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Ultra-sensitive microscope reveals DNA processes
New Scientist ^ | November 15, 2005 | Gaia [sic] Vince

Posted on 11/16/2005 3:40:35 AM PST by 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)


TOPICS: Culture/Society; Extended News; Miscellaneous
KEYWORDS: biology; chemistry; crevolist; dna; microscopy; rna; rnap; science
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To: All

We can jump in here, and mess up THIS thread.

http://www.freerepublic.com/focus/f-news/1525082/posts?page=8#8

After all; they DID say the code word!


1,181 posted on 11/19/2005 5:10:58 AM PST by Elsie (Heck is where people, who don't believe in Gosh, think they are not going....)
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To: Elsie
Gabu, gabu.

I am a medieval man. Full Disclosure: Disco mode.

1,182 posted on 11/19/2005 7:44:42 AM PST by grey_whiskers (The opinions are solely those of the author and are subject to change without notice.)
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To: Dimensio
* Posted by ml1954 to Sir Francis Dashwood

Math is abstract. Science attempts to describe reality.

Mathematics is reality, while your version of science is just a pitiful human attempt to describe it...

_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-

* Posted by Dimensio to Sir Francis Dashwood

I am here to correct the logical fallacies and factual errors often presented by creationists.

That is just my point, neither the so-called Big Bang or evolution theories are proven truth...

Just because you claim they are by your religious faith in them does not lessen the validity my criticism. I'm not an ecumenical or an orthodox atheist. Nothing is sacred to me. Your appeal to false authority is categorically no more true than what you accuse creationists of doing...

Your only purpose here is to advance a religious attack on the godists, your own holy war. This crusade is as illogical as is your lack of evidence in defense of the Big Bang and the evolution of human beings.

The “missing link” is missing still, as is any logic to your arguments. (Don't try to tell me Louis Leaky didn't spend decades looking for the “missing link” when he found Homo habilis and Zinjanthropus either.)

Your version of logic isn't even close to Boolean logic, categorical logic or prepositional logic...

_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-

Both of you are attempting to “cloud the issue” with ancillary and unrelated topics...

The original article that began this thread, one poster pointed out, contains a statement by the author about the “design” of DNA. Logic suggests that would mean some sort of designer, wouldn't it? Not that I would agree, but I do see the fallacy embedded in the story, as I see the fallacies promoted with unproven theories as the sole basis for their use as the only course of research.

What the both of you are doing makes about as much sense as the idiot Pax Macian on the drug threads trying to tell an atheist like me that God wants people to be drug addicts and then giving me long Biblical litanies that have nothing to do with drugs...

1,183 posted on 11/19/2005 8:22:10 AM PST by Sir Francis Dashwood (LET'S ROLL!)
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To: grey_whiskers
"As far as meaningless posts, I have taken it upon myself to liberally populate these threads with bad puns, in order to provide a change of pace from some of the flame wars.

You will find some here altogether too serious for simple attempts at humour. The rest of us appreciate a bit of humour here or there; puns of course being the pinnacle of said humour.

All I ask is that your puns remain on the less obscure side, so even the densest among us (primarily me) can enjoy them.

1,184 posted on 11/19/2005 9:10:03 AM PST by b_sharp
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To: b_sharp
You will find some here altogether too serious for simple attempts at humour. The rest of us appreciate a bit of humour here or there; puns of course being the pinnacle of said humour.

I appreciate your compliment--this is balm to my wounds after being called "mostly harmless" by CarolinaGuitarman. (See also the entry on Earth from the HitchHikers Guide to the Galaxy.)

All I ask is that your puns remain on the less obscure side, so even the densest among us (primarily me) can enjoy them.

We aim to please.

My adjurement to an earlier poster to "Play Fair" was a pun on "Playfair's theorem" from Euclidean geometry, after the poster had mentioned that a**2 + b**2 = c**2 does not hold in some curvilinear coordinate systems. (Playfair's theorem goes along with sum of angles of triangle being 180 degres goes along with ...)

Didja like the mosquito limerick?

1,185 posted on 11/19/2005 9:21:43 AM PST by grey_whiskers (The opinions are solely those of the author and are subject to change without notice.)
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To: highball

:^)


1,186 posted on 11/19/2005 9:24:37 AM PST by b_sharp
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To: Coyoteman

The Canadian judge gives a 5.6


1,187 posted on 11/19/2005 9:26:49 AM PST by b_sharp
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To: Elsie

Ouch!


