Immunology

2009-03-05T16:23:59Z

Able806:

Immunology

2009-03-05T16:18:38Z

Able806: /* History */

Immunology

2009-03-05T16:18:26Z

Able806: /* History */

Immunology

2009-03-05T16:12:54Z

Able806:

NADH

2009-03-05T15:58:26Z

Able806: New page: '''Nicotinamide adenine dinucleotide''' consists of two nucleotides: one nucleotide containing an adenine base, and the other containing nicotinamide, joined by their phosphate groups. NA...

'''Nicotinamide adenine dinucleotide''' consists of two nucleotides: one nucleotide containing an adenine base, and the other containing nicotinamide, joined by their phosphate groups. NAD+ (the abbreviated deprotonated form of NADH) is a coenzyme found in most cellular organisms. The molecule is important in metabolic oxidation-reduction reactions due to its electron transfer capability of its two forms, NADH (reduced form) and NAD+ (oxidized form).

[[Category:Biochemistry]]
[[Category:Chemistry]]
[[Category:Molecular Biology]]

Nicotinamide adenine dinucleotide

2009-03-05T15:48:25Z

Able806: Redirecting to NADH

#REDIRECT [[NADH]]

Ribose

2009-03-05T15:46:14Z

Able806: New page: '''Ribose''' is a 5 carbon cyclic sugar found commonly in nature. The phosphorylated form is often found as a subunit to ATP, NADH and several other metabolic energy compounds. ...

'''Ribose''' is a 5 carbon cyclic sugar found commonly in nature. The phosphorylated form is often found as a subunit to [[ATP]], [[NADH]] and several other metabolic energy compounds.

[[Category:Biochemistry]]
[[Category:Chemistry]]

Adenosine triphosphate

2009-03-05T15:38:06Z

Able806:

'''Adenosine triphosphate (ATP)''' is an organic compound composed of the nitrogenous base [[adenine]], the sugar [[ribose]], and three [[phosphate]] groups arranged in tandem. ATP serves as the major energy source within the cell where it is used to drive a number of biological processes such as [[photosynthesis]], vesicle trafficking, ionic symporters/antiporters (e.g. Na+/K+ pump), muscle contraction, and protein synthesis. It is broken down by [[hydrolysis]] to yield [[adenosine diphosphate]] ([[ADP]]), inorganic phosphate, and energy. [[ADP]] can be further broken down to yield [[adenosine monophosphate]] ([[AMP]]), an additional phosphate ion, and more energy. When the phosphate group and energy are used to drive other reactions, such as the synthesis of [[uridine diphosphate]] ([[UDP]]), an [[RNA]] precursor, from [[uridine monophosphate]] ([[UMP]]), the pair of reactions are said to be coupled. New ATP can be generated by two distinct processes, [[substrate level phosphorylation]] and [[oxidative phosphorylation]]. The latter is the end point of [[cellular respiration]] via the oxidation of glucose.

Extracellularly, ATP has been found to act as a [[neurotransmitter]]. ATP receptors are widespread throughout the body. On its own it is known to have effects on the arteries, intestines, lungs, and bladder. It may also be released in tandem with other neurotransmitters.

[[Image:Atp.gif|Adenosine Triphosphate (ATP, fully protonated)]]

==Structure==
The structure of ATP has an ordered carbon compound as a backbone, but the part that is critical is the triphosphate moiety. Three phosphate groups are connected by oxygens to one another. There are also side oxygens connected to the phosphorous atoms. Under normal conditions in the body, each of these oxygens has a negative charge, the negative charges repel each other resulting in stored potential energy.

==References==
<references/>

[[Category:Biochemistry]]
[[Category:Molecular Biology]]

Talk:Significance of E. Coli Evolution Experiments

2009-03-05T15:29:43Z

Able806:

Talk:Significance of E. Coli Evolution Experiments

2009-03-05T15:27:10Z

Able806: Reply to SJohnson

Talk:Significance of E. Coli Evolution Experiments

2009-03-04T22:00:03Z

Able806: New page: SJohnson, your assessment, while good in the utilization of the chi-squared test is unfortunately incorrect. The Monte Carlo resampling gives a more accurate p-value than the chi-squared....

