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Where can I get some decent Windows-based software for doing genome comparisons?
You might be happy with this.

E-SKEPTIC FOR JUNE 21, 2002
Copyright 2002 Michael Shermer, Skeptics Society, Skeptic magazine, e-Skeptic
magazine (www.skeptic.com and skepticmag@aol.com). Permission to print,
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---------------------------------
Greetings fellow e-Skepticers, and happy summer solstice, the longest day of 
the year. May the sun god continue to shine on us all. The following is a 
result of a recent interesting coincidence that goes a long way toward 
understanding on evolution works.

DARWIN, HAMLET, AND HOW EVOLUTION WORKS:
AN INTERESTING (BUT NOT UNEXPECTED) COINCIDENCE
By Michael Shermer

Here is an interesting coincidence on Darwin, Hamlet, and how evolution 
works, that itself needs no "intelligent designer" to explain.

In the latest issue of Scientific American, the Editor-in-Chief John Rennie 
wrote a brilliant article entitled "15 Answers to Creationist Nonsense," 
debunking creationist arguments 
(http://www.sciam.com/article.cfm?articleID=000D4FEC-7D5B-1D07-8E49809EC588EED

F&pageNumber=4&catID=2). In that article he used an example from my book, Why 
People Believe Weird Things, from Chapter 10 "Confronting Creationists: 
Twenty-Five Creationist Arguments, Twenty-Five Evolutionist Answers" (also 
published as a separate pamphlet and available at www.skeptic.com). In that 
chapter I cite a computer program designed and run by a friend and colleague 
of mine when I was teaching at Glendale College, Richard Hardison, on how 
long it would take a monkey to randomly type "To be or not to be." It would 
take 26 to the power of 13 trials for success, which is 16 times as great as 
the total number of seconds that have elapsed in the 4.5 billion years of our 
solar system. But Hardison designed a computer program that acts like natural 
selection: it preserved the gains and eradicated the mistakes. In other 
words, the computer "selected" for or against letters as they were randomly 
produced (if "T" preserve, if "Z" skip), and took an average of only 335.2 
trials to produce the sequence TOBEORNOTTOBE. It took only 90 seconds. 
Hardison calculated that the entire Hamlet play could be done in 4.5 days. 

This appeared in Richard Hardison's spiral-bound course reading material in 
1984 for a course he and I co-taught on the history of great ideas; it was 
then published in 1985 in book form as "Upon the Shoulders of Giants," 
(University Press of America) published in a second edition in 1988 (as cited 
in my own book).

If that computer sequence sounds familiar to readers, it is because Richard 
Dawkins did something very similar in his book The Blind Watchmaker, except 
he used a different phrase--"Methinks it is like a weasel"--completely 
independent of Hardison, and neither one of them knew about the other's 
program. Dawkins book came out in 1986; he produced his program in 1984. 
There is no way he could have known about Hardison's work because it wasn't 
published in any form that would have been available to anyone but the 
students in our class. And Hardison didn't know about Dawkins' program.


But how interesting or unusual a coincidence is this? Dawkins and I had an 
e-mail exchange about that, and here is his rather satisfactory explanation 
requiring neither Jungian synchronicity nor paranormal shenanigans:

"Thank you for clearing up the mystery. Yes, the coincidence is fascinating.
But it is not all THAT surprising, and you have spotted that it makes a good
lesson in paranormal debunking. Once one has grasped (from Darwin) the
paramount importance of ratcheted CUMULATIVE selection when faced with the
Argument from Statistical Improbability, one's thoughts naturally turn to
the famous monkeys who have so often been used to dramatise that Argument.
It becomes the obvious simulation to do, to get the point across to
doubters. It can easily be done with a little BASIC program, and that is
what both Hardison and I did, at what must have been almost exactly the same
time, 1984 or 1985. As for the superficial details, those pesky monkeys have
always typed Shakespeare. Hamlet is his most famous play. To Be or Not to Be
is the most famous passage from that play.  I would probably have chosen it
myself, except that I thought the dialogue between Hamlet and Horatio on
chance resemblances in clouds would make a neat intro: hence Methinks it is
like a Weasel.

