As of 2/24/2008, Sewell has just responded to this, pretending that he just noticed it. To make discussions easier to follow, I have responded with a new post here, and I would appreciate it if comments could be posted there, to keep it all in one place.
My SciBling Mark Hofnagle over at the Denialist blog wanted me to take a look at the pseudo-mathematical ramblings of Granville Sewell. It actually connects with some of the comments in the thread about the paper by Dembski and Marks – Sewell uses part of the article to make the same kind of quantum nonsense claims that showed up here.
Sewell claims to have written a simulator which simulates the Universe, and is complaining that his supposed simulation didn’t produce things like computers or aircraft carriers. I say claims because I’m pretty convinced that he did no such thing. Actually programming a simulator like the simplest of the several he claims to have done, which produces the results that he claims it produced, would be an absolutely astonishing feat of programming, involving a quantity of data that’s more on the scale of Google than on the scale of Granville Sewell’s laptop.
Here’s what Sewell claims about the first attempt:
A friend read my article and said, computers have advanced a lot in the last seven years, I think we could actually try such a simulation on my new laptop now. So I wrote the program–in Fortran, naturally–and we tried it. It took several minutes, and at the end of the simulation we dumped the final coordinates of all the particles into a rather large data file, then ran MATLAB to plot them. Some interesting things had happened, a few mountains and valleys and volcanos had formed, but no computers, no encyclopedias, and no cars or trucks. My friend said, let me see your program. After examining it, he exclaimed, no wonder, you treated the Earth as a closed system, order can’t increase in a closed system. The Earth is an open system, you need to take into account the effect of the sun’s energy. So I modified the boundary conditions to simulate the effect of the entering solar radiation, and reran it. This time some more interesting things happened, but still no libraries or computers.
So, Sewell claims to have just knocked out a Fortran program which runs a particle-level simulation of the earth, based on classical mechanics, and to have run it on his laptop in “a few minutes”, and to have produced as a result, mountains, valleys, and volcanos. Remember that he’s claiming to be doing full physics – he’s working out the chemical reactions, the physical interactions, everything that’s involved in the environment of an earth-like planet. He claims to have programmed this himself, run it in a few minutes on a laptop, and to have then visualized the data with a simple MATLAB plot.
If he had actually done this – he worked out a way to implement a complete simulation like this that ran to completion in a matter of minutes – he’d be in line for a Nobel prize in physics. All he needs to do is make the data from a run of that program available, and I think we can pretty much guarantee him a date in Stockholm to collect his prize.
But that’s not all he claims to have done. He claims that his “friend” (who I suspect is as imaginary as this program he claims to have written) looked at the program, and saw that he didn’t do quantum physics:
My friend looked more carefully at the program, and said, good grief, you are using classical physics, you can’t simulate the effects of the four forces without quantum mechanics. He explained that according to quantum mechanics, the exact effects of these forces on any particular particle are impossible to predict with certainty, you can only calculate the probabilities. I said, you mean there is a supernatural force at work here?? He said, well, technically, yes, if you define the supernatural to be that which is forever beyond the ability of science to predict or explain–Sir Arthur Eddington said quantum mechanics “leaves us with no clear distinction between the natural and the supernatural”. But there is no reason to doubt that this so-called “supernatural” effect is completely random, you can simulate it using a random number generator. So I completely re-wrote my simulator, I used an IMSL random number generator with a user-supplied probability distribution to simulate this randomness, and computed the required probability distributions by solving the Schrodinger equations with my own PDE solver, PDE2D. Still no luck.
So, not only is Sewell himself a programmer of downright supernatural abilities – but his friend can look at a complete physics simulator, and, in a matter of moments, understand exactly what parts of physics are implemented, and what’s been left out.
I happen to be lucky enough to work at a company with some of the smartest, most skilled programmers in the world. We have a strict policy of code review – which means that every line of code is checked by a second programmer before it gets into a production system. So my coworkers are both brilliant programmers, and incredibly skilled at reading and comprehending code written by other people. But I don’t know anyone who could do what Sewell claims his friend did. I’ve never met anyone who could read code for a universe simulator that could simulate physics well enough to produce volcanoes, and could conclude that the code was correct, but that it didn’t include quantum physics.
But let’s say that Sewell is not only the greatest programmer in the world, but that his buddy is the second-best, and can just glance over Sewell’s Fortran program to see what he left out.
Of course, Sewell, being the genius and impeccably honest individual that we all know he is, claims complete ignorance of quantum physics up until this moment. He didn’t put it in originally, because he didn’t think it was important until his buddy pointed it out. But now that he knows about it, it strikes him – right out of the blue! – doesn’t quantum physics sound almost supernatural? And by golly, his friend reluctantly agrees with him. (And this, of course, has nothing to do with the fact that creationists have been doing the quantum shuffle, trying to shoehorn God into quantum effects for decades. Sewell knew nothing about that argument up until this very moment.)
So, now, Sewell sees the flaw in his system. He then completely rewrites his earth simulator. Not only that, he includes in it a complete and precise simulation of the quantum behavior of every particle in his simulation, using a partial differential equation solver. So he claims to have written complete and detailed physics simulator that can perfectly incorporate quantum behavior of each any every particle. And with this, he claims can still simulate the history of an earth-like planet – on his laptop in a matter of minutes.
I think that accomplishing that would easily win him another Nobel prize, in addition to the Nobel for the non-quantum simulator. All he’d need to do is publish the data. Wouldn’t that be a coup? A creationist professor from a diddly little school in Texas showing up all of the best and brightest physicists in the world, with something he did on a lark with one of his friends? Gosh, why do you suppose that he hasn’t published this? Hasn’t shown anyone the simulation? You think that maybe, just maybe, there’s a reason for that?