Talk:Methodological naturalism

2009-02-26T16:27:46Z

Able806: /* New start */

Circular definition comes into play here:

:Many scientists of faith nevertheless adopt naturalism in their studies. This is because there is simply no way for an experiment to investigate forces which by their nature cannot be investigated scientifically.

The definition of [[scientific investigation]] is "study of the natural (material) world". Science thus ''limits itself'' to investigation of the [[material world]]. By this definition, studying anything beyord the material world is "not scientific". Therefore (by this definition), studying supernatural phenomena is not scientific, and any experiment which investigates the supernatural is not a scientific investigation.

What then is the rationale for limiting investigation to the material world, i.e. natural phenomena. Is it because there is no way at all to study it? Or simply that we have defined "scientific investigation" as "study of the material world only".

This is like defining geography so that it is limited to [[physical geography]] and excluding human culture, trade, etc. So ''National Geographic]] has gone way beyond its bounds, if [[geography]] is limited only to physical aspects such as geology, ecology, wildlife, etc.

It's really a confounding of method and scope. --[[User:Ed Poor|Ed Poor]] [[User talk:Ed Poor|Talk]] 14:30, 13 July 2007 (EDT)

:I don't believe it's possible to say that science limitis itself to the material world... I mean, science is basically testing the testable. So what you are saying is that science is limiting itself to what is possible... It's not as though you can test the untestable.[[User:Raggs|Raggs]] 09:06, 19 March 2008 (EDT)

::Your words simply perpetuate the confusion. Let me try again:

::Liberals and conservatives agree (1) that science should test the testable and that (2) science properly limits itself to investigating the possible. Agreed? --[[User:Ed Poor|Ed Poor]] [[User talk:Ed Poor|Talk]] 14:15, 19 March 2008 (EDT)

==New start==

I had to delete the article, because it simply did not make any sense. Moreover, it completely obscures the main thing that people want to know about science and naturalism:

:Do scientists assume that the material world is all there is?

Now, I've heard it said that "methodological naturalism" is only a self-imposed restriction. That scientists aren't really endorsing materialism but have chosen to look only for physical causes, when studying matters of [[physical science]].

However, the only context in which I've heard this term is in the [[origins debate]], where it's used as the chief pretext for dismissing [[intelligent design]]. Then it starts becoming [[intellectually dishonest]], by using [[circular reasoning]].

They say that ID can't be "scientific" because [[science]] only examines physical causes. But ID says that the decision to confine one's research and study to physical causes is itself the problem! --[[User:Ed Poor|Ed Poor]] [[User talk:Ed Poor|Talk]] 15:30, 13 April 2008 (EDT)

Very interesting conclusion Ed. I would not say that scientists assume that the material world is all there is, as many scientists are of different faiths. I would, however, say that science is limited based on methods of detection. As such it is hard to not study the physical scientifically when the detection methods that currently exist are only able to detect the physical. For example, if I were to say that there is a sunflower in the middle of the room, you could verify this by looking in the room. However, if I were to say there is an invisible sunflower in the room you would be limited to detecting it through means that would not require optics, such as displacement methods. To go further if I were to say there is a mass less, invisible, non-field rendering sunflower in the room you would be unable to verify this based on the current detection methods available currently. The reason why so many scientist say the ID is not scientific is that there is no way to currently detect and research their hypothesis (That life was intelligently designed by something). The reason why evolution does not fall into this situation is based on the hypothesized mechanism of evolution, that mutation can cause the diversity. ID is based on the designer somehow causing the diversity however the mechanism has yet to be explained as to how the designer caused the diversity. The problem, and therefore the reason why science is not accepting of ID, is that we are currently seeing microevolution occur based on the mechanisms explained by evolution however the best explanation that IDists can give is that the designer had predesigned this to occur without providing a mechanism as to how we can detect the hand of the designer or as to how it was preprogrammed.--[[User:Able806|Able806]] 11:27, 26 February 2009 (EST)

Codon

2009-02-20T14:14:29Z

Able806: /* Amino acid codon codes */

A '''codon''' is three bases in a [[DNA]] or [[RNA]] sequence which specify a single [[amino acid]].

