Why is evolution so controversial?

quote:

---

Of course they are. But since we don't have a good direct estimate of their mutation rate, you can't independently check to see whether human/chimpanzee divergence in indels fits with the mutation rate. There's nothing to compare it to.

---

So I have to scratch your 1/7(u)? I was hoping that you would not be so willing as to throw your number under the bus.Move those goal posts a little to the left.

quote:

---

The vast majority of papers dealing with indels having to do with similarity. Indeed, the overall percentage similarity is of very little scientific interest.

---

A minor exception would be the human chimp divergence time.

quote:

---

What paper discounted indels? And what paradigm changed?

---

Nachman and Crowell’s paper, I don’t think you want to claim it did.As the paradigm goes... The paradigm that indels are of no consequence.Since you are retracting the estimate of 1/7(u) that leaves me with a reduced but relevant argument.One last quick question do you agree with a mutation rate of 1.1 x 10^-8 in humans? Or are you moving those goal posts again?

quote:

---

Fine. To go along with that, we'll also need the mutation rate in base pairs per generation. Do you know what it is for indels? It's not the rate you've been quoting -- that's the rate of mutations per generation. If you don't know it, you can't do the calculation.

---

Well you gave me 1/7(u) for indel mutation rate and the empirical measurement of mutations per generation is 70 new mutations per generation or 1.1x 10^-8.

quote:

---

They don't adjust anything. Alignment tools align the parts that align and show gaps where they don’t.

---

They adjust the chimp genome to the human scaffold.You say tomato, I say tamato.And total Bp is not counted just the location of the insertion or deletion and if it is a multiple of 3. If you counted total bp the human chimp genome similarity would be below 70%.

We have, over the past few pages, an inexhaustible gold mine of comments you have made, zaius137, that are manifestly inconsistent with fairly basic and rudimentary biology -- so I'm not sure where to begin my critique. Wrong. The k value is not the total percentage of the number of bases that have changed. I've already pointed this out, so why are you regurgitating this claim? Here's what k is actually about:"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." Do you? Because you keep using k in a grossly inappropriate fashion. You might want to read up on the statistical and bioinformatics literature when it comes to alignment methods. Obviously. If there were no such adjustments, alignment methods would be neglecting a very important part of biological reality -- indels. So gaps are introduced to account for indels, and parsimony (and other methods) are used to determine the most optimal alignment.At this point, the discussion is so convoluted and such a mlange of talking points that it can be hard to follow. But really, I suggest you actually make sound arguments and actually read the papers you cite.

If the substitution rate is 70 and the indel rate is 1/7th of that, then that would be 80 mutations including both substitutions and indels, by my math.If you want to do number of bases, then the mutation rate is 10 indels with an average of 20 bases per indel, or 200 bases plus the 70 bases from substitutions. Therefore, the mutation rate should be 270 if you are using number of bases affected.For divergence, if 35 million substitutions is 1.3% divergence before adding in indels, then the divergence (in number of mutations) should be 1.3 +(1.3/7) = 1.49% for number of mutations. You can adjust this for number of bases by using the math above.Edited by Taq, : No reason given.Edited by Taq, : No reason given.

I will be honest, you make a good point.

quote:

---

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.

---

OK, so my technical language is not up to par.You know I have misplaced my pocket verseion of kimura,1986 also the 1983 copy. My notes from that class of molecular phylogenetics was eaten by my dog.
I do know that kimura along with others developed the Neutral theory of evolution. The theory as I understand it involves random drift as a mechanism for mutation. Indels are also subject to random drift which places them in the realm of the neutral theory of evolution. A clock is a clock although this one runs slower.It seems that the abstract in the following paper does equate substitution mutations with indel mutations

quote:

---

Divergence due to insertions and deletions (indels) along with substitutions was examined separately for different genomic features (coding, noncoding genic, and intergenic sequence). The major part of the genomic divergence could be attributed to indels (5.07%), while the nucleotide divergence was estimated as 1.52%. Thus the total divergence was estimated as 6.58%.

---

Comparative Genomic Analysis of Human and Chimpanzee Indicates a Key Role for Indels in Primate Evolution | SpringerLink

quote:

---

The conclusion is the old saw that we share 98.5% of our DNA sequence with chimpanzee is probably in error. For this sample, a better estimate would be that 95% of the base pairs are exactly shared between chimpanzee and human DNA. In this sample of 779 kb, the divergence due to base substitution is 1.4%, and there is an additional 3.4% difference due to the presence of indels.

---

Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels - PMCIt looks to me as if you can add divergence of indels directly to substitutions. If you want to maintain that indel mutation can not be added directly you must provide citations The ones you did just are not up to date, that doesn’t mean they are bad, just outdated.As I have stated before, new evidence includes indels as significant factors of evolution.

quote:

---

You might want to read up on the statistical and bioinformatics literature when it comes to alignment methods.

