Please don’t use this argument

I got briefly drawn into a twitter argument with a fellow atheist who proudly flashed this image:

badarg
The next time you get bullied by religious people on facebook, remind them that they are using hardware and software invented and built by atheists, including facebook!

That is embarassingly bad. And when I pointed out a few of the flaws in that claim (briefly, ala twitter), he just repeated the claim and then accused me of trolling.

Look, it’s a terrible argument. It annoys me in multiple ways.

  • Have you ever heard Christians claim that all of science is built on a Judeo-Christian foundation? I sure have (WARNING: Creationist video on autoplay at link!). I’ve been told many times that Newton didn’t believe in evolution. It sounds stupid when they say it, it sounds stupid when atheists say it.

  • What, do you really think there are no religious scientists and engineers? Tim Berners-Lee is a Unitarian Universalist. Guglielmo Marconi was both a Catholic and an Anglican. James Clerk Maxwell was a Baptist. I mean, seriously, you’re going to claim our modern technological world is the product of atheists, and you’re going to ignore Maxwell? Jebus. Pretty strong selection bias you’ve got there.

  • I die a little bit inside when you tell me that your paragon of techno-atheist excellence is Mark Zuckerberg and Facebook. Who thinks that Facebook was something that couldn’t possibly have been invented by a devout Christian?

  • All anyone needs to do is cite one Christian who worked on the development of the internet, and your argument dies. Is it wise to stake your claim to something all it takes is one counterexample to shoot down?

  • I notice all the exemplars in the picture are white men. Keep using this logic; let’s start bragging to everyone on the internet that they are using hardware and software invented and built by white people. It’s the same argument. Do you see the flaws yet?

  • We are living in an interesting little bubble of time in which our best educated, most economically stable people are drifting into more secular ways of thinking. Odds are that if you’re sufficiently secure economically that you can go to Harvard in a tech field, even so secure that you can drop out of Harvard, you’re also likely to be secular or liberally religious, and you’re also more likely to be white. Do not confuse cause and effect. You are succeeding because being godless and pale-skinned gives you an edge — you’re looking at people who started out on third base. It’s not because being godless gives you special science powers.

You are not going to find many people who are more adamant than I am that religion and science are incompatible — they are fundamentally different ways of determining the validity of truth claims, and one works while the other perpetuates garbage — but I am not going to confuse that with an incompatibility between religious people and science. Scientists who are religious are quite capable of setting aside supernatural beliefs to work well and succeed in the lab. Being an atheist doesn’t turn you into a scientist or engineer. Avoiding church doesn’t make you a better scientist or engineer — practicing science, no matter how silly the hobbies you practice in your spare time, does that.

Screw it, gimme a steak

As I’ve been shedding the meat from my diet, I don’t need discouragement like this: a fellow ate a vegetarian burrito and picked up a tapeworm from it, which infected his brain. Is there to be no reward for virtue?

Of course, when you think about the mode of transmission, it probably got into the burrito by way of the poor hygiene of the cook, who’d either been handling raw meat or feces…

Wait, take it away, suddenly I don’t want the steak, either.

What I taught today: the great cis vs trans debate

My students get a full exposure to the Sean Carroll perspective in his book, Endless Forms Most Beautiful, and I’m generally pro-evo devo throughout my course. I do try to make them aware of the bigger picture, though, so today we had an in-class discussion/’debate’ (nothing so formal as a debate, and it was more a tool to make them think about the arguments than to actually resolve a question). Fortunately, there’s one really easy exercise we can do in developmental biology, because some big names in the field have already clearly laid out their positions in a couple of relatively succinct papers, so I had a shortcut to bring the students up to speed on the issues. I split the class on Monday, having half read a paper by Hoekstra and Coyne on “The locus of evolution: evo devo and the genetics of adaptation” (pdf), which argues for the importance of trans-acting mutations in evolution, and another by Wray on “The evolutionary significance of cis-regulatory mutations” (pdf), which argues for the importance of developmental changes through changes in cis regulatory regions.

