Introducing Geremy (and Behe)

[Geremy (Geremy D. Lawrence)]

I think that evolutionary algorithms are a actively trying to falsify the null theory that the evolutionary mechanisms are too self limiting to account for biologically equivalent complexity. So their experiments are testing the computational power of evolution itself, making their work highly relevant. Population geneticists are most analogous to the accountants for evolutionary theory, with two unlimited budgets, one for natural selection and the other for neutral theory. Keeping with this analogy they would prefer to spend from neutral theory but will invoke as much natural selection as is needed to explain patterns that contradict neutral theory so that the books stay balanced, as it were.

If we put population genetics aside I know of four examples that contradict the hypothesis that the genetic evidence is best explained by common descent between humans and chimpanzees:

1. The Y chromosomes of humans and gorillas are less divergent than it is for chimpanzees and humans.

Comparing Y Chromosomes of Great Apes Reveals Unexpected Patterns

2. The mitochondrial DNA of ancient humans is more divergent from chimpanzees than modern humans.
   Ancient fossil specimens of extinct species are genetically more distant to an outgroup than extant sister species are

3. ERVs comparisons between humans and chimpanzees do not always match the pattern one would expect if ERVs positions are only due to common descent.

The Chimp Genome Reveals a Retroviral Invasion in Primate Evolution

4. The lack of shared specific genetic characteristics in humans and chimpanzees.

The Origin of the Human Species: a Chromosome Fusion? | OpenMind

I’m sure that population geneticists can invoke some combination of gene deletions and strong selection to explain away the evidence that is contained in the four papers that I linked to. But how are to know if such explanations are accurate without an understanding of the limits of evolutionary mechanisms in the first place? So that is why evolutionary algorithms are so important. Sorry for the long answer.

[Geremy (Geremy D. Lawrence)]

So the oldest algae fossils are about 1.6 billion years old, while unicellular eukaryotes don’t appear at all in the fossil record until 800 million years ago. So the presuppositon that unicellular eukaryotes evolved into multicellular eukaryotes at all is a counterfactual claim based on evolutionary theory.

If we put that aside the similarities between Volvox algae which are motile, and C. reinhardtii algae are also motile, are consistent with common descent within the last few hundred million years. That said it would take a lot less speculation to assume mutations interrupted the development of the Volvox algae led to the evolution of the simpler unicellular algae, than to assume that the developmental process of the Volvox evolved to create the biomechanical process of gastrulation in some unknown way.

Both algae type live in murky waters where sunlight is at the surface and nutrients are subsurface so to survive in nature motility is essential to their environment, and there is no evidence that it was ever different that I am aware of. If you have evidence to the contrary I would love to see it.

[Geremy (Geremy D. Lawrence)]

1. Yes
2. Yes
3. But it would need to.
4. No

The principal algorithm in biology is reproduction not evolution, so the best evolutionary algorithms are inspired by development not evolution. I think evolution is a parasitic algorithm that infects reproduction, in as much as it only exists as a consequence of differential reproduction. The unanswered question is can the natural evolutionary algorithm rewrite the developmental algorithm, in the manner described by evolutionary theory due to some yet to be discovered principle of mathematics? Or is it constrained by known principles of mathematics as described by William Dempski decades ago, and appears to be supported when we look at the the evidence provided by manmade evolutionary algorithms? I don’t pretend to know the answer to that question for certain, but I think it is probably much more limited than evolutionary theory would have us believe.

[Faizal_Ali]

@Geremy

So the oldest algae fossils are about 1.6 billion years old, while unicellular eukaryotes don’t appear at all in the fossil record until 800 million years ago.

I presume you are referring to the one below.

Do you find it surprising or mysterious that we do not find many fossils of non-mineralizing unicellular organisms from billions of years ago?

Single-celled eukaryote fossil with evidence of mineralizing found in Yukon

[Faizal_Ali]

@Geremy

If we put population genetics aside I know of four examples that contradict the hypothesis that the genetic evidence is best explained by common descent between humans and chimpanzees:

If we put population genetics aside (but why would you?) There is certainly genetic evidence that contradicts the hypothesis that you are more closely related to your brother than to your grandfather. Some alleles or other maker sequences would have been passed on to you from your granfather and thru your father to you, but not to your brother.

Therefore, you cannot say you are more closely related to your brother than to your grandfather according to genetics.

Or can you, this evidence notwithstanding? What do you think?

[John_Harshman]

@Geremy

I know of four examples that contradict the hypothesis that the genetic evidence is best explained by common descent between humans and chimpanzees

They don’t, actually.

