Human Evolution Discussion with Ahmed

Wow! That was some discussion, though easy going and pleasant!
In this discussion with Dr. Swamidass, he made a presentation for why he accepted evolution (primarily human common descent). He gave the following arguments and I gave counter arguments:

  1. DNA genome analysis shows more similarity between human and chimp (he said 98%) more than mouse and rat (80%). My response was that human and chimp protein similarity is only 20%, which means that the similarity on DNA level is not indicative of similarity on the ground, which is what makes a difference.

  2. He pointed out that molecular clock measurement using neutral evolution theory appears to be consistent with divergence time of chimps and humans, likewise between mice and rats. My comment is that molecular clocks rely on neutral mutations while the functional differences depend on the beneficial mutations which cannot be (in my opinion) justified by random mutations especially given the little time available for divergence.

  3. He argued that there are types of neutral mutations that are common for mutations that occur between ancestors and off-springs. I commented that there are also more mutations that are not of that type and that those mutations are the ones that are responsible for the phenotypic changes, so focusing one type without explaining the other is not enough.

  4. He argued that the the higher than average mutation in the Y chromosome and the lower than average in the X chromosome are consistent with the nature of the X chromosome which spends more at the female, and the Y chromosome which spends more in the male with higher chances of mutation. I commented that there can be other explanations to this phenomenon which might be just a statistical reflection of the nature of those two chromosomes in chimp and human likewise.

  5. His point of view is that there seems to be no special evidence for design in the human genome variance versus the chimp. I argued that the functional variance is quite obvious, and that if the variance did not require new design then we should expect and should find many creatures that share the human condition just like humans; crocodiles, sharks, … etc. He agrees that this is a mystery and that science does not answer all questions by nature.

  6. He argued that most of the mutations are neutral and that maybe we did not need that much positive mutations after all between humans and great ape ancestors. I argued that actually on the physical level, the great apes (example chimp) have superior physical abilities including an obvious strength advantage and if humans were descendants of chimps (edit correction: chimp ancestors) then it is not reasonable that we lose those abilities (by virtue of natural selection), especially that we needed them, and even that we go to the gym until today to gain the muscle mass that makes us healthy and in good shape, so it is does not compute that we acquire extra positive mutation and meanwhile lose the superior traits that we needed in the process.

  7. I argued that using population genetics it can be shown that there is no available time to collect the needed mutations and fix them, invoking waiting times, generation length, initial population size, and number of off-springs. He argued that maybe those mutations happened in parallel rather than in series. I commented that even if they happen in parallel there is still no available time and that there is the major issue of coherence of the changes. On that topic he invited me to go together into a more involved exercise using simulation software (SLIM, MS Prime) at a later time, or do it with a group of scientists on peaceful science.

We also discussed many other things, and in short he sees that since the math supports it he accepts it and if I reject it then I have to come up with a better mathematical model, though from my side, I argued that I needed the model to produce the predictions that matter most about the human condition (which it doesn’t) and hence I have no reason to accept it.

  1. We also went to discuss more subtle issues about the animals we see around us and whether it is reasonable to think that their behavior can be explained by genetics. I argued that it cannot as they exhibit behaviors that in our experience mandates learning (which can only be explained by a teacher), and he argued that maybe there are explanations that we do not yet know about and that the real behavior might be a step-by-step one that is only apparently well-thought of. I argued, giving examples, that this would be quite a far fetch.

At the end Dr. Swamidass affirms he believes in Divine providence of the creation process, and that what we consider random to us is not random to God.

Dr. Joshua Swamidass, PhD, MD, of Washington University, author of the Genealogical Adam and Eve, a Christian Scientist, computational biologist, also founder of Peaceful Science.

Watch here and share your opinion:


Hi Ahmed! Welcome to the forum. I haven’t watched the discussion yet, I will try to do so tomorrow, but for now I’d like to respond to a couple of your points.

When you say the human and chimp “protein similarity” is 20%, presumably you know that this is approximately the proportion of proteins that are 100% identical (a more accurate figure would be ~29%, see It doesn’t mean that when we compare protein sequences, there is only a 20% similarity. This seems like a very strange metric to use, and doesn’t change the fact that even the proteins are extremely similar between humans and chimps - overall, the coding regions are ~99% identical. In other words, a third of human and chimp proteins are completely identical, and the vast majority of the rest only differ by 1 or 2 amino acids.

