Fodor fails EVOL 101 (in other news, water found to be wet...)

This little article from New Scientist has been circulating about the blogosphere lately:

Survival of the fittest theory: Darwinism's limits by Fodor & Piattelli-Palmarini
(via Jerry Coyne's blog)

Yet another case of New Scientist realising that controversy sells, and so does crappy science journalism. I wouldn't call it anti-science, just horrible misinformed and poorly thought out. But that is not about to stop me from unleashing the mother of all rants. Just because I can. I have a midterm tomorrow, a horribly busy week ahead, and am sort of stressed and grumpy, so what better time is there to rip someone's article to shreds?

Now, I must say, as someone who's rather annoyed by the hyper-adaptationist tones both within and outside biological evolution, I must partly sympathise with some of their argument. But they take it too far, and seriously miss the freaking point. Also, there's a fine line between provocative revolutionaries and drama queens, and they crossed it ages ago.

Let's go!

Much of the vast neo-Darwinian literature is distressingly uncritical. The possibility that anything is seriously amiss with Darwin's account of evolution is hardly considered.

Because we have better things to do than worry about what some guy got wrong 150 years ago?

The methodological scepticism that characterises most areas of scientific discourse seems strikingly absent when Darwinism is the topic.

'Darwinism' is a topic? For the love of FSM, can somebody PLEASE enlighten me on what the fuck IS 'Darwinism'? In all my admittedly still short biological training, I have not once come across such a field. I've scoured evolutionary biology far and wide in search of 'Darwinism', and failed to find it. I know of molecular evolutionary biol, I know of population genetics, I know of cell evolution and genomic evolution and ecological evolution, evolutionary psych, evolutionary linguistics, evolutionary you-name-it... but not once have I c0me across this obscure discipline called Darwinism. Seriously, what am I doing wrong? How can I miss something so well-known by the general public and various outsiders?

OH FOR FUCK'S SAKE EVOLUTION DOES NOT EQUAL DARWINISM!!! I'm not even gonna rebutt that paragraph... *headdesk*

But we don't think it is true. A variety of different considerations suggesting that it is not are mounting up.

Ok, I'm ready. This better be good!

Given a certain amount of conceptual and mathematical tinkering, it follows that, all else again being equal, the fitness of the species's phenotype will generally increase over time, and that the phenotypes of each generation will resemble the phenotype of its recent ancestors more than they resemble the phenotypes of its remote ancestors.

Huh? "Species's phenotype"? I'm definitely no population geneticist (and suck at it), but something seems off about that phrase. Phenotype is something an individual has, not a species! Ok, let's assume they meant the species' average phenotype -- still sounds shaky but meh -- they're trying to say the overall fitness with regards to that trait would gradually increase over time? Well, sure, maybe. That's not really the crux of whatever they call 'Darwinism', since survival is much more important than improvement. 'Improvement' isn't actually necessary, but rather a byproduct of survival. "Survival of the good enough".

And as for the last part, phenotypes resembling those of recent ancestors more so than remote ones...isn't that like, basic inheritance, not selection? What the hell does that have to do with anything?

Skinner's theory, though once fashionable, is now widely agreed to be unsustainable, largely because Skinner very much overestimated the contribution that the structure of a creature's environment plays in determining what it learns, and correspondingly very much underestimated the contribution of the internal or "endogenous" variables - including, in particular, innate cognitive structure.

Oh. So that's where we're going! Skinner's behaviourism became unfashionable in cognitive science and psychology (rightly so, but only because it was extreme -- elements of it may still be quite valid!), and since natural selection is an environmental explanation, it ignores inner developmental constraints and self-organising features. Apparently, Fodor and Piattelli-Palmarini think they're being revolutionary.

Stuart Kauffman beat them to it AGES ago. Thing is, he's a real biologist, and has plenty of modeling and real evidence backing his claims. He's does seem a bit loud about his argument, but considering academia is basically a cage of howler monkeys to begin with, that shouldn't translate to OMG DARWIN IS SO DEAD!!1! (no shit?)