==Amino acid codon codes==
{|class="wikitable" style="text-align:center"
|+
|-
! Amino Acid !! Single Letter Code !! DNA Codons
|-
| Isoleucine || I || ATT, ATC, ATA
|-
| Leucine || L || CTT, CTC, CTA, CTG, TTA, TTG
|-
| Valine || V || GTT, GTC, GTA, GTG
|-
| Phenylalanine || F || TTT, TTC
|-
| Methionine || M || ATG
|-
| Cysteine || C || TGT, TGC
|-
| Alanine || A || GCT, GCC, GCA, GCG
|-
| Glycine || G || GGT, GGC, GGA, GGG
|-
| Proline || P || CCT, CCC, CCA, CCG
|-
| Threonine || T || ACT, ACC, ACA, ACG
|-
| Serine || S || TCT, TCC, TCA, TCG, AGT, AGC
|-
| Tyrosine || Y || TAT, TAC
|-
| Tryptophan || W || TGG
|-
| Glutamine || Q || CAA, CAG
|-
| Asparagine || N || AAT, AAC
|-
| Histidine || H || CAT, CAC
|-
| Glutamic acid || E || GAA, GAG
|-
| Aspartic acid || D || GAT, GAC
|-
| Lysine || K || AAA, AAG
|-
| Arginine || R || CGT, CGC, CGA, CGG, AGA, AGG
|-
| Start Codons || Start || ATG, rarely GTG
|-
| Stop Codons || Stop || TAA, TAG, TGA
|}

[[Category:Genetics]]

Codon

2009-02-20T14:12:32Z

Able806:

A '''codon''' is three bases in a [[DNA]] or [[RNA]] sequence which specify a single [[amino acid]].

==Amino acid codon codes==
{|class="wikitable" style="text-align:center"
|+
|-
! Amino Acid !! Single Letter Code !! DNA Codons
|-
| Isoleucine || I || ATT, ATC, ATA
|-
| Leucine || L || CTT, CTC, CTA, CTG, TTA, TTG
|-
| Valine || V || GTT, GTC, GTA, GTG
|-
| Phenylalanine || F || TTT, TTC
|-
| Methionine || M || ATG
|-
| Cysteine || C || TGT, TGC
|-
| Alanine || A || GCT, GCC, GCA, GCG
|-
| Glycine || G || GGT, GGC, GGA, GGG
|-
| Proline || P || CCT, CCC, CCA, CCG
|-
| Threonine || T || ACT, ACC, ACA, ACG
|-
| Serine || S || TCT, TCC, TCA, TCG, AGT, AGC
|-
| Tyrosine || Y || TAT, TAC
|-
| Tryptophan || W || TGG
|-
| Glutamine || Q || CAA, CAG
|-
| Asparagine || Q || AAT, AAC
|-
| Histidine || Q || CAT, CAC
|-
| Glutamic acid || Q || GAA, GAG
|-
| Aspartic acid || Q || GAT, GAC
|-
| Lysine || Q || AAA, AAG
|-
| Arginine || Q || CGT, CGC, CGA, CGG, AGA, AGG
|-
| Start Codons || Start || ATG, rarely GTG
|-
| Stop Codons || Stop || TAA, TAG, TGA
|}

[[Category:Genetics]]

