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


Message 57 of 98 (182610)
02-02-2005 3:06 PM
Reply to: Message 52 by pink sasquatch
02-02-2005 2:14 PM


Re: Non-random mutation can drive evolution... and disease.
Pink Sasquatch,
Tremendous!
I think this is better than my fuzzy "mechanism." 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? Do all or most traits that vary have this quality of highly repetitive sequences? Are there other mechanisms that work like this?
In the case of repetitive sequence mutation, we have to ask ourselves why an intelligent designer would put the same repeats into important disease suppressor genes as in regulatory elements that could drive evolution.
I understand this. I really do. As far as the Creator making things like cancer and such, the Creator that I follow (the God of the Bible) has made it clear that He has created both health and sickness and that since sin has entered the world death and suffering are the lot of humanity in general in this life. While I'm not enjoying living in a world of suffering, it would be different if the Bible made it sound like all was well with the world...then I might have a different reaction to your question.
Let us not forget that some things the Creator is not responsible for (particularly in "civilized" nations): the effects of junk food, enriched-white bread, vaccines, soda pop, pollution, sewage waste brought about by the adoption of indoor plumbing, nuclear waste, etc.
A tremendous post PS, thanks.
--TL

This message is a reply to:
 Message 52 by pink sasquatch, posted 02-02-2005 2:14 PM pink sasquatch has replied

Replies to this message:
 Message 58 by crashfrog, posted 02-02-2005 3:16 PM TheLiteralist has replied
 Message 62 by pink sasquatch, posted 02-02-2005 3:44 PM TheLiteralist has replied

  
TheLiteralist
Inactive Member


Message 59 of 98 (182614)
02-02-2005 3:20 PM
Reply to: Message 55 by crashfrog
02-02-2005 2:59 PM


gravity analogy
CF,
It may not be possible to tell the difference between gravity and another, previously unknown form of energy that I propose is what holds me, specifically (and not you), down onto my seat; but if it's not, what's the difference?
I guess what I'm wondering would be like seeing some people down and some people floating. Some might be either way on any given day. But some people would always be down. In this case, the theory of gravity would need some tweaking.
So, are there any segments, in any particular organism, that are known not to mutate or that mutate only with extreme rarity, and when they do the organism is debiltated in some way? That would be an important question for this discussion I think.
PS has already indicated that certain segments are much more likely to mutate, which seems to be sort of what I had in mind.

This message is a reply to:
 Message 55 by crashfrog, posted 02-02-2005 2:59 PM crashfrog has not replied

  
TheLiteralist
Inactive Member


Message 60 of 98 (182617)
02-02-2005 3:30 PM
Reply to: Message 56 by crashfrog
02-02-2005 3:05 PM


MUTATIONS
CF,
When I said...
Plus I see here the word "mutations" being used even when the system is doing it on purpose, so to speak.
I meant that my problem with the term "mutations" has been unwarranted. It just means "change," which my model proposes.
My model propose random changes in the DNA sequence. So, it is proposing random mutations--though I've been hard-headed about it.
The difference as far as I can see then is that I am proposing that most changes are due to the construction of the code, which is, as PS posted, also recognized already.
I am then curious about two things: (1) are certain segments in any given genome strangely much less likely to have a random mutation and (2) are there any other code-cause mutation mechanisms such as posted by PS?
Along with the first question, I am also curious if it is known, about any particular genomes, that if these segments that are far less likely to mutate (should they exist) also just happen to be the ones that should a mutation occur have deleterious effects on the resultant organism?
--TL

This message is a reply to:
 Message 56 by crashfrog, posted 02-02-2005 3:05 PM crashfrog has replied

Replies to this message:
 Message 66 by crashfrog, posted 02-02-2005 3:59 PM TheLiteralist has replied

  
TheLiteralist
Inactive Member


Message 61 of 98 (182618)
02-02-2005 3:34 PM
Reply to: Message 58 by crashfrog
02-02-2005 3:16 PM


Nice Chart
CF,
Thanks for posting the chart. I wonder WHY the slippage occurs, though.
--TL

This message is a reply to:
 Message 58 by crashfrog, posted 02-02-2005 3:16 PM crashfrog has replied

Replies to this message:
 Message 63 by crashfrog, posted 02-02-2005 3:48 PM TheLiteralist has replied

  
TheLiteralist
Inactive Member


Message 64 of 98 (182625)
02-02-2005 3:57 PM
Reply to: Message 62 by pink sasquatch
02-02-2005 3:44 PM


Sequences
Well, to me, the mere existence of genetic sequences that get translated is the indication of intelligence. It is sequential information that codes for various processes...including it's own duplication.

