Talk:Genetic recombination

benefits?

What are the benefits of genetic recombination? --Evan 00:21, 12 Dec 2004 (UTC)

See Muller's ratchet

Recombination reduces the degree to which genes in a chromosome are linked. This allows "good" genes to survive and it ensures bad genes do not accumulate within the genome. —The preceding unsigned comment was added by 129.97.248.107 (talk) 08:04, 19 March 2007 (UTC).

imprecise?

It seems imprecise to define recombination as separating genes (this is rather the case with transpositions/translocations). Rather alleles are separated. Sboehringer

Merge: Recombination with crossover

Does this article, perhaps, need to be merged (or merged and re-split along better lines) with chromosomal crossover?--ES2 18:31, 24 Jul 2004 (UTC)

This article was distinct until it was butchered on 23 July 2004. That edit eliminated the general definition of genetic recombination and reduced it to being nothing more than chromosomal crossover--which was addressed in the original article. If I weren't too busy to follow up on this right now, I'd probably revert all the way back to 23 July. AdamRetchless 04:23, 20 Jan 2005 (UTC)

I didn't think that expanding a stub was exactly butchering the article. Thankfully the article has gotten better since that expansion. --ES2 05:01, 26 April 2006 (UTC)

I also think these two articles can be merged - unless someone can make the case that crossover and recombination refer to fundamentally different processes. Dr d12 20:55, 9 December 2006 (UTC)

Intra- vs inter-chromosomal recombination

I have a real problem with the use of intra- vs inter-chromosomal recombination here. Ben Carritt 17:48, 23 December 2005 (UTC)

Cre Recombinase

Cre is a type of Recombinase (read Cyclic Recombinase)which has been found in the Bacteriophage P1. Cre catalyses a reaction between two 'Lox P' (read Loci of X over P1) sites, which are 34 bp sequences, causing splicing of the gene which is flanked by these two Lox P sites, leaving behind just the Lox site. This system is called the Cre-Lox system and has been used in effectively studying Mutations, allelic variations and is currently being used by the Biotechnolgy industry in producing trasgenic species of mice and plants to derive useful biological products. Bold text

New alleles?

Does recombination create new alleles, or does it keep the current ones intact? 5th April 2006

Recombination does not respect reading frame boundaries, and therefore can produce novel alleles. One research article describing this says:

The asymmetric patterns of polymorphism and the absence of simple dinucleotide variation in 23 kb of sequence are compatible with recombination or sister chromatid exchange, but not polymerase slippage. By inference, recombination should underlie the polymorphisms at (GT)n/(AC)n since they are a subset of (RY)n and they commonly occur in the context of longer (RY)n.

Which means that the introductory statement in the main article here:

Recombination therefore only shuffles already existing genetic variation and does not create new variation at the involved loci.

is completely incorrect. Recombination is sufficient to produce novel alleles. It does not necessarily produce novel alleles, though, which is why a misunderstanding such as the quoted statement from the article can become widespread as a meme.

Can somebody fix the main article, please? --Wesley R. Elsberry 22:05, 3 January 2007 (UTC)

Suggested rephrasing of the bad sentence... Was:

Recombination therefore only shuffles already existing genetic variation and does not create new variation at the involved loci.

should become...

Because coding regions are relatively uncommon, in most cases recombination breaks and rejoins genetic material outside those regions, with the effect of "shuffling" already-existing loci. But since recombination does not respect reading frame boundaries, from time to time it will bring together parts of differing alleles, resulting in the production of a novel allele.

How's that sound? --Wesley R. Elsberry 22:20, 3 January 2007 (UTC)

I emphatically disagree with Dr. Elsberry. The sentence should remain unchanged. This article is based on one of the leading cell biology textbooks in the world, co-authored by no less an authority than the late president of the National Academy of Sciences, Bruce Alberts.

Note that the research article quoted by Dr. Elsberry does not say "recombination is sufficient to produce novel alleles." It simply says "By inference, recombination should underlie the polymorphisms ..." Notice the use of the words "by inference" and "should." These are not words indicative of experimental certainty. I would challenge Dr. Elsberry to produce experimental evidence supporting his idea that "recombination can produce novel alleles." To my knowledge, there have been no experiments confirming this. Rather, all experimentation to date has confirmed the sentence as it stands. Therefore, to implement Dr. Elsberry's proposed change would mislead readers. Now it might be acceptable to say something like ...

