Scientific Evidence for Universal Common Descent

[tas8831]

As is often the case, usfan has been making these same dorky "arguments" for some time on other forums. Google him up for some klassic kreatinist komedy!

Observe:

"But if there is no genetic proof of descendancy, it is mere speculation to suggest it happened. How? What mechanism overcame the high genetic walls? It cannot happen, it did not happen, & it will not happen, with what we know of genetic science. Unless a force or mechanism can be defined & demonstrated, the leaps between genome pairs & genetic parameters is impossible. It is a myth based on children's drawings trying to indoctrinate naturalistic origins."



"Genome pairs" and "genetic parameters"...

Klassic!

 

[tas8831]

And yet again you misuse the "ad hominem" fallacy, despite it being explained to you multiple times by multiple posters.

Why are you being so obtuse?

Ultimately, the creationist pretending to be interested in the science of it all has little choice.

 

[Dan From Smithville]

As is often the case, usfan has been making these same dorky "arguments" for some time on other forums. Google him up for some klassic kreatinist komedy!

Observe:

"But if there is no genetic proof of descendancy, it is mere speculation to suggest it happened. How? What mechanism overcame the high genetic walls? It cannot happen, it did not happen, & it will not happen, with what we know of genetic science. Unless a force or mechanism can be defined & demonstrated, the leaps between genome pairs & genetic parameters is impossible. It is a myth based on children's drawings trying to indoctrinate naturalistic origins."



"Genome pairs" and "genetic parameters"...

Klassic!

I am somewhat baffled at his use of technical terms and the creation of technical terms I have never really heard of before.

 

[tas8831]

I am somewhat baffled at his use of technical terms and the creation of technical terms I have never really heard of before.

And all the while calling it "technobabble" meant of obfuscate.....

 

[Dan From Smithville]

And all the while calling it "technobabble" meant of obfuscate.....

These inconsistencies, errors and fallacies have not escaped introspection and become lose on here by accident.

How does one spend decades in personal learning about science and then claim the use of valid technical terms in context is a tool of obfuscation?

 

[tas8831]

These inconsistencies, errors and fallacies have not escaped introspection and become lose on here by accident.

How does one spend decades in personal learning about science and then claim the use of valid technical terms in context is a tool of obfuscation?

Good question.

Of course, he is not alone. At least 2 other creationists on here have engaged in nearly identical antics ( and all others have nibbled at the edges) - proclaiming lengthy tenures at 'debate' and having voluminous knowledge of the topics, only to be handily shown that both assertions are mere pretense. Sad.

 

[Dan From Smithville]

Good question.

Of course, he is not alone. At least 2 other creationists on here have engaged in nearly identical antics ( and all others have nibbled at the edges) - proclaiming lengthy tenures at 'debate' and having voluminous knowledge of the topics, only to be handily shown that both assertions are mere pretense. Sad.

I can understand a desire to know more about science. Personally, I cannot see why a person could not find something interesting there to educate and challenge themselves. I am just not seeing what I would consider to be a garden of understanding based on a study of science, even informally.

What I think I see are people, who have, in exploring their theology, crossed paths with other, similar, people who write erroneous statements and claims about science out of an emotional response to perceived attacks on those theological views. It is these erroneous claims that are used in arguments and poorly and incorrectly identified as science.

That is a fancy way of saying that creationists get their "science" from other creationists that do not understand science.

 

[tas8831]

That is a fancy way of saying that creationists get their "science" from other creationists that do not understand science.

It is those "high genetic walls"....

 

[tas8831]

Cut and pastes of actual scientific papers that we have explained?

You made no points TO refute, just the usual sad, underinformed, Dunning-Kruger-backed creationist assertions.

Genetic walls?

You're a pretender, no question.

Run of the mill desperate self-absorbed creationist.

 

[usfan]

Cut and pastes of actual scientific papers that we have explained?
You made no points TO refute, just the usual sad, underinformed, Dunning-Kruger-backed creationist assertions.
Genetic walls?
You're a pretender, no question.
Run of the mill desperate self-absorbed creationist.

Call names and deflect all you want..

You demonstrate who the real Pretender is.. no science. No reason. No clue.

"You want to argue fossils? Neanderthal? Speciation? Vestigiality? Micro vs macro? Horizontal gene transfer? MtDNA?

Do it, if you dare, and stop depending on your phony narratives, deflections, disruption and heckling. Are all of you so collectively deluded? Does the 'mob mentality' kick in, and you can not reason with your rational brains, but get caught up in the emotional hysteria of groupthink?

I challenge you.. any of you.. to break from the mob rule dynamic, and try Reason and Science. You'll get a Rational Debate the others can only dream of. Want to try it? Or does the mob dynamic have too strong a grip on your minds?"

 

[tas8831]

I propose a discussion about the evidence for this theory of origins. AKA, 'the theory of evolution', it is the most widely believed theory about life in the modern world.

With good reason.

OK, so, here is a bit of evidence.

Molecular phylogenetic analyses of hypotheses of common descent, using tested and verified accurate methods [1, 2, 3] , have overwhelmingly supported non-genetic hypotheses of common descent. That is, two unrelated methods of assessing hypotheses of descent have converged on common results, both indicating the validity of the theory of common descent. In addition, genetic methods have a lower level of subjectivity and employ larger datasets, so are generally considered to be more reliable. The results of these sorts of analyses are demonstrative of valid scientific exploration of evolutionary hypotheses [4, 5, 6].

