Thursday, January 27, 2011

Now that's some efficient health care!

Just had a really bizarre complete waste of my time... Our family practitioner's office called me and said a bunch of claims for my wife and my son were denied -- from 2009. I don't even have the same insurance anymore. The explanation on the EOB was "do not provide that service", and apparently the insurance company told the provider that I would have to call.

So I'm fuming of course... I mean, 2009?! WTF? Luckily I didn't really have to wait on hold, although, the phone menu wanted to fuck me over, but mercifully I got to a point where I could just mash 0 and get to an operator. Talked to the person a bit... apparently there were only two "claims" (although the one on my son was apparently a whole bunch of separate claims that got lumped into one or something) that had failed to go through because there was a computer error while the claim was being submitted.

Yeah, that's it. A short-term computer glitch. All that needed to happen was for the insurance company to resend the claim to their computers.

So I have two questions: What kind of shit-ass IT setup do they have where if there is an intermittent network error while processing a claim -- and it appears to have been internal to the insurance company, no less -- that it requires the intervention of no less than three humans in order to recover? And second, why couldn't the insurance company just work this out with my health care provider?

In a perfect world, the system should have recovered automatically. Transmission error during claim submission? Okay, retry! Failing that, it should have been one phone call between my health care provider and my (former!) insurance company. I mean... really?

Single payer, man, single payer. It's looking better every single day.

Thursday, January 20, 2011

Do atheists spell better?

Well, based on actually empirical data, probably a little bit, but not much. But in my direct experience amongst atheist bloggers and blogophiles? ZOMG, the comments on the blogs I frequent are a joy to read compared to the tripe that infests most of teh interwubz. It's not even just what is said, or the logic and critical thinking that is applied -- though that counts for something too. It's that people seem to care a little bit about spelling and grammar, at least enough to try and make themselves understandable.

What occasioned these remarks is that I happened to stumble upon this while I was Googling for something else. Neither the Creationist nor the person debating him/her comport themselves particularly well. They both come across like idiots. I didn't read the whole thing, so I don't know if "99octane" eventually got around to anything of substance. But "ViRuS"'s initial post is just hilarious. Best line of all:

If evolution is so write then hocome it's still called a theory?

This is not even Poe's Law; this is beyond Poe's Law. If someone were to present this little gem as a parody of intertubian Creationists, I would say that it is not realistic, nobody could be that dense and still manage to find the right buttons to post to a forum. I pray (figuratively!) that English is not his or her first language, because then it would be partially understandable -- although the "hocome" part just blows my mind.

Well, at least "ViRuS" used the proper form of "it's"/"its"...

Tuesday, January 18, 2011

Public perception of journal publication vs. the Scientific Method

[I]f we take the scientific method and the process of peer review seriously, that commits us to occasionally (or even frequently) publishing work that we believe time will eventually prove wrong.
---Tal Yarkoni, writing at [citation needed]

Yarkoni was writing in the context of the recent infamous paper by Daryl Bem published in the prestigious Journal of Personality and Social Psychology, which purports to show evidence of ESP. Yarkoni's analysis of the paper is truly awesome, and worth a read if you are at all interested in research methodology (which means: nobody except for actual researchers, and perhaps hopeless pedants like myself).

Yarkoni's conclusion is in line with the impression I was already getting from reading other bloggers' and pundits' comments on the paper: It's a good paper as far as it goes, even though the conclusions are almost certainly wrong. (I differ from Yarkoni in the weight that I give to good ol' Thomas Bayes in rejecting the ESP hypothesis -- I frankly think that is the most important indicator of how we know this paper is wrong, and the rest is just a post mortem to determine what went wrong) Bem has been admirably transparent and thorough in documenting what exactly he did. As I've written elsewhere, that in many ways redeems the paper's publication, in that it provides the opportunity for a teaching moment in experimental design and what exactly can go wrong.

The quote from Yarkoni with which I open this post is indubitably true from a research perspective, but in a broader societal context, it's highly disturbing. No, I'm not criticizing Yarkoni; he's damn right, and that's exactly what is so disturbing about what he points out. The public doesn't see it that way. The popular press really doesn't see it that way. For science journalists and the lay public, a single provocative paper published in a reputable journal (and even then, the public -- and to a certain extent I include myself in this -- is generally ignorant as to which journals are reputable) is as good as gospel.

