9 Questions

Subduction Zone · Nov 27, 2021

J_B_ said:
Question #7: How common is convergent, divergent, and parallel evolution?

Very. Ask a poorly defined question, get a poorly defined answer.

Question #8: Have examples of convergent, divergent, and parallel evolution been checked for similarity in DNA?

Yes.

Question #9: Is there a way to know if the extant specimens of a given phylogenetic path come from the same population (per the OP definition)?

@Tinker Grey @durangodawood @Yttrium @essentialsaltes @FrumiousBandersnatch @That Guy 11200 @Hans Blaster @sfs

Yes.

durangodawood · Nov 27, 2021

Tanj said:
Opposable thumbs?

I type with 4 fingers.

Subduction Zone · Nov 27, 2021

durangodawood said:
I type with 4 fingers.

What about the space bar?

Tinker Grey · Nov 28, 2021

durangodawood said:
I type with 4 fingers.

Funny, I use at least 8.

sfs · Nov 28, 2021

Subduction Zone said:
What about the space bar?

What do you think your nose is for?

J_B_ · Nov 28, 2021

Question #7: How common is convergent, divergent, and parallel evolution? Very.

What is the basis for distinguishing them?

Question #8: Have examples of convergent, divergent, and parallel evolution been checked for similarity in DNA? Yes.

I would appreciate if someone could summarize the results of these investigations.

Question #9: Is there a way to know if the extant specimens of a given phylogenetic path come from the same population (per the OP definition)? Yes.

What is the basis for placing two fossilized specimens in the same population? If they're lying relatively close to each other, it seems obvious. But given the small numbers indicated in post #88, I'm not sure if they all come from the same site.

If there are differing opinions to the above answers, I'd like to hear it of course. If there's nothing else to say, then thank you everyone. I enjoyed it, and it was helpful. Maybe we'll speak again.

Frank Robert · Nov 28, 2021

Subduction Zone said:
I would disagree with your value of "generation". For humans it is not unreasonable, but we have a rather long time to maturation. But for small mammals a generation can be very short. Mice, for example are sexually mature in as short as 4 weeks and at the most at 7 weeks. The live one to two and a half years on average in the wild. For them a generation would could easily be considered to be about 6 months. I would bump your number of generations by a factor of 4 at least. But then I am not a biologist.

That would bump it up to 160 million generations.

FrumiousBandersnatch · Nov 28, 2021

J_B_ said:
That's what I suspected - that it's based on comparisons of known DNA-morphology sets rather than an ability to model a direct link. However, I'd think some are trying to establish that direct link? Maybe? I don't know of anyone trying to establish direct links from material science to mechanics for my field, and in my opinion it seems a near impossible thing to do, but maybe some in biology are giving it a go.

There's been a lot of research into the genetic basis of morphology - the Hox genes, etc. So I'm sure there are people working on it.

On the other side, I know there is Stuart Kaufmann's camp that is saying biology is emergent, and therefore the link is impossible.

I'm not sure what they mean. Biology is clearly emergent from chemistry, but DNA is on the boundary - I'd suggest it's more a biological structure than a chemical one in this context. Interaction with the environment is important during development, but given normal developmental circumstances, I don't see why it wouldn't be possible to predict gross morphology from DNA - but only where we have already established the relevant genetic contributions to morphology for that species!

E.T.A. Having read the Kaufmann article, it seems he was talking about abiogenesis and the results of evolution being unpredictable rather than the link between morphology and DNA. I'm inclined to agree with him on that.

Frank Robert · Nov 28, 2021

J_B_ said:
I expected there is a practical limit, but I recall some tissue from a T-Rex was found that was 68 million years old. IIRC, they never recovered DNA from it, but still, maybe the limit is farther back than first thought.

I'd like to hear thoughts from @sfs on that.

The dino dna that you refer to is questionable, but even if it turns out to be millions of years old it is a one off find which may never be repeated and certainly not for the millions of presently preserved fossils.

You might want to do some research on DNA or molecular clocks which is a way for estimating the dates of lineage-splitting events.

