Archive for the ‘Evolutionary’ Category
The model suggests that dislocation–dislocation interactions dominate at larger scales, whereas the behavior at the smallest MD scales is controlled by nucleation over energy barriers. These results provide a basic framework for understanding and predicting size-dependent plasticity in nanoscale asperities under contact conditions in realistic engineered surfaces.
Some very interesting papers on Darwin from the Two Centuries of Darwin Sackler Colloquium — examples: Daniel Dennett on Darwin’s “strange inversion of reasoning”, Robert J Richards on Darwin’s place in the history of thought: A reevaluation, Elliott Sober on Did Darwin write the Origin backwards? , and Francisco J Ayala on Darwin and the scientific method. Have fun!
A couple of interesting papers in the latest issue of PNAS!
At the molecular level of biology, the competition for favorable outcomes has been shaped by evolution, just as in more familiar examples from ecological biology. At both levels, this competition is often based on raw speed. There are differences, of course. Most notably, a race between molecules is more often determined by diffusional dynamics than by inertial dynamics. The driving forces on molecules typically comprise electrostatic nudges rather than thundering hooves digging into soil. Electrostatic interactions can be surprisingly effective, however. The rate of degradation of the neurotransmitter acetylcholine by the synaptic enzyme acetylcholinesterase is known to be increased by a factor of up to a few hundred as a result of “electrostatic steering” of the positively charged acetylcholine molecule toward the predominantly negative active-site region of the enzyme [...]. This tends to optimize the clearing and resetting of neuromuscular junctions and other cholinergic synapses, which offered a clear competitive advantage to our successful ancestors, relative to more sluggish individuals of their species who faced the same predators. Such selective pressures are also recorded in proteins at the next level of a hierarchy, in some of the venom molecules of snakes such as the green mamba that prey on small mammals in sub-Saharan East Africa. The green mamba toxin fasciculin-2 is a small protein whose positively charged surface is attracted to, and clamps down on, the active-site entrance of acetylcholinesterase, causing muscular activity of the unfortunate rat or other prey to cease. Here, again, the binding involves electrostatically steered diffusion, and the binding speed is increased by a factor of up to a few hundred by the electrostatic attraction between the proteins (1). Many other examples of electrostatically steered, diffusion-controlled processes are now known, including such familiar ones as the polymerization of actin [...]. In a recent issue of PNAS, a new article by Qin and Zhou greatly deepens our insight into these important processes, and extends the range of analysis to include reactions in which the rates may be influenced by events following the initial diffusional encounter [...].
Emotion research has something in common with a drunk searching for his car keys under a street lamp. “Where did you lose them?” asks the cop. “In the alley,” says the drunk, “but the light is so much better over here.” For emotion research, the light shines most brightly on the face, whose movements can be coded, compared across cultures, and quantified by electromyography. All of the “basic” emotions described by Paul Ekman [...] and others (happiness, sadness, anger, fear, surprise, and disgust) earned their place on the list by being face-valid. The second source of illumination has long been animal research. Emotions that can be reliably triggered in rats, such as fear and anger, have been well-studied, down to specific pathways through the amygdala [...]. But emotions that cannot be found on the face or in a rat, such as moral elevation and admiration, are largely abandoned back in the alley. We know they are there, but nobody can seem to find a flashlight. It is therefore quite an achievement that, as described in this issue of PNAS, Immordino-Yang, McCall, Damasio, and Damasio [...] managed to drag an fMRI scanner back there and have given us a first glimpse of the neurological underpinnings of elevation and admiration.
Few links from Telegraph:
He was also sure that since Strand’s core strength was books, he would be happier with customers who came for books than for a cup of coffee. I doubt the longevity of this faith in a world ruled by business models, but I admire that man for having devoted his life to the printed word and making it accessible to more and more people. Visit the Strand website and you will know what I mean. After a mention of its founding in 1948, the highlights are on its discounts. Strand was the first in the world to offer 20 per cent discount; it now offers up to 50 per cent. The world’s biggest book chain in comparison was late to offer discounts and still does no better than 20 per cent. For me, such an approach, plenty of books and a store owner like Shanbhag, are all that matters. The cappuccino can wait.
