Near-death, rehashed

The story so far: Mario Beauregard published a very silly article in Salon, claiming that Near-Death Experiences (NDEs) were proof of life after death, a claim that he attempted to support with a couple of feeble anecdotes. I replied, pointing out that NDEs are delusions, and his anecdotal evidence was not evidence at all. Now Salon has given Beauregard another shot at it, and he has replied with a “rebuttal” to my refutation. You will not be surprised to learn that he has no evidence to add, and his response is simply a predictable rehashing of the same flawed reasoning he has exercised throughout.

In his previous sally, he cited the story of Maria’s Shoe, a tall tale that has been circulating in the New Age community for decades, always growing in the telling. This story is the claim that a woman with a heart condition was hospitalized, and while unconscious with a heart attack, her spirit floated out of the coronary care unit to observe a shoe on a third-floor ledge. As has been shown, she described nothing that could not be learned by mundane observation, no supernatural events required, and further, that the story is peculiarly unverifiable: “Maria” cannot be found, not even in the hospital records, and no one has been found who even knew this woman. The entire story is hearsay with no independent evidence whatsoever.

Beauregard attempts to salvage the story by layering on more detail. The description of the shoe was very specific, he says, right down to the placement of the laces and the pattern of wear, and she could not possibly have learned this by overhearing staff talking about it because “it would have been difficult for Maria to understand the location of the shoe in the hospital and the details of its appearance because she spoke very little English.” This is a curious observation; the claim is that she could not understand a description of the shoe, but she was able to describe the shoe herself to a woman, Kimberly Clark Sharp, who did not understand Spanish.

“When I got to the critical-care unit, Maria was lying slightly elevated in bed, eyes wild, arms flailing, and speaking Spanish excitedly,” recounts Sharp. “I had no idea what she was saying, but I went to her and grabbed her by the shoulders. Our faces were inches apart, our eyes locked together, and I could see she had something important to tell me.”

The question isn’t whether a seriously ill woman with poor command of English could see the shoe; it’s whether a healthy, ambulatory, English-speaking woman who has made a career out of the myth of NDEs could see the shoe. Beauregard’s additions to the anecdote do not increase its credibility at all.

Beauregard adds another anecdote to the litany, the story of another cardiac patient who was resuscitated and later recounted seeing a particular nurse while his brain was not functional. Seriously — more anecdotes don’t help his case. He threatens to have even more of these stories in a book he’s in the process of publishing, but there’s no point. He could recite a thousand vague rumors and poorly documented examples with ambiguous interpretations, and it wouldn’t salvage his thesis.

This new anecdote is more of the same. The patient is comatose and with no heart rhythm when brought into the hospital; over a week later, he claims to recognize a particular nurse as having been present during his crisis, and mentions that she put his dentures in a drawer.

I am underwhelmed. I must introduce Beauregard to two very common terms that are well understood in the neuroscience community.

The first is confabulation. This is an extremely common psychological process in which we fill in gaps in our memory with fabrications. I described this in my previous response, but Beauregard chose to disregard it. The patient above has a large gap in his memory, but he knows that he existed in that period, and something must have happened; he knows that he was resuscitated in a hospital, so can imagine a scene in which he was surrounded by doctors and nurses; he knows that his dentures are missing, so he suspects that someone put them somewhere, likely one of the people surrounding him during the emergency. So his brain fills in the gap with a plausible narrative. This whole process is routine and unsurprising, and far more likely than that his mind went wandering away from his brain.

The second term is confirmation bias. Only positive responses that confirm Beauregard’s expectations are noted. The patient guessed that a nurse he met during his routine care was also present during his episode of unconsciousness, and he was correct. What if he’d guessed wrongly? That event would be unexceptional, nobody would have made note of it, and Beauregard would not now be trotting out this incident as a vindication of his hypothesis. This is one of the problems of building a case on anecdotes; without knowledge of the range and likelihood of various results, one can’t distinguish the selective presentation of chance events from a measurable phenomenon.