References
1. Science 25 October 1991:
Vol. 254. no. 5031, pp. 554 - 558
Gene trees and the origins of inbred strains of mice

2. Science, Vol 255, Issue 5044, 589-592
Experimental phylogenetics: generation of a known phylogeny

3. Science, Vol 264, Issue 5159, 671-677
Application and accuracy of molecular phylogenies

4. PNAS June 10, 2003 100 (12) 7181-7188; https://doi.org/10.1073/pnas.1232172100
Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: Enlarging genus Homo

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

6. A Molecular Phylogeny of Living Primates

 

[tas8831]

Call names and deflect all you want..

Call names?
Pointing out that you are a pretender is not name calling, it is a conclusion premised on your antics.

Deflect? I demonstrated conclusively that you cannot/do not even understand that which you are ranting about.

I cite multiple scientific papers on molecular phylogenetics and you rant about 'morphology' and 'E.coli' and 'citrate'???

If THAT is not deflecting, it is an unwitting admission of abject ignorance.

You demonstrate who the real Pretender is..

Yes, I do demonstrate it by replying to your laughable rants.

no science. No reason. No clue.

Cool that you can admit this finally.

"You want to argue fossils? Neanderthal? Speciation? Vestigiality? Micro vs macro? Horizontal gene transfer? MtDNA?

LOL!

So precious how you avoided mentioning that which I provided citations to!

You want to argue mtDNA? You cited a paper that you MISREPRESENTED already!!!

But sure, I will argue fossils, Neanderthals, Speciation, vestigiality, micro v. macro, HGT, and mtDNA.

But remember - by YOUR rules, it is one at a time.

You've already lost on molecular phylogenetics (DNA) and mtDNA, and from what I saw you blew it on Neanderthals and HGT, too.

But let's see your "science".

 

[tas8831]

Weird that Mr.Grown-up-creationist totally ignored this....

Underinformed, bombastic, AND desperate! Love it!
Yes, it was a cut and paste of something I've posted before. Is that supposed to be an insult of some kind? Can't you handle it? You, after all, claimed to 'know the material'...

You made no point. You just dismissed it all as being a long cut and paste. You didn't actually think you had made a point, did you? I no more belittled or insulted you than you have done to us. Why the double standard snowflakery?


By technobabble, you are referring to actual scientific terminology? Like.. "the material"? 40 years at this and you've never seen an actual scientific paper's abstract?


I have not once mentioned E. coli or citrates. Sorry.


Again, YOU claimed to know the material. Was that a lie?

Oh, that was from the article I posted on E. coli and citrates...



Your reading comprehension is absolute crap.

Or you are just dodging and flailing out of desperation and panic.

What it is ACTUALLY saying is that while the underlying premises were sound, no actual direct tests had been done because there were few known phylogenies. This was in 1992, by the way. And guess what they did - they found a known phylogeny, and tested the genetic analyses against that known phylogeny, and the molecular methods WORKED! Amazing what you can learn when you actually read and understand the science you claim to!

And I do not need to 'bluff' - if I were going to bluff, I would reply to you and bring up things that you had not even mentioned. You know... like you did.


Are you for real?

Are just TRYING to get flamed? Because not one of the papers I referred to even MENTIONED citrates.

Talk about bluffing - you didn't even TRY to read what I posted, did you?



All of that is bluffing - none of the stuff I presented even mentioned any of that.

Funny - you seem to do an awful lot of the things you accuse others of doing.
Hare brained - you mean like believing a tribal deity made a man from dust 6000 years ago?

And we know that you don't understand what an ad hominem is, but now we see that you don't know what "infer" means, either:


in·fer
/inˈfər/
verb

1. deduce or conclude (information) from evidence and reasoning rather than from explicit statements.
   "from these facts we can infer that crime has been increasing"

Poor fellow - you try so hard!



Desperation - like continuing to refer to E. coli and citrate in response to a series of abstracts that did not once mention either?

You certainly do project and deflect with the worst of your kind...


It isn't, as yet again, I did not once mention E. coli or citrate. Your bluffing is entertaining and informative, though, I must say.

And remind me what YOUR 'belief' is based on? Some tall tales written by pre-technological numerologist mystics in the ancient middle east? Cool!

Cool slogan, bro. Got anything relevant to what I posted?


If you cannot understand the abstracts despite claiming to be a science geek and to have been at this for 4 decades, I have to wonder what you were actually doing all this time.


No, it is pretty obvious any ONE of us is too much for you - you rely WAYYYY too much on these pre-fabricated slogans that you probably scalped from some half-wit professional creationist.

Let me know when you think you can actually address molecular phylogenetics. As it stands, you are way out of your league, but too prideful and too geeked up on the Dunning-Kruger effect to be taken seriously..

In a way, I feel sorry for folks like you - so desperate to try to make your actual religious beliefs seem valid and rational by attacking that which you fear, that you seemingly do not care how foolish you come across.

In another way, I'm totally cool with your antics. Shows the shallowness and desperation of the religious fanatics out there.

 

[usfan]

I would say the best evidence is that genealogy of species via DNA analysis confirms morphology. What this means in basic terms is that the "tree of life" AKA the "family tree" of species based upon their resemblances to each other very closely matches the family tree of species based upon analysis of their DNA.

