Difference between revisions of "Conservapedia talk:Lenski dialog"

Revision as of 01:38, June 27, 2008

The discussion below concerns the letters and response set forth at Conservapedia:Lenski dialog.

Reply to comments in archive

The comments above by defenders of withholding data have been unsatisfactory, to say the least.

Lenski says in his published paper: "Z.D.B. and R.E.L. [Lenski] analyzed data"[1]

So where are all the data Lenski said he analyzed?--Aschlafly 00:27, 25 June 2008 (EDT)

As clearly stated in Professor Lenski's second response:

"Finally, let me now turn to our data. As I said before, the relevant methods and data about the evolution of the citrate-using bacteria are in our paper. In three places in our paper, we did say 'data not shown', which is common in scientific papers owing to limitations in page length, especially for secondary or minor points. None of the places where we made such references concern the existence of the citrate-using bacteria; they concern only certain secondary properties of those bacteria. We will gladly post those additional data on my website."

If the additional data is not on his website by now, I'm sure it will be soon. --DinsdaleP 07:45, 25 June 2008 (EDT)

If "the relevant ... data ... are in our paper," as set forth in the above quote of Lenski, then he would not have much data. So don't pretend the data is too voluminous to turn over. The paper is only 8 pages long!

In fact, the graphs in the paper suggest to a reader that there is underlying data having greater resolution than a graph can provide, and yet those data have not been disclosed for public scrutiny.--Aschlafly 19:24, 26 June 2008 (EDT)

The resolution of the graphs are more than sufficient to communicate the results. If the figures didn't provide sufficient clarity for their purpose the authors would have also provided tables. For example, in figure 1 it's clear the culture shifted its growth pattern. In figure 2, one can see that the Cit+ cultures reach a higher density in the media, as indicated by the higher ODs. To a microbiologist, those results indicate that the Cit+ cells can utilize more of the nutrients in the media (in this case, citrate). --Argon 21:08, 26 June 2008 (EDT)

Lead author won't answer simple, basic questions

IMO the paper has no credibility because the lead author of the paper, Zachary Blount, has refused to give straight consistent answers to the following simple, basic questions about the experiment:

(1) -- whether evolution of citrate-eating (Cit+) E. coli bacteria was a goal of the experiment (I noted that a "goal" does not have to be a sure result), and

(2) -- whether the purpose or one of the purposes of the glucose-cycling (giving insufficient glucose supplies in order to cause alternating glucose feeding and glucose starvation) was to favor the evolution of citrate-eating E. coli bacteria.

Blount's refusal to properly answer these questions is discussed in the following article on my blog --

Co-author of E. coli paper dodges questions

More details concerning Blount's refusal to properly answer these questions are in the comment thread under the following post on Carl Zimmer's "The Loom" blog (note particularly my most recent comments in that thread) -- A new step in evolution

Also, I think Andy Schlafly is wrong to request all of the raw data, because (1) copying all of the raw data to send to him would be a huge job and (2) the raw data might not even be in a form that could be readily understood by someone who did not participate in the research. IMO the citrate-eating bacteria are the best evidence supporting the paper (such as it is).LarryFarma 18:59, 26 June 2008 (EDT)

a reading of the blog reveals that Zachary Blount did indeed address the questions that the above poster named and did so clearly. Please read more carefully next time and don't post falsehoodsDeanWinter 19:10, 26 June 2008 (EDT)

LarryFarma raises an excellent question about whether a goal of Lenski and Blount's project was to generate citrate-eating E. Coli bacteria. (I did not find the answer in the paper.) Did the researchers figure out, after many years of fruitless attempts, how best to promote the percentage of citrate-eating E. Coli bacteria in a population? The details of the data might shed light on how that goal was achieved, if in fact that was the goal. They should turn over the data for public scrutiny so that questions can be resolved.--Aschlafly 19:33, 26 June 2008 (EDT)

Blount's comments on "LarryFarma's" blog make it clear that the evolution of citric eaters was not a goal, but not completely unexpected. The paper, though it was pretty technical for me, seems to indicate that as well. AndyMann 20:15, 26 June 2008 (EDT)

If you're serious, then please provide some quotes and links to back up your statements. Also contribute to entries rather than violating the 90/10 rule.--Aschlafly 20:32, 26 June 2008 (EDT)