While unaware of basic concepts in science, Beauregard seems to readily adopt the most woo-ish buzzwords. His explanation for this purported power of the mind to exist independently of any physical substrate is, unfortunately and predictably, quantum mechanics. Every charlatan in the world seems to believe that attaching “quantum” to a word makes it magical and powerful and unquestionable. I have to accept Terry Pratchett’s rebuttal: “‘Let’s call it Quantum!’ is not an explanation.” And neither is Beauregard’s feeble insistence that the universe possesses quantum consciousness, that psychic powers represent quantum phenomena, or that there is an infinitely loving Cosmic Intelligence.

Beauregard then accuses me of having an ideological bias, and that I’m a fanatical fundamentalist. He, of course, is the dispassionate, objective observer with no axe to grind, only interested in reporting the scientific facts. Unfortunately, his book The Spiritual Brain reveals to the contrary that he has some very, very strange beliefs.

“Individual minds and selves arise from and are linked together by a divine Ground of Being (or primordial matrix). That is the spaceless, timeless, and infinite Spirit, which is the ever-present source of cosmic order, the matrix of the whole universe, including both physics (material nature) and psyche (spiritual nature). Mind and consciousness represent a fundamental and irreducible property of the Ground of Being. Not only does the subjective experience of the phenomenal world exist within mind and consciousness, but mind, consciousness, and self profoundly affect the physical world…it is this fundamental unity and interconnectedness that allows the human mind to causally affect physical reality and permits psi interaction between humans and with physical or biological systems. With regard to this issue, it is interesting to note that quantum physicists increasingly recognize the mental nature of the universe.”

If I am an ideologue, it’s only in that I demand that if you call something science, it bear some resemblance in method and approach to science, not mysticism. Beauregard insists on trying to endorse the babbling piffle above as science by reciting the number of publications he has made, and how much grant money he’s got, when I’m looking for verifiable, reproducible, measurable evidence.

I would also remind him that Isaac Newton, who was probably an even greater scientist than the inestimable Beauregard, wasted much of his later years on mysticism, too: from alchemy and the quest for the Philosopher’s Stone, to arcane Biblical hermeneutics, extracting prophecies of the end of the world from numerological analyses of Revelation. While his mechanics and optics have stood the test of time, that nonsense has not. That his mathematics and physics are useful and powerful does not imply that he was correct in his calculation that the world will end before 2060 AD; similarly, Beauregard’s success in publishing in psychiatry journals does not imply that his unsupportable fantasies of minds flitting about unfettered by brains is reasonable.

(Also on Sb)

Clitoral kludges

My favorite argument against Intelligent Design is the fact that the clitoris is located nowhere near the cervix — for women, reproduction and recreation are fairly effectively uncoupled. But that doesn’t stop some people from imagining the existence of a vaginal source of sexual pleasure, the G-spot. I don’t believe it exists; I do believe that individuals can be sexually stimulated by contact in all kinds of places, from vagina to toes to neck to belly-button, that it varies from person to person, and that you don’t need to find an excuse in sloppy anatomy to justify what makes you feel good.

But I also think it’s an interesting example of chance and contingency in evolution. It would optimize the likelihood of reproduction if women could only find sexual gratification by stimulation deep in the vaginal canal — they’d be more likely to encourage sexual penetration. But the homologous tissue to the penis in women is the clitoris, which is in a fine position for creative external stimulation, but less than optimal for stimulation during intercourse. It’s location is clearly the result not of selection for the function of encouraging female orgasm during reproduction, but as a byproduct of selection for males’ interest in penetration during sex (females have sensitive clitorises because males have sensitive penises), which does enhance reproduction.

So it’s a good article highlighting a weird masculine desire for the vaginal orgasm, but it also illustrates that a fortuitous feature of female anatomy isn’t there for baby-making: it’s there for fun. O happy kludge, I’m so glad you’re there.

Modular gene networks as agents of evolutionary novelty

A while back, I told you all about this small piece of the biochemistry of the fly eye — the pathways that make the brown and red pigments that color the eye.

I left it with a question: if even my abbreviated summary revealed considerable complexity, how could this pathway evolve? Changing anything produces a failure or change in the result. Before I answer, let’s make the problem even harder, because I love a challenge (although actually, I’m cheating — it’s going to turn out that complexity is not a barrier, but an opportunity).