What can be done about this? Yarkoni is right, that if the only papers that got published were the ones which had a very high probability of being correct in their conclusions, it would entirely sabotage the scientific method. In fact, pretty soon you wouldn't be able to publish any papers according to that criterion, because a big part of how certainty is achieved is via a long line of less certain research which all points to the same conclusion. And in any case, many people -- including myself -- are increasingly of the opinion that publication bias is a tremendous problem, resulting in large amounts of waste, as well as retarding the rate of science's natural self-corrective ability. In that light, the last thing we want is to publish fewer papers.

The most effective solution, I think, would be for science journalists to collectively behave more responsibly. But good luck with that. That's only slightly more likely than thinking the entire public is suddenly going to become more skeptical.

There is some hope -- as demonstrated by the recent evisceration of the NASA-funded paper into arsenic-based life forms, the blogosphere is increasingly flexing its muscles in order to keep that sort of credulous nonsense in check. In the past, the blogosphere couldn't really be effective in that role, because even if a zillion science bloggers pointed out the flaws, they were only reaching a niche market of readers -- but now, enough noise in the blogosphere amounts to a news story in itself, one the mainstream media feels obligated to report on.

There's a potential blueprint here: Mainstream science journalists breathlessly report on the latest novel finding of public interest, as if one half-way decent p-value proves some controversial hypothesis beyond a shadow of a doubt; trained researchers blog about how the news stories are all full of shit and explain why the paper is either wrong or should be taken with a grain of salt; other interested bloggers link to and write about these criticisms, and in typical Interwubzian fashion, generate a lot of drama and heat in a short period of time; and finally, that becomes a story in itself, forcing those same mainstream science journalists to write articles playing down the earlier reports.

It's far from a perfect system -- people will in general still remember the early credulous articles rather than the later more skeptical ones, and those with an agenda (Buy my supplements! Don't vaccinate! Religion makes you live longer!) will cite the peer-reviewed-but-wrong papers for decades as if there was nothing wrong with them and they were never contradicted by later research. But the sheer noise the blogosphere is capable of generating, and in such a short time, I think makes the situation somewhat more promising than it has been in the past.

In any case, go back and read the quote from Yarkoni at the top of this post. He's hit the nail on the head here. This sort of thinking should be taught in grade school, and hammered away all through a person's education. Science is messy, and by it's very nature it will frequently produce wrong results -- in fact it is this very embrace of uncertainty which gives science epistemological dominance over all other attempts to get at the truth. We should neither discount science because of its dynamic and ever-changing character (for that is where its power lies!), nor should we assume that every proper application of the scientific method produces an unquestionable truth.

Monday, January 17, 2011

Google's Ngram viewer and the shortcomings of OCR

I was having a bit of fun playing with Google's Ngram viewer, searching for terms that were coined in the 20th century, to see if anybody had used those same words incidentally in the past. Turns out for some of them, most of the results are an OCR failure. For instance, here it mistakes "Jan" for "Jazz" in an 1805 essay. Whoops.

Thursday, January 13, 2011

What the Palin defenders (and even some of her detractors) aren't getting

So I'm not even going to touch Palin's invocation of "blood libel" in her anything-but-an-apology video she released today. It may be some kind of fundamentalist codeword that the likes of us don't understand. In any case, it's deeply, shockingly offensive, and I'm not even going to comment on it beyond this paragraph.

What I want to talk about are the people who don't get why Palin should apologize for the "crosshairs" thing. I take this comment from MarkCC's blog as an example:

You’re touchy about the phrase “blood libel”, but you have no problem falsely blaming someone for a mass shooting.

Okay, look, I'm not blaming her for it. In fact, I think the shooter probably couldn't have cared less about Palin. He may not have even seen the crosshair graphic, and it's a near certainty that he wasn't inspired by it.

Many commentators have focused on the political climate inspired by the militaristic and sometimes even explicitly violent rhetoric coming from the Right. While I agree whole-heartedly -- and in fact, I remember so many people making predictions that an assassination attempt of a national US politician could very well take place sometime in the near future due to the overheated and divisive speech coming from that side -- I think that in terms of why Palin should personally apologize, even that's not the most relevant issue.

