Christopher Hitchens, Rick Santorum

"...the gods that we have made are exactly the gods you'd expect to be made by a species that's about a half a chromosome away from being a chimpanzee."

One of the things I enjoy very much about hearing Christopher Hitchens speak is his capacity to produce pithy phrases.  The above is paraphrased from a "Hitchslap" youtube.com video and it's both a nice soundbite and a good argument. 

Think of religion as a crime scene, humanity as the potential criminal, and ask "well, did they do it?"  There motive is obvious since religion allows certain people to consolidate authority, serious financial benefits accrue to certain people at the center of the religion, and it allows the elite of the religion to manipulate standards of common decency and morality which might otherwise limit the willingness of the masses to follow their "guidance".  Sure plenty of despots over the years have managed to accomplish these things without relying on established religions, but for the rest it's shown itself to be quite handy.

Beyond the motive, human fingerprints are all over the products of religion.  For one thing, religious rules are the sort of generally nasty, controlling, misogynistic mess you would expect from works of convenience written over decades by gangs of fearful male politicians clutching onto power.  It's the sort of thing Rick Santorum or Michelle Bachman might come up with.  Of course Rick Santorum is not one to want to reinvent the wheel (not sure if he could have done it in the first place) and he just wants to go back to the good old days:

 Figure 1: Rick Santorum showing himself unfit for the 

                presidency of the United States of America by being

                incapable of taking the oath of office.

Really, Rick?  Why don't you just go run for president of Iran instead.

Egypt

If you pay attention to the world, you could probably see the recent scenes from Egypt coming.  It's hard to get rid of a police state.  The barrier is not just the leadership, the barrier is made of all the underlings frightened of the day when light will shine on the police files.  The barrier is made of people who go to work everyday to participate in the machinery of repression.  The barrier is the gang of proto-dictators waiting in the wings.  The barrier is the economic interest of the remaining political elite, in this case the military.  In addition, it was pretty clear from the beginning that Egypt's military was quite happy with its position of political and economic power.

May the second revolution go as well as the first, that's about the best you can expect.

Re: Womanspace

Oh Nature, just admit you made a mistake publishing that worthless piece of fiction and move on with being a GlamourMag.

In other news, scientists discover ImmigrantSpace, a parallel dimension accessible only by immigrants trying to learn English and escape from violent gangs in the post-apocalyptic landscape of America's big city public schools.

Penn. state football hides child rapist

Note: this is not a gently written post, it may be upsetting to some.  I also link to the grand jury document which will be upsetting to all.

---

I care about academic institutions because I am a graduate student and I plan on competing for a faculty job one day.  I care about education in general because it can be a great social good, and I care about education as the parent of two small children.  Before starting my current degree program I also worked in a number of labs which made important societal contributions.  In many ways it's a good "business" to be in and very satisfying, but I also have no illusions about the institutional politics of the Academy.  People in academia do unethical things and one of the downsides is that they're all quite good at rationalizing it.  It's that kind of environment, we select for it.

After a grand jury investigation, three men have been charged with either committing child rape or hiding it.  An assistant football coach, Mike McQueary, witnessed the rape of one of the boys and only reported it internally.  Then the otherwise highly respected football coach Joe Paterno also only reported the incident internally.  After these men realized that the internal process didn't reach its appropriate conclusion, neither chose to go to the police independently.

There is a lot in this story to be angry about.  First of all, in 2002, McQueary had the option of stopping the rape and calling 911.  He had the option of calling 911 and having the police intervene.  It was a basic failure of ethics on his part that he could not muster himself to any meaningful action.  His second chance came later, after he (must have) realized that there were no serious consequences for the rapist.  He had at least seven years to consider this possibility, but never made the right decision.  McQueary (after consulting his father!) reported the rape to Joe Paterno the next day (!) and McQueary was involved in a further meeting with perps #2 and #3 from the above grand jury investigation (Curly and Schultz) where he again related his account of the rape.  The consequences to the rapist were minimal (no locker room key for you Mr. Rapist Sandusky!) and the rape was never reported to the police.