1,188 posted on 11/19/2005 9:29:31 AM PST by b_sharp
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To: grey_whiskers
"As far as meaningless posts, I have taken it upon myself to liberally populate these threads with bad puns, in order to provide a change of pace from some of the flame wars.

I LOL. But I thought DDT was illegal?
Here's another version.

A mosquito cried out in pain:
"A chemist has poisoned my brain!"
The cause of his sorrow
was para-dichlorodiphenyltrichloroethane

My daughter told me this one:

Water is composed of two gins, Oxygin and Hydrogin.
Oxygin is pure gin. Hydrogin is gin and water.

1,189 posted on 11/19/2005 9:42:14 AM PST by b_sharp
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To: snarks_when_bored
The more we learn about the microscopic world, the less likely it seems that non-physical (or non-mathematical) principles are needed to explain its behavior.

I think you have that backwards ...

1,190 posted on 11/19/2005 10:04:36 AM PST by WildTurkey (True Creationism makes intelligent design actually seem intelligent)
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To: Sir Francis Dashwood
That is just my point, neither the so-called Big Bang or evolution theories are proven truth...

Absolutely no theory in science is or ever will be "proven truth". You have made it abundantly clear that you have no interest in actually understanding how science works or how science reaches its conclusions. Instead you fundamentally misrepresent science and throw out all manner of lies to support your misrepresntations rather than admit that your understanding is in error. Nothing that you say can be trusted.

Your only purpose here is to advance a religious attack on the godists

When you say this it makes me realise that your claim to being an atheist is also a lie. Only creationist morons think that the theory of evolution is "a religious attack" of any kind. You repeatedly claim that I'm attacking people of religion, yet you can't demonstrate that I'm doing any such thing.
1,191 posted on 11/19/2005 10:24:53 AM PST by Dimensio (http://angryflower.com/bobsqu.gif <-- required reading before you use your next apostrophe!)
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To: snarks_when_bored; All

Science can't speak of ethics and morality since they are religious based or based on unscientific personal biases.

An atheist scientist telling another atheist scientist that it is wrong and a lie to falsify data is speaking gibberish since science can not speak of moral truth. After all, while the scientist can be kicked out of the academy for falsifying data, there is no other moral judgment that can be supplied to brand the man an immoral liar...since science can not make absolute moral judgments!

Perhaps science SHOULD stay out of churches and churches OUT of science. Science can go make bombs...church folk should go fashion constitutions...like the constitution that founded this country 220 odd years ago.

Not a lot of scientists around when the Bill of Rights was established...but there were a bunch of religiously minded folk who were.(and yes I know some were Deists and atheists. but most of them were very well versed in Christian theology and history as well...and horror of horrors..Baptists, methodists and congregationalists as well).

So scientists go ahead and play with your trinkets and fossils and try to sell the rest of us on how you think the world began, and when the world is smoldering from the effects of the amorality that such materialist thought has wrought, it will be Christians trying to put civilization back together(the meek who have just inherited the Earth).

Science can tell how things are put together but it cannot teach how men should LIVE TOGETHER! Science cannot create rights and priviledges that men of Liberty should enjoy, it is the shared consenses of Religion and Morality that undergird our country's freedoms!


1,192 posted on 11/19/2005 11:07:41 AM PST by mdmathis6 ("It was not for nothing that you were named Ransom" from CS LEWIS' Perelandra!)
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To: mdmathis6
So scientists go ahead and play with your trinkets and fossils and try to sell the rest of us on how you think the world began, and when the world is smoldering from the effects of the amorality that such materialist thought has wrought, it will be Christians trying to put civilization back together(the meek who have just inherited the Earth).

If our world were to be smoldering in the near future, who would you call for the tools you need to survive--arrowheads, spears, fire? Would you call the priests or the archaeologists?

You would probably end up as a vegetarian, while you lasted (vegetarian--that's the Indian word for "bad hunter").

1,193 posted on 11/19/2005 11:37:21 AM PST by Coyoteman (I love the sound of beta decay in the morning!)
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To: Coyoteman

It seems that these tools you mentioned were developed by folk who had a rudimentary religious world view even thousands of years(for sake of the arguement) before Oppenheimer quoted a Hindi verse as he watched the Atomic bomb flash into existence"I have become Vishnu, the destroyer or worlds". No scientists running around thousands of years ago...just religious folk...or wannabe's,or lipservice atheists in fear of losing their heads.

