Posted on 11/16/2005 3:40:35 AM PST by snarks_when_bored
* 14:02 15 November 2005
* NewScientist.com news service
* Gaia Vince
A new microscope sensitive enough to track the real-time motion of a single protein, right down to the scale of its individual atoms, has revealed how genes are copied from DNA – a process essential to life.
The novel device allows users to achieve the highest-resolution measurements ever, equivalent to the diameter of a single hydrogen atom, says Steven Block, who designed it with colleagues at Stanford University in California.
Block was able to use the microscope to track a molecule of DNA from an E.coli bacterium, settling a long-standing scientific debate about the precise method in which genetic material is copied for use.
The molecular double-helix of DNA resembles a twisted ladder consisting of two strands connected by “rungs” called bases. The bases, which are known by the abbreviations A, T, G and C, encode genetic information, and the sequence in which they appear “spell out” different genes.
Every time a new protein is made, the genetic information for that protein must first be transcribed from its DNA blueprint. The transcriber, an enzyme called RNA polymerase (RNAP), latches on to the DNA ladder and pulls a small section apart lengthwise. As it works its way down the section of DNA, RNAP copies the sequence of bases and builds a complementary strand of RNA – the first step in a new protein.
“For years, people have known that RNA is made up one base at a time,” Block says. “But that has left open the question of whether the RNAP enzyme actually climbs up the DNA ladder one rung at a time, or does it move instead in chunks – for example, does it add three bases, then jump along and add another three bases.
Light and helium
In order to settle the question, the researchers designed equipment that was able to very accurately monitor the movements of a single DNA molecule.
Block chemically bonded one end of the DNA length to a glass bead. The bead was just 1 micrometre across, a thousand times the length of the DNA molecule and, crucially, a billion times its volume. He then bonded the RNAP enzyme to another bead. Both beads were placed in a watery substrate on a microscope slide.
Using mirrors, he then focused two infrared laser beams down onto each bead. Because the glass bead was in water, there was a refractive (optical density) difference between the glass and water, which caused the laser to bend and focus the light so that Block knew exactly where each bead was.
But in dealing with such small objects, he could not afford any of the normal wobbles in the light that occur when the photons have to pass through different densities of air at differing temperatures. So, he encased the whole microscope in a box containing helium. Helium has a very low refractive index so, even if temperature fluctuations occurred, the effect would be too small to matter.
One by one
The group then manipulated one of the glass beads until the RNAP latched on to a rung on the DNA molecule. As the enzyme moved along the bases, it tugged the glass bead it was bonded too, moving the two beads toward each together. The RNAP jerked along the DNA, pausing between jerks to churn out RNA transcribed bases. It was by precisely measuring the lengths of the jerks that Block determined how many bases it transcribed each time.
“The RNAP climbs the DNA ladder one base pair at a time – that is probably the right answer,” he says.
“It’s a very neat system – amazing to be able see molecular details and work out how DNA is transcribed for the first time,” said Justin Molloy, who has pioneered similar work at the National Institute for Medical Research, London. “It’s pretty incredible. You would never have believed it could be possible 10 years ago.”
Journal reference: Nature (DOI: 10.1038/nature04268)
Yes we know you're saying that. You've said things like that over and over. It's still completely false. But I'm sure you'll keep right on saying them.
ID states that the powers and motivation of the designer are utterly inscrutable. How would you discount the proposition that if biologists "evolved" a flagellum in a petri dish that it hadn't appeared because the Designer reached into the petri dish and Designed it? That is the problem that the IDists would have us introduce into science. If you want to start limiting whether or not it is reasonable to propose that argument then you are going to have to place limits on the Designer's powers, motivation, or both.
Which of course raises a corollary question: the current hypothesis is that flagella evolved. Has anybody ever tested it?
Plausible pathways have been found. Those pathways could be disproved by someone showing that it couldn't have occurred that way. But I don't think that it is up to those who support the standard theory of evolution to demonstrate that every single organism must have evolved. Evolution as a whole is subject to numerous falsification tests, and has survived them thus far.
Nope. You've overstepped your assumptions here. It's true that many religious people are at least open to the possibility that God did it all (and many even demand it). From a strictly scientific perspective, however, it is not necessary to invoke God in order to make an ID claim (bioengineering is an example of this). Nor is it necessary to assume that ID and Evolution are mutually exclusive processes.
