Posts Tagged ‘bacteria’
“Bacteria represent the world’s greatest success story”*…
But as Stephen Jay Gould goes on to observe (in his 1996 book, Full House: The Spread of Excellence from Plato to Darwin), “They are today and have always been the modal organisms on earth; they cannot be nuked to oblivion and will outlive us all. This time is their time, not the ‘age of mammals’ as our textbooks chauvinistically proclaim. But their price for such success is permanent relegation to a microworld, and they cannot know the joy and pain of consciousness. We live in a universe of trade-offs; complexity and persistence do not work well as partners.”
Still, we (more complex) humans have recognized– and accommodated– bacteria for millennia. As We Make Money Not Art explains in a review of a recent book– We The Bacteria. Notes Toward Biotic Architecture by architectural historians Beatriz Colomina and Mark Wigley— that’s fascinatingly apparent in the history of architecture…
This “alternative history of architecture from the point of view of microbes” compiles the research that led to the exhibition We the Bacteria: Notes Toward Biotic Architecture at the 24th Milan Triennale last year. Curated by Colomina and Wigley, the show investigated how microbial ecosystems relate to spatial design and health inequality.
The book argues that microbes have not only built the whole planetary biosphere but they have also been the real architects of our homes and cities throughout the ages. Or rather, it’s the fear and diseases they cause that have shaped our spaces and the ways we move through them.
About ten thousand years ago, humans began retreating into spaces increasingly cut off from the exterior world. Plants, soil and insects could be left outside. But microbes, including pathogenic ones, followed humans inside their homes, where they adapted, mutated and generated new diseases. As our shelters expanded into villages, cities and sprawling empires, so too did the microbial ecosystems.
The authors narrate how buildings and bodies exist in a constant microbial exchange, co-evolving into a single, dynamic ecosystem. The microbiome of a home is highly specific to its inhabitants. Even the microbiome of a frequently cleaned hospital room resembles the microbiome of the previous patient, but starts to resemble that of a new occupant after twenty-four hours.
Architecture cannot exist without microbes, and, by extension, without disease. While scrubbing, spraying and disinfecting may eliminate most microorganisms, these practices also breed extremophiles, species so resistant that they can take over the space.
Throughout history, the book reveals, health crises have dictated architectural and urban design. From toilets to fumigation systems, from the plague hospitals, aka lazarettos, to the sanatoriums for tuberculosis patients; from sewage systems to urban parks, cities have been continually reshaped in response to the threats they sought to contain. Architecture became the first line of defence against microbes…
[More of the intertwined history of bacteria and our reponse to them, with lots of fascinating photos…]
… Given the important role that microbes play for our immune systems and the environments we inhabit, the authors call for a biotic architecture. Biotic architecture is less human-centric than traditional architecture. It learns from microbes rather than resists them. It does, of course, maintain some antimicrobial protocols against pathogens remain crucial. Water, sewage systems, toilets and food preparation areas still need to be cleansed, but cleaning routines should also embrace controlled exposure to microbial diversity. During COVID-19, for example, microbiologist Elisabetta Caselli and her colleagues replaced conventional disinfectants with probiotic-based sanitation in six Italian public hospitals. The result was a decrease in surface pathogens by up to 90% compared to conventional chemical cleaning and lower rates of healthcare-associated infections and antibiotic resistances… For once, here is a book that presents a vision where humans can actively contribute to microbial diversity, collaborate with the unseen world around us and build in ways that nurture rather than harm the environment…
More– and more fascinating images– at: “We The Bacteria. Notes Toward Biotic Architecture.”
###
As we coexist, we might recall that it was on this date in 2012 that Rebekah Speight of Dakota City, Nebraska sold a McDonald’s Chicken McNugget that resembled President George Washington for $8,100 on eBay (the third most expensive McNugget ever sold). She had kept the McNugget in her freezer for 3 years before deciding to sell it…. because bacteria.
“You can swim (uncomfortably) in water at a temperature slightly above freezing; a tiny drop in temperature—or a miracle—allows you to walk on water.”*…
As Elise Cutts explains, making ice requires more than subzero temperatures. The unpredictable process takes microscopic scaffolding, random jiggling and often a little bit of bacteria…
We learn in grade school that water freezes at zero degrees Celsius, but that’s seldom true. In clouds, scientists have found supercooled water droplets as chilly as minus 40 C, and in a lab in 2014, they cooled water to a staggering minus 46 C before it froze. You can supercool water at home: Throw a bottle of distilled water in your freezer, and it’s unlikely to crystallize until you shake it.
Freezing usually doesn’t happen right at zero degrees for much the same reason that backyard wood piles don’t spontaneously combust. To get started, fire needs a spark. And ice needs a nucleus — a seed of ice around which more and more water molecules arrange themselves into a crystal structure.
The formation of these seeds is called ice nucleation. Nucleation is so slow for pure water at zero degrees that it might as well not happen at all. But in nature, impurities provide surfaces for nucleation, and these impurities can drastically change how quickly and at what temperature ice forms.
For a process that’s anything but exotic, ice nucleation remains surprisingly mysterious. Chemists can’t reliably predict the effect of a given impurity or surface, let alone design one to hinder or promote ice formation. But they’re chipping away at the problem. They’re building computer models that can accurately simulate water’s behavior, and they’re looking to nature for clues — proteins made by bacteria and fungi are the best ice makers scientists know of.
Understanding how ice forms is more than an academic exercise. Motes of material create ice seeds in clouds, which lead to most of the precipitation that falls to Earth as snow and rain. Several dry Western states use ice-nucleating materials to promote precipitation, and U.S. government agencies including the National Oceanic and Atmospheric Administration and the Air Force have experimented with ice nucleation for drought relief or as a war tactic. (Perhaps snowstorms could waylay the enemy.) And in some countries, hail-fighting planes dust clouds with silver iodide, a substance that helps small droplets to freeze, hindering the growth of large hailstones.
But there’s still much to learn. “Everyone agrees that ice forms,” said Valeria Molinero, a physical chemist at the University of Utah who builds computer simulations of water. “After that, there are questions.”…
More at: “The Enduring Mystery of How Water Freezes,” from @elisecutts in @QuantaMagazine.
Even more at “Cold, colder and coldest ice” (source of the image above)
* Meteorologist Craig Bohren
###
As we contemplate crystallization, we might send chilly birthday greetings to a man fascinated by ice and its crystalline structure, Walther Hermann Nernst; he was born on this date in 1864. A physicist and physical chemist, he made material contributions to thermodynamics, physical chemistry, electrochemistry, and solid-state physics. But he is best remembered for the Nernst heat theorem, which stated that the entropy (a thermodynamic measure of disorder) in a system approaches zero as the temperature goes towards absolute zero… which led to the development of what Nernst himself called “the third law of thermodynamics,” and to Nernst’s receiving the 1920 Nobel Prize in Chemistry.
“The most outstanding feature of life’s history is a constant domination by bacteria”*…
Jennifer Kahn interviews biochemist Jennifer Doudna (who won the Noel Prize for the gene-editing engine Crispr) on her new focus– our microbiomes, tackling everything from immune disorders and mental illness to climate change—all by altering microbes in the digestive tract…
… what isn’t the microbiome responsible for? It’s been all the rage for the past few years, with scientists hoping it could help treat everything from immune disorders to mental illness. How exactly that will work is something we’re just starting to explore. This spring, the effort got a boost when UC Berkeley biochemist and gene-editing pioneer Jennifer Doudna, who won a Nobel Prize in 2020 for coinventing Crispr, joined the pursuit. Her first order of business, spearheaded by Berkeley’s Innovative Genomics Institute: fine-tuning our microbiome by genetically editing the microbes it contains while they’re still inside us to prevent and treat diseases like childhood asthma. (Full disclosure: I teach at Berkeley.) Oh, she also wants to slow climate change by doing the same thing in cows, which are collectively responsible for a shocking amount of greenhouse gas.
As someone who has written about genetic engineering in the past, I have to admit that my first reaction was: No way. The gut microbiome contains around 4,500 different kinds of bacteria plus untold viruses, and even fungi (so far: in practice we’ve only just started counting) in such massive quantities that it weighs close to half a pound. (Microbes are so tiny that 30 trillion bacteria would weigh roughly 1 ounce. So half a pound is a lot.)
Figuring out which ones are responsible for which ailments is tricky. First you need to know what’s causing the problem: like maybe something is producing too much of a particular inflammatory molecule. Then you have to figure out which microbe—or microbes—is doing that, and also which gene within that microbe. Then, in theory, you can fix it. Not in a petri dish, but in situ—meaning in our fully active, roiling, squishing stomach and intestines while they continue to do all the stuff they usually do.
Until recently, it would have seemed insane—not to mention literally impossible—to edit all the microbes belonging to a species within a vast ecosystem like our gut. And to be fair, Doudna and her collaborator, Jill Banfield, still don’t know quite how it will work. But they think it can be done, and in April, TED’s Audacious Project donated $70 million to support the effort. My own gut feeling (right?) was that this was either brilliant or terrifying, or possibly both at once. Brilliant because it had the potential to head off or treat diseases in an incredibly targeted and noninvasive way. Terrifying because, well, you know … releasing a bunch of inert viruses equipped with gene-editing machinery into the vital ecosystem that is our gut microbiome—what could go wrong? With that in mind, I invited Jennifer Doudna to my house for a chat about the future of microbiome medicine…
Fascinating– and encouraging: “Crispr Pioneer Jennifer Doudna Has the Guts to Take On the Microbiome,” in @WIRED.
(Image above: source)
* Stephen Jay Gould
###
As we investigate our intestines, we might spare a thought for Guido Pontecorvo; he died on this date in 1999. A geneticist, he discovered the process of genetic recombination in the common soil fungus Aspergillus— and as a result the parasexual cycle— in what became the model for the genetic studies in many other fungi. This cycle gives rise to genetic reassortment by means other than sexual reproduction; its discovery provided a method of genetically analyzing asexual fungi…. which, as noted above, populate our microbiomes.
“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: Bacteria, Archaea, and Eucarya.
“Thinking within strict limits is stifling”*…
Affectionately nicknamed “Conan the Bacterium,” Deinococcus radiodurans, a so-called polyextremophile, has an uncanny ability to rapidly repair damage to its genome. As a result, it can resist the most hostile conditions, from drought to radiation to acid baths to a Martian atmosphere. And if Canadian conceptual poet Christian Bök has his way, it will compose verse that will outlive our Sun.
Bök has earned a reputation for conducting extremely difficult poetic experiments and executing them with technical wizardry. In his award-winning 2001 bestseller Eunoia , for example, he uses only a single vowel in each chapter, a constraint that produces a form known as a univocalic . The first section is composed of words that include no vowels other than a , the second includes no vowels other than e , and so on. To build an appropriate lexicon for this demanding work, Bök read through Webster’s Third International Unabridged Dictionary five times and spent six years writing. His latest poetic challenge takes him into trickier and more technically specialized territory. Taking on the very perishability of text, Bök has devised a novel solution: In composing his verse, he is employing the medium of life itself.
The Xenotext: Book 1 represents the first phase of Bök’s wildly ambitious project—nearly 15 years in the making and still ongoing—of encoding poetry into the genome of the bacterium D. radiodurans . Using a substitution cipher, Bök “translates” his poetry into what he calls a “chemical alphabet” representing a genetic sequence. After simulating the resulting protein’s folding pattern, which is essential for its functioning, Bök sends his specifications to a biotechnical lab that engineers the gene accordingly. Finally, Bök’s team of biologists transplants a plasmid carrying the gene into the bacterium.
But why introduce such complexity into the process of poetic composition? The Xenotext provocatively wagers that—in the face of global catastrophe, whether in the form of ecological collapse, drug-resistant pandemic, or nuclear war—D. radiodurans can preserve at least a bit of humanity’s poetic heritage after the apocalypse. DNA, with its remarkable storage capacity and stability, is perhaps the “natural element,” the worthy vessel for the mind’s substance that Wordsworth expresses longing for in the epigraph above…
Writing an eternal poem, one that will survive in the DNA of extremophile bacteria when all other life on the planet is extinguished: “Poetry of the Apocalypse.”
For more on exactly how Bök “writes,” see: “The Making of a Xenotext.”
*
###
As we ponder posterity, we might send straight-forward birthday greetings to Joseph Addison; he was born on this date in 1672. A poet, playwright, and politician, Addison is probably best remembered for The Spectator, a daily publication– a “paper” as it was then called, and as it successors have been known ever since– which he founded in London with his partner Richard Steele.
The Spectator was widely read in London; indeed Jürgen Habermas suggests that the paper was instrumental in the emergence of the public sphere in 18th century England. It also had North American readers (including Benjamin Franklin and James Madison).
You must be logged in to post a comment.