It's just a theory - Page 5

TheSpacePope · 10-23-2005, 05:43 PM

Quote:

Not in terms of DNA sequence

WELL, I am not talking about sequence, I am talking about makeup, ATGCU and the like, 2 polymeraise strips.
90 % the same,
as everything
it is in everything.
or like I said before

Quote:

Originally Posted by myself

just because the basics of DNA are all the same, Adenine, Cytosine, Guanine, and thymine, and uracil. I mean mostly your dealing with the same polynucleotides from bacteria up, however the genomes are what are important there and, The arangement is what is different

so yea

ZAKtheGeek · 10-23-2005, 06:24 PM

But the arrangement is what gives it meaning. Who cares how much of each nucleotide there is? Arrangement is everything when it comes to large molecules like that. I'd love to see how an organism would survive if all the amino acids in its proteins were the same, but in scrambled order...

Skyshot · 10-23-2005, 10:03 PM

Quote:

Originally Posted by krylo

That would be a pretty decent counter-point if not for the fact that most scientists up to the VERY contemporary were religious. They weren't atheists. Darwin himself wasn't an athiest.

Groan. This, kids, is why you don't base discussion points off assumptions. It's like using a card house for the first floor of a skyscraper. I should've remembered Darwin at least started off Christian, even if I didn't have the full story on how that worked out.

Quote:

In fact, I call current athiests illogical for various reasons...

I can respect that, and I'll point out not all theists/deists/non-atheists are particularly logical either. I've seen people from all sides make idiots of themselves. It's happened on these boards; it's happened on other boards; I've seen people in offline life do it. Smart, civil people turned belligerent. One of my goals in this thread is to show certain people creationists aren't all close-minded foaming-at-the-mouth not-gonna-listen-to-arguments what-have-you-for-nouns. At least they can accept I'm being reasonable with the facts I have at hand, even if they don't think my logic ultimately works out. I think I'm doing a decent job so far. (It's sort of one of the reasons I created that thread in General; some creationists make the same assumptions about non-creationists. It's generally a mass case of suppository cranial positioning.)

Dasanudas · 10-24-2005, 01:06 PM

Just briefly, the beliefs of a person becoming a cause for discrediting empirical evidence is a huge indication of bigotry. I will agree that there have been negative reviews on the books I mentioned, there have also been very good reviews. I suggest all with an open mind (as I have seen that all participating in these posts are) check out both.

Now, here's a nifty little blurb from Professor Werner Arber - Nobel Laureate and Emeritus Professor of molecular biology at the University of Basel. This is one small quote from an interview, so feel free to ask for the whole thing in an email, but I don't want to take up too much space with it.

"WA: Well, there are indeed philosophical aspects. I appreciate that you see this while many people don't. Actually, on the basis of these and many other properties of microorganisms, I have formulated, in a crude form, a theory of molecular evolution. This theory postulates that populations of living beings occasioanlly produce genetic variants by using three qualitatively different strategies. One is the gene acquisition strategy which we have already discussed. The second is a reshuffling of DNA segments within the genome. This process is normally mediated by specific recombination enzymes. The third strategy is to generate genetic variants which bring about small local changes in the DNA sequences, such as the substitution of a nucleotide or the deletion or insertion of one or a few nucleotides. These latter changes can occur upon DNA replication because of the limted stability of nucleotides. In literature, such local changes are often described as errors or mistakes. However, I consider this as an unfair interpretation of the observations. From my point of view, such local changes in DNA sequences are a direct consequence of the slight structural and chemical instability of the nucleotides.

TDS (Dr. T. D. Singh, Phd in physical organic chemistry): So, you are saying that, contrary to the opinion of other scientists, mutation is not a mistake or an error in replication; it is a natural process. This is a significant observation.

WA: Yes, indeed. And nature uses that property in order to get some flexibility in the forms of life. Of course, without genetic variation you could not have any evolution, nor biodiversity. Interestingly, in all the three natural strategies of generation of genetic variations, the products of specific genes are involved. We call them evolution genes. Their products act as enzymes that mediate the reactions. Some of the enzymes directly act as generators of gentic variations, while others rather modulate the frequency of genetic variation. Note that the genetic variations of evolutionary relevance must be both non-reproducible from case to case and are relatively pure. The latter condition serves to insure a certain genetic stability to the species of organisms.

