Talk:Natural selection/Archive 8

message: According to Wiki 'In biology, a trait or character is a genetically inherited feature of an organism.' If this is true why does the article say 'but only the heritable component of a trait will be passed on to the offspring'. Which is correct? Is a trait by definition heritable?
— Axel147 20:20, 16 July 2006 (UTC)
replies: text: I corrected the article on that point.  Traits can be fully or partly genetic, or not at all. Hence QTL analysis - carried out when the inheritance of the trait is not exactly known. - Samsara (talk • contribs) 08:17, 17 July 2006 (UTC)
replies: text: Good, what corrrection are you putting in? Maybe I'm just being pedantic here, but we also using trait inconsistently in another respect: in the opening line but not elsewhere it refers to the state or 'value' of a feature (e.g. brown vs. eye colour). Also suggestions traits can be decomposed into parts some of which are heritable - different saying a trait as a single entity has different extents to which it is heritable. — Axel147 08:32, 17 July 2006 (UTC)
replies: text: Unfortunately, trait is not used consistently in genetics.  The Stansfield dictionary equates trait with character and phenotype (as does Hartl's old Human Genetics text).  Some people use trait to refer to carriers, such as talking about individuals who are sickle-cell carriers as having sickle trait (vs. sickle-cell disease for homozygotes).  Still others (myself included) use trait to refer to the gene, with characteristic as the phenotype (I don't know when I picked that up.  It may have been when I was teaching Human Genetics). TedTalk/Contributions 13:47, 18 July 2006 (UTC)
thread_title: Inconsistent use of the word 'trait'

message: The last time that I read this article, some idiot had written something about the new Kim Possible season. If the vandal is reading this, please note that we don't care about Kim Possible and that this page is about NATURAL SELECTION, just in case you haven't noticed that already.
--71.140.114.12 19:45, 11 February 2007 (UTC)
thread_title: Vandalism

message: Guys, seeing how little the article has changed in recent weeks, and noting that it is well referenced and well illustrated, and also noting that my recent experience of peer review shows it to be much less active, and therefore much less useful, than FAC, can I ask you all whether you consider that FA status is desirable for this article, and would therefore like to apply for it? (FA has ups and downs - it will bring more people wanting to "improve" the article, but it also carries prestige...)
Many thanks,
Samsara (talk • contribs) 14:48, 16 August 2006 (UTC)
replies: text: I seem to remember seeing plates of finch beaks in biology textbooks. Maybe a free example exists or could be created. Unfortunately, drawing is not one of my strengths. I don't recall ever seeing an illustration of domestic pigeon diversification. We could try to polish the antibiotic illustration into something more tangible - many bacteria do have a distinct, recognisable shape. - Samsara (talk • contribs) 21:45, 17 August 2006 (UTC)
replies: text: On page 18 of The Beak of the Finch are four finches drawn by Darwin from his journals.  I don't know if these qualify as PD by now via this route, but I'm with Glen, Finches and Pigeons are the ideal candidates for illustrating this article. Pete.Hurd 22:33, 17 August 2006 (UTC)
replies: text: If they're his original figures, then yes, c.f. :Image:Darwins first tree.jpg. Seeing that you seem to have a copy of the book, could you scan and upload the figure? - Samsara (talk • contribs) 14:21, 18 August 2006 (UTC)

text: Is it this image? --Fastfission 17:05, 18 August 2006 (UTC)
replies: text: Aye, that's the one Pete.Hurd 20:09, 18 August 2006 (UTC)
replies: text: Now all it needs is a compelling caption. - Samsara (talk • contribs) 13:50, 19 August 2006 (UTC)
replies: text: I was thinking it would be nice to have some text dealing with character displacement, sympatric and allopatric species and beak shape etc.  It would make the figure all the more worthwhile, and would probably work best as another example section.  What do you think? Pete.Hurd 14:39, 19 August 2006 (UTC)
replies: text: Sounds good. Would also like to see adaptive radiation mentioned. I was intrigued by the fact that there are 13 main islands in the Galapagos archipelago, and 13 species of finch. I don't know the literature on these finches at all, so I'll leave it at that lest I embarrass myself. - Samsara (talk • contribs) 14:54, 19 August 2006 (UTC)
replies: text: Actually, no, the speciation is much more complex, and each island has different species, and the interactions between the species is crucial to explain the variation in beak size. -- Kim van der Linde at venus 15:10, 14 September 2006 (UTC)
thread_title:  Nominate for FA? 