Experiments to date indicate that recombination only shuffles already existing genetic variation and does not create new variation at the involved loci. Some evolutionary biologists have proposed that recombination can produce novel alleles by noting that recombination does not respect reading frame boundaries. However, the notion of novel allele production by recombination has not been confirmed experimentally.

Readers should be aware that this change proposed by Dr. Elsberry was precipitated by a discussion on the "After the Bar Closes" Forum at Panda's Thumb. It appears that evolutionary biologists such as Dr. Elsberry are keen to propose new mechanisms for the generation of novel alleles in the face of accumulating evidence that RM + NS (Random Mutation + Natural Selection) is insufficient to explain all the biological innovations seen in nature. One participant in the discussion--a microbiology professor--even proposed that recombination is a "kind" of mutation. Of course, this would be a significant departure from all previous understandings of the word "mutation."

To make the change proposed by Dr. Elsberry would be misleading to readers and in my opinion would serve to discredit the good name of Wikipedia. --David W. Hawkins 12:15, 4 January 2007 (UTC)

The most likely reason Mr. Hawkins is unaware of research demonstrating that recombination can produce new alleles is that he has not taken the time to research the subject. Allelic recombination is well represented in the scientific literature. For example from PNAS | December 10, 2002 | vol. 99 | no. 25 | 16348-16353 we have:

"Meiotic recombination in the anopheline mosquito is the major mechanism for allelic variation of PfMsp-1 (8); thus, intragenic recombination between unlike alleles generates new alleles in the progeny (10). Recombination sites are confined to the 5' and 3' regions of the gene."

Dr. Elsberry's rewrite is concise, accurate, and easy to understand, and should thus be adopted. The references from the quote are (8) Tanabe, K., Mackay, M., Goman, M. & Scaife, J. (1987) J. Mol. Biol. 195, 273-287 and (10) Kerr, P. J., Ranford-Cartwright, L. C. & Walliker, D. (1994) Mol. Biochem. Parasitol. 66, 241-248. David J. Phippard 17:14, 4 January 2007 (UTC)

In spite of Dr. Phippard's comments, the sentence, as it stands ...

Recombination therefore only shuffles already existing genetic variation and does not create new variation at the involved loci.

is a correct statement. Dr. Elsberry is wrong when he states that it is completely incorrect. Note the following quotes from ...

Annu. Rev. Genet. 2002. 36:75–97 doi: 10.1146/annurev.genet.36.040202.111115 Copyright c° 2002 by Annual Reviews. All rights reserved RECOMBINATION IN EVOLUTIONARY GENOMICS David Posada1,2, Keith A. Crandall3,4, and Edward C. Holmes5 1Variagenics Inc. Cambridge, Massachusetts 02139, 2Center for Cancer Research,Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, 3Department of Integrative Biology, 4Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah 84602, and 5Department of Zoology, University of Oxford,Oxford OX1 3PS, United Kingdom

Recombination can play a dominant role in the generation of novel genetic variants through the rearrangement of existing genetic variation generated through mutation." (p.81)

So while novel alleles can arise through recombination, these novel alleles are simply the rearrangement of existing genetic material which, the above authors believe, was originally created through mutation.

This article also says ...

"Although both [homologous and non-homologous recombination] conform to a broad definition of recombination—[that is,]an evolutionary event that has as a consequence the horizontal exchange of genetic material..." (p.76)

"Horizontal exchange of genetic material" is not a phrase which gives the impression of anything truly novel being created.

Dr. Elsberry's proposed wording ...

Because coding regions are relatively uncommon, in most cases recombination breaks and rejoins genetic material outside those regions, with the effect of "shuffling" already-existing loci. But since recombination does not respect reading frame boundaries, from time to time it will bring together parts of differing alleles, resulting in the production of a novel allele.

would lead readers to believe that new genetic information is being created, when in reality, previously existing information blocks are being reshuffled in a way that is not yet completely understood.

