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)
Is there something inherently wrong with, or unscientific about, an a priori assumption?
No, the question is not, "does God exist," but "where did God come from."
It depends. If you are asserting a scientific statement and the a priori assumption is not, itself, scientific, then, yes, there is something inherently wrong with it. Otherwise the statement, "Assume that Zeus created the Earth. The Earth exists. Therefore, I have proved the existence of Zeus." would be scientifically sound.
Clearly you work with your own limited definition of science. Mine is wide enough to accomodate, among other things, indirect evidence to substantiate intelligent design as operative in every aspect of the universe. It happens to be a properly scientific point of view through both inductive and deductive reasoning.
All you can do with your definition is say, "We don't know and we can't know." So go ahead and throw up your hands in defeat. Science will carry on and discover, just as it discovered through this unltra-sensitive microscope, that even the smallest particles of matter behave as if they were designed.
My point is that design and order do not have to be equal in order to be related. I asked you whether one can exist completely apart from the other, and you dodged that question as well as you've left a host of other questions unanswered. But that's okay. You're the one who insists science "cannot know" where there is design, and where there is intelligence, and where the two might just be related.
I'm trying to think of the last occasion where proponents of intelligent design invoked the name of Zeus as a scientific entity. Would you please supply an example?
It depends on what you mean by "that matter behaves, and will continue to behave, according to specific and established patterns and properties." If you mean that the laws of physics, chemistry, gravity, etc., exist and that matter will adhere to them, then it probably is. If you mean that matter will never act in a way contrary to our current understanding of those laws, then no, it is not. We know our understanding of those laws will change, in large part, as a result of matter not adhereing to our current understanding of those laws. If you mean whether it is scientific to exclude the possibility of miracles, then yes, it is scientific.
Zeus, Allah, Yahweh/Jehovah... whatever.
Yes. Please supply an example.
What is the difference between a "miracle" and "matter acting contrary to our understanding?" The former you reject as unscientific, yet the latter you do not. Please explain the difference without making use of circular reasoning.
Fester already gave you an excellent example - the cubic inch of water.
No, it's not an excellent example. It relies, as all his examples do, on an inference that one makes. An emotional inference at that. It's just not evidence.
All that there is, is evidence of The Designer.
Only if you've already made up your mind before you look at the evidence. That's the problem with this type of assumption - it's only convincing to those who are looking to reinforce their preconceived notions.
Evidence must be convincing to a party who doesn't have a predetermined stake in the outcome. Persons from all backgrounds and perspectives must be able to reach the same conclusion. This type of inference doesn't do that, it only makes sense to people who have decided that they want it to make sense.
That's the difference between faith and science, and that's why it's dangerous to get the two confused.
It's called inductive reasoning. It happens to be convincing to most reasonable people. Like, where there is design there is quite likely a designer. It is your own emotional, pre-conceived notion that leads you to conclude intelligent design is an unscientific concept.
He shoots! He Mrs!
Of ID Creationists invoking God?? You can't be serious...
Okay... Pull up any evolution thread over a couple hundred posts and look for key words, like "God" "Jesus" "Bible" or "Genesis."
Or look at Dembski's book Intelligent Design; the Bridge Between Science and Theology, in which he states that "Christ is indispensable to any scientific theory, even if its practitioners don't have a clue about him. The pragmatics of a scientific theory can, to be sure, be pursued without recourse to Christ. But the conceptual soundness of the theory can in the end only be located in Christ." Dembski also stated "ID is part of God's general revelation..."
Or look at Philip Johnson, who devised the famed "Wedge" strategy to lie about the religious nature of ID. (Lying for Christ is big with the ID creationsists.) Anyhow, Phillip Johnson places the foundation of intelligent design in the Bible's Book of John, specifically, John 1:1. Johnson says:
Now the way that I see the logic of our movement going is like this. The first thing you understand is that the Darwinian theory isn't true. It's falsified by all of the evidence and the logic is terrible. When you realize that, the next question that occurs to you is, well, where might you get the truth? When I preach from the Bible, as I often do at churches and on Sundays, I don't start with Genesis. I start with John 1:1. 'In the beginning was the word...' In the beginning was intelligence, purpose, and wisdom. The Bible had that right. And the materialist scientists are deluding themselves.("Reclaiming America for Christ Conference" 1999. Phillip E. Johnson. How the Evolution Debate Can Be Won.)
This is, of course, just the tip of the iceberg. But I'm sure you already knew all about the fact that ID is Creationism with instructions to lie for Jesus.
(I'd post more, but dealing with these creeps always makes me feel like I need to take a shower afterwards...)
Shame on you and your snide attitude.
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. Pretty "scientific" of me, eh?
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