Why is evolution so controversial?

Would you care to share this evidence of (a) a young genome, and (b) evidence in our DNA that denies common descent? Edited by Genomicus, : No reason given.

The molecular data suggests a recent bottleneck, not a recent origin. See Heng and Durbin (2011). In this study, the researchers used bioinformatic approaches to date the time of the bottleneck. If there were a recent origin, we wouldn't see things like:"Both populations experienced a severe bottleneck between 10—60kya while African populations experienced a milder bottleneck from which they recovered earlier."There's plenty of evidence in the literature -- utilizing different methods -- that suggest a bottleneck, rather than a recent origin. So this argument for a recent origin doesn't really stand up well in the light of scrutiny. Uh, you haven't explained why the theory of common descent is not compatible with the amount of indels that separate our genomes from the genomes of chimps. You're just saying it can't. Back that up with rigorous science.ReferenceInference of Human Population History From Whole Genome Sequence of A Single Individual, 2011.

The paper I cited above gives a neat "when" to your question. How did the bottleneck happen? There are plenty of mechanisms for bottlenecks. Bottlenecks aren't implausible at all; we know they happen.

This doesn't make much sense. Because our genome differs roughly 5% from the chimp genome, that means there couldn't have been enough beneficial mutations? Do you have something to back that line of thought up? And: Selection pressures can lead to a higher-than-average U value. That's nothing new. Edited by Genomicus, : No reason given.

It is true that ~1.7% of the genome is subject to constraint as this is approximately the percentage of the genome that codes for functional proteins (the literature varies a bit on the precise percentage, but that's not really relevant here). However, that there is a constraint in no way implies that every single mutation in this genomic region will be deleterious.Actually, the vast majority of mutations in these regions will be neutral, which throws off your calculations considerably. So I'd suggest that if you want to maintain your argument, you take this into consideration -- it's pretty important and you can't ignore it. Until then, your argument is extremely weak IMHO.On a side note, your calculation for U also fails to correct for multiple amino acid changes at the same site. The formula for that is m/100 = -ln(1 - n/100), where m = the number of amino acid changes that have taken place for a given stretch of 100 amino acids in a protein, and n = the observed number of amino acid changes. I'm pointing this out to highlight your oversimplification of the issue at hand. Edited by Genomicus, : No reason given.

So do you know how these calculations work? Because they got a different U value than you did. Why is that?

I'd suggest that instead of spending most of your time responding to replies of a general nature, you spend some time responding to my Message 548, Message 549, Message 550, and Message 557. I have rather thoroughly excoriated your arguments, and you haven't responded to any of it.If you want to talk molecular phylogenetics and genomics, let's talk about it. If you want to engage with substantive counterpoints to your arguments, I'd suggest you get to it instead of avoiding the issues I brought up. Edited by Genomicus, : No reason given.

This.Edited by Genomicus, : No reason given.

Well, to be fair, he/she made that brief comment based on the graph provided by Cat Sci. So we don't know if his/her line of thinking is based on the same argument as Morris's. Edited by Genomicus, : No reason given.

Correct, yes. With improved bioinformatic/sequence alignment methods, etc., it makes sense that the percentage of sequence identity should change.However, you can't directly plug 5% into the formula you're using. That's because the formula is based on the percent identity estimated from point mutations, not indels. If you trace the formula you're using back to the primary literature, you can see that it's all about point mutations -- indels don't work in the formula if you're going off of gross percent dissimilarity. The formula comes from Kimura's landmark 1983 work. Read it.It's not really biologically appropriate to conflate indels with point mutations in this context, and you can't use that formula with indels unless you count each indel as a single mutational event, instead of treating each difference in base pair as a single mutational event. Make sense?And when you treat each indel as a mutational event, things look different:"This is an observation of the major way in which the genomes of closely related primates divergeby insertion/deletion. More nucleotides are included in insertion/deletion events (3.4%) than base substitutions (1.4%) by much more than a factor of two. However, the number of events is small in comparison. About 1,000 indels listed in Tables 2 and 3 compared with about 10,000 base substitution events in this comparison of 779,142 nt between chimp and human. Little can be said about the effect of these indel events."From: "Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels," 2002.You'll have to rethink your argument considerably based on the points I've raised above.

I'm not quite sure if it's conducive to the clarity of this discussion to go off on slightly different topics/debating points, instead of focusing on the particular argument that he/she put forward. IMHO.Edited by Genomicus, : No reason given.

I'm a little confused on what you mean by this. The difference between two sequences can be quantified relatively easily as the number of differences in aligned base pairs + indels.

Really? You're bringing grammar into this?Edited by Genomicus, : No reason given.

1. It is English. It's just not perfect English.2. He/she might not be a native English speaker.3. Quibbling about your "opponent's" grammar kinda distracts from the issues.I mean, c'mon.

The statistics are often not the same since indels are categorically different than point mutations. And, in particular, the formula you are using is based on point mutations, not indels, so it's completely wrong to figure indels into the formula in the way you're doing it. Just about anyone can do plug-n-chug math. It takes a higher level of expertise to know when it's appropriate to use a given formula -- and when it's not. You're using the formula u= k/(2t+4Ne). But do you know how this formula is derived? Do you understand -- on a rudimentary level, at least -- the different components of this formula? Or are you peeling this off the scientific literature and just plugging numbers in? You need to know the nuances of the formula before you can ever hope to use it effectively.The formula, as I stated, is found in Kimura's 1983 monograph on neutral evolutionary theory. And in this formula, k represents the rate of substitution mutations (see Kimura, 1986). This symbol, k, will be familiar to most students of molecular phylogenetics. It comes in handy in a bunch of formulas. But it represents the rate of substitution mutations, not the gross percent dissimilarity of sequences. Substitution mutations are not indels. They are thoroughly different, and equating the two in this formula is biologically incorrect -- and that's exactly what you've been doing.So will you concede that your initial argument for a recent human origin falls short? Otherwise, I'll be expecting a biologically sound response to my points above.References"DNA and the Neutral Theory," M. Kimura. Philosophical Transactions of the Royal Society of London, 1986.Edited by Genomicus, : Added reference. Have better things to do with my time than format it according to any standard, tho. Edited by Genomicus, : No reason given.Edited by Genomicus, : Fixed typos. Drugged on caffeine.