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)

[Antonello]

This is NOT an answer to my question--what do the verses mean to you?

If you do NOT interpret them 'literally' then what do they mean to you?

Mind if I take a stab at it?

Paul wrote this Epistle to the Church of Rome in anticipation of his upcoming ministry there. However, he harbored fears that anticipated danger he was likely to encounter in Jerusalem prior to his arrival in Rome might cost him his life. Therefore he made sure to spell out the entire strategy he intended to use when preaching to the Jews and non-Christian gentiles so that, if he could not be there, the saints (members of the Church of Rome) could spread his message for him.

After laying out that the Jews were to be condemned for turning away from the gospel of Christ, and the non-believing gentiles were to be chastised that ignorance was no excuse, he layed out his logic as to why. This is where the scriptures you quoted come in...

Citing the parable of the creation of Man from the Old Testament, he used it as an analogy the members of the church could identify with to reinforce the idea that, since all of mankind was created by God, they all were subject to His laws. It did not matter if they rejected them or not, or even if they had ever heard of them or not. Furthermore, he created a logical link between sin and death as evidence that, since all men experienced one, then it followed that all men shared the other.

He continued to capitalize on the parable of Adam to draw on similarities between him and Christ. It fit nicely for illustrative purposes to liken 'one man' to 'one man', as it would make it easier to accept the idea that 'one man' (Christ) could be their salvation if they considered that 'one man' (Adam) caused the whole mess in the first place.

He did have to be careful here, though. The implied comparison between the result of Adam's transgression and the gift of Christ's redemption provided a potential loophole for skeptics: after all, if one affected all mankind without exception, then why not the other? And therefore why bother to accept Christ if the gift is already a guarantee? To combat that, Paul made sure to spell out that while sin propagated simply by virtue of inheritance, salvation was 'downstream', so to speak, and therefore had to be given and accepted.

He ended with the typical promises of bad stuff to those that rejected his sales pitch and eternal sunshine and roses to those that bought into the celestial timeshare he was selling.

Or at least that's my take on it. YMMV.

[UnbelievingScumOnTheOtherSide]

"God built the RNA-DNA engine."

You may be right, of course, but the notion isn't scientific and oughtn't to be taught as such

IF God in fact built it by direct manipulation but "science" reaches a different conclusion, then the shortcoming is in science. But if science shows that it could have happened some other way, then it probably did. Science has the obligation to assume a natural cause in order to try to discover natural processes behind all observations but it has no right to assume there was a natural process and then present that assumption as a fact without filling in every step of the process and answering every question.

Intelligent design is the sudden appearance of purposeful information in nature. Apparent order can appear at random locally within disorder. Such order is indistinguishable from design because science cannot decide whether it had a purpose. But some order, such as a working pocket watch (or a complete living cell?) appearing spontaneously, is so improbable that intelligence and purpose beyond the observable should be inferred. Something that occurs only on an infinitesimal chance is indistinguishable from a "miracle". And a universe of finite size and duration having appeared spontaneously on an infinitesimal chance is too small for another infinitesimal chance occurance to happen within it unrelated to the rise of an anthropic intelligence able to appreciate it. Such an occurance would be proof of intelligent design.

If man is natural, then man's intelligence is natural. If intelligence is natural, then "supernatural" intelligence, if it exists, is perfectly natural and remains a viable alternative explanation so long as any question remains. It becomes the leading explanation if it is shown that but for an infinitesimal chance, something could not have happened except for intelligent intervention. Either way it is amenable to scientific deduction.

[Thatcherite]

If intelligence is natural, then "supernatural" intelligence, if it exists, is perfectly natural...

Does anyone else see a problem with this? :)

[r9etb]

Fine. Give me the quote, "transcript," unquote, so that we can see his exact words, in context, rather than taking it on your say-so. Not too much to ask, eh?

[balrog666]

No. A conservative who understands the purpose and scope of science.

Oh, this I have to read - post it, please.

[BlueStateDepression]

(("You tell them "all or nothing", they can see from the physical evidence that "all" is false, therefore if they follow your logic they must entirely reject the bible."))

I will have to second that notion.

Ill take this time (as I am so new here) to set forth a bit of my position as it relates to this comment.

I take issue with the earth being 6000 years old.

I take issue with Adam being the stand alone first human.

I take issue with anyone that Commands, under threat of punishment, that they be worshipped.

If I am put to the choice of taking all the bible as 100 fact or dismissing it totally, based on these alone I would have to discount it totally.

Ok now that isn't quite what I do, but in that context of either/or I would be compelled to do so.

As a confirmed Lutheran, I have faith that God is a possibility. As a part of my faith I belive it is also possible that there is not. As a stargate FAN, I have faith that there is a bit more to the story than the bible lets on. I find much of the bible honorable, but I also subscribe to the notion that nothing is absolute.

What I do Know, is that some questions are left open and IMHO, the best thing to provide progress in gaining the answers is to seek them out. I would offer that science is the best current method of doing so.

I think that the Bible and organized religion as a whole was designed by Man as a way to answer the question WHY that all people will always ask. It was a way of satisfying the desire to seek out why people should live honorably.

I am trying not to rant, I am just trying to put my comments into context and let people that do not know me where I am coming from. I am not trying to offend.

[Liberal Classic]

It's in one of the recent threads that I have been bookmarked, as well as link to the orig PDF document. I can't find it right now. You're just going to have to take my word for it for now.

[r9etb]

I can't find it right now. You're just going to have to take my word for it for now.

I'll wait until you can find it.

[Liberal Classic]

He said he made this determination based on his personal theology and philosophy.

