(Roughly) Daily

Posts Tagged ‘Natural Selection

“Two obsessions are the hallmarks of Nature’s artistic style: Symmetry- a love of harmony, balance, and proportion [and] Economy- satisfaction in producing an abundance of effects from very limited means”*…

Life is built of symmetrical structures. But why? Sachin Rawat explores…

Life comes in a variety of shapes and sizes, but all organisms generally have at least one feature in common: symmetry.

Notice how your left half mirrors the right or the radial arrangement of the petals of a flower or a starfish’s arms. Such symmetry persists even at the microscopic level, too, in the near-spherical shape of many microbes or in the identical sub-units of different proteins.

The abundance of symmetry in biological forms begs the question of whether symmetric designs provide an advantage. Any engineer would tell you that they do. Symmetry is crucial to designing modular, robust parts that can be combined together to create more complex structures. Think of Lego blocks and how they can be assembled easily to create just about anything.

However, unlike an engineer, evolution doesn’t have the gift of foresight. Some biologists suggest that symmetry must provide an immediate selective advantage. But any adaptive advantage that symmetry may provide isn’t by itself sufficient to explain its pervasiveness in biology across scales both great and small.

Now, based on insights from algorithmic information theory, a study published in Proceedings of the Natural Academy of Sciences suggests that there could be a non-adaptive explanation…

Symmetrical objects are less complex than non-symmetrical ones. Perhaps evolution acts as an algorithm with a bias toward simplicity: “Simple is beautiful: Why evolution repeatedly selects symmetrical structures,” from @sachinxr in @bigthink.

Frank Wilczek (@FrankWilczek)

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As we celebrate symmetry, we might recall (speaking of symmetry) that it was on this date in 1963 that the Equal Pay Act of 1963 was signed into law by president John F. Kennedy. Aimed at abolishing wage disparity based on sex, it provided that “[n]o employer having employees subject to any provisions of this section [section 206 of title 29 of the United States Code] shall discriminate, within any establishment in which such employees are employed, between employees on the basis of sex by paying wages to employees in such establishment at a rate less than the rate at which he pays wages to employees of the opposite sex in such establishment for equal work on jobs[,] the performance of which requires equal skill, effort, and responsibility, and which are performed under similar working conditions, except where such payment is made pursuant to (i) a seniority system; (ii) a merit system; (iii) a system which measures earnings by quantity or quality of production; or (iv) a differential based on any other factor other than sex […].

Those exceptions (and lax enforcement) have meant that, 60 years later, women in the U.S. are still paid less than men in comparable positions in nearly all occupations, earning on average 83 cents for every dollar earned by a man in a similar role.

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“How is it that you keep mutating and can still be the same virus?”*…

Thale cress (Arabidopsis thaliana)

A common plant has yielded insights that question a fundamental assumption in biology– more specifically, an assumption about the mechanism of natural selection…

A simple roadside weed may hold the key to understanding and predicting DNA mutation, according to new research from University of California, Davis, and the Max Planck Institute for Developmental Biology in Germany.

The findings, published today in the journal Nature, radically change our understanding of evolution and could one day help researchers breed better crops or even help humans fight cancer.

Mutations occur when DNA is damaged and left unrepaired, creating a new variation. The scientists wanted to know if mutation was purely random or something deeper. What they found was unexpected.

“We always thought of mutation as basically random across the genome,” said Grey Monroe, an assistant professor in the UC Davis Department of Plant Sciences who is lead author on the paper. “It turns out that mutation is very non-random and it’s non-random in a way that benefits the plant. It’s a totally new way of thinking about mutation.”

Knowing why some regions of the genome mutate more than others could help breeders who rely on genetic variation to develop better crops. Scientists could also use the information to better predict or develop new treatments for diseases like cancer that are caused by mutation.

“Our discoveries yield a more complete account of the forces driving patterns of natural variation; they should inspire new avenues of theoretical and practical research on the role of mutation in evolution,” the paper concludes.

Evolutionary theory revised? A new study challenges the received wisdom that that DNA mutations are random. Read the underlying paper here.

* Chuck Palahniuk, Invisible Monsters

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As we contemplate change, we might send micro-biological birthday greetings to Ruth Sager; she was born on this date in 1918. A geneticist, she had two careers in science.

