13 November 2007

Of Petards and Retards

Two tales tonight of morons caught with their pants down.

First, poor BarryA at UncommonlyDense. He caught wind of the Blog Readability Test, a tool that uses some unknown criteria to report a web site's "reading level." BarryA thought he would use this little webtoy to go nyah-nyah at UD's nemeses at the Panda's Thumb:
Just for fun I inserted UD and it came back “High School,” which means that the general discussion at this blog is at a high school level. I then inserted Pandas Thumb and it came back “Elementary School.”

Make of this what you will.
Not that this little test actually means anything, but unfortunately for BarryA, he got it wrong anyway. Hetyped in the wrong URL. Pandasthumb.com, an unregistered domain, returns the "Elementary School" result. But the actual Panda's Thumb site, pandasthumb.org, returns "College (postgrad)."

Typical of a cdesign proponentsist, to jump at the first inkling of a conclusion that favors their preconceived notions, without checking to see if the conclusion is at all valid. Did he really expect a site that talks about science all day to return an "Elementary School" rating? Did no warning bells go off at all before he rushed to blog about it?

Other bloggers, as well as commenters on the UD post, have already pointed out his error. In response, BarryA says in the comments:
You are right. Ouch; I’ve been hoisted on my own petard.
*sigh* You lose again, Barry. The saying is "hoist by one's own petard." A petard is a little bomb, characteristic of mediƦval siege warfare. To be hoist by one's own petard means to be blown up by your own tool of destruction. To be hoist on your own petard means, well... very little.

It's a little thing, to be sure, but I like the phrase too much to see it abused like that.

Let's move on to the next stupid, shall we?

Dinesh D'Souza.


In his latest screed, D'Souza blames us atheists for spreading lies (LIES, I SAY!) about Christianity:

Have you heard the one about how the dumb, ignorant Christians for
centuries regarded the earth as flat until brilliant scientists like
Galileo came along with their new telescopes and other inventions to
show that it is round? This account of scientific progress can be found
in textbooks and it has also cemented itself in the popular mind.

The only problem with the story is that it is entirely false. It is
a made-up yarn that is supposed to illustrate the so-called war between
science and religion.
D'Souza's one to talk about made-up yarns. Galileo had nothing to do with demonstrating Earth was round; he provided evidence for a heliocentric model of the solar system! Of all the strawmen I've ever seen, this is one of the flimsiest and most disfigured.

Of course, given all the comments to that effect that D'Souza received on his blog, he had to add some sort of response:
Postscript: No sooner did I post than the atheists were in there,
seeking to divert attention from their Flat Earth myth by claiming that
Galileo is actually famous for being the first to demonstrate the truth
of heliocentrism. Even here, they are wrong on two counts: a) It was
Copernicus who advocated heliocentrism more than a half-century before
Galileo and b) Galileo's proofs of heliocentrism were mostly wrong. For
instance, Galileo argued that one reason we know the earth goes around
the sun is because of the ocean tides. Galileo thought it was the
earth's motion that caused the water in the oceans to slosh around!
Actually, the tides are the result of the moon's gravitational force
acting upon the earth. So Galileo was right about heliocentrism, but
largely for the wrong reasons. Count on our "enlightened" atheists to
keep getting their facts wrong.
So instead of admitting his mistake and apologizing, D'Souza has decided that Galileo hasn't contributed jack squat to science anyway. Classy.

There's a big difference between "advocat[ing] heliocentrism" and "demonstrat[ing] the truth of heliocentrism." Copernicus had a lot of fancy-dancy math to show people, but Galileo put forth observable evidence for it. As for that stuff about the tides, way to take one factoid and call it representative of Galileo's entire argument. I... I cannot believe that D'Souza is actually trying to belittle Galileo's contributions to science.

I find this especially amusing in light of the first issue of Dartmouth's new Christian magazine, the "Apologia." You see, they're trying to recast Galileo as a good Christian who deserved to be persecuted by the Church because he hurt the pope's feelings. I wonder how they'd respond if they knew their new hero was just a lucky moron who got on the good side of the atheists who write the history books.

