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Bennett Standeven  
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 More options Jan 15 2004, 7:49 pm
Newsgroups: talk.origins
From: be...@pop.networkusa.net (Bennett Standeven)
Date: Fri, 16 Jan 2004 00:41:15 +0000 (UTC)
Local: Thurs, Jan 15 2004 7:41 pm
Subject: Re: Stacking the Deck

seanpitnos...@naturalselection.0catch.com (Sean Pitman) wrote in message <news:80d0c26f.0401141825.4784ad85@posting.google.com>...
> howard hershey <hersh...@indiana.edu> wrote in message <news:bu46sv$srt$1@hood.uits.indiana.edu>...

> > > Consider the scenario where there are 10 ice cream cones on the
> > > continental USA.  The goal is for a blind man to find as many as he
> > > can in a million years.  

> > Except that is NOT what evolution does.  Evolution starts with an
> > organism with pre-existing sequences that produce products and interact
> > with environmental chemicals in ways that are useful to the organism's
> > reproduction.  

> Yes . . . so start the blind man off with an ice-cream cone to begin
> with and then have him find another one.

OK; the ice cream cones are probably found in shops; so given any
cone, odds are that another cone is just a few inches away. This is
still true even if there is only one shop in the USA.

> > Up is good. Down
> > is bad.

> Ice-cream cone = Good or "Up" (to one degree or another) or even
> neutral depending upon one's current position as it compares to one's
> previous position.  For example, once you have an ice cream, that is
> good.  But, all changes that maintain that ice cream but do not gain
> another ice cream are neutral.

> No ice-cream cone = "Bad", "Down", or even "neutral" depending upon
> one's current position as it compares to one's previous position.

> > Flat is neither good nor bad.

> Exactly.  Flat is neutral.  The more neutral space between each "good"
> upslope/ice-cream cone, the longer the random walk.  The average
> distance between each selectable "good" state translates into the
> average time required to find such a selectable state/ice-cream cone.
> More blind men searching, like 10,000 of them, would cover the area
> almost 10,000 times faster than just one blind man searching alone.
> However, at increasing levels of complexity the flat area expands at
> an exponential rate.

But it does not matter, because the blind men always start out in the
ice cream shop, with an ever increasing selection of cones within
arm's reach. Of course, they'll never find any of the other shops, but
so what?

[...]

> >  And
> > the ice cream cones (the useful functions), remember, are not randomly
> > distributed either.  They are specifically at the tops of these mesas as
> > well.  That is what a fitness landscape looks like.

> Actually, the mesa itself, every part of its surface, represents an
> ice cream cone.  There is no gradual increase here. Either you have
> the ice-cream cone or you don't.  If you don't have one that is even
> slightly "good"/beneficial, then you are not higher than you were to
> begin with and you must continue your random walk on top of the flat
> mesa that you first started on (i.e., your initial beneficial
> function(s)).

> > If this topography of utility only changed slowly, at any given time it
> > would appear utterly amazing to Sean that the blind men will all be
> > found at these local high points or optimal states (the mesas licking
> > the ice cream cones on them) rather than being randomly scattered around
> > the entire surface.

> If all the 10,000 blind men started at the same place, on the same
> point of the same mesa, and then went out blindly trying to find a
> higher mesa than the one they started on, the number that they found
> would be directly proportional to the average distance between these
> taller mesas. If the density of taller mesas, as compared to the one
> they are now on, happens to be say, one every 100 meters, then they
> will indeed find a great many of these in short order.  However, if
> the average density of taller mesas, happens to be one every 10,000
> kilometers,

then each of them is a local high point; only these mesas will have
blind men on them.

> > But you were wondering how something new could arise *after* the blind
> > men are already wandering around the mesas?  The answer is that it
> > depends.  They can't always do so.  

> And why not Howard?  Why can't they always do so?  What would limit
> the blind men from finding new mesas?  I mean really, each blind man
> will self-replicate (hermaphrodite blind men) and make 10,000 new
> blind men on the mesa that he/she/it now finds himself on.

But since the current mesa is a local high point, there is nowhere for
them to go.

[...]

> > Let's say that each mesa top has a different basic *flavor* of
> > ice cream.  Say that chocolate is a glycoside hydrolase that binds a
> > glucose-based glycoside.  Now let's say that the environment changes so
> > that one no longer needs this glucose-based glycoside (the mesa sinks
> > down to the mean level) but now one needs a galactose-based glycoside
> > hydrolase.  

> You have several problems here with your illustration.  First off,
> both of these functions are very similar in type and use very similar
> sequences.

That's not a "problem", it's the whole point. Evolution by definition
involves gradual changes, in which new systems have similar functions
and definitions to the old ones.

> Also, their level of functional complexity is relatively
> low (like the 4 or 5 letter word level).

I don't know exactly what "galactose-based glycoside" is, but
something tells me that it takes more than 4 or 5 amino acids to bind
to it.

> Also, you must consider the likelihood that the environment would change
> so neat so that galactose would come just when glucose is leaving.

Yes. More likely the galactose was always there, but was ignored in
favor of the glucose, until the latter disappeared.

> Certainly if you could program the environment just right, in perfect
> sequence, evolution would be no problem.  But you must consider the
> likelihood that the environment will change in just the right way to
> make the next step in an evolutionary sequence beneficial when it
> wasn't before.

