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A Short History of Nearly Everything - Questions

Old 06-15-05, 01:08 PM
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A Short History of Nearly Everything - Questions

I am nearly through this book. Truly excellent. He covers darn near everything, and covers it well enough to satisfy.

Anyway, on a chapter about biology and how life forms, he goes over the idea that the real problem is with proteins. His example is to imagine if you had a slot machine with 1,000 reels on it, and each reel has 20 different possibilities (which represents the number of proteins and the number of different proteins). He says that if you were to spin the reel to get the correct lineup for a protein, you would basically be spinning the reel forever, and thus it is called "the miracle of life."

But then he goes on to say something like, "but what if you could stop some of the reels when they were on the right protein? Then spin the rest until they got the right protein, stop them, etc."

Okay, that is where I get lost. This seems like the same type of argument made by "The Blind Watchmaker." It seems like that argument had to do with running a computer program to randomly come up with a sentence of words. Basically, it couldn't be done either, but when the program could stop the letters that were correct, and keep randomly trying for the rest, it was completed in a relatively short amount of time.

Okay....isn't that "cheating?" How would a natural process know what proteins (or letters) are the correct ones to stop on?
I am wondering if I have missed something that should be obvious from both of these.
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Old 06-15-05, 06:41 PM
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I'm not real clear about the question but are you talking about the transcription of DNA into mRNA and translating that into a protein.

Or how the tRNA with the amino acid knows where to match up with the mRNA. In that case I'm pretty sure it has to do with the specfic charge on each.
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Old 06-15-05, 07:06 PM
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No, it wasn't that, it wasn't even about getting the amino acids to form a protein. It was getting the proteins to form in a way that was useful. I think the example used was for the protein that is used to make carotene (sp?), or whatever it is that makes a fingernail. You have to first get that protein in the right sequence, and then the DNA will reproduce, etc. but neither is useful without the other. I don't think mitochondrial RNA was discussed.

So anyway, you have to get this protein to form a long chain, and it has to be in a specific order to be any good. If you just threw proteins into the chain randomly, it would be essentially an impossibility to get it right ever. But if you could hold the random ones that happen to be correct, and then keep trying with the others, eventually you would get the protein. That make sense?
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Old 06-15-05, 09:47 PM
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I think I see now. I'm not sure how familiar you are with protein synthesis so forgive me if you know this already.

You need DNA first to get the code for keratin. The DNA is transcribed by an enzyme to make messenger RNA. The messenger RNA(mRNA) now has the code and forms a complex with a ribosome. The transfer RNA(tRNA) brings in one of the 20 amino acids that is unique to that particular part of the mRNA code. It does this one at a time. There is a particular code that stops the elongation of the chain.

This is translation


There isn't any thing like just placing amino acid's at random and then keeping the ones that fit. If you put the wrong amino acids in the protein it will be misshapen and won't function. Sickle-cell anema is caused by one misplaced amino acid, but that is because the code on the DNA is wrong. If you have the right code the wrong amino acid won't be placed in that spot because of the electrical charges in that part of the messenger RNA and tranfer RNA.

What protein you have is determined by the number of amino acids and their sequence.

Keratin shape is called an alpha-helix so it looks similar to DNA. Their's covalent bonding and disulfide bridging between sulfur molecules that bound the individual proteins together. This happens because of the charge on the sulfur molecules.

I think that is on track to what you were looking for.
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Old 06-15-05, 10:55 PM
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Hmmm, it does make me wonder about the book a bit. But I did read a review on it that basically said that Bill Bryson was in over his head on a number of issues, and maybe this was one.

So, which comes first, the protein chain or the DNA? Chicken or egg? Perhaps that was the point he was trying to make. Though he did say something to the effect that they seemed to be made for each other (they need each other to actually do anything useful), but the idea of them forming at the same time to suddenly work together is not probable (I think he says impossible).
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Old 06-15-05, 11:18 PM
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Originally Posted by kvrdave
Though he did say something to the effect that they seemed to be made for each other (they need each other to actually do anything useful), but the idea of them forming at the same time to suddenly work together is not probable (I think he says impossible).
He's probably right in saying that.

I think it's generally believed RNA came first, then protein, then DNA.

Last edited by MrX; 06-15-05 at 11:21 PM.
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Old 06-16-05, 12:23 AM
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I thought I had read that about a year ago or so, but I thought the current idea was than RNA could not have come first. Crap, I hate to have to reread something.

Thanks for the posts.
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Old 06-18-05, 07:22 PM
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I haven't finished this yet. I have in audio format. Maybe I'll try to listen to it again. I found it hard to listen to at work because a lot of ideas were complex enough that it was hard to concentrate on what was being discussed and my work at the same time.
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Old 06-22-05, 01:29 PM
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I would imagine that if humans are the 1,000 reel slot machine ([/b]SUPER MEGA BUCK$ WINNING AMERICAN IDOL PAVILLION JEOPARDY! GAME OF FORTUNE[/b]) then the "cheating" would come from playing the game on the smaller (say, 50 reel) slot machines (ARMANDO'S NON-LICENSED PENNY EXTRAVAGANZA). You don't even need to produce lifeforms, just stuff that starts making sense, like a virus.
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Old 06-22-05, 02:32 PM
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Originally Posted by The Bus
I would imagine that if humans are the 1,000 reel slot machine ([/b]SUPER MEGA BUCK$ WINNING AMERICAN IDOL PAVILLION JEOPARDY! GAME OF FORTUNE[/b]) then the "cheating" would come from playing the game on the smaller (say, 50 reel) slot machines (ARMANDO'S NON-LICENSED PENNY EXTRAVAGANZA). You don't even need to produce lifeforms, just stuff that starts making sense, like a virus.
Except that we aren't talking about producing life, but just the proteins. Those same proteins in a virus, or bacteria, etc. still have huge numbers of amino acids to form the protein. The proteins between all organisms really aren't less complex with less complex life, so you still have that problem. This is talking about even before you get to life.
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Old 06-23-05, 08:08 AM
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I have heard this idea before, from creationists. They want to say that the chances of it "just happening" are too great.