I would be interested to see what Albert's most recent textbook (2002 version) has to say about this, since this article was based on the earlier version of his textbook. I will comment on that when I can obtain a copy. --David W. Hawkins 11:05, 4 January 2007 (UTC)

Can I please say, recombination can provide mutations by accidentally duplicating alleles (a duplication event) during homologous recombination. If you want a source, look up 'homologous recombination' and 'gene duplication' on wikipedia and take the sources from there. It is well known that the third cone that contributes to human colour vision came from a duplication event. So, although recombination is not intended to produce mutations, it does on occasion. 129.67.38.36 (talk) 02:38, 8 February 2011 (UTC)

Santino junction

"...in the first Santino junction..."

What is that? SamEV 10:42, 5 September 2006 (UTC)

Mystery solved. It was vandalism, which I've just removed. SamEV 08:09, 26 February 2007 (UTC)

Contradictory/unclear definition

The definition talks about two parents, and then about "asexually reproducing organisms" in evolutionary biology. Am I missing something? OK, it says that the initially given definition is not commonly used in certain fields (such as evolutionary biology), but it doesn't explain what definition is used in these fields. --194.145.161.227 17:34, 29 December 2006 (UTC)

Information Issue

David Hawkins inserted the following into the main article:

It should be noted that while a novel allele is produced in this way, no new information is being created by this process. Recombination simply rearranges existing genetic information.

This is an antievolution talking point. It comes with no substantiation whatsoever, and depends critically on leaving any coherent definition of "information" out of the discussion. While this may not meet the Wikipedia:Vandalism criteria, it comes pretty close to that. I suggest reverting to the previous version. --Wesley R. Elsberry 17:56, 5 January 2007 (UTC)

I would agree with your justification for removal... what is a novel allele if not new? Recombination rearranges existing genetic information to produce new combinations. The definition of "information" needs to be elucidated to return this statement to NPOV status. -- Serephine ♠ talk - 07:28, 9 January 2007 (UTC)

Information Issue Rebuttal

Dr. Elsberry should not be insinuating a user is a vandal on the article discussion page. He also needs to read policy on Vandalism and Dispute Resolution. I followed policy by adding to the article with well supported information (See policy below).

When someone makes an edit you consider biased or inaccurate, improve the edit, rather than reverting it.

http://en.wikipedia.org/wiki/Wikipedia:Resolving_disputes

This article is now in dispute and IAW policy, I have entered a detailed but courteous dispute essay on Dr. Elsberry's Talk Page and will take up the discussion with him there until this is resolved. David W. Hawkins 02:44, 9 January 2007 (UTC)

If that was "courteous", I will take a pass on seeing what Hawkins says when he gets nasty. Since I have never edited the article, I can hardly be guilty of reverting Hawkins's edit. What I said was, "While this may not meet the Wikipedia:Vandalism criteria, it comes pretty close to that." And it does. Unable to produce a convincing case for his original point, Hawkins inserted an unsupported assertion that had nothing to do with any existing topic within the article, one that is a commonplace in the antievolution literature. When it was properly removed by JoshuaZ as an insertion of a creationist point of view, Hawkins made a false accusation about my actions.

So far as following Wikipedia policy here, I have already been complying with "Step 2" from the "Resolving disputes" page; I have relied upon convincing other editors of the correctness of what I say and allowing them to make, or not make, the changes that I have suggested. It was Hawkins who took direct action to insert a POV assertion without substantiation directly in the main article. --Wesley R. Elsberry 05:25, 9 January 2007 (UTC)

I see that Dr. Elsberry wants to shift responsibility for the recent changes by pointing out the users who actually implemented the changes. Fine. I will retract my accusation. However, it is Dr. Elsberry who is the driving force behind implementing these changes. I would ask Dr. Elsberry to also retract his statement that I came close to vandalism based upon the following definition ...

Vandalism is any addition, deletion, or change of content made in a deliberate attempt to compromise the integrity of Wikipedia.

The most common type of vandalism is the replacement of existing text with obscenities, page blanking, or the insertion of bad jokes or other nonsense. Fortunately, this kind of vandalism is usually easy to spot.

Any good-faith effort to improve the encyclopedia, even if misguided or ill-considered, is not vandalism. Apparent bad-faith edits that do not make their bad-faith nature inarguably explicit are not considered vandalism at Wikipedia. For example, adding a personal opinion once is not vandalism — it's just not helpful, and should be removed or restated.