J_B_ · Nov 28, 2021

Frank Robert said:
You might want to do some research on DNA or molecular clocks which is a way for estimating the dates of lineage-splitting events.

Very interesting. Thanks.

J_B_ · Nov 28, 2021

FrumiousBandersnatch said:
E.T.A. Having read the Kaufmann article, it seems he was talking about abiogenesis and the results of evolution being unpredictable rather than the link between morphology and DNA. I'm inclined to agree with him on that.

True, he does focus more on abiogenesis, but across the spectrum of his work he occasionally touches on evolution as well. For example, he partnered with Soto, Longo, and Montevil in their work: https://bsahely.com/2018/12/31/no-e...-giuseppe-longo-mael-montevil-stuart-kauﬀman/

Subduction Zone · Nov 28, 2021

J_B_ said:
Question #7: How common is convergent, divergent, and parallel evolution? Very.

What is the basis for distinguishing them?

Well they can't interbreed for one thing. By the way, this sort of question again reveals that you may be trying for a "gotcha" question. There are many different degrees of convergent evolution. For example the general shape of dolphins and sharks. Their shape is a result of the environment that they live in and a shape that allows them to move efficiently through it. Yet you would never need to ask if they were different.

Question #8: Have examples of convergent, divergent, and parallel evolution been checked for similarity in DNA? Yes.

I would appreciate if someone could summarize the results of these investigations.

You could easily Google search the topic yourself.

But you would need to ask your questions better. Right now you keep revealing that you do not know enough to ask proper questions yet. Your questions appear to be an attempt to refute evolution and it does not work that way.

Question #9: Is there a way to know if the extant specimens of a given phylogenetic path come from the same population (per the OP definition)? Yes.

What is the basis for placing two fossilized specimens in the same population? If they're lying relatively close to each other, it seems obvious. But given the small numbers indicated in post #88, I'm not sure if they all come from the same site.

If there are differing opinions to the above answers, I'd like to hear it of course. If there's nothing else to say, then thank you everyone. I enjoyed it, and it was helpful. Maybe we'll speak again.

Ask better questions, get better answers.

Frank Robert · Nov 28, 2021

J_B_ said:
Question #7: How common is convergent, divergent, and parallel evolution? Very.

What is the basis for distinguishing them?

This doesn't answer you question but I thought you may be interest in this Scientists Say There May Be “Humans” All Over the Universe because their main reason has to do with convergent evolution.

"In a new interview with the BBC‘s Science Focus magazine, an evolutionary palaeobiologist at the institution’s Department of Earth Sciences named Simon Conway Morris declared that researchers can “say with reasonable confidence” that human-like evolution has occurred in other locations around the universe.

The core of Morris’ belief comes from the theory of convergent evolution, which claims that, as Science Focus put it, “random effects eventually average out so that evolution converges, tending to produce similar organisms in any given environment.” The magazine used the examples of flight, which “has evolved independently on Earth at least four times — in birds, bats, insects and pterosaurs.”

In short, convergent evolution theory posits that evolution itself is a law of nature — and, as a logical endpoint, it’s likely that evolution would operate the same way on different planets as it does here on Earth. In other words, it’s theoretically possible that the blue and green alien humanoids you see on “Star Trek” could be, well, actually out there."

"Morris isn’t the only Cambridge man who believes alien life would have evolved in ways “analogous to a human.”

Occams Barber · Nov 28, 2021

Tinker Grey said:
Funny, I use at least 8.

After much practice I have grossly improved my typing efficiency by reducing it down to occupying only two fingers. This leaves me with six fingers and two thumbs available for parallel multi-tasking should it be required.

OB

Tanj · Nov 28, 2021

J_B_ said:
Question #4: For any given path through a phylogenetic tree, how many generations have passed from a progenitor species to the current species? For example, from Juramaia to Sylvilagus? (feel free to pick another example - maybe the best documented one you are aware of)

Depends on the organism's molecular clock, as well as environmental/random factors as to whether it has the opportunity to speciate., as well how recently the split happened, and finally when someone found the species in question and catalogued them.

