User talk:KimvdLinde/Natural selection/archive

From Wikipedia, the free encyclopedia

For old discussion, see User talk:KimvdLinde/Modern usage of natural selection.

For your example, can you say anything about

a) the size of the genome

b) the spontaneous mutation rate,

c) the generation time

d) the estimated population size

e) the estimated speed of penetration.

This is a case I think where variation is provided solely by spontaneous random mutations. It's a good example to use, but I think the important thing here is to show clearly that the sums add up. ? Gleng 13:55, 6 May 2006 (UTC)

I try to make the first example as easy to understand as possible. I think most of these points need to be included in the more extensive overall and technical explanation of NatSel. KimvdLinde 14:00, 6 May 2006 (UTC)

I should leave the content to you, but sometimes I think it's just easier if I throw in the sort of thing that I think might be needed in the expectation that you'll bin it or put it right...Gleng 17:54, 6 May 2006 (UTC)

Please add what you think is right. I agree that that are topics that need to be covered, although I think they end up at different places in the article. In the course of writing this, I update all kind of linked pages as well, as they sometimes just give plain wrong information. KimvdLinde 18:49, 6 May 2006 (UTC)

Hi Kim: I think that something needs to be said carefully about spontaneous mutations, about time and generations, and about the role of natural selection in rapid vs gradual evolutionary change. I've had a go below, not inserted it because I probably get lots wrong, but I did want to convey a sense of the nature of the evidence that exists, and a sense of how sophisticated the arguments are, without making things just jargon ridden. Let me know what you think, and there is absolutely no need to be polite. This is not my field, so I have absolutely no pretensions to authority of any sort. This is just a (long) suggestionGleng 13:41, 7 May 2006 (UTC)

Denver et al. (Science, 2004) estimated how often spontaneous mutations arise, by studying the nematode worm C. elegans, a species with a generation time of just 4 days. They grew 198 different lines of worms under conditions that minimized natural selection. From each generation, they kept just one worm, and maintained each line for several hundred generations. Then, they sequenced stretches of DNA from each line and compared the sequences with natural populations. They found just 30 mutations. From this, they calculated that, in each generation, there is just one spontaneous non-lethal mutation for every 50 million base pairs of DNA. Humans inherit 3 billion base pairs of DNA from each parent, so this mutation rate would yield 60 new mutations in each of the two genomes that combine to make a baby. This might seem a lot, but humans have about 30,000 genes, and as much as 97% of our DNA does not encode anything. Much of this is so-called "junk" DNA, and mutations here will have no effect; many other changes will be in noncoding regions of DNA that regulate gene expression, and most of these will be neutral; most of the few changes in coding regions will be deleterious. Even if a new mutation is advantageous, there is still a strong chance that it will be lost (i.e. the individuals with the mutation may die without leaving any descendents who carry the mutation). Even if a mutation is not lost, it will take a long time to spread through the population. For example, in a population of 1 million individuals, an allele that confers an advantage of 1% will need about 3000 generations before it becomes “fixed” (i.e. before it spreads to all individuals in the population). Thus, if evolution has to ‘wait’ for appropriate mutations to arise by chance, vast numbers of generations are needed, and for species with a long generation time, this means vast amounts of time. The story of life on earth is one that unfolds over 3 billion years of evolution; typical species of multicellular animals exist for just 10 million years. Nevertheless, there have been times in the history of life when many new species seem to have arisen over relatively short periods – periods too short to be easily explained by the accumulation and selection of new mutations. However, this is not really how all natural selection works. In evolution, it is the individual that is selected, not a gene, and selection is on the basis of the individual phenotype, because of particular traits that the individual possesses. In general, traits are determined by combinations of alleles given particular environmental conditions, although the end result is that particular alleles become more common in a population. The phenotype that is characteristic of a species remains relatively constant for many generations – many millions of years for species of mammals. During this period of “stasis”, deleterious mutations are eliminated by natural selection, but neutral mutations, and mutations with slight beneficial effect become more common. Thus the population becomes more diverse, in that individuals differ more and more from each other in subtle ways. This diversity provides the “raw material” for rapid evolutionary change when environmental conditions change. Environmental conditions can change rapidly because of climate change, but also for example when a species spreads into a new habitat, or when a habitat is disturbed by encroachment of another invading species. In these circumstances, the selection pressure on a species changes; some traits that were neutral or advantageous might become detrimental, while others that were neutral might become advantageous. Accordingly, the frequency distribution of alleles in a population changes, and, as combinations of previously rare alleles become more common, new traits emerge, and can be selected for. This mode of rapid natural selection underlies the theory of “punctuated equilibrium” promoted by Stephen Jay Gould in particular. There is continuing debate about how the different modes of natural selection contribute to evolution. The strongest evidence that species evolved from ancestral species is contained in the records of the genomes of species. These display directly the evidence that all of our genes are, with relatively slight differences, like those of other animals, and that the pattern of differences is consistent with descent of species from common ancestors. Today, we know the full genomes of several species, including our own; we know the differences between species, and how much variation there is within species. We can estimate the rate at which spontaneous mutations arise, and we can determine the phenotypic consequences of mutations. Scientists accept the logical inevitability that natural selection must, in its many ways, affect the distributions of alleles in a population, and can observe this directly in experiments on species with short generation times. Modern evolutionary biology is, to a large extent, calculation of the deduced effects of natural selection, mutation and pre-existing genetic diversity of populations, given different environmental conditions. There are many lively controversies within evolutionary biology, but there are none about the importance of natural selection as the key mechanism underlying evolution

