Human Evolution Discussion with Ahmed

https://www.sciencedirect.com/science/article/pii/S0960982214006678

https://www.pnas.org/content/111/18/6822

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I think your focus on ā€œconclusiveā€ evidence betrays a misunderstanding of science, where all conclusions are ultimately tentative and potentially subject to future change given the right type and amount of new evidence.
There is no objective scale of conclusivity (how much evidence is enough for you might not be enough for someone else).

So the real question is if the current evidence in fact supports one conclusion over another, not whether it is ā€œconclusiveā€. And the current evidence from the relative number of differences in the human and chimp chromosomes in fact only supports common descent, and in no way supports independent creation.

I will also say that I think you probably donā€™t have ā€œconclusiveā€ evidence for what you believe in place of biological evolution.

None of that seems to be relevant to the rather straightforward prediction made by the observed mutation rates on the chimp and human sex chromosomes.

Given that the Y chromosome is evolving faster than the non-sex chromosomes, and the X chromosome is evolving slower - in both chimps and humans - we would expect that a direct comparison between human and chimp chromosomes should show most differences in the Y chromosome, and least differences on the X chromosome, if we share common descent. Since we do in fact observe this result, and since we expect it on common descent, and we do not have a competing hypothesis that yields this same expectation, this is evidence that supports common descent.

Why mutations occur, whether the mutations are neutral, and how the overall rate of mutation differs across species, logically have no effect on this inference.

I hope I have now made it clear both how the logical inference of common descent is made given the Y and X chromosomal rates of mutation, and why seeking the evidence to be ā€œconclusiveā€ is actually not possible in science. There are only degrees of support, and nothing is ever proven conclusively, or beyond possibility of future contradictory evidence.

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Yes and heā€™d be right to say that. I have seen no substantiation of the claim that there are too many millions of mutations separating humans from any of our primate cousins.

No, Iā€™m afraid I donā€™t.

80% of the ~20000 proteins shared among chimps and humans have about one amino acid difference between them. Okay. How does that entail, or indicate, that this approximately one amino acid difference in each of these proteins is not neutral? I genuinely donā€™t see how you arrive at that conclusion.

I think the main problem I see with your argument here is that it is a non-sequitur. I donā€™t think the conclusion follows. Youā€™re going to have to explain yourself better why you think 80% of proteins shared among humans and chimps mean the approximately 1 amino acid difference between them is non-neutral.

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What makes you think we need ā€œmany millionsā€ mutations to get a human from an ancestral ape? What specific evidence can you cite that you think indicates ā€œmany millionsā€ are required, as opposed to a much lower number?

I hope youā€™re misspeaking here, because otherwise you are very confused. To go from ā€œ80% of proteins have at least 1 amino acid difference between humans and chimpsā€ to ā€œ80% of mutations are non-neutralā€ is a complete non sequitur. There is literally no connection whatsoever between these two claims.

BTW, as has been said several times now, itā€™s 71% of proteins of human/chimp proteins that are non-identical, not 80%. Please update the figure in your head.

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Well, you must understand that I donā€™t think the evidence points toward anything other than unguided evolution, and that there is no evidence against gradualism, if by that you mean the absence of saltation. But if we suppose a guided scenario, thereā€™s no reason for anything sudden or drastic, just tweaking the odd mutation to produce, over millions of years, the few thousand differences between us and the chimp-human ancestor that have any effect on phenotype. Nor do any of these mutations have to happen simultaneously in multiple individuals. They just have to happen and then spread through the population, through drift, selection, or divine nudging.

This scenario has the advantage of being consistent with the data, while separate creation isnā€™t. All that stuff Joshua showed you: the genetic similarity, the different rates of evolution in X, Y, and autosomal chromosomes, the mutation spectrum of pedigrees matching that of human/chimp differences, is all explained by common descent but is nonsensical given separate creation. He may not have mentioned my favorite evidence: that the genetic and other data fit a tree of descent for all apes, all primates, all mammals, all amniotes, etc., etc. If thatā€™s special creation, the creator is trying to fool you into believing in common descent. Do you think he would do that?

You canā€™t really spot any of those in the fossil record, though you can find tools. Australopithecines had tools, and theyā€™re intermediate in other ways too. Even chimps make tools. The hominin fossil record is in fact full of intermediate forms.

