An Argument Against Intelligent Design
Feb. 21st, 2012 08:57 pm![[personal profile]](https://www.dreamwidth.org/img/silk/identity/user.png){kind=small}
tanarillToday, I began the third week-long shortcourse; this one is on translational machinery. And also, there was a quite fantastic thing to show how there is no intelligent creator.
The basis of the thing is in tRNAs. These shuttle amino acids along and allow the ribosomes to place a specific one into a growing protein. It recognizes which tRNA it needs using codon-anticodon complimentarity with the mRNA. So far, so simple.
But a three-base codon give sixty-four possible combinations. Even if you use use four of them to say STOP, that's still three times the number of needed codons. So some amino acids have more than one codon. This does not work out to three per amino acid, though; some have four and some have two. The reason is because it allows the third base pair to be "wobbly;" what is there does not matter quite as much as that it is always a purine (A or G) or a pyrimidine (U or C). This wobbly is good, since it means that if the ribosome makes a mistake matching the tRNA, it is less likely to affect the protein.
Then there is the strange case of Isoleucine and Methionine. Methionine is the amino acid that is always the one at the beginning of the protein - the Met codon is also the symbol for "begin!" It is AUG. AUX, where X is A, T, or C, means isoleucine instead. This means that the the ribosome absolutely cannot make a mistake in finding AUG versus AUX, or the protein doesn't start right.
Fortunately, there is the sugar inosine, which we show with I. I is a weird sugar, in that it can pair with A or T or U, but never G. It is made from A by a fairly simple reaction, and it is in fact how the body breaks down adenosine to become uric acid. So an intelligent designer would go, "Ah, the tRNA for isoleucine will have the anticodon TGI, and be able to pair with any AUX that is not AUG." And in fact when I was asked this in class today, this was my answer. It was a good answer, and my teacher went, "Huh. I like that." Is this how it actually works, though?
Of course not.
Instead, biology does the very strange thing of modifying the last base of the Met anticodon, so that instead of being TGC it becomes TG(k2)C. This somehow prevents the ribosome from ever putting the wrong tRNA in there, though mechanisms currently unknown. It is expensive, because instead of using a protein that already hangs around to digest A, there has to be another protein that does the C->(k2)C modification. It is inelegant. It reeks of a quick cludge to fix a problem after the fact.
It is, in short, another argument against intelligent design.
The basis of the thing is in tRNAs. These shuttle amino acids along and allow the ribosomes to place a specific one into a growing protein. It recognizes which tRNA it needs using codon-anticodon complimentarity with the mRNA. So far, so simple.
But a three-base codon give sixty-four possible combinations. Even if you use use four of them to say STOP, that's still three times the number of needed codons. So some amino acids have more than one codon. This does not work out to three per amino acid, though; some have four and some have two. The reason is because it allows the third base pair to be "wobbly;" what is there does not matter quite as much as that it is always a purine (A or G) or a pyrimidine (U or C). This wobbly is good, since it means that if the ribosome makes a mistake matching the tRNA, it is less likely to affect the protein.
Then there is the strange case of Isoleucine and Methionine. Methionine is the amino acid that is always the one at the beginning of the protein - the Met codon is also the symbol for "begin!" It is AUG. AUX, where X is A, T, or C, means isoleucine instead. This means that the the ribosome absolutely cannot make a mistake in finding AUG versus AUX, or the protein doesn't start right.
Fortunately, there is the sugar inosine, which we show with I. I is a weird sugar, in that it can pair with A or T or U, but never G. It is made from A by a fairly simple reaction, and it is in fact how the body breaks down adenosine to become uric acid. So an intelligent designer would go, "Ah, the tRNA for isoleucine will have the anticodon TGI, and be able to pair with any AUX that is not AUG." And in fact when I was asked this in class today, this was my answer. It was a good answer, and my teacher went, "Huh. I like that." Is this how it actually works, though?
Of course not.
Instead, biology does the very strange thing of modifying the last base of the Met anticodon, so that instead of being TGC it becomes TG(k2)C. This somehow prevents the ribosome from ever putting the wrong tRNA in there, though mechanisms currently unknown. It is expensive, because instead of using a protein that already hangs around to digest A, there has to be another protein that does the C->(k2)C modification. It is inelegant. It reeks of a quick cludge to fix a problem after the fact.
It is, in short, another argument against intelligent design.
no subject
Date: 2012-02-22 06:36 am (UTC)I feel like I'm really close to this, I just need a little more light! The gist of the idea is pretty amusing though. Evolution is SUCH a hacker, always doing the expedient thing!
no subject
Date: 2012-02-23 06:01 am (UTC)Okay, I will begin with codons. If you take three nucleotides of an mRNA, that is one codon. The tRNAs have a little loop that pairs with the codon, and this loop is the anticodon. The codons are specific - each one will only pair with certain tRNAs, and each tRNA only carries a specific amino acid, so the end result is being able to put a specific amino acid in at that position.
A ribosome will start at the beginning of an mRNA and ride along until it finds the AUG, which means "start". But if it does not, it will pass it by and keep looking for an AUG. If there is one, it will start there, but the protein it makes has a two-in-three chance of being in the wrong reading frame. Reading frames are the three-nucleotide window the ribosome is looking in:
AUG CTC CTC GTA CTA (correct)
A UGC TCC TCG TAC TA (wrong)
AU GCT CCT CGT ACT A (also wrong)
Proteins that are not in the correct reading frame fail to work, because they are random strings of amino acids instead of real proteins.
So then inosine. It is a non-standard nucleotide that will base pair with anything that is not G. So the anticodon for "start" can be TGC, which matches AUG; the anticodon for isoleucine can be TGI, which pairs with anything else, and means that instead of making three tRNAs, there only needs to be one. This would be sensible, because I is easy for biology to make, and it is elegant, because then there does not need to be an extra protein.
But instead nature goes and does this silly thing where it makes a whole different protein. This new protein have to first fish out the right tRNA, and then it does something to the start anticodon (TGC) to turn it into TG(k2)C. (We know what it does, I'm just not going into the details.) We have no idea why this works to prevent the body from making a mistake. We have no idea why nature came up with this complicated solution instead of the simple and obvious one, which is to use the one sugar that doesn't care what it pairs with as long as it doesn't pair with G.
But the answer is probably not "because God realized the mistake later." There is no design, just luck.