Talk:Point mutation

2009-02-17T20:33:15Z

Able806: /* Genetic information (continued) */

==Genetic Information==
Philip, I have to ask about this addition, point mutations do not add information to the genome. Whereas they do not change the genome size they can change what is actually produced. For example, the sentence "I love my cat" vs. "I love my hat". Both are of the same size however the information is different. While this was a simple explanation it does apply to genomic expression. Many proteins are duplicated on the genome, this actually allows for gene regulation. Based on the promoters and regulatory proteins it is possible to have a point mutation in one of the duplicated sequences that changes the function of the protein expressed, thereby increasing the information (original protein and mutant now expressed) but not changing genomic size. Unless you are equating genomic size with information. It might help if I write about gene regulation sometime, most are not exposed to it in college since it is a very specific topic.--[[User:Able806|Able806]] 09:33, 4 February 2009 (EST)
:: Rather a late response, and pointless, given the merge, but I was primarily correcting the wording to what the reference was actually claiming. [[User:Philip J. Rayment|Philip J. Rayment]] 09:41, 11 February 2009 (EST)
:::Thank you, I had guessed that after reading through the reference a bit. Something I have to ask, the papers published by the ICR and such groups, are they available for scientific review? I would like to research their position about genetic information particularly in relation to increase of information. From what I know of molecular genetics and information molecules, the ability for information to be increased through mutation is possible and has been observed. I would like to research the claims of ICR and such as to why they believe these examples fail. If you could be of assistance with this I would greatly appreciate it.--[[User:Able806|Able806]] 10:33, 11 February 2009 (EST)

::::: Almost all such papers are ''available'' for anybody (scientists or otherwise) to "review" (read and comment on), as they have been published. But is that what you are asking? Are you asking about peer review? Papers published in the ''Journal of Creation'' and the ''CRS Quarterly'' are peer-reviewed. I don't know about ICR papers, but I suspect that ones published in ''Impact'' would be also.
::::: [http://creationontheweb.com/content/view/3012/ This page] list a number of layman's articles and technical papers which cover the [[information]] aspect in more detail. Also, Werner Gitt's ''In the Beginning was Information'' is [http://www.sedin.org/propeng/informat.htm available online].
::::: [[User:Philip J. Rayment|Philip J. Rayment]] 21:08, 11 February 2009 (EST)
Thank you, Philip. This does help. I am looking for tech papers due to the description of the method used to gather the data. I understand their position; I am trying to understand why they believe it to be impossible. A quick example
:The old dog ran.
:The old doe ran.
The first example provides the relative age of the animal, the animal, and the action.
The second example provides the relative age of the animal, the animal, the action, and the gender of the animal.
No increase in letters and only one letter switched however more information is provided.
Now I know this is an overly simplified example but it is possible with codons. I will give an example of a sequence as soon as I find my codons to AA matrix.--[[User:Able806|Able806]] 09:19, 13 February 2009 (EST)

:in my experience people struggle with the concept of a substitution mutation increasing information. Duplication is much easier to understand. Try [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=34156 this]. If you're still not getting through, you need to make sure the subject has an appropriate understanding of the definitions of information and new information. [[User:Alexkm|Alexkm]] 09:59, 13 February 2009 (EST)
:: See the start of the last page (p.31) of [http://creationontheweb.com/images/pdfs/tj/j21_3/j21_3_27-31.pdf this article]. [[User:Philip J. Rayment|Philip J. Rayment]] 00:38, 14 February 2009 (EST)
I have no problem with understanding the idea of information addition, what I am trying to understand is why those who have problems with the idea of mutation leading to new information have issue with it. I want to know what experiments and calculations they have done to infer this. Just saying it does not make it so.--[[User:Able806|Able806]] 15:18, 13 February 2009 (EST)
::: I'll give an expanded answer on this below. [[User:Philip J. Rayment|Philip J. Rayment]] 00:38, 14 February 2009 (EST)