I have tried to incorporate some of these points, but it runs very vrey quickly in a pretty difficutl mass of concepts, mechanisms etc to explain at sufficient accuracy, while at the same time being brief (you have seen the partial versions that included it). One of the major sources of new genetic variation is actually recombinations, they are much more important at the short run than mutations. So, I left it out, and I think this is something that is better covered at a genetic variation page (currently a redirect page to mutation). Kim van der Linde ^{at venus} 13:15, 9 May 2006 (UTC)

That's fine. I just wrote it to flag some points for you to consider including. I totally agree that we need to be both clear and accurate, while providing enough detail to show the kind of evidence and thought that lies underneath the conclusions that are drawn. It's a hard balance to keep. I saw a nice image on Commons for recombination - perhaps it is worth inserting that image with a legend making just the point you raise here?. No, scrub this idea for the moment, talking too fast.Gleng 13:27, 9 May 2006 (UTC)

I have just created the genetic variation page. It is easy to drag all topics into a single article, so I agree, let it out for the moment. Kim van der Linde ^{at venus} 13:39, 9 May 2006 (UTC)

[edit] Check sums?

Is the revision below correct? (8 for 9 etc)

The human genome contains 3.2x10⁹ base pairs, while the effective genome (the functional sequences in which mutations can affect fitness) contains 8.0x10⁷ base pairs. A mutation rate of 2.4x10^-8 acting on the two copies of DNA (one from each parent) will mean that each new baby has, on average, 317 mutations in the whole genome, and 7 mutations in the effective genome; the latter can potentially affect the fitness of the individual

Gleng 19:53, 7 May 2006 (UTC)

Humm, this is a can of worms, so I see if I keep it in. The factor that was still missing is that diploid individuals have actually multiple divisions (~20) before the gamate is completed, increasing the actuall number of mutations. KimvdLinde 20:56, 7 May 2006 (UTC)

Hi Kim. For the moment I cut this out

"Given sufficient time, adaptive evolution can result in speciation and in the evolution of novel traits."

At present it stands as a non-sequitur. I think this argument has to be built up very carefully. I think we must beware of leaping from selection to either emergence of novel traits or speciation, this is where we're most vulnerable to creationist arguments.

If the arguments aren't made here then maybe we should just declare the conclusion but link to places that do fill in the gaps.

Gleng 08:43, 8 May 2006 (UTC)

O yes, i was not done yet, it was late and I just added that sentence for the time being. I will work more on it this evening.KimvdLinde 16:36, 8 May 2006 (UTC)

For your example, might be helpful to have an image here, maybe like that in [1]?Gleng 13:36, 8 May 2006 (UTC)

See [2]? Gleng 16:27, 8 May 2006 (UTC)

Agreed, I just have to make one, to avoid copyvio's. Or are you good with making images? :-) KimvdLinde 16:36, 8 May 2006 (UTC)

I'm just an old dinosaur. I miss Letraset.:-)Gleng 16:41, 8 May 2006 (UTC)

LOL KimvdLinde 16:52, 8 May 2006 (UTC)

[edit] To do

1. Graphics for selection of resistance.
2. competiton for versus competition of

Kim van der Linde ^{at venus} 13:11, 9 May 2006 (UTC)

query - recombination in bacteria? Thought this was all mutation -forgive my ignorance hereGleng 21:56, 9 May 2006 (UTC)

It is indeed mainly mutations in those guys. Kim van der Linde ^{at venus} 02:21, 10 May 2006 (UTC)

Found why you asked, stupid of me :-( Kim van der Linde ^{at venus} 03:34, 10 May 2006 (UTC)

Suggest soon archiving this Talk and inserting a comment both here and on Nat Sel Talk, maybe on the lines of:

This page shows a proposed new version of the article on Natural Selection. This has been developed from 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 here 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.

Gleng 13:18, 10 May 2006 (UTC)

Yup. A friend of me (evolutionary biologist) is going to read through it today (he did a little part yesterday), so that will be a good test on the external side. I agree that we should not just repalce it, but ask a little comment before. Kim van der Linde ^{at venus} 14:12, 10 May 2006 (UTC)

Yup. No I'm not going to start saying yup, it's not me. I put the subheads in for you to think about, take them out or change them as you like, I'm not sure myself. Gleng 12:34, 12 May 2006 (UTC)