I suppose that Granville, modest gentleman that he is, might not like the spotlight that these awards would generate. That must be why he only mentions this astonishing feat of brilliance in a piece of sloppy apologetics.
Anyway, let’s move on. Suppose that Granville and his buddy are the true geniuses that he claims they are, and that he has accomplished this astonishing feat, but that’s he’s two modest to publicly show his work and claim the awards that are his due. What happens next in his little game with his brilliant friend? Why, that should be obvious to you! His brilliant friend – the guy that’s smart enough, and understands math and physics well enough to nigh-unto-instantly notice the lack of quantum phenomena in Granville’- simulation of the universe – this spectacularly brilliant guy spouts out one of the stupidest, most pathetic, transparently wrong canards that is constantly harped on by creationist morons everywhere: the reason that the simulation isn’t creating intelligent life is because it doesn’t include the way that natural selection violates the second law of thermodynamics.
So Sewell’s friend is not only one of the smartest people in the entire world; he’s also a total moron.
What does Sewell conclude from this entire episode? Obviously, intelligent life must not have evolved on earth, because no matter what he did to his simulation, he couldn’t make intelligent life evolve in his simulated world.
I seriously wonder in Sewell actually expects anyone to be taken in by this bullshit. It’s so transparently ridiculous, so full of impossible feats that he claims to have accomplished, I find it difficult to take seriously that he thinks anyone will believe it. It’s so wretchedly dishonest, so obviously dishonest, that I’m truly astonished by it.
Here’s the scary part: all of the stuff I wrote above is a charitable interpretation of his little story. In fact, he never talks about intelligent life. He actually writes as if he expects computers and aircraft carriers to pop out of his simulation directly. According to his argument, if life is a product of the physical laws of the universe, and this non-supernaturally created life can create artifacts like aircraft carriers, then we should expect things like aircraft carriers to simply poof into being by themselves. It’s frighteningly stupid.
To give a sense of the stupidity of that – think about this metaphor. The heavy elements of the universe were created inside of stars. Everything starts with the simplest of matter – basically just hydrogen. Through fusion, helium, and then the heavier elements, are created. They’re scattered around by supernovas when stars die. Stars are natural phenomena – just billions of particles behaving according to the laws of physics. By doing this, stars produce heavy elements, like Carbon and Iron. By Granville’s argument, if we create a simulation of a universe without any stars, we should expect Carbon and Iron to come into being, just like they would if there were stars. If they don’t, then there must be something supernatural about stars.
Mark,
sometimes the idiocy is almost too hard to take, and then there is such a beautiful take-down that it makes you almost happy that there are such nuts in the universe.
Thank you for such a rainbow.
Not to defend Sewell, but I don’t think he means to claim he’s *actually* created such a simulation. I think this was intended to be a satirical piece leading up to the disappointing “punchline,” the already thoroughly debunked “evolution violates 2LT” chestnut.
To create a computer to simulate the complete workings of a planet like Earth (never mind the rest of the universe) would take someone with the talents of Slartibartfast, and running the simulation would take billions of years.
I suppose the whole computer simulation carp was just his way of “framing” his eventual statement that natural selection defies the second law of thermodynamics, and thus would never happen. Which as you point out, is incorrect.
The snark is strong with this one…
Apparently you misunderstand the rules of make-believe.
I remember reading something by Henry Morris, who is usually credited with creating “Creation Science.” Morris thought that life violate 2LT, but that this was OK for a single organism because the books balanced when an organism died. Evolution was out for him of course, because it would decrease the entropy too much. I guess people such as Sewell and Morris don’t ever defecate, because they don’t understand that life follows all the laws that apply to all physical and chemical systems.
Since Sewell didn’t report seeing any fjords, I’m guessing he is not as talented a programmer as Slartibartfast.
I wonder if his fellow programmer might be Kirk Cameron. This makes as much sense as anything cutie Kirk ever said.
I’m curious about the classical part of his simulation. How did he stop the electrons from spiralling into the nuclei and an infinite amount of energy coming out as EM radiation? And did he get chemical bonds in the classical simulation?
But it seems it’s all pretend anyway.
Sewell didn’t intend his piece to be taken literally just as a thought experiment.
To Quote him on the blog
”Sorry. It honestly didn’t even occur to me that anyone would think I was trying to pass this “thought-experiment” off as non-fiction, certainly not anyone who read the whole post. But I guess some people didn’t read past the fold. And I didn’t file under humor because I didn’t consider it to be humorous.”
Having defended him in this respect I still think it is a load of crap. I find it amazing how supposedly intelegent people can think that somehow every scientist has failed to take into account the 2nd law.
The 2LOT problem everyone ignores, though, is the usually unsubstantiated assumption that entropy somehow decreases in the course of evolution. If you took 1 kg of flesh from a human, and 1 kg of Escherichia coli cell paste, I have absolutely no idea which would have the lower entropy, but I know the theory of evolution doesn’t have the remotest relevance to it.
I think the origin of the bad assumption that evolution decreases entropy is the very old fashioned and biologically discredited idea that humans are somehow more ‘evolved’ than E. coli. Of course, since we have a common ancestor, we’ve been at it precisely the same length of time. But even if you restrict yourself to the relatively simple issue of the configurational entropy of the genome, it’s not clear to me the CE of our genome is lower than the genome of a lungfish, say. And the configurational entropy of DNA is a very tiny part of the entropy of a living thing.