----
::::A good, information-increasing point mutation that comes to mind is the [https://content.nejm.org/cgi/content/extract/350/20/2096 LRP5 substitution], which "[enhances] skeletal mass without causing complications of osteopetrosis". Some users may be confused by the term "High-Bone-Mass Disease". If so, please see the medical definition of [http://www.mercksource.com/pp/us/cns/cns_hl_dorlands_split.jsp?pg=/ppdocs/us/common/dorlands/dorland/three/000030493.htm disease]. Some people are unwilling to open their minds to this being an instance of increased information. If that is the case, please proffer a definition of information in this context. [[User:MattL|MattL]] 10:48, 11 February 2009 (EST)
::::: Most claims of information-increasing mutations turn out to nothing of the sort, and the linked extract of this paper does not have enough information to say one way or the other in this case. However, a mutation that merely changes the ''quantity'' of something (mass in this case) is likely ''not'' an information-increasing mutation, just like a cake recipe that has a "mutation" in the quantity of flour is not adding new ''information''. [[User:Philip J. Rayment|Philip J. Rayment]] 21:08, 11 February 2009 (EST)
:::::: I would disagree; most gene regulation is done by concentrations of protein. Therefore changing the amounts would change the expression. A prime example would be the insulin receptor. This transmembrane protein is activated by insulin and causes several things to occur within the cell, however the concentration of insulin determines the order of events therefore, change the concentration gets a different result. {{unsigned|Able806}}
::::::: How different? Anything actually ''new''? [[User:Philip J. Rayment|Philip J. Rayment]] 00:38, 14 February 2009 (EST)

:Can you write some simple introductory material about the [[genome]], [[genome expression]], [[regulatory protein]]s, [[gene regulation]], and [[mutation]]? Nearly all of our readers need to know about the basics before they can learn about advanced topics such as [[point mutation]]. --[[User:Ed Poor|Ed Poor]] [[User talk:Ed Poor|Talk]] 09:39, 4 February 2009 (EST)

::Sure, let me check out what we have already and work with that, many of these topics do overlap.--[[User:Able806|Able806]] 09:57, 4 February 2009 (EST)

After looking at[[Mutation]] I believe this article should be merged with it. There is a section for Substitution mutations where point mutations would fall. Ed, can I move the text over to the mutation article and you can delete this page?--[[User:Able806|Able806]] 10:06, 4 February 2009 (EST)
:How about you move the text over and then reduce this page to a redirect. Do you know how to do that? --[[User:Ed Poor|Ed Poor]] [[User talk:Ed Poor|Talk]] 10:09, 4 February 2009 (EST)

Sure.--[[User:Able806|Able806]] 10:10, 4 February 2009 (EST)

I already added to mutation.--[[User:Able806|Able806]] 10:15, 4 February 2009 (EST)

:Thanks, I see it now. --[[User:Ed Poor|Ed Poor]] [[User talk:Ed Poor|Talk]] 10:30, 4 February 2009 (EST)

== Genetic information (continued) ==

Here I want to elaborate a bit on the various claims about genetic information.

'''Could it occur, in principle?'''.

Werner Gitt, who wrote ''In the Beginning was Information'', argues that information is a ''message'', and that a message requires a message sender. He therefore argues that information ''cannot'' arise naturalistically. Here he is obviously not talking about information of the form that was not intended as a message, such as the "information" we glean from astronomy about the composition of stars, for example. Or the "information" that a particular site must have been inhabited gleaned from the stone tools found there. Indeed, he is talking about ''coded'' information—information that is conveyed by means of arbitrary symbols. That is, symbols that only have meaning to someone who already knows the code. Alphabetic writing uses such arbitrary symbols. This is clear from the fact that the same symbols can mean different things to different people (i.e. different languages using the same alphabet). So in English, a "gift" is a present, whereas in German a "gift" is a poison (which concerns German postal staff handling parcels marked "gift"!). DNA is such a coded information system.

'''Does it occur in observation?'''.

Lee Spetner, who wrote ''Not by Chance''[http://creationontheweb.com/content/view/773], says that information ''has not been observed'' to arise by chance, not that it ''can't''.
{{QuoteBox|All point mutations that have been studied on a molecular level turn out to reduce the genetic information and not increase it. (Spetner, p. 138)}}
Note that this is not the negative argument "we haven't seen it so it doesn't occur". The argument is that "we have seen lots of mutations, and they all ''decrease'' the genetic information". That doesn't say that it's impossible. It says that you're arguing from faith (or wishful thinking), not the evidence, if you want to argue that mutations increase genetic information.