This was presented earlier, and i touched on it, but since the 'looks like!' morphology is one of the main arguments for common descent, it deserves another look.

1. It is primarily circular reasoning. Because you can put together a graphical 'tree', showing plausibility of descent, does not provide evidence for descent. The conjectured graphic does not prove itself.
2. "Analysis of DNA" shows very little similarity, in the actual genes. Certain haplogroups, like canidae, mentioned earler, HAVE the evidence of descendancy. But to extrapolate that to all living things is flawed. It is not the case. There is NO GENETIC EVIDENCE of descendancy in cross genetic architectures. There is real genetic evidence of descendancy within canidae, felidae, equus, etc, but nothing to suggest any of them came from, or are becoming, something else. The 'high genetic walls,' that the hecklers love to ridicule, PREVENT any departure from the parent architecture. That is repeatable, observable, scientific FACT.

Plausibility, and 'looks like!' imagination, is not scientific evidence.

 

[usfan]

I cite multiple scientific papers on molecular phylogenetics and you rant about 'morphology' and 'E.coli' and 'citrate'???

If THAT is not deflecting, it is an unwitting admission of abject ignorance.

You've decided to join the hecklers, so i glaze over any alleged 'rational!' arguments that might be hidden in your bombastic rants.

If you want to make a rational, civil, evidentiary based argument, i will reply. But i won't go through and sift out some alleged nugget of 'proof!' you only allude to.
.especially if it is framed in a deluge of mocking and ridicule.

I do not believe you are a sincere or honest debater, but a heckling True Believer, with jihadist zeal for your cherished beliefs. You have no Reason, just outrage and hysteria.

Can you present a reasoned reply? I don't think you can. Your religious zeal overrides any rational thinking, and the Groupthink loyalties crush any hopes of science or reason..

Enough bluff. Enough pretension. Enough religious hysteria. Do you have any ability to debate this issue rationally? Prove it.

 

[usfan]

Molecular phylogenetic analyses of hypotheses of common descent, using tested and verified accurate methods [1, 2, 3] , have overwhelmingly supported non-genetic hypotheses of common descent.

Seriously? Just repeat the same old asserted 'proofs!'?

Declaring, 'Molecular analysis proves common descent!', is not evidence. None of those studies compel a conclusion of common descent. I have repeatedly quoted, and explained the flaws in the e.coli conclusions, and they do NOT prove horizontal gene transfer, speciation, or anything even remotely resembling common descent. This is just another empty bluff.. repeating techno babble in the hopes of fooling the uninformed.

Here was my LENGTHY reply to this oft repeated reference..

If all that is being said is that organisms vary within their genetic parameters, then there is no debate. E coli is unique, in that it has a wide range of adaptability, but there is NO EVIDENCE that it came from (or is going to), some simpler (or complex) genetic structure.

Here i address the e coli study that has been alluded to. Quotes from the study are italicized.

Contribution of Horizontal Gene Transfer to the Evolution of Saccharomyces cerevisiae

genomic evolution was nearly constant for 20,000 generations. Such clock-like regularity is usually viewed as the signature of neutral evolution, but several lines of evidence indicate that almost all of these mutations were beneficial. This same population later evolved an elevated mutation rate and accumulated hundreds of additional mutations dominated by a neutral signature.

Pathetically, i understand this.. being a bit of a science geek, & having followed with great interest this subject for decades. I take issue with the use of the terminology, 'evolution', as it seems to use circular reasoning.. using the premise (and terminology) to prove itself. If by 'genomic evolution' you merely mean minor changes in generations, or micro evolution, that is plainly obvious. But to correlate it with macro is still a false equivalence.

Now, the study is claiming 'beneficial' mutations, among 'several lines of evidence'. I am a bit confused about the statement above, which seems to conflict with the findings of the study:

Of the 12 populations, six have so far been reported to have developed defects in their ability to repair DNA, greatly increasing the rate of mutation in those strains.[5][19][20] Although the bacteria in each population are thought to have generated hundreds of millions of mutations over the first 20,000 generations, Lenski has estimated that within this time frame,only 10 to 20 beneficial mutations achieved fixation in each population, with fewer than 100 total point mutations (including neutral mutations) reaching fixation in each population.

So there is a question about the results.. were 'almost all mutations beneficial'? Or were there 'only 10-20 beneficial mutations?

That is a fine point, & may be due more to the writer, than the experiment itself.

Ok lets go to the findings, & see what conclusions they compel.
* Change in fitness.
All populations showed a pattern of rapid increase in relative fitness during early generations, with this increase decelerating over time
* defects in genome repair
Of the 12 populations, six have so far been reported to have developed defects in their ability to repair DNA, greatly increasing the rate of mutation in those strains
* increase in cell size, & morphological change
All twelve of the experimental populations show an increase in cell size concurrent with a decline in maximum population density, and in many of the populations, a more rounded cell shape
* Polymorphism & phylogenetic comparison
Two distinct variants, S and L, were identified in the population designated Ara-2 at 18,000 generations based on their formation of small and large colonies, respectively.[25] Clones of the S and L types could co-exist stably in co-culture with each other, indicating they occupied distinct niches in the population
* Citrate usage
The inability to grow aerobically on citrate, referred to as a Cit− phenotype, is considered a defining characteristic of E. coli as a species, and one that has been a valuable means of differentiating E. coli from pathogenic Salmonella. While Cit+ strains of E. coli have been isolated from environmental and agricultural samples, in every such case, the trait was found to be due to the presence of a plasmid containing a foreign citrate transporter.[32] A single, spontaneous Cit+ mutant of E. coli was reported by Hall in 1982.[33] This mutant had been isolated during prolonged selection for growth on another novel substance in a growth broth that also contained citrate. Hall's genetic analysis indicated the underlying mutation was complex, but he was ultimately unable to identify the precise changes or genes involved, leading him to hypothesize activation of a cryptic transporter gene

There is a bit more in this study, & lots of commentary about the findings. But the primary evidence being presented is the ability of e.coli 'to grow aerobically on citrate', when oxygen is present.