The neutral mutations would still point to common ancestry though, even if the beneficial mutations were too numerous to be explained naturally. Do you argue for some kind of guided evolution where common ancestry is true while a creator added/guided beneficial mutations? Otherwise your response is more of a sidestep.

If this was where Josh brought up the mutation spectrum, then my response is the same as for #2.

Humans did not descend from chimps. We share a common ancestor, albeit one that was probably more chimp-like than human-like. What makes you think we “needed” great strength like that of chimps? We seem to have done quite well for ourselves without great strength, don’t you think? Maintaining all that muscle mass requires a lot of energy, and in very simplistic terms, we repurposed those calories from our diets into our large brains, which provides a different benefit compared to great strength.

There are countless animal behaviours that are clearly somehow genetic, as they do not involve any kind of learning. There are also lots of good examples of experiments where we can alter animal behaviours by manipulating the genome. I believe you discussed this with others recently as well: Does Studying Life Lead to Belief in God?| w/ Jackson Wheat, Steve McRae, mod Dapper Dino| Debates 5 - YouTube


I just wanted to say that you are a very clear writer, which I appreciate, so now I am interested in watching the dialogue.


99.5%, according to the chimp genome paper you just cited.

It would be good at that point to introduce the two concepts pleiotropy and tradeoffs. He should look those up.

@Ahmed_AbdelSattar, I think your number one difficulty is that you are conflating two different matters: common descent vs. separate creation and unguided vs. guided evolution. If you think there are too many beneficial mutations in the human lineage to account for by natural processes (which most scientists don’t, but never mind), the overall data would be better explained by guided evolution with common descent rather than separate creation. There are no data supporting separate creation. Separate creation can’t explain any of the things @swamidass brought up. And all your objections were about things that could be explained by guided evolution. Why not go with that? What’s your objection?


Rather than covering all the points and have the discussion all over the place, let’s start with point 1.

What do you mean human chimpanzee similarity is only 20%? Do you have a citation?

Protein coding sequences are 99.1% identical between the two species [86], and in two-thirds of the proteins amino acid sequences are absolutely the same [8].

Source: Differences between human and chimpanzee genomes and their implications in gene expression, protein functions and biochemical properties of the two species | BMC Genomics | Full Text

Now, some might argue that perhaps the minor differences between homologous sequences aren’t the main differences, and that indels and insertions constitute the majority of what is different between humans and chimpanzees.

But, The PATTERN of insertions and deletions ALSO matches that predicted by common descent; they form a nested hierarchy.


That doesn’t appear to be based on a whole-genome comparison, as it (reference 86, I mean) predates publication of the chimp genome paper. And they’re reading reference 8, which is the chimp genome paper, backwards. It’s two thirds that are different, not two thirds that are identical.

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I just want to point out that your response to this argument can be used to dismiss to any imaginable scientific finding. It is always possible, in principle, that some piece of data will be found to have some alternate explanation in the future. For that reason the mere future possibility of alternate explanations-response just isn’t a good argument at all.

The fact is that given the empirical mutation rates measured in these chromosomes, common descent provides us with a perfectly good explanation for the higher and lower fraction of mutations in the Y and X chromosomes respectively, separating humans and chimps, so in the absence of an actual alternate explanation (as opposed to the mere logical possibility that one will be found in the future) - this is de facto evidence for common descent.


Thank you for your comment. Looking forward to your notes.


thoughtful Valerie (non-scientist) Imaginative YEC Mom
June 20

I just wanted to say that you are a very clear writer, which I appreciate, so now I am interested in watching the dialogue.

**Here is the paper I am quoting: Eighty percent of proteins are different between humans and chimpanzees - ScienceDirect **
For some reason the system here is not making me put hyperlinks, so I just put the code!
Now, the point is that to use direct DNA genome comparison, one should first establish that this metric will yield the sought for similarity phenotypically (given all the problems with the comparison method when two species are involved).
Now, the paper actually shows that DNA comparison is not significant, as on the ground, the manifestation of DNA (which is the proteins) is way separated from the DNA similarity.
Another important observation is that the differences between the human and chimp genome are not such innocent differences. If they were primarily neutral, then they would have produced synonyms resulting in the same proteins, but they are obviously not (in 80% of the cases), yielding from my opinion the matter of using neutral theory here not adequate (refer to point 2 also).

Refer to my answer in point 1, and my original quote point 6). In short, it seems that invoking a common ancestor, and a typical neutral accumulation of mutations with little beneficial ones and elimination of deleterious ones does not look to be what is happening there.

