I hope this feature doesn’t turn into Cute Overload…but how can I resist the fennec?
Pharyngula
Evolution, development, and random biological ejaculations from a godless liberal
My students are also blogging here:
A good portion of what I’ve been teaching so far uses Drosophila as a model system — it’s the baseline for modern molecular genetics. Unfortunately, it’s also a really weird animal: highly derived, specialized for rapid, robust development, and as we’ve learned more about it, it seems it has been layering on more and more levels of control of patterning. The ancestral system of establishing the body plan was far simpler, and evolution has worked in its clumsy, chance-driven way to pile up and repurpose molecular patterning mechanisms to reinforce the reliability of development. So I promised the students that this would be the last day I talk about insects for a while…we’ll switch to vertebrates so they can get a better picture of a simpler, primitive system. What we’ll see is many familiar genes from flies, used in some different (but related!) ways in vertebrates.
But today I continued the theme of epistatic interactions from last week. Previously, we’d talked about gap genes — genes that were expressed in a handful of broad stripes in the early embryo, and which were regulated in part by the even broader gradient of bicoid expression. The next level of the hierarchy are the pair rule genes, which are expressed in alternating stripes — 7 pairs of stripes for 14 segments.
First point: notice that we are seeing a hierarchy, a descending pattern of regulatory control, and that the outcome of the hierarchy is increasing complexity. One gene, bicoid sets up a gradient that allows cells to sense position by reading the concentration of the gene; the next step leverages that gradient to create multiple broad domains; and the pair rule genes read concentrations of gap genes and uses the boundaries between them to set up even more, smaller and more precise domains of stripes that establish the animal’s segments.
This is epigenesis made obvious. The 14 stripes of the pair rule genes are not present in the oocyte; they emerge via patterns of interactions between cells and genes. The information present in the embryo, as measured by the precise and reproducible arrays of cells expressing specific genes, increases over time.
So part of the story is hierarchy, where a complex pattern at one stage is dependent on its antecedents. But another part of the story is peer interaction. Cells are inheriting potentials that are established by a cascading sequence of regulatory events, but in addition, genes at the same approximate level of the hierarchy are repressing and activating each other. We can tease those interactions apart by fairly straightforward experiments in which we knock out individual pair rule genes and ask what the effect of the loss has on other pair rule genes. I led the students through a series of epistatic experiments which started out fairly easy. Knock out a pair rule gene that is expressed in odd numbered parasegments, for instance, and it’s complement, the pair rule gene expressed in even parasegments, expands its expression pattern to fill all segments. Sometimes.
Some of the experiments reveal simple relationships: hairy suppresses runt, and runt suppresses hairy. That makes sense. They have mutually exclusive domains, so it’s no surprise that they exclude each other. But then we looked at other pair rule genes which are expressed in patterns slightly out of phase from the hairy/runt pair, and there the relationships start getting complex. Genes like fushi tarazu are downstream from all the others, and their effects are straightforward (their loss doesn’t disrupt the other pair rule genes), but genes like even-skipped have much messier relationships, and the class was stumped to explain the results we get with that deletion.
So I asked them to come up with other experiments to tease apart these interactions. I was somewhat amused: when I think along those lines, I come up with more genetic crosses and analyses of expression patterns — I think about regulatory logic and inferring rules from modifications of the pattern. Students nowadays…they’re so much more direct. They want to go straight to the molecular biology, taking apart the genes, identifying control elements, building reporter constructs to see gene-by-gene effects. I felt so old-fashioned. But we also had to talk about the difficulty of those kinds of experiments, and that often the genetic approach is better for building a general hypothesis that can be fruitfully tested with the molecular approach.
Then we stopped — we’ll come back to flies later, and start looking at some specific subsets of developmental programs. Next, though, we’re going to take a big step backward and look at early events in vertebrates and progress through that phylum until we see how they build segments. I’m hoping the students will see the similarities and differences.
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.
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.
Last year, the Cabrillo Marine Aquarium caught a paper nautilus that survived long enough to lay a few tens of thousands of hatchlings.
It must be nice to be a member of a species that’s beautiful at every stage of life, rather than none.
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.
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.
Speaking of Groening and the Simpsons, Richard Dawkins will be making a cameo voice appearance this Sunday. Tune in!
“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.
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.
If you want to learn more about trilobites, I can’t recommend Richard Fortey’s book, Trilobite: Eyewitness to Evolution
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.
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.
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.
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.
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.
For instance, why do they never give me the seat next to the panda?
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.
