Daily Archives: October 3, 2021

Photo credit: Kumiko SHIMIZU, via Unsplash.

I have been explaining why, if nature is designed, it may exhibit optimal green energy solutions. (See here and here.) Now I will offer an illustration.

The action of removing carbon from the atmosphere and turning it into a sugar molecule is made possible in plants by a very fancy molecular machine called rubisco. Despite being one of a kind, rubisco has received a lot of hate through the years for being slow. Many enzymes process a thousand molecules per second, but rubisco can only process three per second. Because of this, it has been called sluggish and notoriously inefficient. (Bathellier et al. 2018) Justification for these derogatory adjectives does not exist in my personal opinion because, after extensive study for fifty years, no one has been able to make it better. (Bathellier et al. 2018) Id like to suggest (Bathellier et al. 2018) that its slowness might be due to the complexity of the chemical reaction. If one or another function of rubisco were ditched, its mechanism might be able to be enhanced in certain respects. However, there would almost certainly be trade-offs. So I am not suggesting that rubisco cannot be optimized for a different purpose as optimality is always intrinsically tied to function. But I predict that in time it will be recognized for its optimality, given the overall constraints of the ecosystem.

What rubisco actually does is complicated. Rubisco grabs a CO2 molecule (most of the time) and attaches it to a sugar chain. (Bathellier et al. 2018) Rubisco then takes the lengthened carbon chain and clips it, thus producing two identical phosphoglycerate molecules. (PDB-101 Molecule of the Month) Making identical molecules is advantageous because then only a single set of enzymes is required for the remainder of the pathway. Additionally, phosphoglycerate is a highly familiar molecule to the cell. Most of the molecules will be fed back into the carbon fixation cycle, but some of them will also be siphoned off to produce sugars. Every bite of food you have ever taken is directly or indirectly the result of this amazing enzyme.

I said that rubisco grabs CO2 most of the time because occasionally it grabs O2 instead. Thus we have come to the paradox where O2 competes with rubiscos CO2 binding site and this has been said to initiate a wasteful photorespiratory pathway leading to the loss of fixed carbon. (Satagopan and Spreitzer 2008) Id like to throw a wild idea out there that this may be a possible regulatory feature designed to balance carbon and oxygen in the atmosphere, slowing rubisco down if oxygen is already plentiful and CO2 is scarce. (Galms et al. 2014) Others have given better technical explanations, suggesting that the binding of oxygen is likely the result of a compromise between chemical and metabolic constraints:

It is possible that the chemical constraint imposed by CO2 inertness or scarcity (especially in a low CO2 context) is such that the observed specificity represents the best compromise allowing carboxylation at a physiologically acceptable rate. In fact, a recent catalytic survey of Rubisco from diatoms, which possess carbon concentrating mechanisms, strongly suggests that when the pressure on Kc (apparent Michaelis constant for CO2) is relieved (i.e., when CO2 is not limiting), there is an alternative evolutionary path to a better specificity by suppressing oxygenase activity, without impairing carboxylase activity. Therefore, it is very likely that the oxygenase activity is the result of a trade-off: the active site structure adapts to allow maximal enolate twisting and positioning for CO2 reactivity (at the prevailing CO2 mole fraction) even though O2 can also react; alternatively, the enzyme active site can tune its structure (including Mg2+ coordination) to decrease dramatically the probability of the enolate forming a triplet and then reacting with O2, but CO2 reactivity also decreases. In kinetic terms, manipulating oxygenase activity via the geometry of the enolate affects the transition states of oxygenation and carboxylation themselves and consequently can be anticipated to change the energy barrier of CO2 and O2 addition (and thus specificity) as well as the 12C/13C isotope effect associated with CO2 addition, as observed experimentally.

Regardless, rubisco is nothing short of an incredible design, as validated by its abundance in the ecosystem, engineers inability to drastically improve it after fifty+ years of study, and its ability to pull CO2 out of the atmosphere, balancing the atmosphere. (Bathellier et al. 2018)

As Ive indicated, plants are icons of sustainability. They create critical products for other living organisms while utilizing waste products every environmental engineers dream design. Are these ecosystem-level designs mere coincidences of Darwinism? Can consideration of ecosystem constraints really occur without foresight?

These are important questions to consider. Another key question is: Is it possible that because weve been calling rubisco sluggish we have missed the wisdom of its design? Perhaps we incorrectly prioritize efficiency over sustainability. Would this have occurred if we had more respect for the intelligent design in nature for clean, green energy?

Here is the original post:

The Molecular Machine Behind Carbon Balance - Discovery Institute

I entered 2020 thinking of myself as a science writer. I ended the year less sure.

