Later On

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Archive for the ‘Evolution’ Category

A Bird’s-Eye View of Nature’s Hidden Order

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Fascinating article by Natalie Wolchover in Quanta:

Seven years ago, Joe Corbo stared into the eye of a chicken and saw something astonishing. The color-sensitive cone cells that carpeted the retina (detached from the fowl, and mounted under a microscope) appeared as polka dots of five different colors and sizes. But Corbo observed that, unlike the randomly dispersed cones in human eyes, or the neat rows of cones in the eyes of many fish, the chicken’s cones had a haphazard and yet remarkably uniform distribution. The dots’ locations followed no discernible rule, and yet dots never appeared too close together or too far apart. Each of the five interspersed sets of cones, and all of them together, exhibited this same arresting mix of randomness and regularity. Corbo, who runs a biology lab at Washington University in St. Louis, was hooked.

“It’s extremely beautiful just to look at these patterns,” he said. “We were kind of captured by the beauty, and had, purely out of curiosity, the desire to understand the patterns better.” He and his collaborators also hoped to figure out the patterns’ function, and how they were generated. He didn’t know then that these same questions were being asked in numerous other contexts, or that he had found the first biological manifestation of a type of hidden order that has also turned up all over mathematics and physics.

Corbo did know that whatever bird retinas are doing is probably the thing to do. Avian vision works spectacularly well (enabling eagles, for instance, to spot mice from a mile high), and his lab studies the evolutionary adaptations that make this so. Many of these attributes are believed to have been passed down to birds from a lizardlike creature that, 300 million years ago, gave rise to both dinosaurs and proto-mammals. While birds’ ancestors, the dinos, ruled the planetary roost, our mammalian kin scurried around in the dark, fearfully nocturnal and gradually losing color discrimination. Mammals’ cone types dropped to two — a nadir from which we are still clambering back. About 30 million years ago, one of our primate ancestors’ cones split into two — red- and green-detecting — which, together with the existing blue-detecting cone, give us trichromatic vision. But our cones, particularly the newer red and green ones, have a clumpy, scattershot distribution and sample light unevenly.

Bird eyes have had eons longer to optimize. Along with their higher cone count, they achieve a far more regular spacing of the cells. But why, Corbo and colleagues wondered, had evolution not opted for the perfect regularity of a grid or “lattice” distribution of cones? The strange, uncategorizable pattern they observed in the retinas was, in all likelihood, optimizing some unknown set of constraints. What these were, what the pattern was, and how the avian visual system achieved it remained unclear. The biologists did their best to quantify the regularity in the retinas, but this was unfamiliar terrain, and they needed help. In 2012, Corbo contacted Salvatore Torquato, a professor of theoretical chemistry at Princeton University and a renowned expert in a discipline known as “packing.” Packing problems ask about the densest way to pack objects (such as cone cells of five different sizes) in a given number of dimensions (in the case of a retina, two). “I wanted to get at this question of whether such a system was optimally packed,” Corbo said. Intrigued, Torquato ran some algorithms on digital images of the retinal patterns and “was astounded,” Corbo recalled, “to see the same phenomenon occurring in these systems as they’d seen in a lot of inorganic or physical systems.”

Torquato had been studying this hidden order since the early 2000s, when he dubbed it “hyperuniformity.” (This term has largely won out over “superhomogeneity,” coined around the same time by Joel Lebowitz of Rutgers University.) Since then, it has turned up in a rapidly expanding family of systems. Beyond bird eyes, hyperuniformity is found in materials called quasicrystals, as well as in mathematical matrices full of random numbers, the large-scale structure of the universe, quantum ensembles, and soft-matter systems like emulsions and colloids.

Scientists are nearly always taken by surprise when it pops up in new places, as if playing whack-a-mole with the universe. They are still searching for a unifying concept underlying these occurrences. In the process, they’ve uncovered novel properties of hyperuniform materials that could prove technologically useful.

From a mathematical standpoint, “the more you study it, the more elegant and conceptually compelling it seems,” said Henry Cohn, a mathematician and packing expert at Microsoft Research New England, referring to hyperuniformity. “On the other hand, what surprises me about it is the potential breadth of its applications.”

A Secret Order

Torquato and a colleague launched the study of hyperuniformity 13 years ago, describing it theoretically and identifying a simple yet surprising example: “You take marbles, you put them in a container, you shake them up until they jam,” Torquato said in his Princeton office this spring. “That system is hyperuniform.” . . .

Continue reading.

Written by LeisureGuy

15 July 2016 at 5:24 pm

Posted in Evolution, Science

The mystery of tiny forelimbs (T. rex et al.)