See my response to point 2 above.

PS: Thank you for the note about chimps. I edited the text to “chimp-ancestor” to avoid ambiguity. As obvious from the rest of the points and the discussions, I do not think that humans descended directly from chimp.
Mow, concerning your comment about strength, I do think that (if evolution is what happened) as humans ascended the ladder, still living in the wild, strength would for sure give a survival advantage in the wild. We did still need to run fast, climb, and wrestle. A weaker great ape with some intelligence is going to be outperformed and outbred by a stronger great ape with intelligence. I cannot find a justification for this devolution of humanity into weak creatures in comparison with great apes, except that descendance is likely false. Even at the early ages of humanity, warriors and strong men are unarguably at an advantage verses weak comrades!

I am talking about behaviors that involve knowledge typical to learning. Instincts are mysterious too, but even if we accept some of them is genetic, they cannot reasonably lead to a creature having civil engineering skills, or signaling skills. I think the response of Jackson was not satisfactory to my argument too, which I have already explained to him in our discussion.

Yes I do: Eighty percent of proteins are different between humans and chimpanzees - ScienceDirect

Don’t you think that judging based on the final outcome is more objective?

== The system is restricting me to me link per message as a new user, so I had to remove the links from your text! I hope that an admin can help fix this!

Incidentally, this phenomenon has been observed in other species, not just humans and chimps. Chromosomes that spend more time in males accumulate more mutations than autosomes, and chromosomes that spend more time in females accumulate fewer. If I recall, this was first observed in Drosophila. And as you yourself have noted, it’s to be expected given the disparate number of germ line cell divisions in gametogenesis in each sex.


Being different, and the degree of difference, is two different things. Identical twins are not actually completely identical, but they’re still very very similar. All people are “different”, but it is the degree that matters here.

You could have 100% of proteins have one amino acid difference out of 200 total amino acids pr. protein. That would mean all proteins are different, but the difference is only 0.5%.

That is the same sense in which 80% of proteins are different between humans and chimps. They are different by under 1% from each other.


There are several problems here. Trivially, the source is not making use of whole-genome comparisons, and the number is wrong; it should be 71%. The better data come from here: The Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 2005; 437:69-87.
Some quotes:

"• Orthologous proteins in human and chimpanzee are extremely similar, with ,29% being identical and the typical orthologue differing by only two amino acids, one per lineage.

•The normalized rates of amino-acid-altering substitutions in the hominid lineages are elevated relative to the murid lineages, but close to that seen for common human polymorphisms, implying that positive selection during hominid evolution accounts for a smaller fraction of protein divergence than suggested in some previous reports."

So, while a relatively small proportion of proteins are absolutely identical, almost all of them are nearly identical, and in fact more so than when comparing the rat and mouse. Further, most of those amino acid changes appear to be neutral or nearly neutral, not adaptive. There is no justification for calling this “20% similar” or even “29% similar”. Proteins are upwards of 99% similar between humans and chimps if you judge that by counting amino acid differences, as you should.


In one day this restriction will go away.

The paper you cited actually shows, as do many others, that human and chimp proteins are actually more similar to each other than the rest of the genome as a whole. Both give overall similarities >95% - the proteins are >99% identical in terms of their sequence.

Most of the differences between the human and chimp genomes are neutral. The same is true for most of the differences between the protein-coding genes. More than 80% of the nucleotide differences in coding regions result in synonymous codons (they don’t change the protein sequence). This is a much more relevant measure than simply counting the number of proteins that are non-identical.
There is also no reason to believe that all of the minor differences in the protein sequences result in any kind of functional difference - a few of them demonstrably do, but most of them probably don’t.

Even if you disagree about the beneficial mutations, that doesn’t detract from the fact that the neutral mutations clearly point to common ancestry. This is an issue you have to address independently from your objections to the number of beneficial mutations or how the selection pressures would work. Accepting common ancestry is not the same as accepting purely naturalistic evolution.

Do you think that humans today are outcompeted by strong apes? What about tribal communities with extremely limited technology - aren’t they surviving just fine? We obviously survive just fine with the level of strength we have today, whether aided by technology or not. I think you’re severely underestimating how much of an advantage increased intelligence is. We don’t need to wrestle predators or prey and kill with our bare hands - we make tools and hunt in groups, likely over large distances as we are among the best endurance runners in the animal kingdom. It’s really not all about strength. Just look at the diversity of animals alive today, the vast majority don’t rely on any kind of great strength to survive and flourish.

