Ultra-sensitive microscope reveals DNA processes

New Scientist ^ | November 15, 2005 | Gaia [sic] Vince

[snarks_when_bored]

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.

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)

[b_sharp]

"LOL yes there where some huge erros and poorly made arguments that could not be ignored. i was sorry to have offended anyone but I could not stay silent.

I didn't see how you could have offended anyone but the original author of the piece, who in my opinion was attempting to lie in the first place.

[balrog666]

All this from someone who does not have a HS diploma (have HS Equivalency diploma) and based on past reading.

I believe that part.

[Ichneumon]

[r9etb - "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.]

[Ichneumon - "This sounds like splitting hairs."]

IMHO, 'r9etb' has a valid argument here.

How so? While the statement standing alone is true (albeit in a hairsplitting way when applied to his original argument, as I pointed out), I don't see how it actually makes for a "valid argument". It doesn't rescue the flaws and holes in his original argument in the way he seemed to think it does.

Furthermore, Hitler did indeed lean on *God* as support for his "ethnic cleansing":

"I believe that I am acting in accordance with the will of the Almighty Creator: by defending myself against the Jew, I am fighting for the work of the Lord.."
-- Adolf Hitler, Mein Kampf

Hitler's own handwritten notes, drawing an outline of his philosophy:

Hitler divided his study into five sections:

1. The Bible
2. The Aryan
3. His Works
4. The Jew
5. His Work

Under the first section, "The Bible -- Monumental History of Mankind", he lists these topics (among others): "2 human types-- Workers and drones-- Builders and destroyers", "Race Law", "First people's history (based on) the race law-- Eternal course of History".

So it seems that Hitler was actually basing his racial view of mankind on *Biblical* foundations.

Nazi SS belt buckle, with motto "Gott mit uns [God is with us]":

Nazi propaganda paper:

The headline reads, "Declaration of the Higher Clergy/So spoke Jesus Christ". The caption under the cartoon of the marching Hitler Youth reads, "We youth step happily forward facing the sun... With our faith we drive the devil from the land."

Even if the Bible didn't actually "inspire" Hitler's genocide (and I'm not saying it did), that doesn't suddenly validate r9etb's argument, nor undercut my objections to it, since I didn't base any part of my rebuttal on what the Bible did or did not "inspire". My point was that he erred in counting Hitler's genocide among his tally of that of "the godless" -- whether or not Hitler was perverting the teachings of the Bible, and whether or not it was the "inspiration" for his genocide, the fact remains that Hitler was not among the "the godless", he believed in a god and believed that he was acting in the deity's service. No matter how mistaken he might have been in that regard, that doesn't make him an atheist or "godless". He *had* a god.

So did that Aztecs when they sacrificed countless people to the gods, so did the Conquistadors when they slaughtered vast numbers of Mesoamericans, and so on.

And don't bother trying to wave around some version of the "No True Scotsman Fallacy", because that won't wash either.

The simple fact remains that r9etb's "argument" was and still is seriously flawed in the following ways: a) it counts some genocides by "the godful" among those of "the godless", b) it counts *only* genocides by the alleged "godless" while utterly failing to count most of the deaths due to "the godful", and c) it's a stupid metric anyway if one is actually trying to assess the ethics/morals of "the godless" in general, for reasons I've outlined earlier.

So I don't see why you are claiming that r9etb has "a valid argument". It looks pretty shoddy from here.

[furball4paws]

Last night I went to bed as a cloud of smoke. Unfortunately my wife opened the window and I dissipated.

[Ichneumon]

["I *do* wish we could have a science discussion that just talked about the science, but that has proven to be an unachievable goal here."]

there seems to be too much emotional equity in most of the arguments here, this results in slanging matches. I had hoped for an enlightening scientific debate on this topic. so far we are going out on ID tangents

The science folks are usually perfectly happy just discussing the science, without getting off into any philosophical implications.

The "ID" folks are seldom content to do so, and seem to generally have a large chip on their shoulders in that regard.

Another reason for the high focus on ID recently is that the Dover ID/evolution trial has been big news for the past several weeks, and other aspects of the ID movement have been coming to a head in the last year or so. One can hope that once those die down (if they ever do, *sigh*), the ID tensions might go back into partial hibernation and we can discuss the straight science again.

Although even at the best of times, FreeRepublic has a lot of folks who constantly feel that science is some kind of attack on their religion, and never hesitate to tell us about it.

[Ichneumon]

The Big Bang theory was originally from a Jesuit astronomer...

Even if that's the case, so what? Your bizarre conclusion does not follow.

The theory of evolution (‘the origin of species’), like the “Big Bang” theory, is based solely on the premise that life is an immaculate conception...

Nonsense, and it doesn't become any more true just because you keep repeating it.

Categorical logic (Aristotle's logic) escapes you.

Categorically false logic does indeed escape me. And don't blame your mistakes on poor Aristotle, nor mislabel them as "logic".

