(Roughly) Daily

Posts Tagged ‘taxonomy

“The most incomprehensible thing about the world is that it is at all comprehensible”*…

There is an order to the ordered search for ordered understanding…

Science (from Latin scientia, meaning “knowledge”) is a systematic enterprise that builds and organizes knowledge in the form of testable explanations and predictions about the universe.

Modern science is typically divided into three major branches that consist of the natural sciences (biology, chemistry, physics, astronomy and Earth science), which study nature in the broadest sense; the social sciences (e.g. psychology, sociology, economics, history) which study people and societies; and the formal sciences (e.g. mathematics, logic, theoretical computer science), which study abstract concepts. There is disagreement, however, on the formal sciences being a science [as they use an a priori, as opposed to empirical, methodology]. Disciplines that use science, such as engineering and medicine, are described as applied sciences

And there is a dazzling array of “branches” of the scientific endeavor:

Acanthochronology – study of cactus spines grown in time ordered sequence

Acarology – study of mites and ticks

Aceology – science of remedies, or of therapeutics; iamatology

Acology – study of medical remedies

Acoustics – science of sound

Actinobiology – synonymous with radiobiologyAdenology – study of glands…

Browse dozens and dozens at “Index of branches of science,” from Wikipedia… whose contributors may be erring on the generous side, as the list includes such entries as “Hamartiology” (the study of sin) and “Taxidermy” (the art of curing and stuffing animals).

* Albert Einstein

###

As we tackle taxonomy, we might recall that it was on this date in 2013 that Google experienced a five-minute outage affecting all of it’s services, including Google Search, YouTube, and Google Drive. During that brief period global internet traffic dropped 40%.

“Life’s a little weird”…

Needs must…

You may have ridden out the pandemic in compact living quarters without, say, much natural light or air conditioning. Perhaps you lived with roommates or family in an atmosphere that, as time wore on, grew increasingly toxic. 

Things could be worse! You could be a member of the Alviniconcha species—specifically, a small, spike-studded snail who thrives in an environment inhospitable to most aquatic life; mere meters from deep-sea hydrothermal vents that constantly spew toxic chemicals into the water. Think you have limited natural light? Try living nearly 10,000 feet below the surface of the ocean, where complete darkness envelops you 24 hours a day, under pressure so intense all the air pockets in your body would instantly collapse. 

And forget Seamless. Forget food—at least the kind you ingest with your mouth. Your survival hinges on bacteria living in your gills (you have gills!) in a symbiotic relationship that provides you with energy, via a process called chemosynthesis. It’s like photosynthesis, but chemosynthesis is driven by chemical reactions instead of light. As there’s no sunlight and minimal oxygen present, the bacteria that dwell within Alviniconcha use hydrogen and sulfur molecules to produce sugars and other macronutrients that the animals then use as food. “There’s very little food so deep in the ocean,” says Dr. Corinna Breusing, postdoctoral researcher at the University of Rhode Island and co-author of a recent paper on the snails and their symbionts. “Having your own food-producing machine is much better than waiting for it to fall to you.” While chemosynthesis is common around hydrothermal vents, it can occur in places outside of vents, such as in cold seeps and whale falls and even salt marshes: anyplace the proper mélange of inorganic compounds is brewing. 

The researchers studied Alviniconcha living at the bottom of the Lau Basin, in the southwestern Pacific Ocean, and found that the type of bacterial symbiont determined where their particular host species could live. “The symbionts have different metabolic capacities and adaptations, so we think that the symbionts influence the distribution of the animal,” Breusing says, adding that snails with Campylobacteria dominated at vents with higher concentrations of sulfide and hydrogen, while those with Gammaproteobacteria were able to thrive at sites with lower concentrations of sulfide and hydrogen. Meaning: your chef-roommate, who happens to live in your respiratory system, also decides where you hang your hat (so to speak).

