Conservapedia - User contributions [en]

Talk:Letter to PNAS

2008-07-29T15:32:19Z

YoungA:

: It's an excellent draft, DinsdaleP. I made a few minor revisions above. After others improve this, then I'll plan on sending it to PNAS later this week. {{unsigned|Aschlafly}}
::I like it. I'll sign my name to it when the time comes.--[[User:DamianJohn|DamianJohn]] 09:35, 22 July 2008 (EDT)

(unindent)

Thanks for the feedback - When applying changes, please keep in mind that the "Text" section in the final version needs to be 250 words or less. If there are important points to add that would exceed this limit, they could be added to the main [[Flaws in Richard Lenski Study]] article instead since PNAS is being asked to respond to the full list there, and not just the summary. --[[User:DinsdaleP|DinsdaleP]] 09:47, 22 July 2008 (EDT)

: I think if i would have presented some draft of that quality to my supervisor i think i would not have reached the door of his office alive and in one piece. It starts with the fact that the correct citation of the article is missing. Please use the appropriate form, inclucing journal number and page. Please have a look at other PNAS Letters. Restate the central issue you criticise in the first sentence, then explicitely describe what your claim about the same issue is and state using what method you come to your conclusion. Keep a neutral tone. Don't make requests. It is obvious that the original author should respond (please look at PNAS for examples of responses, which are published at the same location). Plese fill in your numbers and precise arguments at the points where i left the dots in the following suggestion ('''Please note that nothing of this is my opinion, i just tried to rephrase your opinions in a way that they have the chance to be exposed to a broader view - i skipped tyhe details, because i will not rephrase your arguments, just the structure'''):
: Recently ...... inferred from their experiments (1) that ...... . We analyzed the statistical analysis in terms of ..... and conclude that several variables do not scale as .... . Using hypothesis tests under such circumstances is, in our opinion, ...... , and we do not understand how the authors of the original publication ..... their results.
: The replay experiments yield an ..... scaling with .... . We do not find a consistent value of ..... between the experiments. Furthermore the statistical deviation due to ...... in each sample set does not allow to infer ..... with a sufficient precision. This lack of scaling makes, in our opionion a constant or random source of contamination a likely explanation for a random observation of the ...... dependence of the mutation rate claimed in the paper. The following calculation supports this hypothesis: ....... .
: Furthermore we point out that Fig. ... contains a serious disagreement with .....: while the data would suggest ..... from gen. ..... the figure suggests .....
: We find the material cited in the original article (2)...(n) about the same long-time experiment not to describe the following procedures and experimental constants in a way accessible to us: Handling of ..., contamination rates of ...., and ..... We would kindly ask the authors to clarify these issues. --[[User:Stitch75|Stitch75]] 12:48, 22 July 2008 (EDT)

::No offense taken. I have no experience in these types of submissions, and would appreciate it if you could restructure the submission improve the quality while adhering to the 250-word limit. As I suggested above, it makes the most sense to incorporate these revisions into the main page for this article, where length is not an issue. --[[User:DinsdaleP|DinsdaleP]] 12:52, 22 July 2008 (EDT)

::: I realized that you have obviously not much experience in it; getting the right tone for a scientific publication is hard and i had to try it quite some times on conferences and i still dont get it right sometimes - and from what you said seem to be a student. Sadly, it is against my conviction to rephrase the original arguments in the right way because it would make me an co-author of argumentations i strongly object. In case you did not realize it, helping here to get the structure right doesn't mean i agree - actually the two reasons i would like to see it published is because then the (wrong) idea that scientific journals are not accepting criticism could be obviously be put aside and because i would like to see the needed scientific rigorousity applied to the arguments presented here, because this would put this discussion onto a scientific basis. Quite frankly - i am a liberal by the standards of this site. But i believe the discussion must be carried out with all respect to define the borders of science. The more effective the discussion is carried out, the better the outcome will be. I am willing to listen, as i have proven here, even when beeing treated by people like Mr. Schlafly as if I would be one of his students, while evaluating his qualification in natural sciences quickly shows that i more likely could supervise him in the issues he discusses here (which is something he has proven all along). Regarding that, i am close to giving up, but nevertheless i have seen that a lot of conservatives actually are willing to lead this discussion in a scientific way, which is something, which fulfills me with hope. I recommend you not to fight a fight in where you don't understand the arguments. Don't pick up arguments from others. If you can not fill in the missing words, numbers and arguments in my text, i cant help you. I see what Mr. Schlafly believes, however i do not know how to get the calculation right to support his hypothesis (random or contant mutation rate) - and, this is most likely not because of a lack of statistical knowledge. The only way i would see is to use the rudest form of descriptive statistics and agreggate the data in a very specific way, while ignoring the structure of the experiment - and ignoring the fact that the authors pointed out the problem they see and adressed them. So i can only give oy a few hints (maybe i can form a short contibution to conservapedia; i am just thinking about the title):

:::: If you claim something is wrong, put your opposing claim in a positive formulation, with a supporting calculation, in contrast . Even if the calculation is simple, this is very important to provide it. E.g. we estimate a rate of x+-y per z for dataset N, in which we aggregated generations a,b,c,d, etc .... In the end, you should either prove a mathematical mistake (which was not done) or shoe you hypothesis is more likely.

:::: Don't be rude. You are not the referee and you are not member of a commitee to examine scientific misbehaviour. Dont act like one (and even referees have a friendlier tone usually). Dont act like an personal enemy either. Don't ask for retraction of the article. It is up to the author to make the conclusion respond or retract. This happens more often than you may think as a response to an critisism (actually it's fun to read the "reply section" of scientific journals - sometimes you find things like: "yes, the commenter was right we copied the paper and retract it"). And you are never requesting, but you are kindly asking. Everybody understands that "kindly asking" does not mean "kindly asking" in this context.

:::: Always give full and specific citations which back your claims. Give it in the form required by the specific journal. General citations like "materials on his website" will make your text bein trown out in the editorial screening (because you can not expect that somebody read trough all information to find something backing you claim - this is your job). See for specific styles [http://en.citizendium.org/wiki/Citation_style[http://en.citizendium.org/wiki/Citation_style]]. Ypu may even reference a page/paragraph/eq/figure number to point the reader to what you mean (for papers longer than 4 pages i usually do that).

:::: Run a style checker over your text to eliminate common style mishaps.

:::: '''Most important''': go to your university library. Take the time to just read a few PNAS Letters and replys, and the original articles (Try to finde some with an easy understandable subject). Understanding how these are written and how authors usually reply will help you to get your one right. You are writing against somebody who has twenty years of experience in a field of publishing in natural sciences. You seem to have little experience and Andrew Schlafly, honestly, neither. This game is an uphill battle and unfair game anyway. Make sure you maximize your chances by understanding the rules of the game.

:::: Focus on a single you are sure about. It is better to present one claim well that two claims badly.

:::: Good luck. You will need it. --[[User:Stitch75|Stitch75]] 14:22, 22 July 2008 (EDT)

::::: "Stitch75", you seem to think that the truth depends on whether PNAS accepts it. It doesn't. Lenski's paper is badly flawed regardless of whether he admits it, PNAS admits it, or you admit it. That's the beauty of the truth: it doesn't require admission by anyone. I'm fine with Lenski and PNAS refusing to admit the flaws in their paper. After all, if they really cared about quality then I doubt they would have published their flawed paper after merely 14 days or less of peer review.--[[User:Aschlafly|Aschlafly]] 15:38, 22 July 2008 (EDT)
I tend to agree with you Andy. I say we get this thing sent to PNAS and see what happens. If they refuse to answer it then we know what that means, and if they thumb their noses at you that's fine too. However I have a little more faith than you in the system and I hold out hope that they'll respond to our queries. Anyway lets get this thing sent. --[[User:DamianJohn|DamianJohn]] 15:50, 22 July 2008 (EDT)

(unindent)

I'd like to thank Stitch75, because he took the time to explain his points constructively, and I learned something from them. (I'm actually an IT Specialist in my 40's, not a full-time student, but learning is a never-ending process and I appreciated the lesson). I consider myself bound by the same ethical constraints on editing that he mentioned, because these objections to Lenski's work are Mr. Schlafly's, not my own. I tend to believe that the Lenski experiment was properly executed, but I'm a strong believer in the scientific process, and Mr. Schlafly's objections deserve a fair hearing whether one believes in them or not. My contribution is to help in the process of getting these objections to the proper forum, namely PNAS, and leaving the response up to them. --[[User:DinsdaleP|DinsdaleP]] 16:20, 22 July 2008 (EDT)

Stich has given you brilliant advice, and you throw it away. He has told you that your letter will not get published, and it will have nothing to do with it's content. And when it doesn't get published you will claim it as a victory. If you take his advice and continue to take it, you will make it so no one can simply claim your letter wasn't accepted because it didn't match the criteria set out for letters to PNAS. Now if you have a well written and correctly laid out letter, and then it isn't published, at least you have a leg to stand on.

As a lawyer I would have expected you to understand that certain documents need to be written in set styles, and obey certain rules. Have you published anything (this isn't meant to be derogatory, it's a geniune request), I am positive you must have done so. When you did your citations would have had to be correctly arranged, and many other rules obeyed. Law suits are written up in a set style, and no one would dream of simply scribbling a note and saying check out this website, and expect to be taken seriously. So why do you expect a scientific journal to accept whatever you send them? Follow the procedures, then you have a right to complain if nothing happens. [[User:Raggs|Raggs]] 10:12, 25 July 2008 (EDT)

Stitch75's advice has already been disregarded, and it seems as though you have arrived at your final word choice for the letter. I think that the letter in its current state is fatally flawed and would not warrant publication by PNAS or any other reputable scientific journal. I say this not because I think that the objections raised in the letter are misguided, but because they are presented as assertions without rationale or supporting evidence. For what it's worth, I'll address the five points individually and offer suggestions to improve them:

: Your insulting tone (any other "reputable" journal) discredits yourself, but I'll respond this one time to you below.--[[User:Aschlafly|Aschlafly]] 22:22, 27 July 2008 (EDT)

:1)Drop the complaint about Fig 3. The paper's hypothesis does not depend upon the jump in mutation rate happening at 31,000 generations; it's merely a graphical representation of the difference between the contingent hypothesis and the rare mutation hypothesis. Nobody has objected that the y-axis of the graph lacks numerical values, have they? Also, since this figure represents the hypothesis formed before the data was obtained, where ''should'' the jump have gone? It's location is arbitrary until the data is collected. The abstract and the results section state that the data supports a potentiating event at the 20,000th generation. Since the paper does state the p-value of the third replay, it's inaccurate to say that the paper fails to admit anything.

:: No scientific paper should present a graphical depiction of a falsehood, without indicating that it is false. Figure 3 suggests that the potentiating mutation occurred at the 31,000th, despite the data proving otherwise. If the authors won't correct that error, then they're unlikely to correct any other error also.--[[User:Aschlafly|Aschlafly]] 22:22, 27 July 2008 (EDT)

:::It is not a falsehood; it is a hypothesis. The hypothesis must be formed before data is collected. They hypothesis was that a potentiating mutation occurred that increased the rate of mutation to Cit+. Prior to running the experiment, it is impossible to know when (or even whether) that potentiating mutation occurred. Given that, it is not an 'error' to show the jump at the 31,000th generation, or the 15,000th, or the 10,000th - any point picked for the figure is abitrary. The hypothesis was not that a potentiating mutation took place ''at the 31,000th generation''. For Lenski to put the graph jump at the 20,000th generation would imply that he got the data and then altered the original hypothesis to make it a perfect fit with the results - and ''that'' would be an ethical breach. The data collected suggest that the hypothesis was correct in that a potentiating mutation took place - and they further suggest that this mutation took place at about the 20k generation point. This does not disprove fig 3; it refines it. Again, you may as well object that fig 3 doesn't provide numerical values on the y-axis.--[[User:Brossa|Brossa]] 10:39, 28 July 2008 (EDT)

:2)This point is where I think your best argument lies, but it should be restated along the lines of: the null hypothesis suggests a fixed mutation rate rather than historical contingency. However, the largest replay experiment did not demonstrate the expected increase in Cit+ mutations, and was consistent with the null hypothesis with a p-value of 0.0823 by the Monte Carlo test method.

:: Your reply to the second point is unresponsive to the flaw. You seem to completely misunderstand it, or hope others do. Any fixed "mutation rate" should scale with sample size, yet the data prove otherwise.--[[User:Aschlafly|Aschlafly]] 22:22, 27 July 2008 (EDT)

::: If you're growing several of the same kind of plant in two different pots, one would expect that under the same conditions total stem growth would scale with sample size (number of plants in the pot). But would you still expect that if one pot received ample water, light and fertilizer while the other was unfertilized in dry, dim conditions? That's an extreme example, but nonetheless you wouldn't expect plants to grow the same way under different conditions. Also in this example, mutation rates in the plants would differ, since one pot received more radiation while the other contained plants that were less healthy and therefore less able to repair DNA damage- different environments lead to different pressures. So, once more, cells, be they bacteria or part of a multicellular plant, do not grow or "behave" the same way under different circumstances, and for someone always claiming that everyone else is erroneously grouping the experiments, you consistently keep doing it yourself here.[[User:Kallium|Kallium]] 23:06, 27 July 2008 (EDT)

:3)The claim that the use of Monte Carlo resampling test was an error is unsupported by argument or counterclaim. ''Why'' is the use of that test an error? Problematically, if the test itself is invalid, why are you willing to accept the p-value for the third replay? Furthermore, the Monte Carlo test was not the test used to combine the three experiments to arrive at the final p-value of p<0.0001 - that was a Z-transformation method. Perhaps your real objection lies with this technique rather than the Monte Carlo test.

:: Monte Carlo resampling will often result in small p values for rarely observed events, and it is error to use that technique to draw conclusions in such circumstances. By the way, I don't accept that approach for analyzing the Third Experiment. The data in the Third Experiment are entirely consistent with the null hypothesis.--[[User:Aschlafly|Aschlafly]] 22:22, 27 July 2008 (EDT)

::: In your own words, "your reply... is unresponsive to the flaw." Would you care to reference that statement about Monte Carlo resampling? Why don't you accept that approach for analyzing the third experiment- would you care to explain that statement or keep repeating it? And what statistical calculations can you present to support how the data for the third experiment are consistent with the null hypothesis? You complain about others' flawed statistics yet your statistics are strangely absent.[[User:Kallium|Kallium]] 23:06, 27 July 2008 (EDT)

:::If you can formalize your objection to the Monte Carlo resampling, then by all means do so and include it in the letter - with a reference, if possible. This is an honest suggestion, not sarcasm. Something along the lines of 'With one million resamplings without replacement, the Monte Carlo technique will potentially underestimate the p-value by x% if the probability of an event is below y; see Statistician et al, 1997'. If you're basing your acceptance of the null hypothesis on some other statistical technique that gives you some other p-value, then you should report the technique and the p-value. If you think that the Monte Carlo technique gives a lower bound to the p-value, such that it must be higher than 0.08, then say so.

:4)It was not 'an error' to include later generations in the replay experiments, because those generations provide information that bears on the contingency hypothesis- they can indicate if the contingency 'window' closes. It would be a valid request that the authors provide an explicit description of the techniques used to exclude the presence of occult Cit+ cells from the samples used in the replay experiments. At some point you will have to accept or reject that it is ''possible'' to do so, routinely, using basic laboratory techniques. If you accept that it is possible, the only way to prove that the routine procedures failed is to repeat the experiment with more rigorous controls and show a different result. Otherwise your objection boils down to "because I said so". If you reject categorically that it is possible to screen all Cit+ cells out, then all of microbiology comes into question, because these are truly fundamental techniques used across thousands of labs for many, many years.

:: Your analysis here is absurd. Trace Cit+ cells inevitably existed after the 31,000th generation, and it's foolish to claim otherwise. It was error to include these generations in the data, and there was no valid reason to do so. The potentiating mutation, if any, would have occurred earlier! Indeed, it occurred before the 20,000th generation according to Lenski's own analysis.--[[User:Aschlafly|Aschlafly]] 22:22, 27 July 2008 (EDT)

:::You completely missed the point of Brossa's comment and again only keep repeating yourself without elaborating. Do you have experience employing the bacteriological methods referred to?[[User:Kallium|Kallium]] 23:06, 27 July 2008 (EDT)

:::The statement that trace cit+ cells inevitably existed after the 31,000th generation requires that there are no techniques to remove them from the mixed-population sample. As others have told you, these techniques do exist and are reliable. You can request that PNAS publish exactly what technique was used (most likely dilution and plating on an indicator medium). Your option then is either to attack the method (difficult, since the techniques have been around for a very long time) or the execution (which would require that you or someone else repeat the experiment with the same technique and obtain different results).
:::Or, taking a different tack - the paper states that it is impossible to exlude an origin for Cit+ that is earlier than the 31,000th generation. So how many generations prior to 31,000 should have been eliminated from the replay?--[[User:Brossa|Brossa]] 10:39, 28 July 2008 (EDT)

:5)This point is, in my opinion, the worst of the lot, mostly because it is meaningless - what does 'combined based on outcome rather than sample size' mean?- but also because it restates the claim in #3, that there was some problem with the technique used to combine the three experiments into a final p-value. If you object to the Z-transformation method, you should state why; if you object to the result, you should be able to say what you think the result should be - with a different p-number that you calculate yourself.

:: The hypothesis of a mutation rate is obviously dependent on sample size, yet the paper combined the results of experiments having vastly different sample sizes as though that did not matter. Point 5 illustrates that the self-contradiction of the statistical analysis in the paper.--[[User:Aschlafly|Aschlafly]] 22:22, 27 July 2008 (EDT)

::: Again, show what you think is wrong by showing statistically what should have been done and what numerical results should have been obtained. Recall the bridge analogy, if you read it.[[User:Kallium|Kallium]] 23:06, 27 July 2008 (EDT)

::: The combination of samples of different sizes is standard practice in the sciences - so you must be objecting to the particular technique used. If you object to the Z-method, state your reasons in the letter. If you have a preferred method, state it in the letter and defend it. Best of all, use your preferred method and present your results. By 'the hypothesis of a mutation rate', are you referring to the calculations of mutation rates? Because the data for those calculations were not obtained from the three replay experiments.--[[User:Brossa|Brossa]] 10:39, 28 July 2008 (EDT)

I would hope that you would at least run this letter past a sympathetic scientist (someone from DI?) before you submit it, to confirm that these concerns are in a legitimate format.--[[User:Brossa|Brossa]] 20:10, 27 July 2008 (EDT)

:: Oh how you cling to the views of others! Logic does not depend on what some think, or the perception of what some think. The readers of this page are smart enough to look at the logic and admit the truth. So are you. Rest assured that logic does not care that some reject it.--[[User:Aschlafly|Aschlafly]] 22:22, 27 July 2008 (EDT)

::: Oh how you cling to your views! The problem with logic is that it only works with knowledge- almost all of the replies on this page have been trying to teach you something about microbiology and/or statistical analysis but you are convinced you understand it better than those who have many years of experience working with them, although you continue to misinterpret basic concepts covered in any undergraduate microbiology, genetics or statistics course. Where is the logic in ignoring the input of all those who have actual training and experience in the fields you are discussing? How is that having an "open mind"?[[User:Kallium|Kallium]] 23:06, 27 July 2008 (EDT)

::: Oh, how I cling to the views of others! Yes, which is why I have an accountant and an attorney and a doctor and a statistician and an architect - I accept that other people have greater experience and knowledge in certain areas than I do. If I want to charge my lawyer with malpractice, it behooves me to check with another lawyer to see if my complaint has merit, or if I'm even articulating the complaint correctly before I show up in a courtroom.--[[User:Brossa|Brossa]] 10:39, 28 July 2008 (EDT)

::::I wasn’t planning on making any more comments, but in perusing other articles on this site I found that part of the Atheism article reminded me of Brossa’s comment:

:::::“Christian apologist JP Holding rightly states that Bible exegesis and Bible exposition is a multi-disciplinary pursuit, and often critics of the Bible have not done a fraction of the due diligence required to make an allegation regarding the Bible. Holding states the following:

:::::““Having now been engaged in apologetics for eight years actively and more years than that on the side, I have long since come to a conclusion that I have shared with others, but will now present in a systematic form here for the first time. My conclusion is a warning that is appropriate for any new readers (hence I link this article from my front page) and will be familiar to veteran ones.

:::::"I'll sum it up to begin: Whenever you run across any person who criticizes the Bible, claims findings of contradiction or error -- they do not deserve the benefit of the doubt. They have to earn it from you. Here's why.

:::::"It doesn't take very long to realize that a thorough understanding of the Bible -- and this would actually apply to any complex work from any culture -- requires specialized knowledge, and a broad range of specialized knowledge in a variety of fields....

:::::"Not even most scholars in the field can master every aspect -- what then of the non-specialist critic who puts together a website in his spare time titled 1001 Irrefutable Bible Contradictions? Do these persons deserves [''sic''] our attention? Should they be recognized as authorities? No, they deserve calculated contempt for their efforts. (By this, I do not mean emotional or behavioral contempt, but a calculated disregard for their work from an academic perspective.) They have not even come close to deserving our attention, and should feed only itching ears with similar tastes.””

::::Now let’s change the academic subject (I leave out the introductory paragraph of Holding’s quote):

:::::“Whenever you run across any person who criticizes ''scientific reports'', claims findings of contradiction or error -- they do not deserve the benefit of the doubt. They have to '''earn''' it from you. Here's why.

:::::"It doesn't take very long to realize that a thorough understanding of ''microbiology and evolutionary biology''-- and this would actually apply to any complex work from any ''field of science'' -- requires specialized knowledge, and a broad range of specialized knowledge in a variety of fields....

:::::"Not even most scholars in the field can master every aspect -- what then of the non-specialist critic who puts together a '''website in his spare time''' titled ''7 Irrefutable Richard Lenski Study Flaws''? Do these persons deserve our attention? Should they be recognized as authorities? No, they deserve calculated contempt for their efforts. (By this, I do not mean emotional or behavioral contempt, but a calculated disregard for their work from an academic perspective.) They have not even come close to deserving our attention, and should feed only itching ears with similar tastes.”

::::I do not post this as satire or mockery, but as another serious attempt to provide perspective. Ironic that Holding’s quote is in an article on Conservapedia, which at the same time is rightly concerned about double standards.[[User:Kallium|Kallium]] 22:38, 28 July 2008 (EDT)

::Brossa has made several excellent points. I would add that there is a disconnect between your primary claim and the list. You should rethink your thesis statement or choose different "flaws" that fit it better, since your primary claim that the flaws "negate [the paper's] claim that E. Coli bacteria underwent an evolutionary beneficial mutation" does not follow from those listed. With your flaws, with the possible exception of #4 depending on interpretation (and even then, where did the undetected Cit+ cells come from?), you are arguing against historical contingency, not whether or not Cit+ cells evolved. In other words, the flaws you claim are questions of mechanism, i.e. the dynamics of how the Cit+ cells arose, but your thesis statement questions whether or not they arose at all from Cit- populations. So even if those flaws were true, they would not negate the "evolutionary beneficial mutation" as you say but rather just historical contingency as a path to it. [[User:Kallium|Kallium]] 21:23, 27 July 2008 (EDT)

: No, point #2 indicates that the paper's data disprove any plausible mutation rate, because the mutations did not scale with sample size. Point #2 thereby negates the claim of "an evolutionary beneficial mutation" as insisted by the paper.--[[User:Aschlafly|Aschlafly]] 22:22, 27 July 2008 (EDT)

::See my above post regarding scaling of mutation rate. As for disproving "any plausible mutation rate", are you referring just to Cit+ variants, or truly ''any'' mutation rate? If the former, where do you propose the Cit+ cells came from in the first place, and if the latter, see my above post about basic microbiology. Also, your letter claims that flaw #2 disproves a ''fixed'' mutation rate, not, as you just said, ''any'' mutation rate. So which are you claiming?[[User:Kallium|Kallium]] 23:06, 27 July 2008 (EDT)

==How about this

I'm not going to say I know much about the science but I made this suggestion a few days ago (in the article page). It is certainly a lot shorter, and I think a little more polite. What do you think Andy

==Word Count==
Is the 250 limit for the body text - the 'meat' of the letter? Or everything? [[User:RobCross|RobCross]] 11:42, 25 July 2008 (EDT)

: I believe it applies only to the Text portion. --[[User:DinsdaleP|DinsdaleP]] 11:44, 25 July 2008 (EDT)

==Completion of the cc: list==

I don't think it's appropriate to submit without specific names in the cc: list. If those were meant to be placeholders then they need to be filled in ASAP. Also, the inclusion of congressional representatives overseeing funding does nothing but add an implied threatening tone to the submission. If this is about questioning his science as reported in the PNAS, then let's keep it focused there - PNAS has nothing to do with the funding of his research and this detracts from the focus of this submission. For that reason, I'm also removing the "refusal to provide data" line from this text, because it's out of the scope for what should be discussed with PNAS. --[[User:DinsdaleP|DinsdaleP]] 11:44, 25 July 2008 (EDT)

:I agree with what you have said. I think we should send out a separate letter to the congresspeople. There are two separate, though very related issues. The rigor of the experiment (this is what PNAS deals with) and the fact that such research is given funding (Congress and the watchdog groups have to do with this part). Lets address the first problem before we look at the second. -[[User:RoyS|RoyS]] 17:05, 25 July 2008 (EDT)

==Link in Letter==
Andy or any of the other sysops: I think it would be a very good idea if you locked the page which the letter refers too. This is necessary, because the last thing we want is to be embarrassed by liberal vandalism that does not reflect what Conservapedia is really about. -[[User:RoyS|RoyS]] 16:57, 25 July 2008 (EDT)

:That makes sense to me - good idea. --[[User:DinsdaleP|DinsdaleP]] 16:59, 25 July 2008 (EDT)

::Thanks. Also, we should completely check all of the sources and make sure each is completely verified, because we don't want are argument to be made less credible by some silly mistakes. -[[User:RoyS|RoyS]] 17:02, 25 July 2008 (EDT)

==Availability of data==
The comment about the availability of data should be removed. The PNAS guidelines for letters [http://www.pnas.org/site/misc/iforc.shtml] state that letters must not include "accusations of misconduct". They have a separate procedure for issues regarding data and material availability. ("Contact pnas@nas.edu if you have difficulty obtaining materials").--[[User:YoungA|YoungA]] 09:18, 26 July 2008 (EDT)

: I thought about this, but PNAS can simply omit the sentence at the end upon publication. It seems unnecessary and inappropriate to break this letter into two separate ones just for one sentence.--[[User:Aschlafly|Aschlafly]] 16:26, 27 July 2008 (EDT)

::It seems more inappropriate to knowingly submit something to PNAS that is against their guidelines and then expecting them to edit the unacceptable comment out on their end. I'd suggest that the "PNAS Letters" submission will be taken more credibly if we respect their guidelines, and instead send the version with the "withholding data" accusation to the appropriate parties separately, and copy PNAS as a courtesy. My grandfather told me I'd never regret taking the high road, and 40-plus years later his advice has served me well. --[[User:DinsdaleP|DinsdaleP]] 10:08, 29 July 2008 (EDT)

==My sixpenn'orth==
I think this reads very sharply and is a pretty punchy 250 words worth - I know it's difficult to express complicated ideas so concisely. A couple of very minor, nitpicky comments: should Lenski's article have its PNAS edition/page citation in brackets? And I'd thought the Editor of PNAS would not be a cc, but the principal recipient.

Congratulations to Andy and all who contributed to this. [[User:Bugler|Bugler]] 15:58, 27 July 2008 (EDT)

: Thanks for your suggestions, which I've incorporated and addressed. Godspeed to you, Bugler!--[[User:Aschlafly|Aschlafly]] 16:25, 27 July 2008 (EDT)

==Mailing==
Has it been sent yet?--[[User:YoungA|YoungA]] 11:32, 29 July 2008 (EDT)

Christianity

2008-07-28T15:57:14Z

YoungA: Undo revision 493422 by CrimsonKing (Talk) Hardly "minor"

{{Christianity}}
'''Christianity''' is a religion taking its name from [[Jesus Christ]] meaning "Jesus the Savior" and "Jesus the Anointed One". Adherents are called Christians, meaning "of Christ" or "belonging to Christ".<ref>[http://dictionary.cambridge.org/define.asp?key=2661&dict=CALD Cambridge Advanced Learner's Dictionary]</ref> It seems that at first the [[religion]] was called "The Way" and the adherents were called Nazarenes (after the city of [[Nazareth]] where Jesus lived). The name Christian arose in [[Antioch]] in the first century A. D. and its use spread, probably closer to mid-century since it is recorded in the [[Acts of the Apostles|Book of Acts]] (Acts:11:26)

== Main Christian groups ==

The three largest self-governing bodies of Christians are:

* the [[Roman Catholic Church]] (approx. 1.1 billion baptized members) traces its roots back to [[Saint Peter]] who Catholic believed established the Church and the succession of the [[Pope]]s as the spiritual authority over the Christian body of believers.

* the [[Orthodox Church]]es (approx. 300 million baptized members) also trace their roots back to the beginnings of Christianity, but do not believe in the Primacy of the Pope. Different theological perspectives led to the [[Great Schism]] between the Roman Catholic Church and the Eastern Orthodox Churches in A.D. 1054.

* [[Protestantism]], the largest Communions are the [[Anglican Church|Anglicans]] (approx. 77 million baptized members) and the Lutheran World Federation (approx. 68 million baptized members). Protestantism has its origins in the European [[Reformation]]. It first broke away from the Roman Catholic Church under [[Martin Luther]] when differences over the nature of faith and works in the role of [[Christianity#salvation|salvation]] could not be adequately reconciled with Papal prescriptions as well as other practices that Luther saw in the Catholic Church at that time that he did not agree with. Other preachers and movements then followed Luther's example and also left the Catholic fold.

== Christian beliefs ==
Theologians, over two millennia, have debated a definitive summary of the Christian faith. While its interpretations vary drastically, probably the most commonly accepted statement of faith is the [[Nicene Creed| Nicea-Constantinopolitan Creed]] below:

<blockquote>I believe in one God, [[God the Father|the Father Almighty]], Maker of [[heaven]] and [[earth]], and of all things visible and invisible. And in one Lord Jesus Christ, the Son of God, the only-begotten, begotten of the Father before all ages. Light of Light; true God of true God; begotten, not made; of one essence with the Father, by whom all things were made; who for us men and for our salvation came down from heaven, and was incarnate of the [[Holy Spirit]] and the [[Virgin Mary]], and became man. And He was crucified for us under [[Pontius Pilate]], and suffered, and was buried. And the third day He rose again, according to the [[Bible|Scriptures]]; and ascended into heaven, and sits at the right hand of the Father; and He shall come again with glory to judge the living and the dead; whose Kingdom shall have no end. And in the Holy Spirit, the Lord, the Giver of Life, who proceeds from the Father; who with the Father and the Son together is worshiped and glorified; who spoke by the prophets. In one Holy, Catholic, and Apostolic Church. I acknowledge one baptism for the remission of sins. I look for the [[Resurrection]] of the dead, and the life of the world to come. Amen.</blockquote>

Christians and Christian denominations agree on many points of doctrine and disagree on others. According to an online Harris poll from 2003 99% of all American Christians believe in God, 96% in the [[Resurrection of Jesus Christ|resurrection of Jesus Christ]], 93% in Heaven, 93% in the virgin birth, 92% in the survival of the soul after death, 82% in Hell, 50% in ghosts, 27% in astrology and 21% in reincarnation. <ref>http://www.harrisinteractive.com/harris_poll/index.asp?PID=359</ref> Note that the latter two beliefs are in opposition to the religious dogma of most Christian denominations.

Nonetheless, the Nicea-Constantinopolitan Creed offers a general overall picture of what Christian theology looks like, and serves as a useful outline.

Other creeds may prove helpful in research. See also: the [[Apostle's Creed]], [[Athanasian Creed]].