In the 1950s and 1960s, she pioneered the field of cytoplasmic genetics by discovering transmission of genetic traits through chloroplast DNA, the first known example of genetics not involving the cell nucleus. The academic community did not acknowledge the significance of her contribution until after the second wave of feminism in the 1970s.

Then, in the early 1970s, she moved into cancer genetics (with a specific focus on breast cancer); she proposed and investigated the roles of tumor suppressor genes.

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“The element of mystery to which you want to draw attention should be surrounded and veiled by a quite obvious, readily recognisable commonness”*…

Day And Night (1938)

An appreciation of the marvelous M.C. Escher…

Despite being a fan of Rennaisance Art and the work of the Impressionists, he feels increasingly pulled in a different direction…

When you look at this picture, you’re flipping between world views. Either you’re seeing the white birds, and the bright, presumably sunlit day scene with its cheerful flotilla of steam ships puffing their way upriver – or you’re seeing the black birds, and your eye is drawn to the night-shrouded landscape where the houses have their lights on and the sky’s already eaten the horizon & is creeping nearer…

Except, that’s not quite right. The black birds are in the daylight side, and the white ones are flying into the night. These aren’t just mirror images: they’re like the Ancient Chinese yin-yang symbol, each side containing part of its opposite…

Escher’s love of the fantastical is primarily inspired by what he sees around him, not what he can dream up out of next to nothing… By looking closely at the real world, and trying to understand how it works, Escher will invite his initially small but intensely loyal fanbase to explore some very strange mysteries indeed.

Ascending And Descending (1960)

It’s the 1960s now, and nonconformity is all the rage. Hair is getting longer, psychedelics-powered artistry is flourishing, and anything that seems to scream to hell with the rules is increasingly in vogue… Because of the fantastical elements of his work, Escher is acquiring a reputation as a surrealist. As a self-identifying “reality enthusiast,” it’s the very last thing he wants. Take Ascending & Descending, where he’s clearly turning his imagination to the futility of so much in the human-centred world. In a letter to a friend, he says:

“Yes, yes, we climb up and up, we imagine we are ascending; one step is about 10 inches high, terribly tiring – and where does it get us? Nowhere.”

But until the end of his career, his work will continue to speak to something deeper – a rebellion against human incuriosity, or a constant rallying-cry for the act of paying attention…

Read it in full: “Fooling With Certainty: The Impossibly Real Worlds Of MC Escher,” from Mike Sowden (@Mikeachim)

* M. C. Escher

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As we look closely, we might recall that it was on this date in 1859 that our perspective was shifted in a different kind of way: Charles Darwin published The Origin of the Species.  Actually, on that day he published On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life; the title was shortened to the one we know with the sixth edition in 1872.

Title page of the 1859 edition

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(Roughly) Daily will be on a brief Thanksgiving hiatus, returning when the the tryptophan haze has passed…

“Nature is pleased with simplicity”*…

As Clare Booth Luce once said, sometimes “simplicity is the ultimate sophistication”…

… The uniformity of the cosmic microwave background (CMB) tells us that, at its birth, ‘the Universe has turned out to be stunningly simple,’ as Neil Turok, director emeritus of the Perimeter Institute for Theoretical Physics in Ontario, Canada, put it at a public lecture in 2015. ‘[W]e don’t understand how nature got away with it,’ he added. A few decades after Penzias and Wilson’s discovery, NASA’s Cosmic Background Explorer satellite measured faint ripples in the CMB, with variations in radiation intensity of less than one part in 100,000. That’s a lot less than the variation in whiteness you’d see in the cleanest, whitest sheet of paper you’ve ever seen.

Wind forward 13.8 billion years, and, with its trillions of galaxies and zillions of stars and planets, the Universe is far from simple. On at least one planet, it has even managed to generate a multitude of life forms capable of comprehending both the complexity of our Universe and the puzzle of its simple origins. Yet, despite being so rich in complexity, some of these life forms, particularly those we now call scientists, retain a fondness for that defining characteristic of our primitive Universe: simplicity.