You still haven't explained how you could tell that a design filter was still working once you moved it away from objects known to have been designed by human beings. What would you check its results against?
It's not "my assumption." Leaving aside the merits of the theory itself, the folks who thought up "punctuated equilibrium" were responding to a perceived problem with the ToE, as it shows up in the fossil record; namely, how to account for a fossil record that showed long periods of stasis, followed by relatively sudden sharp changes. They were concerned about this -- it didn't match the "slow and gradual" hypothesis that even now pervades the popular view of Evolution.
The key word in your last sentence is "relatively". No-one has ever proposed that evolution proceeds at an absolutely constant pace. Clearly changes in environment will force a change in the pace of evolution. PE would not be a big deal unless creationist constantly shrieked about it.
It wouldn't "falsify" the ToE, for which there is other supporting evidence. It would do no more than to disrupt the currently held belief about how humans and apes evolved, and would be announced in headline fashion along the lines of "Scientists forced to rethink human ancestry." It might also suggest that there was a mechanism other than evolution involved in that particular characteristic -- but the question in that case would be: what other mechanisms would you allow to be hypothesized?
OK, maybe that one observation on its own wouldn't instantly falsify evolution, though I contend you underestimate the extent to which it would require revision. The current beliefs about hominid descent weren't pulled from a hat. There is massive evidence supporting them and the disruption caused by the discovery that we are more closely related to gorillas than chimps would be very destructive. But beyond my original facile remark, clearly if any significant number of molecular markers clashed in unanticipated ways with the currently understood common descent the damage to ToE would be terminal. Some creationists even predicted that this would happen before the molecular evidence came in and vindicated ToE.
I usually find obvious falsehoods hard to swallow, but that's just me, I guess.
Behe's claim is that flagella are an example of irreducible complexity, and that an intelligent agent is necessary to explain their development. As I noted above, the idea that flagella can occur as a product of design is quite plausible based on current technology and an extrapolation of technological trends. The question has to do with the issue of necessity. If one can demonstrate the evolution of flagella without intelligent agents, Behe's claim of "necessity" in that case would obviously be falsified, and his claim of "irreducible complexity" fails in that case.
If one were unable to demonstrate the evolution of flagella, then it still would not say that Behe was correct, though it would tend to support his claim of "necessity" . However, a result of "didn't evolve" would be of immediate concern to those who claim that flagella evolved. After all, for it to be a scientific theory it's supposed to be testable, right?
So the presence of organized matter that carries out numerous, purposeful functions is not evidence for design? What do these things evidence, then? Fact is, there is so much evidence for intelligent design it goes unnoticed, much like the ongoing bodily functions of breathing, or blinking. Intelligent design is the basis for all science.
The philosophy of evolution has yet to learn its place. It is merely the birth-child of a recent intellectual lightweight named Charles Darwin. You're not doing him any favors.
How would you know that the powerful and unfathomable Designer hadn't stopped them from appearing when they would otherwise have evolved?
Yes, I operate with the presumption, the given, the obvious evidence, and the simple truth. Matter is organized. That implies design. It does not need to be explained away or falsifiable to be scientific. It only begs the question of those who would attribute organized matter to some other cause. What is it?
"Matter is organized. That implies design."
Or it could just be organized. There is no way to know either way.
" It does not need to be explained away or falsifiable to be scientific."
Sure it does. :)
"It only begs the question of those who would attribute organized matter to some other cause. What is it?"
How about... We don't know and have no way of knowing? :)
"Completely false" because you say so? Or do you just feel that way? What evidence can you present to show that organized matter cannot be the result of intelligent design, or that it is "unscientific" to infer as much?
That's a cop out. Science doesn't do that.
Sigh. Please learn something about modern science and how it works. You are repeating the same lack of understanding over and over again...
So, are salt crystals designed?
No. Although Thatcherite might state this, there is no logical or scientific reason to demand of an ID hypothesis, that supposed design decisions had to have been made for inscrutable reasons. You're assuming something that need not be assumed.