08 November 2007

Deconstructing Tillich

In my German for Theological Reading course over the Summer, I had to translate the following passage:
Tillich fragte sich: "wie die christliche Lehre zu verstehen ware, wenn die Nichtezistenz des historichen Jesus wahrscheinlich wurde." Tillich kam zu der erkenntnis: "Nicht der historische Jesus, sondern das biblische Christusbild is das Fundament des christlichen glaubens."
Which, roughly, equates to the following:
[Theologian Paul] Tillich wondered: "how are the Christian teachings to be understood, if it is likely that 'the historical Jesus' never existed?" Tillich came to the conclusion that "it is not the historical Jesus, but rather the biblical picture of the Church which is the foundation of Christian belief.
I have to wonder if Tillich realized how hollow this sounds: that a religion that is entirely based around the fact that a certain fellow existed simultaneously as both god and man is not impaired by the likelihood that such a man never existed.

This statement is very interesting to me, because in this Tillich and I are in complete agreement: as far as religions are concerned, there needs to be absolutely no historical truth, or even a historical basis for their claims. All belief systems create reality by consensus: for the Christians, that consensus is that there was a fellow called Jesus who set some important ethical standards and performed some miracles, was literally of divine parentage, and died in order to let people into paradise. Whether or not these claims are historically true is immaterial as far as the religion itself is concerned, because its adherents take it to be true.

But the only reason I can make that statement is because I have nothing at stake in Christianity; looking at the phenomenon from the outside, I can say that Christianity is about whatever the Christians say it is about, and nothing else. But what I really want to know is how a believing, practicing Christian can deny the literal truth-value of his most sacred proposition? Put another way, I wonder how Tillich can make this statement and not instantly lose his faith?
In asking this question and finding the answer that he does, Tillich is essentially ripping out the Rappaportian cornerstone on which his entire faith-system is built.* The consensus-effect of Christian belief only works everyone believes (or claims to believe) in the literal truth-value of the central tenet, from which the rest of the faith derives. That's why "faith" is such a buzz-word among Christians: they realize that their beliefs are kind of wacky, but they also recognize (perhaps subconsciously) that questioning those beliefs will lead to chaos in their society (incidentally, that's why they're so afraid of us Atheists, too). And so you have people touting their faith to the heavens: it's like a game where whoever can convince himself the most completely of a silly idea wins. The more demonstratively you suffer for it, the better! (People willing to die for their convictions get bonus points!)

Now, anyone who sees that the historicity of the Jesus figure is immaterial to the Christian faith but paradoxically remains a Christian nevertheless is trying to have his cake and eat it too. Such a man demonstrates his preference of belief over the conclusions of logic, and is shrinking away from an uncomfortable realization to which his conceptual pursuit has taken him. Tillich, in other words, is an intellectual coward.

But more importantly, Tillich's comment I think says a great deal about the Christian response to modern Biblical research. In fact, when I was starting out here at the Div School in September, I overheard a conversation wherein a good friend of mine (an aspiring Catholic Theologian) was trying to define "Systematic Theology" to another student. It's been a while now, so I don't remember his exact words - but when he was finished, I asked the following:
So, let me get this straight. If I may paraphrase, the job of the systematic theologian is to try to pick up the pieces and salvage the god hypothesis after secular Biblical Scholars come in with their facts, potsherds, and scientific method, and ruin your little theological house of cards?
TO which he responded (and for this I love him):
Yeah. Pretty much.
If the historical Jesus never was, or was nothing like the Jesus of later Christianity, then the whole thing is founded on a lie. But Christianity is about far more than the Jesus fellow: it's a culture, it's a history, it's a way of life, it's a linguistic idiom, it's a way of contextualizing one's experience of living in the world. Many Christians can't just abandon it - so what can they do? The answer of Systematic Theology has been to try to save it with endless layers of intellectual band-aids and the compromise of liberal theology. But this, as we know, has its own share of problems. Perhaps this too is a call for a (non-Theological) Humanist version of Christianity?

