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Author Topic:   Genetic evidence of Whale evolution
wj
Inactive Member


Message 20 of 27 (4293)
02-12-2002 7:02 PM
Reply to: Message 19 by wj
02-07-2002 1:32 AM


Is this how you bring the topic back to the front page whilst waiting for JP's response? I wouldn't want to miss it and I'm not sure if I could find the thread again.

Will JP's response also address the apparent sequence of trial and error efforts by the intelligent designer to modify the design to create a fully functioning whale?


This message is a reply to:
 Message 19 by wj, posted 02-07-2002 1:32 AM wj has responded

Replies to this message:
 Message 21 by wj, posted 02-21-2002 9:42 PM wj has not yet responded

  
wj
Inactive Member


Message 21 of 27 (5264)
02-21-2002 9:42 PM
Reply to: Message 20 by wj
02-12-2002 7:02 PM


It appears that JP has returned to this site. I will take the opportunity of reminding him of a number of unanswered questions in this threrad.
This message is a reply to:
 Message 20 by wj, posted 02-12-2002 7:02 PM wj has not yet responded

Replies to this message:
 Message 22 by John Paul, posted 02-22-2002 8:30 AM wj has not yet responded

  
John Paul
Inactive Member


Message 22 of 27 (5288)
02-22-2002 8:30 AM
Reply to: Message 21 by wj
02-21-2002 9:42 PM


Has everyone read the article in question? It can be found here:

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=17876">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.

John Paul

------------------
John Paul


This message is a reply to:
 Message 21 by wj, posted 02-21-2002 9:42 PM wj has not yet responded

Replies to this message:
 Message 23 by mark24, posted 02-22-2002 6:20 PM John Paul has responded
 Message 24 by mark24, posted 02-25-2002 5:23 AM John Paul has not yet responded

  
mark24
Member (Idle past 3275 days)
Posts: 3857
From: UK
Joined: 12-01-2001


Message 23 of 27 (5312)
02-22-2002 6:20 PM
Reply to: Message 22 by John Paul
02-22-2002 8:30 AM


quote:
Originally posted by John Paul:
Has everyone read the article in question? It can be found here:

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=17876">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.

John Paul


What's so unrealistic about assuming SINE/LINEs at homologous loci in extant taxa are a result of common descent?

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?

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.

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.

JP, I wonder,did you wait until the supernatural aspect of the Koran was verified, before you "bought" it? No, you went for it anyway. I find this selective logic, well, illogical. Surely, you would apply the same rigorous criteria to all things before believing them? 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?

Mark

------------------
Occam's razor is not for shaving with.

[This message has been edited by mark24, 02-22-2002]

[This message has been edited by mark24, 02-22-2002]


This message is a reply to:
 Message 22 by John Paul, posted 02-22-2002 8:30 AM John Paul has responded

Replies to this message:
 Message 26 by John Paul, posted 03-10-2002 4:01 PM mark24 has responded

    
mark24
Member (Idle past 3275 days)
Posts: 3857
From: UK
Joined: 12-01-2001


Message 24 of 27 (5444)
02-25-2002 5:23 AM
Reply to: Message 22 by John Paul
02-22-2002 8:30 AM


Bumping to the top, just in case JP makes a reappearance.

Mark

------------------
Occam's razor is not for shaving with.


This message is a reply to:
 Message 22 by John Paul, posted 02-22-2002 8:30 AM John Paul has not yet responded

Replies to this message:
 Message 25 by mark24, posted 03-09-2002 9:20 AM mark24 has not yet responded

    
mark24
Member (Idle past 3275 days)
Posts: 3857
From: UK
Joined: 12-01-2001


Message 25 of 27 (6389)
03-09-2002 9:20 AM
Reply to: Message 24 by mark24
02-25-2002 5:23 AM


And again......

------------------
Occam's razor is not for shaving with.


This message is a reply to:
 Message 24 by mark24, posted 02-25-2002 5:23 AM mark24 has not yet responded

    
John Paul
Inactive Member


Message 26 of 27 (6481)
03-10-2002 4:01 PM
Reply to: Message 23 by mark24
02-22-2002 6:20 PM


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.