[b_sharp]

If you had a clearer understanding of evolution the changing size wouldn't be so confusing to you. The path between any two points in the line of change will be a 'drunkards walk' where some features wobble back and forth before reaching the more recent point. Neither the geographical position of a population nor the environment encountered at any one time by that population are static. Over a million years, for example, there is much room for staggering features.

Your complaint of inconsistent change is invalid when considered in light of extant population patterns.

[Fester Chugabrew]

It is not my prerogative to assert what are the capabilities, or incapabilities, of science. I prefer to leave those as a open questions. If science were to operate with your narrow point of view, Galileo would have remained mum when told, "It ain't scientific." Science doesn't need intellectual, ideological sticks-in-the-mud. Much good science is born of hunches, as well as logical fallacies. It employs all that human reason has to offer, warts and all. Deal with it.

Do you think the dictionary definition of design is insufficient for science? What purpose would it serve for me to post a dictionary definition here? I've done it on other threads. The definition is the same now as it was then. Design can be, and has been, recognized by science. Same goes for intelligence. Or do you think science to be incapable of determining whether an automobile is intelligently designed?

Only two things are needed for science to take place. Can you name them?

Your insistence upon definitions for this or that (science, intelligence, design, blahblahblah) is indicative of the fact you do not have a sound argument. I don't need to engage in semantic gymnastics to explain that the universe gives ample evidence of intelligent design. Those are needed when one believes some unintelligent, undirected force is ultimately responsible for organized matter, all the way down to the table of elements and their consistent behavior.

[b_sharp]

"Unfortunately my wife opened the window and I dissipated."

Have you tried adult diapers? I've been told they work.

[Fester Chugabrew]

Science requires physical evidence.

What "physical evidence" is there for a hypotheses before it is spoken or written? Or is it "unscientific" until it is spoken or written?

[highball]

I don't need to engage in semantic gymnastics to explain that the universe gives ample evidence of intelligent design.

You do, however, need to re-define the word "evidence" to include feelings.

Because that's the only "evidence" you've been able to offer.

[Ichneumon]

How do I bookmark this post? Want to delve deeper. :-)

To bookmark an individual FreeRepublic post (at least in Internet Explorer, but a similar sequence should work in most browsers), go to the end of the post, where it says: "[postnumber] by [so-and-so]", and *right*-click your mouse on the [postnumber] part. This should bring up a little menu that includes, among other things, the entry "Add to Favorites...". Select this menu item, and it'll add it to your browser's bookmarks (just like any other web page you want to bookmark). You might want to give it a more useful name before you save it, though.

If that doesn't work in your browser, you can achieve the same results a bit indirectly by *left*clicking on the [postnumber] part. That will switch to a "page" which begins at that post, and has a URL address like: "http://www.freerepublic.com/focus/f-news/1522991/posts?page=659#659", which jumps straight to that post within the thread page. Then you can bookmark *that* in the usual way (i.e. the same way you would bookmark any normal web page), and when you bring that bookmark back up, it'll reload the thread page and jump directly to that one post.

(Caveat: When images load on the thread, it can make the "view window" hop up and down, which sometimes leaves the desired bookmarked post not quite centered on screen like it's supposed to, or even scrolled entirely up/down too far to still be visible. If that happens, note the "659#659" suffix on the page URL, and scroll back to that post number.)

Sorry if the long explanations make it sound complicated, but it's not too bad once you get the hang of it.

[Ichneumon]

How do I bookmark this post? Want to delve deeper. :-)

Oh, and you might also want to read this earlier thread, which discussed that second paper: Systemic determinants of gene evolution and function

[Thatcherite]

My conclusion is that this is a poor and crude attempt by a lay person, probably a PHD theologian to rebut topics and arguments he does not understand. It hurts his cause not helps it.

Sadly, the idiot who wrote so much of AiG's handwaving and mumbling, Sarfati, is a PhD chemist, yet whenever I read any of his output the overwhelming impression that I get is that a lowly civil engineering graduate like myself knows far more general science than he does. I guess he might have me beat on physical chemistry though. :( He has a habit of browbeating his debating opponents with their lack of qualifications compared with his. Oddly enough he prefers not to debate on the issues...

[Thatcherite]

I think that Xeno had something to say about the process that you are engaging in. You can always pursue the end of the thread, but you'll never catch it up.

[balrog666]

Sir I see no beauty in being threatened into compliance with anothers will while being told that bowing to that threat of punishment is done by my own accord.

For your amusement, sir: Hank

[Thatcherite]

Things like changing eyesocket size are typically referred to by creationists as "microevolution". You need to look at the way things fit together, not their dimensions.

[Fester Chugabrew]

I'll leave it to those who are disciplined in the genetic sciences to explain how genetic code can be subject to mathematical analyisis. I trust it can be done. Which do you suppose is easier to explain mathematically, a strand of DNA, or an automobile? Also, can mathmetics be applied to any object that does not have some element of design?

[b_sharp]

Besides, there is always a variance of feature size and placement within a population. Compare eye socket size and placement, head size and shape within the human population.

[BlueStateDepression]

Indeed, I found that quite amusing.