Jurassic Park is fiction, someone tell Jack Horner

Jack Horner has an ambitious goal. He wants to reverse-engineer birds to recreate dinosaurs.

Dinosaurs could potentially walk among us in real life soon as the paleontologist who inspired the original Jurassic Park movie has announced a research project to bring the extinct creatures back to life. Dr. Jack Horner says scientists are only 5 to 10 years away from genetically engineering dinosaurs into existence.

Yeah, I know. He’s been puttering about with this for years, using every incremental change in bird genetics engineered in a lab as confirmation of his project’s feasibility. It’s interesting developmental biology. It’s not going to get him to his goal.

Horner cited a 2015 study as his “proof of concept,” noting that scientists at Harvard and Yale were able to trick a bird’s head into changing into a dinosaur snout.

“Basically what we do is we go into an embryo that’s just beginning to form, and use some genetic markers to sort of identify when certain genes turn on and when they turn off,” he said.. “And by determining when certain genes turn on, we can sort of figure out how a tail begins to develop. And we want to fix that gene so it doesn t stop the tail from growing.”

And there’s the problem: “that gene”. There isn’t a “that gene” — there is a whole ensemble of interacting genes that work together, and it’s simply not going to be doable in 5-10 years. There will be small changes in the desired direction, but every one of those new changes will have a ripple effect on a dozen or more other genes, and each of them will have to be tweaked to adjust their response, but then each of those will have downstream effects on a dozen other genes.

It’s not impossible, since evolution obviously shaped every species, but evolution is a massive project in parallel processing, with large population numbers and thousands of generations. We don’t know enough to be able to go in and in one grand experiment change all the relevant genes in exactly the right way, with foreknowledge of their interactions, to do what he wants in such a short time.

Also, evolution had an easier job in one sense: it doesn’t work towards a specific goal, but simply takes whatever it gets and accepts it if it survives. There was no intent to take a dinosaur species 150+ million years ago and sculpt it into a chicken, specifically. He’s not going to get a dinosaur — he’s going to get a weird-ass mutant chicken — and it’s going to take a lot more time, effort, and money than he naively expects.

Quoted for truth

From The Seattle 500 Women Scientists:

Despite the popular myth of the lone-wolf genius scientist, science is an inherently social, collaborative endeavor. Intensive scientific training involves close collaboration with a senior advisor. Most scientists can trace their “academic genealogy” through generations linked by formative relationships. Scientific papers typically include many authors who work together to form something greater than the sum of its parts. Conferences and workshops where scientists mingle are petri dishes of new ideas and partnerships—they are nurseries and laboratories for future scientific communities. Scientific progress depends directly on the ability of scientists to discuss, argue, collaborate, and build upon on the knowledge of others.

Yes! I tell my students this: I explain to them that they have to work in teams in lab because that’s the only way they’ll ever succeed in this career.

Brain in a bucket: or, when hype meets ethics

Dr Nenad Sestan has a technique to recover some functioning neurons from dead brains. He’s been collecting decapitated pig heads from slaughterhouses and hooking them up to perfusion pumps and running an oxygenated saline (plus other secret ingredients) through them, and then doing physiological assays on the brain tissue, finding that significant numbers of the neurons are still viable and show signs of cellular activity.

There was no evidence that the disembodied pig brains regained consciousness. However, in what Sestan termed a “mind-boggling” and “unexpected” result, billions of individual cells in the brains were found to be healthy and capable of normal activity.

This work has not yet been published in a peer-reviewed journal, so take that “billions” number with a grain of salt. Even if accurate, and I don’t think there’s any way he could have accurately gotten a good count, it still means that only a small percentage of the cells in the brain retained any capacity to function. It is mostly dead, and ignoring the Princess Bride reference, mostly dead is completely dead. The integrated whole is non-functional. The pig is not thinking, not dreaming, not awaiting the kiss from its true love to awaken. It is unresponsive. It is an ex-pig.