Well, as has been pointed out, atoms only join in certain ways, and molecules only interact in certain ways. If you mix all the chemicals that were in the early Earth, and simulate lightning by zapping it, you get all sorts of lovely amino acids and protiens. They will then interact in predictable (not random) ways.

The "slot machine" analogy is inappropriate. If he wants to show the NON randomness of protien formation, then a jigsaw puzzle would be more apt.
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Old 06-23-05, 10:30 AM
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Originally Posted by Mrs. Danger
I have heard this idea before, from creationists. They want to say that the chances of it "just happening" are too great.

Well, as has been pointed out, atoms only join in certain ways, and molecules only interact in certain ways. If you mix all the chemicals that were in the early Earth, and simulate lightning by zapping it, you get all sorts of lovely amino acids and protiens. They will then interact in predictable (not random) ways.

The "slot machine" analogy is inappropriate. If he wants to show the NON randomness of protien formation, then a jigsaw puzzle would be more apt.
Well, this book is definately not from a Creationist point of view.

The experiment you are talking about is the Miller-Urey experiment, and it has been shown to be pretty much an interesting footnote in science, but does nothing in answering the question of how life begins. This is a pretty brief overview of the experiment and a brief explaination of the problems http://en.wikipedia.org/wiki/Miller_experiment

They actually didn't get any proteins at all, just amino acids. And only one that is actually found in organic material, iirc. They also assumed an atmosphere that was "perfect" for the experiment and that most scientists now believe was not like the atmosphere of the early earth.

And it is random (at least from a non-creationist point of view), so the slot machine would be analogous. The jigsaw puzzle would only work if it were a Creationist argument because not only do you have the pieces, you know how they must be ordered to make sense. The only way a naturalist jigsaw puzzle would work would be is you had 20 different sized pieces and they had to be placed in the right order roughly 1,000 times (and stay there while the others are waiting to form) to form.

Basically from a naturalist point of view, there must be something we aren't thinking of or something we don't know.
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Old 06-23-05, 04:05 PM
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Lol... this is a GREAT thread. My sister-in-law accidentally left a copy of this book on my table this morning! I havn't read this book yet, but I will try to find this chapter and read it tonight.

Here is a suggestion based on what I have read so far in this thread regarding the slot machine analogy.

KVRDAVE wrote: Okay....isn't that "cheating?" How would a natural process know what proteins (or letters) are the correct ones to stop on?
I am wondering if I have missed something that should be obvious from both of these.

Natural selection is the natural process that knows what proteins are the correct ones. Over huge timescales, natural selection will enrich in the population the DNA code that makes up the recipe for the correct protein. It is a gradual step-by-step process, each step meeting pressure from the envoronment that weeds out the "incorrect" proteins and allows the "correct" or "perhaps not correct, but somehow better than the last version" proteins to be inherited in the next generation. If we go back to the slot machine analogy, then each instance of a mutation in a particular protein could be compared to the spin of one reel of the slot machine. The previous generations would have "locked" the reels that led up to your particular protein, and natural selection would cause it to persist in nature. Organisms that have DNA that codes for a particular protein have that DNA because they are the progeny of sucessful parental organisms.


Again, I am only adding my two-cents based on the thread alone. If I am way off track, I apologize!

Rob
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Old 06-23-05, 07:10 PM
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Originally Posted by refeissn
Lol... this is a GREAT thread. My sister-in-law accidentally left a copy of this book on my table this morning! I havn't read this book yet, but I will try to find this chapter and read it tonight.

Here is a suggestion based on what I have read so far in this thread regarding the slot machine analogy.

KVRDAVE wrote: Okay....isn't that "cheating?" How would a natural process know what proteins (or letters) are the correct ones to stop on?
I am wondering if I have missed something that should be obvious from both of these.

Natural selection is the natural process that knows what proteins are the correct ones. Over huge timescales, natural selection will enrich in the population the DNA code that makes up the recipe for the correct protein. It is a gradual step-by-step process, each step meeting pressure from the envoronment that weeds out the "incorrect" proteins and allows the "correct" or "perhaps not correct, but somehow better than the last version" proteins to be inherited in the next generation. If we go back to the slot machine analogy, then each instance of a mutation in a particular protein could be compared to the spin of one reel of the slot machine. The previous generations would have "locked" the reels that led up to your particular protein, and natural selection would cause it to persist in nature. Organisms that have DNA that codes for a particular protein have that DNA because they are the progeny of sucessful parental organisms.


Again, I am only adding my two-cents based on the thread alone. If I am way off track, I apologize!

Rob
Thanks for the reply. I think it is the in one of the last 3 chapters. The whole book is actually worth the read. Very entertaining. I did read one review that mentioned that if was often more entertaining than factual, but the author never claims to be a scientists, so you take it with a grain of salt.

However, I understand your point, but it seems to be more in line with what happens after life has begun. One you have all the amino acids, proteins, DNA, etc. in the right place to make kvrdave, you can then play around with them to make mutant kvrdave (bad) or super kvrdave (which I believe is in process....another thread). But this was specifically about before you have life, in order to get it. So there is no real natural selection in play. You have to have the organism before you start random mutations which might help of hurt.
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