I drew this little cartoon on the board to illustrate the situation: that changes in the coding regions of genes produce mutations that can have broader effects throughout the cell (trans: they can affect other genes not on the same chromosome), while changes in regulatory DNA will have discrete effects on just the gene on the same strand of DNA they are (cis).

cistrans

Then I asked them put together an argument as a group advocating for the significance to evolution of their ‘side’, cis or trans, which they then delivered to their opponent, with opportunities for rebuttal and counter-rebuttal.

Ah, pitting the students against one another…always the fun part of teaching.

There was good friendly discussion. Both sides had to dig into their respective papers to find the arguments, and then restate them to make their point, both of which are good exercises. The battle waged to and fro, and then our hour was up and I asked them to vote for who ‘won’, in the subjective sense of making a good argument and persuasively advancing their position. The results:

Which position do you think makes the best case for the significance of their phenomenon in evolution?

Team trans: 1
Team cis: 0
Both positions are important: 8

Minnesota mildness for the win!

I did think one student comment was perceptive and exposed the whole argument for a sham. If they were to go off to graduate school in developmental biology, they wouldn’t be picking Team trans or Team cis: they’d be pursuing a phenotype or a pattern of interest, and then analyzing how it worked and came to be, and they’d simply accept the evidence, cis or trans or both, however it turned out. Follow the data, always.

Now that’s a healthy attitude.

Halos in the sky

I just got back from this evening’s Cafe Scientifique — where were you guys? — and I got to see lots of pretty pictures of halos and sundogs and light pillars. One of the nice things about living in Morris is that we actually get a lot of that weird atmospheric phenomena here, because we have lots of the raw material for them here: ice crystals. Vast drifting clouds of hexagonal crystals, flat and columnar, of various proportions, floating in the sky at various orientations to both refract and reflect light into our eyes.

I won’t go into all the details, since you weren’t there. And since most of you live in a less blessed place than the cold crisp upper midwest in the wintertime, you won’t get to see them, because your wicked heat melts all those sharp edged crystals into sludgy droopy droplets. Sorry. But I wanted to pass along one tip.

There’s some free software called Halosim that lets you do simulations of ice crystal distributions in the atmosphere. You specify their sizes and proportions and shapes, and then it traces the paths of light rays and produces an idealized image of what you should be able to see.

HaloSim

It’s very cool. You can tinker and see that to make dramatic sundogs, for instance, you need lots of flat hexagonal platelets floating in a mostly horizontal orientation, and presto, you’ll get a pair of virtual suns 22° to either side of the real one.

Well, maybe you can do that. It’s PC only, so I can’t run any of the simulations on my home computers myself. I’ll have to settle for looking at the real thing, darn it.

I can defend both Lawrence Krauss and philosophy!

Philosophers are still grumbling about Lawrence Krauss, who openly dissed philosophy (word to the philosophers reading this: he recanted, so you can put down the thumbscrews and hot irons for now). This is one of those areas where I’m very much a middle-of-the-road person: I am not a philosopher, at least I’m definitely not as committed to the discipline as someone like Massimo Pigliucci, but I do think philosophy is an essential part of our intellectual toolkit — you can only dismiss it if you haven’t thought much about it, i.e., aren’t using philosophy at all.

So I’m pretty much in agreement with this post about the complementarity of philosophy and science. In fact, I’ll emphatically agree with this bit:

Scientists and mathematicians are really doing philosophy. It’s just that they’ve specialised in a particular branch, and they’re employing the carefully honed tools of their specific shard just for that particular job. So specialised, and so established is that toolkit, that they don’t consider them philosophers any more.

I’ll also agree with the flip side, where he defines philosophy:

Philosophy’s method is bounded only by the finite capacities of human thought. To the extent that something can be reckoned, philosophy can get there. As such, philosophy will never stop asking “why”.

But then I start to quibble (oh, no! I must be infected with philosophy!).

