Why is evolution so controversial?

NOOOOO. As a mechanism for fixation. No. That's why it differentiates between them. They are different things. That's why they have different names. Of course you can.This does not justify your error, which has been explained to you, and explained to you, and explained to you, and explained to you.Let's try it again. One substitution explains one divergent base.But one indel can explain the divergence of a million bases.So when you start counting divergence caused by indels as well as substitutions, you are not counting mutations.This has been explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you. Try harder. Because your error has been explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you.If you really don't get it, maybe this is the point at which you should notice that everyone else reading this thread knows that you've made a simple, trivial error. We all know why you're wrong. If you don't, maybe that's your problem.

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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.

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I assume the same holds true with how indels were counted alongside substation sequences, presented in the paper I cited.Comparative Genomic Analysis of Human and Chimpanzee Indicates a Key Role for Indels in Primate Evolution | SpringerLinkI think it might be a good intro to your endeavor. I am making that very argument They describe total changes, not total number of bases changed.Looking forward to your finding. Also I am curious how insertions in multiples of 3 are counted (those that change open reading frames).

Here's an analogy. Not a perfect one, but it's pretty good.Suppose someone wants to know how old I am. But all they know is how far I've walked in my lifetime, and how far an average person walks in a year. Then their best estimate would involve dividing the first number by the second. It might not be a perfect estimate, but given the data they have, it's the best that they can do.Now, suppose someone, as it might be you, comes along and says, well, we should actually measure how far he's traveled by any means, by cars, by trains, by planes, we should add it all up, and then we should divide by how far an average person walks in a year.Then we say: "But you are dividing by the wrong thing". And you answer: "But the people who did the previous calculation also divided by how far an average person walks in a year. I'm just doing what they did, I'm performing the same calculation, if you have a problem take it up with them."

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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.

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I disagree with the premise that the percentage includes total base pair changed. When long segments are compared together between the species, alleles, are not always in one piece. The gap is probably a insertion (previously discarded). It depends if those bp’s are counted as a singular event, if so the percentages are addable. But if you start to count bp totals even in SNP divergence, all bets are off in the resulting divergence numbers. My guess is Nachman and Crowell’s paper did not include indels in the autosomal sequence divergence (there number is too low).

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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.

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I was meaning to address this pointSince indel mutations are on a longer term than SNPs, they probably will not show up in the study that found 70 mutations per generation (unless they are included. As pointed out by sfs the mutation rate per generation is not nailed down in a study that produced 70 mutations per generation. It surprised me that sfs would present a number like 1/7(u). The implication is that there are 10 mutations, including the bp count, totaled in the number (u) of 70 new mutation per generation. That is a question for further investigation.The 270 new mutations per generation is not possible on a number of levels. One being the genome load for humans.

Good post....

To begin with, that no-one proposed it.Please try to find out what a mutation is. This would be kind of essential to the discussion.Sheesh.This has been explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you, and explained to you.You are the one person reading this thread who doesn't understand what mistake you're making. If you are really incapable of understanding it, then you should just resign yourself to the fact that you don't understand it, and move on. Everyone else knows why you're wrong. Your mistake will not deceive anyone but yourself. Try making a different mistake. Move on.

Let's look at the chimp genome paper:"Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements."
Initial sequence of the chimpanzee genome and comparison with the human genome | NatureFor a 3 billion base haploid genome, 35 million substitutions would be 1.16%, consistent with other reports. If just 5 million indel events are added without reference to bases, this would be 40 million, or 1.33%. In order to get to the 5%, you need to transfer those 5 million indels into 90 million bases."The analysis of modest-sized insertions reveals ~32 Mb of human-specific sequence and ~35 Mb of chimpanzee-specific sequence, contained in ~5 million events in each species (Supplementary Information ‘Genome evolution’ and Supplementary Fig. S5)."
Initial sequence of the chimpanzee genome and comparison with the human genome | Nature You are all over the place. First, alleles make up a tiny portion of the overall genome. If we include regulator genes that are not translated into protein, we are only looking at 5% of the genome that has alleles. Since you seem to be referring to introns and exons, as in coding regions, then we are down to about 3% of the genome.If all we have are two species, then we can not tell if a gap is an insertion in one species or a deletion in the other. That is why they are called indels. By comparing the chimp and human genomes to the orangutan and gorilla genomes, we actually can form a consensus sequence and assign insertion and deletion status to some of the gaps. Also, why would a gap be an insertion that was previously discarded? That makes no sense.Next, a 5 bp gap is not considered to be 5 separate 1 base indels. It is considered a single 5 bp indel. It is considered a single event, not 5 individual events. This is based on the rule of parsimony which requires you to have the fewest mutations necessary to reach a consensus sequence. This is the same rule for substitutions. If we see a T substituted for an A, we don't assume that it changed to a G, then a C, then a T, then an A, and then finally a T. Instead, it assumes one mutation, from an A to a T. Then why does Table 1 from their paper include indels? I don't see why they wouldn't be included. The problem is that rare but large indels can really skew the data. For the human and chimp divergence, the rare but large indels account for a hefty portion of the differences while small but plentiful indels account for less of the differences."Analysis of the completely covered insertions shows that the vast majority are small (45% of events cover only 1 base pair (bp), 96% are <20 bp and 98.6% are <80 bp), but that the largest few contain most of the sequence (with the ~70,000 indels larger than 80 bp comprising 73% of the affected base pairs) (Fig. 5). "
Initial sequence of the chimpanzee genome and comparison with the human genome | NatureThis means that you need a very large pool of direct sequencing of family trios to adequately cover the observed occurrence of these rare but important indels. We simply don't have those direct observations. It's as if everything we say is just ignored. 10 indel mutations would be 200 base pairs. It would be 80 new mutations, and 270 base pairs. Like I said, it's as if what we say goes in one ear . . .Edited by Taq, : No reason given.

