The evolution of caffeine

Let us turn now to the One True God of science and atheism, the Ground State of our existence. We shall now contemplate Caffeine. Raise your cup in praise.

caffeine

This morning, as I was sipping the blessed stimulant and browsing the journals, I learned a little something. I learned how caffeine evolved, and it was both unsurprising and surprising. I am not a biochemist, so it’s always enlightening to read a little out of that field. This, for instance, is the chemical precursor in the synthesis of caffeine.

xanthosine

Oh, I said, I certainly do recognize that — I’ve been teaching budding cell biologists about important biological macromolecules for the past few weeks, and that’s a nucleoside. Note the ribose sugar with the attached nitrogenous base, the double ring of one pentagon attached to a hexagon? That’s xanthosine, which is also a precursor in the synthesis of those purines our cells use in signaling and assembling chains of nucleotides in DNA and RNA. That’s obvious. And then you look at caffeine, and it’s also obvious how cells make it: slap a couple of methyl groups (those -CH3s sprinkled around), and presto, you’ve got a happy drug. Easy.

Except…not all cells make significant amounts of caffeine. It takes specific enzymes to glue those methyl groups onto the core base with any reliable yield, and my cells might have xanthosine around, but they aren’t making any for me. I have to raid the vegetable kingdom and tear off their leaves and beans and hit them with boiling water to extract the blessed caffeine. And then not all plants make it — I can’t get a buzz on with a bowl of peas in the morning.

And then I learn that caffeine has evolved independently at least 5 times, and that the distribution of caffeine is patchy — some species in a genus will make it, while other related species in the same genus don’t. The caffeine molecule in Coffea (coffee) and Camellia (tea) and Theobroma is identical, but it’s synthesized by different pathways.

My mind is blown. Excuse me, but I have to take a break and think about this. I’m going to take a walk down to the coffee shop and gurgle down a couple of cups to help absorb this information. I’ll resume this post a little later.

You understand, don’t you? Go have another cup of coffee or tea while you’re waiting.

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Michael Egnor is business as usual for creationism

ignorant

The other day, I wrote about how New Atheists are the same as the Old Atheists, and in particular, how all kinds of atheists are responding to the failure of all religion to answer basic questions about our existence. I could argue that religion is a font of bad ethics, bad philosophy, bad charity, etc., but because I’m a science guy I wrote about how badly it addresses questions of our origin and nature, and how the major premises of all religions are false.

This has roused the indignant jellyfish of the Discovery Institute, Michael Egnor, who has declared that atheism is a catastrophe for science. The most remarkable thing about his complaint is that I asked a number of questions about key premises of faith, like about the existence of a deity, an afterlife, and why we should believe your particular dogma over another, and he doesn’t answer any of them. He doesn’t even try. This isn’t even an argument.

I ask, “Why should I believe one religion over another?”

He harumphs back, Because Christianity is obviously true.

I could ask, “How do you know?”

Because it just is.

This is not a productive direction the discussion could take, but it’s what I expect from a Discovery Institute flunky. The details are not much different from my broad outline. So I bring up this basic question in my post:

Why should I believe in any god? We don’t need an intelligent authority to explain the universe…

His answer:

Of course we need an intelligent authority to explain the universe. The universe is shot through with intelligibility. Nature is governed by astonishingly complex and elegant physical laws, and the laws themselves are written in the language of abstract mathematics. In fact, theoretical physicists must often explore utterly new mathematical theories in order to explain the behavior of inanimate matter.

That’s not an answer. Nothing in that addresses the issue, and when he continues on to babble about the religious beliefs of scientists, claiming that many of them have believed in gods, he is mistaking personal quirks that are irrelevant to question for the facts that support his contention. I could argue that many scientists have been good musicians, but it would not imply that therefore my theory that the universe began with a note on a violin is true; an even more universal truth, that all scientists have possessed nostrils, is not support for my theory that the Big Bang was actually the Big Sneeze. And doesn’t Sandwalk’s list of atheist scientists immediately refute the idea that religiosity is a precondition for good science?

