Stairway to Understanding Hypothesis vs. Common Descent, my presentation to science students and church groups

[colewd (Bill Cole)]

@swamidass

You’ve changed the topic Bill. We are discussing @evograd’s and @glipsnort’s articles, which you seem to have not read.

I will back off. Do you have links easily available?

[glipsnort (Steve Schaffner)]

@r_speir

New answer: Humans and a Proto-great ape.

Baboons aren’t apes – they’re monkeys. What’s your answer now?

[T_aquaticus]

@colewd

A charitable reading of this article will show that a deterministic mechanism is the only credible explanation for the origin of this molecular machine.

Please present the evidence.

[scd]

@glipsnort

Common design isn’t a scientific model because it can’t do either

are you saying that common design cant make any predictions? because its simply not true.

@r_speir

Ok, now I see where you are going

@colewd

I don’t understand your point

its possible that almost all creatures had very similar genome in their initial creation (we already know that since human and chimp for instance are very similar). so they just got neutral mutations over time and thus that result.

[Timothy_Horton]

@colewd

A charitable reading of this article will show that a deterministic mechanism is the only credible explanation for the origin of this molecular machine.

Please present the evidence

“Charitable reading” = “check your mind and scientific knowledge at the door, swallow the DI’s usual evidence-free guff”.

[T_aquaticus]

@scd

its possible that almost all creatures had very similar genome in their initial creation (we already know that since human and chimp for instance are very similar). so they just got neutral mutations over time and thus that result.

Then how do you explain the fact that baboon DNA differs from human DNA by a much larger margin than chimp and human DNA? How do you explain the fact that chimps share more DNA with humans than they do with any other ape or primate?

[scd]

@T_aquaticus

How do you explain the fact that chimps share more DNA with humans than they do with any other ape or primate?

two factors can effect the result: the initial difference among these species (say chimp and human were more similar to each other in their creation), or the time that was past since their creation (shorter between human and chimp).

[Rumraket (Mikkel R.)]

@colewd

I don’t understand your point.

That much is obvious.

Why was his model for common descent inadequate?

Because it doesn’t deal with the tree-structure in the data for individual shared similar (homologous) genes. It does not explain why the sequences of individual homologous genes, shared among species, are different from each other, and it doesn’t explain why they are different from each other in a way that implies a branching process. It also doesn’t explain why different loci would corroborate the same branching topology, whether between different genes, or even different parts of the same gene.

His model deals with only one aspect of the data: The co-occurrence of particular sets of genes in different species. The fact that some genes are found together across different species is explained by appeals to their mutual dependency. And the explanation for the tree-pattern specifically is proposed to be that there are multiple layers of dependency between these different genes.

He was not modeling common descent he was comparing gene families.

We know.

The families were not following a tree pattern that common descent would predict.

Yes they were, Bill, you’ve got it exactly opposite. Winston is proposing to explain that very fact better than common descent. He’s not saying there isn’t a tree pattern, he’s saying the tree pattern is explained better by a dependency graph.

When I looked at a potential smoking gun

A smoking gun for what?

like the data where 100 genes were common to Rats and Chimps and missing in Humans and Mice the data base appeared to be inaccurate.

But then that would also conflict with the dependency graph, as that would predict that if they’re co-dependent in chimps, they’d probably also be co-dependent in humans.

You are deeply infatuated with Ewert’s dependency graph, but you don’t even understand what it forking is.

This is the issue in my mind. If genes are not following the tree pattern then common descent is in trouble.

So it is the dependency graph. The dependency graph is supposed to explain the tree pattern in the distribution of genes among species, just better. That’s the whole goddamn point it was proposed in the first place.

LOL

[T_aquaticus]

@scd

two factors can effect the result: the initial difference among these species (say chimp and human were more similar to each other in their creation), or the time that was past since their creation (shorter between human and chimp).

What would the pattern of those initial differences be with respect to transitions, transversions, and CpG’s, and why?

How far apart in time were these creation events?

[colewd (Bill Cole)]

@Rumraket

So it is the dependency graph. The dependency graph is supposed to explain the tree pattern in the distribution of genes among species, just better. That’s the whole goddamn point it was proposed in the first place.

You are claiming to understand this?

The pattern he is trying to follow is that of a dependency graph as a better explanation of the data than a tree. Genes not following a tree is not a problem for a dependency graph is what the graph predicts which is re use of modules.

[Rumraket (Mikkel R.)]

@colewd

You are claiming to understand this?

The pattern he is trying to follow is that of a dependency graph as a better explanation of the data than a tree.

No, he’s trying to explain the tree-like property of the data with a dependency graph.

Here let me help you by quoting the paper directly:

Winston Ewert - The dependency graph of Life: The essential idea is that the better fitting model is the one that explains the data with least complexity, quantified as improbability. If the dependency graph hypothesis is correct, postulating modules should help explain otherwise improbable distributions of genes. On the other hand, if the dependency graph hypothesis is incorrect, data that deviates from the tree should not fit the graph either, and thus should not be made more probable by the hypothesis.

Did you even read his paper?

Genes not following a tree is not a problem for a dependency graph is what the graph predicts which is re use of modules.

Wrong. The other way around.

By now it is conclusively demonstrated that you have not the slightest clue what is going on here. Holy shirtballs!

[r_speir]

@glipsnort

Baboons aren’t apes – they’re monkeys. What’s your answer now?

Ok, great. Trick question I guess. It does not matter to me. Baboons I guess were from a different stock, kind perhaps. It simply does not matter. What is your point in this?

[glipsnort (Steve Schaffner)]

@r_speir

Ok, great. Trick question I guess.

It was not a trick question. I asked why we see this pattern when we compare humans and baboons, since those two species are more distantly related than humans and chimps. I assumed you knew what a baboon was.

@r_speir

Baboons I guess were from a different stock, kind perhaps. It simply does not matter. What is your point in this?

My point was that your model has no explanation for the patterns we see when we compare genomes. You have just supported that point by failing to provide a creationist explanation.

[nwrickert (Neil Rickert)]

@colewd

The only means of producing a biological organism is a highly deterministic mechanism called reproduction.

I would not describe it that way.

Reproduction is sensitive to environmental conditions. It would be difficult to tell whether or not it is strictly deterministic.

@colewd

These are information based organisms where chemical sequences live in almost infinite sequence space.

Once you get to an infinite sequence space, determinism becomes very iffy. Think about the paradoxes that show up once an infinitude is allowed.

Personally, I see the expression “information based organisms” as meaningless. Information is an abstraction. It has no existence outside of our theories and hypotheses.

@colewd

When are we going to face the reality of what we are observing?

That would be an excellent question for you to pose to yourself.

[Roy (34-year veteran)]

@scd

its possible that almost all creatures had very similar genome in their initial creation (we already know that since human and chimp for instance are very similar). so they just got neutral mutations over time and thus that result.

So, for example, blue whales, coral and millipedes originally all had very similar genomes while still being distinguishable as those very different animals?

[Mercer (John Mercer)]

@Chris_Falter

Evolution, on the other hand, predicts both the similarities and the statistical distribution of nucleotide differences.

Which is why creationists deliberately misrepresent the evidence, not interpretation, as mere similarity.

Both camps are not interpreting the same evidence differently. One camp is ignoring most of the evidence itself.

Right, @Guy_Coe?

[Chris_Falter]

Let’s take a look at the math behind the post 22 by @T_aquaticus .

(1) Let {g_0} = genome of a primate population at time 0 (beginning of analysis)

(2) Let {g_t} = genome of a descendant primate population at later time t. Also, \nabla{g_t} = g_t - g_0 = distribution of differences between that genome and the genome of the ancestral population at time 0.

(3) Let \vec{d} = vector representing expected frequency distribution of each possible nucleotide mutation in one primate generation in sequences not under selection.

(4) Let {f} = inheritance function, representing the transmission of the genome from a primate population to its immediate descendant population.

(5) Then {g_t} = f(g_{t-1}, \vec{d}). For example, {g_1} = f(g_0, \vec{d}).

(6) Similarly, \nabla{g_t} = \nabla_{g_{t-1}} + \vec{d} and \nabla{g_1} = \vec{d}

(7) Extending across time: at generation 2, {g_2} = f(f(g_{0}, \vec{d}), \vec{d}). For simplicity’s sake, the recursive application of the inheritance function f for n generations will be denoted {g_t} = f_n(g_{t-n}, \vec{d}). It follows that \nabla{g_n} = g_0 - f_n(g_{0}, \vec{d})

(8) Let \nabla{g_{n(a,b)}} = distribution of nucleotide-wise differences between 2 primate populations, a and b, that have diverged from a common ancestral primate population for n generations. We expect that \nabla{g_{n(a,b)}} \approx 2\nabla{g_{n(a)}} \approx 2(g_0 - f_n(g_{0}, \vec{d})).

(9) Final step (and thanks for sticking with me!): let \nabla{g_{n(p,h)}} = distribution of nucleotide-wise differences between Pan trogolodytes and Homo sapiens sapiens, let g_h= current genome of Homo sapiens sapiens, and let k = number of primate generations since approximately 6mya. The theory of evolution predicts that \nabla{g_{n(p,h)}} \approx 2(f_k(g_h, \vec{d})) . This is in fact observed to an extraordinarily high degree of statistical significance, as noted in post #22 by @T_aquaticus .

@r_speir - What I have laid out before you is the mathematical model that drives evolution’s predictions about the distribution of nucleotide-wise differences between chimpanzees and humans. Please provide such a mathematically described model for the predictions of special creation with respect to the distribution of nucleotide-wise differences between chimpanzees and humans in sequences not under selection. Neither you nor the resources you have referenced have done anything remotely like this. Until you do, you will be justly accused of hand-waving, and the scientific community will regard your assertions as irrelevant speculation.

@glipsnort, @swamidass, other biologists - please feel free to point out anything that I might have overlooked or gotten wrong in my presentation of an evolutionary mathematical model.

Thanks to all!

Chris

[r_speir]

@glipsnort

My point was that your model has no explanation for the patterns we see when we compare genomes. You have just supported that point by failing to provide a creationist explanation.

I guess I get to call you out now. Because if I am not mistaken, neither do you have any specific data like the study we have been discussing that similarly links baboons and humans. So why are you calling my hand? Show me the genetic studies. I am not asking for the genomes. I am asking for the study between baboons and humans like the human/chimp study we have been discussing. Where is it?

[swamidass (S. Joshua Swamidass)]

@r_speir

My point was that your model has no explanation for the patterns we see when we compare genomes. You have just supported that point by failing to provide a creationist explanation.

I guess I get to call you out now. Because if I am not mistaken, neither do you have any specific data like the study we have been discussing that similarly links baboons and humans.

Yes, you are mistaken. Moreover, you just seem to have ignored both @evograd and @glipsnort’s article. Have you read them yet? You’d find your answer in @glipsnort’s article.

[T_aquaticus]

@r_speir

I guess I get to call you out now. Because if I am not mistaken, neither do you have any specific data like the study we have been discussing that similarly links baboons and humans.

Link to @glipsnort’s article:

https://biologos.org/articles/testing-common-ancestry-its-all-about-the-mutations

Pay close attention to the figure that compares different primate species.