Let us come back to the biological function of restriction-modification systems in bacteria. As we have already discussed, the restriction enzymes cut foreign DNA into fragments when it penetrates into a bacterial cell. Occasionaly, a DNA fragment escapes further degradation and finds a way to incorporate by recombination somewhere into the bacterial genome. Hence, restriction enzymes carry out both properties typical for evolution genes: they seriously reduce the probability of success in horizontal gene transfer and also provide the opportunity for gene aquisition in small steps. In taking the activites of all evolution genes together, we can realize that nature has succeeded in providing means for a steady evolution of life. Evolution does not occur on the basis of errors, accidents or the action of selfish gentic elements. Rather, the evolution genes must have been fine-tunes for their functions to provide and to replenish a wide diversity of life forms capable to cope with the very different conditions of life found on our planet. "

(emphasis is my own) Okay, so it isn't that small, but the interview takes up a few pages, so it's smallER

ZAKtheGeek · 10-24-2005, 03:17 PM

That seems to imply that cells can consciously decide that their existance can improve somehow, and as a result, will modify their DNA (perhaps in a random way?) in order to attempt to produce proteins better fitted to the current situation.

The concept of conscious decisions on a cellular level seems pretty far-fetched. Am I misunderstanding, or do some pretty strange things have to be true in order for that to make any sense?

Azisien · 10-24-2005, 03:23 PM

I think you're misunderstanding. I don't believe there is any evidence at all of 'consciousness' on a cellular level, or even many levels above that. It's all about selection pressures. Back to Darwin, sort of.

Dasanudas · 10-24-2005, 04:38 PM

I simply wanted to put this up to show another researcher's point of view on mutation. It means that the evidence is pointing Professor Abner in the direction that mutations are not mistakes, but rather supposed to happen in the natural event of things.

Now, putting my own spin on this (i.e. - not backed up by anything and probably false, but fun to say so people having something to respond to), evolution is not simply cause and effect of changing environments, but programmed into the different bodies that house life. Of course, that programming may simpl be a fail-safe device in the event of changing environments, so that might not lead anywhere either.

ZAKtheGeek · 10-24-2005, 04:50 PM

Quote:

I think you're misunderstanding. I don't believe there is any evidence at all of 'consciousness' on a cellular level, or even many levels above that. It's all about selection pressures. Back to Darwin, sort of.

The fact that there's no evidence is my point exactly. The exact wording which confuses me:

Quote:

This theory postulates that populations of living beings occasioanlly produce genetic variants by using three qualitatively different strategies.

In the context of mutations not being mistakes, the use of the word "produce" seems to imply that it is not a passive occurrence but instead an active process initiated by the cell for some reason, implying that it, in some way, "realizes" that it needs to help itself somehow.

If it's not random (in other words, a "mistake"), and it's not consciously initiated, then why and when exactly would these processes occur? I couldn't think of anything so I suppose I went with the option of conscious decisions. Which, of course, was problematic in many ways.

Azisien · 10-24-2005, 05:19 PM

Problematic indeed. Just in case anyone could become guilty of affirming the consequent, I should point this out now that Zak brought it up. A random change can occur and it could be labelled as a mistake. For instance, radiation breaking the hydrogen bonds holding nucleotides together and deleting/inserting/swapping around. It would be wrong to then say: therefore, all mistakes within the DNA must be random.

DNA replication is NOT random, it is a triggered event. The enzymes involved in the process are not random either. To address the bad choice of wording, "consciousness," I believe we would have to make some massive reforms to the official definition of the word for it to be valid here. Instead of launching a rather lengthy rant about consciousness on a celluar level, I'll drop that tangent off here.

All functions within the cell are chemically triggered, whether it's by other functions within the cell or by environment triggers. While I have absolutely no difficulty believing in genes that code for proteins that boast controlled variation on a genetic level, I do have a problem with:

"EvoGene 1 to EvoGene 2 do you read, over?"
"EvoGene 2, I read you, over."
"LET'S FUCK UP OUR GENOME TODAY LOL!!!!1111"
"K!!!!111"

Nucleotides are relatively unstable molecules, and they wouldn't hold together at all if it wasn't for countless (more we can count right now, anyway) functional groups and proteins binding them. I urge you not to confuse some kind of controlled variability process with gamma radiation blasting away at a DNA molecule. 99.999999999999999999% or more of all the little mutations that occur to our DNA are mistakes. I may sound like I'm contradicting Mr. Degree from above, but if a cell underwent even one division without the tremendous proofreading it usually performs, well, it probably couldn't divide by that point anyway, and it would be dead.

