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Author Topic:   Redundancy and tolerance in the processes of life
Annafan
Member (Idle past 4579 days)
Posts: 418
From: Belgium
Joined: 08-08-2005


Message 1 of 8 (465486)
05-07-2008 11:20 AM


Content hidden, please see Message 3 for the opening post. --Admin
Edited by Annafan, : Didn't change anything, but already found out that "heterozygous" is not quite what I thought it was
Edited by Admin, : Add forward reference.

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 Message 2 by Admin, posted 05-08-2008 8:53 AM Annafan has replied

  
Admin
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From: EvC Forum
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Message 2 of 8 (465578)
05-08-2008 8:53 AM
Reply to: Message 1 by Annafan
05-07-2008 11:20 AM


Could you add a concluding paragraph that briefly summarizes the conclusions your points lead to, and that makes more clear what it is you'd like to discuss? Please post a note when you're done and I'll take a look.

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 Message 1 by Annafan, posted 05-07-2008 11:20 AM Annafan has replied

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 Message 3 by Annafan, posted 05-08-2008 9:25 AM Admin has not replied

  
Annafan
Member (Idle past 4579 days)
Posts: 418
From: Belgium
Joined: 08-08-2005


Message 3 of 8 (465584)
05-08-2008 9:25 AM
Reply to: Message 2 by Admin
05-08-2008 8:53 AM


edited
Ok, so this is more a matter of a layman wanting to ask a couple specific questions to biochemistry experts than anything else, but it might also be an interesting topic:
One of the big hurdles that creationists and other evolution-doubters have to take, is realizing that "life" is far removed from the Perfect Fragile Machine that they imagine. There are many examples of how the processes of life and evolution contain a lot of redundancy and tolerance for errors in general. Realizing this makes the concept of the combination of random mutation and natural selection as creative force easier to understand.
Here's a list that I came up with from the top of my head for a post on a Muslim forum in a topic meant to give a high-level overview:
- superfluous junk DNA catches most mutations so they don't have detrimental effects (not really completely on-topic in this list)
- cells have a number of verification and repair mechanisms which catch lots of errors
- there are more possible codons (64) than aminoacids(20), which means that there are multiple versions of codons that still result in the same aminoacids. A mutation which turns one version of such codon in another such one, has no implications (silent mutation)
- gene duplication errors create redundant copies of genes. Those copies can take over if the original one is no longer functional due to a bad mutation (q:is it a given that multiple copies will ALWAYS only have positive effect?), and they are also a laboratory to create novel genes
- sexually reproducing organisms can make use of the "heterozygote advantage" because they have all chromosomes/genes duplicate (except X/Y of course). One copy can be dysfunctional without fatal consequences (q:is it categorically NO effect if one is dysfunctional, or is there a whole spectrum from "NO consequence" to "not deadly but still seriously affected"?)
- an example like vitamin C illustrates that often it is possible to take in certain essential substances (like, via food) instead of letting the DNA synthesize them internally. This is why humans and apes (and bats) have a defective gene for vitamin C synthesis without being affected by it. (q:is this a fairly unique (known) example, or is this abundant?)
- a mutation in a gene doesn't have to mean that something simply doesn't work anymore altogether; it could also mean that a biochemical reaction further down the chain will merely execute less efficiently, while possibly they produced an excess of some essential substance already so it would have NO effect at all?
- many genes or groups of genes code for traits that aren't essential anyway (eye color, anyone?), so mutations in them do not have important detrimental effects
And then one that I was using in a translation of the "Cytochrome C" example in Douglas Theobald's "29", and I'd like to know how precise this formulation is:
- biochemistry with complex biochemical molecules like proteins is far more insensitive to changes in the components than the simple inorganic reactions we learn about in highschool. That is, the reactions depend mostly on the shape of the proteins after curling up, and on the amino acids on the "outside". And very often both of these will not be affected much by replacing amino acids "on the other side of the chain" by different, mutated ones. For example, they could be locked up inside once the protein has curled up. (q: Is this a fairly accurate general statement? I've read elsewhere that a small change in amino acid sequence CAN severely destroy the structure of the curled-up protein, but would this be in a minority of cases, or is it that despite this would be the case in the vast majority of cases, there's still an astronomical amount of possibilities to have a mutation NOT influence the structure?)
Taking all this into account, it becomes easier to grasp that a random mutation really does not necessarily stop life in its tracks. That there is room between the extremes "functional" and "non-functional". That different roads lead to Rome on several levels... Life is robust precisely because it is not carefully engineered to work perfectly and optimally. Better to be "good enough" and have backup-strategies to remain "good enough" most of the time, than to work towards something that is perfect, but only under precise circumstances.
It might be interesting to work out the examples I mentioned, or correct the mistakes/oversimplifications(likely ), and to introduce more examples to this list of processes, structures etc. that illustrate the redundancy and tolerance.

