Science

Yellows

Biology, Science
Jan 8, 2021
2 Comments

“A ray of sunshine” is one way to describe a bit of good news. I saw that sunny yellow reflected in the gold medal recently awarded to a brave rat.

You read that right, I am reporting on Magawa, the HeroRat. To date he has found 39 landmines and 28 items of unexploded ordnance in Cambodia. Over the past 4 years he has helped clear over 141,000 square meters of land (the equivalent of twenty football fields), allowing local communities to live, work and play without fear of losing life or limb.

Actually I am introducing a general program, APOPO, that breeds and trains rats for multiple important purposes: detecting landmines, identifying tuberculosis in people, and sniffing out illegally trafficked wildlife. APOPO is an acronym from Dutch which stands for “Anti-Persoonsmijnen Ontmijnende Product Ontwikkeling“, or in English, Anti-Personnel Landmines Detection Product Development. The idea to use rats was born in the mid 1990s in Holland, the choice to train African Giant Pouched rats based on their longevity and origins in Africa where the work was to be done.

Rats get rewarded with treats like ripe, yellow bananas when they detect the correct scent (associated with explosives, or TB or pangolins, one of the most smuggled endangered species) in the lab. Eventually they will do the same in the field, with a speed that escapes their human counter parts, and with more accuracy in detection, as it turns out. Rats can check on 100 TB samples in 20 minutes, for example, which would take 4 days to be done by a doctor with a microscope. You can watch them here.

In 2000, APOPO established office and training facilities in Tanzania, and started developing what would be the most extensive training minefield in Africa in collaboration with local universities and the people defence forces. A year later they were approved by The Geneva International Centre for Humanitarian Demining (GICHD) and expanded to teach the rats to smell remote explosive, and soon started research into detecting tuberculosis via scent. In 2004 the first 11 rats passed International Mine Action Standards accreditation and began to operate in multiple countries in Africa and later Cambodia, Laos, Thailand and Vietnam. By 2015 a country like Mozambique was cleared of all landmines! By 2017 the mine action was invited to Colombia, South America.

Since the APOPO TB-detection research program began in 2007, the rats have checked more than 680.000 patient samples. They discovered 18.300 missed cases, helping not just those patients but preventing another 150,000 likely new infections. APOPO’s programs work within government health systems to support over 100 partner clinics in Tanzania, Mozambique and Ethiopia in their fight against TB. They find both, cases that have been missed – according to estimates of the World Health Organization (WHO), about half of the TB patients in these countries are ‘missed’ – and find TB among non-symptomatic but high-risk population ( like prison inmates.)

I think it is phenomenal to see something this life-saving to develop from the idea of a single person to a global organization in 2 decades. They surely had a lot of help on the way, from educational institutions to stay agencies to business initiatives to NGOs – individuals can and have helped, too – you can adopt a rat to support the program, for example.

It also stands in stark contrast to using animals to enact warfare in the first place. As I learned at the dinner table last night, when talking about today’s subject, B.F. Skinner spearheaded Project Pigeon during WW II. It aimed at using pigeons to guide missiles to their respective targets but apparently never took off. Video describing the idea can be found in this link.

Detecting illness by scent has become a hot topic in scientific study in general, with the hopes of finding helpful markers for diagnosis that avoid intrusive procedures for diseases as varied as cancer, Parkinson’s Disease, asthma and traumatic brain injury. Not all done by rats, of course. Dogs are involved, and electronic “noses,” devices that pick up and analyze scent.

I like to think of it though as if it looks like we’re moving from smelling a rat to have one smell us!

Since I don’t have my own photographs of banana loving rats (rats today are from the APOPO website), I’ll make do with random yellows from my archive that might deliver tasty bits to rats – sunflowers, canola, corn, pears, some odds and ends.

Music depicts rats in a variety of ways….

words by Carl Sandburg :
There was a gray rat looked at me
with green eyes out of a rathole.
“Hello, rat,” I said
“Is there any chance for me
to get on to the language of the rats?”
And the green eyes blinked at me, blinked from a gray rat’s rathole.

Rats away opens the second movement. Hear them scurry!

Matched Pair

Two articles caught my attention last week, reporting on people who at first glance could not be more different. The first appeared in the New York Times, The Social Life of Forests, and (re)introduced Suzanne Simard, a scientist who looks at forest ecosystems. You might have encountered her if you followed my earlier recommendation to read Richard Power’s The Overstory, one of my favorite books of recent years. She was the model for one of the prominent characters in the novel.

The second was a book review in Jacobin Magazine, familiarizing me with William Morris and his conceptions of art and politics, How William Morris became a Socialist.

What could a contemporary professor of forest ecology and a 19th century artist and writer known prominently for his wall paper designs possibly have in common? Lots, I tell you!

Both devoted their lives to exploring new directions in their respective fields, Simard as a researcher who ventures daringly (and brilliantly) far from the main stream science at times, Morris as an artist who is now known as a founding father of the British Arts and Craft movement which upended the trend towards industrialization and mass production in the Great Britain of the 1800s.

Both can be counted as ardent environmentalists.

And, importantly for my spontaneous linking the two in my mind after reading these pieces, both make us see, keenly, the interconnectedness of things in nature as much as in our social, political, and economic lives. Interconnectedness can be a boon, when all pieces work together for maximum achievement, and it can be a bust, if some random (or not so random) interruption paralyzes the system as a whole.

