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


Message 76 of 98 (182710)
02-03-2005 12:25 AM
Reply to: Message 74 by pink sasquatch
02-02-2005 4:42 PM


Re: off-topic?
PS,

I'm sorry. Perhaps I have misunderstood you.

We know that novel, coding genetic sequences can arise by natural means.

I thought this comment was referring to the very origin of the genetic code itself (abiogenesis). If you are referring to abiogenesis, then I think it probably needs to be in a separate thread (not necessarily, just probably). If you're not referring to abiogenesis, then you'll need to help me understand what you're referring to. I can be dense sometimes.


This message is a reply to:
 Message 74 by pink sasquatch, posted 02-02-2005 4:42 PM pink sasquatch has responded

Replies to this message:
 Message 77 by NosyNed, posted 02-03-2005 2:56 AM TheLiteralist has not yet responded
 Message 78 by pink sasquatch, posted 02-03-2005 12:04 PM TheLiteralist has responded

  
NosyNed
Member
Posts: 8829
From: Canada
Joined: 04-04-2003
Member Rating: 4.0


Message 77 of 98 (182749)
02-03-2005 2:56 AM
Reply to: Message 76 by TheLiteralist
02-03-2005 12:25 AM


Translation
We know that novel, coding genetic sequences can arise by natural means.

Without checking back I will try to offer what might be the right translation of the above.

We understand natural mechanisms which can form new genetic sequences which are expressed as proteins. That is they are both new (not in the genome of the ancestors of the individual) and correctly formed sequences (new genes) that will be transcribed to proteins.

There are a number of mechanisms that can do this. Gene duplication and mutation being an obvious one.


This message is a reply to:
 Message 76 by TheLiteralist, posted 02-03-2005 12:25 AM TheLiteralist has not yet responded

  
pink sasquatch
Member (Idle past 4070 days)
Posts: 1567
Joined: 06-10-2004


Message 78 of 98 (182877)
02-03-2005 12:04 PM
Reply to: Message 76 by TheLiteralist
02-03-2005 12:25 AM


back-on-topic...
I thought this comment was referring to the very origin of the genetic code itself (abiogenesis).

No, it wasn't, though I see how you might have read it as such. (There are several abiogenesis threads in the forum that you should look through and 'resurrect' if you are interested - I'll keep an eye out since I find the topic interesting as well.)

I was speaking more at the gene-level - that is, we have evidence that a new gene sequence can arise by natural means. Which leads to my question - why invoke the supernatural in such a case?

I don't think the discussion has (yet) produced any evidence or tests to reveal "the mark of the designer" in DNA. If you think any such points have been made, why don't you give a quick summary/list if you think it will help keep the thread productive and on track?


This message is a reply to:
 Message 76 by TheLiteralist, posted 02-03-2005 12:25 AM TheLiteralist has responded

Replies to this message:
 Message 79 by TheLiteralist, posted 02-03-2005 9:21 PM pink sasquatch has responded

  
TheLiteralist
Inactive Member


Message 79 of 98 (182955)
02-03-2005 9:21 PM
Reply to: Message 78 by pink sasquatch
02-03-2005 12:04 PM


Re: back-on-topic...
PS,

I don't think the discussion has (yet) produced any evidence or tests to reveal "the mark of the designer" in DNA. If you think any such points have been made, why don't you give a quick summary/list if you think it will help keep the thread productive and on track?

Most of the thread has been devoted to helping me see that I was proposing a model whereby RANDOM MUTATIONS are the source of variation.

There IS a difference, though. I am saying that the random mutations are occurring because the code was designed to produce them.

One important point, though, is that once the Designer has implemented the code/organism system, the variations that result are, generally (unless the Designer specifically intervenes--but that is a different subject), of natural origin and not supernatural origin. (Does that addresses your question?)

There is one thing that comes to mind:

I have this idea that certain "core" traits are designed not to variate or to variate in a very limited manner while other traits are designed to variate quite a bit. I think this might explain why bacteria can variate very profusely and yet still be classified as, for example, an E. Coli.

I really am amazed that we can classify bacteria for any length of time given how much they variate.

There might be other things, but nothing comes to mind yet.