===God===
The God of the Christians is a triune being. Though there is only one Divine nature there are three Divine Persons: The Father, the Son, and the Holy Spirit. The three Persons are collectively called the [[Trinity]] or the Holy Trinity. Christians reject the idea that they are polytheists because of the oneness of the divine nature (or essence). Though to non-Christians and even many Christians, it might seem like an inconsequential dogma, the doctrine of the Trinity is central to all of Christian theology and life. This is especially true in the relationship between God and human beings. The major theme of the Bible is love. In the Hebrew [[Old Testament]] the idea is expressed in the Hebrew word ''hessed'', which is variously translated as loyal love, tender mercy, steadfast love, mercy, goodness, etc. in the [[New Testament]] the same idea is expressed in the Greek word ''agape'', which is variously translated as love, compassion, charity, etc. The picture that the Biblical writers draw with these words is of a lover (God) who is entirely self-sufficient, needing nothing, and a beloved (human beings) in desperate need of salvation but unable to obtain it for himself. But God the lover is willing to suffer, knows He is going to suffer, even endure death to save the beloved human beings. This love of God for human beings is an extension of the love the Three Persons in the Trinity have for each other. Each loves the others infinitely. Their love for each other and for their creation is such that the [[Apostle John]] equates God and love, in an almost mathematical way saying, "God is love."

Additionally, the God of the Christians is the creator of all things, is everywhere present, exists in all times, is transcendent, all-knowing (omniscient), just, all-powerful (omnipotent).

===Jesus===
Christians hold that during the reign of [[Caeser Augustus]] the Son (e.g. the second Person of the Trinity) took flesh from a virgin woman and was incarnate as a man. He was born in the town of [[Bethlehem]] and was given the name [[Jesus]]. At the age of thirty he was baptized by his cousin, the [[John the Baptist|Prophet John]], and began to preach in the area [[Palestine]]. About three years after his baptism, he raised his friend Lazarus from the dead, prompting the Jewish power establishment to plot Jesus death. Jesus was [[crucified]]. He came back from the dead and was seen by over 500 people. He ascended to heaven. The four [[Gospels]] contain the records of some of what Jesus did and said, but he did much more than those four books relate, as the Apostle John admitted in his Gospel.

===Jesus' Self Consciousness===

Jesus, conceived of the Holy Spirit, presented a disturbing surprise to his earthly father, Joseph, knowing he had not impregnated his fiancee, Mary. She would ponder the meaning of this miracle all the days Jesus would grow and finally she would behold her son expire on the cross. But Joseph, told by the Lord who his son really was, and how he had come about, and being warned by the Lord to flee the murderous Herod, took his family to Egypt - until the death of Herod made it safe ("Out of Egypt have I called My Son") to return to Israel. The family settled in Nazareth on the elevated rim of the Jezre'el Valley where he grew well and observably no different from the other youth. But when he was about 12 years old, he was taken to the Temple in Jerusalem, and displayed his consciousness that His real Father was God rather than Joseph ("Didn't you know that I must be here about the matters of My Father?".

They returned to Nazereth in Galilee and it wasn't until 28 years later that He began to publicly show His consciousness as to who he was. This was at his baptism at the Jordan River by John, when the voice came, to him, to John, and to the people privileged to be around, "This is my Son, the Beloved, Listen (Shma'a) to Him!" Here and now, against even the desire of John the Baptizer, Jesus, knowing that sin was not in him, chose to identify with sinful mankind in this baptism of John for repentance of sin, knowing that at the end of his time on earth, he would then be giving this sinless life of his on the cross, bearing the sins of the world upon himself.

Back, now, in Galilee, he would begin to do works of mercy, miracles of compassion, healings of deliverance, and overthrowing the devastaions of Satan upon the people of God's compassion - in short, bringing in the Kingdom of Heaven and of God and supplanting the Kingdom of Darkness. He began to gather around him his followers, simple fishing folk and others, spending most of his time in the area around the north shore of the Kinneret (Sea of Galilee). among the Jews of this Jewish area. He was bringing in the Messianic Kingdom to those who would understand it best, the Jews. But all the time, there was burning within him the knowledge that the blessings of Abraham would be extended, according to the promise, to all the peoples of the earth, the Gentiles, and there would be a new Kingdom, a new nation, transcending both Jews and Gentiles, the Kingdom of the people of God the Heavenly Father. He began his forays then into gentile areas, Phoenecia, the Decapolis, and other locales, and finding faith there such as he had not found "even in Israel".

A crossroads occurred, then, in the choice of Jesus, and consequently in the options of his disciples. It occurred in the Tetrarchy of Philip, at the foothills of Mt. Hermon, at the town of Caesarea Philipi. He knowing who he was, would force the question upon others - "Who do people say Me to be?". From the lips of Shim'on, whom he would call Peter, as leader of the others, He would hear - "You are the Messiah, the Son of the Living God!" It was enough. Jesus would then begin imparting to them what the nature of His mission to be - not to expel the Romans from the Holy Land, but to go to Jerusalem, to be betrayed, to be spurned and rejected by the High Priests and the Elders of the People, to be hung on a Roman cross at the hands of the Gentiles, to die. Casesarea Philipi was in between, on one hand, Gentile pervaded Roman Tiberius to the southwest of the Sea, and on the other hand, anti-Roman nationalistic and zealotic Gamla to the north east of the Sea. {This latter would end their rebellion against Rome by suicide on Matzada in 73 A.D). Those two polarities were present in the minds of the disciples and Jesus began, on one hand, to divest from their minds the one, the warrior role of the Messiah against the Romans, and the other, to renew their thinking and their commitment to Him as the self sacrificing Lamb of God, the Prince of Peace and the true Messiah of Israel, on the other hand.

This took place on the long 3 or 4 day journey by foot from Galilee to Jerusalem, along the [[Jordan River]] valley, coming to Jericho, ascending to Jerusalem from the east. It was in Jerusalem that he prepared and settled the matter for the perpetuation of the Church at the Lord's last supper of the Passover, to be made palpable later by the descent of the Holy Spirit. It was in Jerusalem, in the Garden of the Oil Press, that what He had been lead to believe about his mission and the meaning and manner of his death was fully embraced and accepted with no reservation or turning back. "Your will be done, Father, if there is no other way", and "There is no other way, Your will be done Father!" It was a perfect decision and commitment, perfecting his life to be a perfect sacrifice. And it was to the west just outside Jerusalem that His teachings came to a concretization and realization on the cross. And just outside of Jerusalem that His Father would vindicate him by raising him from the dead.

"No man takes my life from me. I have power to take it and I have power to lay it down... I lay down my life for the sheep." <ref>Bible, Gospel of John, 10:18,15 http://etext.virginia.edu/etcbin/toccer-new2?id=KjvJohn.sgm&images=images/modeng&data=/texts/english/modeng/parsed&tag=public&part=10&division=div1</ref>

"Though He was in the form of God, He did not think equality with God something to grasp onto. But He emptied Himself and took to Himself the form of a servant and was made man, And being found in the form of a man, He humbled Himself, becoming obedient unto death, even the death of the Cross. For this reason, God has exalted Him..."<ref>Bible, Philippians 2:6-9a, http://etext.virginia.edu/etcbin/toccer-new2?id=KjvPhil.sgm&images=images/modeng&data=/texts/english/modeng/parsed&tag=public&part=2&division=div1 </ref>

===Morality===
The fundamental principle in Christian moral teaching is love and forgiveness, as expressed by the life and teachings of Jesus Christ and the New Testament. Jesus summarized his teachings in two commandments from the Old Testament:

"'You shall love the Lord your God with all your heart, and with all your soul, and with all your mind.' This is the great and foremost commandment. The second is like it, 'You shall love your neighbor as yourself.' On these two commandments depend the whole Law and the Prophets." ([[Gospel of Matthew|Matthew]] 22:37-39; [[Book of Deuteronomy|Deuteronomy]] 6:5; Leviticus 19:18)

Constant debate has resulted as to how a person should express love for God in their moral behavior. This moral dialogue found expression in the New Testament, where the [[Apostle Paul]] addressed such controversies as [[circumcision]] ([[Book of Romans|Romans]] 2:25-29), eating meat that was sacrificed to [[pagan]] deities (1 Corinthians 8), speculating about myths and genealogies (1 Timothy 1:3-5), and observing ceremonial dates and seasons (Galatians 4:9-11).

Regardless of a person's ethical interpretations, adherents commonly point to New Testament passages John 3:16 and 1 Corinthians 13:4-7 as scriptural depictions of love. The former states that <blockquote>"God so loved the world, that He gave His only begotten Son, that whoever believes in Him shall not perish, but have eternal life."</blockquote> The latter characterizes love, saying <blockquote>"Love is patient, love is kind and is not jealous; love does not brag and is not arrogant, does not act unbecomingly; it does not seek its own, is not provoked, does not take into account a wrong suffered, does not rejoice in unrighteousness, but rejoices with the truth; bears all things, believes all things, hopes all things, endures all things."</blockquote>

Jesus Christ affirmed, "By this all men will know that you are My disciples, if you have love for one another." (John 13:35)

===The Atonement of Jesus on the Cross===

All Christians believe with the New Testament that the death of Jesus, along with His resurrection, is an indispensable proclamation of a crucial event for the reconciliation of lost sinners with God. There are three elements they see to understanding His death on the cross.

# Jesus having the knowledge that His path would lead to his own death, desired and willed that that take place, and persevered in that path though there was opportunity for Him to avoid it. Though there is ample recognition in the New Testament that others desired Him to die, and that the circumstances in which His path took him would bring Him to His end on earth, the mover of all these things was Himself and the will of the Father. "I have power to take my life and I have power to lay down my life. I lay down my life for the sheep."
# Jesus saw that in His death there would be a way for people to be brought back to the God from whom they were alienated and lost because of their sins. This would involve a substitution of Himself to effect that way. "For the Son of Man came not to be served, but to serve and give His life as a ransom for many." How this would take place was not new to the Jews of His day from their understanding of contemporary everyday practice of substitute payment - as in redemption of the first-born (Pidyon Ha Ben), or in the understanding of what aggadic stories such as the Binding of [[Isaac]] implied (see [[Midrash]]), but it was not the prevalent view that the Messiah was to be that payment. Though while alive on earth, he had hinted at it in sayings such as "unless a seed falls and dies, it remains alone, but when it dies, it brings forth..", it was only after He had risen from the dead that He explained Scripture (the Old Testament) clearly about the necessity of His death to have taken place. The disciples would henceforth preach, and Peter among them, that the death of Jesus the Messiah and His resurrection was forplanned and for-ordained by God the Father, and foretold in the Scripture (Isaiah 53). And so, "The Just for the unjust, that He might bring us to God".
# It was the belief in Scripture, that in His death a way back to God was made possible for those that were near to God—the Jews. And a way back to God for those that were far away—the Gentiles. That is why the New Testament saw in the requirements of God for Israel a fulfillment in Jesus the Messiah. He was the perfect Israel, taken out of Egypt, to redeem Israel. And that is why the New Testament saw in Jesus, a deepness to the incarnation of the Son of God, deeper than just a Jew of His time of a certain tribe. He was the "Second Adam" to redeem the sons of Adam. This encompassing perspective had further implications.

Christians of all generations have looked to the perfect Atonement, and the hope for reconciliation, accomplished by Jesus on the cross, to provide the means of understanding the solution to the vexing problems of the mind and of life itself - How can I make reconciliation with my enemies, with even the members of my own family, of race with race and people with people?; Does His death for the sins of the world include those who only partially understand, for the baby aborted, the feeble minded, and severely retarded?; For those who have never heard of Jesus, never been "enlightened", distant and remote in place and time?; Does His death for the sins of the world also include a remedy for the ills that have come as a result of those sins—certain sicknesses, ills of the mind, body and the soul? Do they "hold" for today?; Does His death make good, turn to the better, show the way, effect the way, of the illnesses that have befallen the world, not only by sin, but simply by the circumstances of life, of degeneration, of compounded dysfunction? How does the fruit of His death bring in somehow the Kingdom "among us"?

The death of the Son of God on the cross has provided the solution for sin, and it still holds its sway over the imagination and aspirations for the people of our generation.

===Salvation===
The Bible teaches that "all have sinned and fall short of the glory of God" (Romans 3:23). This is often interpreted to mean that everyone has displeased God and is now separated from him in a kind of alienation and enmity that results from the fundamental conflict between selfish human interests and God's interests (Romans 8:5-8; James 4:4).

However, Jesus offered a solution to this Biblical dilemma in that by repentance of sins and faith in him (Jesus), their sins would be forgiven. He said that "...the Son of man hath power on earth to forgive sins." ([[Gospel of Mark|Mark]] 2:10) Jesus also said, "I came not to call the righteous, but sinners to repentance." (Mark 2:17, and "Verily I say unto you, All sins shall be forgiven unto the sons of men" (Mark 2:28)

Jesus Christ taught that "unless one is born again he cannot see the kingdom of God" ([[Gospel of John|John]] 3:3). Protestant Evangelical Christianity often use the terms "saved" and "born again" interchangeably. Other Christians, notably the Roman Catholic Church and the Orthodox Church use the phrase ''born again'' as a synonym for [[baptism|baptized]]. "Jesus answered, Amen, amen, I say unto thee, Except a man be born of water and [of] the Spirit, he cannot enter into the kingdom of God." (John 3:5)

Christians are expected to continue living by Christ's teachings (John 8:31), as is appropriate for "children of Light" (Ephesians 5:8-10). Some believe that this is necessary in order to stay saved. However, this is a common misconception of the text. It is rather referring to proving that one is a child of God by their "fruit" (things that they do and how they behave). Christians in the Reformed tradition (following the teaching of the 16th century French lawyer [[John Calvin]], as well as the faith outlined in the Belgic and Heidleberg Confessions) say that salvation is irrevocable and that it cannot be lost, if it were genuinely part of one's life to begin with. Reformed Christians (often called [[Calvinists]]) often point to Romans 8:38-39 as validation of their belief: "For I am convinced that neither death, nor life, nor angels, nor principalities, nor things present, nor things to come, nor powers, nor height, nor depth, nor any other created thing, will be able to separate us from the love of God, which is in Christ Jesus our Lord" (Romans 8:38-39; NASB). According to Calvinists, the reason it cannot be lost by natural things is because salvation was obtained through a supernatural being, namely Jesus Christ. This does not negate Jesus' human side, only that he was both one-hundred percent God and one-hundred percent man, according to the [[Council of Chalcedon]] (A. D. 451). The Bible also makes it clear that mankind cannot earn their salvation, and that it is a free gift.

== Resurrection of Jesus Christ ==
The [[Resurrection of Jesus Christ|resurrection of Jesus Christ]] is critical to the Christian faith. The Apostle Paul wrote, "if Christ has not been raised, then our preaching is vain, your faith also is vain" (I Cor:15:14). Traditionally, Christianity has believed in a physical resurrection of Jesus Christ.<ref>http://www.iclnet.org/pub/resources/text/cri/cri-jrnl/crj0056a.txt</ref>

In recent history Gary Habermas is considered the foremost [[Christian apologetics|Christian apologist]] for defending the resurrection of Jesus.<ref>Habermas, Gary, [http://www.garyhabermas.com/articles/dialog_rexperience/dialog_rexperiences.htm Experiences of the Risen Jesus: The Foundational Historical Issue in the Early Proclamation of the Resurrection], ''Dialog: A Journal of Theology'', Vol. 45; No. 3 (Fall, 2006), pp. 288-297.</ref><ref>"Wildcat" and Holding, J.P., [http://www.tektonics.org/books/lichabrvw.html Book review of "The Case for the Resurrection of Jesus"], 22nd June, 2004 (Tektonics)</ref><ref>Habermas, Gary, [http://faculty.gordon.edu/hu/bi/Ted_Hildebrandt/NTeSources/NTArticles/CTR-NT/Habermas-Resurrection1-CTR.pdf Jesus' Resurrection and Contemporary Criticism: An Apologetic] ''Criswell Theological Review'' 4.1 (1989) 159-74.</ref><ref>Habermas, Gary, [http://www.garyhabermas.com/articles/crj_explainingaway/crj_explainingaway.htm Explaining Away Jesus' Resurrection:
The Recent Revival of Hallucination Theories], Christian Research Journal / vol. 23, no. 4, 2001.</ref><ref>Habermas, Gary, [http://www.apologetics.com/default.jsp?bodycontent=/articles/historical_apologetics/habermas-nt.html Why I Believe The New Testament Is Historically Reliable] (Apologetics.com)</ref>
Other notable defenders of the resurrection include: [[William Lane Craig]],<ref>Craig, William Lane, [http://www.leaderu.com/offices/billcraig/menus/historical.html Articles: Historical Jesus]</ref> [[Lee Strobel]], [[Josh McDowell]],<ref>McDowell, Josh, [http://www.leaderu.com/everystudent/easter/articles/josh2.html Evidence for the Resurrection], 1992.</ref> [[Edwin M. Yamauchi]],<ref>Jamauchi, Edwin M., [http://www.leaderu.com/everystudent/easter/articles/yama.html Easter: Myth, Hallucination, or History?]</ref> [[N.T. Wright]]<ref>Wright, N.T., [http://www.ntwrightpage.com/Wright_Early_Traditions.htm Early Traditions and the Origins of Christianity], ''Sewanee Theological Review'' 41.2, 1998.</ref> and [[Michael Horner]].<ref>Horner, Michael, [http://www.michaelhorner.com/articles/resurrection/index.html Did Jesus Really Rise from the Dead?]</ref>

===The Meaning of the Resurrection for Christians===

The Fact of the Resurrection of Christ is a key element of the preaching of the message about Jesus and an essential of Christian belief. But there are also certain effects that this belief has on the lives of believers.

1. It is because Jesus rose from the dead, that believers now can resort to a living Savior to help and deliver them from sin and from situations overwhelming for them by their own powers.

2. The New Testament sees in the resurrection of Christ a certain vindication of what apparently to the world and to all beings was a failure and an overcoming of Him by His crucifixion. He was "declared to be the Son of God" by His resurrection. This brings believers in Him to a strong confidence in the determined power of God to both vindicate in their own lives and to bring His reign upon earth.

3. The coming of Jesus back to life means to the believer that, indeed, their sins are totally forgiven. This is because believers know that His death was as a payment for sins - a "wage of death" for our sins that He received in our stead. If He remained dead, believers would know that the wage had not been fully paid. His resurrection, carries with it our knowledge that our sin with its attendant death has been totally and finally paid for.

4. It is a now living Savior that Christians know can go before them, can closely lead them through life - as He did when He was on earth. This makes following Him practical and real.

5. The New Testament reveals that it is the Risen Christ who received from the Father the Holy Spirit and He, through Himself ascended to the Father, has given the Holy Spirit to us. This gives the believer in Christ both the knowledge and the power to live a godly life, and live a life that can be an intimately and personally directed one.

6. The resurrected Christ was no mere reassembling of the molecules and particles of the Body that had been crucified. It was, indeed, a physical body, but one that was fully under the Spirit's control, guidance, and empowerment. It was a "spiritual body". Christians know that likewise, they will one day be granted the nature of a spiritual body, and full of health. They therefore are full of hope and consolations, and consider that even now in this life, there is an overcoming through Him, a restoration, and that tears, even now, are wiped away.

== Evangelism ==
In what is called the [[Great Commission]], Jesus sent his disciples out into the world to preach the Gospel (literally "good news") and make disciples.
:'''Great Commission'''
:''But the eleven disciples proceeded to [[Galilee]], to the mountain which Jesus had designated. When they saw Him, they worshiped Him; but some were doubtful. And Jesus came up and spoke to them, saying, "All authority has been given to Me in [[heaven]] and on [[earth]]." Go therefore and make disciples of all the nations, baptizing them in the name of the [[#God the Father|Father]] and the [[#God the Son|Son]] and the [[#God the Holy Spirit|Holy Spirit]], teaching them to observe all that I commanded you; and lo, I am with you always, even to the end of the age."'' --[[Gospel of Matthew|Matthew]] 28:16-20 [[New American Standard Bible|NASB]]

It should be noted, however, that Jesus said it was the Holy Spirit, not man, who was sent to convict the world concerning sin and righteousness (John 16:8). This relieves Christians of needing to worry when they evangelize. God is the one who gets the credit with the growth and maturity of the Church: "So then neither the one who plants nor the one who waters is anything, but God who causes the growth" (1 Corinthians 3:7).

==See also==

'''Denominations or branches of Christianity'''
*[[Roman Catholic Church]]
*[[Orthodox Church]]
*[[Protestantism|Protestant]]
**[[Amish]]
**[[Baptist]]
**[[Church of England]] or ''Anglican Church''
**[[Episcopal Church in the United States of America]] (or ''Episcopal Church'' or ''Episcopalians'') (Non-UK branch of the Anglican Church)
**[[Evangelical Christianity]]
**[[Fundamentalism]]
**[[Liberal Christianity]]
**[[Lutheran]]
**[[Mennonite]]
**[[Methodist]]
**[[Pentecostal]]
**[[Plymouth Brethren]]
**[[Presbyterian]]

'''Disputed'''
*[[Church of Jesus Christ of Latter-day Saints]]
*[[Christian Science]]

'''Other articles'''
*[[Cathedral]]
*[[Catholicism]]
*[[Christian apologetics]] (Defense of Christianity)
*[[Christianity and Science]]
*[[Church]]
*[[Conservative Christianity]]
*[[Eucharist]]
*[[Judaism]]
*[[New Testament understanding through the Jewish perspective]]
*[[Passover Seder]]
*[[Persecution of Christians]]
*[[Red-letter Christian]]
*[[Sign of the Cross]]

==References==
{{reflist|2}}

==External Links==
*[http://www.aim.org/wls/category/christians/ What Liberals Say - Category: Christians], [[Accuracy In Media]]

[[Category:Christianity]]
[[Category:Worldviews]]

User talk:Iduan

2008-07-27T21:23:27Z

YoungA: Undo revision 493303 by Wererrrwe (Talk)

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==Liberal Tricks==
The idea of [[liberal tricks]] is more on a personal level, rather than politics that can be best addressed in [[liberal logic]] and [[liberal style]]. So while you're edit is good of [[liberal tricks]], I don't think it belongs there. It's not really a "trick".--[[User:Aschlafly|Aschlafly]] 23:29, 23 February 2008 (EST)
:Ah, my mistake - sorry, --[[User:Iduan|I]][[User_talk:Iduan|Duan]] 23:31, 23 February 2008 (EST)
==I don't suppose you can close the site down==
I would think Andy would have shut off night editing by now, usually he does so at midnight eastern. But he hasn't made an edit since about 11:50. Maybe he went to bed and forgot. [[User:SSchultz|SSchultz]] 00:35, 25 February 2008 (EST)
:Perhaps - he's done that once before I think, aww, that means I have a long night ahead of me, I'll probably stay up and try and make sure no vandals sneak in while most are asleep. Fun times, --[[User:Iduan|I]][[User_talk:Iduan|Duan]] 00:40, 25 February 2008 (EST)
::I'll probably be on vandal watch too, if you don't get them first. --[[User:Liam Spencer|''' L.S. ''']] 00:41, 25 February 2008 (EST)

Talk:Letter to PNAS

2008-07-26T13:18:50Z

YoungA:

User talk:YoungA

2008-07-25T14:10:33Z

YoungA: Removing all content from page

Talk:Flaws in Richard Lenski Study

2008-07-25T13:51:35Z

YoungA: /* The letter is way too long... */ These are OLD jokes

Now, is this page a report over other people thinking Lenski's paper is flawed or is this Aschafly reporting about himself and putting it in the headline of the Front Page? And please specify by references which "two other" experiments are referenced, and explaing how you can see that the "historical contingency" is not true. --[[User:Stitch75|Stitch75]] 23:22, 12 July 2008 (EDT)
And if you think you argue that well, why dont you submit it as a comment òn the paper to PNAS. --[[User:Stitch75|Stitch75]] 23:24, 12 July 2008 (EDT)

:This article is seriously partisan. I see no outside or third party analysis of the paper in the references, just a bunch of cites to the article or conservapedia itself. [[User:Wisdom89|Wisdom89]] 00:34, 13 July 2008 (EDT)

Folks, you're in the wrong place if you're more interested in who says what rather than determining the truth itself. A true wiki gets at the substantive truth rather than trying to rely on biased gatekeepers and filters of the truth.

The flaws in the statistical analysis in Lenski's paper are clearly set forth and well-referenced. If you're interested in the truth, then look at the paper and see the flaws yourself. If you're not interested in the truth and think you can distract people's attention from it by using other tactics, then you're wasting your time here.--[[User:Aschlafly|Aschlafly]] 00:42, 13 July 2008 (EDT)

I agree with Aschlafly on this, there needs to be some kind of admission or response from Lenski but little has been forthcoming and conservapedia itself has taken it on. Notice how no-one, aside from conservapedia (and I think Creationwiki?) has asked such questions of Lenski? All the magazines etc have taken his study at face value without actually taking the time to critique his claims. Aside from the "peer reviewers" of course.
[[User:JJacob|JJacob]] 00:47, 13 July 2008 (EDT)

: The "peer reviewers" who spent somewhere between 0 and only 14 days looking at the paper, and missed an obvious contradiction between Figure 3 (specifying the "Historical contingency" hypothesis) and Table 1, Third Experiment. The statistical analysis in the paper appears so shoddy to me that I doubt anyone with real statistical knowledge or expertise even reviewed it.--[[User:Aschlafly|Aschlafly]] 00:59, 13 July 2008 (EDT)
::I have expertise in research and statistics and I'm just not seeing this shoddiness that you make reference to. You are allowed to have your doubts, but we should get a bunch of people familiar with such fields to examine the paper's statistical analysis. [[User:Wisdom89|Wisdom89]] 01:01, 13 July 2008 (EDT)
::I have the same problem. i hold a Dr.Rer.Nat title and did some statistics (although i am no expert on it) and fail to see the "shoddiness" please help my underdeveloped mind, Mr. Schafly and enlighten me. I it is so obvious it should be a one-liner to formulate it. --[[User:Stitch75|Stitch75]] 09:54, 13 July 2008 (EDT)

::: Please try harder then. I've expanded the explanations a bit also.--[[User:Aschlafly|Aschlafly]] 10:42, 13 July 2008 (EDT)

:::: At least now i can recongnize your statements more or less clearly. Yet i think (cite from the paper) ''We also used the Z-transformation method (49) to combine the probabilities from our three experiments, and the result is extremely significant (P < 0.0001) whether or not the experiments are weighted by the number of independent Cit+ mutants observed in each one.'' has to be addressed more specifically than you do in order to discredit the statistics used --[[User:Stitch75|Stitch75]] 11:54, 13 July 2008 (EDT)
:::::Just for comparative purposes and a frame of reference, a P value that is less than the significance level of 0.05 is considered significant. [[User:Wisdom89|Wisdom89]] 13:10, 13 July 2008 (EDT)

I wonder, do the PNAS allow questions to raised and asked of the "peer reviewers" themselves? Are we able to find out who/what experience they themselves have? Perhaps that is an avenue that we could look at? I apologise in advance if this has already been asked or answered.
[[User:JJacob|JJacob]] 01:07, 13 July 2008 (EDT)

:Definitly not. Peer reviewers are anonymous and only known to the editor, for good reason. Having peer reviewers non-anonymous would cause reviewers to be very careful to step on nobodys foot to evade revenge. --[[User:Stitch75|Stitch75]] 09:54, 13 July 2008 (EDT)

: No, PNAS probably won't disclose who supposedly did the 14-days-or-less peer review on the [[Lenski]] paper. You're right that such disclosure could shed some light on the final product.

: "Wisdom89", your claim that you "have expertise" and don't see the flaws only makes me conclude that you don't really have the expertise that you claim. Judging by your silly user name, perhaps you've tried that approach before. We're not fooled by it here.--[[User:Aschlafly|Aschlafly]] 01:14, 13 July 2008 (EDT)

(removed silly comment by person who has since been blocked for [[90/10 talk]] violation)

==Marginally significant==
In #1, that's not inconsistent. The figure makes it clear that, according to the hypothesis, the mutations should also occur earlier than 31,000, but should become more common at that point. 12/17 mutants occurred after 31,000. The point in #3 is not clear. What do you mean by ''weighting''? In #5, ''Lenski's paper is not clear in explaining how the results of his largest experiment...his paper refers to his largest experiment as "marginally ... significant," which serves to obscure its statistical insignificance.'' Actually, '''marginally significant''' is clear. It means that the p-value is between .05 and .10 (in this case it's .08, table 2). It's a pretty standard phrase to describe an effect that falls into that range. [[User:Murray|Murray]] 13:41, 13 July 2008 (EDT)

: Your defense of Lenski per point #1 is contradicted by the paper's own abstract, and by the comments by the other Lenski defender below. In point #3, proper weighting is needed to combine multiple studies. In point #5, you don't cite any authority for the unscientific claim of being "marginally significant."--[[User:Aschlafly|Aschlafly]] 20:45, 13 July 2008 (EDT)
: Your defense of Lenski per point #1 is contradicted by the paper's own abstract, and by the comments by the other Lenski defender below. In point #3, proper weighting is needed to combine multiple studies. In point #5, you don't cite any authority for the unscientific claim of being "marginally significant."--[[User:Aschlafly|Aschlafly]] 20:45, 13 July 2008 (EDT)
::Define "proper weighting". Are you referring to how they interpreted the sum of the work or to a specific analysis? You're right, I didn't cite any scientific authority. Here's one: Motulsky, H. (1995). ''Intuitive Biostatistics'', Oxford Univ. Press. Chapter 12. Also, try searching for the phrase in Google Scholar or PubMed, you'll find plenty of uses of it. It's a shorthand way of describing an effect that came close to the arbitrary threshold for statistical significance but did not reach it. [[User:Murray|Murray]] 21:55, 13 July 2008 (EDT)

::: You seem unwilling to accept that Point #1 identifies a clear mistake between the figure and the abstract in the paper, which requires correction by Lenski or PNAS. Given that unwillingness, I doubt it will productive discussing the other mistakes further with you. You're right that other usage of the dubious concept of "marginally significant" can be found on the internet, but the first link to such usage on my internet search for it returned the non-rigorous "Intuitive Biostatistics" and the second link returned a criticism of the concept similar to the criticism express here. [http://annhyg.oxfordjournals.org/cgi/reprint/49/1/93-a.pdf] --[[User:Aschlafly|Aschlafly]] 00:42, 14 July 2008 (EDT)
::::It's not a clear mistake in my mind. There does seem to be some confusion or contradiction in terms of the number of generations, but I haven't seen a clear explanation of why this is or is not a mistake. What seems like a contradiction is the abstract statement that no mutations occurred before 31,500, but it's not clear to me whether I'm misunderstanding that. ''I doubt it will productive discussing the other mistakes further with you. '' Of course you doubt it, because you are unlikely to be willing to concede anything no matter what anyone says. Why do you call the concept dubious? The procedure of determining whether an effect is significant requires the setting of an arbitrary threshold, which is usually .05. That means, in analyses of the sort in the Blount et al. paper, that there's less than a 5% chance that the findings are due to sampling error. When an effect comes close to the threshold it is worth noting, because of the problems inherent in significance testing, which itself is widely criticized in the statistical literature. I am not clear what you mean by weighting, as I mentioned before - in the interpretation or statistically? [[User:Murray|Murray]] 13:30, 14 July 2008 (EDT)

== Richard Lenski incorrectly included generations of the E. coli already known to contain Cit+ variants in his experiments.[3] Once these generations are removed from the analysis, the data disprove Len ==

The author of the above statement must not have read the paper or the supplement carefully. Lenski took clones from those cultures that '''weren't Cit+'''. Careful reading of the paper or the supplement reveals that Cit+ mutants appeared at 750 generations or later into the replay experiment. The authors write: "New Cit+ variants emerged between 750 and 3,700 generations..."--[[User:Argon|Argon]] 15:03, 13 July 2008 (EDT)

: Your explanation is not convincing. Show us how Lenski proved that the samples did not have '''any''' Cit+ variants, if you really think he's claiming that.--[[User:Aschlafly|Aschlafly]] 20:51, 13 July 2008 (EDT)

::I count at least four distinct diagnostic methods used in the paper for distinguishing whether clones are Cit+. One in particular they describe as being very sensitive to weakly citrate-using cells. It's not that I 'think' Blount et al. claim they started with Cit- cells. They say that in the 'Supporting information' document.

::Andy, for tonight, I'll leave it as an exercise for you to answer your own question of how one might test a clone to be sure that is was Cit-. Use the paper if you'd like or present another means. Tomorrow evening I'll cite the methods Blount used in the paper.