I happen to have Kauffman's The Origins of Order: Self organisation and selection in evolution sitting on my desk, for no good reason. (had to prepare a small talk on neutral evolution a while ago, but didn't quite swallow enough of Kauffman's rather terrifying math for it to be of any use at the time...)

First of all, what Kauffman attacks is what he calls the Neo-Darwinian Synthesis (Kauffman 1993 p10), which is the 'marriage' of what was at that time a Darwinian view of evolution, and Mendelian genetics into a new form of evolutionary biology. This was happening around the 60's, when it actually became feasible to talk about the stuff of biological inheritance -- DNA, genes, etc. Prior to that, evolutionary biology was mostly environment-oriented, mainly because that's all they had to work with. Perhaps that's what Fodor and Piattelli-Palmarini call 'Darwinism'?

A while later was Kimura's Neutral Theory, which while being quite accepted today apparently caused an uproar back in the day (1970's). This theory showed how some evolutionary change can happen independently of selection, by being selectively neutral. Later on we get Ohta's Nearly Neutral Theory (reviewed in Zuckerdandl 1996 J Mol Evol), where even slightly deleterious mutations can be tolerated, since selection would act much more strongly on greatly deleterious mutations rather than the slightly bad ones.

A common fallacy is to assume selection acts immediately and absolutely -- that any slightly bad change will automatically be removed. First off, selection takes time, and sure, if you randomly mutate a population and leave it static indefinitely, selection will eventually weed out all deleterious traits, even the very nearly neutral ones. But environments are messy and too turbulent to justify modelling selection as acting indefinitely. Secondly, selection follows a bit of a probability curve -- the strongly deleterious traits are much more likely to be erradicated within a certain unit of time, but that does NOT mean they necessarily will be! In summary, selection is not black-and-white, and plenty of neutral processes lurk in the background.

Even most selectionists would agree that selection is not a black-and-white thing, and that it works in conjunction with other processes. Our disagreement is how much emphasis to place on natural selection, not whether or not it exists!

Back to Kauffman. He states four issues he has with modern (as of 1993) Neo-Darwinian Synthesis (p10):
- Selection as the sole source of order in organisms. I agree there is a little too much emphasis on selection being the source of order -- self-organisation doesn't suddenly stop once selection comes into play! But most biologists recognise that, I think.

- The concept of a linear "genetic program". (the genome as a computer) He argues for a 'parallel distributed regulatory network', which is generally how developmental biologists view development today. In fact, networks are quite the hype these days...

- The tendency to see organisms as "ad hoc contraptions cobbled together by evolution." In other words, organisms being viewed as pure historical accidents. He argues that various changes have different probabilities, and that a likelihood model is more suitable than 'pure randomness'.

- The concept of developmental constraints in evolution. What Kauffman alludes to is this notion that if selective pressures would favour a certain trait, the organism would eventually develop it. Nowadays, with the rise of evo-devo and a slightly better understanding for how development actually works, everyone recognises developmental constraints!

Note that nowhere in there does Kauffman claim that natural selection is 'dead' or 'useless' -- instead, he argues that other processes are not to be ignored. Fodor and Piattelli-Palmarini, on the other hand, are little more than ignorant drama queens.

Speaking of drama queens, back to their article.

Over the aeons of evolutionary time, the interaction of these multiple constraints has produced many viable phenotypes, all compatible with survival and reproduction. Crucially, however, the evolutionary process in such cases is not driven by a struggle for survival and/or for reproduction. Pigs don't have wings, but that's not because winged pigs once lost out to wingless ones. And it's not because the pigs that lacked wings were more fertile than the pigs that had them. There never were any winged pigs because there's no place on pigs for the wings to go. This isn't environmental filtering, it's just physiological and developmental mechanics.

And...? You've just shocked the entire evolutionary biology community! Fuck!

And then there is this in March 2009 from molecular biologist Eugene Koonin, writing in Nucleic Acids Research (vol 37, p 1011): "Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected." There's quite a lot of this sort of thing around these days, and we confidently predict a lot more in the near future.

