Posted on 02/21/2005 11:58:57 AM PST by Michael_Michaelangelo
WEST LAFAYETTE, Ind. – The crystallized form of a molecular machine that can cut and paste genetic material is revealing possible new paths for treating diseases such as some forms of cancer and opportunistic infections that plague HIV patients.
Purdue University researchers froze one of these molecular machines, which are chemical complexes known as a Group I intron, at mid-point in its work cycle. When frozen, crystallized introns reveal their structure and the sites at which they bind with various molecules to cause biochemical reactions. Scientists can use this knowledge to manipulate the intron to splice out malfunctioning genes, said Barbara Golden, associate professor of biochemistry. Normal genes then can take over without actually changing the genetic code.
The results of the Purdue study are published in the January issue of the journal Nature Structural and Molecular Biology.
"In terms of human health, Group I introns are interesting because they cause their own removal and also splice the ends of the surrounding RNA together, forming a functional gene," Golden said. "We can design introns and re-engineer them so they will do this to RNA in which we're interested."
Once thought of as genetic junk, introns are bits of DNA that can activate their own removal from RNA, which translates DNA's directions for gene behavior. Introns then splice the RNA back together. Scientists are just learning whether many DNA sequences previously believed to have no function actually may play specialized roles in cell behavior.
(Excerpt) Read more at news.uns.purdue.edu ...
Since "Darwinism" is 145 years old and molecular biology is only 50 years old, I would have to guess that "that certain theory" is some subset of molecular biology.
Whatever happens in the genome and for whatever reason, an organism or phenotype is produced, and that phenotype will be subject of selection.
You seem to be advocating a theory that there is another layer of life within the genome, with selective rules of its own. That would be interesting, but the genome still needs the whole organism to reproduce.
You toss out hints of your beliefs without stating them. How would you describe what you see going on? Are you suggesting saltation, or suggesting that the genome changes itself in anticipation of need?
I have noticed over the years that AC never says what HE really believes. He is very good at picking up on misstatements by Freepers and loose wording by science writers, but he never says exactly what he thinks junk DNA is doing.
I can only assume that this would expose his hypothesis to testing.
What would you expect? Creationists are, by definition, that residue of the population which which elects to know nothing about biology.
Wow, I may have to have that made into a bumper sticker.
Ignorance Is My Strength.
Nice links.
Now I'm bogged down reading again. ;)
In your post, you kept saying "you" as if I wrote the numbers (the numbers were merely a prop for a joke, not an argument I was making).
Thanks for your post. Aside from the usual vitriol it had some interesting information.
If you're that obsessed with staying on "the topic", then maybe you should have stuck to it yourself. Your post #16 had nothing to do with it -- so after *you* had already "rambled" and diverged from "the topic", I replied to the specific post you made.
Was this something you couldn't have figured out yourself?
In your post, you kept saying "you" as if I wrote the numbers (the numbers were merely a prop for a joke, not an argument I was making).
If you post bogus creationist nonsense, which insults biologists in a straw-man manner, you get to take responsibility for its contents, since you're the one spreading it here. And yes, even if (or especially if) you think it's "funny" to do so. Misinformation is misinformation. No one twisted your arm.
Thanks for your post. Aside from the usual vitriol it had some interesting information.
You're welcome.
Dang!
I thought he was reinforcing TRUE bigotry!
(Besides; you guys had it pulled BEFORE I ever got to read it.)
Oh...
So YOUR side can 'joke', but ours can't.
Ok.
Not what I said, but feel free to make up anything you want to.
Now, certainly, you must realize that it probably never was "junk" as you have previously argued. That argument , that it was "junk" had a reason, and that reason was in support of a certain theory. That it is not "junk" is, therefore, in contradiction to that certain theory.(that is, if the theory is to be credibly falsifiable as it is constantly alleged)When did I ever say it had to be junk? Here's the exchange you & I had yesterday:
[JP-19] After all these years I still don't know what the evolutionary argument for the existence of junk DNA was supposed to have been. [I then remind you of my hypothesis for why introns would be advantageous to the evolution of complexity][AC-20] Really, now? It seems to me the argument was that, necessarily, "junk" was a basic component of a "random" process. In fact, most of DNA should be a complete wasteland of unused and "decaying" parts.
[JP-23] But junk DNA would be analogous to an unused organ. Since there's some nonzero cost to keeping & reproducing an unused DNA sequence, any deletion of a truly junk sequence should be slightly favored over time. [Unless the cost is negligible]...
This was my speculation for why we would have so much noncoding DNA when simpler organisms (bacteria) have none. This was before you provided the article that actually presented a bit of the history of mainstream thought on junk DNA, which showed that people on all sides of the issue (regarding introns at least) were using evolution as their starting point. From what I could understand, it looked like each hypothesis implied things we should see if their hypothesis was true. IOW, they all looked quite falsifiable to me.
BTW, here's a study that would be interesting to see the full results for. I don't know what exactly they're calling "junk DNA" - whether they include introns or just LINEs & SINEs, etc. But it's yet again a falsification test for one hypothesis over another:
Proc R Soc Lond B Biol Sci. 1992 Aug 22;249(1325):119-24.This study raises the same issue of the cost of carrying the noncoding DNA as I did. So they show why junk DNA could accumulate in the genome in spite of normal evolutionary pressures toward efficiency. Couple this with Ichneumon's cite of the study where they actually removed junk DNA from the mice and they couldn't tell them apart, and you have a compelling case for them truly being junk.Variation across species in the size of the nuclear genome supports the junk-DNA explanation for the C-value paradox.