The Franciscan friar William of Occam (1285-1347) wasn’t the first to express a preference for simplicity, though he’s most associated with its implications for reason. The principle known as Occam’s Razor insists that, given several accounts of a problem, we should choose the simplest. The razor ‘shaves off’ unnecessary explanations, and is often expressed in the form ‘entities should not be multiplied beyond necessity’. So, if you pass a house and hear barking and purring, then you should think a dog and a cat are the family pets, rather than a dog, a cat and a rabbit. Of course, a bunny might also be enjoying the family’s hospitality, but the existing data provides no support for the more complex model. Occam’s Razor says that we should keep models, theories or explanations simple until proven otherwise – in this case, perhaps until sighting a fluffy tail through the window.

Seven hundred years ago, William of Occam used his razor to dismantle medieval science or metaphysics. In subsequent centuries, the great scientists of the early modern era used it to forge modern science. The mathematician Claudius Ptolemy’s (c100-170 CE) system for calculating the motions of the planets, based on the idea that the Earth was at the centre, was a theory of byzantine complexity. So, when Copernicus (1473-1543) was confronted by it, he searched for a solution that ‘could be solved with fewer and much simpler constructions’. The solution he discovered – or rediscovered, as it had been proposed in ancient Greece by Aristarchus of Samos, but then dismissed by Aristotle – was of course the solar system, in which the planets orbit around the Sun. Yet, in Copernicus’s hands, it was no more accurate than Ptolemy’s geocentric system. Copernicus’s only argument in favour of heliocentricity was that it was simpler.

Nearly all the great scientists who followed Copernicus retained Occam’s preference for simple solutions. In the 1500s, Leonardo da Vinci insisted that human ingenuity ‘will never devise any [solutions] more beautiful, nor more simple, nor more to the purpose than Nature does’. A century or so later, his countryman Galileo claimed that ‘facts which at first seem improbable will, even on scant explanation, drop the cloak which has hidden them and stand forth in naked and simple beauty.’ Isaac Newton noted in his Principia (1687) that ‘we are to admit no more causes of natural things than such as are both true and sufficient to explain their appearances’; while in the 20th century Einstein is said to have advised that ‘Everything should be made as simple as possible, but not simpler.’ In a Universe seemingly so saturated with complexity, what work does simplicity do for us?

Part of the answer is that simplicity is the defining feature of science. Alchemists were great experimenters, astrologers can do maths, and philosophers are great at logic. But only science insists on simplicity…

Just why do simpler laws work so well? The statistical approach known as Bayesian inference, after the English statistician Thomas Bayes (1702-61), can help explain simplicity’s power. Bayesian inference allows us to update our degree of belief in an explanation, theory or model based on its ability to predict data. To grasp this, imagine you have a friend who has two dice. The first is a simple six-sided cube, and the second is more complex, with 60 sides that can throw 60 different numbers. Suppose your friend throws one of the dice in secret and calls out a number, say 5. She asks you to guess which dice was thrown. Like astronomical data that either the geocentric or heliocentric system could account for, the number 5 could have been thrown by either dice. Are they equally likely? Bayesian inference says no, because it weights alternative models – the six- vs the 60-sided dice – according to the likelihood that they would have generated the data. There is a one-in-six chance of a six-sided dice throwing a 5, whereas only a one-in-60 chance of the 60-sided dice throwing a 5. Comparing likelihoods, then, the six-sided dice is 10 times more likely to be the source of the data than the 60-sided dice.

Simple scientific laws are preferred, then, because, if they fit or fully explain the data, they’re more likely to be the source of it.

In my latest book, I propose a radical, if speculative, solution for why the Universe might in fact be as simple as it’s possible to be. Its starting point is the remarkable theory of cosmological natural selection (CNS) proposed by the physicist Lee Smolin. CNS proposes that, just like living creatures, universes have evolved through a cosmological process, analogous to natural selection.

Smolin came up with CNS as a potential solution to what’s called the fine-tuning problem: how the fundamental constants and parameters, such as the masses of the fundamental particles or the charge of an electron, got to be the precise values needed for the creation of matter, stars, planets and life. CNS first notes the apparent symmetry between the Big Bang, in which stars and particles were spewed out of a dimensionless point at the birth of our Universe, and the Big Crunch, the scenario for the end of our Universe when a supermassive black hole swallows up stars and particles before vanishing back into a dimensionless point. This symmetry has led many cosmologists to propose that black holes in our Universe might be the ‘other side’ of Big Bangs of other universes, expanding elsewhere. In this scenario, time did not begin at the Big Bang, but continues backwards through to the death of its parent universe in a Big Crunch, through to its birth from a black hole, and so on, stretching backward in time, potentially into infinity. Not only that but, since our region of the Universe is filled with an estimated 100 billion supermassive black holes, Smolin proposes that each is the progenitor of one of 100 billion universes that have descended from our own.

