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)

[snarks_when_bored]

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.

[snarks_when_bored]

Wake-up ping...

[PatrickHenry]

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.

[Junior]

The CrevoSci Archive Just one of the many services of Darwin Central "The Conspiracy that Cares"

• PatrickHenry's famous List-O-Links
• Webster's On-Line Dictionary:  Creationist

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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CrevoSci Warrior Freepdays for the month of November:
 

2000-11-29 An.American.Expatriate 2000-11-10 AncientAirs 2000-11-21 AndrewC 1998-11-18 angelo 2000-11-10 beavus 1999-11-22 Blood of Tyrants 2003-11-26 blowfish 2004-11-08 CarolinaGuitarman 1997-11-28 cd jones 2001-11-30 claptrap 2001-11-16 CobaltBlue 2005-11-10 culturewars 2002-11-21 DannyTN 2004-11-16 DaveLoneRanger 1997-11-30 Ditto 2001-11-16 dmz 2000-11-11 Ernest_at_the_Beach 2000-11-02 Exigence

2000-11-02 Exit 109 2004-11-05 FeeinTennessee 2000-11-22 FFIGHTER 2000-11-12 ForGod'sSake 2001-11-07 FourtySeven 2000-11-15 freespirited 2000-11-10 Godel 2004-11-06 GreenOgre 2004-11-03 Grey Rabbit 2000-11-04 harbinger of doom 2000-11-28 HiTech RedNeck 1999-11-05 Ichneumon 1998-11-13 jennyp 2005-11-10 jodiluvshoes 1998-11-25 Junior_G 2002-11-17 Just mythoughts 2004-11-11 kaotic133

2005-11-14 knowseverything 2003-11-18 little jeremiah 1998-11-18 malakhi 2000-11-19 Mike Fieschko 2004-11-24 mista science 2003-11-09 MplsSteve 2000-11-06 mrjeff 1999-11-05 muleskinner 2003-11-17 Nathan Zachary 2002-11-12 NCLaw441 1999-11-25 Nebullis 2000-11-13 NYer 2000-11-24 old-ager 2004-11-03 PajamaHadin 2000-11-10 Patriotic Teen 1998-11-01 Pharmboy 2000-11-11 P-Marlowe

2000-11-16 presidio9 1999-11-08 Pyro7480 2002-11-14 Remedy 2000-11-30 Right Wing Professor 2004-11-18 rightwinggoth 1998-11-15 rob777 1998-11-04 RobRoy 2004-11-01 SeasideSparrow 2004-11-05 shadowfighter 1999-11-16 TerP26 2004-11-13 This Just In 2000-11-04 TigerTale 2004-11-11 untrained skeptic 2004-11-21 VictoryGal 2001-11-25 Vote 4 Nixon 2000-11-05 will of the people 2003-11-29 woodb01

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In Memoriam
Fallen CrevoSci Warriors:

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1LongTimeLurker ALS angelo Area Freeper Aric2000 Askel5 Asphalt biblewonk bluepistolero churchillbuff claptrap codebreaker Con X-Poser ConservababeJen DittoJed2 dob

Ed Current f.Christian followerofchrist general_re goodseedhomeschool gopwinsin04 gore3000 IllumiNOTi JediGirl JesseShurun JethroHathaway jlogajan Justice Avenger Kevin Curry kharaku knowquest

Land of the Irish Le-Roy malakhi Marathon medved metacognative mikeharris65 missyme Modernman n4sir NoKinToMonkeys Ogmios peg the prophet Phaedrus Phoroneus pickemuphere

ReasonedThought ret_medic RickyJ SeaLion Selkie Shubi SplashDog The Loan Arranger Tomax tpaine Truth666 twittle Unalienable WaveThatFlag xm177e2

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Bring back Modernman and SeaLion!

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Lost CrevoSci Battlefields (Pulled Threads)

• 2004-04-27 Stop Teaching Our Kids this Evolution Claptrap!
• 2003-10-29 The Mystery of the Missing Links (Intelligent Design vs. Evolution)
• 2003-10-27 Physics Nobelist Takes Stand on Evolution
• 2003-10-23 Gene Found for Obsessive Compulsive Disorder
• 2003-10-21 Artificial Proteins Assembled from Scratch
• 2003-09-23 Solar System Formation Questions
• 2003-07-18 Unlikely Group May Revive Darwin Debate [Evolution v. Creationism]
• 2003-07-02 "Unlocking the Mystery of ""Unlocking the Mystery of Life"""
• 2003-06-26 Darwin Faces a New Rival
• 2003-06-06 Amazing Creatures
• 2002-09-13 Oldest Known Penis Is 100 Million Years Old
• 2002-04-10 (Creationists) CRSC Correction
• 2001-08-28 The Ultimate Creation vs. Evolution Resource [6th Revision]
• 2001-08-26 A Scientific Account of the Origin of Life on Earth [Thread I]
• 2001-01-13 A Christian Understanding of Intelligent Design
• 2000-10-10 Another Lost Generation?
• 2000-08-30 Evil-Ution
• 1999-11-14 Creationism's Success Past 5 Years: (Gallup: 1 in 10 hold secular evolutionist perspective)

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Longest CrevoSci Thread Ever

• 2002-12-11 Evolution Disclaimer Supported (6,879 replies)

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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
Crevo:  Creation vs. evolution
CrevoSci:  Creation 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
Dogma: a religious doctrine that is proclaimed as true without proof
Fact: When an observation is confirmed repeatedly and by many independent and competent observers, it can become a fact
Freepday:  The day a Freeper joined Free Republic
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"
Observation: Any information collected with the senses
Theory: A well-substantiated explanation of some aspect of the natural world; an organized system of accepted knowledge that applies in a variety of circumstances to explain a specific set of phenomena; "theories can incorporate facts and laws and tested hypotheses"; "true in fact and theory"

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The
official beer
of Darwin Central

[agere_contra]

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

[Adder]

Holy Cow! That is awesome!

[nmh]

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.

[snarks_when_bored]

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.

[nmh]

"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.

[snarks_when_bored]

Dang, Junior! Hadn't seen that.

[snarks_when_bored]

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...

[Mark was here]

It is almost like they were able to watch it's shadow as it moved along. Pretty slick.

[snarks_when_bored]

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

[Fester Chugabrew]

. . .but the notion isn't scientific . . .

I hear that often. Is it true?

[Gritty]

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)

[Liberal Classic]

What concerns me is how the godless will use this information. There is no honor amongst them ... . Ethics are not present either.

*sigh*

[Liberal Classic]

Yes.

[Elsie]

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?

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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.

[aruanan]

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.