This message is a reply to:
 Message 62 by pink sasquatch, posted 02-02-2005 3:44 PM pink sasquatch has replied

Replies to this message:
 Message 68 by pink sasquatch, posted 02-02-2005 4:11 PM TheLiteralist has replied

  
TheLiteralist
Inactive Member


Message 65 of 98 (182629)
02-02-2005 3:59 PM
Reply to: Message 63 by crashfrog
02-02-2005 3:48 PM


Slipping
CF,
I gotcha part way--but not all the way I'm afraid. That, in my mind, explains how it can sucessfully slip, but not why it slips in the first place.
I mean it might explain that, too, but I'm not getting it, yet.
--TL

This message is a reply to:
 Message 63 by crashfrog, posted 02-02-2005 3:48 PM crashfrog has replied

Replies to this message:
 Message 69 by crashfrog, posted 02-02-2005 4:14 PM TheLiteralist has replied

  
TheLiteralist
Inactive Member


Message 67 of 98 (182632)
02-02-2005 4:08 PM
Reply to: Message 66 by crashfrog
02-02-2005 3:59 PM


Re: MUTATIONS
CF,
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?
Just curious,
-TL

This message is a reply to:
 Message 66 by crashfrog, posted 02-02-2005 3:59 PM crashfrog has replied

Replies to this message:
 Message 71 by crashfrog, posted 02-02-2005 4:18 PM TheLiteralist has not replied

  
TheLiteralist
Inactive Member


Message 70 of 98 (182636)
02-02-2005 4:17 PM
Reply to: Message 68 by pink sasquatch
02-02-2005 4:11 PM


Re: Sequences (elves?)
PS,
We know that novel, coding genetic sequences can arise by natural means.
I think this is a different topic, but one I'm interested in. Would you like for me to try to get a new thread going about this?
Or do you think we can make short work of it? I really hate off-topic pile-on...now that it's happened to one of my threads I'm starting to understand AdminNosy's harshness about topic purity a bit more.
--TL

This message is a reply to:
 Message 68 by pink sasquatch, posted 02-02-2005 4:11 PM pink sasquatch has replied

Replies to this message:
 Message 74 by pink sasquatch, posted 02-02-2005 4:42 PM TheLiteralist has replied

  
TheLiteralist
Inactive Member


Message 72 of 98 (182638)
02-02-2005 4:22 PM
Reply to: Message 69 by crashfrog
02-02-2005 4:14 PM


Re: Slipping
CF,
Thanks for the link.
We know that novel, coding genetic sequences can arise by natural means.
Hah! I bet it does...probably not so bad as mine would, though, I'm sure.

This message is a reply to:
 Message 69 by crashfrog, posted 02-02-2005 4:14 PM crashfrog has replied

Replies to this message:
 Message 73 by crashfrog, posted 02-02-2005 4:30 PM TheLiteralist has replied

  
TheLiteralist
Inactive Member


Message 75 of 98 (182707)
02-02-2005 11:55 PM
Reply to: Message 73 by crashfrog
02-02-2005 4:30 PM


Re: Cut-n-paste error
CF,
Looks like you had a little "copying error" yourself. I know what you were replying to, though.
ROFL! That is hilarious...I didn't even realize this till hours later!
Clear as mud, I'm sure. My head mostly spins when my wife explains what she's doing in the lab.
That is what was supposed to be in the quote box...if that makes my previous post to you any clearer...
cut-n-paste error, indeed!
--TL

This message is a reply to:
 Message 73 by crashfrog, posted 02-02-2005 4:30 PM crashfrog has not replied

  
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 replied

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

  
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 replied

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

  
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:
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Replies to this message:
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