More SHOCK! OH NOES, NATURAL SELECTION IS DEAD!!! Perhaps instead of criticising us, your should instead focus your energy on criticising your own discipline and your own misinterpretations of evolutionary theory? Just sayin'.

We should stress that every such case (and we argue in our book that free-riding is ubiquitous) is a counter-example to natural selection. Free-riding shows that the general claim that phenotypic traits are selected for their effects on fitness isn't true.

Free-riding as a counter-example to natural selection? Huh? Followed by a complete non-sequitur. My, Jerry Fodor must have gone senile...

The most that natural selection can actually claim is that some phenotypic traits are selected for their effects on fitness; the rest are selected for... well, some other reason entirely, or perhaps for no reason at all.

Doesn't selection by definition act on fitness? If the other traits have nothing to do with fitness, then, by definition, they are not 'selected for'. Why can't we just say 'evolved'?

It's a main claim of our book that, when phenotypic traits are endogenously linked, there is no way that selection can distinguish among them: selection for one selects the others, regardless of their effects on fitness.

Ooooh, you discovered pleiotropy? Congratulations! =D Although the selection part is still muddled up a bit. But yeah, byproduct of selection do happen, quite frequently too. That doesn't mean there is no fitness involved!

Natural selection has shown insidious imperialistic tendencies. The offering of post-hoc explanations of phenotypic traits by reference to their hypothetical effects on fitness in their hypothetical environments of selection has spread from evolutionary theory to a host of other traditional disciplines: philosophy, psychology, anthropology, sociology, and even to aesthetics and theology.

Actually, despite the drama queen -esque language ("insidious imperialistic tendencies" -- what the fuck?), I must kind of agree. Instead of applying evolutionary theory outside biology, the scholars instead just took natural selection, which is but a part of the overall theory. I have issues with that too. But this isn't so much a fault of evolutionary biologists (communication -- sure, but perhaps not so much the field itself) -- but rather the unwillingness of some rash humanities scholars to actually comprehend evolutionary theory prior to shoving it everywhere possible. Natural selection is a powerful concept that does deserve application outside biology, but in conjunction with other parallel processes!

Accordingly, if natural selection disappears from biology, its offshoots in other fields seem likely to disappear as well. This is an outcome much to be desired since, more often than not, these offshoots have proved to be not just post hoc but ad hoc, crude, reductionist, scientistic rather than scientific, shamelessly self-congratulatory, and so wanting in detail that they are bound to accommodate the data, however that data may turn out.

HEY LOOK, WE'RE DRAMA QUEENS! WHEEEEE! Behold our powaz of teh rhetorik! MWAHAHA! But seriously, the very ideo of natural selection disappearing from biology...just...how? Dear FSM, how is that even supposed to be conceived? Any finite system is bound to have selection, just because you will eventually end up with limited resources, and subsequent competition for said limited resources, which will favour entities that are more stable and efficient at procuring said limited resources. If you agree that biological systems are finite (which they ultimately are, to any sane person), then it must follow that there will be competition and selection! It's inherent in the system!

Of course, natural selection is just one process, and that I'll agree with them on (although I seriously doubt that they really understand what they're talking about), and it may perhaps in some cases even not play a major role in order/change in complexity/evolution overall, but it's still there, lurking in the background, and directing evolution when the situation is right.

So it really does matter whether natural selection is true.

How can it be untrue!? I don't get it -- they mean, there is no selection happening, AT ALL? So I guess competition in the business world also goes by some other model, that has nothing to do with natural selection, despite the concept actually originating there? Like...that sentence...makes no sense, actually. They could've asked "whether natural selection is significant in [situation X]" or "whether natural selection is a prominent force" or anything along those lines, but debating its truth value? Huh?

I guess I'm just too scientistically reductionist to comprehend such lofty topics. Oh well.

(I would've typically been more polite about stuff like this, but Jerry Fodor really pisses me off on some other topics too. Don't. Get. Me. Started.)