This seems to be a contentious remark especially when directed at a new user. I made a good-faith effort to improve the encyclopedia, and I am not seeking to insert my POV. From this point forward, I believe policy would dictate that we move any further discussions about rule violations to either of our user Talk Pages.

As for this article, I note that the user "Serephine" states that the definition of "information" needs to be elucidated to return my statement to NPOV status. I submit the following definition for Biological Information from Crick pointed out by Meyer ...

“By information I mean the specification of the amino acid sequence in protein . . . Information means here the precise determination of sequence, either of bases in the nucleic acid or on amino acid residues in the protein”

Crick, F. On Protein Synthesis. Symposium for the Society of Experimental Biology 12:138-63, esp. 144, 153, 1958.

http://www.discovery.org/articleFiles/PDFs/DNAPerspectives.pdf

Meyer also says ...

Thus, molecular biologists beginning with Crick equated information not only with complexity but also with “specificity,” where “specificity” or “specified” has meant “necessary to function” (Crick 1958:144, 153; Sarkar, 1996:191).3 Molecular biologists such as Monod and Crick understood biological information--the information stored in DNA and proteins--as something more than mere complexity (or improbability). Their notion of information associated both biochemical contingency and combinatorial complexity with DNA sequences (allowing DNA's carrying capacity to be calculated), but it also affirmed that sequences of nucleotides and amino acids in functioning macromolecules possessed a high degree of specificity relative to the maintenance of cellular function.

http://www.discovery.org/scripts/viewDB/index.php?command=view&id=2177

In spite of Dr. Elsberry's incorrect statement that ...

Which means that the introductory statement in the main article here:

Recombination therefore only shuffles already existing genetic variation and does not create new variation at the involved loci.

is completely incorrect.

... I do agree with his addition, not because of the reference he cited, but because of David Phippard's citation.

However, my added sentence ...

It should be noted that while a novel allele is produced in this way, no new information is being created by this process. Recombination simply rearranges existing genetic information.

... is correct and helpful in understanding what is really going on. It is well supported by the Posada article, by a statement from Crick, and by further statements with references to the literature by Meyer. I will wait to hear more discussion before editing further. David W. Hawkins Afdave 12:42, 9 January 2007 (UTC)

Hawkins wrote:

I see that Dr. Elsberry wants to shift responsibility

Lack of courtesy noted in the promulgation of a new false accusation.

I made a good-faith effort to improve the encyclopedia, and I am not seeking to insert my POV.

It was because I judged Hawkins to be sincerely misguided that I originally said that his actions may not meet the criteria of Wikipedia:Vandalism. However, the insertion made by Hawkins did reduce the integrity of Wikipedia, and it was quite easily recognizable as POV insertion since it is just a common antievolution argument.

From this point forward, I believe policy would dictate that we move any further discussions about rule violations to either of our user Talk Pages.

Hawkins would be wrong again. Read the policy: "Either contact the other party on that user's talk page, or use the talk page associated with the article in question." This page is perfectly appropriate for handling an exchange over what should -- and should not be -- in the main article.

Stephen C. Meyer is the Director of the Discovery Institute's Center for Science and Culture, a philosopher of science without experience or practice in information theory. What he offers from Crick doesn't even support Meyer's claim that biologists were incorporating functional components into their ideas about information and molecular biology; it reads as a call to determine the sequence of bases or amino acids and not make assumptions about their composition in ignorance, as Meyer documents was commonplace not long before Crick's article was written. Crick was not offering a formal definition of information, but rather identifying an instance of information.

The article from Meyer that Hawkins quotes was repudiated by the publisher. I suggest that it be considered inappropriate as a source of verifiable information per Wikipedia guidelines.

Funny, that I should be incorrect in asserting that a statement was wrong when even Hawkins stipulates that the text that contravened it is correct.

References that show that recombination does cause the formation of novel alleles trumps references that have not taken cognizance of that research. This aspect of science will continue to cause Hawkins trouble until Hawkins learns that he cannot set aside evidence by quoting people who have not yet addressed that evidence. --Wesley R. Elsberry 14:56, 9 January 2007 (UTC)

Hawkins wrote:

However, it is Dr. Elsberry who is the driving force behind implementing these changes.