message: would sympathtic editors consider a positive vote here? Slrubenstein   |  Talk 15:34, 23 August 2006 (UTC)
thread_title:  embryology 

message: Phenotypic plasiticity is heritable in birds and insects as I recollect from more recent studies. I'll find references.GetAgrippa 19:50, 3 September 2006 (UTC)
replies: text: Grin, selection on phentotypic plasticity can even be phenotypically plastic, just to make it even more complex. In the end, phenotypic plasticity is just a version of an GxE interaction. A good article dealing with this is: Schlichting, C. D. and H. Smith (2002). "Phenotypic plasticity: linking molecular mechanisms with evolutionary outcomes." Evolutionary Ecology 16(3): 189-211. -- Kim van der Linde at venus 14:57, 14 September 2006 (UTC)
thread_title: Phenotypic natural selection

message: I feel the example has now become too technical and is likely to put off non-biologists. (HGT etc. are subtleties not really key to natural selection). Does anyone else agree? — Axel147 17:51, 11 September 2006 (UTC)
replies: text: I didn't mean to play down HGT. I just didn't want to scare off the layperson. Maybe it should be mentioned additionally elsewhere in the article? But I don't think the organismic trait 'ability to receive insertion elements' is generally favourable for reproductive success. Insertion elements are preserved, I think, not just because of the reproductive advantage they confer on organisms in which they are housed; they are preserved (partly at least) because of their ability to jump. In other words this is no longer a clear cut example of natural selection acting at the level of the individual phenotype (of the organism). And as such not a clear example of natural selection as described in the opening paragraph? — Axel147 19:55, 11 September 2006 (UTC)

text: Aye, finches would be my pick.  I wish I had time, but I don't. Best Regards, Pete.Hurd 19:30, 11 September 2006 (UTC)
thread_title: Is the example too technical?

message: The picture of the peacock contradicts the peacock article which states in the gallery "The White Peacock is frequently mistaken for an albino, but it is a colour variety of Indian Blue Peacock"
:The file name has it as an albino. - Samsara (talk • contribs) 21:43, 10 October 2006 (UTC)
thread_title:  Picture 

message: It does not state anywhere in the article that this is just a theory and that it has never been proven. That is why I put the weasel word tempelate on it. Everything in the article speaks as if all this is fact and proven when it really has not been proven yet. 69.22.216.252 02:30, 5 November 2006 (UTC)
replies: text: It isn't just a theory, whatever you mean by that. The scientific evidence for the scientific facts of natural selection are well presented in the article. It would appear that you have a mis-understanding of science - or are simply trying to push some religeous POV? Weasel tag goes as it's placement amounts to little more than vandalism. Vsmith 02:44, 5 November 2006 (UTC)
replies: text: Actually there are a huge number of studies demonstrating natural selection, so natural selection is a fact. You could argue is it significant in evolution. There are a large number of studies correlating natural selection with evolution, however there are studies indicating other factors can come into play and/or evolution can be unpredictable.GetAgrippa 19:41, 10 November 2006 (UTC)
replies: text: With all due respect, Vsmith and GA, you are allowing a nobody to waste our time.  The article itself explains these things.  I would say that any registered Wikipedia editor should have no qualms simply reverting nonsense edits from anonymous users who clearly have neither read nor understood the article itself.  Let's save this talk page for talk among people who are serious and deserve to be taken seriously.  For me, actually having read the article is an obvious minimum standard. Slrubenstein   |  Talk 13:42, 12 November 2006 (UTC)

text: Nope, it isn't just correlational, there's experimental and mechanistic support.  Guettarda 20:53, 22 February 2007 (UTC)
replies: text:  Just from the use of "just a", it would be fair to dismiss this anonymous user. If it were a hypothesis, then perhaps yes. But that is not the case. I suggest that you pay a visit to TalkOrigins if you are unsure of terminology or the current standing of evolutionary theory.--THobern 12:50, 13 June 2007 (UTC)
thread_title:  Just a theory 

message: ( Who is Charles Darwin?)
Appeared after a heading resulting in the heading not displaying correctly.
The line seems meaningless so I removed it
Paul Hjul 10:00, 5 December 2006 (UTC)
thread_title:  rv - line "Who is Charles Darwin?" 

message: I began to write a section about the effects of natural selection not taking place, but I realized some of the examples I intended to use were natural selection. Here I'm talking about situations where natural selection has little impact on a trait due to it being of neutral fitness contribution. One example I planned to use was the eyes of moles - how they have diminished due to lack of use. Really it's more a case here of natural selection favoring the removal of the eye as 1) It can be infected by all the dirt and debris in the mole's environment, and to a lesser extent 2) Construction and maintenance of the organ uses up precious energy (here a much weaker force than that of infection, no doubt). However, even without these forces of natural selection favoring the absence of the eye, there is still the force of entropy which simply tends to favor randomness - general loss of orderly arrangement. Even without natural selection there is a tendency to break down progress made in a certain direction, so for example mutations of the eye that were not injurious in other ways would make no difference to the survival rate and hence the careful order of the eye would tend to break down over time without any selective forces acting on it.
(Another force I've neglected to mention is sexual selection, which would act as a backup against the forces of entropy because animals seldom choose partners with strange mutations, even if they aren't deleterious to the species).
I'll try to compose a better section when I have some time, hopefully with some more examples. Comments on the topic are most welcome. Richard001 09:39, 2 January 2007 (UTC)
replies: text: Agree in principle, but please don't equate entropy with randomness: as the linked article states, "Spontaneous changes tend to smooth out differences in temperature, pressure, density, and chemical potential that may exist in a system, and entropy is thus a measure of how far this smoothing-out process has progressed." The "orderly arrangement" is part of a nineteenth century analogy attempting to visualise the motion of energetic molecules as "disorder", and is completely superseded by quantum mechanics. .. dave souza, talk 11:00, 2 January 2007 (UTC)
replies: text: Be careful of introducing material the "seems" correct, but isn't.  It turns out that in lab colonies of Drosophila, at least, there is mate selection favoring the oddballs.  I have not looked for other examples of this phenomenon, so cannot say how common it is. Genetics411 15:10, 3 January 2007 (UTC)