Now, let us examine the claims that this is evidence for macro evolution, which predicts a structural change in the genome.

Has there been a 'structural change' in the dna? No. This is still a strain of e.coli. It is not another, more advanced bacteria, but one of the simplest, most basic ones there is, & even over thousands of generations, it is still e.coli, with a few mutations & variations, perhaps, but genetically, morphologically, & phylogenetically, unchanged. It is just a slightly different genotype, and almost an exact phenotype.

Here are some other facts about this study.

• E.coli is an asexual organism, able to reproduce by itself.
• The study began in 1988, & by 2016 has increased to 66,000 generations.
• E.coli has been found to be extremely adaptive, with ability to survive & adapt to many different conditions.
• There are many criticisms of this study's conclusions, among peer reviewed scientists. Extrapolations not warranted by the data are made, and it has been sensationalized for marketing or hype.
• This study provides no evidence for any structural changes in the genome.

I like this study. I am intrigued by the findings about e.coli, & its amazing adaptability to its environment. It is similar to the shark, in its longevity & ability to live in whatever environmental variables come its way.

But, for those who think this study provide evidence for the ToE, you are greatly mistaken. It does not. It merely illustrates the adaptability of e.coli.

The claim of 'new speciation' is only an arbitrary definition, not anything compelled by any changes in the morphology or genetic structure of the organism. To claim this is 'real evolution!' is absurd. It is obviously just adaptation, & only demonstrates the viability & adaptability of this particular organism. Some organisms do NOT have this capability, but die under unfriendly conditions. So this phenomenon does not apply universally, as would be expected if this were a mechanism for macro evolution, but is unique to e.coli.

Lenski criticizes Van Hofwegen et al.'s description of the initial evolution of Cit+ as a "speciation event" by pointing out that the LTEE was not designed to isolate citrate-using mutants or to deal with speciation since in their 2008 paper they said "that becoming Cit+ was only a first step on the road to possible speciation", and thus did not propose that the Cit+ mutants were a different species, but that speciation might be an eventual consequence of the trait's evolution

So the claim of 'new speciation!' is not even claimed by Lenski, the one doing the study, even though hordes of eager Believers cling to it as 'scientific proof!' of common descent.

This is desperation, not scientific evidence for common descent..

I begin to wonder if you have a clue as to what the study is saying.

You just keep reposting this as some kind of mantra.

 

[It Aint Necessarily So]

You guys are funny.. kind of pathetic

Actually, it is you that is pathetic. Your a walking advertisement against the dangers of excessive faith-based thought. However, I appreciate you serving in that role.

So, you figure, by berating and focusing on me, personally,

What a hypocrite. All you do is complain about others and insult them. How do you expect them to respond to you? I think that the posters on this thread have been kind to you considering how shabbily you treat them after they've tried so hard to teach you.

affirming your collective 'intelligence', by demeaning mine

You demean yourself with your empty posting and insults.

not missing any opportunity for more ad hominem.

Nor are you missing any opportunities to demonstrate how unteachable you are. Have you no self-respect? How can you possibly continue to make this error before the entire forum? Why do you have no interest in how you are perceived by others when trying to convince them of something? Remember ethos, the aspect of argumentation that considers not the argument itself, but how the one making it is perceived by his audience. If you are considered incompetent to discuss common descent, if you are considered unteachable, if you are considered unlikable, or if you are perceived to be promoting an agenda that others don't approve of, they stop listening to you, and their focus goes from your words to you. You don't like that, and do whatever you can to prevent it, but to no avail. Your posting behavior has become the topic of the thread.

your assumptions of 'scientific superiority!', are only assumptions.. assertions to deflect from the dearth of real evidence.

No, they are scientifically superior to you. They understand the science. You don't. They know how to interpret evidence. You won't even look at it.

as if that refutes my points.

Your points need no refutation. They are unsupported claims using nonsense terms as @tas8831 has pointed out. And when your claims are refuted anyway, you ignore the refutation. Just so you know, in academic circles, that's a concession. Creationists hope that if they ignore an argument, it's as if it were never made, but that is incorrect. It's exactly the same as in court of law. The last feasible argument that goes unrebutted or is unsuccessfully rebutted prevails.

If the defense attorney makes a claim of innocence, the prosecutor successfully rebuts the defense - perhaps by discrediting the alibi - and presents compelling evidence and argument in support of guilt, the defense must successfully rebut the prosecutor's argument. If instead, the defense ignores all of that and hopes it goes away, or simply repeats what it said previously unchanged - the same refuted alibi or says nothing at all - the defendant is likely to lose his case and go to prison.That's what you do to yourself by inviting others to provide evidence, telling everybody that you intend to reject it before seeing it, and then ignoring what has so kindly been offered to you. You lose, and your net effect is the opposite of the one you intended.

do any of you pathetic 'debaters' have the balls to deal with science?