Now the mere existence of the RNA/DNA/translation/cell systems IS, to me, strong evidence of a Designer, but THAT is off-topic. I might ressurrect one of those abiogenesis threads (or start one of my own).


This message is a reply to:
 Message 78 by pink sasquatch, posted 02-03-2005 12:04 PM pink sasquatch has responded

Replies to this message:
 Message 80 by jar, posted 02-03-2005 10:33 PM TheLiteralist has not yet responded
 Message 81 by crashfrog, posted 02-03-2005 10:37 PM TheLiteralist has responded
 Message 82 by Quetzal, posted 02-03-2005 11:01 PM TheLiteralist has not yet responded
 Message 83 by pink sasquatch, posted 02-04-2005 2:16 PM TheLiteralist has not yet responded

  
jar
Member
Posts: 30934
From: Texas!!
Joined: 04-20-2004


Message 80 of 98 (182977)
02-03-2005 10:33 PM
Reply to: Message 79 by TheLiteralist
02-03-2005 9:21 PM


Re: back-on-topic...
There IS a difference, though. I am saying that the random mutations are occurring because the code was designed to produce them.

Why would the said designer then design in so many mutations that are either neutral, doing nothing, or harmfull, creating problems? Why does he design in simple copying errors


Aslan is not a Tame Lion
This message is a reply to:
 Message 79 by TheLiteralist, posted 02-03-2005 9:21 PM TheLiteralist has not yet responded

  
crashfrog
Inactive Member


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 responded

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

  
Quetzal
Member (Idle past 3919 days)
Posts: 3228
Joined: 01-09-2002


Message 82 of 98 (182982)
02-03-2005 11:01 PM
Reply to: Message 79 by TheLiteralist
02-03-2005 9:21 PM


Re: back-on-topic...
Hi, TheLit.

There IS a difference, though. I am saying that the random mutations are occurring because the code was designed to produce them.

In a manner of speaking, you're correct. There are areas of the genome that are known as mutational hotspots, or hypervariable regions. Although the mutations are random (as always), these regions are more likely statistically to have mutations occur. I highly recommend Lynn Caporale's quite accessible book, "Darwin in the Genome" for a very detailed discussion. The journal articles I mentioned in my last post show how such hypervariability can serve an adaptive function - in other words can be selected for by natural selection. It's more complicated than this, of course, but this is the short version.

I have this idea that certain "core" traits are designed not to variate or to variate in a very limited manner while other traits are designed to variate quite a bit. I think this might explain why bacteria can variate very profusely and yet still be classified as, for example, an E. Coli.

The obverse of the hypervariable coin are regions that are highly resistant to mutation - we call them "highly conserved". Most of these highly conserved regions are areas where change of any kind - even small changes - have nearly universally fatal effects either for the cell or for the organism itself. So here too you are mostly correct.

However, what you mention isn't really the main problem faced when classifying clonal organisms in general and bacteria in particular. Obviously, the biological species concept falls apart when you are dealing with organisms that not only don't have sex but can actually swap genes across kingdoms! Any mutation that occurs in one bacteria (assuming it is adaptive rather than fatal) will create an entire new clonal lineage - instant "species" if you will (although some bacterial lateral transfers would be the equivalent of giving a mouse functional wings in one generation). Selection operating on one of the new clonal lineages make create "gaps" between bundles of closely related but genetically different clones. Biologists thus use a "typological species concept" when classifying them, which basically classifies "strains" by degree of relatedness. So E. coli might be a nice name for a large bundle of clone lineages that share common typology, but the folks that work with them will qualify that nomenclature with a type name as well. The type may simply be a number, or it may be an alphanumeric string identifying a particular, well studied and carefully screened strain.

More info than you probably wanted, of course. :D

This message has been edited by Quetzal, 02-03-2005 23:03 AM


This message is a reply to:
 Message 79 by TheLiteralist, posted 02-03-2005 9:21 PM TheLiteralist has not yet responded

  
pink sasquatch
Member (Idle past 4070 days)
Posts: 1567
Joined: 06-10-2004


Message 83 of 98 (183109)
02-04-2005 2:16 PM
Reply to: Message 79 by TheLiteralist
02-03-2005 9:21 PM


designed mistakes
Others have already replied well to your points; my additional two cents:

I am saying that the random mutations are occurring because the code was designed to produce them.

I agree with Crashfrog, this seems to be a change from your previous concept that certain areas of the genome were designed to allow mutation, while others are resistant. And again, why is it necessary to invoke "design" for this system?

One important point, though, is that once the Designer has implemented the code/organism system, the variations that result are... of natural origin...

Yet again, I haven't seen any reason to invoke the supernatural in order to "allow" genetic mutation/variation. Mistakes/errors/chaos are a part of most natural processes - are these all the result of design as well?

I have this idea that certain "core" traits are designed not to variate or to variate in a very limited manner while other traits are designed to variate quite a bit.

As Quetzal mentioned, there are highly conserved regions that vary less than other sequences. However, there is an important distinction here - the genes underlying your "not variate" and "variate" traits are all subject to random mutation.

Both categories undergo mutation, it is simply that mutation in a highly conserved region is likely to result in death, sterility, or a severe reduction in fitness; so they are not maintained in the population. Thus, I don't think this at all fits your designed differential mutation rate concept. Does that make sense?

Now the mere existence of the RNA/DNA/translation/cell systems IS, to me, strong evidence of a Designer, but THAT is off-topic.

I don't know that it is so off-topic. You are spending much time in this thread trying to figure out the intent and results of design of the genome, without having provided any specific reasons for your assumption of design. In any case, if you will only present such reasons in another thread... I'll keep an eye out for it...


This message is a reply to:
 Message 79 by TheLiteralist, posted 02-03-2005 9:21 PM TheLiteralist has not yet responded

  
christian atheist
Inactive Member


Message 84 of 98 (183111)
02-04-2005 2:20 PM
Reply to: Message 27 by wj
01-23-2005 6:08 AM


Re: Broken Genes
I have a question on the vitamin c gene. If this gene is a non-functioning gene in humans, I assume they must've first found the functioning version of the gene in another animal. From that, how do the find the same gene in humans? Are there genetic markers on the gene that one can search for?

Finally, do we know what mutation in the gene causes it to not work?


This message is a reply to:
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Replies to this message:
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pink sasquatch
Member (Idle past 4070 days)
Posts: 1567
Joined: 06-10-2004


Message 85 of 98 (183113)
02-04-2005 2:32 PM
Reply to: Message 84 by christian atheist
02-04-2005 2:20 PM


Re: Broken Genes
From that, how do the find the same gene in humans?

I'm not sure how it was specifically done with the GLO gene, but generally the conserved sequence of the gene serves as a 'marker' to identify the same gene in another species using various molecular genetics techniques. Genes generally contain conserved regions that are necessary for basic function of the gene, and are thus less likely to differ between species, and so serve as a starting point for comparative studies. Hopefully that makes some sense...

Finally, do we know what mutation in the gene causes it to not work?

The four species I am aware of that lack a functional GLO gene are humans, chimps, a guinea pig, and a fruit bat. The mutations are known for all four. Humans and chimps have an identical mutation, while the guinea pig and fruit bat have distinct mutations.

It is this sort of pattern, combined with countless other similar genetic patterns, that suggests common ancestry of humans and chimps at the DNA level.


This message is a reply to:
 Message 84 by christian atheist, posted 02-04-2005 2:20 PM christian atheist has not yet responded

  
TheLiteralist
Inactive Member


Message 86 of 98 (183580)
02-06-2005 6:13 PM
Reply to: Message 81 by crashfrog
02-03-2005 10:37 PM


Me? A Programmer?
Hi CF,

No, I'm not a programmer. I'm a breakfast/biscuit cook at Hardee's...if you think you're disappointed, you should be me! :)

I have dabbled in programming only a bit.

TheLit writes:
There IS a difference, though. I am saying that the random mutations are occurring because the code was designed to produce them.

CF asks:
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.

Yes. I'm proposing that the code is designed to produce random mutations. A computer program can be designed to produce randomness. Click Here to see a program that does this (and to get an idea of the limited nature of my programming abilities--I whipped up this amazing programming feat in about 20 minutes).

