An insult to jellyfish everywhere

This is supposed to be an artificially synthesized jellyfish. They layered some rat heart muscle cells on a sheet of elastic silicone polymer, and then applied a current to the medium, causing it to contract.

And they call that a jellyfish! I ask you, does it have a syncytial nerve net to regulate muscle contractions? It does not. Does it have the ability to digest particles in the water to produce energy? It does not. Can it respond to tactile contact, to dissolved chemicals, to light? It can not. Can it reproduce itself? No, not even close.

I say to you, ladies and gentlemen, that is no jellyfish. It is a rubbery toy.

They also hope to reverse-engineer other marine life forms, says Parker. “We’ve got a whole tank of stuff in there, and an octopus on order.”

No way, guy. No freakin’ way.

Why would anyone want a complete simulation, anyway?

The NY Times is touting a computer simulation of Mycoplasma genitalium, the proud possesor of the simplest known genome. It’s a rather weird article because of the combination of hype, peculiar emphases, and cluelessness about what a simulation entails, and it bugged me.

It is not a complete simulation — I don’t even know what that means. What it is is a sufficiently complex model of a real cell that it can uncover unexpected interactions between components of the genome, and that is a fine and useful thing. But as always, the first thing you should discuss in a model is the caveats and limitations, and this article does no such thing.

I’d like to know how fine-grained the model is; I get the impression it’s an approximation of interactions between molecular components based on empirically determined properties of those elements. Again, I don’t think the authors have claimed otherwise, but it’s implied by the NY Times that now we have an electronic simulation that we can plug variables into and get cures for cancer and Alzheimer’s, without ever having to dirty our hands with real cells and animals anymore.

That’s nonsense. Everything in this model has to be a product of analyses of molecules from living organisms; they certainly aren’t deriving the functions and interactions of individual proteins from sequence data and first principles. We can’t do that yet! The utility of a model like this is that it might be able to generate hypotheses: upregulating gene A leads to downregulation of gene Z, a gene distantly removed from A, in the model, and therefore we get a preliminary clue about indirect ways to modulate genes of interest. The next necessary step would be to test potential drug agents in real, living cells. This model will have a huge mountain of assumptions built into it — and you can only build further on those speculations so far before it is necessary to cross-check against reality.

Also, isn’t it a bit of a leap to jump from a single-celled, parasitic organism like M. genitalium to human cancers and brain disease? Yet there it is in the second paragraph, a great big bold exaggeration.

And then there’s the really weird stuff. Some people need to step back and learn some biology.

“Right now, running a simulation for a single cell to divide only one time takes around 10 hours and generates half a gigabyte of data,” Dr. Covert wrote. “I find this fact completely fascinating, because I don’t know that anyone has ever asked how much data a living thing truly holds. We often think of the DNA as the storage medium, but clearly there is more to it than that.”

What the hell…? Look, I could (if I had the skills) generate an hourglass simulator that calculated the shape and bounciness and stickiness of every grain of sand, and stored the trajectory of each as they fell, and by storing enough data for each grain, generate even more than half a gigabyte of data. So? This doesn’t mean that an hourglass is a denser source of information than a cell. The storage requirements for the output of this program do not tell us “how much data a living thing truly holds” — that statement makes no sense.

As for “We often think of the DNA as the storage medium, but clearly there is more to it than that”…jebus, does a professor of bioengineering really need to go back and take some introductory cell biology courses, or what? Heh. “More to it than that.” I’m glad to see that someone needed an elaborate computer simulation to figure that out.

I am, for some reason, reminded of the time I attended a seminar by a computer scientist on an exciting new simulation of the genetic behavior of viruses that I was told would have great predictive power for epidemiology. One of the first things the speaker carefully explained to us was how they’d incorporated sexual reproduction into the model. I wish she’d waited to the end to say that, because it meant that I sat there listening to the whole hour talk with absolutely no interest in any other details.

Anti-Caturday post

All right, the last few times I’ve done this, I’ve hit you with concentrated cuteness. Now, though, it’s a shotgun-blast of multiple qualities: cute, colorful, squishy, stingie, and slimy, all the things we look for in an adorable critter. Nudibranchs!

Creationist FUD refuted

If you’re looking for a meaty weekend read, look no further than Paul McBride’s thorough dismantling of Science and Human Origins, the new bad book from the Discovery Institute, by Gauger, Axe, and Luskin. It’s in 6 parts, taking on each chapter one by one: Part 1, Part 2, Part 3, a prediction about what will be in chapter 4 before reading it, Part 4 (prediction confirmed!), and Part 5.

The creationists are howling. McBride’s evisceration, with Carl Zimmer’s detailed description of the evidence for chromosome fusion, all discrediting what they thought would be a hot new text on the scientific evidence for creation, has made them so furious that they’re even lashing out at me in email — I just linked to the evidence, so I imagine Zimmer and McBride must be seeing some entertaining spectacles in their inboxes. I do so love to see the creationists dancing in the flames of their own immolation.

