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Posts Tagged ‘biology

“Never underestimate how much assistance, how much satisfaction, how much comfort, how much soul and transcendence there might be in a well-made taco and a cold bottle of beer”*…

The tacos estilo Matamoros at El Ultimo Taco Taqueria, in Brownsville

Tacos Estilo Matamoros: a beef and cheese taco that originated in the border town of Matamoros, Mexico

A nod to the Rio Grande Valley’s cattle ranching heritage, tacos estilo Matamoros are made up of small, oily corn tortillas, a beef filling such as bistec or mollejas (beef sweetbreads), and crumbled or shredded queso fresco, and they usually come three to five in an order. Although they are wildly popular in Brownsville, they get their name from the sister city of Matamoros, where El Último Taco: Los Originales claims to have invented the style…

An excerpt from your correspondent’s favorite Holiday wishbook– and your guide to the many types of tacos– José R. Ralat, Texas Monthly‘s Taco Editor‘s “Tacopedia.”

* Tom Robbins


As we lick our fingers, we might send wriggly birthday greetings to Pierre-Joseph van Beneden; he was born on this date in 1809. A zoologist and paleontologist, he discovered the life cycle of the tapeworm (Cestoda).


Written by LW

December 19, 2020 at 1:01 am

“In the space between chaos and shape there was another chance”*…

Prince Hamlet spent a lot of time pondering the nature of chance and probability in William Shakespeare’s tragedy. In the famous “To be or not to be” speech, he notes that we helplessly face “the slings and arrows of outrageous fortune” — though a little earlier in the play he declares that “there’s a special providence in the fall of a sparrow,” suggesting that everything happens because God wills it to be so.

We can hardly fault the prince for holding two seemingly contradictory views about the nature of chance; after all, it is a puzzle that has vexed humankind through the ages. Why are we here? Or to give the question a slightly more modern spin, what sequence of events brought us here, and can we imagine a world in which we didn’t arrive on the scene at all?

It is to biologist Sean B. Carroll’s credit that he’s found a way of taking a puzzle that could easily fill volumes (and probably has filled volumes), and presenting it to us in a slim, non-technical, and fun little book, “A Series of Fortunate Events: Chance and the Making of the Planet, Life, and You.”

Carroll (not to be confused with physicist and writer Sean M. Carroll) gets the ball rolling with an introduction to the key concepts in probability and game theory, but quickly moves on to the issue at the heart of the book: the role of chance in evolution. Here we meet a key historical figure, the 20th-century French biochemist Jacques Monod, who won a Nobel Prize for his work on genetics. Monod understood that genetic mutations play a critical role in evolution, and he was struck by the random nature of those mutations…

Carroll quotes Monod: “Pure chance, absolutely free and blind, at the very root of the stupendous edifice of evolution: This central concept of modern biology is no longer one among other possible or even conceivable hypotheses. It is today the sole conceivable hypothesis, the only one that squares with observed and tested fact.”

“There is no scientific concept, in any of the sciences,” Monod concludes, “more destructive of anthropocentrism than this one.”

From there, it’s a short step to the realization that we humans might never have evolved in the first place…

Preview(opens in a new tab)

The profound impact of randomness in determining destiny: “The Power of Chance in Shaping Life and Evolution.”

See also: “Survival of the Luckiest.”

* Jeanette Winterson, The World and Other Places


As we blow on the dice, we might send carefully-calculated birthday greetings to Gabrielle-Émilie Le Tonnelier de Breteuil, Marquise du Châtelet, the French mathematician and physicist who is probably (if unfairly) better known as Voltaire’s mistress; she was born on this date in 1706.  Fascinated by the work of Newton and Leibniz, she dressed as a man to frequent the cafes where the scientific discussions of the time were held.  Her major work was a translation of Newton’s Principia, for which Voltaire wrote the preface; it was published a decade after her death, and was for many years the only translation of the Principia into French.

Judge me for my own merits, or lack of them, but do not look upon me as a mere appendage to this great general or that great scholar, this star that shines at the court of France or that famed author. I am in my own right a whole person, responsible to myself alone for all that I am, all that I say, all that I do. It may be that there are metaphysicians and philosophers whose learning is greater than mine, although I have not met them. Yet, they are but frail humans, too, and have their faults; so, when I add the sum total of my graces, I confess I am inferior to no one.
– Mme du Châtelet, to Frederick the Great of Prussia


“‘Life’ is of course a misnomer, since viruses, lacking the ability to eat or respire, are officially dead”*…

The human genome contains billions of pieces of information and around 22,000 genes, but not all of it is, strictly speaking, human. Eight percent of our DNA consists of remnants of ancient viruses, and another 40 percent is made up of repetitive strings of genetic letters that is also thought to have a viral origin. Those extensive viral regions are much more than evolutionary relics: They may be deeply involved with a wide range of diseases including multiple sclerosis, hemophilia, and amyotrophic lateral sclerosis (ALS), along with certain types of dementia and cancer.