The reason why Palin should apologize is because if you implicitly wish death on someone, even in jest or in metaphor, and then that person dies or someone tries to kill them -- well, if you have an ounce of humanity in your entire body, then you feel really horribly guilty about that!

Say you were at a party and you got in an argument with one of your friends. A really nasty argument, let's say, that ended in shouting, and as he was storming out, in your rage you shout something vulgar like, "Eat shit and die!" And then let's say he was in a horrible car accident on the way home that left him in critical condition. How would that make you feel? How would you react?

If you were a human being, you would feel awful. You would apologize to everyone at the party. Your soul would be wracked with guilt.

If you were Sarah Palin, you'd make a video painting yourself as a martyr.

This is particularly resonant for me right now, because my wife's and my relationship with our deceased friend had been very rocky towards the end. The reasons make sense now, but that doesn't make it feel any better. The second-to-last e-mail I sent to her before she died was giving her flak about cleaning up her dog's poop when she visits us. That hurts, you know? I mean, I wasn't doing anything wrong, and these things happen... but you always wish the last thing you could say would be something meaningful and heartfelt. I know the world doesn't work that way, and I know -- I think I know better than most -- that in the end it doesn't really matter, that death is death, and that it would sting pretty much just as bad no matter what our final words had been. But I'm human, so I still think about these things.

Now, this situation is pretty different, I guess. Palin was never a friend of Giffords, of course. But then again, I didn't publish a website with a picture of crosshairs over a map of my deceased friend's apartment.

So no, Palin didn't have anything directly to do with this. And as for the extent to which violent political rhetoric created an atmosphere that was encouraging to the Loughners of the world, Palin is hardly the only one who shares blame for that.

None of that matters. Any halfway decent normal human being would feel absolutely awful about the horrible coincidence between the crosshairs incident and the assassination attempt on Giffords. And the fact that Palin apparently doesn't feel bad about it at all -- or at least won't say so in public -- is just fucking sickening.

Wednesday, January 12, 2011

Really, Markuze?

My friend just died, and Dennis Markuze, a.k.a. David Mabus, a.k.a. Makes the Phrase "Has No Life" seem woefully inadequate, is still spamming my blog with his violent hateful brainspooge. He always comments on the most recent post, regardless of what that is... whether it's a rant against religion, or a heartfelt mourning for a deceased friend, Dennis Fucking Markuze doesn't give a shit. Why would he care? He apparently feels nothing. It's an insult to even call him a human being.

So fucking go to it, Dennis. This will be the "most recent post" for a little while, and I'll leave the comments on. Go ahead and toss violent death threats at someone in mourning, with the same nonchalance you always do. Show everyone in the world that you are the most despicable human being on teh interwubz.

The Memetic Equivalent of the Recurrent Laryngeal Nerve

A post over at Epiphenom got me thinking about the old idea of religion as a product of natural meme selection, and how that metaphor could be viewed from different angles.

The recurrent laryngeal nerve is a nerve that provides sensation and motor control to the larynx. It is called "recurrent" because it takes this weird backwards-looping path through the neck, when there is no apparent reason -- without the evolutionary background, that is -- why it shouldn't just descend straight from where it branches off from the vagus nerve down into the larynx.

The reason becomes obvious when you examine the morphological transitions from fish to land animals and eventually to mammals. A common trait in nearly all modern animals is a segmented body plan, which seems to have evolved very long ago. You can often figure out how the segments in one group of animals map to the segments in another group -- adding a segment here, replicating one here, transforming this one for an entirely different purpose... And if you do this morphological comparison with fish vs. mammals, it becomes pretty clear what happened with the recurrent laryngeal nerve. It's morphological equivalent in fish followed a perfectly sensible path, and as the body plan was rearranged, it just got pushed further and further out of the way.

And why didn't natural selection ever fix it? As an engineer, I put it as, "Because evolution by natural selection is an algorithm that is highly susceptible to local maxima." Perhaps a simpler way of saying it is that by the time the laryngeal nerve had developed a routing problem, the type of mutation required to fix it was far too complicated to occur in a single generation -- and a mutant who only got "halfway there" would not be likely to have a functioning laryngeal nerve!

