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Author Topic:   How well do we understand DNA?
crashfrog
Inactive Member


Message 16 of 98 (177834)
01-17-2005 12:19 PM
Reply to: Message 14 by NosyNed
01-17-2005 10:12 AM


I don't see how you think this works. Just because some random mutation happens in the "junk" DNA doesn't mean it won't happen elsewhere in the DNA.

It's simple probability, to me. Lets say that an energetic photon penetrates the cell's nucleus and snips a chromosome in two pieces. The nucleus's repair machinery comes into play but there's always the risk that the DNA won't be repaired quite right at the point where it was broken.

If, say, 70% of that chromosome is non-functional, then there's a 70% chance that imperfect repair occurs at a section where it doesn't matter.

So if the coding DNA is so many base pairs long then it's chances of a really random mutation are just as great no matter what has happened in the other millions of base pairs.

I hope Rrhain can check my math on this. Lets try and work it out together; I hope you'll interject where you disagree.

Lets say that an organism has a genome 100 bp long, and a mutation rate of 1 per hundred base pairs per generation. This organism has no junk DNA whatsoever - every sequence in its genome is either protein-encoding or regulatory. We would therefore expect every generation of this organism to impact a functional sequence.

Now lets double the length of it's genome with junk DNA. Every generation should now have two mutations, but the odds that each one will impact a functional sequence are 50%. The outcome that either mutation impacts a functional sequence is three out of four possible outcomes:

1) First one "hits", second one "misses"
2) First one misses, second one hits
3) First one hits, second one hits
4) First one misses, second one misses

The way I figure it, that's a 75% chance per generation that a mutation has "hit" a functional sequence, down from 100% for no junk DNA. Unless these outcomes are not equally likely, as I have assumed. If my math is flawed, and it feels like it is, I hope it will be pointed out to me.


This message is a reply to:
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Replies to this message:
 Message 17 by Sylas, posted 01-17-2005 2:21 PM crashfrog has responded

  
Sylas
Member (Idle past 3304 days)
Posts: 766
From: Newcastle, Australia
Joined: 11-17-2002


Message 17 of 98 (177870)
01-17-2005 2:21 PM
Reply to: Message 16 by crashfrog
01-17-2005 12:19 PM


This is an intriguing arguement by crashfrog, but flawed. The measure of 1 mutation per hundred base pairs per generation (actually, the real figure is more like 1 per 108 base pairs) is itself a measure of a stochastic process. If you have a genome with 6 by 109 base pairs, it means that you get about 60 mutations per generation. It could be more, and it could be less, but the average is 60.

Crashfrog's argument assumes that the organism will have exactly that many mutations, and that is the error.

Increasing genome length does not change the probability of mutations in the bits you care about.

Cheers -- Sylas


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Replies to this message:
 Message 18 by crashfrog, posted 01-17-2005 5:52 PM Sylas has responded

  
crashfrog
Inactive Member


Message 18 of 98 (177921)
01-17-2005 5:52 PM
Reply to: Message 17 by Sylas
01-17-2005 2:21 PM


Well, there ya go.
This message is a reply to:
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Replies to this message:
 Message 19 by Sylas, posted 01-18-2005 6:37 AM crashfrog has responded

  
Sylas
Member (Idle past 3304 days)
Posts: 766
From: Newcastle, Australia
Joined: 11-17-2002


Message 19 of 98 (178053)
01-18-2005 6:37 AM
Reply to: Message 18 by crashfrog
01-17-2005 5:52 PM


No, no! Don't give up so easily! Damn... the creationists are more fun. Other folks keep learning stuff way too quickly. ;)

(Apologies to the creationists here who do learn things from time to time... I know the above is a cheap shot.)


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Replies to this message:
 Message 20 by crashfrog, posted 01-18-2005 8:30 PM Sylas has not yet responded

  
crashfrog
Inactive Member


Message 20 of 98 (178319)
01-18-2005 8:30 PM
Reply to: Message 19 by Sylas
01-18-2005 6:37 AM


No, no! Don't give up so easily!