Certain areas of the code are meant to produce randomness--i.e., the card's name that is displayed. Unfortunately, I am not able to make a code that produces randomness in the code itself; it can be done, just not by me. Certain areas the code always produces the same results (e.g., the words on the button). Some areas could "mutate" and the program would still kinda run right. For instance, if the button text got garbled to "Coick Horo to Pamk # C$rd", it'd still run right, but people might have trouble figuring out what to do with it (it wouldn't be as efficient). But if the code that is assigned to the button were to change at all, nothing would happen when you clicked on the button. And if the initial "{html}" tag (different brackets would be used, of course) got changed in any way, you couldn't link to it successfully.

Here is a quote from my OP:

How do we know that there is not some method within the genome that is supposed to generate some level of variation--i.e., it's not random mutations but rather variation achieved through randomness generated purposefully by the code? A limited experience in programming has taught me that in many programs it is often useful to have a random generator module.

So, yes...I believe that a genetic code designed to produce variations (random mutations) is what I've been proposing all along, whatever it may have sounded like I was proposing. I just really didn't want to call the variations produced this way "random mutations"--but, as you have helped me to realize, that's what they would be.

The concerns that this raises, I'll have to try to address later (if I can).

--TheLit

This message has been edited by TheLiteralist, 02-06-2005 18:14 AM


This message is a reply to:
 Message 81 by crashfrog, posted 02-03-2005 10:37 PM crashfrog has responded

Replies to this message:
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contracycle
Inactive Member


Message 87 of 98 (183637)
02-07-2005 5:17 AM


Thats a fair point, but: sexual reproduction, by combining two sets of gemes, already produces the kind of effect for whioch an random number generator might be required, I think.
  
Ooook!
Member (Idle past 3862 days)
Posts: 340
From: London, UK
Joined: 09-29-2003


Message 88 of 98 (183897)
02-08-2005 8:03 AM
Reply to: Message 53 by TheLiteralist
02-02-2005 2:35 PM


Hello again, TheLit.

Sorry (again) for the appalling delay in replying Ė I should have warned you how lazy I am :O

A couple of points:

Really, if the issue of intelligent design or evolution etc. could be laid to the side temporarily

Iím not entirely sure you can do this very successfully.† The mechanism you're proposing is† based on an Intelligent Designer after all ;).† But I appreciate that you donít want to get dragged into ĎID is not scienceí debate.† Iíll try not to stray too much.

Having said that:

I don't hold to the first-cell-with-all-the-info-for-everything model that Behe proposes. That is truly a bizarre proposal to me. I seem to recall reading his whole book thinking he was a creationists until I got to the end, and went "WHAT?!?

Now I know other people have expressed similar opinions to mine in the past, and that this has the potential to† go†OT pretty rapidly, but:

I think the reason he has proposed this model is that, as a biochemist he cannot deny the extremely good evidence for common ancestry, but still needs to propose a mechanism that allows the intervention of a Designer.† So thereís the choice between an implausible Uber-cell or have a simple genome in† which the random† mutations are about as targeted as a flamethrower.† Itís something that you need to†tackle.

Of course if you donít accept common ancestry then thatís yet another topic :D

In light of this comment, it may not be possible to even tell the difference between actuall copying errors and those induced on purpose for variation's sake.

The trouble with this is that all of the ways that mutation occurs are essentially copying errors: from point mutations to duplications and large scale rearrangements. Any differences in the rate of mutation can be explained by natural processes (as Crashfrog and PS have pointed out).

Also, don't confuse lack of mutation with conserving vital sequences by natural selection. There are sections of vital genes which are highly conserved between species, but the mutation rate may be just as high as elsewhwere in the genome. It's just that any organism which does have a mutation in those sections doesn't normally hang around for very long. Just a thought.

Hope this hasn't come too late, and is not too repetative. :)


This message is a reply to:
 Message 53 by TheLiteralist, posted 02-02-2005 2:35 PM TheLiteralist has not yet responded

    
crashfrog
Inactive Member


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:
 Message 86 by TheLiteralist, posted 02-06-2005 6:13 PM TheLiteralist has not yet responded

  
crashfrog
Inactive Member


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 responded

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

  
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