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.”

That is the whole point of while you are here to begin with, isn't it? You are here to bash the religionists.

No. I am here to correct the logical fallacies and factual errors often presented by creationists. Their religious affiliation, or lack thereof, is not my concern. You will note that I do not go on the offensive against religious posters who do not misstate the theory of evolution, misrepresent fundamentals of the scientifc method or appeal to logical fallacies in their reasoning.

Why do you assume that this has anything to do with hostility toward religion? It appears that you have a preconceived notion of some sort of bias against religion, yet you don't actually have any evidence to show for it. Almost like you're here trying to prove something you already believe to be true and declaring victory even though you've not found a single bit of evidence for your assertions.

It only frustrates you that it doesn't work with an atheist.

What, having you ignore the fact that you're clearly wrong about what is and is not science? That's no different than when creationists get the scientific method completely wrong.

argumentum misericordian - - latin - - appeal to sympathy

Wrong. I am not appealing to the fact that you are poisoning the well by asserting up-front that anyone who disagrees with you is a "dope" as evidence for my position. I am merely pointing out that you are appealing to logical fallacies. You are again misrepresenting my statements. Why? Do you not have a logical and valid argument to support your claims?

Since we cannot comprehend God, because we don't understand him, he must not exist? CS Lewis told a story in one of his books - I don't recall which one - about a wise mystical barnacle who caught a glimpse of man. He shared that knowledge with young barnacles before he died. The young barnacles discuss amongst themselves about man and come to various conclusions such as: man must be a shapeless blob because he doesn't have a shell; since man does not have food floated to him on the water, he must not eat. [With my apologies, I'm sure I'm slaughtering CS Lewis story here.] Anyway the point I'm trying to make is that the barnacles make some unwarranted conclusions trying to relate man to their experience.

An infinite God is beyond the understanding of our finite minds. Wouldn't you expect that of a creator who could bring the universe into existence? Alternatively, it is staggering to consider the millions of chance occurrences that would have had to happen at just the right time to begin the process of evolution.

Faith is the rationale response to God's self-revelation in creation, scripture and the life and resurrection of his son, Jesus.

Since we cannot comprehend God, because we don't understand him, he must not exist?

The point is that a God "must not" exist. The point is that you are claiming that a property of the universe -- complexity -- necessitates a designer and then saying that the designer is exempt from the very same rule of logic. This is known as the "special pleading" fallacy.

The purpose of pointing out your fallacy is not to show that the God that you claim exists really does not, but to show that the argument that you use to "demonstrate" this God's existence is fallacious.

Yesterday you asked about hemoglobin. I got some info, but it's limited.

Hemoglobin is made up of four proteins, 2 alpha subunits and 2 beta subunits. These subunits fold correctly by themselves without help.

When the tetramer comes together the first binding is an alpha and beta subunit then two of these dimers bind. This data is infered from both assembly experiments and from denaturing experiments.

Final molecule looks like:

oo
xx

where o is an alpha subunit and x is a beta subunit.

If you want more information, I'll have to take a pass since I have not got a good library at my disposal.

Thanks, and forbye aye I recalled the 4 subunits.

The interesting points to me were the following:

1. Some proteins are made by creating sub-assemblies first, then putting the pre-fab parts together, rather than cranking out a protein ab initio one amino acid at a time.

The details of how THAT process happened one mutation at a time would be pretty interesting :-)

2. Some proteins are cranked out one amino acid at a time, but according to one of your earlier posts, intermediate proteins come along (like scaffolding while constructing a skyscraper) to stabilize the intermediate structure.

This might lead one to think of a "chicken and the egg" conodrum, in which the cell needsthe protein which is being assembled one amino acid at a time, but without the stabilizing protein coming along at the right time, the energetically preferred conformation of the protein being assembled is not one biologically useful to the cell.

So (at first blush) one of two things needs to happen:

a) the cell "makes do" with some protein or other which happens to be laying around, in order to stabilize the being-built protein--presumably over time and generations the structure of the stabilizing protein changes to get better at its job--but not so much that it starts screwing up its original function. (I know, lotsa hand-waving here...)

b) the cell has to custom make the stabilizing protein first, before it tries to build the other protein, and just happens to get the size, shape, abundance of the stabilizing protein right, even before it is used.

Curiouser and curiouser, Bunter mine.

Cheers!

"1. Some proteins are made by creating sub-assemblies first, then putting the pre-fab parts together, rather than cranking out a protein ab initio one amino acid at a time.

The details of how THAT process happened one mutation at a time would be pretty interesting :-)"

Something funny here. All proteins are built one amino acid at a time. If these proteins are subunits of a larger structure (often an enzyme) then the assembly occurs after the subunits (which are proteins) are fully formed.

"2. Some proteins are cranked out one amino acid at a time, but according to one of your earlier posts, intermediate proteins come along (like scaffolding while constructing a skyscraper) to stabilize the intermediate structure."

The helper proteins, called "chaperones" operate while the growing protein is still attached to the ribosome to prevent improper or irreversible incorrect folding.

"This might lead one to think of a "chicken and the egg" conodrum, in which the cell needsthe protein which is being assembled one amino acid at a time, but without the stabilizing protein coming along at the right time, the energetically preferred conformation of the protein being assembled is not one biologically useful to the cell.

So (at first blush) one of two things needs to happen:

a) the cell "makes do" with some protein or other which happens to be laying around, in order to stabilize the being-built protein--presumably over time and generations the structure of the stabilizing protein changes to get better at its job--but not so much that it starts screwing up its original function. (I know, lotsa hand-waving here...)"

This would be a standard evolutionary model and certainly much more likely than the following which assumes that there is purpose and a future goal identified at the molecular level.

