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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Maybe they should think about the radiation coming out of their televisions…

I’ve heard you can get eyeball cancer from watching bad televison programming.

No, I lied…but apparently they are people making bank off the idea that cell phones cause ear cancer, which is about as ludicrous. An Australian science show has had to retract another episode after it was exposed as credulous bunk. This show accepted without question the fear-mongering nonsense of Devra Davis, who has written a book claiming that cell phones cause cancer.

I mean, really, the show had some of the most obvious examples of bad methodology I’ve seen in a long time. For example, it purports to show that cell phone radiation is penetrating right into people’s heads with pseudocolored imaging: how horrifying, they show a picture of a child holding a cell phone with a bright red tint over the side of her face with the phone, shading into yellows and greens and blues on the far side of her head. But I’m looking at it and wondering what kind of camera they were using to measure that, and I realize it was no camera…these were stock photos that someone had painted over.

Then Davis makes this claim:

The reality is that every single well-designed study ever conducted finds an increased risk of brain cancer with the heaviest use of cell phones, and the range of the risk is between 50% and eight-fold.

Apparently, her definition of “well-designed study” is one that gives her the results she wants, because that is simply not true. Only a few studies have found a very weak correlation between cell phone use and cancer, and those have tended to be case control studies, in which people with those cancers are asked to retrospectively report on how much they’d used cell phones in the past…and they’re clearly over-reporting their frequency. So quite contrary to what Davis is saying, the studies that find an effect tend to be methodologically flawed.

Here’s a believable analysis of Devra Davis’ work.

Disconnect [Davis’ book] is a good example of the kind of material used by the EMF alarmist movement. Virtually all the alarmist studies that Davis cites used a poor methodology and/or have not been replicated in follow up studies. In fact, most have been refuted by far more comprehensive and rigorous studies. In many cases, serious flaws have been found with studies that show harm. It is at odds with the conclusions of mainstream expert groups such as the SCENHIR (* 5 P 8): It is concluded from three independent lines of evidence (epidemiological, animal and in vitro studies) that exposure to RF fields is unlikely to lead to an increase in cancer in humans. Disconnect is designed to bamboozle and scare the lay reader, not to inform.

But the creators of that science show shouldn’t have needed to read that — they should have been able to see the hokey ‘evidence’ Davis was throwing at them and seen that there was something fishy going on.

If Australians want to be afraid of something, they ought to step outside and look at that giant ball of plasma in the sky that is showering them with intense radiation all the time. Does anyone seriously think that cell phone emissions are at all comparable?

Take the epigenome, please

Larry Moran rips into the latest hype over epigenetics. Good. There is some valuable biology buried in the field, but I see so much nonsense that even as a developmental biologist who wants to seem more attention to regulative changes in the genome, I’m just seeing so much exaggeration that I think it is doing more harm to our understanding than good (see also Carl Zimmer’s latest discussion of epigenetic over-reach). But this video is just too much.

It’s true — region of the genome can be switched on or off in a coarse way by chemical modification of DNA and associated proteins. It happens all the time. But as Larry points out, this doesn’t just happen by magic. There are regulatory factors that change patterns of gene expression, and they’re probably most responsible as well for triggering the establishment of epigenetic marks.

But here’s my objection: the hype seems to be ignoring development (I know, unforgivable). The problem with assigning too much importance to the inheritance of epigenetic marks is that individual cells and tissues acquire them throughout development and even adulthood…but they don’t matter genetically. Have the proponents never heard of Weismann’s Barrier? Changes in the somatic tissues don’t propagate to the next generation. All that matters are changes in a subset of cells in the gonads, the testes and ovaries. So we’re already dealing with a tiny fraction of our cells that also have unique tissue-specific epigenetic marks, and more importantly, their own specialized patterns of gene regulation.

Then, further, gene expression in the germ line is further refined during maturation of the egg and sperm — both of these cell types are highly specialized and gene expression is honed even more during their development. It’s nice to dream that epigenetics influences neurons in the brain, but you’re not going to inseminate anyone with your neurons, nor are those cells going to migrate down into your ovaries and pass their history on to the next generation.

The video does mention that most epigenetic marks are going to be cleared during gamete formation, and other germ-line-specific marks added, but it just blithely slides past that. It seems to me that the clearest example of epigenetic modification in inheritance is genomic imprinting, which is a consequence of differential gamete-specific modification of sperm and egg, and its main effect is in regulating gene dosage.

It’s strange. I don’t even see the appeal of these epigenetic fairy tales; I certainly don’t see any problem in evolutionary theory that requires patching up with this kind of phenomenon. But Larry includes an excerpt from an interview with the creator of the video, and suddenly all is clear. This bastardized, exaggerated version of epigenetics appeals to people who are uncomfortable with the whole central idea of modern evolutionary theory — who dislike seeing gene transmission uncoupled from the will of the individual.