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Very interesting. And the opening paragraph is classic:

For a dinosaur whose scientific name literally translates to tyrant lizard king,Tyrannosaurus rex gets a whole lot of shit for its hilariously puny arms. From the safety of their computer screens, and with the confidence that can come only from 66 million years of evolutionary separation, online artists have documented, time and again, all the things that this vicious predator probably couldn’t do—high five, apply sunscreen, put on a cardigan, do push-ups, etc.

By Alex Kasprak (and I’m going to be looking for that name) at Motherboard.

And, BTW, in the skeletal reconstruction of Gualicho shinyae, you can sort of see how that could become a chicken.

Written by LeisureGuy

13 July 2016 at 1:05 pm

Posted in Evolution, Science

Primeval feelings: Pre-cognitive processes we share with, say, cats

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Today the cleaning ladies are coming, and the preparatory signs are evident (e.g., beds stripped, sheets washed), so Molly knows that this is a Scary Day, though she may be hazy on the details of why.

And she has been unusually persistent and demanding for a lap—she pretty much pushed my computer out of the way— and has curled up and stuck firmly to my lap, even going to sleep, and completely unresponsive to my “I’m getting up” feints.

I’m aware that the obvious explanation is that a lap is a warm place, but the coincidence of her unusually strong lap demand/need (one drives the other) and the fact of the signs of the imminent arrival of the cleaning ladies (whom Molly does not like: she retreats to her hidey-hole in the closet—her version of a safe room—when they arrive and stays there until they leave) make it hard to ignore the possibility that, beyond warmth, Molly is motivated by a demand/need for the comfort of feeling safe.

One doesn’t want to anthropomorphize unnecessarily, of course, so my immediate thought was, “Do cats have feelings?—that is, in general, not just specifically a feeling of being ‘safe’?”

My immediate follow-on thought was that in lifeform evolution, the ability to distinguish “safe” and “not safe” would offer a decided survival advantage, so I would imagine that being able to make that distinction dates way back and is common to many (most? all?) lifeforms, certainly once some level of awareness is achieved. Being able to recognize safety offers a terrific survival advantage over being totally clueless about safety, and of course even better is actually deriving pleasure (an immediate reward that encourages behavior that has significant long-term benefits) from the feeling of being safe.

All organisms must, willy-nilly, be exposed to risks. Those that have a sense of “safety,” and in particular those that derive pleasure from the “safe” side of the menu, will automatically choose the safest course possible—i.e., they will minimize risk. On the whole, organisms that minimize risk will do better than organisms that don’t, pretty much by definition of “risk.” Thus the significant survival advantage that ensures that the ability to recognize safety, once acquired, is passed along.

Thus I would argue that Molly does derive pleasure from feeling safe, and thus her behavior is to some extent guided by feelings. Feelings arise early in evolution, pre-cognitive in origin and even now non-cognitive in operation. Feelings work at a deeper level than cognition, and surely evolution, having found a good device—the reward of immediate pleasure to encourage behavior with long-term evolutionary advantage—we would expect to see it in other contexts. Sex, for example, is important from the gene’s point of view, so it would follow that the pleasure reward would be substantial.

Another example: Consider the feeling of pleasure that one has after a good night’s rest: it’s a definite pleasure, and I think most have experienced it (and have experienced the displeasure of a poor night’s rest). The pleasure, though real, is certainly not so intense as sexual pleasure, but it’s in the same sort of ballpark as the pleasure from feeling safe: it’s better to have the pleasure than not, so one’s choices are pushed in a general direction. In one case, minimizing risk; in the other, being as well-rested as possible under the circumstances, which, along with the similar sort of pleasure that comes from having a substantial and nutritious meal, is known as “taking care of yourself,” which clearly improves chances of survival, so that’s another feeling that goes deep. And presumably Molly would have such feeliings, and indeed evidence shows that Molly seems motivated to be well-rested and thus, presumably, derives pleasure from it.

So I would say that it’s obvious that animals have feelings if not thoughts, and that some of the feelings that a cat, say, experiences are quite similar, as feelings, to those you and I feel. That sort of feeling is basic to the mechanism. And I think that is why some people do not want to eat animals that have such feelings. We’ve read about how pigs show absolute terror in the slaughterhouse. (For some reason, the meat industry wants to make it illegal to reveal (through video, for example—see link) what the industry does: the day-in, day-out routine: nothing special, just their regular work. That’s what they want to hide soe much that they seek to make it a felony to let people know. And such laws have been passed in some states, states in which business interests are more important than free-speech rights.)

I have to say, that took an unexpected direction. I need to think on this.