text: I don't really agree in principle. By defintion this is not natural selection but evolution by another mechanism. I think it is better to cover this in the evolution page rather than here. — Axel147 13:21, 8 January 2007 (UTC)
thread_title: Evolution without natural selection

message: I've removed the preceding passage from the article because of undue weight; it is represents a tiny minority view. Wolfram's ANKOS (A New Kind Of Science) has not been well received in the scientific community at all: [http://www.math.usf.edu/~eclark/ANKOS_reviews.html A Collection of Reviews of ANKOS
and Links to Related Work]. FeloniousMonk 17:04, 14 January 2007 (UTC)
thread_title:  Removed from the article 

message: "The evolutionary process of divergence, which ultimately leads to the generation of new species, is thought to occur usually without any gene exchange between the diverging populations. However, until the recent growth of multi-locus datasets, and the development of new population genetic methods, it has been very difficult to assess whether or not closely related species have, or have not, exchanged genes during their divergence. Several recent studies have found significant signals of gene flow during species formation, calling into question the conventional wisdom that gene flow is absent during speciation."Curr Opin Genet Dev. 2006 Dec;16(6):592-6. Epub 2006 Oct 19. Recent advances in assessing gene flow between diverging populations and species.Hey J. Further while I agree gene flow is homogenizing, it can be useful as gene loss is significant in many examples of speciation and HGT and Hybridization can rejuvenate a genome and generate novelty and speciation. The last year has been a boom for HGT and hybridization studies. I guess we need to address this for NPOV. GetAgrippa 20:46, 15 January 2007 (UTC)
thread_title: Gene flow effects on speciation

