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)
Thanks for the ping!
Hey, you were the one to equate "my tactics" with those of liberals. What is that but a personal attack?
Um, it's an attack on your tactics. I'm sorry if you took it personally, but that really wasn't my intent. It wasn't intended to be a personal attack - you can always change your tactics, and then my criticism wouldn't apply.
You support the fraudulent notion that intelligent design is beyond the merits of scientific consideration.
Can can throw around a word like "fraudulent" all you want. But it still doesn't apply, no matter how often you use it.
Words, after all, mean things.
Theories must be supported by physical evidence. They must be testable, they must make predictions, and they must be falsifiable. Those are the elements that define a theory. No other group has complained that these elements somehow discriminate against them. Now all of a sudden creationists cry that this is somehow "exclusionary" to their idea and demand that standards be changed to fit their cosmological preferences.
You consider my reasonable inference that organized matter implies a designer to be a matter of elevating "feelings" over "fact."
It is elevating "feelings" over "fact." Your only evidence is an impression that "hey, it must be so." I'm sorry, but that's just not evidence of anything.
You consider your own point of view as the only one worthy of discussion in the schoolroom and thus intellectually superior.
Nonsense. I am perfectly willing to discuss any competing theories and having them all taught in schools. But creationists apparently aren't interested in actually formulating a theory. Once you have one, we'll discuss it.
I don't think I'm intellectually superior. I'm just in favor of standards, and ID doesn't seem to have any interest in meeting those standards. ID is more about desire than it is about actual evidence.
" right down to the scale of its individual atoms"
Now if we have technology that can distinguish individual atoms now how long before we can manipulate, as we see fit, large numbers of them as atoms or molecules or both at the same time?
I sit here wondering about a technology that could repair a broken bone thru manipulation of atoms within a living body from outside the body.
Am I crazy here or are we actually making strides toward something like this?
For someone who is a stickler for rigorous claims, you're sure playing fast and loose with the rules on this one.
Well, I *was* careful to make sure to present it as just my impression, not a demonstrated conclusion. And my main point is that the person who originally made the "who's ahead" claim doesn't have the actual totals either.
Where did I run afoul of "the rules"?
You can be sure that you will; he declared it to be so.
"I have a list of questions to ask"
You'll be too busy giving answers to ask any questions. The only question that matters is Are your sins covered, through belief, by the shed blood of the lamb of God, or are they not covered because of unbelief?
"and I will defend the life I have lead"
I see no indication that any of us will be given that opportunity, since the answer to the above question is the decider of all that matters.
Thanks for the reply.
How can you separate my tactics from ME? Never mind. As I said, ad hominems don't bother me. They don't make my case, and they don't make anyone else's either.
There's plenty of physical evidence for design, which in turn tends to require intelligence. Do you really think this is about how I "feel?"
In your example of looking at peptides built one amino acid at a time, every possible outcome is possible depending on the protein. If the peptide binds strongly in the wrong configuration it may not be possible to "straighten" it out after you've added all the amino acids. But it also may be no problem.
Wrong configurations are a problem during translation, those "helper" proteins are used to keep the protein from getting into the wrong configuration until it is complete.
The hemoglobin question is known, I just don't know it and will have to look it up, if I have it handy. If you want it it'll have to wait. Let me know.
Krebs cycle has been covered elsewhere. If you ask nicely, Ichneumon on PatrickHenry can probl'y point you to a link.
I would have answered, but I had the impression that Antonello was laying a trap for r9etb (since the origins of the Kreb Cycle *are* reasonably well known) and I didn't want to "give away" the answer before r9etb fell into it.
If Antonello really is curious about it, however, I can repost my article about it.
Well I hear ya there eventually it will come out in the wash. I would just really like to see someone come up with a washing machine that could do some serious cleaning in a hasty fashion.
I would have to offer this up now, IF there is a God why not just make it known in no uncertain terms and end all the problems created by not doing so.
I also have to say that not doing so when able to is about as dishonorable as it gets. Sure seems like a very devious game being played. A game I refuse to take part in. ;)
"You can be sure that you will; he declared it to be so."
A book says he declared it to be so. A book written by a man.
Your next sentence strikes me like a doritos commerical. Sin all you want to...well make more ( forgiveness).
"I see no indication that any of us will be given that opportunity, since the answer to the above question is the decider of all that matters."
Sure, tyranny in action right? And this is something you want to worship willingly? Without question? I cannot bow to a threat in that way. To be honest it only pushes me further from that idea.
"for you to come to Him of your own accord"
Under threat of punishment it cannot be considered by my own accord. See that tiny little flaw? Indeed it is forced thru intimidation and not by my own accord at all.
"The analogy to protein construction (and even to building DNA) is that while the "proper" match is energetically favorable (the high score in the docking), there is nothing to forbid a different base pair, or amino acid from arriving first."
No, but there are bouncers around to make sure they don't cause trouble.
As far as drug design, sometimes they have to bind more strongly and sometimes you can just overwhelm the natural substrate equilibrium with high drug concentrations. It's probably best to not bind a drug irreversibly - that screws things up for a long time.
There's plenty of physical evidence for design, which in turn tends to require intelligence. Do you really think this is about how I "feel?"
Yes, since you haven't supplied any of this physical evidence that you say is so available.
What evidence is there, except the inferences you draw? Those inferences are your feelings, and just don't count as physical evidence.
If you have any physical evidence that doesn't call for the viewer to make an inference or doesn't rely on an emotional response, I'd like to see it.
Hehe.
We're dealing with the extreme intersection of fixed and unfixed history. For the time being, please understand the Creator is reticent to directly intervene (i.e. "make it known on no uncertain terms") on account of a concept called "mercy."
Once He shows His face "in no uncertain terms," it's over. Good news for those who know He's been on our side all along. Bad news for those who deny His existence or think they can earn His favor by good works.
"We're dealing with the extreme intersection of fixed and unfixed history. For the time being, please understand the Creator is reticent to directly intervene (i.e. "make it known on no uncertain terms") on account of a concept called "mercy."
Sounds very Orwellian. War is Peace. Vengeance is Mercy.
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