The Times (of London) says something weird

The Times has a great article about Richard Dawkins' new book, The Magic of Reality (behind a paywall, but reproduced here), but right in the middle of it they have a couple of paragraphs that leave me scratching my head a bit:

Pitting religion against science, at least in enlightened cultures, is to formalise a dichotomy that need not exist. While [Dawkins] may not agree, many would argue that religion has provided mankind with a moral framework possessed of a strength and clarity that, without God, thinkers since the time of Socrates have struggled to replicate...

The argument that creation requires a sentient creator — the teleological argument — had been ably sunk long before Professor Dawkins’ hero Charles Darwin began to fret whether a benevolent deity would have wilfully created a parasitic wasp that lays its eggs inside the body of a living caterpillar. David Hume perhaps scuttled it best, pointing out that if something as complex as the Universe required a creator, then that creator, being more complex, must have required one, too.

Losing our belief in a creator, though, should not entail we lose our wonder too.

Huh. If I might glibly paraphrase, what I'm hearing here is, "Religion is totally AWESOME! But you know, there's obviously no God, and educated people have known this for centuries..."

(I realize the passage leaves room for a God that is a part of the universe rather than its creator, but... for a lot of people that wouldn't really be God.)

I know what they are trying to do. They are trying to play the usual condescending game of "belief in belief": "I know a lot of you are turned off to Dawkins because he's always hating on religion -- but we don't hate on religion, and we liked this book!" I don't want to get too hung up on this point, it's otherwise a great article. I just feel like the inherent condescension of this position is really on display here. I mean, if I believed in God, I think I'd find that passage a bit off-putting. "I don't believe in that rubbish, but I think it's totally awesome that you are deluded in that way!" Blech. Heh, oh well.

An unconventional take on gender stereotypes and biology

A friend posted a link to Facebook that showed two word clouds, one showing words used in advertising for toys aimed at boys, the other showing words used in advertising for toys aimed at girls. I'm not actually going to post the link here, because while I think the author's point is correct, I think the post itself does nothing to support the point being made, and this is all a distraction from what I actually wanted to talk about. There's been something I've wanted to say for quite some time about gender stereotypes, gender bias, and biology; and thinking about how some toys are perceived as gender-specific finally revealed to me what I think is the right way to say what I am trying to say, without coming across as patronizing.

Is gender discrepancy in toy preference purely a societal construction, or does it have any biological roots? Well, I don't think one can assert a clear answer to this question (it's undeniable that social convention reinforces this discrepancy, even if it didn't create it, which makes it very difficult to measure). But consider the following facts: Men are on average larger and more muscular than women. Babies only come out of vaginas, and milk (generally; don't distract from the central point) only comes out of the nipples of women. Given those realities, I don't think it would be surprising if we were to discover that, independent of culture, boys were more likely to play with fighting superhero toys, and girls were more likely to play with baby dolls. I'm not asserting that as true, but I really don't think it would be surprising.

But that's only a bit of speculation about what is; it says absolutely nothing about what we ought to do about it. Worse yet, it's not even the complete picture: It's undeniable that, even with gender stereotypes being bolstered by powerful cultural reinforcement as they are today, many boys would still rather play with dolls and many girls would still rather play with superheroes. It is not fair that these individuals be short-changed or stigmatized just because they don't fit a stereotypical mold, even if that mold has a perfectly natural origin. (Edit: In re-reading this, I think I inadvertently came across as presenting somewhat of a false dichotomy, i.e. that each individual either likes "boy's" toys or they like "girl's" toys. That's bullocks, and of course equally important is that even if, say, a given boy might usually want to play with superheroes, he should ideally not feel reservations about playing with baby dolls on occasions when it strikes him to do so.) Individuals should be empowered to do what they want, to act according to individual preferences and desires. This personal liberty and autonomy is one of our most important shared human values!

The upshot of this is that if it is the case that gender stereotypes have a biological basis (and again, I do not believe there is sufficient evidence to make an assertion about this either way), then that would only intensify the importance of minimizing any cultural reinforcement of those stereotypes. It might even suggest that we ought to work towards not only elimination of that cultural reinforcement, but an outright reversal of it, i.e. a society where it's "cool" to explore the opposite gender stereotype.

There is absolutely no reason to believe natural selection should be egalitarian in regards to gender. The moderate sexual dimorphism of our species suggests evolution has not been entirely blind to gender in H. sapiens (though thankfully we are quite a bit better off in that regard than C. lectularius!), and therefore we should be prepared that there might very well be natural behavioral differences between men and women. But as organisms with a uniquely powerful ability to reason about concepts of fairness and morality, we owe it to ourselves to do better than unguided evolution in this regard. The possibility that conventional gender roles might have biological roots is not an excuse to shrug our shoulders at stereotyping and inequality: rather, it is a call to redouble our efforts in combating those pernicious effects.

Adaptationists, neutralists, frequentists, and Bayesians -- oh my!

There's a bit of a minor dust-up taking place at Sandwalk, Larry Moran's blog, over adapationism vs. neutralism in regards to evolutionary theory. There are some really great minds engaging in this discussion -- even Richard Dawkins has weighed in! -- so really I'm sure there's nothing a lay person such as myself can meaningfully contribute. But hey, if you thought I was going to go that route, you have significantly underestimated my ego.

A few months ago Bjørn Østman and I were having a discussion about the degree to which selection-for must be thought of as an abstraction rather than a reality, and I presented the following (admittedly somewhat over-the-top) example:

Let's say in the year 5673 BC, one peacock was saved from certain death when his tail got caught in some branches, and that slowed him down enough that an impending avalanche that would otherwise have hit him now missed him -- whereas his brother with a slightly smaller tail continued unimpeded and was killed in the avalanche. Do we now have to include in our analysis a 10^-10% contribution to the selection of the tail by "stops peacocks from walking into the path of avalanches"? If not, why not? (Without invoking agency, that is)

Don't get too distracted by my use of the peacock's tail -- that just happened to be the trait we were talking about at the time. Anyway, I want to flesh out my thoughts on this somewhat in light of the present discussion regarding neutralism.

First, a brief digression on two major schools of thought in probability theory. Let's say I roll a die three times, and I get the sequence 1-3-5. After I have finished the experiment I say, "Now what are the odds I would get that sequence?" A frequentist answer would be 216:1, because, assuming a fair die, if I perform this experiment enough times, I should get the sequence 1-3-5 approximately that often. An extreme Bayesian answer would be 100% -- as long as you were asking the question after performing the experiment. After all, we know that's what I rolled; it can no longer be anything else. Given the state of information we have now, the odds are 100%.

The Bayesian interpretation is not very useful there, but it's quite useful in regards to things like cancer screening. And nobody is so extreme of a Bayesian that they would stubbornly argue for the position in the previous paragraph. Anyway, you can get piles of information on this by Googling, and probably most people who have read this far are already more or less familiar with the concept, so I will not expound on it further.

If we wanted to take the really extremely stubbornly uber-Bayesian interpretation of natural selection, we would have to argue that every single extant trait is adaptive. After all, the a posteriori probability of evolution having taken the path that it has is 100%. Given the information we have now, every trait which exists in the present has perfect inclusive fitness, and every trait which is no longer extant is perfectly unfit.

I am making this rather stubborn and perhaps overly philosophical point in order to drive home the idea that any useful description of selection must inherently be an abstraction. It's not just that we need to use an abstraction in order to analyze it in practice; even in principle, one cannot say anything meaningful about natural selection without taking a frequentist approach, abstracting out the actual environment in which a given organism lives, reproduces and dies, in favor of an idealized, "typical" environment analogous to an idealized fair die roll. Without taking this important step, the most meaningful thing we can say about evolution is, "What happened happened."