@Geremy

The Y chromosomes of humans and gorillas are less divergent than it is for chimpanzees and humans.

You assume that overall similarity is the guide to phylogeny. It isn’t. Evolutionary rates vary, so the most similar taxa, by some measure, may not be the most closely related.

@Geremy

The mitochondrial DNA of ancient humans is more divergent from chimpanzees than modern humans.

That was a paper by a known crackpot published in a journal sympathetic to crackpot claims. I wouldn’t accept any of the assertions made there without corroboration from a more trustworthy source. Note that the data include a dinosaur, but the sequence is extremely short and even that is controversial.

@Geremy

ERVs comparisons between humans and chimpanzees do not always match the pattern one would expect if ERVs positions are only due to common descent.

We’ve already had a discussion of that here. It isn’t what you think.

@Geremy

The lack of shared specific genetic characteristics in humans and chimpanzees.

There are millions of shared specific genetic characteristics, and your reference has nothing to do with that. It’s just a description of the chromosomal fusion that resulted in human chromosome 2.

@Geremy

I’m sure that population geneticists can invoke some combination of gene deletions and strong selection to explain away the evidence that is contained in the four papers that I linked to.

There’s no need to explain anything away.

@Geremy

I think that evolutionary algorithms are a actively trying to falsify the null theory that the evolutionary mechanisms are too self limiting to account for biologically equivalent complexity.

You think wrong. Can you produce any evidence that anyone working with evolutionary algorithms is attempting such a thing? And why would that be the null hypothesis?

[Timothy_Horton]

@Geremy

So the presuppositon that unicellular eukaryotes evolved into multicellular eukaryotes at all is a counterfactual claim based on evolutionary theory.

Why do you think multicellularity couldn’t have evolved more than once?

[Rumraket (Mikkel R.)]

@Geremy

The principal algorithm in biology is reproduction not evolution, so the best evolutionary algorithms are inspired by development not evolution. I think evolution is a parasitic algorithm that infects reproduction, in as much as it only exists as a consequence of differential reproduction.

If this isn’t word-salad, I don’t know what is.

[Rumraket (Mikkel R.)]

@Geremy

So the oldest algae fossils are about 1.6 billion years old, while unicellular eukaryotes don’t appear at all in the fossil record until 800 million years ago. So the presuppositon that unicellular eukaryotes evolved into multicellular eukaryotes at all is a counterfactual claim based on evolutionary theory.

Evidence of single-celled life significantly predates evidence for multicellular life, and since we know from genetics that all life is related, the fossil record (with bacterial and archaeal life much, much older than eukaryotic life) supports a history of single to multi-celled life, even if we don’t specifically have fossils of the first single-celled eukaryotes.

@Geremy

If we put that aside the similarities between Volvox algae which are motile, and C. reinhardtii algae are also motile, are consistent with common descent within the last few hundred million years. That said it would take a lot less speculation to assume mutations interrupted the development of the Volvox algae led to the evolution of the simpler unicellular algae, than to assume that the developmental process of the Volvox evolved to create the biomechanical process of gastrulation in some unknown way.

Both algae type live in murky waters where sunlight is at the surface and nutrients are subsurface so to survive in nature motility is essential to their environment, and there is no evidence that it was ever different that I am aware of. If you have evidence to the contrary I would love to see it

I don’t see how this constitutes a response to anything I’ve said. What point of mine are you supposed to address with this?

[CrisprCAS9]

@Geremy

in the manner described by evolutionary theory due to some yet to be discovered principle of mathematics

I’m pretty sure mathematicians have already ‘discovered’ the principle that big numbers are larger than small ones.

[Geremy (Geremy D. Lawrence)]

Maybe we are just seeing what was actually there. After all bacterial cells seen to fossilize just fine, even when they are over 3 billion years old…

https://ucmp.berkeley.edu/bacteria/bacteriafr.html

[CrisprCAS9]

@Geremy

The Y chromosomes of humans and gorillas are less divergent than it is for chimpanzees and humans.

From your source’s source:

From multispecies alignments ( SI Appendix , Table S2C), the human Y was most similar in sequence to the chimpanzee or bonobo Ys (97.9 and 97.8%, respectively), less similar to the gorilla Y (97.2%), and the least similar to the orangutan Y (93.6%), in agreement with the accepted phylogeny of these species (9).

