A poll on kitty experimentation

There is an extremely common sort of experiment to understand plasticity of the developing brain. These are important experiments to understand an important phenomenon: the brain does not simply unfold ineluctably to produce a fully functional organ, but actually interacts constantly with its environment to build a functioning organ that is matched to the world it must model and work with. This was one of the very first things I learned as a budding neuroscientist; my first undergraduate research experience was in the lab of Jenny Lund at the University of Washington, where we were given prepared slices of embryonic and infant human brains (the products of abortions, stillbirths, and childhood mortality) and counted dendritic spines in the visual cortex. The brain is constantly remodeling itself, and is especially doing so in young individuals.

Now in those old observations, we weren’t really manipulating either the brain or the environment: you don’t get to do that with human babies! All we were doing was documenting the natural progression of synaptic connection density — which, by the way, declines rapidly as the brain learns and refines. What we could see anatomically is that as young children adapt to their environment, the brain is busily pruning and shifting connections — but what we couldn’t see is what was causing those changes, or what effect those anatomical changes had on visual processing.

For that, you have to tinker. And since you can’t do that with human babies, you have to go to animal models.

And the most common animal models for studying the visual system in humans are mammals: cats (also ferrets, for technical reasons involving some of the pathways). And since we’re interested in the plasticity of the brain in young, developing animals, you can see where this is going.

Neuroscientists do experiments on kittens.

THE WHOLE KITTY-LOVING INTERNET EXPLODES IN OUTRAGE.

Actually, it sort of does. The Mirror just put up an article decrying kitten experimentation, with lots of quotes from celebrities moaning in horror.

Ricky Gervais: “I am appalled that kittens are being deprived of sight by having their eyelids sewn shut. I thought sickening experiments like these were a thing of the past.”

Why, no, Ricky. These experiments go on right now. It’s how we learn to understand the role of sensory input in shaping the function of the visual cortex.

Michelle Thew of The British Union for the Abolition of Vivisection: “This is unacceptable cruel research. The public will be shocked to learn of publicly-funded experiments where kittens have been subjected to this.”

Of course they will, because your organization will beat the drum of ignorance and lie about their practice and utility.

Dr Ned Buyukmihci, a vet: “The eyelid procedures would have been painful for the kittens. There are substantial ­differences in cats versus humans. There are ­established methods of obtaining information humanely.”

I’ve done experiments like these in the past, and even more substantial surgical manipulations. The investigators know how to do these experiments humanely: we know about anesthesia, for instance, and anything involving surgery on animals is tightly policed by Institutional Review Boards (actually, they tend to be discouraged by IRBs, but that’s a different complaint), which usually have veterinarians serving on them. If Buyukmihci has evidence that these surgeries were done in a way that did not minimize suffering, he should speak up, and the neuroscience community would join him in deploring them.

But these protocols went through Cardiff University’s ethical review process and the Home Office Animals in Science Regulation Unit. There’s no reason to think they were anything less than impeccable.

Ralph Cook, some politician or bureaucrat: “It’s an academic producing a paper which is meaningless and can’t be transferred to humans. Vivisection is completely wrong.”

No, actually, most of this research isn’t just an abstract pursuit of knowledge (although there’s nothing wrong with that, either). This is research that is directly applicable to alleviating human suffering. Treatment of visual system disorders in children is informed directly by these kinds of experiments: they tell us about the sensitivity of the visual system to abnormalities in inputs and long term effects of sustained aberrations. I had a child with ‘lazy eye’ at birth: the doctors (as well as the parents in this case) knew how important it was to correct this problem as quickly as possible, and gave us protocols (tested in cats!) that we could implement until she was old enough to get surgery.

Ingrid Newkirk, PETA’s fanatical nutball: “Not only is sewing shut the eyes of kittens ­ethically and morally abhorrent, it is so crude and cruel that it sets science back decades. The kittens will suffer from having their eyes sewn shut and will also experience psychological distress from being reared in the dark. We learn far more about what happens in humans by investing in state-of-the-art research methods that provide reliable data on human experience.”