(As a brief aside, I think the primary mistake made by Fodor and Piattelli-Palmarini was their failure to take that next step from the stubborn philosophically pure position to recognizing that the whole enterprise can be handily salvaged by just drawing a few abstractions. In the spirit of full disclosure, I must admit I haven't read their book, but I've read critiques and defenses of it, and unless there's some amazing revelatory concept in the book, this seems to be the rather obvious problem with their entire argument.)

I think this already somewhat undermines the dichotomy of the selectionist/neutralist debate, since both are exposed as abstractions which are (again, by necessity) pretty far removed from the most literal reality of evolution. Because each organism (or each allele if you want to take the gene-centric view) exists in its own actual environment rather than being repeatedly tried in some ideal environment, to even pose the question of whether a particular trait is adaptive or not by necessity admits a sliver of teleology-esque reasoning into your model. By no means am I objecting to this! But it is worth observing.

Of course we can still ask which model is more useful, even if it turns out that the answer is "it varies" -- so there is meaningful discussion to be had. As a lay person, I'm not going to attempt to answer that. But what I will do is point out one problem with the intensely¹ neutralist view espoused by folks like Larry Moran.

Consider the example of the rhinoceros' horn discussed in the comments at Sandwalk. Let's say for sake of argument that, in comparison to each other, the Indian rhino's one horn has no selective advantage over the African rhino's two, and vice-versa. Let's go one step further and assume that sexual selection doesn't even play a role, and that if you could magically give some fraction of Indian rhinos an extra horn, or take away one from some African rhinos, it wouldn't affect the afflicted rhinos' inclusive fitness one iota. Does that necessarily mean that "neutral" is the best way to describe the trait(s)? I'm not so sure.

This is a pretty unrealistic hypothetical, but run with me here for a moment: Let's say the common ancestor of the Indian and African rhinos had a sort of bumpy ridge where the nose is. Two sub-populations become separated, and (here's where the unrealistic part comes in) a single transposition event in one sub-population causes the ridge to grow into a single horn, and a single transposition event in the other causes the ridge to grow into two horns. In each sub-population, only one of those two possible mutations is available, and in both cases the transposition event is so unlikely that we would not expect it to occur again. Assume further that horns -- whether one or two -- have a tremendous selective advantage over the bumpy ridge.

How can one argue with a straight face that either trait is "neutral"? Both mutations are tremendously adaptive over and above the available alternatives in the gene pool. If by the time the two sub-populations are reunited they can no longer produce viable offspring, then we now have two species, each with a mutually exclusive trait that is no better than the other's, but both of which are clearly adaptive. Genetic drift doesn't even come into it, except in the trivial sense that all novel alleles have to arise via random mutation.

I am again being somewhat stubborn and over-the-top, I think, but the point I am making is that in the long term and in a large enough population, every single trait that goes to fixation is adaptive, in the sense that it is superior to the immediately available alternatives present in the gene pool. Now the manifestations of those immediately available alternatives are influenced by effects such as genetic drift, of course. And it's probably fair to argue that it is not uncommon to have multiple available alleles in a population which are (within the limits of our abstraction) no more adaptive than each other, and in those cases the neutralist account would indeed be the most sensible. What I am saying, though, is that just because two potential traits of an organism have no particular selective advantage over one another if both had been readily available in the same population at the same time, that doesn't at all invalidate a selectionist account.

This is all probably hopelessly redundant, covered territory in evolutionary biology, and as a layman I should probably just not blather on about it. But oh well, those are my thoughts on it.

¹I struggled with the wording here... I initially had "extreme" rather than "intensely", but I felt that was unnecessarily -- and unintentionally! -- pejorative. Given our human penchant for promiscuous application of teleology, I think the "extreme" (not in a pejorative sense!) neutralist position is a very necessary part of the tapestry of evolutionary inquiry. Without neutralists like Moran, the adaptationist model could easily get completely out of control. Even great minds like Dawkins, who has been entertainingly referred to as an "uber-adaptationist", have at times seemed a bit too eager to prematurely embrace an adaptationist account. All deserved respect to Larry Moran here, by all means!

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"...

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.

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.

A hypothetical ethical quandary

A comment over at Pharyngula inspired me to ponder the ethical dilemmas that will arise as our ability to cure disease starts to encroach on the fine line between "different" and "pathological". In composing a reply, I came up with a thought experiment that I found compelling enough to warrant inclusion on my blog.

Imagine that a few decades from now, as the study of personal genomics advances, we find a mutation on the X chromosome that causes a slight difference in the sequence/amount of hormones that a woman experiences during pregnancy. And let's say this hypothetical hormonal fluctuation has two effects:

1) It makes her sons significantly more likely to be gay (and in fact, to make it interesting, let's say that scientists estimate that 40-50% of gay men's mothers had this particular mutation, whereas less than 10% of straight men's mothers have it, i.e. while not perfectly correlated, it is highly predictive of sexuality)

2) It causes a modest increase in her sons' risk of a rare type of testicular cancer.¹

Furthermore, let's assume that a simple, safe, and highly accurate screening process can be done for this, and it is cheap enough to be performed as a matter of course (in fact, the incremental cost is essentially zero, since in this not-too-distant future a mother-to-be's genome is routinely sequenced anyway to check for all sorts of other mutations of interest). And finally, let's say there is a safe, effective, cheap, easy "treatment" (e.g. a one-time hormone injection at a certain point in the pregnancy) that will bring the prenatal hormones in line with the "baseline" average in the majority of women.

So... do you offer it? Do you do it as a matter of course?

On one hand, it seems like the answer has to be a resounding "YES!"... The fetus is incapable of making medical decisions for itself, so if a prospective treatment carries little to no risk of (medical) side-effects, and reduces the fetus' risk of developing cancer later in life, even by a little bit, it would seem we are ethically bound to use it.

On the other hand, employing this treatment as a matter of course would significantly reduce the population of a traditionally-oppressed minority. It feels like an attempt to exterminate gays!

Furthermore, if you offer it as an option to mothers-to-be, is that even worse? Are you now allowing a mother to "hetero-ify" her baby without his consent?

I honestly do not know what my answer is to any of these questions. Luckily, this is (right now) nothing more than a flight of fancy. But I suspect we will be facing similar dilemmas in the near future. We are already facing it in regards to cochlear implants, which -- to the surprise of most hearing people, myself included -- have met with stiff resistance from many elements of the deaf community.²

Another hypothetical I mentioned in my Pharyngula comment is, what if we found a treatment that would cure mild cases of Asperger's -- and then, two decades after it started being used as a matter of course, we found ourselves with a shortage of engineers! As I mentioned in the opening paragraph, the line between "different" and "pathological" is not always clear. And, as the present thought experiment seeks to address, the phenomenon of pleiotropy may give us a single allele that simultaneously causes both a "difference" (and one we want to protect) as well as a "pathology"! These will not be easy questions.

Update: A commenter at Pharyngula points out that there is already an eBook with a virtually identical plot! More proof that there's nothing new under the sun, eh?

¹Lest this offend anyone, let me be perfectly clear that this is not a conjecture, nor is it meant to imply anything negative or to suggest that homosexuality is "deviant" or "pathological" or anything remotely of the sort. That ought to go without saying, but I am saying it anyways. I chose this scenario because current research strongly suggests that sexual preference has at least a partial genetic component, other research suggests that sexual preference can be influenced by prenatal hormones, and we also know that some hormones are implicated in certain types of cancer -- so the scenario satisfies a certain baseline plausibility, i.e. it doesn't contradict anything we know about the physical world, and I think that is good enough for a thought experiment.

