Why would anyone want a complete simulation, anyway?

The NY Times is touting a computer simulation of Mycoplasma genitalium, the proud possesor of the simplest known genome. It’s a rather weird article because of the combination of hype, peculiar emphases, and cluelessness about what a simulation entails, and it bugged me.

It is not a complete simulation — I don’t even know what that means. What it is is a sufficiently complex model of a real cell that it can uncover unexpected interactions between components of the genome, and that is a fine and useful thing. But as always, the first thing you should discuss in a model is the caveats and limitations, and this article does no such thing.

I’d like to know how fine-grained the model is; I get the impression it’s an approximation of interactions between molecular components based on empirically determined properties of those elements. Again, I don’t think the authors have claimed otherwise, but it’s implied by the NY Times that now we have an electronic simulation that we can plug variables into and get cures for cancer and Alzheimer’s, without ever having to dirty our hands with real cells and animals anymore.

That’s nonsense. Everything in this model has to be a product of analyses of molecules from living organisms; they certainly aren’t deriving the functions and interactions of individual proteins from sequence data and first principles. We can’t do that yet! The utility of a model like this is that it might be able to generate hypotheses: upregulating gene A leads to downregulation of gene Z, a gene distantly removed from A, in the model, and therefore we get a preliminary clue about indirect ways to modulate genes of interest. The next necessary step would be to test potential drug agents in real, living cells. This model will have a huge mountain of assumptions built into it — and you can only build further on those speculations so far before it is necessary to cross-check against reality.

Also, isn’t it a bit of a leap to jump from a single-celled, parasitic organism like M. genitalium to human cancers and brain disease? Yet there it is in the second paragraph, a great big bold exaggeration.

And then there’s the really weird stuff. Some people need to step back and learn some biology.

“Right now, running a simulation for a single cell to divide only one time takes around 10 hours and generates half a gigabyte of data,” Dr. Covert wrote. “I find this fact completely fascinating, because I don’t know that anyone has ever asked how much data a living thing truly holds. We often think of the DNA as the storage medium, but clearly there is more to it than that.”

What the hell…? Look, I could (if I had the skills) generate an hourglass simulator that calculated the shape and bounciness and stickiness of every grain of sand, and stored the trajectory of each as they fell, and by storing enough data for each grain, generate even more than half a gigabyte of data. So? This doesn’t mean that an hourglass is a denser source of information than a cell. The storage requirements for the output of this program do not tell us “how much data a living thing truly holds” — that statement makes no sense.

As for “We often think of the DNA as the storage medium, but clearly there is more to it than that”…jebus, does a professor of bioengineering really need to go back and take some introductory cell biology courses, or what? Heh. “More to it than that.” I’m glad to see that someone needed an elaborate computer simulation to figure that out.

I am, for some reason, reminded of the time I attended a seminar by a computer scientist on an exciting new simulation of the genetic behavior of viruses that I was told would have great predictive power for epidemiology. One of the first things the speaker carefully explained to us was how they’d incorporated sexual reproduction into the model. I wish she’d waited to the end to say that, because it meant that I sat there listening to the whole hour talk with absolutely no interest in any other details.

Just like Lenin and Stalin!

The residents of Happy Valley have torn down Joe Paterno’s statue. I’m dismayed, though, at the student in this video whining about how it wasn’t fair. Paterno enabled child rape. The kindest thing was to keep the statue’s removal discreet, rather than having a mob strap cables to it and tear it down with trucks, followed by dragging it through the streets and tossing it in the river.

Also, the NCAA will soon be announcing strict penalties on the Penn State football program. PSU football is dead, and unfortunately, this is going to be a major hit on PSU academic programs, too. Never tie your university’s reputation to athletics, people!

The Dark Knight Rises

I saw this new Batman movie last night, and it was fairly good: complex and twisty and dark, mostly, the way I like ’em. It was far from perfect though, so I’ll send you off to this review that lays out the very same problems I had with the movie. No spoilers, it’s safe!

It doesn’t mention one big problem I had with the ending, though, and this one is a bit of a spoiler, so I’m putting it in rot13: Ongzna cbvfbaf bprnaf naq ungrf svfu! I just cringed at the solution to one terrible problem, which treated another serious issue cavalierly.

Also, the ending sets up the possibility of sequels, which is getting mildly annoying. Maybe these stories have roots in pulp serials, but I’d kind of like to see a story with a real ending someday.

I wish we didn’t have atheists saying this

It’s enraging that we have blinkered, stupid Christians declaring that a shooting spree is caused by evolution, or liberals, or atheism. Why? Because there’s the obvious fact that the perpetrators of such crimes are usually not biologists, liberals, or atheists, but also because it is logically fallacious and offensive: the majority of atheists are not committing crimes, and there’s nothing in the principles of atheism that even implies we should be freely slaughtering other members of our communities. It is also the fallacy of mistaking a specific particular for the general properties of the whole; it’s like arguing that one cold day means the climate isn’t warming.

Atheists wouldn’t make such a stupid mistake, though, would they? The killer in Colorado was a church-going Presbyterian — we’re not going to see atheists crowing in triumph and saying that that shows the Christianity turns you into a mass-murderer, are we? That would be just as false as blaming it on evolutionists — the overwhelming majority of Christians feel no compulsion to murder, so it seems to be a rather ineffective ideology for encouraging killing sprees. One could argue that it does short-circuit critical thinking, and that at least the American version seems to endorse destructive policies, but pinning the actions of one unusual individual on the teachings of a religion? We wouldn’t be dumb enough to make that mistake.