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Admin
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Message 4 of 8 (465585)
05-08-2008 9:44 AM


Thread moved here from the Proposed New Topics forum.

  
Annafan
Member (Idle past 4579 days)
Posts: 418
From: Belgium
Joined: 08-08-2005


Message 5 of 8 (465896)
05-11-2008 12:05 PM


Nobody?
Not much interest, it seems.
Could at least any of the biochemists (Wounded King?) address some of the questions, then? I'd like to be sure that I don't blunder when I make my case on the other forum.

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 Message 6 by Wounded King, posted 05-11-2008 7:05 PM Annafan has replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 6 of 8 (465923)
05-11-2008 7:05 PM
Reply to: Message 5 by Annafan
05-11-2008 12:05 PM


Some answers
Hi Annafan,
I had been meaning to reply to this when it got promoted, but I've been a bit distracted.
I think you make a good case in general, I'm not sure of the utility of producing an expanded list of examples of redundancy and robustness since so often the ID/creationist crowd will consider just one example of what they consider an irreducibly complex system to be sufficient proof of some extranatural component. I also agree that the 'junk DNA' point is fairly irrelevant and perhaps confusing, 'junk DNA' is a fuzzily defined term at the best of time, if we consider superfluous 'junk DNA' to be that which is non-functional then we might just as well include it in the set of all effectively non-functional DNA, although this isn't a set we can readily identify either in coding or non-coding sequences.
I'll try and address some of your specific questions.
gene duplication errors create redundant copies of genes. Those copies can take over if the original one is no longer functional due to a bad mutation (q:is it a given that multiple copies will ALWAYS only have positive effect?)
No, it is possible that over expression of a gene by a duplication would be detrimental, although it will vary greatly on a gene by gene basis if a simple duplication would produce a large enough dose for a detrimental response. It could also be argued that as well as adding a layer of redundancy a duplication could increase the chances of a detrimental dominant negative mutation which would block the effect of both copies of the gene.
sexually reproducing organisms can make use of the "heterozygote advantage" because they have all chromosomes/genes duplicate (except X/Y of course). One copy can be dysfunctional without fatal consequences (q:is it categorically NO effect if one is dysfunctional, or is there a whole spectrum from "NO consequence" to "not deadly but still seriously affected"?)
There are many cases where even a totally null allele is no only not fatal but possibly not even phenotypically detectable. n regard to your question; as with duplication there is a possibility of a dose effect and there are known examples of where a low dose causes problems, termed haploinsufficiency.
an example like vitamin C illustrates that often it is possible to take in certain essential substances (like, via food) instead of letting the DNA synthesize them internally. This is why humans and apes (and bats) have a defective gene for vitamin C synthesis without being affected by it. (q:is this a fairly unique (known) example, or is this abundant?
I really don't know about this, I can't think of another example off the top of my head.
biochemistry with complex biochemical molecules like proteins is far more insensitive to changes in the components than the simple inorganic reactions we learn about in highschool. That is, the reactions depend mostly on the shape of the proteins after curling up, and on the amino acids on the "outside". And very often both of these will not be affected much by replacing amino acids "on the other side of the chain" by different, mutated ones. For example, they could be locked up inside once the protein has curled up. (q: Is this a fairly accurate general statement? I've read elsewhere that a small change in amino acid sequence CAN severely destroy the structure of the curled-up protein, but would this be in a minority of cases, or is it that despite this would be the case in the vast majority of cases, there's still an astronomical amount of possibilities to have a mutation NOT influence the structure?)
I don't know about astronomical but there is certainly a large potential for substitutions to be neutral. The most obvious issues for amino acids on the inner core is a change from hydrophobic to hydrophilic,which can radically disturb the proteins conformation, as in the case of the mutation in sickle cell anaemia.
I hope these help answer some of your questions.
TTFN,
WK
Edited by Wounded King, : Changed heading

