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Posts Tagged ‘biology

“To be overly concerned with the original materials, which are merely sentimental souvenirs of the past, is to fail to see the living building itself”*…

The human body replaces its own cells regularly. Scientists at the Weizmann Institute of Science in Rehovot, Israel, have finally pinned down the speed and extent of this “turnover.” About a third of our body mass is fluid outside of our cells, such as plasma, plus solids, such as the calcium scaffolding of bones. The remaining two thirds is made up of roughly 30 trillion human cells. About 72 percent of those, by mass, are fat and muscle, which last an average of 12 to 50 years, respectively. But we have far more, tiny cells in our blood, which live only three to 120 days, and lining our gut, which typically live less than a week. Those two groups therefore make up the giant majority of the turnover. About 330 billion cells are replaced daily, equivalent to about 1 percent of all our cells. In 80 to 100 days, 30 trillion will have replenished—the equivalent of a new you…

Our Bodies Replace Billions of Cells Every Day: “A New You in 80 Days.”

* Douglas Adams, Last Chance to See

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As we sail on the Ship of Theseus, we might spare a thought for Hans Ernst August Buchner; he died on this date in 1902. A bacteriologist, he was a pioneer in the field of immunology, the first to discover a substance in blood, gamma globulins, natural bactericides capable of destroying bacteria.  He also worked with his brother Eduard Buchner, a chemist who won the Nobel Prize in 1907 for his work on fermentation (which helped pave the way for our understanding of the work of enzymes); Ernst had died in 1902, and so did not share in the honor.

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“He was a killer, a thing that preyed, living on the things that lived, unaided, alone, by virtue of his own strength and prowess, surviving triumphantly in a hostile environment where only the strong survive”*…

One notes that there are only three states with unique predators: two with apex predators– Alaska (the polar bear); Florida (the crocodile)– and Hawaii (the domestic cat). A ‘o ia!

The largest land predators in each state. (TotH to @simongerman600)

* Jack London, The Call of the Wild

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As we watch our backs, we might spare a thought for Alexander Emmanuel Rodolphe Agassiz; he died on this date in 1910. Following in his father‘s footsteps, he made important contributions to systematic zoology, serving as curator of Harvard’s Museum of Comparative Zoology (1873-85), which was founded by his father.

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Written by LW

March 27, 2021 at 1:01 am

“Do you think that the soul first shows itself by a gnashing of teeth?”*…

In January 2020, as a new plague began to upend life on Earth, a small research team from Tufts, the University of Vermont, and Harvard announced that they, too, had turned life on Earth upside-down. Their discovery wasn’t quite so dramatic at first glance. Any regular person peering through a microscope at their creation would see little more than a few globs of dirty pond water in a petri dish. But those globs were alive; in fact, they were alive in a way that nothing has ever been alive before, in an uncharted space between biology and technology. They called them Xenobots, the world’s first living robot—the world’s first programmable organism.

Xenobot: Xeno as in Xenopus laevis, a voracious frog native to the wetlands of Sub-Saharan Africa; bot, of course, as in robot. It’s an unconventional name for an unconventional organism, so novel that even its makers struggle to conceptualize it. “The terminology that has served us well for many years is just not any good anymore,” concedes Michael Levin, the team’s iconoclastic biologist. His collaborator Josh Bongard, a computer scientist and robotics expert, has called Xenobots “novel living machines.” Sam Kriegman—the team’s postdoc—prefers the term “Computer Designed Organism,” although he’s been trying on “living deepfake” for size recently.

And they’re all right, in a way. Xenobots are deepfakes in the sense that they aren’t what they seem. They’re robots in the sense that they’re autonomous, programmable agents. They’re Computer Designed in the sense that their morphology—the form their tiny bodies take—was designed by an evolutionary computer algorithm in Bongard’s UVM lab. They’re living in the sense that they’re made of embryonic frog cells, and they’re machines in the sense that humans are machines: biological mechanisms made up of constituent parts.

Xenobots are the first living creatures whose immediate evolution occurred inside a computer and not in the biosphere. The result is a simple organism. Xenobots have no brains; the shape of their bodies is what determines how they behave. And yet, Levin and Bongard do not fully understand why Xenobots behave the way they do. “What you’re seeing de novois a completely novel creature with new proto-cognitive capacities, preferences, capabilities, IQ,” Levin explains. “All of those things appear out of nowhere.” Sometimes a Xenobot will head in one direction and then abruptly double back, as though changing its mind. What force guides such behaviors? Can a frog’s cells, in some way, think? Xenobots seem to have “nano free-will,” Levin jokes.