²After watching a movie about it, I am much more understanding of and empathetic towards the anti-implant position... but I still think that, in cases where the child can expect significant hearing recovery from the implant, it's generally "the right thing to do". I will not pretend that it is an easy call, though, and my heart breaks for deaf parents who have to make this decision. If you were faced with an irrevocable choice that would give your child a valuable new ability, at the cost of possibly reducing the emotional and communal bond between you and her, at the cost of eliminating an entire realm of shared identification, would you do it? I'd like to say I would answer yes, but... I hope I will never have to make such a decision!

A potential explanation for heterogeneity of hereditary propensity for religiosity/credulity?

I was making a comment over at Bruce Hood's blog and a thought occurred to me that I think is worthy of its own blog post.

Pardon me for failing to dig up a citation for this, but there appears to be growing evidence that propensity for religiosity and other o'er-credulous beliefs has a hereditary component. In other words, there could be genes that make you more likely to believe without evidence (or to state it conversely, there could be genes that make you more skeptical).

One problem with this is that it takes very specific conditions to allow genotypic heterogeneity in a population. If there is a clear selective advantage afforded to one phenotype over another, then under normal conditions the corresponding genotype should eventually come to dominate the entire population.

Now, I'm totally a layperson in this regard, and I won't pretend that I understand the mathematics behind what enables heterogeneity, nor that I could list more than a couple of conditions that allow it. But I happen to know offhand that one way you can get heterogeneity is via a host/parasite relationship.

The idea goes like this: Host phenotype A is resistant to parasite phenotype X, but vulnerable to parasite phenotype Y. Host phenotype B is the reverse, i.e. resistant to Y but vulnerable to X. All other things being equal, the prevalence of each phenotype in each population will tend to oscillate, with shifted (or is it opposite?) phases. If the parasite population is dominated by X, then natural selection will cause the host population to tilt towards A... after which natural selection then causes the parasite population to tilt to Y, causing the host population to shift to B, etcetera ad infinitum.

I'm sure there's an evolutionary biologist reading this right now screaming about the horrible state of evolution education in America's schools, but I think I at least got the gist of it... maybe?

Okay, so now on to inherited credulity... one account for why humans are so damn credulous, given by Michael Shermer, is that Type I errors (false positives) tend to be far less costly than Type II errors (false negatives), therefore natural selection will favor individuals who tend to be biased towards Type I errors. Shermer's favored example is the rustle in the grass that might be a tiger. If you assume it's a tiger, and you're wrong, then you waste a little time and energy fleeing from a predator that wasn't there. If you assume it's the wind and you're wrong, then you are dinner.

One thing that's always bothered me about Shermer's account is that he rarely, if ever, explicitly brings probability into it. It's not enough that the cost of a Type I error is less than that of a Type II error -- it must be the case that the cost of a Type I error multiplied by the chance that it is an error must be less than the equivalent calculation for Type II errors. Presumably, most rustles in the grass are in fact not tigers, so for his account to truly show that natural selection would favor "patternicity" requires a bit more than what he has explicitly stated.

It was while complaining about Shermer's omission on Bruce Hood's blog that it occurred to me that we might have a potential solution here for the problem of heterogeneity in inherited credulity. I now copy-paste from my comment on Bruce's blog, with minor edits:

It's just conceivable that there could be an interaction between patternicity and certain environmental conditions (e.g. prevalence of food, prevalence of predation, etc.) that mirrors the interaction between host and parasite — an interaction we already know to mathematically support heterogeneity in a population.

If you'll pardon a "Just So" flight of fancy on my part: We could imagine a population of prey organisms where some individuals are "strongly" biased towards Type I errors, and others are "weakly" biased (whatever that would mean, but run with me here for a second). If conditions of predation were static, we’d expect one of the two phenotypes to become dominant. But if the local density of predators has a cyclic fluctuation, then the ratio of the two phenotypes in the prey population could conceivably track that cycle. In years with an unusually high-density predator population, the "weakly"-biased individuals tend to get eaten before they can reproduce, favoring the "strongly"-biased individuals; while in years with a low predator population, the "weakly"-biased individuals are able to gather more food than their cousins and therefore out-reproduce them.

Furthermore, this very shift could in itself exert a selective influence on the predator population. As the prey population becomes dominated by "weakly"-biased individuals, it's boom time for the predators. Those dumb prey animals just stand there like they didn't even notice that rustling in the grass. The predator population grows, which as we already postulated (remember, this is all wild speculation) will cause the "strongly"-biased phenotype to be favored in the prey population. Suddenly it seems like the prey have smartened up, as they flee even before it's possible they could have even seen the predator. More predators starve, their population wanes, and the cycle begins again with the "weakly"-biased prey being favored.

There's boatloads of math required before we could state that it's truly plausible, but it sounds to me to at least be plausible in principle. IANAEvolutionary Biologist, nor do I have any prayer of working out the mathematical model myself, so for now this will have to stand as merely another "Just So" story by an armchair biologist.

Hey, wait a minute, postulating a superficially-plausible-sounding evolutionary explanation for human behavior, and then throwing it out there like it's fact without even bothering to test it for plausibility against a mathematical model? I think I've found a second career in evolutionary psychology!

NCSE's "Don't Diss Darwin" flyer strikes the appropriate "accomodationist" tone

The National Center for Science Education has generated a flyer to be passed out at college campuses tomorrow in order to counter the distribution of bananaman Ray Comfort's mangled version of Origin of Species. I noticed in the flyer that the NCSE strike the perfect tone for "accommodating" the religious in the fight for evolution, while not alienating atheists or making explicit theological statements:

Comfort implies that it is necessary to reject evolution in
order to be a good Christian.

Ironically, although Comfort quotes Francis Collins, the geneticist who led the Human Genome Project and is now in charge of the National Institutes of Health, he fails to mention that Collins is a committed evangelical Christian who accepts evolution!

People of all faiths and of none have accepted evolution on its scientific merits. The fact that Comfort fails to acknowledge this suggests that he is arguing in bad faith.

Right on. Notice how they never actually say that there is no contradiction between evolution and Christianity (which would be an explicit theological position, and not appropriate to the NCSE's mission statement). They also put in a positive acknowledgment of atheists ("people of all faiths and of none"), a la Obama's inaugural nod to "non-believers".

This is accomodationism done right. They make only factual statements, not theological or philosophical ones¹. They are inclusive. And they don't belabor the point. If this is as far as accomodationism ever went, I would have zero complaints.

¹As is often overlooked, prominent "anti-accomodationists" like Jerry Coyne have clearly stated that the NCSE should also not be saying there is a contradiction between faith and science, because that would also constitute a theological/philosophical position. Based on the NCSE's mission, they need to stick to the facts -- and the bare facts merely say that there are Christians and other theists who believe in evolution. End of sentence.

Accomodationists care more about Darwin than the rights of the oppressed

Okay, the title of this post is needlessly inflammatory, but given how nasty the whole accomodationism debate has gotten, I figure I need to be inflammatory to get anybody's attention, right?

The latest volley from the accomodationist side has been Chris Mooney's contention that Dawkins' atheism advocacy is diluting his pro-evolution message -- specifically, that The God Delusion effectively undermined the mission of The Greatest Show on Earth.

There have been various responses to that argument, mostly focusing on Mooney's very premise, which I agree is weak on evidence. However, I want to pose a completely different response to Mooney's argument:

Yeah, so?

Let's assume for a second that Mooney is completely right: The success and visibility of The God Delusion has had a net negative contribution to the mission of The Greatest Show in Earth to bring people over to the pro-evolution side. However, getting people to come around on evolution is not the only goal in the whole wide world... is it?

Jason Rosenhouse points out:

To this point I have been focused specifically on the evolution issue. Obviously, though, I think religion lies at the heart of a great many other societal ills. It is the primary factor in issues like bigotry towards homosexuals, repressive attitudes toward women, assaults on public education, and a political system in which people must profess the strength of their religious faith to have any hope of a future. Those are just a few examples.

