(Roughly) Daily

Posts Tagged ‘evolution

“Life is a whim of several billion cells to be you for a while”*…

An AI-designed xenobot (parent organism, C shape, red) sweeping up stem cells that have been compressed into a ball (incipient offspring, green)

The more we understand how cells produce shape and form, Philip Ball explains, the more inadequate the idea of a genomic blueprint looks…

Where in the embryo does the person reside? Morphogenesis – the formation of the body from an embryo – once seemed so mystifying that scholars presumed the body must somehow already exist in tiny form at conception. In the 17th century, the Dutch microscopist Nicolaas Hartsoeker illustrated this ‘preformationist’ theory by drawing a foetal homunculus tucked into the head of a sperm.

This idea finds modern expression in the notion that the body plan is encoded in our DNA. But the more we come to understand how cells produce shape and form, the more inadequate the idea of a genomic blueprint looks, too. What cells follow is not a blueprint; if they can be considered programmed at all, it’s not with a plan of what to make, but with a set of rules to guide construction. One implication is that humans and other complex organisms are not the unique result of cells’ behaviour, but only one of many possible outcomes.

This view of the cell as a contingent, constructional entity challenges our traditional idea of what a body is, and what it can be. It also opens up some remarkable and even disconcerting possibilities about the prospects of redirecting biology into new shapes and structures. Life suddenly seems more plastic and amenable to being reconfigured by design. Understanding the contingency and malleability of multicellular form also connects us to our deep evolutionary past, when single-celled organisms first discovered the potential benefits of becoming multicellular. ‘The cell may be the focus of evolution, more than genes or even than the organism,’ says Iñaki Ruiz-Trillo of the Institute of Evolutionary Biology in Barcelona. Far from the pinnacle of the tree of life, humans become just one of the many things our cells are capable of doing.

In one of the most dramatic demonstrations to date that cells are capable of more than we had imagined, the biologist Michael Levin of Tufts University in Medford, Massachusetts and his colleagues have shown that frog cells liberated from their normal developmental path can organise themselves in distinctly un-froglike ways. The researchers separated cells from frog embryos that were developing into skin cells, and simply watched what the free cells did.

Culturing cells – growing them in a dish where they are fed the nutrients they need – is a mature technology. In general, such cells will form an expanding colony as they divide. But the frog skin cells had other plans. They clustered into roughly spherical clumps of up to several thousand cells each, and the surface cells developed little hairlike protrusions called cilia (also present on normal frog skin). The cilia waved in coordinated fashion to propel the clusters through the solution, much like rowing oars. These cell clumps behaved like tiny organisms in their own right, surviving for a week or more – sometimes several months – if supplied with food. The researchers called them xenobots, derived from Xenopus laevis, the Latin name of the African clawed frog from which the cells were taken.

Levin and colleagues have recently found a new type of behaviour that xenobots can exhibit. They discovered that these pseudo-organisms can even replicate, after a fashion. Xenobots placed in a dish of cells will move to marshal those loose cells into piles that, over the course of a few days, cluster into new xenobots that then take off through the liquid themselves. Left to their own devices, the xenobots typically manage to produce only a single generation of offspring. But the researchers wondered if they could do better. They made computer simulations to search for xenobot shapes that were better at making new xenobots, using an AI program devised by their team member Josh Bongard of the University of Vermont. The simulations suggested that structures like C-shaped half-doughnuts could sweep up cells more efficiently than the spheroidal xenobots could, making larger (spherical) clusters of ‘offspring’.

The work shows that, by combining biological xenobots with the exploratory power of AI, it’s possible to make a kind of ‘living machine’ devised for a purpose. ‘AI can be brought in to exaggerate an innate capability,’ says Bongard. ‘The AI can “program” new behaviours into organisms by rearranging their morphology rather than their genes.’ The researchers wonder if the simulations might identify other shapes that can assemble different structures, or perhaps perform other tasks entirely. ‘One of my primary interests in this project is exactly how ‘far’ from the wild type [the natural, spontaneously arising form of xenobots] an AI can push things,’ says Bongard. ‘We’re now working on incorporating several new behaviours into xenobots via AI-driven design.’

This perspective entails a new way of thinking about cells: not as building blocks assembled according to a blueprint, but as autonomous entities with skills that can be leveraged to make all manner of organisms and living structures. You might conceive of them as smart, reprogrammable, shapeshifting robots that can move, stick together, and signal to one another – and, by those means, build themselves into elaborate artifacts.