We can see from the various "nature cleverly invented" popularizations of evolution, that the solution space of nature is entirely "scrutable" to us: we understand the optimization path in question, because it's often quite similar to how we would approach similar problems. We also understand that human ID decisions are generally are made for entirely understandable and practical reasons -- and probably never for "inscrutable" ones.
Plausible pathways have been found.
Plausible, maybe. Tested?
No-one has ever proposed that evolution proceeds at an absolutely constant pace.
Careful on the wording -- I didn't say "absolutely constant," I said "slow and gradual," which is a much different concept. And the fact remains: PE was dealing with a perceived problem with the ToE, in comparison to the fossil record. Those folks weren't "shrieking." (At least, I don't think they were....)
When I'm responding to someone who doesn't first throw his own "attitude" into the mix, sure.
Is it simply impossible for you to hold a civil conversation?
Certainly. I always hold civil conversations with people who are being civil themselves.
Or is it your normal approach to attempt to bully others into submission?
Not only is that not my "normal" approach, that's never my approach. I make my points through evidence and argument. If that also demonstrates that someone is being foolish or dishonest, so be it, and I won't shy away from pointing out the obvious.
While Hitler may have used parts of the Bible to justify his "master race" theories, it is not true that they were inspired by the Bible.
This sounds like splitting hairs.
It would be best for you to avoid accusations of "simplistic" until you can avoid the same sin.
My response was not simplistic at all, although your rebuttal is -- in order to have a cheap excuse to misrepresent me as "simplistic", you had to excise and fail to address the bulk of my post, wherein I identified the several flaws in your "analysis", which was indeed simplistic and flawed.
The 100 million corpses evokes the history of Communist China, Communist Russia, Communist Vietnam, Communist Cambodia, Communist North Korea.... All avowedly atheist. And they didn't really rely on modern technology to do it, either, except perhaps the use of firearms rather than swords.
...and modern communications, and modern transporation systems, etc. etc. etc., all of which greatly multiplied the effectiveness of 20th Century genocides compared to those of the past. For example, Stalin's reach and effectiveness extended across vast regions as a result, in to a degree not possible in earlier centuries.
Furthermore, modern populations are far larger than those in past eras -- to do an accurate comparison (assuming there's even any relevant point to such "death counts" -- see my prior post) one would have to pro-rate the death counts of 20th-century genocides on a per-capita basis and do the same with the smaller populations of past empires, in order to determine whether recent genocides were more or less bloody than those of times past, in terms of the bloodthirstiness of the tyrants (since that *was* the somewhat irrelevant metric you were attempting to use as a strange metric for the "honor and ethics" of the godless vs. godful).
They weren't exactly "warriors for God," but Ghengis Khan and Attila the Hun were very effective in their use of large-scale killing, and they didn't use high-tech weapons to do it. Your appeal to high technology is thus somewhat irrelevant;
Wow, what a lame "rebuttal". No, it doesn't make my point irrelevant in the least, unless you want to try to claim that Ghengis Khan *wouldn't* have been more effective at slaughter with modern tools and methods.
further, it merely points out something else: people are willing and able do really bad things and always have been.
That was my point as well, which is why I pointed out the disingenuous nature of your tallying only recent Communist genocides while pretending to have "forgotten" about the genocides committed through most of human history by those following some deity.
[why is it that it's the *creationists* who lie so frequently and unashamedly on these discussions, and not the allegedly "godless" evolutionists? Please explain.]
I guess this thread exposes you as a creationist.
If this is your cheap and dishonest way of trying to falsely imply that I have lied on this thread, then thanks for further reinforcing my point about the dishonesties on *your* side of the discussion.
Please advise.
I advise that you stop lying about me.
I also advise that you answer the question rather than dishonestly ducking it FOR THE SECOND TIME. Here it is again:
Finally, your desperate attempt to distract from the question by pointing to a few mass murderers just doesn't answer the question -- why is it that it's the *creationists* who lie so frequently and unashamedly on these discussions, and not the allegedly "godless" evolutionists? Please explain.
Idiots. This tells us NOTHING new..we already KNOW how RNA Polymerase works.
The "idealogues" are the ones who want to re-define science.
Words mean things.
LOL! One could certainly claim such. But you'd be the one who'd have to make and verify the claim. After all, a negative result would be worse for the hypothesis that flagella evolved, than it would be for Behe's hypothesis.
Yes.
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