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Gene Silencing
The Wall Street Journal | August 6, 2002 | Antonio Regalado

Posted on 08/10/2002 5:08:09 PM PDT by gore3000

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To: gore3000
Interesting that you mention programming languages in the discussion of gene regulation. You sound like an anti-evolutionist insisting that the genome is a program and was thus intelligently designed. Surely you do not wish to assert that programs are written and modified at random do you?
(gore3000, vigorously waving his hand): OOH! OOH! He said "program"!
41 posted on 08/11/2002 3:30:19 PM PDT by jennyp
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To: jennyp
and then later a regulatory mechanism evolved

But that's the point. The regulatory mechanism seems to have been there all the while in plants and animals. Now we're just recognizing it and starting to understand how to manipulate it.

42 posted on 08/11/2002 3:37:57 PM PDT by Tribune7
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To: Stultis
How did the various species of horsey's all get different chromosome numbers,

Well they are still the same species. It seems that the number of paired chromosomes in horses varies quite wildly amongst thoroughbreds, but they can mate without problems. Don't know the reason for this but they are the same species though.

43 posted on 08/11/2002 7:40:28 PM PDT by gore3000
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To: jennyp
(gore3000, vigorously waving his hand): OOH! OOH! He said "program"!

Not just the writer of the article, but you yourself say it. The comparison is inevitable. In fact from your discussion with tribune7 you are speaking in programming terms. Have you ever heard of a new system inserted in the midst of a program at random? Have you ever heard of a new decision making branch created at random? Of course not.

You see, you describe in post 38 pretty well what has to happen , however you do not see that such could not happen randomly or without specific direction. You cannot just insert what is essentially new code in the middle of a program at random.

44 posted on 08/11/2002 7:52:06 PM PDT by gore3000
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To: gore3000
So whole chromosomes can split and join, but a single gene can't be duplicated and still function. Amazing.

BTW, there are a number of different species of Equids. Off the top of my head I believe there are, in addition to the common horse, two or three species of zebras, two or three of asses, and also several species of other wild horses.

45 posted on 08/11/2002 7:54:22 PM PDT by Stultis
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To: Stultis
So whole chromosomes can split and join, but a single gene can't be duplicated and still function. Amazing.

Yup, and they can still interbreed with no problem. Apparently the extra chromosomes are just duplicates of the basic set so they do not seem to have much influence except in giving a better chance of some of the traits of thoroughbreds being passed on to their progeny. It also should be noted that this is quite unique with horses.

46 posted on 08/11/2002 8:47:07 PM PDT by gore3000
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To: gore3000
You cannot just insert what is essentially new code in the middle of a program at random.

The procedural programming analogy only goes a little ways. The genetic/biological system is more like an event-driven object oriented system. You can plunk down whole libraries of new object classes into a program with no effect at all.

Plus, the way an object method gets invoked is completely different. In a computer program, you have to get the name of the method (or its starting address if we're talking machine code) exactly correct or else the compiler/runtime gives you an error & the whole thing stops. It's all or nothing with traditional programming languages.

If I were to simulate a genetic system, it'd be more like: the probability that an object's method gets invoked is proportional to how correctly it was spelled in the statement that called it. That's just for starters. A totally different programming paradigm.

I've never tried to write a GA program or even seen a genetic programming language, so for all I know they already have languages like that. If they do exist, I'm sure you could duplicate objects & methods and mutate them & have them sometimes end up doing something useful.

47 posted on 08/11/2002 9:00:51 PM PDT by jennyp
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To: gore3000
It shows the existence of double-stranded RNA, something not seen before.

Not to nitpick, but we've seen plenty of double-stranded RNA especially in viruses - have known about it for years. It's this "RNA-interference" that is new.

48 posted on 08/11/2002 9:07:53 PM PDT by realpatriot71
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To: The Great Satan
Indeed, conceptually it may be appropriate to think of RNAi as a particular type of innate immunity.

Bingo!

And now that science is better understanding this phenomenon, we may see many new vaccines, even for HIV.

49 posted on 08/11/2002 9:10:44 PM PDT by realpatriot71
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To: realpatriot71
And now that science is better understanding this phenomenon, we may see many new vaccines, even for HIV.

That is a big part of the importance of this discovery. However, just as important is its use as a tool for discovering just exactly how our bodies function. By selectively silencing genes scientists can get a better handle on how life works. This will certainly lead to many other great discoveries.

50 posted on 08/11/2002 10:35:40 PM PDT by gore3000
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To: realpatriot71
And now that science is better understanding this phenomenon, we may see many new vaccines, even for HIV.

