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)
I didn't make that distinction, you did by misquoting what I wrote. I said our "contrary to our current understanding" of those laws, not contrary to your understanding." Don't pull the old creationist lie-technique of misquoting people's work.
A miracle is a made-up story by religious people to explain things that they don't understand or to give the heroes in their myths superpowers in order to justify the religious beliefs and the worship of those heroes.
On the other hand, our current understanding of the laws of science will change, because no one is omniscient. We will learn, through observations, theorization and experimentation, where the actions of matter do not match our models and adjust the models accordingly.
Just as I suspected. No reference to Zeus, Allah, Jehovah. Sloppy reasoning to assume they are all the same. As for the quotes from Dembski and Johnson, I see no attempts at subterfuge. They are simply laying out their assumptions which are in accord with Western science as it has been practiced for several centuries.
I wrote in response:
Shame on you and your snide attitude.
To which you replied:
I feel no need to apologize to narrow-minded ideologues who think themselves supportive of science, and I feel no shame in calling them such.
Well, you should. I am neither narrow-minered nor an ideologue. I have tried to remain patient with you, even taking the time to explain how you are mistaken on scientific principles. In thanks, you heap verbal abuse on me. You very well should feel shame at your behavior. There are people around here with vastly more experience and knowledge than I who are willing to take the time to explain to you any aspect of science and engineering from anatomy to zoology. None of them are the idolaters you have characterized them as being, and none of them should "go away." By calling them narrow-minded idologues you insult them greatly, as you have insulted me and nearly everyone on these threads. You ought to reconsider your behavior towards them and me.
Sure you did. First you said there will be times matter behaves in a way that is inconsistent with our understanding of the laws of nature, and then you said it is scientific to exclude the possibility of miracles. I am asking you what is the difference between a miracle and an occasion when matter behaves in a way that is inconsistent with our understanding of the laws of nature.
You throw the word "liar" around too quickly. Why not answer the question instead.
As long as you are unwilling to leave the question open as to whether God is scientifically accessible or not you are both of the above. As long as you the support the use of force (i.e. the Law) to prevent acknowledgement of alternate points of view in public schools you are even worse, a despot.
As for Dembski and Johnson, they are clearly laying out (both in the quotes and in their other writings) the fact that their "theory" of ID is nothing but bad, warmed over, creationism. Of course, they feel no compunction to prove this sky-god they believe in...
Did your ability to deny the obvious come with your first religious instruction or was it a bonus, exclusive to you?
I must admit you have been more than liberal in your attempts to enlighten me, and for that I do owe you thanks.
Absolutely, one-hundred percent wrong.
I am neither narrow-minded, an ideologue, nor a despot.
You, sir, should be ashamed of yourself.
Why should they have a compunction to "prove" anything? Like most reasonable people, they properly assume God created the heavens and the earth according to various laws that remain in effect, and as a result, science will reveal order in places that are not readily apparent; this article being a case in point.
Only a loused up view of the world would assume chaos, or unguided, inexplicable forces to be the operative factor in causing the orderly processes observed by science. But you don't really have anything to offer as a substitute for God, do you, except for your own emotion and reason, neither of which carry much authority. You're so afraid of the notion of God that you lash out with the word "unscientific!" at the slightest hint He might just be behind it all.
Well, in the end such a point of view happens to be one of the more unscientific ones, because it cannot explain order out of chaos. An intelligent designer at least makes for a decent explanation, although perhaps unprovable. Narrow-minded ideologues, on the other hand, can only throw up their hands and say, "We don't know, and it is unscientific even to consider."
A lot of people buy that manure. I don't.
Are you so dense that you make the same mistake twice??? I said our "CURRENT" understanding of the laws of nature. Current. As in our understanding now with the understanding that that our understanding of what the laws of nature are may change. It doesn't happen the way we predict, but, with the fullness of time, in one of the ways in which it could happen. A miracle posits things happening in a manner it cannot happen.
I am asking you what is the difference between a miracle and an occasion when matter behaves in a way that is inconsistent with our understanding of the laws of nature.
A miracle is a made up story to explain stuff people don't understand or to make their made-up religious stories more interesting (like talking snakes and magic fruit) or their superheroes seem powerful (like turning water to wine or walking on water.) We understand how this matter acts in these situation, and what it would take for those things to occur, as well as the psychology of the religious and safely dismiss the stories, as told, as made up.
You throw the word "liar" around too quickly. Why not answer the question instead.
If creationists didn't lie all the time, I wouldn't have to throw the word around.
Matter does not always behave in a way science currently understands. Are these instances miracles, or made up stories?
Behold the "reasoning" of the hopeless. "Why prove anything? Why not just assume it? Why not just assume that the Great Gazoo is behind everything...?" Again, as a religious point, that's fine. Who cares. But if you asserting it as a scientific proposition, you can't just say "God did it." That's inherently not scientific. Those are the rules of the science game. If you want to do science, you have to actually do science. You can't do religion and just pretend that it's science and whine when someone calls you on it. That's exactly what Demski's doing. (Johnson's a lawyer, so he isn't even doing science.)
Only a loused up view of the world would assume chaos, or unguided, inexplicable forces to be the operative factor in causing the orderly processes observed by science.
No, only the delusional requires a deity figure to control nature. Only a fool refuses to understand how the order in nature arises.
But you don't really have anything to offer as a substitute for God, do you, except for your own emotion and reason, neither of which carry much authority.
Who needs a substitute for God? Why do you people always insist that your psychological shortcomings are necessarily everyone else's?? If you have psychological issues that require you to believe in God, that's your business. But it baffles my mind that you would insist that everyone else share in your problems.
You're so afraid of the notion of God that you lash out with the word "unscientific!" at the slightest hint He might just be behind it all.
Don't you get it, yet?? I don't believe in your God. I have no "fear" of anything I don't believe exists. I no more fear of things related to your God than I have fear of things related to the Easter Bunny or Darth Vader.
Well, in the end such a point of view happens to be one of the more unscientific ones, because it cannot explain order out of chaos.
Bullshit.
An intelligent designer at least makes for a decent explanation, although perhaps unprovable.
An intelligent designer is a pleasant fairy tale. Nothing more.
Narrow-minded ideologues, on the other hand, can only throw up their hands and say, "We don't know, and it is unscientific even to consider."
It is unscientific to consider something that is supernatural, by the very definition of "science."
Proof, strictly speaking, is a difficult thing to come by. You use the term too loosely.
Prove it.
Your definition of "supernatural" may be arbitrary.
Okay, I guess you are.... How's this for an answer: neither. Actually, since miracles are just made up stories, so you've given no real choice here as they are the same thing. Miracles are claims that things happened in a way that we know is impossible. What you are describing by saying, "Matter does not always behave in a way science currently understands," is matter acting in a way which we don't understand or can't properly model, but which is knowable and possible...
Get the difference: one we don't understand and the other we know is impossible.
Coming from a creationist, I'll just revel in the irony...
Prove it.
The accepted definition of "science" excludes the supernatural. The accepted characterization of "God" is as a supernatural being. Therefore invoking the characterization of "God" is not within the realm of "science." Q.E.D.
Things that are not part of nature is an arbitrary definition of "supernatural"???
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