Yes, anyone who points out an error in a Wikipedia article is the driving force behind getting it changed to a more accurate state. Is there a problem in that? --Wesley R. Elsberry 15:00, 9 January 2007 (UTC)

Several points here ...

1) Crick's statement is a very good formal definition of "biological information", which is what is being discussed here and he makes himself quite clear. However, I am not omniscient and I am willing to research the other sources that Meyer and others cite to ensure we achieve accuracy.

2) Dr. Elsberry seems to be using the fact of a later editorial committee not liking Dr. Meyer because they are anti-ID, to somehow reduce the value of the Crick statement.

3) Dr. Elsberry speaks of Dr. Meyer's lack of experience or practice in information theory, yet history is replete with examples of scientists and philosophers who crossed boundaries in varying degrees successfully. Further, is not Crick an authority?

4) Dr. Elsberry says

References that show that recombination does cause the formation of novel alleles trumps references that have not taken cognizance of that research. This aspect of science will continue to cause Hawkins trouble until Hawkins learns that he cannot set aside evidence by quoting people who have not yet addressed that evidence.

Why does Dr. Elsberry imagine that Posada et. al. are not cognizant of the mentioned research? Both the Posada article and the PNAS article which admittedly support Dr. Elsberry's added language were both 2002 articles.(note that Dr. Elsberry's original citation did not support changing the article)

5) Note that Dr. Elsberry still does not understand how his early statement was incorrect. He writes ...

Funny, that I should be incorrect in asserting that a statement was wrong when even Hawkins stipulates that the text that contravened it is correct.

Yes. You said that the original sentence was "completely incorrect." But this is not true. It was quite correct as the Posada article clearly shows. Had you said that it was "incomplete" or "could be expanded to include recent research" you would have been correct. But the statement you made was incorrect.

6) But that does not matter WRT the added sentences. I have accepted your added sentence and I am merely asserting that my sentence (or something very similar) should also be added

7) I will answer your last question (or further questions pertaining to rules and etiquette) on your Talk page as that seems to be more in line with Wikipedia rules where it says ...

Never carry on a dispute on the article page itself.

From a comprehensive reading of the rules it does appear that pros and cons related to the article itself belong here, but that arguments over etiquette and rules should stay on the User Talk pages. David W. Hawkins Afdave 17:36, 9 January 2007 (UTC)

Meyer is not a reliable source for these purposes. He is for obvious reasons very biased and is a philosopher and theologian with no training in mathematics or biology. it is not Wikipedia's concern that "history is replete with examples of scientists and philosophers who crossed boundaries in varying degrees successfully" - if actual biologists pick up on the idea then Wikipedia could cite it. As to the Crick matter, there are a variety of defintions of information and it isn't even clear to me from the Crick quote that he wouldn't consider this to be an increase in information and concluded that it wouldn't be is thus original research. Now, if you can get a specific defintion of information and get a reliable source that specifically says that these novel allels are not adding information then we can consider including it. JoshuaZ 00:01, 16 January 2007 (UTC)

Nothing else needs to be said, the above sums it up perfectly. Please, to parties involved, don't drag this out further, suck it up and do what's best in the interests of Wikipedia. It's getting tiresome and petty. -- Serephine ♠ talk - 00:14, 16 January 2007 (UTC)

JoshuaZ said ...

As to the Crick matter, there are a variety of defintions of information and it isn't even clear to me from the Crick quote that he wouldn't consider this to be an increase in information and concluded that it wouldn't be is thus original research. Now, if you can get a specific defintion of information and get a reliable source that specifically says that these novel allels are not adding information then we can consider including it.

You say there are a variety of definitions of information, yet you don't provide any. In contrast to this, I have provided one from a quite authoritative source. And I have also provided a reliable source that says that these novel alleles simply reshuffle existing variation.

Recombination can play a dominant role in the generation of novel genetic variants through the rearrangement of existing genetic variation generated through mutation." (p.81) (From the Posada article above)

You appear to be quibbling over the exact choice of words - "variation" vs. "information". What authoritative source can you provide that refutes the clear statement from the Posada article above? How is "variation" not equivalent to "biological information" especially in light of the Crick quote?