message: dave souza, alright, this seems kind of desperate (for me to post a bunch of page numbers), but at your request here are some citations which you can check out yourself …
p.14
“Evolution Theory.  The Darwinian theory of evolution by natural selection is often assumed to explain the complexity we see in biological systems – and in fact in recent years the theory has increasingly been applied outside of biology.  But it has never been at all clear just why this theory should imply that complexity is generated.  And indeed I will argue in this book that in many respects it tends to oppose complexity.…..”
p.383 – 432.   Most of Chapter 8 starting with Fundamental Issues in Biology showing something other than Natural Selection as responsible for adaptations.
p.383
“… And in fact what I have come to believe is that many of the obvious examples of complexity in biological systems actually have very little to do with adaptation or natural selection.  And instead ….”
p.391-392
“ … So why should this be? My guess is that in essence it reflects limitations associated with the process of natural selection.  For while natural selection is often touted as a force of almost arbitrary power, I have increasingly come to believe that in fact its power is remarkably limited.  And indeed, what I suspect is that in the end natural selection can only operate in a meaningful way on systems or parts of systems whose behaviour is in some sense quite simple. …”
He goes on to justify his belief natural selection is a force of limited power into the next pages arguing that natural selection is not sufficient to produce complexity we see in nature.
p.393
“In a sense it is not surprising that natural selection can achieve little when confronted with complex behaviour. ….”
“It has often been claimed that natural selection is what makes systems in biology able to exhibit so much more complexity than systems that we explicitly construct in engineering.  But my strong suspicion is that in fact that main effect of natural selection is exactly the opposite: it tends to make biological systems avoid complexity and be more like systems in engineering.”
p.397 Criticism of Natural selection as a predictive theory …
p.400 Constructing growing plants by means other than natural selection …
p.402-404 Constructing the shape of leaves by means other than natural selection …
p.408-410 Constructing the arrangement of leaves by means other than natural selection ..
p. 411 Constructing plant geometries by means other than natural selection …
p.414-417 Constructing the Shape of Shells by means other than natural selection …
Just a comment on Wolfram’s views of Biological Evolution found on p. 414-417:  It was Stephen Jay Gould who argued in his doctoral thesis on shells that natural selection is necessary to pare down the evolution of thousands of potential shell shapes in the world to only about the half dozen that actually exist in shell forms.  He used this as evidence of natural selection.  In these 3 pages Wolfram proves mathematically that in fact there are only six possible shell shapes possible in the world, and all of them exist proving Gould wrong.
p.423-425 Constructing pigment patterns by means other than natural selection …
p.842 when a process repeatedly makes random modifications and then applies natural selection, only fairly simple aspects are yielded (i.e. diversity does not result).
p.861 Natural Selection is identified as the basis of many phenomena in biology …. But biology still continues to concentrate on very specific observations with no serious theoretical discussion on complexity.
:You can see his above comment to be true by witnessing the resistance being applied to including a single criticism of Natural Selection in this article.
p.1001 In the history of Natural Selection (Fundamental Issues of Biology) Wolfram comments that continuing controversies with religious accounts of creation have caused biologist’s to adamantly refuse to consider anything other than natural selection in shaping biological systems.
:We don’t see a touch of that here do we?
p.1001 cont.  In the late 1980’s natural selection had become firmly enshrined as a force of practically unbounded power, assumed-through without specific evidence to be capable of solving almost any problem and producing almost any degree of complexity.
:This sounds like it might be noteworthy in this article.  A credible scientist placing limits on the value of a theory.
p.1002 Genetic programs:
“… there is no uniform correspondence between sophistication of organism and length of genetic program …”
:Ok he’s not directly criticising natural selection here, but its deficiency is implied.
p.1002 Natural Selection section suggests that more work needs to be done to map out the exact limits of the usefulness of the theory of natural selection.
p.1104 Growth in plants section asserts that diversity in plant growth patterns in best explained by rules (not natural selection)
p.1104 Branch patterns in plants suggests the same …..
p.1007 Shape of Cells, Symmetries in Nature, Isotropic growth ……
p.1008 Shape of Antlers also …..
p.1008 Shapes of shells suggests the same again …
p.1009 Embryonic Development ….
p.1011 Growth of Tumours, Pollen, Animal Behaviour …
p.1012 Pigmentation patterns does too ….
Etc. through for hundreds of pages (not all dealing with natural selection)
1185 Molecular Biology: … DNA as biological artifacts having very simple origins .. (Same with some animals traits such as the mollusc shell, or the radiolarian skeletons etc)
I’ve provided at least some evidence that Wolfram is not glossing over natural selection.  To be fair he is equally rigourous with other fields.  Clearly, he was critically examining natural selection - and this makes his views pertinant.  My point again, is that a credible scientist has raised criticisms about the value of, and placed limits on the subject of this article.  Reading it over the not a single critical viewpoint is included.  This is either because natural selection is beyond criticism or their are none.  I don't know about the former, but I do now about the latter.  So I suggest at least let us include Wolfram’s view as being possibly the only valid criticism raise so far.WikiRat1 03:48, 21 January 2007 (UTC)
replies: text: Pages in what? Mathematical principals apply to biological systems because of physical laws-like the law of laplace in blood vessels or Murray's law in dividing blood vessels. I don't see that providing other possible mechanisms PROVES natural selection is wrong. It only proves that mathematical models can mimick natural selection. Of course work needs to be done in natural selection that is why the thirty year study of Darwin's finches showed evolution was unpredictable. Constructing pigment patterns is not based on mathematics but genetics and environment-phenotype. To say there is more than one way to achieve an end does not demonstrate which path is for real. Nothing against his work but I don't see that is appropriate for a encyclopedia article. As you state they are his views which is POV, and just cause a mathematical model can mimic natural selection it in no way proof of its existence or significance. There are numerous models for all kinds of biological phenomena just cause they may work does not prove significance. Has he designed experiments to test his hypotheses or is it just theoretical? I too have pushed lesser know areas of interest to be added to this article, but it is an encyclopedia and it just doesn't add to the subject so I backed off. Besides there are plenty of examples of the influence of the environment on developmental and phenotypic plasticity and stress induced mutagenesis. The influence of the environment on the development and life cycle of about every form of life you can think of has been demonstrated so it is difficult to deny the impact of the environment on molding life. Further complex behavior such that competition, predator-prey, etc. add another dimension of environmental influence. There is significance evidence to indicate that environmental change has influenced the tempo of evolution and speciation. GetAgrippa 04:49, 21 January 2007 (UTC)
replies: text: This seems to be very much a strawman argument against alleged claims that natural selection creates complexity, rather than disputing fundamental tenets. There appear to be no such claims in this article. Wolfram’s view of natural selection promoting repeatable simplicity rather than maximum mathematical complexity, thus producing relatively simple engineering style contrivances, fits well with homology. Similarly his view that variability and complexity is greatest in features not subject to selective pressure accords with the theory as I understand it. Gould does not seem to be mentioned in the book, and in any case it would hardly be astonishing if modern computer based studies found flaws in work that Gould presumably did before 1967. Wolfram’s text is repeatedly qualified by terms such as "what I suspect" and "seems likely" – when Wolfram or someone using his approach produces peer reviewed papers on biology giving detailed clarification of these vague opinions, then the work will merit appropriate treatment in this overview of natural selection. However a balanced article incorporating Wolfram’s ideas together with relevant assessment or criticism could make a useful main article which could be linked from the Information theory section, and allow a suitably brief summary style mention here. .. dave souza, talk 10:27, 21 January 2007 (UTC)

text: Just to clarify, I was thinking of an article about Information theory and evolution or something on these lines, to include more than Wolfram’s contribution. However that may be too closely associated with Information Theory and Creationism which isn't the aim, so the title needs some thought. .. dave souza, talk 18:25, 21 January 2007 (UTC)

