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Author Topic:   Genetic Equidistance: A Puzzle in Biology?
molbiogirl
Member (Idle past 954 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 6 of 89 (596859)
12-17-2010 11:54 AM


LM writes:

Since flowers are less epigenetically complex than mammals, if my assertion is correct, there would be more genetic diversity among flowering plants than among mammals.

Can I assume that by "genetic diversity" you are referring to the coding regions of DNA?

If so, then you run into the problem that Taq raised in the last thread.

To wit:

Taq writes:

However, coding DNA makes up a tiny portion of the whole genome, somewhere around 3%. In this model, the other 97% of the genome is diverging through drift so the predominant force of genetic change is still drift.

And:

Selection is hard to put into the calculations so population geneticists try to use selectively neutral DNA seqeunces that can be readily identified (especially for genomic position to rule out duplication events). One good source for these sequences is pseudogenes, which is exactly what this group used:

http://www.ncbi.nlm.nih.gov/pubmed/8364591


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molbiogirl
Member (Idle past 954 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 8 of 89 (596876)
12-17-2010 2:03 PM


Just FYI for everyone
This is where LM seems to be getting his ideas:

http://thegoldengnomon.blogspot.com/

In particular, this page (see comments):

http://thegoldengnomon.blogspot.com/...r-first-axiom-of.html

And this paper:

http://precedings.nature.com/documents/1751/version/2


Replies to this message:
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molbiogirl
Member (Idle past 954 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 21 of 89 (596944)
12-18-2010 11:40 AM
Reply to: Message 14 by crashfrog
12-17-2010 7:10 PM


I'm not sure you know any biochemistry.

Crash, he claims to be a biochemist.

LM writes:

Being the author of two technical papers in biochemistry (manuscript under review), I can understand most technical terminology

http://thegoldengnomon.blogspot.com/...r-first-axiom-of.html


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molbiogirl
Member (Idle past 954 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 23 of 89 (596950)
12-18-2010 12:47 PM
Reply to: Message 12 by Livingstone Morford
12-17-2010 6:25 PM


If complexity has some relationship to diversity, then how do you explain the significant differences within taxa?

For example:

... among fish, marine species showed a significantly higher heterozygosity than the geographically restricted freshwater species ...

And:

... among mollusks, the terrestrial pulmonates were substantially less polymorphic than marine bivalves or gastropods ...

http://www.sciencemag.org/content/312/5773/570.full

And how would you explain these findings?

Genetic diversity is largely higher (i) in species living in broader environmental spectra, (ii) in large species with patchy population structure and limited migration, as well as in solitary or social species, and (iii) species with small body size, annuals or long-lived perennials that are older in time with diploid chromosome numbers, primarily out-crossed, and plant species reproducing sexually and pollinated by wind. Species with the above characteristics harbor, generally, more genetic diversity than their opposite counterparts.

Genetic diversity is correlated and predictable by 3-4 variable combinations of ecological, demographic, and life-history variables, largely in this order.

Nevo E. (2001). Evolution of genome-phenome diversity under environmental stress. Proc. Natl. Acad. Sci. USA 98:6233-6240.

Nevo E, Beiles A, and Ben-Shlomo R. (1984a). The evolutionary significance of genetic diversity: Ecological demographic and life history correlates. Lect Notes Biomath 53, 13-213.

ABE: Another question. Can you explain this quote from Shi?

However, for macroevolution of distinct species of different biological complexity such as yeast versus drosophila or orangutan versus human...

http://thegoldengnomon.blogspot.com/...r-first-axiom-of.html

That is, why are humans and orangs "of different biological complexity"?

Edited by molbiogirl, : No reason given.


This message is a reply to:
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molbiogirl
Member (Idle past 954 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 24 of 89 (596956)
12-18-2010 2:57 PM
Reply to: Message 15 by crashfrog
12-17-2010 7:43 PM


No, it's not. If Shi Huang says this, Shi is wrong.

Really wrong, Crash.

Shi writes:

Dr. Shi Huang has now come up with a more complete theory unifying epigenetics and genetics. His new theory, the maximum genetic diversity hypothesis ... explains more facts than Darwinism and has yet to meet a single exception within its domain of application.

From a book review he posted on Amazon. Gotta love the third person.
http://www.amazon.com/review/R160K7033BB22Y

And:

Shi writes:

Thus, macroevolution is the opposite of microevolution. While randomness is good and a source of innovation/variation for microevolution, it is mostly harmful for macroevolution of greater complexity and must be suppressed.