In viruses, but not in the human organism, that I know of. In fact, the article seems to imply that they are regarded as intruders and not part of the organism: " The kind of molecules created by Dr. Fire - long, double stranded RNA molecules - were known to be toxic to animal cells. The big molecules triggered the cells' sophisticated defenses against viral invaders, throwing them into a panic mode and causing them to commit cellular suicide."

Do you know of any examples besides this of a normal production of double stranded RNA in organisms?

51 posted on 08/11/2002 10:43:45 PM PDT by gore3000
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To: jennyp
The procedural programming analogy only goes a little ways. The genetic/biological system is more like an event-driven object oriented system. You can plunk down whole libraries of new object classes into a program with no effect at all.

Plus, the way an object method gets invoked is completely different. In a computer program, you have to get the name of the method (or its starting address if we're talking machine code) exactly correct or else the compiler/runtime gives you an error & the whole thing stops. It's all or nothing with traditional programming languages.

If I were to simulate a genetic system, it'd be more like: the probability that an object's method gets invoked is proportional to how correctly it was spelled in the statement that called it. That's just for starters. A totally different programming paradigm.

Well, you have a problem there with chance mutations already don't you? Wrong spelling. To get correct spelling by chance seems an unreasonable assumption.

However, the big problem with your explanation is that all programs are in machine language. What you call object classes are just for ease of writing programs. When turned into executables, they are all machine language programs and cannot be changed by random insertions of code.

Also you need to realize that any program needs to differentiate between data and code, in the case of an organism between the gene data and the DNA code to make them work. It requires intelligent interpretation of the DNA 'bits' to accomplish this. More importantly though, what this shows ( the presence of both data and code) is that you cannot just change a gene, add a gene, to get new functioning, but you also have to simultaneously change the code. This is a bit much to expect from random mutations.

52 posted on 08/11/2002 11:03:47 PM PDT by gore3000
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To: jennyp
What happens to "information" in the quantum eraser experiment?
53 posted on 08/12/2002 7:07:56 AM PDT by AndrewC
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To: AndrewC
What happens to "information" in the quantum eraser experiment?

Amazingly, I have no idea what you're talking about.

54 posted on 08/12/2002 1:02:41 PM PDT by jennyp
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To: jennyp
Amazingly, I have no idea what you're talking about.

From Quantum mysteries

In fact, the team has carried out several tests of the stranger predictions of quantum theory, but the most dramatic is what they call the "quantum eraser". In this variation on the Young's slit theme, the experiment is first set up in the usual way, and run to produce interference. Quantum theory says that the reason why interference can occur, even if light is a stream of photons, is that there is no way to find out, even in principle, which photon went through which slit. The "indeterminacy" allows fringes to appear.

But then Chiao and his colleagues ran the same experiment with polarising filters in front of each of the two slits. Any photon going one way would become "labelled" with left-handed circular polarization, while any photon going through the other slit is labelled with right-handed circular polarization. In this version of the experiment, it is possible in principle to tell which slit any particular photon arriving at the second screen went through. Sure enough, the interference pattern vanishes -- even though nobody ever actually looks to see which photon went through which slit.

Now comes the new trick -- the eraser. A third polarising filter is placed between the two slits and the second screen, to scramble up (or erase) the information about which photon went through which hole. Now, once again, it is impossible to tell which path any particular photon arriving at the second screen took through the experiment. And, sure enough, the interference pattern reappears!

The strange thing is that interference depends on "single photons" going through both slits "at once", but undetected. So how does a single photon arriving at the first screen know how it ought to behave in order to match the presence or absence of the erasing filter on the other side of the slits?

All of these experiments were carried out using beams of individual photons, and there is no way in which the results can be explained by using classical physics. They lay bare the mysteriousness of quantum mechanics in all its glory, and in particular demonstrate its "non local" nature -- the way in which a photon starting out on its journey behaves in a different way for each experimental setup, as if it knew in advance what kind of experiment it was about to go through.

My point is that more "things" do not necessarily connote more "information". In the QM experiment the evidence of information is a direct pattern.

55 posted on 08/12/2002 3:03:15 PM PDT by AndrewC
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To: AndrewC
I'm so glad we don't live in a quantum size-scale!
56 posted on 08/12/2002 11:14:48 PM PDT by jennyp
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To: jennyp
I'm so glad we don't live in a quantum size-scale!

Are you certain of that?

57 posted on 08/13/2002 6:56:48 AM PDT by AndrewC
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