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Double Helix: 50 Years of DNA
Dr from the Source writes "Despite previous posts, tomorrow (April 25, 2003) is the real 50th anniversary of the publication of the famous paper by J. D. Watson and F. Crick in the Nature journal. Readers can download such paper, along with a few other classic ones from Nature's archive."
Nova had a really great program this week about Rosalind Franklin who did all the crystallography work. Apparently Watson and Crick stole her data and that's what enabled them to come up with the double helix model.
If tits were wings it'd be flying around.
For those who didn't catch the Nova episode.
Rosalind Franklin
Rosalind Franklin was a brilliant [female] scientist specializing in x-ray crystalography. It was Rosalind Franklin that identified two forms of DNA, and correlated their diffraction images with the helix shape. Watson and Crick were secretly, and intentionally passed Franklin's in-depth research (some would say "stole"). If Franklin had not died of cancer (probably due to working so much with radiation) at such a young age she would have undoubtedly presented the discovery of the helix nature of DNA (she was far ahead of Watson and Crick, while they were still fscking around with broken models). Watson went on to write The Double Helix, which slandered Franklin, to which even Crick objected. Franklin's paper on DNA was published in the same journal as two other papers (one of which was Watson/Crick's), AFTER the other two, and EDITED without her knowledge to imply that her research merely confirmed rather than provided the foundation for Watson's and Crick's work. After being made so miserable working at the same lab with Watson and Crick, she went on to other things briefly virus research, in which her partner, surprise again, also won a Nobel prize.
Personally I think it is a damned shame. We should be celebrating Rosalind Franklin. Or at the VERY LEAST we should have (and should still) heard her name. Crick and Watson really come off as clueless chauvanistic assholes. Granted, a Nova episode is one data point, but usually their programs are really good, and I'd like to hear other opinions if other people know more about this issue.
It's 10 PM. Do you know if you're un-American?
Then:
I believe Watson and Crick's solution to DNA structure was a fabulous achievement, but press should also be given to Hershey and Chase's 1952 experiment proving DNA as the genetic material. Of course, they too rested on the shoulders of giants in chemistry and biology, but their work has equal claim to initiating an era of reverse engineering hereditary mechanisms.
Now:
Biology has come a long way reverse engineering life, but still has a long way to go. Unlike systems composed of similar components interacting to create a complex and often unpredictable outcome, life is composed of a huge variety of components which can interact to create stable outcomes (homeostasis). As we identify the individual components and subsystems, a new field is emerging. This field, called systems biology, is about modeling this complexity.
Now/Next:
Perhaps most exciting, there now exists enough information to begin forward engineering life. In living systems we have the ultimate collection of both components and subsumption architectures for making complex systems. Rodney Brooks was brilliant for modeling his robots after living systems, but a living system can be the starting point for further engineering. This work has begun, but consists mostly as limited applied science with pharmaceutical, agricultural, or industrial enzyme goals. Is anyone (else) engineering life for the sake of engineering?
First entomology, then virology, and finally bioinformatics systems. Bugs follow me wherever I go.
For the curious, googling for "Rosalind Franklin" is rather informative.
And no, this isn't offtopic.
The Christian Right are just one example among many of the dangers inherent in misreading or ignoring the manufacturer's instructions (you're another). Your brains work a lot better if you don't constantly abuse them in lifestyle and diet.
Sit down for a few hours and figure out the odds against enough genetic material arising spontaneously (together with a framework to support and replicate it all), no matter how many or how few steps it's done in, to produce the most basic lifeform. It lends new depth and richness of meaning to the term "impossible". The Medieval people called it "spontaneous generation" and we laugh at that concept - but the only new ingredient we add is time.
Even living critters like us, if we die, don't spontaneously burst back into life again or spawn simpler critters. All of the ingredients are there, in the right arrangements and ideal concentrations, an immensely better situation than any of the ephemeral "primordial soup" scenarios, yet we don't get new life from dead bodies, we just get food for worms and bacteria.
So if it didn't happen by accident, it happened by design. Is there a third alternative?
Got time? Spend some of it coding or testing
Y'know, given how difficult it is for us and all of our technology to even consider forward-engineering from borrowed parts, one has to wonder how life as we know it came together in the first place. The complexity involved is well over the top of anything which can be produced by randomising and selecting - without a plan for making those selections - in any finite time.
Got time? Spend some of it coding or testing
kc + ScottK ----^
but the only new ingredient we add is time
If you add a grain or two of sand to your soup, you are unlikely to notice it.
Now add a handful of sand. You begin to notice the grittiness.
Now dump an entire beach of sand onto your dining room table.
Adding ingredients is relative, even if it is only one new one.
Now, I know you're a troll (even if you may not realize it), but go read this, take a look at the image it talks about, then have a little sit down and realize that this planet we're on (and all of your "intelligent designs") are more meaningless than one microscopic speck of silica in the entire ocean.