*Anthropologist Roy Rappaport wrote a fantastic paper once (whose title escapes me at present) whose thesis was essentially thus: that at the heart of every religious belief system is a central, paradoxical, supernatural claim; that the power of this central image derived from the fact that it was illogical; therefore the fact that it was illogical meant that it could not be logically falsified; and thus all other statements of truth value in a society were made in reference to that central symbol (i.e. swearing to a god as a way of making an oath). The direct result of this thesis, for our purposes, is that people who question that central tenet (*cough cough*) threaten to destabilize the entire culture, because if the truth value of the central proposal is called into question, then all derivative claims can no longer be trusted. I don't do the theory justice, and I'm not sure I agree with everything he says, but he brings up some very interesting points that are always worth considering.

A Minor Irritation

So: my dear, darling Divinity school just came out with its staff/student/faculty directory the other day, and (being narcissistic and wondering how my ID photo looked in grainy black and white) I of course decided to look up my name.

The photo was about as good as could be expected (read: not), so no surprises there. But I was incredibly irritated by the fact that under the religious tradition category they had listed me as "No Denominational Affiliation."

Now, I remember very, very clearly designating "Other: Atheist" (Atheist was never an actual choice) on every form I ever filled out for HDS. Now, as always, I don't want to be one of those angry, loud atheists...but believing as I do that we ought to have the right to be open and unashamed of our non-theistic identity, then I have to be willing to own the label and any consequences it may entail. Which is why it bothers me so much that the administrators seem to have decided that I didn't really mean to be open about my beliefs and have them listed along with my contact information. As though they felt they had to be ashamed of my atheism on my behalf.

Moreover, many many of my classmates opted not to have their denominations published - so not only is my information incorrect (well...misleading), but it seems to be an emphatic statement of fabulous agnosticism or fear of commitment (so non-committal that I'm even apparently afraid to be a Unitarian!).

I had hoped that perhaps there might be other atheists hiding in the woodworks here, who might be surprised and pleased to see a fellow free-thinker in their ranks. Maybe we could get together and have those interesting talks about religion that I had always hoped I'd have in grad school, but which have been entirely lacking for the last two months. But alas - such is not to be.

Still, I don't want to be a dick about it, so I'm not going to try to bring it to administrative attention. But I felt I needed to share that little bit of frustration with you all, if only for my own peace of mind.

Dinesh D'Lusional

I think it may have been a mistake to subscribe to Dinesh D'Souza's blog (it's in the "christofascists" folder in my Google Reader). This can't be good for my heart blood pressure.

The blog is basically one big advertisement/masturbation session over his new book, What's So Great About Christianity. (Don't be misled by the title. From the looks of it, the book is much less about why Christianity is supposedly good and much more about why atheism is supposedly bad.) I was going to give D'Souza the benefit of the doubt and go buy a copy of his book (mostly so I could make angry notes in the margins), but there's no way I'm shelling out thirty dollars for that shitbrick. There's probably nothing in there I haven't heard before anyway... just the same tired old apologetics and smears of atheism, cobbled together by someone I hate who, to my embarrassment, happens to share my alma mater.

But that's okay, because I don't need to give any money to the Hindenburg (Blake, that one made my day!) to give his writing a thrashing... there's plenty of fodder on his blog, much of it excerpted from the book.

And sometimes, it's just too easy. Here's a quote from a recent post:
Yes, I know that some of today's leading atheists like Richard Dawkins and Daniel Dennett have advanced degrees. By itself this proves nothing, since we all know people who are educated beyond their intelligence.
I'm pretty sure that has applied to D'Souza since his freshman fall at Dartmouth.

I seems to be a favorite theme with D'Lusional that atheists--especially contemporary atheists--are all stupid, which means poor li'l Dinesh doesn't have a worthy opponent. He has another post up today to that extent, wherein he writes:
He bought into the atheist canard that somehow theism is inconsistent with reason and science. Of course Boyle and Keppler [sic] and Copernicus and Newton didn't think so, but somehow biology major Sam Harris and literary essayist Christopher Hitchens think they know something that these great scientists didn't.
Here's the thing, Dinesh: Hitchens and Harris DO know something those scientists didn't. They know a hell of a lot more than those scientists did. So do I. And so, perhaps, do you.

