Live! From an alien world!

Yeah, yeah, NASA has probes going off to space, but the University of Washington has installed a probe in a much more interesting location: around an active hydrothermal vent off the coast of Oregon. I just learned that they also have a live camera feed 4 times a day, accessible from your local internet.

The next 14 minute stream will be in about half an hour from when I post this. The vent is covered in tube worms, palm worms, scale worms and limpets, so it’s much more interesting than anything the Mars Curiosity Rover has found, and it’s been ongoing every day, for years.

I hope that doesn’t hurt the Rover’s feelings. It’s been doing a good job, it’s just such a dead planet that it’s been banished to.

How eugenics fails

Selecting for one trait, or a small number of them, and failing to recognize that individual organisms must be integrated with their environment, leads to catastrophe, as this interview with Bill Muir explains.

Almost everyone who thought about eugenics at that time unquestionably assumed that creating a better society was a matter of selecting the most able individuals, or “hereditary genius”, as Galton put it. Against this background, consider an experiment conducted in the 1990’s by William M. Muir, Professor of Animal Sciences at Purdue University. The purpose of the experiment was to increase the egg-laying productivity of hens. The hens were housed in cages with nine hens per cage. Very simply, the most productive hen from each cage was selected to breed the next generation of hens.

badchickens

If egg-laying productivity is a heritable trait, then the experiment should produce a strain of better egg layers, but that’s not what happened. Instead, the experiment produced a strain of hyper-aggressive hens, as shown in the first photograph. There are only three hens because the other six were murdered and the survivors have plucked each other in their incessant attacks. Egg productivity plummeted, even though the best egg-layers had been selected each and every generation.

The reason for this perverse outcome is easy to understand, at least in retrospect. The most productive hen in each cage was the biggest bully, who achieved her productivity by suppressing the productivity of the other hens. Bullying behavior is a heritable trait, and several generations were sufficient to produce a strain of psychopaths.

In a parallel experiment, Muir monitored the productivity of the cages and selected all of the hens from the best cages to breed the next generation of hens. The result of that experiment is shown in the second photograph. All nine hens are alive and fully feathered. Egg productivity increased 160% in only a few generations, an almost unheard of response to artificial selection in animal breeding experiments.

Weirdly, though, Muir goes on to claim that this experiment shows that capitalism is the best possible system, which just goes to show that American indoctrination is very effective. It seems to me, rather, that it shows that you can’t decide ahead of time what traits are desirable, but that they have to emerge organically in concert with other properties of the organism, and deciding ahead of time that humans must be guided by one ideology or the other is a huge mistake.

Carl Zimmer is defective

But it’s all right, we all are. Zimmer has begun a series called Game of Genomes in which he has had his whole genome sequenced, and is being led by a group of scientists through the analysis. So far he’s made a good summary of the procedure, and a general overview of the state of his genome.

In my own genome, Gerstein and his colleagues discovered 13 genes in which both copies appear to be broken. I have another 42 genes in which only one copy looks like it’s defunct.

It may sound strange that my genome has dozens of broken genes that cause me no apparent harm. If it’s any consolation, I’m no freak. The 1000 Genomes Project revealed that everyone has a few dozen broken genes.

Our genomes are not finely engineered machines that can’t tolerate a single broken flywheel or gear shaft. They’re sloppy products of evolution that usually manage to work pretty well despite being riddled with mutations.

I’ve probably passed down some of my uniquely broken genes to my children. Perhaps, long in the future, one of those broken genes will become more common in humans, and end up in every member of our species. That’s certainly happened in the past. My genome catalog includes about 14,000 genes that have been broken for thousands or millions of years, known as pseudogenes. Once they lost the ability to make proteins, they simply became extra baggage carried down from one generation to the next. Thanks to a genetic roll of the dice, they ended up becoming common. Now these 14,000 pseudogenes are found in all humans today.

As you can tell, it’s a nicely written summary that doesn’t require a huge amount of scientific background to understand. Good stuff!

Conodontia

conodonts

Conodonts are strange and extinct animals that left behind lots of fossils: their teeth. Practically nothing else but teeny-tiny, jagged, pointy teeth. I remember when the animals themselves were total mysteries, and no one even knew what phylum they belonged to — it was only in the 1980s that a few eel-like soft tissue fossils were found, and they were recognized as chordates (very small chordates, on the order of millimeters to centimeters long) with big eyes and membranous fins.

CarboniferousConodont

And now today I find two artistic reconstructions of the conodont animal that please me.

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Friday Cephalopod: They can see color?

cuttleeye

This is kind of awesome: cephalopods only have one kind of photoreceptor, so it was thought that they would be only able to see the world in shades of gray. Those amazingly clever camouflage tricks they pull? That was just matching intensities and textures, fooling our eyes. But now someone has figured out a way they could see color, and special bonus, it also explains those funky weird pupil shapes, like you see in the cuttlefish eye to the right.

They use chromatic aberration! We think of chromatic aberration as an imaging problem — it’s caused by the fact that the degree refraction of light is partly dependent on wavelength, so the blue light in an image focuses closer to the lens than the red light. When you focus optimally on the green wavelengths, for instance, that means that the red and blue colors form an out of focus, blurry image on top of the sharp greens, producing a pattern of color fringes around objects. They jump out clearly to me when I use the cheap student microscopes here, and are why I spent a lot of extra money getting planapochromat lenses for my microscope. They have lots of corrective glass to tweak the different wavelengths into the same focal plane.