While the first sparks of the COVID-19 pandemic ignited at the end of 2019, I was traipsing through a hillside in search of radio-tagged rattlesnakes, allowing myself to get electrocuted by an electric catfish, and cradling loggerhead-turtle hatchlings in the palm of my hand. As 2020 began and the new coronavirus commenced its ruinous sweep of the world, I was marveling at migratory moths and getting punched in the pinky by a very small and yet surprisingly powerful mantis shrimp. We share a reality with these creatures, but we experience it in profoundly different ways. The rattlesnake can senseperhaps seethe body heat of its mammalian prey. The catfish can detect the electric fields that other animals involuntarily produce. The moths and the turtles can both sense the magnetic field of the planet and use it to guide their long navigations. The mantis shrimp sees forms of light that we cannot, and it processes colors in a way that no one fully understands. Each species has its own unique coterie of senses. Each is privy to its own narrow slice of the total sights, smells, sounds, and other stimuli that pervade the planet.

My plan was to write a book about those sensory experiencesa travelogue that would take people through the mind of a bat, a bird, or a spider. Such a journey, not to visit strange lands but to possess other eyes, as Marcel Proust once said, is the only true voyage.

It quickly became the only voyage I could make. As the pandemic spread, the possibility of international travel disappeared. Commuting turned from daily reality to fading memory. Restaurants, bars, and public spaces closed. Social gatherings became smaller, infrequent, and subject to barriers of cloth and distance. My world contracted to the radius of a few blocks, but the sensory worlds of other animals stayed open, magical and Narnia-like, accessible through the act of writing.

When I had to pause my book leave to report full-time on the pandemic, those worlds closed too.

In theory, 2020 should have been a banner year for science writers. A virus upended the world and gripped its attention. Arcana of epidemiology and immunologysuper-spreading, herd immunity, cytokine storms, mRNA vaccinesbecame dinner-table fodder. Public-health experts (and pseudo-experts) gained massive followings on social media. Anthony Fauci became a household name. The biggest story of the yearperhaps of the decadewas a science story, and science writers seemed ideally placed to tell it.

Read: Why the coronavirus is so confusing

When done properly, covering science trains a writer to bring clarity to complexity, to embrace nuance, to understand that everything new is built upon old foundations, and to probe the unknown while delimiting the bounds of their own ignorance. The best science writers learn that science is not a procession of facts and breakthroughs, but an erratic stumble toward gradually diminished uncertainty; that peer-reviewed publications are not gospel and even prestigious journals are polluted by nonsense; and that the scientific endeavor is plagued by all-too-human failings such as hubris. All of these qualities should have been invaluable in the midst of a global calamity, where clear explanations were needed, misinformation was rife, and answers were in high demand but short supply.

But the pandemic hasnt just been a science story. It is an omnicrisis that has warped and upended every aspect of our lives. While the virus assaulted our cells, it also besieged our societies, seeping into every crack and exploiting every weakness it could find. It found many. To understand why the United States has fared so badly against COVID-19, despite its enormous wealth and biomedical savvy, one must understand not just matters of virology but also the nations history of racism and genocide, its carceral state, its nursing homes, its historical attitudes toward medicine and health, its national idiosyncrasies, the algorithms that govern social media, and the grossly deficient character of its 45th president. I barely covered any of these issues in an 8,000-word piece I wrote for The Atlantic in 2018 about whether the United States was ready for the next pandemic. When this pandemic started, my background as a science writer, and one who had specifically reported on pandemics, was undoubtedly useful, but to a limited degreeit gave me a half-mile head start, with a full marathon left to run. Throughout the year, many of my peers caviled about journalists from other beats who wrote about the pandemic without a foundation of expertise. But does anyone truly have the expertise to cover an omnicrisis that, by extension, is also an omnistory?

Read: The next plague is coming. Is America ready?

The all-encompassing nature of epidemics was clear to the German physician Rudolf Virchow, who investigated a typhus outbreak in 1848. Virchow knew nothing about the pathogen responsible for typhus, but he correctly realized that the outbreak was possible only because of poverty, malnutrition, poor sanitation, dangerous working conditions, and inequities perpetuated by incompetent politicians and negligent aristocrats. Medicine is a social science and politics is nothing but medicine in larger scale, Virchow wrote.

This viewpoint was championed by many of his contemporaries, but it waned as germ theory waxed. In a bid to be objective and politically neutral, scientists focused their attention on pathogens that cause disease and ignored the societal factors that make disease possible. The social and biomedical sciences were cleaved apart, separated into different disciplines, departments, and scholars. Medicine and public health treated diseases as battles between individuals and germs, while sociologists and anthropologists dealt with the wider context that Virchow had identified. This rift began to narrow in the 1980s, but it still remains wide. COVID-19 landed in the middle of it. Throughout much of 2020, the United States (and the White House, specifically) looked to drugs and vaccines for salvation while furiously debating about masks and social distancing. The latter were the only measures that controlled the pandemic for much of the year; billed as non-pharmaceutical interventions, they were characterized in opposition to the more highly prized biomedical panaceas. Meanwhile, social interventions such as paid sick leave and universal health care, which could have helped essential workers protect their livelihoods without risking their health, were barely considered.

To the extent that the pandemic has been a science story, its also been a story about the limitations of what science has become. Perverse academic incentives that reward researchers primarily for publishing papers in high-impact journals have long pushed entire fields toward sloppy, irreproducible work; during the pandemic, scientists have flooded the literature with similarly half-baked and misleading research. Pundits have urged people to listen to the science, as if the science is a tome of facts and not an amorphous, dynamic entity, born from the collective minds of thousands of individual people who argue and disagree about data that can be interpreted in a range of ways. The long-standing disregard for chronic illnesses such as dysautonomia and myalgic encephalomyelitis meant that when thousands of COVID-19 long-haulers kept experiencing symptoms for months, science had almost nothing to offer them. The naive desire for science to remain above politics meant that many researchers were unprepared to cope with a global crisis that was both scientific and political to its core. Theres an ongoing conversation about whether we should do advocacy work or stick to the science, Whitney Robinson, a social epidemiologist, told me. We always talk about how these magic people will take our findings and implement them. We send those findings out, and knowledge has increased! But with COVID, thats a lie!

Virchows experiences with epidemics radicalized him, pushing the man who would become known as the father of pathology to advocate for social and political reforms. COVID-19 has done the same for many scientists. Many of the issues it brought up were miserably familiar to climate scientists, who drolly welcomed newly traumatized epidemiologists into their ranks. In the light of the pandemic, old debates about whether science (and science writing) is political now seem small and antiquated. Science is undoubtedly political, whether scientists want it to be or not, because it is an inextricably human enterprise. It belongs to society. It is interleaved with society. It is of society.

Read: How the pandemic defeated America

This is true even of areas of science that seem to be sheltered within some protected corner of intellectual space. My first book was about the microbiome, a bustling area of research that went unnoticed for centuries because it had the misfortune to arise amid the ascent of Darwinism and germ theory. With nature red in tooth and claw, and germs as the root of disease, the idea of animals benefiting from cooperative microbes was anathema. My next book will show that our understanding of animal senses has been influenced by the sociology of sciencewhether scientists believe one another, whether they successfully communicate their ideas, whether they publish in a prestigious English journal or an obscure foreign-language one. That understanding has also been repeatedly swayed by the trappings of our own senses. Science is often caricatured as a purely empirical and objective pursuit. But in reality, a scientists interpretation of the world is influenced by the data she collects, which are influenced by the experiments she designs, which are influenced by the questions she thinks to ask, which are influenced by her identity, her values, her predecessors, and her imagination.

When I began to cover COVID-19 in 2020, it became clear that the usual mode of science writing would be grossly insufficient. Much of journalism is fragmentary: Big stories are broken down into small components that can be quickly turned into content. For science writing, that means treating individual papers as a sacrosanct atomic unit and writing about them one at a time. But for an omnicrisis, this approach leads only to a messy, confusing, and ever-shifting mound of jigsaw pieces. What I tried to do instead was unite those pieces. I wrote a series of long features about big issues, attempting to synthesize vast amounts of information and give readers a steady rock upon which they could observe the torrent of information rushing past them without drowning in it. I treated the pandemic as more than a science story, interviewing sociologists, anthropologists, historians, linguists, patients, and more. And I found that the writing I gravitated toward did the same. The pandemic clarified that science is inseparable from the rest of society, and that connection works both ways. Science touches on everything; everything touches on science. The walls between beats seemed to crumble. What, I found myself asking, even counts as science writing?

Read: How the pandemic now ends

There has long been a view of science writing that imagines its about opening up the ivory tower and making its obscure contents accessible to the masses. But this is a strange model, laden with troubling corollaries. It implicitly assumes that science is beleaguered and unappreciated, and that unwilling audiences must be convinced of its importance and value. It equates science with journals, universities, and other grand institutions that are indeed opaque and cloistered. And treating science as a special entity that normies are finally being invited to take part in is also somewhat patronizing.

Such invitations are not anyones to extend. Science is so much more than a library of publications, or the opinions of doctorate holders and professors. Science writing should be equally expansive. Ultimately, What even counts as science writing? is a question we shouldnt be able to answer. A womans account of her own illness. A cultural history of a color. An investigation into sunken toxic barrels. A portrait of a town with a rocket company for a neighbor. To me, these pieces and others that I selected for the 2021 edition of the Best American Science and Nature Writing anthology show that science is intricately woven into the fabric of our livesso intricately that science writing should be difficult to categorize.

There is an obvious risk here. Of the typical journalistic beats, science is perhaps the only one that draws us out of our human trappings. Culture, politics, business, sport, food: These are all about one species. Science covers the other billions, and the entirety of the universe besides. I feel its expansive nature keenly. I have devoted most of my career to writing about microbes and lichens, hagfish and giraffes, duck penises and hippo poop. But I do so now with a renewed understanding that even as we step away from ourselves, we cannot fully escape. Our understanding of nature has been profoundly shaped by our culture, our social norms, and our collective decisions about who gets to be a scientist at all. And our relationship with naturewhether we succumb to it, whether we learn from it, whether we can save itdepends on our collective decisions too.

This article was excerpted from Ed Yongs introduction in The Best American Science and Nature Writing 2021.

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Ed Yong: The Pandemic Changed How I Think About Science Writing - The Atlantic