Ciliate orgies and barnacles with twin penises

Like any other human beings on the planet, scientists too are enamoured with sex and genitalia. After all, procreation (self-replication) is the central theme in biology, and we tend to find it more fun when more than one individual is involved. Especially when these individuals differ anatomically into categories, in our case, two types, since that is what's most familiar to us. As far as I know, no lineage has evolved obligatory triple conjugations of three different mating types, although such a thing can be induced in the lab. But for now, let's have a look at a particularly unusual developmental glitch in an individual barnacle, and an even more surreal publication accompanying it:

An Individual Barnacle, Semibalanus balanoides, with Two Penises (Hoch & Yuen2009 J Crustacean Biol) [NOT SAFE FOR WORK due to images of genitalia. Unless you work in biology...]

I came across this while responding to someone's comment, and chuckled. Then I checked whether it really was a single individual case, and whether it really was published in a real journal. In 2009. Yes and yes. It was a rather entertaining read as well. Now, I would go off on a rant about some of their hypotheses and assumptions, but the type of work and the following accompanying note in the acknowledgements suggest this was actually an undergrad project, and I should be nice to my brethren:

"This work was partially supported by a Student Research Fellowship from the American Microscopical Society to [author] and a Crustacean Society Summer Research Fellowship to [author]."

"So, what did you do this summer?" "Found a barnacle with two penises, and you?"

Damn, I wish my summers were as exciting. They usually get spent in a dark room staring at blue [DAPI] dots all day. Sometimes I surgically rape a tiny flower with a pair forceps. Other times I drown my poor seedlings in nasty cytotoxins, and wonder why how they die. This guy got to measure barnacle genitalia. And infer about its sex life.

Here are the two penises in all their glory:

Lemme paraphrase all the scientific lingo: "OMG, TWO penises!" (Hoch & Yuen 2009 J Crustacean Biol)

So why barnacles, of all things? Thing is, upon reaching maturity, they glue themselves to the rock. And become stuck there. And then they get horny, but they can't go out. Kind of like that basement-dwelling 4chan crawling internet loser nerd stereotype. With one key difference: in the barnacle case, size does matter. A lot. Maybe that's not such a key difference, and we won't go there in this polite company (LOL!), but the barnacles can do it without ever going out. All they need is really loooooong penises, long enough to reach the next mother's basement-dwelling geek barnacle. And those beyond it. You can see how this particular sticky situation can lead to evolutionary peddling of male organ enlargment solutions*.

*My horrible, horrible mind is trying to imagine what molecular spam would look like... alas, my imagination does not stretch as far as barnacle penises If only they were immersed in some serious horizontal gene transfer...

They've proposed that at least one of the penises is fully functional, as the sole nearby barnacle has been fertilised. Then they wonder whether this was a genetic or developmental accident. Well, when your sample size is...ONE...it becomes very difficult to separate the two. Especially when you terminate the sole specimen by chopping its penises off. A regularly inherited twin penis trait would be rather unlikely; it's quite improbable for a genetic change to result in the doubling of an entire organ in the metazoan version of multicellularity. So it's likely just a chance developmental glitch. I've seen a photo of a tulip with half its leaf converted to a petal, but only one tulip and a single leaf -- another example of an entertaining, but biologically unimportant, developmental glitch.

So, to summarise:

Lab slave: Holy shit guys, this one has two penises!
PI: OMG, let's see if we can publish that!
Slave: LOL nice joke, buddy!
PI: No, seriously!
[...]
Reviewer: So what's the scientific significance of this work?
Authors: It has two penises, lol XD!
Reviewer: *giggle* Ah what the hell, we need our [juvenile] entertainment too! *accept*

So what is their actual stated conclusion?

"The result is significant because it shows that the mating ability of the barnacle is resilient to developmental instability and able to overcome extreme departure from normal morphology."

For a sample size of ONE. Remember guys, this isn't a mutant line or anything, this is ONE single freak case. But they had to write something ^_~ Still amused by this getting published though...