Sestan now says the organs produce a flat brain wave equivalent to a comatose state, although the tissue itself “looks surprisingly great” and, once it’s dissected, the cells produce normal-seeming patterns.

The lack of wider electrical activity could be irreversible if it is due to damage and cell death. The pigs’ brains were attached to the BrainEx device roughly four hours after the animals were decapitated.

Put that four hours in context. If your brain is deprived of oxygen for four minutes, irreversible damage begins. After about six minutes, you are dead and typically beyond resuscitation. Within that window between the onset of damage and death, the functional network of the brain begins to break down, and victims have an increasing chance of being reduced to a comatose vegetable.

Those pig brains were deprived of all oxygen and nutrients for 240 minutes. “Comatose” is a generous assessment of their state. You’ve no longer got a brain, you’ve got a scattering of individual cells that no longer work together, but haven’t quite gotten the message that they’re supposed to decay, or haven’t yet been chewed up by bacteria or the wash of lytic enzymes released by their definitely dead neighbors.

This is not a surprising result. No one expects that there is an instant of death in which every cell ruptures their membranes and disintegrates into a liquid acellular mass. It takes time for a mass of meat to break down completely. It is a slight surprise that they can salvage useful single cells after hours of breakdown, but only slightly.

Is this a useful observation? Yes. It would be nice to have another source of neurons for laboratory work that doesn’t require maintaining a colony of animals that you have to personally kill to extract the very freshest cells. You can also use this surviving subset to trace functional activity, which is apparently the goal of the research. It’s going to have new problems, though: how do you interpret the cellular activity of a neuron that has been hypoxic for four hours? Is it actually comparable to newly isolated or cultured cells? The Sestan lab has a lot of work ahead of them. It’s also likely to be extendable to animals other than pigs: human brains donated to research might provide a pool of living cells for physiological work.

But realistically, this is more like discovering that you can go down to the local junkyard and find an unbroken passenger side front window for a 1998 Toyota Corolla that you can use to replace the one someone broke on your car, or a replacement starter motor for your Jeep Cherokee. It does not mean that we can expect a zombie car uprising as the whole junkyard starts up and rushes to clog up the nearest freeway.

Unfortunately, it is also priming unrealistic and irrelevant ethical dilemmas.

The one type of research he thinks may call for quick action to set up rules of the road is Sestan’s unpublished brain preservation technique (which the Nature editorial did not discuss). “If people want to keep human brains alive post mortem, that is a more pressing and realistic problem,” says Hyman. “Given that it is possible with a pig brain, there should be guidelines for human tissue.”

It is not a pressing or realistic problem. What is described as a concern is not possible with a pig brain — I have to say it again, those are dead, non-functional, unsalvageable brains, although a tiny fraction of the cells might have some utility for research. Still, it could become a legitimate ethical issue, so I can see where the responsible ethicist will set up guidelines before it becomes a problem.

Imagine a situation where a patient is dying of organ failure, but their brain is still healthy. If we could decapitate them, hook them up within seconds to the pumps and fluids that Sestan pioneers, keeping their brain intact and undamaged and healthy in a nice little vat, should we? Given that there is no known technique for reconnecting such a brain, it might be greater torment than allowing them to die — would you want to spend decades in a sensory deprivation tank, just for the sake of living? That’ll be a fun one for the bioethicists to wrestle with.

But this technique is not currently anywhere close to raising this problem.

What I see as a greater problem is this annoying essentialism. It’s HUMAN, it’s a HUMAN brain, therefore we need to regard it with the same requirement of respect we accord to HUMAN BEINGS. There is a difference between an adjective and a noun. It is human tissue, yes, but it has none of the properties essential to a good definition of a sapient human being (which we don’t have in most people’s heads: they’ll talk about 46 chromosomes, or parentage, or attributes of the human body like having one head and two arms and two legs, which are all pretty much irrelevant to personhood, I would think), so people freak out over human organoids, little blobs of brain tissue around a millimeter across in a dish, or over chimeras, small subpopulations of human cells in an animal host.

