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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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Anybody who reads this article and feels no astonishment is either stupid or not paying attention.

As an aside, note that the RNA polymerase, once brought into contact with the DNA strand, simply begins its replicative journey, moving along the strand one base pair at a time (as the experiment apparently demonstrates for the very first time). Now why does the RNA do this? Nobody (in their right mind) would suggest that it has a will and is acting intentionally, or that some unseen deity's hand is continually pushing it along, so it must be acting as its chemical structure compels it to act. This base-pair by base-pair copying motion must simply be what the chemical structure of RNA does. So why this chemical structure and not some other? This is a question that doesn't appear to lend itself to a scientific answer. Perhaps an ID'er would suggest that a higher intelligence designed the chemical structure of RNA to do just what it does. That may or may not be, but, clearly, it's not an hypothesis of empirical science. As a consequence, prolonged examination of such a hypothesis—as if it were a scientific hypothesis—has absolutely no place in a science classroom.

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.

1 posted on 11/16/2005 3:40:36 AM PST by snarks_when_bored
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To: RadioAstronomer; longshadow; grey_whiskers; headsonpikes; Iris7; PatrickHenry

Wake-up ping...


2 posted on 11/16/2005 3:41:03 AM PST by snarks_when_bored
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To: VadeRetro; Junior; longshadow; RadioAstronomer; Doctor Stochastic; js1138; Shryke; RightWhale; ...
Evolution Ping

The List-O-Links
A conservative, pro-evolution science list, now with over 320 names.
See the list's explanation, then FReepmail to be added or dropped.
To assist beginners: But it's "just a theory", Evo-Troll's Toolkit,
and How to argue against a scientific theory.

3 posted on 11/16/2005 3:48:05 AM PST by PatrickHenry (Expect no response if you're a troll, lunatic, retard, or incurable ignoramus.)
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The CrevoSci Archive
Just one of the many services of Darwin Central
"The Conspiracy that Cares"

CrevoSci threads for the past week:

  1. 2005-11-16 Ultra-sensitive microscope reveals DNA processes
  2. 2005-11-15 Early Humans Settled India Before Europe, Study Suggests
  3. 2005-11-15 'Perception' gene tracked humanity's evolution, scientists say
  4. 2005-11-15 'Perception' gene tracked humanity's evolution, scientists say [Locked]
  5. 2005-11-15 Stanford Scientists' Discovery of Hormone Offers Hope For Obesity Drug
  6. 2005-11-15 The Intrinsic Evil of Evolutionary Humanism
  7. 2005-11-14 A column about Kansas Science Standards
  8. 2005-11-14 Darwin And The Origin Of ….The Racist?
  9. 2005-11-14 For Republicans, a debate over the party's design
  10. 2005-11-14 THE CATHOLIC CHURCH EMBRACES EVOLUTION!!!!
  11. 2005-11-13 Intelligent Design Grounded in Science
  12. 2005-11-13 Intelligent Design, Part 1
  13. 2005-11-13 Pope states the universe is a product of an 'intelligent project'
  14. 2005-11-13 Santorum: Don't put intelligent design in classroom
  15. 2005-11-13 Vietnam study shows bird flu virus mutating - media
  16. 2005-11-12 [Kansas Gov. Kathleen] Sebelius criticizes State Board of Education's move [new science standards]
  17. 2005-11-12 ID [Intelligent Design] Opens Astronomer’s Mind to Universe’s Surprises
  18. 2005-11-11 A revolution for evolution - Intelligent design must not replace hard science in classrooms.
  19. 2005-11-11 Dover results disputed: School board candidate says machine was faulty
  20. 2005-11-11 FR Debate: Intelligent Design vs. Birth Defects, Can They Be Reconciled?
  21. 2005-11-11 Potential Origins of Europeans Found
  22. 2005-11-11 The Real Evil of Evolutionary Humanism
  23. 2005-11-10 Culture War Briefing, weekday news guide
  24. 2005-11-10 Fossils of fierce-looking dinosaur found in Argentina (Godzilla)
  25. 2005-11-10 Is Intelligent Design a Bad Scientific Theory or a Non-Scientific Theory?
  26. 2005-11-10 Kansas educators clear way for evolution criticism
  27. 2005-11-10 Pat Robertson has a message for Dover, PA: Don't ask God to help.
  28. 2005-11-10 Pat Robertson Warns Pa. Town of Disaster
  29. 2005-11-10 US states divide over creationism [the view from the UK]
  30. 2005-11-10 Why the conspiracy theorizing about theories? (Freeper op-ed)

CrevoSci Thread Count, 2005 YTD:  1103


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2000-11-29 An.American.Expatriate
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2000-11-02
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1998-11-13 jennyp
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2002-11-17 Just mythoughts
2004-11-11
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1998-11-18 malakhi
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Longest CrevoSci Thread Ever


Glossary of Terms

Assumption: Premise: a statement that is assumed to be true and from which a conclusion can be drawn; "on the assumption that he has been injured we can infer that he will not to play"
Belief: Any cognitive content (perception) held as true; religious faith
CrevoCreation vs. evolution
CrevoSciCreation vs. evolution/Science
CrevoSci Warriors:  Those who take part on CrevoSci threads
Data: factual information, especially information organized for analysis or used to reason or make decisions
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Hypothesis: A tentative theory about the natural world; a concept that is not yet verified but that if true would explain certain facts or phenomena; "a scientific hypothesis that survives experimental testing becomes a scientific theory"; "he proposed a fresh theory of alkalis that later was accepted in chemical practices"
Impression: A vague idea in which some confidence is placed; "his impression of her was favorable"; "what are your feelings about the crisis?"; "it strengthened my belief in his sincerity"; "I had a feeling that she was lying"
Law: A generalization that describes recurring facts or events in nature; "the laws of thermodynamics"
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The
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4 posted on 11/16/2005 3:48:56 AM PST by Junior (From now on, I'll stick to science, and leave the hunting alien mutants to the experts!)
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To: snarks_when_bored

God built the RNA-DNA engine. A very beautiful thing.