Well, I mean, it wasn't even my idea - it was just something I heard from somewhere, and it sounded plausible. Now I know that it isn't. It's not like my scientific career was on the line, because I don't have one. :)


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TheLiteralist
Inactive Member


Message 21 of 98 (179821)
01-23-2005 12:42 AM
Reply to: Message 6 by Sylas
01-16-2005 4:27 AM


Conserved Sequences
Hi Sylas,

I am thinking of the genetic code like a programming language. So just as a programmer might use a certain code module (for instance, a code sequence that makes highlighted text bold) in many programs; so the Creator might have numerous genetic modules which can be used in many creatures to accomplish similar tasks in all the many organisms.

How can one distinguish between a conserved genetic sequence and a particular genetic module that the Creator might have used in various organisms (to achieve similar functions in various organisms)?

Thanks,
--TL

This message has been edited by TheLiteralist, 01-23-2005 00:43 AM

This message has been edited by TheLiteralist, 01-23-2005 00:47 AM


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TheLiteralist
Inactive Member


Message 22 of 98 (179823)
01-23-2005 1:02 AM
Reply to: Message 9 by NosyNed
01-16-2005 10:50 AM


Broken Genes
NosyNed,

Also we see that what are obviously broken genes are carried along for a pretty significant time. It is unlikely that these are both broken genes and of some other value (unless pure bulk is of value).

In my mind, the "broken" genes might simply be genetic modules that look very similar to other genetic modules but serve somewhat, or even altogether, different purposes. It is easy enough to make a few adjustments to a computer code module and have it serve a completely different function in the same or different program. (Why re-invent the wheel for each program, right?)

Also remember that the original designation of junk was based on the fact that it does not code for proteins.

So, apparently, there was a time when we didn't realize there was a purpose for non-protein-coding DNA; now we realize that there is.

Could it be that the "broken" genes serve legitimate purposes that are simply unknown at this time?

--TL

This message has been edited by TheLiteralist, 01-23-2005 01:02 AM


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Replies to this message:
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TheLiteralist
Inactive Member


Message 23 of 98 (179826)
01-23-2005 1:26 AM


random mutations v. purposed variation
I can conceive writing a computer program that copies itself and, each time it does, changes certain sections of the program on a random basis. Certain core areas of the program could be identified so that they could be prevented from being changed (or else the whole thing would quit or go haywire). Also, while randomness could be introduced into the program via a random generator module, test modules could be set up to ensure that the randomly generated code sequences met certain criteria (e.g., were valid code segments, weren't detrimental to the overall program, etc.) Or, the program could contain a sort of database of various code seqence snippets, and depending on results from the random generator module, various of these snippets could be copied into active modules. Thus, either way, the overall program sequence changes upon each copy (or it could be set up to change after X copies have been made, where X could be constant, variable, or randomly variable), yet the basic program remains the same AND the variants are a result of the original program AND each variant has the capability of making variants, too.

I don't think anybody on this thread has yet satisfactorily shown how we can distinguish between random mutations and on-purpose but randomly generated changes in the sequence due to some function or functions of the original sequence.

I would really like to know if and how such could be distinguished.

--TL


Replies to this message:
 Message 24 by crashfrog, posted 01-23-2005 1:38 AM TheLiteralist has responded

  
crashfrog
Inactive Member


Message 24 of 98 (179830)
01-23-2005 1:38 AM
Reply to: Message 23 by TheLiteralist
01-23-2005 1:26 AM


I don't think anybody on this thread has yet satisfactorily shown how we can distinguish between random mutations and on-purpose but randomly generated changes in the sequence due to some function or functions of the original sequence.

There's simply no physical way in a thermodynamic universe to prevent mutation in any part of DNA. It can be reduced, and is, but it cannot be prevented completely as you suggest.

Also, while randomness could be introduced into the program via a random generator module, test modules could be set up to ensure that the randomly generated code sequences met certain criteria (e.g., were valid code segments, weren't detrimental to the overall program, etc.)

There's no test that operates on DNA except the expression of genetics in the morphology of individuals who are then selected for or against by the environment. If there were, we could detect the cellular machinery that did so; if you believe it exists its inbumbent on you to prove it, not us to prove you wrong.