In other words: No, it isn’t. The only way humans and gorillas are closer than humans and chimps is the structure, which is consistent with the substantial size reduction of the chimpanzee Y. You might as well say that ‘Pride and Prejudice’ is more similar to ‘Pride and Prejudice and Zombies’ than the first draft of the first half of the book is to its published form.

@Geremy

The mitochondrial DNA of ancient humans is more divergent from chimpanzees than modern humans.

https://www.nature.com/articles/ncomms16046

Definitely not.
I mean, really:

@Geremy

ERVs comparisons between humans and chimpanzees do not always match the pattern one would expect if ERVs positions are only due to common descent.

Yes, because some are explained by independent insertions. Your source’s source found the insertions to be non-orthologous, so a non-issue.

@Geremy

The lack of shared specific genetic characteristics in humans and chimpanzees.

The ~99% coding identity, ~96-98% nucleotide similarity (including and excluding indels, respectively) is a ‘lack’? Okay.

@Geremy

contained in the four papers that I linked to.

You linked to one paper by a crank obsessed with a notion of Chinese origins of humanity, and three popular-level write-ups.

[Geremy (Geremy D. Lawrence)]

@John_Harshman

There are millions of shared specific genetic characteristics, and your reference has nothing to do with that. It’s just a description of the chromosomal fusion that resulted in human chromosome 2.

Okay perhaps we are talking about two different things, I am less than 2% Neanderthal, according to genetic testing so what percentage of chimpanzee am I? No one can tell me, the author speculates:

This would also explain why traces of their genetic characteristics remain in our genome , as shown by the comparative genomic analysis of the three species. However, the hypothetical descendants of breeding between the three hominid species mentioned (46 chromosomes) and their large ape ancestors (48 chromosomes) would have had problems of chromosome incompatibility and would probably not have been viable. In fact, no traces of specific genetic characteristics of the large apes have been found in our genome.

That was a paper by a known crackpot published in a journal sympathetic to crackpot claims.

I actually agree but crackpots have a way of getting some things right every once in a while, but not knowing where to end their speculation. There was this 19th century crackpot that I know of who was severely emotionally ill to the point of not being able to leave the house, named Charles Darwin that we all know had some strange ideas about biology. So perhaps we can both agree to avoid the genetic fallacy, and look at just the data as it relates to chimpanzees, modern humans, ancient Aborigines and Neanderthal.

You assume that overall similarity is the guide to phylogeny. It isn’t. Evolutionary rates vary, so the most similar taxa, by some measure, may not be the most closely related.

Not, exactly I simply think that extrapolating mutation rates to be whatever it needs to be to confirm the evolutionary narrative to be a very efficient way to avoid contradicting it even when findings conflict with it.

We’ve already had a discussion of that here. It isn’t what you think.

Fair enough, I will not comment on that point until I read the other conversation.

You think wrong. Can you produce any evidence that anyone working with evolutionary algorithms is attempting such a thing? And why would that be the null hypothesis?

We will (before long) be able to run genetic algorithms on computers that are sufficiently fast to recreate on a human timescale the same amount of cumulative optimization power that the relevant processes of natural selection instantiated throughout our evolutionary past . .

.39

[John_Harshman]

@Geremy

Okay perhaps we are talking about two different things, I am less than 2% Neanderthal, according to genetic testing so what percentage of chimpanzee am I?

You are zero percent chimpanzee. Whatever are you talking about here? Now of course 98.7% of the bases in your genome are inherited from the human-chimp common ancestor, if that’s what you mean. A reasonable proportion of those are new since the separation of that lineage from the gorilla lineage, if that’s what you’re talking about. But I don’t know what you’re talking about.

@Geremy

In fact, no traces of specific genetic characteristics of the large apes have been found in our genome.

I have no idea what that was supposed to mean. Do you? Also, the author grossly exaggerates the difficulty in interbreeding caused by the chromosomal fusion. There are a great many species today in which chromosomal fusions are polymorphic, and heterozygotes are not uncommon.

@Geremy

So perhaps we can both agree to avoid the genetic fallacy, and look at just the data as it relates to chimpanzees, modern humans, ancient Aborigines and Neanderthal.

As has been pointed out, the data have been misinterpreted by you and the crackpot you rely on.

@Geremy

I simply think that extrapolating mutation rates to be whatever it needs to be to confirm the evolutionary narrative to be a very efficient way to avoid contradicting it even when findings conflict with it.

No idea what you mean by that either. But if you present your own hypothesis, perhaps that would clarify. What do you propose to replace common descent with?

