Genetic evidence of Whale evolution

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Originally posted by lbhandli:
John Paul has claimed only genetic evidence will do for demonstrating whale evolution from hippos. He should do some more reading because the work was published in the Proceeding of the National Academy of Science in August of 1999:
Masato Nikaido, Alejandro P. Rooney, and Norihiro Okada
Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: Hippopotamuses are the closest extant relatives of whales

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abstract:Insertion analysis of short and long interspersed elements is a powerful method for phylogenetic inference. In a previous study of short interspersed element data, it was found that cetaceans, hippopotamuses, and ruminants form a monophyletic group. To further resolve the relationships among these taxa, we now have isolated and characterized 10 additional loci. A phylogenetic analysis of these data was able to resolve relationships among the major cetartiodactyl groups, thereby shedding light on the origin of whales. The results indicated (i) that cetaceans are deeply nested within Artiodactyla, (ii) that cetaceans and hippopotamuses form a monophyletic group, (iii) that pigs and peccaries form a monophyletic group to the exclusion of hippopotamuses, (iv) that chevrotains diverged first among ruminants, and (v) that camels diverged first among cetartiodactyls. These findings lead us to conclude that cetaceans evolved from an immediate artiodactyl, not mesonychian, ancestor.

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Comments? Please be specific if you are going to criticize the analysis.

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Cheers,
Larry

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John Paul:
To be frank, I have read this and similar diatribe. Very unimpressive because it offers nothing for the betterment of mankind."Hippopotamuses are the closest extant relatives of whales"But related how, exactly? Common Creator, common Intelligent Designer, common descent (ie shared a common ancestor)?- please be specific in your rhetoric Can you take this paper to the lab to verify the the so-called 'tests' are valid?How does this phylogenic analysis of the alleged evolution of cetaceans aid us in the research for a cure for cancer or any disease for that matter?IOW, what good does 'theorizing' what organisms share an alleged closer common ancestor than do others?When I first learned of the switch in positions of the alleged lineage of alleged cetacean evolution, I sent emails to, vistited several aquariums and cetacean institutes. I asked how this recent discovery (that caused the switch) would affect their research (pertaining to cetaceans). The overall answer was clear- "Not one bit."Go figure.------------------
John Paul

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Originally posted by joz:
In other words this research doesn`t give results that fit into JP`s personal opinion of how the world is so they are obviously worthless and completely spurious...

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Sorry JP but your going to have to do better than vague aspersions and questioning the worth of the knowledge....

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John Paul:
Sorry, joz. It ain't just me. If it were, you might have a point. I am hard pressed to find any cetacean expert who thinks theoretical musings of the past have any practical bearings on today's marine life.------------------
John Paul

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Originally posted by John Paul:
John Paul:
To be frank, I have read this and similar diatribe. Very unimpressive because it offers nothing for the betterment of mankind.--------------------------------------------------------------------------------
Mark:
WTF has cetacean phylogenies to do with the betterment of mankind? Does 6 day genesis better mankind?John Paul:
WTF does cetacean phylogenies have to do with anything? The only 'relevance' it may have is to determine relationships, and even with that we wouldn't be able to verify in what way the relationship works- related via Common Creator, common Intelligent Designer or common ancestor.Mark:
Having nothing for the betterment of mankind is UTTERLY IRRELEVANT to the validity of the conclusion.John Paul:
IMHO the conclusion is irrelevant if it can't be verified and brings absolutely nothing to the operational/ application table.quote:
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Originally posted by John Paul:"Hippopotamuses are the closest extant relatives of whales"
But related how, exactly? Common Creator, common Intelligent Designer, common descent (ie shared a common ancestor)?- please be specific in your rhetoric

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Can you take this paper to the lab to verify the the so-called 'tests' are valid?

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How does this phylogenic analysis of the alleged evolution of cetaceans aid us in the research for a cure for cancer or any disease for that matter?

