Archives December 2008

Irreducible Complexity Still Not Disproven… Wait, What?

The story so far:

Back in 1996, when Intelligent Design was in its infancy (and pretty
much indistinguishable from today’s Intelligent Design), Michael Behe
defined an irreducibly complex system as:

composed of several well-matched, interacting parts that
contribute to the basic function, wherein the removal of any one of
the parts causes the system to effectively cease
functioning.

Recently, the Disco Tute
presented the bicycle
as an example of an irreducibly complex system, on the grounds that if
you remove one of the wheels, it doesn’t work anymore.

Carl Zimmer
responded
with a video of someone riding a bicycle with only one wheel. So
presumably bicycles aren’t irreducibly complex after all.

Now DonaldM at Uncommon Blithering
presents
this bizarre counterargument:

if you look closely at the photo you’ll notice it isn’t
just the front wheel that’s missing from this bicycle, but the entire
front wheel assmembly, including the handle bars and wheel
frame.

So, um, I guess the point is that if you remove exactly one part from
an IC system, it doesn’t work, but you can remove a whole bunch of
parts from an IC system, and it still works. Wait, what?

Elsewhere in the same post, Donald asks:

Perhaps the good Dr. Z would be so kind as to provide a
bibliography listing all the peer reviewed scientific research studies
that provide the detailed, testable (and potentially falsifiable)
biological models for any of the IC systems that Mike Behe
described in his ground breaking book Darwin’s Black
Box.

Might I suggest that Donald start with the articles and books about
blood clotting and the human immune system that were literally piled
up in front of Behe on the witness stand at the Dover trial? There’s a
good boy.

I’d like to remind him that “nuh-uh” is not a rebuttal.

Audacity Tip: Cleaning up Scratches

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Just something I discovered recently while using Audacity to clean up some old vinyl recordings:

The Click Removal tool does a darn good job of cleaning up most scratches, but not all. IME it’s still necessary to go back after it to fix what it missed (I find that the Repair tool works well for small scratches).

Unfortunately, a lot of scratches are hard to see with the default waveform view: a scratch can have a small amplitude (smaller than the clean waveform around it); it’s annoying because it shows up as a short burst of white noise in the middle of a tune.

The black bars mark the location of an audible but invisible click.

However, white noise shows up as a vertical bar in spectrum view. So what I did was:

  1. Duplicate the track I’m cleaning up.
  2. Mute the copy.
  3. Switch the copy to spectrum view; leave the original in waveform view.

That way, you can zoom out and easily find scratches on the spectrum view. By the time you zoom in and the spectrum becomes too smeared out to be useful, you can see the scratch in the waveform view, so you can fix it.

In spectrum view, the scratch is clearly visible as a bar that goes all the way to the top.

The downside of this technique is that Audacity has to do lots of FFTs to show the spectrum. So you may want to use a fast machine for this.

As we zoom in, the spectrum becomes too smeared out to be useful, but in waveform view, the scratch becomes obvious.

The other downside, of course, is that since you can see a lot more flaws, it takes ten times longer to fix a track.

Merry War on Christmas Eve!

I can only assume that BillDo took heed of my strategy paper on the War on Christmas™, because here‘s what he’s moaning about now:

“The latest gambit by the anti-Christmas Czars is to flood public parks with a vast array of cultural symbols. For example, at the Fort Collins Museum in Colorado, in addition to a nativity scene and a menorah, they are displaying the Indian Diwali Festival of Lights, the Thailand Buddhist celebration of Loy Krathong, the Chinese Lantern Festival, African-American Kwanzaa, Muslim Ramadan, and the Scottish Hogmanay festival.

“It is insulting to Christians and Jews to dilute their long-standing holidays in a country founded on Judeo-Christian principles by turning public areas into a junk-yard clutter of cultural artifacts, and that is why only the nativity scene and the menorah should be allowed in the same place at this time of the year. The real goal of the cultural fascists is to water down the meaning of Christmas (and to a much lesser extent Hanukkah) via contrived competition. Let the others find another spot or another time to display their symbols.”

In other words, “it’s our country, and our holiday. We’ll share with the Jews, but the rest of you can just fuck off.”

No word from the Indian, Thai, Chinese, African-American, Muslim, or Scottish communities on how they feel about their culture being dismissed as “junk-yard clutter”. (Besides, I thought Scotland was Christian, and celebrated Christmas. Maybe BillDo resents them because they’re mostly Protestant. And besides, Hogmanay is a new year celebration. Is Bill going to lay claim to New Year’s Day now as well?)