Thatā€™s by no means obvious. Why should God guide evolution similarly in different lineages, if you want to go that way? Why should the same mutations show up by chance in different lineages, if you want to go that way? Chimps and humans have diverged from their common ancestor in different directions, and thatā€™s how evolution generally works.

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No, it doesnā€™t mean that. First, it isnā€™t 80%; itā€™s 71%. Second, the differences are almost all one or two amino acids, and half of those are in the chimp lineage. Third, your basic assumption is incorrect: many amino acid changes have no significant effect on the proteinā€™s function, and are thus evolving neutrally. In fact, I have already cited evidence that most of these differences are neutral, if you will look back.

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Youā€™re welcome. Iā€™m less than a year studying this topic with no background so I appreciate these kinds of dialogues, as it helps clear up misunderstandings I had or gives new information as someone who is also a skeptic. Iā€™ve only watched the first 40 minutes so far but it seems like a very nice dialogue and I appreciate you both giving that much time to it. Btw, happy Fatherā€™s Day to all the dads here and those celebrating.

One question I had after watching the beginning and I decided to look up, is whether the y chromosome pattern hold up across the great apes. If it isnā€™t as clear, does that undermine the hypothesis even if there isnā€™t a competing one? Perhaps Iā€™ve brought this up before.

Among great apes, the Y has so far been assembled only in human (6), chimpanzee (7), and gorilla (8). A comparative study of these Y assemblies (8) uncovered some unexpected patterns which could not be explained with the data from three species alone. Despite a recent divergence of these species (āˆ¼7 million years ago [MYA]) (9), their Y chromosomes differ enormously in size and gene content, in sharp contrast to the stability of the rest of the genome. For example, the chimpanzee Y is only half the size of the human Y, and the percentage of gene families shared by these two chromosomes (68%) that split āˆ¼6 MYA (9) is similar to that shared by human and chicken autosomes that split āˆ¼310 MYA (7). Puzzlingly, in terms of shared genes and overall architecture, the human Y is more similar to the gorilla Y than to the chimpanzee Y even though human and chimpanzee have a more recent common ancestor (8). Y chromosomes from additional great ape species should be sequenced to understand whether high interspecific variability in gene content and architecture is characteristic of all great ape Ys.

https://www.pnas.org/content/117/42/26273

It holds up across a lot more than the great apes. Itā€™s a general phenomenon among species that have eggs and sperm. Works for birds, works for flies, etc. The reference you cite has nothing to do with any of that.

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@Ahmed_AbdelSattar this is just not a valid summary of the evidence. Are you ready to understand why?

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I think I wasnā€™t explaining well what I meant by a pattern - I meant whether the y-chromosome would form the same phylogeny with the great apes as the entire genome (if each was considered completely independently) and whether the apes that are farther from each other on the tree would have a more dissimilar y-chromosome. Neither appears to be the case from what I read of that paper; perhaps Iā€™m understanding it incorrectly.

Also if the percentage of gene families in the human y-chromosome is the same compared to the chicken as to the chimpanzee, yet I think it said sequences are similar in the human as to the chimpanzee, then should we put any confidence in similar sequences in the rest of the genome as to showing recent common ancestry?

Just thoughts off the top of my head - no idea if they are valid questions or not.

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Not true. Here you go, from the paper:

Primate Phylogeny based on Ychromosome

The paper says gene death rates are markedly higher in the Pan lineages relative to humans on the Y-Chr, indicating that lineage-specific gene loss is a most likely explanation for this observation. From the paper:

and

Common ancestry is determined by looking at certain patterns, not just similarities. If those patterns expected from common descent are present in datasets, we conclude ancestry regardless of the number of gene families shared. We expect some genes or gene families derived from a common ancestor to be lost or gained over evolutionary time in lineages from that common ancestor.

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Downhill?

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You believe that there are ā€œtoo many millions of mutationsā€ are needed, but you need to actually provide evidence for that claim, besides a mere appeal to your belief in human exceptionalism.

Furthermore, just as Evograd pointed out, the figure is not 80% it is actually 71%, and that figure specifically means the following: Of the ~20 thousands protein orthologs shared between humans and chimpanzees, 71% of them differ by at least 1 amino acidā€¦and they often differ by one or a few amino acids at the most.