And now for another anomaly:

Ciliate orgies
Ciliates are obligate sexual organisms. If they don't have sex within a certain number of generations (~50 for Paramecium), their somatic nucleus basically rots away. Thing is, they actually have two different nuclei - one the pass on, and one they use (ie transcriptionally active). The transcriptionally active 'macronucleus' (MAC) is essentially a giant bag of linear plasmids, sometimes having upwards of ~9000 copies of a single unigenomic, or just really short, chromosome. A problem with having so many chromosomes is evident at mitosis -- how do you attach a bundle of microtubules to every single chromosome of the thousands there are? Well, you just...don't.

Ciliate MACs undergo a special form of nuclear division termed 'amitosis', where the nucleus is more or less pinched in half (ciliates do closed mitosis where the nuclear membrane remains intact the whole time), more or less evenly. Sort of. This is roughly compensated for by some rather crazy DNA replication regulation stuff, but eventually the organism may start losing genes. (how it corrects for the ever-changing gene copy numbers is beyond me...*)

This is were sex comes in -- the ciliate exchanges its germline 'pronuclei' (haploid gametes, if you will) with that/those of its partner (in some species, it gets complicated...), and makes a new MAC. Actually, the making of a new MAC heavily depends on the preceding one, which gets destroyed just as the new one is formed, yet its information can still influence it...basically, a paradise for anyone obsessing over epigenetics! In fact, I've done an essay on that stuff for a class: Ciliate genome rearrangements pdf (not my best writing as I spent way too much time reading stuff and not enough time constructing sensible sentences...)

*Hmmm, just thought of this: overexpression lines might be a problem in a ciliate model, no? It may well be that just like what seems to be happening with the polycistronic gene situation in trypanosomes, may be also happening here: namely -- highly emphasised post-transcriptional and post-translational regulation of gene expression levels rather than direct regulation of the promoter... thus would mean that driving a gene with a highly expressed promoter might be compensated for by some pathways specific to regulating that gene (or its class), thereby screwing with your overexpression attempts. Any thoughts?

So, before I get too carried away with this, ciliates need sex. Furthermore, I'll argue that sex was a prerequisite for such a ridiculous genomic system to evolve in the first place -- frequent sex allowed their genomes to get loose like that, for it could be easily compensated for by more sex. Perhaps this is what fundies fear under 'sex addiction'? In a way, sex does a wonderful job at screwing up otherwise perfectly self-sufficient organisms. So yeah, they're right, sex is a sin. Remember the poor barnacles? Divine punishment.

On the topic of impure deviations and dirty sex, ciliates have been observed having orgies. Like the more familiar fungi, ciliates too have multiple mating types, and avoid breeding with their own. If you have a culture with, say, three mating types, you may, occasionally, see orgies of three (rarely four) organisms. Even when such orgies do occur, most often they feature a pair of ciliates conjugating, while the third kind of sits there sadly and has sex with itself. Literally (autogamy)*. (Chen 1940 PNAS)

The big solid black things are MACs, the things undergoing meiosis are the smaller germline nuclei, which are about to be exchanged. Don't you feel sorry for the poor little guy who got left out? =( (Chen 1940 PNAS)

However, sometimes they can arrange themselves into a circle and pass around the pronuclei in a circular fashion. A true triple conjugation where all the participants can get their fair share:

Wheee - a circular orgy! I suspect there may be enough material for a ciliate Kama Sutra out there... (Preparata & Nanney 1977 Chromosoma)

They also had ways to induce massive group copulation (I guess also orgies, to some extent) using a sex-inducing mystery fluid; which caused massive autogamy sprees in populations of a single mating type -- Chen (1945) proposes it was actually a 'killer', toxic substance secreted by bacterial endosymbionts which render their host immune, and kill off everything else (I don't think they knew about the endosymbionts yet at the time). Basically, their defense response to the threat of death seems to be...having sex.

I think I've just ruined ciliates for you too. You're welcome ^_^

Note: Nice picture of ciliate triple conjugation on its way when I finally scan this Russian paper I 'had' to order through the library...

*When it gets too old and still solitary and mateless, the ciliate can also cure that by having sex with itself. Ciliate microbial sex life would be an awesome topic for a popular book...