So what this is really saying is that science is a bounded domain of philosophy, while philosophy is unlimited, which sounds like philosophy has the better deal. But I’d argue otherwise: what’s missing in philosophy is that anvil of reality — that something to push against that allows us to test our conclusions against something other than internal consistency. It means philosophy is excellent at solving imaginary problems (which may be essential for understanding more mundane concerns), while science is excellent at solving the narrower domain of real problems. Science has something philosophy lacks: a solid foundation in empiricism. That’s a strength, not a weakness.

I think that’s where philosophers begin to annoy us, when they try to pass judgment using inappropriate referents — which is also how scientists like Krauss can annoy philosophers. And philosophers are so good at rationalizing disagreement away while carping on others. For instance…

Because scientists have a rather poor track record when it comes to doing philosophy.

Sam Harris’s attempt to provide a scientific basis for morality springs to mind, where he poo poos metaethics only to tread squarely in a metaethical dilemma. Or Richard Dawkins and his dismissal of religion as a false belief system, meanwhile dismissing the rather significant psychological and cultural functional roles it has played throughout human history, and may still play today.

Or Krauss, who without a hint of irony, suggests that good philosophers are really just bad scientists, when in fact he’s a good scientist doing philosophy badly. His definition of “nothing” comes not from within science, but is a grope in the dark for a definition that conforms with his particular theoretical predilections. That’s not how one defines things in polite (philosophical) circles, as David Albert pointed out.

After stating that scientists are philosophers and that science is a branch of philosophy, we’re now told that scientists do philosophy poorly. So is he saying that scientists must do science poorly? I know who’s not going to get invited to my next cotillion, that’s for sure.

Rather, scientists do their brand of philosophy very, very well — philosophers seem to be playing a two-faced game here of wanting to claim science as one of their own when they like what it accomplishes, but washing their hands of it when they don’t like it. Nuh-uh, people, you want to call us philosophers, you have to live with the stinking chemicals and the high energy discharges and the reeking cadavers now too.

His examples aren’t persuasive. I’ll skip over Harris, I’m not particularly fond of his efforts to explain morality, but the Dawkins complaint is weird. He does not disregard the immense psychological and cultural roles of religion: in fact, those are reasons why he and I both detest religion, because we’re aware of all the harm it does and has done. That we think the physical and psychological harm is enough that we should change it is not a sign that we’re doing bad philosophy at all; it’s a sign that we scientifical philosophers consider reality and empiricism to be extremely important factors in our thinking…apparently to a greater degree than many non-scientifical philosophers.

As for Krauss, I thought the Albert review was awful — typical unbounded philosophy with no anchor to the truth. Krauss’s definition of “nothing” was not just a grope in the dark. It was a definition built on empirical and theoretical knowledge of what “nothing” is like. Krauss is describing the nothing we have, Albert is describing the nothing he thinks we ought to have. Krauss is being the scientist, Albert is being the philosopher, and the conflict is driven because the philosopher is unable to recognize the prerequisites to doing science well.

I think that appreciating the boundaries of both disciplines as well as their strengths is important for getting along. Krauss may not have appreciated what philosophy has to offer, but a substantial reason for the friction is the smugness of philosophers who disrespect the functional constraints required for doing good science. Scientists don’t get to be “bounded only by the finite capacities of human thought”. We also have to honor the physical nature of reality.

In my head I have the capacity to flap my arms and fly. In the real working world…not so much.

Cafe Scientifique tonight!

I was up early this morning and just got off the radio, where I told you the whole story. Were you listening? KKOK/KMRS out of Morris, Minnesota? You get it every day with the weather and the farm report?

Oh, OK, I’ll repeat myself. Tonight, Tuesday the 26th of February, at 6pm in the Common Cup Coffeehouse, Sylke Boyd will be talking about “Sundogs and Halos and Pillars—oh my”. This is an informal, casual conversation about science — she’ll talk about what causes these strange atmospheric phenomena, and also be showing lots of lovely pictures of the strange skies above Morris, Minnesota.

Come on down, everyone!