As far as I’m concerned, the Sestan experiment has been grossly overhyped, although it has real potential, and the ethical gasps are actually in response to an imaginary situation, rather than anything that has happened yet.

Lest anyone think I said anything the ethicists don’t already know, I should include this bit from one of them:

Hyman…thinks most of the scenarios are exaggerated or unlikely. It’s hardly possible a tiny brain organoid will feel or think anything, he says.

Have you ever noticed how often the origin of breasts is explained as “for men”?

I made a video about hypotheses for the evolution of breasts in women. Sort of a video. It’s not very visual, and is just me talking, because I didn’t want anyone distracted by sexy pictures — that wasn’t the point. I even left my sexy face out of it.

Since it’s just me droning on, I include my script below, so you can skip the video altogether and just read what I said.

[Read more…]

Writing synopses of science articles is hard

Really, it’s harder than you think. Individual science papers typically build on a larger body of knowledge and don’t stand alone; it is assumed that the reader has significant amounts of training in the subject at hand so that the authors don’t bother to fill in all the background. When writing a summary of the article for a general audience, one has to provide a lot of context, without simply reiterating the contents of, for instance, a molecular biology textbook and a year’s worth of upper level biology education. And if someone writing a summary of an article lacks that knowledge altogether, the misinterpretations can be disastrously wrong.

Take this article in TechTimes, Massive Genetic Study Reveals 90 Percent Of Earth’s Animals Appeared At The Same Time. The title alone is creationist clickbait, and the author of the story clearly didn’t understand the article at all. She gets it all wrong.

Landmark new research that involves analyzing millions of DNA barcodes has debunked much about what we know today about the evolution of species.

In a massive genetic study, senior research associate at the Program for the Human Environment at Rockefeller University Mark Stoeckle and University of Basel geneticist David Thaler discovered that virtually 90 percent of all animals on Earth appeared at right around the same time.

More specifically, they found out that 9 out of 10 animal species on the planet came to being at the same time as humans did some 100,000 to 200,000 years ago.

No, it didn’t. The paper says nothing of the kind.

The paper is an analysis of DNA barcodes. DNA barcoding is a process that uses a short stretch of mitochondrial DNA to map an individual organism to a species — it’s a technique that lets you look at a sample of a few cells, amplify and sequence a single gene (COI or COX1 are commonly used in animals), and then unambiguously identify the specific species those cells came from. Being able to do this relies on an interesting property of a species: there is limited variance in the barcode sequence within the species, but there has to be greater variance of that sequence from other, even closely related species. In other words, DNA barcodes form tight little clusters of similarity that correlate well with other criteria for defining a species.

That raises questions. You can read the original article, Why should mitochondria define species?, for yourself and see. The question is about why variations within a species should cluster so tightly. Stoeckle and Thaler propose a couple of hypotheses to explain that phenomenon.

Either 1) COI barcode clusters represent species-specific adaptations, OR 2) extant populations have recently passed through diversity-reducing regimes whose consequences for sequence diversity are indistinguishable from clonal bottlenecks.

It’s a meaty paper that goes through the evidence for both of those hypotheses, and I’m wishing I’d seen this paper last semester, when I was teaching evolutionary biology — there is a lot of useful evolutionary thinking going on here. Maybe I can revoke all of my students’ degrees and tell them they have to come back for one last thing? I think we can go through the paper adequately in about a week, so I’m sure they won’t mind.

Their final conclusion, after analyzing millions of barcodes, is fairly straightforward, I think.

The simple hypothesis is that the same explanation offered for the sequence variation found among modern humans applies equally to the modern populations of essentially all other animal species. Namely that the extant population, no matter what its current size or similarity to fossils of any age, has expanded from mitochondrial uniformity within the past 200,000 years.

This is not saying that there was a single instant in the last 200,000 years from which all modern species arose simultaneously. It’s a statement about the process of speciation: species arise from isolation of a limited subset of an existing population, which is why they have limited variation in their DNA barcodes, followed by an expansion of the new species’ population, during which the DNA barcodes accumulate variation slowly.

