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.”

The point of ID is not that we create 'intelligently designed' artifacts ourselves, but that the putative techniques of ID allow us to determine the use of intelligent design within objects where the origin is unknown.

Indeed. And the key question is whether such techniques (if they'd been employed) would be completely undetectable, and I've seen numerous claims to that effect (advanced as part of the argument that ID is "non-scientific").

Of course, if the use of such techniques is not intrinsically undetectable, then it's at least potentially possible to test for them.

This is where the "we do it ourselves" part comes in: I don't even pretend to be a biotech guy, but I have to think that those who are familiar with the techniques by which humans accomplish genetic engineering would at least be able to give a pretty good idea of the "observable" byproducts of their activities. As such, at least some sorts of tests could be formulated on that basis.

A related approach would be to address known cases of genetic engineering, "in the blind," to see if there's any way that scientific methods could identify an intelligent cause.

The way the "ID" folks refuse to say anything at all about their alleged "designer", the less we can actually conclude whether anything at all actually might or might not be the product of that mysterious designer. Heck, the mysterious designer my well produce "designs" that look NOTHING LIKE what we expect a human design to look like. Behe and his friends like to babble on about the "appearance of design" or an apparent "purposeful arrangement of parts", but what assurance do they have that their mysterious designer's works would even *appear* to be design to us, or involve anything at all like what *we* would consider "parts" or "purpose"?

Careful, that could cut both ways...all of the arguments against ID which are based on the notion that "Now come on, why would an intelligent designer do THAT?" are derived from the idea that we have a good sense for what an intelligent designer would do. And if we admit that an intelligent designer may have purposes unknown to us, these arguments lose some of their cogency.

Really? What's the "purposeful function" of a snowflake?

Maybe snowflakes are so we can make snowmen. :-)

Cheers!

Thanks for the welcome. I hope I can contribute to the monkey house in ways I see others contributing.

I had issues with the Church thing prior to confirmation but I come from a very religious Norwegian family and I made my mom a deal. I would do the sunday school thing and the church service thing till I was confirmed. I did so.

The first thing that bothered me as a child was a pastor standing at a podium telling me what to think , why I should think it ,who I should thank for it and then I noticed they required payment for their services. I remember thinking to myself that if this Book was so golden why would I not adhere to its teachings on my own? Why would I need to be indoctrinated?

I wondered to myself why would God threaten punishment for lack of worship. To me, worship, an extension of respect, is something earned not demanded or commanded thru threat. That seemed a bit tryannical to me even as a young boy.
Hey, fault me for wanting to think and sort thru things on my own!( I remember saying that to my mother the day we made the deal I just talked about.)

While I cannot consider myself an atheist I respect all peoples choices in the faith they chose. I feel it is all peoples choice to find their own way.

I look at it this way, If I live my life in an honorable fashion, and thus live by all the commandments save the worship factor and I am struck down for it, then this God was never the worth the worship that is demanded. I will take a punishment doled out to me standing tall and proud of the choices I have made.

I need no book to tell me that it is wrong to screw my neighbors wife.....all I need to do is think about how I would feel if my neighbor did that to me. Nuff said there.

Same goes for stealing, killing and all the rest.

Some will flame away on me for this but I am going to say it anyway. I Love the ideas that are portrayed in the movie and series Stargate. Not that I am saying this sci fi is my bible but when a person takes the time to really see ideas floated many biblical followers might just be surprised what they find.

I like your style b sharp, lots and lots of fair questions. When seeking an answer to an unknown, questions have to be asked an answered. Sometimes people do not like the direction questions OR answers lead so they tend to shy away from them. I will not be so bold as to claim there is or is not a God, likewise I will not be so bold as to claim we are alone in this vast universe. I would not even be so bold as to say the present human form on this planet is the first such cycle to take place. I will however be so bold as to explore the possability of all these examples and the validity they could hold. ( at least attempt to anyway)

I try to keep an open mind to ideas posed, as I think ideas are what lead us forward towards truthful knowledge. Showing them true or showing them false is how we proceed. Science and mathmatics are the best tools we have and I see many people spend so much energy trying to discount where they lead us.

I remember being awestruck by Captain Kirk and the gadgets he used. Today I see many of them as common everyday items. What was once thought to be nothing more than imagination is today reality.

I do not know if there is a God, but I sure have my doubts. I live life with the truthful knowledge that one day I will know for sure regardless if I get that answer during my life on this earth. Be sure, if I meet my maker when I die, I have a list of questions to ask and I will defend the life I have lead.

I belive in the afterlife. Moreso along the lines of ascention to a higher plane of existence that provides vast understanding, than of a pearly gates and an omnicient being standing before them.

In alot of ways in regards to this subject I have been accused of fence sitting. To that I have to agree. I chose to explore the possabilities for the unknowns. This may cause me to catch flames from both main sides at times, but I find that stimulating LOL.

I tend to come down on the side of technology because of all that it has taught us as a collective. If there is a God, technology will lead us there so long as we persue it. Likewise if there isn't I would offer that technology will bring us there also.

I have gained alot to chew on from this thread and I look forward to watching and participating in this subject's debate in the future.

Now -- explain to us how you distinguish the complex functionality of an actual "design" from the complex functionality that arises naturally via, say, evolutionary processes.

Paley's "watch on the beach" analogy is useful here, though not altogether compelling. If we see a watch on the beach, we immediately identify it as designed because a) we never see watches assembling by evolutionary processes, and b) we recognize it as the sort of thing that is commonly designed.

The point being that we know it when we see it, even if there were no explicit test to demonstrate our conclusion.

Now, obviously "I know it when I see it" is a very poor scientific argument, but there may be a nugget of truth buried there: there are certain characteristics of "designed" things that we can immediately recognize. (We're often able to do this even if it's a fragment of a part of we don't know what.) If one could formalize those characteristics it might be possible to formulate a test on that basis. (Pattern recognition algorithms are based on this principle.)

Note, BTW, that we need not make any assumptions regarding the properties or motives of the designer in order to identify the characteristics of design.

We would, however, have to assume that we could recognize at least some characteristics of non-human design. That's not a show-stopper. If the assumption is correct, then testing is possible. If it turned out to be impossible to recognize the characteristics of a non-human design, we'd end up a false negative result, which would be indistinguishable from a "no design" conclusion.

Disclaimer: Opinions posted on Free Republic are those of the individual posters and do not necessarily represent the opinion of Free Republic or its management. All materials posted herein are protected by copyright law and the exemption for fair use of copyrighted works.