Only mostly dead

Sometimes, New Scientist puts a strange twist on their stories — like this one, Universal ancestor of all life on Earth was only half alive. I got stuck on just the title. “Half alive”? What does that mean? It’s describing a paper that did a comparative analysis of genes found in 1800 bacteria and 130 archaea to identify what was common between them, which would suggest what genes were present in the last universal common ancestor.

Now we have the best picture yet of what that ancestor was like and where it lived, thanks to a study that identified 355 genes that it probably possessed.

“It was flabbergasting to us that we found as many as we did,” says William Martin of the University of Dusseldorf in Germany, who led the study. The findings support the idea that the last universal common ancestor (LUCA) lurked in hydrothermal vents where hot water rich in hydrogen, carbon dioxide and minerals emerged from the sea floor.

“It’s spot on with regard to the hydrothermal vent theory,” Martin says. He describes LUCA as half-living, because it may have depended on abiotic reactions in the vents to produce many of the chemicals it needed.

That last bit is where they lost me. I’m about 0.4% salt, which is abiotically derived…does that mean I’m only 99.6% alive? And what about water? I’m 60% water, which means I’m now 39.6% alive, or mostly dead. If you’re just talking about chemical reactions, I don’t have an autonomous power source, but rely on daily input of organic material produced by other living creatures. So by that definition, I am a mostly dead, or undead, zombie PZ that lives by ghoulishly feasting upon the bodies of the living.

When I put it that way, it doesn’t sound so bad.

But I think what is messing us up here is a continuing bias towards vitalism — there is no distinction between “life” and “chemistry”. If you just accept that, we’ll all stop wasting our time trying to figure out what part of our biology is life vs. not-life. This video is a nice simplified approach to the problem of the origin of life, but it also seems hung up on a pointless distinction between “dead chemicals” and “living cells”.

At least the story does make the case for the increasingly dominant hypothesis for the origin of life on earth — that it came from reactions that exploited electron gradients found at deep-sea hydrothermal vents.

One characteristic of almost all living cells is that they pump ions across a membrane to generate an electrochemical gradient, then use that gradient to make the energy-rich molecule ATP. Martin’s results suggest LUCA could not generate such a gradient, but could harness an existing one to make ATP.

That fits in beautifully with the idea that the first life got its energy from the natural gradient between vent water and seawater, and so was bound to these vents. Only later did the ability to generate gradients evolve, allowing life to break away from the vents on at least two occasions – one giving rise to the first archaea, the other to bacteria.

Zika and political obstructionism

Maki Naro has a very good overview of the Zika virus in comic form.

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naro-zika-3a

The effects of the virus are actually easy to understand: mild, flu-like symptoms in adults, but a significant chance of debilitating brain damage to developing fetuses. You don’t want to get Zika because it’s unpleasant and nasty, but your fetus must be protected from it because it’s devastating.

Unfortunately, the USA has a dysfunctional congress that can’t respond to serious problems anymore. An effort to dedicate money (to the tune of almost two billion dollars) to preventing the spread of the disease was killed because Republicans loaded it with irrelevant, poisonous addenda — baggage to snipe at Planned Parenthood (an organization that is vital to putting together a response) or to allow Confederate flags to fly, for instance.

But especially unfortunately, diseases that cause birth defects are a vector for the pro-life-at-any-cost fanatics to gallop in and wreck any process with their delusional antics. We are supposed to love that tiny slug of human fetal tissue so much that we’ll defy any attempt to combat a virus that will poison its nervous system, and don’t you dare think about abortions. A fetal slug with a deformed, shriveled brain is still to be regarded as a full human person!

If you think I’m making this up, listen to Marco Rubio.

Obviously, microcephaly is a terrible prenatal condition that kids are born with. And when they are, it’s a lifetime of difficulties. So I get it.

I’m not pretending to you that that’s an easy question you asked me. But I’m pro-life. And I’m strongly pro-life. I believe all human life should be protected by our law, irrespective of the circumstances or condition of that life.

No, he doesn’t get it. He’s lying.

He also doesn’t believe in protecting life, because he’s also in favor of the death penalty, and in fact thinks the big problem with capital punishment is that we don’t shuffle the condemned into the death machine fast enough.

zikacuts

Meanwhile, Donald Trump thinks we have Zika under control, and is praising Florida governor Rick Scott for how he’s handling it. His little PR helpers are arguing for inaction because birth defects are nothing new.

The United States has been paralyzed by the Republican virus. They know nothing, they do nothing, and they actively interfere with necessary responses to problems. We need to do something about that. Never vote for any Republican, ever.

If you’re not an activist, you must be a do-nothing passivist

A True Scientist is supposed to be aloof, objective, dispassionate, and unemotional. This isn’t just a stereotype, it’s part of a set of social mores that are imposed on individuals who belong to this community of scientists.

