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Author Topic:   Evolution Simplified
crashfrog
Member (Idle past 1544 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 106 of 170 (311268)
05-11-2006 11:11 PM
Reply to: Message 102 by robinrohan
05-11-2006 7:07 PM


Re: Generalizations
I am referring to whether or not they are theoretically inevitable, and if so, whether it is theoretically inevitable that some of these be non-neutral.
If outcomes are statistically random, then every possible outcome occurs given sufficient time. (This is similar to the mathematical phenomenon that, given a statistically random series of numbers of sufficient length, like the decimal expansion of pi, you can prove that any arbitrary, finite sequence of numbers is contained within it.)
Since there's no physical law apparently preventing alternate energy states and chemical outcomes of the molecular interactions involved in the replication of genetic material, we know that all those alternate outcomes are possible. And since they're possible, they'll happen given sufficient opportunities for them to do so, at random.
So, yeah. Seems like, to me, there's a pretty good reason to assume that mutations are inevitable. The same reasoning applies to the question of those mutations being silent or not. Since there's a non-zero probability that a random change to a polypeptide sequence will alter the chemistry of the resulting protein, the outcome that such a change does alter that chemistry is inevitable, given sufficient time.
Since it turns out that those things have a pretty substantial probability, that sufficient time turns out not to be very long.

This message is a reply to:
 Message 102 by robinrohan, posted 05-11-2006 7:07 PM robinrohan has replied

Replies to this message:
 Message 107 by robinrohan, posted 05-11-2006 11:33 PM crashfrog has replied

  
robinrohan
Inactive Member


Message 107 of 170 (311282)
05-11-2006 11:33 PM
Reply to: Message 106 by crashfrog
05-11-2006 11:11 PM


Re: Generalizations
If outcomes are statistically random, then every possible outcome occurs given sufficient time.
The amount of time is limited.

This message is a reply to:
 Message 106 by crashfrog, posted 05-11-2006 11:11 PM crashfrog has replied

Replies to this message:
 Message 108 by crashfrog, posted 05-11-2006 11:35 PM robinrohan has replied

  
crashfrog
Member (Idle past 1544 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 108 of 170 (311283)
05-11-2006 11:35 PM
Reply to: Message 107 by robinrohan
05-11-2006 11:33 PM


Re: Generalizations
The amount of time is limited.
That's a different question, though.
As it stands, the rate for mutagenesis in mammalian nuclear DNA, in terms of single-point substitutions, is 1 per every 3.6 billion base pair replications, according to my wife's phylogenetics text.

This message is a reply to:
 Message 107 by robinrohan, posted 05-11-2006 11:33 PM robinrohan has replied

Replies to this message:
 Message 109 by robinrohan, posted 05-11-2006 11:48 PM crashfrog has replied

  
robinrohan
Inactive Member


Message 109 of 170 (311294)
05-11-2006 11:48 PM
Reply to: Message 108 by crashfrog
05-11-2006 11:35 PM


Re: Generalizations
As it stands, the rate for mutagenesis in mammalian nuclear DNA, in terms of single-point substitutions, is 1 per every 3.6 billion base pair replications, according to my wife's phylogenetics text.
I'm not sure what that 7th word means, but it sounds like mutation doesn't happen very often.

This message is a reply to:
 Message 108 by crashfrog, posted 05-11-2006 11:35 PM crashfrog has replied

Replies to this message:
 Message 110 by kuresu, posted 05-12-2006 12:00 AM robinrohan has not replied
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kuresu
Member (Idle past 2590 days)
Posts: 2544
From: boulder, colorado
Joined: 03-24-2006


Message 110 of 170 (311300)
05-12-2006 12:00 AM
Reply to: Message 109 by robinrohan
05-11-2006 11:48 PM


Re: Generalizations
actually, they do happen often. Just a ball park figure, but if every gene had, say, ten base pairs, and we have roughly twenty thousand genes, that's 200000. And at ten per gene, that's only three amino acids per protein, and most proteins in our body are much, much longer.
Then, how many times do our cells divide? plenty, so even if there were only 200000 base pairs, there are trillions of cells in the body.
The mutations that are important are those in gametic cells, as those are the ones passed on to the offpsring. Guys produce millions of sprem cells weekly, if not daily. Think of how many base pairs total there are in that number. Point is, mutations happen, and happen often.