I don’t know who is arguing that civil engineering skills are genetic and don’t involve learning. Hopefully no one. Can you give some examples of what sort of behaviours you think involve knowledge that are unexplained by biology, and where you think they come from instead?


Thank you for your note. I am looking forward to your comments.

So, if we invoke guided evolution, and in the absence of gradualism from the evidence, would you suggest that we start with a great ape ancestor, and then his genome is suddenly rewritten, and likewise a female counterpart? How would that be different, in principle, from a separate creation?

If you alternatively say that the genome will be edited gradually, over the same divergence time, then where are the gradual transitions which should reflect onto great apes that have intellect, language, mathematics, tools, … etc. Obviously a medium level of any of those would make an ape that is superior to the extant ones today, so it is not reasonable that inferior ones survive and the superior ones don’t!
PS: probably this matter would be different if we look at other animal transitions.


What I am saying is that this is not conclusive evidence. The matter of understanding of muta-genesis and what affects it, and the variances in mutation rates between primates, and between paternal and maternal germlines, and even the reason of mutations (DNA Damage / replication error) together with many confounding factors, seems to be under review even as we speak.
I have come across this interesting (and pretty recent) paper that you might find informative: Evolution of the mutation rate across primates - ScienceDirect

If you think that this evidence is conclusive, please tell me why. I am open to suggestions.

Ok, let me expand on this…
So, Josh invokes neutral theory. He also says that the majority of the mutations are probably neutral when I say that we need too many millions of mutations to reach to a human from an ape…
So, the empirical evidence has things to say here… and the evidence say a different story!
The fact that 80% of proteins are different means that in coding regions at least 80% of mutations are not neutral, and they are even fixed nevertheless!
You see where this is going.
I see this has two implications:

  1. It confirms my argument that there are too many non-neutral mutations to account for.
  2. It suggests that the invocation of neutral theory may be inadequate in this context altogether.

If you think differently, let me know, and tell me why.

The fact that Aghmed specifically said “ascended the ladder” it already reveals that he has a gross misconception of evolution.

The “ladder” he is referring to is a cultural hangover of Aristotle’s Scala Naturae or the “great chain of being”, where humans are on the top of the “higher” beings and with “lower” beings on the bottom. Prior to the 1930’s ““modern”” synthesis (quotes are there for a reason), one of the competing alternatives to Darwinian evolution by natural selection was “orthogenesis”, which says that evolution progresses to some teleological goal. Climbing up the evolutionary ladder! This idea has fallen out of favor and evolution is NOT a progressive process that aims towards some predetermined end goal.

Trying to order organisms across a scale from “lower” to “higher” based on traits that you happen to to value is completely arbitrary. Evolution doesn’t care about what you happen to value, and it produces organisms not along an arbitrary ladder, but a tree.

And there is no “higher” or “lower” place on the tree, just like there is no UP or DOWN with respect to the universe. Hence, any complaint about our species not being “stronger” (or whatever attribute you might think of) than you would otherwise would’ve thought to be “better” is like asking whether the earth is above or below the sun.

“It is absurd to talk of one animal being higher than another. We consider those, when the cerebral structure / intellectual faculties most developed, as highest. A bee doubtless would when the instincts were.”
— Charles Darwin (1837), notebook jottings

“Never use the words higher or lower .”
— Charles Darwin, note written on the margin of his copy of Robert Chambers’ 1844 Vestiges of The Natural History of Creation

“With respect to ‘highness’ and ‘lowness’, my ideas are only eclectic and not very clear . It appears to me that an unavoidable wish to compare all animals with men, as supreme, causes some confusion; and I think that nothing besides some such vague comparison is intended, or perhaps is even possible, when the question is whether two kingdoms such as the articulata or mollusca are the highest. Within the same kingdom, I am inclined to think that ‘highest’ usually means that form, which has undergone most morphological differentiation’ from the common embryo or archetype of the class; but then every now and then one is bothered (as Milne Edwards has remarked) by ‘retrograde development’, i.e. the mature animal having fewer and less important organs than its own embryo. The specialization of parts to different functions, or ‘the division of physiological labor’ of Milne Edwards exactly agrees (and to my mind is the best definition, when it can be applied) with what you state is your idea in regard to plants. I do not think zoologists agree in any definite ideas on this subject; and my ideas are not clearer than those of my brethren.”
— Charles Darwin “Letter to Joseph Hooker”, Jun 27