Reddit could be excellent

Rebecca Watson has a very good summary of her SXSW panel on Reddit. Reddit has an introspection problem (they don’t) and a criticism problem (they don’t accept it, even when they have a serious problem that needs correcting).

The panel then moved on to discussing where Reddit came from, how it differed from other forums and communities, and how its features have impacted both the internal community and the outside world.

On that last point, I talked a bit about how I think that Reddit’s shared values of “freedom of speech” and anonymity combine with the “karma” voting system to create an ideal environment for the proliferation and normalization of bigotry and hate. I showed screenshots that I grabbed from just the previous few days of posts on r/ShitRedditSays, with credit given and a brief detour for us to talk about whether the existence of a self-critical subreddit like SRS is cause for hope (my answer being “no,” because SRS is popularly seen by other Redditors not as a helpful part of Reddit but as a hateful, misguided, humorless, and occasionally dangerous outside threat, an idea that supports my forthcoming point that Redditors hate and resist criticism). I pointed out that the karma system resulted in bigoted ideas being not just tolerated but rewarded, sometimes by people thinking they were being edgy and ironic and sometimes by actual hate groups like Stormfront, a racist forum that encourages users to game Reddit so that their ideology is represented prominently.

Free speech is a good thing except when you fetishize it to such a degree that it gets elevated well above personal responsibility.

Also, I think the majority of Reddit users are basically good people; their success at promoting great causes (which Rebecca talks about) is testimony to that. However, by refusing to address reasonable limits on what ought to be said, they’ve privileged a tiny minority of trolls and wreckers and parasites who love to rampage and ruin the site’s reputation for others…and management vacillates over doing anything about it, because they seem to think they need to worship the 4chan version of ‘free speech’.

Seriously: does encouraging the existence of a “jailbait” forum that tramples over the civil rights of the targets of their surreptitious photography represent a net increase in civil liberty, or a net decrease? If that’s what you care about, this ideal of personal freedom, then handing it to abusers at the expense of the innocent is not advancing your goals at all. Unless your goal is just making cheap porn and trampling on women.

A nice illustration of the problem:

reddit

Prediction: Some of you will read this and grab a roll of tape

“Ratters”. Ick.

These are pathetic people who use a canned remote administration tool (RAT) to seize control of other people’s computers…especially to activate their laptop cameras so they can spy on them (which is why I predict some of you will want to tape over your camera). Ars Technica has a whole article on these deeply creepy human beings.

Not all human beings, obviously. Unfortunately, most of them seem to be feeble little child-men.

By finding their way to forums filled with other ratters, these men—and they appear to be almost exclusively men—gain community validation for their actions. “lol I have some good news for u guys we will all die sometime, really glad to know that there are other people like me who do this shit,” one poster wrote. “Always thought it was some kind of wierd sick fetish because i enjoy messing with my girl slaves.”

Please, guys, could you stop making me ashamed of my sex? What the fuck is the matter with you?

What I taught today: farewell to flies (for a while)

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.

Slides for this talk (pdf)

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

`

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.