ZAKtheGeek · 10-24-2005, 05:39 PM

It would be difficult to have a chemical messenger to signal, "Change now please, we need help. Kthxbai." This is because it's hard to define, without some sort of conscious process, at what point exactly it becomes necessary for a variation to occur. It doesn't even have to be necessary, by evolution, really, just helpful. I mean, if a cell can make ATP, it's happy. It could make it faster, maybe, but what would spontaneously trigger a mesenger to tell it to change its DNA a bit in hopes of a faster production method? If there's no problem, there's nothing to stimulate a messenger; if it ain't broke, don't fix it.

I assume you are agreeing with me in the above post, based on this.

10-23-2005, 06:24 PM	#42
ZAKtheGeek Worth every yenny Join Date: Jul 2005 Location: not my mind that's for sure! Posts: 1,299	But the arrangement is what gives it meaning. Who cares how much of each nucleotide there is? Arrangement is everything when it comes to large molecules like that. I'd love to see how an organism would survive if all the amino acids in its proteins were the same, but in scrambled order... __________________ Pyro Icon - It needs your love. I haven't looked at it in months.

10-24-2005, 01:06 PM	#44
Dasanudas Bhaktisiddhanta = Lion Guru! Join Date: Oct 2005 Location: the spiritual embassy Posts: 365	another wrench in the gears Just briefly, the beliefs of a person becoming a cause for discrediting empirical evidence is a huge indication of bigotry. I will agree that there have been negative reviews on the books I mentioned, there have also been very good reviews. I suggest all with an open mind (as I have seen that all participating in these posts are) check out both. Now, here's a nifty little blurb from Professor Werner Arber - Nobel Laureate and Emeritus Professor of molecular biology at the University of Basel. This is one small quote from an interview, so feel free to ask for the whole thing in an email, but I don't want to take up too much space with it. "WA: Well, there are indeed philosophical aspects. I appreciate that you see this while many people don't. Actually, on the basis of these and many other properties of microorganisms, I have formulated, in a crude form, a theory of molecular evolution. This theory postulates that populations of living beings occasioanlly produce genetic variants by using three qualitatively different strategies. One is the gene acquisition strategy which we have already discussed. The second is a reshuffling of DNA segments within the genome. This process is normally mediated by specific recombination enzymes. The third strategy is to generate genetic variants which bring about small local changes in the DNA sequences, such as the substitution of a nucleotide or the deletion or insertion of one or a few nucleotides. These latter changes can occur upon DNA replication because of the limted stability of nucleotides. In literature, such local changes are often described as errors or mistakes. However, I consider this as an unfair interpretation of the observations. From my point of view, such local changes in DNA sequences are a direct consequence of the slight structural and chemical instability of the nucleotides. TDS (Dr. T. D. Singh, Phd in physical organic chemistry): So, you are saying that, contrary to the opinion of other scientists, mutation is not a mistake or an error in replication; it is a natural process. This is a significant observation. WA: Yes, indeed. And nature uses that property in order to get some flexibility in the forms of life. Of course, without genetic variation you could not have any evolution, nor biodiversity. Interestingly, in all the three natural strategies of generation of genetic variations, the products of specific genes are involved. We call them evolution genes. Their products act as enzymes that mediate the reactions. Some of the enzymes directly act as generators of gentic variations, while others rather modulate the frequency of genetic variation. Note that the genetic variations of evolutionary relevance must be both non-reproducible from case to case and are relatively pure. The latter condition serves to insure a certain genetic stability to the species of organisms. Let us come back to the biological function of restriction-modification systems in bacteria. As we have already discussed, the restriction enzymes cut foreign DNA into fragments when it penetrates into a bacterial cell. Occasionaly, a DNA fragment escapes further degradation and finds a way to incorporate by recombination somewhere into the bacterial genome. Hence, restriction enzymes carry out both properties typical for evolution genes: they seriously reduce the probability of success in horizontal gene transfer and also provide the opportunity for gene aquisition in small steps. In taking the activites of all evolution genes together, we can realize that nature has succeeded in providing means for a steady evolution of life. Evolution does not occur on the basis of errors, accidents or the action of selfish gentic elements. Rather, the evolution genes must have been fine-tunes for their functions to provide and to replenish a wide diversity of life forms capable to cope with the very different conditions of life found on our planet. " (emphasis is my own) Okay, so it isn't that small, but the interview takes up a few pages, so it's smallER __________________ People are so much apt to indulge in transitory speculations even when they are to educate themselves on a situation beyond their empiric area or experiencing jurisdiction...This impulse moves them to fix the position of the immanent to an indeterminate impersonal entity, no clue of which could be discerned by moving earth and heaven through their organic senses. -Srila Bhaktisiddhanta Thakur Hare Krishna Hare Krishna Krishna Krishna Hare Hare Hare Rama Hare Rama Rama Rama Hare Hare

10-24-2005, 03:17 PM	#45
ZAKtheGeek Worth every yenny Join Date: Jul 2005 Location: not my mind that's for sure! Posts: 1,299	That seems to imply that cells can consciously decide that their existance can improve somehow, and as a result, will modify their DNA (perhaps in a random way?) in order to attempt to produce proteins better fitted to the current situation. The concept of conscious decisions on a cellular level seems pretty far-fetched. Am I misunderstanding, or do some pretty strange things have to be true in order for that to make any sense? __________________ Pyro Icon - It needs your love. I haven't looked at it in months.