Shi writes:

Most of today's species are terminally highly derived or differentiated. So, macroevolution would be extremely rare in today's Earth.

Shi writes:

Chimpanzee is closer to orangutan or gorilla than human is in DNA.

http://thegoldengnomon.blogspot.com/...r-first-axiom-of.html

Edited by molbiogirl, : No reason given.


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molbiogirl
Member (Idle past 954 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 25 of 89 (596962)
12-18-2010 3:54 PM


LM. Can you explain this to me?

Shi writes:

The genetic non-equidistance to a more complex outgroup despite equidistance in time or genealogy, as described here, shows that higher sequence similarity to a complex outgroup cannot be used to infer closer genealogical relationships.

http://precedings.nature.com/documents/3794/version/1

Why can't sequence similarity be used to infer closer genealogical relationships?


  
molbiogirl
Member (Idle past 954 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 31 of 89 (597080)
12-19-2010 1:01 PM


Dr. Shi Huang
I've been reading his blog and some of his papers.
Just want to get some facts on the table.

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 here's what Dr. Katz had to say when she reviewed one of his papers for Journal of Experimental Zoology Part B: Molecular and Developmental Evolution:

Dr. Katz writes:

Dear Dr. Huang,

I have now had a chance to read your manuscript and I regret that I am not recommending publication in JEZ-B. While the ideas presented are very intriguing, several key elements lack rigorous definitions and, as written, are inconsistent with observations from across the tree of life. For example, the view of phylogenetic diversity is more consistent with the Scala Natura than current understanding of the tree of life and the nature of biological diversity on Earth. Similarly, the treatment of the term complexity is simplistic at times. For example, limb number is certainly one measure of complexity (e.g. snakes vs. other reptiles) but, if "complex organisms are here defined as those that have complex epigenetic programs" then organisms like ciliates, which rely on epigenetic mechanisms to scan the last generation's somatic genome in forming the next generation's somatic genome, may also be worth considering. As written, the manuscript reads as if humans are the pinnacle of both the tree of life and complexity. Further, the treatment of genetic distance is also simplistic at times, particularly given what we know about patterns and processes driving molecular evolution across genomes.

I do hope that this quick turn around enables you to find a more appropriate journal for your interested manuscript without any unnecessary delay.

Sincerely

Laura Katz

His reply is telling. Some excerpts:

Shi writes:

You did not object to my outrageous statement in the paper that the MGD explains all relevant facts and has yet to meet a factual contradiction. You also did not object to my outrageous claim that the MGD is a better theory than all existing ones based on the best and only criterion that counts, which is to explain all facts and is contradicted by none. ... Therefore, the only realistic way of publishing the MGD is a book. If Darwin changed history by publishing a book, it may well take another book to reset history.

Edited by molbiogirl, : No reason given.

Edited by molbiogirl, : No reason given.


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molbiogirl
Member (Idle past 954 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 32 of 89 (597101)
12-19-2010 5:34 PM
Reply to: Message 29 by crashfrog
12-19-2010 12:28 PM


Re: The Crash Promise
Here are some of LM's thoughts on cytochrome c (from his blog, talkbio.blogspot.com, October 19 post):

Now, the idea that a neutral mutation in yeast is not necessarily neutral in say, humans, is consistent with observations from cytochrome c sequences.
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.

From the dot-matrix alignment and the ClustalX alignment one can see that there is obviously more sequence conservation in human and tuna cytochrome c than in the cytochrome c of the two unicellular organisms. This is what would be expected if a substitution in a unicellular organism was not necessarily neutral for a multicellular organism.

Have a look at the rest here, Crash:

http://talkbio.blogspot.com/search?updated-max=2010-11-04...


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molbiogirl
Member (Idle past 954 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 33 of 89 (597102)
12-19-2010 5:35 PM
Reply to: Message 26 by Livingstone Morford
12-19-2010 12:44 AM


Re: A General Response To Comments Regarding My Character
Is this one of the papers?

I submitted a manuscript to the Journal of the Royal Society Interface. My paper was a critique of a paper by Dryden et al. 2008, "How much of protein sequence space has been explored by life on Earth?"

https://docs.google.com/fileview?id=0B0x8Ne67j7k4NTZiNWY1...