The NYT article is an easy read, and reveals some astonishing scientific findings in everyday language. (It also reinforces things we have learned form another book about the secret life of trees, which is reviewed here.) Among other things,

“….Simard has discovered that fungal threads link nearly every tree in a forest — even trees of different species. Carbon, water, nutrients, alarm signals and hormones can pass from tree to tree through these subterranean circuits. Resources tend to flow from the oldest and biggest trees to the youngest and smallest. Chemical alarm signals generated by one tree prepare nearby trees for danger. Seedlings severed from the forest’s underground lifelines are much more likely to die than their networked counterparts. And if a tree is on the brink of death, it sometimes bequeaths a substantial share of its carbon to its neighbors.”

Underground fungal networks that improve the overall health of the forest system by re-directing needed resources are, of course, affected by indiscriminate logging, or other forms of environmental degradation. William Morris thought the same to be true for art when the benefits it bestows on a given society are endangered. Environmental degradation, either in the literal sense of destroying the beauty and health of nature, or in the figurative sense of our lives being accosted by industrialization and labor exploitation, was the main culprit in his view when it came to the disappearance of art in everyday life.

If you have the time and interest, here is a prescient lecture that Morris gave on the relationship between destroying the earth, undermining its beauty and the pernicious effects of wage labor, all of which alienates humans from their creative capacities. In general, he believed that “art was man’s expression in his joy of labor,” art encompassing not just the intellectual achievements of a chosen few, but the daily beautification of one’s environment that across centuries was part of society’s existence.

He implored us “to take in not only painting and sculpture, and architecture, but the shapes and colors of all household goods, nay, even the arrangement of the fields for tillage and pasture, the management of towns and of our highways of all kinds; in a word, to extend to the aspect of the externals of our life.” That could be accomplished by a medieval potter’s careful decorations, a glass blower’s feel for form, a cottage gardener’s lush color schemes up to the hand-pressed paper, hand-printed and colored designs of Morris’ famous tapestries. The very ideas of combining the higher arts with applied art eventually found their homes in the German Bauhaus in the 1920s and its contemporary Russian twin, Vkhutemas, the most fascinating art school you have never heard of. The workshops had artistic and industrial faculties; the art faculty taught courses in graphics, sculpture and architecture while the industrial faculty taught courses in printing, textiles, ceramics, woodworking, and metalworking.

By no means did Morris imply that industrialization and machine production were the causal agent in the disappearance of daily creativity. It was the fact that only capital, not laborers benefitted from the automization and speed of production, workers receiving no increased leisure time to use for creative activities to make up for the increasingly non-creative work serving the machines. His writings on socialist models to remedy the unfairness were astoundingly clear-sighted and pragmatic.

He was also quite the character, which, as you all know by now, always excites me. A rich Bourgeois drawn to Ruskin and Marx, an artist and successful business man who marries a working class girl who happens to be his painting model, leaves him for his best friend and then they all manage to establish a menage à trois, a risk taker who late in life shifts gear from designing pretty things (if you like flowery wall paper) to establishing a printing press – it’s all pretty fascinating. Details here.

For a final bit of reading on new claims about the ultimate biological interconnectedness, the Gaia Hypothesis, go here. Would love to know what either Simard or Morris or for that matter Darwin would have thought about this view of an evolving planet.

Photographs of Pacific Northwest forests from this spring. Wallpaper has to wait….

And here are Silent Woods by Dvorak.

Re-distribution

There it was again. Bobbing for seconds above the water, then disappearing, leaving a bunch of seagulls screaming in its wake. The head, then the rump of a sea lion, about 100 miles upstream from where it was supposed to be, surfacing as little speck in front of me in the Willamette river yesterday.

Sea lions are driven upriver by hunger, and find a veritable feast in salmon that return to their spawning grounds. To protect the fish whose numbers are in dire decline due to human intervention, people now kill the sea lions, whose numbers are on the rise, due to human intervention.

“Sea-lion populations were once declining, too, but they have rebounded under the Marine Mammal Protection Act. Such is the challenge for humans trying to manage vast, interconnected ecosystems. Put a thumb on one part of the scale, and something somewhere else goes out of whack. Try to correct that, and you create another problem. Eventually, you end up with a policy of fisheries managers killing sea lions.” (Ref.)

Walking downstream, my thoughts stayed on hunger. A passage from the book I am currently reading, Tyll by Daniel Kehlmann, had uncomfortably lodged in my brain. It described a man condemned to die for witchcraft having the first real meal ever – soup, meat, cake – as his last meal. He realizes then that he has been hungry all his life with no exception, an awarenesses only revealed in the hours before his church tribunal – imposed execution.

Put a thumb on one part of the scale, and something somewhere else goes out of whack. Set in early 17th century Europe, in the wake of the disastrous 30 Years’ war (1618- 1648), the novel weaves a tale with the help of its protagonist, the trickster Tyll Ulenspiegel (Till Eulenspiegel,) that draws us deeply into a world of hunger, catastrophe, superstition, religious fervor and conspiracy theories. In some ways, one might argue, not quite unlike our own.

It was Emperor Ferdinand II, a staunch Catholic, who put his thumb on the scale, trying to force his religion on the uneasy detente of Europeans states that had emerged after the upheavals of the Reformation. Hell ensued, and as with all catastrophes in human history, drove people into ever cruel and persecutory forms of thinking and behavior, seeking salvation in authority, often church-associated, and scape goats often linked to the devil and magic.