Science can't create a civilization...at best it exists as civilization's servant; at worst it becomes the club of tyrants who scurge the virtuous and powerless into slvery with it!


1,194 posted on 11/19/2005 11:51:53 AM PST by mdmathis6 ("It was not for nothing that you were named Ransom" from CS LEWIS' Perelandra!)
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To: mdmathis6
Science can't speak of ethics and morality since they are religious based or based on unscientific personal biases.

Several reading assignments for you:

C.P. Snow, The Search
C.S. Lews, The Abolition of Man
D.L. Sayers,Gaudy Night

Cheers!

1,195 posted on 11/19/2005 3:22:51 PM PST by grey_whiskers (The opinions are solely those of the author and are subject to change without notice.)
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To: Coyoteman
If our world were to be smoldering in the near future, who would you call for the tools you need to survive--arrowheads, spears, fire? Would you call the priests or the archaeologists?

You would probably end up as a vegetarian, while you lasted (vegetarian--that's the Indian word for "bad hunter").

"The only tool you own is a set of toenail clippers. Whereas Steve has a wide assortment of both jacks and winches. Steve's children play with jacks and winches. Steve has every kind of tool he'll ever need for anything, right in his truck. If the world economy ever collapses, and mankind regresses to a primitive state, guys like Steve will be living in sturdy, safe shelters that they built with their own hands, eating food that they grew or caught. Whereas guys like you will be passing through the digestive systems of wolves."

--Dave Barry's Complete Guide to Guys

Cheers!

1,196 posted on 11/19/2005 3:28:04 PM PST by grey_whiskers (The opinions are solely those of the author and are subject to change without notice.)
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To: grey_whiskers; Coyoteman

I've read the Abolition of Man, where CS Lewis writes of the creation of "Men without Chests" by Britain's "modern school curricula...he is very scathing in his assessment of where modern materialism is going "We have created men who think critically with their brains and act sensually with their bodies(the exact quote may be off a bit but I know I am quoting the substance), but are devoid of age old virtue...we have created "en without Chests"


1,197 posted on 11/19/2005 3:36:05 PM PST by mdmathis6 ("It was not for nothing that you were named Ransom" from CS LEWIS' Perelandra!)
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To: Dimensio
Absolutely no theory in science is or ever will be "proven truth".

Many of them have been proven true (i.e., the earth is not flat).

But since you flat earth types will falsely claim that is not so, you cannot also logically claim the creationist theory a falsehood, as both evolutionary theory and creation theory “appeal to false authority,” an informal fallacy in logic.

This makes neither of them any more valid than the other, nor are either of them any more valid than the zany theory life came to this planet via extra terrestrials.

Evolution is nothing more than a religious science you defend.

So, I'm a heretic... As I said, I am not an orthodox atheist, nor am I an ecumenical atheist (there is no such thing).

1,198 posted on 11/19/2005 3:39:50 PM PST by Sir Francis Dashwood (LET'S ROLL!)
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To: Sir Francis Dashwood
Many of them have been proven true (i.e., the earth is not flat).

"The earth is not flat" is not a theory, it's a single statement. If you don't understand what a theory is then you carry no credibility here.

So, I'm a heretic... As I said, I am not an orthodox atheist, nor am I an ecumenical atheist (there is no such thing).

An atheist is simply someone who lacks belief in gods. But god-belief isn't the issue here, the dishonesty and scientific ignorance of creationists is. And your dishonesty and scientific ignorance.
1,199 posted on 11/19/2005 3:44:49 PM PST by Dimensio (http://angryflower.com/bobsqu.gif <-- required reading before you use your next apostrophe!)
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To: mdmathis6
There were other points in that book I was referring to as well...

1) Uniformity of ethics across cultures

2) The idea that the reputation of those attacking morality as more intellectual was an illusion.

In other words, there is a difference between knowledge and wisdon; the old quote about "the heart has its reasons, of which reason knows nothing"; the difference between connaitre and savoir (sorry about the missing circumflex...); etc.

Try The Search and Gaudy Night too. Things aren't always as clear in practice as they are in FR bull sessions. :-)

Cheers!

1,200 posted on 11/19/2005 3:47:18 PM PST by grey_whiskers (The opinions are solely those of the author and are subject to change without notice.)
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