I will say this, though: I did get one very polite email from a creationist, who told me that he was not a scientist, but that he’d read a couple of articles that sounded impressively sciencey to him, and asked if they didn’t represent a legitimate criticism of the chromosome fusion idea? And he very nicely sent along the two papers for me to read. Here they are:

Bergman J, Tomkins J (2011) The chromosome 2 fusion model of human evolution—part 1: re-evaluating the evidence. Journal of Creation 25(2):106-110.

Tomkins J, Bergman J (2011) The chromosome 2 fusion model of human evolution—part 1: re-evaluating the evidence. Journal of Creation 25(2):111-117.

Two things jumped out at me: it’s by batty Jerry Bergman, no credible source at all, and it’s published in the inbred in-house journal of the Institute for Creation Research. These are not legitimate science papers, although they do throw around enough science terms and techniques, and follow the form of a real science paper, to generate confusion in the mind of the naive reader. They’re beautiful examples of cargo cult science by creationists. Would you like to read them, or use them as bad examples? Here you go, download it for entertainment purposes only.

I read them anyway. I’m not going to bother with a detailed refutation, but I’ll give you the gist. The fundamental confusion in both papers is the nature of the evidence for an ancestral chromosome fusion, and a focus on irrelevant details that are not central to the argument.

The story is this. At some time after the separation of the human and chimpanzee lineages, two ancestral chromosomes, #12 and #13 in the chimpanzee, fused end-to-end to form a single chromosome, #2, in humans. Chimpanzee chromosome 13 forms the short arm (2p) and part of the long arm (2q) of human chromosome 2, while chimpanzee chromosome 12 forms most of the long arm (2q) of chromosome 2.

The primary evidence for this fusion is the comparative genetic content of these chromosomes. That is, most of the genes in chimpanzee chromosome 13 are found in human 2p, and most of the genes in chimpanzee chromosome 12 are in human 2q. The chromatin binding patterns line up, the sequence analysis confirms, and there have been some lovely FISH studies that show the correspondence.

What has since been done is that a prediction was made that there ought to be fragments of telomeres (the end caps of chromosomes) in the middle of chromosome 2, at the fusion site. Which has been examined. And the prediction has been confirmed.

Bergman and Tomkins ignore every single bit of that. Instead, what they do is focus on just the region of the fusion, and complain that it is a tangled mess and hard to interpret — that it is a degenerate telomeric region, rather than a complete and intact telomere, which is what they demand be present. This is an unrealistic expectation, given that every paper on the structure of the fusion region makes the point that it is degenerate.

An analogy: imagine a red Ford Mustang and a blue BMW X6 are in a head-on collision, and both have totally wrecked front ends, with bumpers and radiators and headlights interlocked and everything about their grilles in tangled confusion, and with bits and pieces torn loose and flung about. You’d be able to look at the crash and still tell by everything in and behind the engine compartment that Car #1 was a Mustang and Car #2 was an X6.

Bergman and Tomkins are the bewildered and incompetent investigators who ignore every other factor in the crash, look at a few particularly mangled bits of the wreckage, and declare that they can’t identify it, therefore…the two vehicles were assembled at the factory in this particular configuration, and no crash occurred. But they use lots of sciencey language to explain this at tendentious length, which is sufficient to convince non-scientists that the interpretation of an obvious historical event has been refuted. And that’s all they need to do to accomplish their goals: fling about unfounded fear, uncertainty, and doubt to win over the ignorant.

Forever disappointed

I always have unwarrantedly high expectations of creationists. I know that there are some flamingly ignorant nutjobs out there, all your Hams and Hovindses and Luskins, but lurking in my mind is always this suspicion that somewhere there has to be one or two biologically competent ideologues on their side of the fence. And I am always disappointed.

For example, there’s this one fellow, Douglas Axe, who has a legitimate and well-earned doctoral degree in chemical engineering, and several published papers in real science journals (not the fake journals creationists create). The Discovery Institute tapped him to head their Biologic Institute, their attempt to create an organization that would do genuine biological research (it hasn’t, so far). And I thought, hey, maybe this guy at last is a worthy opponent.

But let’s be honest here. I have no illusions that I’m a super-mega-genius, or that I have high standing as a researcher in my field. I’m a grunt in the army of biology, not an officer. So I can imagine someone smarter than me in opposition; I certainly know many on my side who are far more accomplished and intelligent than I am. So you can imagine my disappointment at looking over Axe’s ideas and seeing that he, too, is an incompetent twit.

I was really shocked when he revealed that he didn’t understand coalescence theory at all. It may be a bit esoteric for the lay public, but if you’re a critic of genomics and population genetics, you must at least comprehend the basics. And he doesn’t.