Daniel Kehlmann’s Measuring the World, a small novel linking the 19th century explorer and mathematician Alexander von Humboldt and Carl Friedrich Gauss respectively, was a literary sensation. When it appeared in 2006, it replaced Harry Potter and Dan Brown from the charts in Germany, no small feat for a historical novel. It had to do something right, given that it elicited major praise across the literary reviews of the globe and major condemnation by the folks at the American Mathematical Society.

The book delivered easy-access, colorfully wrapped, inventively speculated bites of historical facts. You felt smarter afterwards without having to stretch your brain all too much. Tyll, I have to say, is much different. Although it echoes Kehlmann’s earlier writing with its reliance on wit and comical relief, it is much darker, much more opaque, and in some ways much smarter in its subtle ways of drawing parallels between a world from the past and our own. It makes your brain work, while your heart beats faster, more defensively.

A smart review in The New Yorker spells out the focus on magic and survival. It links to historical views of Tyll Ulenspiegel as “a dangerous vagrant, a folk hero, a journeyman magician, a bawdy circus performer, a jester and prankster who, like the Shakespearean Fool, recklessly needled those in power into looking honestly at themselves.” It also provides a perceptive enumeration of all the interesting characters populating the novel, testament to the author’s depth and breadth at this go-around, since historical sources to fall back on are much sparser.

My own reading was hooked more by the narrative line throughout the book of how unequal distribution of riches and power – from the village level to the international state players, the intra-religion conflicts to those between world religions, between emerging scientific rationality and religion-fervored superstition – affect human behavior and its psychological consequences.

Hunger creates catastrophe, a hunger driven by the inhuman conditions of a world divided into those who hold the goods and those who fight for daily survival. Without giving away too much, the small child Tyll, during a traumatic event, is driven by hunger to sacrifice the only thing he is attached to. The psychological consequences forcibly stamp out what we call conscience. Tyll, for no fault of his own, morphs into an amoral and untrustworthy hero, so vividly imagined and described that you see the world through his eyes, and blanche.

How many children are driven by hunger, by daily experience of unfairness and injustice, into life paths that end in catastrophe? Finding the escape as a jester (or a tycoon, a rap star or a sports hero) is the exception to the rule, thus making it into the canon of cautionary or triumphant tales, I gather. Well, here is one number: 13.9 million children in the US alone lived in a household characterized by child food insecurity as of late June. School lunch programs were already struggling to meet rising demand before the pandemic. With COVID-19 now keeping children out of school, many don’t have access to school lunches at all. (Ref.) And we don’t even know the dark numbers, or what it will look like when people start to be evicted from their homes by the end of the year. Nor can we wrap our minds around the likely numbers in even poorer parts of the world.

And no Willamette to fish from…..

Time to think seriously about forms of re-distribution.

Thoughts on Flatulence

Flatulence, you know, the activity that releases methane into the atmosphere, is not usually a topic discussed in polite company. But since we all appreciate some good news these days, flatulence it shall be. Or the absence thereof.

Many of you might have heard the report already on NPR 2 days ago. It has been picked up all over the place: one of the major sources of methanol emissions, gas with high global warming potential, heating up the atmosphere, are the burps and farts of cows. There, I said it.

Cows have several stomach chambers, in which microbes help digest the food. They belch due to enteric fermentation, which is the digestive process of converting sugars into simple molecules for absorption into the bloodstream and which produces methane as a by-product. On the other end of the cow, manure is dropped which contains and releases methane as well.

It turns out (and it seems to be a bit of a rediscovery, if you look at what the ancient Greeks or 18th century Icelanders reported,) adding seaweed to the bovine feed helps reduce methane emission by an astonishing 98%. Minute amounts of those submarine grasses seem to be enough.

Asparagopsis taxiformis and Asparagopsis armata are 2 species of a crimson submarine grass that drifts on waves and tides all around the world’s oceans. These 2 species are emerging as an effective tool in innovative, regenerative, and cleaner production for the wider agriculture sector. Asparagopsis and other types of seaweed have specialized gland cells that make and store bromoform, an organic compound. When this deep red seaweed is freeze-dried, powdered, and sprinkled as a garnish on a cow’s meal, bromoform blocks carbon and hydrogen atoms from forming methane in the stomach. (Ref.)

Given that there are about 1.5 billion cows on our planet, this seems an exciting step forward in our attempts of decarbonization to save the earth.

Incidentally it also seems to make the cows healthier and increase milk production. The whole seaweed issues started in this newest version, in fact, when a farmer noticed that his cows that feed near the ocean shore thrived in comparison to his other ones that fed at higher pastures. The power of observation, leading to scientific exploration.

Unclear to me, though, is how large-scale seaweed production will impact marine environments, and how much global efforts to get people away from eating beef will be undermined if we now think cows are no longer complicit in climate change. There are still the countless acres of Amazon rainforest cut down to make pastures for cows, who surely will not be fed seaweed in the first place…

But for now, let’s celebrate diminished flatulence – we take our small victories where we can find them these days – and amuse ourselves by going back to what Benjamin Franklin had to say in 1781 on the very topic. “It is universally well known, That in digesting our common Food, there is created or produced in the Bowels of human Creatures, a great Quantity of Wind.” The essay can be found here. A fun read. It is titled: A Letter to a Royal Academy about Farting. Gone with the wind, I guess, since it never arrived at that august body.