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molbiogirl
Member (Idle past 954 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 34 of 89 (597103)
12-19-2010 5:36 PM


Livingstone Morford's blog
For those who might be interested:

http://talkbio.blogspot.com/


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molbiogirl
Member (Idle past 954 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 48 of 89 (597209)
12-20-2010 11:51 AM
Reply to: Message 37 by Livingstone Morford
12-19-2010 6:27 PM


Re: The Crash Promise
I will respond to those posts which I think are the most pertinent and most important to this topic.

1. Do you agree with Dr. Huang that there are .1% neutral mutations in the genome? If so, how do you explain your response in Message 12?

2. Do you agree with Dr. Huang that humans and orangs are "of different biological complexity"? If so, why?

3. Do you agree with Dr. Huang that sequence homology cannot be used to infer genealogical relationships? If so, why?

4. Do you agree with Dr. Huang that any exception to a biological "rule" negates that rule?

Edited by molbiogirl, : No reason given.


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molbiogirl
Member (Idle past 954 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 49 of 89 (597211)
12-20-2010 12:12 PM
Reply to: Message 42 by Livingstone Morford
12-19-2010 7:09 PM


There is a difference between a direct effect and a mere effect, however discernible.

What effect? And please support your assertion with cites.

Okay, so finally we agree on one thing: and that is that a neutral substitution in a protein in one cell type is not necessarily neutral in another.

It's a far cry from "There is some constraint" to "All mutations are deleterious in all cases".

Please provide cites that support your contention that all mutations are deleterious in all tissues in all cases.


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Replies to this message:
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molbiogirl
Member (Idle past 954 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 50 of 89 (597213)
12-20-2010 12:24 PM
Reply to: Message 37 by Livingstone Morford
12-19-2010 6:27 PM


Slow genes and the molecular clock
The idea that different proteins evolve at different rate is not new.

Other proteins also showed a constant rate of molecular evolution across species, but with each protein having a different characteristic rate: histones were exceptionally slow, cytochrome c was faster (but slower than hemoglobins) and fibrinopeptides were faster still.

http://www.nature.com/nrg/journal/v4/n3/abs/nrg1020.html

Please explain to me how slow genes are a problem for the molecular clock.

Please provide cites.

And no, a cite that suggests the mere existence of slow genes is not enough.


This message is a reply to:
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molbiogirl
Member (Idle past 954 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 52 of 89 (597216)
12-20-2010 12:32 PM
Reply to: Message 51 by Dr Adequate
12-20-2010 12:25 PM


Is that in fact his contention? If so, I missed it.

What I meant to say is "Please provide cites that support your contention that all deleterious mutations are deleterious in all tissues in all cases."

My bad.

And, as he is parroting Dr. Huang's assertions, I can only assume he agrees with Dr. Huang that SNPs are the only neutral mutations.

Dr. Huang is quite adamant that there are virtually no neutral mutations. .1% in fact.

Which means that 99.9% of all mutations are either beneficial or deleterious. I'd like him to provide support for that assertion too.


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molbiogirl
Member (Idle past 954 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 54 of 89 (597246)
12-20-2010 2:53 PM


Dr. Shi Huang again
The paper LM is relying on, Huang, S. (2009) Inverse relationship between genetic diversity and epigenetic complexity, has not been peer reviewed.

http://precedings.nature.com/documents/1751/version/2

They are not subjected to editorial or peer review for quality or significance ... Documents on Nature Precedings are not peer-reviewed and, as such, should not be considered 'published' works.

http://precedings.nature.com/about

ABE: Whoa. Just found this in the conclusion of the "paper".

Shi writes:

The inverse relationship between genetic diversity and epigenetic complexity is the first axiom in biology. It does not need independent validation of empirical facts, just like the intuition that a complex system is more selective in building materials than a simple system.

Does not need independent validation!!!

I knew it. The guy has no data. No support.

And Shi got banned on another site because he refused to support his assertions:

I have teminated gnomon's [Shi's] membership. I afforded him ample opportunity to participate in the discussion, but his refusal to deal with the comments made by Easy, Dorids and me finally got to be too much. He constantly mis-directed us away from those criticisms, and blantantly stated that he didn't need to provide either evidence or definitions of his terms.

http://fundiesvatheists.lefora.com/...ic-diversity-and/page4

Emphasis added.

Edited by molbiogirl, : No reason given.

Edited by molbiogirl, : No reason given.


  
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