For many years, biologists had little understanding of how that connection worked—so little that they came to refer to the viral part of our DNA as dark matter within the genome. “They just meant they didn’t know what it was or what it did,” explains Molly Gale Hammell, an associate professor at Cold Spring Harbor Laboratory. It became evident that the virus-related sections of the genetic code do not participate in the normal construction and regulation of the body. But in that case, how do they contribute to disease?

An early clue came from the pioneering geneticist Barbara McClintock, who spent much of her career at CSHL. In the 1940s, long before the decoding of the human genome, she realized that some stretches of our DNA behave like infectious invaders. These DNA chunks can move around through the genome, copying and pasting themselves wherever they see fit, which inspired McClintock to call them “jumping genes.” Her once-controversial idea earned her a Nobel Prize in 1983.

Geneticists have since determined that jumping genes originate in the viral portion of the genome. Many of these genes turn out to be benign or even helpful. “But some of the things are full-on parasites,” Hammell says, like infections embedded within our own DNA. All it takes to set these bad actors loose, she is finding, is a slip-up in the body’s mechanisms that normally prevent the genes from jumping around and causing harm…

Half of your genome started out as an infection; if left unchecked, some parts of it can turn deadly all over again: “The Non-Human Living Inside of You.”

See also: “The Wisdom of Pandemics– viruses are active agents, existing within rich lifeworlds. A safe future depends on understanding this evolutionary story.”

* “‘Life’ is of course a misnomer, since viruses, lacking the ability to eat or respire, are officially dead, which is in itself intriguing, showing as it does that the habit of predation can be taken up by clusters of molecules that are in no way alive.” – Barbara Ehrenreich, Living with a Wild God: A Nonbeliever’s Search for the Truth about Everything


As we check our baggage, we might send reforming birthday greetings to Abraham Flexner; he was born on this date in 1866.  The founding director of Princeton’s Institute for Advanced Studies, Flexner is best remembered for his pioneering work as a reformer of American higher education, especially medical education.  On the heels of his 1908 study, The American College, in which he effectively critiqued the university lecture as a method of instruction, he published the Flexner Report, which examined the state of American medical education and led to far-reaching reform in the training of doctors.  The report called on American medical schools to enact higher admission and graduation standards, and to adhere strictly to the protocols of mainstream science in their teaching and research.  While one unintended consequence of Flexner’s impactful advocacy was the reversion of American universities to male-only admittance programs to accommodate a smaller admission pool (female admissions picked up again only later the century), most historians agree with his biographer, Thomas Bonner, that Flexner was “the severest critic and the best friend American medicine ever had.”


“We are what we pretend to be, so we must be careful about what we pretend to be”*…

There is just something obviously reasonable about the following notion: If all life is built from atoms that obey precise equations we know—which seems to be true—then the existence of life might just be some downstream consequence of these laws that we haven’t yet gotten around to calculating. This is essentially a physicist’s way of thinking, and to its credit, it has already done a great deal to help us understand how living things work…

But approaching the subject of life with this attitude will fail us, for at least two reasons. The first reason we might call the fallacy of reductionism. Reductionism is the presumption that any piece of the universe we might choose to study works like some specimen of antique, windup clockwork, so that it is easy (or at least eminently possible) to predict the behavior of the whole once you know the rules governing how each of its parts pushes on and moves with the others…

The second mistake in how people have viewed the boundary between life and non-life is still rampant in the present day and originates in the way we use language. A great many people imagine that if we understand physics well enough, we will eventually comprehend what life is as a physical phenomenon in the same way we now understand how and why water freezes or boils. Indeed, it often seems people expect that a good enough physical theory could become the new gold standard for saying what is alive and what is not.

However, this approach fails to acknowledge that our own role in giving names to the phenomena of the world precedes our ability to say with any clarity what it means to even call something alive. A physicist who wants to devise theories of how living things behave or emerge has to start by making intuitive choices about how to translate the characteristics of the examples of life we know into a physical language. After one has done so, it quickly becomes clear that the boundary between what is alive and what is not is something that already got drawn at the outset, through a different way of talking than physics provides…

Physics is an approach to science that roots itself in the measurement of particular quantities: distance, mass, duration, charge, temperature, and the like. Whether we are talking about making empirical observations or developing theories to make predictions, the language of physics is inherently metrical and mathematical. The phenomena of physics are always expressed in terms of how one set of measurable numbers behaves when other sets of measurable numbers are held fixed or varied. This is why the genius of Newton’s Second Law, F = ma, was not merely that it proposed a successful equation relating force (F), mass (m), and acceleration (a), but rather that it realized that these were all quantities in the world that could be independently measured and compared in order to discover such a general relationship.

This is not how the science of biology works. It is true that doing excellent research in biology involves trafficking in numbers, especially these days: For example, statistical methods help one gain confidence in trends discovered through repeated observations (such as a significant but small increase in the rate of cell death when a drug is introduced). Nonetheless, there is nothing fundamentally quantitative about the scientific study of life. Instead, biology takes the categories of living and nonliving things for granted as a starting point, and then uses the scientific method to investigate what is predictable about the behavior and qualities of life. Biologists did not have to go around convincing humanity that the world actually divides into things that are alive and things that are not; instead, in much the same way that it is quite popular across the length and breadth of human language to coin terms for commonplace things like stars, rivers, and trees, the difference between being alive and not being alive gets denoted with vocabulary.

In short, biology could not have been invented without the preexisting concept of life to inspire it, and all it needed to get going was for someone to realize that there were things to be discovered by reasoning scientifically about things that were alive. This means, though, that biology most certainly is not founded on mathematics in the way that physics is. Discovering that plants need sunlight to grow, or that fish will suffocate when taken out of water, requires no quantification of anything whatsoever. Of course, we could learn more by measuring how much sunlight the plant got, or timing how long it takes for the fish-out-of-water to expire. But the basic empirical law in biological terms only concerns itself with what conditions will enable or prevent thriving, and what it means to thrive comes from our qualitative and holistic judgment of what it looks like to succeed at being alive. If we are honest with ourselves, the ability to make this judgment was not taught to us by scientists, but comes from a more common kind of knowledge: We are alive ourselves, and constantly mete out life and death to bugs and flowers in our surroundings. Science may help us to discover new ways to make things live or die, but only once we tell the scientists how to use those words. We did not know any physics when we invented the word “life,” and it would be strange if physics only now began suddenly to start dictating to us what the word means.

The origin of life can’t be explained by first principles: “Why Physics Can’t Tell Us What Life Is.”

See also this interview with Jeremy England, the author of the article linked above (and of the book from which it is excerpted): “The Physicist’s New Book of Life.”

  • Kurt Vonnegut, Mother Night


As we live and let live, we might spare a thought for Ernest Everett Just; he died on this date in 1941.  A pioneering biologist, academic, and science writer, he contributed mightily to the understanding of cell division, the fertilization of egg cells, experimental parthenogenesis, hydration, cell division, dehydration in living cells, and the effect of ultra violet rays on egg cells.

An African-American, he had limited academic prospects on his graduation from Dartmouth, but was able to land a teaching spot at Howard University.  Just met  Frank R. Lillie, the head of the Department of Zoology at the University of Chicago and director of the Marine Biological Laboratory (MBL) at Woods Hole, Mass.  In 1909 Lillie invited Just to spend first one, then several summers at Woods Hole, where Just pioneered the study of whole cells under normal conditions (rather than simply breaking them apart in a laboratory setting).  In 1915, Just was awarded the first Spingarn Medal, the highest honor given by the NAACP.

But outside MBL, Just experienced discrimination.  Seeking more opportunity he spent most of the 1930s in various European universities– until the outbreak of WW II hostilities caused him to return to the U.S. in late 1940.  He died of pancreatic cancer on this date the next year.



Written by LW

October 27, 2020 at 1:01 am

“The daily hummingbird assaults existence with improbability”*…

Black Metaltail Hummingbird (Metallura phoebe), Peru

High in the Andes, thousands of meters above sea level, speedy hummingbirds defy near-freezing temperatures. These tiny flyers endure the cold with a counterintuitive trick: They lower their body temperature—sometimes as much as 33°C [over 90°F] —for hours at a time, new research suggests…

Among vertebrates, hummingbirds have the highest metabolism for their size. With a metabolic rate roughly 77 times that of an average human, they need to feed nearly continuously. But when it gets too cold or dark to forage, maintaining a normal body temperature is energetically draining. Instead, the small animals can cool their internal temperature by 10°C to 30°C. This slows their metabolism by as much as 95% and protects them from starvation, says Blair Wolf, a physiological ecologist at the University of New Mexico, Albuquerque.

In this state, called torpor, a bird is motionless and unresponsive. “You wouldn’t even know it was alive if you picked it up,” Wolf says. But when the morning comes and it’s time to feed, he says, the birds quickly warm themselves back up again. “It’s like hibernation but regulated on an even tighter schedule.”…

One of Nature’s (many) marvelous tricks: “To survive frigid nights, hummingbirds cool themselves to record-low temperatures.”

* Ursula K. Le Guin, No Time to Spare: Thinking About What Matters


As we admire adaptation, we might send closely-observed birthday greetings to Antonie Philips van Leeuwenhoek; he was born on this date in 1632. A largely self-taught man in science, he is commonly known as “the Father of Microbiology“, and one of the first microscopists and microbiologists (he discovered bacteria, protists, sperm cells, blood cells, and numerous structures in animal and plant tissues). A central figure in the Golden Age of Dutch science and technology, his letters to the Royal Society were widely read and richly influential… which is fair dues, as it’s widely believed that van Leeuwenhoek was inspired by illustrations in  Robert Hooke’s earlier book, Micrographia [and here].


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