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 Myth

It 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


This message is a reply to:
 Message 23 by mark24, posted 02-22-2002 6:20 PM mark24 has responded

Replies to this message:
 Message 27 by mark24, posted 03-13-2002 4:25 PM John Paul has not yet responded

  
mark24
Member (Idle past 3275 days)
Posts: 3857
From: UK
Joined: 12-01-2001


Message 27 of 27 (6755)
03-13-2002 4:25 PM
Reply to: Message 26 by John Paul
03-10-2002 4:01 PM


quote:
Originally posted by 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 Myth

It 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)


Firstly, ancient SINE locations ARE affected by mutations. 3-4 fixed mutations per nucleotide site per 10^9 years are expected (Molecular Evolution: A Phylogenetic Approach. RDM Page & EC Holmes. p159). Given the average SINE is 300 bp long this means 3-4 mutations are fixed per 33 1/3 million years, well within the range of the paper in question. It’s a shame it’s not higher, as these fixed mutations are informative in phylogenetic relationships in their own right. So SINEs are a valid source of data going back 50 my + .

The creator DIDN’T use similar DNA sequences in different organisms. I think you mean similar sequences in similar organisms, pedantic, but important to make the distinction. Also, your talking genes here, not SINES. There is absolutely no reason a creator would need to make homologous gene sequences between humans & chimps, but not humans & crocodiles, where genes are necessary for both taxa. It is entirely feasible to create a chimp with zero homologous gene sequences if there was a creator. The relationship between those sequences only makes sense with common descent with modification. The gene sequences between taxa correlate less the further they are apart, this need not be true if a recent ID was involved.

Regarding accuracy of derived phylogenies. There are several reasons a phylogeny may not produce the correct tree. If the sequences aren’t homologous, sampling error, incomplete data, mismatching method & genetic information, long branch attract, method limiltations etc. “Molecular Evolution” (referenced above) is full of examples of incorrect phylogenies, & goes on to explain why those phylogenies are incorrect. In fact, if your interested in molecular phylogeny, this book is excellent in that it spends half the time explaining what CAN go wrong. In the vast majority of cases, however, highly concordant trees are derived. This is unexpected if an ID is involved recently. There is no reason a phylogeny derived from gene sequences, pseudogenes, retroviral insertions, nucleotide sequences, amino acid sequences, SINEs, LINEs, etc. should produce phylogenies that match at all, let alone to the high degree that they do. Taking cytochrome c as an example, it is an enzyme used in Krebbs Cycle, & as such is used by ALL life, so why is there such a disparity in nucleotide & amino acid sequences for the molecule? They ALL do exactly the same job. If your argument is that similar organisms have similar gene sequences, then why don’t similar protein function have similar sequences? In some cases the conserved sites number only 10% of the sequence without functionality loss.

quote:
Originally posted by John Paul:

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).


1/ What would remove SINEs from the genome with such regularity that these losses would be fixed? I’m sure it happens, but removing a SINE in an individual is different to then having it removed from a POPULATION. See above for the FIXATION rates of sine mutations.

2/ Random? Yes & no. They aren’t random in the true quantum mechanical sense, but they are random in the sense that they can appear anywhere in the genome, even smack bang in the middle of coding genes, depending on sequences at the insertion site.

3/ Some SINEs have assumed functions as transcription promoters, source of polyadenylation signals, & a source of regulatory elements, but most are functionless self replicators on the genome. The majority, ie the functionless ones aren’t selected for or against, they are neutral. There are even deleterious ones, eg Neurofibromatosis is caused by an Alu element in the NF1 gene

4/ i.e. Godidit

quote:
Originally posted by John Paul:

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.


The basic architecture of the organism is due to DNA.

quote:
Originally posted by John Paul:

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.


The prediction of evolution that was borne out is that at every stage of the enzymes evolution, it must function. It can’t go away for 1,000 generations while it works out how to perform xyz.

Yes we would expect to see non-functional homologous DNA similarities in common ancestors, as I have shown, the rate of point mutation fixation of SINEs is low enough to identify those homologous SINEs in mammals. The AF locus SINE (in the paper) is in an intron, indicating it is functionless. Even if SINEs are functional we would expect to see those same homologous sequences. The functionality that SINEs have aquired can be carried out by other non-SINE sequences, as indeed they are in other taxa, & even other mammals, providing the SINE was transposed AFTER speciation.

“All” that is needed for DNA to replicate efficiently are the enzymes, mRNA, tRNA, ribosomes, supporting structures, etc. ALL are the product of DNA. A sexual organism will receive a payload of these molecules & structures from its parents in the fertilised egg. These structures & molecules are a product of DNA. An asexual organism will get the same as the cell divides, all a product of DNA.

So, knowing that these support structures & molecules are necessary (once again, the product of DNA) casts no doubt whatsoever on DNAs “transforming” abilities.

Mark

------------------
Occam's razor is not for shaving with.


This message is a reply to:
 Message 26 by John Paul, posted 03-10-2002 4:01 PM John Paul has not yet responded

    
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