Yeah, but you're not qualified to discuss the subject. Most of your detractors have been dealing with science all of their lives, which is why they know it. They're people that have been fascinated by science since childhood. They asked for chemistry sets and Radio Shack kits as kids. They read about science in their Highlights magazines. They enjoyed biology, chemistry and physics in high school and needed no prompting to study and learn it. They took science electives in college. They may have majored in one or two of the sciences and chosen a career in science. They were glued to the TV during the Apollo missions and have been following the space program ever since. They subscribed to Scientific American and Sky & Telescope. Many owned telescopes and became amateur astronomers. And they continued their science education after graduating with pop science books at Barnes & Noble or B. Dalton written by people like Davies, Gribben, Dawkins, Weinberg, and Prigogine, watched uncounted science documentaries from NatGeo and Nova, watched every episode of both Sagan's and Tyson's Cosmos series, and the like.And it shows.

Not so much with you. Your interest in science seems to be to try to use it against itself in support of your religious beliefs, a foolish endeavor. You came to attack, but unarmed.

Show me the evidence.

Nah. Why bother? Others are still providing evidence to you, but I won't. Your game, the creationist two-step, is obvious, and not one I want to play. My interest is not in trying to teach you when you have already announced an unwillingness to learn and demonstrated it as well (your ad hom nonsense has hurt you), but in assessing how your faith has affected you. I see an interesting spectrum of Christians on these threads. Some seem to be well educated and competent critical thinkers. They say nothing I disagree with. Their religious beliefs don't seem to have had any ill effect on them. On the other end, are the intellectual and moral roadkill the Christianity also generates. Every new Christian debater is a data point.

I do the same with the Muslims, the Baha'i, the pagans and polytheists, the deists, the irreligious, etc., and eventually come to an understanding of which of these helps people or harms them. Nobody outperforms the secular humanists, but some of the religious do as well.

the intent is to flood the thread with 30 - 1 heckling, deflections, pissing contests, and juvenile bickering?

No. The intent is to rebut your absurd claims.

How separated from evidence are you? The whole thread is telling you the same thing, something that ought to be important to you. But you are blissfully ignorant of the damage you do to your case with your debating etiquette, which you beg others to forgive and ignore, but as I said, you've made that the topic of the thread with that behavior.

You've decided to join the hecklers, so i glaze over any alleged 'rational!' arguments that might be hidden in your bombastic rants.

So this isn't an example of you heckling? You're doing exactly what you falsely accuse others of. You're the ranter here, ranting about heckling and ad hom. Your complete lack of insight as to how others perceive you is among the damage done to you by this path you've chosen. How can you possibly not know how much damage you do to your position after being told and shown repeatedly?

 

[tas8831]

There is a saying about how lies go around the world twice before the truth gets out of bed. There is a similar saying about how it takes 10 pages of facts to refute one page of misrepresentation. This could take a while...
PART 1

What does man's best friend have to say about universal common descent?

I'm not sure canid evolution actually ADDRESSES "universal common decent", - why do you think it does?

I encountered a creationist one time that used a newspaper article about a paper on felid phylogeny to claim support for evolution only within "kinds". But the actual paper included non-felids in their phylogeny. When I showed him this, he deflected and dissembled for weeks, but never could bring himself to admit his error.

I read the following study several years ago, and found a wealth of information about canidae..

However did you make it through all the technobabble?

many old beliefs or assumptions have been corrected by hard genetic evidence

Can't wait to see it. What do consider "hard genetic evidence"? Because when I presented some of what I consider hard genetic evidence, you blew it off as too long a cut and paste.

It has interesting facts about dogs, & their genetic base.

What is a "genetic base"? I have taught both genetics and evolution and have never seen this phrase used. Educate me.
Regarding your post, I will emphasize points for rebuttal/refutation purposes (i.e., emphases mine, except for italics which were in the original post).

Relaxation of selective constraint on dog mitochondrial DNA following domestication

Here is a summary of some of the points, with quotes from the study in italics:

1. The ancestor of wolves, coyotes, dogs, and other canidae is unknown, appears suddenly, and contained all the genetic information for each haplotype. the origin of the huge morphological diversity that led Darwin to his speculation remains largely unknown

Your interpretation does not follow from the quote (nor the context).

Here is the quote in context:

In The Origin of Species, Darwin (1859) suggested that “several wild species of Canidae have been tamed and that their blood, in some cases mingled together, flows in the veins of our domestic [dog] breeds”. We now know that dogs (Canis familiaris) are entirely derived from the domestication of wolves (Canis lupus) (Vilà et al. 1997); however, the origin of the huge morphological diversity that led Darwin to his speculation remains largely unknown (Sutter and Ostrander 2004). The domestic dog is the most phenotypically diverse mammal on earth. The large differences in size, conformation, behavior, and physiology between dog breeds exceed the differences among species in the dog family, Canidae (Coppinger and Coppinger 2001; Wayne 2001). Recent studies show that the origin of most dog breeds may derive from very recent selective breeding practices and are probably <200 yr old (Parker et al. 2004). However, selection acts upon existing variability. It is remarkable that the potential for such large diversification existed in the ancestral wolf population from where the domestication process was initiated. Furthermore, the time since domestication (at least 14,000 yr; Vilà et al. 1997; Sablin and Khlopachev 2002; Savolainen et al. 2002) seems insufficient to generate substantial additional genetic diversity. What is the origin of this diversity? We hypothesize that changes in the living conditions of dogs as a result of domestication resulted in the release of selective constraint allowing a faster accumulation of functional (non-silent) genetic diversity in a large array of genes.​

Further, nothing in the paper indicates that the origins of wolves, etc., are "unknown." That is your editorializing.