So, even if 2LOT prevented local decreases in entropy, which it emphatically does not, that still does not prove that evolution couldn’t have happened!
I’ve tried to understand Sewell’s argument, BTW, and I think it’s simply waffle. To use Pauli’s hackneyed phrase, he isn’t even wrong. He just doesn’t say anything that can be disproven.
Sewell’s claims about his “simulation” are absurd on their face. The closest thing I can think of to what he’s describing is an N-Body Simulation, which has O(N2) complexity and is thus an expensive computation on even small scales (it’s typically used for global illumination, explosions, etc.). Running it on the scale he’s taking about would likely be impossible even on a huge computing cluster, let alone your garden-variety laptop.
Some people act as if computers are magic artifacts that always produce the correct result instantly no matter what.
Remember the old story about the NASA orbital simulation that supposedly threw up a red flag confirming that sun stood still at some time in the past so the Hebrews could win a battle?
I suspect this is another case of the “computers are magic” thinking. One of my favorite creationist “proof” programs was a program that would attempt to get the random number generator in BASIC to produce, in order, the ASCII codes for the letters in “evolution”. It showed a stunning ignorance in that it had no check for the period of the BASIC interpreter’s PRNG. (I think it was written in Commodore BASIC.)
These people act as if computers are divine oracles, but only when they agree with the results.
Nice ending, a rebuttal with your own creationist story (formation of heavy elements from a hydrogen universe). This is one of the most beautiful and well supported theories of astronomy/cosmology. Yet we haven’t directly observed the conditions at the center of stars (beyond a few neutrinos), and only have a few low-res snapshots of supernovas and star formation. We depend on well supported modeling simulation for confirmation of this story.
Clumping of hydrogen to form the initial stars is the weakest link, although it seems that classical mechanics should be sufficient. We’d be blessed (by the reviewers) if his simulation demonstrated the mechanism behind early galactic and stellar evolution.
Well, *I* for one think Sewell did a great job of showing evolution to be a farce. In the same spirit, I went outside today, picked up some mud and formed it into a humanoid shape. Unfortunately, it didn’t come alive and start walking around. I even tried breathing on it! I think this pretty much proves that life on earth couldn’t have had a creator – it didn’t work for me, so it simply doesn’t work.
Seriously, you did not take this seriously. It is obviously comedy.
Did he have to claim to do this in FORTRAN? Makes the rest of us look bad. Of course what do you expect from someone who doesn’t even capitalize it correctly. Unless he meant Fortran 90, but everyone knows if you are going to simulate something totally insane, FORTRAN 77 is the only way to go.
please read the (new) postscript to Sewell and erase your embarrassing post
Not to defend Sewell, but I don’t think he means to claim he’s *actually* created such a simulation. I think this was intended to be a satirical piece leading up to the disappointing “punchline,” the already thoroughly debunked “evolution violates 2LT” chestnut.
We could practically make t-shirts at this point: “Intelligent Design: For heaven’s sake people, THIS IS A P-A-R-O-D-Y!!”
(You can tell they’re joking when they say that they’ve been doing experiments.)
MarkCC’s post rightly focuses mainly on the many things that are wrong with Sewell’s thought experiment, but keeps dramatically returning to an unnecessarily detailed discussion of how such a grandiose program could never actually work.
I’m aware that ID people are cranks and sometimes even knowingly misrepresent the facts, but this and the Denialism discussions about this particular ID post make me a little uncomfortable.
I get the feeling people are pretending not to be sure he’s joking.
Yeah, I know, I’m a big fat faker-pants.
So apparently mountains, valleys and volcanos don’t count as ‘order.’ Fascinating.
I can’t but help find it amusing when:
1. Sewell makes a parody, which defeats itself by relying on IDC’s parody of science. Seriously (or humorously :-), how can you tell an IDCist making a parody from an IDCist making an argument?
2. Mark H and Mark CC both, gets fired up into rant mode by the display of enormous stupidity. (Oh yes, it burns, you have my sympathy.)
3. Sewell is forced to amend his text:
But in the creo way there isn’t any revision number that shows it is changed.
4. People get uncomfortable by analyses of exactly how stupid Sewell is.
And is Sewell stupid! He wrote an anti-evolution 2LOT addendum in his math textbook, where he both manage to display his ignorance of physics (unwarrantably assuming perfect differentials) and errors of math.
The later, in the form of sign errors that makes his ‘derivation’ of a model for entropy calculations go through, may or may not be accidentally introduced. In any case it should embarrass him.
Now, it seems I may have missed a lot of entertaining quantum nonsense on the other GMBM thread due to lack of time. Rats!
Do’h! I forgot to note another amusing point: Sewell claims he couldn’t incorporate intelligence in his model.
So we are led to conclude that Sewell claims he has proved that intelligent design is also impossible. 🙂
#2: “Not to defend Sewell, but I don’t think he means to claim he’s *actually* created such a simulation. I think this was intended to be a satirical piece leading up to the disappointing “punchline,” the already thoroughly debunked “evolution violates 2LT” chestnut.”
You know, as satire Sewell’s piece is even worse than as simple creationist crap. Postulating that a perfect simulation of the universe can’t produce intelligence? Without any sort of actual evidence to back it up, he’s really just saying, “My shoddy understanding of the laws of physics and computer science reinforce my shoddy understanding of the laws of biology.”
I’m reminded of Scott Adams (of Dilbert fame) writing silly ID blog posts and then, when attacked, claiming it was all just a satirical exercise. I suspect that Sewell and his ilk wouldn’t be terribly upset if they won a few converts from gullible people who really believed that they had developed a “program of the universe.”