People need to stop asking to "turn over the data for public scrutiny" before they've fully read and comprehended the papers and information released to date. E. Coli don't live off of citrate - it's a characteristic of the species - so there was no "goal to promote the percentage that could do it". The fact that a certain population were able to after after thousands of generations of reproduction in a controlled, monitored setting was the key observation, and Lenski's team is still investigating the specifics of when and how that characteristic was enabled. It reflects poorly on an online encyclopedia that the leadership is still questioning whether sufficient data to understand the experiment has been released. The most relevant data from the experiment is the actual bacteria itself, and Lenski has publicly offered to share samples of them with any scientist qualified to handle them, who follows the proper, professional protocols. The Consevapedia community has yet to see a specific, professional response to Professor Lenski's second letter other than a flippant remark about attitude and a continued insistence that data has not been revealed when it clearly has.

I'll probably earn another 90/10 block for this, but when you continue to question Lenski's work while admitting that you've only skimmed the related paper, you accomplish nothing but setting a poor example of intellectual honesty for the students who use CP as a trustworthy resource. With all respect, I would ask that instead, you retain the services of a qualified scientist who can engage in a proper review of Lenski's work, whose could then post an ongoing journal of the review process and its findings here on CP. That would be an appropriate lesson for the students in the proper application of scientific scrutiny to findings that some find questionable. Godspeed. --DinsdaleP 20:20, 26 June 2008 (EDT)

The development of citrate metabolizers wasn't the main intent (see Lenski's early papers) and it's actually tangential in the overall context of the long-term experiment. Zachary Blount describes the purpose of citrate in the media in his responses at Carl Zimmer's blog, The Loom. http://scienceblogs.com/loom/2008/06/02/a_new_step_in_evolution.php (see replies #115 & #270). Citrate was not added to be a carbon nutrient in the media but as a non-metabolizable chelator (the three carboxyl groups of citrate can bind certain cations in solution). The recipe for the medium was taken from other microbiologists who developed the recipe as a general culture medium back in 1949. Lenski's description of the DM25 media is here: https://myxo.css.msu.edu/ecoli/dm25liquid.html. Glucose was the intended carbon source. If you read the Lenski article cited by Blount (Phenotypic and genomic evolution during a 20,000-generation experiment with the bacterium Escherichia coli. -- available here: https://www.msu.edu/~lenski/, you'll see the setup and reasons for performing the experiments (An earlier article at generation 2000 is here: http://myxo.css.msu.edu/lenski/pdf/1991,%20AmNat,%20Lenski%20et%20al.pdf). Basically, Lenksi wanted to see how mutations arise and move through populations over time. Even if the media and growth conditions remain pretty consistent over time, the populations continuously shift and change. That is because for a bacterium in the experiment the 'environment' is not just made up of the flask and media but also the *other cells in the flask* with which it must compete. This results in a continuously shifting competitive environment as mutations arise in lineages. Citrate utilization was just one of the many interesting variations acquired over the course of the experiment. Read his other papers for more details and a fuller understanding of the open-ended experiment's scope.--Argon 21:16, 26 June 2008 (EDT)

With regard to 'competent scientists' consider that Behe, in his discussions on this topic has not argued about the 'mechanics' and data presented in Lenski's paper. In his review that can be found on the amazon.com website, he calls Lenksi's work 'fascinating' (and means it in a good way).--Argon 21:29, 26 June 2008 (EDT)

removal of content from this page removes context of Lenski's second reply

I'm sure it's an oversight but Lenski, in his second letter, made several direct references to the discussion that has been removed from this page. Some of his comments thus appear inappropriately to lack context. I'm sure you did not intend to remove significant parts of this debate, especially when the result seems so one-sided.AndyMann 20:09, 26 June 2008 (EDT)

Archive Link?

Can a link be provided to the archive for this page? Thanks. --DinsdaleP 20:48, 26 June 2008 (EDT)

Oops. Did my edits delete the earlier sections? If so, I'm sorry. Could someone restore the original? --Argon

No, your edits were not a problem. It was the edits of those individuals who decided to use this talk page as an attack forum. Karajou 21:02, 26 June 2008 (EDT)