The model Smolin proposed includes a kind of universal self-replication process, with black holes acting as reproductive cells. The next ingredient is heredity. Smolin proposes that each offspring universe inherits almost the same fundamental constants of its parent. The ‘almost’ is there because Smolin suggests that, in a process analogous to mutation, their values are tweaked as they pass through a black hole, so baby universes become slightly different from their parent. Lastly, he imagines a kind of cosmological ecosystem in which universes compete for matter and energy. Gradually, over a great many cosmological generations, the multiverse of universes would become dominated by the fittest and most fecund universes, through their possession of those rare values of the fundamental constants that maximise black holes, and thereby generate the maximum number of descendant universes.

Smolin’s CNS theory explains why our Universe is finely tuned to make many black holes, but it does not account for why it is simple. I have my own explanation of this, though Smolin himself is not convinced. First, I point out that natural selection carries its own Occam’s Razor that removes redundant biological features through the inevitability of mutations. While most mutations are harmless, those that impair vital functions are normally removed from the gene pool because the individuals carrying them leave fewer descendants. This process of ‘purifying selection’, as it’s known, maintains our genes, and the functions they encode, in good shape.

However, if an essential function becomes redundant, perhaps by a change of environment, then purifying selection no longer works. For example, by standing upright, our ancestors lifted their noses off the ground, so their sense of smell became less important. This means that mutations could afford to accumulate in the newly dispensable genes, until the functions they encoded were lost. For us, hundreds of smell genes accumulated mutations, so that we lost the ability to detect hundreds of odours that we no longer need to smell. This inevitable process of mutational pruning of inessential functions provides a kind of evolutionary Occam’s Razor that removes superfluous biological complexity.

Perhaps a similar process of purifying selection operates in cosmological natural selection to keep things simple…

It’s unclear whether the kind of multiverse envisaged by Smolin’s theory is finite or infinite. If infinite, then the simplest universe capable of forming black holes will be infinitely more abundant than the next simplest universe. If instead the supply of universes is finite, then we have a similar situation to biological evolution on Earth. Universes will compete for available resources – matter and energy – and the simplest that convert more of their mass into black holes will leave the most descendants. For both scenarios, if we ask which universe we are most likely to inhabit, it will be the simplest, as they are the most abundant. When inhabitants of these universes peer into the heavens to discover their cosmic microwave background and perceive its incredible smoothness, they, like Turok, will remain baffled at how their universe has managed to do so much from such a ‘stunningly simple’ beginning.

The cosmological razor idea has one further startling implication. It suggests that the fundamental law of the Universe is not quantum mechanics, or general relativity or even the laws of mathematics. It is the law of natural selection discovered by Darwin and Wallace. As the philosopher Daniel Dennett insisted, it is ‘The single best idea anyone has ever had.’ It might also be the simplest idea that any universe has ever had.

Does the existence of a multiverse hold the key for why nature’s laws seem so simple? “Why simplicity works,” from JohnJoe McFadden (@johnjoemcfadden)

* “Nature does nothing in vain when less will serve; for Nature is pleased with simplicity and affects not the pomp of superfluous causes.” – Isaac Newton, The Mathematical Principles of Natural Philosophy

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As we emphasize the essential, we might spare a thought for Martin Gardner; he died on this date in 2010. Though not an academic, nor ever a formal student of math or science, he wrote widely and prolifically on both subjects in such popular books as The Ambidextrous Universe and The Relativity Explosion and as the “Mathematical Games” columnist for Scientific American. Indeed, his elegant– and understandable– puzzles delighted professional and amateur readers alike, and helped inspire a generation of young mathematicians.

Gardner’s interests were wide; in addition to the math and science that were his power alley, he studied and wrote on topics that included magic, philosophy, religion, and literature (c.f., especially his work on Lewis Carroll– including the delightful Annotated Alice— and on G.K. Chesterton).  And he was a fierce debunker of pseudoscience: a founding member of CSICOP, and contributor of a monthly column (“Notes of a Fringe Watcher,” from 1983 to 2002) in Skeptical Inquirer, that organization’s monthly magazine.

