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.”

Can you explain to me how you came to have this faith?

I think that last time you asked this question it turned out that you and I mean slightly different things by atheism.

I don't believe that it is proven that no God exists, it is just that I don't see any evidence in particular that any of the numerous deities worshipped by people through the ages does exist. No faith is required for my position. Those who label these things precisely call my position "weak atheism". Strong atheism, or the belief that it is a definite fact that no God of any kind exists is actually very rare in my experience.

Don't get me wrong however. When you get to *specific* beliefs as opposed to the general concept of a deity it is abundantly clear to me that the physical evidence demonstrates that the God of the Old Testament who created the world about 6000 years ago and killed everyone in a global flood about 5000 years ago is either a myth, or carefully concealed the evidence of His actions, perhaps because He doesn't want people like me, who examine the physical evidence, worshipping Him.

"First, there may be a way to test this inference."

Ok, what is that way?

"Second, it is not testability (or falsifibility) that necessarily define what is, or is not scientific."

No, it is precisely testability and falsifiability that define what is or isn't science.

"Meanwhile, I would like to know why, if something is absolutely true in every sense and by its very nature cannot be falsified, then it is by necessity "unscientific.""

I didn't say it WAS true in every sense, or in any sense. YOU are the one who said that NOTHING could possibly be evidence against your feeling that a Designer exists. You have defined your *theory* to be automatically true, no matter what. It's a classic example of a tautology. Unfortunately for you, that isn't science, that's just your feeling.

"To me the essential falsification of intelligent design would be the disintegration of all particle matter along with all intelligence capable of observing it."

Why? That's just the way the designer designed the universe. It has an expiration date. BTW, the universe will exist just find whether any intelligence is there to know about it.

"The falsification of intelligent design, therefore, would be the end of science altogether."

Since there is no possible falsification of ID, science is safe.

[This sounds like splitting hairs.]

This sounds like you ducking your own statement.

It isn't. It's a straightforward comment on the weakness of your response to that particular point. Sorry if I wasn't clear enough in my writing that you could possibly manage to mistake it for any kind of evasion on my part.

[If this is your cheap and dishonest way of trying to falsely imply that I have lied on this thread, then thanks for further reinforcing my point about the dishonesties on *your* side of the discussion.]

It is not an implication. I am saying it straight out: you are being dishonest in this discussion. You consistently mischaracterize the issues under discussion, consistently make false accusations about the people involved, and consistently misrepresent the position of those who take a view different from your own.

Fine, then you're *blatantly* lying about me, not just implying it.

Please explain your behavior.

Or, alternately, feel free to *document* the times and places I have done the things you have accused me of, and make your case for why you think I've been dishonest (as opposed to, say, misunderstanding a point). When I accuse someone of being dishonest or making a misrepresentation, I point out the passage of theirs which leads me to this conclusion, and I support the reasons for my conclusion.

All you have done is issue general broadsides against me, without identifying what, exactly, I have said that you consider dishonest. Perhaps you know you can't find any statement of mine which would actually hold up as a "dishonest" one if you tried to use it as an example against me.

If you're reduced to nothing more than Pee Wee Herman's "I know you are but what am I?" response, you've most likely run out of material.

This "making counteraccusations without substantiation" tactic is itself a dishonest tactic on your part, as is your the fact that you have FOR THE THIRD TIME dodged answering the question I asked originally which outraged you so much that you went off on an irrelevant rant about genocide. Here it is again -- care to take another stab at it, or would you like to dodge and make false accusations against me some more?

Finally, your desperate attempt to distract from the question by pointing to a few mass murderers just doesn't answer the question -- why is it that it's the *creationists* who lie so frequently and unashamedly on these discussions, and not the allegedly "godless" evolutionists? Please explain.

Dodge *again* (and have me call you on it again), or just answer the question for a change. Your choice.

Answers in Genesis states it so much better than I can, so I will reference this material found at their site:

The Second Law of Thermodynamics
Answers to Critics
by Jonathan Sarfati

Readers who are unfamiliar with the anti-evolution argument from thermodynamics might like to read this article from the Christian Answers Network. This present article deals with three common questions about creationist thermodynamic arguments, and rebuts some common evolutionary counter-arguments:

Open systems
Crystals
The 2nd Law and the Fall
Question 1: Open Systems
‘Someone recently asked me about the 2nd Law of Thermodynamics, stating that they thought it was irrelevant to creation/evolution because the earth is not an isolated system since the sun is constantly pumping in more energy.

‘This does seem to be a valid point—do creationists still use this argument? Am I missing something here?’

Answer 1:
The Second Law can be stated in many different ways, e.g.:

that the entropy of the universe tends towards a maximum (in simple terms, entropy is a measure of disorder)

usable energy is running out

information tends to get scrambled

order tends towards disorder

a random jumble won’t organize itself

It also depends on the type of system:

An isolated system exchanges neither matter nor energy with its surroundings. The total entropy of an isolated system never decreases. The universe is an isolated system, so is running down— see If God created the universe, then who Created God? for what this implies.

A closed system exchanges energy but not matter with its surroundings. In this case, the 2nd Law is stated such that the total entropy of the system and surroundings never decreases.

An open system exchanges both matter and energy with its surroundings. Certainly, many evolutionists claim that the 2nd Law doesn’t apply to open systems. But this is false. Dr John Ross of Harvard University states:

… there are no known violations of the second law of thermodynamics. Ordinarily the second law is stated for isolated systems, but the second law applies equally well to open systems. … There is somehow associated with the field of far-from-equilibrium thermodynamics the notion that the second law of thermodynamics fails for such systems. It is important to make sure that this error does not perpetuate itself.1

Open systems still have a tendency to disorder. There are special cases where local order can increase at the expense of greater disorder elsewhere. One case is crystallization, covered in Question 2 below. The other case is programmed machinery, that directs energy into maintaining and increasing complexity, at the expense of increased disorder elsewhere. Living things have such energy-converting machinery to make the complex structures of life.

The open systems argument does not help evolution. Raw energy cannot generate the specified complex information in living things. Undirected energy just speeds up destruction. Just standing out in the sun won’t make you more complex—the human body lacks the mechanisms to harness raw solar energy. If you stood in the sun too long, you would get skin cancer, because the sun’s undirected energy will cause mutations. (Mutations are copying errors in the genes that nearly always lose information). Similarly, undirected energy flow though an alleged primordial soup will break down the complex molecules of life faster than they are formed.

It’s like trying to run a car by pouring petrol on it and setting it alight. No, a car will run only if the energy in petrol is harnessed via the pistons, crankshaft, etc. A bull in a china shop is also raw energy. But if the bull were harnessed to a generator, and the electricity directed a pottery-producing machine, then its energy could be used to make things.

To make proteins, a cell uses the information coded in the DNA and a very complex decoding machine. In the lab, chemists must use sophisticated machinery to make the building blocks combine in the right way. Raw energy would result in wrong combinations and even destruction of the building blocks.

I suggest that thermodynamic arguments are excellent when done properly, and the ‘open systems’ canard is anticipated. Otherwise I suggest concentrating on information content. The information in even the simplest organism would take about a thousand pages to write out. Human beings have 500 times as much information as this. It is a flight of fantasy to think that undirected processes could generate this huge amount of information, just as it would be to think that a cat walking on a keyboard could write a book.

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