Most hydrothermal vent-dwelling animals, such the aforementioned snails and deep-sea anemones, as well as some species of mussels and tube worms, depend on bacteria that they pick up from the environment, but there is a species of deep-sea clam that passes their symbiont down from mother to offspring, like a fancy set of dinner plates. (This is rare in the marine world, Breusing says.) In the case of the deep-sea clams, where the symbiont is inherited, the symbiont cannot thrive outside the host and dies with it. But if a symbiont is taken up from the environment, it can be released back into the environment after its host dies, ready to help feed a brand-new host.

Alviniconcha might not pack the same visual punch as much marine life does much closer to the surface, but their very existence points to the origins of life on Earth. Before oxygen was free and plentiful, microbial life had to work with inorganic compounds like methane and ammonia, which over millennia dissolved into the seas. Much is still murky about how these little snails co-evolved with the bacteria that enable them to survive, but these fascinating ecosystems indicate that our education about life at the margins is just getting started…

Life at the Edge of Impossible“: ten thousand feet under the sea, these snails thrive with a little help from their friends; from Adrienne Day (@adrienneday).

* Dr. Seuss

###

As we examine extremes, we might send redefining birthday greetings to Carl Woese; he was born on this date in 1928. A microbiologist and biophysicist, he made many contributions to biology; but he is best remembered for defining the Archaea (a new domain of life).

For much of the 20th century, prokaryotes were regarded as a single group of organisms and classified based on their biochemistry, morphology and metabolism. In a highly influential 1962 paper, Roger Stanier and C. B. van Niel first established the division of cellular organization into prokaryotes and eukaryotes, defining prokaryotes as those organisms lacking a cell nucleus. It became generally assumed that all life shared a common prokaryotic (implied by the Greek root πρό [pro-], before, in front of) ancestor.

But in 1977 Woese (and his colleague George E. Fox) experimentally disproved this universally held hypothesis. They discovered a kind of microbial life which they called the “archaebacteria” (Archaea), “a third kingdom” of life as distinct from bacteria as plants are from animals, Having defined Archaea as a new “urkingdom” (later domain) which were neither bacteria nor eukaryotes, Woese redrew the taxonomic tree. His three-domain system, based on phylogenetic relationships rather than obvious morphological similarities, divided life into 23 main divisions, incorporated within three domains: BacteriaArchaea, and Eucarya.

source

source

“And God said, Behold, I have given you every herb bearing seed, which is upon the face of all the earth, and every tree, in the which is the fruit of a tree yielding seed”*…

The first patent on an animal was granted in the U.S. in 1988. But the first agricultural patents date back to 1930 and the Plant Patent Act (PPA). Since then, patent protection on seeds has been both broadened and lengthened; in the 1980’s, protection was extended beyond “utility” (a plant that uniquely did one thing or another) to the living thing itself. And the seed industry has consolidated…

For years Haribhai Devjibhai Patel has been growing cotton, peanuts and potatoes in the western Indian state of Gujarat. For years he and his family have used seedlings from one harvest to plant the next year’s crops on his four acre field.

Last year he planted a new potato variety known as FC5. It was a decision that ultimately landed him in court, because the US company PepsiCo had already claimed the rights to that very same potato variety. Patel claims he wasn’t aware of the potato’s name, much less PepsiCo’s claim…

According to the plaintiffs’ lawyer, Anand Yadnik, the lawsuit alleges that the FC5 potato is especially bred for PepsiCo’s subsidiary company Lays and their internationally distributed product: potato chips. PepsiCo was seeking 10 million Rupies or $140.000 (€ 126.000).

“I was completely devastated. I was afraid. Not in my lifetime would I ever have been able to pay the kind of damages that were being claimed by PepsiCo,” Patel said. The 46-year-old farmer has two children and earns around $3,500 per year.