Realising that this is a powerful argument against evolution, evolutionists now make various claims that new information ''has'' arisen from mutations, and various claims about how it could in theory. Both groups of claims have been answered by creationists, and I think it's fair to say that ''most'' such claims have been debunked. For example, two of the arguments are that organisms acquire new genetic information from other organisms, and that they acquire new genetic information by means of gene duplication. But both these arguments don't stand up to scrutiny. Acquiring genetic information from other organisms explains nothing about where the genetic information came from in the first place. It is ''existing'' genetic information, not ''new'' information. And duplication is a second copy of ''existing'' information, not ''new'' information. But of course then they go on to more sophisticated arguments. Another very common argument is acquired resistance to antibiotics and the like, but most if not all of these turn out to be either an ''existing'' resistance that natural selection causes to become widespread in the population, or due to a ''loss'' of information.

'''Would a few examples solve the problem?'''

For microbe-to-man evolution to have occurred, a ''huge'' amount of new information would have had to be generated. So supplying a handful of questionable examples, which is all that has been offered so far, hardly solves the problem. And when Richard Dawkins was interviewed for a video, he was unable to supply ''any'' examples of new genetic information arising in nature.

Indeed, a creationary biologist has told me that he doesn't totally rule out the possibility of the extremely rare trivial information-gaining mutation. I've seen this alluded to in creationary literature, although I'm not sure that I've ever seen it said explicitly. However, I gather that Michael Behe's ''The Edge of evolution'' (which I haven't read) covers this point. See [http://creationontheweb.com/content/view/6207/#txtRef19 here] for a mini-review of Behe's book.

John Sanford (''Genetic Entropy and the Mystery of the Genome''), writing mainly about human evolution, points out that a few examples wouldn't solve the problem anyway.
{{QuoteBox|We can, at best, wave our hands when we speculate about how selection might synthesize ''new'' information. It is inherently hypothetical. In a sense it becomes a philosophical question and is not really subject of scientific analysis. Strong arguments can be made against mutation/selection creating new information, but theorists can always speculate to the contrary (it is very difficult to prove that something can never happen). However I believe the "going down" aspect of the genome is subject to actual scientific analysis. It is for this reason that I have focused on the issue of the degradation of information. I believe that it is subject to concrete analysis. Such analysis persuasively argues that ''net'' information must be declining. If this is true, then even if it could be shown that there were specific cases where new information ''might'' be synthesized via mutation/selection, it would still be meaningless since such new information would promptly then begin to degenerate again. The net direction would still be ''down'', and complex genomes could never have arisen spontaneously. (Sanford, p. 105, his italics)}}

[[User:Philip J. Rayment|Philip J. Rayment]] 02:32, 14 February 2009 (EST)

:Thank you, for your summary. I will take some time out to read some of these recommendations. I believe the issue at the base of all of this is the term '''information'''. I do not know if the issue with this term is the fact that the encoded proteins are not just the result of the code from the DNA, thereby making the term '''information''' an oversimplification or if it is the inference of some needed form of result due to the order of the code. I will write more on this at a later date, I am a bit behind this week.--[[User:Able806|Able806]] 15:33, 17 February 2009 (EST)

Talk:Point mutation

2009-02-13T20:18:44Z

Able806:

Talk:Point mutation

2009-02-13T20:15:27Z

Able806:

Talk:Point mutation

2009-02-13T14:19:20Z

Able806: /* Genetic Information */

2009-02-04T21:24:10Z

2009-02-04T20:44:39Z

Able806:

A '''DNA nucleotide''' is made of a [[phosphate]], a molecule of [[ribose]], and another molecule called a [[nitrogenous base]]. The initial letters of the base names that spell out the [[genetic code]].
A, T, G, and C stand for the chemicals [[adenine]], [[thymine]], [[guanine]], and [[cytosine]], respectively. In base pairing, adenine always pairs with thymine, and guanine always pairs with cytosine.

== Sources ==
*[http://www.blurtit.com/q145909.html What Is A DNA Nucleotide?]
*[http://www.genome.gov/glossary.cfm?key=base%20pair Courtesy: National Human Genome Research Institute]

[[Category:Genetics]]

Talk:DNA nucleotide

2009-02-04T20:43:30Z

Able806: