polymania

Over at Pharyngula, PZ Myers notes the latest silliness from one of the most ardent Intelligent Design advocates, William Dembski:

William Dembski asks an odd question:

Ask yourself, Why do biological systems exhibit molecular machines at the smallest level permissible by the properties of matter? “Evolution” provides less and less a convincing answer.

I have a different question. What process or protein would the Intelligent Design creationists not call a "molecular machine"?

Myers fumbles a little in his answer; however, one of the commenters, Martin Striz, provided the best summary of why notions of irreducible complexity and the specious "747 built by a tornado" arguments are fundamentally unsound. He writes:

In one sense, a machine is any system that performs a thermodynamically improbable transformation. A car doesn't spontaneously drive you to the mall, but given energy input and your coordination, it will make that transformation (of your location). Machines at the macro level are human-made systems designed to make such nonspontaneous events happen.

Enzymes are also systems that make chemical transformations with low thermodynamic velocity more probable. Except that enzymes can be constructed from the bottom up because they have smooth fitness gradients, while human-made macro machines do not.

IDists never mention this difference to their audiences, and probably don't understand it themselves. It's the key reason why the "tornado making a 747" analogy is horrendously wrong.

As to the question, "Why do biological systems exhibit molecular machines at the smallest level permissible by the properties of matter?", I don't understand what the issue is. They exhibit machines at the smallest level of organization precisely because evolution is a bottom-up process. Organisms are complex interwoven sets of thermodynimically imporbable chemical reactions, and the only way that they can arise, ontogenetically and phylogenetically, is through the smallest units of chemical conversion "machinery" permissible by the laws of physics/chemistry.

And yes, another commenter was unclear on what he meant by "fitness gradient", just as I was. His followup indicated that he basically is referring to the robustness of the reaction. At the molecular or even the cellular level, the likelihood of chemicals to still engage and complete reactions even under suboptimal conditions is far greater than what can happen for a complex entity on a larger or "macro" scale:

It means that slightly changing some variable only changes the activity of the system/enzyme slightly, it doesn't completely knock it out. For example, if you look at a graph of the activity of an enzyme over, say, temperature, you'll typically see a parabolic curve, it looks like a hill (or less often a hyperbolic curve). At some temperature, the enzyme has maximum activity. In humans, this is usually 37C, which is why it's so important to maintain thermal homeostasis. If you change the temperature to 38 or 36C, the enzyme doesn't just stop working. It merely slows down.

If you make a single amino acid substitution in an enzyme, it (usually) doesn't just stop working as well. You change the conformation of the enzyme slightly, you alter the size or shape of the binding pocket, and therefore the affinity of the substrate for the enzyme. It works a little better or a little worse. The fitness function for this enzyme is smooth. It doesn't just stop working.

With macro machines, if you cut the right wire in a car, it does stop working. That's a discontinuous fitness function. Only specific states work at all.

[...]

The reason, I think, that enzymes and other nanosystems have smooth fitness gradients is because physics becomes a lot more probabilistic, a lot fuzzier, at smaller and smaller scales. All chemical reactions are thermodynically probabilistic, although most macro objects aren't.

Evolution works by accruing complexity through small changes over smooth fitness gradients, because that's the only way that it could happen from the bottom up. And since the smallest systems are likely to have the smoothest fitness gradients, it shouldn't be a surprise to Dembski why biological systems have tiny "machines." At least not if he knows some biochemistry.

This is the clearest refutation of that old complexity canard I've come across.

The implications of these ideas are far-reaching. Not only do they help us understand how the myriad of enzymatic reactions that happen in organisms eventually came to be, but they even give us a hint as to how abiogenesis - an idea beyond the purview of evolution proper, but not science - could well occur. Indeed, Dembski has it completely backwards - when it comes to understanding the origin of these processes, Evolution provides the only convincing answer.

tags: evolution, intelligent design, abiogenesis

Well, another Thanksgiving in the can. You know, I like the idea of this holiday just fine, but it seems to me that the timing of it is ridiculous. Why have a nice family oriented holiday just one month before another one? Any why have a holiday that supposedly represents an autumn harvest festival long after any real harvest actually occurs? It's late November, for pete's sake, right on the verge of winter.

I am going to start a movement, a real Movement, to Move Thanksgiving to some other date.

I'll blog more on this later, but I just wanted to get the idea out there. It's gonna happen. Oh yes it will.

Our family does a random drawing every year, around Thanksgiving time, to determine who gives a present to whom for Christmas. (In the interest of not engaging in total consumerist gluttony, we try to reduce the total amount and cost of gifts exchanged in the holiday season.) We've always cut up little pieces of paper, and drawn them from a basket to assign the names. Pretty 19th-century, don't you think?

So, with plenty of free time at hand, I whipped up a couple Perl scripts to make these random assignments for us. This one takes a list of names of assigns gift recipients to each one randomly:

#!/usr/bin/perl -w

@givers    = ('Dan','Lori','Connie','Dave','Chet','Cindy','Eric','Mom','Kent');
@receivers = @givers ;

foreach $giver (@givers) {
    $num_receiver = int(rand(@receivers)) ;
    $receiver = $receivers[ $num_receiver ];
    redo if $giver eq $receiver;
    print "======++++++ $giver will give a present to $receiver\n" ;
    splice (@receivers,$num_receiver,1);
}

My mother also suggested today that we come up with a similar scheme for having the adults give a gift to one child. The constraint was that a parent could not give a gift to their own child, but other than that, every assignment was random. I also cranked out a script for that:

#!/usr/bin/perl

my $adult;
my $kid;
my $num;

my %parents = (
   'Gabby'  => ['Dan','Lori'],
   'Grant'  => ['Dan','Lori'],
   'Alissa'  => ['Dan','Lori'],
   'Bianca'  => ['Dan','Lori'],
   'Caitlin'  => ['Dan','Lori'],
   'Zack' => ['Connie','Dave'],
   'Nick' => ['Connie','Dave'],
);

my @adults = ('Dan','Lori','Connie','Dave','Chet','Cindy','Eric');
my @kids =  ("Gabby","Grant","Alissa","Bianca","Caitlin","Zack","Nick");

BLOCK: foreach $child (@kids) {
    $num = int(rand(@adults));
    $adult = $adults[ $num ];
    foreach $parent ( @{$parents{ $child }} )  {
        redo BLOCK if $parent eq $adult ;
    }
    print "======++++++ $child will get a present from $adult\n" ;
    splice (@adults,$num,1);
}

As it turns out, we probably won't even use this second script, since there are some issues about the purpose of even doing this random assignment thingy in the first place. But I felt compelled to prove to myself that I can still create something from scratch on a moments notice, even after a full year away from programming at Yahoo. Thanks to Apple and Mac OS X, where I can easily graft together Perl in a UNIX environment.

I just discovered that Norah Jones sings and plays along on "Virginia Moon", on the Foo Fighters' latest album "In Your Honor".

I love it when my favorite artists collaborate, especially when I would never have imagined that they might. In the biz we call that "thinking outSIDE the box."