User talk:KimvdLinde/Natural selection

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This page shows a proposed new version of the article on Natural Selection. This has been developed using parts of the existing version by Kim van der Linde and Gleng, following the discussions on the Natural selection talk page. We have tried to produce an article that will be both clear and rigorously accurate. If there is general agreement that this version is an improvement over the existing version, then we will replace it. Please put any comments and criticisms about this proposed new version on [[this Talk page, and in particular please indicate your support for, or opposition to, replacement of the existing version. Please do not edit this version except for any minor corrections at this stage. Kim van der Linde ^{at venus} 05:13, 13 May 2006 (UTC)

I just got this message: "Thumbs up from me. If it comes to a vote, please include my comment (I really won't be around after today)." User:Guettarda 23:07, 13 May 2006 (UTC) (Retrieved from "http://en.wikipedia.org/wiki/User_talk:Slrubenstein")

Nice, and let see if the rest thinks the same (I expect some will be away for mothers day) and if the tone remains the same, lets replace it. I will also get a outside review for a non-wikipedia biologist who I respect for his insights. Kim van der Linde ^{at venus} 23:21, 13 May 2006 (UTC)

Contents 1 some comments 2 Illustrations 3 Quotation marks and other emphasis 4 References 5 Done? 6 what is born out of spite... 7 Axel147 on new version

[edit] some comments

Italic is my response. Kim van der Linde ^{at venus} 16:02, 14 May 2006 (UTC)

looks good. some things to consider:

• the bit about resequencing MRSA is off topic
  • Agreed and removed.
• you've covered this, but maybe make it clear: natural selection does not necessarily lead to adaptation
  • Agreed and done.
• natural selection does not always enhance the fitness of a population (e.g., selfish genetic elements -- Alu elements in the human genome)
  • Agreed and done.
• direct selection "speeds up" change while balancing selection "slows down" change
  • I would say it stronger, balancing selection does not lead to change at all, it just conserves. Added as such.
• natural selection can adapt populations and build adaptations, which may deterioriate in the absense of selection
  • Agreed and added.
• the natural selection syllogism is good to include (organisms are variable, some of that variation is heritable, overproduction of offspring, but stable populations)
  • I will think about how to deal with this, as there is the issue of the two definitions for NatSel that are used. The sequence you give focusses on the inclusive def, which we not really use here.
  • What you describe here is in my pinion more evolution by means of natural selection. In the first two paragraphs under that header, this is exactly explained, although I can see the addition of many offspring (overpopulation) and stable populations.
• the fact that fitness is more generally understood today than it was by Darwin -- it's more than survival -- should be pointed out to some extent; at least point out that fitness is more than survial
  • Was already explained, but I have added that it was in the past more resitictive.
• a little bit of math could be mentioned... maybe
  • Personally, I would leave it out. I think this would be a great seperate article but makes this article to long and to complex.
• the controversy over the extent to which the history of life can be accounted for by natural selection
  • I leave this point to someone else, as I do not feel comfortable enough to discuss this in detail. But i agree, it should be mentioned. Maybe we can ask he editors of the creationism and such pages as they deal with this contrioversy all the time.

Think maybe what is needed is just point to the problems with "Origins of life" i.e. that this is still unexplained?Gleng 18:44, 14 May 2006 (UTC)

Mmm, I was thinking of the debate about the extent to which life was determined by natural section to have taken the forms that it has as compared to alternative forms, such that if you "wind back the clock" (that's not quite right) you'd get a different outcome. Gould was a proponent of the different outcome view. --Rikurzhen 21:50, 14 May 2006 (UTC)

Good point, but maybe beyond this article - the contingent path of evolution is as much about the role of catastrophic environmental change, random mutation, accidents of survival and founder effects as natural selection. Certainly worth an allusion, but to cover in depth would be a significant diversion. I'll look for a quote from Gould perhaps, who had a good way with words on this.Gleng 10:54, 15 May 2006 (UTC)

I am aware of that discussion, but I do not know enough to add something about it. Also, I think this is more an evolution issue than a NatSel issue. Generally, NatSel on the same trait with the same pressures and the same genetic context will result in comparable solutions. It is the wider context that makes it different, such as random mutations (do the same mutations occur, if not, NatSel will have a different result (see for example the body size clines in D. melanogaster in Australia and South America who had different mechanistic solutions for the same problem and resulted in the same pattern at the phenotypic level. Kim van der Linde ^{at venus} 13:18, 15 May 2006 (UTC)