This more recent paper (2017) indicates:

Abstract
There are nearly 400 modern domestic dog breeds with a unique histories and genetic profiles. To track the genetic signatures of breed development, we have assembled the most diverse dataset of dog breeds, reflecting their extensive phenotypic variation and heritage. Combining genetic distance, migration, and genome-wide haplotype sharing analyses, we uncover geographic patterns of development and independent origins of common traits. Our analyses reveal the hybrid history of breeds and elucidate the effects of immigration, revealing for the first time a suggestion of New World dog within some modern breeds. Finally, we used cladistics and haplotype sharing to show that some common traits have arisen more than once in the history of the dog. These analyses characterize the complexities of breed development resolving long standing questions regarding individual breed origination, the effect of migration on geographically distinct breeds, and by inference, transfer of trait and disease alleles among dog breeds.​

and

Previous studies have addressed the genomic makeup of a limited number of breeds, demonstrating that dogs from the same breed share common alleles and can be grouped using measures of population structure (Irion et al., 2003; Koskinen, 2003; Parker et al., 2004), and breeds that possess similar form and function often share similar allelic patterns (Parker et al., 2004; Parker et al., 2007; Vonholdt et al., 2010). However, none of these studies have effectively accounted for the variety of mechanisms through which modern breeds may have developed, such as geographic separation and immigration; the role of hybridization in the history of the breeds; and the time-line of the formation of breeds. In this study we overcome these barriers by presenting an expansive dataset including pure-breeds sampled from multiple sections of the globe and genotyped on a dense scale. By applying both phylogenetic methods as well as a genome-wide analysis of recent haplotype sharing, we have unraveled common population confounders for many breeds leading us to propose a two-step process of breed creation beginning with ancient separation by functional employment followed by recent selection for physical attributes. These data and analyses provide a basis for understanding which and why numerous, sometimes deleterious, mutations are shared across seemingly unrelated breeds.​

And regarding the origin of the Canidae ("The ancestor of wolves, coyotes, dogs, and other canidae is unknown, appears suddenly"), well, you are way wrong:

Carnivora

Man's Best Friend

"Domestic dogs, wild dogs, and wolves all belong to the Family Canidae, which also contains jackals, coyotes, and foxes. Canidae is contained within the group caniformia which is contained within the Order Carnivora, one of the eighteen current groups of Eutherians, or placental mammals. A full list of the groups contained in Canidae is provided below.

Within the Canidae are 14 groups, or genera. Contained within those 14 genera are at least 34 species and two subspecies (a chart showing all members in the Canidae is provided below). The genus Canis contains dogs, jackals, and wolves. The gray wolf, Canis lupus, is among 7 species of canids and also related to two subspecies, Canis lupus dingo and Canis lupus familiaris, which are known commonly as the dingo and the domestic dog, respectively."​

Some relevant refererences provided for the two links above:

Lindlad-Toh, K. et al. (2005) Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature. 438, 803-819.
Arnason, U., A. Gullberg, A. Janke, and M. Kullberg. 2007. Mitogenomic analyses of caniform relationships. Molecular Phylogenetics and Evolution 45 (3): 863-874.
Bininda-Emonds, O. R. P., J. L. Gittleman, and A. Purvis. 1999. Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia). Biological Reviews of the Cambridge Philosophical Society 74:143-175.
Delisle, I. and C. Strobeck. 2005. A phylogeny of the Caniformia (order Carnivora) based on 12 complete protein-coding mitochondrial genes. Molecular Phylogenetics and Evolution 37(1):192-201.
Dragoo, J.W. and R. L. Honeycutt. 1997. Systematics of mustelid-like carnivores. Journal of Mammalogy 78:426-443.
Flynn, J. J., J. A. Finarelli, S. Zehr, J. Hsu, and M. A. Nedbal. 2005. Molecular phylogeny of the Carnivora (Mammalia): Assessing the impact of increased sampling on resolving enigmatic relationships. Systematic Biology 54(2):317-337.
Schreiber, A., K. Eulenberger, and K. Bauer. 1998. Immunogenetic evidence for the phylogenetic sister group relationship of dogs and bears (Mammalia, Carnivora : Canidae and Ursidae) - A comparative determinant analysis of carnivoran albumin, C3 complement and immunoglobulin mu-chain. Experimental and Clinical Immunogenetics 15:154-170.
Wyss, A. R. and J. J. Flynn. 1993. A phylogenetic analysis and definition of the Carnivora. Pages 32-52 in Mammal Phylogeny. Volume 2. Placentals. (F. S. Szalay, M. J. Novacek, and M. C. McKenna, eds.) Springer Verlag, New York.
Zhang, Y. P. and O. A. Ryder. 1993. Mitochondrial-DNA sequence evolution in the Arctoidea. Proceedings of the National Academy of Sciences (USA) 90:9557-9561.​

I know, I know - citation bombing.... Lengthy cut and paste, right? No - these are references showing that your implication about the origin of the Canidae is bogus. Deal with it.