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Mark:
Common Creator, ID, or abiogenesis is irrelevant to common descent. [b]John Paul:
Why is that? Because you say so?Mark:
What is the purpose of this question?John Paul:
Larry posted that hippos were related to whales. I wanted to know specically how he thought they were related.Mark:
Yes, the genomal positions of interspersed elements (transposons) can be repeatedly tested.John Paul:
Go buy a vowel. The conclusions can't be tested and verified.Mark:
Phylogenetic analysis doesn’t help find a cure for cancer? Well, there's a nobel prize winging it's way towards you now, mate.Since when was medical value a criteria to make research "valid" in other fields? [b]John Paul:
OK what good is this research? It's one thing (meaning it's OK) if this research is privately funded, but if my tax dollars are being spent on theoretical musings that is another story (meaning it sucks).Mark:
Does 6 day genesis help us cure cancer?John Paul:
Did you read the thread on biological origins and why it doesn't matter? The only reason a literal Genesis is being touted at all is because materialistic naturalism is trying to dominate world-view. Can't let that go unchecked...Mark:
Good grief.quote:
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Originally posted by John Paul:IOW, what good does 'theorizing' what organisms share an alleged closer common ancestor than do others?--------------------------------------------------------------------------------
Mark:
What good does theorising 6 day genesis do?John Paul:
Actually we don't theoize a 6 day Genesis. We read about it.Mark:
It attempts to draw up a universal phylogeny of all organisms. With which we can better understand the place of human & other organisms place on earth.John Paul:
But that hypothesis can't be verified- whichever it is- related via common ancestor, Common Creator or common ID. We can't take whatever conclusion we may reach with such research, to the lab and verify that conclusion is indicative of reality. Sure it may strengthen one's PoV- but so what?Mark:
Most people find that of interest. Even fundamentalist christians.John Paul:
I think it's interesting too, not being a fundamenatist or a Christian and all. I'm just glad that most people have enough sense not to fret about such tripe. Where would we be if everyone just worked on theoretical musings that have no practical value?

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That was one of the main reasons I choose engineering- APPLIED/ OPERATIONAL science.quote:
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Originally posted by John Paul:When I first learned of the switch in positions of the alleged lineage of alleged cetacean evolution, I sent emails to, vistited several aquariums and cetacean institutes. I asked how this recent discovery (that caused the switch) would affect their research (pertaining to cetaceans). The overall answer was clear- "Not one bit."
Go figure.--------------------------------------------------------------------------------
Mark:
Go figure what? Your entire post is dedicated to the assumption that there should be some overriding clear benefit for mankind, or the conclusion has no validity. [b]John Paul:
The fact that the conclusion can't be verified demonstrates its lack of validity.Mark:
What’s wrong with knowledge for knowledges sake?John Paul:
Is it 'knowledge' if it can't be verified?Mark:
How has the bible helped in the struggle against cancer, not one bit, by your argument, you may as well use it for toilet paper, for the medical use it’s been.John Paul:
Um, the Bible is a collection of historical and philoshical books.Mark:
This post was another sour graped evasion, you haven’t addressed any points Larry raised. I can only conclude you have no rebuttal with substance, or you would have made it by now.John Paul:
Truthfully I haven't seen anything of substance to rebut. You haven't told me how hippos and whales are related, how can you tell the difference between that conclusion and the Creationists' conclusion (Common Creator), from the same evidence.

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So let me get this straight- To evolutionists hippos and whales are related, ie they shared a common ancestor in the distant past. We don't know (and probably never will) what that ancestor was but we find 'comfort' in the 'knowledge' that a hippo and whale shared it.

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Great. Thank you. I will be able to rest better now. ------------------
John Paul

Has everyone read the article in question? It can be found here:Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: Hippopotamuses are the closest extant relatives of whalesDid you understand this?:Interpretation of the SINE/LINE Results. Copies of the same SINE shared in a unique locus of two different taxa are assumed to be derived from the same initial insertion event in the germ line of a common ancestor, thereby defining monophyletic groups (21).Taxa lacking SINE insertions for the same locus (SINE-minus bands) are assumed to retain the ancestral condition (21). (emph. in original)John Paul:
Studies like these require unverfifiable assumptions, like the one stated above. This, like alleged fossil transitions, are more of "I wouldn't have seen it if I didn't believe it."If you want to use this data to infer common descent, even though we don't have the DNA of that alleged common ancestor, go ahead. I am not buying it until those assumtions are replaced by verifiable data.John Paul------------------
John Paul

quote:Originally posted by John Paul:
Has everyone read the article in question? It can be found here:
Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: Hippopotamuses are the closest extant relatives of whales
Did you understand this?:
Interpretation of the SINE/LINE Results. Copies of the same SINE shared in a unique locus of two different taxa are assumed to be derived from the same initial insertion event in the germ line of a common ancestor, thereby defining monophyletic groups (21). Taxa lacking SINE insertions for the same locus (SINE-minus bands) are assumed to retain the ancestral condition (21). (emph. in original)
John Paul:
Studies like these require unverfifiable assumptions, like the one stated above. This, like alleged fossil transitions, are more of "I wouldn't have seen it if I didn't believe it."
If you want to use this data to infer common descent, even though we don't have the DNA of that alleged common ancestor, go ahead. I am not buying it until those assumtions are replaced by verifiable data.