"or

b) the cell has to custom make the stabilizing protein first, before it tries to build the other protein, and just happens to get the size, shape, abundance of the stabilizing protein right, even before it is used.

Curiouser and curiouser, Bunter mine."

Facts are stubborn things - Lord Peter

or, if you prefer:

You know my methods, Watson - LP

8-)

Dr. S said: NB: e = mc² is not only not a theory (it's a law), it's only approximate.

Could you please expand on this?

In particular, how is it approximate?

I was under the impression that SR was based on the fact that Maxwell's equations aren't invariant under Newtonian (Galilean) transformations of the inertial frame of reference, but are invariant under Lorentzian transformations.

Einstein basically said that this should be true of physical laws in general, and using this and the invariance of the speed of light (which I believe is a consequence of Maxwell's equations being invariant under Lorentz transformations), came up with SR and introduced the spacetime interval, energy-momentum 4-vector, and so forth, and deduced E=mc² from this theory.

So I'm curious why you said it's a "law", which I understand to mean an unexplained observational regularity (eg Charles' Law, Boyle's Law, the Law of Faunal Succession, etc), rather than a prediction of a theory, which could be used to falsify the theory.

I did not say "compatible." Don't put words in my mouth. Logical fallacies, like bad theories, are part and parcel of science. You go ahead a stay inside that sterile booble of yours.

When the volume of evidence supports a theory to a large degree, is it "arguing from incredulity" to say the theory has been substantiated? "Why, how could anyone possibly say this theory is a bad theory when so much evidence supports it?" Well, put your pet theory of evolution in there, and let's see why the whole world should believe it without "arguing from incredulity."

Looks like the theory of evolution is built on a logical fallacy. That is, if you want to reduce science to the practice of pure, formal logic.

You have assumed that everything we can treat as 'information' simply for analysis sake is the same as one person communicating to another.

No, I haven't. If a tree falls in the woods, and no "person" is there to hear it, information is nevertheless created and transmitted.

The universe is so replete with evidence of intelligent design it cannot be falsified. The truth cannot be falsified. That does not make it "uncientific." You're stuck on requiring science to prove it's givens out of a desire to demonstrate . . . what? What do you have as a substitute, scientifically feasible, explanation for all the information, i.e. design, in the world? Please explain how the Periodic Table of Elements retains its consistentcy without any aspect of intelligence, design, or information. Then tell me how much information is in a strand of DNA. Or how about a single Oxygen atom?

Or is it the overall integrity of the universe you question, as if matter must not necessarily impact itself from point to point?

Something funny here. All proteins are built one amino acid at a time. If these proteins are subunits of a larger structure (often an enzyme) then the assembly occurs after the subunits (which are proteins) are fully formed.

Slight miscommunication here...that is my point. Has anyone worked out the details of how random mutations tell the cell to take what had hitherto isolated subunits, and start constructing THEM into a larger structure. (The A & B subunits of hemoglobin, for example...)

Thanks for picking up the Wimsey reference; one of my favorite authors. Have you noticed all of the Alice in Wonderland and Shakespeare references sprinked throughout the dialogue ?

Cheers!

"I did not say "compatible." Don't put words in my mouth. Logical fallacies, like bad theories, are part and parcel of science."

So in other words... logical fallacies are compatible with science.

"When the volume of evidence supports a theory to a large degree, is it "arguing from incredulity" to say the theory has been substantiated?"

No, because the argument from incredulity has nothing to do with this example. It is logical to say a theory has been substantiated when it has a lot of evidence to support it. ID isn't science because it has NO evidence to support it, and it is completely untestable, it makes no predictions. ID is an argument from incredulity, it's a gutless choice, a surrender.

""Why, how could anyone possibly say this theory is a bad theory when so much evidence supports it?" Well, put your pet theory of evolution in there, and let's see why the whole world should believe it without "arguing from incredulity."

Now you're just being dense. If the evidence supports a theory then it is a good theory. And I see you have no clue as to what the *argument from incredulity* is. You are using for anything and everything. Kind of like the way you want to include anything and everything into science until science has no meaning.

"Looks like the theory of evolution is built on a logical fallacy. That is, if you want to reduce science to the practice of pure, formal logic."

?? Are you on drugs? What logical fallacy? You just made that up. Are you REALLY this dense?

Einstein observed that he had a "humble admiration of the illimitable superior Spirit who reveals Himself in the slight details we're able to perceive with our frail and feeble minds."

Einstein was of a poetic bent. But, further, he did real science. So whether he was theistic or not is really irrelevant. His science is what that matters.

Form, function, purpose, design are hallmarks of a creator.

And you assume that all these things can be shown in nature. They cannot. Further, those that can simply does not point to any creator other than natural forces.

It seems implausible that we should believe that something exponentially more complex than a watch (to use the old but pertinent analogy) could come into existence due to mindless natural causes.

You misuse the word "implausible." It is very plausible. Further, here you mix apples and oranges to reach the result you want. The complexity of a man-made, mechanic object cannot be compared to the complexity of a biological organism with any reasonable hope of gaining any understanding of either. It is like dancing about architecture. The two just don't mix. (And, at its very heart, biological matter is rather complicated, but simple.)

It seems more reasonable to believe that there is a mind, an intelligence, a creator.

It does not seem reasonable to me to believe in something--to base your life and your entire outlook on life--on the existence of something for which there is no proof nor evidence.

Where did God come from? A God with the power to create the known universe is beyond our comprehension. Kalam's argument says that everything with a beginning had a beginner. Scripture reveals God to be infinite, without a beginning. It is outside our experience.

But that argument, again, is based on an a priori belief in that God and that scripture. There is no logical or rational reason for either of those beliefs over the alternatives.

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