Where I’m coming from

Before plunging into some very long (and quite overdue ) responses to people good enough to comment on previous posts about whether chance alone is enough to explain our existence, it’s time for a few words why I’m so skeptical about the received wisdom, particularly in molecular biology.  Psychological background can never alter scientific facts, but it certainly alters  the way theories are viewed.

The commenters I’ll be addressing are quite sophisticated, so this and the next post will likely be tough going for those outside the field.  For some background see https://luysii.wordpress.com/2010/07/07/molecular-biology-survival-guide-for-chemists-i-dna-and-protein-coding-gene-structure/ and https://luysii.wordpress.com/2010/07/11/molecular-biology-survival-guide-for-chemists-ii-what-dna-is-transcribed-into/

I was in grad school studying organic chemistry ’60 – ’62, a time when the actual genetic code was being worked out (e.g. which triplet of nucleotides coded for which amino acid).  Given that background, it was fairly easy to keep up with molecular biology as it grew and flowered (also it gradually became more and more important for medicine).  

This means that I’ve seen statements given by the highest authorities turn out to be absolutely wrong.  Gunther Stent proclaimed in 1969 that the end of molecular biology had been reached.  No small fry, he later went on to become chair of the molecular biology department at Berkeley from ’80 – ’86 (he must have recanted).

Consider the statement that Chimps and Humans were so close genetically that they should be considered the same species.  Genes in this case being the 1.5 % of the genome coding for protein.  The rest being Junk DNA (and considered unimportant at the time the statement was made).   

Consider Paul Ehrlich’s Population Bomb which predicted we’d be starving in the dark 10 years ago, or the prognostications of the Club of Rome in 1972 “The Limits to Growth” which sold 30,000,000 copies and was taken very seriously.  

No one believes that our genome is junk any more, but the nomenclature lives on.  Look at Cell vol. 143 pp. 46 – 58 ’10 (1 October issue).  “Long Noncoding RNAs with Enhancer-like Function in Human Cells”  Another term for them is lincRNAs (long INTERGENIC RNAs), the implication of intergenic being that they aren’t genes.  But of course they are.  A mere 3,000 of them were found looking at about 1/3 of the genome, implying that they are probably half as abundant as proteins.  Just because they don’t code for protein doesn’t mean they aren’t genes.  The paper shows that some of them modify protein expression (increasing it, unlike microRNAs of which we have at least 1,000, which usually decrease protein levels).  

For most of you, this is ancient history, but I’ve lived through it, which makes me skeptical about grand pronouncements such as global warming or the idea that the complexity of life (which grows more complex all the time as we discover new players like microRNAs, lincRNAs, etc. etc.) just arose by chance.  If it doesn’t make sense to me, I’m not going to buy it, no matter how eminent the authority. This is NOT the same thing as saying they’re wrong.

Among the things I don’t understand (1) why a protein should have one or a few shapes — clearly 20,000 of them do or we wouldn’t be here  (2) why the side chains of proteins don’t react with each other more often, a la Green Fluorescent Protein (3) how the incredible fidelity of DNA replication could have arisen — see https://luysii.wordpress.com/2010/05/23/how-fast-is-your-biological-clock-ticking-well-know-soon/ where the error rate between parent and child is 1/100,000,000 (in one family anyway) (4) how the elaborate dance of the topoisomerases with DNA could have arisen by random mutation.

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