The pigment pathways above are far downstream: they operate in the differentiated compound eye of the fly. Long before that, there are a set of genes that have to be activated first to trigger formation of the head and eye in the larva. And this is that pathway:

Regulatory scheme on the top of the eye developmental pathway. Twin of eyeless (toy), eyeless (ey), and possibly eyegone (eyg), three Pax genes, are master control genes on the top of the hierarchy. Sine oculis (so), eyes absent (eya), dachshund (dac), and optix are second-order transcription factors regulated by the master control genes. Note that the pathway is not linear, but rather a network interconnected by feedback loops.

At the top of the hierarchy are two genes in Drosophila, eyeless (ey) and twin of eyeless (toy). Remember, genes are named for their mutant effect, so the normal function of eyeless is to initiate eye development. These genes switch on sine oculis and eyes absent (notice the effort to find synonyms to describe genes that cause missing eyes when broken) that activate each other and feed back on eyeless to generate a robust response. Another gene, dachshund (this one named for another part of its phenotype: it makes flies with very short legs) also feeds back on eyeless.

This circuit has multiple outputs: so, dac, optix and eyg. All of these have effects further downstream, in that catch-all category labeled “eye development” here. In that broad label lie multiple processes: the pigment pathways above, but also all kinds of elaborate interactions that recruit cells to specific photoreceptor functions, that organize supporting cells, like hair cells and lenses, and that induce the neural tissue of the retina and deeper parts of the nervous system. The genes ey and toy initiate a whole deep, branching network of genes that cascade together to build the many bits and pieces of the eye.

These two master control genes, eyeless and twin of eyeless, also have a synonym. To everyone’s surprise, versions of this circuit are found in all animals with eyes, and the common name for this universal regulator of eye formation is Pax6, and that’s what I’ll call it in the rest of this article.

And look at this! Isn’t it cool? All these eyes use this same Pax6 gene regulatory network to initiate development.

General scheme of eye evolution. The first step in eye evolution is the evolution of a light receptor molecule which in all metazoans is rhodopsin. In the most ancestral metazoa, the sponges, a single Pax gene, but no opsin gene has been found. In the cubozoan jellyfish Tripedalia, a unicellular photoreceptor has been described in the larva. The adult jellyfish has complex lens eyes that form under the control of PaxB, whereas the eyes of a hydrozoan jellyfish (Cladonema) are controlled by PaxA. We propose that from the unicellular photoreceptor cell, the prototypic eye postulated by Darwin originated by a first step of cellular differentiation into a photoreceptor cell and a pigment cell, controlled by Pax6 and MITF, respectively. From this prototype, all the more complex eye types arose monophyletically. As a mechanism, we propose intercalary evolution of progressively more genes such as lens genes into the eye developmental pathway (after Gehring and Seimiya 2010). Starting from the common prototype, the various eye types evolved by divergent, parallel, and convergent evolution, generating a magnificent biodiversity.

That’s the power of a gene regulatory network. Switch on just one of the key genes, and it recruits all the downstream genes and triggers a whole series of actions to assemble a complex structure. That strange grey object to the right is a developing Drosophila wing — the dark fringe is the line of bristles that surround the leading and trailing edges of the fully-formed wing — which has had the Pax6 gene inappropriately expressed in a few cells at the base. Just switching on that one gene has led to the construction of an eye with its red pigment right there, where flies should not have eyes.

The ability to build elaborate organs with a simple switch is a reflection of the modular nature of developmental programs. It also simplifies evolution; small, simple changes can lead to dramatic novelties. Zap, one mutation can lead to an abrupt saltational change.

Now wait a moment, you will say. Suddenly plopping an eye onto a wing sounds disastrous: it really is a kind of hopeful monster, emphasis on “monster”, and is almost always going to be grossly deleterious. This can’t be a viable pathway for evolutionary change, can it? And you’d be right. But what about portions of a pathway? Look back up at the eye development pathway, the second figure in this article. What if you just switched on optix, one of the second-order transcription factors? Then you’d just activate some of the tools of eye construction.