- but there are never the same pressures (because the environment is not independent of the ecosystem, and never the same genetic context. Species attain local maxima of fitness, not a global maximum, and slightly divergent paths across the landscape might take a species to a quite different local maximum, so re-run the tape and everything might be different. Anyway, I think we agree, too much to take on for this articleGleng 13:30, 15 May 2006 (UTC)

Exactly, it is evolution, which includes all those aspects, and NatSel is just an aspect of it. Kim van der Linde ^{at venus} 13:54, 15 May 2006 (UTC)

--Rikurzhen 00:12, 14 May 2006 (UTC)

Thanks a lot for the comments. They seem more accents than anything else.Kim van der Linde ^{at venus} 16:02, 14 May 2006 (UTC)

All great points to be included; thanksGleng 11:06, 14 May 2006 (UTC)

[edit] Illustrations

Hi Kim et al.,

It looks engaging thus far. The illustration (resistance evolution) came out very similarly to what I had imagined when making the suggestion - well done and many thanks for taking the time to create it! Figure 2 seems to be missing survival selection during the reproductive period, but it's a nice figure otherwise.

It's nice that the passage on Lamarck at least partly incorporates Michael T. Ghiselin's view. I'll post more comments as I progress through the document. - Samsara (talk • contribs) 11:27, 14 May 2006 (UTC)

[edit] Quotation marks and other emphasis

As you may have seen from my suggested edits, I don't see any grounds for distinguishing between double and single quotes, unless double quotes are to be reserved for literal quotations from historical sources. In any case, it may be worth considering whether phrases in quotes should be replaced by italics on all occasions, and whether some terms should be in bold font. - Samsara (talk • contribs) 11:37, 14 May 2006 (UTC)

I personally think quotes (and foreign words) should go in italic between double quotes, and emphasizing should be in single quotes. But I have no strong opinion about this. Kim van der Linde ^{at venus} 15:23, 14 May 2006 (UTC)

I try to use double quotes for identifying quotations, single quotes for identifying definitions or unconventional uses of words, and italics for added emphasis whether in quotes or not (and foreign words). Hard to keep consistent, but I agree there should be consistency, whatever convention is adopted, and have no strong feelings about which convention is adopted. There are a few places I'd favour the use of bold, but if overdone it gets ugly. Gleng 15:36, 14 May 2006 (UTC)

I think consistency is the main things. I think what you propose is good. We can tinker around with that. Kim van der Linde ^{at venus} 17:06, 14 May 2006 (UTC)

[edit] References

I'm also very pleased to note that the reference count has increased from 7 in the original to 15 in your new version of the article! (See Wikipedia:WikiProject Unreferenced GA.) Several references were dropped in the process, these are:

• Nachman, M.W. & Crowell, S.L. 2000. Estimate of the Mutation Rate per Nucleotide in Humans. Genetics 156, 297-304.PMID 10978293
• Siller, S. (2001). Sexual selection and the maintenance of sex. Nature 411: 689-692
• Lewontin, R. C. (1997). Dobzhansky's genetics and the origin of species: is it still relevant? Genetics. 147(2): 351-355.PMID: 9071586

Samsara (talk • contribs) 11:44, 14 May 2006 (UTC)

Yup, a large section was created from the bottum up, without using anything of the old stuff. The first reference should remain out because mutation rates are not mentioned in detail as it opens a can of worms such as variation between species, neutral mutations (no-coding and synonymious in coding), functional genome, effective population size, etc etc etc. The other wtwo can be reinserted at appropriate places, and I definately want to add more references when it developes. Kim van der Linde ^{at venus} 15:28, 14 May 2006 (UTC)

I would say that once you are satisfied you have incorporated/responded to Rikurzhen's points (and unless FrankWSweet or Graft object) you should make this the actual Natural Selection page. Slrubenstein | Talk 16:04, 14 May 2006 (UTC)

O yes, as soon as it seems that we get stable, I will paste it over, archive the talk page and such to save the discussion with the page. There will be some discussion of Rikurzhen comments, but they are mainly clarifications. Kim van der Linde ^{at venus} 16:27, 14 May 2006 (UTC)

[edit] Done?

I think we are done (for the moment). There is always new stuff, and the article is never finished. If there is no objection, lets plant it over. I think I will move this page to a subpage of Natural selection for example Natural selection/development to preserve the history of this new page. We can than copy and paste the content over the old NatSel page. Any objections? Kim van der Linde ^{at venus} 00:40, 16 May 2006 (UTC)

[edit] what is born out of spite...

