Monday, November 20, 2006

Chemical Codes

This is the second of a multi-part series related to David Berlinski's essay entitled 'On the Origins of Life.'

Berlinski noted that two very different structures- information management and chemical activity- must be coordinated and that this is accomplished by the genetic code. Berlinski emphasizes the word code. He goes on to state the following:

"By itself, a code is familiar enough: an arbitrary mapping or a system of linkages between two discrete combinatorial objects."1

This arbitrary property is distinct from a linkage dictated by underlying chemical forces that would make the linkages inevitable under specified conditions. The genetic code operates in conformity to laws of physics and chemistry even as they do not explain its origin. More from Berlinski:

"To note that codes are arbitrary is to note the distinction between a code and a purely physical connection between two objects. To note that codes embody mappings is to embed the concept of a code in mathematical language. To note that codes reflect a linkage of some sort is to return the concept of a code to its human uses."2

The arbitrariness of codes is linked to the question of whether the genetic code was generated by chemical properties of nucleic acids and proteins through which the code is manifested. If the genetic code is not the inevitable outcome of a specified series of reactions or of a stochastic selection process then there is little reason to think the biochemical objects forming the code are not like other objects expressing other codes. The objects in these codes are intelligently linked. An ID hypothesis would infer that shared properties result from the shared cause namely, intelligence. A prominent alternative cites a preponderance of amino acids in tRNA as an explanation for a chemically based origin of the genetic code. RNA molecules have been shown to bind tightly to some amino acids in vitro selection experiments. Note the following comment made about this.

"The nucleotide sequences of these RNAs often contain a disproportionately high frequency of codons for the amino acid that is recognized. For example, RNA molecules that bind selectively to arginine have a preponderance of Arg codons and those that bind tyrosine have a preponderance of Tyr codons. This correlation is not perfect for all the amino acids, and its interpretation is controversial, but it raises the possibility that a limited genetic code could have arisen from the direct association of amino acids with specific sequences of RNA, with RNAs serving as a crude template to direct the non-random polymerization of a few different amino acids."3

How does a "limited genetic code" arise? The direct association alluded to is not a chemically based explanation for an tRNA molecule. A detailed look at tRNAs reveals why. There are invarient properties common to all tRNAs. For example, structually all tRNAs have four tRNA stems, which are sometimes referred to as arms and all acceptor stems contain the sequence "CCA." The sequence is also found in the same location- the 3' end of the RNA chain. Acceptor regions and anti-codon regions are 76 Å apart. No doubt theoretical explanations can be concocted that explain forces leading to both invariance and variations. But where does selection play into this and why are there tRNAs that do not have a preponderance of the amino acid associated with them? How useful are constructs that seek to simultaneously explain both a particular property (tRNAs and an amino acid linkage) and its counterpart (the absence of such linkage) without furnishing the chemical details of how this was accomplished?


1. 'On the Origins of Life.'

2. Ibid

3. Molecular Biology of the Cell; Fourth Edition; Bruce Alberts, Alexander Johnson, Julian Lewis, Martin raff, Keith Roberts and Peter Walter; Garland Science; Chapter 6; Page 372.



At 3:11 PM, Blogger Doug said...

Have you ever seen or heard the Berlinski-Dawkins debate? I only heard that they had one. Sorry this is off topic.

Also, I'm going to be going back to college for a degree in biochemistry soon. Wish me luck!

At 4:36 PM, Blogger William Bradford said...

Hi Doug. I had not heard of this debate. I think Berlinski is as sharp a thinker as there is and I would place my bet on him in a debate. Smokey would stand a better chance than Dawkins and I mean that respectfully.

I hope you do well at school. Whatever you do now will stick with you for the rest of your life so resist the urge to party if there is work to do. I like your major. My son is a sophmore in college and is majoring in mathematics. He is growing in knowledge and maturing as well. Drop by from time to time whenever you get the chance.

At 10:38 AM, Blogger Doug said...

Hi William,

Thanks for the words of advice. I initially graduated from college with a B.A. in psychology from St. Norbert's College in De Pere, WI (right next to Green Bay). This was in 2000.
My wife (just married less than 3 months ago) received her doctorate in physical therapy from Marquette University. I am working in a field very different from what my degree is in.
While I was in college I wasn't really into it. Now I am motivated. I only wish that I had this motivation that I have now back then. But oh well.... I've been looking at a few colleges to see what they offer in regards to biochemistry/molecular biology programs.

At 5:47 PM, Blogger William Bradford said...

Go after it Doug. Motivation, (like inspiration was for Edison), is 98% of the battle. If you do not have it, mediocrity is inevitable despite natural ability. This country could use a good, motivated scientist with a biochemistry background. Your life still lies ahead of you.


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