References
Chen, T. (1940). Conjugation of Three Animals in Paramecium bursaria Proceedings of the National Academy of Sciences, 26 (4), 231-238 DOI: 10.1073/pnas.26.4.231

Chen, T. (1945). Induction of Conjugation in Paramecium bursaria Among Animals of One Mating Type by Fluid from Another Mating Type Proceedings of the National Academy of Sciences, 31 (12), 404-410 DOI: 10.1073/pnas.31.12.404

Hoch, J., & Yuen, B. (2009). An Individual Barnacle, Semibalanus balanoides, with Two Penises Journal of Crustacean Biology, 29 (1) DOI: 10.1651/08-3037.1

Preparata RM, & Nanney DL (1977). Cytogenetics of triplet conjugation in Tetrahymena: origin of haploid and triploid clones. Chromosoma, 60 (1), 49-57 PMID: 870290

I've wondered about this too...

In this week's Nature:

"Overzealous use of decimal places has wrong kind of impact"
by J. M. D. Coey 23 Sep 2009

"Scientists teach students to evaluate critically the significance of their measurements, and to eschew meaningless decimal places thrown up when pocket calculators work out a quotient of two integers. So what are we to make of the recently released impact factors, including Nature's much advertised rating of '31.434' (see also http://www.nature.com/nature/about)? Has Thomson Reuters discovered a protocol that allows it to measure the impact of a journal with an accuracy of 32 p.p.m.?

Quoting this figure conveys the wrong impression — that innumerate marketing is trumping common sense at the heart of science's leading journal."

So what does a thousandth of an impact factor rating look like anyway? Also, how much does Thomson Reuters charge per point? ^_^

Butterfly = Worm + Insect (2009, PNAS)

Shit, is it really that easy to get published? Seriously, what the fuck:

Caterpillars evolved from onychophorans by hybridogenesis
PNAS 2009 AOP

I reject the Darwinian assumption that larvae and their adults evolved from a single common ancestor. Rather I posit that, in animals that metamorphose, the basic types of larvae originated as adults of different lineages, i.e., larvae were transferred when, through hybridization, their genomes were acquired by distantly related animals. “Caterpillars,” the name for eruciforms with thoracic and abdominal legs, are larvae of lepidopterans, hymenopterans, and mecopterans (scorpionflies). Grubs and maggots, including the larvae of beetles, bees, and flies, evolved from caterpillars by loss of legs. Caterpillar larval organs are dismantled and reconstructed in the pupal phase. Such indirect developmental patterns (metamorphoses) did not originate solely by accumulation of random mutations followed by natural selection; rather they are fully consistent with my concept of evolution by hybridogenesis. Members of the phylum Onychophora (velvet worms) are proposed as the evolutionary source of caterpillars and their grub or maggot descendants. I present a molecular biological research proposal to test my thesis. By my hypothesis 2 recognizable sets of genes are detectable in the genomes of all insects with caterpillar grub- or maggot-like larvae: (i) onychophoran genes that code for proteins determining larval morphology/physiology and (ii) sequentially expressed insect genes that code for adult proteins. The genomes of insects and other animals that, by contrast, entirely lack larvae comprise recognizable sets of genes from single animal common ancestors.

This? In PNAS of all places?

Basically, worm hybridised with insect to make grub-like larval forms. Yeah. I thought "k, maybe the paper itself may have some data, or something", and even VPN'd to get it. It actually wasn't really worth it. At all. There was nothing of substance there .I expected some grotesquely misinterpreted data. It was disappointing: a few drawings pointing out the visual similarities (very robust methodology, especially for constructing phylogenetic trees. Absolutely failproof.), some rather sketchy-looking tree I was too lazy to figure out in the 2min I could spare for that paper. And discussiony-looking text. Kinda reminiscent of a certain creationist 'journal' we do not speak of in fear of death by laughter...


Via Musings of The Mad Biologist, wherein the paper is gently chewed up (could be worse). I really like the phrase 'clusterfuck of genes'. I'll be sure to steal it when necessary. Because that's really the only argument you need against this paper. And also, genes don't work like that. Really, they don't.

Come to think of it, neither does evolution. Or decent science.