This message is a reply to:
 Message 5 by Annafan, posted 05-11-2008 12:05 PM Annafan has replied

Replies to this message:
 Message 7 by Annafan, posted 05-13-2008 5:26 AM Wounded King has replied

  
Annafan
Member (Idle past 4579 days)
Posts: 418
From: Belgium
Joined: 08-08-2005


Message 7 of 8 (466108)
05-13-2008 5:26 AM
Reply to: Message 6 by Wounded King
05-11-2008 7:05 PM


Re: Some answers
Wounded King writes:
I think you make a good case in general, I'm not sure of the utility of producing an expanded list of examples of redundancy and robustness since so often the ID/creationist crowd will consider just one example of what they consider an irreducibly complex system to be sufficient proof of some extranatural component.
The crowd I'm addressing there is largely unaware of the finer points of the discussion. At the moment they are just against evolution, but they don't seem to have a very good idea of what it is or any of the claims against.
wounded king writes:
I don't know about astronomical but there is certainly a large potential for substitutions to be neutral. The most obvious issues for amino acids on the inner core is a change from hydrophobic to hydrophilic,which can radically disturb the proteins conformation, as in the case of the mutation in sickle cell anaemia.
In his 29+, Theobald mentions that only 30% of the amino acids in cytochrome C are necessary for the functionality, and that human cytochrome C can be put into yeast without consequences, and 40% of its amino acids is different. It was also estimated that there are more than 2x10^93 different amino acid combinations that would result in functional cytochrome C. I thought all this warranted "astronomical"
Thanks for the feedback!

This message is a reply to:
 Message 6 by Wounded King, posted 05-11-2008 7:05 PM Wounded King has replied

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 Message 8 by Wounded King, posted 05-13-2008 6:39 AM Annafan has not replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 8 of 8 (466119)
05-13-2008 6:39 AM
Reply to: Message 7 by Annafan
05-13-2008 5:26 AM


Re: Some answers
In his 29+, Theobald mentions that only 30% of the amino acids in cytochrome C are necessary for the functionality, and that human cytochrome C can be put into yeast without consequences, and 40% of its amino acids is different. It was also estimated that there are more than 2x10^93 different amino acid combinations that would result in functional cytochrome C. I thought all this warranted "astronomical"
The qualifier for this would be that a gene can still be functional but not equivalent in fitness to a wild type gene, i.e. while they may not be null mutants they may still be deleterious.
As far as Yockey's estimate goes Theobald uses the probability measure as an effective point to emphasise the lack of any need for such homologies outside of an evolutionary framework, I don't think it fits quite as well into your argument about redundancy although it does work.
Looking back I can't actually work out quite where Theobald gets his 30% figure, it is in a sentence with no reference and could be talking about either the study referenced just before, just after or some calculation extrapolated from several of the studies. I'm also not quite clear what he means by 'necessary to specify its function', if he means that there are 30 amino acid position that can't accept any substitutions at all then I would say that was actually a quite stringently defined sequence. If he means that there are 70 positions that can accept absolutely any substitution with no functional effect then obviously that is much more permissive. I suspect that the truth lies somewhere between these 2, some sites will not accept any substitutions, some will accept a number of similar residues with little functional effect and some may accept any and all substitutions with no effect. I'm just not quite sure what Theobald is describing when he says it.
TTFN,
WK

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 Message 7 by Annafan, posted 05-13-2008 5:26 AM Annafan has not replied

  
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