What I taught today: maternal effect genes

You know I teach the 8am courses every term, right? Every semester for years I get my oddball classes that weren’t present in the curriculum 13 years ago (when I started here) stuffed into the cracks of the schedule. I’m slowly getting to be a little pushier and am gradually making my way into wakier hours with other classes, but so far, developmental biology is still in the darkness. Fortunately, this talk was so jam-packed with excitement and action that they couldn’t possibly sleep through it! Right?

Just a word about the presentation slides: I’m a firm believer that less is more. My goal is not to display my lecture notes, or lists of bullet point slides that make my points for me, but to show complex and interesting illustrations that I talk about and explain — whoa, I know, how radical. I’ve sat through too many talks that flash 60-80 slides at me in an hour, and it’s too much. Take your time, people! That said, I used 18 slides in a 65 minute lecture today, which I felt was a little excessive — I aspire to someday do a lecture with half that number. But I am weak and need the crutch now.

Also, I returned exams today. People asked if I’d post their answers. No way in hell! These are exams and have the privilege of privacy. I will say that in general the students answered well. The goal of that kind of exam isn’t to confront students with a question that has a specific answer, but with a problem that they should explore, defend, or criticise.

So the subject today was maternal effect genes in Drosophila, specifically the prepatterning information that specifies the anterior-posterior and dorsal-ventral axes. Yes! I can tell you’re all excited!

So I gave them the precursor observations to the actual molecular biology, all this lovely modeling of gradients and information domains that was rich with Turing elegance, and then I dashed their optimism with the cold water of reality: molecular biology has shown that instead of beautifully designed systems, we’ve got bits and pieces cobbled together in a functional kludge. Any pretty patterns we do see are the product of brute force coding.

So they got the overall picture of A/P patterning in flies: a gradient of the Bicoid protein, high in front and low in back, is read by cells to determine their location — its the GPS signal of the early fly. The Nanos protein, also found in a gradient but from back to front, is a hack: it’s only purpose is to clear away a leaky remnant of another gene, Hunchback, which isn’t supposed to be expressed yet (although Nanos may be the diminished rump of a more elaborate ancestral posterior patterning scheme). And the Torso related genes are specifically involved in ‘capping’ the front and back ends of the fly.

The main point of interest about the terminal genes like Torso is their mechanism: we sometimes talk about maternal genes as like a paint-by-number system in which Mom lays out the lines for different areas of differentiation in Baby, and then the embryo fills in the details. The terminal genes are like a perfect example of that: in the follicle, cells literally paint the vitelline membrane of the fly with different informational molecules during the construction of the egg, and then as the embryo develops, these molecules trickle across the perivitelline space (a gap between the outer membrane and embryo proper) to bind receptors and trigger regional differentiation.

It’s also a nice segue into the dorsal/ventral patterning genes, because flies do something similar there: proteins imbedded in discrete regions of the vitelline membrane diffuse to Toll receptors, where they selective activate the Dorsal protein by freeing it from the Cactus inhibitor. We go from a paint-by-number kit to a restored gradient from back to belly side of localization of free Dorsal protein to the cell nucleus. By the way, in case they were getting bored with flies, Dorsal is homologous to NF-κB in us vertebrates, using the same nuclear exclusion/inclusion mechanism, and NF-κB is a hot molecule in biomedicine and cancer research right now.

That was my hour. I closed by threatening them with talk of zygotic genes, specifically the gap genes, next week.

Also, Wednesday we’re going to try something a little different. We’ve finished chapter 5 of Carroll’s book Endless Forms Most Beautiful so they should be ready to weigh the importance of various mechanisms, so I split the class in two and told half of them to read Wray’s article on the importance of cis-regulatory mutations in evolution, and Hoekstra and Coyne’s article that argues for a more balanced emphasis. I’d love to have a fight break out in the room.