text: I endorse Dave souza's suggestion of a "a suitably brief summary style mention" (I suggest c1 sentence) to link to another article (I suggest linking to A new kind of science, in the absence of an Information theory and evolution article, should such article come to be, then redir then, but I don't think a specific article needs to be created if the essence of the material exist in the A new kind of science article). Also note that GetAgrippa is correct in pointing out that there's nothing inherent in Nat Sel leading to greater complexity. Pete.Hurd 19:17, 21 January 2007 (UTC)
thread_title:  Some Citations 

message: Just a reply to all this talk about Wolfram, and self-organisation in general. It is a fact that rich, complex dynamics do arise "spontaneously" in certain systems, without any natural selection or evolution. It's called self-organisation, and it is not new. At any rate, it certainly doesn't make natural selection "unnecessary" to explain the complexity of living beings, because it does not explain adaptation. Under the proper conditions, brute matter will spontaneously create a range of diverse forms - but very, very few of them will result in anything useful. Complex, well-adapted organs cannot be explained by spontaneous assembly. Self-organisation makes it easier for natural selection to come up with complex designs, but does not replace it. 
Complexity is not just the result of evolution by natural selection alone, or self-organisation alone. If there were no natural selection, adaptive complexity would be unheard of. If there were no self-organisation, then the amount of complexity available for evolution to "play" with would be vastly diminished; for example, building well-organised regulatory networks would be much more difficult without the "self-organising" properties of random boolean networks discovered by Stuart Kauffman. 
In any case, I'm not sure this page is the place to mention these things. This is an article about natural selection, not about the emergence of complexity in nature. The respective roles of self-organisation and natural selection could be discussed in other pages. No? --Thomas Arelatensis 14:05, 26 January 2007 (UTC)
replies: text: No doubt others will accuse Wolfram of rediscovering self-organisation as you have.  Unfortunately our views as editors of Wikipedia is to ensure that balance, objectivity and neutrality all somehow influence the development of articles.  Therefore, POVs are represented in articles that we, ourselves may agree with.  Nonetheless for the sake of reflecting the current debates about things our own personal view points are not sufficient to exclude or otherwise monopolize content.  In this case, you can the reaction to including Wolfram's views, and how animated it got.  Similarly, a debate is festering between bioinformaticists and biologists on Wolframs views. Wolfram asserts that Natural Selection is unnecessary given his views views of complexity.  Undoubtedly, some of his critics will put their disagreement to peer review, but I suggest that I am having a hard time finding any who have refuted him anything more than casually. Wolframs' views are certainly out in the open now, a list of references has been published above about his views dealing with natural selection, so that others may check out my claims about him (to ensure I am representing his view faithfully).  Because Wolfram himself opposes the scope or power of Natural Selection, I can personally think of no better article to include his criticism (and as I pointed out above, does this article really contain any other valid criticisms about the subject?).  I am glad you disagree with Wolfram.  Perhaps it will motivate you to assist me in finding scholars who have examined his criticism.  If you can find some scholarly sources accusing Wolfram of rediscovering self-organisation, or even better outright refuting his criticism of Natural Selection, could you kindly include it here also? WikiRat1 05:08, 2 February 2007 (UTC)
replies: text: Have you examined these? Pete.Hurd 05:29, 2 February 2007 (UTC)

text: This Science article review was similar in tone:Science 4 October 2002: Vol. 298. no. 5591, pp. 65 - 68 DOING SCIENCE: Is the Universe a Universal Computer?A review by Melanie Mitchell*. In relation to Natural selection the review states: "Less compelling are Wolfram's speculations on natural selection. He contends that because the generation of complexity is so common in simple cellular automata, it must be common in nature as well and, therefore, natural selection is not needed to create complexity in biology. In his view, biological systems are complex merely because evolution has sampled a huge number of simple programs and these often give rise to complex behavior. Wolfram offers no convincing evidence for this claim, nor does he discuss where these programs are implemented--at the level of the genome? of cells? Although cellular automata provide plausible models of biological pigmentation and some aspects of morphology, there is as yet no compelling link between simple programs and complex biological systems such as the brain, the immune system, or cellular metabolism. On the contrary, it is increasingly clear that notions of selection and adaptation are crucial for understanding such systems."
The review gives the impression he tends to bloviate, he is dogmatic with narrow views discounting other concerns with weak arguments, and fails to provide few real advancements or real proof. Although they do say positive things that his research is useful. Just not grandiose as Wolfram suggests. I guess we need to add some kind of statement and references to detract from Wolfram's beliefs for NPOV. GetAgrippa 05:45, 3 February 2007 (UTC)

text: Fine by me the way it is, but "if it is not related to Natural selection [...] why have it?" yep, fine by me if the paragraph goes entirely. Pete.Hurd 00:09, 4 February 2007 (UTC)
replies: text: Axel I apologize for speaking in your behalf- putting words in your mouth, but it sounded like the voice of reason and I thought it was worth mentioning on the Talk. There is a disconnect between his idea as a mathematical model and biology-he doesn't propose where his ideas fit in, and he does propose a form of natural selection as he believes nature has selected through the possiblities to use simple programs to generate complexity. I think the Science review excerpt I posted says it well and is relatively complementary compared to those that Pete Hurd posted. Most appear to think his reference to natural selection was just an egomaniacal rant rather anything with substance. Wasn't there some mathematician who "proved" the existence of God by mathematical proof or model or discovery (or is it some academic legend). I don't know why that comes to mind. GetAgrippa 02:47, 5 February 2007 (UTC)
thread_title: The respective roles of natural selection and self-organisation in the emergence of complexity.