Pagel M, Johnstone RA.
Harvard University, Cambridge, Massachusetts 02138.
The amount of DNA in the nuclear genome (the DNA C-value) of eukaryotes varies at least 80,000-fold across species, and yet bears little or no relation to organismic complexity or to the number of protein-coding genes. This phenomenon is known as the C-value paradox. One explanation for the C-value paradox attributes the size of the nuclear genome to 'junk' (typically non-coding) genetic elements that accumulate until the costs to the organism of replicating excess DNA select against it. Across species, organisms that develop at a slower rate should tolerate more junk DNA. Alternatively, junk DNA may function as a nucleo-skeleton to maintain the volume of the nucleus at a size proportional to the volume of the cytoplasm in the cell. Across species, the DNA C-value is predicted to vary with the nuclear and cytoplasmic volumes of cells. Previous studies have not been able to distinguish between the skeletal-DNA and junk-DNA explanations for the C-value paradox. We report a study of DNA content in 24 salamander species which does. The size of the nuclear genome is correlated with developmental rate even after the effects of nuclear and cytoplasmic volume have been removed. However, genome size is not correlated with cytoplasmic volume after controlling for developmental rate. These results support the view that junk DNA accumulates in the nuclear genome until the costs of replicating it become too great, rather than that it functions as a nucleo-skeleton.
Now, the cost of introns must be higher than simple psuedogenes & LINEs & SINEs, since introns are processed whenever a gene is transcribed - there's the whole spliceosome that needs to be in place to help excise them from the RNAs. So the cost of having introns should be higher than for the other noncoding DNA, so it would be more likely that they'd get selected out of the genome. Since we have so many introns in spite of this, that would argue for introns having some positive role to play that the other noncoding regions wouldn't have.
So far all I see are lots of good, falsifiable hypotheses getting generated for why introns exist, all using the truth of evolution as a starting point. What's not to like? And where are all the falsifiable creationism-inspired hypotheses & studies showing why introns exist?
The really good question is, who is doing research on the possible function of non-coding DNA, creationists or mainstreamers? Is it really a crisis if you can't explain everything today?
Evolution chugged along with useful findings for decades before genetics reached a point where it could be useful.
Now if someone finds an encrypted text of Genesis in one of thos conserved regions...
;-)
Yes, even though some choose to name-call and belittle. Now as you can see Dr. Shapiro stated long ago what this thread discusses. And despite what jennyp is now saying, in 2001 she was saying something quite different.
The deletions in the mouse genome when announced brought gasps from biologists, not because it was something expected, but something quite different than expected.
All of these findings are significant, not because they are run of the mill, but because they are different than what the expectation was.
Ouch!
So your rebuttal is based upon a 13-year old finding?
In any case what is the explanation for the conservation of "junk"?(the reason for the gasps)
What is your explanation? Why do you find it important, other than that it was unexpected?
Dark matter and energy were unexpected. Physics is in ruins.
This study raises the same issue of the cost of carrying the noncoding DNA as I did. So they show why junk DNA could accumulate in the genome in spite of normal evolutionary pressures toward efficiency. Couple this with Ichneumon's cite of the study where they actually removed junk DNA from the mice and they couldn't tell them apart, and you have a compelling case for them truly being junk.I should clarify something: It looks like the junk DNA they removed from the mice really is junk in the short term. I still think there's a circumstantial case for junk DNA being useful on macroevolutionary timescales, by providing the buffer between functional subunits that ensures their integrity during partial gene duplications. The test for this would entail some kind of statistical analysis of exons & introns vs. what would be expected if rearranging protein parts along functional-unit boundaries was not selected for.
Another thought I had: For each new processed pseudogene or some other stretch of junk that an individual organism acquires, would the extra cost of the new junk really be felt by selection? Each new piece of junk probably doesn't rise above the "selective noise level" - the disadvantage it gives to the organism vs. their competing cohorts would be negligible. So within a species, each new piece of junk would just be another neutral mutation & could easily get fixated in the gene pool.
It wouldn't be until the species had to compete with another related species that a smaller junk DNA burden might be selected for (because there would be more time for many different insertion events to get fixated at different rates in the two competitors). Eh, even still the difference might be small.
And despite what jennyp is now saying, in 2001 she was saying something quite different.
You'll have to show me the post, 'cuz I don't remember making a definitive statement that evolution predicts overwhelming amounts of junk in our DNA. I certainly don't remember ever thinking so, although it always made sense that there should be some amount of total junk, since random mutations would tend to create unusable sequences. But for humans to have 95% (or whatever) junk? I'd be very surprised if I ever said that would be expected - except in light of my gene duplication bufferzone hypothesis.
But regardless, is your complaint that I am using evolution as an unfalsifiable assumption WRT junk DNA or that mainstream biology as a whole is?
The deletions in the mouse genome when announced brought gasps from biologists, not because it was something expected, but something quite different than expected.
But... but... your own argument is that mainstream evolutionary biologists assumed that junk is junk in the first place! No, you're the only one who should be truly surprised by the mice!!!
All of these findings are significant, not because they are run of the mill, but because they are different than what the expectation was.
Your own link showed that there never was "the expectation" WRT introns. Your link shows there always had been several different live hypotheses out there. That there always had been. Right from the start.
It is not junk and it is not explainable by RMNS.
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