And now he lets me down again. The Biologic Institute is putting out some fresh horror of pseudoscience, a book called Science and Human Origins, in which they presumably bring all their scientific guns to bear in order to question human evolution. And what do they do? They question the evidence of a fusion of chromosome two, something I’ve hammered on Luskin before. And they bumble it up completely.

This stuff isn’t that hard. I’ve explained the basics of synteny, or conserved linkage blocks; fragments of chromosomes are constantly getting shuffled about, inverted, duplicated, and deleted, and we can compare chromosome structure between two species and see exactly how they’ve been juggled. These movements leave traces, and are mechanically well understood; we can see the evidence right therein the sequences.

So Carl Zimmer engaged the Biologic Institute ideologues on their facebook page. They denied that a fusion had occured, and claimed that the evidence was actually against such an event. So Zimmer hit them right where they’re weakest: he asked them to cite that evidence. And what did they do? You know it, it’s familiar. They went dumb and stopped answering. They couldn’t answer the basic question. And this is why I’m vaguely disappointed. Even their self-proclaimed science stars can’t explain something a small-town teaching professor in the Midwest can see laid out plainly in the data.

One benefit, though, is that Carl Zimmer summarized the whole affair in a must-read post. He explains step by step with simple cartoons every event that occurred in the chromosomal fusion, and what the molecular evidence for the phenomenon is. And he shows up the creationists for frauds who won’t address a simple question of sources.

For added hilarity, David Klinghoffer of Evolution News & Views, the DI’s dishonest propaganda organ, has challenged Carl to debate the issue. I don’t know what there is to debate; Gauger, Axe, and Luskin claim there is evidence against a chromosome fusion in human history, Carl asked what it was, and they refused to give it.

So he flatly turned them down, as was sensible to do. Debating creationists is a waste of time. Now that refusal is getting trolled by creationists, accusing him of being ‘afraid’ to debate…and I still don’t know what he’s supposed to argue about. Did the Discovery Institute refuse to cite any evidence supporting their claim? Yes. We’re done.

And my quest for an honest, scientifically competent creationist continues, fruitlessly.

This is why I could never be an anthropologist

Somedays, it’s just awful to have the mind of a 12 year old boy. So I’m reading this serious and interesting paper on Neandertals, and learn something new.

Two particular characteristics have received considerable attention; pronounced humeral diaphysis strength asymmetry and anteroposteriorly strengthened humeral diaphyseal shape. In particular, humeral bilateral asymmetry for cross-sectional area, and torsional and average bending rigidity, appear exceptionally high in Neandertals (averaging 24–57%) compared to skeletal samples of modern Holocene H. sapiens (averaging 5–14%).

That’s science-speak for “Neandertals had massively muscular right arms compared to their left.” And my mind went right into the gutter.

Anthropologists had their own less juvenile explanations: their strong right arms were a response to extreme muscular activity of repetitive thrusting (ack, back into the gutter) with long, heavy spears (slap me hard.) The paper, though, analyzed muscular activity in experimental subjects who made spear thrusts while hooked up to loads of instrumentation, and discovered that, contrary to their expectations, it was the left arm, the off hand, that carried the largest load in stabilizing the thrust. So that hypothesis simply doesn’t work.

So they tested an alternative explanation, and it wasn’t the first one that leapt to my mind. One of the most common kinds of tools found at Neandertal sites are scrapers —if you’re using hides for clothing and shelter, there is a lot of processing involved — prolonged, repetitive scraping motions while stripping excess flesh from the underside of skins. I imagine scraping a mammoth skin is a huge endeavor that does involve a lot of work. They reviewed ethnographic studies, and discovered that processing a single cow hide, for instance, takes 6-10 hours of work. So they hooked up their test subjects to instruments and measured muscle activity during scraping…and it matches, generating forces that could lead to a build-up of muscle and bone in the right arm.

Unfortunately for my adolescent Neandertal wanking hypothesis, though, the comparison probably doesn’t hold up. Even the most obsessive individual is going to be hard up to maintain 6-10 hours of constant activity. Rats, I guess I’m not going to be making a novel contribution to anthropology. Besides, I imagine this guess was made many times before, and for some reason never made it into print.

Shaw CN, Hofmann CL, Petraglia MD, Stock JT, Gottschall JS (2012) Neandertal Humeri May Reflect Adaptation to Scraping Tasks, but Not Spear Thrusting. PLoS ONE 7(7): e40349. doi:10.1371/journal.pone.0040349.

Watch out for the GMWs: Genetically Modified Women

I’ve been hoping that someone would come out and explain how this claim that women are becoming smarter than men was accomplished. I need to know the scenario and the mechanism, so I’ve developed a few of my own that I hope to see appearing soon in the Daily Mail.