message: Sorry to be a bit slow here, but when registering to look at the website I tactfully asked a couple of questions and forgot to check that mail account for a while, Here's the first response:
They helpfully sent a more detailed response: 
Hope this helps, dave souza, talk 19:03, 20 February 2007 (UTC)
thread_title: Response from Wolfram Science Group

message: Natural selection still does not have any criticism of the idea in it.  There should at least be on paragraph near the bottom labelled criticism.  Steven Wolfram is not the only critic.  I have heard complaints such as Selection just reduces the genetic diversity in a population.  Even if a criticism is wrong, if it common it deserves a mention. GB 10:03, 12 February 2007 (UTC)
replies: text: However, it is not common, relative to the support. Undue weight applies. Adam Cuerden talk 10:49, 12 February 2007 (UTC)

text: The laws of thermodynamics also have their "critics" (namely the "free energy" enthusiasts), yet there is no "Criticism" section in the related articles. Similarly, not a word on "Einstein debunkers" in the Special Relativity article. --Thomas Arelatensis 13:45, 13 February 2007 (UTC)

text: By the way, of course selection reduces genetic diversity within a closed population (though it can also maintain it by enforcing a blance between different sub-populations), but it does not "just" do that. It does it asymmetrically, by retaining and propagating newly found, well-adapted characters. This allows for gradual accumulation of small (or even not-so-small) improvements, the secret of evolution's power. Mutation and speciation -> diversity, natural selection -> adaptation and improvement.
--Thomas Arelatensis 13:45, 13 February 2007 (UTC)
replies: text: All the talk of Mutationism is that proposed by Thomas Morgan who dismissed natural selection as a minor process and he proposed mutations as the driving force for evolution. Of course mutations don't have to precede evolution, as epigenetic heritable change driven by the environment can isolate phenetically a species long before a genetic change and reproductive isolation (biological speciation). Also hybridization and HGT can promote speciation which is not mutation. GetAgrippa 17:26, 13 February 2007 (UTC)
replies: text: Mutations are a driving force behind evolution, but I think natural selection is the driving force behind adaptive evolution. That seems to be the difference. — Axel147 14:39, 21 February 2007 (UTC)
thread_title:  Still not NPOV 

message: Also the example of antibiotic resistance in golden staph is not that great an example.  Much of antibiotic resistance in bacteria is the result of horizontal gene transfer between different bacteria, rather than by mutation. GB 10:03, 12 February 2007 (UTC)
thread_title: resistance

message: Overly long, disproportionately footnoted... reeks of old edit war. Can anyone who's been active on this article longer than I've been watching recall why this is and whether it needs to stay as long as it is? Opabinia regalis 07:53, 6 March 2007 (UTC)
replies: text: Ummm, IIRC, Axel held that "Natural Selection" required phenotypic change in subsequent generations. Others (Kim, Samsara, myself) felt that such a definition made "Natural Selection" & "Evolution" synonymous when they were in fact different concepts, and Nat Sel applied only to the first half, the selection, and not the response to selection.  Yeah, old edit war. Some of your recent edits to the lead seemed to relate to this.  Cheers, Pete.Hurd 17:10, 6 March 2007 (UTC)
replies: text: Hmm, I don't know about 'synonymous', but I agree with your definition, as you've described it. I wasn't trying to stir up definitional issues in the lead, but it did need to be a better summary of the article. At any rate, I think this section needs a good trim; it impedes the flow from basic to more complex, and... well, anybody who knows how wikipedia articles get written can see what caused it ;) I'm always a month behind on these collaboration things, but I thought I should do something on this article, since I nominated it for SCOTM and all. Opabinia regalis 02:39, 7 March 2007 (UTC)
replies: text: Trim as you see fit, Cheers. Pete.Hurd 03:06, 7 March 2007 (UTC)
replies: text: Seconded. Samsara (talk • contribs) 03:43, 7 March 2007 (UTC)

text: Yes indeed it was an old edit war. But at least KimvdLinde and I agreed on one thing — that there are two widely used definitions with an important difference betwen them. KimvdLinde asserts that natural selection can occur without heritability: in this case there would be no evolutionary response. On the other hand I assert that heritability is a pre-requisite and without heritability it cannot happen. My version does not require evolutionary repsonse (because the effects could be cancelled out by other 'evolutionary forces') but requires the possibility of it. (It is close to being synomymous with 'evolution by natural selection' not evolution per se.) The article seems unwittingly to have moved back towards my preference by including the word 'heritable' in the opening line. — Axel147 13:44, 20 March 2007 (UTC)
thread_title:  Nomenclature section 