@Geremy

We will (before long) be able to run genetic algorithms on computers that are sufficiently fast to recreate on a human timescale the same amount of cumulative optimization power that the relevant processes of natural selection instantiated throughout our evolutionary past . .

Sorry, but that isn’t the claim you said it was. Read it again, more carefully.

[Rumraket (Mikkel R.)]

@Geremy

After all bacterial cells seen to fossilize just fine, even when they are over 3 billion years old…

Fossil Record of the Bacteria

So can you show me a continuous lineage of fossil cyanobacteria going back 3 billion years? Finding a small handful of examples of fossil cyanobacteria, interrupted with blanks extending through billion-year intervals, hardly counts as support for the claim that “bacterial cells seen to fossilize just fine”.

You seem to have confused the probability of fossilization together with preservation (and finding the fossil) with a statement that it isn’t possible at all. Nobody says bacteria don’t fossilize, but rather that it is relatively rare for unicellular lifeforms to fossilize. Given that we can find almost billion-year intervals without any direct bacterial fossils (where instead we only find trace evidence, such as stromatolites and isotope ratios), it shouldn’t come as a surprise that we can find ~500-million-year intervals without any single-celled eukaryotes.

[Rumraket (Mikkel R.)]

@Geremy

You think wrong. Can you produce any evidence that anyone working with evolutionary algorithms is attempting such a thing? And why would that be the null hypothesis?

We will (before long) be able to run genetic algorithms on computers that are sufficiently fast to recreate on a human timescale the same amount of cumulative optimization power that the relevant processes of natural selection instantiated throughout our evolutionary past . .

.39

The reference literally argues that simulating evolution on the scale it has occurred on our planet is pretty much impossible, and the phrase you lift is actually a sort of paraphrase of an “argument” that the authors are trying to rebut.

You also seem to have completely misunderstood what is being argued about here. Reference 39 there is an article about the possibility of using a sort of selection algorithm to evolve artificial intelligence.

There’s nothing there about the makers of algorithms are “actively trying to falsify the null theory that the evolutionary mechanisms are too self limiting to account for biologically equivalent complexity.”

[Faizal_Ali]

@Geremy

Maybe we are just seeing what was actually there. After all bacterial cells seen to fossilize just fine, even when they are over 3 billion years old…

Fossil Record of the Bacteria

Did you read the link?

It may seem surprising that bacteria can leave fossils at all. However, one particular group of bacteria, the cyanobacteria or “blue-green algae,” have left a fossil record that extends far back into the Precambrian - the oldest cyanobacteria-like fossils known are nearly 3.5 billion years old, among the oldest fossils currently known. Cyanobacteria are larger than most bacteria, and may secrete a thick cell wall. More importantly, cyanobacteria may form large layered structures, called stromatolites (if more or less dome-shaped) or oncolites (if round). These structures form as a mat of cyanobacteria grows in an aquatic environment, trapping sediment and sometimes secreting calcium carbonate. When sectioned very thinly, fossil stromatolites may be found to contain exquisitely preserved fossil cyanobacteria and algae.

[Mercer (John Mercer)]

@Geremy

So perhaps we can both agree to avoid the genetic fallacy, and look at just the data as it relates to chimpanzees, modern humans, ancient Aborigines and Neanderthal.

The genetic fallacy works both ways. Are you really proposing to look at just the data? All the data?

That would be awesome.

[John_Harshman]

@CrisprCAS9

The only way humans and gorillas are closer than humans and chimps is the structure, which is consistent with the substantial size reduction of the chimpanzee Y.

I think that what he was saying, whether he knew it or not, was that humans and gorillas are closer than chimps and gorillas, and this appears to be true, as shown in tree A of the figure you reproduced. As I said, evolutionary rates vary, and phylogeny doesn’t work by molecular clocks. Here’s what the authors said, as quoted in the story:

“We found that the genus Pan , which includes chimpanzee and bonobo, experienced accelerated substitution rates,” the article’s authors wrote. “ Pan also exhibited elevated gene death rates. These observations are consistent with high levels of sperm competition in Pan .

Nothing to see here, in other words. @Geremy is practicing the old creationist sport of misreading evidence to fit his story. Though we don’t actually know what his story is yet.

[Rumraket (Mikkel R.)]

@Geremy

So perhaps we can both agree to avoid the genetic fallacy, and look at just the data as it relates to chimpanzees, modern humans, ancient Aborigines and Neanderthal.

Hey, why don’t we proceed to look at a large collection of genetic data from most living primates instead of just chimps and humans? That could be informative.

For example, there’s this:

A Molecular Phylogeny of Living Primates