END PART 1

 

[tas8831]

PART 2


Moving on...

2. All of the current variety of dogs are recent developments, less than 200 yrs old. Recent studies show that the origin of most dog breeds may derive from very recent selective breeding practices and are probably <200 yr old

Again, you are editorializing and engaging in some of the tactics you imply/accuse others if using - that quote is in context above, and one can note a single ref from 2004 supporting the claim about 200 years - one can also see the word "most" in the original.
Regarding these breeding practices - what leads you to believe that all of the diversity was in the 'original' canids? Where is the evidence? It is not in the paper you refer to.And by the way - how do you define "haplotype"? Because it does seem like you are using it the way you think you are.

3. Selection acts on EXISTING variability. It is not created on the fly, & is assumed to take thousands or millions of years to come about.selection acts upon existing variability

In context:

"It is remarkable that the potential for such large diversification existed in the ancestral wolf population from where the domestication process was initiated. Furthermore, the time since domestication (at least 14,000 yr; Vilà et al. 1997; Sablin and Khlopachev 2002; Savolainen et al. 2002) seems insufficient to generate substantial additional genetic diversity. What is the origin of this diversity? We hypothesize that changes in the living conditions of dogs as a result of domestication resulted in the release of selective constraint allowing a faster accumulation of functional (non-silent) genetic diversity in a large array of genes."​

That is one answer, another, again from the 2017 study, is this:

"The large haplotypes specifically target admixture resulting from breed formation rather than domestication, which previous studies have not addressed. The total length of the shared haplotypes was summed for each pair of dogs. Individuals from within the same breed-clade share nearly four times more of their genome within large IBD haplotype blocks than dogs in different breed clades [median shared haplotype lengths of 9,742,000bp and 2,184,000bp, respectively, P(K-S and Wilcox) < 2.2e-16 (Figure 3a)]. Only 5% of the across-breed pairings have a median greater than 9,744,974bp. These exceptions argue for recent admixture events between breeds..."​

And please document the claim that "EXISTING variability. It is not created on the fly, & is assumed to take thousands or millions of years to come about". I think maybe you are referring to speciation, not variation?

4. ALL of this variability EXISTED in the ancestral wolf/parent, according to the time frame in the UCD model. It is remarkable that the potential for such large diversification existed in the ancestral wolf population

More editorializing. Again, I refer to the 2017 paper in which more extensive analyses revealed admixtures with other populations of dogs.

5. The recent time for the variety of dog breeds is incongruent with the assumption of 'millions' or even thousands of years of evolution, to generate such variety. Furthermore, the time since domestication seems insufficient to generate substantial additional genetic diversity.

One part at a time -
"The recent time for the variety of dog breeds is incongruent with the assumption of 'millions' or even thousands of years of evolution, to generate such variety"

Again, please document the notion that it takes thousands or millions of years to generate variety/diversity.

Next part - please re-read your 'supporting' quote:

"Furthermore, the time since domestication seems insufficient to generate substantial additional genetic diversity."

But adding more diversity from 'external' dog populations - as documented in the 2017 study - does nto require the generation of this diversity:

"These exceptions argue for recent admixture events between breeds, as evidenced by the example of the Eurasier breed, created in the 1970's by mixing Chow Chow with other spitz-type breeds"

Does it?

The child [???] branches within canidae show REDUCING variability, as the diverse genetic information became localized in the various phenotypes.

So much technobabble meant to obfuscate - can you explain that in simpler terms? I have only been at this for about 25 years...
Also - please explain the genetic mechanism whereby all of this already-present 'diversity' was held in check. I mean a wolf does not look at all like a chihuahua, so how did the wolf genome 'suppress' the chihuahua haplotyes/information? You must have an explanation, or is it all just editorializing and supposition and speculation on your part?

The mtDNA provides clear evidence of the descendancy within canidae, but the time frame is incompatible with the UCD model.

You do know, do you not, that mtDNA has little if anything to do with morphology, right?

But cool extrapolation from mtDNA haplotypes on hundred-to-thousand year time scales to nuclear genome process on hundreds of thousands to millions of years time scales.

You can see from the following chart, where they mapped the genome sequence, & followed the trail of the mtDNA:

From the link:
"Phylogenetic tree of wolf (W), dog (D), and coyote (C) mtDNA sequences. The tree was constructed using a Bayesian approach. The same topology was obtained with a neighbor-joining approach. Support is indicated at the nodes as percent bootstrap support for 1000 neighbor-joining replicates and Bayesian posterior probabilities. Four clades of dog sequences (I to IV) are indicated as in Vilà et al. (1997). Internal dog branches are marked in orange, and internal wolf branches are marked in light blue. The branch leading to wolf haplotype W1 was basal to the rest of the tree and it was also considered internal. Internal branches that could not be conclusively associated to dogs or to wolves are indicated in discontinuous green."

So cool how you accept without question molecular phylogenetics results when you think they are supporting your cause.

As you can see, the mtDNA shows the ancestry line.[sic].

And yet you dismiss something like this?:

That study used mtDNA, too. It shows "the ancestry line".