Is the modern concept of prayer the memetic equivalent of the recurrent laryngeal nerve?

First, an obligatory caveat: Whenever we talk about memetic evolution, we must remember that we are just drawing an analogy. Genetic evolution only works "right" because it is digital (i.e. each base pair has a discrete value -- each base is either A, C, T, or G, and you cannot have a base that is 75% A and 25% T!). This turns out to be really important in making the math work out, because it enables traits to be inherited as a discrete unit. As an example, if your mother has green eyes and your father has brown eyes, probably you will get one or the other, but you will not get a blend. If genes were not digital, and if sexual reproduction produced a blend rather than a discrete sampling, evolution via natural selection would not work.

Memes are sometimes digital, as when the meme is a particular phrase or perhaps a particular translation of a book. In those cases, evolutionary analysis tends to work quite well (nearly identical techniques are applied by both evolutionary cladists as well as those examining the "mutations" over time of copied manuscripts). But memes are often not digital -- as, I would argue, in the case of religions themselves, even if the texts are digital -- and in those cases it is not clear to what extent evolutionary theory really works. So when we talk about a meme like religion "evolving", we might just be blowing smoke.

With that out of the way, let's assume it's valid to talk about religion "evolving" by natural memetic selection. When we look at the evidence for biological evolution, there are certain fingerprints of natural selection that we expect to see, and -- as the Intelligent Design losers are always pointing out -- if we didn't see these fingerprints, it would be pretty disturbing to current theory. These fingerprints are things like the recurrent laryngeal nerve. That's an extreme example, but the point is that we should see animals "designed" in a way that betrays a compromise modification of an earlier design, rather than an optimal "clean sheet" design.

So do we see those fingerprints on religion? Yes we do. And I think that the concept of prayer, at least as it relates to most modern religions, is a real doozy. I haven't posted much about it, but I've discussed with my wife the bizarre contradiction among virtually all modern religions between belief in a God that is omnipotent and omniscient and benevolent and has a perfect "plan" vs. the habit of prayer. If God's plan is perfect, why are you bothering her with suggestions?

This logical clunker is a damn good candidate for the Abrahamic equivalent of a recurrent laryngeal nerve. If you look at the Judaic God, omnipotence and omniscience (but not necessarily benevolence or possession of a perfect "plan") are important adaptive traits, which the Torah hammers home again and again in pointing out that if you mess with God, he will mess with you -- and how! (visited upon the third and fourth generations, etc.) The same is true of Yahweh's predecessors and rough contemporaries, but I mostly want to look at the Abrahamic lineage here. (On a side note, another distinctive "adaptation" of Judaism is the idea of a chosen people. This trait seems to be a big winner early on, but it also seems to be directly in contradiction with that whole "evangelical zeal" thing, which turns out to be hugely adaptive, for obvious reasons.)

For an omnipotent -- but not necessarily benevolent -- God, prayer makes perfect sense. "Please sir, if you could just find it in your heart to not kill us all today, that would be great." She can do whatever she wants to you, but if you ask nicely, there is still room for convincing.

Now, I am not an expert on the development of early Christianity, but at some point there seems to have been a definite shift towards the idea of a benevolent God. I suppose one could argue that this shift had already begun with Judaism. As megalomaniacal and erratic as the God of the Torah is, his capriciousness does not rise quite to the level of the Greek Gods, for example. Yahweh might kill every living thing on Earth except for one family just because he thought some of them were dicks, but he wouldn't turn into a bull and go rape some people on a whim. Christianity pushed things even further in this direction: God is perfect and fair and benevolent (and by the way, if that seems to be a laughable impossibility in the face of the evidence, it's Your Fault for not understanding his "mysterious ways").

The adapative benefit of this is obvious as well. The Greeks had less incentive to devote themselves to their gods, because who knows when Poseidon will just randomly trick your wife into cheating on you. The Jews have more incentive, because God at least claimed to have specific enumerable rules that one could follow if you wanted to stay on his good side. And the Christians had more incentive still, because not only was God supposedly perfectly fair and just, but he also really wants to help you out. He's on your team. Work with him. Be his buddy.