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 Message 23 by TheLiteralist, posted 01-23-2005 1:26 AM TheLiteralist has responded

Replies to this message:
 Message 25 by TheLiteralist, posted 01-23-2005 2:14 AM crashfrog has responded

  
TheLiteralist
Inactive Member


Message 25 of 98 (179841)
01-23-2005 2:14 AM
Reply to: Message 24 by crashfrog
01-23-2005 1:38 AM


Crashfrog,

There's simply no physical way in a thermodynamic universe to prevent mutation in any part of DNA. It can be reduced, and is, but it cannot be prevented completely as you suggest.

I have not said that mutations do not or cannot occur. I am asking how could random mutations be distinguished from on-purpose variations produced as a function of the code itself.

There's no test that operates on DNA except the expression of genetics in the morphology of individuals who are then selected for or against by the environment.

I certainly am not an expert on cellular biology. I believe that there are cell components that "correct" many "copying errors"...could that actually be a test similar to what I have stated in my programming analogy? (Perhaps it isn't...I don't know.)

If there were, we could detect the cellular machinery that did so; if you believe it exists its inbumbent on you to prove it, not us to prove you wrong.

Rather than making any assertions, I felt more like I was asking a question: "How can we distinguish between random mutations and on-purpose but randomly generated changes in the sequence due to some function or functions of the original sequence?" My analogies to computer programs are simply to give a better understanding of what I mean by the question. It is highly unlikely that I will ever find myself in a lab working with DNA. Yet, the question seems valid and easy enough to answer one way or the other for those, whose field is in an area dealing regularly with genetic operations and/or functions.


This message is a reply to:
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Replies to this message:
 Message 30 by crashfrog, posted 01-23-2005 10:58 AM TheLiteralist has responded

  
NosyNed
Member
Posts: 8829
From: Canada
Joined: 04-04-2003
Member Rating: 4.2


Message 26 of 98 (179844)
01-23-2005 2:18 AM
Reply to: Message 22 by TheLiteralist
01-23-2005 1:02 AM


Re: Broken Genes
Could it be that the "broken" genes serve legitimate purposes that are simply unknown at this time?

Yes that is possible. However, there isn't any hint of it yet.

There was (referenced elsewhere I don't have it) a study where large segements of mouse "junk" was stripped out. IIRC, the result was -- no change. The animals seemed perfectly normal.

This is the type of experiment that will have to be done over generations to be sure there is no effect but it is indicative.

As I noted, if there is no significant cost to carry extra DNA then there is nothing to remove it. With that the case we can expect DNA to pile up that would be really non functional.

This would supply a source for new funtions with further mutations of course. It may be that this is a long term advantage that actually selects for having "junk" DNA but I'm n ot sure that can be the case.

I expect the regulating parts of non coding DNA will be shown to have certain properties. I will be very surprised if those include looking just like a working gene that has had a hit by a mutation.

You may continue to hope for some new discoveries in this area but I don't see it likely that it will help you. These same discoveries are very likely to further strengthen our understanding of how we and chimps evolved from a common source. You should not pin your faith on what will be found out in genetics.


This message is a reply to:
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wj
Inactive Member


Message 27 of 98 (179858)
01-23-2005 6:08 AM
Reply to: Message 22 by TheLiteralist
01-23-2005 1:02 AM


Re: Broken Genes
TheLiteralist writes:

In my mind, the "broken" genes might simply be genetic modules that look very similar to other genetic modules but serve somewhat, or even altogether, different purposes.

Such supposition is contrary to reality. Most mammals have a GLO gene which produces an enzyme involved in the synthesis of ascorbic acid (vitamin C). Humans have an analogous gene which has a mutation which codes for a premature sop codon and renders the resultant protein useless. This explains why humans must get their ascorbic acid from their dietary intake. Chimpanzees, gorillas and orangutans have the same disabling mutation which inactivates their GLO genes.

The original gene does not serve its original purpose. It does not serve any other purpose. It is shared by a number of species which are relatively closely related. The simplest hypothesis is that all of these primate species are descended froma common ancestor which contained the GLO pseudogene and it has been passed to descendent species.