END PART 2

 

[tas8831]

And PART 3:

The canid ancestor preceded the wolf, the dog, & the coyote, as well as other canidae not listed. I have seen them in other genetic studies.

In the many references I list above, the ancestor of the Candiae is indicated. And it was not a canid.

But all this does is indicate descendancy,

Right - ancestor-descendant relationships.

and shows the variability to be INHERENT in the genes.

In the genes at present yes.
You understand that, right?

This is why I asked about haplotypes.

You should not employ technobabble that you do not understand. I mean, we sort of know where haplotypes and new alleles and such come from...
And do you think that all variability is inherent in all genomes of a particular 'kind'? Again, if so, please provide the mechanism by which hundreds of alleles/haplotypes are 'silenced' while they are not being used.

It was not created on the fly, or mutated over millions of years.

What do you mean "on the fly"?
Do you really not understand what a haplotype is?

There is no evidence for those speculations.

So it this how you will operate - editorialize, extrapolate, dismiss?

Canidae shows diversity and adaptability. There is no evidence they shared ancestry with felids, equids, or any other haplogroup.

Sure there is - I provided (cut and pasted) about a dozen papers providing such evidence - evidence that you accepted above.

We can follow the MICRO variations within canidae, but there is NOTHING to suggest they were once of a different genetic structure, or varied to or from a MACRO change.

Sure there is - the exact same type of analyses that you approved of above:

"The mtDNA provides clear evidence of the descendancy..."
"You can see from the following chart, where they mapped the genome sequence, & followed the trail of the mtDNA"
"As you can see, the mtDNA shows the ancestry line."

Amazingly, those are the very things that my abstracts showed (that you dismissed because of the fact that you thought I was making several arguments via one long copy paste, as opposed to using several papers to support one line of argument).

Like nearly all creationists, you just accept the science when you think it supports your position, and reject the exact same science when it doesn't. Pretty immature and disingenuous.

Canids have always been canids, and always produce canids,

Except that their "line of descendancy", when traced using your already-approved-of-methods of analysis shows that they were not yet canids. Like here:

https://media.springernature.com/fu...aObjects/12915_2011_Article_534_Fig1_HTML.jpg


from "Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates"

though with reduced variability, as we reach the ends of the branches in their haplotree.

So... what is the mechanism by which diversity is lost upon breed formation?

And btw, this phylogenetic tree has evidence to support it. The genetic lines can be traced, not just presumed.

Really? How did they get mtDNA from the 'original' canids?

How does this study, specifically, differ in reliability from this one:

Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes

"Here we present a comprehensive mitogenomic study of primates. We assembled 87 mammalian mitochondrial genomes, including 62 primate species representing all the families of the order. We newly sequenced eleven mitochondrial genomes, including eight Old World monkeys and three strepsirrhines. Phylogenetic analyses support a strong topology, confirming the monophyly for all the major primate clades. In contrast to previous mitogenomic studies, the positions of tarsiers and colugos relative to strepsirrhines and anthropoids are well resolved. "​

That study is actually far more comprehensive that your canid "descendancy" one is, so please provide a valid rationale for rejecting this and accepting the canid one.

Lack of such a valid criterion shows that what you accept and what you reject is not based on any valid scientific footing, but rather on a decidedly non-scientific, arbitrary prejudice.

But leaping to 'common descent!', based on the diversity within canidae is unwarranted, unscientific, and unbelievable..

Agreed - who would have used a paper on the canidae to argue for UNIVERSAL common descent? Why would you suggest such a thing? Why employ logical fallacies - I thought you had prohibited them from this thread by decree?

Yup - rule 2:

"Be logical. Try to use sound reason & avoid logical fallacies."

Nice strawman.

Also, to clarify terms, 'haplotype' is the specific clade or branch in this tree, like dogs, coyotes, etc.

No, that is not what a haplotype is.

"A haplotype is a group of genes within an organism that was inherited together from a single parent. The word "haplotype" is derived from the word "haploid," which describes cells with only one set of chromosomes, and from the word "genotype," which refers to the genetic makeup of an organism. A haplotype can describe a pair of genes inherited together from one parent on one chromosome, or it can describe all of the genes on a chromosome that were inherited together from a single parent. This group of genes was inherited together because of genetic linkage, or the phenomenon by which genes that are close to each other on the same chromosome are often inherited together. In addition, the term "haplotype" can also refer to the inheritance of a cluster of single nucleotide polymorphisms (SNPs), which are variations at single positions in the DNA sequence among individuals."

Please learn to use science terms correctly - 40 years at this? You 'know the material'? OK...

The haplogroup is all the haplotypes together.

Nope - that is wrong, too.

"Haplogroups are mtDNA sequence polymorphism variations that have occurred over more than 150 000 years and correlate with the geographic origins of populations traced through the maternal lineages."


Too much technobabble?

Canidae, for the most part, consists of the single haplogroup of genetic commonality and evidenced descendancy. Genetics has replaced and updated the old morphological taxonomic classifications, which were one limited to 'looks like!' correlation. Now, we have hard science, not just speculation.

FINALLY you got one thing correct!!! <--- LINK


By the way - old morphological classifications were originally done by a creationist. And as it turns out, genetic systematics is generally not terribly different from morphological schemes. But with 40 years of debating this, and being a science geek, you must already know that...