Indeed, and in fact I have to criticize Jason just a little bit for failing to follow up on this point as much as he might. I'm going to go out on a limb and argue that bigotry and repression of women and homosexuals are more important issues than evolution education. Not that the latter isn't critically important, and I believe there is synergy between these various goals -- but if I were offered a choice between ending Creationism and ending bigotry, I wouldn't even have to think about that one.

So, as I said, let's say Mooney is right. So what? Is he saying that The God Delusion was completely worthless in all respects, then? That it has not had any positive effect on the public conversation about the false respect accorded to religion and religious prejudice? Well, maybe Mooney is saying that, but I think that's ridiculous.

Rosenhouse says something very similar, that the long-term goal is moving towards a more godless society, but he puts it firmly within the context of the Creationism problem, i.e. he argues that as the American and UK mainstream stop giving so much undue deference to religious belief, ideas like "Teach the controversy" will fade into crackpot obscurity, where they belong.

I think Rosenhouse is exactly right, that there is synergy here. But I'm going to go one step further and say that the goal of tearing down religion's wall of protection is the more important aim even if it had no effect, or even a negative effect, on the fight against creationism. As atheists and other nontheists are further emboldened to speak out, it helps in so many other struggles as well: In countering those who would use religiously-motivated scare-mongering to fight against marriage equality, in deflating the silly faux-liberal belief that equates criticism of misogyny with ethnocentric intolerance, and in combating dangerous nigh-genocidal prohibitions issued by a certain "rat" of a pontiff. All of these things are important -- at least as important as whether evolution gets taught properly in schools, don't you think?

When making grand pronouncements on the wisdom of writing The God Delusion, one cannot take into account only the costs and benefits in regards to evolution education and future books on evolution -- one must look at all the costs and benefits. And I say, even if The God Delusion did have some small deleterious effect on evolution education (an unproven allegation to begin with), it still would be a net positive, because it helped to bring atheism and frank religious criticism into the mainstream. It seems to me that to argue otherwise is rather short-sighted and narrow-minded.

In defense of speciesism

I finally got around to reading The Selfish Gene. One of the themes of that book is a purely gene-centric view of natural selection. Dawkins has even spoken in later writing of the idea of "speciesism", that it is irrational to discriminate purely on the basis of species, since a species often has no sharp boundary, and in the end is nothing but a pool of genes that tends to (but doesn't always) congregate together. The analogy is, of course, to racism, which is irrational for multiple reasons -- both because the whole concept of races has been demonstrated to be on shaky biological footing, and because it would be wrong anyway even if there had turned out to be a clear delineation between races and a significant difference in their talents.

I think this analogy between speciesism and racism is completely inapt, and I respectfully disagree that it is irrational to discriminate on the basis of species alone. It is partially other insights from The Selfish Gene that leads me to this conclusion.

I am not going to make an attempt to justify omnivorousness, though I do eat meat. I try to get it only from smaller farms, better yet if I can get a look at how they keep the animals, since factory farming practices multiply the ethical and environmental issues of meat consumption a hundredfold. I simply intend to make a case that it is quite rational to apply radically different standards to an individual of a different species, extending even to putting a significantly lower value on that individual's life, irrespective of any other concerns.

The boring obvious part
The obvious problem with the idea of "speciesism" being a bad thing is that there are massive differences between species, and these do matter.

One recent debate that has continued to fascinate me is the controversy over whether lobsters feel pain -- and therefore, is it cruel to dip them headfirst into boiling water. I think the whole conversation is absurd, or at least barking up the wrong tree, because we have failed to clearly articulate what we mean by "feel pain." If we define "pain" as "the response of a nervous system to negative stimuli, causing the organism to try and avoid said stimuli", then of course lobsters feel pain. Anything with a nervous system feels pain by that definition.

But any attempt to base ethical decisions around this definition will quickly veer into the ridiculous. I could write a computer program that puts a dot on the screen, and whenever the mouse cursor comes within a certain distance of the dot, the computer says "Ouch!" and tries to move the dot away from the mouse cursor. Is this not a "negative stimulus" of sorts? After all, it provokes a reaction from the computer to try to avoid repetition of that stimulus. Does the computer feel pain?

Ah, you say, but a computer's CPU, memory, etc., are not a "nervous system" per se. Exactly right. So, it is not just that a certain thing tries to avoid a certain class of stimuli. The structure of the mechanism engaging in the avoidance response is critical in whether we would consider it to be pain.

So how close does a nervous system have to be in structure before we call it "pain" and actually give a shit? Clearly a computer loses. It seems to me that a lobster loses as well -- it clearly is experiencing something we might call "pain", but it's specific biological embodiment is not much more similar to the phenomenon we experience as "pain" than my hypothetical mouse-avoiding computer program is.

This does not apply only to pain, but in terms of any evaluation of a different organism. I do not mean to revert to the language of the past where animals were by definition viewed as mere automatons -- but in regards to very simple nervous systems, it is hard to reach any other conclusion. Without ridiculous concepts like a "soul" or "life essence", it becomes very difficult to justify the idea that a lobster's nervous system has any special properties that differentiate it from a robot's control system.

I think so far, Dawkins would agree with me. I think the idea of speciesism is meant primarily in regards to bird and mammals, particularly higher primates, where their nervous systems are so similar to ours that it is indeed meaningful to think of their experiences as being analogous to ours.

The interesting part
While I think that absolutely a more complex nervous system entitles an animal to greater protections, I will now argue that it is both rational and ethically defensible to discriminate against an organism solely because they are a member of a different species. This means that if we encountered another sapient species with nervous systems identical to ours, while we would be obliged to treat that species with the same dignity and respect with which we would expect them to treat us, it would be quite acceptable to value a human life over the lives of the organisms belonging to the other species.

In arguing this, I am going to dig into what we mean when we say that apparent "altruism" is the result of selfish genes. As Dawkins expounds on at length, any evolutionarily successful action taken by a gene must be "selfish" from the gene's point of view. But what about from the point of view of the organism? Is it always selfish from the organism's point of view, or can the action be truly "altruistic" in the sense that the organism itself gains no benefit?

At one point in The Selfish Gene, Dawkins postulates that it may be inappropriate to differentiate between symbiotic relationships among different species vs. cooperative relationships within the same species. I could not disagree more, and the reason is because the answer to the question at the end of the preceding paragraph is markedly different depending on whether the participants in the symbiotic/cooperative relationship are drawn from a compatible gene pool.

When considering interactions between two different species, any behavior that is "selfish" for the gene must also be "selfish" for the organism. (This of course excludes misfiring of "selfish" instincts, where by a parasitic species like a cuckoo capitalizes on the "selfish" impulses of another species) There is simply no way that an interaction between two organisms of different species can be, for one of the parties, good for the gene yet bad for the individual. (And thus the previous parenthetical remark is addressed -- subversion of "selfish" impulses by a parasitic species is both bad for the gene and bad for the individual) The highest form of interspecies altruism that can evolve is delayed reciprocal altruism.

Within the same species, the story is entirely different, as a result of kin selection. This is explained at length in Dawkins' book, but for those who are unfamiliar with the concept, in brief: I know that (statistically speaking) my first cousin shares 1/4 of my DNA. If I can take an action that will harm myself, but will benefit my first cousin more than four times as much as it harms me, then on average that will do more to spread my DNA than if I had failed to take that action. So natural selection will select for genes which inspire me to take such an action, even at a net loss to the individual organism in question. In other words, from the point of view of the individual, apparently "genuine" altruism.