And this is where the can of worms—or tadpoles, maybe—pops open…

The word “robot” recently celebrated its centennial. It comes from the Czech playwright Karel Čapek’s 1920 play “Rossum’s Universal Robots,” about a worker uprising in a robot factory. Čapek’s robots are biological, the result of a vaguely alchemical process involving “albumen” with a “raging thirst for life.” Our conception of a robot as being something metallic, with clanging gears and servo-motors, is more recent baggage, a consequence of the science-fiction stories and films of the mid-twentieth century. In order to understand what Xenobots might mean for our future, we’ll have to divest ourselves from the idea that a robot—or any kind of autonomous being—can be wholly defined by its materiality…

As Norbert Weiner, the father of cybernetics, observed: “Let us remember that the automatic machine is the precise economic equivalent of slave labor. Any labor which competes with slave labor must accept the economic consequences of slave labor.”

Claire Evans (@TheUniverse) explains how “Xenobots may change how we think about intelligence.”

For apposite background, see also “The Link Between Bioelectricity and Consciousness.”

Karel Čapek, R.U.R. (Rossumovi Univerzální Roboti, or in English, Rossum’s Universal Robots)

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As we ponder life itself, we might recall (with, perhaps, a touch of nostalgia) that it was on this date in 1959 that Texas Instruments (TI) demonstrated the first working integrated circuit (IC), which had been invented by Jack Kilby. Kilby created the device to prove that resistors and capacitors could exist on the same piece of semiconductor material. His circuit consisted of a sliver of germanium with five components linked by wires. It was Fairchild’s Robert Noyce, however, who filed for a patent within months of Kilby and who made the IC a commercially-viable technology. Both men are credited as co-inventors of the IC. (Kilby won the Nobel Prize for his work in 2000; Noyce, who died in 1990, did not share.)

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Written by LW

March 24, 2021 at 1:01 am

“Man tends to define in terms of the familiar. But the fundamental truths may not be familiar.”*…

Most of us probably do not need to think too hard to distinguish living things from the “non-living”. A human is alive; a rock is not. Easy!

Scientists and philosophers do not see things quite this clearly. They have spent millennia pondering what it is that makes something alive. Great minds from Aristotle to Carl Sagan have given it some thought – and they still have not come up with a definition that pleases everyone. In a very literal sense, we do not yet have a “meaning” for life.

If anything, the problem of defining life has become even more difficult over the last 100 years or so. Until the 19th Century one prevalent idea was that life is special thanks to the presence of an intangible soul or “vital spark”. This idea has now fallen out of favour in scientific circles. It has since been superseded by more scientific approaches. Nasa, for instance, has described life as “a self-sustaining chemical system capable of Darwinian evolution”.

But Nasa’s is just one of many attempts to pin down all life with a simple description. In fact, over 100 definitions of life have been proposed, with most focusing on a handful of key attributes such as replication and metabolism.

To make matters worse, different kinds of scientist have different ideas about what is truly necessary to define something as alive. While a chemist might say life boils down to certain molecules, a physicist might want to discuss thermodynamics…

A comparative survey of the definitions that currently exist concludes…

To properly define life, we might need to find some aliens.

The irony is that attempts to pin down a definition of life before we discover those aliens might actually make them more difficult to find. What a tragedy it would be if in the 2020s the new Mars rover trundles straight past a Martian, simply because it does not recognise it as being alive.

“The definition can actually hinder the search for novel life,” says [Carol] Cleland. “We need to get away from our current concept, so that we are open to discovering life as we don’t know it.”

It is surprisingly difficult to pin down the difference between living and non-living things: “There are over 100 definitions of ‘life’ and all are wrong.

* Carl Sagan

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As we strive for beginner’s mind, we might send exploratory birthday greetings to John Theophilus Desaguliers; he was born on this date in 1683. A natural philosopher, clergyman, and engineer, he is best remembered as the experimental assistant to Isaac Newton, who went on to popularize Newton’s work in public lectures and publications. On the strength of that work, Desaguliers was elected to the Royal Society and ultimately became its curator.

In his own work he coined the terms conductor and insulator. He repeated and extended the work of Stephen Gray in electricity. He proposed a scheme for heating vessels such as salt-boilers by steam instead of fire. And he made inventions of his own (e.g., a planetarium), and material improvements to others’ machines, such as Thomas Savery’s steam engine (by adding a safety valve and using an internal water jet to condense the steam in the displacement chambers) and a ventilator at the House of Commons. 

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“In so far as a scientific statement speaks about reality, it must be falsifiable: and in so far as it is not falsifiable, it does not speak about reality.”*…

Kirsten Thompson, the lead scientist on the Arctic Sunrise, takes water samples for eDNA sampling near Paulet Island at the entrance to the Weddell Sea. Photo by A Trayler-Smith/Greenpeace/Panos

If you ask philosophically minded researchers – in the Anglophone world at least – why it is that science works, they will almost always point to the philosopher Karl Popper (1902-94) for vindication. Science, they explain, doesn’t presume to provide the final answer to any question, but contents itself with trying to disprove things. Science, so the Popperians claim, is an implacable machine for destroying falsehoods.

Popper spent his youth in Vienna, among the liberal intelligentsia. His father was a lawyer and bibliophile, and an intimate of Sigmund Freud’s sister Rosa Graf. Popper’s early vocations draw him to music, cabinet making and educational philosophy, but he earned his doctorate in psychology from the University of Vienna in 1928. Realising that an academic post abroad offered escape from an increasingly antisemitic Austria (Popper’s grandparents were all Jewish, though he himself had been baptised into Lutheranism), he scrambled to write his first book. This was published as Logik der Forschung (1935), or The Logic of Scientific Discovery, and in it he put forward his method of falsification. The process of science, wrote Popper, was to conjecture a hypothesis and then attempt to falsify it. You must set up an experiment to try to prove your hypothesis wrong. If it is disproved, you must renounce it. Herein, said Popper, lies the great distinction between science and pseudoscience: the latter will try to protect itself from disproof by massaging its theory. But in science it is all or nothing, do or die.

Popper warned scientists that, while experimental testing might get you nearer and nearer to the truth of your hypothesis via corroboration, you cannot and must not ever proclaim yourself correct. The logic of induction means that you’ll never collect the infinite mass of evidence necessary to be certain in all possible cases, so it’s better to consider the body of scientific knowledge not so much true as not-yet-disproved, or provisionally true. With his book in hand, Popper obtained a university position in New Zealand. From afar, he watched the fall of Austria to Nazism, and commenced work on a more political book, The Open Society and its Enemies (1945). Shortly after the war, he moved to the UK, where he remained for the rest of his life.

For all its appealing simplicity, falsification was quickly demolished by philosophers, who showed that it was an untenable way of looking at science. In any real experimental set-up, they pointed out, it’s impossible to isolate a single hypothetical element for disproof. Yet for decades, Popperianism has nonetheless remained popular among scientists themselves, in spite of its potentially harmful side-effects. Why should this be?

The notion that science is all about falsification has done incalculable damage not just to science but to human wellbeing. It has normalised distrust as the default condition for knowledge-making, while setting an unreachable and unrealistic standard for the scientific enterprise. Climate sceptics demand precise predictions of an impossible kind, yet seize upon a single anomalous piece of data to claim to have disproved the entire edifice of combined research; anti-vaxxers exploit the impossibility of any ultimate proof of safety to fuel their destructive activism. In this sense, Popperianism has a great deal to answer for.

When the constructive becomes “deconstructive”– Charlotte Sleigh (@KentCHOTS) explains how a powerful cadre of scientists and economists sold Karl Popper’s “falsification” idea to the world… and why they have much to answer for: “The abuses of Popper.”

See also: “Why ‘Trusting the Science’ Is Complicated.”

* Karl Popper, The Logic of Scientific Discovery

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As we re-engage with epistemology, we might recall that it was on this date in 1997 that Ian WilmutKeith Campbell, and their colleagues at the Roslin Institute (part of the University of Edinburgh, Scotland) announced that they had successfully cloned a sheep, Dolly, who had been born on July 5, 1996. Dolly lived her entire life at the Institute, where (bred with a Welsh mountain ram) she gave birth to six lambs. She died in February, 2003.

 Dolly’s taxidermied remains

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