Human Evolution Discussion with Ahmed

[thoughtful (Valerie (non-scientist))]

@John_Harshman

I don’t understand what you mean here. Chickens don’t even have Y chromosomes. Where did it say tlhis?

Sorry, I misread that part of the paper. It said the amount of shared gene families with chimp y-chromosome was the same as humans to chickens autosomes.

[Faizal_Ali]

@CrisprCAS9

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

I’m really having a hard time following the argument @Ahmed_AbdelSattar is trying to make here. If the difference between humans and chimps can be attributed merely to a number of SNP’s or similarly minor mutations in a number of proteins doesn’t that strengthen the argument for common descent? i.e. very small changes can have very big effects?

That is to say: He’s wrong, but even if he was right, he’d still be wrong.

[John_Harshman]

@thoughtful

It said the amount of shared gene families with chimp y-chromosome was the same as humans to chickens autosomes.

What that just means is that chimp Y chromosomes have lost a lot of genes. Y chromosomes are losing genes all the time. That’s why they’re so much smaller than X chromosomes. Chimps just did it faster. I would actually expect the chimp Y chromosome to evolve faster than that in other apes, given the extreme sperm competition in chimps. The more sperm they make, the more gametogenesis they have to do, and that increases the number of germ line replications. Human Y should evolve a bit more slowly and gorillas even more slowly.

[Argon]

Most of the points were long ago addressed in the Talk.Origins FAQs. A year or so of genetics or molecular biology coursework with a decent introduction to population genetics would really go a long way. Would anyone like to suggest a couple good evolution-relevant genetics texts for Ahmed? The math shouldn’t be a problem but gaining the background information and contextual knowledge would clearly help.

[Rumraket (Mikkel R.)]

This lecture series - Introduction to Genetics and Evolution, by Mohamed Noor - is quite good:

[Faizal_Ali]

@Argon

Would anyone like to suggest a could good evolution-relevant genetics texts for Ahmed? The math shouldn’t be a problem but gaining the background information and contextual knowledge would clearly help.

@swamidass provided him such information in the video. Do you think he was grateful for this and found it helpful? Did it help him realize that he does not understand the topic nearly as well as he thinks? I have not yet watched the whole thing, so I will withhold judgment for now. But that should give an idea of how likely he is to benefit from such education.

[Rumraket (Mikkel R.)]

Oh and here’s a link to the actual course, I think it starts today (if it has not already):

Introduction to Genetics and Evolution

[John_Harshman]

@CrisprCAS9

@Ahmed_AbdelSattar

THEN, when looking at the result of the coding reasons (which produces the proteins), and we find that 80% of the proteins are different

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

This bears amplification: it’s very likely that most of the phenotypic difference between humans and chimps is the result of changes in regulatory sequences like transcription factor binding sites, not proteins.

[T_aquaticus]

@Ahmed_AbdelSattar

A. Well, 80% difference in what makes a difference on the ground i obvious enough…

Here are two short amino acid sequences:

YCHASQMLNH
YCHAPQMLNH

There are 10 amino acids and they differ by 1 amino acid. Are those amino acid sequences 0% similar or 90% similar?

@Ahmed_AbdelSattar

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.

Coding regions make up ~1% of the genome. This means that 99% of mutations occur outside of coding regions. Only 5% of the human genome shows evidence of function. Conservatively, more than 80% of mutations are going to be neutral.

[T_aquaticus]

@Ahmed_AbdelSattar

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…

Yes, you say that. However, you have yet to produce any evidence that this is the case. What evidence are you basing this on?

Let’s do some back of the envelope calculations. Let’s say the mutation rate is 50 mutations per person per generation. We have a generation time of 25 years, a population of just 100,000 individuals, and 5 million years since divergence. That’s 5 million mutations per generation over 200,000 generations, or 1E12 mutations (i.e. 1 trillion mutations).

Humans and chimps are separated by ~40 million mutations. If we assume half of those mutations occurred in each lineage that leaves 20 million mutations that can now be seen in the human population. As I showed above, trillions of mutations occurred in the lineage over that time, and we only see 20 million of them now.

So how can you say that 20 million is too many to have made it into the modern human population?

[Ahmed_AbdelSattar]

@Nesslig20

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.

Hi @Nesslig20 ,
Hope this message finds you well.
We are talking in the context of reaching to the human condition, with is at the pinnacle of intellect, and consciousness, and rationality. It is due to those features that we have gained dominance.
Now, whether evolution cares or not, this is a fact… and remember that the very point of the discussion is whether humans evolved from great apes or not in the first place … so, as your comment involves a presupposition of evolution as a given, I think it is out of context. You cannot assume evolution when the debate is about evolution.

In any case, you can take my expression as poetic if you’d like and skip it. To me it is intentional, because obviously I do believe in intentionality behind the whole scene (regardless if common descent is accepted or not).

Hope that helps clarify.

[John_Harshman]

Just to point out, population size is irrelevant for neutral evolution. If the mutation rate per person per generation is µ, the number of alleles fixed per generation is also µ.