Good grief, now he’s blaspheming! We all know who his imaginary friend is.
Not so much parody as parable. Since Sewell can’t convince with logic, he’s going for folksy humor, safe in the assumption that most denizens of UD can’t see the holes in his argument.
A simulation that ran on a laptop would be doing a creditable job if it had plate tectonics (mountains and volcanoes) after 4 Gya. What’s he complaining about?
As I said else ware
How do the IDists think we’d take it when their serious posts are almost exactly in the same vein as their “street theater”.
I like how at the end of paragraph two, Mark CC divulges a secret of his new employer: Google has the power to model the universe! Wow j/k.
I read this post yesterday, but something just occured to me.
If it was all a “thought experiment,” Sewell must have “written” and “run” the simulation all in his head. If he’s claiming that’s as good as doing it in the real world, then he must be smarter than Reed Richard, Victor von Doom, The Mad Thinker and The Leader all put together.
Ben:
“More on the scale of” does not imply “capable of” 🙂
I have no concept of how much data Google stores. (I just write build tools!) All that I know is that it’s mind-boggling. It’s a hell of a bloody lot of storage. But it’s nowhere near enough to do a particle-model simulation of the earth.
How can I be so sure? Because a particle level simulation of the earth would have to include every particle that makes up those disk drives. Which would mean storing (at least) the position and velocity of each of those particles. It takes more than one magnetic atom on a disk to store the information about one of those particles – so the disks couldn’t store enough information to do a particle-level simulation of the particles that would eventually wind up becoming those disks.
And those disk drives are a virtually infinitessimal part of the number of particles that make up the entire earth.
I’d guess that with a volume of storage on the scale of all matter in the solar system – every planet, every comet, every speck of dust – that we still wouldn’t be able to store enough information to do a precise particle level simulation of the earth.
In response to No.11, I don’t know which of a random 1kg lump of people-flesh and E. coli paste would have greater entropy, but I’m pretty sure that if we compared an entire person and their weight in E. coli cultures, the person would have higher entropy, if only because human body temperature is higher than a free-living bacterial culture’s is.
I think part of the reason the second law canard is so staying is that religion tends to have a very strong and important sense of order and disorder, so mention of those concepts resonates strongly. Unfortunately, religious ideas of order have only the most misleading superficial resemblances to physical ideas like entropy, much like religious ideas of purity and cleanliness have only accidental resemblances to modern sanitation guidelines.
Re Sewell
I worked in the area of simulating automobile traffic on signalized urban networks and freeways. The model which we developed had some 200,000 FORTRAN statements, just for traffic simulation. The notion that this schmuck Sewell could develop a model to simulate the entire universe in a few days and run it on a laptop is utter nonsense. This guy is such a total numbnuts that he makes Michael Behe look like a competent scientist.
Sewell’s essay was obviously a parody. I just cant work out what it is supposed to be a parody of.
To me it seems to be an hilarious parody of silly ID arguments regarding computer simulations of evolution and stupid scientifically illiterate arguments about the second law of thermodynamics.
On the other hand the people at UD seem to think it is a parody targetting evolution.
Damn Heisenberg got us again…
I just wanted to point out that there was plenty of helium before the existence of stars. Much of the universe’s helium was produced in Big Bang nucleosynthesis.
As someone that spent the summer doing particle simulations, here’s a typical time scale to compare numbers with. Yes, his post was farce, and yes, MarkCC pointed out the impossibility of the simulation, so this is just provided as a factoid.
Simulating 10,000,000 photons moving through ~2cm of human skin (using no math more complicated than tan()) for ~500 iterations (until all the photons have
Maybe Sewell is framing?
(sorry)
Wait, I thought he was supposed to use FORTH?
Driving Force Of Evolution? Evolution Of Proteins Linked To Species’ Metabolic Rate
Source: University of Florida
Date: October 4, 2007
Keywords:
Evolution, Evolutionary Biology, Charles Darwin, Biology, Origin of Life, Human Evolution
Science Daily — “Survival of the fittest” has popularly described evolution for more than a century, but a new study published in the Royal Society journal Biology Letters provides further evidence that random genetic mutations over millions of years may also play a powerful role.
Florida and California scientists are the first to link the evolution of proteins — the organic compounds that determine the structure and function of living things — to a species’ metabolic rate.
Across species from fish to mammals, they found that rates of protein evolution showed the same body size and temperature dependence as metabolic rate. Specifically, their mathematical model predicts that a 10-degree increase in temperature across species leads to about a 300 percent increase in the evolutionary rate of proteins, while a tenfold decrease in body size leads to about a 200 percent increase in evolutionary rates.
“It does suggest that if there were an evolutionary arms race between a small, hot animal and a cold, big animal, it’s going to be awfully hard for the cold, big animal to keep up,” said James F. Gillooly, an assistant professor of zoology in the University of Florida College of Liberal Arts and Sciences and a member of the UF Genetics Institute. “But really, what we are showing is that neutral processes, processes that do not depend on natural selection, are important in governing its evolution.”
Natural selection, a concept first introduced by British naturalist Charles Darwin in 1859, is a cornerstone of biology that says evolution is driven by organisms passing along beneficial traits that help them survive and reproduce while weeding out unfavorable ones.
“We know evolution depends on the environment in which an animal lives,” Gillooly said. “And yet this study suggests that you can look at different species — and without knowing anything at all about their pressures to survive and reproduce in their respective environments — you can draw conclusions about their rates of protein evolution over millions of years. It’s pretty exciting.”