This is fundamentally different from what takes place between species. While two individuals of two different species might share quite a large number of genes, the fact that the two species represent separate gene pools makes the evolution of "genuine" altruism impossible. The key point is that kin selection doesn't actually work because your first cousin shares 1/4 of your DNA -- it works because, if you have the "help your first cousin" mutation, then there is a 25% chance your cousin has the mutation as well. The other shared DNA that is being propagated does not affect the selective pressure on the gene one whit.

It might be conceivable to artifically create a stable situation where several species shared the same gene for inter-species altruism only among the species who have that gene in their gene pool (I'm not even sure that could be made stable) but you could never have that in the first place because there's no way such a gene could evolve. If a mutation for it developed in one species, there would be no way for it to jump to the other species. No, "genuine" altruism -- in the sense that the individual never reaps any benefit for her altruism -- can only exist within a species.

Now, some might argue cases of "genuine" intra-species altruism are no different from the case of a parasitic species (like the cuckoo) using trickery to exploit intra-species altruism for its own benefit -- only in this case, the parasite is the gene, and the rube is the altruistic individual.

Hogwash!

Dawkins closes The Selfish Gene with a call to escape the "tyranny of our genes". I have written in the past about how I find this to be a rather paradoxical exhortation. This to me seems no more meaningful than to say that if I were to install an after-market stereo system in the family's minivan, I would be emancipating it from the "tyranny of Toyota".

Certainly humans are in a unique position to rise above the short-sightedness of our genes. Furthermore, we can say that humans are in a position to empower the individual with respect to the gene pool -- but it would be silly to say that we could empower the individual with respect to genes in general, because what is the individual but the manifestation of a specific permutation of genes, combined with environment?

Our far-sightedness in comparison to natural selection allows us to make decisions that go against the "purposes" our genetic program in startling ways, contraception being a convenient example. But even in the case of contraception, we are not overthrowing the "tyranny of our genes" -- quite the opposite, it seems to me that we should be rather glad that our genes are configured in such a way as to afford so much pleasure.

Only if one gets sloppy with the metaphor (as Dawkins repeatedly promises he won't do, but occasionally does anyway) would one argue that we have subverted the "motives" of our genes by doing so -- genes after all do not have any motives to speak of. They just are. That their ultimate cause was different is somewhat irrelevant today.

Thus I assert: If we are to say that apparent altruism which harms the individual but benefits the genes is parasitic rather than "genuinely" altruistic, then it follows also that sex doesn't "genuinely" feel good. And I for one am not willing to say such a thing.

To restate: We must discard this silly idea of escaping the "tyranny of our genes", and realize that what Dawkins is really exhorting us to do in the final chapter of his book is to 1) rise above the short-sightedness of our genes, and 2) to empower specific permutations of genes with respect to the gene pool at large. But in terms of what is "genuinely" good, the genes -- that is, the specific permutations of genes -- are still very much running the show.

At this point I'm sure some people would say I am engaging in the naturalistic fallacy. But I believe this argument is subtly different. I am not saying that "Our genes make us want to do X, therefore doing X must be good." Rather, I am saying that if our genes make us want to do X, and X is not in conflict -- either short-term or long-term, directly or indirectly -- with anything else that our genes make us want to do, then doing X must "genuinely" be a good thing to do.

I say this because I don't see any other objective way to define what is good. As I blogged about in the post I linked to before, even the Golden Rule, the apparent foundation of higher ethical behavior, is rooted in our affinity for reciprocal altruism -- an affinity we only have because of our genes.¹ (It occurs to me at this moment that if one were to really truly escape the "tyranny of our genes" then one would also have to reject reciprocal altruism, and therefore the Golden Rule as well!)

So what does all this have to do with "speciesism"? Well, as I said, "genuine" altruism, i.e. non-reciprocal altruism, can only evolve within a species. Therefore, it is not surprising that we have a strong impulse towards speciesism. In the same way that we find sex quite pleasurable, independent of the gene-selfish ultimate cause, we can also say that we find human life to be worth some apparently irrational sacrifice. We also sometimes find non-human life to be worth apparently irrational sacrifices (my rather large outstanding vet bill being a vivid demonstration of this), most likely because of a "misfiring" (from the gene pool's point of view) of our impulse to make irrational sacrifices for other humans. But it seems fairly clear to me that the impulse to sacrifice for other members of the species is far more powerful than the impulse to sacrifice for other species.

The remaining question is, does this natural impulse have any unforeseen conflict with any other imperatives we have inherited from our genes? If not, I cannot see any basis on which to pronounce this impulse "wrong". In the absence of some unforeseen conflict I am missing, it seems to me that the statement "It is fine to discriminate heavily against members of different species" is as true as the statement "It is fine to have sex for pleasure."

It's worth reiterating in closing what I am not saying: I don't mean this as a defense of eating meat. Factory farming causes so much suffering -- and to species some of whose nervous systems are strikingly similar to ours -- that it is quite rightly seen as an affront to both our impulse towards reciprocal altruism, as well as even our limited impulses towards inter-species non-reciprocal altruism. Even if not, the environmental disaster of modern factory farming is clearly in long-term conflict with a number of our other impulses, e.g. the impulse to NOT FREAKING DIE.

More humane forms of animal farming are much murkier. Our sense of reciprocal altruism may rightly see it as a raw deal for the animal -- "we feed you for a couple years, but then it's choppy-choppy time" -- but I believe this is weighted against a lot of other factors that I would prefer not to get into at this time, since this post is already way too long.

¹Of course, as I also said in the previous post I linked to, it is my opinion (and I think game theory backs me up on this) that any organism we might refer to as "sapient" in the slightest must have evolved some form of reciprocal altruism. In this sense I postulate that a limited form of reciprocity may represent a gene-transcendent ethic. However, I do not think this impacts my argument here.

Happy Blasphemy Day!

(For more lolgodz fun, check this old post)



Update: Since apparently I worship Darwin (why didn't anybody tell me I had to worship Darwin when I enlisted to be a Militant Atheist?), I decided to rise to Dembski's challenge and do some "blasphemy" about old Chuckie as well:

Pascal's Wager presented and then discredited in rhyming form. For real.

This song is awesome:

You can't escape it

PZ writes this morning about some asshats who are offended that the awesome band They Might Be Giants sings a children's song that (gasp!) promotes the idea of evolution and refers to angels as unscientific.

Later, I was checking out some stunning photos of volcano lightning (seriously, you gotta see that shit) and when I

I have a dream... that someday my children's children will be able to look at a stunning and starkly beautiful picture like this without some fuckhead ruining the whole thing by insisting that GODDIDIT.

get to the bottom, lo and behold, there is an argument in the comments over whether this is some kind of penis-wielding display by an angry god.

Meanwhile, I've been conversing with HuffPo's resident "yoga chickie" over in the comments section at Joel's blog, trying to explain to her why us "atheist fundamentalists" feel the need to be so vocal. It's because the other side¹ will not shut the fuck up, and uses every possible context to prattle on not just about their absurd delusions, but also why we should all cower in terror of their warmongering sky daddy.

I did not go looking for some theological discussion today. Well, okay, I got pointed to the TMBG thing via a hardcore atheist blog, but PZ originally posted about it just because TMBG is awesome, and I would have clicked the link and listened to the song anyway. In the case of the volcano lightning, I was just looking at some cool pics that I found out about from Snopes. And yet, everywhere I turn, there are theistic blowhards trying to tarnish everything that is beautiful and wondrous in this world with their dumbass sectarian viewpoint.

You can't escape it. Not in today's world. And given that, we have two choices: Run away, or take a stand.

¹I want to clarify that by "the other side" in this case I do not mean moderate theists, and especially not "imaginary friend"-style pseudo-theists like Lauren... I waffle on whether moderate theism is potentially harmful or not -- and you can read a lot of my thoughts about that in my conversation with Lauren at Joel's blog -- but that's a subtlety that's not very important right now. I'm not inclined to spend much time arguing the finer points of whether a mature form of theism is a net positive or a net negative, when our politics and our daily lives are under constant assault by an infantile and intolerant form of theism.