::Meanwhile, here's another question to ponder: If the colonies used to start the 'replay' cultures were Cit+ at the start, why is it that no Cit+ cells were found in such cultures before 750 generations? These cultures were all started from single clones which must have either had the Cit+ phenotype or not.--[[User:Argon|Argon]] 18:38, 14 July 2008 (EDT)

-
How did Lenski obtain Cit- clones from later populations after Cit+ had become the dominant phenotype? It's pretty standard procedure. First, keep in mind that these populations contained a minority of Cit- cells. Now, a small liquid growth is made from the frozen glycerol stock of cells from a given generation, say 32,000. This is grown to an appropriate OD and then plated on a standard rich media agar plate. Provided that the plated sample isn't too dense, this plating will deposit somewhere between 15-100 individual cells on the agar, with plenty of spacing between them. The plate is then incubated at 37 C for a given time, during which the individual cells replicate to form small, visible colonies. These colonies will consist solely of cells that are genetically identical to the original cell deposited on the agar. This is all well and good, but how do you find which of the colonies are Cit-? Here you use a technique called replica plating. The agar plate is gently inverted onto a sterile swatch of velvet so that some of the cells from each colony are deposited onto the fabric. Next, a citrate-only agar plate is pressed against the velvet, transferring cells from the fabric to the new plate in exactly the same spacial orientation as the first plate. The cells are then allowed to grow on the citrate-only plate. When we then compare the two plates, we look for colonies on the rich plate that did not grown on the citrate-only plate. These colonies will be Cit-, and can be used for the replay experiments. [[User:Gerlach|Gerlach]] 13:45, 14 July 2008 (EDT)

:Just a correction: The Cit+ cells didn't dominate the cultures at generations 32,000 & 32,500. Cit+ mutants represented 12% and 19% of the population at these times points, respectively. Replica plating is definitely one means of identifying Cit- and Cit+ clones but because the Cit+ cells represented a fraction of the total, it is simple enough to streak the samples to individual colonies (founded by single cells) and test each colony individually. Otherwise, a nice description of replica plating (a technique developed by Joshua Lederberg that allowed him do the research for which he was awarded one of the 1958 Nobel Prizes in Medicine)--[[User:Argon|Argon]] 18:38, 14 July 2008 (EDT)

::Oops, you're right, Argon. Cit+ wasn't dominant at generation 32,000, so replica plating might not be the best option. Still, in the case of almost 20% Cit+, I think replica plating might be labor reducing. I'm a biochemist by training, not a microbiologist, but I'm sure there are other methods that could be used. For example, Christensen's agar appears to provide a sensitive, colorimetric method of identifying even weakly citrate-utilizing colonies, so one might be able to plate cells on a Christensen's agar plate and pick uncolored colonies. Again though, I'm no microbiologist so I don't know the best method. However, there are ways to easily pick Cit- clones from later generations in this case. That said, I think that this specific "flaw" cited in Lenski's paper should be removed from the main article. Clearly, Cit+ were not used in the replays from later generations, so Conservapedia's objection is totally baseless.[[User:Gerlach|Gerlach]] 19:19, 14 July 2008 (EDT)
:::All appropriate descriptions. For generating estimates of the population distribution (Cit-/Cit+) in a culture, replica plating would certainly be applicable. The main point is that identifying and isolating Cit- clones from the generations used in the experiment is straightforward. I agree that it would be a mistake to keep that objection in the article (actually that thread runs across several points in the article).--[[User:Argon|Argon]] 20:12, 14 July 2008 (EDT)

:::: Nothing in the paper rules out contamination of those samples by Cit+ variants, and you quote nothing in the paper to rule it out. There was no reason to use and rely on these samples that already have Cit+ variants.--[[User:Aschlafly|Aschlafly]] 23:04, 14 July 2008 (EDT)
:::::The whole point of the discussion above was to illustrate that there are methods to isolate cells with a particular genotype from a mixed population. Suppose we used the replica plating method (maybe not the best choice, but it's standard procedure). Care to explain where the Cit+ contaminants could possibly come from? And the naivete inherent in objecting that "nothing in the paper" rules it out is simply astounding. Standard laboratory procedures, like isolating specific clones, typically don't show up in papers. For example, if I to write a paper on my research, it would not include a detailed discussion of the construction of my expression plasmid. I might mention that I cloned my gene into a particular vector, but there wouldn't a discussion of how I did my PCR, restriction digests, or transformations. Things like that are simply extraneous details that are taken for granted by experienced researchers. There is simply no reason for Lenski et al. to include a discussion of their method for isolating specific clones. This is why this whole exercise of Conservapedia criticizing Lenski's paper is folly, because most Conservapedia users simply don't know standard laboratory techniques. It's kind of important to know what scientists today are able to do on a routine basis before wading in to claim that they couldn't have done what they claim.[[User:Gerlach|Gerlach]] 09:05, 15 July 2008 (EDT)

:::::***** *****
:::::Actually the methods cited in the paper would separate the Cit+ lines from the Cit-. They took single colonies (founded by single cells), and tested them on selective agar (minimal citrate media - MC agar) and an indicator medium, Christensen's citrate agar (Product information from Sigma here: http://www.sigmaaldrich.com/sigma/datasheet/c7595dat.pdf). As Gerlach notes from the Blount paper, Christensen's citrate agar is very sensitive to citrate utilization. Typical ''E. coli'' strains do not produce a color change but other citrate-using enterics like ''S. typhimurium'' and Cit+ ''E. coli'' mutants appear pink/red on the plates.

:::::This conclusion is further validated (as I mention above), by the fact that Cit+ mutants did not appear immediately in the replay experiments (Others have also noted this). For example, in replay set-1, it took 750 generations before the first Cit+ mutants were isolated. Many didn't produce Cit+ cells after 3700 generations. If the starting line was Cit+, *all* the cells in the culture would have show up as Cit+ in the first pass.

:::::Overall, it is abundantly clear that the cell lines used in the replay experiments were not Cit+ at the beginning.--[[User:Argon|Argon]] 19:44, 15 July 2008 (EDT)

== 1. Lenski's "historical contingency" hypothesis, as specifically depicted in Figure 3, is contradicted by the data presented... ==

Again, more issues with comprehension: The authors did not know when the potentiating mutation first arose but they knew it was before generation 31,500. Figure 2 is merely figurative, being an illustration, and not quantitative. Their analyses suggested that the potentiating mutation did arise at about the 20,000 generation point or later. Their conclusion is that Cit+ mutation rate is low even in a potentiated background but apparently distinguishable from a low-incidence single, unpotentiated event.--[[User:Argon|Argon]] 15:04, 13 July 2008 (EDT)

== Statistics101 package: ==

What does the author imply by writing: "...Lenski himself does not have any obvious expertise in statistics. In fact, Richard Lenski admits in his paper that he based his statistical conclusions on use of a website called "statistics101"?

From the web site:
''Professionals: Although it was originally developed to aid students, the Statistics101 program is suitable for all levels of statistical sophistication. It is especially useful for Monte Carlo, resampling, and bootstrap applications. It has been used by professionals in many fields. These include anthropology, biology, ecology, evolutionary biology, epidemiology, marine biology, psychology, toxicology, veterinary pathology.''
It would appear that the package from the web site (not the web site itself) was used to perform the Monte Carlo resampling tests. Is there any evidence that the package produces incorrect results?--[[User:Argon|Argon]] 19:41, 13 July 2008 (EDT)

==Formal Response to PNAS==

''I've moved this thread from the open section above since this page is being categorized.'' --[[User:DinsdaleP|DinsdaleP]] 21:52, 13 July 2008 (EDT)

:::I think this article presents very sound arguments. Conservapedia should now take action, offering to publish a rebuttal of Lenski in the PNAS journal.--[[User:JBoley|JBoley]] 11:31, 13 July 2008 (EDT)

I agree with JBoley in that if Conservapedia wants to present a formal, professional response to Professor Lenski's paper that questions specifics within his paper, then it should happen. That is the proper execution of the scientific method, and I'm certain that a professional response to PNAS would yield better results than vague "give us all the data " demands. Is a formal response to PNAS from Conservapedia in the works, or is this article the only place these questions/objections were intended to be raised? --[[User:DinsdaleP|DinsdaleP]] 11:52, 13 July 2008 (EDT)

: I don't know if PNAS would embarrass itself by printing a rebuttal, or whether it has the integrity to retract Lenski's paper. Conservapedia's audience is probably bigger than PNAS's, and we're certainly not going to suspend our exposure of the truth here in order to await correction by PNAS.

: PNAS publishes, quite easy to find Rules for "Rebuttals" (they call it "Letter"). It is specifically what you want. [http://www.pnas.org/site/misc/iforc.shtml PNAS:Information for Authors] . I cite: ''Letters are brief online-only comments that contribute to the discussion of a PNAS research article published within the last 3 months. Letters may not include requests to cite the letter writer's work, accusations of misconduct, or personal comments to an author. Letters are limited to 250 words and no more than five references.'' --[[User:Stitch75|Stitch75]] 13:25, 14 July 2008 (EDT)

: In addition, Lenski has already demonstrated how he reads this site and he can certainly correct his own paper, and he should do so. Indeed, professionalism might support giving Lenski the time to correct it himself first.--[[User:Aschlafly|Aschlafly]] 12:14, 13 July 2008 (EDT)

::I understand what you're saying, but there's nothing improper or unprofessional in submitting a formal request to PNAS to have the points in this article addressed by Professor Lenski and his team. To be frank, you've been adamant in your insistence that PNAS has been less than rigorous in the review of Lenski's paper, so if one of your intentions is to demonstrate this then having PNAS respond to a formally submitted response to the paper in public would serve that purpose. This can be done in addition to publishing these objections on Conservapedia--[[User:DinsdaleP|DinsdaleP]] 12:21, 13 July 2008 (EDT)

:::If not PNAS, then perhaps some other public forum? I know Andy Schlafly has appeared on television, effectively arguing against gardisal and other dangerous vaccines. Perhaps if a TV program were interested you could argue against Lenski? You could be the spokesperson against these false claims of evolution.--[[User:JBoley|JBoley]] 12:24, 13 July 2008 (EDT)

:::: I'm not opposed to the above suggestions, but the future is here, folks. Lenski, PNAS editors and television producers have free will to reject or ignore the truth, and I'm more interested in getting the truth out here than trying to persuade someone in dying media like print or television. Lenski and his defenders can see the truth here, and they can decide for themselves whether to reject or admit it.--[[User:Aschlafly|Aschlafly]] 12:30, 13 July 2008 (EDT)

:::::I agree with you about the dying nature of print (I don't think television is dying, merely changing). The problem is that information about the flaws in Lenski's study are not registering outside of sites like Conservapedia. In effect, Conservapedia is an echo chamber. People that come to this site already agree with its point of view. I encourage you to attempt to attract the attention of other forms of media, or Lenski's false claims will simply be accepted as fact by the public and even worse, by educators.--[[User:JBoley|JBoley]] 12:36, 13 July 2008 (EDT)

::::::While there's nothing wrong with taking one's message to various forums or outlets, I believe there's a specific value in submitting these objections as a formal response to PNAS. Conservapedia was established as a trustworthy resource for students, and in my mind all of it's actions should be done with the goal of informing and educating. The Lenski debate is over the findings published in a scientific journal after undergoing a peer-review process. The objections to this paper by the CP leadership are not just about its content, but to the process by which it was reviewed and published in the timeframe it was. Talking about these objections is fine, but it's more instructional to the students using Conservapedia, and a better example of the scientific method in action, to respond to a scientific paper published in a journal through the formal process by which such papers are either defended or corrected. In the end, Lenksi's work will either stand up as good science, or any errors will be addressed and the paper's conclusions modified accordingly, which is also good science. Seeing this process in action regarding a such a significant paper is a great learning opportunity, and the Conservapedia leadership would be remiss in not standing by their conviction in these objections and submitting them formally to PNAS. --[[User:DinsdaleP|DinsdaleP]] 12:38, 13 July 2008 (EDT)

PNAS has a letters section available with the online edition. Many journals have a letters section for rebuttals or clarification. Legitimate corrections are welcome. Andy, have you run your list of 'flaws' past any biologists?--[[User:Argon|Argon]] 15:36, 13 July 2008 (EDT)

: Funny, Argon, how you don't apply your demand of expertise to Lenski himself. What are Lenski's credentials with respect to statistical analysis? Has he even taken and passed an upper-class statistics course of any substance?--[[User:Aschlafly|Aschlafly]] 00:45, 14 July 2008 (EDT)

::I don't follow. Are you suggesting that Lenski doesn't understand the proper application of the statistical methods used in his paper? If so, I haven't seen a description of which alternate methods you'd employ, let alone any output from such an analysis. Here's a thought: Why don't you substantiate your claims by writing up the work and submitting it as a correction letter to PNAS?--[[User:Argon|Argon]] 18:46, 14 July 2008 (EDT)

::: Argon, if you really "don't follow," then try harder. You insist on credentials by others who criticize Lenski, and yet you do not insist on expertise by Lenski in statistics with respect to his "analysis". Perhaps Lenski should first take and try to pass "Statistics 101" before trying to use a website by its name to draw flawed conclusions.--[[User:Aschlafly|Aschlafly]] 22:36, 14 July 2008 (EDT)

::::Do you really think that Lenski went to statistics101.net to learn about statistics and how to apply them? That simply is not the case. The Lenski group knew that they needed to do a Monte Carlo resampling analysis on the results of their replay experiments. In this situation, they are faced with two choices: either code an appropriate program themselves, or utilize one that has already been developed and is readily available to researchers. Since statistics101 had such a program available, they chose the latter option. Statistics101.net was simply the source of the program that the Lenski group used to perform the statistical analysis. If you want to argue against that choice, then you need to examine the source code for the statistics101 package and enumerate why it should not have been used.[[User:Gerlach|Gerlach]] 11:40, 15 July 2008 (EDT)

::::***** *****
::::I don't insist on credentials per se. I *recommend* developing a working understanding of the experiments or a willingness to do the necessary background research to get the details straight before heading off on possibly the wrong direction. It saves a lot of thrashing about. It's perfectly OK to raise questions but before leveling accusations it might be nice to do that privately and discuss that with others who can provide useful feedback. Just my 2 cents.--[[User:Argon|Argon]] 19:48, 15 July 2008 (EDT)

::Mr. Schlafly, does your response above, "I'm more interested in getting the truth out here than trying to persuade someone in dying media like print or television", mean that you will not be submitting a response with these identified flaws directly to PNAS? As I mentioned above, it takes nothing away from the value of posting these statements here on CP to also submit them to PNAS, but the proper way to prompt a journal to review and correct an article is through a direct response, not publication on an unrelated website like CP. It's not proper for anyone but the author(s) of the objections in this article to make that submission, so I'm hoping they step up with the conviction of their beliefs and respond to PNAS directly. Thanks. --[[User:DinsdaleP|DinsdaleP]] 12:32, 14 July 2008 (EDT)

::: By now Lenski has probably seen the flaws identified on the content page here. What's "proper" is for him to correct his own paper in PNAS. The criticism will likely continue as long as he declines to do so. If anyone here would like to educate the PNAS editors about the flaws, then please feel free to do so.--[[User:Aschlafly|Aschlafly]] 22:36, 14 July 2008 (EDT)

::::I'll be glad to submit these items to PNAS on behalf of Conservapedia using the "Letters" forum described by Stitch75 above. Should I cite you the author of this analysis, and is there an email you'd prefer me to include instead of my personal one for any PNAS response? I'll put up a draft of the Letters submission here for your approval before sending anything out. Thanks. --[[User:DinsdaleP|DinsdaleP]] 18:39, 15 July 2008 (EDT)

:::::It would have a very strange scientific taste should somebody else that Mr. Schlafly be the first author of the letter (however, if you insist on that, i suggest "personal communications" as the right kind of citing the work here.). It is his turn to stand up to his claims in this way (by publishing it into a Forum which he is not the owner of). I personally share the doubts of many here about his argumentation (and his understanding os the experiments), but i am sure only more of his dismissive comments will follow. However i see that he comes up with a clear alternate Hypothesis (contamination), so he is free to show that this is more likely (calculations please) and peform Monte-Carlo simulations on it (for a person complaining that statistics101 is to simple that should be no difficult task). As far as i understood and see the data Lenski and coworkers did the best to exclude this Hypothesis, however i did not run own simulations (And I won't do it, because i think nothing will come out - furthermore Mr. Schlaflys personal style in the communication "you have to try harder" is not the style i am used to be adressed by people whose qualification in a subject is appearlingly nor more than mine). So running the simulation, evaluating his own hypothesis using a valid statistical method is now Mr. Schlaflys job - if he come up with a decent calculation showing this Hypothesis is more likely, the letter would for sure be accepted and Lenksi would have to react. If Mr. Schlafly is not the first author of the letter he could evade the critics after that by saying that he was misunderstood, which means somebody else take the risk of submitting the letter, but in case of success Mr. Schlafly would take the glory. --[[User:Stitch75|Stitch75]] 20:10, 15 July 2008 (EDT)

::::::I would prefer that Mr. Schlafly submit his objections to PNAS directly as well, but since he has declined to do so the next best response is to submit it "on behalf of Conservapedia", which he has authorized above. I'll post the draft letter tomorrow, and it will credit him as the author unless I'm asked to include other individuals who contributed to the analysis. --[[User:DinsdaleP|DinsdaleP]] 22:05, 15 July 2008 (EDT)

:::::::I hope ASchlafly does offer a rebuttal of Lenski's flawed "study." However, if he does not, I am all for DinsdaleP's suggestion. I look forward to reading your draft. If you take all the objections that Conservapedians have raised to Lenski's paper, I do not see how PNAS can possibly object.--[[User:JBoley|JBoley]] 11:28, 16 July 2008 (EDT)

::::::::They could object because Conservapedia's criticisms are obviously false. If this page hasn't made that clear, I don't know what could.[[User:Gerlach|Gerlach]] 13:44, 16 July 2008 (EDT)

:::::::::They would have to prove that Conservapedia's criticisms are false, and they cannot do that. You sound like a Lenski supporter. You need to open your mind to the truth.--[[User:JBoley|JBoley]] 13:59, 16 July 2008 (EDT)

:::::::::Gerlach, the most obvious lesson from this page is how a few, yourself included, seem determined to defend a flawed paper no matter what the truth brings. You have free will to reject whatever you want, but you're only hurting yourself by that approach. People who do open their minds are amazed by the insights and happiness it brings.--[[User:Aschlafly|Aschlafly]] 21:54, 16 July 2008 (EDT)

:::::::::This is such a strange response, Andy. The attitude that you and several of your defenders seem to have is that the criticisms you have made of Lenski's paper cannot be rebutted. However, the fact that you ''can'' level criticism at something doesn't make that criticism true. That is, you may be wrong. And that is the case here. Myself and others have pointed out that your alleged flaws in Lenski's paper are incorrect, and based on misunderstanding it, or, even worse, simply not reading it carefully. There has been little to no substantive response to our detailed rebuttals. Replies from you or other defenders of the Conservapedia article amount to little more than brazen declarations that we are wrong or "nonresponsive", and that criticisms in the original article remain unscathed. But for people who claim to have "the truth" on their side, this is simply baffling. If the veracity of your claims against Lenski's paper is so obvious, then it should be an easy task to provide in depth responses to the points that we have been raising against your article. I'm not above criticizing scientific papers. Bad papers get published frequently, after all. However, Lenski's paper does not appear to be one of those. Notice, though, that I am not claiming it to be perfect, no paper is. That said, whatever flaws the paper may have, those presented in the Conservapedia article are not among them. [[User:Gerlach|Gerlach]] 11:43, 17 July 2008 (EDT)

:::::::::: Gerlach, now you seem to admit that the Lenski paper may be flawed, but that Conservapedia has not identified any of those flaws! With all due respect, you seem to have taken closemindedness to new heights.

:::::::::: Lenski claims there is a mutation rate, yet his presented data show that the number of mutations do not scale with sample size. His presented data disprove both of his hypotheses.--[[User:Aschlafly|Aschlafly]] 13:27, 17 July 2008 (EDT)

:::::::::: First, we need to clarify what we mean by "flaw". Are we talking about serious methodological flaws or errors in interpretation that fatally undermine the paper's conclusion? If so, I fail to see any such flaws. Of course, any honest scientist recognizes that any work at the frontier of science has the potential to be wrong. It ''may'' be that future work shows Lenski to be wrong. But let's not confuse this possibility with actuality: saying that something might be wrong is not the same as saying that it is. On the other hand, by "flaw" we may mean minor experimental details that could have been better. In this case, the paper is flawed, and Lenski himself admits this in the supporting information. But ''every'' paper is flawed in this manner, and I doubt you'll find any investigator who wouldn't say that they wish they had done some things differently during the course of their research. As an example of what I'm talking about, the Lenski group's statistical analysis would have been improved if they could have accounted for the evolution of increased cell size (and, therefore, decreased cell density) in later generations. As it stands, their analysis ''underestimates'' the potentiation effect in these generations because replays of later generations involved fewer cells. But this flaw, and other flaws of this type, do not undermine the conclusion of the paper.

:::::::::: Regarding the mutation rate argument, see the earlier discussion on this page. The third experiment was significantly different than the first two. The experimental scheme was different, it was performed at at different time and with different conditions, and utilized, for the most part, different clones than the first two. And Lenski doesn't just claim there is a mutation rate in potentiated cells, he ''actually measures it''. But frankly, I don't understand your argumentation here. It seems that you are trying to suggest that all the Cit+ mutants isolated were the result of contamination. This clearly isn't the case, for several reasons. However, this isn't the place for this particular discussion, as there is already such a discussion elsewhere on this page. I still haven't seen any adequate response to our points against the Conservapedia article, and I don't think I am closed-minded for expecting such a response. As I said, I'm open to the possibility that the Lenski paper is flawed, but I expect cogent argumentation to support any such flaws. I haven't seen that here.[[User:Gerlach|Gerlach]] 15:09, 17 July 2008 (EDT)

::::::::::: Gerlach, look at how many words you used to sidestep my simple explanation of a flaw in Lenski's work: "Lenski claims there is a mutation rate, yet his presented data show that the number of mutations do not scale with sample size. His presented data disprove both of his hypotheses." If the third experiment of Lenski's was independently flawed as implied by your response, then that does not help your defense. Note that in Lenski's second experiment the mutations also failed to scale with sample size.--[[User:Aschlafly|Aschlafly]] 18:26, 17 July 2008 (EDT)

::::::::::::I think there is a misunderstanding. Blount et al. did not say that the absolute mutation rate was constant for the generation of Cit+. After all, they found that variations in culture conditions had some effect. The replay experiment was performed to determine if clones from later cultures were more or less likely to give rise to Cit+ cells than clones from earlier generations. The authors' hypothesis was that a potentiating mutation was required before the Cit+ mutations could arise. If that was the case then clones from later generations would be more likely to produce Cit+ cells. If the Cit+ capability was the result of an extremely rare, single mutation, then any generation of clones would be equally likely to produce Cit+ cell. The hypothesis is that in a particular experiment, the '''relative probability''' of generating a Cit+ mutant would be greater with clones from later generations. '''Absolute mutation rates''' (which appear to be Andy's concern) may be contingent on the growth conditions, which differed between the three replay experiments but '''''within any particular set of conditions''''', one might expect the relationships between Cit+ recovery and the generations from which the starting clones were derived would still hold.

::::::::::::pg 7902 of the paper in the journal:
::::::::::::"According to the rare-mutation hypothesis, Cit+ variants should evolve at the same low rate regardless of the generation of origin of the clone with which a replay started. By contrast, the historical-contingency hypothesis predicts that the mutation rate to Cit+ should increase after some potentiating genetic background has evolved. Thus, Cit+ variants should re-evolve more often in the replays using clones sampled from later generations of the Ara-3 population."

::::::::::::From the abstract:
::::::::::::"The long-delayed and unique evolution of this function might indicate the involvement of some extremely rare mutation. Alternately, it may involve an ordinary mutation, but one whose physical occurrence or phenotypic expression is contingent on prior mutations in that population. We tested these hypotheses in experiments that ‘‘replayed’’ evolution from different points in that population’s history. We observed no Cit+ mutants among 8.4 x 10^12 ancestral cells, nor among 9 x 10^12 cells from 60 clones sampled in the first 15,000 generations. However, we observed a significantly greater tendency for later clones to evolve Cit+, indicating that some potentiating mutation arose by 20,000 generations. This potentiating change increased the mutation rate to Cit+ but did not cause generalized hypermutability."

::::::::::::What the authors found was that the later generations really did produce more Cit+ mutants than you'd expect if the Cit+ mutation was instead randomly distributed (or, as Andy has claimed and not yet retracted, contaminated by Cit+ cells). Yes, the absolute rates didn't scale across the three different conditions but within each experiment it is clear that the Cit+ mutants arose from cells taken at later generations. Yes, there were differences in the absolute rates under different conditions but that doesn't mean the results and conclusions about potentiated clones are wrong.

::::::::::::As for calculations of mutation rates: Blount et al. performed additional fluctuation experiments (journal pg. 7903) in an attempt to estimate the relative effect of the potentiating mutation and to calculate a rough estimate of the mutation rates. Keep in mind, those rates '''''are referenced to growth under the specific conditions used in that particular experiment''''' and were used to provide ballpark estimates for comparison to other classes of known mutations. As for the second experiment not 'scaling' (with the first?), I wouldn't expect that. The first involved clones grown in continuous liquid subcultures and both the total number of generations, cells/generation and growth conditions (e.g. liquid with nutrient replenishment vs. solid agar) are very different.--[[User:Argon|Argon]] 19:20, 17 July 2008 (EDT)

::::::::::: I have not "sidestepped" your point, Andy. Your claim is that the number of Cit+ mutants obtained did not scale with sample size in the third experiment. In response, I reiterated what Argon and I have said previously, specifically that there are differences between the third and second experiments that make a straight comparison between the two inappropriate. That said, if anyone is sidestepping the issue, it is you. Argon and I have addressed your objection previously, but your only response has been to stubbornly restate the original claim. If you don't agree with our statements, then you must explicate why. Additionally, I did not say or imply in any way that the third experiment was flawed. I said that it was significantly different from the second, but this is not the same as saying it was flawed. Argon has provided a response to the scaling of the second experiment to the first.[[User:Gerlach|Gerlach]] 20:21, 17 July 2008 (EDT)

:::::::: In response to earlier postings about drafting and submitting a letter to PNAS, I'm for it and would be happy to contribute. In response to a comment above, I don't want any "glory" and learned a long time ago that nobody gets credit or money for telling the truth. More often those who speak the truth are reviled and insulted, but mockery doesn't bother the truth as much as it bothers falsehoods.--[[User:Aschlafly|Aschlafly]] 22:01, 16 July 2008 (EDT)

::::::::: (removed false and baseless claim by Argon about sponsorship of this site)

==Draft of PNAS Letters Response from Conservapedia==

''Apologies for the delay in following up on this - I've spent the past few days attending to family priorities, and this is my first CP-related priority now that I have time at my PC again.''

''Since the guidelines for submitting PNAS Letters restricts the submissions to 250 words, the following is the draft submission I'd like to send pending Andy Schlafly's approval:''

:: ''Title:''

::: Identification of procedural and statistical flaws in the paper "Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli".

:: ''Author:''

::: Andrew Schlafly, B.S.E., J.D.

:: ''Author Affiliations:''

::: www.conservapedia.com

:: ''Text:''

::: Flaws in this PNAS paper negate its claim that ''E. Coli'' bacteria underwent an evolutionary beneficial mutation. See http://www.conservapedia.com/Flaws_in_Richard_Lenski_Study and its talk page. The flaws include:

:::: 1. Figure 3 depicts an "historical contingency" hypothesis at about the 31,000th generation, but the abstract states that "some potentiating mutation arose by 20,000 generations." The paper fails to admit that the Third Experiment disproved the hypothesis depicted in Figure 3.
:::: 2. The hypotheses suggest a fixed mutation rate, but the failure of the mutations to increase based on scale disproves the hypotheses. If the Second and Third experiments were so dissimilar to the First Experiment that they cannot be compared for scale, then it was error to treat them as similar for the statistical analysis.
:::: 3. The paper incorrectly applied a Monte Carlo resampling test to exclude the null hypothesis for rarely occurring events. The Third Experiment results are entirely consistent with the null hypothesis.
:::: 4. It was error to include generations of the E. coli already known to contain trace Cit+ variants, and the otherwise highly improbable occurrence of four Cit+ variants from the 32,000 generation in the Second Experiment suggests an origin from undetected pre-existing Cit+ variants.
:::: 5. The Third Experiment was erroneously combined with the other two experiments based on outcome rather than sample size, thereby yielding a false claim of overall statistical significance.

::: The underlying data for this taxpayer-funded has not been released to the public, despite requests to do so.

cc: Editor-in-Chief, PNAS
 New Scientist
 Selected Congressmen having oversight for research budgets
 Selected watchdog groups

''Mr. Schlafly, please let me know if this is acceptable, and apply any revisions as you see fit, thanks. --[[User:DinsdaleP|DinsdaleP]] 10:38, 21 July 2008 (EDT)''

: It's an excellent draft, DinsdaleP. I made a few minor revisions above. After others improve this, then I'll plan on sending it to PNAS later this week. {{unsigned|Aschlafly}}
::I like it. I'll sign my name to it when the time comes.--[[User:DamianJohn|DamianJohn]] 09:35, 22 July 2008 (EDT)

(unindent)

Thanks for the feedback - When applying changes, please keep in mind that the "Text" section in the final version needs to be 250 words or less. If there are important points to add that would exceed this limit, they could be added to the main [[Flaws in Richard Lenski Study]] article instead since PNAS is being asked to respond to the full list there, and not just the summary. --[[User:DinsdaleP|DinsdaleP]] 09:47, 22 July 2008 (EDT)

: I think if i would have presented some draft of that quality to my supervisor i think i would not have reached the door of his office alive and in one piece. It starts with the fact that the correct citation of the article is missing. Please use the appropriate form, inclucing journal number and page. Please have a look at other PNAS Letters. Restate the central issue you criticise in the first sentence, then explicitely describe what your claim about the same issue is and state using what method you come to your conclusion. Keep a neutral tone. Don't make requests. It is obvious that the original author should respond (please look at PNAS for examples of responses, which are published at the same location). Plese fill in your numbers and precise arguments at the points where i left the dots in the following suggestion ('''Please note that nothing of this is my opinion, i just tried to rephrase your opinions in a way that they have the chance to be exposed to a broader view - i skipped tyhe details, because i will not rephrase your arguments, just the structure'''):
: Recently ...... inferred from their experiments (1) that ...... . We analyzed the statistical analysis in terms of ..... and conclude that several variables do not scale as .... . Using hypothesis tests under such circumstances is, in our opinion, ...... , and we do not understand how the authors of the original publication ..... their results.
: The replay experiments yield an ..... scaling with .... . We do not find a consistent value of ..... between the experiments. Furthermore the statistical deviation due to ...... in each sample set does not allow to infer ..... with a sufficient precision. This lack of scaling makes, in our opionion a constant or random source of contamination a likely explanation for a random observation of the ...... dependence of the mutation rate claimed in the paper. The following calculation supports this hypothesis: ....... .
: Furthermore we point out that Fig. ... contains a serious disagreement with .....: while the data would suggest ..... from gen. ..... the figure suggests .....
: We find the material cited in the original article (2)...(n) about the same long-time experiment not to describe the following procedures and experimental constants in a way accessible to us: Handling of ..., contamination rates of ...., and ..... We would kindly ask the authors to clarify these issues. --[[User:Stitch75|Stitch75]] 12:48, 22 July 2008 (EDT)

::No offense taken. I have no experience in these types of submissions, and would appreciate it if you could restructure the submission improve the quality while adhering to the 250-word limit. As I suggested above, it makes the most sense to incorporate these revisions into the main page for this article, where length is not an issue. --[[User:DinsdaleP|DinsdaleP]] 12:52, 22 July 2008 (EDT)

::: I realized that you have obviously not much experience in it; getting the right tone for a scientific publication is hard and i had to try it quite some times on conferences and i still dont get it right sometimes - and from what you said seem to be a student. Sadly, it is against my conviction to rephrase the original arguments in the right way because it would make me an co-author of argumentations i strongly object. In case you did not realize it, helping here to get the structure right doesn't mean i agree - actually the two reasons i would like to see it published is because then the (wrong) idea that scientific journals are not accepting criticism could be obviously be put aside and because i would like to see the needed scientific rigorousity applied to the arguments presented here, because this would put this discussion onto a scientific basis. Quite frankly - i am a liberal by the standards of this site. But i believe the discussion must be carried out with all respect to define the borders of science. The more effective the discussion is carried out, the better the outcome will be. I am willing to listen, as i have proven here, even when beeing treated by people like Mr. Schlafly as if I would be one of his students, while evaluating his qualification in natural sciences quickly shows that i more likely could supervise him in the issues he discusses here (which is something he has proven all along). Regarding that, i am close to giving up, but nevertheless i have seen that a lot of conservatives actually are willing to lead this discussion in a scientific way, which is something, which fulfills me with hope. I recommend you not to fight a fight in where you don't understand the arguments. Don't pick up arguments from others. If you can not fill in the missing words, numbers and arguments in my text, i cant help you. I see what Mr. Schlafly believes, however i do not know how to get the calculation right to support his hypothesis (random or contant mutation rate) - and, this is most likely not because of a lack of statistical knowledge. The only way i would see is to use the rudest form of descriptive statistics and agreggate the data in a very specific way, while ignoring the structure of the experiment - and ignoring the fact that the authors pointed out the problem they see and adressed them. So i can only give oy a few hints (maybe i can form a short contibution to conservapedia; i am just thinking about the title):

:::: If you claim something is wrong, put your opposing claim in a positive formulation, with a supporting calculation, in contrast . Even if the calculation is simple, this is very important to provide it. E.g. we estimate a rate of x+-y per z for dataset N, in which we aggregated generations a,b,c,d, etc .... In the end, you should either prove a mathematical mistake (which was not done) or shoe you hypothesis is more likely.

