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Author Topic:   Genetic Equidistance: A Puzzle in Biology?
derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 74 of 89 (599140)
01-05-2011 8:22 AM
Reply to: Message 11 by Livingstone Morford
12-17-2010 6:24 PM


Just a few thoughts on this.
It appears that Huang is one of those few scientific folks who simply cannot accept the notion that humans are closely related to chimps and so goes to great lengths to try to justify his prejudices.
One should check out his amazon.com review of Coyne's book - he comes across more as an anti-evolution zealot than a legitimate scientist. His frequent references to Lovtrup and the like indicate a rather skewed view of what constitutes valid science.
He is a classic ReMine-style huckster - from one of his comments on Amazon:
"If this result supports rather than contradicts NeoDarwinism, Coyne's book or any Darwinist's would be all over it. Instead, the Darwinists have managed to keep this result unknown to 100% of lay people and 99% of all biologists for 46 years. I have to re-discover it independently a few years ago."
He is talking about genetic equidistance. Something one can read about in any molecular biology textbook. And something one does not actually see when one looks at large datasets.
I liked this response to Huang as well:
"To those who are wondering, Nature describes the forum in which Huang deposited his work thusly: "Documents on Nature Precedings are not peer-reviewed and, as such, should not be considered 'published' works."
IOW, Huang, on these issues anyway, has about as much credibility as Rush Limbaugh has on family values.
Edited by derwood, : added link

This message is a reply to:
 Message 11 by Livingstone Morford, posted 12-17-2010 6:24 PM Livingstone Morford has not replied

  
derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 75 of 89 (599146)
01-05-2011 8:41 AM
Reply to: Message 1 by Livingstone Morford
12-16-2010 6:46 PM


quote:
Here I wish to discuss my thesis that the phenomenon of genetic equidistance presents a problem in biology: how do we know if this phenomenon is the result of the amount of time that has lapsed since any two or more organisms have diverged, or is it largely the result of the epigenetic complexity of organisms imposing restraints on the amount of mutations those organisms tolerate?
As it appears that Huang has read the Wiki entry on the molecular clock (as he uses the same ref and quote found there in one of his Amazon.com comments), I should like ot also quote the Wiki entry on Molecular Clocks in regards to equidistance:
For example, the difference between the cytochrome C of a carp and a frog, turtle, chicken, rabbit, and horse is a very constant 13% to 14%. Similarly, the difference between the cytochrome C of a bacterium and yeast, wheat, moth, tuna, pigeon, and horse ranges from 64% to 69%.
1% off here, 5% off there, but 'equidistance' nonetheless.
As has been, I believe, pointed out, the 'epi' part of epigenetics must work on the 'genetics' part. Methylation, etc. does not constrain the underlying sequence; quite the opposite.
Epigenetics is the new buzzword, especially among anti-evolutionist propagandists. But buzzwords co-opted by such folk often have a way of biting them in the arse, once their intellectually capable targets actually look into the issues themselves and discover that their handlers have been overstating their case, such as what happened re: junkDNA.
quote:
On a slight tangent, if this was the case, then functionally redundant protein sequences cannot always give us accurate conclusions with regards to phylogenetic relationships.
Which is probably why DNA sequence data is preferred in such analyses.

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derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 76 of 89 (599150)
01-05-2011 9:23 AM
Reply to: Message 17 by Dr Jack
12-18-2010 5:00 AM


quote:
The simple fact is that the genetic distance do not follow simple complexity connection lines.
Especially when "complexity" is defined idiosyncratically and arbitrarily.

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derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 77 of 89 (599151)
01-05-2011 9:26 AM
Reply to: Message 18 by Dr Jack
12-18-2010 5:02 AM


quote:
You'd use non-coding regions to compare human populations, for example, but they're useless for comparing humans and yeast.
You can use noncoding DNA in larger scale phylogenetic analyses as well, such all vertebrates. Humans to yeast is a stretch, to say the least, but humans and alligators could still be done.

