🚀 go-pugleaf

john baez (baez@guitar.ucr.edu) wrote:
> In article <4fd9gs$ueu@ds2.acs.ucalgary.ca> kmuldrew@acs.ucalgary.ca (Ken Muldrew) writes:
> >baez@guitar.ucr.edu (john baez) wrote:

> >>I'm mainly interested in how many bits of information needed to create
> >>a new organism are contained in the phenotype and NOT in the DNA.  This
> >>seems to be a much trickier and less-studied question.    

...

> Here's what I mean in concrete terms.  In the movie Jurassic Park the
> idea is that scientists find the DNA for dinosaurs and use it to clone
> dinosaurs.  The details are omitted.  Viewers ignorant of biology might
> think that you just hand a biologist the genome of a dinosaur and then
> they mix up a bunch of chemicals and it turns into a baby dinosaur. 
> Of course it isn't quite like that.  There is no stage in the life
> cycle of a dinosaur when all its information is in the DNA.

> So what I'm wondering is this: given the complete genome of an organism, how
> much *additional information* would you need to give someone for them to
> be able to build a living copy of that organism?  

An interesting analogy could be made by thinking of the DNA as the main
memory of a computer, and the mechanisms which translate that information
into proteins/structures/etc. as the central processor of a computer.

So what you're asking is, in essence, "What is the structure of that
processor, and what is the minimal amount of information needed to
describe it?"  Since I am not well-versed in molecular biology, I
can't give a very detailed answer, but I suspect it isn't *that* huge --
perhaps on the same order of magnitude as the amount information in the
DNA; perhaps even less.

One interesting twist about this "processor", relative to a computer's
processor, is that the "program" stored in the main memory can affect
the structure of the processor itself.  Each gene codes for a particular
protein, right?  And the mechanics of a cell depend heavily on the
actions of quite a wide variety of proteins.  Therefore, since the
information describing many (or all?) of those proteins is already
contained in the DNA, we don't have to include a description of them
when we describe our "processor".  That might cut out a lot of the
information right there.

What remains, then, would be to describe the basic mechanisms by
which those genes are translated into proteins, and any other items
whose structure is not specified in the DNA (e.g. the cell membrane).

You would also need some kind of "boot sequence"; i.e. a
specification about which of these proteins encoded in the DNA
must already exist in the intracellular environment in order
for the cell to start functioning.

So I would guess that the amount of additional information needed
really isn't very large at all.  In the example of telling aliens
about how to build a human, we would probably only really need to
give them the genome + the additional structures + the boot sequence
for a zygote.  Although, in addition, we would also probably want to
include the ideal environmental conditions for the growth of this
embryo, and what to expect in terms of how this embryo will grow, and
how to take care of it.  However, this additional information would
not be *absolutely* necessary -- if we assume our alien friends are
pretty bright, they would probably be able to figure out the right
environmental conditions, etc. to get the thing to work.

------

On the issue of "junk" DNA, I would suspect that it's main
role would be in providing additional evolutionary flexibility.
Obviously it must be doing *something*, since longer DNA strands
would require more maintenance, and hence more energy, to maintain.
If they were doing nothing, a mutation which happens to cut out
a section of junk DNA would give the resulting individual a
distinct survival advantage.  So this evolutionary pressure
towards downsizing of junk DNA must be offset by some kind
of advantage it offers.

So let us for a moment assume that junk DNA really is is just
a random stream of base pairs.  Now, it's defined as "junk"
because the sequences don't correspond to any of the amino
acids that would ever be present in the cell, right?  But
what about a sequence that *almost* does -- one that just
has one bit flipped the wrong way, as it were.  A mutation
in this "wrong" base pair may enable the larger sequence
to start coding for an amino acid.  That amino acid might in
turn have been a missing "piece" in a larger sequence which
will build a protein.  So in other words, this "junk" DNA
could contain a huge number of latent, potential genes just
waiting to surface.  Those "hidden" genes could code for
proteins that offer benefit to the organism in its present
environment, or could be useless now but advantageous if the
environment changes a certain way, or even be harmful (e.g.
it could happen to be the code for a virus).

Without the existence of this "junk" DNA, an organism would have
to rely on altering one of the genes already in use in order to
evolve.  So before a new useful protein could be produced, one
of the existing ones would need to be sacrificed -- the cell
would have to "break" some of its machinery temporarily in order
to make improvements.  The odds of producing a new, useful protein
in this way, while allowing the cell to survive in the process, are
probably much lower than if the cell had lots of "junk" DNA.

-------

Whew.  Well, I guess that's everything I wanted to say.  I hope
it's not too naive.  All comments will be appreciated.

- Doug