[continued from previous message]   
      
   >>> The issue though is not what fraction of the possible protein space   
   >>> life has explored, but rather how explorable is it? E.g. is it sparse   
   >>> plains with occasional local maxima, or is it a rugged terrain of   
   >>> endless valleys and ridges? In either case, the maxima will be mostly   
   >>> undiscoverable to incremental search relying on incremental   
   >>> improvements each conferring survival advantage sufficient to drive   
   >>> the associated mutation to fixation in the population.   
   >>   
   >> Your adaptive immune system would not work if the search parameters   
   >> were what you want them to be.  Biological evolution by descent with   
   >> modification works because the space that needs to be searched is   
   >> minimal and within what is possible.  Really, new antibodies that bind   
   >> specific antigens would not be routinely selected for by an immune   
   >> response if the search parameters were too distant from the existing   
   >> protein sequences.  If you look up the abzyme work where they use the   
   >> adaptive immune system to evolve new enzymatic activity you will find   
   >> that they have found that less than 10 changes in the antibody   
   >> sequence can produce the new enzymatic activity that was selected   
   >> for.  It wasn't just any enzymatic activity, but the one that they   
   >> were selecting for.   
   >>   
   >> The paper that you put up trying to claim that too many new genes   
   >> needed to be produced to evolve multicellular animals should have told   
   >> you that very little protein space seems to have been needed to be   
   >> searched. Those thousands of new genes evolved after a basic set of   
   >> genes had already evolved, and they evolved over a billion year period   
   >> before the Cambrian explosion.  The initial gene set had been evolving   
   >> for over 2 billion years to produce that Eukaryotic gene set.  It   
   >> looked like nearly all the new genes that evolved within the billion   
   >> year period before the Cambrian explosion had evolved from an existing   
   >> gene.  You should have seen that in their tables of the origins of the   
   >> new genes.   
   >>   
   >> It just turns out that very little protein space has had to be tested   
   >> to get to where we are now.   
   >>   
   >>>   
   >>> The way to and up countless Mount Improbables need to be largely   
   >>> smooth and monotonically increasing.   
   >>   
   >> The mount improbables are only in your head.  What exists are just   
   >> additions to what had already existed.   
   >>   
   >>>   
   >>> I realise too that this not a settled question, and in some instances   
   >>> a random polymer can be effecively to function, e.g. https://   
   >>> journals.plos.org/plosone/article?   
   >>> id=10.1371%2Fjournal.pone.0000096&utm_source=chatgpt.com   
   >>   
   >> The likely reason that nearly all new genes have evolved from existing   
   >> genes is that just a random sequence of amino acids will fold up and   
   >> could have some function, but most random sequences do not efficiently   
   >> produce the same structure.  It can take time to fold up, and the   
   >> sequence might not fold up into the same structure every time.  De   
   >> novo coding sequence that produces a new protein has to go through a   
   >> selective process where the sequence needs to further evolve so that   
   >> it will efficiently fold up into its functional structure.  Genes that   
   >> have existed for billions of years already fold up efficiently, and it   
   >> turns out that just changing the sequence a little can produce a new   
   >> function, so we end up with related gene families.   
   >>   
   >> There is even some stability issues with existing proteins, and   
   >> chaperone proteins have evolved to help them maintain the shape they   
   >> need to be in in order to function.   
   >>   
   >> It is just how life has adapted to reality.   
   >>   
   >> Ron Okimoto   
   >>>   
   >>>   
   >>>>   
   >>>>>   
   >>>>> ID posits a lawlike conservation of information, which I find   
   >>>>> intuitively appealing, but Dembski's efforts to formally define   
   >>>>> this have yet to land it seems.   
   >>>>>   
   >>>>>   
   >>>>>   
   >>>>>   
   >>>>>   
   >>>>   
   >>>   
   >>   
   >   
      
   --- SoupGate-Win32 v1.05   
    * Origin: you cannot sedate... all the things you hate (1:229/2)