There have been some great critical responses to some of the posts, which deserved a reply long ago. All the posts criticized involve either a chemical, molecular biological or numeric argument about the macromolecules making us up. Here they are in a semi-logical sequence. I’ll deal with the actual criticisms in the next post(s).
Two posts involve simple calculations about how many distinct proteins or polynucleotides life could have made given the mass of the earth to do so and 14 billion years. Here are the links. (1) https://luysii.wordpress.com/2009/12/20/how-many-proteins-can-be-made-using-the-entire-earth-mass-to-do-so/ (2) https://luysii.wordpress.com/2009/12/28/how-many-distinct-rna-polymers-can-be-made-using-the-mass-of-the-earth-to-do-so/.
No one has criticized the correctness of the calculations, which show that life on earth could have made only an infinitesmal fraction of the possible proteins of only 100 amino acids, or polynucleotides of 100 bases. If you disagree say so now. There has been severe criticism of the implication that evolution works by randomly trying out all such possibilities. I didn’t really say that, and will deal with this in the next post. I do think that all of us agree that mutations occur randomly (recombination hotspots excepted) so that the grist for the evolutionary mill is formed essentially willy nilly. If you disagree say so now.
What I was really getting at, is that I find the proteins which make us up rather miraculous in that (1) they have one or just a few conformations which give then a fairly stable shape — they certainly do or we wouldn’t be here. For details see http://luysii.wordpress.com/2010/08/04/why-should-a-protein-have-just-one-shape-or-any-shape-for-that-matter/. (2) their side chains don’t react with each other. For details see https://luysii.wordpress.com/2010/05/13/protecting-groups/.
I think proteins with such magical properties are exceedingly uncommon. So how would you know how common such proteins actually are ? While possible in theory, the experiment to investigate the structures of a random sequence of amino acids is impossible to carry out fully. For details see htts://luysii.wordpress.com/2010/08/08/a-chemical-gedanken-experiment/. It still might give an answer if nearly every random sequence of say 60 – 100 amino acids had just one or a few structures.
I’m unimpressed with the argument that there are only 1000 or so protein folds, which significantly narrows the search space. There are huge numbers of proteins in the microorganisms living in the sea which far outnumber what we’ve already studied. Even if correct, how would random mutation find them? I’d love to see the results of the ‘glass eye’ experiment — for details see http://luysii.wordpress.com/2009/11/29/time-for-the-glass-eye-test-to-be-inserted-into-casp/
Finally, I must admit that these speculations provided a certain degree of comfort as I watched patients I was unable to help get worse and worse and finally die. For details see –http://luysii.wordpress.com/2009/09/17/the-solace-of-molecular-biology/. If our existence is as miraculous as I think it to be, then what really needs to be explained is not suffering and disease, but health and the gift of life. At long last, a semi-answer to Camus “The Plague” which affected me profoundly as an undergraduate years ago.