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

by dhw, Saturday, February 02, 2019, 14:19 (1911 days ago) @ David Turell

DAVID: You still seem totally confused about the issue of information in the genome. I see the cells as actively entering their genome for instructions to be activated. The information is always available, just as you enter a library to review a subject from inactive books. As Davies points out life runs on information.

dhw: The genome is part of the cell, so you now have the cell consciously entering part of itself to look for instructions to tell it how to use the part of itself which it has entered....And you have now gone back on your original agreement that information (a passive data base) “cannot possibly serve as instructions”. You also agreed when I wrote: “I would say, then, that life “runs on” cells being aware of and actively using the passive information that is lying there inactive.” Life does not run on information, it runs on the active use of passive information. But you think I’m confused.

DAVID: This is just semantics.

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.] Note the entry on stickleback fish evolution. ( 2019-01-31, 01:22 ) [dhw: I answered it on this thread, 31 January at 12.15]

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: There must be a misunderstanding. I don't understand the bolded quote. It does not represent any of my thinking. I have always viewed the genome as creating structure, but also instructions for biochemical reactions and also responses to stimuli. I'd like to see the entire context of the quote.

See our exchanges on this thread, 14/15 January: You wrote initially: “The original DNA may have contained all the info for evolution”, and when I asked you for a definition of info, you wrote: “a complete set of instructions for cells to respond to all the stimuli they must deal with.”

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)

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.”