In the end it was the original victim who, years later, relayed the story to his mother.  She notified the school district in 2009, the district notified the police, which led to the grand jury investigation.  It turns out that the mother and the victims who were willing to speak to the grand jury were quite brave.  The rest?  Cowards.  Men in power, three of them at the core of a sport which glorifies testosterone and aggression, completely lacking cojones and drifting through life without a functioning moral compass.

It also makes me angry that I can imagine the meeting McQueary had with Curly and Schultz.  I don't know if he was inclined to report the rape to the police before the meeting, but I'm sure soothing words were deployed about taking care of the "situation" internally and quietly.  Like in other big institutions, it's quite easy to get blacklisted in an academic setting.  People like McQueary work for years to get into the sort of career they want, all the while assiduously avoiding making enemies.  Once you've made that sort of investment it's hard to decide to risk it on your morals.  The investment itself is corrosive.

You might have months or years where the worst you witness is somebody stealing pipette tips from your lab, or trashing your paper in review only to publish first on the same topic.  Sooner or later something real will go down with you in the middle of it, and when it does, please remember that keeping your humanity really is worth risking your PhD/grant/reputation.  Consider it as an extra incentive to network broadly.

After stewing on this for a few days, I discovered that Jon Stewart put it quite succinctly, and is quite effective at conveying his anger as well.

The unholly alliance between \(\phi_t\) and AIC

In the wild world of mark-recapture analysis, there is a well-worn path to publication.  Two of the key parameters are the survival and recapture probabilities in the marked population[1].  One of mile-markers is comparing two models for each parameter: either the parameter is constant, or it is different for each interval (survival) or occasion (recapture).  Sometimes an enlightened paper will skip this comparison, but there's really no guarantee.
Clearly, it's crucial to know whether the survival rate varies over time.

If you were looking at this question using hypothesis testing, you would take the following as your null hypothesis.

\[H_0 : \phi_1 = \phi_2 = ... = \phi_K
\]
The alternative would be that each phi is independent at each time step or something in between.  If you're using hypothesis testing, this brings up, front and center, the problem that H_0 is crazy.  No ecologist would honestly accept that as a null hypothesis.  Survival varies over time, end of story.  I'm pretty sure that the reason this test comes up is that MARK has a button for it.

Besides the fact that the null hypothesis is crazy[2] (though related), small mark-recapture studies, and most are small, will lack the power to find important temporal variation in survival[3].  If biologists were willing to give their theory a little bit more weight in deciding the issue, it would be sensible to take \phi to have some distribution over time (a "random" effect) and just deal with the estimates.  Even if the estimates were nothing special, at least it would save the world from the umpteenth discussion of whether \phi varies over time.

To further muddy the waters, these days the comparison is carried out using AIC rather than hypothesis testing.  I like ranking a set of well-fitting models as well as anybody else, but in this case it just masks the fact that the study was too underpowered to even contemplate the comparison to begin with.  At least when a hypothesis-driven comparison is not significant most biologists know that you shouldn't make a big deal of it without a power analysis[4].  With a table of AIC values, an inappropriate comparison is harder to spot.  One indicator is a slew of "comparable" models which ought to remind the reader that the models are only "comparable" in light of the data on hand. 

Now back to that paper...


[1] Survival in the marked and unmarked populations can be quite different, I'm sure hawks love mice with neon marker on their back.
[2] Common, there's survival variation when you look within a single manufacturing lot of CPU's, forget frogs in the wild.
[3] I just read one in a reasonable journal where the 95% confidence intervals basically stretched from 0.5-0.95, and the _title_ of the paper relied on the statistical lack of difference.
[4] Through the hard work of generations of biostatisticians, most biologists will recognize that making a big deal from a lack of significance is questionable.

The Shotgun Approach to Hypothesis Formation

It's like going into a dark basement in a zombie movie.  You know there are zombies down there, so you might as well start shooting.  Each shotgun blast illuminates more zombies for you, and the process continues.  This is why academics start on a topic and continue until it sucks all the life out of them.  To continue the analogy, if you die at your desk it's because you ran out of bullets.

If ... then ...

If P then Q is only false if P and not Q, if not P, then whatever.  Who knew?

It does help to get these things straight from a blog post if you don't breathe math in your career.