:::: Don't be rude. You are not the referee and you are not member of a commitee to examine scientific misbehaviour. Dont act like one (and even referees have a friendlier tone usually). Dont act like an personal enemy either. Don't ask for retraction of the article. It is up to the author to make the conclusion respond or retract. This happens more often than you may think as a response to an critisism (actually it's fun to read the "reply section" of scientific journals - sometimes you find things like: "yes, the commenter was right we copied the paper and retract it"). And you are never requesting, but you are kindly asking. Everybody understands that "kindly asking" does not mean "kindly asking" in this context.

:::: Always give full and specific citations which back your claims. Give it in the form required by the specific journal. General citations like "materials on his website" will make your text bein trown out in the editorial screening (because you can not expect that somebody read trough all information to find something backing you claim - this is your job). See for specific styles [http://en.citizendium.org/wiki/Citation_style[http://en.citizendium.org/wiki/Citation_style]]. Ypu may even reference a page/paragraph/eq/figure number to point the reader to what you mean (for papers longer than 4 pages i usually do that).

:::: Run a style checker over your text to eliminate common style mishaps.

:::: '''Most important''': go to your university library. Take the time to just read a few PNAS Letters and replys, and the original articles (Try to finde some with an easy understandable subject). Understanding how these are written and how authors usually reply will help you to get your one right. You are writing against somebody who has twenty years of experience in a field of publishing in natural sciences. You seem to have little experience and Andrew Schlafly, honestly, neither. This game is an uphill battle and unfair game anyway. Make sure you maximize your chances by understanding the rules of the game.

:::: Focus on a single you are sure about. It is better to present one claim well that two claims badly.

:::: Good luck. You will need it. --[[User:Stitch75|Stitch75]] 14:22, 22 July 2008 (EDT)

::::: "Stitch75", you seem to think that the truth depends on whether PNAS accepts it. It doesn't. Lenski's paper is badly flawed regardless of whether he admits it, PNAS admits it, or you admit it. That's the beauty of the truth: it doesn't require admission by anyone. I'm fine with Lenski and PNAS refusing to admit the flaws in their paper. After all, if they really cared about quality then I doubt they would have published their flawed paper after merely 14 days or less of peer review.--[[User:Aschlafly|Aschlafly]] 15:38, 22 July 2008 (EDT)

:::::: Maybe its because English is not my native language. Somehow you seem not to understand what i am saying. I try to rephrase it so that there is no room for misunderstanding: I never can talk about truth, which is a religious thing. I talk about science and observable reality. Primarily i can tell you only what it takes that your thoughts are at least looked at. If rejection happens du to formal reasons (like using unsuitable Formulations, etc) it's not good to draw conclusions on the content or the scientific community. The strong formalism is to save time. And in turn the taxpayers money. I am screening the title of approx. 70 articles per day (10 Minutes), namely everything which come in on the preprint servers on my subject. From approx 70 titles, 10 are interesting enough to read the abstract (6 Minutes), and 2 are interesting enough to look at the summary (4 Minutes) and one in two days in interesting enough to read Section 2 (10 Minues), skipping the introduction, one in a week in interesting enough to print it out and read it (2-4 Hours). Something which does not follow the form end up with beeing thrown out of my rss feed quite quickly. The editors of the journals know that and in a refereed journal such thigs may even be trown out by the editor (and not the referee). Claiming from not getting a response published that "the article is still wrong, no matter what others say, and i am rights anyway" doesnt sound very scientific to me. From everything you have said here, you are unwilling to learn, and you don't expect a response. If you formulate your comment in that way, then skip it. Publishing a letter should stimulate a discussion, if it's not meant to, seen from the style, it will not be accepted. Moreover, according to everything i have seen here, Mr. Schlafly, you seem to have no clue what you are talking about. Please at least consider one time that you could be wrong and try to follow the statistical arguments in the paper - and build up own one on a real calculation (and show the numbers you get). --[[User:Stitch75|Stitch75]] 20:55, 22 July 2008 (EDT)

::::::::: Stitch75 - you are too far inside the belly of the beast to understand what ASchalfly is talking about. You have probably spent your (young, naive?) life as a scientist, or inside the sciences, and as such you are blinded and cannot think with real, free logic. If you look at ASchlafly's arguments with an open mind, and not the blinkered mentality you seem to want to perpetrate, you'll see he's got many excellent points, and I'm convinced that the PNAS will ask Lenski to retract major conclusions of his obviously flawed study once ASchalfly submits this letter. Try to open your mind more to other ways of thinking and you'll see the truth for what it is. [[User:RobCross|RobCross]] 21:01, 22 July 2008 (EDT)

::::::Stitch75 just went far out of his way to be helpful and yet you still continue to respond with hostility and a self-righteous attitude. You explicitly stated that now matter what response you get, you won't accept the conclusions of the paper. That is your prerogative, but you are directly stating that their replies, other than a retraction, will be irrelevant and/or wrong, despite the '''many decades''' of combined practical experience of the authors compared with your complete lack of such. So why is it again that you're even bothering? Several contributors to this forum and others related to it on this website have addressed your questions in great detail- repeatedly- and you continue make vague, unspecific accusations. As Stitch75 discussed, something like "table X is wrong because of figure Y" is nonproductive. Furthermore, if you want to have PNAS readers listen to you- your flaws should be real. For instance, even now your fifth "flaw" is that the statistical results of the third experiment are "obscured" and "not defin[ed]... in the traditional way". Well, the p-value for the third experiment is 0.0823. It took me literally four seconds of flipping through the PDF to find it. It's even in a nice table to make it easy to find. How is that obscure? (I might add that considering P<0.05 significant and P=0.0823 not statistically significant is '''completely arbitrary'''. If the observed pattern wasn't at all what was expected, the P value would be roughly around 0.8-1.0 or so. So 0.0823 ''does'' suggest that the underlying idea is correct in '''exactly''' the same way that P=0.05 would. That is a fundamental concept in basic statistics.) The final problem is that your arguments have drifted from your original concern- whether or not a new trait evolved- since only one of your listed "flaws" actually addresses this issue. The others are tangential and relate to interpretation and mechanisms. Even ''if'' 6 of your 7 flaws were so, the core finding of the paper- around which all else is based- would still hold: in earlier generations, there weren't Cit+ E. coli, in later generations, there were. The mathematical analyses and timeline of occurrence don't change this qualitative, directly observable fact.

::::::I do encourage you to refine the letter and submit it to PNAS- I really do- but Stitch75 is very correct in saying that if you submit it in its current shoddy form it will be laughed at and promptly ignored. You would do well to take the advice of people who actually work in the field when it comes to considering how something will be received. Also, your comment about peer review above indicates that your still have not learned anything at all about how it actually works despite the long discussions previously.

::::::As you said, the truth doesn't require admission. But it does require empirical support, which Lenski provided in ample quantities- but you still have yet to provide anything even beginning to resemble scientific rigor. That is why Stitch75 wrote that response- to ''help you'' improve your letter from that condition.[[User:Kallium|Kallium]] 21:36, 22 July 2008 (EDT)

::::::: You have it backwards, "Kallium". Lenski has the burden of providing "scientific rigor," and his paper falls short. In fact, the data presented in the paper tend to ''disprove'' his hypothesis about a mutation rate, as the mutations identified in his paper do not scale in a meaningful way with sample size.--[[User:Aschlafly|Aschlafly]] 23:11, 22 July 2008 (EDT)

:::::::: I honestly don't know how to make this any more clear. Yes, Lenski does have the burden of providing scientific rigor, as any scientist does. I never said otherwise. However, to claim flaws in any study requires that they be presented with equal rigor. This is just rewording the last statement of my previous post. Simply making vague, unspecified and unsubstantiated hand-waving claims won't get you anywhere. Consider an analogous situation in an appeals court: someone doesn't like the decision of a lower court, so they go to a higher level to present their objections. Now, to do this requires legal rigor to the same degree with which the decision was originally made. The defendant would need to address specifics in the decision and explain exactly why they were incorrectly interpreted. If, however, that defendant were to waltz into the higher court and simply read quotes from the decision and say "that's illogical" or "those statements are self-contradictory" or "that's unfair", without going into detail to explain their reasoning and without addressing the previous cases cited in the decision or providing any further legal precedents, they would utterly fail to make their case and likely be chastised by the judge for wasting the court's time. Now replace the court references with their respective scientific analogs and you have exactly what is going on here. That is why both Stitch75 and I have been giving you this advice- to ''help you present your case''. Lastly, you haven't developed your arguments since you first posted them but keep relisting them. You have yet to show in detail how the data disprove the hypothesis (which you also vaguely define), and as others have explained repeatedly, mutation rates are only expected to scale with sample size under identical conditions, which were not used. That's why your letter needs improvement- it simply won't be taken seriously if it shows a flawed understanding of basic experimental biology. You can't pass rigor completely off of your shoulders; you have to make your case or it will get thrown out of court.[[User:Kallium|Kallium]] 12:12, 23 July 2008 (EDT)
:::::::::You are correct that the truth does not require acceptance. Kallium is not quite correct in in saying that it requires empirical support. It does not, the truth is the truth is the truth and that’s an end to it. The ''search'' for truth, however, requires certain actions and, in this case, Stitch75’s advice should be welcome. Following Stitch75’s advice will not alter the truth one little bit, but will aid the search for it. According to you the truth is that this was a flawed paper that was published, demonstrating flaws in the peer review process. It gets science nowhere, the public scrutiny of science nowhere and the use of public money nowhere for this simply to ''be'' the truth. The scientific community would need to see your objections in the "correct" format before it would do anything about it.

:::::::::You may say that the scientific community should be doing this already. (We might also question whether the format stipulated by the scientific community really is "correct"). Whether they should or should not is moot: the simple fact is that they aren’t and are unlikely to start anytime soon without a “correctly” prepared objection. Stitch75’s advice is designed to help you prepare the objection “correctly” and, in doing so, aid the search for truth.--[[User:YoungA|YoungA]] 09:26, 24 July 2008 (EDT)

::::::::::YoungA, I think we're thinking along the same lines, just using different vocabulary. As you said, reality is what reality is (in that sense of the word "truth"- I changed words to avoid the usual connotation of the vague philosophical ideal, which is itself unproductive). My meaning was the same as yours, referring to "truth" requiring empirical support in the sense that any given claim to it must be backed up by real evidence. But thanks for explaining the situation from a different angle.[[User:Kallium|Kallium]] 15:55, 24 July 2008 (EDT)

I tend to agree with you Andy. I say we get this thing sent to PNAS and see what happens. If they refuse to answer it then we know what that means, and if they thumb their noses at you that's fine too. However I have a little more faith than you in the system and I hold out hope that they'll respond to our queries. Anyway lets get this thing sent. --[[User:DamianJohn|DamianJohn]] 15:50, 22 July 2008 (EDT)

(unindent)

I'd like to thank Stitch75, because he took the time to explain his points constructively, and I learned something from them. (I'm actually an IT Specialist in my 40's, not a full-time student, but learning is a never-ending process and I appreciated the lesson). I consider myself bound by the same ethical constraints on editing that he mentioned, because these objections to Lenski's work are Mr. Schlafly's, not my own. I tend to believe that the Lenski experiment was properly executed, but I'm a strong believer in the scientific process, and Mr. Schlafly's objections deserve a fair hearing whether one believes in them or not. My contribution is to help in the process of getting these objections to the proper forum, namely PNAS, and leaving the response up to them. --[[User:DinsdaleP|DinsdaleP]] 16:20, 22 July 2008 (EDT)

While some here are willing to discuss, obviously Mr. Schlafly seems to be not. This will be the last thing i say before i see a calculation by Mr. Schlafly and everything else has been said already. I point out that submitting an Letter to any journal will involve the "editor in chief" exactly if the internal handling process of the journal involves this. So it is arrogant to prescribe the journal who should read the submission. Furthermore i think, that if you send this with a cc to "watchdog" groups, you should read the publication guidelines of PNAS. it might be that it collides with the publication guidelines to publish the contribution somewhere else at the same time. This most likely holds for articles, and maybe for comments/letters as well. To put congressmen on the cc is, in my opinion a waste of taxpayers money. it would be much better to wait until you have something in your hands. Right now you havent. The only rational reason for congressmen in the cc is to hope for an intimidating effect on somebody. Be assured, if you are long enough in science you are not scared easily. If this would be meant to intimidate the editors of PNAS, be assured that- if they have mood- will pin your Letter to their door to have something to laugh. And for new scientist, i can assure you, nothing will happen before the Reaction of PNAS. based on that you can write one more comment on the "New Scientist" article. --[[User:Stitch75|Stitch75]] 12:15, 24 July 2008 (EDT)

:Listen Stitch75- Right now, there are some pretty serious flaws in the Lenski study. Conservapedia has identified enough of them to put the entire conclusion in doubt, and even if one of our arguments turns out to be not valid, I am sure that because we raised so many valid points at least part of the paper will need to be reconsidered. You claim to have so much respect for the scientific process and scientific work, but you contradict this because you yourself refuse to allow a piece of scientific work to be legitimately challenged. If you truly believed that the work was infallible, you wouldn't mind us scrutinizing it. Please stop telling us about how to follow a good scientific method, when as you know the most important part is checking your work. We are contributing to the scientific community by revising a conclusion that is fatally flawed. Try to open your mind a bit more.--[[User:RoyS|RoyS]] 15:26, 24 July 2008 (EDT)

::By using "fatally flawed" in an ''a priori'' fashion, you contradict your own words regarding opening one's mind. Read more carefully- Stitch75 did '''not''' try to keep you from submitting your letter-, but rather tried to help you improve it. It seems you immediately criticize anyone you've decided to disagree with regardless of what they say. As several others here have said, you '''should submit a letter''' but with its current form of poor scholarship and misunderstanding of basic microbiology techniques, it won't be taken seriously. You haven't given it a reason to be. And Stitch75 is right about all the CCs: they serve only to undermine your argument and erode your credibility. Unfortunately, with each revision the letter becomes less and less tactful, thus further reducing the likelihood of it being posted by PNAS. Stitch75 gave that detailed advice because he does have "respect for the scientific process and scientific work"- thus helping you develop your letter in a scientifically acceptable format. Also, if you've already decided that you won't agree with any response other than retraction, there's not much point in the effort because that in itself is not a scientific approach. Through this and already calling it "fatally flawed" before any formal scientific response to those claims, you've already made up your minds. Again, submit a letter, really, but if you want them to take you seriously you should reciprocate in due course and not pass judgment before even sending it.[[User:Kallium|Kallium]] 15:55, 24 July 2008 (EDT)

:::ASchlafly's statement, "''In fact, while the paper states the generation periods for the First (replay) Experiment, it does not disclose the generation periods for the Second and Third Experiments''" demonstrates a surprising lack of comprehension of the procedures described for the second and third replay experiments. There were no generation periods for the second and third experiments, because the bacteria in those experiments were not serially cultured. They were plated once onto MC agar (which contains no glucose) and allowed to sit on those same plates for 59 days (replay 2) or 49 days (replay 3).

::: If you continue your insulting tone, then you'll join others who have been blocked. If you're claiming that the Second and Third replay Experiments did not have new generations during their 59 and 49 day periods, then please clearly say so. Note that Lenski does not observe when the Cit+ variants were allegedly observed during those periods.--[[User:Aschlafly|Aschlafly]] 23:07, 24 July 2008 (EDT)

:::Similarly, his statement "''The same reason that the paper admits an inability to "exclude an earlier origin" (p. 7901) for the Cit+ variants also results in an inability to exclude Cit+ variants from the samples taken after generation 31,000''" is also wrong. It is impossible to exclude an earlier origin ''in a population of millions of cells'' because it is impractical to plate all of the cells for each generation out so thinly that each and every cell gives rise to a unique colony which can then be tested for the Cit+ trait. For each generation you would have to run thousands of plates to determine ''exactly'' when the first Cit+ cell arose. Conversely, if you wish to sample only a few hundred or thousand cells, rather than multiple millions, it is straightforward to plate them out at such a great dilution that every cell in the sample gives rise to a unique colony, separated in space from all the others, which can then be tested individually for the traits you wish to identify. Since each colony arises from a single cell in the sample, after generation 31,000 you will have colonies that are entirely Cit+ and those that are entirely Cit-. His claim that "''there is no scientific basis for including these Cit+ populations in this study, and it only serves to distort the results''" is also wrong - there is a basis to include those populations - or to be more specific, the Cit- subset of those populations. At the time the replay experiments were designed, before there was any evidence for a potentiating mutation at 20,000 generations, it was impossible to know which generations were more likely to give rise to the Cit+ trait. Suppose that a potentiating mutation arose at the 25,000th generation and expanded through the population or simply persisted at a low level through the 31,000th generation, ''by which time it was outcompeted by some other mutation, or was lost through drift''. It could have been the case that the Cit+ mutation could ONLY have arisen between, say, the 25,000th and 31,500th generations, with no 'potentiated-but-not-Cit+' cells lasting past the 31,500th generation. As it turns out, it appears that the potentiated cells continue to persist in the Cit- population through the 32,500th generation. If you are trying to determine whether the Cit+ trait is contingent or simply random, it absolutely makes sense to include Cit- cells of later generations.

:::: The alleged potentiating mutation must have occurred prior to the 31,500th generation, and it makes no sense to test subsequent generations for the potentiating mutation. Rather, including later generations only distorts the statistical analysis.--[[User:Aschlafly|Aschlafly]] 23:07, 24 July 2008 (EDT)

:::His statement "''The paper incorrectly combined the Third Experiment with the other two based on outcome rather than sample size, thereby yielding a false claim of overall statistical significance''" is meaningless. If ASchlafly objects to the statistical method used, he should recalculate the results using his preferred test and then present both his results and a defense of the alternate statistical method. If you send a letter to PNAS that includes such obvious errors of fact and unsupported conclusions, it will only embarrass ASchlafly and Conservapedia further.--[[User:Brossa|Brossa]] 16:20, 24 July 2008 (EDT)

:::: You resort to insults when you lack substance. One need not propose an alternative, or a solution, in order to identify a flaw. One may announce that a bridge is defective and should be closed prior to figuring out how it can be fixed, if indeed it can be fixed.--[[User:Aschlafly|Aschlafly]] 23:07, 24 July 2008 (EDT)

:: Dear RoyS, my mind is open enough and I listened long enough, and I would appreciate if you would contribute to the discussion instead of accusing me of beeing closed-minded and acting as if we sat in the pub. If the flaws are so obvious, please present your calculations. Lenski presented his, So unless you show that, using a specific method of calculation, you get other numbers, there is not much of an argument. --[[User:Stitch75|Stitch75]] 20:27, 24 July 2008 (EDT)

== Expertise in Statistics ==
I don’t mind admitting that I have none! The article states that Lenski combined the three trials incorrectly and that he doesn’t make the insignificance of the third clear. Now it may well be very clear to others but, unfortunately, the article doesn’t make clear to people like me what was wrong. Can someone expand on this point? Is anyone able to explain to a layman what Lenski should have done and the conclusions he should have reached? It's all getting a little technical for me. --[[User:Billd|Bill Dean]] 12:10, 14 July 2008 (EDT)

: OK, here's point 4 in layman's terms: Lenski's hypotheses of a mutation rate imply that a ten-fold increase in sample size should result in a ten-fold increase in mutations. But it doesn't. In fact, a nearly ten-fold increase in sample size results in only a slight increase in mutations in Lenski's data. These data, as presented by Lenski in his paper, suggest (if properly interpreted) that there is no mutation rate at all. Rather, these data are more consistent with occasional contamination, broadly defined.--[[User:Aschlafly|Aschlafly]] 23:15, 14 July 2008 (EDT)

::Except that the growth pattern of the Cit+ cells in the third replay experiment demonstrated that there were no Cit+ cells in the cultures at the time of plating. Control plates with a mix of Cit- and Cit+ cells were done which showed rapid development of Cit+ colonies, whereas the experimental plates did not show any Cit+ colonies for at least 8 days and up to 28 days. If you believe that the plates became randomly contaminated during the course of the incubation, rather than at the initial plating, the post-plating contamination should have affected all generations equally, but it did not--[[User:Brossa|Brossa]] 12:46, 15 July 2008 (EDT)

::Blount et al. discussed the unexpectedly low Cit+ conversion rate for the third replay set in the supplementary document. They have some speculations but don't know why it occurred. They are dealing with low probability events. I don't agree that the 'proper' interpretation is contamination. First, they isolated and tested each Cit+ isolate for the markers and sequences we've discussed on earlier Conservapedia pages. Second, the distribution of Cit+ isolates does not appear to be random: They correlate strongly with the later generations. If undetected contamination was random, it's unlikely the Monte Carlo resampling tests would reject the null hypothesis of the 'rare-mutation' hypothesis over the 'potentiated' hypothesis. As Brossa correctly notes, contamination would have affected all generations. Blount et al. write in the paper's supplement: "To facilitate handling and minimize possible confounding variables, we divided this third experiment into 20 blocks of 14 clones each. All of the clones within a block came from different generations, and the single ancestral clone was included in all 20 blocks."--[[User:Argon|Argon]] 20:01, 15 July 2008 (EDT)
::: Good and detailed analyis and conclusion, Argon. I had no time to read everything in that detail, but i think you present exactly the arguments (contant background would favour rare mutation hypothesis) would be exactly the one i had in mind, so let's see how Mr. Schlafly will bend his own Monte-Carlo simulations to showing several 1000 times no mutation into accordance with any reasonable background explaining a significant number of counts in *some* samples --[[User:Stitch75|Stitch75]] 20:20, 15 July 2008 (EDT)

:::: The above comments are non-responsive. The essence of ''both'' of Lenski's hypotheses is that there is a fixed, or stepped, mutation rate. But any such rate would be roughly proportional with sample size. Yet his three experiments prove otherwise, which Lenski fails to address in a satisfactory manner. Indeed, Lenski's presentation of his data disproves the very thing he claims to have shown.--[[User:Aschlafly|Aschlafly]] 20:40, 15 July 2008 (EDT)

::::: Mr. Schlafly, please answer: Which the of the two hypotheses is, according to your calculations the most likely? --[[User:Stitch75|Stitch75]] 20:47, 15 July 2008 (EDT)

::::::The first replay experiment was run under different conditions - roughly 3700 generations in continuous subcultures. One can't compare population sizes or rates between the first and last two replay experiments. As I noted, Blount et al. acknowledged the possible anomaly of lower than expected mutants in the third run. Still, the second and third experiments were run under different conditions. The plates in the second replay experiment were seeded with fewer cells per plate than in the third experiment. That change can affect the survival rates of cells on plates over time (e.g. different rates of nutrient exhaustion). Given the extremely low mutation rates involved, there is no simple means of normalizing the numbers of mutants recovered for the second and third experiments. One might expect 'roughly' 10x more mutants in the third experiment but that's truly a 'rough' estimate that would be affected by conditions under which cells are exposed. It's certainly a question that remains and they may be able to clear up with future research. In any case, the pattern of data does not support Andy's claims of contamination or that the hypotheses of the paper is in error.--[[User:Argon|Argon]] 21:27, 15 July 2008 (EDT)

::::::: Argon, you have free will and it's clear to me that you are going to exercise it to the point of embracing absurdities. This time you claim that "extremely low mutation rates" would not result in mutations that scale with sample size (of course they would), and that density completely alters mutation rate (if that silly claim were true, then Lenski's experiment was flawed from the get-go). Your belief system is remarkable, but it's not logical.--[[User:Aschlafly|Aschlafly]] 23:38, 15 July 2008 (EDT)

::::::::Fair enough, but let's be clear: That's my take on the paper and that of most of the scientists who reviewed the paper, read the paper and commented upon the paper so far. For that matter, Michael Behe didn't call the data flawed, nor did those commentators at Dembski's Uncommon Dissent blog, nor did Dr. Georgia Purdom at Answers in Genesis. In contast, those who think the work is flawed appears to be limited mostly to you, Andy. It is true that 'scaling' was not seen in this case but as we've seen, the conditions were not quite the same and it is known that this can have an impact.

::::::::However, the fact that the conditions were not identical doesn't detract from the fact that the emergence of Cit+ clones *still* correlated with the sampling of the later generations. What this means is that with three separate experiments and under three sets of conditions, the constant-rate-mutation hypothesis doesn't hold. What the differences between the second and third replay experiments demonstrates is that they were run under different conditions that affected the overall rate of conversion, not that the 'potentiated mutation' hypothesis is wrong. Those are actually distinct questions. Andy, the data simply does not support your claims that the cultures were contaminated (we'd expect random distribution), or that the 'scaling' variations ruined the experiment. In my opinion, you seem focused on red herrings to the exclusion of evaluating the data in the overall context of the experiment which demonstrates a correlation of Cit+ clones emerging from samples taken at later generations. Would you care to address that pattern and discuss why your 'contamination hypothesis' doesn't appear to hold up?--[[User:Argon|Argon]] 09:29, 16 July 2008 (EDT)

:::::::There is nothing absurd in what Argon said. As he mentioned, the third experiment was performed under different conditions and at a different time than the first or second experiments. The key here is that there are plenty of variables, some unknown, that simply aren't controlled for between the experiments. For example, take the fact that it was performed at a different point in time than the first two. The third experiment, then, is almost certainly being performed with different batches of growth media, liquid and solid. Anyone who has spent any significant time growing cells knows that media can vary significantly in growth characteristics between batches, despite the same recipe being used. The reasons for this can be many. Perhaps the balance or pH meter was off calibration one day, or a different bottle of reagent was used. Take an analytical chemistry course, you'll spend plenty of time talking about this. It is true that, for the most part, this sort of variability has minimal impact. But when you're examining something like an extremely rare mutation, or you're trying to make an extremely accurate measurement, intra-lab variability like this can be significant. For an extremely rare mutation like Cit+, which involved at least two additional mutations in potentiated cells, any change in mutation rate can have a significant effect on your ability to obtain mutants. Mutation rate is sensitive to growth conditions, so cells grown in different conditions are likely to experience a different rate of Cit+ mutation.

:::::::Regardless of the reason for the lower-than-expected number of Cit+ mutants in the third experiment, however, the Cit+ mutants isolated absolutely did not arise from contamination. This is clear if you read the paper. You're still left, then, with the two hypotheses presented, and the results support historical contingency.[[User:Gerlach|Gerlach]] 09:45, 16 July 2008 (EDT)
Is there anyone here with expertise in statistics who could give an analysis? [[User:Fyezall|Fyezall]] 16:15, 15 July 2008 (EDT)

:Hello Fyezall. I rearranged the position of your question to hopefully keep the conversations clearer. It boils down to this: The researchers found that mutant Cit+ strains arose over the course of time in their long term growth experiment. They wanted to learn something about how that strain acquired this ability. They wondered, 'Was this the result of a single, very low frequency mutation or did some other mutation have to precede it in earlier generations, followed by the final mutation(s) that allowed the cells to grow on citrate?'

:If the Cit+ change required a single mutation with a low but constant probability over time one would expect Cit+ mutations to be distributed across cells taken from any generation of the experiment. On the other hand, if a 'potentiating' mutation had to arise at some point in the cultures before the final Cit+ mutation could function, then one would expect the probability for Cit- cells to mutate to Cit+ cells would increase with samples of cells taken from later cultures.

:Blount ran the experiment and found that Cit+ mutants arose more frequently in cells taken from later generations in the culture. The Monte Carlo resampling tests were used to assess how likely the pattern of results would fit the models. The statistical significance (smaller P-values mean greater significance), was calculated for each experiment and the combination of experiments. The numbers suggest the distribution of mutants was not randomly distributed across the experimental generations, they tended to appear in cells taken from the later generations. This would argue against the single-mutation, constant, low-probability hypothesis. It appears that a pre-adaptive mutation had to have arisen first, followed by the mutation that finally allowed the cells to utilized citrate. Future work in Lenski's lab will focus on trying to identify the various mutations involved. I hope this brief explanation helps.--[[User:Argon|Argon]] 20:25, 15 July 2008 (EDT)

==What I have noticed==
I tell you what strikes me the most about this discussion - Its watching evolutionists do whatever they can to keep their precious beliefs above question or scrutiny. Its as if they know that it will come toppling down so they must resort to side-lining the hard questions.
[[User:JJacob|JJacob]] 21:43, 15 July 2008 (EDT)
==[[Social Text]]==
This well known hoax ''does'' support Aschlalfy's position that the paper was reviewed by PNAC ''rather quickly'', since (apparently) the paper supported the editors/reviewers point of view. Perhaps this would have beeen better placed on the [[Richard Lenski]] page rather than here since this deals only with the 6/10/08 PNAS paper ''per se'' and not the review process. [[User talk:MargeryCampbell|Marge]] 12:45, 16 July 2008 (EDT)

:I fail to see the relevance of the Sokal Hoax here. You should also know that Social Text was not a peer-reviewed journal when Sokal submitted his paper. That doesn't excuse the credulity of its editors, but Sokal's paper was not sent out for review. Not to say that it would have mattered, postmodernism is just meaningless word salad.[[User:Gerlach|Gerlach]] 13:39, 16 July 2008 (EDT)

== The letter is way too long... ==

from what I understand, PNAS has a 250 word limit on letters. The above proposed letter is too long. [[User:Leonard|Leonard]] 00:04, 25 July 2008 (EDT)

: Looks like we need to start trimming, then. Intelligent suggestions are welcome.--[[User:Aschlafly|Aschlafly]] 09:05, 25 July 2008 (EDT)

York

2008-07-24T15:43:18Z

YoungA:

A city in [[Yorkshire]], '''York''' was founded by the Romans as Eboracum. The [[Vikings]] renamed it Jorvik, whence the contemporary name stems. York is one of the few remaining walled cities in [[England]].

The Grand Old Duke of York, son of King George I, had an army of ten thousand men which he marched to the top of the hill and then marched down again.

In addition to the medieval defensive wall, York is also known for:

* York ham
* York Minster, the largest Gothic cathedral in northern Europe
* The National Railway Museum, the world's largest railway museum
* York Railway station, known for its architecture
* Yorkie bars
* The York Rite (see [[Freemasonry]])

The American municipality of [[New York]] is named after York.