Egnor is simply making a fallacious assertion, and is begging the question. I will reply with a quote from Percy Shelley, published in 1814, which the Intelligent Design creationists will ignore, as they’ve been doing for two centuries.

Design must be proved before a designer can be inferred. The matter in controversy is the existence of design in the Universe, and it is not permitted to assume the contested premises and thence infer the matter in dispute. Insidiously to employ the words contrivance, design, and adaptation before these circumstances are made apparent in the Universe, thence justly inferring a contriver, is a popular sophism against which it behoves us to be watchful.

Shouldn’t Milo’s 15 minutes be over by now?

It’s not as if Yiannopoulis is contributing anything interesting. But, as Shiv mentions, he’s got a new profile published which throws him softballs. It’s the equivalent of Jimmy Fallon’s Trump interview — it presents a dangerous crackpot as just another goofball, rather than as an inflammatory bomb-thrower.

ThinkProgress protests his presentation as a representative of the LGBT community.

The Out profile of Yiannopoulos represents the peak of this harm. Here is a white supremacist whose entire career has been built on the attention he can get for himself through provocation. His attacks against women, people of color, Muslims, transgender people, and basically anybody who doesn’t like him are as malicious as they come, and he catalyzes his many “alt-right” followers to turn on any target he deems worthy of abuse. This puff piece — complete with a cutesy clown photoshoot — makes light of Yiannopoulos’s trolling while simultaneously providing him a pedestal to further extend his brand of hatred. Indeed, he does so in the profile itself, openly slurring the transgender community, which Out published without any apparent concern.

Amanda Marcotte was at the photo shoot and took the opportunity to grill him on his views. He likes to claim that he’s just a troll who is trying to get a response, but Amanda found him to be completely serious about being an anti-feminist, anti-immigrant, far right wing bigot.

Milo Yiannopolous is not playing around. He is utterly sincere about his far-right views.

He is sincere enough that he lectured me for about 15 minutes and was so caught up in the moment that he seemingly forgot that he was half naked while wearing a wig and makeup. He was sincere enough to get genuinely wound up during this time.

Yiannopolous was so sincere that when the Salon team shut off the cameras so as to move to another vantage point, he demanded that I leave the room, refused to answer any more questions and called me a “bitch.”

Well, now we know how to get under his skin: actually talk about what he really believes.

Allow me to complain some more about SETs

You might also like reading about the reification of student evaluations. I’ve witnessed this so many times — another thing I detest is the sacred mean, which must climb ever higher, or you’re a bad teacher. It doesn’t seem to matter that students are diverse and there cannot be a single professors who personifies the ideal for every single person. One of the terrible things about is that it assumes our student bodies have the consistency of mashed potatoes, and we just have to find the strategy to teach the mass. How can you even contemplate reducing a complex task like teaching to a single representative number?

Student Evaluations of Teaching don’t

I love student evaluations. I hate student evaluations.

Every semester, at the end, I’m required to go through this rigamarole where we give students an opportunity to evaluate our teaching, by handing out a standardized form with a Likert scale for telling us how wonderful or awful we are. It’s useless. They get to color in little dots that put us on a scale of quality, and most students don’t seem to enjoy it, and I’ve also noticed that the way they score the teacher is more reflective of how well they’re doing in the class than how well they were taught. I could easily boost my score by giving out more A grades.

And, unfortunately, they’re taken way too seriously by our review committees. I’ve seen committees split hairs over a hundredth of a point, or compare faculty on the basis of sample sizes of less than 10 students. Worst of all, I’ve been in meetings where faculty seriously insist that every instructor ought to be getting above average scores on student evaluations. And you can’t speak out against them, because then they’ll get revenge by carefully scrutinizing your scores.

In their defense, though, people have argued for years that student evaluation scores are positively correlated with academic effectiveness. Only that turns out to be not necessarily true.

A new study suggests that past analyses linking student achievement to high student teaching evaluation ratings are flawed, a mere “artifact of small sample sized studies and publication bias.”

“Whereas the small sample sized studies showed large and moderate correlation, the large sample sized studies showed no or only minimal correlation between [student evaluations of teaching, or SET] ratings and learning,” reads the study, in press with Studies in Educational Evaluation. “Our up-to-date meta-analysis of all multisection studies revealed no significant correlations between [evaluation] ratings and learning.”