Just this morning I was discussing with a colleague of mine about the service, sincerity and the discounts at Strand, Bangalore which made book buying such a pleasure (not to mention Kadambam next to it, as long as it lasted — which was not for too long).
… the true force of Darwinism in nonsense literature comes through in the works of Sukumar Ray (1887-1923), the poet, printer, humorist and illustrator from Bengal. From his early poem, “Khichudi”, Ray disclosed a playfully witty, yet empathetic, understanding of the inner lives of animals. He not only created a menagerie of fantastic creatures here, but also endowed each of them with a fantasy life. In the poem, the duck (hans) fuses with a porcupine (sajaru) to become hansjaru, the caterpillar chooses to merge with the goat for mysterious reasons. Some of these strange meetings are self-conscious, as if out of some evolutionary design the best of two disparate worlds have conspired to become one: the lion with horns like the deer or the giraffe with the torso of a grasshopper. Such a mix-up, of herbivore and carnivore or winged and terrestrial beings, hints at — and parodies — an evolutionary process (like Darwin’s natural selection) that allows only the best features to endure by coming together.
The Darwinian urge in nature to favour the fittest is also explored in the figure of Kimbhut, another bizarre assembly of body parts giving rise to a hotchpotch animal. In the poem, “Kimbhut”, a sniffling, disgruntled creature longs for the voice of the cuckoo, the tail of an iguana, wings of a bird, the elephant’s snout, and the kangaroo’s legs. The end product is so fearfully ugly that it only inspires jeers. That Ray was deeply fascinated by Darwin is evident from the mini-biography he wrote for the young readers of the Sandesh magazine, which he edited. In that article, Ray explained the scientific premises of Darwin’s theories — why weaker species, unable to adapt themselves to changes in the environment, become extinct, how bodily features evolve through use and disuse.
The rationalism of this piece also pervades the origins of Ray’s nonsense animals, even though wish-fulfilment need not always bring a happy ending.
Reminds me that I should get that Rupa published translation of one of Sukumar Ray’s books (about some owl or something, if I remember correct).
Like the search for the most authentic portrait of Shakespeare, the debate over what the dodo looked like is yet to be over. A Dutch illustration going back to 1598 shows a gawky little creature with tiny wings like stumps, looking like a Walt Disney cartoon. In 1651, Jan Savery painted the dodo as an obese, smug bird with ugly, beady eyes. George Edwards painted it as a colourful, glamorous bird in 1759.
These striking disparities were not due to artistic errors alone. In its natural habitat, on the island of Mauritius, the dodo may have been a slim, even unremarkable, bird. When explorers started taking dodos to Europe, the birds lost touch with their natural diet. As their eating habit changed, so did their body structure. Still the bird proved inedible for humans because of its coarse, tasteless flesh. But dogs, cats, rats and pigs ate up its eggs, leading to its extinction in the 17th century.
J F Crow in Journal of Biology (free registration required to read the article) discusses the relevance of mathematical models in evolutionary studies — in a piece that has some interesting academic gossip too:
In 1959 Ernst Mayr (…) flung down the gauntlet [...] at the feet of the three great population geneticists RA Fisher, Sewall Wright and JBS Haldane (…): “But what, precisely,” he said, “has been the contribution of this mathematical school to the evolutionary theory, if I may be permitted to ask such a provocative question?” His skepticism arose in part from the fact that the mathematical theory at the time had little to say about speciation, Mayr’s major interest. But his criticism was more broadly addressed to the utility of the entire approach. A particular focus was the simplification that he called “beanbag genetics”, in which “Evolutionary genetics was essentially presented as an input or output of genes, as the adding of certain beans to a beanbag and the withdrawing of others.” [...].
Mayr was, however, criticizing textbook simplifications, rather than the actual work of the three pioneers. Far from treating gene frequency changes as analogous to the consequence of beans jostling at random in a bag, both Fisher and Wright considered gene interactions in detail. Fisher (…) showed that, despite interactions between genes, natural selection acts on the additive component of the genetic variance. It is as if nature were familiar with least squares. The beanbag criticism was particularly inappropriate for Wright (…), who specifically devised his ‘shifting balance’ theory as a way for a population to go from one harmonious gene combination (Mayr would say “integrated genotype”) to another when intermediates were disadvantageous.
