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Author Topic:   Genetic Equidistance: A Puzzle in Biology?
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 28 of 89 (597062)
12-19-2010 10:35 AM
Reply to: Message 14 by crashfrog
12-17-2010 7:10 PM


This makes no sense. Every single amino acid can be found in every single human cell, so there's no such thing as a substitution that would be "incompatible" with the cell.
He jus means a deleterious point mutation.
No, this makes no sense. Protein A may not be expressed in X, Y, or Z, or it may be subject to alternate splicing such that the mutation in the gene for A is in a region that is not expressed in one of those cells. And really, there's no such thing as "cell type", there's just different patterns of gene expression and regulation in different cells. The fact that two different cells may have different patterns of gene expression really doesn't say anything at all about which mutations will prove fatal in which cells.
But it is a priori less likely that a mutated protein will be neutral with respect to its function in the brain and the liver and the pancreas and the bone marrow and ... so on ... then with respect to its function in a single cellular environment.
This still leaves certain questions:
(1) What is the magnitude of this effect?
(2) What is the magnitude of this effect in the proteins used in molecular phylogeny?
(3) What in the world can this have to do with IDiocy?

This message is a reply to:
 Message 14 by crashfrog, posted 12-17-2010 7:10 PM crashfrog has replied

Replies to this message:
 Message 30 by crashfrog, posted 12-19-2010 12:32 PM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 35 of 89 (597105)
12-19-2010 6:13 PM
Reply to: Message 30 by crashfrog
12-19-2010 12:32 PM


I don't think a priori you can make such a statement, since there's too many confounding factors. Most proteins in the cell have no idea whether they're in a liver cell, or a brain cell, or a pancreatic cell.
Well, all of them have "no idea", poor little things. But all that is necessary is that some mutation which is neutral with respect to one cellular environment should be harmful in another (in which it is also expressed, otherwise examples, while commonplace, would also be irrelevant).
For example, No webpage found at provided URL: here's an account of the research of one Kevin Talbot:
The commonest and most debilitating of these diseases is amyotrophic lateral sclerosis, which is relentlessly progressive and fatal on average 3 years after onset. The key question for our research is why mutations in genes which are expressed in every cell in the body result in specific and selective degeneration of motor neurons. Using primary neuronal cell culture systems his group has explored the effect of mutant small heat shock protein on axonal function. Mutations in the gene for glycyl tRNA synthetase lead to another form of lower motor neuron degeneration. He is using a combination of structural, biochemical and cellular studies to understand why mutations in a ‘house-keeping’ gene expressed in all cells lead to specific neuronal degeneration.
It would seem, then, that the mutations he's studying would be neutral in an organism too primitive to have motor neurons.
Obviously cell environment has an effect on which mutations prove to be deleterious, because some of that effect is the result of changes in a protein's interactions with other components of the cell environment. But to predict the effect of diversity of cell environment on a mutated protein (and vice-versa) you need a finer-grained study than "liver cell; muscle cell."
Yes ... but we don't need to be able to predict the effects of a mutation to support the thesis that number of cell types correlates inversely with neutrality of mutations.
Well, it's a standard practice in constructing phylogenies to use proteins with identical function across the compared clades. That would seem to rule out any effect of diversity of cell environment.
The site quoted above specifically mentions glycyl-tRNA synthetase. This, as the name suggests, attaches glycine to transfer RNA with glycine antocodons. Hence glycyl-tRNA synthetase performs a very basic (and ancient) function --- which is the same function performed by glycyl-tRNA synthetase in prokaryotes. And yet there are mutations to it which apparently in humans only produce problems with motor neuron cells.
---
The questions remain: what is the magnitude of this proposed effect? And how on Earth are IDiots weaving this hypothesis into their tissue of nonsense? I don't see how this would help them any.

This message is a reply to:
 Message 30 by crashfrog, posted 12-19-2010 12:32 PM crashfrog has not replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 36 of 89 (597108)
12-19-2010 6:22 PM
Reply to: Message 34 by molbiogirl
12-19-2010 5:36 PM


Re: Livingstone Morford's blog
For those who might be interested:
BioTalk
I notice that his subtitle is "The biological ramblings of a dwarf struggling to stand on the shoulders of giants."
"Stand on the shoulders"? Shouldn't that be "kick at the ankles"?

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 Message 34 by molbiogirl, posted 12-19-2010 5:36 PM molbiogirl has not replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 41 of 89 (597118)
12-19-2010 6:59 PM
Reply to: Message 37 by Livingstone Morford
12-19-2010 6:27 PM


I still don't see what this has to do with cdesign proponentism. Perhaps you could explain. So far as I can see, you are proposing that an eminently Darwinian mechanism would plausibly account for certain observations. There is nothing in such a suggestion to keep a biologist awake at night or give consolation to a crank.
Am I missing something?

This message is a reply to:
 Message 37 by Livingstone Morford, posted 12-19-2010 6:27 PM Livingstone Morford has replied

Replies to this message:
 Message 43 by Livingstone Morford, posted 12-19-2010 7:12 PM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 45 of 89 (597129)
12-19-2010 8:09 PM
Reply to: Message 43 by Livingstone Morford
12-19-2010 7:12 PM


So I guess because I happen to disagree with the orthodox view that the phenomenon of genetic equidistance is best explained by the time lapsed since divergence, and since I am proposing another model ...
It's not clear that that's what you are doing. Thus far, clarity has not been your strongest suit.
... that all of a sudden means that I am using this as evidence for intelligent design?
No, but your blog where you say that you're an "staunch proponent of intelligent design" and the fact that you seem to have drawn your idea from an IDiot suggest that there may be some relationship between ID and whatever idea it is that you're currently advocating.
If you will clearly and distinctly say that none of this is evidence for ID then I shall not ask you any further questions about their possible connection.

This message is a reply to:
 Message 43 by Livingstone Morford, posted 12-19-2010 7:12 PM Livingstone Morford has not replied

Replies to this message:
 Message 53 by New Cat's Eye, posted 12-20-2010 12:34 PM Dr Adequate has not replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


(1)
Message 51 of 89 (597214)
12-20-2010 12:25 PM
Reply to: Message 49 by molbiogirl
12-20-2010 12:12 PM


Please provide cites that support your contention that all mutations are deleterious in all tissues in all cases.
Is that in fact his contention? If so, I missed it.

This message is a reply to:
 Message 49 by molbiogirl, posted 12-20-2010 12:12 PM molbiogirl has replied

Replies to this message:
 Message 52 by molbiogirl, posted 12-20-2010 12:32 PM Dr Adequate has not replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 87 of 89 (599179)
01-05-2011 10:54 AM
Reply to: Message 86 by Admin
01-05-2011 10:37 AM


Please read through the thread first and then post a single message.
Hold on. He's replying to different messages. And whenever someone replies to several different messages in a single post we all (including the moderators) tell him not to do that.

This message is a reply to:
 Message 86 by Admin, posted 01-05-2011 10:37 AM Admin has seen this message but not replied

  
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