At any rate, as I sit here admiring the Christmas tree and listening to Bing Crosby, with a Christmas LOLcat on my lap helping me type (and, incidentally, preventing me from getting up and getting the glass of egg nog that I want), yes, I am diluting the True Meaning of Christmas™.

If you didn’t want other people enjoying the secular stuff that’s been glommed onto your religious holiday over the centuries, you shouldn’t have made it so much fun. So now all the kids are playing in your sandbox. Whatcha gonna do about it?

I know what I’m going to do about it: pick the cat off of my lap, get a glass of Christmas cheer, and use it to dilute Christmas some more. And maybe water the tree with Bill’s tears.

Happy Solstice!

Summer solstice for our friends south of the equator, but up north, it’s the winter solstice, the shortest day of the year. This celestial event occurs every year at the peak of the holiday shopping frenzy, as millions of people step out of malls and pronounce the traditional phrase, “Holy crap! The sun’s down already? And I still haven’t found anything for uncle Rupert!” (An alternate theory states that this is caused by millions of children going to bed early to make Christmas morning arrive sooner.)

And remember, you can balance an egg on its point on the winter solstice. Or the vernal equinox. Or any day you like, actually.

Exploiting Personal Tragedy to Advance Ideology

You may have heard of the tragedy of Jesse Kilgore, the college
sophomore who commited suicide after, as
WingNut Daily reported,
reading The God Delusion and having a crisis of faith.

Now, just when you thought the Disco Tute couldn’t sink any lower,
they’ve produced a
melodramatic episode
of their Intelligent Design the Future podcast about this
(the “melo” part is literal: the whole ten-minute episode is
underscored with soft minor-key acoustic guitar and piano music, so
that it sounds like a cross between a eulogy and a soap opera). It
presents the same story that the WND article does: that Kilgore was a
good Christian kid who went off to a secular college, where a
professor either assigned, or challenged him to read The God
Delusion. After Kilgore went out to the woods and committed
suicide, his father found the book under his son’s bed, with a
bookmark on the last page.

The narrative is that Jesse Kilgore killed himself because he read
Dawkins’s book and lost both his faith and his will to live. Yes, it’s
as bad as I make it sound. If you thought the WND article was sleazy,
this is worse.

Now, I don’t know why Jesse Kilgore decided to end his life. No one
life can be summarized in an article and a ten-minute show. I’m sure
there was a lot more to him than we’ve seen. For all I know, he got a
girl pregnant and couldn’t live with that. He didn’t leave a suicide
note, so we’ll probably never know for sure. All we have is
speculation, mostly by grieving friends and relatives.

With that out of the way, the ID the Future show is a treasure trove
of wingnut tropes: we’ve got Good Kid vs. Bad College; Brainwashing
Professor; Reading Opposing Ideas Will Poison You; and many more. For
a group that keeps insisting that they’re not creationists, they seem
to have borrowed an awful lot of ideas from
Big Daddy.

There’s the assertion that Jesse felt alone because he was one of the
only Christians on campus. The school that he was attending,
SUNY Jefferson Community College,
is in northern New York state (unless, of course, both WND and IDtF
got it wrong, which is not something that can be excluded). I can’t
imagine any college campus in North America where most of the
population isn’t Christian.

Then there’s the notion that the nameless biology professor was using
his authority to tell students what to believe. From what little I’ve
seen of religious homeschooling techniques, I suspect that this is
projection: these people teach their kids that “these are the facts,
and they’re true because I said so”, and can’t imagine teachers
leading students to conclusions by showing them the evidence. And in
my experience, the latter is far more common on college campuses than
the former.

PZ Myers put it best (paraphrased from memory): “We don’t teach
students that the sky is blue. We teach them how to go outside and
look up. And yeah, if they come from an environment where they were
told that the sky is green, that’s likely to cause problems.”

And, of course, there’s the elephant in the room: Jesse killed himself
after reading The God Delusion, therefore he did so
because of it. Classic
post hoc ergo propter hoc.

The subtext, of course, is that learning is dangerous. So don’t go
getting any ideas about going to college and exposing yourself to
foreign ideas.

In fact, this theme is repeated several times: Jesse is said to have
been a fervent debater and defender of The Faith; he went to a secular
school because he wanted to challenge himself; everyone was sure he
could withstand anything secular academia could throw at him.
Throughout the piece, foreign ideas are talked about in the same terms
one would describe a disease.