Well, I think we can see why. Zaius has put forward his best "scientific" attempt at trying to controvert evolution, and everyone with a brain in his head can see why it's a ludicrous failure. So we think: if this is the best anyone can do to argue against it, it must be pretty much perfect. A scientific theory stands by the efforts made to controvert it, and on that basis --- well, we've seen what creationists can do. So on that basis, the theory of evolution is the most reliable scientific theory we have.

Here is my attempt at using Zaius math to show that it is impossible to drive to a store just 5 km away.We will be using a car. In order for a car to be a viable mode of transportation, it will need to be able to reach the store within the lifetime of an individual (80 years) at the speed it was designed to go (100 kph). I will show that a car is not a viable means of getting to the store.First, we need to know the distance to the store. According to my calculations from the first paragraph, that would be 5 x 10^15 picometers. As I discussed above, a car is designed to go 100. Therefore, it would take 5 x 10^13 hours to reach the store. By my calculations, that is 5703979438 years. Therefore, it is impossible to get to the store 5 km away using a car.

How many indels were there? What was the average size of the indels? Indels of 1 base or more are counted as single indels. A 3 base indel is one indel. An 18 base indel is 1 indel. A 5 base indel is 1 indel.

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I don't see why they wouldn't be included. The problem is that rare but large indels can really skew the data. For the human and chimp divergence, the rare but large indels account for a hefty portion of the differences while small but plentiful indels account for less of the differences.

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That's one issue. Another is that it's much harder to accurately detect indels, especially ones that are more than a few base pairs. The direct estimate of mutation rates in humans that I'm most familiar with (this one) only looked at single base substitutions. They're just a lot easier to deal with.

Is this due to the difficulty of aligning gappy sequence and distinguishing indels from DNA that wasn't sequenced? Could these problems by solved by using slower, but more accurate sequencing methods on BAC clones?Edited by Taq, : No reason given.Edited by Taq, : No reason given.

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Is this due to the difficulty of aligning gappy sequence and distinguishing indels from DNA that wasn't sequenced? Could these problems by solved by using slower, but more accurate sequencing methods on BAC clones?

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I'm not a sequencer, so I don't know all of the issues. With diploid sequence, you'll have some reads with and some without the indel. If you're doing lowish coverage, short-read sequencing, there may not be very many reads of both type, and the indel is going to be near the end of some of them, making it hard to distinguish indels from SNPs. BACs would definitely be easier, since they're haploid. Of course, you'd need to sequence multiple BACs from the same chromosome segment, since you'd need to have BACs with both versions of the sequence.

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Let's look at the chimp genome paper:
"Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements."
Nature - Not Found

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I am sure this is accurate for what genes this paper looked at. These numbers do vary from paper to paper according to the focus of the researchers.

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For a 3 billion base haploid genome, 35 million substitutions would be 1.16%, consistent with other reports.

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I agree for the gene segments analyzed.

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If just 5 million indel events are added without reference to bases, this would be 40 million, or 1.33%. In order to get to the 5%, you need to transfer those 5 million indels into 90 million bases.

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I would say you can not get to 5% from 1.33% in these results. Like I say, different findings for different genes investigated.Here is a paper comparing different genes ( it covered exclusively chromosome 21 in humans and chromosome 22 in chimps) high-quality BAC clone sequences of the homologous chimpanzee chromosome 22 quote.

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The analysis of modest-sized insertions reveals ~32 Mb of human-specific sequence and ~35 Mb of chimpanzee-specific sequence, contained in ~5 million events in each species (Supplementary Information ‘Genome evolution’ and Supplementary Fig. S5)."
Nature - Not Found

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Fine for the segments selected by the authorsHere is a link to the paper again that promotes 5% sequence divergence.Comparative Genomic Analysis of Human and Chimpanzee Indicates a Key Role for Indels in Primate Evolution | SpringerLinkHere is a shameless repost of the calculation I did with only using indel variables from the proceeding paper and reduced mutation rate for indels. As I have stated over and over indel and substitution rates are addable. They both reflect autosomal sequence divergence for the (k) in the calculation in question.

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Indels of 1 base or more are counted as single indels. A 3 base indel is one indel. An 18 base indel is 1 indel. A 5 base indel is 1 indel.

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Just what I was looking for. thanks.