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Ben!
Member (Idle past 1666 days)
Posts: 1154
From: San Diego, CA
Joined: 10-14-2004


Message 28 of 98 (179859)
01-23-2005 6:56 AM
Reply to: Message 27 by wj
01-23-2005 6:08 AM


Re: Broken Genes
The original gene does not serve its original purpose. It does not serve any other purpose. It is shared by a number of species which are relatively closely related.

Seems to me that you're simply stating the same thing again rather than providing an argument. As far as I can understand, just because a gene is mutated and does not serve its' original purpose does not mean that it serves no purpose.

In fact, isn't the whole neo-evolutionary theory predicated on the fact that (in super simple terms) mutations can occur to change the function of a gene? Clearly this gene does not serve it's original purpose. That does not allow us to conclude that it serves no purpose. In fact, I think it really has little to do with the argument.

It seems to me that the only way we could determine that it serves no purpose is to knock it out and see what happens. Or to determine, in another way, that there are no proteins being transcribed from this sequence. Or, if there are proteins being transcribed, to show that they do not participate in any functional role within or outside of the cell.

Or am I way off? I'm kind of out of the loop here.

Edited to clear up a poorly worded sentence, and clear up an ambiguity that crashfrog picked up on.

This message has been edited by Ben, Thursday, 2005/04/14 05:27 PM


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Lizard Breath
Member (Idle past 4739 days)
Posts: 376
Joined: 10-19-2003


Message 29 of 98 (179867)
01-23-2005 7:52 AM
Reply to: Message 9 by NosyNed
01-16-2005 10:50 AM


Re: Tidying up
quote:
Also we see that what are obviously broken genes are carried along for a pretty significant time. It is unlikely that these are both broken genes and of some other value (unless pure bulk is of value).

Could one of the reasons why organisms like humans have more junk dna is because humans have a slower reproductive rate than bacteria so they have fewer generations to sort through the closet and discard unused and unwanted code?

Like if my nerd neighbor cleans his garage every other weekend but I only clean mine in the spring and the end of fall, I will have more junk on hand at any given time? Except for those two times when I clean it and then that is like a quantum jump in the condition of my garage verses his more stable situation.


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crashfrog
Inactive Member


Message 30 of 98 (179912)
01-23-2005 10:58 AM
Reply to: Message 25 by TheLiteralist
01-23-2005 2:14 AM


I have not said that mutations do not or cannot occur.

Er, no, you have, remember? When you said this?

quote:
I can conceive writing a computer program that copies itself and, each time it does, changes certain sections of the program on a random basis. Certain core areas of the program could be identified so that they could be prevented from being changed (or else the whole thing would quit or go haywire).

The reason we know that random mutation operates, and that all mutations are not simply pre-programmed randomness restricted to certain sequences, is that all sequences mutate. It's impossible to completely protect a given sequence from mutation.

I am asking how could random mutations be distinguished from on-purpose variations produced as a function of the code itself.

There's no way to distinguish them, because those are exactly the same thing. We find that some genetic locii mutate more frequently than others, due to their chemical structure (some nucleotide sequences are physically less resistant to mutation than others) or their position in the chromosome. This may even be a circumstance that can be selected for.

But unless you're proposing that cells actually determine the mutational outcome in response to need, what you're proposing is not at all different than a random mutation.

Consider a casino. The fact that you can only gamble at card tables, and not the middle of the men's room, doesn't make the games themselves any less random.

I believe that there are cell components that "correct" many "copying errors"...could that actually be a test similar to what I have stated in my programming analogy?

The way they correct them is by comparing sequences to their opposing side of the helix. They don't, for instance, predict the consequences of the mutation and then excise sequences that are deleterious. All genetic sequences are the same to the cellular repair mechanism, except insofar as they're complimentary to their opposite helix.

The only process that removes mutations because of their survival consequences is natural selection.

How can we distinguish between random mutations and on-purpose but randomly generated changes in the sequence due to some function or functions of the original sequence?

As I said, there is absolutely no difference between these situations. Both cases would be random mutation because the outcome of the mutation was not determined by need.

It's certainly the case that some organisms respond to environmental stress by "turning up" the mutation rate of their DNA. This is still random mutation.

This message has been edited by crashfrog, 01-23-2005 11:01 AM


This message is a reply to:
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