message: In case anybody misses it in the thicket of header banners, I've put this article up for peer review. I've been picking at it for the last couple of weeks, but I really think it could use some fresh eyes, especially from non-biologists. Opabinia regalis 03:45, 18 March 2007 (UTC)
replies: text: Specific question arising from the quite lengthy peer review: should anything be done with the last sentence of the lead, which mentions that some genetic diversity is better explained by genetic drift and the neutral theory of molecular evolution? On the one hand, it may be distracting to readers unfamiliar with the subject to mention a related theory without explaining it, and could be a wedge for people to try to downgrade selection to more 'just a theory, so creationism might be true!' nonsense. On the other hand, it's an important point from a molecular perspective. Any thoughts from the rest of the watchers of this page? Opabinia regalis 03:39, 22 March 2007 (UTC)
replies: text: I'm fine if it moves out of the lead into a later section, such as the "Selection and genetic variation" section. I think it'll have to expand a bit.  I think mentioning it in the lead and not addressing it further in the main body is kinda poor. Pete.Hurd 04:42, 22 March 2007 (UTC)

text: I think it's important to somehow point out the distinction between evolution (change in genetic makeup of populations, which can be adaptive or random) and natural selection (one of the factors which cause this change).  Confusion between the two is rife. Natural selection is one of the driving forces of evolution - arguably the most interesting one, because it explains adaptation. There are other forces, such as genetic drift. I'm not sure about mentioning the neutral theory, which AFAIK is purely molecular and explicitly does not consider phenotypic changes (does it?).--Thomas Arelatensis 13:11, 22 March 2007 (UTC)
replies: text: I think it's more true to say 'does not explicitly consider phenotypic change'. It was certainly formed for molecular data, and has been interpreted as being most relevant in non-coding regions and in synonymous substitutions, but it doesn't exclude the possibility of neutral changes that have only entirely irrelevant effects on phenotype. Opabinia regalis 02:49, 30 March 2007 (UTC)

text: On an unrelated note, does anyone know of a good, non-quantitative textbook that covers the material in the 'fitness' and 'genetical theory' sections? The text I have on hand (Rice) is very mathematical and not accessible to general audiences, so an additional recommendation to supplement the sources in those sections would be helpful. Opabinia regalis 02:49, 30 March 2007 (UTC)
thread_title:  Peer review request 

message: I know I have raised this before but there seems to be inconsistency in the use of phenotype/genotype now in the opening paragraph.
: 'Natural selection acts on the phenotype, or the observable characteristics of an organism, such that individuals with favorable phenotypes are more likely to survive and reproduce than those with less favorable phenotypes. If these phenotypes have a genetic basis, then the genotype associated with the favorable phenotype will increase in frequency in the next generation.' 
This implies an organism has one phenotype (not one for each characteristic) which is mapped to a single genotype. But how can the genotype increase in frequency unless I am producing clones of myself? Surely it's clearer to say genes (or alleles) increase in frequency? — Axel147 05:17, 21 July 2007 (UTC)
thread_title: Genotype

message: The Fitness section has some problems. Firstly no quotes, no sources, no citations.  
Secondly "Modern evolutionary theory defines fitness in terms of reproduction rather than survival." -This should be changed. Dawkins proposed DNA "gene reproduction" as a better explainer, and others in "modern evolutionary theory" have also moved away from simple "reproduction". Here's one reason why- in ants and bees and termites and other haplodiploid insects, the colonies are mainly composed of "sisters." The female workers and soldiers forgo reproduction so that their queen will produce sisters instead (brothers too, but relatively few). In other words, Evolution works for family members other than direct offspring. In fact in any creature, uncles and aunts, even cousins, can pass genetic material and their associated traits without reproducing.(through survival of nephews and nieces, etc) While it may seem a minor point at first, as stated now in the article, the whole theory breaks down the when any example of any creature forgoes reproduction for any reason(including humans)
Thirdly the sickle-cell anemia is potentially offensive as well as factually incorrect.  "as in extreme examples include many human genetic disorders like sickle-cell anemia"-- Sickle-cell anemia turns out to have great survival value in areas with high malaria infection.  This is why many descendants of Africans who lived in malaria ridden areas have sick-cell anemia.  Sickle cell disease is the most common inherited blood disorder in the United States, affecting 70,000 to 80,000 Americans. The disease is estimated to occur in 1 in 500 African Americans and 1 in 1,000 to 1,400 Hispanic Americans. (http://ghr.nlm.nih.gov/condition=sicklecelldisease)  So to call it an extreme example is, at best, misleading, and unfortunately, one could read into it a racist bias. This could be easily avoided.
I am going to edit out "extreme," for now, but the example itself isn't very good (unless someone wants to greatly expand upon how sickle-cell relates to "genetic fitness") 76.19.28.24 15:17, 23 July 2007 (UTC)
replies: text: I'm not sure what you're trying to say on these points.  Modern evolutionary theory does stick with reproduction as fitness.  However, if you're trying to discuss something more than fitness, I'm losing your message in the your commentary.  As for sickle-cell anemia, what are you trying to say?  Sickle cell anemia is a genetic disorder.  It might have some fitness benefit with malaria, but even so, non-sickle cell humans have advantages over sickle-cell carriers, even in malarial areas.  I don't think it's a "racial" comment whatsoever.  Orangemarlin 18:00, 23 July 2007 (UTC)