"A well-known example of natural selection is the development of antibiotic resistance in microorganisms."

let's dissect the very first sentence above: "an example of selection is the development of antibiotic resistance..."

kim, i thought you aggreed that selection is not evolution. !? now the whole new article is full of such high-school-level imprecisions and sloppy formulations.

and, posibly more serious, the new article is mainly about evolution !

everybody should welcome additions and revisions to the existing article as long they are done orderly and carefully.

but one must correct any imprecisions, and one must refocus back to selection any additions that focus mainly on evolution.

note that i am an evolutionary biologist but i couldn't care less about selection for scientific reasons that are not simple.

however, the article about selection must be about selection, i.e. about the generation of fitness differences.

Marcosantezana 04:21, 16 May 2006 (UTC)

I have seen no spite in anything that Kim has said or done. I am a biologist (and mathematician) but certainly not an evolutionary biologist, though I guess that doesn't make me immune from spite. Douglas Futayama is an evolutionary biologist though. Here is part of what he said when asked to give an example of natural selection:

"ActionBioscience.org: Could you give us an example of natural selection at work in the recent past? Futuyma; There are so many examples of that! ....the single greatest crisis in medicine: antibiotic resistance. The fact is that enormous numbers of the most dangerous bacteria and viruses have evolved to be resistant to the antibiotics or other drugs that used to be effective against them." The link to that interview is in the new version of the article.

I wanted to see an article that was clear, interesting and accurate. I felt that the old version was none of these. The new version will no doubt get better, provided editors do what is always needed, discuss their edits on Talk pages to establish reasonable consensus before implementing major changes. Isn't that what we have been doing here?Gleng 08:36, 16 May 2006 (UTC)

I respond later longer, but your Appeal on Authority is completly misplaced. I think it is very nice of you to pretty much dismis all standard textbooks for biology students regarding natural selection. Furthermore, you do not own the article. Kim van der Linde ^{at venus} 12:03, 16 May 2006 (UTC)

I have decided to not respond to Marcos in a longer reply. I had enough of his patronizing way of approaching people and the way he is telling that others are wrong on things. I will wait till the ArbCom case will be concluded. Kim van der Linde ^{at venus} 19:53, 17 May 2006 (UTC)

I'd have to disagree with Doug. If there ever was a strong case for "Evolution by Founder Effect," antibiotic resistance would be it. Possibly, you could make a decent case for Tb and other slow bacteria, however, in most cases you completely wipe out the infection. The more times you have to use antibiotics (or, use antibiotics when it is not necessary), the more founder populations you go through, increasing the chance to get one that has resistance to your antibiotic. I definitely don't think you should go through this in the current article, but it might be better to use a different example. Antibiotic resistance is one of those cases we use while teaching, but it isn't really true. I guess we could also debate if that might be an OK strategy for Wikipedia. As for the figure, the caption is good, but the titles in the figure are hard to understand. Maybe it is the difference between British and American English. Even so, there really is no reason to skimp on words (e.g., what does Direct After mean? After antibiotic treatment? Then say it.). I suppose someone could also make a case that this is really a case of artificial selection, albeit for a trait we don't want.

Sorry for sticking my nose in again. I'll leave you to your own devices, although you'll never know when I'll drop in from more esoteric realms to catch up on what is happening. Cheers! Ted 05:30, 17 May 2006 (UTC)

(edit conflict)What you just described is exactly NatSel, and not a founder effect. Founder effects could equally result in ultra receptive populations. Repeateed founder effects have generally the tendency to increase the variation in resistance at the level of all the newly created populations, not at the population level at large and the overall average remains the same. The combination of repeated founder effects with repeated whiping out of those subpopulations, is nothing different than natsel occuring in a metapopulation. As for the image, I will think about whether to change the text in the image of the caption under it. Kim van der Linde ^{at venus} 13:15, 17 May 2006 (UTC)

To clarify a metapopulation consists of many smaller populations, with frequent colonisations and extinctions. You could call the frequent colonisations founder effects, but that is not what they are normally called, and it would erode the meaning of the term founder effect. Kim van der Linde ^{at venus} 14:18, 17 May 2006 (UTC)

Really? Interesting. What do you view as the unit of selection here? Ted 03:32, 19 May 2006 (UTC)

Individual bacteria. Kim van der Linde ^{at venus} 03:51, 19 May 2006 (UTC)

