Human Evolution Discussion with Ahmed

I think you misunderstood me. I mean there is no gradual transitions, so guided evolution will be abrupt too… So, few thousand mutations happening over millions of years would better produce those gradual transitions… where are they?
If on the other side of the argument, you accept an abrupt divine change to the DNA of great apes… I am asking you: why would that to you be less miraculous than a denovo creation… but since you do not accept guided evolution anyway, there is no context.

No, he is not doing that. He is just giving you evidence that He is one creator, same signature across various creatures. Again, if you want to think other primates are a guided series of evolution into each other, then you can choose that, except that you don’t.

Why didn’t the transitional forms in the path to homo-sapiens survive and we see them in the wild? For sure they would be better than the chimps. Is it logical they perish and the chimps don’t?

I agree it doesn’t on the DNA level. By result, it is though.

Yes, and I never stated otherwise. You know that emergent complexity doesn’t necessarily mean that the parts are “simple” by themselves. It just means that the parts, as well as the mere sum of the parts, are simpler with respect to the whole. The ants by themselves are dumb compared to the emergent intelligence of the whole colony. So to point out that the water molecules are not “simple” in an absolute sense does not refute the point of the emergent complexity of snowflake crystals.

When the video went over this, they weren’t trying to explain HOW life emerged. They just pointed out the basic observation that pretty much everything that we interact with is composed of atoms, which is organized into bigger complex structures, at several levels…i.e. atoms > molecules > proteins > cells > organs > individuals > societies. Although cells are of course build from more than proteins, besides that, this observation is simply a fact.

The hexagon structure isn’t observed in the water molecules by themselves. Individual ants cannot exhibit the same behavior seen from the colony as a whole. As I said previously, unless you believe that a God is somehow guiding all ants and designing each individual snowflake behind the curtain, you don’t have an objection to this.

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Nope. Conclusion based on facts. Facts of which you are clearly ignorant;

The Case for Junk DNA

The math showing your presumptions are wrong is quite simple, and is summarized here

The human and chimp genomes are 98.6% identical or 1.4% different. That difference amounts to 44.8 million base pairs distributed throughout the entire genome. If this difference is due to evolution then it means that 22.4 million mutations have become fixed in each lineage (humans and chimp) since they diverged about five million years ago.

The average generation time of chimps and humans is 27.5 years. Thus, there have been 185,200 generations since they last shared a common ancestor if the time of divergence is accurate. (It’s based on the fossil record.) This corresponds to a substitution rate (fixation) of 121 mutations per generation and that’s very close to the mutation rate as predicted by evolutionary theory.

Any questions?

You do understand that most species go extinct, right? Why would Homo be an exception?

It is an interesting question why only one species of Homo has persisted to now. But it should present no problem for accepting common ancestry.

What is your explanation for the existence of all these transitional forms? According to you, there should be none. Yet there they are, by the dozens. Where do these human- like apes (or ape-like humans) fit in with Allah’s creation? Why are they never mentioned in the Quran?

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That is clearly false, as you are not looking at the results presented in the paper you cite. You are merely quoting text that, put charitably, you have grossly misinterpreted.

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In the fossil record?

It wouldn’t be less miraculous, but it would be more in line with the actual evidence. That’s why guided evolution is preferable to separate creation.

But it isn’t the same signature. It’s different signatures, organized in a special way, the way that common descent would be expected to produce.

Who says they’re better than chimps? Are humans better than frogs? Better than maple trees? That’s the same sort of question. Now why don’t we see transitional forms today? Many possible explanations: some populations could be directly ancestral to humans and could all have transformed (through ordinary processes of mutation, gene flow, etc.); some populations could have been in competition with better-adapted populations and have gone extinct; some populations could just have been unlucky, in the volcano’s path at the wrong time. The point is that we do see such populations in the fossil record. What do you think they’re doing there?

No, as you’ve been told several times, it doesn’t. Most protein differences between chimps and humans are probably neutral or nearly so. And it isn’t even 80%. Why can’t you get that one simple point, if nothing else?

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That is utterly, objectively incorrect. Would you like to know why your claim is so directly contradicted by relatively simple evidence?

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That parenthetical comment is one of the better indications here of how profound is your misunderstanding of evolution. By what objective criteria would a particular phenotype be defined as an “abomination”?

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It is obvious that @Ahmed_AbdelSattar has a repertoire of pre-written responses that he just copy/pastes when he feels he needs to say something, whether or not it pertains to the current discussion. The 80% is probably included in them, and he can’t be bothered to edit it.

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I just rejected a couple snarky posts. I try to be fairly light-handed with the moderation but this thread is getting a bit aggressive and we don’t want it to get nasty.

So let me just remind everyone of some our community guidelines and expectations.

Especially as this is in the Conversation category, please try to keep the professionalism up and be hospitable as you engage with those you disagree. As much as possible try to keep criticism constructive. Posts should include questions, information, or otherwise move the conversation forward. You can be honest and to the point without being uncivil.

Remember, these are among our values:

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And many of those residues can be substituted by others with little to no functional effect.
That a protein’s amino acid sequence determines it’s structure and function does not mean many alternative amino acids can not do the job equally well, which as @John_Harshman also told you about, is revealed by the variants that exist in the human population.