But now what of prayer? The Torah speaks of an antecedent religion that used human sacrifice, which mutated to animal sacrifice, which finally mutated away from even that at some point in the development of Christianity. The methods of supplication kept getting pushed in a more humane direction, in a direction where god was less of an "insane bully" and more of a "protective father". Just like the laryngeal nerve, the method of placating one's god kept shifting to accommodate newer adaptations. And just like the laryngeal nerve, by the time this gradual shifting becomes a problem, it's too late to do anything about it.

Surely many thinkers over the centuries must have realized the inanity of pleading with an omniscient being who already has a "perfect" inalterable plan. But what are you going to do? "The Pope has determined that prayer doesn't make any damn sense any more, so although Mass will still include communion, confession, etc., there will be no more prayers." No, of course not. Prayer was such a fixture of the religion by that point, it couldn't be changed. Even if prayer makes as much sense in modern interpretations of Christianity as it does to get from the vagus nerve to the larynx by looping underneath the thorax.

There are more obvious "fingerprints" of the evolution of religion, of course -- basically, anything that can be traced back to syncretism, such as celebrating the alleged birth of Jesus (which, if one takes the Bible literally, can be inferred to have probably occurred in September, or maybe in the spring, but most certainly not in winter!) over the same time frame as a pagan winter festival, and adopting numerous traditions from said festival. But those syncretic fingerprints are neutral. There is no horrible logical contradiction in choosing an arbitrary date for celebrations, and plenty of practical value in lining it up to coincide with other religions' festivals.

But I think that prayer in the face of omniscience is a really interesting one, because it really demonstrably is a suboptimal solution. I'm not the only one to realize that it doesn't make any sense. One of the most visible and frequently practiced aspects of your religion is a bald logical contradiction. Even with most homo sapiens being rather poor critical thinkers, that still can't be good for business. And yet, it ain't gonna change, because to fix it without doing damage would require a radical memetic reorganization, one that is unlikely to occur naturally.

This is important because it really drives home the fact that even if religion became so dominant because it evolved to confer certain social benefits, that tells us nothing. Just as with the laryngeal nerve -- which, to be fair, works just fine -- with human foresight we might just put together a system that's far superior and far more sensible.

Friday, January 7, 2011

Take lots of pictures of yourself, just in case you die young

I've been going through all of the remaining online photo albums that belonged to my deceased friend, as we're putting together a memorial slideshow for this Sunday. Of course, since she took the pictures, she's hardly in any of them!

So the lesson is: If you think you might die a tragic untimely death, make sure to take lots of pictures of yourself. heh...

Wednesday, January 5, 2011

Chris Mooney's Peace Anthem for Science and Religion

Mooney's got an article in Playboy touting his most recent tactic for denying the science/faith conflict, the one I call the Spirituality Gambit. The basic ploy is this: If you use a rather fuzzy definition of "spirituality" -- you might call it a feeling of awe or transcendence -- then it is true that scientific understanding can inspire this fuzzy "spirituality" in even the most secular-minded folk. So there you go! Everybody, theist or atheist, experiences "spirituality". Why not work there for common ground?

I must confess to not having read the current article. I don't feel I need to, because the Spirituality Gambit is a mess. The main criticism is that Mooney is engaging in semantic trickery. "Spirituality" is an ill-defined word. Certainly it no longer retains its etymological roots denoting a belief in spirits. But even then, many religious people mean it much more specifically than this fuzzy "feeling of transcendence." Even if they don't, I think it is safe to say that most people who would identify as "spiritual" believe there is something literal about what they feel, i.e. it is more than a feeling.

But that's already been well-covered (see here and here). I want to focus on a different, and equally serious problem with Mooney's Spirituality Gambit, one I have mentioned before in comments on other blogs, but which I think deserves its own post.

If you've never heard Tim Minchin's Peace Anthem for Palestine, you owe it to yourself to scroll down to the bottom of this post and check it out. The song consists of one repeated refrain:

You don't eat pigs, we don't eat pigs
It seems it's been that way forever
So if you don't eat pigs and we don't eat pigs
Why not not eat pigs together?