It appears to me that Dr. Elsberry wants you to disallow my added sentence because of his own Darwinist POV. You have labeled my sentence as Creationist POV which clearly it is not. We even had another editor weigh in and say ...

The definition of "information" needs to be elucidated to return this statement to NPOV status.

which I promptly did from an authoritative source. You have two authoritative sources from me which clearly establish the validity of my added sentence.

In my experience, I have found that the only ones confused about the meaning of "biological information" are those seeking to find new mechanisms for Darwinian Evolution POV in the face of accumulating evidence that previously proposed mechanisms such as Random Mutation + Natural Selection are inadequate. It appears that this might the case here with Dr. Elsberry.

A quick Google search of "biological information" turned up this 2005 article ...

In order to come up with such a concise definition, we should first consider what systems biology aims to achieve, that is, the understanding of biological information, specifically the information encoded in the linear nucleotide sequence of a genome. Like written language texts, genome sequences can be represented as letters (nucleotides) and words (genes). However, understanding the lingual information of such texts requires knowledge not only of the letters and words, but also of the syntax, that is, the ordering of and relationship between the words in phrases and sentences. Likewise, understanding the biological information of genomes requires an understanding of not only the nucleotides and their arrangement into genes, but also of the syntax of biological information. http://www.nature.com/msb/journal/v1/n1/full/msb4100009.html

It seems that many practicing biologists have a very clear understanding of the meaning of "biological information" and that the notion that my statement is "Creationist POV" is itself "Darwinist POV." You have rightly asserted that Wikipedia should be impartial and not promote POV. It seems that disallowing my sentence would be a clear example of doing just that. David W. Hawkins Afdave 11:24, 19 January 2007 (UTC)

Dave said:

How is "variation" not equivalent to "biological information" especially in light of the Crick quote?

If it is, then you're sunk, since Posada's clear statement clearly states that rearrangement of existing genetic variation creates novel variants; ie, more variation, and an increase of information. Tsumetai 17:25, 19 January 2007 (UTC)

Hmmm ... interesting how you added "and an increase of information" to the Posada statement. Would you please cite where in the Posada article you found that phrase? Thanks. David W. Hawkins Afdave 10:55, 22 January 2007 (UTC)

I never presented it as an exact quote. Are you seriously going to argue that "variation" and "biological information" are equivalent, but "more variation" and "more biological information" are not? Tsumetai 14:40, 31 January 2007 (UTC)

I am arguing that it is misleading to say that "recombination ... can produce novel alleles" without further explaining that these novel alleles are created from "existing genetic variation" as the Posada article makes clear.

Recombination can play a dominant role in the generation of novel genetic variants through the rearrangement of existing genetic variation generated through mutation." (p.81)

"Although both [homologous and non-homologous recombination] conform to a broad definition of recombination—[that is,] an evolutionary event that has as a consequence the horizontal exchange of genetic material..." (p.76) [Posada, Reference given above]

IOW, we should not be giving readers the impression that there is new biological information (as defined by Crick) being created through this process. You could silence me on this issue by adding the following wording ...

But since recombination does not respect reading frame boundaries, from time to time it will bring together parts of differing alleles, resulting in the production of a novel allele [current wording] through the rearrangement of existing genetic variation. [added] [Straight from the Posada article]

This way we don't get into the debate over the definitions of "biological information", yet we don't mislead our readers by implying that new biological information is being created through this process.

Is that a fair compromise? JoshuaZ, can you please implement this change? Thx. 71.1.124.104 11:34, 12 February 2007 (UTC)Afdave

That clarification might be redundant, but the opening paragraph is a bit clunky and that little bit of "increased information" might be helpful. I've made the change. Dphippard 23:44, 13 February 2007 (UTC)

"This way we don't get into the debate over the definitions of "biological information", yet we don't mislead our readers by implying that new biological information is being created through this process."

It would be misleading to readers to pretend that a novel allele, however it comes into existence, is anything other than new biological information. The objection that a novel allele made by rearranging existing genetic information cannot be considered new biological information is parallel to the objection that a book comprised of words found in a dictionary cannot be considered a new literary work. --Wesley R. Elsberry 10:37, 20 February 2007 (UTC)

Genetic Recombination Does Not Create Biological Innovations

I like analogies also. But I believe Dr. Elsberry's analogy is flawed. His book analogy implies that recombination is responsible for the origination (innovation) of form in addition to the diversification (variation) of form. Muller and Newman address this thoroughly ...