==External Links==
*[http://www.vryork.com Take Java + Quicktime VR tours of the City]
*[http://www.visityork.org/ Official York tourism website]
*[http://www.nrm.org.uk/ The National Railway Museum]
*[http://www.yorkminster.org/ Official York Minster website]
*[http://members.virtualtourist.com/m/65d99/49d7d/ VirtualTourist - York]

[[Category:United Kingdom Cities and Towns]]

Talk:Flaws in Richard Lenski Study

2008-07-24T13:27:37Z

YoungA: /* Draft of PNAS Letters Response from Conservapedia */

Now, is this page a report over other people thinking Lenski's paper is flawed or is this Aschafly reporting about himself and putting it in the headline of the Front Page? And please specify by references which "two other" experiments are referenced, and explaing how you can see that the "historical contingency" is not true. --[[User:Stitch75|Stitch75]] 23:22, 12 July 2008 (EDT)
And if you think you argue that well, why dont you submit it as a comment òn the paper to PNAS. --[[User:Stitch75|Stitch75]] 23:24, 12 July 2008 (EDT)

:This article is seriously partisan. I see no outside or third party analysis of the paper in the references, just a bunch of cites to the article or conservapedia itself. [[User:Wisdom89|Wisdom89]] 00:34, 13 July 2008 (EDT)

Folks, you're in the wrong place if you're more interested in who says what rather than determining the truth itself. A true wiki gets at the substantive truth rather than trying to rely on biased gatekeepers and filters of the truth.

The flaws in the statistical analysis in Lenski's paper are clearly set forth and well-referenced. If you're interested in the truth, then look at the paper and see the flaws yourself. If you're not interested in the truth and think you can distract people's attention from it by using other tactics, then you're wasting your time here.--[[User:Aschlafly|Aschlafly]] 00:42, 13 July 2008 (EDT)

I agree with Aschlafly on this, there needs to be some kind of admission or response from Lenski but little has been forthcoming and conservapedia itself has taken it on. Notice how no-one, aside from conservapedia (and I think Creationwiki?) has asked such questions of Lenski? All the magazines etc have taken his study at face value without actually taking the time to critique his claims. Aside from the "peer reviewers" of course.
[[User:JJacob|JJacob]] 00:47, 13 July 2008 (EDT)

: The "peer reviewers" who spent somewhere between 0 and only 14 days looking at the paper, and missed an obvious contradiction between Figure 3 (specifying the "Historical contingency" hypothesis) and Table 1, Third Experiment. The statistical analysis in the paper appears so shoddy to me that I doubt anyone with real statistical knowledge or expertise even reviewed it.--[[User:Aschlafly|Aschlafly]] 00:59, 13 July 2008 (EDT)
::I have expertise in research and statistics and I'm just not seeing this shoddiness that you make reference to. You are allowed to have your doubts, but we should get a bunch of people familiar with such fields to examine the paper's statistical analysis. [[User:Wisdom89|Wisdom89]] 01:01, 13 July 2008 (EDT)
::I have the same problem. i hold a Dr.Rer.Nat title and did some statistics (although i am no expert on it) and fail to see the "shoddiness" please help my underdeveloped mind, Mr. Schafly and enlighten me. I it is so obvious it should be a one-liner to formulate it. --[[User:Stitch75|Stitch75]] 09:54, 13 July 2008 (EDT)

::: Please try harder then. I've expanded the explanations a bit also.--[[User:Aschlafly|Aschlafly]] 10:42, 13 July 2008 (EDT)

:::: At least now i can recongnize your statements more or less clearly. Yet i think (cite from the paper) ''We also used the Z-transformation method (49) to combine the probabilities from our three experiments, and the result is extremely significant (P < 0.0001) whether or not the experiments are weighted by the number of independent Cit+ mutants observed in each one.'' has to be addressed more specifically than you do in order to discredit the statistics used --[[User:Stitch75|Stitch75]] 11:54, 13 July 2008 (EDT)
:::::Just for comparative purposes and a frame of reference, a P value that is less than the significance level of 0.05 is considered significant. [[User:Wisdom89|Wisdom89]] 13:10, 13 July 2008 (EDT)

I wonder, do the PNAS allow questions to raised and asked of the "peer reviewers" themselves? Are we able to find out who/what experience they themselves have? Perhaps that is an avenue that we could look at? I apologise in advance if this has already been asked or answered.
[[User:JJacob|JJacob]] 01:07, 13 July 2008 (EDT)

:Definitly not. Peer reviewers are anonymous and only known to the editor, for good reason. Having peer reviewers non-anonymous would cause reviewers to be very careful to step on nobodys foot to evade revenge. --[[User:Stitch75|Stitch75]] 09:54, 13 July 2008 (EDT)

: No, PNAS probably won't disclose who supposedly did the 14-days-or-less peer review on the [[Lenski]] paper. You're right that such disclosure could shed some light on the final product.

: "Wisdom89", your claim that you "have expertise" and don't see the flaws only makes me conclude that you don't really have the expertise that you claim. Judging by your silly user name, perhaps you've tried that approach before. We're not fooled by it here.--[[User:Aschlafly|Aschlafly]] 01:14, 13 July 2008 (EDT)

(removed silly comment by person who has since been blocked for [[90/10 talk]] violation)

==Marginally significant==
In #1, that's not inconsistent. The figure makes it clear that, according to the hypothesis, the mutations should also occur earlier than 31,000, but should become more common at that point. 12/17 mutants occurred after 31,000. The point in #3 is not clear. What do you mean by ''weighting''? In #5, ''Lenski's paper is not clear in explaining how the results of his largest experiment...his paper refers to his largest experiment as "marginally ... significant," which serves to obscure its statistical insignificance.'' Actually, '''marginally significant''' is clear. It means that the p-value is between .05 and .10 (in this case it's .08, table 2). It's a pretty standard phrase to describe an effect that falls into that range. [[User:Murray|Murray]] 13:41, 13 July 2008 (EDT)

: Your defense of Lenski per point #1 is contradicted by the paper's own abstract, and by the comments by the other Lenski defender below. In point #3, proper weighting is needed to combine multiple studies. In point #5, you don't cite any authority for the unscientific claim of being "marginally significant."--[[User:Aschlafly|Aschlafly]] 20:45, 13 July 2008 (EDT)
: Your defense of Lenski per point #1 is contradicted by the paper's own abstract, and by the comments by the other Lenski defender below. In point #3, proper weighting is needed to combine multiple studies. In point #5, you don't cite any authority for the unscientific claim of being "marginally significant."--[[User:Aschlafly|Aschlafly]] 20:45, 13 July 2008 (EDT)
::Define "proper weighting". Are you referring to how they interpreted the sum of the work or to a specific analysis? You're right, I didn't cite any scientific authority. Here's one: Motulsky, H. (1995). ''Intuitive Biostatistics'', Oxford Univ. Press. Chapter 12. Also, try searching for the phrase in Google Scholar or PubMed, you'll find plenty of uses of it. It's a shorthand way of describing an effect that came close to the arbitrary threshold for statistical significance but did not reach it. [[User:Murray|Murray]] 21:55, 13 July 2008 (EDT)

::: You seem unwilling to accept that Point #1 identifies a clear mistake between the figure and the abstract in the paper, which requires correction by Lenski or PNAS. Given that unwillingness, I doubt it will productive discussing the other mistakes further with you. You're right that other usage of the dubious concept of "marginally significant" can be found on the internet, but the first link to such usage on my internet search for it returned the non-rigorous "Intuitive Biostatistics" and the second link returned a criticism of the concept similar to the criticism express here. [http://annhyg.oxfordjournals.org/cgi/reprint/49/1/93-a.pdf] --[[User:Aschlafly|Aschlafly]] 00:42, 14 July 2008 (EDT)
::::It's not a clear mistake in my mind. There does seem to be some confusion or contradiction in terms of the number of generations, but I haven't seen a clear explanation of why this is or is not a mistake. What seems like a contradiction is the abstract statement that no mutations occurred before 31,500, but it's not clear to me whether I'm misunderstanding that. ''I doubt it will productive discussing the other mistakes further with you. '' Of course you doubt it, because you are unlikely to be willing to concede anything no matter what anyone says. Why do you call the concept dubious? The procedure of determining whether an effect is significant requires the setting of an arbitrary threshold, which is usually .05. That means, in analyses of the sort in the Blount et al. paper, that there's less than a 5% chance that the findings are due to sampling error. When an effect comes close to the threshold it is worth noting, because of the problems inherent in significance testing, which itself is widely criticized in the statistical literature. I am not clear what you mean by weighting, as I mentioned before - in the interpretation or statistically? [[User:Murray|Murray]] 13:30, 14 July 2008 (EDT)

== Richard Lenski incorrectly included generations of the E. coli already known to contain Cit+ variants in his experiments.[3] Once these generations are removed from the analysis, the data disprove Len ==

The author of the above statement must not have read the paper or the supplement carefully. Lenski took clones from those cultures that '''weren't Cit+'''. Careful reading of the paper or the supplement reveals that Cit+ mutants appeared at 750 generations or later into the replay experiment. The authors write: "New Cit+ variants emerged between 750 and 3,700 generations..."--[[User:Argon|Argon]] 15:03, 13 July 2008 (EDT)

: Your explanation is not convincing. Show us how Lenski proved that the samples did not have '''any''' Cit+ variants, if you really think he's claiming that.--[[User:Aschlafly|Aschlafly]] 20:51, 13 July 2008 (EDT)

::I count at least four distinct diagnostic methods used in the paper for distinguishing whether clones are Cit+. One in particular they describe as being very sensitive to weakly citrate-using cells. It's not that I 'think' Blount et al. claim they started with Cit- cells. They say that in the 'Supporting information' document.

::Andy, for tonight, I'll leave it as an exercise for you to answer your own question of how one might test a clone to be sure that is was Cit-. Use the paper if you'd like or present another means. Tomorrow evening I'll cite the methods Blount used in the paper.

::Meanwhile, here's another question to ponder: If the colonies used to start the 'replay' cultures were Cit+ at the start, why is it that no Cit+ cells were found in such cultures before 750 generations? These cultures were all started from single clones which must have either had the Cit+ phenotype or not.--[[User:Argon|Argon]] 18:38, 14 July 2008 (EDT)

-
How did Lenski obtain Cit- clones from later populations after Cit+ had become the dominant phenotype? It's pretty standard procedure. First, keep in mind that these populations contained a minority of Cit- cells. Now, a small liquid growth is made from the frozen glycerol stock of cells from a given generation, say 32,000. This is grown to an appropriate OD and then plated on a standard rich media agar plate. Provided that the plated sample isn't too dense, this plating will deposit somewhere between 15-100 individual cells on the agar, with plenty of spacing between them. The plate is then incubated at 37 C for a given time, during which the individual cells replicate to form small, visible colonies. These colonies will consist solely of cells that are genetically identical to the original cell deposited on the agar. This is all well and good, but how do you find which of the colonies are Cit-? Here you use a technique called replica plating. The agar plate is gently inverted onto a sterile swatch of velvet so that some of the cells from each colony are deposited onto the fabric. Next, a citrate-only agar plate is pressed against the velvet, transferring cells from the fabric to the new plate in exactly the same spacial orientation as the first plate. The cells are then allowed to grow on the citrate-only plate. When we then compare the two plates, we look for colonies on the rich plate that did not grown on the citrate-only plate. These colonies will be Cit-, and can be used for the replay experiments. [[User:Gerlach|Gerlach]] 13:45, 14 July 2008 (EDT)

:Just a correction: The Cit+ cells didn't dominate the cultures at generations 32,000 & 32,500. Cit+ mutants represented 12% and 19% of the population at these times points, respectively. Replica plating is definitely one means of identifying Cit- and Cit+ clones but because the Cit+ cells represented a fraction of the total, it is simple enough to streak the samples to individual colonies (founded by single cells) and test each colony individually. Otherwise, a nice description of replica plating (a technique developed by Joshua Lederberg that allowed him do the research for which he was awarded one of the 1958 Nobel Prizes in Medicine)--[[User:Argon|Argon]] 18:38, 14 July 2008 (EDT)

::Oops, you're right, Argon. Cit+ wasn't dominant at generation 32,000, so replica plating might not be the best option. Still, in the case of almost 20% Cit+, I think replica plating might be labor reducing. I'm a biochemist by training, not a microbiologist, but I'm sure there are other methods that could be used. For example, Christensen's agar appears to provide a sensitive, colorimetric method of identifying even weakly citrate-utilizing colonies, so one might be able to plate cells on a Christensen's agar plate and pick uncolored colonies. Again though, I'm no microbiologist so I don't know the best method. However, there are ways to easily pick Cit- clones from later generations in this case. That said, I think that this specific "flaw" cited in Lenski's paper should be removed from the main article. Clearly, Cit+ were not used in the replays from later generations, so Conservapedia's objection is totally baseless.[[User:Gerlach|Gerlach]] 19:19, 14 July 2008 (EDT)
:::All appropriate descriptions. For generating estimates of the population distribution (Cit-/Cit+) in a culture, replica plating would certainly be applicable. The main point is that identifying and isolating Cit- clones from the generations used in the experiment is straightforward. I agree that it would be a mistake to keep that objection in the article (actually that thread runs across several points in the article).--[[User:Argon|Argon]] 20:12, 14 July 2008 (EDT)

:::: Nothing in the paper rules out contamination of those samples by Cit+ variants, and you quote nothing in the paper to rule it out. There was no reason to use and rely on these samples that already have Cit+ variants.--[[User:Aschlafly|Aschlafly]] 23:04, 14 July 2008 (EDT)
:::::The whole point of the discussion above was to illustrate that there are methods to isolate cells with a particular genotype from a mixed population. Suppose we used the replica plating method (maybe not the best choice, but it's standard procedure). Care to explain where the Cit+ contaminants could possibly come from? And the naivete inherent in objecting that "nothing in the paper" rules it out is simply astounding. Standard laboratory procedures, like isolating specific clones, typically don't show up in papers. For example, if I to write a paper on my research, it would not include a detailed discussion of the construction of my expression plasmid. I might mention that I cloned my gene into a particular vector, but there wouldn't a discussion of how I did my PCR, restriction digests, or transformations. Things like that are simply extraneous details that are taken for granted by experienced researchers. There is simply no reason for Lenski et al. to include a discussion of their method for isolating specific clones. This is why this whole exercise of Conservapedia criticizing Lenski's paper is folly, because most Conservapedia users simply don't know standard laboratory techniques. It's kind of important to know what scientists today are able to do on a routine basis before wading in to claim that they couldn't have done what they claim.[[User:Gerlach|Gerlach]] 09:05, 15 July 2008 (EDT)

:::::***** *****
:::::Actually the methods cited in the paper would separate the Cit+ lines from the Cit-. They took single colonies (founded by single cells), and tested them on selective agar (minimal citrate media - MC agar) and an indicator medium, Christensen's citrate agar (Product information from Sigma here: http://www.sigmaaldrich.com/sigma/datasheet/c7595dat.pdf). As Gerlach notes from the Blount paper, Christensen's citrate agar is very sensitive to citrate utilization. Typical ''E. coli'' strains do not produce a color change but other citrate-using enterics like ''S. typhimurium'' and Cit+ ''E. coli'' mutants appear pink/red on the plates.

:::::This conclusion is further validated (as I mention above), by the fact that Cit+ mutants did not appear immediately in the replay experiments (Others have also noted this). For example, in replay set-1, it took 750 generations before the first Cit+ mutants were isolated. Many didn't produce Cit+ cells after 3700 generations. If the starting line was Cit+, *all* the cells in the culture would have show up as Cit+ in the first pass.

:::::Overall, it is abundantly clear that the cell lines used in the replay experiments were not Cit+ at the beginning.--[[User:Argon|Argon]] 19:44, 15 July 2008 (EDT)

== 1. Lenski's "historical contingency" hypothesis, as specifically depicted in Figure 3, is contradicted by the data presented... ==

Again, more issues with comprehension: The authors did not know when the potentiating mutation first arose but they knew it was before generation 31,500. Figure 2 is merely figurative, being an illustration, and not quantitative. Their analyses suggested that the potentiating mutation did arise at about the 20,000 generation point or later. Their conclusion is that Cit+ mutation rate is low even in a potentiated background but apparently distinguishable from a low-incidence single, unpotentiated event.--[[User:Argon|Argon]] 15:04, 13 July 2008 (EDT)

== Statistics101 package: ==

What does the author imply by writing: "...Lenski himself does not have any obvious expertise in statistics. In fact, Richard Lenski admits in his paper that he based his statistical conclusions on use of a website called "statistics101"?

From the web site:
''Professionals: Although it was originally developed to aid students, the Statistics101 program is suitable for all levels of statistical sophistication. It is especially useful for Monte Carlo, resampling, and bootstrap applications. It has been used by professionals in many fields. These include anthropology, biology, ecology, evolutionary biology, epidemiology, marine biology, psychology, toxicology, veterinary pathology.''
It would appear that the package from the web site (not the web site itself) was used to perform the Monte Carlo resampling tests. Is there any evidence that the package produces incorrect results?--[[User:Argon|Argon]] 19:41, 13 July 2008 (EDT)

==Formal Response to PNAS==

''I've moved this thread from the open section above since this page is being categorized.'' --[[User:DinsdaleP|DinsdaleP]] 21:52, 13 July 2008 (EDT)

:::I think this article presents very sound arguments. Conservapedia should now take action, offering to publish a rebuttal of Lenski in the PNAS journal.--[[User:JBoley|JBoley]] 11:31, 13 July 2008 (EDT)

I agree with JBoley in that if Conservapedia wants to present a formal, professional response to Professor Lenski's paper that questions specifics within his paper, then it should happen. That is the proper execution of the scientific method, and I'm certain that a professional response to PNAS would yield better results than vague "give us all the data " demands. Is a formal response to PNAS from Conservapedia in the works, or is this article the only place these questions/objections were intended to be raised? --[[User:DinsdaleP|DinsdaleP]] 11:52, 13 July 2008 (EDT)

: I don't know if PNAS would embarrass itself by printing a rebuttal, or whether it has the integrity to retract Lenski's paper. Conservapedia's audience is probably bigger than PNAS's, and we're certainly not going to suspend our exposure of the truth here in order to await correction by PNAS.

: PNAS publishes, quite easy to find Rules for "Rebuttals" (they call it "Letter"). It is specifically what you want. [http://www.pnas.org/site/misc/iforc.shtml PNAS:Information for Authors] . I cite: ''Letters are brief online-only comments that contribute to the discussion of a PNAS research article published within the last 3 months. Letters may not include requests to cite the letter writer's work, accusations of misconduct, or personal comments to an author. Letters are limited to 250 words and no more than five references.'' --[[User:Stitch75|Stitch75]] 13:25, 14 July 2008 (EDT)

: In addition, Lenski has already demonstrated how he reads this site and he can certainly correct his own paper, and he should do so. Indeed, professionalism might support giving Lenski the time to correct it himself first.--[[User:Aschlafly|Aschlafly]] 12:14, 13 July 2008 (EDT)

::I understand what you're saying, but there's nothing improper or unprofessional in submitting a formal request to PNAS to have the points in this article addressed by Professor Lenski and his team. To be frank, you've been adamant in your insistence that PNAS has been less than rigorous in the review of Lenski's paper, so if one of your intentions is to demonstrate this then having PNAS respond to a formally submitted response to the paper in public would serve that purpose. This can be done in addition to publishing these objections on Conservapedia--[[User:DinsdaleP|DinsdaleP]] 12:21, 13 July 2008 (EDT)

:::If not PNAS, then perhaps some other public forum? I know Andy Schlafly has appeared on television, effectively arguing against gardisal and other dangerous vaccines. Perhaps if a TV program were interested you could argue against Lenski? You could be the spokesperson against these false claims of evolution.--[[User:JBoley|JBoley]] 12:24, 13 July 2008 (EDT)

:::: I'm not opposed to the above suggestions, but the future is here, folks. Lenski, PNAS editors and television producers have free will to reject or ignore the truth, and I'm more interested in getting the truth out here than trying to persuade someone in dying media like print or television. Lenski and his defenders can see the truth here, and they can decide for themselves whether to reject or admit it.--[[User:Aschlafly|Aschlafly]] 12:30, 13 July 2008 (EDT)

:::::I agree with you about the dying nature of print (I don't think television is dying, merely changing). The problem is that information about the flaws in Lenski's study are not registering outside of sites like Conservapedia. In effect, Conservapedia is an echo chamber. People that come to this site already agree with its point of view. I encourage you to attempt to attract the attention of other forms of media, or Lenski's false claims will simply be accepted as fact by the public and even worse, by educators.--[[User:JBoley|JBoley]] 12:36, 13 July 2008 (EDT)

::::::While there's nothing wrong with taking one's message to various forums or outlets, I believe there's a specific value in submitting these objections as a formal response to PNAS. Conservapedia was established as a trustworthy resource for students, and in my mind all of it's actions should be done with the goal of informing and educating. The Lenski debate is over the findings published in a scientific journal after undergoing a peer-review process. The objections to this paper by the CP leadership are not just about its content, but to the process by which it was reviewed and published in the timeframe it was. Talking about these objections is fine, but it's more instructional to the students using Conservapedia, and a better example of the scientific method in action, to respond to a scientific paper published in a journal through the formal process by which such papers are either defended or corrected. In the end, Lenksi's work will either stand up as good science, or any errors will be addressed and the paper's conclusions modified accordingly, which is also good science. Seeing this process in action regarding a such a significant paper is a great learning opportunity, and the Conservapedia leadership would be remiss in not standing by their conviction in these objections and submitting them formally to PNAS. --[[User:DinsdaleP|DinsdaleP]] 12:38, 13 July 2008 (EDT)

PNAS has a letters section available with the online edition. Many journals have a letters section for rebuttals or clarification. Legitimate corrections are welcome. Andy, have you run your list of 'flaws' past any biologists?--[[User:Argon|Argon]] 15:36, 13 July 2008 (EDT)

: Funny, Argon, how you don't apply your demand of expertise to Lenski himself. What are Lenski's credentials with respect to statistical analysis? Has he even taken and passed an upper-class statistics course of any substance?--[[User:Aschlafly|Aschlafly]] 00:45, 14 July 2008 (EDT)

::I don't follow. Are you suggesting that Lenski doesn't understand the proper application of the statistical methods used in his paper? If so, I haven't seen a description of which alternate methods you'd employ, let alone any output from such an analysis. Here's a thought: Why don't you substantiate your claims by writing up the work and submitting it as a correction letter to PNAS?--[[User:Argon|Argon]] 18:46, 14 July 2008 (EDT)

::: Argon, if you really "don't follow," then try harder. You insist on credentials by others who criticize Lenski, and yet you do not insist on expertise by Lenski in statistics with respect to his "analysis". Perhaps Lenski should first take and try to pass "Statistics 101" before trying to use a website by its name to draw flawed conclusions.--[[User:Aschlafly|Aschlafly]] 22:36, 14 July 2008 (EDT)

::::Do you really think that Lenski went to statistics101.net to learn about statistics and how to apply them? That simply is not the case. The Lenski group knew that they needed to do a Monte Carlo resampling analysis on the results of their replay experiments. In this situation, they are faced with two choices: either code an appropriate program themselves, or utilize one that has already been developed and is readily available to researchers. Since statistics101 had such a program available, they chose the latter option. Statistics101.net was simply the source of the program that the Lenski group used to perform the statistical analysis. If you want to argue against that choice, then you need to examine the source code for the statistics101 package and enumerate why it should not have been used.[[User:Gerlach|Gerlach]] 11:40, 15 July 2008 (EDT)

::::***** *****
::::I don't insist on credentials per se. I *recommend* developing a working understanding of the experiments or a willingness to do the necessary background research to get the details straight before heading off on possibly the wrong direction. It saves a lot of thrashing about. It's perfectly OK to raise questions but before leveling accusations it might be nice to do that privately and discuss that with others who can provide useful feedback. Just my 2 cents.--[[User:Argon|Argon]] 19:48, 15 July 2008 (EDT)

::Mr. Schlafly, does your response above, "I'm more interested in getting the truth out here than trying to persuade someone in dying media like print or television", mean that you will not be submitting a response with these identified flaws directly to PNAS? As I mentioned above, it takes nothing away from the value of posting these statements here on CP to also submit them to PNAS, but the proper way to prompt a journal to review and correct an article is through a direct response, not publication on an unrelated website like CP. It's not proper for anyone but the author(s) of the objections in this article to make that submission, so I'm hoping they step up with the conviction of their beliefs and respond to PNAS directly. Thanks. --[[User:DinsdaleP|DinsdaleP]] 12:32, 14 July 2008 (EDT)

::: By now Lenski has probably seen the flaws identified on the content page here. What's "proper" is for him to correct his own paper in PNAS. The criticism will likely continue as long as he declines to do so. If anyone here would like to educate the PNAS editors about the flaws, then please feel free to do so.--[[User:Aschlafly|Aschlafly]] 22:36, 14 July 2008 (EDT)

::::I'll be glad to submit these items to PNAS on behalf of Conservapedia using the "Letters" forum described by Stitch75 above. Should I cite you the author of this analysis, and is there an email you'd prefer me to include instead of my personal one for any PNAS response? I'll put up a draft of the Letters submission here for your approval before sending anything out. Thanks. --[[User:DinsdaleP|DinsdaleP]] 18:39, 15 July 2008 (EDT)

:::::It would have a very strange scientific taste should somebody else that Mr. Schlafly be the first author of the letter (however, if you insist on that, i suggest "personal communications" as the right kind of citing the work here.). It is his turn to stand up to his claims in this way (by publishing it into a Forum which he is not the owner of). I personally share the doubts of many here about his argumentation (and his understanding os the experiments), but i am sure only more of his dismissive comments will follow. However i see that he comes up with a clear alternate Hypothesis (contamination), so he is free to show that this is more likely (calculations please) and peform Monte-Carlo simulations on it (for a person complaining that statistics101 is to simple that should be no difficult task). As far as i understood and see the data Lenski and coworkers did the best to exclude this Hypothesis, however i did not run own simulations (And I won't do it, because i think nothing will come out - furthermore Mr. Schlaflys personal style in the communication "you have to try harder" is not the style i am used to be adressed by people whose qualification in a subject is appearlingly nor more than mine). So running the simulation, evaluating his own hypothesis using a valid statistical method is now Mr. Schlaflys job - if he come up with a decent calculation showing this Hypothesis is more likely, the letter would for sure be accepted and Lenksi would have to react. If Mr. Schlafly is not the first author of the letter he could evade the critics after that by saying that he was misunderstood, which means somebody else take the risk of submitting the letter, but in case of success Mr. Schlafly would take the glory. --[[User:Stitch75|Stitch75]] 20:10, 15 July 2008 (EDT)

::::::I would prefer that Mr. Schlafly submit his objections to PNAS directly as well, but since he has declined to do so the next best response is to submit it "on behalf of Conservapedia", which he has authorized above. I'll post the draft letter tomorrow, and it will credit him as the author unless I'm asked to include other individuals who contributed to the analysis. --[[User:DinsdaleP|DinsdaleP]] 22:05, 15 July 2008 (EDT)

:::::::I hope ASchlafly does offer a rebuttal of Lenski's flawed "study." However, if he does not, I am all for DinsdaleP's suggestion. I look forward to reading your draft. If you take all the objections that Conservapedians have raised to Lenski's paper, I do not see how PNAS can possibly object.--[[User:JBoley|JBoley]] 11:28, 16 July 2008 (EDT)

::::::::They could object because Conservapedia's criticisms are obviously false. If this page hasn't made that clear, I don't know what could.[[User:Gerlach|Gerlach]] 13:44, 16 July 2008 (EDT)

:::::::::They would have to prove that Conservapedia's criticisms are false, and they cannot do that. You sound like a Lenski supporter. You need to open your mind to the truth.--[[User:JBoley|JBoley]] 13:59, 16 July 2008 (EDT)

:::::::::Gerlach, the most obvious lesson from this page is how a few, yourself included, seem determined to defend a flawed paper no matter what the truth brings. You have free will to reject whatever you want, but you're only hurting yourself by that approach. People who do open their minds are amazed by the insights and happiness it brings.--[[User:Aschlafly|Aschlafly]] 21:54, 16 July 2008 (EDT)

:::::::::This is such a strange response, Andy. The attitude that you and several of your defenders seem to have is that the criticisms you have made of Lenski's paper cannot be rebutted. However, the fact that you ''can'' level criticism at something doesn't make that criticism true. That is, you may be wrong. And that is the case here. Myself and others have pointed out that your alleged flaws in Lenski's paper are incorrect, and based on misunderstanding it, or, even worse, simply not reading it carefully. There has been little to no substantive response to our detailed rebuttals. Replies from you or other defenders of the Conservapedia article amount to little more than brazen declarations that we are wrong or "nonresponsive", and that criticisms in the original article remain unscathed. But for people who claim to have "the truth" on their side, this is simply baffling. If the veracity of your claims against Lenski's paper is so obvious, then it should be an easy task to provide in depth responses to the points that we have been raising against your article. I'm not above criticizing scientific papers. Bad papers get published frequently, after all. However, Lenski's paper does not appear to be one of those. Notice, though, that I am not claiming it to be perfect, no paper is. That said, whatever flaws the paper may have, those presented in the Conservapedia article are not among them. [[User:Gerlach|Gerlach]] 11:43, 17 July 2008 (EDT)

:::::::::: Gerlach, now you seem to admit that the Lenski paper may be flawed, but that Conservapedia has not identified any of those flaws! With all due respect, you seem to have taken closemindedness to new heights.

:::::::::: Lenski claims there is a mutation rate, yet his presented data show that the number of mutations do not scale with sample size. His presented data disprove both of his hypotheses.--[[User:Aschlafly|Aschlafly]] 13:27, 17 July 2008 (EDT)

:::::::::: First, we need to clarify what we mean by "flaw". Are we talking about serious methodological flaws or errors in interpretation that fatally undermine the paper's conclusion? If so, I fail to see any such flaws. Of course, any honest scientist recognizes that any work at the frontier of science has the potential to be wrong. It ''may'' be that future work shows Lenski to be wrong. But let's not confuse this possibility with actuality: saying that something might be wrong is not the same as saying that it is. On the other hand, by "flaw" we may mean minor experimental details that could have been better. In this case, the paper is flawed, and Lenski himself admits this in the supporting information. But ''every'' paper is flawed in this manner, and I doubt you'll find any investigator who wouldn't say that they wish they had done some things differently during the course of their research. As an example of what I'm talking about, the Lenski group's statistical analysis would have been improved if they could have accounted for the evolution of increased cell size (and, therefore, decreased cell density) in later generations. As it stands, their analysis ''underestimates'' the potentiation effect in these generations because replays of later generations involved fewer cells. But this flaw, and other flaws of this type, do not undermine the conclusion of the paper.

:::::::::: Regarding the mutation rate argument, see the earlier discussion on this page. The third experiment was significantly different than the first two. The experimental scheme was different, it was performed at at different time and with different conditions, and utilized, for the most part, different clones than the first two. And Lenski doesn't just claim there is a mutation rate in potentiated cells, he ''actually measures it''. But frankly, I don't understand your argumentation here. It seems that you are trying to suggest that all the Cit+ mutants isolated were the result of contamination. This clearly isn't the case, for several reasons. However, this isn't the place for this particular discussion, as there is already such a discussion elsewhere on this page. I still haven't seen any adequate response to our points against the Conservapedia article, and I don't think I am closed-minded for expecting such a response. As I said, I'm open to the possibility that the Lenski paper is flawed, but I expect cogent argumentation to support any such flaws. I haven't seen that here.[[User:Gerlach|Gerlach]] 15:09, 17 July 2008 (EDT)

::::::::::: Gerlach, look at how many words you used to sidestep my simple explanation of a flaw in Lenski's work: "Lenski claims there is a mutation rate, yet his presented data show that the number of mutations do not scale with sample size. His presented data disprove both of his hypotheses." If the third experiment of Lenski's was independently flawed as implied by your response, then that does not help your defense. Note that in Lenski's second experiment the mutations also failed to scale with sample size.--[[User:Aschlafly|Aschlafly]] 18:26, 17 July 2008 (EDT)

::::::::::::I think there is a misunderstanding. Blount et al. did not say that the absolute mutation rate was constant for the generation of Cit+. After all, they found that variations in culture conditions had some effect. The replay experiment was performed to determine if clones from later cultures were more or less likely to give rise to Cit+ cells than clones from earlier generations. The authors' hypothesis was that a potentiating mutation was required before the Cit+ mutations could arise. If that was the case then clones from later generations would be more likely to produce Cit+ cells. If the Cit+ capability was the result of an extremely rare, single mutation, then any generation of clones would be equally likely to produce Cit+ cell. The hypothesis is that in a particular experiment, the '''relative probability''' of generating a Cit+ mutant would be greater with clones from later generations. '''Absolute mutation rates''' (which appear to be Andy's concern) may be contingent on the growth conditions, which differed between the three replay experiments but '''''within any particular set of conditions''''', one might expect the relationships between Cit+ recovery and the generations from which the starting clones were derived would still hold.