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crashfrog
Member (Idle past 1544 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 111 of 170 (311301)
05-12-2006 12:01 AM
Reply to: Message 109 by robinrohan
05-11-2006 11:48 PM


Re: Generalizations
'm not sure what that 7th word means, but it sounds like mutation doesn't happen very often.
Your genome is upwards of 3 billion base pairs long, and that genome is fully replicated every time one of your cells undergoes meiosis or mitosis. Which happens, in your body:
1) hundreds of times every second in your skin as new skin cells and hair are grown and the lining of your digestive tract is replaced, plus
2) thousands of times per second as your bone marrow replicates and differentiates new cells to replace the contents of your blood; plus
3) 1.5 million times a day as your testes produce sperm (assuming you're a man), plus
4) whatever assorted other cell division is going on in your body.
So, for every act of cell division per day that comes to (millions), we should expect the new sequence of DNA to differ from the old one in 1 or 2 different places.

This message is a reply to:
 Message 109 by robinrohan, posted 05-11-2006 11:48 PM robinrohan has replied

Replies to this message:
 Message 112 by robinrohan, posted 05-12-2006 12:04 AM crashfrog has replied

  
robinrohan
Inactive Member


Message 112 of 170 (311303)
05-12-2006 12:04 AM
Reply to: Message 111 by crashfrog
05-12-2006 12:01 AM


Re: Generalizations
1) hundreds of times every second in your skin as new skin cells and hair are grown and the lining of your digestive tract is replaced, plus
2) thousands of times per second as your bone marrow replicates and differentiates new cells to replace the contents of your blood; plus
3) 1.5 million times a day as your testes produce sperm (assuming you're a man), plus
4) whatever assorted other cell division is going on in your body.
So, for every act of cell division per day that comes to (millions), we should expect the new sequence of DNA to differ from the old one in 1 or 2 different places.
So are mutations frequent or not?

This message is a reply to:
 Message 111 by crashfrog, posted 05-12-2006 12:01 AM crashfrog has replied

Replies to this message:
 Message 113 by crashfrog, posted 05-12-2006 12:06 AM robinrohan has replied

  
crashfrog
Member (Idle past 1544 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 113 of 170 (311304)
05-12-2006 12:06 AM
Reply to: Message 112 by robinrohan
05-12-2006 12:04 AM


Re: Generalizations
So are mutations frequent or not?
If my post didn't answer your question, I guess I don't know what you mean by "frequent." We estimate that any one human being has between 5 and 500 mutations. Every single human. Would you characterize that as "frequent"? I'd say that it's "sufficient."

This message is a reply to:
 Message 112 by robinrohan, posted 05-12-2006 12:04 AM robinrohan has replied

Replies to this message:
 Message 114 by robinrohan, posted 05-12-2006 12:08 AM crashfrog has replied

  
robinrohan
Inactive Member


Message 114 of 170 (311305)
05-12-2006 12:08 AM
Reply to: Message 113 by crashfrog
05-12-2006 12:06 AM


Re: Generalizations
If my post didn't answer your question, I guess I don't know what you mean by "frequent." We estimate that any one human being has between 5 and 500 mutations. Every single human. Would you characterize that as "frequent"? I'd say that it's "sufficient."
I mean in the ones that matter as regards evolution--the ones that get passed on. Say, in your standard litter of pups.
--------------------------------------------------------------------------------
This message has been edited by robinrohan, 05-11-2006 11:08 PM

This message is a reply to:
 Message 113 by crashfrog, posted 05-12-2006 12:06 AM crashfrog has replied

Replies to this message:
 Message 115 by crashfrog, posted 05-12-2006 12:12 AM robinrohan has replied

  
crashfrog
Member (Idle past 1544 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 115 of 170 (311308)
05-12-2006 12:12 AM
Reply to: Message 114 by robinrohan
05-12-2006 12:08 AM