  • Late at night, when no one was looking, UFOs have been abducting our women and enslaving them in the Love Factories on Mars (because as we all know, Mars Needs Women). So that we don’t catch on, they’ve been replacing them with femdroids with cybernetic brains that are very good at cheating on tests.

  • Beginning in about 1980, all female infants were selectively injected with a Communist mind control virus that turned them into soulless, freedom-hating machines who were good at gymnastics and engineering. When the time is ripe, their programming will be activated and they will rise up to overthrow Western running dog democracies.

  • The government has top secret labs where clone babies with enhanced genetically engineered intelligence are being raised. Only females are used in this project for technical cloning reasons. They’ve been swapping out normal babies in maternity wards and replacing them with these Humanity 2.0 versions for years.

  • Big Pharma has been testing brain-enhancing drugs by hiding them in birth control pills. The recent results are the consequence of clandestine human trials. Little known, related fact: they’re also doping Viagra with a stupidity drug.

  • A select team of exceptionally intelligent pick-up artists have been using their talents to inseminate a majority of women around the world, cuckolding all the dumber men, and increasing the frequency of their super-smart alleles in the population to a remarkable degree. They also all fortuitously carry a Y-dominant allele that causes defective Y-bearing sperm, so all of their children are female. Which increases the frequency of babes, schwing!

Unfortunately, there’s one little problem with those scenarios: they’re all ridiculous, requiring large-scale changes in the genetic composition of a world-wide population numbering in the billions within a few generations, and that all of the positive changes would be selective for one sex. You simply can’t argue in any coherent way that women are becoming smarter than men or that women are the smarter sex. You can reasonably say that the evidence shows that women have higher IQ scores than men now.

Because, as I’ve been saying for a long time, there’s a difference between IQ scores and the actual potential for knowledge, learning, and that general poorly defined thing we call ‘intelligence’.

What this current study by James Flynn of worldwide intelligence test scores actually shows is that a) whatever intelligence tests measure is plastic, b) the variation in those scores is not a measure of biological limitations (although I’d argue that our intelligence is a biologically human property), and c) shifting cultural environments can induce relatively rapid changes in the responses of developing human minds.

Women aren’t getting smarter. They have the same biological properties in this generation that they had in the previous generation, and the generation before that. What’s changing is a culture that allows women to slip free of sociological limitations at a young age and encourages them to practice using those brains. Their grandmothers were just as smart, but were molded in ways that limited expression of their intelligence. I also suspect that there are factors emerging which are imposing limits on male behavior and experiences — there are some troubling signs that some social expectations are imposing a new kind of stereotype threat on men.

Of course, there is some anecdotal counter-evidence. I have a daughter who went from being totally reliant on Mommy and Daddy to being an independent young woman, almost overnight. The alien pod-person/cybernetic brain implant/radical brain-enhancement doping theories do have some attractiveness.

Camille Marino is probably going to jail

Marino is a demented fanatical animal rights activist who runs a website called “Negotiation is Over”. NIO is notorious as the site of some of the most frothingly furious denouncers of all animal research. Marino is from Florida; she was arrested and extradited to Michigan in March to be tried for words she wrote on the internet.

Whoa. That ought to give one pause — arrested for free speech, you’re thinking? That does cause one’s knee to jerk.

But then she was also arrested in May when she chained herself to a library door to protest being banned from the Wayne State campus in Detroit. She’s been ordered to stay away from the researchers she threatens, but then she travels to their university to harass them — that sounds like stalking to me.

The situation here is that Marino’s got nation-wide bands of dedicated followers, those followers have in the past shown a willingness to undertake violent, destructive action on behalf of their cause, and Marino has been actively inciting others to kill researchers. You want an example? Here’s an example, and it’s also a great example of her incoherent state of mind.

The image on this page [a chalk outline labeled “animal abuser was here”] is not a cute logo. It is my personal belief that if you are a sadistic animal torturer, that is all you deserve – a chalk outline. That’s my opinion, not a threat. It’s not even inciting anyone because, unless you read my words and run out and murder David Jenstch (sic) (an idea that amuses me immensely), I’m not responsible. If you have time to think about it and form your own conclusions, my words cease being the impetus. Eh, that used to be the law at least. Who knows? Who cares? We have a job to do and that’s all that matters…. NIO is no longer mincing words. This is war!… Nothing is off limits at NIO!

…

if there are no consequences, there is no threat. If you spill blood, your blood should be spilled as well…. Some of the more high profile pacifists have said that I am “violent” and “unbalanced”. I think they finally may be right about something!

If I have my way, you’ll be praying to us for mercy!

It’s just her “opinion”, she’s not inciting anyone — she would just be amused by David Jentsch being murdered by someone who read her suggestion to go murder him. She’s not responsible, she’s just telling everyone that researchers’ blood should be spilled, and that nothing is off limits.

She’s a danger to others. It’s good news that she’s being constrained to protect the citizenry.