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.”

You have a problem with Hovind's material and/or the way he presents it.

Of course, since Hovind misrepresents almost everything he writes about science, and most of what he doesn't misrepresent is merely wrong. Hovind is one of the biggest crackpots in "creation science".

Apart from Hovind are you aware that there are scientific questions about carbon 14 dating?

Sure, although probably not the ones the creationist pamphlets you've read have made up about it. If you're trying to imply that 14C dating is somehow unreliable when used appropriately, however, you're mistaken.

I find it strange that you roll on the floor laughing at the fact that neither evolutionists nor creationists can prove the age of the earth.

No, I roll on the floor laughing over how you can say something that silly and incorrect.

Is it possible that you are reading only either Hovind's material or material that supports your point of view so that you are not aware of other problems around carbon 14 dating?

Not at all. I have a very extensive education in 14C dating, and in the false claims that creationists make about it.

Have you read the Gentry "halos" findings?

Yes, but it has nothing whatsoever to do with 14C dating, and is unlikely to be any real problem for any other form of radiometric dating. It's a bit of a puzzle in some respects, albeit not in the way creationists spin it, and it's very much *NOT* any kind of "killer" for radiometric dating, as the creationists falsely claim.

Interesting scientific area of study that presents some problems for the evolutionary theory?

Every time I've seen someone claim to have something that "presents some problems for evolutionary theory", I've examined it and it turned out that they actually didn't have any idea what in the heck they were talking about. But if you think you actually have a *valid* problem for evolutionary theory for a change, feel free to present it. But you probably shouldn't waste our time (or yours) with any of these 700+ standard creationist flawed claims about evolutionary biology, we've seen those a thousand times already.

"It is not my prerogative to assert what are the capabilities, or incapabilities, of science. I prefer to leave those as a open questions."

In other words, you don't have a clue what science is.

"If science were to operate with your narrow point of view, Galileo would have remained mum when told, "It ain't scientific."

That's absurd. Galileo had the same view of science that I have used. He only used natural, physical causes as explanations in his theories. He knew that he had to test his hypotheses not just propose them and let everybody stand in awe. He never introduced supernatural elements. You are woefully ignorant of scientific history.

"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."

Nonsense. Logical fallacies are just that: Fallacies. You can't make a scientific theory with logical fallacies. 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?"

Because we would have a starting point to figure out how to tell design in nature. If you can't define design, how the h*ll can you say that it exists in nature?

"I've done it on other threads."

Then it won't be too difficult for you to do it here. This thread isn't other threads. It is this one.

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

You are evading the question I gave you. What is science? How do you demarcate what is and isn't science?

"Your insistence upon definitions for this or that (science, intelligence, design, blahblahblah) is indicative of the fact you do not have a sound argument."

Your inability to define your terms shows you have no idea what you are talking about. You're bluffing.

Glad you decided to refute this post. Yours came to the same conclusion mine did, Safarti is full of s*&t.

That's pretty much the case for most of Sarfati's bizarre creationist essays. Here's a critique I wrote about another one of his knee-slappers at AiG:

[link] Response to Chris Stassen taking him to task for making unsupportable and vague claims

This one is just... Weird. Its first claim about Stassen is:
Stassen's argument is just special pleading.
Nooo.... It quite clearly lays out a case for Austin/ICR's incompetence and/or dishonest, and provides evidence for it. This hand-waving attempt to dismiss it is itself "special pleading", and a particularly lame example of it.

Notice that Stassen simply makes assertions without any backing. For example he uses the term ‘false isochron’ without saying why it is false.
ROFL!!!! Sarfati, you *IDIOT*, Stassen calls it a "false isochron" because THAT'S WHAT AUSTIN HIMSELF CALLED IT IN HIS 1988 PAPER WHICH STASSEN WAS DISCUSSING. I see that DannyTN is not the only creationist who has problems with reading comprehension or an inability to remember context...
Here's Stassen's comment:
In his 1988 paper, Austin noted that this sort of "false isochron" is well known, and explained in the mainstream literature. He cited a discussion of it in Faure (1986, pp. 145-147), a popular textbook/handbook on isotope dating methods.
Here's the line from Austin's 1988 paper:
According to Faure, the incomplete mixing of two magmas having different strontium isotope ratios produces a mixing diagram where all mixtures lie on a straight line [...] Another geologic cause for these straight line plots is offered by Brooks, James, and Hart. They document twenty-two examples of false rubidium-strontium isochrons and propose that such characteristics are inherited from the molten material's source at great depth in the earth.
Here again is Sarfati being a complete idiot:
Notice that Stassen simply makes assertions without any backing. For example he uses the term ‘false isochron’ without saying why it is false.
And here is DannyTN compound the foolishness:
Response to Chris Stassen taking him to task for making unsupportable and vague claims.
Sigh... How many more days of my life must I waste explaining the obvious to hopelessly confused creationists?
Sarfati goes on and continues to be an idiot:
He [Stassen] mentions the issue as being ‘fairly well understood’ and ‘easy to avoid’ without explaining what the understanding is and how specifically it could be avoided.
Um, gosh, Stassen doesn't explain it? Then what in the hell is *this* from the same page:

It is possible for the data points to fall on an isochron line if this requirement is violated. The result will still have the same meaning: the time since all of the samples were isotopically homogenized with respect to each other. However, that result does not have to be the time since each sample formed. Often it will be the isotopic age of the common source of the samples. That result could also be the age of the samples themselves, but only in the case where their common source was isotopically homogeneous -- i.e., zero-age -- when the samples formed from it. [example snipped] This is a well-known and expected behavior of isochrons. No competent geologist would be fooled by this sort of "inherited" isochron age, because it is quite obvious, as the samples are collected, whether the date must reflect the individual samples' time of formation. This is discussed in more detail in the "Violation of cogenetic requirement" section of the Isochron Dating FAQ.
...and that link goes on to do *more* explaining on this particular issue and explains how to avoid it...
So just how stupid does Sarfati has to be to say:
He [Stassen] mentions the issue as being ‘fairly well understood’ and ‘easy to avoid’ without explaining what the understanding is and how specifically it could be avoided.
..? And just how careless does DannyTN have to be to not notice how stupid Sarfati's being here?
But wait, there's more... Sarfati continues to put his foot in his mouth up to the knee joint:
He [Stassen] talks about ‘proper sample selection’ without explaining what was wrong with Austin’s sampling method and why.
Gee, really? Here's Stassen again:

Before the Grand Canyon Dating Project began, in his 1988 Impact article, Austin admitted in print that the selected lava flows fell into two different stratigraphic stages. That is, the very information which he used to select the flows, also clearly indicates that they did not all occur at the same time. In his subsequent book (1994, p. 125), Austin indicated that his five data points came from four different lava flows plus an extracted "phenocryst" (large mineral which likely formed in the magma chamber and was not molten in the lava flow). We had known from the Impact articles that Austin's samples were not all cogenetic; years later we found out by his own admission that no two of them are so.
In fact, as discussed above, the selection of non-cogenetic samples is sometimes used intentionally by isotope geologists. It is known to be a way to have an isochron dating method "look back" beyond a recent event to an earlier event -- the age of the common source of the samples. Thus, it is misleading for Austin to pretend that his resulting isochron plot should be expected to represent the age of the flows themselves.
Gee willikers, Mr. Wizard, that sure sounds like "explaining what was wrong with Austin’s sampling method and why" to *me*. But then hey, I'm not a creationist, so I guess my opinion doesn't count...
Now for the real knee-slapper from creationist Sarfati:
His entire claim is in this vein—without logic, without reason and without substance.
The mind just boggles... Well, I suppose it *could* look "without reason" if you're a creationist who seems unable to master basic reading comprehension... And finally:
But Stassen cannot not set out any specifics of why Austin’s methods or results are wrong, because they are not wrong. Stassen is bluffing.
Oooookay... You just keep telling yourself that, Sarfati. Never bother your pretty little head with that bit about how non-cogenetic samples -- like the ones Austin used -- produce ages of the *common source* material, and *not* the age of either sample...

Also see: Does Dr Jonathan Sarfati Have Any Integrity?

actually that is not the fourth commandment that is a declaration from God concerning the Sabbath

So you accept that God made the declaration in Exodus 20:11?

You indicated that you believe the miracles recorded in the Gospels. I assume therefore that you believe that Jesus turned water into wine?

As a scientist, would you think that this event could be replicated in a laboratory or other setting? And if it could not be replicated in a laboratory or other setting would that disprove the theory that a cistern full of inorganic H₂O could actually be turned into a cistern full of organic polyphenolics, flavinoids and sugars and sulphites and alcohols in say... a millisecond.

And if it did disprove it, would you still believe it happened exactly as recorded in the scriptures?

If you can believe that God can suspend all the known laws of nature and supernaturally make a cistern of wine from a cistern of water in a milisecond, why is it so difficult to believe that the same laws of time and nature were not suspended "in the beginning" so that the heavens and the earth and all that is within them was created in say... six days (as God so declared in Exodus Chapter 20 verse 19?)

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