(Where's a Total Perspective Vortex when you need one....)
I watched C-beams glitter in the dark near the Tannhauser gate.
The actual article is funny because they never would have gotten it published if they didn't propose the mechanism for DNA replication in the same breath.
At the time, crystallography was something geologists did in order to study the composition of rocks. The idea of using xrays to study the crystal patterns of biological molecules was really new at the time. Franklin deserves credit for being innovative in that regard. The real credit that Watson and Crick deserve was that once Crick saw that the structure was a double helix, they were able to put together a decent model for DNA replication. Something people had only guessed about before. Their model wasa still a guess, at best, but they turned out to be right!
The funny part about the whole thing is that the diffraction pattern that they analyzed was no bigger than your fingernail. The picture in the Nature article has actually been blown up from its original size, if you can believe that. Kind of scary how something so important could have been determined by studying something so blurry and small...
Those who can, do. Those who can't, simulate.
You cannot add enough time to make spontaneous generation work. The closest anyone has come is (in their head only) adding an infinitude of extra universes to reality in the (forlorn) hope that if you toss a coin often enough, you'll come up with 10^umptysquillion heads in a row. Not only are those extra universes strictly an article of faith, but the way odds work the universe we would find ourselves in under those circumstances is extremely unlikely to be anything like as favourable to life as the one we're in. Arguments about "we're here because we're here" are just plain dumb - and the tautology they represent points once again to an article of faith.
I realise that your nickname is "Cyclops", but aside from the fact that a perspective in which we are insignificant and intrinsically worthless is a useful one - it makes the value placed on each of us so much more meaningful - our planet is indeed special, since it's a cosmic hop, skip and jump from the centre of the universe (in a universe which you hold as an article of faith as having no centre).
Now I'm wondering why my comment above got modded offtopic and your's didn't. I guess it's a political thing: "I disagree (as an article of faith, not based on complete observations), so I'll blast him". Very SlashDot. (-:
Got time? Spend some of it coding or testing
DNA is one of the best demonstrations in existence that we cannot have arrived here as the culmination of a long series of accidents. If you've got a problem with that, explain your problem to us all instead of voting pointlessly. Even an AC comment is better than an "Offtopic" mod.
Got time? Spend some of it coding or testing
I'm glad you had something objective to say, and didn't stoop to an ad hominem argument.
In point of fact, given the existence of creationists - and even asserting that they're all literally insane - the odds against one of them thinking objectively are many thousands of orders of magnitude more likely than even the simplest concievable life-form having formed entirely by accident out of 10^81 atoms (the vast majority of those being hydrogen) within 10^17 seconds even aided by the most eye-poppingly optimistic assumptions about the environment(s) that this may have occurred in.
Now take your religious zealotry elsewhere, materialist (-: or at least get some objectivity of your own installed :-)
Got time? Spend some of it coding or testing
I once published a monograph on this subject in the old Journal of Irreproducible Results. (I am most emphatically not making this up.) The phylogenetic tree was something like this:
primordial slime ---> creationist
primordial slime ---> fish ---> frog ---> lizard ---> lemur ---> ape ---> evolutionist
Huxley said it better, of course...
"Obviously, I'm not an IBM computer any more than I'm an ashtray" (Bob Dylan)
And Avogadro's number has what to do with probability?
Well, you've made a start, I guess. Pick a lifeform of the order of 10^8 atoms and structure them in all chemically possible ways (ie, all combinations of 10^7 through 10^9 atoms). How many of those ways represent a living organism? Let's be generous and call it one in 10^9 possible arrangements. What does this organism eat/breathe? What proportion of possible locations in the universe contain those substances? Of those locations, what proportion fall within habitable ranges of temperature and radiation? What proportion of them contain no significant concentration of chemicals lethal to our organism-to-be? What mechanism(s) are you proposing to rearrange these auto-polymerising carbon chains? Is this "lifeform" that you've chosen standalone, or a virus? If it's a virus, what are you proposing to use for a host?
I don't think you're reading from the same page as me. Limiting yourself to a planetary surface would tilt the calculations dramatically toward "my" end of the table.
Way less than 1% of the atoms in the universe are other than hydrogen (92.5%) or helium (7.4%); oxygen (0.06%) and carbon (0.03%) are among the most abundant of those; but we'll ignore that, even though it's critical (because there are even more critical things to consider). If you rearrange every one of the (roughly) 10^81 atoms in the universe stupidly often (say, 10^9 times a second) for the (roughly) 10^17 second nominal life of the universe and ignore the effects of distance, you get 10^107 possible combinations of atoms (which certainly is a shitload of combinations).
Over against this, we set out the need for at least something like 100 functional proteins to appear in the same location simultaneously. Nothing this simple has been observed in the wild, "simple" one-celled lifeforms like E.Coli are enormously more complex. A protein is constructed from roughly 200-1000 amino acids, so let's select shortish ones that average 300 aminos to improve the odds. This yields 4^300 possible proteins (10^180) at each site. Grant that any one of a million different proteins will function in any particular slot and we're down to odds of 10^174 against; look for 100 such proteins and we're up to 10^176. Not that it makes any difference.
