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Author Topic:   How well do we understand DNA?
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 58 of 98 (182613)
02-02-2005 3:16 PM
Reply to: Message 57 by TheLiteralist
02-02-2005 3:06 PM


Could this fact that copying errors are inherent in certain sequences where there is a lot of repetitiveness be the mechanism I'm looking for?
I'm not trying to agree or disagree in this post, but I myself had a hard time understanding the relationship between repetitive sequences and mutation until I saw diagrams of it. So maybe you would find the same thing helpful.
Repetitive sequences are vulnerable to something called "slipped-strand mutation", which can be both additive or subtractive to the genetic material based on the direction of the slippage:

This message is a reply to:
 Message 57 by TheLiteralist, posted 02-02-2005 3:06 PM TheLiteralist has replied

Replies to this message:
 Message 61 by TheLiteralist, posted 02-02-2005 3:34 PM crashfrog has replied

  
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 63 of 98 (182622)
02-02-2005 3:48 PM
Reply to: Message 61 by TheLiteralist
02-02-2005 3:34 PM


Re: Nice Chart
Thanks for posting the chart. I wonder WHY the slippage occurs, though
It's not obvious? It slips because it can slip; a non-repetitive sequence cannot slip because there's no way to skip a gene and have the opposing strand bind correctly. (You remember of course that A can only bind to T and G can only bind to C.)
For instance, if I have:

5' AGA AGA AGA AGA 3'
3' TCT TCT TCT TCT 5'

You can lose/slip the first triplet and get

5' AGA AGA AGA 3'
3' TCT TCT TCT TCT 5'

and your strands still bind because the right nucleotides still pair up.
On the other hand, if you have

5' AGC CGT TGG GAA 3'
3' TCG GCA ACC CTT 5'

and slip the first triplet, you get

5' CGT TGG GAA 3'
3' TCG GCA ACC CTT 5'

and the strands wouldn't bind because they're not complimentary.

This message is a reply to:
 Message 61 by TheLiteralist, posted 02-02-2005 3:34 PM TheLiteralist has replied

Replies to this message:
 Message 65 by TheLiteralist, posted 02-02-2005 3:59 PM crashfrog has replied

  
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 66 of 98 (182630)
02-02-2005 3:59 PM
Reply to: Message 60 by TheLiteralist
02-02-2005 3:30 PM


Re: MUTATIONS
I am then curious about two things: (1) are certain segments in any given genome strangely much less likely to have a random mutation
I believe that's what's meant by a "conserved" gene. For instance my wife is working with COI, a mitochondrial gene that is highly conserved across insect species. But maybe I'm wrong.
I don't know that there would be anything "strange" about a gene that did not mutate as often; we would probably find that one or more of several things was true:
1) The gene was non-repetitive
2) The gene was not expressed or transcribed often;
3) The gene was located in a section of the DNA that was not often "unwound" or "unzipped"
In other words mutations are often "opportunistic" in that they happen when normal cell machinery doesn't quite work right. A gene that was not often manipulated by the cell would probably not often mutate. Sort of like, we might find that collector automobiles are involved in less fatal accidents per car than, say, the Honda Civic; not because of any flaw in the Civic or virtue of a collector's car, but simply because a collector automobile isn't taken out on the road that often.
also just happen to be the ones that should a mutation occur have deleterious effects on the resultant organism?
I dunno. There are a number of speculations I could make about what might happen to the genetics of a population of organisms burdened by a gene very vulnerable to mutation, and how that population might evolve to deal with that vulnerability. But I don't have the data to answer your question.

This message is a reply to:
 Message 60 by TheLiteralist, posted 02-02-2005 3:30 PM TheLiteralist has replied

Replies to this message:
 Message 67 by TheLiteralist, posted 02-02-2005 4:08 PM crashfrog has replied

  
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 69 of 98 (182634)
02-02-2005 4:14 PM
Reply to: Message 65 by TheLiteralist
02-02-2005 3:59 PM


Re: Slipping
That, in my mind, explains how it can sucessfully slip, but not why it slips in the first place.
It slips because there's nothing preventing it from doing so. Just like you "slip" on a puddle because there's no friction preventing you from doing so, and you fall on your ass because there's no magic hand that reaches out to catch you.
The question that might make it clearer in your head is to ask instead of what makes it "slip", what makes it come together in the first place? These are all just chemical reactions happening in water, and the complimentarity of nucleotides is the only thing that makes the two strands of DNA "zip up" correctly. Repetition compromises the effecacy of that complimentarity, and so they don't "zip up" quite right.
Does that help any? I think a better understanding of the genetic transcription/replication mechanisms might aid you.
DNA - Wikipedia
The wiki article is pretty comprehensive, and should give you an idea about how DNA is strutured, stored in the cell, transcripted, and replicated. Also you might follow the link and read about Polymerase Chain Reaction, or PCR, which is the lab process for replicating DNA. It proceeds much like the cellular version (indeed, uses most of the same enzymes, I believe. Well, not exactly. Specifically it uses the polymerase enzyme from thermophile bacteria, which can survive the heating process needed to cleave the two strands.)
Clear as mud, I'm sure. My head mostly spins when my wife explains what she's doing in the lab.