text: 'I wish, therefore to suggest to you the possibility of entirely avoiding this source of misconception in your great work (if now not too late)...by adopting Spencer's term viz. 'Survival of the Fittest'. This term is a plain expression of the fact; 'Natural Selection' is a metaphorical expression of it, and to a certain degree indirect and incorrect, since, even personifying Nature, she does not so much select special variations as exterminate the most unfavourable ones. ' 
It is clear that "survival of the fittest" was intended to apply to variations not to individuals. (Or perhaps it could be viewed as applying to lineages or 'races' consistent with Darwin's title of the Origin describing natural selection as 'the Preservation of Favoured Races in the Struggle for Life'.) It is so obvious that being the fittest individual, if this simply means living a long time, is not sufficient per se to propagate characteristics to the next generation it is hardly worth mentioning the point! Darwin in any case clears the matter up,  'I should premise that I use the term Struggle for Existence in a large and metaphorical sense, including dependence of one being on another, and including (which is more important) not only the life of the individual, but success in leaving progeny.'  — Axel147 12:03, 25 July 2007 (UTC)
thread_title:  FITNESS NEEDS REWRITING 

message: I note that this article doesn't even link to the slightly broader article selection, which is in a fairly poor state. Do we want to have this broader article? I'd probably be in favour of keeping it since heaping everything into this article and having nothing linking the other forms together is probably a bad idea. Selection can provide an overview of the subject, such as classification e.g. natural vs. artificial, stabilizing vs. directional etc, as well as levels of selection and other related topics. Another much smaller article is evolutionary pressure. Should this one be merged into selection? I'm not very familiar with the finer details of evolutionary biology so I'm not sure exactly how much potential this one would have. If it is kept as is, perhaps we should look at whether evolutionary pressure or selective/selection pressure is more commonly used, and consider moving it. Richard001 04:11, 28 August 2007 (UTC)
thread_title:  Selection and evolutionary pressure 

message: The Darwin's hypothesis section contains a fraudulent misquotation: I have called this principle, by which each slight variation, if useful, is preserved.
:The full quotation is:
I have called this principle, by which each slight variation, if useful, is preserved, by the term natural selection, in order to mark its relation to man's power of selection.  and the next paragraph
But the expression often used by Mr. Herbert Spencer, of the Survival of the Fittest, is more accurate, and is sometimes equally convenient. We have seen that man by selection can certainly produce great results, and can adapt organic beings to his own uses, through the accumulation of slight but useful variations, given to him by the hand of Nature. But Natural Selection, we shall hereafter see, is a power incessantly ready for action, and is as immeasurably superior to man's feeble efforts, as the works of Nature are to those of Art.
 
Darwin seems to imply that Natural Selection as some sort of nature selection force is superior to mans "feeble" efforts. His intent with the phrase Artificial selection also alludes to this. What confuses the matter is that nobody knows what was his or Spencer's intent with Survival of the Fittest. It could mean anything you want it to mean. Natural selection must be discussed in terms of Artificial selection and Survival of the Fittest since Darwin said SoF is more "accurate" and how it relates to "feeble man" and "nature's power of selection" as he put it in the passage dealing with Artificial Selection. It is not clear what was Darwin's intent with these three phrases and how they relate. He seems to be invoking nature as some sort of conscious "selection" force, unless there are passages that proves that it is not so. 
:from http://www.gutenberg.org Darwin used artificial selection only once in the book Origin of Species
Slow though the process of selection may be, if feeble man can do much by artificial selection, I can see no limit to the amount of change, to the beauty and complexity of the coadaptations between all organic beings, one with another and with their physical conditions of life, which may have been effected in the long course of time through nature's power of selection, that is by the survival of the fittest.
I propose that we at least cite the full sentence as written down by Darwin? TongueSpeaker 14:27, 12 September 2007 (UTC)
thread_title:  Darwin's hypothesis section fraudulent misquotation 

message: This sentence appears in the 'Fitness' section. I don't understand what the very last 'or unfavorable...' clause is supposed to mean.
" Since fitness is an averaged quantity, however, it is possible a favorable mutation may arise in an individual that does not survive to adulthood for unrelated reasons, or unfavorable mutations to have a for unrelated reasons."Johnor 01:50, 1 October 2007 (UTC)
replies: text: Looks like the author didn't get out what they meant to say: . It was an IP so I can't really contact them, but I presume they were saying unfavourable mutations can survive among mostly 'good' genes, as long as there aren't too many, and they aren't too harmful. Richard001 04:19, 1 October 2007 (UTC)
thread_title:  Clarification needed