The most modern of those four, Sir Isaac Newton, died in 1727. That means the four scientists D'Souza lists knew about neither general relativity nor quantum mechanics. They didn't know about atomic theory, and they didn't have the periodic table of elements. They didn't know about the expansion of the universe, cosmic microwave background radiation, cosmological redshift, the Big Bang. They didn't know about Maxwell's equations for electromagnetism. Newton and maybe Boyle might have known about Hooke's and von Leeuwenhoek's observations of cells, but they knew nothing of cell theory as credited to Schwann, Schleiden, and Virchow. They didn't know about the role of DNA in the cell, much less its structure. They didn't know about evolution. They didn't know anything about the science of psychology. They didn't know jack.

Copernicus, Kepler, Boyle, and Newton are recognized as having been great minds NOT because they were prophets with magical Knowledge of All. We remember them because they were great puzzlers who drew strong conclusions from what evidence they had. Nowadays, we have a vastly expanded reservoir of data from which to draw new conclusions. I'm not going to say Newton would be an atheist if he were alive today, because some people prefer to blind themselves to certain evidences (especially when it comes to religion) and for all I know Newton might have done the same. Newton was kind of a dick. But the data available does not support the truth of Christianity as a conclusion.

So fuck you, Dinesh.

Here now, to help me blow off a little more steam, are Tony Montana and friends:

06 November 2007

Worst. Mad Lib. Ever.

I just stumbled across an ad for the Personal Promise Bible, a sort of vanity publication where you give them your name and they print a bible that makes specific references to you. For example, if your name is Betty Lou:
Even when Betty Lou was dead in her trespasses, God made her alive together with Christ (by grace Betty Lou has been saved), and raised Betty Lou up with Him and made Betty Lou to sit with Him in heavenly places in Christ Jesus. (Eph. 2:5-6)
Now imagine a whole bible like that. I'm not sure what's creepier, a personalized bible or the fact that there's apparently a demand out there for personalized bibles.

Not that I'd want to give these freaks any money, but I have to say, the opportunity for mischief is sacrilicious. I wonder if they screen for pranksters. Just imagine...
Toilet, believing in Him, shall not perish, but have eternal life. For God so loved Toilet, that He gave His one and only Son, that Toilet, believing in Him, should not perish, but have eternal life. (John 3:15-16)
I'd get that sucker leather-bound.

05 November 2007


So I spent most of last night and today trying to install the latest "fglrx" driver in Ubuntu so my graphics card would have some improved functionality, but to no avail. I'm stuck with the out-of-date one for now. I guess I'll just have to be patient until issues are resolved... at least there's always Windows to fall back on.

It looks like Tim Mills (a.k.a. the Friendly Humanist) has been busy with Ubuntu as well. He's apparently been exploring some of the various Ubuntu distributions and spinoffs. In particular, he's found two custom distribution packages: Ubuntu CE (Christian Edition) and Ubuntu ME (Muslim Edition).

I'm sorry, but can I just say, the Ubuntu CE logo is lame:

The standard Ubuntu logo with a Jesus fish in the middle? They couldn't be more creative than that?

The Muslims at least put in a little more effort:

But what really strikes me about all this is, there doesn't seem to be any custom alternative for the third of the big three Abrahamic religions. Where's the operating system for Jews?!

I'm not much of a Linux programmer (or a Jew), or else I'd get cracking on a chosen OS for His chosen people myself. I can, however, at least contribute a logo design:


Doesn't that just make you want to convert? From Windows, that is. ;-)

03 November 2007



I've just accepted a position as research assistant with the Broad Institute of Harvard/MIT. I'm going to be a professional scientist!