X-Men take over the world

"We are all mutants!" blares the headline, and I suppose it's true: According to a paper published in Current Biology, we each have about 100 to 200 mutations in our gene sequences. I guess that's not too surprising, considering we are talking about using biological (i.e. messy) transcription methods to copy billions of individual data points. Getting a several dozen of them wrong is to be expected.

I post this for two reasons: First of all, I'm sure PZ will be posting something about this, and I wanted to beat him to it. heh... also, this has some relevance to a blog post I am currently composing that explores a new metaphor that helps a simple computer engineer like me understand how such complexity could arise out of a relatively small genome.

The evolutionary implications of our preference for the Maillard reaction

This is something that has been bugging me the last couple of days... As many of the foodies out there may know, the Maillard reaction (pronounced may-ARD) is that incredible magic chemistry that happens when you sear meat, roast coffee, or malt barley to make whiskey and beer. In a nutshell, heat applied to certain proteins causes them to get all jumbled up and rearrange themselves into literally hundreds of different complex flavor compounds. Okay, that was probably an imprecise lay explanation, but you get my point.

How can this delicious piece of seared meat help my genes to replicate themselves?

Make no mistake, the products of the Maillard reaction taste fucking good. In fact, it is so tasty that this is where the myth developed that searing meat helps to "hold in the juices". It doesn't, and in fact roasted meat that has not been seared will actually have very slightly higher moisture content than meat that has been properly seared. However, unseared meat will taste drier because the Maillard reaction is so (literally) mouth-wateringly good that it will actually make you salivate more while eating and make the seared meat taste tender and moister.

But here's the question: From an evolutionary perspective, why does it taste good?

I suppose its possible that a preference for cooked food was such a beneficial adaptation for us that we evolved a taste for charred meat in a relatively short amount of time, a hundred thousand years or so. I mean, our jaw structure definitely reflects the shift in selective pressures brought about by the advent of cooking, so it's not inconceivable. But I tend to doubt this explanation for a couple of reasons.

One is that there is a big difference between a modified jaw structure vs. the ability to detect and seek out a whole new class of flavor compounds. It seems the latter would take a lot longer to arise as a result of natural selection.

The other reason I doubt that this preference was selected due to cooking is because there doesn't seem to be any reproductive benefit to preferring charred meat over, say, boiled meat. I suppose our ancestors may just have used fire-roasting more than boiling -- but I have to imagine that the two techniques were invented around the same time, and if our ancestors did not already prefer the flavor of seared meat, I don't see why they wouldn't just boil it to save time, as well as to capture any rendered fat in a broth rather than letting it drip wastefully into the fire.

It seems most likely to me that we already had a taste for these flavor compounds prior to learning how to create them via cooking, and that it was a side effect of some other adaptation. But what?

The Wikipedia article talks about a similar reaction occurring naturally in our bodies... I wonder if that could have any bearing on it? I don't know, I am not an evolutionary biologist, or any kind of biologist for that matter. Anybody have any ideas?

Biology and Morality, Or How I Learned to Stop Worrying and Love My Selfish Genes

I was reading Stephen Pinker's excellent book The Blank Slate this morning and I had some thoughts about a topic that's been rattling around in my brain. In the passage I was reading, Pinker was asserting that humans are neither inherently good or evil, but that people most likely have both good and evil tendencies, and whether or not they are acted on is a function of each individual's neurological processes. His reference to "good and evil" without qualification inspired me to think once again about what is meant by this -- but this time, I was doing so in the context of Pinker's ideas about human nature.

In a previous post, I railed against the idea of relativism, both in terms of interpretation of factual data, as well as -- to a more limited extent -- in determining morality. I probably should have been a little more guarded when I maintained that some things were "absolutely" right or wrong. "Absolute" is probably too strong, but what I meant is that much of what constitutes morality is both non-arbitrary and independent of culture. Clearly morality does not exist on its own. There are no absolute moral laws woven into the fabric of reality in the same manner as physical laws.

This of course prompts the question: Whence this morality, if not from culture?

Perhaps the obvious answer is biology. The concepts of "good" and "evil" can be viewed as products of natural selection, a natural extension of various instincts we have evolved over time. In the case of altruism, this is not just speculation; as I'm sure everyone reading this post knows, there is growing evidence that genuine altruism is a side-effect of a sort of selfish altruism evolved by our primate ancestors. The so-called Golden Rule can be seen as the logical conclusion of our altruistic natures, i.e. the product of instinctual altruism multiplied by abstract reasoning ability is the mandate that others ought to be treated in a way we would prefer to be treated.

But there's even more to this. It seems obvious, but it is easy to ignore that the way we prefer to be treated is itself determined by our biology. Consider a harmless but painful electric shock. There is clearly no eternal abstract reason why a harmless jolt of electricity is undesirable, but we find it painful because it stimulates systems within our bodies which have evolved to warn against possible harm. In other words, the reason I don't want to be shocked is itself a byproduct of biology. And therefore, the reason it is not cool to go around shocking people with a hand buzzer is due not just to our altruistic nature, but to other features of biology.

To what extent can we take this without it becoming absurd? What if instead of a hand buzzer, I am talking about lopping off your arm? Is this only "wrong" because of instincts that make me want to keep my arm? Well, no, there are plenty of practical reasons why we might want to keep both arms anyway. But aren't those reasons also the product of our biology? Having one arm may make it harder to do everyday tasks like tying my shoes, but why do I want to tie my shoes in the first place? Isn't it because not wearing shoes damages my feet, and I have a biological imperative not to damage my feet?

Logically extending this idea, I could argue that it's only wrong to kill people because they have evolved the desire not to die. Well, maybe. But I am not entirely sure whether this takes us all the way to explaining all manifest morality.

What I mean by this is best explained by a thought experiment: Consider an alien race -- call them the Eschatolians -- which for whatever reason have not evolved an altruistic instinct. Perhaps their civilization is structured more like an ant colony, where loyalty to some "Queen"-like being is the driving moral code rather than a do-unto-others ethic. This of course might make them seem quite evil by human eyes, but I don't think that is entirely fair. Eschatolian individuals are not treated with respect, but they don't even have the evolved desire to be treated in this way. Who are we to judge that?

Now suppose the Eschatolians invent a technology that can please and protect their Queen -- the highest form of morality in their civilization -- but it will set in motion a process that will significantly hasten the heat death of the universe. The Eschatolians' sun will be long dead by this time, so it's no skin off their (or their Queens') backs, but it will lop untold trillions of years off the meaningful life of the universe.

Now is there some arbitrary standard that makes the Eschatolians "evil" -- beyond even our specifically human concepts of morality? Every fiber of my being wants to say yes: destroying the universe for short-term gain is wrong, independent of biology. But how can I say this without invoking some sort of morality from the clear blue sky?

I think today I have a partial answer, but before that, I want to digress into a different thought experiment, so that when I propose my answer to the Eschatolian problem, it will be clear what I am not saying. I was once challenged with the question, if only one human woman remained on earth, and she refused to have sex, would it be moral to rape her?¹ To me, this is a fascinating question, and I still haven't made up my mind entirely. (Update 2010/08/17: FWIW, I am now leaning towards no.) Debating this question is beyond the scope of this post, but I want to address one particular fallacious argument against it.

When I first heard it, some who answered "absolutely not!" asserted that our desire to reproduce and to propagate the human race was nothing more than the parasitic effect of our "selfish genes", and that a rejection of those imperatives was necessary to "liberate" ourselves from the "tyranny" of our genes. (Some of this, I realize, is straight from Dawkins, but I don't know how much. I unfortunately have not read The Selfish Gene yet, so I am not aware if my objections to this line of reasoning would apply to his ideas, or merely to the interpretation of them presented by some folks on PZ's blog. I apologize if some of what follows comes across as strawman-ish.)