[Ahmed_AbdelSattar]

No, @Faizal_Ali , the argument is in the context of the discussion, where Josh was arguing for neutral theory and that potentially, positive mutations were not that much out of the 35Million SNP’s and 5million insertions that are the difference in the genome (if at all we take the higher than 98pct estimate he presented).
The point I am making is double fold:

1. Empirical evidence is that the mutations are predominantly not neutral (obviously because proteins are 80% different).
2. It means that invoking neutral theory may be inadequate.

You can refer to a thread with Josh that I am having here that has more on this: HYG: Human Evolution Discussion - #34 by Ahmed_AbdelSattar

[Ahmed_AbdelSattar]

I just provided evidence for the protein variance; the origin of which and what else is impacted can be looked at…
For example, I think it is also reasonable to expect that GRN’s are also affected, maybe as hard as protein coding regions (and maybe not)! If this is the case, then it will be a more serious issue, because a significant level of mutation of GRN’s typically causes the death of the being. Anyway, if you have literature on this, I’d be happy to know about them.

[Faizal_Ali]

@Ahmed_AbdelSattar

In any case, you can take my expression as poetic if you’d like and skip it. To me it is intentional, because obviously I do believe in intentionality behind the whole scene (regardless if common descent is accepted or not).

Common descent is an important part of evolutionary theory, and you have stated that you do not accept it.

@swamidass went to great lengths in the video to present some of the evidence that supports this, then he would ask if separate creation has any mathematical model that better explains these observations. You would, instead, ignore the question and instead just ask some silly and irrelevant question like “Why aren’t there talking sharks?”

Would like to take the opportunity now to answer some of the questions he was asking? Pick any of the mathematical arguments he presented in the video, and show how creation better models the observations.

@Ahmed_AbdelSattar

The point I am making is double fold:

1. Empirical evidence is that the mutations are predominantly not neutral (obviously because proteins are 80% different).

Your conclusion does not follow from your claim. Your claim is wrong as has already been demonstrated here: Human Evolution Discussion with Ahmed - #37 by Faizal_Ali. But since your logic is deeply flawed that doesn’t even matter.

[Ahmed_AbdelSattar]

@T_aquaticus

Here are two short amino acid sequences:

YCHASQMLNH
YCHA P QMLNH

There are 10 amino acids and they differ by 1 amino acid. Are those amino acid sequences 0% similar or 90% similar?

I think in this context the point is whether they are similar or not, because the nucleotide sequences that generated both of those are not synonymous, and if one mutated into the other, it means the mutation also got fixed while it is not neutral.

@T_aquaticus

Coding regions make up ~1% of the genome. This means that 99% of mutations occur outside of coding regions. Only 5% of the human genome shows evidence of function. Conservatively, more than 80% of mutations are going to be neutral.

Do you think that all what we don’t yet understand is non-functional?
Maybe consult the E.N.C.O.D.E project?

Side-note: Yet, I have to ask you a question to ponder upon: replicating DNA takes up significant energy and materials… if all the 99% is junk, wouldn’t it make sense that “evolution” would have gotten rid of it?

[Ahmed_AbdelSattar]

Your math leads no where, as it treats mutations as if they just happen and fix!
You are ignoring: the core of the matter which is the beneficial mutations (which look to be quite plenty, e.g. changing 80% of proteins and fixing), how rare beneficial mutations are, fixation probability and time, and coherence of those mutations.
You will also have to factor in the deleterious mutations that also got fixed (refer to the discussion about humans losing physical advantages of the alleged chimp-ancestors).
If you consider those, then the case is hopeless.

You can have only have a valid case if you can prove that the non-neutral mutations are really very few… which the evidence is quite against.

[T_aquaticus]

@John_Harshman

Just to point out, population size is irrelevant for neutral evolution.

You are absolutely right. However, I was calculating the total number of mutations that would have happened, not the rate of fixation.

[evograd (Blogging Graduate Student)]

@Ahmed_AbdelSattar

Side-note: Yet, I have to ask you a question to ponder upon: replicating DNA takes up significant energy and materials… if all the 99% is junk, wouldn’t it make sense that “evolution” would have gotten rid of it?

Do you know how much energy and materials it takes to replicate the human genome? Have you actually looked into this, or are you relying on your intuition? Because the actual answer isn’t that hard to find - it’s a tiny fraction of the cell’s energy budget, not enough to cause selection to favour losing the excess.

https://www.pnas.org/content/112/51/15690

[evograd (Blogging Graduate Student)]

@Ahmed_AbdelSattar

Empirical evidence is that the mutations are predominantly not neutral (obviously because proteins are 80% different).

Can you please lay out the logic that gets you from “80% of human chimp proteins are different by at least one amino acid” to “therefore most mutations are non-neutral”? I think you have some grave misunderstandings that need to be resolved before any worthwhile discussion can be had.

You have also been corrected at least a half-dozen times on the 80% figure - it’s 71%, NOT 80%. Please stop using the incorrect figure.