Genome complexity: what genes do and don't do (Introduction)

by dhw, Sunday, February 03, 2019, 10:12 (1910 days ago) @ David Turell

dhw: There is a world of difference between passive information and active use of information. Our whole discussion revolves around what it is that uses the passive information.

DAVID: What I bolded in your comment is correct. My library analogy is correct. A library is passive, but one can actively use it. Cells use their library of information in the genome. There are instructions telling cells how to act.[dhw: The whole article clearly distinguishes between information and instructions, but you refuse to do so.]

dhw: So (a) the “reviewer” cells know how to pick out one set of instructions from the billions stored in the 3.8 billion-year-old library, or (b) there are no instructions, and they work out for themselves how to use the passive information in the genome, as you agreed earlier: [DNA] offers nothing but passive information which “cannot possibly serve as instructions”. The genome can be restructured, but we do not know what organizes the restructuring.

DAVID: I'm convinced there are instructions, but nothing as simple as DNA coding for protein. There are many other layers of the genome which modify coded instructions. HOX genes run a committee of lesser genes, but we have idea how. We identify genes that control a function, but have no idea how that really works.

You are echoing my last sentence (now bolded), and have ignored the rest. I know you are convinced that the genome stores billions of instructions planted 3.8 billion years ago, and the cell enters the genome and picks out the relevant one. I find it less than convincing.

dhw: However, I pointed out that this contradicted the article you were agreeing with, and you responded: “Sloppy thinking and writing. My boldings above and below are my thoughts exactly.” Now you have reverted to exactly the same “sloppy thinking and writing”. Here are the two quotes:

QUOTE: "Scientists now understand that the information in the DNA code can only serve as a template for a protein. It cannot possibly serve as instructions for the more complex task of putting the proteins together into a fully functioning being, no more than the characters on a typewriter can produce a story."(David’s bold)
QUOTE: "as the British biologist Denis Noble insists in an interview with the writer Suzan Mazur,1 “The modern synthesis has got causality in biology wrong … DNA on its own does absolutely nothing until activated by the rest of the system … DNA is not a cause in an active sense. I think it is better described as a passive data base which is used by the organism to enable it to make the proteins that it requires.”(David’s bold)

dhw: If DNA is a passive data base which cannot possibly serve as instructions, does nothing and is incapable of forming a fully functioning being but is used by the organism, how can you argue that it is a library of instructions telling the organism how to form a fully functioning being (I don't think you can have evolution without fully functioning beings)? The article itself tells us that cells “learn” and “create instructions on the hoof”, and “instructions are, again, created de novo”, and the “glorious ballet of different cells finding just the right places at the right times “could not have been specified in the fixed linear strings of DNA.”

DAVID: Note my above comment. We know what a gene controls, but not how it is actually done. That is exactly what the quotes are saying. I've pointed out the 3-D relationships in the coils of DNA. What the article says to use your words differently is that the cells appear to 'learn' and 'construct information on the hoof', but it is my word 'appear' that applies.

The article does not use the word “appear”, unless you have misquoted it. The quotes with which you agreed are unequivocal.

DAVID: We are still looking in from the outside and making assumptions. Yes, DNA is a passive code but we see the system creating life running intelligently, and I propose there are layers of the genome where Davies 'ghost in the system' exists. That is what activates. It is all still a black box. As usual I am interpreting the bolded statements in my way.

Yes, the system runs intelligently. I also propose a “ghost in the system”, which is cellular intelligence. Your “ghost” is a 3.8-billion-year old library of instructions, and presumably another set of instructions instructing the ghost to pick out volume 3,000,000,007, under “fin”, or “camouflage”, or “flight path”, or “nest”. You described as “sloppy thinking and writing” your earlier proposal – that DNA may have contained all the info for evolution, and “info” meant a complete set of instructions. The only change appears to be that you have substituted “genome” for DNA.