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“Nothing so much assists learning as writing down what we wish to remember”*…

Lewis Carroll’s commonplace shows his musings on ciphers and detailed handwritten charts exploring labryinths. [source]

Your correspondent is away for the rest of this month; regular service will resume on or around September 1st. For the hiatus, a little something to occupy you…

As readers of this blog will have deduced, (Roughly) Daily is a kind of commonplace book…

Commonplace books (or commonplaces) are a way to compile knowledge, usually by writing information into books. They have been kept from antiquity, and were kept particularly during the Renaissance and in the nineteenth century. Such books are similar to scrapbooks filled with items of many kinds: sententiae, notes, proverbs, adages, aphorisms, maxims, quotes, letters, poems, tables of weights and measures, prayers, legal formulas, and recipes… Commonplaces are used by readers, writers, students, and scholars as an aid for remembering useful concepts or facts. Each one is unique to its creator’s particular interests but they almost always include passages found in other texts, sometimes accompanied by the compiler’s responses.

Commonplace book

As Steven Johnson points out, commonplace books have a storied history…

Scholars, amateur scientists, aspiring men of letters — just about anyone with intellectual ambition in the seventeenth and eighteenth centuries was likely to keep a commonplace book. In its most customary form, “commonplacing,” as it was called, involved transcribing interesting or inspirational passages from one’s reading, assembling a personalized encyclopedia of quotations. It was a kind of solitary version of the original web logs: an archive of interesting tidbits that one encountered during one’s textual browsing. The great minds of the period — Milton, Bacon, Locke — were zealous believers in the memory-enhancing powers of the commonplace book. There is a distinct self-help quality to the early descriptions of commonplacing’s virtues: in the words of one advocate, maintaining the books enabled one to “lay up a fund of knowledge, from which we may at all times select what is useful in the several pursuits of life.”

The philosopher John Locke first began maintaining a commonplace book in 1652, during his first year at Oxford. Over the next decade he developed and refined an elaborate system for indexing the book’s content. Locke thought his method important enough that he appended it to a printing of his canonical work, An Essay Concerning Human Understanding

The Glass Box And The Commonplace Book

Perhaps because in these interconnected days almost anything seems re-retrievable at a click, not too many bother keeping commonplaces. That’s a shame. Your correspondent can testify that the habit– whether practiced in a book or digitally– is a powerful aid both to learning and to writing.

Happily, there are lots of sources of good advice for getting started, e.g., here, here (source of the image above), and here. There’s even a Masterclass.

* Marcus Tullius Cicero

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As we live and learn, we might recall that it was on this date in 1858 that (prodigious journaler and commonplace keeper) Charles Darwin and Alfred Russel Wallace published “On the tendency of species to form varieties; and on the perpetuation of varieties and species by natural selection” in the Journal of the Proceedings of the Linnean Society. This was the first printed formal exposition of the theory of evolution by natural selection.

Darwin had developed the essential elements of his theory by 1838 and set them on paper in 1844; however, he chose to keep his work on evolution unpublished for the time, instead concentrating his energies first on the preparation for publication of his geological work on the Beagle voyage , and then on an exhaustive eight-year study of the barnacle genus Cirripedia.

In 1856, at the urging of Charles Lyell, Darwin began writing a vast encyclopedic work on natural selection; however, it is possible that the extremely cautious Darwin might never have published his evolutionary theories during his lifetime had not Alfred Russel Wallace, a naturalist born in New Zealand, independently discovered the theory of natural selection. Wallace conceived the theory of natural selection during an attack of malarial fever in Ternate in the Mollucas, Indonesia (Febuary, 1858) and sent a manuscript summary to Darwin, who feared that his discovery would be pre-empted.

In the interest of justice Joseph Dalton Hooker and Charles Lyell suggested joint publication of Wallace’s paper prefaced by a section of a manuscript of a work on species written by Darwin in 1844, when it was read by Hooker, plus an abstract of a letter by Darwin to Asa Gray, dated 1857, to show that Darwin’s views on the subject had not changed between 1844 and 1857. The papers by Darwin and Wallace were read by Lyell before the Linnean Society on July 1, 1858 and published on August 20.

Darwin & Wallace Issue the First Printed Exposition of the Theory of Evolution by Natural Selection

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