Then you might want to read DR Cox's excellent book, "Planning of Experiments", Wiley 1958. While it deals with experimental units, it is readily transfered to units of selection. Ted 08:42, 19 May 2006 (UTC)

I think it's worth remembering exactly what this is a good example of and why it's such a popular example, because there is a sense in which this is anything but "natural" selection. However, the example shows how, from a population of individuals that differ genetically only by random mutations, an adapted population can arise by selective reproduction of individuals that are best fit to survive a particular environmental challenge. The important things to emphasise are i) that it is not that individual organisms that adapt - they don't, each plays out its genetically predetermined destiny, and ii) despite the "appearance" of intelligence or "purpose" in the bacterial response, the outcome is not a consequence of design but of a simple blind process acting in the presence of random variation. In this it is a great "example" of natural selection in action; perhaps a better word would be model, but this would not be understood. I had thought of founder effects as referring primarily to the consequences of initial fixation of neutral or near neutral mutations that happen to by chance to characterise a founder population; in this sense I don't recognise your comment aboveGleng 12:58, 17 May 2006 (UTC)

It seems to me that antibiotic resistance selection is as close as you're going to get to seeing selection in isolation, without the other microevolutionary forces, because the population sizes are large (disposes of drift) and mortality is high (effect is instant, so mutation does not plays any role on the relevant timescale); gene flow, similarly, is not relevant on the short timescale. - Samsara (talk • contribs) 18:07, 17 May 2006 (UTC)

I find the comment about mutation interesting. Where, exactly, does the antibiotic resistance come from? (Assuming it is not transformed from another species.) Also, how is this "natural" selection and not "artificial" selection? I'm not necessarily opposed to using the example. All examples use simplifications. The problem arises when examples are remembered without an understanding of the simplifications used. How is this better than, say, evolution of insecticide resistance among insects? (Outside of the natural vs artificial problem which is still present here.) Now you see why there are very few good examples of natural selection, particularly since the use of industrial melanism is out of favor. I find it somewhat amusing that the best way to describe natural selection is in analogy with artificial selection -- which Darwin did 140 years ago. Ted 03:32, 19 May 2006 (UTC)

As far as I know, you need a conscious choice about which individuals are used for the next generation. In antibiotic resistance, that is not occuring. What does happen is the introduction of an artificial component to the environment of the individuals. IF you call that artificial selection, the introduction of CO2 to the atmosfeer results in world wide artificial selection (although no intentional choice is made on what to select for). Kim van der Linde ^{at venus} 03:51, 19 May 2006 (UTC)

Conscious choice. Good. It is what makes artificial selection different from natural selection--by definition. Of course, that's not very satisfying, either. How is mass selection in crops really any different from natural truncation selection, particularly outside of agri-business? Is the selection of hip dysplasia or "dumbness" in dogs (St. Bernard's is a good example) now natural selection since I don't consciously choose either trait? Kim, I understand from our past conversations that your training is in quantitative ecological genetics (or, your thesis advisor is so trained). The reason it works is that natural selection and artificial selection are essentially the same process--just a different way of creating fitnesses (for the simplist of models). I believe Darwin knew this. As did the giants of the 20th century, such as Fisher and Wright (at the extreme ends of theoretical development) who developed and applied theory to both artificial and natural selection. Ted 05:47, 19 May 2006 (UTC)

Indeed, conscious choice. There is no aim in selection for antibiotics resistance. There is an aim in mass selection in agriculture. Selection of hip dysplasia or "dumbness" in dogs is indeed what it is, selection OF, not selection FOR. It is correlated selection, a side effect of selection for something else. And yes, it is always about fitness. Kim van der Linde ^{at venus} 05:59, 19 May 2006 (UTC)

OK, finally my recommendation. If you want to discuss the high school experiments with E. coli and the artificial selection for antibiotic resistance and think of it as a "simulation," that's OK. However, comparing it to the very real public health problem of development of antibiotic resistance through selection is misleading. It is common among students and recent graduates to think there is only one possible unit for selection (their major professor's choice). Life is not so easy. The high school experiment does have individual bacteria as the unit of selection, but the real-life situation is different. That said, I'd go for just getting the labels in the figure less confusing. Wikipedia simply isn't designed for topics such as these. Ted 08:42, 19 May 2006 (UTC)