Don’t let Catholics run hospitals

Imagine if you lived in a town where the only hospital was owned by the Jehovah’s Witnesses, and you were in a car accident — you’ve got a ruptured spleen, you’re bleeding internally, and your life is at risk. The surgeon is going to go in and stitch up and cauterize everything, but you’re warned that they don’t keep any kind of blood supply in the hospital, and they refuse to do blood transfusions — they have an in-house professional ethicist (who is a Jehovah’s Witness, of course) who rejects the morality of exchanging sacred blood, and the administrators have signed an agreement with the church to never, under any circumstances, carry out blood transfusions.

If you need a blood transfusion, they say, don’t worry, the ambulance will take you to a different hospital…50 miles away. You, unfortunately, are in shock, you’ve got a gusher pouring blood into your body cavity, and this is not an option. You get to die.

We would not tolerate this situation. That hospital would have a change of ownership as fast as the public could drive it, and if anyone did die because of that kind of criminal neglect and refusal to follow standard medical procedure, a malpractice suit would be the least of their worries. Someone would be going to jail.

So why are Catholics allowed to buy up and impose Catholic dogma on hospitals? Is it because their ignorant dogma does the greatest harm to women (especially those slutty ones who have sex) and bizarre rules about reproduction don’t directly harm men?

But Catholics are buying up hospitals all over the country. They’ve got declining attendance, they’re closing churches, they’re having trouble recruiting priests, but they’ve still got buckets of money, and they’re using that money to impose control in another way — by taking over your health care.

Catholic institutions across the nation are merging with secular hospitals, clinics, and even small private practices at an unprecedented rate. Optimists explain that the consolidation and shared infrastructure help reduce costs. Pessimists point out that the aggressive mergers come at a time when Catholic bishops are exerting and expanding their authority. “I see it as a conscious effort to achieve through the private market what they failed to achieve through the courts or at the ballot box,” says Monica Harrington, a San Juan Island resident who’s spent the last year fighting a Catholic hospital in her town.

Three of the largest health-care systems in the Northwest—PeaceHealth, Providence Health & Services, and Franciscan Health System—are Catholic entities, and they’re busy making new deals in our state. According to MergerWatch, a nonprofit that tracks Catholic hospital mergers across the nation, there was a record-breaking 10 mergers announced in Washington State in 2012.

It’s a chilling story. Catholics can’t get their way in popular opinion, so they’ve followed another path, buying up and limiting health care options so that you have no choice but to follow their ancient biblical rules. The linked article is an examination of the growing move to limit your medicine to Catholic medicine in the Pacific Northwest, but it applies everywhere. They interviewed doctors who reported on their constraints.

Three physicians working in Whatcom County eventually agreed to speak with me. PeaceHealth bought out the secular hospital in 2008. Since then, PeaceHealth has systematically bought up nearly every specialty clinic in the area, from cardiologists to pediatricians, hospice to oncology. The physicians who agreed to meet me for coffee talked about the mindfuck of being raised Catholic, turning to atheism, and excelling in medicine—only to wake up one day with the church as your boss. The first physician joked grimly about the religious directives being “medieval torture porn.” He talked about the struggle of trying to balance his duty to patients with the edicts of a Catholic hospital.

These religious directives are nightmarish. They aren’t always followed — these really are rules laid down by religious fanatics who have no experience or connection to the actual practice of medicine, and conscientious doctors try to find workarounds — but what limits them now is competition. If Catholics get a monopoly on health care in an area, then the trouble really begins.

To understand Catholic health care, it’s important to know the rules that guide Catholic hospitals, otherwise known as Ethical and Religious Directives (ERDs). These directives are drafted and tweaked by the rotating cast of mostly white, mostly celibate bishops couch-surfing at the Vatican. ERDs operate like a code of conduct that medical staff in Catholic hospitals agree to abide by, regardless of whether or not a particular staffer is Catholic. For the most part, the directives aren’t suggestions—they’re prescriptive.

“Any partnership… must respect church teaching and discipline,” one directive states. The church monitors the implementation of these directives through hospital ethic committees overseen by regional bishops like our very own Archbishop Peter Sartain.