With collaborator Michael W. McCoy, Ph.D., a postdoctoral associate in UF’s department of zoology, scientists studied three cellular protein families from fish, amphibians, reptiles, birds and mammals — the only proteins for which sufficient data exist to perform the analyses.
“Generally, there are two schools of thought about what affects evolution,” said Andrew P. Allen, Ph.D., a researcher with the National Center for Ecological Analysis and Synthesis in Santa Barbara, Calif. “One says the environment dictates changes that occur in the genome and phenotype of a species, and the other says the DNA mutation rate drives these changes. Our findings suggest physiological processes that drive mutation rates are important.”
In a previous study, Gillooly and Allen determined how temperature controls rates of speciation — when animals and plants evolve into a new species. The latest research takes those findings to the genomic level.
“We’re not saying when this and that occur, an animal is going to grow a tail,” Allen said. “We can’t make these sorts of predictions, but this study suggests that we can perhaps predict how quickly an animal can evolve in the face of some environmental challenge. That is, we are defining constraints on the overall rate of evolution.”
Ultimately, the researchers found that rates of protein evolution are largely controlled by mutation rates, which in turn are strongly influenced by individual metabolic rates.
“There is an ongoing debate about what is driving the forces of evolution, and this is one of the clearest studies that say mutation is a driving force,” said Dan Graur, Ph.D., the John and Rebecca Moores professor of biology and biochemistry at the University of Houston, who was not involved in the research. “If you want to put a catch phrase on it, it is not so much the survival of the fittest, but survival of the luckiest. The outcome is not determined by the ‘fitness’ of a particular trait, in terms of whether the trait affects an animal’s ability to compete and survive.
“The database of proteins the researchers have used is limited, but at this time it is all there is to work with,” Graur continued. “The sampling of the various species, however, is amazing. The paper reinforces the view that proteins evolve mainly by mutation, although it is possible that the evolution of ‘important’ traits is driven by positive Darwinian selection. Unfortunately, at present we do not know how to identify and quantify important traits.”
Note: This story has been adapted from material provided by University of Florida.
Copyright © 1995-2007 ScienceDaily LLC — All rights reserved — Contact: editor@removeme.sciencedaily.com
I got to this post late, but excellent, excellent takedown, Mark.
I really like the backpedal into “parody” by the crank. Sometime, I’d like to get someone to do that followed by me requesting a detailed explanation of the “humor” in the “parody”.
Funny on one hand, sad on another. Honestly, as I understand it Bremmerman’s limit basically implies that no one will ever accomplish such a simulation even if the computer were the size of the Earth.
Behold! This didn’t even take a fake simulation. Interesting clues about biogenesis which, as we’ve said before, is not Evolution by Naturwal Selection as such.
Tiny DNA Molecules Show Liquid Crystal Phases, Pointing Up New Scenario For First Life On Earth
[A colorful microscope image showing that a solution of tiny DNA molecules has formed a liquid-crystal phase. The DNA molecules pair to form DNA double helices, which, in turn stack end-to-end to make rod-shaped aggregates that orient parallel to one another. (Credit: Michi Nakata)]
ScienceDaily (Nov. 23, 2007) — A team led by the University of Colorado at Boulder and the University of Milan has discovered some unexpected forms of liquid crystals of ultrashort DNA molecules immersed in water, providing a new scenario for a key step in the emergence of life on Earth.
CU-Boulder physics Professor Noel Clark said the team found that surprisingly short segments of DNA, life’s molecular carrier of genetic information, could assemble into several distinct liquid crystal phases that “self-orient” parallel to one another and stack into columns when placed in a water solution. Life is widely believed to have emerged as segments of DNA- or RNA-like molecules in a prebiotic “soup” solution of ancient organic molecules.
Since the formation of molecular chains as uniform as DNA by random chemistry is essentially impossible, Clark said, scientists have been seeking effective ways for simple molecules to spontaneously self-select, “chain-up” and self-replicate. The new study shows that in a mixture of tiny fragments of DNA, those molecules capable of forming liquid crystals selectively condense into droplets in which conditions are favorable for them to be chemically linked into longer molecules with enhanced liquid crystal-forming tendencies, he said.
“We found that even tiny fragments of double helix DNA can spontaneously self-assemble into columns that contain many molecules,” Clark said. “Our vision is that from the collection of ancient molecules, short RNA pieces or some structurally related precursor emerged as the molecular fragments most capable of condensing into liquid crystal droplets, selectively developing into long molecules.”
Liquid crystals — organic materials related to soap that exhibit both solid and liquid properties — are commonly used for information displays in computers, flat-panel televisions, cell phones, calculators and watches. Most liquid crystal phase molecules are rod-shaped and have the ability to spontaneously form large domains of a common orientation, which makes them particularly sensitive to stimuli like changes in temperature or applied voltage.
RNA and DNA are chain-like polymers with side groups known as nucleotides, or bases, that selectively adhere only to specific bases on a second chain. Matching, or complementary base sequences enable the chains to pair up and form the widely recognized double helix structure. Genetic information is encoded in sequences of thousands to millions of bases along the chains, which can be microns to millimeters in length.
Such DNA polynucleotides had previously been shown to organize into liquid crystal phases in which the chains spontaneously oriented parallel to each other, he said. Researchers understand the liquid crystal organization to be a result of DNA’s elongated molecular shape, making parallel alignment easier, much like spaghetti thrown in a box and shaken would be prone to line up in parallel, Clark said.
A paper on the subject was published in the Nov. 23 issue of Science. The paper was authored by Clark, Michi Nakata and Christopher Jones from CU-Boulder, Giuliano Zanchetta and Tommaso Bellini of the University of Milan, Brandon Chapman and Ronald Pindak of Brookhaven National Laboratory and Julie Cross of Argonne National Laboratory. Nakata died in September 2006.