I think this whole debate is going to be curbed by discussing a single round of selection, along the lines of, "Now, if we consider how exposure to antibiotic affects a single generation of bacteria [...]" And then offer the multi-generational view as an extension of that. - Samsara (talk • contribs) 11:56, 19 May 2006 (UTC)

If, absenting Marcos's opinions,l there is general agreement in this section, Kim you should make this the main article (or I can). As any main contributor registered any objections? have all main concerns been addressed? Slrubenstein | Talk 09:12, 18 May 2006 (UTC)

I strongly support that suggestion. Release early (and I think this is quite late already...)! - Samsara (talk • contribs) 19:29, 19 May 2006 (UTC)

Done. I did not get the impression that anyone, except Marcos had major objections. Kim van der Linde ^{at venus} 20:39, 19 May 2006 (UTC)

[edit] Axel147 on new version

Moved here from NatSel talkKim van der Linde ^{at venus} 20:23, 18 May 2006 (UTC)

I generally like it!! Here are some hopefully constructive comments...

• I think the example is given too much prominence and is a bit scary for the layman.

The only way to really explain it is by an example, and there was some activity in that section. Have a look a little later when I am done with it. Kim van der Linde ^{at venus} 01:34, 19 May 2006 (UTC)

• On Sober's distinction the emphasis should be 'cause of selection' vs. 'free rider' (not trait vs. individual).

I have look at it, ut as far as I can see, this is semantics. Selection does take place on a trait. The trait is connected to an individual. After that, many things can doa free ride, be it directly through the same trait, or indirect because it is linked to the individuals that cary the trait. Kim van der Linde ^{at venus} 01:34, 19 May 2006 (UTC)

To add, Sober talks about selection OF objects (aka individuals) versus selection FOR properties (aka funtions or traits), So, this is the same here. You could start with the trait and the other traits that take a free ride, but than you have retrospectibe to explain how (genetic linking, multiple functions oer trait. Kim van der Linde ^{at venus} 04:22, 19 May 2006 (UTC)

• I think I object to the sentence 'For Darwin, fitness was equivalent to survival'. Darwin did not really use the term 'fitness' obviously undertood the importance of fecundity so I think this is misleading. ('Fittest' is really Spencers.) And is it survival of individuals or families of indiviuals etc.?

You're right; tweaked here.Gleng 21:32, 18 May 2006 (UTC)

• The article descibes natural selection in different places as a 'process', 'principle' and an 'idea'. Is this consistent?

Thanks for the alert. I've made a few suggested tweaks to use natural selection consistently as if it stands for "the mechanism of natural selection", but where there are historical references, different shades of use become apparent. Gleng 21:48, 18 May 2006 (UTC)

Depending on context, yes. Maybe we have slipped a few, those will be weeded out in due time. Kim van der Linde ^{at venus} 04:24, 19 May 2006 (UTC)

• The wider defintion is also a 'mechanistic' one: it is just that the mechanism of selection is combined with a mechanism for propagation (inheritance).

No, a result is not mechanistic, but the result of an mechanism. The generation of heritable genetic variation is mechanistic, but that is a far cry from being included in natural selection, and it is not even in the inclusive defintion. What is in the definition is the result, which is a static something, not a mechanism. Kim van der Linde ^{at venus} 01:34, 19 May 2006 (UTC)

• I hadn't read Petri Krohn trivia up until now! If only Darwin had used the term 'natural preservation' we wouldn't have had the mass discussions on this page! I'm not so sure this is trivial though as this confirms (if there was any doubt) that Darwin meant natural selection in the wide sense. However 'preservation' is not quite synonymous with 'evolution by natural selection'. New variation is required for (substantial) evolution but not for preservation. So let's get this part right!

I am perfectly fine if you want to change the appropriate sections in the historical context that are wrong, but I am going to resist changing this article to Darwinism, as there is already an article about that. Kim van der Linde ^{at venus} 04:32, 19 May 2006 (UTC)

— Axel147 19:55, 18 May 2006 (UTC)

I think the example should stay up front, though exactly how it's explained can be tweaked. Difficult to judge whether it's scary. My feeling is that, if the logic is there that any intelligent person can follow with minimal prior specialist knowledge, then it's right. The important thing is to be able to follow the logic through to the important conclusions, so that it becomes clear that natural selection is not an article of faith but has a carefully reasoned inevitability to it, that anyone can reach. We don't need experts to tell us that natural selection makes sense, we can conclude that for ourselves. Let's move it now, I think there's a general constructively critical support for it to be ready.Gleng 09:27, 19 May 2006 (UTC)