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derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 78 of 89 (599152)
01-05-2011 9:28 AM
Reply to: Message 20 by Theodoric
12-18-2010 9:47 AM


Re: Just FYI for everyone
quote:
Hello, my name is Livingstone Morford (Morford being an alias and a variation of my real name, for anonymity).
I am a staunch Intelligent Design proponent, and an avid opponent of Darwinian evolution.
But he comes across so level-headed and open minded and objective....

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derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 79 of 89 (599153)
01-05-2011 9:31 AM
Reply to: Message 23 by molbiogirl
12-18-2010 12:47 PM


quote:
That is, why are humans and orangs "of different biological complexity"?
Why, because orangs do not know Jesus, of course.
After reading through Huang's screeds at Amazon.com, I would not be surprised if he, in fact, was to make such a claim.

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derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 80 of 89 (599154)
01-05-2011 9:32 AM
Reply to: Message 24 by molbiogirl
12-18-2010 2:57 PM


quote:
Chimpanzee is closer to orangutan or gorilla than human is in DNA.
Which is simply factually incorrect. Surely Mr.Morford knows this?
Edited by derwood, : typo

This message is a reply to:
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derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 81 of 89 (599156)
01-05-2011 9:37 AM
Reply to: Message 31 by molbiogirl
12-19-2010 1:01 PM


Re: Dr. Shi Huang
quote:
Shi believes:
1. There are virtually no neutral mutations (only SNPs).
2. Coding DNA is 99.9% of the genome.
3. By "epigenetics" he means "epigenetics".
4. Sequence homology cannot be used to infer genealogical relationships.
5. Micro is the opposite of macro evolution.
6. There is no macroevolution going on right now.
7. There is a "60% maximum because any more mutations will hit the key residues and will abolish gene function and thus affect organism viability" (aka MGD) for all organisms.
8. "The more function a gene performs, the more functional constraints on its mutation, and the less the MGD for this gene."
9. "Humans are the pinnacle of both the tree of life and complexity" and are not apes.
10. Any exception to a "rule" in evolutionary theory negates the theory. Period.
11. MGD has no exceptions. Period.
And as such, it is wise for one with common sense and bit of relevant knowledge to believe that Shi is a crackpot and a poseur.

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derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 82 of 89 (599157)
01-05-2011 9:42 AM
Reply to: Message 32 by molbiogirl
12-19-2010 5:34 PM


Re: The Crash Promise
quote:
I compared the cytochrome c sequence of two unicellular organisms: Naegleria gruberi and Dictyostelium discoideum.
Next, I aligned the cytochrome c sequence of two organisms as distant as the tuna and humans.
I wonder if Mr.Morford realizes that Naegleria and Dictyostelium are from different PHYLA, whereas humans and tuna are not?

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derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 83 of 89 (599158)
01-05-2011 9:44 AM
Reply to: Message 42 by Livingstone Morford
12-19-2010 7:09 PM


The accumulation of mutations in tissue-specific genes would have no affect on tissues in which the genes are not used.

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derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 84 of 89 (599159)
01-05-2011 9:50 AM
Reply to: Message 52 by molbiogirl
12-20-2010 12:32 PM


quote:
Dr. Huang is quite adamant that there are virtually no neutral mutations. .1% in fact.
Then I submit that Huang has never bothered to do sequence comparions. Even comparing members of the same species one can find numerous real differences. Steven Pinker and Craig Venter's genomes, for example, differed by many millions of bps, in addition to a nearly 1 million bp indel. Is the correct conclusion really that only a few thousand of those were neutral? Absurd. What is Huang's actual area of expertise? Does anyone know?

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derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 85 of 89 (599162)
01-05-2011 9:58 AM


I see that Huang has also had a paper published in Rivista di Biologica, that crack outfit run by a creationist in which one can find pubs by Johnny Wells and John Davison. Of note is how Huang responds to criticisms.
Classic crackpottery. Shame so many have latched onto his nonsense.
Molbiogirl also mentioned this conversation.
Reading Huang's comments, it comes across as classic 'angry arrogant IDcreationist' boilerplate stuff - none of his coworkers thnk much of evolution, evolutionists hatemath, blah blah blah.
Pathetic.
Edited by derwood, : No reason given.
Edited by derwood, : addenda

Replies to this message:
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