No, they did not find out “that 9 out of 10 animal species on the planet came to being at the same time as humans did some 100,000 to 200,000 years ago”. New species arise continuously, but they do so by going through a population bottleneck in geologically recent times. Homo sapiens arose as a distinct species between 100,000 and 200,000 years ago, but that notorious London Underground mosquito may have evolved in the 18th century…which is still within the past 200,000 years, you may notice.

It’s a bit like reading a statement that almost all people are less than 100 years old, and then wondering, publicly and in print, about what happened in 1918 to cause every human being on Earth to have been suddenly born in that year. That must have been some orgy to celebrate the end of the Great War.

Flattered, then humbled

Today I read an article that listed a few of the colossal errors of Jordan Peterson, and I was flattered to be cited by the author.

However, using the coincidence of serotonin as the supposed basis for behavioural parallels between lobsters and humans – trumpeted during the Channel 4 interview, again to give off the impression of scientific authority – has been expertly dismantled by the biologist PZ Myers. Evidently irked by Peterson’s intellectual overreaching, Myers claims that Peterson has “built a case on false facts and distortions of general observations from the scientific literature. He has not demonstrated anything about socio-cultural constructions. Not only does he get the evidence wrong, he can’t construct any kind of logical argument…”

Worse still, Myers argues, there is an ideological motive for all this: “Peterson is distorting the evidence to fit an agenda… It’s appalling the degree to which this man is asserting nonsense with such smug confidence. This man is lying to you.”

Oh, “expertly dismantled”…thank you, thank you, I wave to the audience and blush charmingly. I am gratified to be appreciated. But then…Google throws a bucket of ice-cold humility in my face and suggests that I go read this excellent article in the Washington Post by Bailey Steinworth.

Oh, man, it is so good. She points out that “in asking us to consider the lobster, he’s cherry-picking one model of social behavior when there’s a whole ocean full of equally relevant examples”, and then…she gives several examples. It’s beautiful.

As a psychologist, Peterson understandably seems to favor lobsters because of their well-characterized behavioral repertoire, citing among other things research on the neurotransmitter and antidepressant target serotonin. But they’re not the only inhabitant of the ocean that’s been studied in this way. He might also be interested in Aplysia. Like lobsters, sea hares of the genus Aplysia — sea slugs named for sensory structures that resemble rabbit ears — have been used extensively in serotonin studies. Behaviorally, however, lobsters and sea slugs could hardly be more different: While a lobster rarely wants to see another lobster, a sea hare placed on its own will crawl toward chemical cues indicating the presence of other sea hares. In fact, being with other members of its species improves a sea hare’s ability to learn and remember. Peterson’s opening chapter emphasizes that male lobsters compete for the best territory to win access to the most females. By contrast, in sea hare sex, everyone gets a turn. They’re hermaphrodites that mate in groups, alternating between the “male” and “female” roles.

Now that’s an expert dismantling. Go read the whole thing. Of of the dismaying truths of our woefully inadequately educated public, which includes a certain pretentious professor of psychology, is how unaware they may be of the diversity of biological strategies. Nature ain’t respectin’ your Biblical mores, people.

Do not play gotcha games with @upulie, even if you are a billionaire

You all know I’m not a fan of Elon Musk — I think he’s something of a looter, a guy who’s good at PR (usually) and knows what bandwagons to leap upon. But lately he’s been working so hard to confirm all of my biases against him.

He announced a plan to fund a media watchdog site that would rank news sources…which is a fine idea, except that his criteria seemed to be self-serving. A news source that was critical of Elon Musk would be “fake news”, obviously. And then what happens? Musk endorses a propaganda site run by a sex cult.

But what really annoyed me was his ignorance and arrogance when he sneered at Upulia Divisekera because she studies nanotechnology.

So Upulie responded with a whole series of tweets outlining the importance of nanotechnology. But guess what? After his initial snipe, he just ignored her altogether. I think that means that she kicked his ass.

At least a nice summary of the Musk mythos emerged out of that mess.