5 posted on 11/16/2005 3:54:58 AM PST by agere_contra
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To: snarks_when_bored

Holy Cow! That is awesome!


6 posted on 11/16/2005 3:55:57 AM PST by Adder (Can we bring back stoning again? Please?)
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To: snarks_when_bored

Amazing!

Do I see cloning as a common reality coming?

Me thinks so ... .

I'm not convinced knowing how this works will lead to good things considering the mindset of MANY in the field of science.


7 posted on 11/16/2005 3:59:50 AM PST by nmh (Intelligent people believe in Intelligent Design (God).)
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To: agere_contra
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 (which, of course, was the point of my little aside).

A very beautiful thing.

Completely true.

8 posted on 11/16/2005 4:02:55 AM PST by snarks_when_bored
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To: agere_contra
"God built the RNA-DNA engine. A very beautiful thing."

No doubt about that!

What concerns me is how the godless will use this information. There is no honor amongst them ... . Ethics are not present either.
9 posted on 11/16/2005 4:03:14 AM PST by nmh (Intelligent people believe in Intelligent Design (God).)
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To: Junior

Dang, Junior! Hadn't seen that.


10 posted on 11/16/2005 4:08:52 AM PST by snarks_when_bored
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To: nmh
What concerns me is how the godless will use this information. There is no honor amongst them ... . Ethics are not present either.

This is far from true, as some thought and some attention to history would show. And (by way of anecdote) don't forget that the BTK monster was a well-respected Lutheran congregant...

11 posted on 11/16/2005 4:14:50 AM PST by snarks_when_bored
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To: snarks_when_bored
It is almost like they were able to watch it's shadow as it moved along. Pretty slick.
12 posted on 11/16/2005 4:15:01 AM PST by Mark was here (How can they be called "Homeless" if their home is a field?.)
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To: Mrs Mark

Slick, indeed. A kind of Glasperlenspiel. Hesse might have been pleased.


13 posted on 11/16/2005 4:18:49 AM PST by snarks_when_bored
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To: snarks_when_bored; gobucks; mikeus_maximus; MeanWestTexan; JudyB1938; isaiah55version11_0; ...
(((Creationist Ping)))



You have been pinged because of your interest regarding matters of Creation vs. Evolution - from the Creationist perspective. Freep-mail me if you want on/off this list.

Colossians 1:16 "For by him all things were created: things in heaven and on earth, visible and invisible, whether thrones or powers or rulers or authorities; all things were created by him and for him."



DNA: marvelous messages or mostly mess?
There is no known non-intelligent cause that has ever been observed to generate even a small portion of the literally encyclopedic information {DNA} required for life.

How does anyone look at the wonder of DNA and think "accident" and "random chance"?
14 posted on 11/16/2005 4:41:47 AM PST by DaveLoneRanger (As long as liberalism and I exist, neither one of us is safe.)
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To: snarks_when_bored
. . .but the notion isn't scientific . . .

I hear that often. Is it true?

15 posted on 11/16/2005 5:25:07 AM PST by Fester Chugabrew
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To: snarks_when_bored
What an ingenious and elegant process!

For since the creation of the world God's invisible qualities—his eternal power and divine nature—have been clearly seen, being understood from what has been made, so that men are without excuse. (Romans 1:20)

16 posted on 11/16/2005 5:26:50 AM PST by Gritty ("The GOP is the party of small government, big government, and of all points in between - Mark Steyn)
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To: nmh
What concerns me is how the godless will use this information. There is no honor amongst them ... . Ethics are not present either.

*sigh*

17 posted on 11/16/2005 5:30:01 AM PST by Liberal Classic (No better friend, no worse enemy. Semper Fi.)
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To: Fester Chugabrew

Yes.


18 posted on 11/16/2005 5:30:20 AM PST by Liberal Classic (No better friend, no worse enemy. Semper Fi.)
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To: snarks_when_bored
So why this chemical structure and not some other? This is a question that doesn't appear to lend itself to a scientific answer.

It DOESN'T???

Why not?


Perhaps an ID'er would suggest that a higher intelligence designed the chemical structure of RNA to do just what it does.

Perhaps a scientist will be able to show how something OTHER than a copy manages to get into the strand.

Since this is the very essence of Evolution, THAT is what is needed now to blast the IDer's out of the water.

19 posted on 11/16/2005 5:32:53 AM PST by Elsie (Heck is where people, who don't believe in Gosh, think they are not going....)
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To: snarks_when_bored
Nobody (in their right mind) would suggest that it has a will and is acting intentionally, or that some unseen deity's hand is continually pushing it along, so it must be acting as its chemical structure compels it to act. This base-pair by base-pair copying motion must simply be what the chemical structure of RNA does. So why this chemical structure and not some other? This is a question that doesn't appear to lend itself to a scientific answer. Perhaps an ID'er would suggest that a higher intelligence designed the chemical structure of RNA to do just what it does. That may or may not be, but, clearly, it's not an hypothesis of empirical science. As a consequence, prolonged examination of such a hypothesis—as if it were a scientific hypothesis—has absolutely no place in a science classroom.

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.


You sound like a 19-year-old who's just started college and is new to the wonders of both science and philosophy. Your conclusion is a perfect example of a non-sequitur and reveals gigantic gaps in your knowledge of both science and philosophy.
20 posted on 11/16/2005 5:35:40 AM PST by aruanan
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