Well, I’m sorry, but if your ideas can’t survive contact with reality,
they’re not worth holding on to. I’d say the lying taint-pustules at
the DI should be ashamed of themselves for promulgating such crap, if
I thought they could feel shame.

Me? Pissed? Oh, just a tad.

(See also
Ed Brayton’s post
at Dispatches from the Culture Wars.)

(Update, Dec. 19, 18:49: Oh, lookee! I beat that hack, O’Leary, to this story.)

Arthur Dent’s Procedural Filibuster

Anyone who’s watched Frank Capra’s
Mr. Smith Goes to Washington
knows what a filibuster is: the Senate has no time limit on debate, so
a senator can just talk and talk and talk for hours, thus preventing
the Senate from taking a vote. This can be stopped if 60 senators vote
to halt debate (a cloture vote), allowing Senate business to resume.

Gary Gamber has a
history
of the filibuster. One interesting twist, though, is that — if
that site is correct — since 1975 Senate rules allow for the
procedural filibuster: if 41 or more senators to simply say that they
intend to filibuster, the filibuster is assumed, the motion is
dismissed, and business resumes.

In other words, a senator can say “I intend to filibuster. Then you’ll
have a cloture vote to shut me up, but 40 of my colleagues and I will
vote against cloture, so the motion will fail; I’ll keep talking until
I run out the clock, and the vote on the issue I care about won’t take
place. So let’s just save ourselves some time and simply pretend that
that’s what happened.”

This seems very similar to the scene in
The Hitch-Hiker’s Guide to the Galaxy
where Arthur Dent is lying in front of the bulldozers to prevent them
from demolishing his house.
He[1]
tells the foreman that since he’s going to be doing this all day, and
since the workers are resigned to this anyway, then they don’t
actually need Arthur there, and he can just run down to the
pub.

[1] Or Ford, in the TV series.

Unlike the Senate, Douglas Adams’s fictional bulldozers do demolish
Arthur’s house as soon as he’s not there to stop them.

And this illustrates a weakness of the procedural filibuster.
Filibusters work because people can and do tie up the floor of the
Senate, preventing real business from occurring. Filibusters are also
a good thing, because they prevent the majority from running roughshod
over the minority. If a senator feels strongly enough about an issue,
he can prevent the vote from occurring, even though he is in the
minority, as long as he can convince 40 others to let him go on. At
the same time, the fact that a filibuster is physically demanding
helps reserve it for those cases when negotiation fails.

But ultimately, it depends for its effectiveness on the senator in
question being able and willing to walk the walk: to talk for as long
as it takes, without a bathroom break if necessary, until either he or
the rest of the Senate gives in. (Though I think there are rules for
allowing two or more senators to take turns, to give each other a
break.)

Fortunately, the majority leader has the option of calling the
filibustering senator’s bluff: bypass the procedural part where the
majority and minority anticipate each other’s moves, and actually go
through the motions: talk, cloture motion, count the votes.
Unfortunately, I understand the current majority leader, Harry Reid,
has failed to use this power, leading to an unprecedented number of
procedural filibusters.

Anticipating a series of events and acting as if they had actually
happened only works if all of the players agree that that’s how things
will play out. In reality, a lot of senators are old, and while they
love to hear themselves talk, even they aren’t necessarily up to the
task of speaking for 20 hours straight, or whatever it actually takes
to block a vote. It wouldn’t hurt Reid to remind those who are abusing
the power of the filibuster what a real one actually entails.

Pursuit of Happiness

Greta Christina
makes a great point:
if conservatives want to argue that gay marriage goes against the
principles that America was founded on, remind them of that founding
principle explicitly spelled out in the declaration of independence:

We hold these truths to be self-evident, that all men are
created equal, that they are endowed by their Creator with certain
unalienable Rights, that among these are Life, Liberty and the pursuit
of Happiness.

If marrying the person you love isn’t pursuit of happiness, I don’t
know what is.

But don’t take my word for it. In the
Loving v. Virginia
decision, SCOTUS chief justice Warren wrote:

The freedom to marry has long been recognized as one of
the vital personal rights essential to the orderly pursuit of
happiness by free men.

Character Encodings Are a PITA

Character encoding schemes (UTF-8, ASCII, ISO-8859-1/-15,
Windows-1252, etc.) are an incredible source of headaches. Stay away
from them.