And yet, at the same time, we’re part of a larger society that sometimes has serious problems that scientists are among the first to see. Should climate scientists be dispassionate about global climate change? Should medical doctors be unemotional about dishonest tobacco advertisements? The best scientists I’ve known have also had causes: for instance, George Streisinger, the fellow who started this whole business of zebrafish as a model system, was also a peace activist who was very concerned about nuclear war.

So when Shiv writes about the use of the word “activist” to demean scientists, I know exactly where that’s coming from. I’ve seen it way too many times.

Being an activist means you are aware and working to change the world. There’s nothing in that that implies you are cavalier with the evidence — often, it means you are acutely conscious of the facts, and passionate about the truth.

Watching zebrafish make stripes

Our summer research program is winding down, and preparation for the fall semester teaching is winding up. My student, Katrine Sjovold, and I have been trying to figure out what early melanocytes are doing — it’s a very simple and accessible system to observe cell motility, because the cells label themselves with melanin and we don’t need to do any of that persnickety cell injection stuff, or buy expensive dyes, or buy expensive cameras capable of detecting fluorescence (although we’ve tried a little of that here at the end of the summer, and I’ve been appropriately impressed that my research camera actually can see DiI fluorescence, even if it’s not designed for it).

Anyway, one of the things we’ve been doing is making time-lapse videos of melanocytes after they start making pigment and as they’re linking up and consolidating to form stripes. Here’s one example, a time-lapse where we take one image every 3 minutes over a day and an evening of growth.

You can see that we’re looking down on the dorsal side of the animal, in the region of the hindbrain (see the fourth ventricle, and the ears, deep and out of focus?). You may also notice that one of the melanocytes spontaneously decides to die and quickly breaks down into a few darkly pigmented blobs.

I’ve also uploaded a few other videos, but keep in mind these aren’t polished, perfect videos — these are bits and piece of our working data collection.

[Read more…]

Let’s all make chimeras

manbearpig

Government regulation of research to enforce ethical concerns is a good idea, and I support the general idea. I’d like them to be based on reasonable concerns, though. I’m actually glad that the NIH has ended a ban on research into human-animal chimeras, although I know some people are going to freak out over it, pointlessly.

Here’s the basic idea. Mammalian embryos are relatively plastic. If you take a mouse embryo at the blastocyst stage, when the embryo is just a small number of cells in a spherical capsule, and you take a few cells from a human blastocyst and inject them into the mouse embryo, those human cells will be readily incorporated into the developing mouse. They can then be incorporated into the mouse’s tissues, so you end up with an adult mouse that has a liver made up of human liver cells. Or a human pancreas. Or, what really scares some people, human-derived brain tissue. Or human-derived gonadal tissue — the mouse could be making human sperm or human eggs, and if a boy mouse with human testes meets a girl mouse with human ovaries…well, you can imagine the concerns.

One issue is that scientists might inadvertently create animals that have partly human brains, endowing them with some semblance of human consciousness or human thinking abilities. Another is that they could develop into animals with human sperm and eggs and breed, producing human embryos or fetuses inside animals or hybrid creatures.

That was the thinking that led to the moratorium on such experiments, now lifted. Which is good.

All of those troubling possibilities are rather easily prevented, and also rather unlikely.

The concerns about animals with “some semblance of human consciousness or human thinking abilities” is simply silly. They already do, and you could also argue that humans have some semblance of animal consciousness. Mice aren’t going to be able to construct whole human brains in their tiny little skulls, although maybe a pig chimera could; but even there, our brains have co-evolved with all kinds of circulatory adaptations, and I rather suspect that a chimera with a significant amount of human brain tissue isn’t going to be viable. And most importantly, the point of such research isn’t to make a human brain in an experimental animal — it’s to get human nervous tissue that will have human-like responses to, for instance, pharmacological treatments.

It’s the same with the reproductive tissue. Making male and female pigs with human reproductive organs would be cool and useful, but bringing them together to do something as mundane as producing a human baby is not — and would be a catastrophic result of the research that would probably lead to the shutting down of the lab and massive legal consequences, all to produce a totally useless result. These are labs that are interested in studying the mechanisms of human sperm maturation, or oocyte development, not the mad scientist nonsense of creating ManBearPig.

Of course, some people don’t like the idea of ending the moratorium.

But critics denounced the decision. “Science fiction writers might have imagined worlds like this — like The Island of Dr. Moreau, Brave New World, Frankenstein,” says Stuart Newman, a biologist at New York Medical College. “There have been speculations. But now they’re becoming more real. And I think that we just can’t say that since it’s possible then let’s do it.”

Let’s do what? That’s the crux of this disagreement — no one is interested in creating The Island of Dr. Moreau in reality. Moreau was an idiot who didn’t do anything practical or informative with his imaginary technology, and using dystopian science fiction as your counter-argument really says you don’t understand the motivations behind this research.