Scientists don’t do these experiments to get their jollies torturing kittens. These are experiments that advance our understanding of the wiring of the brain.

I agree that there is an amount of suffering involved, and having done similar work, I also know that good investigators do their best to minimize it. My second job as an undergraduate was as an animal care assistant in a surgery, and one of the things I was paid to do was to spend a few hours a day just playing with post-op cats and kittens, and making sure that their housing was clean and comfortable. These were conscientious scientists. They needed to do these experiments, but they also cared about the animals. I was really impressed with their concern and respect for the animals they had to do experiments on.

(By the way, this was an animal surgery that was also used as a training unit for the medical school. One other thing I learned there was that while Ph.D. researchers were people with a deep affection for their subjects, M.D. students were assholes who didn’t give a damn. I hope they learned some humanity later in their careers, because I didn’t see it at the early stage when they were practicing on animals.)

So, after doing a hatchet job on the research and quoting lots of ignorant celebrity wankers and cranky nobodies, the Mirror has a poll. This will be a challenge: you’re going to have to go up against the whole kitty-loving internet to shift this one.

Is the scientific experiment on kittens acceptable?

Yes 7.44%

No 92.56%

Good luck with that one.

Why I am an atheist – Leon Baradat

The defining moment in my search for religious truth came when I took a step back and looked at all the world’s religions.  I realized that many of them make claims that contradict other religions, which means they can’t all be right.  I also noticed that, if you’re not predisposed to think one of them is right over all the others, they all look about equally believable–which is to say, not very.  I’m open to the possibility that there might be a god (or gods) out there, but I’m going to need a very good reason to think that’s true.  So far, no religion has been able to offer any solid evidence that it’s right over all the others, so I see no reason to give any of them special treatment…even the religion I happen to be surrounded by here in the US.

Leon Baradat
United States

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.

Mike Adams one-ups everyone

We’ve been seeing the spectacle of everyone with a cause blaming the Colorado massacre on every tinge of ideological difference they want to oppose. Now Mike Adams, the chronic wackjob behind the deranged alt medicine site Natural News, brings the lunacy to put everyone to shame. First claim: Adams rides his anti-pharmaceutical hobby horse to make a completely unsupported assertion: “James Holmes may have been involved in mind-altering neuroscience research”.

But that’s just the beginning. The rest is a wacky conspiracy theory fit for a 9-11 Truther: Holmes was set up by the FBI through “drugs, hypnosis, or trauma” to carry out a government-planned terrorist attack, all to the purpose of driving a UN-inspired effort to confiscate all of our guns. And then? “government genocide really kicks in like we saw with Hitler, Stalin, Pol Pot, Mao and other tyrants”.

Don’t read the comments. A few brave critics express their incredulity, but the rest are saying, “it does make some sense.”

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.

Give ’em a little time, the merely rancid turn rotten

I’ve criticized both atheists and the religious for trying to turn the recent tragedy in Colorado into an ideological battleground. You’d think at some point they’d learn that the best thing to do is shut up about how it shows Christians or atheists are evil, but no…one evangelical fruitcake, Jerry Newcombe, has taken it to the next level. He’s now arguing that not only did the shooting occur because Americans aren’t fearful enough of hell, but that the victims who were not Christian are now burning in hell.

While I appreciate his honesty and commitment to the principles of his religion, I can’t help but feel a little nauseous.

A few well-deserved words for Peter Leschak

Peter Leschak writes in the Star Tribune about his conversion from creationist to rational human being. He used to be a smug, condescending, young earth creationist idiot, but he got better. Good for him! He still has a few things to learn, though.

Why is it that despite convincing scientific evidence so many Americans are creationists? For me, at least, the answer was clear: I had never seriously studied evolution and the facts supporting it. I’d graduated high school and college with honors and continued to read widely, and yet was not adequately exposed to a key concept of science. The chief fault lies with the scientific establishment.

[Read more…]