The CU-Boulder and University of Milan team began a series of experiments to see how short the DNA segments could be and still show liquid crystal ordering, said Clark. The team found that even a DNA segment as short as six bases, when paired with a complementary segment that together measured just two nanometers long and two nanometers in diameter, could still assemble itself into the liquid crystal phases, in spite of having almost no elongation in shape.
Structural analysis of the liquid crystal phases showed that they appeared because such short DNA duplex pairs were able to stick together “end-to-end,” forming rod-shaped aggregates that could then behave like much longer segments of DNA. The sticking was a result of small, oily patches found on the ends of the short DNA segments that help them adhere to each other in a reversible way — much like magnetic buttons — as they expelled water in between them, Clark said.
A key characterization technique employed was X-ray microbeam diffraction combined with in-situ optical microscopy, carried out with researchers from Argonne and Brookhaven National Laboratories. The team using a machine called the Argonne Advanced Photon Source synchrotron that enabled probing of the “nano DNA” molecular organization in single liquid crystal orientation domains only a few microns in size. The experiments provided direct evidence for the columnar stacking of the nano DNA pieces in a fluid liquid crystal phase.
“The key observation with respect to early life is that this aggregation of nano DNA strands is possible only if they form duplexes,” Clark said. “In a sample of chains in which the bases don’t match and the chains can’t form helical duplexes, we did not observe liquid crystal ordering.”
Subsequent tests by the team involved mixed solutions of complementary and noncomplementary DNA segments, said Clark. The results indicated that essentially all of the complementary DNA bits condensed out in the form of liquid crystal droplets, physically separating them from the noncomplementary DNA segments.
“We found this to be a remarkable result,” Clark said. “It means that small molecules with the ability to pair up the right way can seek each other out and collect together into drops that are internally self-organized to facilitate the growth of larger pairable molecules.
“In essence, the liquid crystal phase condensation selects the appropriate molecular components, and with the right chemistry would evolve larger molecules tuned to stabilize the liquid crystal phase. If this is correct, the linear polymer shape of DNA itself is a vestige of formation by liquid crystal order.”
Adapted from materials provided by University of Colorado at Boulder.
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University of Colorado at Boulder (2007, November 23). Tiny DNA Molecules Show Liquid Crystal Phases, Pointing Up New Scenario For First Life On Earth. ScienceDaily. Retrieved November 23, 2007, from http://www.sciencedaily.com /releases/2007/11/071122151148.htm
Behold! This didn’t even take a fake simulation. Interesting clues about biogenesis which, as we’ve said before, is not Evolution by Natural Selection as such.
[resubmitted from first time on November 23, 2007 2:28 PM]
Tiny DNA Molecules Show Liquid Crystal Phases, Pointing Up New Scenario For First Life On Earth
[A colorful microscope image showing that a solution of tiny DNA molecules has formed a liquid-crystal phase. The DNA molecules pair to form DNA double helices, which, in turn stack end-to-end to make rod-shaped aggregates that orient parallel to one another. (Credit: Michi Nakata)]
ScienceDaily (Nov. 23, 2007) — A team led by the University of Colorado at Boulder and the University of Milan has discovered some unexpected forms of liquid crystals of ultrashort DNA molecules immersed in water, providing a new scenario for a key step in the emergence of life on Earth.
CU-Boulder physics Professor Noel Clark said the team found that surprisingly short segments of DNA, life’s molecular carrier of genetic information, could assemble into several distinct liquid crystal phases that “self-orient” parallel to one another and stack into columns when placed in a water solution. Life is widely believed to have emerged as segments of DNA- or RNA-like molecules in a prebiotic “soup” solution of ancient organic molecules.
Since the formation of molecular chains as uniform as DNA by random chemistry is essentially impossible, Clark said, scientists have been seeking effective ways for simple molecules to spontaneously self-select, “chain-up” and self-replicate. The new study shows that in a mixture of tiny fragments of DNA, those molecules capable of forming liquid crystals selectively condense into droplets in which conditions are favorable for them to be chemically linked into longer molecules with enhanced liquid crystal-forming tendencies, he said.
“We found that even tiny fragments of double helix DNA can spontaneously self-assemble into columns that contain many molecules,” Clark said. “Our vision is that from the collection of ancient molecules, short RNA pieces or some structurally related precursor emerged as the molecular fragments most capable of condensing into liquid crystal droplets, selectively developing into long molecules.”
Liquid crystals — organic materials related to soap that exhibit both solid and liquid properties — are commonly used for information displays in computers, flat-panel televisions, cell phones, calculators and watches. Most liquid crystal phase molecules are rod-shaped and have the ability to spontaneously form large domains of a common orientation, which makes them particularly sensitive to stimuli like changes in temperature or applied voltage.
RNA and DNA are chain-like polymers with side groups known as nucleotides, or bases, that selectively adhere only to specific bases on a second chain. Matching, or complementary base sequences enable the chains to pair up and form the widely recognized double helix structure. Genetic information is encoded in sequences of thousands to millions of bases along the chains, which can be microns to millimeters in length.
Such DNA polynucleotides had previously been shown to organize into liquid crystal phases in which the chains spontaneously oriented parallel to each other, he said. Researchers understand the liquid crystal organization to be a result of DNA’s elongated molecular shape, making parallel alignment easier, much like spaghetti thrown in a box and shaken would be prone to line up in parallel, Clark said.