---

Well, I will just take that long needed vacation and spend it locked in a room with all the research I can dig up.

quote:

---

Obviously. If there were no such adjustments, alignment methods would be neglecting a very important part of biological reality -- indels. So gaps are introduced to account for indels, and parsimony (and other methods) are used to determine the most optimal alignment.
At this point, the discussion is so convoluted and such a mlange of talking points that it can be hard to follow. But really, I suggest you actually make sound arguments and actually read the papers you cite.

---

I always try and understand what I use in my citations. If you feel that I am in error, you too can cite away, but not from some dusty text book that is out of print since 1990.

From what I have read and seen, the indel clock tends to run a bit ragged, faster at times and slower at other times. The SNP clock seems to run at a much steadier rate. This is one of the reasons that they have focused on divergence caused by substitutions, because the rate of mutations is understood a lot better. The author clearly describes them separately. For what purpose and in what context? Obviously, you can't add the number of indels directly to the number of substitutions to get the number of bases affected. 10 indels plus 70 substitutions will probably affect more than 80 bases.

Is that the exception that proves the rule?

I just realized something You posted the following: The k in the paper we are discussing is the autosomal sequence divergence not the rate of substitution mutations. (u) is the rate of substitution mutations.Thought I would clear that up Maybe my def. was better.Estimate of the Mutation Rate per Nucleotide in Humans | Genetics | Oxford Academic

It runs slower than what? Than a molecular clock based on substitutions? Sometimes, sometimes not. It's wholly context-contingent. You're going to get far more indels in fibrinopeptides than you'll have substitutions in cytochrome c, if we're looking at a pair of species. No, it does not equate the two. It simply analyzes the two. But they aren't equated, because they're different -- especially when you're using them in mol clock equations. You can only equate the two if you are treating indels as substitutions in the sense that 1 indel = 1 substitution (instead of using k to mean the gross base pair/aa dissimilarity between any two biological sequences). Because they are. That's not under debate here. Yea, I have a mol phylo textbook published in 2009 only inches away from me. Then there's this 2003 bioinformatics textbook on hand, and it confirms what I said about k values. Getting papers published means getting the terminology right. And that means actually examining the primary literature. You might say that's too much to ask for in an online discussion, but that's kinda the price you have to pay for getting into a nitty-gritty technical debate.

The k value is typically treated as the number of substitutions per site. Calling it "the autosomal sequence divergence" doesn't change the fact that it still represents the number of substitutions per site.

(k) is autosomal sequence divergence (a percentage).(u) is the mutation per generation figure (rate of mutations).You don’t get it the (u) and (k) are reversed. Look at the paper

quote:

---

It seems that the abstract in the following paper does equate substitution mutations with indel mutations

​

No, it does not equate the two. It simply analyzes the two. But they aren't equated, because they're different -- especially when you're using them in mol clock equations.

---

Could you add the percentage if they are different?The major part of the genomic divergence could be attributed to indels (5.07%), while the nucleotide divergence was estimated as 1.52%. Thus the total divergence was estimated as 6.58%.From that citation... Did they add the percentages or not?So I can add apples and oranges to figure out how much citrus in the fruit bowl?

Evolution is not controversial, not among scientists.Therefore any attempt to answer this question is invariably going to veer off topic to things like "Any real evidence for evolution" which I have pointed out elsewhere is also a piss poor question because the answer is, that in order to be a valid scientific theory one considers all of the evidence. If the theory is the best explanation for the data, it is a valid scientific theory and that fact will not be controversial. That doesn't mean there aren't controversies about specifics - for example, what individual fossils tell us, etc. - lots of controversy about that.

Here is the legend for Table 1 of the paper:"Divergence per site between human and chimpanzee (Kimura 1980) is given for transitions (Kts) and transversions (Ktv) at CpG sites and at non-CpG sites, all single nucleotide changes (Kn), insertion-deletions (Ki), and total changes including both point mutations and insertion-deletions (Kt). Mean values are weighted by the number of sites in each locus. "They describe total changes, not total number of bases changed. They have the accession numbers for the genes they compared, so I may try to do my own alignments at a later time to show that multiple base indels are counted as single changes.Edited by Taq, : No reason given.

The problem is that you are not adding two percentages. You are adding the percentage of bases changed for substitutions to the number of indel events for your mutation rate. You need to convert the number of indel events to the number of bases changed if you want to add the two together for your mutation rate.I already did this math earlier. Indels are 1/7th the number of substitutions. If the number of substitutions is 70, then there are 10 indels. The average size of an indel is 20 bases. Therefore, the mutation rate in the units of bases changed is 70 bases from substitutions and 200 bases from indels for a total of 270.