10^176 may not look so bad over against 10^107, but that's 10^69 short and in order for the numbers to be comparable we'd have to presume that every atom in the universe was an amino acid molecule. Statisticians generally quote somewhere between 10^30 and 10^50 as "impossible", so taking the stricter end of this spectrum and laying it alongside our universe made of amino acids with no space between them, we find that a working lifeform - any working lifeform - is 10,000,000,000,000,000,000 times impossible. This is a fantastic distance from even odds, and you've got to admit, I don't pull any punches when I use phrases like "wildly optimistic" to describe those starting conditions. (-:
Firstly, no it couldn't. Silicon has different properties to carbon, and those properties won't allow it to form the kinds of compounds necessary to life. And if it could, why didn't it?
No, it doesn't. Argument f
Got time? Spend some of it coding or testing
Nature v. 171, p. 737-738 (1953) was published on April 2, 1953. See: here, and here
Ya just did, ya drongo! (-:
If you were truly interested in not arguing you would simply have dropped it.
I saw the logic in your statement, it was broken, I pointed it out, and now you're having a hissy fit and leaving. Very reasonable... (-:
Got time? Spend some of it coding or testing
I'm going to borrow a couple of basic analogies to illustrate the point. Don't get carried away nitpicking the details of each analogy, just consider the broad view. The porpose of the analogies is not to prove or disprove evolution, but to illustrate some things about statistics.
If you sent a tornado through a junkyard, would you expect it to form a working B52?
My answer: No. I suspect your answer would be "what are you? nuts? the cases aren't comparable!" - but they are. A tornado brings with it energy, which is needed for assembling things, and the junkyard suplies raw materials, something for the energy to act on. In fact, this analogy gives you the advantage, since a tornado has a good deal more structure available than raw energy does.
If you sent a trillion tornados, one at a time, through the same junkyard, would you expect a working B52 to form as a result?
My answer: I would expect it to form a very fine metallic sand. Your answer?
OK, let's abandon illustrations connected with reality, and start giving you som serious ground. If you sent a trillion tornados through a trillion junkyards, would you expect to see a working B52 formed? Would it help to re-run the experiment a trillion times?
My answers: no, and no. Your answers?
If you sent a trillion tornados across a trillion copies of the biggest B52 junkyard in the world, would you expect to get a working B52 in the process? Or even something that flew under its own power, maybe a mutant with nineteen jet engines (three of which worked) and seven wings?
My answers: no, and no. Your answer?
Let's go back to that most popular of analogies, the infinite number of monkeys.
We don't have an infinite number of monkeys, so let's consider a very large number of them. Their task is to type out The Origin of Species, starting with the title. We'll use Golden Tamarinds, because they're small, and pack them and a little typewriter into a cage 10cm on a side. Given a surface area of 500,000,000 square kilometers, if we paved the entire Earth, oceans too, with cages, we'd fit 50,000,000,000,000,000 (5x10^15) cages on Earth. Let's stack those a kilometer high to get 5x10^19 cages. We don't know how many planets there are in the universe, but let's guess that there are 10^22, roughly one for every single star in the universe, and that they're Earth-sized. Cover those with tamarinds too. We're up to 5x10^41 tamarinds - oh, the plumbing...! Being fast little buggers, they type ten random characters a second, so we have 5x10^42 random keystrokes available every second to apply to our manuscript. That's a lot of keystrokes!
The title of Darwin's work is `On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life.' That's 21 words in 119 characters, and a boring typewriter keyboard like this one has 63 symbols available. We'll tape over keys like tab, carriage return and backspace because layout is of no interest to us. Because we don't want to spend forever dithering around about how often a tamarind will hit shifted keys, or how much favour the spacebar gets because it's bigger, or ASDFGHJKL get because they're central - and also to maintain that typing speed - we'll arrange those 63 symbols in a "mammary" style keyboard with equal-sized unshifted keys and an equal chance of each being hit.
Ready to roll... each keystroke stands a 1/63 chance of being the right one, so it will take an average of a bit over 10^214 keystrokes to complete the title. Dividing by 5x10^42 gives 2x10^171 seconds to type out the heading... but the universe is less
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Not exactly, and the difference between "very many" and "virtually infinite" is a crucial one.
If in practically every example you can find or analogy you can invent, the probability is always negative, zero or infinitesimal, this is an indication (not a proof, but certainly an indication) that in reality the probability is effectively zero (-: "or less" :-)
As I mentioned, it's also important that "lots" is not the same as "infinite". If you can fine your answers down to within, say, 5000 orders of magnitude <grin> then side-issues that only count for a hundred or so orders of magnitude are - in the statistical sense - insignificant.
Got time? Spend some of it coding or testing