Who was to answer Mayr’s criticism? Fisher was already dead, and in any case preferred attack to defense, and Wright was too gentle – though admittedly not always when Mayr was involved: returning from Italy where he had received the prestigious Balzan Prize in 1984, Wright told me that the value of the prize was considerably diminished when he discovered that Mayr had won it the year before. In the event, however, it was Haldane (…) who took up the challenge. And he did it with flair and gusto. The result was “A defense of beanbag genetics” [...]. This was Haldane at his best – witty, spirited, informed, interesting and convincing.
But the larger question remains: what indeed has been the contribution of mathematical theory to evolution? Mathematics is not central to evolution in the way it has been in theoretical physics. Solid advances have been made without using mathematics, much being due to Mayr himself [...]. And these continue. Yet, I shall argue that mathematical ideas have made important, and often essential, contributions, and still do. Many concepts that are now established were arrived at mathematically, although their origins have since been forgotten.
People who say that Darwin didn’t have many ideas usually haven’t read any Darwin. Now, I might say this about many nineteenth-century thinkers. When you go through the works of Spencer, or Haeckel, or Wundt, you discover that these people were remarkably thoughtful. They went through reams of examples — the kind of writing you rarely see people do anymore. Darwin was one of this number, perhaps the foremost. So it should come as no surprise that his works were full of details that would precipitate or presage developments as much as 150 years later.
But there’s something more. Darwin threaded many needles in his writing, finding the right solution for many contradictions — not only in his naturalism but also in the way his theory provoked social resistance. Darwin had the first theory of human evolution. It wasn’t correct, as we now know, but it did the essential thing: it showed a way that human features could have emerged by natural pressures of the environment. Darwin found a plausible explanation for the diversity of races — one not rooted in the divine order, but in natural history. He championed the monogenetic theory against polygenists who held that human races had separate origins. And he integrated the best empirical data from animal and plant breeding into the understanding of the natural world. Possibly most important, he insisted on the testability of his hypotheses, and gave specific criteria that would falsify them.
Sure, many of Darwin’s ideas now seem obvious. When different varieties have different rates of intrinsic growth, one will inevitably supersede the others. Small changes add up to big changes over long times. Common descent explains common morphology.
But it is precisely the reams of details that remind us so forcefully that there is more to being a scientist than having good ideas. You also have to have the courage to tell the world exactly how your ideas could be rejected. We have rejected many of Darwin’s in the succeeding 150 years. Still the core remains.
A very well written piece. Take a look!
Grrlscientist explains the paradox and its resolution in a story that involves Ernst Mayr and Jared Diamond, among others, with some oh so… lovely photographs! A must-read!
Even though not quite in the same league as the ideas discussed, this post, touched a cord with me since I also face so many of my close relatives and friends who believe that all the ills and diseases that we face today were either absent in an earlier “golden” Indian era or were completely treatable and curable by the local doctors and physicians of that period!
As an evolutionary biologist, I was filled with enthusiasm at first over the idea of a modern mismatch between everyday life and our evolutionary past. But a closer look reveals that not all evolutionary ideas are created equal; even for Darwinians, the devil is in the details. The notion that there was a time of perfect adaptation, from which we’ve now deviated, is a caricature of the way evolution works.
Take a look!
The publci outreach page of the New York Academy of Sciences, Science and the city has a few interesting pieces that have been published recently:
Lax is passionate about the need for education reform. “I’ve seen for a long time what I call the paradox of education: Science and mathematics are growing by leaps and bounds on the research frontier, so what we teach in high school, college, and graduate school is falling behind by leaps and bounds.” But by fostering intimate cooperation between research mathematicians and educators, he says, we can “simplify the teaching of old topics, and make room for new ones.”
A few years ago I had a series of conversations with the Dalai Lama about the nature of emotion and compassion reported in our book Emotional Awareness. I explained recent research in which a monkey could get food only by delivering a shock to another monkey. If it was a familiar monkey, the hungry monkey did not attempt to get food for many days. The amount of delayed gratification decreased if it was an unfamiliar monkey, and even more if it was a monkey from a different species.
 Of course, the master himself: an excerpt from Darwin’s Origin of species.