Then for something like the human/chimp split, which happened about 4 million years ago, if we assume 20 years for a human generation then you get 200 000 generations.

Question #5:

Click to expand...

For that series of generations how many have an extant specimen (living, preserved, remains, fossil, etc.)?

What? You do realise there's at least 1 million species of insect out there (possibly up to 10 million), and that's just the insects.

Question #6:

Click to expand...

Of the extant specimens, how many come as a DNA-morphology set?

We have about 200 000 eu/archa- bacter genomes, if we throw in the few thousand eukaryote genomes it still comes to about 200 000.

tas8831 · Nov 29, 2021

J_B_ said:
That's what I suspected - that it's based on comparisons of known DNA-morphology sets rather than an ability to model a direct link.

I forget now who originally posted these on this forum, but I keep it in my archives because it offers a nice 'linear' progression of testing a methodology and then applying it.

The tested methodology:

Science 25 October 1991:
Vol. 254. no. 5031, pp. 554 - 558

Gene trees and the origins of inbred strains of mice

WR Atchley and WM Fitch

Extensive data on genetic divergence among 24 inbred strains of mice provide an opportunity to examine the concordance of gene trees and species trees, especially whether structured subsamples of loci give congruent estimates of phylogenetic relationships. Phylogenetic analyses of 144 separate loci reproduce almost exactly the known genealogical relationships among these 24 strains. Partitioning these loci into structured subsets representing loci coding for proteins, the immune system and endogenous viruses give incongruent phylogenetic results. The gene tree based on protein loci provides an accurate picture of the genealogical relationships among strains; however, gene trees based upon immune and viral data show significant deviations from known genealogical affinities.

======================

Science, Vol 255, Issue 5044, 589-592

Experimental phylogenetics: generation of a known phylogeny

DM Hillis, JJ Bull, ME White, MR Badgett, and IJ Molineux
Department of Zoology, University of Texas, Austin 78712.

Although methods of phylogenetic estimation are used routinely in comparative biology, direct tests of these methods are hampered by the lack of known phylogenies. Here a system based on serial propagation of bacteriophage T7 in the presence of a mutagen was used to create the first completely known phylogeny. Restriction-site maps of the terminal lineages were used to infer the evolutionary history of the experimental lines for comparison to the known history and actual ancestors. The five methods used to reconstruct branching pattern all predicted the correct topology but varied in their predictions of branch lengths; one method also predicts ancestral restriction maps and was found to be greater than 98 percent accurate.

==================================

Science, Vol 264, Issue 5159, 671-677

Application and accuracy of molecular phylogenies

DM Hillis, JP Huelsenbeck, and CW Cunningham
Department of Zoology, University of Texas, Austin 78712.

Molecular investigations of evolutionary history are being used to study subjects as diverse as the epidemiology of acquired immune deficiency syndrome and the origin of life. These studies depend on accurate estimates of phylogeny. The performance of methods of phylogenetic analysis can be assessed by numerical simulation studies and by the experimental evolution of organisms in controlled laboratory situations. Both kinds of assessment indicate that existing methods are effective at estimating phylogenies over a wide range of evolutionary conditions, especially if information about substitution bias is used to provide differential weightings for character transformations.

Application of the tested methodology:

Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: Enlarging genus Homo

"Here we compare ≈90 kb of coding DNA nucleotide sequence from 97 human genes to their sequenced chimpanzee counterparts and to available sequenced gorilla, orangutan, and Old World monkey counterparts, and, on a more limited basis, to mouse. The nonsynonymous changes (functionally important), like synonymous changes (functionally much less important), show chimpanzees and humans to be most closely related, sharing 99.4% identity at nonsynonymous sites and 98.4% at synonymous sites. "

Mitochondrial Insertions into Primate Nuclear Genomes Suggest the Use of numts as a Tool for Phylogeny

"Moreover, numts identified in gorilla Supercontigs were used to test the human–chimp–gorilla trichotomy, yielding a high level of support for the sister relationship of human and chimpanzee."

A Molecular Phylogeny of Living Primates

"Once contentiously debated, the closest human relative of chimpanzee (Pan) within subfamily Homininae (Gorilla, Pan, Homo) is now generally undisputed. The branch forming the Homo andPanlineage apart from Gorilla is relatively short (node 73, 27 steps MP, 0 indels) compared with that of thePan genus (node 72, 91 steps MP, 2 indels) and suggests rapid speciation into the 3 genera occurred early in Homininae evolution. Based on 54 gene regions, Homo-Pan genetic distance range from 6.92 to 7.90×10−3 substitutions/site (P. paniscus and P. troglodytes, respectively), which is less than previous estimates based on large scale sequencing of specific regions such as chromosome 7[50]. "

Catarrhine phylogeny: noncoding DNA evidence for a diphyletic origin of the mangabeys and for a human-chimpanzee clade.

"The Superfamily Hominoidea for apes and humans is reduced to family Hominidae within Superfamily Cercopithecoidea, with all living hominids placed in subfamily Homininae; and (4) chimpanzees and humans are members of a single genus, Homo, with common and bonobo chimpanzees placed in subgenus H. (Pan) and humans placed in subgenus H. (Homo). It may be noted that humans and chimpanzees are more than 98.3% identical in their typical nuclear noncoding DNA and probably more than 99.5% identical in the active coding nucleotide sequences of their functional nuclear genes (Goodman et al., 1989, 1990). In mammals such high genetic correspondence is commonly found between sibling species below the generic level but not between species in different genera."

On the other side, I know there is Stuart Kaufmann's camp that is saying biology is emergent, and therefore the link is impossible.

Do you know of ANY original research being done by IDCs/YECs/OECs to test their hypotheses re: creation ?

J_B_ · Nov 29, 2021

tas8831 said:
I forget now who originally posted these on this forum, but I keep it in my archives because it offers a nice 'linear' progression of testing a methodology and then applying it.

The tested methodology:

Science 25 October 1991:
Vol. 254. no. 5031, pp. 554 - 558

Gene trees and the origins of inbred strains of mice

WR Atchley and WM Fitch

Extensive data on genetic divergence among 24 inbred strains of mice provide an opportunity to examine the concordance of gene trees and species trees, especially whether structured subsamples of loci give congruent estimates of phylogenetic relationships. Phylogenetic analyses of 144 separate loci reproduce almost exactly the known genealogical relationships among these 24 strains. Partitioning these loci into structured subsets representing loci coding for proteins, the immune system and endogenous viruses give incongruent phylogenetic results. The gene tree based on protein loci provides an accurate picture of the genealogical relationships among strains; however, gene trees based upon immune and viral data show significant deviations from known genealogical affinities.

======================

Science, Vol 255, Issue 5044, 589-592

Experimental phylogenetics: generation of a known phylogeny

DM Hillis, JJ Bull, ME White, MR Badgett, and IJ Molineux
Department of Zoology, University of Texas, Austin 78712.

Although methods of phylogenetic estimation are used routinely in comparative biology, direct tests of these methods are hampered by the lack of known phylogenies. Here a system based on serial propagation of bacteriophage T7 in the presence of a mutagen was used to create the first completely known phylogeny. Restriction-site maps of the terminal lineages were used to infer the evolutionary history of the experimental lines for comparison to the known history and actual ancestors. The five methods used to reconstruct branching pattern all predicted the correct topology but varied in their predictions of branch lengths; one method also predicts ancestral restriction maps and was found to be greater than 98 percent accurate.

==================================

Science, Vol 264, Issue 5159, 671-677

Application and accuracy of molecular phylogenies

DM Hillis, JP Huelsenbeck, and CW Cunningham
Department of Zoology, University of Texas, Austin 78712.

Molecular investigations of evolutionary history are being used to study subjects as diverse as the epidemiology of acquired immune deficiency syndrome and the origin of life. These studies depend on accurate estimates of phylogeny. The performance of methods of phylogenetic analysis can be assessed by numerical simulation studies and by the experimental evolution of organisms in controlled laboratory situations. Both kinds of assessment indicate that existing methods are effective at estimating phylogenies over a wide range of evolutionary conditions, especially if information about substitution bias is used to provide differential weightings for character transformations.

Application of the tested methodology:

Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: Enlarging genus Homo

"Here we compare ≈90 kb of coding DNA nucleotide sequence from 97 human genes to their sequenced chimpanzee counterparts and to available sequenced gorilla, orangutan, and Old World monkey counterparts, and, on a more limited basis, to mouse. The nonsynonymous changes (functionally important), like synonymous changes (functionally much less important), show chimpanzees and humans to be most closely related, sharing 99.4% identity at nonsynonymous sites and 98.4% at synonymous sites. "

Mitochondrial Insertions into Primate Nuclear Genomes Suggest the Use of numts as a Tool for Phylogeny

"Moreover, numts identified in gorilla Supercontigs were used to test the human–chimp–gorilla trichotomy, yielding a high level of support for the sister relationship of human and chimpanzee."

A Molecular Phylogeny of Living Primates

"Once contentiously debated, the closest human relative of chimpanzee (Pan) within subfamily Homininae (Gorilla, Pan, Homo) is now generally undisputed. The branch forming the Homo andPanlineage apart from Gorilla is relatively short (node 73, 27 steps MP, 0 indels) compared with that of thePan genus (node 72, 91 steps MP, 2 indels) and suggests rapid speciation into the 3 genera occurred early in Homininae evolution. Based on 54 gene regions, Homo-Pan genetic distance range from 6.92 to 7.90×10−3 substitutions/site (P. paniscus and P. troglodytes, respectively), which is less than previous estimates based on large scale sequencing of specific regions such as chromosome 7[50]. "

Catarrhine phylogeny: noncoding DNA evidence for a diphyletic origin of the mangabeys and for a human-chimpanzee clade.

"The Superfamily Hominoidea for apes and humans is reduced to family Hominidae within Superfamily Cercopithecoidea, with all living hominids placed in subfamily Homininae; and (4) chimpanzees and humans are members of a single genus, Homo, with common and bonobo chimpanzees placed in subgenus H. (Pan) and humans placed in subgenus H. (Homo). It may be noted that humans and chimpanzees are more than 98.3% identical in their typical nuclear noncoding DNA and probably more than 99.5% identical in the active coding nucleotide sequences of their functional nuclear genes (Goodman et al., 1989, 1990). In mammals such high genetic correspondence is commonly found between sibling species below the generic level but not between species in different genera."

Thanks. I'll look through these. Hopefully I don't get buried.

tas8831 said:
Do you know of ANY original research being done by IDCs/YECs/OECs to test their hypotheses re: creation ?

Kauffman is not a creationist. As best I can tell, he's a well respected biologist who has paid his dues to the evolutionary country club.

But, to answer your question, no I'm not aware of any creationist research. IMO, what I have seen of creationist attempts is completely off-track.

Tanj · Nov 29, 2021

J_B_ said:
Question #7: How common is convergent, divergent, and parallel evolution?

Question #8: Have examples of convergent, divergent, and parallel evolution been checked for similarity in DNA?

Question #9: Is there a way to know if the extant specimens of a given phylogenetic path come from the same population (per the OP definition)?

Very
Yes
Not just from the phylogeny. e.g. ring species sit on the same phylogenetic node. Probably don't count as the one population.

tas8831 · Dec 9, 2021

J_B_ said:
Do you know of ANY original research being done by IDCs/YECs/OECs to test their hypotheses re: creation ?

Click to expand...

Kauffman is not a creationist.

Um... OK...

As best I can tell, he's a well respected biologist who has paid his dues to the evolutionary country club.

Great, not what I asked, but sure.

But, to answer your question, no I'm not aware of any creationist research. IMO, what I have seen of creationist attempts is completely off-track.

Same.
So why not badger them?

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