Reverting to Richard Hardison, the one thing he did which I did not (and I
am now kicking myself for not thinking of it) was to extrapolate to the time
it would take to type the entire play. The speed at which computers happened
to run in 1985 is, of course, not particularly interesting now: just an
arbitrary point on the Moore's Law curve. But it would now be interesting to
do the extrapolation again for (a) modern computers and (b) monkeys. Make
some sort of conservative estimate for how much slower a monkey is than a
computer. 4.5 days would expand to  --  what?  --  tens of millions of
years? Hundreds of millions? It will still be very very short compared to
the random monkey without cumulative selection."
----------------------
Here is the section from Hardison's 1985 edition, with the narrative passage 
from pages 123-124 and the computer program from Appendix E. I typed the 
entire thing in for interested readers. Remember, this program was for a 
computer from the early 1980s--very primitive!

IN "UPON THE SHOULDERS OF GIANTS" BY RICHARD HARDISON, 1985, University Press 
of America, pp. 123-124:

"Taking exception to the view that orderliness could be chance-determined, 
the anti-evolutionists point out that while the monkeys might type Hamlet in 
theory, they could not do so in the real world, for the time required would 
be much too great. 

Let us imagine an intrepid monkey punching away at a typewriter keyboard. For 
the monkey to stumble onto just the few words, "To Be Or Not To Be" would 
require a prohibitive improbability. Mathematical expectancy would lead us to 
anticipate some 26 to the 13th power number of trials before the litttle 
rascal prints out the desired sequence and sends his typewriter off for a 
much-needed ribbon replacement. This number of trials is so large that it is 
roughly 16 times as great as the total number of seconds that have elapsed in 
the four and one half billion years of the solar system's existence.

These enormous numbers apply for just the first 13 letters of Hamlet's 
siloloquy, and for every additional letter, the odds against continued 
success grow by leaps and bounds. More significant still is the fact that 
producing Hamlet is child's play when compared with constructing the human 
eye or inventing the process of reproduction. Rather discouraging.

However, this just isn't the way evolution works. To the contrary, nature 
keeps the successes and discards the failures. The gains are perpetuated, so 
to continue the typewriter analogy, when our simian friend happens upon a T, 
that letter is kept and he goes on randomly typing until he strikes an O, 
which in turn is retained. And so on.

What then are the chances of arriving at the opening line of Hamlet's 
question with this scheme of modified randomness? At first glance, this may 
seem the kind of problem that is not suited to calculation (since one end of 
the distribution curve is infinite) but it is possible, using a simple 
formula that is proved by calculus and infinite geometric series, to arrive 
at the theoretical number of trials that would be expected (338), and it is 
also possible to program a computer to test the calculations empirically. Let 
us have the computer randomize alphabet selection until a T is drawn. Then it 
will be programmed to do the same for the O and continue accordingly for the 
desired 13 letters. Interested readers should consult APPENDIX E for a print 
out of the "Basic" program that will perform this test of empirical 
probability ten successive times.

When running the program through a home computer 1000 times, it developed 
that an average of 335.2 trials were required in order to produce the 
sequence of letters "TOBEORNOTTOBE." Small computers do not have perfect 
random number generators, but the outcome gives reasonable support to the 
theoretical expectancy of 338. Clearly 338 is a number of vastly different 
magnitude than the number of seconds that have elapsed in the history of the 
solar system.

Extending this computer program so that it would construct the entire play 
would be a task of Herculean proportions, but if this were done, the actual 
writing of the play would require only about four and one half days for the 
relatively slow home computers of today."

THE COMPUTER PROGRAM IN APPENDIX E IN "UPON THE SHOULDERS OF GIANTS" BY 
RICHARD HARDISON

10 REM 1984 R. HARDISON
11 PRINT "RANDOMIZING ALPHABET"
12 PRINT "WRITE HAMLET, KEEPING"
13 PRINT "SUCCESSES."
14 PRINT :; REM N-COUNTER: # OF TRIALS
15 REM T=COUNTER:REUSE "TO BE"
16 PRINT "SUBROUTINE TO
17 PRINT "RANDOMIZE AND SELECT"
18 PRINT "LETTER"
30 N = 0
40 FOR G = 1 TO 10
50 T = 0
60 GOTO 80
70 X = INT (26 * RND (1)) + 1: RETURN
80 GOSUB 70
90 N = N + 1
ETC.