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John Paul
Mark:
What's so unrealistic about assuming SINE/LINEs at homologous loci in extant taxa are a result of common descent?John Paul:
It assumes quite a bit. It assumes that such great transformations are possible and that these regions were not affected by mutations. It also assumes Crick’s theory on DNA is correct, which as you should know by now would be denying reality.Unraveling the DNA MythIt also assumes a Common Creator wouldn’t use similar DNA sequences in different organisms and that similar DNA sequences wouldn’t react in similar ways.Furthermore it is my understanding that different molecules lead to very different phylogenetic trees and sometimes bizarre trees result from some molecular analyses. (from Icons of Evolution) A 1996 study using 88 protein sequences grouped rabbits with primates instead of rodents; a 1998 analysis of 13 genes in 19 animals species placed sea urchins among the chordates; and another 1998 study based on 12 proteins put cows closer to whales than to horses. (but I take it the last one would be considered by some to be a prediction of evolution)Mark:
1/ SINEs are hereditary.
2/ They are transposable elements.
3/ If speciation occurred, those inherited TEs would be extant in both species. It is ENTIRELY reasonable to infer that these very SPECIFIC sequences are a result of common descent.
4/ If not, then what?John Paul:1)Transposons:
SINES (Short interspersed elements)
SINES are short DNA sequences that represent reverse-transcribed RNA molecules originally transcribed by RNA polymerase III; that is, molecules of tRNA, 5S rRNA, and some other small nuclear RNAs.
The most abundant SINES are the Alu elements. There are about one million copies in the human genome (representing about 11% of the total DNA).
Alu elements consist of a sequence of 300 base pairs containing a site that is recognized by the restriction enzyme AluI. They appear to be reverse transcripts of 7S RNA, part of the signal recognition particle.
SINES do not encode any functional molecules and (like LINES) their presence in the genome is a mystery. Like LINES, they seem to represent only "junk" or "selfish" DNA. Why would we expect SINEs to stick around for millions of years if they are indeed junk or selfish DNA?2) Transposable elements are not random in the same sense that copying errors (i.e. point mutations) are. Wouldn’t it be better to wait until we deciphered the genetic code so that we understand what it is doing before basing any inferences upon its actions?3) Why, if they provide no function and therefore no apparent benefit? Why would they be selected?4) Something we don’t yet understand that the Common Creator did (understand).Mark:
It seems to me this is a retreat to "if I can't see it with my own eyes, I won't believe it" land.John Paul:
It seems to me your approach is from I wouldn’t have seen it if I didn’t believe it land. For all we know DNA is only responsible for an organism’s traits and basic bio-chemical system repair but not the basic architecture of the organism itself.Mark:
Secondly, although we don't have the DNA of those ancestors, nucleotide sequences can be inferred. Of course, evolution dictates that any protein being coded for, must be functional at all stages of a molecular phylogeny.
"In a pioneering study by Jernmann & colleagues the sequences for 13 ancestral RNAses were inferred for artiodactyl mammals (this order includes the pig, camel, deer, sheep, & ox) using parsimony. These hypothetical ancient proteins were then synthesised in a laboratory & their properties compared to present day RNAses. All 13 RNAses had catalytic activity consistent with being functional enzymes."
(Molecular Evolution, A phylogenetic Approach. Roderick D.M. Page & Edward C. Holmes Blackwell Science 1998 pp 168-9)
If you imagine a common ancestor of artiodactyls 50 million years ago, & picture an evolutionary tree, branching many times, each line ultimately representing the extant artiodactyls we know today. This was the tree inferred. Each branch represents speciation, involving a common ancestor. For nine of these common ancestors, going back 50 million years, the 13 RNAses nucleotide sequences were inferred.
Evolutions prediction was born out in spectacular fashion, each of the 13 RNAses were functional enzymes in all nine ancestors. Such reasoned assumptions cannot be so easily cast off, when such predictions are born out, without exception.
An assumption can, & in the particular case of the SINEs/LINEs , & molecular phylogenies in general, is, very well supported. Hardly shooting in the dark.John Paul:
Might not be shooting in the dark but could be a case of painting the target around the arrow.What predictions? That if cetaceans did evolve from land animals and if mutating DNA sequences can bring about the great transformations required by the ToE, we would expect to see similar non-functional DNA sequences in cetaceans and some land animals? Even though we haven’t deciphered the genetic code and have little clue to what it says. Even though we know through cloning that more than DNA is required to give rise to an organism casting more doubt on DNA’s powers of transforming organisms. More like accommodations to me.Mark:
JP, I wonder,did you wait until the supernatural aspect of the Koran was verified, before you "bought" it?John Paul:
Actually my copy of the Noble Qur’an was given to me by a Saudi Naval officer.Mark:
No, you went for it anyway.John Paul:
Not really. There are many religious writings I am skeptical of. Some in the Qur’an, some in the Bible. Nothing’s perfect, not even a perfect stranger.Mark:
I find this selective logic, well, illogical. Surely, you would apply the same rigorous criteria to all things before believing them?John Paul:
Yes, I do.Mark:
Rather than a lesser criterial model to things you WANT to be true, compared to a strict, empirical criteria for something that you don't?John Paul:
I actually apply the same standards to each & every model.------------------
John Paul