It’s been done. The hideous blob to the left is the nascent antenna of a fruit fly, and optix has been inappropriately switched on…and what do you get? It activates the pigment pathway (that biochemical sequence illustrated in the first image at the top of this page), and it creates a bright red spot on the antenna. This is non-trivial; it means the precursors and transporters are all at work, and all the enzymes in the xanthomattin and drosopterin pathways are doing their job. One switch, and you get a whole hierarchy of genes producing a complex output. This could be one way new traits appear, by redeploying genes from established pathways.

Saying they could isn’t the same as saying they did, of course. But here are a few examples that suggest that eye network genes have been redeployed to create morphological novelties. In Heliconius butterflies, for instance, the red spots on their wings can be traced back to embryonic patterns of expression of optix in the developing wings.

Heliconius butterflies express optix in wing epidermal cells that will produce red ommochrome pigments. A: Heliconius erato. B: Forewing and hindwing patterns from different races of H. erato (top: H. e. petiverana; bottom: H. e. erato). C: Pupal wings expressing optix mRNA in a pattern corresponding to the areas of red pigment in wings depicted in (B).

Even more dramatically, here’s an extinct biting midge preserved in amber, and look at that wing: what was I saying about switching on eye genes inappropriately in the wing would be deleterious? I was wrong. This is an insect with a compound eye growing in its wing.

A. The extinct biting midge, Eohelea petrunkevitchi, with a unique wing organ that resembles the surface of its compound eye. B: The dorsal surface of the wing organ. C: The midge’s compound eye. D: The ventral surface of the wing organ.

It’s extremely unlikely that that alar eye functioned as a visual organ: any photoreceptor signals coming from a platform flapping several times a second would be hopelessly confusing. Most likely what it was was a species-specific sexual signal, like the spots on many fly wings — this one is just more elaborately structured and expensive than most. Alternatively, one hypothesis for the formation of spots on insect wings is that they are intended to resemble eyes — large eyes, far apart, making the animal look much larger to predators — so Eohelea may have just been carrying the eyespot mimicry to an extreme. Either way, building these eyes is developmentally trivial.

It may also represent a transitional state: first the initiator of a genetic cascade is co-opted and expressed at a novel time or place, and then selection can hone it down over time, adding new control points that, for instance, suppress irrelevant ommatidium formation in the alar eye while allowing the functional pigment expression to continue.

One last example: this is the Cambrian worm, Microdictyon. Notice anything unusual?

Microdictyon sinicum, a Cambrian Lobopodian fossil from Chengjiang (China) with compound eye on every annulus (segment) above every leg. (A) Reconsruction (after Bergström and Hou). (B) Lateral view.

There’s a pair of eyes in the head, where you’d expect them…but all those other eyes along the sides are morphologically indistinguishable from the anteriormost pair. There is some argument about whether these structures actually are eyes, but they are definitely hexagonal arrays that closely resemble the hexagonally structured ommatidia of the compound eyes of insects. If they weren’t functional eyes, it seems likely that they are at least produced by the redeployment of the structural genes of the compound eye.

And if they were functional eyes, well, that is just freakin’ cool.

The bottom line, though, is that because complex developmental networks are functionally constrained — think of them as software modules that respond to molecular inputs and produce morphological outputs — their complexity is not a barrier to evolution at all, but instead provide opportunities for generating interesting evolutionary novelties.

Gehring WJ (2012) The animal body plan, the prototypic body segment, and eye evolution. Evolution & Development 14(1):34-36.

Monteiro A (2012) Gene regulatory networks reused to build novel traits. Bioessays 34:181-186.

(Also on Sb)

Now you, too, can be a cephalopedant

You remember all those dinosaur books you read as a kid, page after page listing species, with illustrations? (Wait, you don’t? What was wrong with you?) Well, now you’ve got the same thing for cephalopods, and it’s all free. You can download two volumes in pdf form of a massive catalog of species, all for yourself. Put ‘em on your iPad, and then you can read it under the covers in bed. Hey, I just realized…this generation may be the last to do the ol’ “smuggling books and a flashlight into bed to read past your bedtime” thing — tablets make the whole procedure so much easier.

Here are the two volumes; each is about 20Mb.

