Love in Afghanistan

Spring is in the air! Young hearts turn to thoughts of love, and romance flowers everywhere, even in the darkness of Taliban-ruled Afghanistan. A young couple there, their union frowned upon by their families, eloped to marry anyway, a gesture I find wonderfully romantic and sweet. I’m a little biased — my own parents were discouraged from marrying by their families, and they too ran off to marry without permission (in liberal Idaho, in their case). I wouldn’t be here without youthful affection and passion!

Alas, no such happy result comes from a region poisoned by fanatical Islam. Mullahs seized the rebellious couple, issued a religious decree, and had them shot on the street in front of a mosque, symbol of their religion of peace.

I think the true symbol of their religion should be a pair of bloody corpses, dreams dead, hopes destroyed, all joy crushed.

Spring will still come and the poppies will blossom, and the air will warm and the sun will shine—but where is the meaning of it all when minds are shackled and love is shunned, when happiness is replaced with regimented dogmatism? A season of rebirth should be accompanied by an expansion of ideas and feelings and human connections, not repression. There can be no springtime for the Taliban, except as a series of dates on a calendar.

Atheist calls Christians “non-human”, commits murder

Oh, wait — I got the headline backwards. The real story is that a mentally disturbed, fanatical Christian/creationist and misogynist, went nuts, killed a young woman on a community college campus, and then killed himself. It’s a tragedy, but not at all exceptional, I’m afraid — the man was delusional and depressed, apparently frustrated that women weren’t obedient to him, and he decided to erupt into hateful violence.

The disturbing twist this time, though, is that the killer was a youtuber — and a big fan of VenomFangX, the infamously vapid creationist. You can see some of his pre-suicidal rants preserved for posterity, and they will make you wonder why he wasn’t getting psychiatric help. And yes, the lunatic does literally accuse atheists of being non-human and evil, but that doesn’t seem to have been the trigger for his break from reality…that seems to have stemmed more from his proprietary feelings towards women.

Ignorant old fuddy-duddy finds god, doesn’t like atheists or evolutionists anymore

It’s an article about yet another Christian who was once an atheist, telling us how awful and unfulfilling life was until he found Jebus. The guy is a fool, and just to spice it up, they threw in…a poll! A poll that needs fixing!

Should creationism have a place in the curriculum?

54% are saying yes
46% are saying no

So fix it already. Go ahead and leave a comment there, too, although the comments so far all seem to be going our way anyway.

Snails have nodal!

i-e88a953e59c2ce6c5e2ac4568c7f0c36-rb.png

My first column in the Guardian science blog will be coming out soon, and it’s about a recent discovery that I found very exciting…but that some people may find strange and uninteresting. It’s all about the identification of nodal in snails.

i-9814996ee90947e59439af12f03a03db-nodal_guts.jpg

Why should we care? Well, nodal is a rather important — it’s a gene involved in the specification of left/right asymmetry in us chordates. You’re internally asymmetric in some important ways, with, for instance, a heart that is larger on the left than on the right. This is essential for robust physiological function — you’d be dead if you were internally symmetrical. It’s also consistent, with a few rare exceptions, that everyone has a stronger left ventricle than right. The way this is set up is by the activation of the cell signaling gene nodal on one side, the left. Nodal then activates other genes (like Pitx2) farther downstream, that leads to a bias in how development proceeds on the left vs. the right.

In us mammals, the way this asymmetry in gene expression seems to hinge on the way cilia rotate to set up a net leftward flow of extraembryonic fluids. This flow activates sensors on the left rather than the right, that upregulate nodal expression. So nodal is central to differential gene expression on left vs. right sides.

i-21bda85fe662c24fe34efc609dcbf4ac-nodal_cilia.jpg

What about snails? Snails are cool because their asymmetries are just hanging out there visibly, easy to see without taking a scalpel to their torsos (there are also internal asymmetries that we’d need to do a dissection to see, but the external markers are easier). The assymetries also appear very early in the embryo, in a process called spiral cleavage, and in the adult, they are obvious in the handedness of shell coiling. We can see shells with either a left-handed or right-handed spiral.

i-d03d89cba8e1ae44e04152b3d93bf105-nodal_spiral.jpeg
(Click for larger image)
Chirality in snails. a, Species with different chirality: sinistral
Busycon pulleyi (left) and dextral Fusinus salisbury (right). b, Sinistral (left)
and dextral (right) shells of Amphidromus perversus, a species with chiral
dimorphism. c, Early cleavage in dextral and sinistral species (based on ref.
27). In sinistral species, the third cleavage is in a counterclockwise direction,
but is clockwise in dextral species. In the next divisions the four quadrants
(A, B, C and D) are oriented as indicated. Cells coloured in yellow have an
endodermal fate and those in red have an endomesodermal fate in P. vulgata
(dextral)15 and B. glabrata (sinistral)28. L and R indicate left and right sides,
respectively. d, B. glabrata possesses a sinistral shell and sinistral cleavage
and internal organ organization. e, L. gigantea displays a dextral cleavage
pattern and internal organ organization, and a relatively flat shell
characteristic of limpets. Scale bars: a, 2.0 cm; b, 1.0 cm; d, 0.5 cm; e, 1.0 cm.

Until now, the only organisms thought to use nodal in setting up left/right asymmetries were us deuterostomes — chordates and echinoderms. In the other big (all right, bigger) branch of the animals, the protostomes, nodal seemed to be lacking. Little jellies, the cnidaria, didn’t have it, and one could argue that with radial symmetry it isn’t useful. The ecdysozoans, animals like insects and crustaceans and nematodes, which do show asymmetries, don’t use nodal for that function. This suggests that maybe nodal was a deuterostome innovation, something that was not used in setting up left and right in the last common ancestor of us animals.

That’s why this is interesting news. If a major protostome group, the lophotrochozoa (which includes the snails) use nodal to set up left and right, that implies that the ecdysozoans are the odd group — they secondarily lost nodal function. That would suggest then that our last common ancestor, a distant pre-Cambrian worm, used this molecule in the same way.

Look in the very early mollusc embryo, and there’s nodal (in red, below) switched on in one or a few cells on one side of the embryo, the right. It’s asymmetrical gene expression!

i-6daa81c2edebfc143fde371c4849c1cf-nodal_early_exp.jpeg
(Click for larger image)
Early expression of nodal and Pitx in snails. a, 32-cell stage L.
gigantea expressing nodal in a single cell. b, Group of cells expressing Pitx in
L. gigantea. c, Onset of nodal expression in B. glabrata. d, A group of cells
expressing Pitx in B. glabrata. e, 32-cell L. gigantea expressing nodal (red) in
a single cell (2c) and brachyury (black) in two cells (3D and 3c).
f-h, brachyury (black) is expressed in a symmetrical manner in progeny of 3c
and 3d blastomeres (blue triangles in g), thus marking the bilateral axis, and
nodal (red) is expressed on the right side of L. gigantea in the progeny of 2c
and 1c blastomeres, as seen from the lateral (f) and posterior (g, h) views of
the same embryo. i, A group of cells expressing nodal (red) in the C quadrant
and Pitx (black) in the D quadrant of the 120-cell-stage embryo of L.
gigantea. j, nodal (red) and Pitx (black) expression in adjacent areas of the
right lateral ectoderm in L. gigantea. L and R indicate the left and right sides
of the embryo, respectively. The black triangle in b and i, the green, yellow
and pink arrows in f and i, and the black and pink arrows in f and h point to
the equivalent cells. Scale bars: 50µm.

Seeing it expressed is tantalizing, but the next question is whether it actually does anything in these embryos. The test is to interfere with the nodal-Pitx2 pathway and see if the asymmetry goes away…and it does, in a dramatic way. There is a chemical inhibitor called SB-431542 that disrupts this pathway, and exposing embryos to it does interesting things to the formation of the shell. In the photos below, the animal on the left is a control, and what you’re seeing is a coiled shell (opening to the right). The other two views are of an animal treated with SB-431542…and look! Its shell doesn’t have either a left- or right-handed twist, and instead extends as a straight tube.

i-055b648d0eaf32f767e5cc31f9f9a19b-nodal_shell.jpeg
(Click for larger image)
Wild-type coiled and drug-treated non-coiled shells of B.
glabrata. Control animals
(e) display the normal sinistral shell morphology. Drug-treated animals
(f, g, exposed to SB-431542 from the 2-cell stage onwards) have straight
shells. f and g show an
individual, ethanol-fixed, and shown from the side (f) and slightly rotated
(g).

What this all means is that we’ve got a slightly better picture of what genes were present in the ancestral bilaterian animal. It probably had both nodal and Pitx2, and used them to build up handedness specializations. Grande and Patel spell this out:

Although Pitx orthologues have also been identified in non-deuterostomes such as Drosophila melanogaster and
Caenorhabditis elegans, in these species Pitx has not been reported in
asymmetrical expression patterns. Our results suggest that asymmetrical expression of Pitx might be an ancestral feature of the bilaterians.
Furthermore, our data suggest that nodal was present in the common
ancestor of all bilaterians and that it too may have been expressed
asymmetrically. Various lines of evidence indicate that the last common ancestor of all snails had a dextral body. If this is true, then our
data would suggest that this animal expressed both nodal and Pitx on
the right side. Combined with the fact that nodal and Pitx are also
expressed on the right side in sea urchins, this raises the possibility
that the bilaterian ancestor had left-right asymmetry controlled by
nodal and Pitx expressed on the right side of the body. Although
independent co-option is always a possibility, the hypotheses we present can be tested by examining nodal and Pitx expression and function in a variety of additional invertebrates.

It’s also, of course, more evidence for the unity of life. We are related to molluscs, and share key genes between us.

Grande C, Patel NH (2009) Nodal signalling is involved in left-right asymmetry in snails. Nature 457(7232):1007-11.

Registration now required to comment

I hated doing this, but it has become necessary. You now have to register with an off-site authentication service in order to leave a comment here. It’s not hard; just follow the links at the Typekey page, and it should sail through and let you comment freely afterwards. (In theory, you should also be able to use OpenID authorization — I’ve toggled it on in the Pharyngula master control panel, let me know if it works).

In other news, you are a cruel bunch, and the overall response to my Pilate-like offer to turn the responsibility of banning Alan Clarke over to you was that most of you declined to shut him down, the reaction that he himself argued would be most civil. He has a temporary reprieve now, although if he keeps whining that goddidit I may smite him anyway. The argument most often given for sparing him is that he is a really good training dummy — he makes truly stupid arguments that inspire informative rebuttals — so I expect you to continue to abuse him in that tradition.

John Maddox dead at 84

I’m sad to report that John Maddox, former editor of Nature, has died. He was one of those fellows who shaped the direction of science for quite a long period of time with the power of one of the most influential science journals in the world.

I suspect every scientist of my generation read his editorials in our weekly perusal of the journal. The one I remember most vividly, and probably the one that got the most attention in general, was his ferocious denunciation of Rupert Sheldrake’s work — he went so far as to say that if ever there was a book suitable for burning, it was that one. So of course, I had to read it (that’s one of the pitfalls of calling for the destruction of books). And then, also of course, I discovered that Maddox was right on the money — that book was an astonishing pile of B.S. masquerading as science, and it’s true that Sheldrake is still peddling his nonsense.

We’ve lost a vigorous skeptic and humanist.

Where a troll comes from

As many of you know, Alan Clarke is a fundamentalist/creationist kook who has been babbling in the comments for a while now. A reader alerted me to how Clarke found his way here: he was posting his silliness on a powerbasic support forum, and was warned that we would “kick his butt” if he came here. He’s just as obtuse there as he is here, so nothing has changed…and yes, his butt has been kicked up and down the threads here.

This is no big deal, and completely unsurprising, but Clarke left one comment there that made me think.

I took your advice and have been hanging out on the Pharyngula site:

Thread 1
Thread 2

Bob Zale would have shut these threads down long ago for the abusive language. I appreciate him even more when his civility is contrasted to that of P.Z. Myers’.

That last paragraph is…enlightening. Mr Clarke seems to think that civility is equivalent to silencing argument, and that I would be more civil if I had shut down the discussion. Interesting. It raises a conundrum that my poor brain cannot resolve; I had thought that it was better that I allow Mr Clarke to continue his ignorant ravings without taking a hand, but apparently Mr Clarke himself thinks that was uncivil.

So, I leave it to the readers. Shall I be civil and boot Clarke’s badly bruised butt from the site entirely, or should I be abusive and allow him to continue to comment here?

If you’re having trouble deciding, too, just follow his comments on these pages…I am actually relieved that commenters don’t have the ability to freely insert cartoons and caricatures here, because Mr Clarke can create quite a circus.