Sure, in 43 pages of Ethical and Religious Directives, there’s some common-sense guidance to be found. But they’re also flush with horrifying detail. As you’d expect, the directives pertaining to women’s fertility read like a misogynist romance novel or found art from the Middle Ages: “Catholic health institutions may not promote or condone contraceptive practices.” Emergency contraception can only be given to rape victims, and even then only “if, after appropriate testing, there is no evidence that conception has occurred already.” Vasectomies and tubal ligations are also prohibited. Egg and sperm donors are deemed “contrary to the covenant of marriage,” surrogate motherhood is prohibited because it denigrates “the dignity of the child and marriage,” and doctors at Catholic hospitals can’t help infertile couples conceive artificially—using their own eggs and sperm—because test-tube babies “separate procreation from the marital act in its unitive significance.”

Then there’s this: “Abortion… is never permitted.”

Not even when the egg attaches outside the uterus and puts a mother’s life in danger: “In case of extrauterine pregnancy, no intervention is morally licit which constitutes a direct abortion.”

The short-sighted and selfish male readers out there (and we know we have no shortage of those assholes in the atheist community) aren’t possibly quite as outraged as they should be. These rules affect women, right? I got mine, let them worry over it, it’s not my fight.

Unfortunately, Catholics also have some weird ideas about LGBT relationships. Another set of people who are going to be hurt by this Catholic takeover are those who are in any kind of relationship that doesn’t fit their narrow definition of one man, one woman…and give them the power to flex their ideological muscle, and you might find yourself snubbed if you’re divorced.

So maybe you aren’t gay and your sexual relationships are conservative and conventional. The other big problem is death, which all of us will do someday. Washington state passed a death with dignity law a few years ago, allowing physician-assisted suicide in terminal cases. Guess which hospitals ignore the law and will prolong your suffering indefinitely?

Don’t let Catholics control your hospitals. Keep the church out of your health care decisions. Make Catholic Ethical and Religious Directives (ERDs) illegal — individuals may follow them at their personal discretion, but no health care facility gets to impose them on their patients, especially when they defy the law.

Not to mention the excessive reductionism…

Wow. Talk about major failure. A new study out correlates levels of Foxp2 with levels of vocalization in rats: basically, male rats squeak more than female pups when they’re stressed by separation from their mothers, and mothers tend to rescue the rat who squeaks the loudest. They then found higher levels of Foxp2 in males, and also found that reducing male Foxp2 levels in male pups with siRNA also reduced vocalizations. So far, so good; looks like a reasonable and interesting experiment. Then they extended it to humans half-assedly, finding that 4 year old boys have lower levels of Foxp2 in their left hemisphere (the side that largely controls speech) than 4 year old girls; they could not do the siRNA experiment in human children, obviously.

And that’s where it goes so, so wrong. The researchers assumed that women talk more than men, four-year old girls have more Foxp2, therefore their results conform neatly to what they observed in rats.

You know all the times that men complain about women talking too much? Apparently there’s a biological explanation for the reason why women are chattier than men. Scientists have discovered that women possess higher levels of a "language protein" in their brains, which could explain why females are so talkative.

Previous research has shown that women talk almost three times as much as men. In fact, an average woman notches up 20,000 words in a day, which is about 13,000 more than the average man. In addition, women generally speak more quickly and devote more brainpower to speaking. Yet before now, researchers haven’t been able to biologically explain why this is the case.

The only problem here is that that statistic is false, and men and women talk at about the same rate. Oops.

female-vs-male-word-counts

This is so unfortunate. There is evidence that girls on average learn to talk a little earlier than boys, and that would have been a safer correlation, especially since they’re describing different levels in young children. That interpretation is still fraught, though: they haven’t worked out cause and effect, they know nothing about how Foxp2 mediates this vocalization difference (and we don’t even know if it’s a direct effect on vocalization; it could also modulate a stress response), and in humans, we don’t know if different socialization pressures could be causing differences in the expression of this gene.

This is why scientists are supposed to be cautious in their interpretations. Especially when trying to explain human behavior, there’s far too much temptation to push the results to fit stereotypes as a kind of unconscious validation.