But where I see an annoyance, cephalopods evolved an opportunity. Where an object comes into sharpest focus on the eye can actually tell you what wavelengths are — so by focusing backwards and forwards on something, they can extract a rough idea of its color.

And that leads into the next nifty explanation. Where I want to minimize chromatic aberration, cephalopods want to increase it…and as it turns out, having weird off-axis apertures causes more disparity in the focal plane of different wavelengths of light, which makes it easier to discriminate color using this mechanism.

Chromatic blur and pupil geometry. The (A) full and (C) annular aperture pupils produce more chromatic blurring (CB) than (B) the small on-axis pupil, because they transmit rays with a larger ray height h. Vertical lines show best focus positions for blue, green, and red light.

Chromatic blur and pupil geometry. The (A) full and (C) annular aperture pupils produce more chromatic blurring (CB) than (B) the small on-axis pupil, because they transmit rays with a larger ray height h. Vertical lines show best focus positions for blue, green, and red light.

It’s settled then. Cephalopods are cleverer than we are. Or maybe it’s evolution that is smarter than we are. One of those two.


Stubbs AL, Stubbs CW (2016) Spectral discrimination in color blind animals via chromatic aberration and pupil shape. Proc Natl Acad Sci U S A. 2016 Jul 5. pii: 201524578. [Epub ahead of print]

Gene activity in the dead

Now you’ve got another paper you can file with that dead salmon fMRI paper: one that analyzes the transcriptome, or excuse me, the thanatotranscriptome, of dead zebrafish and mice.

You should not be surprised to learn that when a multicellular organism dies, it’s not as if every single cell is abruptly extinguished: the integrated, functional activity of the individual as a whole ceases, but individual cells struggle on for a while — they’re not getting oxygen or nutrients, in a mouse they’re experiencing thermal stress as the body rapidly cools, but it takes a while for all of the cells to starve or suffocate or undergo necrosis. It seems to take a couple of days, actually. You can measure the declining amounts of RNA present in the dead animals, and yep, it looks like everything is done after a few days. This kind of study has also been done in human corpses, which show that RNA transcription continues for a couple of days.

Total mRNA abundance (arbitrary units, a.u.) by postmortem time determined using all calibrated microarray probes. A, extracted from whole zebrafish; B, extracted from brain and liver tissues of whole mice. Each datum point represents the mRNA from two organisms in the zebrafish and a single organism in the mouse.

Total mRNA abundance (arbitrary units, a.u.) by postmortem time determined using all calibrated microarray probes. A, extracted from whole zebrafish; B, extracted from brain and liver tissues of whole mice. Each datum point represents the mRNA from two organisms in the zebrafish and a single organism in the mouse.


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Meanwhile, in Kentucky…

This week, Nature has an article on the reconstruction of global tectonics during the past 200 million years.

a–c, Maps are separated by 10 Myr. The shapes of the large plates do not change much, whereas the adjustment of the small plates evolves quickly. d, 90 Myr after the first snapshot (a), the distribution of the large plates and smaller plates has evolved substantially. In a–d, the top panels show the viscosity of the mantle (colour scale); the bottom panels show the different boundary types (coloured lines) and plate sizes (shading) within the boxed regions in the top panels (which focus on longitudes between −30° and 90° and latitudes between −30° and 30°). The arrows indicate the direction and magnitude (represented by arrow length) of the mantle flow.

a–c, Maps are separated by 10 Myr. The shapes of the large plates do not change much, whereas the adjustment of the small plates evolves quickly. d, 90 Myr after the first snapshot (a), the distribution of the large plates and smaller plates has evolved substantially. In a–d, the top panels show the viscosity of the mantle (colour scale); the bottom panels show the different boundary types (coloured lines) and plate sizes (shading) within the boxed regions in the top panels (which focus on longitudes between −30° and 90° and latitudes between −30° and 30°). The arrows indicate the direction and magnitude (represented by arrow length) of the mantle flow.

In Science, we can read about a thorough analysis of a site where a mastodon was butchered by North American hunter-gatherers 14,550 years ago.

(A) Location of Page-Ladson in northwestern Florida. (B) Map of the Page-Ladson underwater excavations, showing the entire sinkhole and previous excavation areas, as well as excavation areas and sediment cores reported in this paper. Core 4A is marked with a blue star. Other cores are marked with blue circles. Previous excavations are marked with yellow. Our excavations are marked with red. Contours are in meters below datum. (C) Detailed map displaying the location of bones (gray), drawn to scale, and artifacts (black) recovered from geological Units 3a to 3c and 4a to 4b

(A) Location of Page-Ladson in northwestern Florida. (B) Map of the Page-Ladson underwater excavations, showing the entire sinkhole and previous excavation areas, as well as excavation areas and sediment cores reported in this paper. Core 4A is marked with a blue star. Other cores are marked with blue circles. Previous excavations are marked with yellow. Our excavations are marked with red. Contours are in meters below datum. (C) Detailed map displaying the location of bones (gray), drawn to scale, and artifacts (black) recovered from geological Units 3a to 3c and 4a to 4b

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And of course, the big news, scientists have put a probe in orbit around Jupiter.

junoart

Meanwhile, in Kentucky…

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