This message is a reply to:
 Message 65 by TheLiteralist, posted 02-02-2005 3:59 PM TheLiteralist has replied

Replies to this message:
 Message 72 by TheLiteralist, posted 02-02-2005 4:22 PM crashfrog has replied

  
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 71 of 98 (182637)
02-02-2005 4:18 PM
Reply to: Message 67 by TheLiteralist
02-02-2005 4:08 PM


Re: MUTATIONS
Hey, has your wife seen this thread? If she has, has she found it interesting...or has she had a roll-your-eyes type reaction?
She posts here, ever-so-rarely, as "Entomologista". (For some reason, no matter how she tries to log on with her computer, her posts wind up under my name, even though I've never logged on at her machine. Maybe the new BB code has fixed that, though. I don't think she's tried recently.)
As a biologist, though, she's not really that interested in the creationism debate. You'd be surprised, I think, how much of a non-entity the creationism movement is to actual biology professionals. It's only us amateurs for whom the debate doesn't go right under the radar. She's too busy doing real work.

This message is a reply to:
 Message 67 by TheLiteralist, posted 02-02-2005 4:08 PM TheLiteralist has not replied

  
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 73 of 98 (182643)
02-02-2005 4:30 PM
Reply to: Message 72 by TheLiteralist
02-02-2005 4:22 PM


Cut-n-paste error
Looks like you had a little "copying error" yourself. I know what you were replying to, though.

This message is a reply to:
 Message 72 by TheLiteralist, posted 02-02-2005 4:22 PM TheLiteralist has replied

Replies to this message:
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crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 81 of 98 (182978)
02-03-2005 10:37 PM
Reply to: Message 79 by TheLiteralist
02-03-2005 9:21 PM


There IS a difference, though. I am saying that the random mutations are occurring because the code was designed to produce them.
Are you sure that's what you're proposing? I thought you proposed a model where mutations are occuring because the code was designed to allow them.
Do you see the difference? If you believe that the mutations are not simply allowed by the code, but are in fact produced by the code, how does that work, exactly? How does a deterministic chemical process generate a random output?
You've mentioned, I think, that you're a computer programmer; you must therefore know that computers are incapable of generating random numbers. The best they can do is choose a pesudorandom number from a preset list of random values.
You're proposing that cells act like computers; but you're proposing that they do something very un-computer-like, which is generate random output. I guess I'd like to know how you propose they do that.
On the other hand, if you propose that mutations are occuring in certain circumstances because they're being allowed to occur by the "design" of the code; well, we see that anyway, and it doesn't take design to arrive at that outcome.
I really am amazed that we can classify bacteria for any length of time given how much they variate.
I thought I already explained how we classify based on heredity, not strictly morphology.

This message is a reply to:
 Message 79 by TheLiteralist, posted 02-03-2005 9:21 PM TheLiteralist has replied

Replies to this message:
 Message 86 by TheLiteralist, posted 02-06-2005 6:13 PM crashfrog has replied

  
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 89 of 98 (183915)
02-08-2005 10:40 AM
Reply to: Message 86 by TheLiteralist
02-06-2005 6:13 PM


Re: Me? A Programmer?
Yes. I'm proposing that the code is designed to produce random mutations. A computer program can be designed to produce randomness.
Strictly speaking, no, it cannot. It can only provide pesudorandom output. There's no way to get a deterministic system to provide truly random output. Your computer program (I assume, since you don't provide source code) essentially looks up a number from a table of random numbers. If you could duplicate the exact state of the computer at the time you first ran your program, you could get the same "random" output each time.
By what cellular mechanism is random genetic output created? I don't understand how that would be possible.
At any rate, I don't yet understand why you believe that the code has to produce random mutations when most of the activity in the nucleus is working to suppress mutation as much as possible. If a cell wanted some mutations (if you'll pardon an amazingly simplistic model of what occurs), all it would have to do is simply relax. The "natural" state of DNA is to mutate; it hardly needs any help in that regard.

This message is a reply to:
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crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 90 of 98 (183916)
02-08-2005 10:45 AM
Reply to: Message 84 by christian atheist
02-04-2005 2:20 PM


Re: Broken Genes
Finally, do we know what mutation in the gene causes it to not work?
It's my understanding, perhaps erroneously, that there's a "stop" codon right in the middle of it.

This message is a reply to:
 Message 84 by christian atheist, posted 02-04-2005 2:20 PM christian atheist has replied

Replies to this message:
 Message 91 by christian atheist, posted 02-13-2005 7:51 PM crashfrog has replied

  
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 94 of 98 (185207)
02-14-2005 3:46 PM
Reply to: Message 91 by christian atheist
02-13-2005 7:51 PM


Couldn't we cut out that stop codon and put it in the right place?
It's not quite that simple; there's control genes that regulate expression of genes. Control genes that currently have this gene turned off. We'd have to turn those back on, and we don't know enough about them to know how to do that. Lord only knows what we might activate by mistake. The vast, vast majority of your chromosomes are genetic information from viruses, etc.
And why bother? I love eating citrus. We wouldn't have the broken gene in the first place if we couldn't get away with not having it, via diet.

This message is a reply to:
 Message 91 by christian atheist, posted 02-13-2005 7:51 PM christian atheist has replied

Replies to this message:
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 Message 98 by Godfearingatheist, posted 08-28-2005 5:12 PM crashfrog has not replied

  
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