10-24-2005, 04:38 PM	#47
Dasanudas Bhaktisiddhanta = Lion Guru! Join Date: Oct 2005 Location: the spiritual embassy Posts: 365	speculation aside I simply wanted to put this up to show another researcher's point of view on mutation. It means that the evidence is pointing Professor Abner in the direction that mutations are not mistakes, but rather supposed to happen in the natural event of things. Now, putting my own spin on this (i.e. - not backed up by anything and probably false, but fun to say so people having something to respond to), evolution is not simply cause and effect of changing environments, but programmed into the different bodies that house life. Of course, that programming may simpl be a fail-safe device in the event of changing environments, so that might not lead anywhere either. __________________ People are so much apt to indulge in transitory speculations even when they are to educate themselves on a situation beyond their empiric area or experiencing jurisdiction...This impulse moves them to fix the position of the immanent to an indeterminate impersonal entity, no clue of which could be discerned by moving earth and heaven through their organic senses. -Srila Bhaktisiddhanta Thakur Hare Krishna Hare Krishna Krishna Krishna Hare Hare Hare Rama Hare Rama Rama Rama Hare Hare

10-24-2005, 05:39 PM	#50
ZAKtheGeek Worth every yenny Join Date: Jul 2005 Location: not my mind that's for sure! Posts: 1,299	It would be difficult to have a chemical messenger to signal, "Change now please, we need help. Kthxbai." This is because it's hard to define, without some sort of conscious process, at what point exactly it becomes necessary for a variation to occur. It doesn't even have to be necessary, by evolution, really, just helpful. I mean, if a cell can make ATP, it's happy. It could make it faster, maybe, but what would spontaneously trigger a mesenger to tell it to change its DNA a bit in hopes of a faster production method? If there's no problem, there's nothing to stimulate a messenger; if it ain't broke, don't fix it. I assume you are agreeing with me in the above post, based on this. __________________ Pyro Icon - It needs your love. I haven't looked at it in months.

10-24-2005, 03:23 PM	#46
Azisien wat Join Date: Jan 2005 Posts: 7,177	I think you're misunderstanding. I don't believe there is any evidence at all of 'consciousness' on a cellular level, or even many levels above that. It's all about selection pressures. Back to Darwin, sort of.

10-24-2005, 05:19 PM	#49
Azisien wat Join Date: Jan 2005 Posts: 7,177	Problematic indeed. Just in case anyone could become guilty of affirming the consequent, I should point this out now that Zak brought it up. A random change can occur and it could be labelled as a mistake. For instance, radiation breaking the hydrogen bonds holding nucleotides together and deleting/inserting/swapping around. It would be wrong to then say: therefore, all mistakes within the DNA must be random. DNA replication is NOT random, it is a triggered event. The enzymes involved in the process are not random either. To address the bad choice of wording, "consciousness," I believe we would have to make some massive reforms to the official definition of the word for it to be valid here. Instead of launching a rather lengthy rant about consciousness on a celluar level, I'll drop that tangent off here. All functions within the cell are chemically triggered, whether it's by other functions within the cell or by environment triggers. While I have absolutely no difficulty believing in genes that code for proteins that boast controlled variation on a genetic level, I do have a problem with: "EvoGene 1 to EvoGene 2 do you read, over?" "EvoGene 2, I read you, over." "LET'S FUCK UP OUR GENOME TODAY LOL!!!!1111" "K!!!!111" Nucleotides are relatively unstable molecules, and they wouldn't hold together at all if it wasn't for countless (more we can count right now, anyway) functional groups and proteins binding them. I urge you not to confuse some kind of controlled variability process with gamma radiation blasting away at a DNA molecule. 99.999999999999999999% or more of all the little mutations that occur to our DNA are mistakes. I may sound like I'm contradicting Mr. Degree from above, but if a cell underwent even one division without the tremendous proofreading it usually performs, well, it probably couldn't divide by that point anyway, and it would be dead.