[hershey]

Astonishing, amazing, wonderful.

[Ichneumon]

[furball4paws:] When you pin down any IDer he/she will eventually say the designer is God

[r9etb:] Oh? Are you God, then? Are the folks who produce my son's insulin, God?

[blah blah blah]

Nevertheless, I note you're not addressing the fact that you're an intelligent designer who is not God. Thus we see that it is not necessary to invoke God when making the hypothesis.

Oh, for pete's sake...

Read this again until it sinks in (from post #160):

Yawn -- yet another dishonest straw man. Look, son, no one has ever denied that "intelligent design" as a *process* works. That would be immensely stupid, which is a) why no one ever makes that claim, and b) why it's immensely stupid *and* dishonest for you to try to imply that we ever had.

Instead, as we are quite clear to anyone with working reading comprehension (admittedly, this leaves out a lot of "IDers"), is that the "Intelligent Design postulate" (as held by the Intelligent Design movement) which hypothesizes that there was "design" in the formation of life as we know it is, in its current state, utterly unscientific and untestable. It consists of nothing more than the postulate (it doesn't even rise to the level of "hypothesis", much less "theory") that: some (unspecified) form of (unspecified) intelligence added some (unspecified) amount of (unspecified) "design" into life on Earth at some (unspecified) time(s).

This comment was made in a post ADDRESSED TO YOU, and you HAVE ALREADY RESPONDED TO IT, so you can hardly pretend that you didn't see it.

*HE's* talking about "the ID postulate", the one the "Intelligent Design" folks want to squeeze into schools, the one the Discovery Institute wants to pretend is actual science.

For some reason, whenever we talk about THAT movement and its positions, *YOU* want to keep blathering on about the fact that people can design things. Well no s**t, Sherlock, WE KNOW THAT. What *you* don't seem to grasp is that this childish point ("people make things!") is irrelevant to the discussion of that THE ID MOVEMENT itself is up to, what they claim and don't claim, and so on.

Look, we "get" your blindingly obvious point -- the one you keep trying to bring into a mind-numbing number of your replies -- the one we already realized years ago and doesn't have to be explained to us 99 times by you -- *AN* ID hypothesis need not involve the supernatural or be hopelessly vague. But so freaking what? WE KNOW THAT. So stop trying to explain the obvious to us, son, we're WAY ahead of you.

What *we're* talking about -- what you either keep missing like a blind man looking for a crow in a coal mine at midnight, or keep bringing up as a diversion from the *actual* topic *we're* discussing -- is the claims and failuers of THE CURRENT ID MOVEMENT. Now do you want to discuss *those*, or do you want to keep blathering on about "gosh, people can make things!"?

Your choice -- keep up your end of the conversation, or stop wasting our time.

[Antonello]

>>[Why isn't Krebs Cycle cited as an example of IC?]

>Is this Maynard's bike?

Even at the risk of encouraging your often inane comments on these threads, I have to admit -- *that* one was *funny*.

I find it a bit funny too, but I am disappointed it wasn't followed with 'But seriously, here's why...' or 'That's a good example; let's discuss it...'.

Sadly, all my question got was a cheap joke and a brushoff.

[Doctor Stochastic]

I do note that the IDers do not disclaim Dembski's equating ID with Theology (albeit a particular type thereof.) The phrase "Forked Tongue" does come to mind.

[VadeRetro]

I don't see anything in your post except for the rehashed 19th century interpretations of the second law and some out of context quotations.

Actually, it's rehashed creationist crap--just for instance: no real law of physics uses the phrase "tends to"--plus Demski's Specific Complex Obfuscation. ("Raw energy cannot generate the specified complex information in living things.") Again, the real second law of thermodynamics makes no appeal to such nonsense.

Prigogene got a Nobel for his work demonstrating that Dembski was wrong, long before Dembski ever typed. Yes, even as Ross says in the quoted bit, the second law of thermodynamics operates even in systems far from thermodynamic equilibrium. However, all kinds of complex interactions do tend to happen so long as said system has not run down. The operation of the second law does not prevent these things.

Oddly enough, GOPPachyderm, although you "responded" to my point by going out and getting an AiG article to paste in, that article contains the very kind of nonsense I anticipated and already answered.

information tends to get scrambled

order tends towards disorder

a random jumble won’t organize itself

If these were, as advertised, real ways of stating the second law of thermodynamics, hurricanes could not form from already-diffuse warm air masses in the Atlantic off North Africa. You could never get the concentrated fury (and structure) of a tornado. You could never get the order and beauty of a snowflake.

The version of the second law of thermo cited by Sarfati is not the one used by physics and it's wrong. Don't make me tell you again, OK?

[furball4paws]

Still coy, huh. Read the trial transcript. I believe PH has it in his links.

[Doctor Stochastic]

Sautéed energy?
Parboiled energy?
Roasted energy?
Toasted energy?
Poached energy?
Deep fried energy?

[b_sharp]

Here I go again, poking my nose in.

"I'm not being coy. What you do is design -- intelligent design. You are a living, breathing example of the fact that supernatural actions and agents are neither necessary nor sufficient to put forth an intelligent design hypothesis."

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.

[Rudder]

Mext time you need surgery, call upon your local piano player.

[VadeRetro]

Medium rare energy works best for me. With a nice salad and a good dry red wine.

[b_sharp]

"Bare facts and "random bits of information" are not synonymous, but both can be scientific."

I did not say they were. I said that without collecting, analyzing and interpreting the 'facts' within a theoretical framework the 'facts' are nothing but random bits of information.

It sounds like you think science is nothing but the collection of 'random bits of information'.