::::::::::::pg 7902 of the paper in the journal:
::::::::::::"According to the rare-mutation hypothesis, Cit+ variants should evolve at the same low rate regardless of the generation of origin of the clone with which a replay started. By contrast, the historical-contingency hypothesis predicts that the mutation rate to Cit+ should increase after some potentiating genetic background has evolved. Thus, Cit+ variants should re-evolve more often in the replays using clones sampled from later generations of the Ara-3 population."

::::::::::::From the abstract:
::::::::::::"The long-delayed and unique evolution of this function might indicate the involvement of some extremely rare mutation. Alternately, it may involve an ordinary mutation, but one whose physical occurrence or phenotypic expression is contingent on prior mutations in that population. We tested these hypotheses in experiments that ‘‘replayed’’ evolution from different points in that population’s history. We observed no Cit+ mutants among 8.4 x 10^12 ancestral cells, nor among 9 x 10^12 cells from 60 clones sampled in the first 15,000 generations. However, we observed a significantly greater tendency for later clones to evolve Cit+, indicating that some potentiating mutation arose by 20,000 generations. This potentiating change increased the mutation rate to Cit+ but did not cause generalized hypermutability."

::::::::::::What the authors found was that the later generations really did produce more Cit+ mutants than you'd expect if the Cit+ mutation was instead randomly distributed (or, as Andy has claimed and not yet retracted, contaminated by Cit+ cells). Yes, the absolute rates didn't scale across the three different conditions but within each experiment it is clear that the Cit+ mutants arose from cells taken at later generations. Yes, there were differences in the absolute rates under different conditions but that doesn't mean the results and conclusions about potentiated clones are wrong.

::::::::::::As for calculations of mutation rates: Blount et al. performed additional fluctuation experiments (journal pg. 7903) in an attempt to estimate the relative effect of the potentiating mutation and to calculate a rough estimate of the mutation rates. Keep in mind, those rates '''''are referenced to growth under the specific conditions used in that particular experiment''''' and were used to provide ballpark estimates for comparison to other classes of known mutations. As for the second experiment not 'scaling' (with the first?), I wouldn't expect that. The first involved clones grown in continuous liquid subcultures and both the total number of generations, cells/generation and growth conditions (e.g. liquid with nutrient replenishment vs. solid agar) are very different.--[[User:Argon|Argon]] 19:20, 17 July 2008 (EDT)

::::::::::: I have not "sidestepped" your point, Andy. Your claim is that the number of Cit+ mutants obtained did not scale with sample size in the third experiment. In response, I reiterated what Argon and I have said previously, specifically that there are differences between the third and second experiments that make a straight comparison between the two inappropriate. That said, if anyone is sidestepping the issue, it is you. Argon and I have addressed your objection previously, but your only response has been to stubbornly restate the original claim. If you don't agree with our statements, then you must explicate why. Additionally, I did not say or imply in any way that the third experiment was flawed. I said that it was significantly different from the second, but this is not the same as saying it was flawed. Argon has provided a response to the scaling of the second experiment to the first.[[User:Gerlach|Gerlach]] 20:21, 17 July 2008 (EDT)

:::::::: In response to earlier postings about drafting and submitting a letter to PNAS, I'm for it and would be happy to contribute. In response to a comment above, I don't want any "glory" and learned a long time ago that nobody gets credit or money for telling the truth. More often those who speak the truth are reviled and insulted, but mockery doesn't bother the truth as much as it bothers falsehoods.--[[User:Aschlafly|Aschlafly]] 22:01, 16 July 2008 (EDT)

::::::::: (removed false and baseless claim by Argon about sponsorship of this site)

==Draft of PNAS Letters Response from Conservapedia==

''Apologies for the delay in following up on this - I've spent the past few days attending to family priorities, and this is my first CP-related priority now that I have time at my PC again.''

''Since the guidelines for submitting PNAS Letters restricts the submissions to 250 words, the following is the draft submission I'd like to send pending Andy Schlafly's approval:''

:: ''Title:''

::: Identification of procedural and statistical flaws in the paper "Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli".

:: ''Author:''

::: Andrew Schlafly, B.S.E., J.D.

:: ''Author Affiliations:''

::: www.conservapedia.com

:: ''Text:''

::: An analysis of the paper and the supporting information on Professor Lenski's website has led to the identification of significant flaws which, if not refuted, negate the claim that E. Coli bacteria underwent an evolutionary beneficial mutation in the experiment.

::: The full description of these flaws exceeds the submission length allowed for PNAS Letters, but can be found at http://www.conservapedia.com/Flaws_in_Richard_Lenski_Study. In summary, the flaws are:

:::: - The "historical contingency" hypothesis depicted in Figure 3 is contradicted by the abstract and by the data presented in the Third Experiment in Table 1 of his paper.
:::: - Lenski incorrectly included generations of the E. coli already known to contain Cit+ variants in his experiments and had no means to exclude their presence in the samples.
:::: - Lenski's Third Experiment failed to support his hypothesis with statistical significance, even with the incorrect inclusion of the Cit+ variant generations.
:::: - Lenski's two alternative hypotheses suggest a fixed mutation rate, but the failure of the mutations in his experiments to increase based on scale tends to disprove both hypotheses.
:::: - The lag time between the potentiating mutation in the largest experiment disproves Lenski's implicit assumption that it likely occurred in proximity with the occurrence of the Cit+ variant.
:::: - Lenski has not disclosed key portions of his data, such as how thoroughly the samples were screened for pre-existing Cit+ variants.

::: I am requesting that the authors of the paper respond to each of the flaws in this forum and explain the withholding of the data, and submit a revision or retraction of their paper if any are held valid.

''Mr. Schlafly, please let me know if this is acceptable, and apply any revisions as you see fit, thanks. --[[User:DinsdaleP|DinsdaleP]] 10:38, 21 July 2008 (EDT)''

: It's an excellent draft, DinsdaleP. I made a few minor revisions above. After others improve this, then I'll plan on sending it to PNAS later this week. {{unsigned|Aschlafly}}
::I like it. I'll sign my name to it when the time comes.--[[User:DamianJohn|DamianJohn]] 09:35, 22 July 2008 (EDT)

(unindent)

Thanks for the feedback - When applying changes, please keep in mind that the "Text" section in the final version needs to be 250 words or less. If there are important points to add that would exceed this limit, they could be added to the main [[Flaws in Richard Lenski Study]] article instead since PNAS is being asked to respond to the full list there, and not just the summary. --[[User:DinsdaleP|DinsdaleP]] 09:47, 22 July 2008 (EDT)

: I think if i would have presented some draft of that quality to my supervisor i think i would not have reached the door of his office alive and in one piece. It starts with the fact that the correct citation of the article is missing. Please use the appropriate form, inclucing journal number and page. Please have a look at other PNAS Letters. Restate the central issue you criticise in the first sentence, then explicitely describe what your claim about the same issue is and state using what method you come to your conclusion. Keep a neutral tone. Don't make requests. It is obvious that the original author should respond (please look at PNAS for examples of responses, which are published at the same location). Plese fill in your numbers and precise arguments at the points where i left the dots in the following suggestion ('''Please note that nothing of this is my opinion, i just tried to rephrase your opinions in a way that they have the chance to be exposed to a broader view - i skipped tyhe details, because i will not rephrase your arguments, just the structure'''):
: Recently ...... inferred from their experiments (1) that ...... . We analyzed the statistical analysis in terms of ..... and conclude that several variables do not scale as .... . Using hypothesis tests under such circumstances is, in our opinion, ...... , and we do not understand how the authors of the original publication ..... their results.
: The replay experiments yield an ..... scaling with .... . We do not find a consistent value of ..... between the experiments. Furthermore the statistical deviation due to ...... in each sample set does not allow to infer ..... with a sufficient precision. This lack of scaling makes, in our opionion a constant or random source of contamination a likely explanation for a random observation of the ...... dependence of the mutation rate claimed in the paper. The following calculation supports this hypothesis: ....... .
: Furthermore we point out that Fig. ... contains a serious disagreement with .....: while the data would suggest ..... from gen. ..... the figure suggests .....
: We find the material cited in the original article (2)...(n) about the same long-time experiment not to describe the following procedures and experimental constants in a way accessible to us: Handling of ..., contamination rates of ...., and ..... We would kindly ask the authors to clarify these issues. --[[User:Stitch75|Stitch75]] 12:48, 22 July 2008 (EDT)

::No offense taken. I have no experience in these types of submissions, and would appreciate it if you could restructure the submission improve the quality while adhering to the 250-word limit. As I suggested above, it makes the most sense to incorporate these revisions into the main page for this article, where length is not an issue. --[[User:DinsdaleP|DinsdaleP]] 12:52, 22 July 2008 (EDT)

::: I realized that you have obviously not much experience in it; getting the right tone for a scientific publication is hard and i had to try it quite some times on conferences and i still dont get it right sometimes - and from what you said seem to be a student. Sadly, it is against my conviction to rephrase the original arguments in the right way because it would make me an co-author of argumentations i strongly object. In case you did not realize it, helping here to get the structure right doesn't mean i agree - actually the two reasons i would like to see it published is because then the (wrong) idea that scientific journals are not accepting criticism could be obviously be put aside and because i would like to see the needed scientific rigorousity applied to the arguments presented here, because this would put this discussion onto a scientific basis. Quite frankly - i am a liberal by the standards of this site. But i believe the discussion must be carried out with all respect to define the borders of science. The more effective the discussion is carried out, the better the outcome will be. I am willing to listen, as i have proven here, even when beeing treated by people like Mr. Schlafly as if I would be one of his students, while evaluating his qualification in natural sciences quickly shows that i more likely could supervise him in the issues he discusses here (which is something he has proven all along). Regarding that, i am close to giving up, but nevertheless i have seen that a lot of conservatives actually are willing to lead this discussion in a scientific way, which is something, which fulfills me with hope. I recommend you not to fight a fight in where you don't understand the arguments. Don't pick up arguments from others. If you can not fill in the missing words, numbers and arguments in my text, i cant help you. I see what Mr. Schlafly believes, however i do not know how to get the calculation right to support his hypothesis (random or contant mutation rate) - and, this is most likely not because of a lack of statistical knowledge. The only way i would see is to use the rudest form of descriptive statistics and agreggate the data in a very specific way, while ignoring the structure of the experiment - and ignoring the fact that the authors pointed out the problem they see and adressed them. So i can only give oy a few hints (maybe i can form a short contibution to conservapedia; i am just thinking about the title):

:::: If you claim something is wrong, put your opposing claim in a positive formulation, with a supporting calculation, in contrast . Even if the calculation is simple, this is very important to provide it. E.g. we estimate a rate of x+-y per z for dataset N, in which we aggregated generations a,b,c,d, etc .... In the end, you should either prove a mathematical mistake (which was not done) or shoe you hypothesis is more likely.

:::: Don't be rude. You are not the referee and you are not member of a commitee to examine scientific misbehaviour. Dont act like one (and even referees have a friendlier tone usually). Dont act like an personal enemy either. Don't ask for retraction of the article. It is up to the author to make the conclusion respond or retract. This happens more often than you may think as a response to an critisism (actually it's fun to read the "reply section" of scientific journals - sometimes you find things like: "yes, the commenter was right we copied the paper and retract it"). And you are never requesting, but you are kindly asking. Everybody understands that "kindly asking" does not mean "kindly asking" in this context.

:::: Always give full and specific citations which back your claims. Give it in the form required by the specific journal. General citations like "materials on his website" will make your text bein trown out in the editorial screening (because you can not expect that somebody read trough all information to find something backing you claim - this is your job). See for specific styles [http://en.citizendium.org/wiki/Citation_style[http://en.citizendium.org/wiki/Citation_style]]. Ypu may even reference a page/paragraph/eq/figure number to point the reader to what you mean (for papers longer than 4 pages i usually do that).

:::: Run a style checker over your text to eliminate common style mishaps.

:::: '''Most important''': go to your university library. Take the time to just read a few PNAS Letters and replys, and the original articles (Try to finde some with an easy understandable subject). Understanding how these are written and how authors usually reply will help you to get your one right. You are writing against somebody who has twenty years of experience in a field of publishing in natural sciences. You seem to have little experience and Andrew Schlafly, honestly, neither. This game is an uphill battle and unfair game anyway. Make sure you maximize your chances by understanding the rules of the game.

:::: Focus on a single you are sure about. It is better to present one claim well that two claims badly.

:::: Good luck. You will need it. --[[User:Stitch75|Stitch75]] 14:22, 22 July 2008 (EDT)

::::: "Stitch75", you seem to think that the truth depends on whether PNAS accepts it. It doesn't. Lenski's paper is badly flawed regardless of whether he admits it, PNAS admits it, or you admit it. That's the beauty of the truth: it doesn't require admission by anyone. I'm fine with Lenski and PNAS refusing to admit the flaws in their paper. After all, if they really cared about quality then I doubt they would have published their flawed paper after merely 14 days or less of peer review.--[[User:Aschlafly|Aschlafly]] 15:38, 22 July 2008 (EDT)

:::::: Maybe its because English is not my native language. Somehow you seem not to understand what i am saying. I try to rephrase it so that there is no room for misunderstanding: I never can talk about truth, which is a religious thing. I talk about science and observable reality. Primarily i can tell you only what it takes that your thoughts are at least looked at. If rejection happens du to formal reasons (like using unsuitable Formulations, etc) it's not good to draw conclusions on the content or the scientific community. The strong formalism is to save time. And in turn the taxpayers money. I am screening the title of approx. 70 articles per day (10 Minutes), namely everything which come in on the preprint servers on my subject. From approx 70 titles, 10 are interesting enough to read the abstract (6 Minutes), and 2 are interesting enough to look at the summary (4 Minutes) and one in two days in interesting enough to read Section 2 (10 Minues), skipping the introduction, one in a week in interesting enough to print it out and read it (2-4 Hours). Something which does not follow the form end up with beeing thrown out of my rss feed quite quickly. The editors of the journals know that and in a refereed journal such thigs may even be trown out by the editor (and not the referee). Claiming from not getting a response published that "the article is still wrong, no matter what others say, and i am rights anyway" doesnt sound very scientific to me. From everything you have said here, you are unwilling to learn, and you don't expect a response. If you formulate your comment in that way, then skip it. Publishing a letter should stimulate a discussion, if it's not meant to, seen from the style, it will not be accepted. Moreover, according to everything i have seen here, Mr. Schlafly, you seem to have no clue what you are talking about. Please at least consider one time that you could be wrong and try to follow the statistical arguments in the paper - and build up own one on a real calculation (and show the numbers you get). --[[User:Stitch75|Stitch75]] 20:55, 22 July 2008 (EDT)

::::::::: Stitch75 - you are too far inside the belly of the beast to understand what ASchalfly is talking about. You have probably spent your (young, naive?) life as a scientist, or inside the sciences, and as such you are blinded and cannot think with real, free logic. If you look at ASchlafly's arguments with an open mind, and not the blinkered mentality you seem to want to perpetrate, you'll see he's got many excellent points, and I'm convinced that the PNAS will ask Lenski to retract major conclusions of his obviously flawed study once ASchalfly submits this letter. Try to open your mind more to other ways of thinking and you'll see the truth for what it is. [[User:RobCross|RobCross]] 21:01, 22 July 2008 (EDT)

::::::Stitch75 just went far out of his way to be helpful and yet you still continue to respond with hostility and a self-righteous attitude. You explicitly stated that now matter what response you get, you won't accept the conclusions of the paper. That is your prerogative, but you are directly stating that their replies, other than a retraction, will be irrelevant and/or wrong, despite the '''many decades''' of combined practical experience of the authors compared with your complete lack of such. So why is it again that you're even bothering? Several contributors to this forum and others related to it on this website have addressed your questions in great detail- repeatedly- and you continue make vague, unspecific accusations. As Stitch75 discussed, something like "table X is wrong because of figure Y" is nonproductive. Furthermore, if you want to have PNAS readers listen to you- your flaws should be real. For instance, even now your fifth "flaw" is that the statistical results of the third experiment are "obscured" and "not defin[ed]... in the traditional way". Well, the p-value for the third experiment is 0.0823. It took me literally four seconds of flipping through the PDF to find it. It's even in a nice table to make it easy to find. How is that obscure? (I might add that considering P<0.05 significant and P=0.0823 not statistically significant is '''completely arbitrary'''. If the observed pattern wasn't at all what was expected, the P value would be roughly around 0.8-1.0 or so. So 0.0823 ''does'' suggest that the underlying idea is correct in '''exactly''' the same way that P=0.05 would. That is a fundamental concept in basic statistics.) The final problem is that your arguments have drifted from your original concern- whether or not a new trait evolved- since only one of your listed "flaws" actually addresses this issue. The others are tangential and relate to interpretation and mechanisms. Even ''if'' 6 of your 7 flaws were so, the core finding of the paper- around which all else is based- would still hold: in earlier generations, there weren't Cit+ E. coli, in later generations, there were. The mathematical analyses and timeline of occurrence don't change this qualitative, directly observable fact.

::::::I do encourage you to refine the letter and submit it to PNAS- I really do- but Stitch75 is very correct in saying that if you submit it in its current shoddy form it will be laughed at and promptly ignored. You would do well to take the advice of people who actually work in the field when it comes to considering how something will be received. Also, your comment about peer review above indicates that your still have not learned anything at all about how it actually works despite the long discussions previously.

::::::As you said, the truth doesn't require admission. But it does require empirical support, which Lenski provided in ample quantities- but you still have yet to provide anything even beginning to resemble scientific rigor. That is why Stitch75 wrote that response- to ''help you'' improve your letter from that condition.[[User:Kallium|Kallium]] 21:36, 22 July 2008 (EDT)

::::::: You have it backwards, "Kallium". Lenski has the burden of providing "scientific rigor," and his paper falls short. In fact, the data presented in the paper tend to ''disprove'' his hypothesis about a mutation rate, as the mutations identified in his paper do not scale in a meaningful way with sample size.--[[User:Aschlafly|Aschlafly]] 23:11, 22 July 2008 (EDT)

:::::::: I honestly don't know how to make this any more clear. Yes, Lenski does have the burden of providing scientific rigor, as any scientist does. I never said otherwise. However, to claim flaws in any study requires that they be presented with equal rigor. This is just rewording the last statement of my previous post. Simply making vague, unspecified and unsubstantiated hand-waving claims won't get you anywhere. Consider an analogous situation in an appeals court: someone doesn't like the decision of a lower court, so they go to a higher level to present their objections. Now, to do this requires legal rigor to the same degree with which the decision was originally made. The defendant would need to address specifics in the decision and explain exactly why they were incorrectly interpreted. If, however, that defendant were to waltz into the higher court and simply read quotes from the decision and say "that's illogical" or "those statements are self-contradictory" or "that's unfair", without going into detail to explain their reasoning and without addressing the previous cases cited in the decision or providing any further legal precedents, they would utterly fail to make their case and likely be chastised by the judge for wasting the court's time. Now replace the court references with their respective scientific analogs and you have exactly what is going on here. That is why both Stitch75 and I have been giving you this advice- to ''help you present your case''. Lastly, you haven't developed your arguments since you first posted them but keep relisting them. You have yet to show in detail how the data disprove the hypothesis (which you also vaguely define), and as others have explained repeatedly, mutation rates are only expected to scale with sample size under identical conditions, which were not used. That's why your letter needs improvement- it simply won't be taken seriously if it shows a flawed understanding of basic experimental biology. You can't pass rigor completely off of your shoulders; you have to make your case or it will get thrown out of court.[[User:Kallium|Kallium]] 12:12, 23 July 2008 (EDT)
:::::::::You are correct that the truth does not require acceptance. Kallium is not quite correct in in saying that it requires empirical support. It does not, the truth is the truth is the truth and that’s an end to it. The ''search'' for truth, however, requires certain actions and, in this case, Stitch75’s advice should be welcome. Following Stitch75’s advice will not alter the truth one little bit, but will aid the search for it. According to you the truth is that this was a flawed paper that was published, demonstrating flaws in the peer review process. It gets science nowhere, the public scrutiny of science nowhere and the use of public money nowhere for this simply to ''be'' the truth. The scientific community would need to see your objections in the "correct" format before it would do anything about it.

:::::::::You may say that the scientific community should be doing this already. (We might also question whether the format stipulated by the scientific community really is "correct"). Whether they should or should not is moot: the simple fact is that they aren’t and are unlikely to start anytime soon without a “correctly” prepared objection. Stitch75’s advice is designed to help you prepare the objection “correctly” and, in doing so, aid the search for truth.--[[User:YoungA|YoungA]] 09:26, 24 July 2008 (EDT)

I tend to agree with you Andy. I say we get this thing sent to PNAS and see what happens. If they refuse to answer it then we know what that means, and if they thumb their noses at you that's fine too. However I have a little more faith than you in the system and I hold out hope that they'll respond to our queries. Anyway lets get this thing sent. --[[User:DamianJohn|DamianJohn]] 15:50, 22 July 2008 (EDT)

(unindent)

I'd like to thank Stitch75, because he took the time to explain his points constructively, and I learned something from them. (I'm actually an IT Specialist in my 40's, not a full-time student, but learning is a never-ending process and I appreciated the lesson). I consider myself bound by the same ethical constraints on editing that he mentioned, because these objections to Lenski's work are Mr. Schlafly's, not my own. I tend to believe that the Lenski experiment was properly executed, but I'm a strong believer in the scientific process, and Mr. Schlafly's objections deserve a fair hearing whether one believes in them or not. My contribution is to help in the process of getting these objections to the proper forum, namely PNAS, and leaving the response up to them. --[[User:DinsdaleP|DinsdaleP]] 16:20, 22 July 2008 (EDT)

== Expertise in Statistics ==
I don’t mind admitting that I have none! The article states that Lenski combined the three trials incorrectly and that he doesn’t make the insignificance of the third clear. Now it may well be very clear to others but, unfortunately, the article doesn’t make clear to people like me what was wrong. Can someone expand on this point? Is anyone able to explain to a layman what Lenski should have done and the conclusions he should have reached? It's all getting a little technical for me. --[[User:Billd|Bill Dean]] 12:10, 14 July 2008 (EDT)

: OK, here's point 4 in layman's terms: Lenski's hypotheses of a mutation rate imply that a ten-fold increase in sample size should result in a ten-fold increase in mutations. But it doesn't. In fact, a nearly ten-fold increase in sample size results in only a slight increase in mutations in Lenski's data. These data, as presented by Lenski in his paper, suggest (if properly interpreted) that there is no mutation rate at all. Rather, these data are more consistent with occasional contamination, broadly defined.--[[User:Aschlafly|Aschlafly]] 23:15, 14 July 2008 (EDT)

::Except that the growth pattern of the Cit+ cells in the third replay experiment demonstrated that there were no Cit+ cells in the cultures at the time of plating. Control plates with a mix of Cit- and Cit+ cells were done which showed rapid development of Cit+ colonies, whereas the experimental plates did not show any Cit+ colonies for at least 8 days and up to 28 days. If you believe that the plates became randomly contaminated during the course of the incubation, rather than at the initial plating, the post-plating contamination should have affected all generations equally, but it did not--[[User:Brossa|Brossa]] 12:46, 15 July 2008 (EDT)

::Blount et al. discussed the unexpectedly low Cit+ conversion rate for the third replay set in the supplementary document. They have some speculations but don't know why it occurred. They are dealing with low probability events. I don't agree that the 'proper' interpretation is contamination. First, they isolated and tested each Cit+ isolate for the markers and sequences we've discussed on earlier Conservapedia pages. Second, the distribution of Cit+ isolates does not appear to be random: They correlate strongly with the later generations. If undetected contamination was random, it's unlikely the Monte Carlo resampling tests would reject the null hypothesis of the 'rare-mutation' hypothesis over the 'potentiated' hypothesis. As Brossa correctly notes, contamination would have affected all generations. Blount et al. write in the paper's supplement: "To facilitate handling and minimize possible confounding variables, we divided this third experiment into 20 blocks of 14 clones each. All of the clones within a block came from different generations, and the single ancestral clone was included in all 20 blocks."--[[User:Argon|Argon]] 20:01, 15 July 2008 (EDT)
::: Good and detailed analyis and conclusion, Argon. I had no time to read everything in that detail, but i think you present exactly the arguments (contant background would favour rare mutation hypothesis) would be exactly the one i had in mind, so let's see how Mr. Schlafly will bend his own Monte-Carlo simulations to showing several 1000 times no mutation into accordance with any reasonable background explaining a significant number of counts in *some* samples --[[User:Stitch75|Stitch75]] 20:20, 15 July 2008 (EDT)

:::: The above comments are non-responsive. The essence of ''both'' of Lenski's hypotheses is that there is a fixed, or stepped, mutation rate. But any such rate would be roughly proportional with sample size. Yet his three experiments prove otherwise, which Lenski fails to address in a satisfactory manner. Indeed, Lenski's presentation of his data disproves the very thing he claims to have shown.--[[User:Aschlafly|Aschlafly]] 20:40, 15 July 2008 (EDT)

::::: Mr. Schlafly, please answer: Which the of the two hypotheses is, according to your calculations the most likely? --[[User:Stitch75|Stitch75]] 20:47, 15 July 2008 (EDT)

::::::The first replay experiment was run under different conditions - roughly 3700 generations in continuous subcultures. One can't compare population sizes or rates between the first and last two replay experiments. As I noted, Blount et al. acknowledged the possible anomaly of lower than expected mutants in the third run. Still, the second and third experiments were run under different conditions. The plates in the second replay experiment were seeded with fewer cells per plate than in the third experiment. That change can affect the survival rates of cells on plates over time (e.g. different rates of nutrient exhaustion). Given the extremely low mutation rates involved, there is no simple means of normalizing the numbers of mutants recovered for the second and third experiments. One might expect 'roughly' 10x more mutants in the third experiment but that's truly a 'rough' estimate that would be affected by conditions under which cells are exposed. It's certainly a question that remains and they may be able to clear up with future research. In any case, the pattern of data does not support Andy's claims of contamination or that the hypotheses of the paper is in error.--[[User:Argon|Argon]] 21:27, 15 July 2008 (EDT)

::::::: Argon, you have free will and it's clear to me that you are going to exercise it to the point of embracing absurdities. This time you claim that "extremely low mutation rates" would not result in mutations that scale with sample size (of course they would), and that density completely alters mutation rate (if that silly claim were true, then Lenski's experiment was flawed from the get-go). Your belief system is remarkable, but it's not logical.--[[User:Aschlafly|Aschlafly]] 23:38, 15 July 2008 (EDT)

::::::::Fair enough, but let's be clear: That's my take on the paper and that of most of the scientists who reviewed the paper, read the paper and commented upon the paper so far. For that matter, Michael Behe didn't call the data flawed, nor did those commentators at Dembski's Uncommon Dissent blog, nor did Dr. Georgia Purdom at Answers in Genesis. In contast, those who think the work is flawed appears to be limited mostly to you, Andy. It is true that 'scaling' was not seen in this case but as we've seen, the conditions were not quite the same and it is known that this can have an impact.

::::::::However, the fact that the conditions were not identical doesn't detract from the fact that the emergence of Cit+ clones *still* correlated with the sampling of the later generations. What this means is that with three separate experiments and under three sets of conditions, the constant-rate-mutation hypothesis doesn't hold. What the differences between the second and third replay experiments demonstrates is that they were run under different conditions that affected the overall rate of conversion, not that the 'potentiated mutation' hypothesis is wrong. Those are actually distinct questions. Andy, the data simply does not support your claims that the cultures were contaminated (we'd expect random distribution), or that the 'scaling' variations ruined the experiment. In my opinion, you seem focused on red herrings to the exclusion of evaluating the data in the overall context of the experiment which demonstrates a correlation of Cit+ clones emerging from samples taken at later generations. Would you care to address that pattern and discuss why your 'contamination hypothesis' doesn't appear to hold up?--[[User:Argon|Argon]] 09:29, 16 July 2008 (EDT)

:::::::There is nothing absurd in what Argon said. As he mentioned, the third experiment was performed under different conditions and at a different time than the first or second experiments. The key here is that there are plenty of variables, some unknown, that simply aren't controlled for between the experiments. For example, take the fact that it was performed at a different point in time than the first two. The third experiment, then, is almost certainly being performed with different batches of growth media, liquid and solid. Anyone who has spent any significant time growing cells knows that media can vary significantly in growth characteristics between batches, despite the same recipe being used. The reasons for this can be many. Perhaps the balance or pH meter was off calibration one day, or a different bottle of reagent was used. Take an analytical chemistry course, you'll spend plenty of time talking about this. It is true that, for the most part, this sort of variability has minimal impact. But when you're examining something like an extremely rare mutation, or you're trying to make an extremely accurate measurement, intra-lab variability like this can be significant. For an extremely rare mutation like Cit+, which involved at least two additional mutations in potentiated cells, any change in mutation rate can have a significant effect on your ability to obtain mutants. Mutation rate is sensitive to growth conditions, so cells grown in different conditions are likely to experience a different rate of Cit+ mutation.

:::::::Regardless of the reason for the lower-than-expected number of Cit+ mutants in the third experiment, however, the Cit+ mutants isolated absolutely did not arise from contamination. This is clear if you read the paper. You're still left, then, with the two hypotheses presented, and the results support historical contingency.[[User:Gerlach|Gerlach]] 09:45, 16 July 2008 (EDT)
Is there anyone here with expertise in statistics who could give an analysis? [[User:Fyezall|Fyezall]] 16:15, 15 July 2008 (EDT)

:Hello Fyezall. I rearranged the position of your question to hopefully keep the conversations clearer. It boils down to this: The researchers found that mutant Cit+ strains arose over the course of time in their long term growth experiment. They wanted to learn something about how that strain acquired this ability. They wondered, 'Was this the result of a single, very low frequency mutation or did some other mutation have to precede it in earlier generations, followed by the final mutation(s) that allowed the cells to grow on citrate?'

:If the Cit+ change required a single mutation with a low but constant probability over time one would expect Cit+ mutations to be distributed across cells taken from any generation of the experiment. On the other hand, if a 'potentiating' mutation had to arise at some point in the cultures before the final Cit+ mutation could function, then one would expect the probability for Cit- cells to mutate to Cit+ cells would increase with samples of cells taken from later cultures.

:Blount ran the experiment and found that Cit+ mutants arose more frequently in cells taken from later generations in the culture. The Monte Carlo resampling tests were used to assess how likely the pattern of results would fit the models. The statistical significance (smaller P-values mean greater significance), was calculated for each experiment and the combination of experiments. The numbers suggest the distribution of mutants was not randomly distributed across the experimental generations, they tended to appear in cells taken from the later generations. This would argue against the single-mutation, constant, low-probability hypothesis. It appears that a pre-adaptive mutation had to have arisen first, followed by the mutation that finally allowed the cells to utilized citrate. Future work in Lenski's lab will focus on trying to identify the various mutations involved. I hope this brief explanation helps.--[[User:Argon|Argon]] 20:25, 15 July 2008 (EDT)

==What I have noticed==
I tell you what strikes me the most about this discussion - Its watching evolutionists do whatever they can to keep their precious beliefs above question or scrutiny. Its as if they know that it will come toppling down so they must resort to side-lining the hard questions.
[[User:JJacob|JJacob]] 21:43, 15 July 2008 (EDT)
==[[Social Text]]==
This well known hoax ''does'' support Aschlalfy's position that the paper was reviewed by PNAC ''rather quickly'', since (apparently) the paper supported the editors/reviewers point of view. Perhaps this would have beeen better placed on the [[Richard Lenski]] page rather than here since this deals only with the 6/10/08 PNAS paper ''per se'' and not the review process. [[User talk:MargeryCampbell|Marge]] 12:45, 16 July 2008 (EDT)

:I fail to see the relevance of the Sokal Hoax here. You should also know that Social Text was not a peer-reviewed journal when Sokal submitted his paper. That doesn't excuse the credulity of its editors, but Sokal's paper was not sent out for review. Not to say that it would have mattered, postmodernism is just meaningless word salad.[[User:Gerlach|Gerlach]] 13:39, 16 July 2008 (EDT)

Talk:Flaws in Richard Lenski Study

2008-07-24T13:26:11Z

YoungA: /* Draft of PNAS Letters Response from Conservapedia */

Now, is this page a report over other people thinking Lenski's paper is flawed or is this Aschafly reporting about himself and putting it in the headline of the Front Page? And please specify by references which "two other" experiments are referenced, and explaing how you can see that the "historical contingency" is not true. --[[User:Stitch75|Stitch75]] 23:22, 12 July 2008 (EDT)
And if you think you argue that well, why dont you submit it as a comment òn the paper to PNAS. --[[User:Stitch75|Stitch75]] 23:24, 12 July 2008 (EDT)

:This article is seriously partisan. I see no outside or third party analysis of the paper in the references, just a bunch of cites to the article or conservapedia itself. [[User:Wisdom89|Wisdom89]] 00:34, 13 July 2008 (EDT)

Folks, you're in the wrong place if you're more interested in who says what rather than determining the truth itself. A true wiki gets at the substantive truth rather than trying to rely on biased gatekeepers and filters of the truth.

