Bring back the Shasta ground sloth

Bringing extinct animals back to life is big news this week. Not because there’ve been any particular recent breakthroughs, but because the upcoming issue of National Geographic features the topic as a cover story, and is hosting a related TEDx meeting this Friday in Washington D.C. that’s also sponsored by Stewart Brand’s Long Now Foundation. There’s a Twitter hashtag for the meetup, National Geographic has set up a portal page for the topic (credit Brian Switek for that labor), and the event is driving a lot of traffic to the Long Now site — which is worth checking out, especially its FAQ and its list of criteria for choosing extinct animals to bring back.

But I see no mention of bringing back the extinct animal we actually really need.

[Read more…]

Sadly, it’s International Women’s Day

It’s that day when we’re supposed to celebrate the accomplishment’s of women. I say “sadly,” because unfortunately there are way too many people out there who would rather sneer at and diminish women’s status in the world.

Case in point: on twitter, I ran across this lovely tweet from one of those repugnant slymepitters.

On #IWD remembered the nearly 0 wimmin – Nobels in science, highbrow art, chess GMs, great standups, but 100s of pop-culture hos #ftbullies

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Yes. Let’s remember those women.

Let’s remember Lise Meitner, Hilde Mangold, Chien-Shiung Wu, Rosalind Franklin, and Jocelyn Bell — who were all well-qualified (men won the prizes for work equivalent to what they did, instead) to win a Nobel but didn’t get one.

Rather than 0 women, perhaps we should remember Marie Curie and Maria Goeppert Mayer, who won Nobels in physics; Irène Joliot-Curie, Dorothy Crowfoot Hodgkin, and Ada E. Yonath in chemistry; Barbara McClintock, Carol W. Greider, Christiane Nüsslein-Volhard, Elizabeth H. Blackburn, Françoise Barré-Sinoussi, Gertrude B. Elion, Gerty Cori, Linda B. Buck, Rita Levi-Montalcini, and Rosalyn Yalow, in physiology or medicine. Clearly women are not intrinsically incapable of scientific work at the highest levels. Of those whose work I’m familiar with in detail, I have to tell you that McClintock blows me away with the stunning brilliance of her abstract reasoning — I know of no other male scientist whose work is at all comparable (that of course is a matter of taste!)

The relatively lower frequency of women recieving Nobels is not something any man should take pride in; what it really indicates is that we’ve been shortchanging half the human population, depriving them of opportunities to excel. Wait — we’ve been doing worse than shortchanging women; we’ve been depriving all of humanity of the potential in those minds. This pattern of discrimination against women has hurt us all.

Let’s not forget also all the people, men and women alike, deprived of opportunities because of their race or class — deprived by the kind of endemic bigotry that would, for instance, denigrate an entire group of people as “pop-culture hos”. And it’s not just science — it was good of our petty MRA to remind us that we’ve also lost their contributions to art and theater and games.

That’s what I think of everytime some bigot crows about the absence of some group of people from some field of endeavor — it’s a reminder of all that we’ve lost to selfish stupidity.

Damsel in Distress

Anita Sarkeesian has released the first of her series on sexist tropes in video games.

I notice that the comments on the youtube video are disabled. I wonder why?

No, I actually don’t.

Rebecca Watson points out something interesting. In all the noise surrounding Sarkeesian’s initial campaign to raise money (you don’t need that much cash to make youtube videos, it’s a biased project, Sarkeesian is a &$@##$&, etc.), a competing group tried to raise money to produce an alternative series of videos on male tropes in video games…which I think would be an excellent idea, actually. Men are also subject to sexist stereotypes in games.

Only one problem: The men behind the male tropes proposal seem to have absconded with the money, and even apparently photoshopped fake charitable donation receipts. Whoops.

I remember that poster!

Back in the dim dark distant days of yore, Matt Groening actually did some promotional artwork for Apple — all at about the same time he started up with some little show called the Simpsons, and when he’d apparently doodle up a poster for them for the price of a Laserwriter.

Bongos-Dream-Dorm-aopg

Speaking of Groening and the Simpsons, Richard Dawkins will be making a cameo voice appearance this Sunday. Tune in!

What’s Jimmie Walker’s favorite arthropod?

“TRI-LO-BIIITE!”

Oh, no, that was a terrible opening. You’ll only know what the heck I’m talking about if you remember JJ from the television show Good Times, and it’s such a pathetic joke it’s only going to appeal to grade schoolers. So if you’re a time-traveling 8 year old from the 1970s, you’ll appreciate the reference. How many of those are reading this right now?

Maybe this will work better. Here’s a small chip of shale I keep at my desk.

trilobite

My son Alaric and I collected that on a trip to Delta, Utah over 20 years ago. We had permission from the owner of a commercial dig site to rummage around in their tailings*, and we ambled about picking up chunks of rock and splitting them with a hammer. Everywhere we looked were trilobites. We brought home a good haul, chiefly Elrathia, like that one, and lots of Peronopsis. I keep it at my desk as a token of a good memory, and also because it’s about half a billion years old.

I can reach over and touch a half billion year old fossil at will, which I find to be an awesome thrill. That it’s also from a subphylum that was so successful, swarming in our oceans for about 300 million years, yet that ended so finally in the Permian extinction, is humbling. Puny ephemeral humans — we can only dream of achieving the glories of the Trilobite empire.

trilobiterichness
Summary of the evolutionary history of the major trilobite clades plotted against stratigraphic time. The y-axis scale approximates a log scale to permit the more detailed illustration of the Cambrian and Ordovician diversifications. Numbers refer to age in millions of years (Ma). Although the spread along the x axis approximates the morphological diversity within a clade at any given stratigraphic level, horizontal distances between groups should not be interpreted to suggest degrees of phenetic difference. The diagram is not meant to imply that maximal phenetic variance was present in the early part of the Cambrian, even though groups such as Agnostida and Corynexochida form the extremes along the x axis. This is an artifact of the mode of representation. Trilobite color represents the condition of dorsal exoskeletal trunk tagmosis: orange is the homonomous condition, pink is the heteronomous condition in which the batch boundary occurs within the holaspid thorax, blue is where this boundary occurs within the holaspid pygidium, and green where it occurs at the thoracic/holaspid pygidial boundary. The representation is schematic and not meant to imply that all members of these clades younger than the image shown had that condition.

If you want to learn more about trilobites, I can’t recommend Richard Fortey’s book, Trilobite: Eyewitness to Evolution, highly enough. It’s an excellent, enthusiastic, readable overview of the group. There’s also a gorgeous online guide to the orders of trilobites that’s full of fossil photos and detailed information. But I also recently stumbled across a review paper by Nigel Hughes that looked at them from the perspective of development — O Rhapsody! It’s beautiful!

Despite being extinct for 250 million years, and despite being nothing but fossils, we still have a pretty good idea of the development of trilobites, because they were so numerous and we can find great drifts of entire populations of the animals embedded in lagerstätten. That allows us to see the range of variation and the distribution of different developmental stages, and further, because they’re arthropods, we can see well preserved cuticles of both intact animals and molted shells. And with almost 300 million years of recorded species, we’ve also got a good picture of their evolution. This is a classic evo-devo story.

So, quick, here’s a general introduction to trilobite anatomy. First thing to know is that the ‘three lobes’ of the word ‘trilobite’ refer to the longitudinal divisions of the animal: a central axis with a lateral or pleural lobe on either side of it. There are also, usually, three transverse divisions: cephalic (head) segments, thoracic segments in the middle, and a pygidium or tail.

trilobiteanat
Basic anatomy of the dorsal surface of two trilobites. (Left panel ) The figure is based on a generalized olenelloid trilobite, which had a boundary between two distinct or heteronomous batches of segments located within the thorax, dividing the protrunk from the opisthotrunk. (Right panel ) Aulacopleura konincki displayed the homonomous trunk condition in which all trunk segments shared a similar morphology. A, anterior; Opi, opisthotrunk; P, posterior; Pyg, pygidium.

Not usually shown are the limbs. If you flip over a trilobite, you discover that each segment, except the anterior- and posterior-most, has a pair of biramous appendages — they’re branched legs, with one branch functioning as the walking limb, and the outer branch being lamellate (thin and flat) and probably functioning as a gill. They’re surprisingly uniform and consistent in general structure, from head to thorax to pygidium. One of the curious features of trilobites is that most species are marked by this homonomous condition (that is, maintaining identity or close similarity between adjacent segments), while most of the extant arthropods are strongly heteronomous, making strong distinctions in the structure of adjacent segments.

trilobiteseg
Major divisions of the anterior-posterior (a-p) body axis in trilobites. The letter M indicates an individualized segment morphotype. Colors indicate major morphological divisions along the axis, with shading approximating the degree of morphological difference between adjacent segments. Segments in red are cephalic, those in light blue are thoracic, those in dark blue are pygidial, and the terminal piece is in purple. Thoracic segments articulate with one another, whereas those in the cephalon and pygidium are conjoined.

Now here’s the cool bit: a generalized staging series for trilobites. There are some broad terms for different stages — protaspid, then meraspid, then holaspid — but this diagram makes it clear that growth was by sequential addition of new segments to the posterior end of the animal. This is not an unusual pattern: vertebrates also build segments sequentially from front to back, as do many insects (the short germ band insects), but others, long germ band insects like flies, build the whole collection nearly simultaneously.

trilobitegrowth

Generalized trilobite ontogeny showing the boundaries of ontogenetic stages based on three aspects of the development of trunk segments: generation (Gn), articulation (Art), and morphology (Form). The generation state contains a poorly known initial stage that may have had a constant set of cephalic segments, the anamorphic phase during which new segments appeared in the trunk, and the epimorphic phase after which the exoskeletal segment number was constant despite continued molting. The articulation state is based on dorsal sclerite articulation pattern, with the onset of the protaspid stage marked by the development of the dorsal facial suture, onset of the meraspid stage marked by the onset of trunk articulation, and the onset of the holaspid stage marked by the completion of trunk articulation. The morphology state refers to the form of trunk segments, which in some trilobites are divided into discrete, heteronomous batches of anterior (protrunk) and posterior (opisthotrunk) segments. The site of the appearance of new trunk segments is shown for the first trunk segment only. Segment color scheme as in previous figure. Individualized segments, such as those that bore unusually large axial or pleural spines (i.e., a macrospinous condition), retained the same position relative to the cephalic margin following their first appearance, indicating that the site of appearance of new segments was subterminal, and the boundary between articulating and conjoined segments migrated posteriorly during the meraspid phase.

Development is the foundation of evolutionary change, and I can’t help but wonder how this pattern, and the unknown genetic constraints behind it, affected trilobite evolution. The early history of arthropods seems to be one of exuberant exploration of the potentials of that modular segmental organization, with trilobites tending to be more conservative than other arthropods. What that means is tricky to interpret: the more inventive arthropods still have descendants around, while trilobites are extinct without issue. But 300 million years is still a fantastically good run, and clearly they had the flexibility to survive major changes in geological history.

The real mystery is why the clade as a whole began to decline after the Ordovician, and how the end of the Permian could so thoroughly quench this gigantic group.

Hughes NC (2007) The Evolution of Trilobite Body Patterning. Annu. Rev. Earth Planet. Sci. 35:401–34.

*By the way, I recommend digging in fossil beds as a great way to connect with the history of the planet with your kids. You can’t make it to Delta? There are quarries that will sell you crates of unprocessed rock, 30 pounds for $75, and you can take them apart in your back yard.

Bora 1, Climate Denialist Kooks 0

This is really a thing of beauty: climate pseudoscientist Willis Eschenbach whines at the inadvertent comedy blog Watt’s Up With That that Bora Zivkovic has been moderating comments on his SciAm blog.

Eschenbach, who’s also a Mass Extinction denialist, objects to Bora’s having instituted some basic anti-troll measures at A Blog Around The Clock that relegate comments with certain field marks of the climate denialist loon to the spam bin. Says Bora, in a passage that apparently made Eschenbach’s cranial temperature spike like a Warmist hockey-stick graph:

If I write about a wonderful weekend mountain trek, and note I saw some flowers blooming earlier than they used to bloom years ago, then a comment denying climate change is trolling. I am a biologist, so I don’t write specifically about climate science as I do not feel I am expert enough for that. So, I am gradually teaching my spam filter to automatically send to spam any and every comment that contains the words “warmist”, “alarmist”, “Al Gore” or a link to Watts. A comment that contains any of those is, by definition, not posted in good faith. By definition, it does not provide additional information relevant to the post. By definition, it is off-topic. By definition, it contains erroneous information. By definition, it is ideologically motivated, thus not scientific. By definition, it is polarizing to the silent audience. It will go to spam as fast I can make it happen.

What Eschenbach doesn’t mention, and a basic point of Bora’s post on how trolls derail substantive conversation, is that climate denialism is just the most pernicious and prevalent of a number of kinds of pseudoscience that have afflicted some of the sites on SciAm of late:

I know that I used the example of Global Warming Denialism here the most – mainly because it is currently the most acute problem on our site – but the same goes for people harboring other anti-scientific ideas: creationists, anti-vaxxers, knee-jerk anti-GMO activists, and others.

This post is not about climate denial, it is about commenting and comment moderation. It is about the fact that eliminating trolls opens the commenting threads to more reasonable people who can actually provide constructive comments, thus starting the build-up of your own vigorous commenting community.

There are seven billion people on the planet, many of them potentially useful commenters on your site. Don’t scare them away by keeping a dozen trolls around – you can live without those, they are replaceable.

Eschenbach’s month-late response to Bora’s post is as pure and canonical a paean to the hallowed practice of JAQing off as I have seen. A sample:

I can only bow my head in awe. I mean, what better way is there to keep you from answering people from WUWT and other sites who might want answers to actual scientific questions, than not allowing them to speak at all?… See, Bora, the beauty of your plan is, you don’t even have to think about censorship once you do that. The computer does the hard work for you, rooting out and destroying evil thoughtcrimes coming from … from … well, from anyone associated with Watts Up With That, or with Steven McIntyre’s blog Climate Audit, or anyone that you might disagree with, or who is concerned about “alarmists”, you just put them on the list and Presto!

No more inconvenient questions!

I probably ought to feel sorry for Eschenbach: anyone who would proudly link to a piece like this alleged debunking of extinctions — as opposed to deleting it, salting the earth of the server on which it once resided, and denying under oath that you’d ever heard of the thing — is definitely more properly pitied than mocked. “No continental forest bird or mammal is recorded as having gone extinct from any cause,” Eschenbach says. That’s some Time-Cube-level obliviousness.

But I can’t help snickering, and feeling slyly jealous that Bora was able to elicit a response like that just by mentioning idly that he’s keeping his own comment threads on topic despite a massive campaign by a few fanciers of metallic haberdashery to disrupt them. Well done, my friend. Well done.

Pricing, hell: I’ll never understand airline seating policies

For instance, why do they never give me the seat next to the panda?

pandaplane

 

Must be a smart panda, as it’s sitting in the emergency exit aisle and they only let competent individuals capable of assisting others do that. Remember, in the unlikely event that the oxygen masks are released from the overhead panel, always help the panda affix her mask securely before putting on your own.

Via.

What I taught today: heavy on the epistasis

Today we talked about gap genes and a little bit about pair rule genes in flies, and to introduce the topic I summarized genetic epistasis. Epistasis is a fancy word for the interactions between genes, and we’ve already discussed it on the simplest level. You can imagine that a gene A, when expressed, activates the expression of gene B. The arrow in this diagram? That’s epistasis.

epi1

So far, so simple. This could describe how bicoid activates zygotic hunchback for instance. But of course not all epistatic interactions are linear and one dimensional; often one transcription factor will turn on or repress multiple genes — so A might switch on genes B, C, and D.

epi2

But wait! Now there is the potential for all kinds of combinatorial interactions: maybe C has positive feedback back on A, and B activates D and C, and D activates B, and C represses B. There’s a whole mathematically bewildering world of possibility here.

epi3

And it gets worse and worse. B, C, and D could have downstream effects on other genes, like E, F, G, and H, and each of those interact with each other and can have feedback effects as well. It’s not at all uncommon to be taking apart the sequence of events of a developmental pathway and discover a whole tangled snarl of epistatic interactions that lead to complicated patterns of gene expression.

epi4

And that’s molecular geneticists and developmental biologists do: they try to tease apart the snarl, asking how each gene interacts with all the other genes in the system, working out the kind of genetic circuitry shown in those diagrams. Often the approach is take it one gene at a time: knock out F, for instance, and ask what happens to the expression patterns of A, B, C, D, E, G, and H. Or upregulate D, and ask what all those other genes do. If you like logic puzzles, you’ll love epistatic studies, because that’s what they are: grand complicated logic puzzles with multiple cascading effects and usually only partial knowledge about what each component does. You’ll either have great fun with it all, or cultivate great headaches.

So most of the class hour was spent going through examples of these puzzles. The gap genes, for instance, are expressed in broad stripes in the embryo, and we can try to decipher the rules that establish the boundaries by taking out components. If hunchback is deleted, what do the giant, krüppel, and knirps stripes look like? Take out krüppel, what happens to knirps? So I led them through this series of experiments, asking them to come up with general rules regulating the expression of each stripe, and then using those rules to predict what would happen if we did a different experiment. I think they mostly got it.

But of course the discussion today was mostly about the gap genes, which are the second tier of genetic interactions (analogous to my third figure above). Next I introduced the pair rule genes, the third tier, rather like my fourth diagram. These are genes that are expressed in alternating stripes corresponding to parasegments in the fly…so we’ve gone from a few broad stripes to many narrow stripes. Each of those stripes, too, is independently regulated, with distinct control regions for each.

The real nightmare begins in the next class, when we start taking apart the many ways all of the pair rule genes interact with each other, and how their position is established partly by regulation by the gap genes and partly by mutual sorting out with combinations of activating and repressing interactions. It’s going to be loads of fun!

Today’s slides.

A little blogging exercise for my students

In my development class, students have been blogging away for the last few weeks, and I asked them to send me links to ones they wouldn’t mind seeing advertised. I’ve told them that an important part of effectively blogging is to link and comment, so they’re supposed to write something this week that adds to one of these posts and links to it on their own blog, and they’re also supposed to leave a comment on their fellow students’ work.

I warned them too that I’d highlight these publicly and urge my readers to look and say a few things: so go ahead and comment, criticize, praise, whatever — I told them that the good will come with the bad.

I suspect I’ll have to explain to them how to kill spam and remove irrelevant or outrageous comments in the next class…