Posted on 11/16/2005 3:40:35 AM PST by snarks_when_bored
* 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)
Yes, BUT, the point the IDers keep missing is that "detecting a designer" depends heavily upon specific knowledge of the designer's abilities, methods, and purpose.
We can "detect design" when we find an ancient astrolabe because it is very much the kind of thing that humans are *known* to make, for *known* purposes, via *known* methods and materials, etc. etc.
However, the "IDers" keep refusing to pin down *anything* about the alleged "ancient designer(s)". Without knowing anything about an alleged "designer's" methods, purpose, capabilities, intelligence, history, etc., it is epistemologically impossible to determine whether any given object is or is not an instance of that hypothetical designer's "design". Is the pile of rocks in yon forest "designed" by this hypothetical designer in their current configuration? Maybe, maybe not -- who the hell can say?
If we find something on a distant planet that *looks* like a machine, can we determine whether it was "designed" by some unspecified and unknown designer of unknown purposes and unknown abilities? How the heck would we be able to know? What exactly would we test for? It might turn out that the *puddles* on the planet were designed by aliens who wanted puddles for some reason, while the "machine" was the result of some natural process like the formation of a clamshell or some bizarre natural process resulting from the planet's unique chemistry and weather which we did not yet understand.
The point is that in order to tell if thing X is the product of process Y, we *must* know enough about process "Y" in order to be able to determine what kinds of things it actually *is* likely to produce, and what it's not likely to produce, *and* enough about other processes that might be at work in order to make sure that we're not mistaking the results of process Y for the results of another process Z.
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"?
You stretch science to the point of a gross caricature of reason in suggesting there is "no evidence for intelligent design" when so much matter is organized to carry out purposeful function on a scale both micro and macroscopic.
Really? What's the "purposeful function" of a snowflake?
You've indulged your hatred of God to the point of insanity, and it is unbecoming.
Now you're just ranting.
Conflation of molecular entropy and informational entropy.
As it applies to biology it is more correctly stated as: Energy spontaneously tends to flow from being concentrated to being diffused or dispersed if not hindered. Entropy is a measurement of the amount of energy that has been diffused.
"An open system exchanges both matter and energy with its surroundings. Certainly, many evolutionists claim that the 2nd Law doesn’t apply to open systems. But this is false. Dr John Ross of Harvard University states:
"… there are no known violations of the second law of thermodynamics. Ordinarily the second law is stated for isolated systems, but the second law applies equally well to open systems. … There is somehow associated with the field of far-from-equilibrium thermodynamics the notion that the second law of thermodynamics fails for such systems. It is important to make sure that this error does not perpetuate itself.1
This is not what evolutionists say at all. The 2LoT applies everywhere, however it can be held off by various mechanisms (it is not immediate). Further, the application of energy can trigger (overcome the activation energy) a reaction which in the case of chemical bonds allows complex (3 atoms or more) molecules to form. The point is that an open system makes more energy available to do work.
"Open systems still have a tendency to disorder. There are special cases where local order can increase at the expense of greater disorder elsewhere. One case is crystallization, covered in Question 2 below. The other case is programmed machinery, that directs energy into maintaining and increasing complexity, at the expense of increased disorder elsewhere. Living things have such energy-converting machinery to make the complex structures of life.
Note the use of the term 'machinery' in an attempt to inject ID into the system. Living organisms have chemical molecules that in the process of putting externally sourced energy to work by either combining smaller molecules into more complex molecules (and diffusing a small amount of energy) or overcoming activation energies of 'stored' energy to make it available to do work (thus diffusing the energy).
"The open systems argument does not help evolution. Raw energy cannot generate the specified complex information in living things.
This assumes the premise that CSI is part of biological organisms. Without some verification that the premise is valid any argument using it should be ignored.
"Undirected energy just speeds up destruction.
This is another attempt to inject ID into the argument. It completely ignores the use of entropy to accomplish work. It also ignores the possibility of having the energy flow obstructed until the activation energy is overcome. Energy can be obstructed for any length of time.
"Just standing out in the sun won’t make you more complex—the human body lacks the mechanisms to harness raw solar energy.