Re: Generalizations
I mean in the ones that matter as regards evolution--the ones that get passed on. Say, in your standard litter of pups.
I would estimate that each pup would have between 5 and 500 mutations, individually. That's a wide range because I don't know how long the dog genome is, or the precise rate of mutation in nuclear dog DNA.
Excellent way of framing the question, though. I'm sorry I wasn't clearer before. You're right, of course, that there's a difference between the mutations that are passed along from the parents' gametes and the somatic mutations that an organism naturally accrues in its lifetime. In a sense, an organism is born with all the mutations that it will ever possess that are relevant in an evolutionary context. It will then pass along those mutations, possibly; also, as it generates gametes, mutations will form that aren't relevant to the parent's fitness but become part of the genome of the offspring.
This message has been edited by crashfrog, 05-12-2006 12:18 AM

This message is a reply to:
 Message 114 by robinrohan, posted 05-12-2006 12:08 AM robinrohan has replied

Replies to this message:
 Message 116 by robinrohan, posted 05-12-2006 12:16 AM crashfrog has replied

  
robinrohan
Inactive Member


Message 116 of 170 (311309)
05-12-2006 12:16 AM
Reply to: Message 115 by crashfrog
05-12-2006 12:12 AM


Re: Generalizations
I would estimate that each pup would have between 5 and 500 mutations, individually.
Just a question:
Mutation is not the same thing as imperfect replication, is it? I thought that meant that the female and male combinations would result in a baby that did not look exactly like the mamma or the papa due to the combination.

This message is a reply to:
 Message 115 by crashfrog, posted 05-12-2006 12:12 AM crashfrog has replied

Replies to this message:
 Message 117 by crashfrog, posted 05-12-2006 12:21 AM robinrohan has replied

  
crashfrog
Member (Idle past 1544 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 117 of 170 (311312)
05-12-2006 12:21 AM
Reply to: Message 116 by robinrohan
05-12-2006 12:16 AM


Re: Generalizations
Mutation is not the same thing as imperfect replication, is it?
Mutation includes changes that happen due to imperfect replication, as well as changes that happen when DNA is damaged and then repaired improperly.
I thought that meant that the female and male combinations would result in a baby that did not look exactly like the mamma or the papa due to the combination.
That's sexual recombination. Sexual organisms have two alleles per gene (usually), one of which they inherit from each parent. The phenotype of the offspring depends on how those two alleles interact. Those interactions are what people are talking about when they talk about dominant and recessive traits.

This message is a reply to:
 Message 116 by robinrohan, posted 05-12-2006 12:16 AM robinrohan has replied

Replies to this message:
 Message 118 by robinrohan, posted 05-12-2006 12:46 AM crashfrog has replied
 Message 126 by EZscience, posted 05-12-2006 3:06 PM crashfrog has not replied

  
robinrohan
Inactive Member


Message 118 of 170 (311318)
05-12-2006 12:46 AM
Reply to: Message 117 by crashfrog
05-12-2006 12:21 AM


Re: Generalizations
So the term "imperfect replication" does not mean the same thing as "sexual recombination"?
One does get mixed signals on this forum.

This message is a reply to:
 Message 117 by crashfrog, posted 05-12-2006 12:21 AM crashfrog has replied

Replies to this message:
 Message 120 by Brad McFall, posted 05-12-2006 8:24 AM robinrohan has not replied
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Lithodid-Man
Member (Idle past 3008 days)
Posts: 504
From: Juneau, Alaska, USA
Joined: 03-22-2004


Message 119 of 170 (311330)
05-12-2006 4:50 AM
Reply to: Message 100 by robinrohan
05-11-2006 5:15 PM


Re: questioning facts
quote:
I think we are talking about a particular effect not just any effect. It has to have an effect on which creatures reproduce and which don't, I think. Some trait that on the face of it seems like a survival advantage might have no effect on which life forms reproduce, those with or those without the trait. It depends on the entire environmental situation and the other traits possessed by the organism. One might even imagine a situation where having vision--which seems like an obvious advantage--might be a negative trait, depending on other factors.
So perhaps it is not a simple matter at all determining which traits are neutral and which not.
Robin,
You are actually dead-on in your question here. It is the nature of mutation that it be random. Whether it is neutral, beneficial, or harmful is more often than not a factor of the environment. Obviously a mutation that causes a zygote to abort during somite formation is harmful and impossible to be passed onto the next generation. But more often mutations are not as easily classifible.
The same mutation can be neutral in one environment, while being beneficial or harmful in another. I am sure there are better examples out there, but one that comes to mind are mutations in cell transport proteins in Nucella snails (I am going from memory here). In the general population there is a mutated protein that enables the snail (because of it's ability to transport material in and out of the cell) to function in warm temperatures. In the majority of the snail's range the gene that codes this protein exists and seems to arise frequently and is neutral. During warming events (like el Nino) the gene is favored. During cold events (such as when the cold-phase Pacific Decadal oscillation coincides with non-el Nino years) the gene is not favored (the daughter protein doesn't function as well as the standard protein). So the same mutation is usually neutral, but can be beneficial in warm water and detrimental in cold water. I am searching for my refs on this, but they seem to be buried. I suspect that many EvC people have even better examples.
quote:
So the term "imperfect replication" does not mean the same thing as "sexual recombination"?
Mutation (imperfect replication) is not the same sexual (genetic) recombination, although both can have selective consequences. Mutation refers to an accident in a gene that results in a new sequence (usually tiny, insignificant, and often lost or repaired but can be none of the above). Genetic recombination is when whole genes are mixed during sexual reproduction and different alles may be expressed.
quote:
One does get mixed signals on this forum.
I can see where you get this (at least on this topic) but try to understand that the concept itself is pretty complicated, and there are many different terms that are used. Often these terms differ in meaning between scientists and laymen. In my opinion you have asked good questions on this topic.

Doctor Bashir: "Of all the stories you told me, which were true and which weren't?"
Elim Garak: "My dear Doctor, they're all true"
Doctor Bashir: "Even the lies?"
Elim Garak: "Especially the lies"

This message is a reply to:
 Message 100 by robinrohan, posted 05-11-2006 5:15 PM robinrohan has replied

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Brad McFall
Member (Idle past 5110 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 120 of 170 (311354)
05-12-2006 8:24 AM
Reply to: Message 118 by robinrohan
05-12-2006 12:46 AM


Re: Generalizations
Yep, confusing indeed. It gets just as confusing when one reads non-EVC literature too. Ya know, I found this particularly frustrating but after I found out what people in New Zealand were writing about biology, and it was all in English, I just dismissed most of these confusion comaparisons as academic. Maybe that is why I never got on at Cornell not that I was psychologically disposed to do so. Anyway..
This difference you were able to get a good sequence of discussion on, shows how important it is to think about a single "generation" when discussing the relation of form-making and translation in space to "mutations" of any polyvocal crack er,, at it...
Before the force of Crick's DNA was around, Weismann, thinking through selection selectively on more than one level had thought that any form changes had to come "molecularly" from without, outside the organism. It has always been an academic point with me why molecular biologists (not organacists) have not since WWII tried to group mutations acros one or a determinate number of generations into physically caused classes that in effect might be statistically tested for seperability in... Maybe a particular lineage or monophyla has a group of mutations caused by photons in divided phases, another a group by subatomic particles, another by human electricity, another by a comination of macro-physical troque combined with circular chemcial rxn networks, another by a quantum mechanical difference in the energy levels of the ad hoc chemicals in the larger clade the monophyla is in. These particulars are not mutually exclusive.
Instead because of the differnt affects on thoughts about levels of selection and levels of organization one can find (in Science vol 312 May 5, 2006 on sexual selection) an example which makes your point.
J Stewart responding to Roughgarden et. al said,
quote:
"Choices could also be made by females in this manner: for example, a chemical push evolved in female lions that causes them to prefer male lions with darker manes. Whether this push results in better genetics for lions is irrelevant. Once females mate and have a litter, another set of chemical signals takes over that pushes her to take care of her offspring rather than abandon them. In other species, there is no chemcial push, so femalses abandon their offspring and survive on their own."
Here Stewart DID seperate mutations in prior generations ("whether this push results in better genetics for lions is irrelevant") from the divided push chemcial system that manifests itself AFTER some mutation (push better manes, push parental care) but Stewart and no one I know of then tries to say if this chemical push category itself cannot itself have a biophysical reduction of a group of physical "agents" that cause just this push not the "pull" in any other spieces with a better genetics or not!! Roughgarden et. al. point out the problem in general with Stewart was that Stewart thought that Roughgarden et al were talking about SPECIES not individuals but then if we raise the discussion to a "third" level of species selection and individuality the whole discussion gets so very complicated.
That is why I find it incumbent on biologists to be as redutionist as possible but this is in material reality not theoretical biology only.

This message is a reply to:
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