This might also be a better way to conceptualise how our own bodies are built during embryogenesis…

The generative potential of cells equipped for multicellular construction was evident almost as soon as this became a lifestyle option, in evolutionary terms. In the Cambrian explosion around 540 million years ago, all manner of strange body shapes appeared, many of which are no longer exhibited by any creatures on Earth. Perhaps we should regard those forgotten ‘endless forms most beautiful’, to borrow Charles Darwin’s resonant phrase, as an illustration of the constructive potential of the metazoan cell – an exuberant expression of the palette of solutions to the problem of cell assembly, which natural selection then stringently pruned.

Acknowledging that the human form is a contingent outcome of the way our cells are programmed for construction raises some mind-bending questions. Are there, for example, human xenobots (perhaps we might call them anthrobots)? If so, are they truly ‘human’? Might there be a kind of organ or tissue that our cells could make but don’t normally get the chance to? Might our still cells ‘remember’ older evolutionary body shapes?…

How our understanding of genetics is changing– a fascinating dispatch from the frontiers of experimental biology: “What on earth is a xenobot?,” from @philipcball in @aeonmag. Eminently worth reading in full.

* Groucho Marx

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As we ponder possibility, we might spare a thought for Hans Spemann; he died on this date in 1941. An embryologist, he was awarded the Nobel Prize for Physiology and Medicine in 1935 for his discovery of embryonic induction, an effect involving several parts of the embryo in directing the development of the early group of cells into specific tissues and organs.

In a way that can be said to have foreshadowed the work described above, Spemann showed that the in the earliest stage, tissue may be transplanted to different areas of the embryo, where it then develops based on the new location and not from where it came. (For example, early tissue cut from an area of nervous tissue might be moved to an area of skin tissue where it then grows into the same form as the surrounding skin.)

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Written by (Roughly) Daily

September 12, 2022 at 1:00 am

“What is the pattern that connects the crab to the lobster and the primrose to the orchid, and all of them to me, and me to you?”*…

Crab-like body plans have evolved independently at least five times. As Jason P. Dihn explains, biologists are still trying to figure out exactly why…

In 1989, paleontologist Stephen Jay Gould proposed a thought experiment: What would the world look like if we turned back time and replayed the evolutionary tape? “I doubt that anything like Homo sapiens would ever evolve again,” he concluded. Maybe not. But crabs might.

Evolution just can’t stop creating crabs. Believe it or not, the flat-and-wide body plan has evolved at least five different times. The process is called carcinization, and it’s inspired comics, memes and entire subreddits.

Still, biologists don’t know why crabs keep evolving. Figuring it out would satisfy the online masses, sure, but it would also be a step toward solving other important scientific mysteries. For instance, why some species share evolutionary paths while others forge unique ones (looking at you, platypus)…

Convergent evolution: “Evolution Only Thinks About One Thing, and It’s Crabs,” from @JasonPDinh in @DiscoverMag.

Will crabs need to (re-)evolve a sixth time? “Alaska’s snow crabs have disappeared. Where they went is a mystery.”

(Image above: source)

* Gregory Bateson

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As we fiddle with phylogeny, we might spare a thought for Walter Rothschild, 2nd Baron Rothschild; he died on this date in 1937. A British banker, politician and soldier, he is best remembered for his pursuit of his passion— zoology and his collection of species. At its largest, Rothschild’s collection included 300,000 bird skins, 200,000 birds’ eggs, 2,250,000 butterflies and 30,000 beetles, as well as thousands of specimens of mammals, reptiles, and fishes. They formed the largest zoological collection ever amassed by a private individual (and are now part of the Natural History Museum). He named dozens of animal taxa, published Novitates Zoologicae, and authored or co-authored scores of scientific papers.

Related: “How Bird Collecting Evolved Into Bird-Watching.”

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Written by (Roughly) Daily

August 27, 2022 at 1:00 am

“Simplicity is the ultimate sophistication”*…

Sometimes less is more…

Scientists have identified evolutionary modifications in the voice box distinguishing people from other primates that may underpin a capability indispensable to humankind – speaking.

Researchers said… an examination of the voice box, known as the larynx, in 43 species of primates showed that humans differ from apes and monkeys in lacking an anatomical structure called a vocal membrane – small, ribbon-like extensions of the vocal cords.

Humans also lack balloon-like laryngeal structures called air sacs that may help some apes and monkeys produce loud and resonant calls, and avoid hyperventilating, they found.

The loss of these tissues, according to the researchers, resulted in a stable vocal source in humans that was critical to the evolution of speech – the ability to express thoughts and feelings using articulate sounds. This simplification of the larynx enabled humans to have excellent pitch control with long and stable speech sounds, they said.

Sound production mechanisms in people and nonhuman primates are similar, with air from the lungs driving oscillations of the vocal cords. Acoustical energy generated this way then passes through the pharyngeal, oral and nasal cavities and emerges in a form governed by the filtering of specific frequencies dictated by the vocal tract.

“Speech and language are critically related, but not synonymous,” said primatologist and psychologist Harold Gouzoules of Emory University in Atlanta, who wrote a commentary in Science accompanying the study. “Speech is the audible sound-based manner of language expression – and humans, alone among the primates, can produce it.”

Paradoxically, the increased complexity of human spoken language followed an evolutionary simplification.

“I think it’s pretty interesting that sometimes in evolution ‘less is more’ – that by losing a trait you might open the door to some new adaptations,” Fitch said…

Pivotal evolutionary change helped pave the way for human speech,” from Will Dunham @Reuters.

[Image above: source]

* Leonardo da Vinci

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As we simpify, we might send thoughtfully-analyzed birthday greetings to Karl Gegenbaur; he was born on this date in 1826. An anatomist and professor, he was the first to demonstrate that the field of comparative anatomy offers important evidence supporting of the theory of evolution— of which, he became one of Europe’s leading proponents.

Gegenbaur’s book Grundzüge der vergleichenden Anatomie (1859; English translation: Elements of Comparative Anatomy) became the standard textbook, at the time, of evolutionary morphology, emphasizing that structural similarities among various animals provide clues to their evolutionary history. In a way that prefigured the research featured above, Gegenbaur noted that the most reliable clue to evolutionary history is homology, the comparison of anatomical parts which have a common evolutionary origin.

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Written by (Roughly) Daily

August 21, 2022 at 1:00 am

“Homo sapiens, the only creature endowed with reason, is also the only creature to pin its existence on things unreasonable”*…

We appeared 800,000-300,000 years ago, or in the last 1.5%-5.3% of hominid history

How, Sarah Constantin asks, did we humans get so smart?

If you zoom way out and look at the history of life on Earth, humans evolved incredibly recently. The Hominidae — the family that includes orangutans, chimpanzees, bonobos, gorillas, and humans — only arose 20 million years ago, in the most recent 0.5% of evolutionary history.

Within the Hominidae, in turn, Homo sapiens is a very recent development [see image at top]. We appeared 800,000-300,000 years ago, or in the last 1.5%-5.3% of hominid history.

If you look at early hominid “technological” milestones like tool use or cooking, though, they’re a lot more spread out over time. That’s interesting.

There’s nothing to suggest that a single physical change in brains should have given us both tool use and fire, for instance; if that were the case, you’d expect to see them show up at the same time.

Purposeful problem-solving behaviors like tool use and cooking are not unique to hominids; some other mammals and birds use tools, and lots of vertebrates (including birds and fish) can learn to solve puzzles to get a food reward. The general class of “problem-solving behavior” that we see, to one degree or another, in many vertebrates, doesn’t seem to have arisen surprisingly fast compared to the existence of animals in general.

However, to the extent that Homo sapiens has unique cognitive abilities, those did show up surprisingly recently, and it makes sense to privilege the hypothesis that they have a common physical cause.

So what are these special human-unique cognitive abilities?…

Is Human Intelligence Simple? Part 1: Evolution and Archaeology,” from @s_r_constantin. Part 2 is here.

* Henri Bergson

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As we study our species, we might send self-examining birthday greetings to Giambattista Vico; he was born on this date in 1668.  A political philosopher, rhetorician, historian, and jurist, Vico was one of the greatest Enlightenment thinkers.  Best known for the Scienza Nuova (1725, often published in English as New Science), he famously criticized the expansion and development of modern rationalism and was an apologist for classical antiquity.

He was an important precursor of systemic and complexity thinking (as opposed to Cartesian analysis and other kinds of reductionism); and he can be credited with the first exposition of the fundamental aspects of social science (and so, is considered by many to be the first forerunner of cultural anthropology and ethnography), though his views did not necessarily influence the first social scientists.  Vico is often claimed to have fathered modern philosophy of history (although the term is not found in his text; Vico speaks of a “history of philosophy narrated philosophically’).  While he was not strictly speaking a historicist, interest in him has been driven by historicists (like Isaiah Berlin).

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“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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