The flaws in the statistical analysis in Lenski's paper are clearly set forth and well-referenced. If you're interested in the truth, then look at the paper and see the flaws yourself. If you're not interested in the truth and think you can distract people's attention from it by using other tactics, then you're wasting your time here.--[[User:Aschlafly|Aschlafly]] 00:42, 13 July 2008 (EDT)

I agree with Aschlafly on this, there needs to be some kind of admission or response from Lenski but little has been forthcoming and conservapedia itself has taken it on. Notice how no-one, aside from conservapedia (and I think Creationwiki?) has asked such questions of Lenski? All the magazines etc have taken his study at face value without actually taking the time to critique his claims. Aside from the "peer reviewers" of course.
[[User:JJacob|JJacob]] 00:47, 13 July 2008 (EDT)

: The "peer reviewers" who spent somewhere between 0 and only 14 days looking at the paper, and missed an obvious contradiction between Figure 3 (specifying the "Historical contingency" hypothesis) and Table 1, Third Experiment. The statistical analysis in the paper appears so shoddy to me that I doubt anyone with real statistical knowledge or expertise even reviewed it.--[[User:Aschlafly|Aschlafly]] 00:59, 13 July 2008 (EDT)
::I have expertise in research and statistics and I'm just not seeing this shoddiness that you make reference to. You are allowed to have your doubts, but we should get a bunch of people familiar with such fields to examine the paper's statistical analysis. [[User:Wisdom89|Wisdom89]] 01:01, 13 July 2008 (EDT)
::I have the same problem. i hold a Dr.Rer.Nat title and did some statistics (although i am no expert on it) and fail to see the "shoddiness" please help my underdeveloped mind, Mr. Schafly and enlighten me. I it is so obvious it should be a one-liner to formulate it. --[[User:Stitch75|Stitch75]] 09:54, 13 July 2008 (EDT)

::: Please try harder then. I've expanded the explanations a bit also.--[[User:Aschlafly|Aschlafly]] 10:42, 13 July 2008 (EDT)

:::: At least now i can recongnize your statements more or less clearly. Yet i think (cite from the paper) ''We also used the Z-transformation method (49) to combine the probabilities from our three experiments, and the result is extremely significant (P < 0.0001) whether or not the experiments are weighted by the number of independent Cit+ mutants observed in each one.'' has to be addressed more specifically than you do in order to discredit the statistics used --[[User:Stitch75|Stitch75]] 11:54, 13 July 2008 (EDT)
:::::Just for comparative purposes and a frame of reference, a P value that is less than the significance level of 0.05 is considered significant. [[User:Wisdom89|Wisdom89]] 13:10, 13 July 2008 (EDT)

I wonder, do the PNAS allow questions to raised and asked of the "peer reviewers" themselves? Are we able to find out who/what experience they themselves have? Perhaps that is an avenue that we could look at? I apologise in advance if this has already been asked or answered.
[[User:JJacob|JJacob]] 01:07, 13 July 2008 (EDT)

:Definitly not. Peer reviewers are anonymous and only known to the editor, for good reason. Having peer reviewers non-anonymous would cause reviewers to be very careful to step on nobodys foot to evade revenge. --[[User:Stitch75|Stitch75]] 09:54, 13 July 2008 (EDT)

: No, PNAS probably won't disclose who supposedly did the 14-days-or-less peer review on the [[Lenski]] paper. You're right that such disclosure could shed some light on the final product.

: "Wisdom89", your claim that you "have expertise" and don't see the flaws only makes me conclude that you don't really have the expertise that you claim. Judging by your silly user name, perhaps you've tried that approach before. We're not fooled by it here.--[[User:Aschlafly|Aschlafly]] 01:14, 13 July 2008 (EDT)

(removed silly comment by person who has since been blocked for [[90/10 talk]] violation)

==Marginally significant==
In #1, that's not inconsistent. The figure makes it clear that, according to the hypothesis, the mutations should also occur earlier than 31,000, but should become more common at that point. 12/17 mutants occurred after 31,000. The point in #3 is not clear. What do you mean by ''weighting''? In #5, ''Lenski's paper is not clear in explaining how the results of his largest experiment...his paper refers to his largest experiment as "marginally ... significant," which serves to obscure its statistical insignificance.'' Actually, '''marginally significant''' is clear. It means that the p-value is between .05 and .10 (in this case it's .08, table 2). It's a pretty standard phrase to describe an effect that falls into that range. [[User:Murray|Murray]] 13:41, 13 July 2008 (EDT)

: Your defense of Lenski per point #1 is contradicted by the paper's own abstract, and by the comments by the other Lenski defender below. In point #3, proper weighting is needed to combine multiple studies. In point #5, you don't cite any authority for the unscientific claim of being "marginally significant."--[[User:Aschlafly|Aschlafly]] 20:45, 13 July 2008 (EDT)
: Your defense of Lenski per point #1 is contradicted by the paper's own abstract, and by the comments by the other Lenski defender below. In point #3, proper weighting is needed to combine multiple studies. In point #5, you don't cite any authority for the unscientific claim of being "marginally significant."--[[User:Aschlafly|Aschlafly]] 20:45, 13 July 2008 (EDT)
::Define "proper weighting". Are you referring to how they interpreted the sum of the work or to a specific analysis? You're right, I didn't cite any scientific authority. Here's one: Motulsky, H. (1995). ''Intuitive Biostatistics'', Oxford Univ. Press. Chapter 12. Also, try searching for the phrase in Google Scholar or PubMed, you'll find plenty of uses of it. It's a shorthand way of describing an effect that came close to the arbitrary threshold for statistical significance but did not reach it. [[User:Murray|Murray]] 21:55, 13 July 2008 (EDT)

::: You seem unwilling to accept that Point #1 identifies a clear mistake between the figure and the abstract in the paper, which requires correction by Lenski or PNAS. Given that unwillingness, I doubt it will productive discussing the other mistakes further with you. You're right that other usage of the dubious concept of "marginally significant" can be found on the internet, but the first link to such usage on my internet search for it returned the non-rigorous "Intuitive Biostatistics" and the second link returned a criticism of the concept similar to the criticism express here. [http://annhyg.oxfordjournals.org/cgi/reprint/49/1/93-a.pdf] --[[User:Aschlafly|Aschlafly]] 00:42, 14 July 2008 (EDT)
::::It's not a clear mistake in my mind. There does seem to be some confusion or contradiction in terms of the number of generations, but I haven't seen a clear explanation of why this is or is not a mistake. What seems like a contradiction is the abstract statement that no mutations occurred before 31,500, but it's not clear to me whether I'm misunderstanding that. ''I doubt it will productive discussing the other mistakes further with you. '' Of course you doubt it, because you are unlikely to be willing to concede anything no matter what anyone says. Why do you call the concept dubious? The procedure of determining whether an effect is significant requires the setting of an arbitrary threshold, which is usually .05. That means, in analyses of the sort in the Blount et al. paper, that there's less than a 5% chance that the findings are due to sampling error. When an effect comes close to the threshold it is worth noting, because of the problems inherent in significance testing, which itself is widely criticized in the statistical literature. I am not clear what you mean by weighting, as I mentioned before - in the interpretation or statistically? [[User:Murray|Murray]] 13:30, 14 July 2008 (EDT)

== Richard Lenski incorrectly included generations of the E. coli already known to contain Cit+ variants in his experiments.[3] Once these generations are removed from the analysis, the data disprove Len ==

The author of the above statement must not have read the paper or the supplement carefully. Lenski took clones from those cultures that '''weren't Cit+'''. Careful reading of the paper or the supplement reveals that Cit+ mutants appeared at 750 generations or later into the replay experiment. The authors write: "New Cit+ variants emerged between 750 and 3,700 generations..."--[[User:Argon|Argon]] 15:03, 13 July 2008 (EDT)

: Your explanation is not convincing. Show us how Lenski proved that the samples did not have '''any''' Cit+ variants, if you really think he's claiming that.--[[User:Aschlafly|Aschlafly]] 20:51, 13 July 2008 (EDT)

::I count at least four distinct diagnostic methods used in the paper for distinguishing whether clones are Cit+. One in particular they describe as being very sensitive to weakly citrate-using cells. It's not that I 'think' Blount et al. claim they started with Cit- cells. They say that in the 'Supporting information' document.

::Andy, for tonight, I'll leave it as an exercise for you to answer your own question of how one might test a clone to be sure that is was Cit-. Use the paper if you'd like or present another means. Tomorrow evening I'll cite the methods Blount used in the paper.

::Meanwhile, here's another question to ponder: If the colonies used to start the 'replay' cultures were Cit+ at the start, why is it that no Cit+ cells were found in such cultures before 750 generations? These cultures were all started from single clones which must have either had the Cit+ phenotype or not.--[[User:Argon|Argon]] 18:38, 14 July 2008 (EDT)

-
How did Lenski obtain Cit- clones from later populations after Cit+ had become the dominant phenotype? It's pretty standard procedure. First, keep in mind that these populations contained a minority of Cit- cells. Now, a small liquid growth is made from the frozen glycerol stock of cells from a given generation, say 32,000. This is grown to an appropriate OD and then plated on a standard rich media agar plate. Provided that the plated sample isn't too dense, this plating will deposit somewhere between 15-100 individual cells on the agar, with plenty of spacing between them. The plate is then incubated at 37 C for a given time, during which the individual cells replicate to form small, visible colonies. These colonies will consist solely of cells that are genetically identical to the original cell deposited on the agar. This is all well and good, but how do you find which of the colonies are Cit-? Here you use a technique called replica plating. The agar plate is gently inverted onto a sterile swatch of velvet so that some of the cells from each colony are deposited onto the fabric. Next, a citrate-only agar plate is pressed against the velvet, transferring cells from the fabric to the new plate in exactly the same spacial orientation as the first plate. The cells are then allowed to grow on the citrate-only plate. When we then compare the two plates, we look for colonies on the rich plate that did not grown on the citrate-only plate. These colonies will be Cit-, and can be used for the replay experiments. [[User:Gerlach|Gerlach]] 13:45, 14 July 2008 (EDT)

:Just a correction: The Cit+ cells didn't dominate the cultures at generations 32,000 & 32,500. Cit+ mutants represented 12% and 19% of the population at these times points, respectively. Replica plating is definitely one means of identifying Cit- and Cit+ clones but because the Cit+ cells represented a fraction of the total, it is simple enough to streak the samples to individual colonies (founded by single cells) and test each colony individually. Otherwise, a nice description of replica plating (a technique developed by Joshua Lederberg that allowed him do the research for which he was awarded one of the 1958 Nobel Prizes in Medicine)--[[User:Argon|Argon]] 18:38, 14 July 2008 (EDT)

::Oops, you're right, Argon. Cit+ wasn't dominant at generation 32,000, so replica plating might not be the best option. Still, in the case of almost 20% Cit+, I think replica plating might be labor reducing. I'm a biochemist by training, not a microbiologist, but I'm sure there are other methods that could be used. For example, Christensen's agar appears to provide a sensitive, colorimetric method of identifying even weakly citrate-utilizing colonies, so one might be able to plate cells on a Christensen's agar plate and pick uncolored colonies. Again though, I'm no microbiologist so I don't know the best method. However, there are ways to easily pick Cit- clones from later generations in this case. That said, I think that this specific "flaw" cited in Lenski's paper should be removed from the main article. Clearly, Cit+ were not used in the replays from later generations, so Conservapedia's objection is totally baseless.[[User:Gerlach|Gerlach]] 19:19, 14 July 2008 (EDT)
:::All appropriate descriptions. For generating estimates of the population distribution (Cit-/Cit+) in a culture, replica plating would certainly be applicable. The main point is that identifying and isolating Cit- clones from the generations used in the experiment is straightforward. I agree that it would be a mistake to keep that objection in the article (actually that thread runs across several points in the article).--[[User:Argon|Argon]] 20:12, 14 July 2008 (EDT)

:::: Nothing in the paper rules out contamination of those samples by Cit+ variants, and you quote nothing in the paper to rule it out. There was no reason to use and rely on these samples that already have Cit+ variants.--[[User:Aschlafly|Aschlafly]] 23:04, 14 July 2008 (EDT)
:::::The whole point of the discussion above was to illustrate that there are methods to isolate cells with a particular genotype from a mixed population. Suppose we used the replica plating method (maybe not the best choice, but it's standard procedure). Care to explain where the Cit+ contaminants could possibly come from? And the naivete inherent in objecting that "nothing in the paper" rules it out is simply astounding. Standard laboratory procedures, like isolating specific clones, typically don't show up in papers. For example, if I to write a paper on my research, it would not include a detailed discussion of the construction of my expression plasmid. I might mention that I cloned my gene into a particular vector, but there wouldn't a discussion of how I did my PCR, restriction digests, or transformations. Things like that are simply extraneous details that are taken for granted by experienced researchers. There is simply no reason for Lenski et al. to include a discussion of their method for isolating specific clones. This is why this whole exercise of Conservapedia criticizing Lenski's paper is folly, because most Conservapedia users simply don't know standard laboratory techniques. It's kind of important to know what scientists today are able to do on a routine basis before wading in to claim that they couldn't have done what they claim.[[User:Gerlach|Gerlach]] 09:05, 15 July 2008 (EDT)

:::::***** *****
:::::Actually the methods cited in the paper would separate the Cit+ lines from the Cit-. They took single colonies (founded by single cells), and tested them on selective agar (minimal citrate media - MC agar) and an indicator medium, Christensen's citrate agar (Product information from Sigma here: http://www.sigmaaldrich.com/sigma/datasheet/c7595dat.pdf). As Gerlach notes from the Blount paper, Christensen's citrate agar is very sensitive to citrate utilization. Typical ''E. coli'' strains do not produce a color change but other citrate-using enterics like ''S. typhimurium'' and Cit+ ''E. coli'' mutants appear pink/red on the plates.

:::::This conclusion is further validated (as I mention above), by the fact that Cit+ mutants did not appear immediately in the replay experiments (Others have also noted this). For example, in replay set-1, it took 750 generations before the first Cit+ mutants were isolated. Many didn't produce Cit+ cells after 3700 generations. If the starting line was Cit+, *all* the cells in the culture would have show up as Cit+ in the first pass.

:::::Overall, it is abundantly clear that the cell lines used in the replay experiments were not Cit+ at the beginning.--[[User:Argon|Argon]] 19:44, 15 July 2008 (EDT)

== 1. Lenski's "historical contingency" hypothesis, as specifically depicted in Figure 3, is contradicted by the data presented... ==

Again, more issues with comprehension: The authors did not know when the potentiating mutation first arose but they knew it was before generation 31,500. Figure 2 is merely figurative, being an illustration, and not quantitative. Their analyses suggested that the potentiating mutation did arise at about the 20,000 generation point or later. Their conclusion is that Cit+ mutation rate is low even in a potentiated background but apparently distinguishable from a low-incidence single, unpotentiated event.--[[User:Argon|Argon]] 15:04, 13 July 2008 (EDT)

== Statistics101 package: ==

What does the author imply by writing: "...Lenski himself does not have any obvious expertise in statistics. In fact, Richard Lenski admits in his paper that he based his statistical conclusions on use of a website called "statistics101"?

From the web site:
''Professionals: Although it was originally developed to aid students, the Statistics101 program is suitable for all levels of statistical sophistication. It is especially useful for Monte Carlo, resampling, and bootstrap applications. It has been used by professionals in many fields. These include anthropology, biology, ecology, evolutionary biology, epidemiology, marine biology, psychology, toxicology, veterinary pathology.''
It would appear that the package from the web site (not the web site itself) was used to perform the Monte Carlo resampling tests. Is there any evidence that the package produces incorrect results?--[[User:Argon|Argon]] 19:41, 13 July 2008 (EDT)

==Formal Response to PNAS==

''I've moved this thread from the open section above since this page is being categorized.'' --[[User:DinsdaleP|DinsdaleP]] 21:52, 13 July 2008 (EDT)

:::I think this article presents very sound arguments. Conservapedia should now take action, offering to publish a rebuttal of Lenski in the PNAS journal.--[[User:JBoley|JBoley]] 11:31, 13 July 2008 (EDT)

I agree with JBoley in that if Conservapedia wants to present a formal, professional response to Professor Lenski's paper that questions specifics within his paper, then it should happen. That is the proper execution of the scientific method, and I'm certain that a professional response to PNAS would yield better results than vague "give us all the data " demands. Is a formal response to PNAS from Conservapedia in the works, or is this article the only place these questions/objections were intended to be raised? --[[User:DinsdaleP|DinsdaleP]] 11:52, 13 July 2008 (EDT)

: I don't know if PNAS would embarrass itself by printing a rebuttal, or whether it has the integrity to retract Lenski's paper. Conservapedia's audience is probably bigger than PNAS's, and we're certainly not going to suspend our exposure of the truth here in order to await correction by PNAS.

: PNAS publishes, quite easy to find Rules for "Rebuttals" (they call it "Letter"). It is specifically what you want. [http://www.pnas.org/site/misc/iforc.shtml PNAS:Information for Authors] . I cite: ''Letters are brief online-only comments that contribute to the discussion of a PNAS research article published within the last 3 months. Letters may not include requests to cite the letter writer's work, accusations of misconduct, or personal comments to an author. Letters are limited to 250 words and no more than five references.'' --[[User:Stitch75|Stitch75]] 13:25, 14 July 2008 (EDT)

: In addition, Lenski has already demonstrated how he reads this site and he can certainly correct his own paper, and he should do so. Indeed, professionalism might support giving Lenski the time to correct it himself first.--[[User:Aschlafly|Aschlafly]] 12:14, 13 July 2008 (EDT)

::I understand what you're saying, but there's nothing improper or unprofessional in submitting a formal request to PNAS to have the points in this article addressed by Professor Lenski and his team. To be frank, you've been adamant in your insistence that PNAS has been less than rigorous in the review of Lenski's paper, so if one of your intentions is to demonstrate this then having PNAS respond to a formally submitted response to the paper in public would serve that purpose. This can be done in addition to publishing these objections on Conservapedia--[[User:DinsdaleP|DinsdaleP]] 12:21, 13 July 2008 (EDT)

:::If not PNAS, then perhaps some other public forum? I know Andy Schlafly has appeared on television, effectively arguing against gardisal and other dangerous vaccines. Perhaps if a TV program were interested you could argue against Lenski? You could be the spokesperson against these false claims of evolution.--[[User:JBoley|JBoley]] 12:24, 13 July 2008 (EDT)

:::: I'm not opposed to the above suggestions, but the future is here, folks. Lenski, PNAS editors and television producers have free will to reject or ignore the truth, and I'm more interested in getting the truth out here than trying to persuade someone in dying media like print or television. Lenski and his defenders can see the truth here, and they can decide for themselves whether to reject or admit it.--[[User:Aschlafly|Aschlafly]] 12:30, 13 July 2008 (EDT)

:::::I agree with you about the dying nature of print (I don't think television is dying, merely changing). The problem is that information about the flaws in Lenski's study are not registering outside of sites like Conservapedia. In effect, Conservapedia is an echo chamber. People that come to this site already agree with its point of view. I encourage you to attempt to attract the attention of other forms of media, or Lenski's false claims will simply be accepted as fact by the public and even worse, by educators.--[[User:JBoley|JBoley]] 12:36, 13 July 2008 (EDT)

::::::While there's nothing wrong with taking one's message to various forums or outlets, I believe there's a specific value in submitting these objections as a formal response to PNAS. Conservapedia was established as a trustworthy resource for students, and in my mind all of it's actions should be done with the goal of informing and educating. The Lenski debate is over the findings published in a scientific journal after undergoing a peer-review process. The objections to this paper by the CP leadership are not just about its content, but to the process by which it was reviewed and published in the timeframe it was. Talking about these objections is fine, but it's more instructional to the students using Conservapedia, and a better example of the scientific method in action, to respond to a scientific paper published in a journal through the formal process by which such papers are either defended or corrected. In the end, Lenksi's work will either stand up as good science, or any errors will be addressed and the paper's conclusions modified accordingly, which is also good science. Seeing this process in action regarding a such a significant paper is a great learning opportunity, and the Conservapedia leadership would be remiss in not standing by their conviction in these objections and submitting them formally to PNAS. --[[User:DinsdaleP|DinsdaleP]] 12:38, 13 July 2008 (EDT)

PNAS has a letters section available with the online edition. Many journals have a letters section for rebuttals or clarification. Legitimate corrections are welcome. Andy, have you run your list of 'flaws' past any biologists?--[[User:Argon|Argon]] 15:36, 13 July 2008 (EDT)

: Funny, Argon, how you don't apply your demand of expertise to Lenski himself. What are Lenski's credentials with respect to statistical analysis? Has he even taken and passed an upper-class statistics course of any substance?--[[User:Aschlafly|Aschlafly]] 00:45, 14 July 2008 (EDT)

::I don't follow. Are you suggesting that Lenski doesn't understand the proper application of the statistical methods used in his paper? If so, I haven't seen a description of which alternate methods you'd employ, let alone any output from such an analysis. Here's a thought: Why don't you substantiate your claims by writing up the work and submitting it as a correction letter to PNAS?--[[User:Argon|Argon]] 18:46, 14 July 2008 (EDT)

::: Argon, if you really "don't follow," then try harder. You insist on credentials by others who criticize Lenski, and yet you do not insist on expertise by Lenski in statistics with respect to his "analysis". Perhaps Lenski should first take and try to pass "Statistics 101" before trying to use a website by its name to draw flawed conclusions.--[[User:Aschlafly|Aschlafly]] 22:36, 14 July 2008 (EDT)

::::Do you really think that Lenski went to statistics101.net to learn about statistics and how to apply them? That simply is not the case. The Lenski group knew that they needed to do a Monte Carlo resampling analysis on the results of their replay experiments. In this situation, they are faced with two choices: either code an appropriate program themselves, or utilize one that has already been developed and is readily available to researchers. Since statistics101 had such a program available, they chose the latter option. Statistics101.net was simply the source of the program that the Lenski group used to perform the statistical analysis. If you want to argue against that choice, then you need to examine the source code for the statistics101 package and enumerate why it should not have been used.[[User:Gerlach|Gerlach]] 11:40, 15 July 2008 (EDT)

::::***** *****
::::I don't insist on credentials per se. I *recommend* developing a working understanding of the experiments or a willingness to do the necessary background research to get the details straight before heading off on possibly the wrong direction. It saves a lot of thrashing about. It's perfectly OK to raise questions but before leveling accusations it might be nice to do that privately and discuss that with others who can provide useful feedback. Just my 2 cents.--[[User:Argon|Argon]] 19:48, 15 July 2008 (EDT)

::Mr. Schlafly, does your response above, "I'm more interested in getting the truth out here than trying to persuade someone in dying media like print or television", mean that you will not be submitting a response with these identified flaws directly to PNAS? As I mentioned above, it takes nothing away from the value of posting these statements here on CP to also submit them to PNAS, but the proper way to prompt a journal to review and correct an article is through a direct response, not publication on an unrelated website like CP. It's not proper for anyone but the author(s) of the objections in this article to make that submission, so I'm hoping they step up with the conviction of their beliefs and respond to PNAS directly. Thanks. --[[User:DinsdaleP|DinsdaleP]] 12:32, 14 July 2008 (EDT)

::: By now Lenski has probably seen the flaws identified on the content page here. What's "proper" is for him to correct his own paper in PNAS. The criticism will likely continue as long as he declines to do so. If anyone here would like to educate the PNAS editors about the flaws, then please feel free to do so.--[[User:Aschlafly|Aschlafly]] 22:36, 14 July 2008 (EDT)

::::I'll be glad to submit these items to PNAS on behalf of Conservapedia using the "Letters" forum described by Stitch75 above. Should I cite you the author of this analysis, and is there an email you'd prefer me to include instead of my personal one for any PNAS response? I'll put up a draft of the Letters submission here for your approval before sending anything out. Thanks. --[[User:DinsdaleP|DinsdaleP]] 18:39, 15 July 2008 (EDT)

:::::It would have a very strange scientific taste should somebody else that Mr. Schlafly be the first author of the letter (however, if you insist on that, i suggest "personal communications" as the right kind of citing the work here.). It is his turn to stand up to his claims in this way (by publishing it into a Forum which he is not the owner of). I personally share the doubts of many here about his argumentation (and his understanding os the experiments), but i am sure only more of his dismissive comments will follow. However i see that he comes up with a clear alternate Hypothesis (contamination), so he is free to show that this is more likely (calculations please) and peform Monte-Carlo simulations on it (for a person complaining that statistics101 is to simple that should be no difficult task). As far as i understood and see the data Lenski and coworkers did the best to exclude this Hypothesis, however i did not run own simulations (And I won't do it, because i think nothing will come out - furthermore Mr. Schlaflys personal style in the communication "you have to try harder" is not the style i am used to be adressed by people whose qualification in a subject is appearlingly nor more than mine). So running the simulation, evaluating his own hypothesis using a valid statistical method is now Mr. Schlaflys job - if he come up with a decent calculation showing this Hypothesis is more likely, the letter would for sure be accepted and Lenksi would have to react. If Mr. Schlafly is not the first author of the letter he could evade the critics after that by saying that he was misunderstood, which means somebody else take the risk of submitting the letter, but in case of success Mr. Schlafly would take the glory. --[[User:Stitch75|Stitch75]] 20:10, 15 July 2008 (EDT)

::::::I would prefer that Mr. Schlafly submit his objections to PNAS directly as well, but since he has declined to do so the next best response is to submit it "on behalf of Conservapedia", which he has authorized above. I'll post the draft letter tomorrow, and it will credit him as the author unless I'm asked to include other individuals who contributed to the analysis. --[[User:DinsdaleP|DinsdaleP]] 22:05, 15 July 2008 (EDT)

:::::::I hope ASchlafly does offer a rebuttal of Lenski's flawed "study." However, if he does not, I am all for DinsdaleP's suggestion. I look forward to reading your draft. If you take all the objections that Conservapedians have raised to Lenski's paper, I do not see how PNAS can possibly object.--[[User:JBoley|JBoley]] 11:28, 16 July 2008 (EDT)

::::::::They could object because Conservapedia's criticisms are obviously false. If this page hasn't made that clear, I don't know what could.[[User:Gerlach|Gerlach]] 13:44, 16 July 2008 (EDT)

:::::::::They would have to prove that Conservapedia's criticisms are false, and they cannot do that. You sound like a Lenski supporter. You need to open your mind to the truth.--[[User:JBoley|JBoley]] 13:59, 16 July 2008 (EDT)

:::::::::Gerlach, the most obvious lesson from this page is how a few, yourself included, seem determined to defend a flawed paper no matter what the truth brings. You have free will to reject whatever you want, but you're only hurting yourself by that approach. People who do open their minds are amazed by the insights and happiness it brings.--[[User:Aschlafly|Aschlafly]] 21:54, 16 July 2008 (EDT)

:::::::::This is such a strange response, Andy. The attitude that you and several of your defenders seem to have is that the criticisms you have made of Lenski's paper cannot be rebutted. However, the fact that you ''can'' level criticism at something doesn't make that criticism true. That is, you may be wrong. And that is the case here. Myself and others have pointed out that your alleged flaws in Lenski's paper are incorrect, and based on misunderstanding it, or, even worse, simply not reading it carefully. There has been little to no substantive response to our detailed rebuttals. Replies from you or other defenders of the Conservapedia article amount to little more than brazen declarations that we are wrong or "nonresponsive", and that criticisms in the original article remain unscathed. But for people who claim to have "the truth" on their side, this is simply baffling. If the veracity of your claims against Lenski's paper is so obvious, then it should be an easy task to provide in depth responses to the points that we have been raising against your article. I'm not above criticizing scientific papers. Bad papers get published frequently, after all. However, Lenski's paper does not appear to be one of those. Notice, though, that I am not claiming it to be perfect, no paper is. That said, whatever flaws the paper may have, those presented in the Conservapedia article are not among them. [[User:Gerlach|Gerlach]] 11:43, 17 July 2008 (EDT)

:::::::::: Gerlach, now you seem to admit that the Lenski paper may be flawed, but that Conservapedia has not identified any of those flaws! With all due respect, you seem to have taken closemindedness to new heights.

:::::::::: Lenski claims there is a mutation rate, yet his presented data show that the number of mutations do not scale with sample size. His presented data disprove both of his hypotheses.--[[User:Aschlafly|Aschlafly]] 13:27, 17 July 2008 (EDT)

:::::::::: First, we need to clarify what we mean by "flaw". Are we talking about serious methodological flaws or errors in interpretation that fatally undermine the paper's conclusion? If so, I fail to see any such flaws. Of course, any honest scientist recognizes that any work at the frontier of science has the potential to be wrong. It ''may'' be that future work shows Lenski to be wrong. But let's not confuse this possibility with actuality: saying that something might be wrong is not the same as saying that it is. On the other hand, by "flaw" we may mean minor experimental details that could have been better. In this case, the paper is flawed, and Lenski himself admits this in the supporting information. But ''every'' paper is flawed in this manner, and I doubt you'll find any investigator who wouldn't say that they wish they had done some things differently during the course of their research. As an example of what I'm talking about, the Lenski group's statistical analysis would have been improved if they could have accounted for the evolution of increased cell size (and, therefore, decreased cell density) in later generations. As it stands, their analysis ''underestimates'' the potentiation effect in these generations because replays of later generations involved fewer cells. But this flaw, and other flaws of this type, do not undermine the conclusion of the paper.

:::::::::: Regarding the mutation rate argument, see the earlier discussion on this page. The third experiment was significantly different than the first two. The experimental scheme was different, it was performed at at different time and with different conditions, and utilized, for the most part, different clones than the first two. And Lenski doesn't just claim there is a mutation rate in potentiated cells, he ''actually measures it''. But frankly, I don't understand your argumentation here. It seems that you are trying to suggest that all the Cit+ mutants isolated were the result of contamination. This clearly isn't the case, for several reasons. However, this isn't the place for this particular discussion, as there is already such a discussion elsewhere on this page. I still haven't seen any adequate response to our points against the Conservapedia article, and I don't think I am closed-minded for expecting such a response. As I said, I'm open to the possibility that the Lenski paper is flawed, but I expect cogent argumentation to support any such flaws. I haven't seen that here.[[User:Gerlach|Gerlach]] 15:09, 17 July 2008 (EDT)

::::::::::: Gerlach, look at how many words you used to sidestep my simple explanation of a flaw in Lenski's work: "Lenski claims there is a mutation rate, yet his presented data show that the number of mutations do not scale with sample size. His presented data disprove both of his hypotheses." If the third experiment of Lenski's was independently flawed as implied by your response, then that does not help your defense. Note that in Lenski's second experiment the mutations also failed to scale with sample size.--[[User:Aschlafly|Aschlafly]] 18:26, 17 July 2008 (EDT)

::::::::::::I think there is a misunderstanding. Blount et al. did not say that the absolute mutation rate was constant for the generation of Cit+. After all, they found that variations in culture conditions had some effect. The replay experiment was performed to determine if clones from later cultures were more or less likely to give rise to Cit+ cells than clones from earlier generations. The authors' hypothesis was that a potentiating mutation was required before the Cit+ mutations could arise. If that was the case then clones from later generations would be more likely to produce Cit+ cells. If the Cit+ capability was the result of an extremely rare, single mutation, then any generation of clones would be equally likely to produce Cit+ cell. The hypothesis is that in a particular experiment, the '''relative probability''' of generating a Cit+ mutant would be greater with clones from later generations. '''Absolute mutation rates''' (which appear to be Andy's concern) may be contingent on the growth conditions, which differed between the three replay experiments but '''''within any particular set of conditions''''', one might expect the relationships between Cit+ recovery and the generations from which the starting clones were derived would still hold.