This does not in any way mean that 71% of all fixed mutations are non-neutral. It doesnā€™t even mean that 71% of all fixed mutations within the protein coding sequences are non-neutral. In order to determine the actual percentage of neutral vs non-neutral mutations, you would need to know the exact number of synonymous and non-synonymous mutations. With regard to the number of synonymous mutations, the 71% figure canā€™t tell you anything about that since it explicitly ignores the synonymous mutations. Hence why you cannot refer to this 71% figure to say anything about what percentage of all fixed mutations were non-neutral.

And this is similarly the case for the ā€œimplicationsā€ you outlined. The first that says there are ā€œtoo many (millions) of non-neutral mutations to account forā€ is completely unsupported by this 71% figure. As explained before, all it says is that there is at a minimum 1 amino acid difference in 71% of the protein coding genes shared between humans and chimps. Given that there are roughly 20.000 genes shared, that means that there are at minimum 14.200 non-synonymous mutations that separate us. But you would also need to divide this by 2, since the amino acid differences is also caused by the changes that have occurred in the chimpanzee line as well as the human line. In order to get to your ā€œtoo many millions of mutationsā€ from the 71% figure, you would have to argue that each of the protein orthologs that differs between humans and chimps differ on average by more than 140 amino acids. Calculation: >140 amino acids x (~20.000 protein coding genes x 71% differ) = more than 2 million or ā€œtoo many millions of mutationsā€ But we already know that this is wrong, since most of these proteins only differ by one or a few amino acids at the most - not even close to 140 - just as mentioned previously.

And regarding the second implication, @swamidass has given ample evidence to show that (nearly) neutral theory applies in accounting for the genetic differences observed between, and you have yet to make a sound counterargument against this.

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Sure, I am always open to understand betterā€¦
I am not sure however if you have been looking into all threads open here, so, I have posted few comments about why this piece of evidence is enough, even it is seem as giving a hint:

  1. The matter of mutation rates seems to have plenty of unknowns including their reasons, correlations, and implications. I would like to draw your attention to this paper:
    Evolution of the mutation rate across primates - ScienceDirect

  2. Neutral theory itself is being challenged as a good explanation for molecular evolution, and I would like to refer to this paper, and seek your opinion:
    I quote: ā€œWe argue that the neutral theory was supported by unreliable theoretical and empirical
    evidence from the beginning, and that in light of modern, genome-scale data, we can firmly reject its universality. The ubiquity of adaptive variation both within and between species means that a more comprehensive theory of molecular evolution must be sought.ā€
    Neutral Theory in Light of Natural Selection | Molecular Biology and Evolution | Oxford Academic (oup.com)
    I also quote: ā€œWe have presented accumulated evidence from the past 50 years that natural selection has played the predominant role in shaping within- and between-species genetic variation. As a consequence, we believe that the neutral theory has been overwhelmingly rejected, and that as a field we must continue to develop alternate theories of molecular evolution.ā€

So, if Selection is the master of the game, then the matter that we have 80% proteins difference should very well draw our attention to where this is going.
Quoting the paper again here:
Eighty percent of proteins are different between humans and chimpanzees - ScienceDirect
(I couldnā€™t add the link because the system still prevents me from adding more than two links!).

Once again, appealing to divine providence can solve any problemā€¦ but my point here in response to what you have remarked ā€œIf God wanted it to be obvious, he would have made it obvious that humans are not descendants of apesā€.

So, my comment would be:
A. Well, 80% difference in what makes a difference on the ground i obvious enoughā€¦
B. more than 35 differences in DNA is obvious enough,
C. on top of them 5 million insertions are obvious enough,
D. And then, we have to note that we really only understand some ~2% pf what the human genome is actually doing, so we cannot safely say that the changes are neutralā€¦
E. THEN, when looking at the result of the coding reasons (which produces the proteins), and we find that 80% of the proteins are different, then it does not seem that things are really neutral here.

Bottom-line, seems neutral theory is doubly adequate at its own standing, in the matter of measurement at hand, and in this specific case it seems the evidence is contradictory to what we expect if it was even true here a a special case.