Origination of Organismal Form: The Forgotten Cause in Evolutionary Theory

Gerd B. Müller and Stuart A. Newman

http://mitpress.mit.edu/books/chapters/0262134195chap1.pdf

(Cited in Meyer's "Smithsonian" paper found here http://www.discovery.org/scripts/viewDB/index.php?command=view&id=2177)

pp. 1-2

Evolutionary biology arose from the age-old desire to understand the origin and the diversification of organismal forms. During the past 150 years, the question of how these two aspects of evolution are causally realized has become a field of scientific inquiry, and the standard answer, encapsulated in a central tenet of Darwinism, is by “variation of traits” and “natural selection.” The modern version of this tenet holds that the continued modification and inheritance of a basic genetic tool kit for the regulation of developmental processes, directed by mechanisms acting at the population level, has generated the panoply of organismal body plans encountered in nature. This notion is superimposed on a sophisticated, mathematically based population genetics, which became the dominant mode of evolutionary biology in the second half of the twentieth century. As a consequence, much of present-day evolutionary theory is concerned with formal accounts of quantitative variation and diversification. Other major branches of evolutionary biology have concentrated on patterns of evolution, ecological factors, and, increasingly, on the associated molecular changes. Indeed, the concern with the “gene” has overwhelmed all other aspects, and evolutionary biology today has become almost synonymous with evolutionary genetics.

These developments have edged the field farther and farther away from the second initial theme: the origin of organismal form and structure. The question of why and how certain forms appear in organismal evolution addresses not what is being maintained (and quantitatively varied) but rather what is being generated in a qualitative sense. This causal question concerning the specific generative mechanisms that underlie the origin and innovation of phenotypic characters is probably best embodied in the term origination, which will be used in this sense throughout this volume. That this causal question has largely disappeared from evolutionary biology is partly hidden by the semantics of modern genetics, which purports to provide answers to the question of causation, but these answers turn out to be largely restricted to the proximate causes of local form generation in individual development. The molecular mechanisms that bring about biological form in modern-day embryos, however, should not be confused with the causes that led to the appearance of these forms in the first place. Although the forces driving morphological evolution certainly include natural selection, the appearance of specific, phenotypic elements of construction must not be taken as being caused by natural selection; selection can only work on what already exists. Darwin acknowledges this point in the first edition of The Origin of Species, where he states that certain characters may have “originated from quite secondary causes, independently from natural selection” (Darwin, 1859, 196), although he attributes “little importance” to such effects. In a modified version of the same paragraph in the sixth edition (Darwin, 1872, 157), he concedes that “we may easily err in attributing importance to characters, and in believing that they have been developed through natural selection.”

It is the aim of the present volume to elaborate on this distinction between the origination (innovation) and the diversification (variation) of form by focusing on the plurality of causal factors responsible for the former, relatively neglected aspect, the origination of organismal form. Failure to incorporate this aspect represents one of the major gaps in the canonical theory of evolution, it being quite distinct from the topics with which population genetics or developmental genetics is primarily concerned. As a starting point, we will briefly outline the central questions that arise in the context of origination.

I think the book/dictionary analogy would be good if we compared, for example, Homer's Iliad to the human genome and Gone With the Wind to the horse genome, to pick some higher organisms. I will allow the geneticists here to correct me if I am wrong, but my understanding is that genetic recombination would be analogous to writing a new book using only the existing words in a particular book, such as one of the examples above, NOT the whole dictionary. Yes, the reading frame boundaries are not always respected, implying an analogy of selecting the new word 'HERE' from the previously existing words 'tHE REal story', for example. But this is quite a different analogy from the one given by Dr. Elsberry. Nature does not select a subset of the 'words' in the 'dictionary' to create biological innovation, as Dr. Elsberry's analogy implies. Nature selects ALL the existing 'words' and 'letters' of the genome, recombines them under tight cellular control and produces a new organism displaying relatively minor differences from the previously existing organism. Nothing resembling the creation of biological innovation has ever been demonstrated by recombination. David W. Hawkins Afdave 15:57, 13 March 2007 (UTC)

Muller and Newman don't address the role of recombination as a source of novel alleles. "Recombination" does not even appear in the linked PDF. Muller and Newman argue for non-genetic components and processes as being the locus of most evolutionary innovation; they do not argue for exclusive generative ability being due to those components and processes. The linked text is very much high-level and their references to actual research are few in number. The linked article does not in any case set aside the research cited by Phippard, which Hawkins has already stipulated does establish the ability of recombination to produce novel alleles. Novel alleles are new biological information, contrary to Hawkins's idee fixe and title of this subsection. Certainly the fact of citation of Muller and Newman by Meyer adds nothing to the discussion.