Speaking of proteins more generally, biochemical experiments have routinely revealed that variant sites in proteins (those that aren’t conserved) also have little to no functional effects if substituted. Just to pick an example, check this reference on biochemical characterizations of mutations on a human G-protein coupled receptor:

Here they experimentally characterize the functional effects of almost all possible single amino acid substitutions in all positions on the protein, and the result is revealed in Figure 4c:
Fig4 C
The residues colored pale green tolerate all possible amino acid substitutions:

Unsupervised learning reveals functionally relevant groupings of residues

Given that our data spans thousands of mutations across several treatment conditions, we used unsupervised learning methods to reveal hidden regularities within groups of residues’ response to mutation. In particular, we applied Uniform Manifold Approximation and Projection (UMAP) (McInnes and Healy, 2018) to learn multiple different lower dimensional representations of our data and clustered the output with density-based hierarchical clustering (HDBSCAN; Figure 4—figure supplement 1; Campello et al., 2013). We found residues consistently separated into six clusters that exhibit distinct responses to mutation (Figure 4A,B). Clusters 1 and 2 are globally intolerant to all substitutions, whereas Cluster 3 is vulnerable to proline and charged substitutions. Cluster 4 is particularly inhibited by negatively charged substitutions and Cluster five by proline substitutions, while Cluster 6 is unaffected by any mutation.

As the paper also states, the tolerance to mutations of individual positions in the protein well predicted by comparative genetics:

Metrics for sequence conservation and covariation are often used to predict the effects a mutation will have on protein function (Adzhubei et al., 2013; Capra and Singh, 2007; Hopf et al., 2017). Mutational tolerance, the mean activity of all amino acid substitutions per residue at each agonist concentration, is highly correlated to conservation, both across species for the β2AR (Figure 3—figure supplement 1A; Spearman’s ρ = −0.74; 55 orthologs, predominantly mammals but including a few other vertebrates as well as a small number of invertebrate beta-like sequences, identified from the OMA Database, Supplementary file 1), and across all Class A GPCRs (Spearman’s ρ = −0.68; Figure 3A and Figure 3—figure supplement 1B; Altenhoff et al., 2018; Capra and Singh, 2007; Hopf et al., 2017) at EC100.

Results like these are not at all unusual, so the burden of proof is on you to explain why your non-sequitur has any merit. I remind you that you are the one who attempted to derive the conclusion that the very few amino acid differences between proteins shared among human and chimp must have a functional consequence simply because the majority of proteins have a tiny handful of such differences.

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I think that we all understand you very well.

Here are photos of fossil skulls. If, as you claim, there are no gradual transitions, at which point do you draw the line between human and nonhuman?

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Ahmed: “There are no transitional forms leading to humans.”

Also Ahmed: “Why did all the transitional forms leading to humans, that we know exist because they are found in the fossil record, go extinct?”

SMH

(Not direct quotes, just paraphrases of things he has said here.)

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I’m sorry but these are just assertions.

Again I have to say you seem to have a difficult time with the concept of evidence. Evidence does not MAKE anything be true. Something is either true or it is not, regardless of what we happen to have evidence for. But evidence is what should guide our beliefs about what is true.

But what conclusions we, as human beings, should draw about what is true about the world(what should we believe and why?), depends on what evidence we have available to us when we have searched for and collected it.

Given that we have a pattern in the data supporting a hypothesis that explicitly predicts that pattern, and we do not have any competing hypothesis that predicts that same pattern of data, the fact that we do have a hypothesis that predicts it then becomes a reason to accept the hypothesis as likely being true. The data is expected given the hypothesis.

So no, there is no argument from ignorance going on. I am appealing to the fact that we have a hypothesis that makes a whole lot of sense of the data.

No, because I am not saying it’s true just because no alternative hypothesis is known. I’m saying evidence should guide our beliefs, and the evidence only supports one hypothesis.

I can’t make sense of that statement. What is a “general homoplasy”?

That’s a nice assertion, but that is all it is.

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And to do the exercise, we should assume random normal distribution of mutations, I suppose?

@Rumraket What do you make out of that, yourself, and the rest of it?

So, if the difference between the processing power of the basic desktop PC and the largest cray computer is way larger than the difference between the PC and a calculator… does that make a calculator a computer??!

You reasoning is quite flawed.

You don’t do intra-category comparisons versus inter-category comparisons and reach to anything.

The problem is circular logic again. You start by presupposing common descent, so humans and chimps are great apes, and them you give yourself a green card for doing such a comparison.

I have to tell you it is irrelevant and misleading.

:ok_hand:
I vouch for that!

That the Y-chromosome is fast-evolving compared to the rest of the genome, and therefore the prediction that if humans and chimps share a common ancestor, the Y chromosome should be more different on average, than the rest. The authors explain why the chimpanzee Y is more different from human and gorilla with a rather straightforward inference based on observation, and that explanation makes logical sense.

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Normal in what sense?

Location? Type ie transversions/transitions? Fitness effect? Size of proteins?

Mutations in coding regions are more likely to be deleterious, and deleterious mutations usually don’t fix.

A preponderance of a type of mutation may make identical mutations between clades marginally higher.

Fitness effects - again, deleterious mutations usually do not fix.

Smaller proteins obviously would have a higjer chance of being identical.

Counting the above, the actual proportion of identical proteins should be a bit higher than calculated.