I came from the world of evolutionary biology. I have always been interested in evolutionary theory but I was never convinced by the neo-Darwinian argument that environmental factors are not a big player in the generation of genetic changes. On the other hand, I never understood the fierce dismissal and often mocking of the Lamarckian ideas in schools and universities; particularly, because Darwin himself never denied Lamarck’s ideas. In epigenetics I found the mechanisms that allow you to understand the action of environmental exposures on the genome.

Whoa. That environmental factors are not a big player in the generation of genetic changes is sort of true; the environment can influence the rate of genetic changes, but doesn’t play a big role in shaping the direction of that change — that’s all a consequence of changing the frequency of representation of those changes in the population. That he brings up the idea of Lamarck is telling. Lamarckian evolution ain’t coming back, although it’s surprising how often people want it.

Also, Darwin himself never denied Lamarck’s ideas? Does he know nothing about the history of evolutionary theory? Darwin did not deny them, because his theory of inheritance was all about the inheritance of acquired characters and pangenesis, the generation of a gamete by contributions from all tissues (which, come to think of it, is what you’d need for the epigenetics hype to have any hope of working). He was pre-Mendelian genetics. He was wrong. You can’t defend Lamarck by citing a guy, no matter how influential, who had no viable theory of genetics, and who wrote in the era just before genetics was explored and understood. He might as well support it by announcing that Aristotle didn’t deny Lamarck.

As for the idea that epigenetics somehow explains the effects of environmental exposure to damaging agents…I’m trying to think of any clear examples of how that occurs, and I’m a developmental biologist who has been studying teratology for a few decades. We don’t invoke epigenetics to account for abnormal cell death, or signaling failures, or mismigration, or endocrine disruption, or any of the phenomena that are commonly responsible for non-genetic errors in development. His example is to claim that exposure to DDT in the 50s and 60s somehow led to the current high frequency of obesity.

He’s got no evidence. He has no mechanism, other than to say, “epigenetics!”

The thing to watch out for next is revealed at about 4:00 in the video, where he talks about using diet and behavior to give yourself a “healthy epigenome”, whatever that is. I’m sure some unscrupulous, dishonest someone, somewhere is writing a diet book about super-foods to super-charge your epigenome for you and your baby.

I’m calling it. There are already plenty of pseudoscientific books that mangle the concept of epigenetics. I’m sure the ones that will turn it into a marketing fad are coming up soon. We’ve already got a lot of books touting the microbiome as the cure-all for everything — I can easily imagine the fusion of the epigenome and microbiome hype machines popping up on Amazon.

Can I claim royalties for predicting it?

Yes, you are a fish

I get this question all the time, and I just got asked it again: “Did you really say that humans are fish in that Ray Comfort video?” Yes, I did, and I guess I have to explain it again.

There are multiple meanings of “fish”. We can use it to refer to specific species or an extant category of animals: salmon are fish, halibut are fish, herring are fish. No one objects to that, and they all understand that if I said “humans are still salmon”, that would be wrong.

But another way the term is used is as a descriptor for a clade. A taxonomic clade is a “grouping that includes a common ancestor and all the descendants (living and extinct) of that ancestor”.

clade

So, for instance, humans belong to the mammalian clade, which includes mice and cats and cows. If we have transhuman, part-cyborg descendants, they will still be mammals, because, note, by definition a clade must include all the descendants of an ancestor. We’re trapped! There’s no way our progeny can exit the clade!

We’re also members of multiple clades. For example, the tetrapod clade is the group that descended from a 4-limbed ancestor, an early amphibian, so it includes frogs and salamanders, and also reptiles, mammals, and birds, and the fact that we’re weird bipeds that have specialized our two pairs of limbs in odd ways, or that birds have turned a forelimb into a wing, doesn’t get us out of the club labeled “four footed”.

The thing about the clades of mammals and tetrapods, though, is that we have convenient generic labels for the groups: we can say “humans are mammals”, and we don’t get hordes of clueless people gawping and saying, “Did he just call me a mouse? That’s absurd!” But we belong to another clade, all the organisms descended from an ancient fish, and “fish” is the common label there. People generally have such a dim comprehension of the diversity of the fishes, though, that they hear a biologist pointing out that we belong, and will always belong, to the fish clade, and they think, “Did he just call me a sturgeon? That’s absurd!”

One way to get around the problem is to get technical. I could say we’re all gnathostomes, and nobody would freak out because most of them wouldn’t have the slightest idea what I was talking about. So I could hide in technical obfuscation. But the point is that you are descended from an ancestor that was a torpedo-shaped aquatic vertebrate with gills, a fish. You can never escape your ancestry. Embrace Your Inner Fish.

innerfish

By the way, another way “fish” is defined taxonomically is as a craniate that is not a tetrapod, and if you use that definition, we are not fish. But that requires explicitly creating a paraphyletic group (that’s what you call it when you take a clade and willfully exclude a smaller clade), and that’s just annoying.