While I think it is incredibly valuable to have an awareness of how our behavior is shaped by evolution, and while I think Dawkins is quite right in pointing out that genes act in their own self-interest rather than in the interest of the collective of genes we refer to as an organism, at the same time I think this idea of becoming "liberated" from the "tyranny" of our genes is utter nonsense. Who, exactly, is being liberated? This smells like Cartesian dualism, like we are saying there is some ghost imprisoned in our DNA that is just waiting to be freed.

Hogwash! What are we if not the product of our genes and our environment? To dismiss our innate impulses and desires because they are also a product of our genes is a futile attempt to divorce our selves from our selves. Certainly, our instinctual preferences will conflict with each other, and an awareness of how these preferences have developed from the "selfish" nature of genes can inform the conflict and help us reach a decision. But even if we do decide to suppress an instinctual impulse, it will not be because of some external moral code that hangs in the air sui generis, or because of the willed choice of some mythical "soul" -- it will be because we have decided to favor a different instinctual impulse that is itself a result of selfish genes.

In the case of the Last Woman on Earth thought experiment, if we decide that rape is not acceptable even in a last ditch attempt to save the human species from extinction, it will not be because we have "liberated" ourselves from the parasitic impulse to propagate our selfish genes. It will be because the logical extension of our altruistic instincts -- also a parasitic impulse wrought by our selfish genes -- has convinced us that the rights of the individual are more important.

So if morality cannot exist independent of selfish genes, then what of the Eschatolians? Can we possibly say they are "evil" in some non-arbitrary sense for wanting to destroy the universe, without engaging in human chauvinism? Isn't there some meta-morality we can invoke, that transcends individual gene pools?

I am going to tentatively answer yes, though my reasoning relies quite heavily on speculative assumptions about the extent to which evolution is convergent on different planets (if life even exists elsewhere, that is, which itself is uncertain). This species-independent morality I am positing cannot exist independent of the phenomenon of selfish replicators², but it is not tied to the specifics of an individual pool of replicators.

I think it is quite reasonable to assert that any successful form of life will have evolved biological imperatives which resist extinction. Individuals may not necessarily have self-preservation or self-reproduction impulses (e.g. ant worker castes), but must have some impulses which would be violated by pretty much any mechanism forcing the species into extinction, or else natural selection is going to get rid of such a species in a big hurry.

If we accept that morality must be a product of instinctual impulses, then I think it logically follows that from the perspective of species X, the extinction of species X is immoral. That doesn't mean the extinction of species Y is immoral from the perspective of species X, of course, but we have established here a species-transcendent moral pattern.

How much more would it take to transform this into a species-transcendent moral code? I suppose I might invoke a sort of vague "galactic utilitarianism" and argue that if a particular act -- e.g. destroying the universe -- violates the morality of enough species, then it is perhaps also immoral in some universal and non-arbitrary sense. Of course, utilitarianism almost certainly has its roots in our altruistic instincts, and it is clearly not the case that all species have a similar instinct. But I think we are almost there.

It is conceivable that altruistic impulses are a likely/necessary feature of sapient life. How realistic is it to envision a civilization with an ant-like social structure that has developed enough self-awareness to start talking about morality? Of course this question is impossible to answer, as it is asking about convergent evolution on an interplanetary basis, and for all we know the question itself is invalid.

But I think it's an interesting question nonetheless. Depending on the answer, this could establish some basic moral codes, not quite as immutable laws, but as an inevitable byproduct of sapience. There are not many things that fall into this category -- basically, just don't destroy stuff for no reason or for reasons which are insignificant compared to the destruction -- but it still seems like an appealing idea, not just because it provides a possible answer to the Eschatolian thought experiment, but because it provides a much firmer underpinning for environmentalism than might otherwise be achieved.

This still does not justify the absurd notion that we can be "liberated" from our selfish genes. If this transcendent morality is justifiable, it will still be because of selfish replicators, not in spite of them. To denigrate our instinctual impulses because they exist solely for the purpose of propagating DNA is to practice self-contradiction in the name of some mythical ghost in the machine. It is both Puritanical and delusional.

¹Unfortunately, the rather shrill and unimpressive person asking me this question merely wanted to use it to accuse me of being a "rape apologist," which it seems to me relied on a rather preposterous definition of "apologist": that if you say X is acceptable under any circumstances you are by definition an "X apologist". If I think it is acceptable under some circumstances for police to forcibly detain and imprison an individual, does this make me a kidnapping apologist? If I think chemotherapy is a good thing, does this make me a poison apologist? If I think that yelling "Fire!" in a crowded theatre is not protected speech, does this make a censorship apologist? If I think a hysterectomy is acceptable for medical reasons, does that make me an apologist for forced sterilization?

This kind of context-free morality is not just absurd; it is dangerous. It is a close cousin of the kind of lazy and asinine reasoning that compels idiots to assert that gay marriage will lead inexorably to a legalization of incest and pedophilia.

²I steer away from the word "gene" from this point on, because I am now speculating about how life might evolve on other planets. Presumably, though, some kind of gene-like "replicator" would be necessary for natural selection to evolve life, so I will content myself to refer to it as such.

Robots evolve to deceive -- how could they evolve to cooperate?

Note: I am pretty sure I use the term "Bayesian network" completely incorrectly throughout this entire post. Just pretend I used the more general term "neural network". Or, if that's wrong too, just pretend I said whatever thing that wouldn't make me sound stupid and pretentious.

I have this vision in my head from school days of a bunch of inputs and outputs connected by some number of intermediate nodes that do a weighted sum of the inputs -- with the weights being the coefficiencts that change over time, whether by "training" the network or via genetic algorithm. Whatever that thing is called, that's what I meant. (That'll teach me to try and talk authoritatively about stuff I learned eight years ago and never applied...)

The scienceblog-o-sphere is mildly abuzz with a fun new study about Bayesian-network controlled robots evolving the ability to deceive each other. Click the link for details, but to very briefly summarize: The robots can only detect a "food" source at very close range, but they also have the ability to flash a light which the other robots can detect at a distance. They start off flashing randomly and searching randomly. Within a few generations, some robots evolved an attraction to the flashing lights, since it might indicate the discovery of a food source. Within a few more generations, though, many of the robots started to control when they flashed the light so as to "remain silent" when in proximity to a food source, thereby preventing others from discovering it and crowding them out for resources.

Neat stuff. I can't help but think the same thing probably could have been done with a computer simulation, but doing it with robots is just so cool. (It probably also has the advantage of removing a number of possible experimenter biases in the computational model of how to represent movement, sight, overcrowding, etc., since you can just let the laws of the physical world handle it.)

This got me to thinking, how would the conditions have to be different in order for the robots to evolve cooperative behavior? Could the conditions of the experiment be modified so that, after enough generations, some robots intentionally signaled the presence of a food source to their peers?

It is very difficult to see this happening in the present setup, where all the robots can see the "signal" emitted by all the other robots. A "gene"¹ would have no selfish reason to alert its peers to the presence of food, because there is no mechanism within that experimental framework to signal robots who shared the gene at a higher frequency than those who did not share the gene.²

But what if we change the experiment to involve several different "species" of robots. Some of them emit blue light, some green light, some red light, etc. Furthermore, a robot can only see the color of light it itself emits, i.e. it can only "see" the signals of members of the same species. The species all compete for food in the same common area, and the selection criteria applies cross-species, i.e. survival is awarded to the 200 fittest robots regardless of species. "Mating", on the other hand, is constrained to within species.