The lab in which I'll be working is dedicated to creating deletion libraries for a few different bacteria, including Mycobacterium (the pathogen responsible for tuberculosis) and Pseudomonas (an opportunistic pathogen--meaning it tends only to cause problems if you're already sick--that's especially fond of causing respiratory infections in people with cystic fibrosis). Creating a deletion library means deleting a single gene from the bacterial chromosome, and repeating the process for every gene in the genome. So in the end you have thousands of bacterial colonies, each with a different single gene deleted.

What's really great about this particular project is that we'll be making our deletion library freely available to other researchers. So if a researcher somewhere is interested in a specific gene and wants to know what happens when it's deleted, they don't need to go through creating the deletion themselves, they can just look up the gene in our library and request a sample.

How excited am I to be making that kind of contribution to the scientific community?

Pretty damn excited.

But how, you may be wondering, does one delete a gene from a chromosome? The trick is homologous recombination. If two strands of DNA have a region that matches the other in sequence, that region is said to be homologous between the two. In a cell, two homologous DNA regions can line up, break at the same place, switch pieces, and fuse back together; this is called homologous recombination, or "crossing-over."

Let's say the section of chromosome in which we're interested looks like this:

. . . ====[ Upstream DNA ][ GENE ][ Downstream DNA ]==== . . .

We can build a plasmid (little circle of DNA, kind of like a mini-chromosome for bacteria) that has a section looking like this:

. . . ====[ Upstream DNA ][ Downstream DNA ]==== . . .

(For ease of visualization later, DNA from the chromosome is red and DNA from the plasmid is green.) We can stick that plasmid in the bacteria, and hope for homologous recombination between the chromosome and the plasmid. Recombination only occurs in a few of the cells, though, so we need a means of selecting for those cells that do cross-over.

We need two different recombination events to occur, one on either side of the gene. So we'll stick two marker genes on our plasmid: a strength (like resistance to ampicillin, an antibiotic) and a weakness (like a gene that makes sucrose toxic). First we grow the bacteria on plates containing ampicillin; only those cells that have the plasmid (meaning they've had one cross-over event) will survive. Then we take those survivors and grow them on plates containing sucrose; now only those cells that got rid of the plasmid (meaning they had a second cross-over event) will survive.

So after two rounds of selection, the bacterial chromosomes hopefully look something like this:

. . . ====[ Upstream DNA ][ Downstream DNA ]==== . . .

However, that assumes that one recombination event occurred in the upstream region and one occurred in the downstream region. If both events occurred in the same region, then the chromosome could look like:

. . . ====[ Upstream DNA ][ GENE ][ Downstream DNA ]==== . . .


. . . ====[ Upstream DNA ][ GENE ][ Downstream DNA ]==== . . .

So after all that selection, about 50% of our bacteria colonies still have the gene! We therefore need to add one more step: we pick a bunch of bacteria colonies and sequence that part of the chromosome to see if the gene was deleted successfully. The colonies that pass sequencing get added to our deletion library!

So that's how you delete a single gene from a bacterial chromosome. Part of my job will be figuring out how to optimize that process to handle tens or hundreds of genes at once. That means I get to use robots!

This is going to be awesome.

(Oh, and in case you were curious, the opening to this post comes from this Homestar Runner cartoon.)

01 November 2007

I Have a Friend in Vincent

Sara and I have been watching through Season One of "The Muppet Show" on DVD, and tonight the episode that just happened to come up was the one guest-starring Vincent Price. How incredibly appropriate for Hallowe'en! And even if it weren't Hallowe'en, who doesn't love Vincent Price?

But all is not well, for apparently the Season One release cuts out an entire scene from this episode. Now, that's bad enough in of itself. But dear friends, do you know what scene was omitted? Why, none other than Vincent's big closing number.


You have no idea how upset that makes me. I mean, what decent person leaves a man's big musical number on the cutting room floor? So much for the "complete" first season. Just one more reason to loathe Disney executives.

Thankfully, the episode is included in its entirety in the "Best of the Muppet Show" DVD collection, which I also own. And of course, there's always the magic of the Internet. So now let's take a moment to enjoy Vincent's big finish. Together. As a family.