Meme lovers will note the absence of the meme, but feelings arrive in the organism’s evolution long before the ability to imitate behaviors and thus play host to memes. Feelings have meme-independent pathways, though I imagine memes can co-opt feelings (“… moon, … June”).

Written by LeisureGuy

6 July 2016 at 3:23 pm

Mene, mene, tekel, upharsim: Mosquitoes Have Developed Resistance to Every One of Our Malaria-Fighting Tools

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Note that the article, foreboding as it is, is one of a series. And truly, take the impact of climate change (in spreading this mosquito that has evolved to resist all our tools by expanding the mosquito’s habitat, northward into the U.S., not to mention the upcoming famines) and add to that the growing list of systemic failure in our most fundamental institutions (about which I earlier blogged), the warning does seem not totally off the wall, as it were.

We unfortunately live in interesting times.

Written by LeisureGuy

28 June 2016 at 11:16 am

Hair, feathers, scales: Much of a muchness

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Kate Lunau has an interesting article in Motherboard. The lede:

Lizard scales and feathers seem like they’re a long way from human hair. But it turns out that fur, feathers, and scales all evolved from one common ancestor, no matter how different these adornments seem: they can all be traced back to a lizardlike creature that roamed the Earth some 310 million years ago. . .

Written by LeisureGuy

24 June 2016 at 3:48 pm

Posted in Evolution, Science

DNA: A Metaphor?

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A very interesting exchange of letters in the NY Review of Books:

In response to:

DNA: ‘The Power of the Beautiful Experiment’ from the June 9, 2016 issue

To the Editors:

H. Allen Orr in his review of Matthew Cobb’s Life’s Greatest Secret [NYR, June 9] gives us a beautifully clear exposition of modern genetics, perhaps the clearest I have ever read. He notes that developments in mathematical information theory and cybernetics soon after World War II had a strong influence on the way biologists began to talk about life and heredity—specifically the idea that DNA contains a “genetic code” replete with “information.” Much the same point can be made about psychology and neuroscience: they too were influenced by these developments in the mathematical theory of information, introducing this notion into the heart of theories of the mind and the brain. But Orr goes on to remark:

In the end, the information sciences provided biologists with loose but useful metaphors and analogies, a language that allowed scientists to think and speak in new ways. But the high-powered mathematics of these fields proved mostly impotent in biology [I would add in psychology and neuroscience too]. No one, for instance, used Shannon’s equations to say anything especially interesting about organisms.

This raises a troubling question: If these recent ways of talking in biology, psychology, and neuroscience are really just loose but useful metaphors, now deeply ingrained in these sciences, what is the literally true way of speaking for which they substitute? How can we reformulate these sciences in such a way that the information metaphors are replaced by sober statement of fact? And do scientists now agree that the borrowed way of talking really is just loose metaphor, or have they come to take it for literal truth? This question seems to me not sufficiently addressed, though very important.

Colin McGinn
Miami, Florida

H. Allen Orr replies:

I thank Colin McGinn for his letter. As usual, he has recognized a key conceptual problem and one that often goes undiscussed—as, for instance, in my review of Life’s Greatest Secret (though not in the book itself). It’s important to note, however, that Matthew Cobb’s claim that mathematical information theory contributed little to the rise of molecular genetics does not itself settle the question of whether DNA harbors information. At least two possibilities present themselves.

The first is that information theory contributed little because the idea of information in DNA is fundamentally mistaken. This is (roughly) the view of some philosophers of biology. One kind of molecule (DNA) is associated with another (protein) but talk of information is mostly metaphorical.

The second possibility is that mathematical information theory contributed little because Claude Shannon’s theory considered the wrong kind of information, not because there’s no information in DNA. Cobb, for instance, notes in Life’s Greatest Secret that Shannon’s measure of information features no clear sense of meaning. For example, two alternative DNA sequences at a gene might show the same amount of Shannon information although one sequence “means” that the resulting protein, say, detoxifies a compound and therefore allows an organism to live while the second sequence “means” that the resulting protein does not detoxify the compound and so lets the organism die. A mathematical theory that is blind to such distinctions is unlikely to be of much use to biologists. But something that is loosely analogous to Shannon’s information and that takes this sort of biological “meaning” into account could still reside in DNA.

McGinn asks how biologists view the idea of information in biology now. He will not be surprised to hear that few consider the question explicitly. If pushed, some biologists may incline to the first view but I suspect that most would favor the second. Whether they are fundamentally right to do so is subject to some debate among philosophers.

Written by LeisureGuy

23 June 2016 at 9:44 am

Posted in Evolution, Math, Science

New Life Found That Lives Off Electricity

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Evolution will eventually find a way to exploit any niche at all.

Written by LeisureGuy

21 June 2016 at 3:26 pm


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