Now let's assume that "somehow or other" -- and I'll come back to this, because it's quite a large bit of hand-waving -- one of the species develops a significant sub-population with the "cooperative" gene. Call it the Green species, for sake of convenience. Robots of the Green species would, on average, be alerted to food sources much quicker than robots of other species, and so ought to tend to outperform them in each round. While the within-species selection would be against the "cooperative" gene, it might in the short term tend to out-reproduce the various genes of other species simply by virtue of random mating with more selfish Greens. In other words, a sub-population of selfish Blues might be more individually fit than cooperative Greens, but the selfish Greens are crowding out the selfish Blues and forcing them to disappear. Meanwhile, the few cooperative Greens that do manage to survive could continue to sprinkle the "cooperative" gene amongst the burgeoning Green population.

I think this might be a bit fanciful in that form. It doesn't sound particular sustainable to me, and more damning is that I can think of no evolutionary process by which the Greens would develop a significant sub-population of cooperatives to begin with. (This is the frantic hand-waving I referred to earlier) If a Green mutated to show cooperative tendencies, the selective pressures would be strongly against that mutant. The species-wide benefit would have to be immense in order to facilitate the by-chance propagation of a gene that was so clearly bad for the individual, but a large species-wide benefit would not be able to develop until the "cooperative" gene constituted a sizeable sub-population. It seems to me this is an unsurmountable can't-get-there-from-here problem.

Unless the inheritance were somehow tweaked to behave in a Mendelian fashion, with the "cooperative" gene being a recessive trait. Now I think maybe we are getting somewhere. A "cooperative carrier" can still behave selfishly, but it also benefits from the fact that 1/4 of its brethren are pure cooperatives. There is still a bit of a jump start here, because cooperative carrier Greens are, within the species itself, no better off than pure selfish Greens. But if one species were to develop even a relatively small population of cooperatives and cooperative carriers, that species could suddenly start to significantly outperform other species. The selective benefit to the cooperative carrier is clear: it surrounds itself with cooperatives that it can exploit in order to out-compete other species.

Hmmm, this makes me want to try to duplicate the experimenters' results in software and then start playing with the model... Of course, the fact that I've never directly worked with Bayesian networks or genetic algorithms could put a damper on that...

¹Depending on the experimenters' exact implementation of the neural network and the inheritance scheme, it is probably not quite accurate to use the word "gene" here. At this time, by "gene" I am simply referring to some group of coefficients in the Bayesian network which produce a particular behavior. I am also going to pretend that this "gene" is atomically heritable, for purposes of this thought experiment, even though that may not reflect the experiment at hand.

²We can maybe envision a group of robots which devised a special "code", i.e. a series of pulses of light, that signified the presence of food only to others who were genetically "in the know", but this is fraught with all sorts of difficulties. For one, even a brief code would likely attract robots who did not comprehend the code. For another, robots who did not have the "cooperative" gene could still develop the capability to understand the code and exploit the cooperative robots. Perhaps most damningly, the development of this code is too complex to evolve all at once, and looking only within the context of food-signalling, there is no evolutionary advantage to a partial or weakly-comprehended code. In order to surmount this, the robots would have had to evolve a coded communication ability for some other purpose, which was then co-opted into food signalling -- and that is going way beyond the scope of even this quite fanciful thought experiment.

Faith: One word, two meanings

I was reading an interesting (and very old) post at the Gene Expression blog that, among other things, dealt with the fact that the vast majority of people who believe in evolution don't actually understand it at all, and simply accept that evolution is true because it is the scientific consensus. One interesting conundrum this raises is that it makes me question whether I understand the ideas behind natural selection as well as I think I do, but that's a topic for another post.

The other thing the post reminded me of was that I've been planning to write a blog post about the unfortunate double meaning of the word "faith." In the comments on that post, the phrase "faith in science" was used, and while I agree with what the commenters and the blog author were getting at, I am not comfortable with that word being used. I think there are two meanings of the word faith, and I think this is confusing for theists and results in that whole "Well, I have faith in Christ, you have faith in science. No difference!" fallacy.

Both meanings of the word faith involve believing something with insufficient evidence, or at least, without enough evidence to justify the level of confidence. So there is a similarity there. The two major differences, in my mind, are in 1) the presence of a pragmatic justification in one case for believing with insufficient evidence, and 2) the amount of contradictory evidence required to change the belief. I think these differences are distinct enough to make the two meanings of faith entirely different concepts.

As the post at Gene Expression describes, having "faith in science" is usually a matter of recognizing that reality is often counterintuitive, that as a result the scientific method is a better way of discerning truth than common sense, and lastly that it takes specialized knowledge to really understand the truth in a particular field.

The logical conclusion of this is that one's own intuition in a field where one does not have specialized knowledge is probably not going to be particularly accurate. The alternatives are to try to become educated in every possible area (which is not practical for those of us who have jobs and/or social lives), or to put tentative implicit trust in what the "experts" say about fields in which we are not knowledgable.

Of course, figuring out who is an "expert" worth listening to is easier said than done, and hence this is why I say that this is believing on insufficient evidence. I can't check out the claims of every expert I chose to trust. I can educate myself and see if their claims even make sense, but in many cases I'm ultimately going to have to chose between people who strongly disagree and yet whom I have no way of knowing who is right. We just do the best we can in these cases, because pragmatism dictates it must be so.

The other thing that makes so-called "faith in science" different from religious faith is the standard of disproof. This is not to say that those of us who chose to put stock in the consensus of "experts" are always perfect at reacting to solid evidence that our previous beliefs were false. It's always hard to change one's beliefs; that's human nature.

In some ways, this is even a good thing: As previously mentioned, reality is often counter-intuitive, so if I am presented with evidence that seems to me to contradict the established scientific paradigm, I would be well-advised to be resistant to accepting that evidence until I gather more information, no matter how plain the evidence may seem to me. This is because there may be some grievous error in the argument that I am not aware of due to my ignorance in a particular field.

The result of this is an undue preference for the current scientific orthodoxy. This has been historically demonstrated, with a recent example being the powerful resistance to plate tectonics theory. However, I don't see any reasonable way of avoiding this momentum for the status quo. The other alternatives are to either become 100% educated about everything (impossible), or to shift undue stock in our own personal intuition about things which we know nothing about -- and most educated people understand that doesn't usually work out so well.

But while pragmatism may lead us to exhibit an undue preference for scientific orthodoxy, this is nothing compared to the immutability of religious faith. This is complete apples and oranges.

For one thing, religious faith is mostly atomic, or at least highly interconnected. If one part is proven to be abjectly false, then sometimes it becomes difficult to continue to justify belief in the rest, e.g. if the story of Moses is shown to be pure fable, then the rest of Judaism kind of falls by the wayside. In contrast, the body of scientific knowledge is constantly changing, with old ideas shown to be mistaken, misunderstood, or even abjectly false, yet this does not in any way impact the validity of the scientific method -- or even in the idea of "faith in science" in the sense I am referring to it in this post.

For another, religious faith seems uniquely capable of spreading unwavering crankery more effectively than any other ideas. Certainly, you will get the rare cantankerous old scientist who does all sorts of mental contortions to stick to an old idea from the scientific orthodoxy which has since been proven false -- perhaps even contortions on the order of what Young Earth Creationists are known to do. But this is rare. YECs make up a non-trivial percentage of the American population. Not sure one can say the same about Flat-Earthers... and yet both ideas are equally ridiculous and require similarly fantastic mental contortions.

Recognizing these differences, I think it would be preferable to use a different word for the "faith in science" idea. I'm not sure what that word would be... but it should be a word that captures the idea that, yes, although I believe this with insufficient evidence, I am ready to change my mind or adopt a more nuanced position if presented with sufficient evidence to justify the change.

This post is already too long and I need to get to work. I may revise it or expand on it later..