These findings “suggest that institutions focused on student learning and career success may want to abandon SET ratings as a measure of faculty’s teaching effectiveness,” the study says.

Oh, please, yes, make it so. Kill these things. Not only would it stop wasting our time, but it would end pointlessly innumerate conversations in faculty meetings.

But wait, I also said I love student evaluations. I do! But not the numbers. Our forms also have an open space for free-form student comments, and those are often very useful. They’re also abused (one year a group of students colluded to write the same thing on every form: “This class taught me to love Jesus even more”, because of my reputation as an atheist. I hadn’t mentioned anything, pro or con, about Christianity in the course — it was a cell biology class, but I had brought up evolution quite a bit), but they also tell me what students found memorable or problematic. That’s good to know, and I try to reduce the problems and use the memorable strategies more in subsequent classes.

Also, believe it or not, grades aren’t just a way of punishing and rewarding students. I have goals for my courses, and they also tell me if I’m getting essential concepts across. So, for instance, the first exam in my cell bio course this term was intended to evaluate whether students had a good grasp of basic general chemistry; if they didn’t, I would have to go over redox reactions yet again before I plunged into oxidative phosphorylation. There’s no point in pushing on into more complex topics if they don’t have a good grip on the basics. (I’m relieved to say they did surprisingly well on the first exam, so our general chemistry course has clearly prepared them well.)

There are better ways of assessing whether a course is accomplishing its goals than handing students who don’t see the big picture a Likert scale and asking them to state whether the course and teacher are good or not. And do I need to even go into the superficial biases that color SETs? It matters whether you are good-looking or not, and students are nests of gender biases. I know that a benefit from being male — I’m not judged on appearance as much — but suffer a bit from being older and less attractive. But those are things that shouldn’t matter at all in judging teaching effectiveness.

The Democrats are doing it again

I’ve made a few small donations to the Democratic party, and you know what that means: I now receive a flock of email — almost hourly — begging for more donations. And I’ve noticed something ugly about that email. It’s all about fear.

We’ve rightly berated the media for plumping up Trump’s prominence, but the Democrats are doing it, too. Nearly every email is moaning about the polls. The latest is telling me how terrified we should be, because Nate Silver says Trump has a 2 in 5 chance of winning the election. In fact, nearly every email from them is all about the growing power of this ogre who is crushing the opposition and growing in popularity every day, so give us more money.

Just stop it. Of course Trump has a chance; there are a lot of stupid, bigoted people in this country. But I don’t want to hear doom and gloom from his opposition, because it sounds like you’re already giving up. Tell me why the Democratic party is better, what you’ll do if we give you our vote, and how your policies are superior to those of the corrupt orange toad. And most of all, don’t give a good goddamn about the polls. I’m not going to vote for someone because they’re ahead or behind in some poll — that doesn’t influence me in the least, although apparently the Democrats want that to be the major factor in my decision about who I should support, because it’s all they talk about.

Also, I’m more than a little tired of anything to do with Nate Silver, who is the political equivalent of a horse racing tout. Don’t care. Shut up about polls, tell me more about policy.

Terry Gross forces me to question my marriage

It’s a brutal question. Suddenly, my whole life has become a lie because Terry Gross asked a penetrating question of a gay soccer player, Abby Wambach.

So I want to ask you more about like comprehending your sexuality, your sexual orientation. You’d had a boyfriend in high school. You went to the prom together. You were considered, like, the jock couple of Rochester, New York. Was it helpful on Long Island to have had a boyfriend, to have had sex with a boy, so that you could know with more certainty, “no, I love women?”

Dang, Ms Gross, you made me realize…I went through all of high school (and my life since high school) not even dating any boys, let alone having sex with them. With that huge lack of experience, how can I possibly know whether I’m sexually attracted to women, especially my wife? I’m supposed to be all about prioritizing empirical research, and apparently desire has to be evaluated like a taste test, and I have to sample all the varieties before I can truly love someone.