(Oh, and if you tell me I mean “raw character encoding” or “codepoint
set” some such, I’ll whack you upside the head with a thick Unicode
reference.)

In case you hadn’t noticed, I upgraded WordPress not too long ago.
Being the cautious sort, I did a dump of the back-end database before
doing so, as I’ve done every other time I upgraded. And, like every
other time, I noticed that some characters got mangled. This time
around, though, I decided to do something about it.

It turned out that when I originally set up the database, I told it to
use ISO-8859-1 as the default text encoding. But later, I told
WordPress to use UTF-8. And somewhere between dumping, restoring, and
WordPress’s upgrade of the schema, various characters got mangled. For
the most part, various ISO-8859-1 quotation marks got converted to
UTF-8, then interpreted as ISO-8859-1, and converted again. On top of
which, some commenters used retarded software to post comments, which
insisted on using cp1252 or cp1258 (and I even saw something which
might’ve been IBM-CP1133), which also got converted to and from UTF-8
and ISO-8859-1 or -15.

Obviously, with 13 Mb of data, I wasn’t going to correct it all by
hand; I needed to write a script. But that introduced additional
problems: a Perl script that’s basically “s/foo/bar/g” is
pretty simple, but when foo and bar are strings that
represent the same character using different encodings, things can get
hairy: what if bar is UTF-8, but Perl thinks that the file is
in ISO-8859-15?

On top of that, you have to keep track of which encoding Emacs is
using to show you any given file.

iconv turned out to be an invaluable forensic tool, but it has one
limitation: you can’t use it to simply decode UTF-8 (or if you can, I
wasn’t able to figure out how to do so). There were times when I
wanted to decode a snippet of text and look at it to see if I could
recognize the encoding. But iconv only allows you to convert from one
encoding to another; so if you try to convert from UTF-8 to
ISO-8859-1, and the resulting character isn’t defined in ISO-8859-1,
you get an error. Bleah.

The moral of the story is, use UTF-8 for everything. If the software
you’re using doesn’t give you UTF-8 as an option, ditch it and use
another package.

Foxholes and Shoe Leather

Carnival of the Godless
We’ve all heard the expression “There are no atheists in foxholes”. As I understand it, it means something like:

It’s easy to be self-reliant when everything’s going well. But when times are tough, when the situation is desperate, you will find that you’re not able to fix everything by yourself, and will need to turn to someone else for help. And in really dire straits, you will swallow your pride and turn to God.

Yes, in desperate times people resort to desperate measures. But they’re called desperate measures for a reason: they’re things you normally want to avoid doing.

If I collapse and my heart stops, I’ll be happy for the EMTs to beep-beep-beep-clear!-Zap! me back to life. But that doesn’t mean that I want people to go around zapping me with 1000 volts through the chest.

Starving people will eat anything that looks even vaguely edible, including tree bark and shoe leather. It even helps a little, in that they feel less empty. But that doesn’t mean we should stop eating apples in favor of apple tree bark (though I’m sure you could charge a pretty penny for it in certain boutiques).

The thing about desperate measures is that they come with huge down sides. In certain situations, amuptation, lobotomization, and even suicide may be the best available option. But it’s a good idea not to resort to them before you have to.

And those are just the desperate measures that work. Many desperation measures don’t. In the Middle Ages, plague-ridden towns would exterminate the local cat population, under the belief that said cats had to do with evil magic. And, of course, desperate people have always prayed to whichever gods they thought might help.

As a rule, “If I had no option but to do X, so I’ll do X when I do have other options” is not a good way to live one’s life. And while I’m not so arrogant to say “fontaine, je ne boirai pas de ton eau” — who knows, I might one day resort to prayer in case there’s someone out there — in my right mind, I see no reason to believe that it does any good, and honesty compels me to atheism.

War on Christmas

Carnival of the Godless
Dear Fox News pundits and assorted wingnuts,

I assume that this year, as has become tradition, you will once again be talking up the War On Christmas™. Since I am a liberal godless atheist who supports both separation of church and state and the ACLU, presumably this makes us enemies in this war.

So I thought I’d let you know how I plan to wage war on Christmas.

Oh, I know, giving information to the enemy is usually treasonous, but Christmas is the season for giving, so what the hey. Pull up a yule log and I’ll tell you all my plans. I won’t even make you eggnog-board me.

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