That's pretty easy; following the mesa analogy, either the high mesa
drops to be lower than the formerly low one, or the low one rises
above the formerly high one. Happens all the time.

> The odds
> that such changes will happen in just the right way on both the
> molecular level and environmental level get exponentially lower and
> lower with each step up the ladder of functional complexity.

No; the chance that two sequences will interchange in relative fitness
does not depend on how complex they are.

> What was so easy to evolve with functions requiring no more than a few
> hundred fairly specified amino acids at minimum, is much much more
> difficult to do when the level of specified complexity requires just a few
> thousand amino acids at minimum.  It's the difference between evolving
> between 3-letter words and evolving between 20-letter phrases.  What
> are the odds that one 20-letter phrase/mesa that worked well in one
> situation will sink down with a change in situations to be replaced by
> a new phrase of equal complexity that is actually beneficial? -

Quite good, I'd say. I can easily imagine the relative fitness of
"Today we'll talk about unicorns" exchanging places with that of
"Today we'll talk about unicode", for example. Those are 25-letter
phrases; making them even longer would only increase the number of
nearby phrases with potential value.

> Outside of intelligent design?  That is the real question here.

> > Notice that the difference in need here is something more
> > like wanting chocolate with almonds than wanting even strawberry, much
> > less jalapeno or anchovy-flavored ice cream.  The blind man on the newly
> > sunk mesa must keep walking, of course, but he is not thousands of miles
> > away from the newly risen mesa with chocolate with almonds ice cream on
> > top.  

> He certainly may be extremely far away from the chocolate with almonds
> as well as every other new type of potentially beneficial ice cream
> depending upon the level of complexity that he happens to be at (i.e.,
> the average density of ice-creams of any type in the sequence space at
> that level of complexity).

Yes; the higher the lever of complexity, the more likely that the new
ice cream cone is nearby, since the fancier (more complex) flavors
tend to appear in the stores with the largest selection.

> > Changing from one glucose-based glycoside hydrolase to one with a
> > slightly different structure is not the same as going from chocolate to
> > jalapeno or fish-flavored ice cream. Not even the same as going from
> > chocolate to coffee.  The "island" of chocolate with almonds is *not*
> > going to be way across the ocean from the "island" of chocolate.

> Ok, lets say, for arguments sake, that the average density of
> ice-cream cones in a space of 1 million square miles is 1 cone per 100
> square miles.  Now, it just so happens that many of the cones are
> clustered together.  There is the chocolate cluster with all the
> various types of chocolate cones all fairly close together.  Then,
> there is the strawberry cones with all the variations on the
> strawberry theme pretty close together.  Then, there is the . . .
> well, you get the point.  The question is, does this clustering of
> certain types of ice creams help is the traversing the gap between
> these clustered types of ice creams?  No it doesn't.  If anything, the
> clustering only makes the average gap between clusters wider.  The
> question is, how to get from chocolate to strawberry or any other
> island cluster of ice creams when the average gap is still quite
> significant?

You don't; if you want to get from chocolate to strawberry, you need
to do it early on, when the distance is smaller. That's why
fundamental differences between organisms (such as between chocolate
and strawberry ice cream) are taken as evidence that they are only
distantly related.

> You see, the overall average density of cones is still significant to
> the problem no matter how you look at it.  Clustering some of them
> together is not going to help you find the other clusters

Who said we had to find all of the clusters?

> > It will  be nearby where the blind man is.  *And* because chocolate with
> > almonds is now the need, it will also be on the new local high mesa
> > (relative to the position of the blind man on the chocolate mesa).  The
> > blind man need only follow the simple rules (Up good.  Down bad. Neutral
> > neutral. Keep walking.) and he has a good chance of reach the 'new' local
> > mesa top quite often.

> And what about the other clusters?  Is the environment going to change
> just right a zillion times in a row so that bridges can be built to
> the other clusters?

No; the blind men at the other clusters reached them when they were
still a part of this one. Eventually the clusters split apart and
"drifted" away from each other. (Much as galaxies "drift" apart due to
cosmic expansion.)

[...]

> >  My
> > presumption is that the successful search is almost always going to
> > start from the pre-existing mesa

> Agreed.

> >  with the closest flavor to the new need
> > (or from a duplicate, which, as a duplicate, is often superfluous and
> > quickly erodes to ground level in terms of its utility).

> This is where we differ.  Say you have chocolate and vanilla.  Getting
> to the different varieties of chocolate and vanilla is not going to be
> much of a problem.  But, say that neither chocolate nor vanilla are
> very close to strawberry or to each other.  Each cluster is separated
> from the other clusters by thousands of miles.  Now, even though you
> already have two clusters in your population, how are you going to
> evolve the strawberry cluster if an environmental need arises where it
> would be beneficial?

In that case, you wouldn't. You'd have to settle for chocolate ice
cream with strawberries or some such.

Similarly, we would not expect birds to evolve jet engines, as they
are too different from any system the birds possess now.

[...]

> The suggestion that absolutely all of the clusters are themselves
> clustered together in a larger cluster or archipelago of clusters in a
> tiny part of sequence space is simply a ludicrous notion to me -
> outside of intelligent design that is.  Oh no, you, Robin, Deaddog,
> Sweetness, Musgrave, and all the rest will have to do a much better
> job and explaining how all the clusters can get clustered together
> (when they obviously aren't) outside of intelligent design.

It isn't necessary that they _all_ be clustered in that fashion; only
that some of them are.

 
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