The lawsuit was based on findings that PepsiCo gathered from Patel’s field. According to his lawyer, the company hired a private detective agency to provide the data. “They took secret video footage and collected samples from farmers fields’ sans disclosing their real intent”…

The case is another example of  an ongoing global trend of companies claiming property rights for plants or genetic material of plants  across the globe. 

“Resources that used to be available to mankind as a community have now been confined to privatization,” Judith Düesberg from NGO Gene Ethical Network… The number of patents on plants worldwide has increased a hundredfold from just under 120 in 1990 to 12,000 today – 3500 of them are registered in Europe,according to the European initiative No-Patents-On-Seeds

Critics argue that patents block access to genetic material for farmers and minimize biodiversity, the diversity of species and increase farmers’ dependency on seed producers.

But Bayer, Monsanto’s parent company, told DW in a written statement: “Farmers have the choice of whether and which products they buy from which supplier. [… ] Each farmer decides freely. […] Farmers will only use our products if they gain a clear advantage.”

In Europe, a case involving Monsanto and a particular breed of melon drew media attention several years ago. Monsanto had discovered that an Indian melon variety was naturally resistant to a specific virus. At the European Patent Office it then successfully applied for a patent on that trait after breeding into other melons. 

From this moment on, not only did this trait belong to Monsanto, but so did every melon variety containing it, including the Indian melon from which it originated. Patent opponents call this practice  biopiracy

According to the Indian-based market research agency Mordor Intelligence, revenue in the seed sector will reach $90 billion by 2024 compared to about $60 billion in 2018. And over 50% of the worldwide market share is in the hands of Bayer-Monsanto, Du Pont and Syngenta…

The UN report “The right to food” has raised concerns about food security caused by “the oligopolistic structure of the input providers” warning that it could also cause food prices to increase and deprive the poorest of food.

A further concern is who owns the seeds and who produces the food. According to the NGO Germanwatch, most of the seed producing industry comes from the Global North, but 90% of biological resources (agricultural products, natural materials come) from the Global South. 

While patenting laws remain more restrictive in the Global South, an Oxfam Study shows that big global players appear to be finding loopholes

A few companies are angling to sew up the world’s seed supply: “Patents on plants: Is the sellout of genes a threat to farmers and global food security?

* Genesis, 1:29 (KJV)

###

As we reap what we sow, we might send well-organized birthday greetings to Antoine Laurent de Jussieu; he was born on this date in 1748.  A botanist, he is best remembered as the first to publish a natural classification of flowering plants; much of his system– which was, in part, based on unpublished work by his uncle, Bernard de Jussieu— remains in use today.

220px-Jussieu_Antoine-Laurent_de_1748-1836

 source

Written by (Roughly) Daily

April 12, 2021 at 1:01 am

“Taxonomy is described sometimes as a science and sometimes as an art, but really it’s a battleground”*…

Dorothy Porter in 1939, at her desk in the Carnegie Library at Howard University.

In a 1995 interview with Linton Weeks of the Washington Post, the Howard University librarian, collector, and self-described “bibliomaniac” Dorothy Porter (1905–95) reflected on the focus of her 43-year career: “The only rewarding thing for me is to bring to light information that no one knows. What’s the point of rehashing the same old thing?” For Porter, this mission involved not only collecting and preserving a wide range of materials related to the global Black experience, but also addressing how these works demanded new and specific qualitative and quantitative approaches in order to collect, assess, and catalog them…

As Thomas C. Battle writes in a 1988 essay on the history of the Moorland-Spingarn Research Center, the breadth of the two collections showed the Howard librarians that “no American library had a suitable classification scheme for Black materials.” An “initial development of a satisfactory classification scheme,” writes Battle, was first undertaken by four women on the staff of the Howard University Library: Lula V. Allen, Edith Brown, Lula E. Conner, and Rosa C. Hershaw. The idea was to prioritize the scholarly and intellectual significance and coherence of materials that had been marginalized by Eurocentric conceptions of knowledge and knowledge production. These women paved the way for Dorothy Porter’s new system, which departed from the prevailing catalog classifications in important ways.