Music today is by Tcherepnin from his Le Monde en Vitrine – The Greyhounds and the Cow. It was incited by the vitrine of a patron of the arts that held numerous chachkas. “The first movement,” the composer wrote, “is inspired by a group of miniature greyhounds in glass, which in the show-case stands next to a massive porcelain cow. The greyhounds are full of action, whilst the cow is placid. This contrast inspired me deeply. How often in life is our enthusiasm thwarted by something as placid as a cow!” To which I say: Give me placidity any day….

(Placidity – a feeling of calmness; a quiet and undisturbed feeling. placidness. calmness – a feeling of calm; an absence of agitation or excitement. 2. placidity – a disposition free from stress or emotion.)

Here is fuller menu of his piano works, if you click play all.

Thoughts on Vaccination

· ·

Health, Science
Dec 1, 2020
4 Comments

It looks like we will be able to get vaccinated to be (somewhat) protected against Covid-19 in the near future. Or will we? There are many questions attached to the issues of vaccines: their development, their approval, their distribution, their side effects and the (un)willingness of the population to be inoculated, to name a few. I’ll try and report on some of these issues today, including the fascinating fact of people volunteering to be infected with the virus in so-called challenge trials for vaccine development that risk their deaths, given the absence of definitive treatment options for the disease when it hits you hard.

First a lightning round on what vaccines do in general: they basically fake the disease without making you sick, helping the body develop protective immune responses so when the actual crud arrives you have a shield. There are three established ways to accomplish this and one that has never been approved before but seems to be a valuable candidate in the fight against Covid-19.

For one you can take a virus, inactivate it so it can no longer multiply in your body and expose your system to it to develop a defense. Successfully done in cases of the flu, polio, hepatitis A, and rabies, for example. Secondly you can work with a viral vector that carries the immobilized virus. Loosely put, scientists use DNA as a vector (often from chimpanzee adenoviruses) that your own system copies into RNA and then acts with a protective response. It worked for Ebola, some retroviruses, and small pox among others. Third, there are protein-based vaccines, which work with viral proteins only from the spike of the virus that tries to invade your cells. These vaccines are historically very safe and effective, among others protecting against hepatitis B virus, shingles, and whooping cough. And last, there are genetic vaccines, which introduce genes directly as either DNA or messenger RNA, which is used by the cell as a template to build a protein through a process of translation, then activating the protective response. They are easier to manufacture and distribute, but we have never used them before outside cancer research, and they also will require 2 doses.

Ok, let’s say you have developed something that seems to work, like Pfizer, Moderna, Astra Seneca and various other international pharmaceutic industries claim. Now what? You need approval – usually only given for vaccines that can prove to protect for longer than a year. We have no data on that and do not know how long each vaccine will protect you. This is particularly relevant in the light of the fact that we now have cases of re-infection after 4 months.

Then you need to manufacture on a grand scale, under sterile conditions. There are shortages of the glass containers and the custom bags that line the bioreactors in which vaccines are produced. In some cases, the vaccine ingredients are so unstable that they need to be kept at insanely cold temperatures( – 94 degrees Fahrenheit!) and expire after 10 days, a problem for distribution that relies on dry ice – also in short supply, as are syringes. The vaccine must be mixed at the administration site with a sterile liquid — usually water — and given within six hours of creating the solution. Since the vaccine will be shipped in cases with a high volume of doses, rural communities may not have the population, or infrastructure, to administer a case of doses while still cold. Hospitals across the country might also not have funds available to buy the fancy freezers that can be used where there is lots of electricity. (Ref.)

Then you have to decide who gets it first, since vaccines will be in limited supply (to achieve herd immunity, we need to inoculate about 5 billion people across the world, but we, if all get approved, are only likely to have enough for 2.5 billion people, given that the vaccine needs two doses.) First responders, health professional and old people, who are the most at risk? Younger people who are the super spreaders? People in certain areas of the country, so-called hotspots? Decision vary from country to country and are based on political reasons as well as medical evaluations. Details of allocation issues can be found here.

Given that we need more vaccines, people are trying to speed up development, and one way to do so is to run studies that use far fewer than the 10thousands of participants in normal randomized trials where you wait for people to get naturally infected, a process that takes time.

These faster studies are called “challenge” trials in which half of a group of a hundred or so participants gets actively infected with the virus, with the other half being the control group after they all received the developing vaccine. No longer using your gardener’s son (as Edward Jenner did in 1796 with small pox), or prison- or developing world populations who sign up under duress or are simply forced, these trials use volunteers. The World Health Organization has established complex protocols to insure ethical proceedings, but the ethics are still a hot topic of debate.

Would you sign up to be infected by this disease when we have no known treatments that are certain to cure? Would you risk long-term impairment, even if you can avoid death under the stellar medical care these programs provide? Would you agree to isolation for months on end to be under close supervision? Well, 37.000 people have signed up for this since May alone. PBS aired a segment on the One Day Sooner website that calls for volunteers and had an insane response.

When journalists from the Radiolab Podcast asked participants for their reason they found them all over the map. From gas station attendants to Nobel Prize Winners in Physics, they calculated the gain for humanity vs. their own vulnerability, they wanted to protect their parents, or escape boredom, they felt they were dying in a short time anyhow and might as well help science, they urged a commitment to our nation and community after these years of division, they wanted to have a voice at the table for underrepresented communities, and so on. It’s an interesting short listen, if you ignore the small numbers of respondents.

In contrast to those willing to face the disease personally and help develop vaccines against it, there are the many who are not willing to be vaccinated in the first place. There are multiple reasons why they might refuse. For one, there is a large anti-vaccine and anti-science movement in this country, amplified by the partisan divide in the Covid-19 case of acknowledging the danger of the disease. If it is all a hoax, why would I allow the state to prick me with a needle and have me suffer the side-effects (by all reports getting the vaccine will make you feel sick for a bit, with fevers and aches common) or worse inject some – insert your favorite conspiracy theory here – into me. The Lancet reports: “31 million people follow anti-vaccine groups on Facebook, with 17 million people subscribing to similar accounts on YouTube. The CCDH calculated that the anti-vaccine movement could realise US$1 billion in annual revenues for social media firms.” They are also an easy target for further radicalization.

Secondly, there are understandable reason for subparts of the population to be wary of being exposed to unproven substances. The experience of poor and people of color populations in our history has been exposure to forced experimentation in combination with much reduced access to good health care and pre- existing, poverty-related vulnerabilities. A devastating summary can be found here. Suffice it to say that the Nazi defense (!) at the Nürnberg Trial used the fact of experimentation by the US Army and the University of Chicago that infected prison population with malaria in the 1940s, and many such other cases, as justification for “international practice.” Current estimates say that only 42% of the US population is willing to get vaccinated, a number too low to achieve a win in the fight against the disease (and a number much lower than comparable choices in other western nations.)

In sum, do we know if and when we will get vaccinated? Can we trust the voices that claim we’ll be well into it at the beginning of next year? I fear so many things can go wrong, so many factors will influence distribution and allocation, that there is no way to be sure. But I do know that the minute the scientific sources I trust give the green light, I will still wait a month or two to see how things unfold and also give priority to those with a more and immediate need for limited supplies. But then I will stand in line and do my part to protect the community as a whole. No worries, you’ll hear about it!

Photographs are from my local Jackson Middle School on whose fields I walk my dog. The students have decorated their buildings with totem pole-like assemblages with abundant creativity – made me think again how hard these times are on children and how much we owe them to make this a better, less dangerous and more equitable world.

And here is music from illness-induced periods of social isolation of various composers. I found the source here.

Chopin wrote this while isolated during a bout with tuberculosis.

Stravinsky wrote this while recovering from typhoid (contracted from eating oysters…) in a nursing home.

And Rachmaninoff transcribed and played this after he was stricken with the Spanish Flu upon arrival in the US in 1918.

Of sheep and peas

Literature, Science
Jun 22, 2020
1 Comments

In truth, today is all about peas, their luminescence, their daintiness, their curlycues and their service to science. The sheep play a minor role, just in as much as they were of great economic value to the monasteries that raised and sold them 150 years ago. When imports of Australian wool tightened the financial competition in the mid 1800s at least one Abbot, Cyril Knapp of St. Thomas monastery in Brünn (Brno, Czech Republic,) was prescient enough (and worried enough about profit margins) to allow in-house scientific studies to understand the laws of inheritance, which might help breed sheep for better quality or faster growing wool.

Luckily a scientist was at hand, a novice who had chosen St. Thomas as an order known for enlightened thinking. With its Augustinian credo per scientiam ad sapientiam (“from knowledge to wisdom”), the monks focused on scholarly teaching and research, as well as having a reputation for being culinary wizards.

His name was Mendel, of course. Formerly Johann, now novice Gregor, son of poor peasants, protégé of numerous professors at the university in Vienna where he studied mathematics, botany and physics (which he failed miserably just as he failed later teachers’ exams, twice…) Haunted by depression and too poor to continue his studies, he was persuaded to join the monks.

The Mendel, who chose peas as his field of study after the monks discovered his laboratory of black and white mice in his monastery cell, promptly nixing in vivo experiments involving sex.

What Mendel brought to the field of genetics, (he is really assumed by many to be the actual father of that field,) was rigorous scientific experimentation, botanical research techniques – and mathematics. He basically figured out fundamental laws of inheritance and ALSO calculated their statistical probability. (Ref.)

5 acres of garden, one greenhouse. 28.000 to 29.000 pea plants cultivated between 1854 and 1856, because they were easy to grow, came with visibly different traits, and could be easily pollinated. For two years he grew strains that were absolutely pure, along one of 7 dimensions that he chose to observe: the height of the plant (short or tall) the color of the flower (white or purple,) its position on the stem, the seed shape and color, the pod shape and color. Literally he grew and tested 34 varieties of garden peas for these traits to be consistent across several generations. Two full years devoted to a base-line control group!

Then he started to explore what would happen when he hybridized these pure varieties. Would cross-pollinating a tall plant with a short one create medium height? Would cross-pollinating a white flowering plant with a purple one lead to pink blossoms when you planted the seed?

Surprise. Some “factors” (what we call genes today) were dominant, while others were recessive for certain traits. In the first generation of cross-pollinated peas, for example all would have purple flowers, the white ones being masked. However, and here is where his mathematical observation started to reveal new insights, if you counted what happened in the next generation, you would find a 3:1 ratio – for every 3 purple flowering plants, a white one would re-emerge. It took almost a decade to reveal a truly reliable pattern. Ten years of growing, pollinating, observing, measuring, recording peas. Nothing but peas.

Eventually he published his work, “Experiments in Plant Hybridization” in 1866 in Proceedings of the Natural History Society of Brünn.

Deafening silence. About three citations over the next 35 years. He died, painfully, of kidney disease before the importance of his discoveries were understood and the hereditary factors he had inferred identified by modern genetics. Contemporary research on genetics has, of course, revealed more complicated patterns of inheritance, including the fact that sometimes there can be co-dominance of two traits, or incomplete dominance of one, but the basic ideas stand: he figured out how living systems send their genes down to the next generations, and how dominant genes mask recessive ones until they don’t.

I am trying to grapple with the psychology of this scientific mind. Having ideas that were revolutionary for the times, and no one, really, to talk to. He sent a manuscript to Darwin, but that was found among the latter’s papers, unread. He prayed with his monks, he administered the monastery, (appointed abbot at some later point,) he taught some kids, but where would he find the discussion partners so necessary to develop ideas and have them questioned? Dedicated to a single type of plant, its size and color, the smoothness of its seeds, doggedly pursuing the idea that there needed to be something, some thing that made off-spring carry the traits of its progenitor, that made children look like their parent, or have certain traits skip generations (one wonders if there was a history of depression in his family or hair color that might have been recessive.) Next time I complain about lack of mobility in these Covid – 19 times, I will just think: 3000 or so days with nothing but peas behind the cloister walls!

The mechanisms of inheritance is a fascinating topic, made even more interesting when you have a person who is in equal parts gifted writer and scientist, help you understand its history. Siddhartha Mukherjee does just that in his book “The Gene.” Here is a review that could not be more enthralled if it tried…. and here is a link to a trailer of the PBS program they filmed, based on the book. Full program is available if you are a member of your public station. Given the author’s stunning success with The Emperor of all Maladies one might have wondered how that can be followed up. Wonder no more.

Music by Dvorak, Mendel’s Czech compatriot, the most bucolic of his Symphonies – maybe there are sheep to be heard in there after all…….

I, Borage, bring Courage.

Nature, Science
Jun 2, 2020
5 Comments

Yesterday I wrote about Hemlock, a poisonous plant that can kill. In the interest of fair and balanced reporting – and no, no false equivalencies here – I will today introduce a plant that heals, in ways just called for by our current times where war-like action by state and military forces start to dominate our streets, tear gassing peaceful protesters, if only to create photo-ops near churches.

The outside beauty of Borage, Borago officinalis L., is matched by the positive effects of the chemical properties contained inside. The leaves, flowers and seeds of the plant stimulate the adrenaline gland when ingested, helping to produce adrenaline which enables flight or fight responses in times of stress. In fact, Roman soldiers prepared themselves for battle by drinking Borage wine, claiming: “Ego borago gaudia semper ago” – I, Borage, will always bring courage. Both ancient Greeks and Romans also believed that it was useful as an anti-depressant, or, as they put it, cheer the heart and lift melancholia. Aren’t we in dire need of that? Courage and less sadness, so we can resume to act rather than feel paralyzed?

Liquid distilled from the leaves helps with the damage of steroid therapy (often use while fighting cancer,) alleviates dry coughs (lingering effects from Covid-19 infections,) and eases the effects of menstrual disorders. Borage poultices can help with inflamed skin and eczema.

Throughout the centuries, healers and now contemporary naturopathic practitioners all incorporated Borage into their arsenal of medicines. Eventually, science caught up: Borage is used by pharmacological industries as an antioxidant due to its bioactive compound content, called phenolics. These acids exert antioxidant and anti-inflammatory properties, and, as it turns out, anti-carcinogenic effects. Put simply, both wild and cultivated Borage provides chemical blueprints that can be used in the fight against cancer, infection and improve the immune-system.

And if that isn’t enough to lift your spirits, the plant also makes for one of the best sauces around – the traditional green sauce of the region around Frankfurt am Main. Here is the recipe. ( I assume it’s a sauce. Or is it gravy? Or dressing? How many more decades do I need to live here to figure out the difference? For once German is simple: it uses one word for all three! Soße.

And here’s the last bit of cheery news: Borage is quite effective to protect neighboring plants in your garden from pests and diseases. It attracts a lot of bees (as you can verify in the photographs) which also helps to pollinate your vegetable patch.

People have obviously always known it for its value – if you look at 17th century flemish paintings, for example, you find quite a lot of Borage blossoms mixed in with the other flowers that signify importance, either in terms of economic or religious value (tulips, lilies, carnations.) I am posting a few samples here but encourage those who love a good still life to check out the National Galleries’ recent exhibition. There is barely a flower painting that does not have Borage flowers peek through here or there.

*Insects with Creeping Thistle and Borage* Jan van Kessel the Elder

*Bouquet in Clay Vase* Jan Brueghel the Elder (Excerpt)

*Flowers in a White Stone Vase, Dirck de Bray (Borage on the marble slab)*

Bonus: here is a clip of how British florists recreated a Dutch masterpiece with real flowers, in huge dimensions, in honor of the exhibit.

And if you think we should not spend time with trifling issues like beauty while our country burns – I politely disagree. We need to preserve our sanity, keep our mental resources together, and that can only happen if we look at beautiful and hope-instilling things as well. That is how other generations survived far worse as well. Here is a reminder: Shostakovitch’s Symphony #11, commemorating the violent crushing of the 1905 uprising, Bloody Sunday, in Russia (and also hinting at the Hungarian Uprising in 1956.) (Music starts at 5:48)

But yes, courage is needed. Plant the Borage!

Overcoming Aloneness

Art, Science
May 27, 2020
0 Comments

Even for people like me who like being alone, at times even crave aloneness, the recent lonely days smear solitude with fear at times.

What if we all end up alone? Truly alone, not just the state that we currently experience, in our respective living conditions, geographic locations, separated from family and friends? The kind of alone where you lost the one closest to your heart, or take your last breath being surrounded by strangers, if surrounded at all?

I find comfort, when these threatening thoughts crop up, in thinking of a German scientist, Ernst Haeckel (1834–1919), who conquered an immense loss when his wife-to-be suddenly died, by throwing himself into work and art. In fact, he confronted the pain of aloneness with creating a whole worldview of systemic connectedness – ecology – and devoted himself to promote Darwin’s theory of evolution. The fate of the individual, the very fact of individuation, could be subsumed into ideas of connectedness and dominant needs within and for the preservation of the species. He and Darwin became close friends, and cooperated on numerous scientific explorations.

Haeckel’s scientific methods as a zoologist and professor of comparative anatomy as well as his philosophy where not uncontroversial – to this day creationist websites call him Darwin’s lap dog and the German menace – his Tree of Life was and is incendiary to religious folks clinging to biblical literalness of creation. The Nazis, long after his death, selectively picked some of his writings on the political and religious implications of Darwinism to justify their racial programs, perhaps one of the reasons that he has fallen into obscurity more so than Darwin.

Within the scientific community some of Haeckel’s biological assumptions are no longer accepted. Inferring from his work with radiolarians, tiny plankton that is found in the ocean, he believed that an individual’s biological development mirrors the evolutionary one of the entire species – ontogeny recapitulates phylogeny. Not so.

He is heralded, though, as a brilliant naturalist and discoverer of multiple new species.

Whatever you think of his science, or his beliefs, there is no controversy around the fact that he was an amazing artist.

In fact, it was his art that introduced him to Darwin in the first place when he sent him portfolios with his drawings of jelly fish and other maritime creatures. The drawings in Kunstformen der Natur – Art Forms in Nature – are breathtaking, you can judge for yourself, of course.

I can vividly imagine how the painstaking creation of these detailed drawings and watercolors of jelly fish and other creatures distracted him from his loss; the embrace of a theory that celebrates interconnectedness in nature must have helped to transmute his grief into a sense of belonging. We should all be so lucky to find appropriate distractions and beliefs ourselves.

Or we could engage in truly downward comparison to make us feel better if we are really desperate: over dinner, the time of day where we try to cheer each other up by reporting useless factoids, I learned that marine biologists discovered, deep, deep at the floor of the ocean, a species of octopus that has to sit on her eggs (all 155 of them) for a gestation period of 4.5 years. Not eating during all this time, not moving once other than fending off ravenous crabs, the emaciated Mama dies when the little ones emerge. Now there is loneliness. To the bitter end.

Below is a 4 minute art film that uses Haeckel’s concepts and drawings to explain some of the things I mentioned. Nothing but wonder.

Music today fits the topic, I think. Anything and everything is captured in this concerto, from lonely distance, listlessness, determination to intense joy (Hindemith wrote it while still in the killing fields of WW I – art transmuting fear here as well.)

Photographs are of jelly fish at diverse aquariums, in Newport, OR, Vancouver BC and Charleston, SC.

Your Brain is Not an Onion with a tiny Reptile inside.

Science
May 19, 2020
2 Comments

Every so often there is a scientific article that should be read and shared for the title alone. I mean, how can you not revel in the image of your head consisting of layer after tear-producing layer enshrouding a lizard?

The one in question, a paper by scientists Joseph Cesario, David J. Johnson, and Heather L. Eisthen at Michigan State University, should be read for a more important insight, though. Not only do many of us, influenced by thinkers as long ago as the Greek philosophers, or as influential as Freud in our own times, conceive of our brain in ways that are wrong, but the majority of psychology textbooks, never mind common literature, perpetuate the false beliefs.

Put simply: we cling to the notion that there is an old reptilian part of the brain, that controls basic functions. Layered onto it is the limbic system that controls our emotional responses. On top of it is another layer, the cerebral cortex, which controls language, reasoning and rational actions. The tug of war between emotional reactions (hot) and deliberate reason (cold) is assigned to these regions and reserved for the evolutionary most complex species.

This notion includes some basic assumptions: that there are older anatomical structures (the animalistic drive center that only allows reflexive responses) and that there are newer structures that are reserved for more complex organism like humans, allowing for rational decision making, overriding the emotional response. They are seen as layered on top of each other, like geological strata that you can identify when you dig ever deeper onto the earth. And the notion assumes that we have evolved linearly from simple animals to highly complex ones, our own species included at the very top.

We’ll have to let go of this view. For one, neural and anatomical complexity evolved repeatedly within many independent lineages. Simply put, there is increasing complexity to be found in mammals and non-mammal species, octopus, sharks, birds for example show ever evolving incredible brain complexity and corresponding behavior.

The notion of layers of new structures added to existing structures across evolutionary time as species became more “complex” is also incorrect. All mammals, not just humans, have a pre-frontal cortex the part that controls reasoning, it is not uniquely human.

Most importantly, evolution does not proceed by laying down geological strata, one over the other, instead evolution changes existing parts, transforming them. That does not mean that everything earlier is completely wiped out (the “head vs. heart” tug of war is something we do still experience) but the belief that emotion and reason are located in evolutionary independent, untouched structures is scientifically untenable.

The paper goes on to discuss why it matters to change our mistaken views. I’ll leave it to you to read up on it if that is of interest. I will cheer us up in the short run with something related that I read yesterday referring to science, by Jan Mieszkowski, a Reed College professor in the German department:

Lizards come in all sizes – one of the biggest is the green iguana. Iguanas are a favorite American pet, and all too often released into the wild after people get bored – there they wreck havoc. Florida, where today’s photographs were taken some time back, suffers substantial damage from these creatures who have not many natural predators, proliferate and threaten eco system and structures, river banks and golf courses alike. The video below is pretty graphic in what iguana hunters do, catching the lizards for kill, or to be sold to restaurants (their meat is a favorite for caribbean cuisine, “tree chicken,”) or to be sold for pets. It is an interesting sociological snapshot, though, which is why I decided to include it.

And here is the biggest lizzard of them all in a wonderful 1924 Fritz Lang rendition….of a Wagnerian Tarzan slaying the dragon.

Music is self explanatory….

Freedom From vs Freedom To

Bullypulpit here. Essential reading. Sweetened by the sweetest birds, I believe Wilson warblers, photographed from my window during their fleeting, skipping, hopping, fluttering visit on Saturday. Tired of birds yet? Tired of politics of racism? Granting the former, but we don’t have the luxury of fatigue for the latter. As I said, bullypulpit today.

In a friendlier, pleading voice: please read this short essay by Ibram X. Kendi. It is enlightening, non-belligerent, and so, so timely. (Alternatively, I put the key paragraphs below to get the message in plain view.)

In a nutshell he argues that we see parallels between the American history of slaveholding mentality and the division in approaches to containing the Covid-19 pandemic today. Embedded in some plain teaching about historical facts of our founding fathers and the Civil War is this core insight:

Slaveholders desired a state that wholly secured their individual freedom to enslave, not to mention their freedom to disenfranchise, to exploit, to impoverish, to demean, and to silence and kill the demeaned. The freedom to. The freedom to harm. Which is to say, in coronavirus terms, the freedom to infect.

Slaveholders disavowed a state that secured any form of communal freedom—the freedom of the community from slavery, from disenfranchisement, from exploitation, from poverty, from all the demeaning and silencing and killing. The freedom from. The freedom from harm. Which is to say, in coronavirus terms, the freedom from infection.

From the beginning of the American project, the powerful individual has been battling for his constitutional freedom to harm, and the vulnerable community has been battling for its constitutional freedom from harm. Both freedoms were inscribed into the U.S. Constitution, into the American psyche. The history of the United States, the history of Americans, is the history of reconciling the unreconcilable: individual freedom and community freedom. There is no way to reconcile the enduring psyche of the slaveholder with the enduring psyche of the enslaved.

Much has been written about the origins of individualism, the settler mentality, the connection to the belief in the doctrine of exceptionalism and the fact that it is a specifically Western value, so different from the rest of the world which cherishes communal values.

Here is another take that I found quite interesting. New research published six months ago explores a connection between the teachings of the Catholic Church and the rise of individualism, including its specific beliefs in independence, agency and autonomy, starting in the 6th century. In essence there was a church directive to cease intrafamily marriages – to stop marrying your cousins, eventually up to the 6th degree (so not just an incest taboo,) or their widows or adopt their orphans, which changed the traits shared by most people in the world to something different, individualistic, specifically Western.

The research used an enormous range of data to look at correlations between time and intensity spent under the directions of the church, and development of these Western values, including comparisons within one and the same country (Italy) that provided two parts differentially dependent on the church, the industrial North and the poor South. The data “included historical records of church exposure in every nation on Earth, beginning in the first century and ending in 1500 C.E., when European society had become nearly fully Christianized. They also looked at they consulted anthropological data to assign a kinship intensity score to each of the world’s major ethnolinguistic groups. This score was based on historical rates of cousin marriage, polygamy, and other factors. Finally, they drew on dozens of studies that used established psychological measures such as the World Values Survey to determine modern population-level scores for traits such as individualism, creativity, nonconformity, obedience, and ingroup/outgroup trust.”

The large family clans that had been constituted by these family connections guaranteed survival. Growing crops and protecting land required cooperation, and marrying cousins was an easy way to get it. When these kinship systems were broken apart it had enormous consequences, not all good. On the one hand, less dependency and obedience to clans, elders, community did lead to more freedom of choice for the individual, less forced obedience and conformity. Individualistic people working together across family boundaries (and thus with less in-group conformity) formed a precursor civic society that eventually enabled democracy.

The disruption of extended family systems in favor of a nuclear family, however, also meant less security in case of emergencies, famine, disease, with no familial system to fall back on. This is where the church jumped in, corralling the poor in their alms/work houses. Depriving folks of the leadership of their elders left space for the church to take over as authority, requiring obedience, extending influence. The disruption of family ties also led to less land consolidation among the intermarried, from which the church benefited by snatching it up for itself. This was particularly the case during the demise of entire family branches when the lack of succession through adoption was blocked and the estates fell by default to the church.

And, of course, the prime value that we eventually put on individualism weakened the values attached to communal existence.

The interconnection between human psychology, religion, economy and politics never ceases to amaze me. As does our willingness to ignore history and look away from causal factors – like the ongoing effects of slavery or the disadvantages of individualistic societal structuring – when we try to move towards solutions in crises. The worst thing, though, is the fact that so often the price for acting in our self-interest is paid by others, the masses who are granted neither: the freedom for or the freedom from.