A paper on the subject was published in the Nov. 23 issue of Science. The paper was authored by Clark, Michi Nakata and Christopher Jones from CU-Boulder, Giuliano Zanchetta and Tommaso Bellini of the University of Milan, Brandon Chapman and Ronald Pindak of Brookhaven National Laboratory and Julie Cross of Argonne National Laboratory. Nakata died in September 2006.
The CU-Boulder and University of Milan team began a series of experiments to see how short the DNA segments could be and still show liquid crystal ordering, said Clark. The team found that even a DNA segment as short as six bases, when paired with a complementary segment that together measured just two nanometers long and two nanometers in diameter, could still assemble itself into the liquid crystal phases, in spite of having almost no elongation in shape.
Structural analysis of the liquid crystal phases showed that they appeared because such short DNA duplex pairs were able to stick together “end-to-end,” forming rod-shaped aggregates that could then behave like much longer segments of DNA. The sticking was a result of small, oily patches found on the ends of the short DNA segments that help them adhere to each other in a reversible way — much like magnetic buttons — as they expelled water in between them, Clark said.
A key characterization technique employed was X-ray microbeam diffraction combined with in-situ optical microscopy, carried out with researchers from Argonne and Brookhaven National Laboratories. The team using a machine called the Argonne Advanced Photon Source synchrotron that enabled probing of the “nano DNA” molecular organization in single liquid crystal orientation domains only a few microns in size. The experiments provided direct evidence for the columnar stacking of the nano DNA pieces in a fluid liquid crystal phase.
“The key observation with respect to early life is that this aggregation of nano DNA strands is possible only if they form duplexes,” Clark said. “In a sample of chains in which the bases don’t match and the chains can’t form helical duplexes, we did not observe liquid crystal ordering.”
Subsequent tests by the team involved mixed solutions of complementary and noncomplementary DNA segments, said Clark. The results indicated that essentially all of the complementary DNA bits condensed out in the form of liquid crystal droplets, physically separating them from the noncomplementary DNA segments.
“We found this to be a remarkable result,” Clark said. “It means that small molecules with the ability to pair up the right way can seek each other out and collect together into drops that are internally self-organized to facilitate the growth of larger pairable molecules.
“In essence, the liquid crystal phase condensation selects the appropriate molecular components, and with the right chemistry would evolve larger molecules tuned to stabilize the liquid crystal phase. If this is correct, the linear polymer shape of DNA itself is a vestige of formation by liquid crystal order.”
Adapted from materials provided by University of Colorado at Boulder.
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University of Colorado at Boulder (2007, November 23). Tiny DNA Molecules Show Liquid Crystal Phases, Pointing Up New Scenario For First Life On Earth. ScienceDaily. Retrieved November 23, 2007
I found the ‘it was all a joke’ bit the most offensive. Like a child molester crying himself to sleep.
We really ought to defend the integrity of thought experiments. It’s not just making up shit.
Actually Granville thought the “simulation” was so obviously and absurdly beyond the capability of any practical computing device that no one would need to have it explained it was a thought experiment.
The most common elements in the universe are hydrogen and stupidity. Granville’s attackers sure showed that to be a truism.
I can’t believe how many folks on this site continue to be duped by this “thought experiment.” If you can be duped by this, imagine how easy it would be to be duped by something like, say, a theory of evolution! I think Granville has achieved a double coup here. First by a spoof on a thought experiment that was taken literally, and now by pointing out how gullible evolutionists are, he has heaped on them a second helping of ridicule!
Undergirding the rebuttals is the notion of the absurdity of a mere mortal designing a complex program to “simulate” the universe in a few hours when it would take, by their estimate, a few billion years (and certainly not in FORTRAN).
Let’s look at the facts.
1. The Universe exists (at least I think I do, and maybe you do too)
2. It is of unimaginable complexity and design as to defy simulation (all the posters agree on this point)
3. A simulation of it cannot be programmed by mere humans (all the posters agree on this point).
4. The complexity and design of the Universe arose out of nothing (big bang theory) in just a few billion years, all by itself, with no assistance from humans obviously.
5. The complexity and design of life similarly arose out of random collisions of molecules, and continues today based on chance collisions of molecules.
6. Yet all of this is so complex and intricately designed that no one can simulate it on a computer, even one the size of the earth, given billions of years of programming effort.
I can’t help but shake my head in astonishment that the obvious answer is rejected with such arrogance and vehemence. “In the beginning God created the heavens and the earth.” What drives the fear that underlies acceptance of this proposition? I wonder…
Sewell’s now complaining that people took the time to point out the ridiculousness of what he’d written, and saying it was just a parable clearly not meant to be taken seriously. I agree that what Sewell wrote was obviously absurd and couldn’t be taken seriously. But as recently as January this year he was describing it as a “simple, clear, proof”.
(I would have pointed this out on the appropriate threads over at uncommondescent, but I’m banned from commenting there).
How the hell is that obvious at all? Saying “oh look, the world is big and complex” in no way implies god. That’s just stupid.
“That’s just stupid.”
Sounds like a vehement denial to me.
ROTFLMAO
For a PhD, you’re not so bright. I bet you thought for a moment that he actually made the program.
If you are truly interested in the debate I suggest you pick up a copy of Mike Gene’s book, The Design Matrix. He lays out how one should go about thinking about the problem.
“Mike” is a mere troll, pushing a thoroughly debunked book, written by a liar, hoping to persuade fools.
The back cover text, according to Amazon, gives us sufficient clues as to the deluded and dishonest nonsense infesting the waste of paper:
From the Back Cover:
“Looking at a living cell is like looking into the future of our own designs. Within the cell, the chemical processes that make life possible are under the control of coded information and sophisticated molecular machines. Could life be a true example of carbonbased nanotechnology that originated from a Mind? Could an intelligent agent possibly have designed life to exploit evolution? Could evolution and Intelligent Design be intimately linked in an elaborate dance we call life? Culminating with an insightful twist, Mike Gene has devised a unique,open-ended scoring methodology to help resolve such questions. With an analysis and approach that circumvents the polarization that typically plagues this discussion, he offers a truly fresh perspective on the continuing and controversial debate between evolution and Intelligent Design. The Design Matrix: A Consilience of Clues is unlike any other book on Intelligent Design and evolution you will ever read. It is the beginning of a journey.”
“Mike” — there IS NO CONTROVERSY. There IS NO DEBATE between “evolution and Intelligent Design.”
The Theory of Evolution by Natural Selection is the central paradigm of Biology, supported by billions of data by tens of thousands of researchers.
Intelligent Design, on the other hand, has been proven in a court of law to be a religious dogma fraudulently repackaged as if science, while having zero scientific content.
You and your colleagues are liars for profit, and enemies of the entire scientific world, from whose benefits you live as grotesque parasites.
You are a dirty rat in the basement of a magnificent palace, the Darwin Bicentennial Skyscraper, squeaking that there is no building at all, but that you are the designer of a vast rat-nest which is the very future of architecture.
Go peddle your drugs someplace else. Your hallucinations are uninteresting to those of us who can apply rational means and mathematical methods to appreciating the cosmos.
Also, to the extent that you are a fraudulent religious fanatic, your theology has been condemned by professional theologians of every major religion.
You have nothing to sell. Nobody here is buying.
Apologies to the readers for my being so mild and forgiving in this comment.
Wow, #51, you are so angry.
Here are some of the epithets you just used.
“dirty rat”
“fraudulent religious fanatic”
“condemned by professional theologians”
“grotesque parasites”
“liars for profit”
“enemies of the entire scientific world”
“hallucinations”
I know you said you were holding back, but nevertheless, you sound terrified and fearful. I have noticed a pattern on all the pro-darwinian blogs: people come out in attack mode when they’re afraid of something. But what exactly are you people afraid of? That’s what I’m very curious to know.
Thus showing that both Granville’s article and the post went past this commenter. Whether one believes Granville’s blather is a spoof or not, they have nothing to do with the science he (tries but ridiculously fail) to criticize.
Yes, yes, we got it, bh didn’t understand the post, nor has he any better understanding of the science than Granville. For the love of science, quit boring us with repetitions!
How anyone can imagine that the complexity and contingencies of a problem makes a scientific theory, say of gravitation, unpredictable is beyond most persons who have studied even a little bit of science.
Do we deny Newton’s mechanics just because we can’t solve the three-body system analytically? Do we deny solid state physics underlying the integrated electronics in the laptop I’m currently blogging with just because we can’t simulate all the impurities that goes into defining donors and acceptors?
bh is as deluded by the IDC scam as Granville. But he makes a much more pitiful effort of concealing it.
Oh, another incompetent unable to recognize his incompetence! Figures, those are the easiest to delude.
@ bh # 52:
As it is easy to peg you as an incompetent by your other comments here, it is fairly meaningless to answer your delusions. It would work both against your basic inability to learn and your willingness to embrace a movement that perverts available knowledge.
But you made such a ridiculous attack on Jonathan, so for the record:
Jonathan is one of the most literate bloggers you will ever have the enjoyment to read. This is something you could easily have ascertained before posting a comment based on the commenter not having the means to support his comment.
Unfortunately for you, Mike, Granville, Gene and the IDC scam, evolution is a venerated and amply verified scientific theory (that is, containing 150 years worth of facts verifying its predictions) that is nothing like your confabulations. If any of its results, methods or theories can be criticized, as they are daily, it is from within the science itself.
This is what infuriates scientists and science supporters as Mark and Jonathan, that a religious scam attacks a basic science in guise of a pseudoscience (or not, when the religious underpinnings becomes visible, as in your own comments).
Btw, “pro-darwinian” – as there are no “darwinians” among scientists and science supporters, would you care to define your terms rigorously? If you do, you must also show why “scientists and science supporters” wouldn’t suffice to describe those who support basic biology.
Shakespeare once eloquently said “The lady doth protest too much, methinks.”
Once again, in an attempt to sway a poster to his point of view, Torbjörn resorts to invective, dismisses the poster as incompetent, and uses vehemence to overwhelm his opponent.
I make no effort to conceal my epistemological approach to science. Everyone has a starting point. Either you believe in a transcendent God, or you don’t. If you don’t, then you are going to filter science differently than if you do.
Considering the heightened tensions introduced by Torbjörn to a simple question, it’s no wonder that the general public smells a rat when these kinds of tactics are employed.
You might benefit more from reading “How to Win Friends and Influence People” and less time reading a thesaurus for alternative ways to say confabulation. My suggestion to you would be to learn how to ratchet down the rhetoric, and get off your high horse where you have somehow convinced yourself you have God-like knowledge no one else does.
The problem with these high horses come from the ever changing nature of scientific “knowledge”. Every year someone debunks some long held theory, a theory that those with the “knowledge” were willing to fight to the death to defend. Darwinism is no different. The more you learn, the more you realize just how much you really don’t know.
If you’re so sure of your knowledge, why the tirade, the string of provocative adjectives? If you’re right, you have room for some humility. On the other hand, if you doubt yourself, you have nowhere to go but into the attack mode.
My question remains unanswered. Where does the fear response come from?