I’m disappointed to see that we do have stupid atheists. Witness Why James Holmes’ Rampage is the Result of the Teachings of Christianity. I hang my head in shame. That’s no different than what Rick Warren or the American Patriarchy Association or any of a thousand other ideologues playing the blame game have done.

Christianity is piss-poor at doing more than providing lip-service against violence, but it’s at best a passive enabler. Blame it on the real causes: a culture that glorifies violence, easy availability of deadly weapons, and mostly James Fucking Holmes. Anything else is a distraction from correcting the real causes.

Gotcha!

This is an account from Connie Schultz’s facebook page, so I’ll put the whole thing here for you fb-haters.

Email from conservative blogger, dated July 9, 2012:

Dear Ms. Shultz,

We are doing an expose on journalists in the elite media who socialize with elected officials they are assigned to cover. We have found numerous photos of you with Sen. Sherrod Brown. In one of them, you appear to be hugging him.

Care to comment?

An exposé! Of the elite media! And he’s got the photographic evidence! It sounds so Breitbartian. And the followup is a classic Breitbartian pratfall.

Response, dated July 10, 2012:

Dear Mr. [Name Deleted]:

I am surprised you did not find a photo of me kissing U.S. Sen. Sherrod Brown so hard he passes out from lack of oxygen. He’s really cute.

He’s also my husband.

You know that, right?

Connie Schultz.

I’m sure this will make headlines at the Drudge Report or the Daily Caller or The Blaze or some similar right-wing schlock factory.

Burzynski is still bilking dying children

And credulous newspapers are helping that quack. The latest case is a little girl in Ireland with a disfiguring and deadly rhabdomyosarcoma who is trying to raise money to get the useless and totally fraudulent Burzynski antineoplaston treatment … and this article makes the good point that newspapers are helping to defraud sick people. Both the Irish Times and the Irish Independent reported on the poor girl’s struggle, and they called the fake treatment “pioneering” or “advanced”.

Each uncritical article published about clinics like the Burzynski clinic amounts to free advertising for a treatment which is at best, as yet unproven, and at worst, much more damaging than it is claimed. Though articles about individual patients and families must tread a careful line between criticism of the clinic and the feelings of those involved, the current standard of reporting on these clinics ultimately helps no one. It’s time to stop hiding the controversy, and sweeping it under the carpet. Patients deserve information, not infomercials.

It’s a shame. If you google Burzynski, the first page is full of bullshit promoting the fake treatment — one thing his clinic is good at is SEO — but still, there’s quackwatch and Orac and Larry Moran buried in the muddle, pointing out that this is flaming quackery. You’d think a reasonably intelligent journalist would notice that there’s some controversy here. And even better, you’d expect a reasonably intelligent journalist to pick up a phone, call an oncologist, and ask what they thought of antineoplaston therapy.

But they don’t.

And Burzynski gets free advertising for his $200,000 urine treatments.

Portland, Oregon is having a humanist film festival!

I wish I could be there. The Humanist Film Festival is happening on 26-28 October, and they’re looking for submissions. If you’ve got anything that fits their categories, send them in soon. They’re looking for films that speak to humanist themes, including:

  • Reason, Critical Thinking and Skepticism (such as claims of the paranormal, critical thinking education, rational living, etc.)

  • Ethics and Human Wellbeing (including human rights, women’s rights, gay rights, rational ethics, challenging scriptural ethics, sex education and attitudes about sex, etc.)

  • Science and the Natural World (e.g. science appreciation, science education, evolution, global warming, pseudo-science and pseudo-medicine etc.)

  • Freedom of Thought, Speech and Critical Inquiry

  • Challenging the Claims and Value of Religion (e.g. anti-apologetics, education about atheism and atheists, uncovering problems with religion, etc.)

  • Separation of Church and State

  • Joie de vivre and human thriving (art and aesthetics, living the good life, human progress etc.)

And here’s their mission:

The Portland Humanist Film Festival is an outreach event designed to broaden the understanding and acceptance of a secular, humanist world view. It specifically addresses audiences who are friendly to our views but who are not necessarily familiar with atheism or humanistic ethics, or why we value reason and scientific thinking. The Film Festival presents these themes through an accessible, entertaining medium.

Got any suggestions? If you’re a godless filmmaker, think about sending them something!

Have you ever felt like you were hanging out with a mob of anti-social, clumsy nerds who need everything spelled out literally for them?

I know I do. When the minimal basics of simple social interactions have to be spelled out, you know you’re in trouble.

I say that as someone who has always been a shy and cautious wallflower, too. If I understood this stuff all along, and you didn’t, you’ve really got a problem.

Of course, an alternative hypothesis is that you’re hanging out with a bunch of predatory assholes who are pretending to be unable to understand social mores so they can violate them.

Another thing that bugs me: if you’re bragging about how you feel safe at an event, so what? I’ve always felt safe in my travels, because I’m a cocky brash guy who has never been seriously threatened in my life, and because most of the events I attend are safe — going to an academic conference is not like walking into a biker bar. To deny someone you want on your side even the slightest reassurance of security because you have to preen about your privileges just tells me that you lack the slightest modicum of empathy.