Except to make vitamin D. This is a strawman argument. Humans use energy from the sun indirectly, through eating plants and animals. These sources 'store' energy that is obstructed from diffusing until we ingest it. During the process of our using and storing that energy some of it diffuses as body heat and bodily excretions. (Anytime energy diffuses, entropy increases meaning that the 2LoT is being followed).
"If you stood in the sun too long, you would get skin cancer, because the sun’s undirected energy will cause mutations. (Mutations are copying errors in the genes that nearly always lose information).
The only time this is a problem for evolution is if the mutation occurs in the gamete. Skin cancer or other radiation damage that occurs in any other cell does not affect the inheritance of DNA. You will note that the majority of mutations in germ cells is due to copy errors during meiosis, are primarily neutral and are not related to radiation. Using the term 'undirected' is simply a red herring.
"Similarly, undirected energy flow though an alleged primordial soup will break down the complex molecules of life faster than they are formed.
It will, depending on the temperature, also allow complex molecules to form by overcoming any activation energy. It is only a problem it the temperature is high enough to break the chemical bonds.
This entire paragraph is a strawman.
"It’s like trying to run a car by pouring petrol on it and setting it alight.
This is a huge strawman and a false analogy to boot. The use of energy for work and the increase of entropy as used in biological organisms is in no way similar to pouring gas on a car. Biological organisms (other than plants with chlorophyll) use the sun's energy indirectly, by pouring the gas into the gas tank.
"No, a car will run only if the energy in petrol is harnessed via the pistons, crankshaft, etc. A bull in a china shop is also raw energy. But if the bull were harnessed to a generator, and the electricity directed a pottery-producing machine, then its energy could be used to make things.
The creation of molecules takes energy. Work done in chemical reactions takes energy. Complexity is created by all sorts of natural processes that use energy, much of it energy being diffused by an external source, which of course increases the entropy of that source.
Got an example for that one, baldie?
Just more projection - this is a considerably more stupid Fester than we usually see.
Harumpf.
r9etb implied I was God, and did I get a placemarker? Huh?
You guys are a kick. :)
"The design itself is proof of a designer."
An earthquake shakes a container of salt on the counter to the edge and it falls over. On the floor there is pattern, a design.
Is the designer circumstance at random or is there a designer of biblical proportion involved?
Two further points:
1. Are we sure the mass of the glass bead being tugged along did not affect the mechanics?
2. I'd been playing in my mind with just such a mechanism: often people trying to get protein structure from ab initio sequences take some molecular dynamics program and let the protein "relax" to a preferred structure. But of course this isn't how proteins are constructed in vivo: if you add one peptide at a time, the lowest energy configuration of an intermediate fragment might be different than the preferred configuration of that same subsequence in the full chain. What effects would there be on predicted protein folding starting from one peptide at a time? Do we have enough CPU time to model this properly?
Extra credit: Are all proteins build "one peptide at a time" or are significant sub-assemblies built first and then put together using enzymes? I dunno? Any biochemists here have any ideas?
Cheers!
Full Disclosure: Thanks, Snarks!
There's GOT to be a pun in there about Santa Claus and mythological beliefs-- "making a list, checking it twice" etc.
Cheers!
More food for thought: has anyone looked into error rates of base pair substitution in DNA replication as a function of nearest neighbor or nearby sequence?
E.g. is there more likely to be an error in the nucleotide after every GTCGGA than after every GGGAAT?
Are some amino acids in the protein more "error prone" than others?
Full Disclosure: I mean in the original expression rather than in animals with these defects, which subsequently survive long enough to be tagged and/or breed...
Don't get the cart before the horse. :-)
The flame wars in Crevo Threads on Free Republic! :-)
"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."
You've only shown that man's intelligence is natural, not all intelligence. This means that supernatural intelligence may not necessarily be natural and your argument falls apart. You still need to show that supernatural intelligence is natural. This will be difficult because of the definition of 'supernatural' which means, I believe, above nature. It appears that anything supernatural is not natural by definition.
You didn't see it, the author apparently did. You read a posted excerpt of what the author reported that they saw. :-)
Sorry, just makin' waves tonight. I had a hard week at work today. :-(
Cheers!
That would be not only classically forbidden, but completely degenerate :-)
Are you Hermitian?
Welcome to the monkey house.
Just for information purposes, I too was a confirmed Lutheran... at 14. I am now what is generally called a strong atheist.
500
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