And then, apart from this, we still have the problem that the mandatory predictions of common descent given the obvious external functional difference between humans and apes, lacking gradualism, and being the singular case of human condition on the planet, and other topics that we have gone through, really make the argument of common descent with apes so highly unlikely to me from a secular perspective (set aside the theological aspect now, which weā€™ve gone through before, that I find still good for those who would accept common descent as it gives them flexibility for co-existence).
Hope that helps to clarify where I stand.

But that isnā€™t what @swamidass was talking about. Werenā€™t you responding to the video? And you are understanding the paper incorrectly. The Y chromosome does form the same phylogeny as the entire genome. Itā€™s just that certain structural features of the chromosome have evolved quickly in the chimpanzee lineage, making it different in that way from the other apes. Technically, those are called autapomorphies, just a fancy way of saying things that happen on a single lineage at the tip of a tree. They arenā€™t informative of phylogeny, just as our loss of body hair tells us nothing about human relationships.

I donā€™t understand what you mean here. Chickens donā€™t even have Y chromosomes. Where did it say tlhis?

Yes, we should.

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Did you get past the abstract? I quote, from the introduction, no less:

ā€œTo begin, we should make clear what the neutral theory claims about nature. It is not simply a statement about the presence of neutral mutations, nor about the large fraction of eukaryotic genomes that are nonfunctionalā€”neither of these assertions would be contested by current competing hypotheses.ā€

You keep ignoring repeated corrections: the true figure is 71%.

Thatā€™s not 80% difference. It isnā€™t even 71% difference. Percentage of non-identical proteins is not a reasonable measure of difference.

The vast majority of those are neutral. The paper you just cited even says that.

Still mostly neutral.

That just isnā€™t true. 2% of the genome is protein-coding sequences. Another 8% or so of the sequence is transcribed into functional RNAs or is a target for transcription factors. There is good evidence that the rest is junk, and that isnā€™t just because we donā€™t understand what itā€™s doing.

Not everything is neutral, of course. Just a small percentage of changes are not. In protein-coding sequences, fewer changes are neutral compared to those in junk DNA; silent changes are close to neutral and so are some non-silent changes.

I think your bias is blinding you to any secular perspective. The predictions of common descent that @swamidass showed you, and others that have been mentioned here, are indeed borne out, the greatest of them being that nested hierarchy in which humans are embedded. Differences in function can be accounted for by a small number of mutations, and you are free to consider those divinely guided if you prefer. And there is indeed gradualism in the hominin fossil record. So your stand is puzzling unless we assume that you are highly resistant to data.

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It has already been explained to you that we do NOT have ā€œ80% protein difference,ā€ not in the sense you seem to understand the term.

Perhaps an example will help you?

I am going to create two hypothetical, very simple organisms, who each possess only two proteins that are each 250 amino acid residues in length:

Organism A:

YDDTCNKHHPNQDQMPQCNEECNGWVTSTSTLIDNGYGYCHMIDNVFNDFKQPAGRRWLM
DRMKNVGWMMKASGVVGYIIHCYMCKQWMCSLQSQVVCKDCEGQFKNVYDGKCTFSDTRG
VWQEGTSNYLAWYTENRVSVIFNPSCHMYRTTSGDYVALYHWTKAFQTADIEDWDRICAR
YFAVPLDMTRNDNFTTIPTMGQAGFHGLVHWTGMHERFQNWQCVVENPRICLFDNPPIGK
IYHAIRNFCP

TRNAMYWSICKYNAWNCQYVGSDIFFCYFEHFLAESVVTVPKCTPTICNKNEDTFALRWF
WRPVSWWQSENIGWVQKSMSPAERDKKVQIHDPIRDATKLWMWKKGEKPDSTGSTMWLLW
VPMEPCRWCTLAAKGYKDIPNSMNPPALWPRVNVILKGGVQWSWMVHLICKHDLVESQQP
VMQYKGFVMNGWEYFLLNTAAAPRHSTCFCHCIRSDFFCWLPKQVQDFTGSRLAHREDGY
MTFEFWCMKF

Organism B:

YDDTCNKHHPNQDQMPQCNEECNGWVTSTSTLIDNGYGYCHMIDNVFNDFKQPAGRRWLM
DRMKNVGWMMKASGVVGYIIHCYMCKQWMCSLQSQVVCKDCEGQFKNVYDGKCTFSDTRG
VWQEGTSNYLAWYTENRVSVIFNPSCHMYRTTSGDYVALYHWTKAFQTADIEDWDRICAR
YFAVPLDMTRNDNFTTIPTMGQAGFHGLVHWTGMHERFQNWQCVVENPRICLFDNPPIGK
IYHAIRNFCP

TRNAMYWSICKYNAWNCQYVGSDIFFCYFEHFLAESVVTVPKCTPTICNKNEDTFALRWF
WRPVSWWQSENIGWVQKSMSPAERDKKVQIHDPIRDATKLWMWKKGEKPDSTGSTMWLLW
VPMEPCRWCTLAAKGYKDIPNSMNPPALWPRVNVILKGGVQWSWMVHLICKHDLVESQQP
VMQYKGFVMNGWEYFLLNTAAAPRHSTCFCHCIRSDFFCWLPKQVQDFTGSRLAHREDGY
MTFEFWCMKW

The only difference between the two is the last residue in the 2nd protein, which I have bolded.

By your measure, these two organisms are only 50% similar.

Do you really think that is a reasonable interpretation?

How about these two:

Organism A (same as above):

YDDTCNKHHPNQDQMPQCNEECNGWVTSTSTLIDNGYGYCHMIDNVFNDFKQPAGRRWLM
DRMKNVGWMMKASGVVGYIIHCYMCKQWMCSLQSQVVCKDCEGQFKNVYDGKCTFSDTRG
VWQEGTSNYLAWYTENRVSVIFNPSCHMYRTTSGDYVALYHWTKAFQTADIEDWDRICAR
YFAVPLDMTRNDNFTTIPTMGQAGFHGLVHWTGMHERFQNWQCVVENPRICLFDNPPIGK
IYHAIRNFCP

TRNAMYWSICKYNAWNCQYVGSDIFFCYFEHFLAESVVTVPKCTPTICNKNEDTFALRWF
WRPVSWWQSENIGWVQKSMSPAERDKKVQIHDPIRDATKLWMWKKGEKPDSTGSTMWLLW
VPMEPCRWCTLAAKGYKDIPNSMNPPALWPRVNVILKGGVQWSWMVHLICKHDLVESQQP
VMQYKGFVMNGWEYFLLNTAAAPRHSTCFCHCIRSDFFCWLPKQVQDFTGSRLAHREDGY
MTFEFWCMKF

Organism C

YDDTCNKHHPNQDQMPQCNEECNGWVTSTSTLIDNGYGYCHMIDNVFNDFKQPAGRRWLM
DRMKNVGWMMKASGVVGYIIHCYMCKQWMCSLQSQVVCKDCEGQFKNVYDGKCTFSDTRG
VWQEGTSNYLAWYTENRVSVIFNPSCHMYRTTSGDYVALYHWTKAFQTADIEDWDRICAR
YFAVPLDMTRNDNFTTIPTMGQAGFHGLVHWTGMHERFQNWQCVVENPRICLFDNPPIGK
IYHAIRNFCP

DMFDMTTSCGVHVFMMNALHYGPFAILKHFSYAWGQWSCSGNVCWSFPWWTFLYFGYPDV
CVIFPRSRNSKRAKDFKHEWNMDQAVFQFMACLRLRVYICVVQLSMMLAYELMVPTMIRR
KFDDWRTSYVRQLSLKMMVTFIPYVRLKCQKKTTYPGCDAFLMNEDILAQQGEESYNDWH
KRHWAVFVSVYTYNDHNMNWATKLISPRVHHKPRCCRNEAYHMTFVQWAHSAVKWGQHPF
QTFCWMNSVF

The first protein for Organisms A and C are identical.

The 2nd proteins are completely different.

Again, by your measure, the similarity between the two organisms is 50%.

So, according to the metric you are using, the degree of difference between A and B is identical to that between A and C.

That seems absurd to me.

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You are standing on shaky grounds.

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And I would refer to this paper, which points out a series of fundamental errors in yours.
https://onlinelibrary.wiley.com/doi/full/10.1111/evo.13650

We understand that a great deal of the human genome isnā€™t doing anything.

You have yet to provide a single scrap of evidence that a single one of those sequence differences results in any functional difference.

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Chimps beat humans at some cognitive tasks.

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