All of the libraries that Porter consulted for guidance relied on the Dewey Decimal Classification. “Now in [that] system, they had one number—326—that meant slavery, and they had one other number—325, as I recall it—that meant colonization,” she explained in her oral history. In many “white libraries,” she continued, “every book, whether it was a book of poems by James Weldon Johnson, who everyone knew was a black poet, went under 325. And that was stupid to me.”

Consequently, instead of using the Dewey system, Porter classified works by genre and author to highlight the foundational role of Black people in all subject areas, which she identified as art, anthropology, communications, demography, economics, education, geography, history, health, international relations, linguistics, literature, medicine, music, political science, sociology, sports, and religion.

This Africana approach to cataloging was very much in line with the priorities of the Harlem Renaissance, as described by Howard University professor Alain Locke in his period-defining essay of 1925, “Enter the New Negro.” Heralding the death of the “Old Negro” as an object of study and a problem for whites to manage, Locke proclaimed, “It is time to scrap the fictions, garret the bogeys and settle down to a realistic facing of facts.” Scholarship from a Black perspective, Locke argued, would combat racist stereotypes and false narratives while celebrating the advent of Black self-representation in art and politics. Porter’s classification system challenged racism where it was produced by centering work by and about Black people within scholarly conversations around the world.

How Dorothy Porter assembled and organized a premier Africana research collection– and helped change academia: “Cataloging Black Knowledge.”

See also “African American Print Culture.”

* Bill Bryson, A Short History of Nearly Everything

###

As we contemplate cataloguing, we might recall that it was on this date in 1909 that a group including W. E. B. Du Bois, Mary White Ovington, Moorfield Storey, and Ida B. Wells formed the NAACP— The National Association for the Advancement of Colored People– an interracial organization dedicated to advancing justice for African Americans. 112 years later, its work continues.

source

“If you cannot teach me to fly, teach me to sing”*…

 

Chutney

A map of “chutney,” a genre based in the southern Caribbean, especially Trinidad and Tobago, which was most popular in the 1980s

 

You could argue that on the face of it, the project Every Noise At Once feels like staring into the abyss, and that the abyss is a completely straight line. The site, designed by Glenn McDonald, is an effort to visually map all the world’s musical genres algorithmically using Spotify data. Through the miracle of computer programming, the collective artistic genius and work of diverse individuals and cultures is flattened out into a single sprawling word cloud, with rock genres cluttering in the center, and other more remote musics pulsing off in seemingly stochastic drifts. Some might view it as a sign of impending doom, I suppose. But you could also see it as beautiful, fractal representation of the joys to be had in crossing cultures and musical styles; a vision of a world with the walls taken out…

McDonald is cheerfully upfront about the fact that Every Noise At Once isn’t a definitive single view of the world of music, but a discussion about possible landscapes. “Our computers can now enter plausibly into arguments over almost 500 genres, from a cappella to zydeco,” he says in an explanation of the project. Genres are always fuzzy, porous, and changeable anyway. Every Noise at Once updates and rearranges itself regularly, offering not a single vision of global sound, but a more tentative invitation to explore outside of your comfort zone.

And exploring is really a blast. It’s great fun to scroll around the map, looking for genres you’ve never heard of, and taking a moment to try to figure out what it is, where it’s from, and what it sounds like…

An attempt to map every music genre that exists, no matter how obscure: “Every Noise at Once” does its darnedest to create order out of chaos.  Explore for yourself here.

* Sir James Barrie, Peter Pan

###

As we hum along, we might recall that it was on this date in 1986 that Dan Rather began to sign off his CBS Evening News broadcasts with the word “courage.”  He insisted that it was just a signature line and had nothing to do with the news at the time.  In any case, other newscasters ridiculed and parodied Rather, and he dropped it one week later.

 

Written by (Roughly) Daily

September 1, 2019 at 1:01 am

%d bloggers like this: