Illusions of Phylogeny

[PhantomGaze]

Wow - I must have never received the Official Notification that Shapiro Speaks For ALL and that his personal opinions (which seem to be based more on the fact that most scientists do not accept his bizarre extrapolations) are to be Written in Stone.

I think Shapiro's natural genetic engineering is some pretty serious business.

 

[Loudmouth]

I think Shapiro's natural genetic engineering is some pretty serious business.

I think it is salesmanship. I have seen his stuff, and it stops well short of redefining evolution as he claims.

 

[PsychoSarah]

I mentioned the platypus. Someone argued it was a transitional form between mammals and reptiles. Which of course is true imo, but they completely ignored it's avian characteristics as an area of interest.

Or its weird poison glands that males have. The animal is so freaky that when people first brought examples of them in for the scientific community, they were thought to be fakes, beaver and duck parts sewn together.

 

[Split Rock]

This says it all. When the "molecular clock" seems to agree with standard phylogeny, then it "works". When the MC disagrees with standard phylogeny then the "species evolved at unequal rates", or some other kind of irregularity occurred.

More of the same non-falsifiable, ad-hoc, save-the-theory-with-rescue-devices nonsense.

Being a biologist, I would expect you to recognize this type of problem.

We actually know that species do not evolve at the same rate all the time. There is nothing ad hoc about it. Nor is there anything ad hoc about the mechanisms you yourself mentioned as explanations for irregularities in phyogenetic analysis. When exceptions are explainable by recognized natural mechanisms, they are not a problem for a scientific theory.

I will still very much like to know what you expect to be different in nature, if common descent were true.

 

[lifepsyop]

Wow - I must have never received the Official Notification that Shapiro Speaks For ALL and that his personal opinions (which seem to be based more on the fact that most scientists do not accept his bizarre extrapolations) are to be Written in Stone.

No need to get upset, it's just one man's opinion. Shapiro is an expert geneticist, an evolutionist, and openly hostile to creationism. Yet he casually points out the religious conviction of many evolutionary theorists. Struck a chord in you, I see.

Honestly, you can cut the religious fervor of most evolutionists with a knife. They absolutely hate to have their origins beliefs questioned. It's just nice to have it confirmed by a hostile witness every now and then.

 

[lifepsyop]

Say, that is super clever. But do you really think that strawman nonsense will convince anyone that you are out of your league?

Maybe you could stop spamming nonsense all over the thread and actually respond to the original content? Or are you just here to stamp your feet?

 

[PsychoSarah]

Maybe you could stop spamming nonsense all over the thread and actually respond to the original content? Or are you just here to stamp your feet?

Will you listen to what we have to say and be respectful with your questions?

 

[lifepsyop]

I mentioned the platypus. Someone argued it was a transitional form between mammals and reptiles. Which of course is true imo, but they completely ignored it's avian characteristics as an area of interest.

Interesting article. Thanks.

This is another example of how the supposed "nested hierarchy of common descent" is contradicted by out of place traits and then saved by ad hoc explanations.

Here we see the same kind of rescue devices at work that was pointed out earlier with platypus (monotreme) phylogeny. First they pull out the "convergent evolution" card.

And then, they save the phylogeny by pushing the problem back into the mystical evolutionary past. That is they say the Bird trait existed in a "common ancestor" of birds and monotremes, but not carried to other mammalian lineages, and this is why the trait is found in birds and platypus.

Of course if the trait was found in only birds and placentals, the explanation would be that it was simply lost in the monotreme lineage.

So, in short, evolutionists can keep making up stories about mystical events that occurred at these imaginary nodes (common ancestors) millions of years ago to explain why traits end up where they do in modern species.


Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes 2008

The sex-determining gene that initiates testis development is also different; for instance, there is no SRY in non-mammal vertebrates, and sex determination in birds seems to be largely controlled by dosage of a Z-borne gene (possibly DMRT1) (Raymond et al. 1999) rather than a male-dominant gene. The similarities shared by sex chromosomes are thus the results of convergent evolutionary forces in different vertebrate lineages.

In complete contradiction to early data, we find that the 10 sex chromosomes of platypus share no homology with the ancestral therian X chromosome, which is homologous to platypus chromosome 6. Instead, we find that regions homologous to the chicken Z are scattered throughout the chain, principally on X5 and X3. These results have major implications for our understanding of mammalian sex chromosome evolution.

The chicken Z is homologous to regions of human chromosomes 9 and 5. The mixture of HSA 9 and HSA 5 genes on platypus X5 and X3 implies that a region corresponding to the chicken Z was intact in an ancestor of monotremes and birds 310 Mya.

Platypus sex chromosomes are more bird-like than mammal-like

Our findings mean that the egg-laying monotreme mammals, representing the basal mammalian group, have an XY sex determination system quite unlike that of the therian mammal XY, but one derived from an ancestral bird-like ZW system.

These results demand reconsideration of the theories of sex chromosome evolution in vertebrates. Previous demonstrations that the mammal XY and bird ZW chromosomes share no homology were interpreted as independent evolution from different autosomes in a common ancestor that probably had a temperature-dependent sex determination. However, our mapping results suggest that the amniote ancestor may have had a bird-like ZZ male: ZW female sex chromosome system, from which all other unrelated ZW and XY systems evolved

Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes

 

[lifepsyop]

Yeah, those were some of the redflags for me, too. And that was just in the abstract. And of course it just looks to creationists like we are handwaving articles away that we don't like...really not our fault that they are incabable of recognizing poor scientific writing when they see it.

It's a shame some of that stuff manages to get a "peer reviewed" tag on it. Unfortunately, its only going to get worse until they crack down on some of these open access journals.

I notice none of you are commenting on the Schwartz,Maresca article which lists numerous literature references of molecular clock discordance and failed predictions.

Do Molecular Clocks Run at All? A Critique of Molecular Systematics

http://www.pitt.edu/~jhs/articles/Schwartz&Maresca_Mol_clocks.pdf


The funny part is that none of you will make any major claims about the molecular clock now. As Split Rock already conceded, sometimes it matches up, sometimes it doesn't because "species do not always evolve at equal rates". How do you know if the rate of evolution is unequal? Because the molecular clock says so. Heads: Evolution. Tails: Evolution.

The molecular clock is just more circular ad-hoc evo fluff that darwin spokespeople use to confuse the unwitting public.

 

[PhantomGaze]

Or its weird poison glands that males have. The animal is so freaky that when people first brought examples of them in for the scientific community, they were thought to be fakes, beaver and duck parts sewn together.

Electrolocation Platypus - Wikipedia, the free encyclopedia

This little guy becomes weirder the more we learn.

 

[Split Rock]

IThe funny part is that none of you will make any major claims about the molecular clock now. As Split Rock already conceded, sometimes it matches up, sometimes it doesn't because "species do not always evolve at equal rates". How do you know if the rate of evolution is unequal? Because the molecular clock says so. Heads: Evolution. Tails: Evolution.

No, we know because we can watch evolution, and sometimes it can occur very quickly, such as with Stickleback fish studies:
Stickleback genome holds clues to adaptive evolution -- ScienceDaily
The Foster/Baker Lab at Clark University in Worcester, Mass., studies the post-glacial adaptive radiation of the threespine stickleback fish

It's all about actually looking at the world and basing your theories on what we see there, rather than basing our theories on a book written centuries ago by men who didn't understand the world around them as well.

The molecular clock is just more circular ad-hoc evo fluff that darwin spokespeople use to confuse the unwitting public.

Really? I guess that's why scientists rarely talk about the molecular clock with the public.
Molecular clock research is done by scientists for science.
Here's a PubMed search for "molecular clock"
"molecular clock" - PubMed - NCBI
Results: 1 to 20 of 1736
How many of these journals are intended for public consumption? None.

As usual, you are more interested in bluster, rhetoric and conspiracy fantasies than reality.

 

[46AND2]

I notice none of you are commenting on the Schwartz,Maresca article which lists numerous literature references of molecular clock discordance and failed predictions.

Do Molecular Clocks Run at All? A Critique of Molecular Systematics

http://www.pitt.edu/~jhs/articles/Schwartz&Maresca_Mol_clocks.pdf


The funny part is that none of you will make any major claims about the molecular clock now. As Split Rock already conceded, sometimes it matches up, sometimes it doesn't because "species do not always evolve at equal rates". How do you know if the rate of evolution is unequal? Because the molecular clock says so. Heads: Evolution. Tails: Evolution.

The molecular clock is just more circular ad-hoc evo fluff that darwin spokespeople use to confuse the unwitting public.

No...the funny part is that I never made any major claims about the molecular clock in the first place. In fact, I distinctly said that I don't care if it works or not.

I commented on the particular paper you posted, because it was very obviously substandard. Even if I was arguing for your case, I'd not have used it as evidence, because it was poorly written. I wasn't harping on it because I thought it was WRONG, but because I thought it lacked scientific professionalism.

I'm well aware of the limitations of the molecular clock, and treat results for what they are...inferred, SUPPORTING evidence...that is to say, not direct, infallible, stand-alone evidence.

It's useful in certain studies, to scientists, who know that they are not engraved in stone.

 

[SLP]

Yeah, those were some of the redflags for me, too. And that was just in the abstract. And of course it just looks to creationists like we are handwaving articles away that we don't like...really not our fault that they are incabable of recognizing poor scientific writing when they see it.

It's a shame some of that stuff manages to get a "peer reviewed" tag on it. Unfortunately, its only going to get worse until they crack down on some of these open access journals.

Indeed. I had my doubts about open access way back when - and my concerns just keep getting more and more data in their support.

 

[SLP]

I think Shapiro's natural genetic engineering is some pretty serious business.

Great.

That means he speaks for all science?

 

[SLP]

No need to get upset, it's just one man's opinion. Shapiro is an expert geneticist, an evolutionist, and openly hostile to creationism. Yet he casually points out the religious conviction of many evolutionary theorists. Struck a chord in you, I see.

Good for him - yes, the chord it struck was the arrogant hypocrisy that he exudes. He is building a cult of personality, little more.

Honestly, you can cut the religious fervor of most evolutionists with a knife. They absolutely hate to have their origins beliefs questioned. It's just nice to have it confirmed by a hostile witness every now and then.

Whatever. For me, it is more of an annoyance to see so many creationists pretend to understand things they don't.

And their arrogant ignorance is explained by the Dunning-Kruger effect coupled with their religious fervor.

 

[SLP]

Maybe you could stop spamming nonsense all over the thread and actually respond to the original content? Or are you just here to stamp your feet?

The original content is a load of baloney - typical creobabble.

I know that many YECs like to stroke their egos by pretending to know more than they do, then acting indignant when others point out the flaws in their reasoning,

Pitiful lot.

 

[SLP]

Can you provide an example of the molecular clock actually being used to infer phylogenies?

Thanks, sport!

Isn't it interesting to see what posts creationist pseudo-know-it-alls ignore?

 

[SLP]

More ignored stuff for the YEC bloviators.

Found this on another forum:

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."





What are the methods used to assess creationism's claims? Are they testable? have they been tested on knowns?

Nested hierarchies are predictions of evolution which have been confirmed via tested methodologies.

All you are offering is inflammatory assertions coupled with unwarranted condescension produced by the Dunning-Kruger effect, as best I can tell.

And no mention of molecular clocks!

Amazing what one can see when one actually understands the material!

 

[SLP]

No...the funny part is that I never made any major claims about the molecular clock in the first place. In fact, I distinctly said that I don't care if it works or not.

I commented on the particular paper you posted, because it was very obviously substandard. Even if I was arguing for your case, I'd not have used it as evidence, because it was poorly written. I wasn't harping on it because I thought it was WRONG, but because I thought it lacked scientific professionalism.

I'm well aware of the limitations of the molecular clock, and treat results for what they are...inferred, SUPPORTING evidence...that is to say, not direct, infallible, stand-alone evidence.

It's useful in certain studies, to scientists, who know that they are not engraved in stone.

I'll never get used to these YEC types that read a few websites and fancy themselves experts on all things related to evolution.

 

[SLP]

So, in short, evolutionists can keep making up stories about mystical events that occurred at these imaginary nodes (common ancestors) millions of years ago to explain why traits end up where they do in modern species.

The hypocritical projection is astounding.

Standard YEC blowhard fare.