Jereb, P.; Roper, C.F.E. (eds) Cephalopods of the world. An annotated and illustrated catalogue of cephalopod species known to date. Volume 1.
Chambered nautiluses and sepioids (Nautilidae, Sepiidae, Sepiolidae, Sepiadariidae, Idiosepiidae and Spirulidae).
FAO Species Catalogue for Fishery Purposes. No. 4, Vol. 1. Rome, FAO. 2005. 262p. 9 colour plates.

This is the first volume of the entirely rewritten, revised and updated version of the original FAO Catalogue of Cephalopods of the World (1984). The present Volume is a multiauthored compilation that reviews six families: Nautilidae, Sepiidae, Sepiolidae, Sepiadariidae, Idiosepiidae and Spirulidae, with 23 genera and the 201 species known to the date of the completion of the volume. It provides accounts for all families and genera, as well as illustrated keys to all taxa. Information under each species account includes: valid modern systematic name and original citation of the species (or subspecies); main synonyms; English, French and Spanish FAO names for the species; illustrations of dorsal and ventral aspect of the whole animal (as necessary) and other distinguishing illustrations; field characteristics; diagnostic features; geographic and vertical distribution, including GIS map; size; habitat; biology; interest to fishery; local names when available; a remarks section (as necessary) and literature. The volume is fully indexed and also includes sections on terminology and measurements, an extensive glossary, an introduction with an updated review of the existing biological knowledge on cephalopods (including fisheries information and catch data for recent years) and a dedicated bibliography.

Jereb, P.; Roper, C.F.E. (eds) Cephalopods of the world. An annotated and illustrated catalogue of cephalopod species known to date. Volume 2.
Myopsid and Oegopsid Squids.
FAO Species Catalogue for Fishery Purposes. No. 4, Vol. 2. Rome, FAO. 2010. 605p. 10 colour plates.

This is the second volume of the entirely rewritten, revised and updated version of the original FAO Catalogue of Cephalopods of the World (1984). The present Volume is a multiauthored compilation that reviews 28 families, i.e. (in alphabetical order), Ancistrocheiridae, Architeuthidae, Australiteuthidae, Bathyteuthidae, Batoteuthidae, Brachioteuthidae, Chiroteuthidae, Chtenopterygidae, Cranchiidae, Cycloteuthidae, Enoploteuthidae, Gonatidae, Histioteuthidae, Joubiniteuthidae, Lepidoteuthidae, Loliginidae, Lycoteuthidae, Magnapinnidae, Mastigoteuthidae, Neoteuthidae, Octopoteuthidae, Ommastrephidae, Onychoteuthidae, Pholidoteuthidae, Promachoteuthidae, Psychroteuthidae, Pyroteuthidae and Thysanoteuthidae, with 83 genera and the 295 species known and named to the date of the completion of the volume. It provides accounts for all families and genera, as well as illustrated keys. Information under species accounts includes: valid modern systematic name and original citation of the species (or subspecies); synonyms; English, French and Spanish FAO names for the species; illustrations of dorsal and ventral aspects of the whole animal (as necessary) and other distinguishing illustrations; field characteristics; diagnostic features; geographic and vertical distribution, including GIS map; size; habitat; biology; interest to fishery; local names when available; a remarks section (as necessary) and literature. The Volume is fully indexed and also includes sections on terminology and measurements, an extensive glossary, an introduction with an updated review of the existing biological knowledge on squids (including fisheries information and main catch data for recent years) and a dedicated bibliography. Due to the conspicuous amount of literature addressing many squid species, an appendix is included in the online version, where those references considered most pertinent to the species are listed, by family and species, in alphabetical order by author; key words, also, are reported.

There. Now everybody should be happy.

More juicy stuff for Minnesotans

Sorry, all you foreigners who don’t live in an awesome state like Minnesota, but I have to mention another cool local series of events. The Hennepin County Library is sponsoring DNA Day, with multiple opportunities to learn about genetics, genetic diseases, cancer genetics, and genetic family trees. I don’t know why it’s called DNA Day, though, because they have multiple events spread out between 19 April and 1 May at various libraries around Minneapolis. There is limited space, so registration is required (these events are free, though), and you’d better get in there fast.