At the risk of ruining a good joke by explaining the punchline, the song is funny because it naively suggests that a long-standing enmity between two violently opposed groups can be resolved by focusing on a superficial similarity -- in this case, that both Jewish and Muslim orthodoxy prohibit the consumption of pork. Of course this is absurd, because the conflict between Israeli Jews and Palestinian Muslims has nothing to do with dietary requirements. While finding some common ground is often a first step in conflict resolution, it's usually expected that the common ground will have something to do with the conflict in question.

And so it is with the Spirituality Gambit. Yes, it is true: To borrow Obama's inaugural phraseology, "people of all faiths and none" experience feelings of awe and transcendence. Your point? We also all (presumably) wipe our asses after going to the bathroom, but that hardly addresses the epistemological divide between scientific inquiry and revealed truth, does it?

Even if Mooney weren't engaging in clever word games, his point would still fall flat. In fact, many people have maintained that this is an argument in favor of discarding faith -- countless people, myself included, have found that they can accept the reality of a harsh uncaring universe without giving up their sense of wonder and fulfillment. This helps dispel the myth of secularists as some kind of emotionless Spocks, and undermines one of the more common arguments against embracing a nontheistic worldview.

The Spirituality Gambit is nothing more than a distraction. If it tells us anything, it's that atheists aren't as scary as many people make us out to be. But it tell us nothing about the epistemological (il)legitimacy of faith, nor about the societal effects of religion. Calling it a red herring would be an insult to Clupea harengus.

Tuesday, January 4, 2011

Lehrer's getting a raw deal, but...

Jonah Lehrer is getting a lot of flak from the skeptic community over an article in the New Yorker he wrote about the "decline effect", whereby some statistically significant correlations tend to "wear off" over time as more and more attempts are made to replicate them.

It's an interesting problem, and for the most part he gave a thoughtful examination of the issues and their causes (the primary cause, IMO, being simple publication bias). However, he was harshly criticized -- and rightly so -- for the final paragraph of the original article in which he seems to flirt with a destructive form of post-modernism, a rejection of the very nature of objective fact. The worry is that he has given more fodder for science deniers of all stripes to ignore the overwhelming evidence in favor of evolution, climate change, etc. and against most forms of alternative medicine, psychic ability, etc.

I felt his first follow-up (sorry, I can't find the link at the moment) clarified his position sufficiently, and I sort of think the continued criticism he is receiving is overblown. I do want to highlight one rhetorical question from his most recent follow-up, however, because I think this question is very answerable. The context here is that he is discussing how the theory in evolutionary biology of "fluctuating asymmetry" initially got several false positives in numerous studies, before the preponderance of evidence turned against it.

This raises the obvious problem: If false results can get replicated, then how do we demarcate science from pseudoscience?

In principle, there is a very simple answer to this question, though of course applying it is often quite messy in practice: Bayes' theorem.

I'm a bit too busy at work right now to give even a brief treatment of the Bayesian mode of thought, but the Wikipedia article does a nice job, so read that if you are unfamiliar. As it applies to Lehrer's present question, we can (usually) demarcate science from pseudoscience by taking a guess at the prior probability.

Fluctuating asymmetry falls in the "science" camp, despite the fact that it ultimately turned out to be false, and even despite the fact that it was prematurely elevated to the status of "true" based on an (in retrospect) insufficient number of positive results, because it was a priori plausible. Homeopathy, on the contrary, falls in the "psuedoscience" camp, despite the fact that some trials of homeopathy have achieved positive results, because it is completely implausible.

As I said, this can get messy in practice. How would one classify early trials of acupuncture, when plausibility could be argued either way? And how much undue resistance was there to the theory of continental drift (now solidified in the more complete theory of plate tectonics) because most scientists at the time found the idea of moving continents to be a priori implausible?

But we already knew science is messy, and I think that overall Lehrer's original article and follow-ups have helped illuminate one of those messy aspects to a lay audience. I must reiterate that I agree with those who found the concluding paragraph of the original article to be severely misguided -- and I think in this most recent reply, he also missed an opportunity for a teaching moment by not digging deeper into his self-posed question. The question about demarcation does have an answer, one that is relatively simple in principle, if not in practice.