Nor did I offer the literary scenario as an analogy for the genetics. Please read more carefully in the future. --13:35, 15 March 2007 (UTC)

Hmmm ... I did read you very carefully (Dr. Elsberry I assume?) and it appears that you did indeed offer the literary scenario as an analogy for the genetics. You wrote ...

The objection that a novel allele made by rearranging existing genetic information cannot be considered new biological information is parallel to the objection that a book comprised of words found in a dictionary cannot be considered a new literary work. --Wesley R. Elsberry

It would therefore appear that my analysis of your analogy is accurate. Afdave 14:57, 26 April 2007 (UTC)

Merging chromosomal crossover into genetic recombination

If anyone has an argument against this, please say something. In fact, I notice now that the argument has been made before now, but no merge tag had been placed on the article. -Madeleine 01:20, 29 March 2007 (UTC)

A decision was made against a merge last time (by the nominator shortly after making the nomination). I think the crossover page is useful as a stand alone page - since there are types of recombination that aren't due to crossover. I disagree with a the merge proposal. Ideally some more of the text about crossover would be moved form this article to that one. --Peta 01:46, 29 March 2007 (UTC)

Sorry, I wasn't aware that there'd been a recorded decision made about it. Was there discussion about it that isn't on this talk page? -Madeleine 03:32, 29 March 2007 (UTC)

It's on the crossover talk page. --Peta 03:33, 29 March 2007 (UTC)

Okay, there's a "decision", but I'm not seeing a lot of discussion that gives the reasoning against merger. Peta - I resent that you didn't bother to give a reason. I'm going to decide against the merge, but I'm also going to record why: yes, chromosomal crossover is one of several types of recombination -- that alone isn't justification, because all could be covered on one page. I missed this before, but all of these others types of recombination also have their own subpages linked from this main page -- site-specific recombination, transposons, and nonhomologous end joining -- just as for chromosomal crossover. Now that I realize this, my mind is changed. Here's my ideas on how to edit this article:

• Add to each of sections for other types of recombination the same "Main article: Foo" note at the top.
• Homologous recombination should point here rather than to chromosomal crossover, and there should be information on homologous vs. nonhomologous recombination here. I have to think about how to actually summarize the topic on this page, but the redirect to chromosomal crossover contributed to my initial suggestion to merge.
• The category levels of "crossing over" vs. "other types of recombination" needs to be reconsidered. Perhaps all types of recombination should be categories on the same level. Alternatively, it could be "homologous" vs "nonhomologous" recombination, with the different types of recombination within each, but since site-specific recombination uses "partial" homology this is might just be confusing to the reader.
• As Peta suggested, information specific to chromosomal crossover should be moved to the crossover page such that chromosomal crossover does not dominate the information content of this article.

-Madeleine 17:15, 3 April 2007 (UTC)

Error in first paragraph - asexually

The sentence

"In evolutionary biology this shuffling of genes is thought to have many advantages, including that of allowing sexually reproducing organisms to avoid Muller's ratchet."  should say asexually instread of sexually.

Bindi13 (talk) 06:51, 14 April 2008 (UTC)

I think perhaps you are misreading it, it looks correct to me... Madeleine ✉ ✍ 13:35, 14 April 2008 (UTC)

This extra 'a' has caused me so much trouble... It should in fact be 'sexually', pointing out that asexual organisms must deal with Muller's Ratchet. If you think about it, recombination between two chromosomes in an asexual organism would merely pass a mutated allele from one chromosome to another, it would not deal with it. If only I'd thought about that before I spent about an hour trawling through wikipedia and the internet trying to discover if asexual organisms undergo recombination.