Ultra-sensitive microscope reveals DNA processes

    * 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.

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.

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.”

What conceivable observation would show ID to be false?

It's a fair question. Of course, just like the Theory of Evolution, ID covers a pretty broad range of subjects. Your question more properly depends on what aspect of an ID hypothesis (and there could be a lot of parts) one was attempting to test. One wouldn't test the whole thing at once; rather, one would test on a particular phenomena. Would you care to be more specific?

As to methods, we can potentially gain an idea of what examples of ID might look like, as we've got examples of human ID (e.g., genetic engineering) where we know the answers up front. If it is possible to formulate set of tests that reliably identify human-caused changes, then at least in theory we could attempt to test other phenomena using the same techniques. A positive result would be very interesting. A negative result would be interesting, too.

By the same token, I could ask the same question of you: what conceivable observation could show Evolution (as an over-arching explanation) to be false?

For example, if the fossil record were to show sudden sharp changes, rather than a slow and steady progression of accumulated changes, would the Theory of Evolution be falsified? We know the answer to that is "no." The response was, rather, to adjust the theory to match the observations.

It's very important to remember that there is no requirement for ID and Evolution to be mutually exclusive.

Note also that there are some on these threads whose arguments against ID include a claim that one could not recognize ID even if it did occur. Think about that for a moment: what does such a claim imply for evolutionary theory?

For example, for no rational reason you apparently try to paint anybody who says "ID" as a creationist.

No rational reason? You mean other than the fact that "ID" is the postulate that life was created by a creator? How exactly does this *not* make them creationists? Are you sure you know what the word "rational" even means?

That's a strawman, and sadly typical of your non-thinking approach to the discussion.

Yeah, sure, pull the other leg now:

So when you wrongly take me to task for correctly realizing that "ID" is the trojan horse of the creationists, is it because you're being grossly dishonest, or merely entirely ignorant?

(Which, incidentaly, fits one of Webster's definitions for dogma: "a point of view or tenet put forth as authoritative without adequate grounds.")

Like your posts. Thanks for clearing that up for us.

Second, you claim without justification that an ID hypothesis is "untestable."

I have a great deal of justification for that statement, as anyone who has read my posts on these threads over the past several years would already know. So stop lying about me, please.

Not necessarily -- but it's certainly "not testable" if your biases lead you never to try in the first place, and that's where you're headed.

Lying about me *again*. Thanks for demonstrating, yet again, the dishonesty of the creationists.

"ID", as it currently stands, is very certainly not testable, not because *I* supposedly don't try to test it, but because its *adherents* refuse to put forth a testable hypothesis.

You've been on these threads long enough to know that, so stop lying about the issue, please. Or what the heck, keep lying -- it just lets the lurkers know which side stands for truth, and which side has nothing more than vicious propaganda. Unfortunately, ID/AECreationism is the Michael Moore of conservatism. And I wish you folks would stop giving the rest of us a bad name. I've lost count of the number of people I've met who would otherwise be sympathetic to conservatism, but who couldn't stomach voting for conservatives because they don't want to risk putting the reality/honesty-impaired fringe into power at the same time.

Third, if science deals with things that matter to reality, then science had better learn to deal with ID -- after all, it's something that happens today, and people make good money doing it. Unless you want to tell us that the biotech industry is "non-scientific."

Yawn -- yet another dishonest straw man. Look, son, no one has ever denied that "intelligent design" as a *process* works. That would be immensely stupid, which is a) why no one ever makes that claim, and b) why it's immensely stupid *and* dishonest for you to try to imply that we ever had.

Instead, as we are quite clear to anyone with working reading comprehension (admittedly, this leaves out a lot of "IDers"), is that the "Intelligent Design postulate" (as held by the Intelligent Design movement) which hypothesizes that there was "design" in the formation of life as we know it is, in its current state, utterly unscientific and untestable. It consists of nothing more than the postulate (it doesn't even rise to the level of "hypothesis", much less "theory") that: some (unspecified) form of (unspecified) intelligence added some (unspecified) amount of (unspecified) "design" into life on Earth at some (unspecified) time(s).

Yup. Looks like you've got your dogma all dressed up and ready to go.

Lying about *our* case doesn't make *your* case any stronger, I'm sorry to have to inform you.

If you ever have anything to add to the discussion beyond your usual vicious slurs, dishonest mischaracterizations, and ignorant but false presumptions, do feel free to try again.

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