::::::::::::pg 7902 of the paper in the journal:
::::::::::::"According to the rare-mutation hypothesis, Cit+ variants should evolve at the same low rate regardless of the generation of origin of the clone with which a replay started. By contrast, the historical-contingency hypothesis predicts that the mutation rate to Cit+ should increase after some potentiating genetic background has evolved. Thus, Cit+ variants should re-evolve more often in the replays using clones sampled from later generations of the Ara-3 population."

::::::::::::From the abstract:
::::::::::::"The long-delayed and unique evolution of this function might indicate the involvement of some extremely rare mutation. Alternately, it may involve an ordinary mutation, but one whose physical occurrence or phenotypic expression is contingent on prior mutations in that population. We tested these hypotheses in experiments that ‘‘replayed’’ evolution from different points in that population’s history. We observed no Cit+ mutants among 8.4 x 10^12 ancestral cells, nor among 9 x 10^12 cells from 60 clones sampled in the first 15,000 generations. However, we observed a significantly greater tendency for later clones to evolve Cit+, indicating that some potentiating mutation arose by 20,000 generations. This potentiating change increased the mutation rate to Cit+ but did not cause generalized hypermutability."

::::::::::::What the authors found was that the later generations really did produce more Cit+ mutants than you'd expect if the Cit+ mutation was instead randomly distributed (or, as Andy has claimed and not yet retracted, contaminated by Cit+ cells). Yes, the absolute rates didn't scale across the three different conditions but within each experiment it is clear that the Cit+ mutants arose from cells taken at later generations. Yes, there were differences in the absolute rates under different conditions but that doesn't mean the results and conclusions about potentiated clones are wrong.

::::::::::::As for calculations of mutation rates: Blount et al. performed additional fluctuation experiments (journal pg. 7903) in an attempt to estimate the relative effect of the potentiating mutation and to calculate a rough estimate of the mutation rates. Keep in mind, those rates '''''are referenced to growth under the specific conditions used in that particular experiment''''' and were used to provide ballpark estimates for comparison to other classes of known mutations. As for the second experiment not 'scaling' (with the first?), I wouldn't expect that. The first involved clones grown in continuous liquid subcultures and both the total number of generations, cells/generation and growth conditions (e.g. liquid with nutrient replenishment vs. solid agar) are very different.--[[User:Argon|Argon]] 19:20, 17 July 2008 (EDT)

::::::::::: I have not "sidestepped" your point, Andy. Your claim is that the number of Cit+ mutants obtained did not scale with sample size in the third experiment. In response, I reiterated what Argon and I have said previously, specifically that there are differences between the third and second experiments that make a straight comparison between the two inappropriate. That said, if anyone is sidestepping the issue, it is you. Argon and I have addressed your objection previously, but your only response has been to stubbornly restate the original claim. If you don't agree with our statements, then you must explicate why. Additionally, I did not say or imply in any way that the third experiment was flawed. I said that it was significantly different from the second, but this is not the same as saying it was flawed. Argon has provided a response to the scaling of the second experiment to the first.[[User:Gerlach|Gerlach]] 20:21, 17 July 2008 (EDT)

:::::::: In response to earlier postings about drafting and submitting a letter to PNAS, I'm for it and would be happy to contribute. In response to a comment above, I don't want any "glory" and learned a long time ago that nobody gets credit or money for telling the truth. More often those who speak the truth are reviled and insulted, but mockery doesn't bother the truth as much as it bothers falsehoods.--[[User:Aschlafly|Aschlafly]] 22:01, 16 July 2008 (EDT)

::::::::: (removed false and baseless claim by Argon about sponsorship of this site)

==Draft of PNAS Letters Response from Conservapedia==

''Apologies for the delay in following up on this - I've spent the past few days attending to family priorities, and this is my first CP-related priority now that I have time at my PC again.''

''Since the guidelines for submitting PNAS Letters restricts the submissions to 250 words, the following is the draft submission I'd like to send pending Andy Schlafly's approval:''

:: ''Title:''

::: Identification of procedural and statistical flaws in the paper "Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli".

:: ''Author:''

::: Andrew Schlafly, B.S.E., J.D.

:: ''Author Affiliations:''

::: www.conservapedia.com

:: ''Text:''

::: An analysis of the paper and the supporting information on Professor Lenski's website has led to the identification of significant flaws which, if not refuted, negate the claim that E. Coli bacteria underwent an evolutionary beneficial mutation in the experiment.

::: The full description of these flaws exceeds the submission length allowed for PNAS Letters, but can be found at http://www.conservapedia.com/Flaws_in_Richard_Lenski_Study. In summary, the flaws are:

:::: - The "historical contingency" hypothesis depicted in Figure 3 is contradicted by the abstract and by the data presented in the Third Experiment in Table 1 of his paper.
:::: - Lenski incorrectly included generations of the E. coli already known to contain Cit+ variants in his experiments and had no means to exclude their presence in the samples.
:::: - Lenski's Third Experiment failed to support his hypothesis with statistical significance, even with the incorrect inclusion of the Cit+ variant generations.
:::: - Lenski's two alternative hypotheses suggest a fixed mutation rate, but the failure of the mutations in his experiments to increase based on scale tends to disprove both hypotheses.
:::: - The lag time between the potentiating mutation in the largest experiment disproves Lenski's implicit assumption that it likely occurred in proximity with the occurrence of the Cit+ variant.
:::: - Lenski has not disclosed key portions of his data, such as how thoroughly the samples were screened for pre-existing Cit+ variants.

::: I am requesting that the authors of the paper respond to each of the flaws in this forum and explain the withholding of the data, and submit a revision or retraction of their paper if any are held valid.

''Mr. Schlafly, please let me know if this is acceptable, and apply any revisions as you see fit, thanks. --[[User:DinsdaleP|DinsdaleP]] 10:38, 21 July 2008 (EDT)''

: It's an excellent draft, DinsdaleP. I made a few minor revisions above. After others improve this, then I'll plan on sending it to PNAS later this week. {{unsigned|Aschlafly}}
::I like it. I'll sign my name to it when the time comes.--[[User:DamianJohn|DamianJohn]] 09:35, 22 July 2008 (EDT)

(unindent)

Thanks for the feedback - When applying changes, please keep in mind that the "Text" section in the final version needs to be 250 words or less. If there are important points to add that would exceed this limit, they could be added to the main [[Flaws in Richard Lenski Study]] article instead since PNAS is being asked to respond to the full list there, and not just the summary. --[[User:DinsdaleP|DinsdaleP]] 09:47, 22 July 2008 (EDT)

: I think if i would have presented some draft of that quality to my supervisor i think i would not have reached the door of his office alive and in one piece. It starts with the fact that the correct citation of the article is missing. Please use the appropriate form, inclucing journal number and page. Please have a look at other PNAS Letters. Restate the central issue you criticise in the first sentence, then explicitely describe what your claim about the same issue is and state using what method you come to your conclusion. Keep a neutral tone. Don't make requests. It is obvious that the original author should respond (please look at PNAS for examples of responses, which are published at the same location). Plese fill in your numbers and precise arguments at the points where i left the dots in the following suggestion ('''Please note that nothing of this is my opinion, i just tried to rephrase your opinions in a way that they have the chance to be exposed to a broader view - i skipped tyhe details, because i will not rephrase your arguments, just the structure'''):
: Recently ...... inferred from their experiments (1) that ...... . We analyzed the statistical analysis in terms of ..... and conclude that several variables do not scale as .... . Using hypothesis tests under such circumstances is, in our opinion, ...... , and we do not understand how the authors of the original publication ..... their results.
: The replay experiments yield an ..... scaling with .... . We do not find a consistent value of ..... between the experiments. Furthermore the statistical deviation due to ...... in each sample set does not allow to infer ..... with a sufficient precision. This lack of scaling makes, in our opionion a constant or random source of contamination a likely explanation for a random observation of the ...... dependence of the mutation rate claimed in the paper. The following calculation supports this hypothesis: ....... .
: Furthermore we point out that Fig. ... contains a serious disagreement with .....: while the data would suggest ..... from gen. ..... the figure suggests .....
: We find the material cited in the original article (2)...(n) about the same long-time experiment not to describe the following procedures and experimental constants in a way accessible to us: Handling of ..., contamination rates of ...., and ..... We would kindly ask the authors to clarify these issues. --[[User:Stitch75|Stitch75]] 12:48, 22 July 2008 (EDT)

::No offense taken. I have no experience in these types of submissions, and would appreciate it if you could restructure the submission improve the quality while adhering to the 250-word limit. As I suggested above, it makes the most sense to incorporate these revisions into the main page for this article, where length is not an issue. --[[User:DinsdaleP|DinsdaleP]] 12:52, 22 July 2008 (EDT)

::: I realized that you have obviously not much experience in it; getting the right tone for a scientific publication is hard and i had to try it quite some times on conferences and i still dont get it right sometimes - and from what you said seem to be a student. Sadly, it is against my conviction to rephrase the original arguments in the right way because it would make me an co-author of argumentations i strongly object. In case you did not realize it, helping here to get the structure right doesn't mean i agree - actually the two reasons i would like to see it published is because then the (wrong) idea that scientific journals are not accepting criticism could be obviously be put aside and because i would like to see the needed scientific rigorousity applied to the arguments presented here, because this would put this discussion onto a scientific basis. Quite frankly - i am a liberal by the standards of this site. But i believe the discussion must be carried out with all respect to define the borders of science. The more effective the discussion is carried out, the better the outcome will be. I am willing to listen, as i have proven here, even when beeing treated by people like Mr. Schlafly as if I would be one of his students, while evaluating his qualification in natural sciences quickly shows that i more likely could supervise him in the issues he discusses here (which is something he has proven all along). Regarding that, i am close to giving up, but nevertheless i have seen that a lot of conservatives actually are willing to lead this discussion in a scientific way, which is something, which fulfills me with hope. I recommend you not to fight a fight in where you don't understand the arguments. Don't pick up arguments from others. If you can not fill in the missing words, numbers and arguments in my text, i cant help you. I see what Mr. Schlafly believes, however i do not know how to get the calculation right to support his hypothesis (random or contant mutation rate) - and, this is most likely not because of a lack of statistical knowledge. The only way i would see is to use the rudest form of descriptive statistics and agreggate the data in a very specific way, while ignoring the structure of the experiment - and ignoring the fact that the authors pointed out the problem they see and adressed them. So i can only give oy a few hints (maybe i can form a short contibution to conservapedia; i am just thinking about the title):

:::: If you claim something is wrong, put your opposing claim in a positive formulation, with a supporting calculation, in contrast . Even if the calculation is simple, this is very important to provide it. E.g. we estimate a rate of x+-y per z for dataset N, in which we aggregated generations a,b,c,d, etc .... In the end, you should either prove a mathematical mistake (which was not done) or shoe you hypothesis is more likely.

:::: Don't be rude. You are not the referee and you are not member of a commitee to examine scientific misbehaviour. Dont act like one (and even referees have a friendlier tone usually). Dont act like an personal enemy either. Don't ask for retraction of the article. It is up to the author to make the conclusion respond or retract. This happens more often than you may think as a response to an critisism (actually it's fun to read the "reply section" of scientific journals - sometimes you find things like: "yes, the commenter was right we copied the paper and retract it"). And you are never requesting, but you are kindly asking. Everybody understands that "kindly asking" does not mean "kindly asking" in this context.

:::: Always give full and specific citations which back your claims. Give it in the form required by the specific journal. General citations like "materials on his website" will make your text bein trown out in the editorial screening (because you can not expect that somebody read trough all information to find something backing you claim - this is your job). See for specific styles [http://en.citizendium.org/wiki/Citation_style[http://en.citizendium.org/wiki/Citation_style]]. Ypu may even reference a page/paragraph/eq/figure number to point the reader to what you mean (for papers longer than 4 pages i usually do that).

:::: Run a style checker over your text to eliminate common style mishaps.

:::: '''Most important''': go to your university library. Take the time to just read a few PNAS Letters and replys, and the original articles (Try to finde some with an easy understandable subject). Understanding how these are written and how authors usually reply will help you to get your one right. You are writing against somebody who has twenty years of experience in a field of publishing in natural sciences. You seem to have little experience and Andrew Schlafly, honestly, neither. This game is an uphill battle and unfair game anyway. Make sure you maximize your chances by understanding the rules of the game.

:::: Focus on a single you are sure about. It is better to present one claim well that two claims badly.

:::: Good luck. You will need it. --[[User:Stitch75|Stitch75]] 14:22, 22 July 2008 (EDT)

::::: "Stitch75", you seem to think that the truth depends on whether PNAS accepts it. It doesn't. Lenski's paper is badly flawed regardless of whether he admits it, PNAS admits it, or you admit it. That's the beauty of the truth: it doesn't require admission by anyone. I'm fine with Lenski and PNAS refusing to admit the flaws in their paper. After all, if they really cared about quality then I doubt they would have published their flawed paper after merely 14 days or less of peer review.--[[User:Aschlafly|Aschlafly]] 15:38, 22 July 2008 (EDT)

:::::: Maybe its because English is not my native language. Somehow you seem not to understand what i am saying. I try to rephrase it so that there is no room for misunderstanding: I never can talk about truth, which is a religious thing. I talk about science and observable reality. Primarily i can tell you only what it takes that your thoughts are at least looked at. If rejection happens du to formal reasons (like using unsuitable Formulations, etc) it's not good to draw conclusions on the content or the scientific community. The strong formalism is to save time. And in turn the taxpayers money. I am screening the title of approx. 70 articles per day (10 Minutes), namely everything which come in on the preprint servers on my subject. From approx 70 titles, 10 are interesting enough to read the abstract (6 Minutes), and 2 are interesting enough to look at the summary (4 Minutes) and one in two days in interesting enough to read Section 2 (10 Minues), skipping the introduction, one in a week in interesting enough to print it out and read it (2-4 Hours). Something which does not follow the form end up with beeing thrown out of my rss feed quite quickly. The editors of the journals know that and in a refereed journal such thigs may even be trown out by the editor (and not the referee). Claiming from not getting a response published that "the article is still wrong, no matter what others say, and i am rights anyway" doesnt sound very scientific to me. From everything you have said here, you are unwilling to learn, and you don't expect a response. If you formulate your comment in that way, then skip it. Publishing a letter should stimulate a discussion, if it's not meant to, seen from the style, it will not be accepted. Moreover, according to everything i have seen here, Mr. Schlafly, you seem to have no clue what you are talking about. Please at least consider one time that you could be wrong and try to follow the statistical arguments in the paper - and build up own one on a real calculation (and show the numbers you get). --[[User:Stitch75|Stitch75]] 20:55, 22 July 2008 (EDT)

::::::::: Stitch75 - you are too far inside the belly of the beast to understand what ASchalfly is talking about. You have probably spent your (young, naive?) life as a scientist, or inside the sciences, and as such you are blinded and cannot think with real, free logic. If you look at ASchlafly's arguments with an open mind, and not the blinkered mentality you seem to want to perpetrate, you'll see he's got many excellent points, and I'm convinced that the PNAS will ask Lenski to retract major conclusions of his obviously flawed study once ASchalfly submits this letter. Try to open your mind more to other ways of thinking and you'll see the truth for what it is. [[User:RobCross|RobCross]] 21:01, 22 July 2008 (EDT)

::::::Stitch75 just went far out of his way to be helpful and yet you still continue to respond with hostility and a self-righteous attitude. You explicitly stated that now matter what response you get, you won't accept the conclusions of the paper. That is your prerogative, but you are directly stating that their replies, other than a retraction, will be irrelevant and/or wrong, despite the '''many decades''' of combined practical experience of the authors compared with your complete lack of such. So why is it again that you're even bothering? Several contributors to this forum and others related to it on this website have addressed your questions in great detail- repeatedly- and you continue make vague, unspecific accusations. As Stitch75 discussed, something like "table X is wrong because of figure Y" is nonproductive. Furthermore, if you want to have PNAS readers listen to you- your flaws should be real. For instance, even now your fifth "flaw" is that the statistical results of the third experiment are "obscured" and "not defin[ed]... in the traditional way". Well, the p-value for the third experiment is 0.0823. It took me literally four seconds of flipping through the PDF to find it. It's even in a nice table to make it easy to find. How is that obscure? (I might add that considering P<0.05 significant and P=0.0823 not statistically significant is '''completely arbitrary'''. If the observed pattern wasn't at all what was expected, the P value would be roughly around 0.8-1.0 or so. So 0.0823 ''does'' suggest that the underlying idea is correct in '''exactly''' the same way that P=0.05 would. That is a fundamental concept in basic statistics.) The final problem is that your arguments have drifted from your original concern- whether or not a new trait evolved- since only one of your listed "flaws" actually addresses this issue. The others are tangential and relate to interpretation and mechanisms. Even ''if'' 6 of your 7 flaws were so, the core finding of the paper- around which all else is based- would still hold: in earlier generations, there weren't Cit+ E. coli, in later generations, there were. The mathematical analyses and timeline of occurrence don't change this qualitative, directly observable fact.

::::::I do encourage you to refine the letter and submit it to PNAS- I really do- but Stitch75 is very correct in saying that if you submit it in its current shoddy form it will be laughed at and promptly ignored. You would do well to take the advice of people who actually work in the field when it comes to considering how something will be received. Also, your comment about peer review above indicates that your still have not learned anything at all about how it actually works despite the long discussions previously.

::::::As you said, the truth doesn't require admission. But it does require empirical support, which Lenski provided in ample quantities- but you still have yet to provide anything even beginning to resemble scientific rigor. That is why Stitch75 wrote that response- to ''help you'' improve your letter from that condition.[[User:Kallium|Kallium]] 21:36, 22 July 2008 (EDT)

::::::: You have it backwards, "Kallium". Lenski has the burden of providing "scientific rigor," and his paper falls short. In fact, the data presented in the paper tend to ''disprove'' his hypothesis about a mutation rate, as the mutations identified in his paper do not scale in a meaningful way with sample size.--[[User:Aschlafly|Aschlafly]] 23:11, 22 July 2008 (EDT)

:::::::: I honestly don't know how to make this any more clear. Yes, Lenski does have the burden of providing scientific rigor, as any scientist does. I never said otherwise. However, to claim flaws in any study requires that they be presented with equal rigor. This is just rewording the last statement of my previous post. Simply making vague, unspecified and unsubstantiated hand-waving claims won't get you anywhere. Consider an analogous situation in an appeals court: someone doesn't like the decision of a lower court, so they go to a higher level to present their objections. Now, to do this requires legal rigor to the same degree with which the decision was originally made. The defendant would need to address specifics in the decision and explain exactly why they were incorrectly interpreted. If, however, that defendant were to waltz into the higher court and simply read quotes from the decision and say "that's illogical" or "those statements are self-contradictory" or "that's unfair", without going into detail to explain their reasoning and without addressing the previous cases cited in the decision or providing any further legal precedents, they would utterly fail to make their case and likely be chastised by the judge for wasting the court's time. Now replace the court references with their respective scientific analogs and you have exactly what is going on here. That is why both Stitch75 and I have been giving you this advice- to ''help you present your case''. Lastly, you haven't developed your arguments since you first posted them but keep relisting them. You have yet to show in detail how the data disprove the hypothesis (which you also vaguely define), and as others have explained repeatedly, mutation rates are only expected to scale with sample size under identical conditions, which were not used. That's why your letter needs improvement- it simply won't be taken seriously if it shows a flawed understanding of basic experimental biology. You can't pass rigor completely off of your shoulders; you have to make your case or it will get thrown out of court.[[User:Kallium|Kallium]] 12:12, 23 July 2008 (EDT)
:::::::::You are correct that the truth does not require acceptance. Kallium is not quite correct in in saying that it requires empirical support. It does not, the truth is the truth is the truth and that’s an end to it. The ''search'' for truth, however, requires certain actions and, in this case, Stitch75’s advice should be welcome. Following Stitch75’s advice will not alter the truth one little bit, but will aid the search for it. According to you the truth is that this was a flawed paper that was published, demonstrating flaws in the peer review process. It gets science nowhere, the public scrutiny of science nowhere and the use of public money nowhere for this simply to ''be'' the truth. The scientific community would need to see your objections in the "correct" format before it would do anything about it.

You may say that the scientific community should be doing this already. (We might also question whether the format stipulated by the scientific community really is "correct"). Whether they should or should not is moot: the simple fact is that they aren’t and are unlikely to start anytime soon without a “correctly” prepared objection. Stitch75’s advice is designed to help you prepare the objection “correctly” and, in doing so, aid the search for truth.--[[User:YoungA|YoungA]] 09:26, 24 July 2008 (EDT)

I tend to agree with you Andy. I say we get this thing sent to PNAS and see what happens. If they refuse to answer it then we know what that means, and if they thumb their noses at you that's fine too. However I have a little more faith than you in the system and I hold out hope that they'll respond to our queries. Anyway lets get this thing sent. --[[User:DamianJohn|DamianJohn]] 15:50, 22 July 2008 (EDT)

(unindent)

I'd like to thank Stitch75, because he took the time to explain his points constructively, and I learned something from them. (I'm actually an IT Specialist in my 40's, not a full-time student, but learning is a never-ending process and I appreciated the lesson). I consider myself bound by the same ethical constraints on editing that he mentioned, because these objections to Lenski's work are Mr. Schlafly's, not my own. I tend to believe that the Lenski experiment was properly executed, but I'm a strong believer in the scientific process, and Mr. Schlafly's objections deserve a fair hearing whether one believes in them or not. My contribution is to help in the process of getting these objections to the proper forum, namely PNAS, and leaving the response up to them. --[[User:DinsdaleP|DinsdaleP]] 16:20, 22 July 2008 (EDT)

== Expertise in Statistics ==
I don’t mind admitting that I have none! The article states that Lenski combined the three trials incorrectly and that he doesn’t make the insignificance of the third clear. Now it may well be very clear to others but, unfortunately, the article doesn’t make clear to people like me what was wrong. Can someone expand on this point? Is anyone able to explain to a layman what Lenski should have done and the conclusions he should have reached? It's all getting a little technical for me. --[[User:Billd|Bill Dean]] 12:10, 14 July 2008 (EDT)

: OK, here's point 4 in layman's terms: Lenski's hypotheses of a mutation rate imply that a ten-fold increase in sample size should result in a ten-fold increase in mutations. But it doesn't. In fact, a nearly ten-fold increase in sample size results in only a slight increase in mutations in Lenski's data. These data, as presented by Lenski in his paper, suggest (if properly interpreted) that there is no mutation rate at all. Rather, these data are more consistent with occasional contamination, broadly defined.--[[User:Aschlafly|Aschlafly]] 23:15, 14 July 2008 (EDT)

::Except that the growth pattern of the Cit+ cells in the third replay experiment demonstrated that there were no Cit+ cells in the cultures at the time of plating. Control plates with a mix of Cit- and Cit+ cells were done which showed rapid development of Cit+ colonies, whereas the experimental plates did not show any Cit+ colonies for at least 8 days and up to 28 days. If you believe that the plates became randomly contaminated during the course of the incubation, rather than at the initial plating, the post-plating contamination should have affected all generations equally, but it did not--[[User:Brossa|Brossa]] 12:46, 15 July 2008 (EDT)

::Blount et al. discussed the unexpectedly low Cit+ conversion rate for the third replay set in the supplementary document. They have some speculations but don't know why it occurred. They are dealing with low probability events. I don't agree that the 'proper' interpretation is contamination. First, they isolated and tested each Cit+ isolate for the markers and sequences we've discussed on earlier Conservapedia pages. Second, the distribution of Cit+ isolates does not appear to be random: They correlate strongly with the later generations. If undetected contamination was random, it's unlikely the Monte Carlo resampling tests would reject the null hypothesis of the 'rare-mutation' hypothesis over the 'potentiated' hypothesis. As Brossa correctly notes, contamination would have affected all generations. Blount et al. write in the paper's supplement: "To facilitate handling and minimize possible confounding variables, we divided this third experiment into 20 blocks of 14 clones each. All of the clones within a block came from different generations, and the single ancestral clone was included in all 20 blocks."--[[User:Argon|Argon]] 20:01, 15 July 2008 (EDT)
::: Good and detailed analyis and conclusion, Argon. I had no time to read everything in that detail, but i think you present exactly the arguments (contant background would favour rare mutation hypothesis) would be exactly the one i had in mind, so let's see how Mr. Schlafly will bend his own Monte-Carlo simulations to showing several 1000 times no mutation into accordance with any reasonable background explaining a significant number of counts in *some* samples --[[User:Stitch75|Stitch75]] 20:20, 15 July 2008 (EDT)

:::: The above comments are non-responsive. The essence of ''both'' of Lenski's hypotheses is that there is a fixed, or stepped, mutation rate. But any such rate would be roughly proportional with sample size. Yet his three experiments prove otherwise, which Lenski fails to address in a satisfactory manner. Indeed, Lenski's presentation of his data disproves the very thing he claims to have shown.--[[User:Aschlafly|Aschlafly]] 20:40, 15 July 2008 (EDT)

::::: Mr. Schlafly, please answer: Which the of the two hypotheses is, according to your calculations the most likely? --[[User:Stitch75|Stitch75]] 20:47, 15 July 2008 (EDT)

::::::The first replay experiment was run under different conditions - roughly 3700 generations in continuous subcultures. One can't compare population sizes or rates between the first and last two replay experiments. As I noted, Blount et al. acknowledged the possible anomaly of lower than expected mutants in the third run. Still, the second and third experiments were run under different conditions. The plates in the second replay experiment were seeded with fewer cells per plate than in the third experiment. That change can affect the survival rates of cells on plates over time (e.g. different rates of nutrient exhaustion). Given the extremely low mutation rates involved, there is no simple means of normalizing the numbers of mutants recovered for the second and third experiments. One might expect 'roughly' 10x more mutants in the third experiment but that's truly a 'rough' estimate that would be affected by conditions under which cells are exposed. It's certainly a question that remains and they may be able to clear up with future research. In any case, the pattern of data does not support Andy's claims of contamination or that the hypotheses of the paper is in error.--[[User:Argon|Argon]] 21:27, 15 July 2008 (EDT)

::::::: Argon, you have free will and it's clear to me that you are going to exercise it to the point of embracing absurdities. This time you claim that "extremely low mutation rates" would not result in mutations that scale with sample size (of course they would), and that density completely alters mutation rate (if that silly claim were true, then Lenski's experiment was flawed from the get-go). Your belief system is remarkable, but it's not logical.--[[User:Aschlafly|Aschlafly]] 23:38, 15 July 2008 (EDT)

::::::::Fair enough, but let's be clear: That's my take on the paper and that of most of the scientists who reviewed the paper, read the paper and commented upon the paper so far. For that matter, Michael Behe didn't call the data flawed, nor did those commentators at Dembski's Uncommon Dissent blog, nor did Dr. Georgia Purdom at Answers in Genesis. In contast, those who think the work is flawed appears to be limited mostly to you, Andy. It is true that 'scaling' was not seen in this case but as we've seen, the conditions were not quite the same and it is known that this can have an impact.

::::::::However, the fact that the conditions were not identical doesn't detract from the fact that the emergence of Cit+ clones *still* correlated with the sampling of the later generations. What this means is that with three separate experiments and under three sets of conditions, the constant-rate-mutation hypothesis doesn't hold. What the differences between the second and third replay experiments demonstrates is that they were run under different conditions that affected the overall rate of conversion, not that the 'potentiated mutation' hypothesis is wrong. Those are actually distinct questions. Andy, the data simply does not support your claims that the cultures were contaminated (we'd expect random distribution), or that the 'scaling' variations ruined the experiment. In my opinion, you seem focused on red herrings to the exclusion of evaluating the data in the overall context of the experiment which demonstrates a correlation of Cit+ clones emerging from samples taken at later generations. Would you care to address that pattern and discuss why your 'contamination hypothesis' doesn't appear to hold up?--[[User:Argon|Argon]] 09:29, 16 July 2008 (EDT)

:::::::There is nothing absurd in what Argon said. As he mentioned, the third experiment was performed under different conditions and at a different time than the first or second experiments. The key here is that there are plenty of variables, some unknown, that simply aren't controlled for between the experiments. For example, take the fact that it was performed at a different point in time than the first two. The third experiment, then, is almost certainly being performed with different batches of growth media, liquid and solid. Anyone who has spent any significant time growing cells knows that media can vary significantly in growth characteristics between batches, despite the same recipe being used. The reasons for this can be many. Perhaps the balance or pH meter was off calibration one day, or a different bottle of reagent was used. Take an analytical chemistry course, you'll spend plenty of time talking about this. It is true that, for the most part, this sort of variability has minimal impact. But when you're examining something like an extremely rare mutation, or you're trying to make an extremely accurate measurement, intra-lab variability like this can be significant. For an extremely rare mutation like Cit+, which involved at least two additional mutations in potentiated cells, any change in mutation rate can have a significant effect on your ability to obtain mutants. Mutation rate is sensitive to growth conditions, so cells grown in different conditions are likely to experience a different rate of Cit+ mutation.

:::::::Regardless of the reason for the lower-than-expected number of Cit+ mutants in the third experiment, however, the Cit+ mutants isolated absolutely did not arise from contamination. This is clear if you read the paper. You're still left, then, with the two hypotheses presented, and the results support historical contingency.[[User:Gerlach|Gerlach]] 09:45, 16 July 2008 (EDT)
Is there anyone here with expertise in statistics who could give an analysis? [[User:Fyezall|Fyezall]] 16:15, 15 July 2008 (EDT)

:Hello Fyezall. I rearranged the position of your question to hopefully keep the conversations clearer. It boils down to this: The researchers found that mutant Cit+ strains arose over the course of time in their long term growth experiment. They wanted to learn something about how that strain acquired this ability. They wondered, 'Was this the result of a single, very low frequency mutation or did some other mutation have to precede it in earlier generations, followed by the final mutation(s) that allowed the cells to grow on citrate?'

:If the Cit+ change required a single mutation with a low but constant probability over time one would expect Cit+ mutations to be distributed across cells taken from any generation of the experiment. On the other hand, if a 'potentiating' mutation had to arise at some point in the cultures before the final Cit+ mutation could function, then one would expect the probability for Cit- cells to mutate to Cit+ cells would increase with samples of cells taken from later cultures.

:Blount ran the experiment and found that Cit+ mutants arose more frequently in cells taken from later generations in the culture. The Monte Carlo resampling tests were used to assess how likely the pattern of results would fit the models. The statistical significance (smaller P-values mean greater significance), was calculated for each experiment and the combination of experiments. The numbers suggest the distribution of mutants was not randomly distributed across the experimental generations, they tended to appear in cells taken from the later generations. This would argue against the single-mutation, constant, low-probability hypothesis. It appears that a pre-adaptive mutation had to have arisen first, followed by the mutation that finally allowed the cells to utilized citrate. Future work in Lenski's lab will focus on trying to identify the various mutations involved. I hope this brief explanation helps.--[[User:Argon|Argon]] 20:25, 15 July 2008 (EDT)

==What I have noticed==
I tell you what strikes me the most about this discussion - Its watching evolutionists do whatever they can to keep their precious beliefs above question or scrutiny. Its as if they know that it will come toppling down so they must resort to side-lining the hard questions.
[[User:JJacob|JJacob]] 21:43, 15 July 2008 (EDT)
==[[Social Text]]==
This well known hoax ''does'' support Aschlalfy's position that the paper was reviewed by PNAC ''rather quickly'', since (apparently) the paper supported the editors/reviewers point of view. Perhaps this would have beeen better placed on the [[Richard Lenski]] page rather than here since this deals only with the 6/10/08 PNAS paper ''per se'' and not the review process. [[User talk:MargeryCampbell|Marge]] 12:45, 16 July 2008 (EDT)

:I fail to see the relevance of the Sokal Hoax here. You should also know that Social Text was not a peer-reviewed journal when Sokal submitted his paper. That doesn't excuse the credulity of its editors, but Sokal's paper was not sent out for review. Not to say that it would have mattered, postmodernism is just meaningless word salad.[[User:Gerlach|Gerlach]] 13:39, 16 July 2008 (EDT)