A new electrically conductive “eSoil” could make hydroponic farming even more productive — and help ensure a sustainable new source for the human food supply.

“[W]e can get seedlings to grow faster with less resources,” said Eleni Stavrinidou, leader of the Linköping University team that developed the new substrate.

The challenge: Much of the world is perpetually in a food crisis. An estimated 735 million people experienced chronic undernourishment in 2022, a number that has increased by 122 million since 2019, a major setback after decades of progress. The struggle to expand food supply is likely to face new stresses in the future. 

“The world population is increasing, and we also have climate change,” said Stavrinidou. “So it’s clear that we won’t be able to cover the food demands of the planet with only the already existing agricultural methods.”

The idea: Hydroponic farming — a technique where plants are grown in water rather than soil — could help the world meet some of its future food needs. 

Not only does it enable farming in places that lack arable land, hydroponic systems can also be paired with lights to grow plants indoors. Trays of crops can then be layered vertically, allowing more food to be grown in an area than would be possible with traditional farming.

​​“We can’t say that hydroponics will solve the problem of food security, but it can definitely help, particularly in areas with little arable land and with harsh environmental conditions,” said Stavrinidou.

The biggest challenge with indoor hydroponic farming is the cost — it’s far cheaper to let the sun provide light than it is to power LEDs — so finding ways to make the process more efficient is key to helping it meet its potential.

What’s new? Stavrinidou’s team has now developed a new substrate for hydroponic farming. This is the material the plants’ roots attach to in a hydroponic system, instead of soil, and the standard option is mineral wool, which is made through an energy-intensive process.

The new substrate, called “eSoil,” is made out of cellulose, a material found in plant walls, and PEDOT, an electrically conductive polymer.

This conductivity made it possible to apply a small voltage to the roots of barley plants growing in the substrate. That electrical stimulation made the plants grow 50% larger (by dry weight) than control seedlings grown in eSoil with no stimulation during a 15-day study.

The cold water: This isn’t the first study to show that electrical stimulation can help plants grow. However, the Linköping team says previous studies have used higher voltages, while their eSoil requires a low voltage and has a very low energy consumption, which could make it more practical.

Because the controls were also grown in eSoil without electrical stimulation, though, it’s not clear how this approach compares to barley grown in a traditional substrate. The study also ended while the plants were still seedlings, so more research is needed to test the longer term impact of the eSoil and stimulation.

Looking ahead: The next step for the Swedish scientists will be figuring out how their approach works so that they can further optimize it for use during hydroponic farming.

“We don’t yet know how it actually works [or] which biological mechanisms that are involved,” said Starvrinidou. “What we have found is that seedlings process nitrogen more effectively, but it’s not clear yet how the electrical stimulation impacts this process.”

This article Zapping plants in “eSoil” makes them grow 50% larger is featured on Big Think.

For the first time, scientists have mapped the process of limb development in human embryos down to the individual cell — and the stunning result could help prevent a common type of birth defect in the future.

The challenge: At four weeks old, the parts of a human embryo that will eventually be arms and legs are essentially buds of undifferentiated cells. By week 8, though, the limbs are well-defined, with visible fingers and toes, and we’ve never really understood how we get from point A to B. 

In part, that’s because researchers have traditionally only been allowed to grow human embryos in the lab until about day 14. While that restriction is loosening, we don’t know if it’s even possible to get an embryo to develop to week 4, let alone week 8, outside a womb.

Studying young embryos inside a womb, meanwhile, is logistically tricky — at 8 weeks, an embryo is only about an inch long. Studies of animal limb development, meanwhile, might be telling us what’s going on, but we don’t know for sure since we can’t validate them.

Because we don’t fully understand the limb development process, we also don’t understand much about why it goes wrong so frequently — 1 in 500 babies is born with some significant limb abnormality, such as shortened fingers or extra toes — or how to prevent it.

What’s new? An international team of researchers, led by scientists at the Human Cell Atlas initiative, has now traced the expression of genes and differentiation of individual cells in donated fetal tissue to create the first map of human limb development.

“For the first time, we have been able to capture the remarkable process of limb development down to single cell resolution in space and time,” said senior author Sarah Teichmann.

This work led to the discovery that our fingers and toes actually don’t grow out from the clumps of limb cells we have at week 4. Instead, they form inside the buds — extra cells around them then die off to reveal the digits.

“What we reveal is a highly complex and precisely regulated process,” said senior author Hongbo Zhang. “It is like watching a sculptor at work, chiseling away at a block of marble to reveal a masterpiece. In this case, nature is the sculptor, and the result is the incredible complexity of our fingers and toes.”

Aside from exposing this remarkable process for the first time, the researchers also identified connections between common limb abnormalities and disturbances in specific genes through their study, which could be the key to preventing those abnormalities in the future.

“Our work in the Human Cell Atlas is deepening our understanding of how anatomically complex structures form, helping us uncover the genetic and cellular processes behind healthy human development, with many implications for research and healthcare,” said Teichmann.

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Thirty-five years ago, the waters of Lake Colden in New York’s Adirondack Mountains were found to be too acidic to support fish, making the picturesque, high-altitude body of water one of the signature casualties of acid rain. Red spruce trees in New England were also showing signs of strain as the rain leached vital calcium from the soil, severely stunting the trees’ growth. Today, Lake Colden’s trout have returned and the spruce trees are flourishing, tangible signs that the decades-long effort to mitigate acid rain has worked.

Now that sulfur dioxide and nitrogen oxide emissions — the causes of acid rain — are greatly reduced in Europe and North America, a success based on capstone environmental legislation, it’s easy to look back on the panicked news stories from the 1980s and 1990s and wonder if acid rain was really more of a “nuisance, not a catastrophe,” as William Reville, an emeritus professor of Biochemistry, wrote for the Irish Times. Seeing as how we dealt with the problem, we may never conclusively know the answer.

What we do know is that scientists in the U.S. and Scandinavia originally discovered acid rain in the 1960s and chose to gather evidence for years — more than a decade in some cases — before sounding the alarm in the 1970s and 1980s. American ecologist Gene Likens and his colleagues found that while rainwater was often slightly acidic, with a pH of 5.6, by 1980 the average rainfall in the U.S. was at a pH level of 4.6, about ten times more acidic! And it was getting worse.

In areas downwind of coal power plants — the primary sources of sulfur dioxide emissions — the problem was even more acute. The pH of individual rainstorms sometimes dropped to 3 or below, similar to that of grapefruit juice or soda. These sorts of downpours weathered buildings, dissolved nutrients in the ground that trees need to survive, and caused aluminum to be released in the soil.

Across the Atlantic Ocean in Sweden, scientists warned that half of the country’s lakes and rivers would reach a critical pH level by the early-mid 21st century and cause mass fish die-offs if actions weren’t taken to stop acid rain.

Whether these scenarios constitute “hype,” a “nuisance,” or a “catastrophe” might depend on one’s feelings towards scientific predictions, the environment, and wildlife, but there was no question that acid rain was a growing problem, and one that humans were responsible for.

That’s why, after years of public debate and amendments to the Clean Air Act in 1990, legislators in the U.S. instituted a bipartisan cap and trade program that capped sulfur dioxide emissions in the power industry at a drastically lower level compared to 1980 and allowed companies to either lower their emissions or buy and trade credits from companies that did. Limits were also placed on nitrogen oxide emissions.

The free-market program was a resounding success. The national average of sulfur dioxide annual ambient concentrations in the U.S. decreased a whopping 93% between 1980 and 2018.

But while the cloud of acid rain has all but vanished from much of Europe, North America, Australia, and Japan, it is a surging problem in places like India and China, where coal power is still widely used. Urbanizing areas of Latin America and Africa are also seeing precipitation grow increasingly acidified.

For these places, reducing noxious emissions that fuel acid rain is a tandem goal with lowering air pollution as a whole. Four million people die prematurely due to outdoor air pollution globally. Making air more breathable and rain less acidic benefits everyone, regardless of whether or not acid rain is a hyped problem or a genuine one.

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“Anthropogenic” is a key word of our time. It means caused by, and/or originating with, humans. It’s generally used to refer to climate change. But anthropogenic warming isn’t the only thing we’re collectively causing here on earth. Humans have become a major evolutionary force. In fact, we may be the most powerful evolutionary force going. We are driving rapid evolution—contemporary evolutionary change—in other species at rates that seem to be faster than anything else in history, barring the five great mass extinctions of earth history.

In their introduction to a special issue of Philosophical Transactions: Biological Sciences on human influences on evolution and the ecological and societal consequences thereof, Andrew P. Hendry, Kiyoko M. Gotanda, and Erik I. Svensson list some of the anthropogenic factors influencing evolution today, which include

[p]ollution, eutrophication, urbanization, habitat fragmentation, climate change, domestication/agriculture, hunting/harvesting (including fishing), invasion/extinction, medicine and emerging/disappearing diseases.

It’s a lot. And, of course, these factors aren’t necessarily separate and distinct. Consider fish, for instance, beset by hotter, more acid waters; many different kinds of pollution; and eutrophication, among other things.

Antibiotic resistance is the best known of our evolutionary forcings. With too-liberal use of antibiotics in both human and domestic animal populations, we’ve channeled pathogens into evolving super-resistance against antibiotics.

There any many other examples. The peppered moth is a now classic one, but it’s only the most famous of more than 100 other species of moth affected by industrial melanism. Formerly rare dark (melanic) versions of peppered moths began to predominate as the Industrial Revolution coated England’s Midlands with dark industrial filth. The dark ones blended in, so they were less likely to be picked off by predators and more likely to pass on their genes. Once the air got cleaner, the lighter ones returned to their former prominence.

Killifish are another example. These small fish are now able to survive in polluted environments that would normally kill most species. Populations in places like Newark Bay have evolved enormous resistant to industrial pollutants.

Rapid evolution has also been seen and studied in such animals as wolves (Chernobyl Exclusion Zone), Crested Anoles (Puerto Rico), Fairy-wrens (Australia), Spotted Hyenas (Tanzania), Red Deer (Scotland), and Red Squirrels (Canada). Fish have gotten smaller because we’ve removed the large ones out of the gene pool and smaller ones get through nets easier. Female elephants are losing their tusks in response to slaughter by ivory poachers.

Hendry et al. draw distinctions between “how humans interact with their ‘enemies’ (or ‘adversaries’) versus their ‘friends.’” Enemies are things like “weeds, pests, and pathogens” which we want to decrease. Efforts to do so can favor resistance/tolerance to our control efforts. Friends are things like crops, natural resources, and biodiversity, which we strive to increase. Here we can facilitate adaptive evolution that benefits the target species. In the case of both enemies and friends, there can be “spillover to influence non-target species.”

The authors also write that some species may be “frenemies,” that is, good or bad at different times and places. Meanwhile, many species (“neighbors”) are just there, living besides us, neither “good” nor “bad” for us, but just just as likely to be driven to evolve because of the multi-pronged pressures we put on them, often quite unintentionally.

Without even realizing it, we’ve actually become pretty god-like in our powers. We’re controlling what lives and dies; what evolves and what becomes extinct. Our domesticated species dominate the biosphere: 34.4 billion chickens, 1 billion cattle, 784 million pigs. Our stuff—roads, buildings, phones, daily coffee cups—may now outweigh all the life on earth.

Welcome to Anthropogenic Earth.

“From our increasing knowledge of how humans influence evolution comes the opportunity, perhaps even the responsibility, for humans to do something about it,” conclude Hendry, Gotanda, and Svensson, noting numerous ways we already do so. “The future affords even greater opportunities to influence evolution in informed, effective, restrained and safe directions.”

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Could a jellyfish tell you why the ocean is near the shore, or think of things never thunk before — if it only had a brain? Maybe, but jellyfish don’t have brains. They instead have simple nervous systems dispersed throughout their transparent bodies. For this reason, it has been long thought that they are incapable of learning beyond a basic level, and research seems to back up this notion.

In 2021, biologist Ken Cheng wrote a systematic review of learning in cnidarians — the phylum that consists of jellyfish, hydras, and sea anemones. He found substantial evidence of habituation among these animals, meaning they can grow accustomed to a stimulus. In other words, super basic learning.

Only a few studies showed the potential for associative learning in sea anemones. In these, the anemones were shocked while also being shown a light. In time, the animals would retract their bodies when the light was shown, even without a concurrent shock. It’s classic conditioning and does suggest that the anemones formed a memory and adapted their behavior accordingly.

But there’s a concern. Because anemones rarely encounter shock-happy scientists in the wild, it’s not entirely clear whether these studies demonstrated learning that aids survival or simply induced an unnatural behavior in the creatures.

To see if and how cnidarians learn, researchers at the University of Kiel and the University of Copenhagen created a more natural school for Caribbean box jellyfish. Their results challenge the belief that advanced learning requires a brain.

A school for jellyfish

For brainless, spineless, blueberry-sized predators, Caribbean box jellyfish have it pretty good. They spend their days swimming in sunlit tropical waters among the prop roots of mangrove trees. These roots provide protection as the jellies hunt their prey of choice, tiny crustaceans called copepods.

It all sounds idyllic, but as always in nature, dangers abound. One such danger is the roots themselves. Should a box jellyfish’s fraile body collide with a root, it could injure the creature. The weather also poses risks. It can churn up silt and other particles to make the water murky, inhibiting a box jelly’s ability to see the prop roots and navigate them safely. (Caribbean box jellyfish are unique among jellies for having eyes on their bells. Most other jellyfish can only sense light and dark.)

The researchers wanted to determine if box jellyfish learn to avoid the prop roots or have to mindlessly take their licks. To test this, they brought the jellies into the lab and created three experimental conditions using round tanks.

The first tank sported high-contrasting black-and-white stripes. This condition was meant to simulate clear-water days where the prop roots are easily visible. The second tank also contained stripes but with low-contrast colors to simulate murky days. The final tank had uniformly gray walls.

The researcher’s aim was to create conditions analogous to those the box jellyfish actually encounter in the wild — and not the cnidarian equivalent of a close encounter with the third kind.

“Learning is the pinnacle of performance for nervous systems,” Jan Bielecki, the study’s first author and a postdoctoral researcher at Kiel University, said. “It’s best to leverage its natural behaviors, something that makes sense to the animal, so it reaches its full potential.”

Learning is a no-brainer

Turns out, these “brainless” creatures are quick studies. In the low-contrast bucket, the jellies initially collided with the wall, but in less than 8 minutes, they began swimming an average of 50% farther away. They also quadrupled their number of quick turn maneuvers to avoid collisions.

In the high-contrast bucket, the jellyfish managed to avoid the walls altogether by sticking to the center. Conversely, in the gray bucket, they continuously bonked their bells. Taken together, these results suggest that the box jellyfish began associating the murky stripes with collisions and adjusted their behavior accordingly.

In short, they learned.

“We can see that as each new day of hunting begins, box jellyfish learn from the current contrasts by combining visual impressions and sensations during evasive maneuvers that fail,” Anders Garam, one of the study’s lead authors and an associate professor of marine biology at the University of Copenhagen, told Genetic Engineering & Biotechnology News.

He added: “So, despite having a mere one thousand nerve cells [per eye-bearing structure] — our brains have roughly 100 billion — they can connect temporal convergences of various impressions and learn a connection — or what we call associative learning.”

Specifically, this is a type of associative learning known as operant conditioning. This advanced learning occurs when an organism learns to associate a voluntary behavior with a stimulus or result. The classic example is the lab mouse taught to push a blue button for a treat and avoid the red button that gives it a zap.

As the researchers note in their study: “[This] suggests the intriguing possibility that advanced neuronal processes, like operant conditioning, are a fundamental property of all nervous systems.” And not just those based on a centralized brain.

In the 24 eyes of the beholder

To tease out how the box jellyfish learn without a brain, the researchers tested the creature’s rhopalia — sensory structures located on a box jellyfish’s bell. An adult box jelly will have four such structures, each one housing six eyes. These structures also generate “pacemaker signals” that control the jelly’s pulsing movement and spike in frequency when avoiding obstacles.

The researchers positioned isolated rhopalium in a Petri dish to face a screen. The screen projected images showing moving bars of different contrasts — similar to the tank experiment. During the pre-trial runs, the rhopalium did not respond to the gray or light gray bars, seemingly because it interpreted them as distant. It did, however, generate pacemaker signals for the dark gray bars.

During the trials, the researchers trained the rhopalium by giving it a small electric shock when any colored bar appeared on the screen. Within five minutes of testing, the rhopalium began generating pacemaker signals in response to the gray bars and even the light gray ones. These results suggest that the rhopalial nervous system is the learning center of the Caribbean box jellyfish and that the species combines visual and mechanical stimuli to learn.

“Our behavioral experiments demonstrate that three to five failed evasive maneuvers are enough to change the jellyfish’s behavior so that they no longer hit the roots. It is interesting that this is roughly the same repetition rate that a fruit fly or mouse needs to learn,” Garm said. 

The researchers published their results in the peer-reviewed journal Current Biology.

Relearning our understanding of learning

In future research, the team hopes to identify which cells precisely control the box jellyfish’s ability to learn, and how those cells translate that information into behavior. There is also the question of how the jellyfish form memories and how long they retain them. 

The research also opens the question of whether more natural studies will demonstrate similar results among other cnidarians.

“This is only the third time that associative learning has been convincingly demonstrated in cnidarians,” Cheng, who was not involved with the study, told The New York Times. “And this is the coolest demonstration, replete with physiological data.”

The findings have implications for our understanding of the evolution of learning, too. They suggest that associative learning may be a property of all nervous systems, not just those centralized around a brain. That has the potential to shake up how much and how far back learning may have shaped our shared evolutionary history.

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A herd of wooly mammoths march across the snowy tundra steppe. Close by, human hunters scavenge meat from a dead elk with stone-flint tools while their compatriots scanned the horizon, wary that their kill might attract neighboring steppe lions. Against this ancient backdrop, something historic happened: A group of nematodes (also known as roundworms) became trapped and frozen in an arctic gopher burrow.

Granted, it didn’t seem all that historic at the moment. The nematodes are only about one millimeter long, so it’s unlikely even the gophers took notice. But one Ice Age later, Anastasia Shatilovich, a scientist working at the the Institute of Physicochemical and Biological Problems in Soil Science RAS, would unearth the burrow in the Siberian permafrost near the Kolyma River and discover something quite amazing. The nematodes were still alive.

Just add water for life

Radiocarbon dating of plant material found alongside the nematodes showed the specimens were frozen around the end of the Pleistocene epoch — sometime between 45,839 and 47,769 years ago. They managed to survive the intervening millennia thanks to a survival strategy known as cryptobiosis.

Cryptobiosis is a state some plant and animal species can undergo in response to overly harsh environmental conditions, such as freezing or extreme dryness. Essentially, the organism slows down biological functions to nearly undetectable levels to preserve itself. When environmental conditions return to livable, the organism revs up its metabolism and starts “living” again.

Perhaps the best-known cryptobiotic species is the tardigrade (also known as the water bear). This most extreme of extremo-tolerant animals can use cryptobiosis to survive freezing, high temperatures, and even exposure to outer space. For a more everyday example, you need only look to your cupboard. The fungal cells in active dry yeast have been desiccated to the point of entering cryptobiosis. When yeast and water combine as part of a recipe, the yeast returns to life (albeit shortly before being baked).

Even for cryptobiosis, the nematodes’ 46,000-year stint on ice is impressive. They handily beat the previous nematode record of 39 years and even the rotifer record of 24,000 years. It may ultimately prove to be the longest cryptobiotic hibernation — for an animal, that is. But it’s nowhere near the longest. Scientists were able to revive a bacterial spore from an extinct bee’s abdomen. The bee had been preserved in amber for 25 to 40 million years.

So, how did Shatilovich revive a pair of the prehistoric nematodes? Like all good bakers, she just added water and waited for life to rise.

Ancestor or contemporary?

The ancient nematodes would die several days later, as part of their natural life cycle, but not before spawning more than 100 generations of descendants. Shatilovich then took her discovery to researchers in Dresden and Cologne to have its DNA sequenced and morphology analyzed.

The researchers discovered that the nematodes belonged to the genus Panagrolaimus, a genus of nematodes that survives to this day. In fact, the Antarctic nematode Panagrolaimus davidi is known for its ability to survive in sub-zero temperatures. However, genome analysis showed that these nematodes belonged to a previously unknown species. The researchers named them Panagrolaimus kolymaensis, after the Kolyma River where they were discovered.

They also compared the genome to another contemporary species of nematode, Caenorhabditis elegans. Their analysis shows that both species prepare their bodies for cryptobiosis by upregulating a sugar, trehalose, which makes them more tolerant by protecting cellular membranes. They also discovered similar genes present in each species’ genomes.

However, they could not determine if those similar genes functioned the same way in both species or if P. kolymaensis had other biochemical pathways that helped it survive. In future studies, they hope to use RNA experiments to determine the species’ cryptobiosis mechanisms and determine if they are the result of convergence (the independent evolution of a similar trait in two unrelated organisms) or parallelism (the evolution of such a trait in a common ancestor).

“Our experimental findings also show that Caenorhabditis elegans can remain viable for longer periods in a suspended state than previously documented. Overall, our research demonstrates that nematodes have developed mechanisms that allow them to preserve life for geological time periods,” Temo Kurzhchalia, professor emeritus at the Max Planck Institute of Molecular Cell Biology and Genetics and one of the study’s authors, and Vamshidhar Gade, another study author, said in a news release.

The researchers published their findings in a study in the peer-reviewed journal PLOS Genetics.

Reconsidering the road of evolution

That life can be preserved across such periods of time further challenges a simplistic conception of evolution as a successive series of species, one progressing into the next. Consider, for example, the famous Road to Homo Sapians illustration: A chimp progresses into a bipedal primate into an upright primate into a tool-wielding primate into a modern human.

Cryptobiosis on a geologic scale complicates this simple idea of evolutionary processes. Prehistoric species — particularly microscopic ones like nematodes, bacteria, and viruses — may be out there alive and, well, not well but ready to reemerge. Ancestors might one day become contemporaries with their progeny, and as environments alter from climate change, previously unknown species may reappear. This makes the road to nematodes — and potentially other species — less a straight path and more an evolutionary highway system.

“Our findings are essential for understanding evolutionary processes because generation times can range from days to millennia and because the long-term survival of a species’ individuals can result in the re-emergence of lineages that would otherwise have gone extinct,” Philipp Schiffer, another study author and the co-lead of the Biodiversity Genomics Center at the University of Cologne, said in the same release.

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The scale of humanity’s meat consumption is enormous. 360 million tonnes of meat every year.

This number is so large that I find it impossible to comprehend. What helps me to make these numbers more relatable is to turn them from the weight of meat to the number of animals and from the yearly total to the daily number. This is what I have done in the graphic below. It shows how many animals are slaughtered on any average day.

About 900,000 cows are slaughtered every day. If every cow was 2 meters long, and they all walked right behind each other, this line of cows would stretch for 1800 kilometers.¹ This represents the number of cows slaughtered every day.

For chickens, the daily count is extremely large – 202 million chickens every day. To comprehend the scale, it is better to bring it down to the average minute: 140,000 chickens are slaughtered every minute.

The number of fish killed every day is very uncertain. I discuss this in some detail at the end of this article. But while the uncertainties are large, it is clear that the number of fish killed is large: certainly, hundreds of millions of fish are killed every day.

If you believe that the slaughter of animals causes them to suffer and attribute even a small measure of ethical significance to their suffering, then the moral scale of this reality is immense.

From the perspective of animal suffering, it is the absolute numbers of animals that matter, but if you want to explore this data in per capita terms, you can do so in our Animal Welfare Explorer.

It’s not just about how many farm animals are killed but also the suffering they endured while they were raised. The majority of the world’s farm animals are raised in dismal conditions. Pigs are held in cramped, stressful conditions, living a life in chronic discomfort and distress. Cows get their calves taken away to produce milk for human consumption, a practice under which both the mother and the calf suffer. Many animals are castrated without anesthetic. Chickens are often debeaked to stop them from fighting with other chickens out of discomfort and pain; many cannot turn around their entire lives.

What would be the benefits of reducing our meat consumption?

Meat production has a number of large negative impacts on the environment, wildlife, and our health.

Viewed from the other side, this means that the benefits of reducing meat consumption are large. What would some of these benefits be?

Less land use for agriculture and more biodiversity: The use of land for agriculture is the main driver of biodiversity loss.³ Today, almost half of the world’s ice- and desert-free land is used for agriculture, and most of this land is used by livestock. The total global land use for meat and dairy production sums up to 37 million square kilometers, an area as large as the entirety of the Americas — from Alaska in the North to Cape Horn in the South.For the data, see our page on land use.

As my colleague Hannah Ritchie showed, if we didn’t eat meat, it would be possible to reduce agricultural land from 4 to 1 billion hectares. Changes towards less meat consumption would have large benefits for animals around the world as wilderness could regrow to provide habitats for wildlife.⁴

Benefits for the world’s climate: Reducing global meat consumption would also help to address climate change: it would reduce direct emissions from burping cows and nitrous oxide from manure, but also reduce emissions from deforestation and land use change.

Less antibiotic resistance: Reducing the world’s meat consumption would decrease the use of antibiotics in livestock farming, a practice that contributesto the rise of antibiotic-resistant bacteria. This reduction could preserve the efficacy of existing antibiotics and the health of people around the world.

Lower risk of pandemics: Many infectious diseases originate in other animals. The high-density conditions in many meat production facilities create ideal environments for the mutation and spread of pathogens. Reducing global meat consumption would reduce the risk of zoonotic diseases and the risks of suffering another pandemic.

Less animal suffering: Coming back to the starting point of this short text, less meat consumption would mean less suffering for animals.

I think this future is possible. I can imagine a future in which our grandchildren look back at our time and find it hard to believe that we today are living in a world in which we kill hundreds of millions of fish, 900,000 cows, 1.4 million goats, 1.7 million sheep, 3.8 million pigs, 11.8 million ducks, and more than 200 million chicken every day.

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So what’s their cutest feature? Is it their squashy little faces? Their grunting pants? Their double-curled tails?

That coiled tail is possibly less endearing when you know it’s a purpose-bred genetic defect, which in its most serious forms leads to paralysis. And their squished noses? That’s been selectively bred to become ever shorter and smaller, making it difficult for the dogs to breathe and eat, causing trickle down effects like cardiovascular stress, eye prolapses, overheating (dogs don’t sweat, so they need to pant to expel heat through evaporation), weight gain because of that sedentary overheated lifestyle, dental crowding, soft palate collapse, and skinfold dermatitis. More of an “anatomical disaster” than the patron saint of cuteness.

Despite performing corrective surgeries and designing pain treatment plans for these dogs, veterinarians don’t often speak up about the unethical nature of buying and creating demand for genetically impaired dogs for one simple reason: It’s bad for business. “If I stood up and told the truth about these breeds,” says an anonymous vet to The Guardian, “I would immediately alienate [their owners] and they would up sticks and move to the neighboring practice where the vet was not as outspoken. Vets in general practice simply cannot afford to be honest and to speak out.”

Perturbed by pugs

The British Veterinary Association (BVA), which represents vets across the UK, is in a better position to do so. It has made several statements this year on the breeding and buying practices of brachycephalic dogs, expressing the trend as a concern in dog health and welfare. “The surge in popularity of these dogs has increased animal suffering and resulted in unwell pets for owners, so we strongly encourage people to think about choosing a healthier breed or crossbreed instead,” Sean Wensley, president of the BVA, says to The Guardian.

Mixed breed dogs are said to be much healthier than pure bred dogs, a claim that is contested by dog breeders, but a study from 2013 inserts some much-needed data into an argument that is skewed by passion and profit. Using medical records from more than 27,000 dogs and comparing the incidence of 24 genetic disorders in mixed versus pure bred dogs, the researchers found that 10 of those genetic disorders had a significantly higher incidence among pure bred dogs, and just one was greater among mixed breeds. For the remaining disorders, the incidence was fairly even in both groups.

Funny looks, serious problems

Why has this peculiar set of physical traits become so popular in dogs — and for that matter, in cats? While dogs are America’s #1 pet, cats are arguably more famous in the digital world. Two of the most viral cat celebrities with millions of fans were Lil Bub (who died at age 8) and Grumpy Cat (who died at age 7).

Why were they so cute and famous? Because they had health problems. Lil Bub was the runt of her litter and had a tongue that always hung out of her mouth because of her abnormally short lower jaw and toothlessness. She also had serious osteoporosis and was medicated for it. Lil Bub eventually died from a bone infection. Grumpy Cat had feline dwarfism and an underbite, which caused her famous frown. She succumbed to complications of a urinary tract infection.

If you look at Bored Panda’s list of the most famous internet cats, many of them have disabilities or genetic mutations such as vision impairment (Honey Bee), a missing nasal bridge (Monty the Cat), and a cleft palate (Lazarus the Vampire Cat). There is a big ethical difference, however, in loving an animal with a debilitating genetic mutation and intentionally breeding animals to have more of them.

Among domesticated pets, there is an increasing fetishization of the weird. Ugly is cute, and deformed is unique. This is the new Victorian freak show — and we love them so.

This article Top vets urge dog lovers to stop buying pugs and bulldogs is featured on Big Think.

One of humans’ key characteristics, and a major reason we’ve been so successful, is that we can adapt to a huge range of environments and lifestyles. For instance, while modern changes in our diet may have caused an increase in certain inflammatory bowel conditions, we can now consume a wide range of calorie-dense, complex foods previously unimaginable to our hunter-gatherer forebears.

Humans have not evolved alone. In our settled agricultural wake, we brought along a whole host of animals. We domesticated the wild. We tamed the beast. One of the first examples of this is the dog. While it might be hard to imagine in some cases, modern dogs do share a common ancestry with the wild gray wolf.

This has been a pretty good deal for the dogs, on the whole, but even pampered dogs are known to suffer from gastrointestinal conditions that their wolf cousins generally do not. One plausible reason is that we give them our processed foods, but they lack an accompanying effective and adaptive gut microbiome to help them deal with them.

Knowing this, a recent study from a team of researchers at Oregon State University-Cascades explored an interesting way to improve dogs’ gut health.

Trouble in the dog bowl

A gray wolf eats predominantly raw meat, hunted or scavenged. So, a wolf’s gut will contain certain microbiota that are specifically designed to aid in digesting carcass meat. The Paenibacillus species of bacteria is the main ally here. This stomach bacteria will produce certain advantageous antimicrobials, antibacterials, and antifungals that improve the overall health of the wolf. For instance, Paenibacillus reduces E. coli in the lower intestine and strengthens the immune system more broadly. In short, Paenibacillus is a good thing for a wolf.

The problem is that when you stop eating only raw meat, your gut biome will adapt. Modern dogs eat a different and more varied diet than gray wolves or their ancestors ever had. Most importantly, domesticated dogs have been eating more food high in carbohydrates made up of cereal grains — in the past, scraps and food waste from humans, and more recently, commercial dog foods.

So, over time, dogs have developed GI tracts suitable for this polysaccharide metabolism. In some ways, our pet companions are better for this diversification of diet because they are exposed to more nutrients, vitamins, and calorific foods. Diets only made up of meat can place strain on the kidneys and cause renal failure.

In one very important way, however, the move from a meat diet to a carbohydrate one exaggerates and multiplies the incidence of inflammatory bowel conditions in modern dogs, by changing their microbiome.

A difficult resolution

If the inflammatory bowel conditions are caused by a deficit in Paenibacillus, and if that in turn caused by eating less meat and more other foods, surely giving your dog more meat would resolve the issue? Sometimes, yes. But as McCabe et al reveal, “even when switched to a raw meat diet, a dog’s fecal microbiota only partially resembles that of a wolf.” You cannot change millennia of canine stomach adaptation with a bit more offal.

You generally cannot currently cure IBCs. Diet changes can and do help, but most cases in dogs are treated with antibiotics or anti-inflammatory medications from the vet. These can be expensive and might have other knock-on effects on a dog’s gut microbiome and general health.

Now, we have a different solution. What the team from Oregan State University-Cascades has discovered is a strain of Paenibacillus that could be turned into an effective prebiotic or probiotic. Up until now, it’s been hard to isolate and locate a suitable microbe to make such a formula, and this novel strain, which the team calls ClWae2A, makes for an optimistic change in fortune. This strain, collected from a freshly killed wolf hit by a car, is able to “encode enzymes that would be of value in digesting carbohydrates and could contribute to energy metabolism for a monogastric animal.”

If you don’t have a dog or you take only passing interest in canine intestinal microbiota, this all might seem a touch irrelevant to you. It’s the parochial esoterica of dog-lovers and biologists. But Americans spend $36 billion on veterinary care, and it can cost around $850 a year to treat IBCs. The pet food industry is estimated to be worth $170 billion by the end of the decade. That’s a lot of money, and it’s just possible that this new discovery, and ones like it, could one day help pet owners treat or prevent this condition. That will make for a lot of happy dogs and happy owners, too.

This article Do wolves harbor the secret to curing dogs’ bowel problems? is featured on Big Think.

After investigating the origin of the species, Charles Darwin lunged into an exploration of something that seemed, by comparison, terribly minute: orchids. By 1862, he’d traveled the world wide and far, encountering incredible organisms like giant tortoises, seafaring iguanas, and fossils of giant ground sloths. But he couldn’t stop thinking about a delicate, white star-shaped flower he’d been sent as a gift by his acquaintance James Bateman, an English horticulturalist with a penchant for rare flora from Madagascar. The flower’s odd shape—with an extremely long nectar pouch hanging under its crown—stirred in him a deep, almost inexplicable fascination.

“Orchids have interested me as much as almost anything in my life,” Darwin wrote. In their forms, he saw a vast landscape of the forces of selective evolution, a dance they played with their environment and their pollinators. “My little darlings,” as he sometimes referred to orchids, became his model for further exploring the forces he so broadly described in The Origin of Species. Just three years after the publication of that shattering work, he had produced his tome puzzling over the multitudinous, striking habits of orchids: On the Various Contrivances by Which British and Foreign Orchids Are Fertilised by Insects, and On the Good Effects of Intercrossing.

How a single family of flowers could vary so widely—from small and frilly, almost invisible to see, to large, gaudy and with a front pouch—left Darwin baffled. He called this, and flower diversity as a whole, an “abominable mystery.” Indeed, there are upward of 28,000 species of orchids worldwide and new ones cropping up every so often—sometimes even right under our noses. They have made their homes on all contemporary continents save for Antarctica—from the Arctic north, across the equator, and reaching south through all but the tip of South America.

“I think the reason people become obsessed with them is because of that mystery: Why are there so many?” says Jamie Thompson, a life sciences researcher at the University of Bath, in the United Kingdom. Yet the scientific jury is still out—and fervently debating—how many species there are exactly, what secret makes them so brilliant at diversifying, and when and where orchids evolved in the first place. Getting to the bottom of these mysteries could help us better understand the evolutionary dynamism of this massive group of alluring plants, and how we might help them fend off upcoming decimation.

Phallaenopsis orchid in bloom. (John Wiesenfeld / Unsplash)

To search for answers, researchers have spent decades digging into the orchid’s past. For plants, fossil records are often hard to come by because soft organic matter is less likely to be preserved than, say, bones. To track when a plant first appeared on this planet, experts now tend to rely on phylogenetic profiling: They use DNA from different species to plot them onto a tree of life, and then use a statistical model to pull them back into the past and recreate their history. 

When, in 2015, researchers used this technique to sequence 39 species from all major orchid groups, as well as data from some fossils, their findings suggested that orchids originated between 102 and 120 million years ago, most likely in Australia.¹ Ancient orchids then spread to the tropics by making their way through Antarctica—which was then connected and flourishing with vegetation. And since then, Southeast Asia is where most of their speciation has taken place.

Darwin couldn’t stop thinking about a delicate, white star-shaped flower.

Or at least, this is currently the leading theory about orchid origins. It may soon be upended, though, according to new preliminary findings.² An international team of researchers has drafted a study using DNA from more than 1,900 species of orchids and pinpointed their origin north, in Laurasia, modern-day Europe, Asia, and North America. The majority of diversification happened just over the past 5 million years, their work suggests, and southern Mesoamerica, such as the lush Costa Rica and Panama, actually hosts the fastest speciation of orchids.

This paper, posted to a preprint site in September, hasn’t yet been peer-reviewed, and some outside experts don’t think this new hypothesis is any good. But Oscar Pérez-Escobar, the lead author of the study and a researcher at the Royal Botanic Gardens, Kew in the United Kingdom, doesn’t think his findings are controversial at all. “Understanding where things come from can help us understand why we have X or Y species, and why there are so many,” Pérez-Escobar says.

Today, it takes a long logbook to account for orchids’ present diversity of appearances and habits. “There’s quite a number of innovations that orchids can do that other plants can’t, or not so well,” says Katharina Nargar, an orchid researcher at James Cook University, in Australia who contributed to the new study.

The neatest and most helpful of these tricks, according to Nargar, is that more than 70 percent of orchids have developed the ability to grow out of tree trunks and branches instead of soil—a capability known as epiphytism. This allows them to exploit new territories other plants cannot use, giving them “free rein,” says Nargar. Studies suggest that epiphytism evolved independently at least 14 times throughout the orchid family tree, and epiphytic orchids are “significantly richer in species” than terrestrial ones, write the authors of one study of their diversity.³ To successfully live in trees, orchids have developed the ability to absorb moisture from the air via a succulent spongy outer coating on their stem and leaves, as well as to use their roots directly to photosynthesize. The Taeniophyllum orchid, for instance, doesn’t even have any leaves: it just uses its roots for all energy production from the sun.

For the species that haven’t evolved to live in trees, the other main running theory for their inexplicable ability to diversify lies in how specialized their flowers are at getting pollinated. For one, some orchid species are the ultimate swingers—they’re very lenient in their sex lives and can produce fertile offspring with orchids from some other species, making them more likely to reproduce and more likely to often birth unique, new hybrid species, according to Nargar.

Marsh helleborine, a species of orchid native to Europe and Asia. (Hans-Juergen Roessler / Unsplash)

To ensure pollination, some orchids also strike up an evolutionary deal with local fauna: The plant evolves a flower so intricate it’s only accessible to a couple types of insects, and those insects are sure to only really ever pollinate other orchids. One of these striking examples is the Angraecum sesquipedale, the orchid Darwin had grown obsessed with, which has evolved a 12-inch long and narrow satchel for its nectar so that only the Hawk moth, with an exceptionally long proboscis, can access it. Although Darwin had already mused on this possibility, the moth hadn’t yet been discovered, so his theory was only confirmed almost four decades later, in 1903.

Some orchids are very lenient in their sex lives. 

In order to fine-tune their ability to accommodate just certain pollinators, orchids have also grown very meticulous about how they deliver their pollen gifts. Some orchids bundle their pollen in tailor-made, measured, sticky packages and fling them onto their preferred pollinators with precision so that no grains are wasted and lost along the way once they fly off, and they can only be dislodged once they reach their destination. This push to specialize pollen packaging according to available pollinators—maybe a moth, maybe a bee—has also pushed diversification. And it allows one mutant orchid to have a higher chance of having loads of offspring because less pollen goes to waste than with traditionally dispersed grains. The branch of the orchid family tree that has evolved this trick called “pollinia” has a higher speciation rate than orchids that have stuck with traditional pollen grains.⁴

To take their specialization a step further, some orchids have evolved to mimic the mate of their preferred pollinator, or their favorite snack through looks, scent, and the release of special chemicals.⁵Unknowing insects show up on their flower crown hoping to get lucky, and get duped into picking up the flower’s pollen instead. Ophrys apifera orchids look and smell like female bees. The Hammer orchid eerily resembles a female wasp. The Satyrium pumilum orchid, in South Africa, imitates the scent of dead animals to attract fruit flies, while Disa pulchra orchids pretend to be other nectar-offering flowers, like the pink iris, to fool insects into coming looking for a sweet reward. Since bees, wasps, and butterflies alike would clock the ploy if it were too common, it’s possible this has led orchids to vary in their mimetics as much as possible, spurring the birth of so many different species and tactics.

These unique flower morphology strategies are “fundamental,” to diversification according to Dewi Pramanik, an orchid morphology researcher at the Naturalis Biodiversity Center, in the Netherlands. One of her favorites is the Serapias cordigera orchid, which has evolved to shape its hairy, burgundy flower like a comfortable resting place for the Hoplitis adunca male bee, which will conveniently stop to rest there in between bouts of foraging, accidentally pollinating the flower.

Dust-like seeds are also likely among the orchid’s arsenal for rapid diversification. A single orchid seed packet can contain up to 4 million seeds, sometimes as tiny as 0.05 mm in length—the smallest in the plant kingdom—meaning plenty can easily disperse with a single gust of wind. Although most of the dust seeds won’t ever germinate, this tiny seed technique does increase the odds for diversification compared to a plant with a heartier seed bulk because new plants can crop up quickly in new locations without too much energy expenditure, and rapidly adapt accordingly.

Though orchid excellence might not all be down to just tricks pulled by the plants themselves, according to Thompson—there are external factors at play, too. When Thompson ran another phylogenetic statistical analysis on nearly 1,500 species of terrestrial orchids, his data suggested that their diversification “exploded” specifically when temperatures started dropping across the globe, somewhere around 10 million years ago.⁶ Global cooling is 700 times more likely to have influenced the rate at which orchids speciated than just time alone, Thompson says, making orchids “the best example of climate-driven speciation.”

Unfortunately, this also suggests extra trouble for the challenges orchids will face as the world warms. “I think extinction will increase, because a lot of them are cold-adapted, and we’ve seen in Europe, how hot it’s been this year,” says Thompson. Climate changes also put orchids at additional risk due to their hyper-specializing for one pollinator that might die off or be forced out of their habitat.

Going by their evolutionary history, orchids should continue to proliferate, and we should continue to discover new ones. “If you look at the number of orchid species described against time, it’s not really showing any evidence of leveling off,” according to Thomas Givnish, a professor of botany and environmental studies at the University of Wisconsin-Madison, who penned that seminal Australia-orchid-origin research. But human-caused climate change and other habitat destruction are spelling out a different future for many of these species of flower.

Some calculations suggest that plant species are dying out at least 500 times faster than before 1900, with orchids high on the threat list. Bangladesh has lost 32 of its 188 identified orchid species since 1996; in the Czech Republic, the suitable habitat for endemic orchids has declined up to 92 percent; in Florida, the number of famed ghost orchid (the sought-after subject of The Orchid Thief) has declined by half; orchids in India are blooming earlier than they should, potentially disrupting pollination. And according to a study published earlier this year, almost 280 known orchid species are in need of “immediate conservation action” but most of these still lack adequate protection.

If most of the diversity arose in the past 10 to 5 million years, the rapid loss of species we’re experiencing now might be too late to counteract, according to Pérez-Escobar. “We are kind of stuck,” he says. “If we don’t protect the orchids that we have left, the time it will take for that orchid diversity to bounce back is millions of years.” He’s on a mission to gather additional international collaboration to sample the DNA of all existing orchid species—however many they may be—because he thinks that will help him definitively plot out the plant’s evolutionary history.

The one thing experts seem to all agree on is that perhaps the best way to come up with strategies to effectively stop orchids’ decline⁷—whether it’s going to be saving the habitats they reside in, focusing on the pollinators they rely on, cutting down on their illegal trade, or all of the above—is to somehow answer the big questions of the “abominable mystery”: What are the secrets to their success in speciation? Further parsing these details about orchid diversity can help conservationists home in on their rapid and wild evolutionary plasticity to, hopefully, give them a fighting chance at adapting to a rapidly changing world.

After all, Darwin, himself noted that orchids had been “eminently useful” for him to learn how every little element, “even most trifling details of structure,” are somehow a result of natural selection.⁸ As he writes in a letter replete with exclamation points to a fellow botanist: “The beauty of the adaptations of parts seems to me unparalleled.”

References

1. Givnish, T.J., et al. Orchid historical biogeography, diversification, Antarctica, and the paradox of orchid dispersal. Journal of Biogeography 43, 1905-1916 (2016).

2. Perez-Escobar, O.A., et al. The origin and speciation of orchids. BioRxiv (2023).

3. Gravendeel, B., Smithson, A., Slik, G.J.W., & Schuiteman, A. Epiphytism and pollinator specialization: Drivers for orchid diversity? Philosophical Transactions of the Royal Society B 359, 1523-1535 (2004).

4. Givnish, T.J., et al. Orchid phylogenomics and multiple drivers of their extraordinary diversification. Proceedings of the Royal Society B 282, 20151553 (2015).

5. Ackerman, J.D., et al. Beyond the various contrivances by which orchids are pollinated: Global patterns in orchid pollination biology. Botanical Journal of the Linnean Society 202, 295-324 (2023).

6. Thompson, J.B., Davis, K.E., Dodd, H.O., Wills, M.A., & Priest, N.K. Speciation across the Earth driven by global cooling in terrestrial orchids. Proceedings of the National Academy of Sciences 120, e2102408120 (2023).

7. Fay, M.F. Orchid conservation: How can we meet the challenges in the twenty-first century? Botanical Studies 59, 16 (2018).

8. Darwin, C. Letter to J.D. Hooker. Darwin Correspondence Project. University of Cambridge (1862).

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More than 1.5 billion years ago, a momentous thing happened: Two small, primitive cells became one. Perhaps more than any event — barring the origin of life itself — this merger radically changed the course of evolution on our planet.

One cell ended up inside the other and evolved into a structure that schoolkids learn to refer to as the “powerhouse of the cell”: the mitochondrion. This new structure provided a tremendous energetic advantage to its host — a precondition for the later evolution of complex, multicellular life.

But that’s only part of the story. The mitochondrion is not the only important structure within complex, eukaryotic cells. There’s the membrane-bound nucleus, safekeeper of the genome. There’s a whole system of internal membranes: the endoplasmic reticulum, the Golgi apparatus, lysosomes, peroxisomes and vacuoles — essential for making, transporting and recycling proteins and other cargo in and around the cell.

Where did all these structures come from? With events lost in the deep past and few traces to serve as evolutionary clues, it’s a very tough question to tackle. Researchers have proposed various hypotheses, but it is only recently, with some new tools and techniques, that cell biologists have been able to investigate the beginnings of this intricate architecture and shed some light on its possible origins.

A microbial merger

The idea that eukaryotes originated from two cells merging dates back more than 100 years but did not become accepted or well known until the 1960s, when the late evolutionary biologist Lynn Margulis articulated her theory of endosymbiosis. The mitochondrion, Margulis said, likely originated from a class of microbes known as alphaproteobacteria, a diverse group that today includes the bacterium responsible for typhus and another one important for the genetic engineering of plants, among many others.

Nothing was known about the nature of the original host cell. Scientists proposed that it already was fairly complicated, with a variety of membrane structures inside it. Such a cell would have been capable of engulfing and ingesting things — a complicated and energetically expensive eukaryotic feature called phagocytosis. That might be how the mitochondrion first got into the host.

But this idea, called the “mitochondria late” hypothesis, doesn’t explain how or why the host cell had become complex to begin with.

In 2016, evolutionary biologist Bill Martin, cell biologist Sven Gould and bioinformatician Sriram Garg, at the University of Dusseldorf in Germany, proposed a very different model known as the “mitochondria early” hypothesis. They argued that since no primitive cells today have any internal membrane structures, it seems very unlikely that a cell would have had these over 1.5 billion years ago.

Instead, the scientists reasoned, the endomembrane system — the whole hodgepodge of parts found inside complex cells today — could have evolved soon after the alphaproteobacterium took up residence inside a relatively simple host cell, of a kind from a class called archaea. The membrane structures would have arisen from bubbles, or vesicles, released by the mitochondrial ancestor.

Free-living bacteria shed vesicles all the time, for all sorts of reasons, Gould, Garg and Martin note, so it seems reasonable to think they’d continue to do that when enclosed inside a host.

Eventually, these vesicles would have become specialized for the functions that membrane structures perform today inside eukaryotic cells. They would even fuse with the host cell’s membrane, helping to explain why the eukaryote plasma membrane contains lipids with bacterial features.

Vesicles could have served an important initial function, says biochemist Dave Speijer of the University of Amsterdam. The new endosymbiont would have generated plenty of poisonous chemicals called reactive oxygen species, by oxidizing fatty acids and burning them for energy. “These destroy everything, they are toxic, especially on the inside of a cell,” Speijer says. Sequestering them inside vesicles would have helped keep the cell safe from harm, he says.

Another problem created by the new guest could also have been helped by making membranes barriers, Gould, Garg and Martin add. After the alphaproteobacterium arrived, bits of its DNA would have mixed with the genome of the archaeal host, interrupting important genes. Fixing this would mean evolving machinery to splice out these foreign pieces — today they’re known as introns — from the messenger RNA copies of genes, so those protein-making instructions wouldn’t be garbled.

But that created yet another problem. The protein-making machinery — the ribosome — works extremely fast, joining several amino acids together per second. In contrast, the intron-removing system of the cell is slow, snipping out about one intron per minute. So unless the cell could keep the mRNA away from ribosomes until the mRNA was properly processed, the cell would produce many nonsensical, useless proteins.

The membrane surrounding the nucleus provided an answer. Serving as a spatial barrier, it allows mRNA splicing to finish up in the nucleus before the intron-free mRNA is translated in the cell’s internal fluid, the cytosol. “This is the selective pressure behind the origin of the nucleus,” Martin says. To form it, vesicles secreted by the endosymbiont would have flattened and wrapped around the genome, creating a barrier to keep ribosomes out but still allowing small molecules to pass freely.

An inside-out explanation

In short, Gould, Garg and Martin’s hypothesis explains why endomembrane compartments evolved: to solve problems created by the new guest. But it doesn’t fully explain how the alphaproteobacterium got inside the host to begin with, says cell biologist Gautam Dey at EMBL in Heidelberg, Germany; it assumes the endosymbiont is already inside. “This is a massive problem,” Dey says.

An alternative idea, proposed in 2014 by cell biologist Buzz Baum of University College London (with whom Dey once worked) and his cousin, University of Wisconsin evolutionary biologist David Baum, is the “inside-out” model. In this scenario, the alphaproteobacterium and the archaeal cell destined to be its eventual host would have lived side by side for millions of years in an intimate symbiosis, each depending on the other’s metabolic products.

The archaeal cell would have had long protrusions, as seen on some modern-day archaea that live in close association with other microbes. The alphaproteobacterium would have nestled up against these slender extensions.

Eventually, the protrusions would have wrapped around the alphaproteobacterium and enclosed it completely. But during the long stretch of time before that happened, the archaeal cell would have begun some spatial division of labor: It would keep information-processing jobs in its center, where the genome was, while functions like protein building would take place in the cytosol within the protrusions.

The power of the inside-out model, Buzz Baum says, is that it gives the cell eons of time, before the alphaproteobacterium becomes fully enclosed, to evolve ways to regulate the number and size of the mitochondrion and other membrane compartments that would eventually become fully internal. “Until you can regulate them, you’re dead,” Buzz Baum says.

The model also explains why the nucleus has the shape that it does; in particular, it provides an explanation for its unusually large pores. Viewed from inside the center of an archaeal cell, the long protrusions would be openings that could naturally become big pores like those, Baum says.

Most important, the inside-out model explains how the alphaproteobacterium would have gotten inside the archaeal host in the first place.

Still, the inside-out model has features it needs to explain. For example, the mitochondrion would end up in the wrong place — inside the endoplasmic reticulum, the network of tubes on which sit the cell’s protein-making ribosomes, as the archaeal protrusions wrapped around it. And so an additional step would be required to get the alphaproteobacterium into the cytoplasm.

But Martin’s main objection is that the inside-out model does not provide an evolutionary pressure that would have caused the nucleus or other membrane-bound compartments to arise in the first place. The inside-out model “is upside-down and backwards,” Martin says.

The nucleus: A riddle in the middle

Though the models agree that the mitochondrion evolved from an alphaproteobacterium, they have very different ideas about the origin of the nucleus and other organelles.

In the Gould, Garg and Martin model, the source for all of the structures would have been vesicles released by the evolving mitochondrion. Vesicles to contain reactive chemicals or cellular cargo, and the ability to move this cargo around, would have evolved very early. The nucleus would have come later.

In the inside-out model, the nucleus was, essentially, the remains of the archaeal cell after it wrapped its membranes around the alphaproteobacterium. So it would have appeared immediately. The endoplasmic reticulum also would have formed early, created from those squished-together protrusions. Other organelles would have come later — arising, Buzz Baum says, from buds of archaeal membrane.

Thus the models also make different predictions about the chemical nature of the membranes of cell organelles — at least originally — and how today’s complex cells came to have membrane lipids that are all chemically like the ones in bacteria, not archaea.

In the Gould, Garg and Martin model, in the beginning all the membranes except for the host cell’s outermost one would have been bacterial, like the membranes of the new resident. Then, as bacterial vesicles fused with this archaeal outer membrane, the bacterial lipids would slowly replace the archaeal ones.

In the inside-out model, the membranes of the nucleus and endoplasmic reticulum — and probably others — would have been archaeal, like the host, to start. Only later on, after genes from the bacterial genome moved over to the archaeal genome, would the lipids become bacterial in nature, Baum suggests.

How to test these ideas? Through experiments, cell biologists are starting to glimpse ways in which simple vesicles could have diversified into different organelles with distinct jobs — by taking on different shapes, like the layered membrane stacks of the modern endoplasmic reticulum or the Golgi body, or by ending up with different proteins inside them or on their membranes.

They are also highlighting the dynamism of the modern-day mitochondrion — and its potential to spawn new membrane structures.

Take, for example, the compartment that Speijer thinks evolved early in order to deal with reactive oxygen species: the peroxisome.

In 2017, cell biologist Heidi McBride of McGill University in Montreal reported that cells lacking peroxisomes could generate them from scratch. Working with mutant human fibroblast cells without peroxisomes, her team found that these cells put proteins that are essential for peroxisome function into mitochondria instead. Then the mitochondrial membrane released them as little bubbles, or vesicles.

These vesicles, or proto-peroxisomes, matured into true peroxisomes when they fused with another type of vesicle derived from endoplasmic reticulum, which carry a third necessary peroxisome protein. “It’s a hybrid organelle,” McBride says.

For McBride, this is an indication that peroxisomes — and probably other organelles — originally came from mitochondria (not exclusively from the endoplasmic reticulum, as previously believed). “The presence of mitochondria launched the biogenesis of new organelles,” she says. “In the case of peroxisomes, it’s quite direct.”

Other mitochondrion antics have also been noted.

First, a 2021 report from the lab of biochemist Adam Hughes at the University of Utah found that when yeast cells are fed toxic amounts of amino acids, their mitochondria will shed vesicles that are loaded with transporter molecules. The transporters move amino acids into the vesicles, where they won’t poison the mitochondria.

Hughes also discovered that the vesicles shed by the mitochondria can form long, tubule-like extensions with multiple layers, reminiscent of the layered stacks of the endoplasmic reticulum and the Golgi body. The structures persist in the cell for a long time. “They’re definitely their own unique structure,” Hughes says. 

And in 2022, immunologist Lena Pernas, now at UCLA, showed that multilayered, mitochondria-derived structures can form in other contexts, too. When a cell is infected by the parasite Toxoplasma, her team found, the mitochondria surround the parasite and change shape. The parasite responds, and the upshot is that the mitochondrion ends up shedding large bits of outer membrane.

Pernas, who wrote about mitochondrial remodeling in the Annual Review of Physiology in 2016, recently discovered that these structures, which initially look like simple vesicles, also can grow and take on more complex shapes, such as stacks of sheet-like layers. What’s more, the stress of infection changes what sorts of proteins are placed on these shed bits of mitochondrial membrane. Such changes open the door for the stacked sheets to behave in different ways than they normally would, presenting the opportunity to take on new jobs, Pernas says.

The more Pernas and Hughes study these structures — found in quite different cells and conditions — the more similar they look. It’s tantalizing, says Hughes, to imagine how a structure like this, forming in the early days of eukaryote evolution, could have evolved over eons of natural selection into some of the endomembrane compartments existing in cells today.

It may never be possible to know for sure what happened such a very long time ago. But by exploring what can happen in today’s living bacterial, archaeal and eukaryotic cells, scientists can get more clarity on what was possible — and even probable. A cell moves into another cell, bringing benefits but also problems, setting off a complex cascade. And then, McBride says, “all this stuff blooms and blossoms.”

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You’re twisted. Sorry, but we all are. The molecules most central to life twist one way or the other. Your most famous molecule, DNA, a spiraling helix like the thread of a screw, is right-handed. The molecules encoded by your DNA, proteins, are left-handed. Even humble sugars like glucose have a twist to their shape.

Why does this handedness, called chirality after the Greek word for hand, feature in the molecules (clusters of atoms) from which all life on Earth is constructed? How and when was the left-or-right chiral twist of life’s components decided? No one knows—even though the chirality of life has been recognized for more than a century and a half.

But we do know that living organisms are exquisitely sensitive to this handedness. Feed bacteria with left-handed amino acids, and they’ll incorporate them into their proteins. Feed them right-handed amino acids, and they are likely to ignore them, even though these are the same molecules but inverted as though in a mirror.

There might be a dark biosphere—a whole ecosystem of mirror-image life forms.

Maybe we just need to accept this is how life is. It exists on one side of the looking glass. But some researchers think there could be equivalent lifeforms on the other side too—if only we could make them. They are already making mirror-image versions of proteins and nucleic acids like DNA. These molecules could be valuable drugs—all the more effective because their looking-glass structure should allow them to operate out of sight of the body’s usual defense mechanisms for breaking apart foreign molecules.

But biochemist Ting Zhu of Westlake University in Hangzhou, China, is determined to go much further than that. He’s made it his mission to create mirror-image versions of the key molecular ingredients of life. In principle, it might be possible to assemble those components into synthetic cell-like entities that can replicate and metabolize: a kind of primitive form of life, but inverted relative to every known organism, and therefore the first truly non-natural life form.

“I believe there are many alternative possibilities for life,” says Zhu. “But among all of these, there is one that we know for sure would work, and that’s the exact mirror-image version of ourselves.” No one knows how such mirror-image cells would get along with ordinary ones—maybe they’d ignore each other, or compete? Might our planet have already conducted a version of that experiment in the wild, billions of years ago when life began?

Over the past several years, Zhu and his colleagues have performed the monumental task of making, from their constituent molecular parts, mirror-image versions of the key biomolecules in living cells: DNA, its sibling RNA, and the enzymes for replicating them and translating their sequences into proteins. He hasn’t got the full set yet, but he is getting very close. Only a few components are still to be added to the basic biomolecular toolkit needed by stripped-down, minimal versions of mirror-image life.

“Ting’s work is really impressive,” says biochemist and Nobel laureate Jack Szostak at Harvard University, who was Zhu’s Ph.D. advisor. “Making a mirror-image cell with a complete mirror-image protein synthesis system is a hugely ambitious goal. But I think it’s worth trying, just to see what the hardest problems are.”

“This could be the beginning of a new form of life,” says Zhu. A lot of people think it can’t be done—but he is determined to try, just to see if it’s possible. “Indeed, it’s difficult and challenging, but that also makes it exciting, like climbing a high mountain.”

The hand(s) of love

Mirror-image life was first imagined by the man who discovered the chirality of life’s molecules: French chemist Louis Pasteur. In 1848, Pasteur deduced that a byproduct of winemaking called tartaric acid may crystallize in two mirror-image crystal shapes because their constituent molecules have opposite chirality. After carefully separating the two types of crystal by hand, Pasteur dissolved them separately in water and found that when polarized light passed through the solutions, the plane of polarization was rotated in opposite directions: to the left and to the right. Mirror- image molecular structures are called enantiomers, and are distinguished by the prefixes D and L, for the Latin words for right (dextera) and left (laeva). They are distinguished by the way their component atoms are arranged in space.

Pasteur became convinced that molecular chirality was a fundamental feature of living things: what distinguished them from the non-living world. He was wrong about that but correct that chirality is omnipresent in biomolecules. Pasteur wondered if chirality was induced by forces such as magnetism, electricity, or light, and in the 1850s he conducted a series of experiments that from today’s vantage point might look borderline cranky: crystallizing compounds in magnetic fields, growing plants in sunlight with its polarization inverted with mirrors. Those efforts never led anywhere, although recently researchers at Harvard University have proposed that magnetism in minerals might indeed have played a role in giving the earliest life its particular chirality.

But Pasteur also examined the chirality of some natural molecules and showed that the amino acid asparagine, isolated from plants (the name comes from its discovery in asparagus juice), is present in just the L-form. In 1886 the Italian chemist Arnaldo Piutti discovered the D-form of asparagine and found that, while L-asparagine is tasteless, D-asparagine is sweet. In other words, mere mirror-image inversion is enough to produce different biological effects. Such distinctions became tragically apparent when it was found in the early 1960s that the two enantiomers of the drug thalidomide, prescribed for anxiety and for morning sickness in pregnant mothers, have very different effects: One is a sedative, the other can cause serious birth defects.

Mirror drugs

We now know that all natural amino acids in proteins are L-enantiomers. But protein-like molecules made from D-amino acids by chemical synthesis have been investigated for several decades as potential drugs.

The creation of mirror-image proteins was pioneered several decades ago by chemist Stephen Kent of the University of Chicago and his co-workers. In the early 1990s, Kent and colleagues were able
to chemically synthesize the enzyme HIV-1 protease, which the HIV virus uses to degrade other proteins. This allowed researchers to obtain the first crystal structure of the enzyme, assisting the development of drugs that combat AIDS by blocking the enzyme from working. Having acquired that facility for building proteins from scratch, in 1992 Kent’s team made a mirror-image version of HIV protease just to see what it would do. They found that the molecule would cut up only peptides also made from D-amino acids, while ignoring those made from natural L-versions.

Kent realized that such reversed proteins could be useful for drug discovery. Many drugs aim to bind to and block the action of natural proteins, and such compounds are typically found by a screening procedure: The protein target is exposed to a wide variety of compounds to see if any bind to it. Many such compounds are chiral, and a mirror-image version of the target protein could double the chances of finding a good match, because a candidate in the screening library could have the correct handedness to stick only to the mirror-image form. If so, the other enantiomer, once chemically synthesized, should stick to the natural target.

D-proteins (and small fragments of them called peptides) could also be useful as drugs, for example by binding to and blocking the activity of natural proteins that are therapeutic targets. Around 80 or so normal L-peptides that do this are already on the market, but D-peptides have a distinct advantage. One of the obstacles for protein-based drugs is that natural protease enzymes quickly break them apart. But those enzymes don’t work on D-peptides, and so they “are expected to be largely invisible to metabolic degradation,” says Kent.

What’s more, D-proteins wouldn’t cause the immune system to trigger an inflammatory response, because this only happens once foreign proteins are chopped into fragments by proteases. Studies in mice have shown that D-proteins can pass harmlessly through the body before being cleared by filtration in the kidneys.

D-proteins are being explored for cancer treatment, among other things. For example, Kent’s group has explored one that can interfere with blood-vessel formation in tumors. But it’s still early days for mirror-image protein drugs. “To the best of my knowledge, none has yet been approved for use as a therapeutic,” says Kent.

Biochemist Sven Klussmann is hoping that mirror-image nucleic acids too will find uses as drugs, and he has launched two companies based in Germany to develop them. As with D-peptides, naturally occurring enzymes that degrade nucleic acids, called nucleases, cannot degrade mirror-image nucleic acids, and they are not so easily recognized by the immune response and so are less apt to trigger inflammatory reactions.

Life’s essential machines

While Pasteur was conducting his weird experiments on molecular chirality with magnets and light in the 1850s, he admitted, “One had to be a little mad to undertake what I am trying to do now.” That’s a sentiment Zhu might well sympathize with. His determination to build mirror-image versions of life’s key molecules from scratch, assembling their long chains piece by piece with meticulous, painstaking chemistry, goes way beyond earlier efforts to make right-handed proteins. When he began in the early 2010s, his goal must have looked crazily ambitious. But many are astonished at the progress he has made. The work “is fascinating, pushing the limits,” says Klussmann.

A bare-bones form of mirror-image life would need just a few key molecular ingredients—a little biology primer will help to explain what those are.

In cells, the enzyme DNA polymerase makes copies of DNA molecules as the cell prepares to replicate, while RNA polymerase creates so-called messenger RNA (mRNA) molecules that carry the information for making proteins. In both cases, the sequence of nucleotides made by the polymerase is determined by that in the DNA “template” strand on which the enzyme puts together the new nucleic acid. DNA nucleotides come in four varieties, distinguished by the molecules called nucleotide bases they contain: adenine (A), cytosine (C), thymine (T), and guanine (G). Each base is attached to a sugar molecule called deoxyribose and a phosphate group, which together form the backbone of the double helix on which the bases hang. Deoxyribose is a chiral molecule, and in natural DNA it is always the D-enantiomer, which is what makes the helix twist in a right-handed fashion.

The nucleotide bases can stick to one another in pairs via weak chemical bonds called hydrogen bonds. These pairs have distinct preferences because of the way the bases fit together: A sticks to T, and C to G. So the twin strands of DNA are zipped up by hydrogen bonds, and they have complementary sequences: where one has an A, the other has a T, and so on. Crudely speaking, some DNA sequences—those of the regions corresponding to genes—encode the structures of proteins, which are crumpled-up chains of amino acids. Each triplet of DNA bases, called a codon, encodes a single amino acid: This correspondence is called the genetic code.

Base pairing allows a new DNA strand to be put together on an existing one, once that part of the double helix is unzipped. The complementary pairing means that the new strand has a sequence complementary to that of the template strand: The information encoded in the sequence is preserved. All the DNA polymerase enzyme needs to do is to join together the backbone segments of new nucleotides as they dock onto the template strand.

The assembly of an RNA molecule on a DNA template strand, catalyzed by RNA polymerase, relies on the same rules of base pairing except that in RNA a base called uracil substitutes for DNA’s thymine. Once a protein-coding gene (which might typically be a few hundred bases long) has been transcribed into mRNA, the RNA molecule floats free from the DNA template strand and is translated into a protein by a large cluster of proteins and RNA molecules called the ribosome. Amino acids are brought to the ribosome attached to small RNAs called transfer RNA (tRNA), which dock onto the mRNA so that the amino acids get linked into the corresponding sequence.

The processes of information transfer involved in DNA replication, transcription, and translation comprise the so-called Central Dogma of molecular biology adduced in 1957 by British biologist Francis Crick, co-discoverer of DNA’s double-helical structure. Information goes from DNA to DNA during replication, said Crick, and from DNA to RNA to protein during transcription and translation. He also allowed for the possibility that it could pass from RNA back to DNA—a suggestion validated in the 1970s when researchers discovered that viruses that encode their genes in RNA (examples now include HIV and SARS-CoV-2) could insert them into the host DNA. This “reverse transcription” is orchestrated by a polymerase called reverse transcriptase, which itself is encoded in the viral genome.

Reversing the parts

Zhu’s aim is to create mirror-image versions of all the components involved in enacting the Central Dogma. Then he can progress from DNA to proteins in this looking-glass world, as well as enabling DNA replication. This would give him the minimal set of biomolecules needed for putting together an inverted life form.

His first target, attained in 2016 while he was based at Tsinghua University in Beijing, was an inverted DNA polymerase. Wisely, he chose to synthesize the smallest such protein known, called African swine fever virus polymerase X. To make the inverted enzyme, Zhu’s team used now well-established chemical methods for joining amino acids one by one, although it was challenging to apply them to such a long chain. A mechanical engineer by training, Zhu learned his chemical craft under the expert guidance of Szostak, who has long pursued the challenge of making rudimentary synthetic living entities called protocells from scratch.

Once Zhu’s team had put the enzyme together, they verified that it was able to complete a 12-base strand of L-DNA on an 18-base template strand, filling in the remaining six nucleotides. The enzyme did that job rather slowly compared with natural polymerases, however, taking about four hours: Because the African swine fever virus polymerase X is so small, it isn’t terribly efficient. Given even longer—a day and a half—the enzyme was able to extend such a 12-base “primer” strand all the way along a 56-nucleotide template. Better still, the mirror-image polymerase worked for making RNA too, transcribing L-RNA on an L-DNA template.

“The devil is in the details,” he says cautiously, “and there are a lot of devils.”

It would be useful to use such a mirror-image DNA polymerase to amplify strands of L-DNA—that is, to make copies from which it can make further copies, boosting the number of strands exponentially. That’s what happens in the process called the polymerase chain reaction (PCR), ubiquitous in genetic biotechnology for making lots of DNA from tiny samples. (It’s the process used in the PCR test for COVID-19, where tiny amounts of viral genome in swab samples are amplified so that they can be identified.) To conduct PCR, the double-strands made by a DNA polymerase are separated so that each strand can act as a template for further replication, and the cycle is repeated many times. The strands are separated by warming them up, which unzips the hydrogen bonds holding them together. This heating is apt to destroy most polymerase enzymes, but standard PCR uses one taken from a thermophilic (“heat-loving”) bacterium that lives in hot thermal springs, which is more resistant to heat.

As his next target for mirror-image biochemistry, Zhu chose a DNA polymerase called Dpo-4 from a heat-tolerant microbe, Sulfolobus solfataricus. The researchers made it in 2017 and showed that indeed it could be used for looking-glass PCR. In 2019, Zhu’s team made a mutant form of the polymerase that could not only transcribe L-RNA from L-DNA but also reverse-transcribe it, writing an RNA sequence back into DNA: another link of the information-transfer network in the Central Dogma.

In 2022, Zhu and colleagues synthesized the mirror-image form of the massive 883-amino-acid protein RNA polymerase used by the T7 bacterial virus, a widely used enzyme for transcription because of its efficiency and accuracy. This achievement, says chemical biologist Richard Payne of the University of Sydney, “represents a monumental feat of total chemical synthesis and a pivotal breakthrough on the journey toward mirror-image life.”

With nucleic-acid polymerization under his belt, Zhu moved on to the biggest challenge for a mirror-image Central Dogma: a reversed ribosome capable of translating L-RNA into D-proteins. The ribosome is not a single enzyme but a huge piece of biochemical machinery, with many component parts. In the ribosomes used by the common gut bacterium Escherichia coli, for example, there are around 55 proteins and three ribosomal RNAs.

Zhu began working toward this goal in 2019, and the following year his group at Tsinghua reported that they had synthesized mirror-image versions of three key ribosomal proteins. They used their polymerases also to make a mirror-image ribosomal RNA molecule and showed that the three proteins would assemble spontaneously with this RNA into the complex found in the ribosome.

Now Zhu says that he and his team at Hangzhou have made nearly all the molecular components of the ribosome, although they have not yet published this work. How close is he? “The devil is in the details,” he says cautiously, “and there are a lot of devils.”

Life, inverted?

If Zhu succeeds in making a mirror-image ribosome, it could be a huge boost for D-protein therapeutics, because then such proteins could be made simply by producing the corresponding mirror-image DNA—a simpler task—and transcribing and translating it.

“A working synthetic ribosomal system for making mirror-image proteins would be a practical demonstration of the power of chemical synthesis applied to enzyme protein molecules,” Kent says. “It would show that we do in fact understand the key aspects of how proteins are biosynthesized.”

Yet Zhu’s ultimate goal is not drugs but life itself: making a mirror-image protocell with all that it needs to replicate and to use its genome to generate the enzymes it needs to function and metabolize. That would arguably constitute the first genuinely artificial life form. Goodness knows what such a thing might be used for, but Kent attests this curiosity-driven work—what he calls “ambitious and excellent science”—is its own justification. “Good research does not need to be justified by practical applications,” he says.

Can such mirror-image life ever be made in the lab? A minimal protocell that can transcribe and translate its genome into functional proteins need only have the basic molecular ingredients encapsulated within a lipid membrane. A more ambitious goal would be an entire mirror-image bacterium, with all its nucleic acids, proteins, and sugars inverted. If such an organism is ever made, it should look and act no different from a normal bacterium. Only by zooming in on the individual molecules would the looking-glass difference become apparent.

Right now, though, all this is still fantasy. Zhu points out that no one has yet made a replicating synthetic protocell even using the normal biomolecular machinery. He thinks it makes sense to wait until that is done before trying to do it with mirror-image molecules.

Mirror-image life might also help to explore “one of the biggest mysteries surrounding the origin of life on Earth,” says Zhu—its “homochirality,” or why it uses only D-nucleic acids and L-proteins. Some think the choice was entirely random: Perhaps both enantiomers existed among the prebiotic building blocks, and some random fluctuation in the concentrations of one type got amplified by feedback processes and gained precedence. Others wonder if some tiny chiral bias might have been introduced by more fundamental factors, such as the left-right symmetry-breaking called parity violation, known to occur in nuclear processes involved in radioactive beta decay.

Having a mirror-image biochemistry might not answer the question of homochirality, but it could supply a new direction to probe: by putting both enantiomers of the biomolecules together in the same test tube and seeing what happens, especially if the molecules can mutate and evolve. Zhu says that in dilute solutions, mirror-image proteins and nucleic acids seem to ignore one another. But if they interact in more concentrated conditions, might just a single chirality emerge from the melee?

There is another possibility, too. “Is life on Earth really homochiral, or do we just not have the right tools to look for the other chiral version?,” Zhu asks. What if mirror-image life exists in some corners of the natural environment that we’ve overlooked because we don’t have the means to detect it? There might be a dark biosphere—a whole ecosystem of undetected mirror-image life forms. If so, a PCR system that can amplify the inverted DNA from such organisms could help to bring it to light.

Once he has made a working mirror-image ribosome, however, Zhu says he’ll probably leave the challenge of complete mirror-image protolife to others. At that point, he’ll be ready to move on to other projects. Besides, he has another way to explore the dreams of alternative life. “Things I can do, I’ll do in the lab,” he says. “Things I cannot do yet, I’ll write them as science fiction.”

This article The “dark biosphere”: Do mirror-image lifeforms exist? is featured on Big Think.

Last week, I was contacted by a German documentary producer, asking if I was willing to be interviewed about two mummified bodies presented at a Mexican congressional hearing by TV personality Jaime Maussan, who claimed they were aliens.

I declined, explaining that I didn’t have any inside knowledge about the alleged discovery. But I did say in a written statement that I was skeptical. The “bodies” shown at the hearing look a little too humanoid to me. That is what we have come to expect from decades of science fiction movies, but in actuality, I would not necessarily expect aliens to look like us.

Most outside observers also were skeptical about Maussan’s “mummies,” with many dismissing them as outright fakes. But it got me thinking: If one day, somebody comes forward with a body that appears at first glance to be extraterrestrial in origin, how would we know for sure? How would we positively identify an alien?

“Ata”

There’s actually a precedent for the “aliens” shown to the Mexican Congress. Similar claims were made about a six-inch-long skeleton called “Ata” discovered in the Atacama desert of Chile 20 years ago. Several investigators proposed that the tiny body was of alien origin because of its elongated cranium, accelerated bone age, and the fact that it had fewer ribs than a typical human.

After a research group led by Sanchita Bhattacharya from the University of California-San Francisco performed whole-genome sequencing, however, Ata turned out to be a human with previously unknown genetic mutations that caused abnormal tissue growth. Two subsequent papers, one by Gary Nolan and Atul Butte, and one by a team led by Siân Halcrow from the University of Otago in New Zealand, confirmed that assessment. While Ata’s specific mutations were new to scientists, it was widely known that mutations can greatly disfigure a human body. Such abnormalities have long fascinated the general public as well as scientists, even ending up as curiosities in places like the Mütter Museum in Philadelphia. 

So, DNA analysis provided clear evidence that the skeleton was human. In fact, if we find DNA at all, it is safe to say the body is probably from Earth. DNA is just one of many possible nucleotides that could form the basis of life elsewhere in the Universe.

Francis Crick, co-discoverer of DNA, referred to our genetic code as a “frozen accident.” Many deviations from the code could have been possible, including the substitution of bases that we see in RNA right here on Earth. Steven Benner from the Foundation for Applied Molecular Evolution has shown convincingly that nucleotides with six bases instead of four (as in DNA) could effectively transfer genetic information. Work by Ned Budisa from the University of Manitoba in Canada suggests that extraterrestrials might use a different set of amino acids for coding. Gerald Feinberg and Robert Shapiro went even further and speculated that information transfer could occur magnetically rather than chemically. While there is no question that DNA is a highly optimized code for life, significantly better alternatives would exist under slightly different environmental conditions.

Alien biochemistry

For the sake of discussion, let’s not rule out that an alien body could have DNA like ours. It still would very likely have a completely different biochemistry. Their cells might not use ATP for energy production, as human cells do. Alien blood might not be red or have hemoglobin at all. It could be any color, in fact — there are lizards on Earth with green blood and octopuses with blue blood. Even on a planet with an environment exactly like Earth’s, different biological solutions might evolve from chance events, since the same functions can be provided by different biochemistries. Photosynthesis, for example, can be done with chlorophyll in plants, but also with rhodopsin and carotenoids. The chemicals in an alien’s body might have isotopes that are rare on Earth, and that might be a clue to an extraterrestrial origin.

But unless the biochemistry is fundamentally different from ours, we would still have to assume the body is from Earth. And that poses a dilemma. While difference is a useful criterion for identifying aliens, creatures from another planet, which evolved under physical conditions unlike those on Earth, might be so different as to be unrecognizable at first glance. We are intrigued by bodies like Ata’s precisely because they look like us, but not quite. If they looked too different, we might miss noticing them altogether.

Calling Fox Mulder

It is no surprise, then, that most reported “aliens” look humanoid. There is a lot to be said about the advantages of bipedal anatomy for evolving intelligence, given that nature, when faced with a similar set of environmental challenges, tends to come up with similar solutions — a principle called convergent evolution. But I think nature is much more creative than many of us think, particularly on an alien planet with a different origin story for life and a different history.

Every astrobiologist I know, myself included, wants to find an alien. But I am skeptical when the “aliens” look like tiny humans.

This article How could we tell if those “alien bodies” in Mexico are legit? is featured on Big Think.

This article is an installment of Future Explored, a weekly guide to world-changing technology. You can get stories like this one straight to your inbox every Thursday morning by subscribing here.

Extinction is a regular part of nature. An estimated 99% of all species that have existed on Earth have gone the way of the dodo, sometimes because a fitter competitor came along or their environment changed (often because of humans) and they couldn’t adapt.

While life can go on relatively unchanged after the extinction of some species, the loss of a keystone species — one that plays a significant role in its environment — can upend an ecosystem. 

Now, researchers exploring the idea of “de-extinction” believe that science might be able to intervene and restore the balance.

Australia’s loss

The thylacine, or “Tasmanian tiger,” is a prime example of what can happen when a keystone species goes extinct — when these carnivorous marsupials, which look like dogs, but with kangaroo-like pouches and tiger stripes, went extinct in 1936, it had a domino effect in Australia.

“We lost this incredibly unique animal that sat right at the top of a food chain,” Andrew Pask, head of the University of Melbourne’s Thylacine Integrated Genetic Restoration Research (TIGRR) Lab, told the Dallas Morning News in 2022.

“It does destabilize all the species that sit beneath them in that ecosystem,” he continued. “So there’s already been a lot of ripple effects that have happened as a result of the loss of the thylacine.”

One example of those effects can be seen in the Tasmanian devil population, according to Pask — a facial tumor disease that nearly wiped out the species over the past few decades might not have spread so widely had thylacines been around to kill the infected and weak animals.

“We lost this incredibly unique animal that sat right at the top of a food chain.”

ANDREW PASK

Between de-extinction and creation

Pask is now working with Colossal Biosciences — a company focused on using genetic engineering to resurrect extinct species — to explore the possibility of “de-extincting” the Tasmanian tiger.

The goal wouldn’t be to produce an exact replica of the animal — that’s likely impossible — but to create a proxy that could take its place in the Australian ecosystem.

“We think that bringing that animal back to Tasmania would have incredible benefits, not just for the Tasmanian devil population but for all sorts of unforeseen parts of that ecosystem,” Pask told Al Jazeera.

Colossal, which is also working to resurrect the woolly mammoth due to its potential to reduce permafrost thawing in Siberia, believes the Tasmanian tiger is particularly well suited to de-extinction research.

“The thylacine is a great candidate for de-extinction because it only went extinct in 1936 due to human hunting and the ecosystem we are looking to return it to is still intact,” Ben Lamm, Colossal’s co-founder and CEO, told Discovery.

“Furthermore, we have incredible tissue samples and genomes assembled as well as many additional pelts that are being sequenced for population genomics studies,” he continued.

“We are essentially engineering our dunnart cell to become a Tasmanian tiger cell.”

ANDREW PASK

That’s the first step in bringing the Tasmanian tiger (or any species) back from extinction, according to Colossal: you need to sequence its genome, the complete collection of DNA that can be found in almost every cell in its body.

Pask published the first thylacine genome in 2018, after two decades of work, using DNA extracted from a 108-year-old thylacine preserved at an Australian museum, and his team is still working to improve upon that draft, filling in missing gaps as new technology allows.

The next step is to sequence the genomes of living animals similar to the target species to find the one that’s closest to it genetically. Surprisingly, that turned out to the fat-tailed dunnart, a tiny, mouse-sized, carnivorous marsupial.

“We then take living cells from our dunnart and edit their DNA every place where it differs from the thylacine,” Pask told Discovery. “We are essentially engineering our dunnart cell to become a Tasmanian tiger cell.”

The nucleus from a thylacine-like cell can then be transferred into a dunnart egg cell to create an embryo (that process, somatic cell nuclear transfer, is the classic technique for cloning animals, like Dolly the sheep). 

Once the embryo is ready, it can be implanted into a surrogate mother. Because thylacines are (or were) only slightly larger than a grain of rice when they’re born, a dunnart could plausibly be used for this. 

After birth, the babies would be transferred to an artificial marsupial pouch designed to mimic the one a real mother thylacine would have had, until they can survive outside of it.

What’s new?

That’s the goal, at least — Colossal researchers are still in the beginning of the process where they try to make a dunnart genome as thylacine-like as possible. New research from the SciLifeLab research center and Center for Paleogenetics in Sweden could help there.

The group has published a study in the journal Genome Research detailing how it recovered and sequenced RNA from a room-temperature Tasmanian tiger specimen at the Swedish Museum of Natural History in Stockholm.

“Most researchers have thought that RNA would only survive for a very short time — like days or weeks — at room temperature,” researcher Love Dalén told Reuters. “This is likely true when samples are wet or moist, but apparently not the case when they are dried.”

“Resurrecting the Tasmanian tiger… will require a deep knowledge of both the genome and transcriptome regulation.”

EMILIO MÁRMOL

RNA is a nucleic acid, like DNA, and the major type — messenger RNA — plays a key role in turning the instructions coded in DNA into actual proteins. 

While practically every cell in an animal contains the same genome, the collection of mRNA in a cell — called its “transcriptome” — can vary widely between cells, depending on their role in the body. 

The Swedish team has produced transcriptomes for thylacine skin and skeletal muscle tissues, and while they aren’t working to resurrect the species, they believe their research could be useful for de-extinction efforts.

“Resurrecting the Tasmanian tiger or the woolly mammoth is not a trivial task, and will require a deep knowledge of both the genome and transcriptome regulation of such renowned species, something that only now is starting to be revealed,” said lead author Emilio Mármol.

Looking ahead

The thylacine isn’t going to be resurrected overnight — the University of Melbourne’s Pask told Al Jazeera he believes it could take his team until 2033 to create their thylacine-like cell, and it may be decades after that before the first Tasmanian tiger proxy is born. 

Colossal’s Lamm is far more optimistic — he thinks the first one could be birthed within the next five years.

If/when the researchers are able to produce thylacine proxies, they’ll study how groups of the animals fare in large areas of enclosed land over many years before considering their release into the wild.

A lot of time and money is going to go into the project, and it could be for naught. 

Because the proxies won’t be exactly like the original species, they might not be able to fill the exact same role in the ecosystem, and they could end up with health issues that prevent them from being able to survive in the wild.

“The best thing we can do to protect our ecosystems is to prevent species extinctions.”

ANDREW PASK

Still, the work going into de-extincting the Tasmanian tiger could aid other conservation efforts — the Tasmanian devil is an endangered keystone species, and the artificial pouch Colossal is developing could be used to increase the survival rates for its joeys, for example.

Ultimately, Pask believes the potential benefits of returning the thylacine to Australia alone make the project worth the effort.

“The best thing we can do to protect our ecosystems is to prevent species extinctions,” said Pask. “But where a corner-stone species has been lost from that environment, the next best thing we can do is try to bring that animal back.”

This article CRISPR is helping “de-extinct” the Tasmanian tiger is featured on Big Think.

Toward the end of the 19th century, lurid tales of killer plants began popping up everywhere. Terrible, tentacle-waving trees snatched and swallowed unwary travelers in far-off lands. Mad professors raised monstrous sundews and pitcher plants on raw steak until their ravenous creations turned and ate them too.

The young Arthur Conan Doyle stuck closer to the science in a yarn featuring everyone’s favorite flesh-eater, the Venus flytrap. Drawing on brand-new botanical revelations, he accurately described the two-lobed traps, the way they captured insects, and how thoroughly they digested their prey. But even his flytraps were improbably large, big enough to entomb and consume a human. Meat-eating, man-eating plants were having a moment, and for that you can thank Charles Darwin.

Until Darwin’s day, most people refused to believe that plants ate animals. It was against the natural order of things. Mobile animals did the eating; plants were food and couldn’t move — if they killed, it must only be in self-defense or by accident. Darwin spent 16 years performing meticulous experiments that proved otherwise. He showed that the leaves of some plants had been transformed into ingenious structures that not only trapped insects and other small creatures but also digested them and absorbed the nutrients released from their corpses.

In 1875, Darwin published Insectivorous Plants, detailing all he had discovered. In 1880, he published another myth-busting book, The Power of Movement in Plants. The realization that plants could move as well as kill inspired not just a hugely popular genre of horror stories but also generations of biologists eager to understand plants with such unlikely habits. 

Today, carnivorous plants are having another big moment as researchers begin to get answers to one of botany’s great unsolved riddles: How did typically mild-mannered flowering plants evolve into murderous meat-eaters?

Tales of killer plants were popular in the late 19th century. In 1887, American author James William Buel described the fantastical man-eating tree Ya-te-veo (“I see you”) in his book Land and Sea. (CREDIT: J.W. BUEL / PUBLIC DOMAIN)

Since Darwin’s discoveries, botanists, ecologists, entomologists, physiologists and molecular biologists have explored every aspect of these plants that drown prey in fluid-filled pitchers, immobilize them with adhesive “flypaper” leaves or imprison them in snap-traps and underwater suction traps. They’ve detailed what the plants catch and how — plus something of the benefits and costs of their quirky lifestyle.

More recently, advances in molecular science have helped researchers understand key mechanisms underpinning the carnivorous lifestyle: how a flytrap snaps so fast, for instance, and how it morphs into an insect-juicing “stomach” and then into an “intestine” to absorb the remains of its prey. But the big question remained: How did evolution equip these dietary mavericks with the means to eat meat?

Fossils have provided almost no clues. There are very few, and fossils can’t show molecular details that might hint at an explanation, says biophysicist Rainer Hedrich of the University of Würzburg in Germany, who explores the origins of carnivory in the 2021 Annual Review of Plant Biology. Innovations in DNA sequencing technology now mean that researchers can tackle the question another way, searching for genes linked to carnivory, pinpointing when and where those genes are switched on, and tracing their origins.

There’s no evidence that carnivorous plants acquired any of their beastly habits by hijacking genes from their animal victims, says Hedrich, although genes do sometimes pass from one type of organism to another. Instead, a slew of recent findings point to the co-option and repurposing of existing genes that have age-old functions ubiquitous among flowering plants.

“Evolution is sneaky and flexible. It takes advantage of preexisting tools,” says Victor Albert, a plant-genome biologist at the University at Buffalo. “It’s simpler in evolution to repurpose something than make something new.”

Road to predation

Quirky though it is, carnivory has evolved repeatedly over the 140 million-plus years that flowering plants have been around. The adaptation arose independently at least 12 times, says Tanya Renner, an evolutionary biologist at Penn State.

Each time, the driving force for evolution was the same: the need to find an alternative source of vital nutrients. Carnivorous plants grow in swamps and bogs, in nutrient-poor bodies of water or on thin tropical soils, all habitats short on the nitrogen and phosphorus essential for growth. Protein-packed insects and other small invertebrates are rich sources of both, as well as other elements plants need to flourish. “A Venus flytrap can live for three weeks on a single large insect,” says Hedrich. “If it captures lots of insects, it produces more leaves and more traps.”

Today there are some 800 known carnivorous species. Some, like pitcher plants and many sundews, are passive receivers of prey — albeit with ingenious adaptations such as slippery rims and gluey-tipped hairs that help to secure a meal. Others are more active: Some sundews curl inward, nudging prey into the trap’s stickier center, while a few have an outer ring of fast-moving tentacles that hurl victims to their doom. Most sophisticated of all is the Venus flytrap, Dionaea muscipula, with its sensitive trigger hairs and snap-traps that can distinguish the touch of an insect from a falling raindrop or dead leaf and can judge the size of prey and respond accordingly.

Despite huge differences in shape and form and mode of killing, all traps are modified leaves or parts of leaves. “That means these plants not only get nutrients from a different source but by a different route, primarily through their leaves rather than their roots,” says Renner. 

How did leaves come to perform such un-leaf-like functions? To find out, researchers have turned to a mix of “omics” techniques — genomics, transcriptomics and proteomics. They compare genomes of carnivorous and non-carnivorous plants; sequence the RNA transcripts that carry a gene’s instructions to see which genes are switched on where and when; and draw up inventories of proteins to find out which ones the traps manufacture at mealtimes.

New jobs for old genes

Many features of the carnivorous lifestyle have yet to give up their genetic secrets. But studies of two of its grislier elements — digestion and absorption — are revealing how evolution repurposed existing genes, putting some to work in new places and giving others new functions and the odd tweak to suit them better to their new roles. In many cases, plants that evolved carnivory entirely independently have repurposed the same genes. Faced with the problem of consuming flesh, they all hit on the same solution, Albert says. And central to the transformation was the plant’s age-old system of defense.

Back in the 1970s, researchers recognized that the digestive fluid they found in traps contained enzymes that functioned in very similar ways to many of the chemical weapons that plants wield against harmful bacteria, fungi and hungry herbivorous insects. Initially, it wasn’t clear whether carnivorous plants made the enzymes themselves or if microbes living in their traps did. Since then, botanists have confirmed that carnivorous plants do produce many of those enzymes and have discovered dozens more. Today’s fast and cheap sequencing technology has enabled molecular scientists to identify many of the genes encoding these digestive enzymes and to monitor their activity as plants trap and process prey.

The roster of enzymes includes chitinases, which break down the chitin of insect exoskeletons; flesh-dissolving proteases, which break down proteins; and purple acid phosphatase, which enables plants to extract usable phosphorus from their victims’ deconstructed corpses. All played roles in the ubiquitous and ancient defenses of flowering plants. “The genes for those enzymes were repurposed when plants started to eat the things they were originally protecting themselves from,” says Albert. “Chitinases most likely were for defense against fungi, which have chitin in their cell walls. Later, after arthropods evolved, they helped defend against them.” Protein-digesting enzymes also helped to repulse attackers.

Evolution’s tendency to adopt and adapt existing tools goes beyond digestion. As chitin, proteins and DNA are broken into smaller molecules, the trap must move them from the outside world to the inside of the plant. In ordinary plants, uptake of nutrients is the job of a root, where transporter proteins continually shuttle them from the soil into the plant. “You might not expect to find those proteins working in a leaf,” says Renner.

Yet that’s precisely what Hedrich’s colleague Sönke Scherzer found in the Venus flytrap as it processes prey: He recently identified transporters for two of the most vital plant nutrients, nitrogen and potassium. To enable a leaf to absorb nutrients, it seems, evolution co-opted root genes and put them to work somewhere new. The difference is that transporter genes are always active in roots, but in traps they are switched on only once nutrients begin to flow from decomposing prey.

The way of all flesh-eaters?

Co-option is an important driver of evolutionary innovation, and often begins with the accidental duplication of genes during cell division. Most duplicate genes serve no purpose and are eventually lost. But if spare genes acquire useful mutations, that can pave the way for a change in function. “Duplication of genes is always happening and sometimes it’s highly adaptive,” says Albert. This seems to have been the way carnivorous plants evolved their meat-eating abilities — at least for those genes examined so far. 

What came as more of a surprise was the discovery that whenever and wherever a new line of carnivores arose, evolution worked on the same genes.

In 2017, evolutionary biologist Kenji Fukushima, Hedrich’s colleague and coauthor of the 2021 Annual Review article, joined Albert and an international team of researchers to sequence the genome of an Australian carnivorous plant called Cephalotus follicularis. Like many carnivores, it traps prey in pitchers — in this case, small, squat, toothy-mouthed pitchers — but it sits on its own separate branch of the plant family tree.

Australia’s unique pitcher plant, Cephalotus follicularis, grows only in peaty swamps in the far southwest corner of the country. Genetic analysis of this species revealed how unrelated plants evolved meat-eating skills by co-opting and repurposing the same genes. (CREDIT: H. ZELL / WIKIMEDIA COMMONS)

The team identified many genes linked to different aspects of its meat-eating habits, from how the plant attracts prey to how it makes the inside of its pitchers too slippery for insects to escape. The big surprise came when they probed the origins of digestive enzymes in Cephalotus and three more, unrelated, species: Nepenthes alata (an Asian pitcher plant), the North American pitcher Sarracenia purpurea and a sundew, Drosera adelae. All of them, it turned out, had repurposed the same ancient enzymes — matching ones identified previously in the Venus flytrap. Between them, these five species represent three independent lines of carnivores. This was a classic case of convergent evolution, says Albert. It suggested there were only limited pathways to becoming a carnivorous plant.

Delving deeper, Fukushima discovered that convergent evolution went beyond co-opting the same genes. Once enzymes had taken on their new, carnivory-related roles, they continued to evolve, swapping some of their amino acids for others that improved their performance, probably by prolonging their activity in an inhospitable stew of protein-busting chemicals. Fukushima found the very same amino acid substitutions in unrelated plants.

Fly in the ointment

As they continue to explore carnivory, researchers are identifying many more enzymes. “But time and time again we’re finding that they have similar functions across distantly related species,” says Renner, who heads a major investigation into the role of co-option in the making of meat-eaters. Yet while that bolsters the idea that carnivorous plants acquired their new digestive skills in much the same way, there’s growing suspicion that the same might not be true for the all-important mechanism that controls the whole operation by switching on the right genes at the right time.

The chain of events in trapping and digestion is best understood for the Venus flytrap, the most scrutinized of carnivorous plants. If an unwary insect settles on one of its traps and touches one sensory hair, it triggers an electrical signal. If it touches a second hair — proof that it’s prey and not a speck of dirt or dead leaf — then the trap snaps shut.

As the insect struggles and sets off more electrical signals, the trap also begins producing chemicals called jasmonates, which provide the signal to seal the edges of the trap and start filling it with enzymes. As the insect corpse breaks down, the trap ratchets up its output of enzymes and starts production of nutrient transporters, again under the control of jasmonates. It’s a direct steal from the plant defense system, which responds to an insect attack by sending electrical signals to raise the alarm in neighboring cells — which then synthesize jasmonates, which then activate production of defensive proteins.

As it’s ubiquitous to all flowering plants, the jasmonate defense response is a prime candidate for recruitment to the cause of carnivory. In fact, says Renner, “our initial expectation was that the control process might be the same in all carnivorous plants.” And it does turn out to be the same for Nepenthes pitcher plants and sundews as well as flytraps, but those three belong to the same order of plants, so that’s not entirely surprising. Look beyond this trio, however, to the somewhat neglected butterworts, and there’s a tantalizing glimpse of otherness.

Butterwort (Pinguicula moranensis). Taken in situ in Oaxaca, Mexico. (Noah Elhardt / Wikimedia Commons / CC BY-SA 3.0)

Butterworts (Pinguicula) are unshowy plants, with small rosettes of leaves covered in tiny glands that ooze sticky mucilage and digestive enzymes. Most butterworts are entirely passive, although a few can curl the edges of their leaves inward, covering more of the insect in lethal goo. In 2020 the butterwort began to attract a lot more attention following a report from Andrej Pavlovič’s biophysics lab at Palacký University in the Czech Republic.

Pavlovič and his colleagues found that when they fed butterworts a generous helping of fruit flies, the plants responded by churning out enzymes, many of them the same as those identified in other carnivorous plants. So far, so similar. But when it came to the role of jasmonates in switching on production of enzymes, the story was very different.

As in other flowering plants, jasmonates orchestrate the butterwort’s defense against its enemies. Jabbing leaves 10 or 15 times with a needle to mimic attack by an insect prompted a big buildup of jasmonates in the leaves. Prey, on the other hand, triggered almost no response. The team tried another tactic, spraying jasmonate directly onto leaves: In Venus flytraps and sundews that produces a surge of digestive enzymes. In butterworts — zilch.

So butterworts do things differently, although exactly what they do is not yet known. “Butterworts have left us scratching our heads,” says Renner. “The question is, how many other carnivorous plants have figured out their own way?”

If Darwin were here today, he’d pile right in to solve the remaining mysteries of his “most wonderful plants.” He wouldn’t recognize the techniques modern investigators have at their disposal and would be amazed at the quantities of data that can be processed in seconds. But when it comes to designing elegant ways to test theories, he’d be on familiar ground. “Sequencing genomes, counting and analyzing genes are not enough,” says Renner. “You still have to do experiments to find out what genes do, and how they work.”

And that means feeding hungry plants. Darwin fed his on roast meat and hard-boiled egg, cheese, peas and other protein-packed morsels. Today the menu more often consists of less appetizing-sounding “substrate” dosed with precisely measured amounts of nitrogen — but there’s little doubt that Darwin would feel right at home.

This article How some plants became carnivorous predators is featured on Big Think.

Every day, we rely on our past experiences to make informed decisions. When we’re stuck in traffic, we quickly debate changing routes, recalling important information like the day of the week, time, and past traffic conditions. We use this information to determine which route is likely to be less congested at that moment.

This thought process is an example of “statistical inference,” in which we draw conclusions based on previous data. Scientists once believed that using statistical inference for decision-making was an exclusively human trait, akin to language. However, recent research challenges this notion by showing that crows exhibit impressive reasoning skills based on statistical inference.

The researchers, from the University of Tübingen in Germany, demonstrate that these birds can grasp how one choice may be optimal in one context but not in another — a bit like how one traffic route might be the go-to choice on a Monday, but not on a Saturday. They published their findings in the journal Current Biology.

Counting crows

The researchers trained two carrion crows to associate nine shapes with a probability of receiving food (from 10% to 90%). When the image appeared on a screen and the crow responded by pecking at it, the researchers rewarded the crow according to the associated probability. For example, if a crow pecked at an image of a cross that was assigned “20% probability,” the researchers would give it food 20% of the time.

Then, the task got trickier. Instead of flashing one symbol, two would appear on the screen. Now, the crow had to choose which image to respond to — and they had eight seconds to do it. If the crows used true statistical inference, the researchers expected them to peck at the shape with the highest probability of a reward. For example, if the cross image (assigned a 20% probability) appeared with another shape (like a square) assigned a 50% probability, the crow should pick the square.
However, if the 20% cross appeared with a shape associated with a 10% probability of reward, the cross is the better choice.

If the crows were pecking randomly and not making informed decisions, we would expect them to make the right choice 50% of the time. Instead, both crows selected the optimal shape 76% of the time. Furthermore, the crows seemed to understand the “game” immediately. Over the course of about 5,000 trials, their performances did not improve. They also easily retained the information; they kept up their performance a month later, without any reminders or additional training.

The crows were also better at making the right choice when the difference in probabilities between the options was larger. For example, when faced with a choice between a 50% and 10% chance of reward, they performed better than when the probabilities were closer, like 50% versus 40%. This finding suggests that they found it easier to understand extreme probabilities.

Statistical wizards

The researchers went a step further to understand how the crows made decisions. They wanted to figure out if the crows were simply picking the shape that had given them rewards the most times throughout the experiment (absolute frequency) or if they were thinking about the chance of getting a reward compared with the other choice (relative frequency).

To explore this idea, the researchers introduced two new stimuli in a second experiment: one associated with an 80% probability of receiving a reward and another with a 40% probability. During their training, the researchers showed the crows the choice with a 40% chance of getting a reward twice as often as the choice with an 80% chance. This setup made it such that if the crows always picked the 40% option, they would get the same number of rewards as if they had always picked the 80% option.

During the test, both crows consistently chose the 80% option, indicating their ability to compare probabilities rather than simply focusing on reward frequency.

Smarter than the average bird

It doesn’t end with statistical prowess. Crows can recognize faces and hassle scientists who had captured them for research in the past. They also create tools, like making “hooks” out of sticks to forage and then storing them carefully for later reuse. When a crow turns its eye toward you, it is not simply looking; it is also calculating.

This article Crows use statistical inference to make informed decisions is featured on Big Think.

Deep in the Bavarian woods of Southeast Germany roam scores of wild boars—prized game in a country where hunting is akin to a national tradition. But most hunters would think twice before venturing into the woods to chase these fat and fleshy pigs. Even if they track one and take it down, chances are they won’t be able to enjoy the meat. The boars are too dangerous to eat.

They are radioactive. 

In some cases, the Bavarian boars are several hundred times more radioactive than what’s considered safe for human consumption. The hunters are well aware of this phenomenon, typically attributed to the 1986 Chornobyl accident, during which radioactive fallout drifted over to Europe. (Chornobyl is the preferred spelling in Ukraine.) “Europe is pretty much a mess in terms of radioactive contamination,” says Georg Steinhauser, professor of physical radioecology at the Vienna University of Technology.

For a few years after the Chornobyl accident, all forest animals—including deer, hares, and pheasants—were highly radioactive. But eventually these levels waned in most game. Curiously, the wild boars remained radioactive. “The phenomenon of wild boars being so radioactive after such a long time has been termed the wild boar paradox,” says Steinhauser. “It’s so unusual. No other species does this.”

It turns out that the pigs picked up radioactive Cesium, a heavy metal, from eating Elaphomyces, a particular type of underground fungi they feed on, also known as deer truffles (humans eat a different variety). Unlike many other plants, fungi are really good at absorbing heavy metals from the soil in which they grow, says Steinhauser. They accumulate lead, cadmium, mercury, and in this specific case two radioactive heavy metal isotopes, Cesium 135 and Cesium 137.

For a long time, it was believed that the radioactive Cesium the boars carry in their bodies came from the Chornobyl accident. But a recent study conducted by Steinhauser and his colleagues pointed to other surprising sources: the atmospheric, or aboveground, nuclear bomb testing of 1940s to 1960s, before this toxic practice was stopped. 

Southern Bavaria gets more rain and snow than some other parts of Europe, concentrating the fallout from atmospheric testing in the soil. “The southern rim of Bavaria, which is where the Alps get really steep, has higher precipitation rates,” says Steinhauser—and that’s where the radioactive isotopes eventually flow and settle.

The boars are too dangerous to eat.

Prompted by Bavarian hunters, the researchers examined samples of wild boar meat. From 2019 to 2021, hunters sent wild boar samples to Leibniz University Hannover, where they were processed and analyzed for the presence of Cesium 135 and 137.

Cesium 137 is a product of both nuclear weapons explosions and nuclear reactor fission. However, Cesium 135 is mostly a product of nuclear explosions, so nuclear reactors generate very little of it. Calculating the ratio of Cesium 135 to Cesium 137 in a radioactive sample generates a “fingerprint,” says Steinhauser, that helps identify the origin of the radioactive contamination. “If the ratio is high, most of the radioactivity originated from nuclear weapons. If the ratio is low, then it’s mostly from a nuclear reactor.” The samples taken from Bavarian wild boars have a high ratio of Cesium 135 to Cesium 137, which indicates that the contamination must have come from nuclear bomb testing performed 60 to 80 years ago.

It is an eye-opening discovery because “nobody even thinks about nuclear weapons tests these days anymore,” says Steinhauser—but the radioactivity of wild boar meat in Bavaria will likely exceed safety limits for many more decades. While the radioactivity of the boars itself poses no health threats to humans who do not eat them, the disinterest of some European hunters in their meat has helped drive the explosion in population—to the point that the boars have begun venturing into cities and attacking humans. Germany and Austria are fortunate to not depend on wild boars for sustenance, Steinhauser says, but in other countries where hunting helps put food on the table—for example in Belarus—people are likely consuming Cesium-laden meat.

The scientists haven’t taken any stands on nuclear energy, Steinhauser says, but they do want to spread awareness that radioactive contamination persists in the food chain for generations. “Our study is a cautionary tale.”

This article The paradox of the radioactive boars is featured on Big Think.

Some 900 miles off the coast of Portugal, nine major islands rise from the mid-Atlantic. Verdant and volcanic, the Azores archipelago hosts a wealth of biodiversity that keeps field research scientist, Marlon Clark, returning for more. “You’ve got this really interesting biogeography out there,” says Clark. “There’s real separation between the continents, but there’s this inter-island dispersal of plants and seeds and animals.”

It’s a visual paradise by any standard, but on a microscopic level, there’s even more to see. The Azores’ nutrient-rich volcanic rock — and its network of lagoons, cave systems, and thermal springs — is home to a vast array of microorganisms found in a variety of microclimates with different elevations and temperatures.

Clark works for Basecamp Research, a biotech company headquartered in London, and his job is to collect samples from ecosystems around the world. By extracting DNA from soil, water, plants, microbes and other organisms, Basecamp is building an extensive database of the Earth’s proteins. While DNA itself isn’t a protein, the information stored in DNA is used to create proteins, so extracting, sequencing, and annotating DNA allows for the discovery of unique protein sequences.

Using what they’re finding in the middle of the Atlantic and beyond, Basecamp’s detailed database is constantly growing. The outputs could be essential for cleaning up the damage done by toxic chemicals and finding alternatives to these chemicals.

Catalysts for change

Proteins provide structure and function in all living organisms. Some of these functional proteins are enzymes, which quite literally make things happen.

“Industrial chemistry is heavily polluting, especially the chemistry done in pharmaceutical drug development. Biocatalysis is providing advantages, both to make more complex drugs and to be more sustainable, reducing the pollution and toxicity of conventional chemistry,” says Ahir Pushpanath, who heads partnerships for Basecamp.

“Enzymes are perfectly evolved catalysts,” says Ahir Pushpanath, a partnerships lead at Basecamp. ”Enzymes are essentially just a polymer, and polymers are made up of amino acids, which are nature’s building blocks.” He suggests thinking about it like Legos — if you have a bunch of Lego pieces and use them to build a structure that performs a function, “that’s basically how an enzyme works. In nature, these monuments have evolved to do life’s chemistry. If we didn’t have enzymes, we wouldn’t be alive.”

In our own bodies, enzymes catalyze everything from vision to digesting food to regrowing muscles, and these same types of enzymes are necessary in the pharmaceutical, agrochemical and fine chemical industries. But industrial conditions differ from those inside our bodies. So, when scientists need certain chemical reactions to create a particular product or substance, they make their own catalysts in their labs — generally through the use of petroleum and heavy metals.

These petrochemicals are effective and cost-efficient, but they’re wasteful and often hazardous. With growing concerns around sustainability and long-term public health, it’s essential to find alternative solutions to toxic chemicals. “Industrial chemistry is heavily polluting, especially the chemistry done in pharmaceutical drug development,” Pushpanath says. 

Basecamp is trying to replace lab-created catalysts with enzymes found in the wild. This concept is called biocatalysis, and in theory, all scientists have to do is find the right enzymes for their specific need. Yet, historically, researchers have struggled to find enzymes to replace petrochemicals. When they can’t identify a suitable match, they turn to what Pushpanath describes as “long, iterative, resource-intensive, directed evolution” in the laboratory to coax a protein into industrial adaptation. But the latest scientific advances have enabled these discoveries in nature instead.

Enzyme hunters

Whether it’s Clark and a colleague setting off on an expedition, or a local, on-the-ground partner gathering and processing samples, there’s a lot to be learned from each collection. “Microbial genomes contain complete sets of information that define an organism — much like how letters are a code allowing us to form words, sentences, pages, and books that contain complex but digestible knowledge,” Clark says. He thinks of the environmental samples as biological libraries, filled with thousands of species, strains, and sequence variants. “It’s our job to glean genetic information from these samples.”

Basecamp researchers manage this feat by sequencing the DNA and then assembling the information into a comprehensible structure. “We’re building the ‘stories’ of the biota,” Clark says. The more varied the samples, the more valuable insights his team gains into the characteristics of different organisms and their interactions with the environment. Sequencing allows scientists to examine the order of nucleotides — the organic molecules that form DNA — to identify genetic makeups and find changes within genomes. The process used to be too expensive, but the cost of sequencing has dropped from $10,000 a decade ago to as low as $100. Notably, biocatalysis isn’t a new concept — there have been waves of interest in using natural enzymes in catalysis for over a century, Pushpanath says. “But the technology just wasn’t there to make it cost effective,” he explains. “Sequencing has been the biggest boon.”

AI is probably the second biggest boon.

“We can actually dream up new proteins using generative AI,” Pushpanath says, which means that biocataylsis now has real potential to scale.

Glen Gowers, the co-founder of Basecamp, compares the company’s AI approach to that of social networks and streaming services. Consider how these platforms suggest connecting with the friends of your friends, or how watching one comedy film from the 1990s leads to a suggestion of three more.

“They’re thinking about data as networks of relationships as opposed to lists of items,” says Gowers. “By doing the same, we’re able to link the metadata of the proteins — by their relationships to each other, the environments in which they’re found, the way those proteins might look similar in sequence and structure, their surrounding genome context — really, this just comes down to creating a searchable network of proteins.”

Uwe Bornscheuer, professor at the Institute of Biochemistry at the University of Greifswald, and co-founder of Enzymicals, another biocatalysis company, says that the development of machine learning is a critical component of this work. “It’s a very hot topic, because the challenge in protein engineering is to predict which mutation at which position in the protein will make an enzyme suitable for certain applications,” Bornscheuer explains. These predictions are difficult for humans to make at all, let alone quickly. “It is clear that machine learning is a key technology.”

Benefiting from nature’s bounty

Biodiversity commonly refers to plants and animals, but the term extends to all life, including microbial life, and some regions of the world are more biodiverse than others. Building relationships with global partners is another key element to Basecamp’s success. Doing so in accordance with the access and benefit sharing principles set forth by the Nagoya Protocol — an international agreement that seeks to ensure the benefits of using genetic resources are distributed in a fair and equitable way — is part of the company’s ethos. “There’s a lot of potential for us, and there’s a lot of potential for our partners to have exactly the same impact in building and discovering commercially relevant proteins and biochemistries from nature,” Clark says.

Bornscheuer points out that Basecamp is not the first company of its kind. A former San Diego company called Diversa went public in 2000 with similar work. “At that time, the Nagoya Protocol was not around, but Diversa also wanted to ensure that if a certain enzyme or microorganism from Costa Rica, for example, were used in an industrial process, then people in Costa Rica would somehow profit from this.”

An eventual merger turned Diversa into Verenium Corporation, which is now a part of the chemical producer BASF, but it laid important groundwork for modern companies like Basecamp to continue to scale with today’s technologies.

“To collect natural diversity is the key to identifying new catalysts for use in new applications,” Bornscheuer says. “Natural diversity is immense, and over the past 20 years we have gained the advantages that sequencing is no longer a cost or time factor.”

This has allowed Basecamp to rapidly grow its database, outperforming Universal Protein Resource or UniProt, which is the public repository of protein sequences most commonly used by researchers. Basecamp’s database is three times larger, totaling about 900 million sequences. (UniProt isn’t compliant with the Nagoya Protocol, because, as a public database, it doesn’t provide traceability of protein sequences. Some scientists, however, argue that Nagoya compliance hinders progress.)

“Eventually, this work will reduce chemical processes. We’ll have cleaner processes, more sustainable processes,” says Uwe Bornscheuer, a professor at the University of Greifswald.

With so much information available, Basecamp’s AI has been trained on “the true dictionary of protein sequence life,” Pushpanath says, which makes it possible to design sequences for particular applications. “Through deep learning approaches, we’re able to find protein sequences directly from our database, without theneed for further laboratory-directed evolution.”

Recently, a major chemical company was searching for a specific transaminase — an enzyme that catalyzes a transfer of amino groups. “They had already spent a year-and-a-half and nearly two million dollars to evolve a public-database enzyme, and still had not reached their goal,” Pushpanath says. “We used our AI approaches on our novel database to yield 10 candidates within a week, which, when validated by the client, achieved the desired target even better than their best-evolved candidate.”

Basecamp’s other huge potential is in bioremediation, where natural enzymes can help to undo the damage caused by toxic chemicals. “Biocatalysis impacts both sides,” says Gowers. “It reduces the usage of chemicals to make products, and at the same time, where contamination sites do exist from chemical spills, enzymes are also there to kind of mop those up.”

So far, Basecamp’s round-the-world sampling has covered 50 percent of the 14 major biomes, or regions of the planet that can be distinguished by their flora, fauna, and climate, as defined by the World Wildlife Fund. The other half remains to be catalogued — a key milestone for understanding our planet’s protein diversity, Pushpanath notes.

There’s still a long road ahead to fully replace petrochemicals with natural enzymes, but biocatalysis is on an upward trajectory. “Eventually, this work will reduce chemical processes,” Bornscheuer says. “We’ll have cleaner processes, more sustainable processes.”

This article Scientists find enzymes in nature that could replace toxic chemicals is featured on Big Think.

Evolution is in a perpetual cycle of churning out new pathogens. Luckily for us humans and many other animals, we have a very advanced immune system — known as the adaptive immune system — that allows our bodies to very precisely target pathogens using antibodies and a whole host of other weapons, like T cells. When we get vaccinated against a disease-causing organism such as measles or COVID, we are prepping this adaptive immune system for future encounters with the pathogen.

Plants lack this. While they do have a more general immune system — known as innate immunity — it is not nearly as precise or powerful as adaptive immunity. While this innate immune system has withstood the test of time, it leaves plants, including important food crops, vulnerable to new strains of pathogens.

What if it was possible to bioengineer plants to have an adaptive immune system? That’s precisely what Jiorgos Kourelis and his colleagues did, and their results were reported in the journal Science. Their method could provide a path toward the long-sought goal of rapidly and precisely modifying susceptible crop species to give them resistance to emergent pathogens and pests.

An evolutionary dance

Plant immunity can be divided into cell-surface and intracellular immunity. Coating the surface of plant cells, immune receptors monitor for ancient pathogen-associated molecular patterns (PAMP). These are non-specific markers that simply indicate a microbial threat is present. A rough analogy is a security camera. The immune receptors act like security cameras, setting off an alarm when they recognize something suspicious, say, a person with a mask (this is the pathogen-associated molecular pattern in this analogy) trying to break into the house. But the camera isn’t precise enough to determine who it is.

When these surface-bound receptors are triggered, they initiate a cascade of protective measures that kill the pathogen. To avoid this, pathogens have evolved to release an arsenal of immune sabotaging agents called effectors, which are injected into plant cells to disrupt cellular functions. In response, plants have evolved their own strategy to counteract effectors. They use a repertoire of intracellular immune receptors called NLRs (nucleotide-binding, leucine-rich repeat immune receptors) that recognize and neutralize pathogen effectors.

For millions of years, plants and pathogens have engaged in a never-ending evolutionary dance, with plants evolving NLRs that can detect and disarm pathogen effectors, and pathogens evolving effectors that are undetectable by plant NLRs.

However, when this evolutionary dance affects a staple food crop, it can pose a serious threat to millions of people. For example, a single fungal pathogen, Magnaporthe oryzae, is responsible for 30% of rice production loss globally, destroying food that could have fed 60 million people. That’s why scientists like Kourelis want to find ways to give crops a little help.

A hybrid plant-animal immune system

The part of the NLR protein that recognizes suspicious pathogenic molecules is called an integrated domain (ID). Scientists have identified a few hundred unique IDs in rice plants, suggesting that the plants can detect a few hundred different effectors. That might sound like a lot, but remember that plants possess a generic immune system capable of recognizing only general patterns. The antibodies produced by humans, on the other hand, have the potential to recognize one quintillion (one million trillion) different and highly precise molecular patterns.

Given that the animal adaptive immune system can generate antibodies against virtually any foreign protein it is exposed to, Kourelis and his team wondered if they could harness the power of antibodies to help plants fight against pathogens. In a proof-of-principle study, Kourelis modified a protein called Pik-1, one of the NLRs produced by a rice plant. The team replaced Pik-1’s ID region with an antibody fragment that binds to fluorescent proteins. Next, they exposed bioengineered and control (unaltered) plants to a pathogen (Potato virus X) that itself was genetically modified to express fluorescent proteins. The bioengineered plants showed significantly less fluorescence, suggesting that the NLR-antibody hybrid molecules produced by the plants successfully blocked the virus from replicating.

The authors suggest that this technology could yield “made-to-order resistance genes” to protect crops against pathogens and pests. That would be a welcome development for the world’s farmers and the people they feed.

This article Scientists bioengineer plants to have an animal-like immune system is featured on Big Think.

Bacteriophages, known simply as “phages” for short, are viruses that infect and kill bacteria. Essentially harmless to humans, they exist solely to inject their genes into bacterial cells, where they can either lurk indefinitely or replicate madly. In the latter case, they cause their unfortunate host’s metabolism to go haywire, churning out copies of the virus instead of the mater­ials it needs to sustain itself. When the time is right, the new viruses burst the bacteria open like a popped water bomb and spill out to find new hosts in which to repeat the process.

The vast majority of these viruses are so-called “tailed” phages. Along with a sinister-looking 20-faced head, known as a capsid, these viruses have a distinctive protein tube, or tail, which they use to inject their DNA into their unfortunate host like a tiny syringe. Even finer, spider-like legs fold out from the base of the phage to help it detect and bind to the surface of the bacterial cell, like an unfathomably tiny lunar lander.

Confusingly, bacteria and viruses are often grouped together simply as “germs,” but they are distinct in important ways. The most basic difference between them is that bacteria are cells and viruses are not. Cells are biology’s basic units of life — microscopic capsules with everything needed for life and replication contained within a fat-based membrane and, sometimes, a tough outer wall. All life on the planet — except viruses — consists of cells, either working in concert with one another (like the human body, for example, a network of trillions of related cells arranged to form tissues and organs) or existing just fine as single cells.

Viruses, conversely, are far less complex. At their simplest, they are little more than a length of genetic material (normally DNA, deoxyribonucleic acid, but sometimes its chemical cousin, RNA, ribonucleic acid) wrapped in a protective protein capsule. Outside of a host, they are inert, lifeless even, lacking the biochemical components to do anything with the information contained in their genes.

In order to replicate, the virus must get inside a cell. Viruses have been described as living “a kind of borrowed life,” only ever able to exert an influence on the world when inside a host cell. It’s a little like how a computer virus is just a piece of code on a USB stick — unable to do anything when lying in a drawer — until it is placed into a computer, when it can suddenly instruct that computer’s systems to send copies of itself to a thousand inboxes around the world. This reliance on other life is, in part, why there has always been a debate over whether viruses are “alive” or not. To me, the question is unhelpful, suggesting that viruses are somehow not a proper, paid-up member of our wonderful living world.

Whether or not viruses meet the criteria we have decided characterizes a distinct living being, they are an essential biological component of the ecosystems that have developed on Earth. They are built from the same basic building blocks as life, use the same chemical language as life, evolve and replicate alongside life, and interact with and transform life. Some scientists believe that all life may have evolved from self-replicating entities more akin to viruses than cells. And by operating in the fascinating and illuminating grey area where complex chemistry becomes simple biology, they can arguably tell us more about what life is than living creatures so complex that they may never be fully understood.

For every type of cellular life on earth — bacterial, fungal, animal or plant, and the weird things somewhere in between — there are viruses that have evolved to infect them, and together these viruses outnumber all other living entities on Earth. While we commonly associate viruses with disease and death, just a tiny fraction are a danger to us. The vast majority are phages. And it is only very recently that we have begun to understand that phages are an essential part of the living fabric of the planet, drivers of innovation, diversification and change.

Bacteria are also essential to all life on Earth. Although we have “learnt to hate and fear them,” as the science writer Ed Yong puts it, just a hundred or so of the many thousands of species of bacteria in the world colonize our body in a way that makes us ill or causes disease. Even these mostly live quite happily on and around us without our noticing, only causing ill health when a vulnerability in our immune systems is exposed. The rest perform a suite of essential environmental services that make our planet hospitable. They capture chem­ical and solar energy to form the foundational layer of the food chains that support the rest of life on Earth; they take inorganic material, waste products, and dead things and re­cycle them back into forms that can be used by other life. They produce 20% of the atmospheric oxygen we breathe. They help us digest our food, help plants absorb nutrients, protect us from other microbes, and ferment some of our favorite foods. They have adapted and co-evolved to live in almost every environmental niche on the planet, from boiling vents at the bottom of the sea to the internal organs and tissues of other life, from lakes with the acidity of battery acid to the nodules in the roots of our most important crops.

They, and other similar single-celled life that together are known as prokaryotes, have been growing and multiplying on Earth ceaselessly for almost four billion years, since life first emerged on our scorching, primordial rock. Among the most ancient forms of life on the planet, they have evolved into thousands, probably millions of different species, exploiting and colonizing virtually every environment possible. They are literally everywhere. Just on the sponge in your kitchen sink, there are probably more bacteria than the total number of humans who have ever lived.

For as long as all this bacteria has been around, however, phages have been perfecting the art of infecting and destroying them. For every single one of the immense number of bacter­ial cells on the planet, there are thought to be at least ten phages — perhaps more. Anywhere and everywhere a bacterial strain has evolved to exploit an ecological niche, there will be viruses that have evolved to exploit that bacteria. This makes these seemingly obscure viruses easily the most abundant biological entity on Earth.

Sail out into the middle of the ocean and scoop up a cup of water and it will contain millions, possibly hundreds of millions of phages. Take some water from a briny marsh or your local stream, a caustic alkaline lake, or a scorching hydrothermal vent and still you’ll find millions of phages in every milliliter. On land, there can be even higher concentrations — billions of phages in a single gram of rich soil. Even a gram of baked desert earth or frozen Arctic peat contains an active community of millions of phages, locked in a never-ending dance with their bacterial hosts.

There are so many phages on this planet that they can even be found floating in thin air. When one group of researchers installed collection devices on a concrete platform almost 3 km above sea level in the Sierra Nevada mountains in Spain, they found that hundreds of millions and sometimes billions of viruses rained down onto their equipment every day. Researchers estimate there may be as many as 10³¹ phages on Earth — that’s 10 with 30 zeros after it — a truly preposterous number that equates to around a trillion phages for every grain of sand on the planet. The biologist J.B.S. Haldane famously quipped that if God created all the living organisms on Earth, then the creator must have “an inordinate fondness for beetles”: it seems God is even fonder of bacterial viruses.

This article Phage: The most abundant life form on Earth has a unique license to kill is featured on Big Think.

Let’s begin, as so many things do, with Aristotle. His view of life was a hierarchy called “The Ladder of Life” (or Scala Naturae in Latin). He set inanimate life at the bottom and humans at the top of the ladder (angels and gods and such would be added later by others as the ladder transformed into the “Great Chain of Being”). 

Aristotle’s work was the most important influence on the West’s understanding of the natural world for more than 1,000 years, and the Ladder of Life/Great Chain of Being metaphor is still how many people understand (or rather misunderstand) evolution — that is, as a linear process with bacteria and plants at the bottom as “primitive” and a straight line from fish → amphibians → reptiles → mammals and then humans as a distinct category at the top.

The problem with that antiquated, single-file view of how life is organized is that it makes you think of life as evolving in a straight line. Even people who accept evolution can get things wrong by taking this linear view. They see all other living things besides us as subordinate precursors leading to humans. They see chimpanzees as a step before humans as if we evolved directly from them. With that view, they see chimps and other apes as “primitive” antecedents of humans, which they are not. They also see a fish as a step before a frog, and a frog as a step before an alligator or some other reptile. 

Linear thinking can result not only in a very poor understanding of evolution but also in a distorted sense of ourselves, especially when we push this thinking to include socially constructed views of human races and genders.

In his bestselling, overtly macho self-help book 12 Rules for Life, Jordan B. Peterson argues in “Rule 1” that you should “Stand up straight with your shoulders back,” building his argument based on the mistaken notion that our ancient shared ancestry with lobsters means we should somehow maintain certain shared innate behaviors with them. Peterson explains how lobsters that are the victors of battles have upright postures: Only losers slouch. Okay, I suppose slouching is bad, but we are not lobsters, nor did we evolve from them. We do share a common ancestor with them, however, we share common ancestors with all living things on Earth, and one of those ancestors gave us some common hormones like serotonin (which we have in common with many other multicellular life forms — pineapples have serotonin, for instance). 

We did not receive our behavioral traits from some lobster ancestor, as implied by Peterson. And why cherry-pick behaviors anyway? Why not fixate on how some species of lobsters form “Conga lines,” marching in long, single-file migrations. Apparently, that part of lobster behavior isn’t something he thought relevant to the modern-male human condition.

In the same book, Peterson argues that human sexuality and gender are essentially fixed because sex and distinct sexes were invented millions of years ago, and that the mother/father-child relationship is the oldest in our evolutionary history. But if you look closer at that evolutionary history or throughout the Tree of Life, asexual reproduction is certainly the oldest form of reproduction (many bacteria and archaea are clonal). There are also all-female species (like Amazon mollies, Poecilia formosa), multisex/intersex/no-sex species (as in many fungi that have “mating types” or slime molds that have hundreds of “sexes”), species that change sex (many fish species), and, indeed, there are species that reproduce without needing to find a mate (again, asexual reproduction) in every phylum of the animal kingdom. You could certainly argue for a variety of sexualities being “age-old.” 

The misguided linear view of life — this false hierarchy — led some people to argue that white men are at the top of the evolutionary ladder, a convenient argument to enslave people of “lesser” races or to keep the womenfolk at home barefoot and pregnant. But this kind of thinking is insidious and, in its worst form, leads to racism, classism, sexism, transphobia, homophobia, and all manner of pernicious prejudices.

To be fair, for a long time most Tree of Life illustrations (many by well-meaning people) almost always picked an image of an old white guy to represent all of humanity — “man” — on the branch that represents humans, even though a child, a woman, or Jackie Chan could also have been picked to represent “man.” Nothing against old white men, but representation matters; seeing a member of the same subgroup of humans represented as the ideal human on nearly every evolutionary tree is damaging, and evolutionary biologists need to do better. 

We also tend to draw these trees with single-celled or “primitive” living things on the left, and humans on the right, which again gives the impression that evolution is linear; but because the descendants from the same node are “sister lineages” that can be flipped, you can also draw the tree with humans in the middle without any of the relationships depicted changing.

Let’s go back to Aristotle’s hierarchy. Most people today don’t think of humans as having evolved from plants or fungi, so those who conceptualize evolution see that there was at least some distinct branching off from different forms of life. We often visualize the evolution of life as a branching tree, as in the Tree of Life, but there are other ways of visualizing it. Many people revert to the mistaken linear view because it is easy to organize the evolution of life with us humans at the end and everything else behind us. 

But it would be much more accurate if we visualized the evolution of life as a bush or bursting firecracker, expanding from a center. The living things around us are part of a process that started billions of years ago, with every living thing alive today nearly equidistant from a center point. 

Think of the origin of life as the “Big Birth,” like the Big Bang that formed our universe, except with life radiating out from that center (first living thing, or last common ancestor of all living things), and with us and every other living species on the outer edge. The fossil forms from millions and billions of years ago are closer to that center; they are long extinct, as are many other forms of life from the past that have left no trace. Just like a fading firework in the sky, when the center has burst and faded into darkness, all that remains are the flaming edges expanding outward: These are the forms of life we see living today, and it is just a little snapshot of the evolutionary history of life.

This article The Great Chain of Being: The evolutionary misconception that just won’t go extinct is featured on Big Think.

Bob Vonderheide, a friend and colleague who studies cancer and immunology, teases me for having once remarked, “You are a developmental biologist, Bob, you just don’t know it.”

My lighthearted statement was a throwback to the notion that almost all fields of biomedical research —​ cell biology, genetics, physiology, immunology, cancer biology, neuroscience — ​have their roots in the study of embryonic development. Theodosius Dobzhansky, the Ukrainian-​born biologist who helped unify evolutionary biology and genetics, is most famous for stating, “Nothing in biology makes sense except in the light of evolution.” But he could just as easily have asserted that nothing in biology makes sense except in the light of development. Embryogenesis is as central to the body’s operations as a building’s architectural designs and assembly are to its flow and structural integrity.

Nearly two centuries have passed since we realized that life is built from cells, and embryos have been among our best teachers and guides ever since. Sea urchin blastomeres (the cells of the early embryo) and fly larvae gave us a road map for understanding the mechanics of heredity, while a command of mouse embryology provided an entry point for modeling human diseases and mastering the alchemy of reprogramming. Thanks to the teachings of these diverse animal species, we have a much clearer picture of how we humans come into existence.

Still, there is much we don’t know. Some of the most basic questions — ​What controls an organ’s shape and size? What determines life span? How does development foster consciousness? — remain confined to the land of night science. Although the answers to these questions may elude us for some time, we can use what we have already learned to develop new therapies. We have seen a sampling of these remedies — ​cell therapies for cancer and degenerative diseases, DNA editing to correct inborn genetic errors, novel reproductive technologies — ​but the biggest breakthroughs to come will probably be the ones we haven’t yet conceived of.

Embryonic development has the effect of changing your perception of time. In our day-​to-​day (postnatal) lives, change comes slowly. The transitions our bodies make as we mature from toddlers to young adults and from young adults to old adults are subtle, recognizable only if we look for them across the span of months or years. But during development, things happen quickly. Dramatic changes can occur in the span of hours. In less than a day, a sheet of cells may roll itself into a tube, or an organ may “bud” like a seedling erupting from the ground. And yet, the embryo also embodies a greatly protracted timescale, as it reflects “designs” worked out over hundreds of millions of years. Observing an embryo mature is like viewing two sets of overlapping time-​lapse images at once — ​one developmental and one evolutionary — ​intersecting in the present. It is a backstage peek at nature’s grandest production.

Despite working with embryos for more than 20 years, I still have no answer to the question that stumped Aristotle and drove developmental biologist Hans Driesch to the paranormal: What life force, or entelechy, compels the inanimate substances surrounding us to self-​assemble into cells, embryos, tissues, and bodies? At an intellectual level, it is easy enough to view it all as a matter of chemistry, an assortment of organic reactions, each governed by a thermodynamic calculation taking the reactants to a lower energy state. But at a gut level, this remains unsatisfactory. It is something the mind can know but not comprehend, like the near impossibility of perceiving that there are more stars in the universe than grains of sands on earth.

As cosmologist Carl Sagan asserted, “Science is not only compatible with spirituality; it is a profound source of spirituality.” He was right. Most parents will tell you that there is no experience in life as transcendent as the birth of a child, with its mix of jubilation, humility, and awe. This was certainly the case for me. And yet my sense of wonderment — ​my spirituality — ​has only grown as my understanding of embryonic development has ripened.

As human beings, we tend to focus on our differences, which too easily blind us to our far-​more-​abundant similarities. That we all began unpretentiously, as a single cell, should be a source of solidarity, a reminder of our deep and irrevocable connections. Viewed from this vantage point, and embracing our shared origin, it is much easier to celebrate, rather than disparage, our differences.

“Every one of us is, in the cosmic perspective, precious,” Sagan reminds us. “If a human disagrees with you, let him live. In a hundred billion galaxies, you will not find another.”

This article How a single human cell connects us to the spiritual essence of Carl Sagan’s cosmos is featured on Big Think.

Genes are needed in development and tissue maintenance, but from the laying out of the body plan to the organization and functioning of our nervous system, cells rule their expression and make us who and what we are.

Throughout the 20th century and continuing to the present day, the common assumption has been that our identity is tightly linked to our DNA. While there’s some truth here — as Shakespeare said, “What’s past is prologue” — when it comes to development, cells and genes have very different relationships with history. It is therefore worth pausing for a moment to recap briefly the reasons behind the dominant view of the genome as the master of our being. 

This view lies in the essence of DNA, those strings of Gs, Cs, As, and Ts that configure the hardware store catalogue that is your genome. This catalogue has been updated over millions of years and is unique to each of us, not in its repertoire of tools and materials but in their colors and design details. It is through these subtle differences that, in the same manner you can follow the transformation of the clumsy computers of the 1950s into your iPhone, you can trace history in your genome, a history based on the relatedness of the differences and similarities of the script. Add some historical narrative to these genetic relationships — genealogies — and you will have ancestries, lineages that, so you are told, link you to remote people and places and, if you go back far enough, link all people to each other.

We humans feel a great need to belong, to know our origins, and because we’ve been fixated on genes over the past hundred years, we’ve been using the language of genetics to write our stories. The big hitters in commercial DNA testing, Ancestry.com and 23andMe, together maintain the genomes of more than 30 million people in their books. Based on these data, you might be told you’re 37% Western Bantu, 27% Germanic, 26% Scottish, and 10% Nigerian, give or take 10 to 20%, or that 2% of your DNA is Neanderthal (as it is, on average, for all people living today, because of how humans evolved). Some companies claim the ability to compare your DNA to that of, say, Vikings, ancient Egyptians, Chumash Indians, and other populations who lived a few thousand years ago. To be descended from a pharaoh! 

There’s immense allure to imagining connections to such remote peoples, places, and times. But as the organization Sense About Science says of such claims, “They are little more than genetic astrology.” Geneticist Adam Rutherford has also rightly pointed out that if you go back far enough — and “far enough” isn’t all that long ago in human history — we’re all related to each other. This is a fact. The tools and fixtures in the genome are what we need to be an animal, a primate, a human, so it’s not very remarkable that there’s so much overlap.

Genetic ancestries can be quantified, saying that we are 50% this or 25% that, but what do these numbers really mean? Do these numbers say anything about who we are today? A history of our species may be carried in our genome, but our genome does not make us who and what we are.

An equally interesting view of human history is contained in the story of how our cells create us, division by division, starting from the zygote’s very first division and building differences along the way. Recall the feature of embryonic development first noticed by Karl Ernst von Baer: that, just after gastrulation, the process that lays down the blueprint of an organism, we look very similar to a chicken, fish, and frog. The similarities in animal embryos connect us to the first multicellular organisms. Eukaryotic cells — those with a “true,” or well-formed, nucleus — began to use the genome in novel ways, controlling genes so that they could come together to build a robust, efficient organism that could conquer the planet. 

To achieve this, cells found a handful of approaches that worked well, such as a bilaterian body plan (mirrored left and right sides) and gastrulation. Across all animals, cells draw upon the same set of tools and fixtures to lay the foundation for the body. Then, after gastrulation, they go their separate ways, building species-specific features and unique, individual beings, based on their interactions with each other and, because we’re mammals, our intercellular connections to our mother. The process of building does not end at birth; it continues throughout our lifetimes, so long as our stem cells generate new cells to keep our bodies running in good form.

Our genes aren’t our identity, no matter what the DNA testing companies say in their advertising campaigns. Indeed, these companies use the DNA from people’s tests to research how diseases caused by a single genetic mutation might be treated. In other words, they know that genes are tools, and they’re looking for ways to capitalize on the fact that these tools can sometimes be repaired.

This article Ancestry tests are “genetic astrology.” We must re-learn everything we know about DNA and cells is featured on Big Think.

For 35 years, Discovery Channel’s annual Shark Week has entertained audiences with shows about our fishy, elasmobranch friends. Unfortunately, however, Shark Week often does sharks (not to mention humans) a disservice, sharing a staggering amount of incorrect or wildly misleading information, as a group of marine biologists reported last year after watching every Shark Week episode ever broadcast. This year, Discovery Channel continued this regrettable trend with the release of “Cocaine Sharks” last week.

“Cocaine Sharks”

No doubt intended to mirror the viral success that was Cocaine Bear, a movie released earlier this year about a bear that goes on a murderous rampage after consuming a large amount of cocaine discarded in the woods, “Cocaine Sharks” represents an attempt to explore whether sharks off the Florida Keys are getting high on and even addicted to cocaine occasionally dropped by drug smugglers in the coastal waters, potentially turning them hyperactive and aggressive. For decades, newspaper stories have highlighted how bundles of cocaine wash up on Florida’s shores after apparently being lost by smugglers. The reports are echoed by fishermen who have told tales of sharks biting into the bundles and becoming hyperactive and aggressive.

In “Cocaine Sharks,” marine biologist Tom Hird and environmental scientist Tracy Fanara teamed up to test whether there is any truth to these claims. They first jumped into shark-filled waters off the Florida Keys and observed local lemon, sandbar, and hammerhead sharks, watching for any unusual behavior potentially indicative of cocaine exposure. This was a fruitless exercise, as cocaine is a fairly fast-acting and rapidly-metabolized drug, so they would never be able to conclusively attribute any abnormal behavior to cocaine. After noting some “tweaked” behavior in a potential “junkie shark,” they concluded their dive, subsequently admitting that nobody knows what a shark high on cocaine looks like.

Hird and Fanara then conducted an experiment, plopping a few square, white bundles in the water meant to mimic bales of cocaine. Nearby, they positioned a few plastic swans, intended to represent a sleeping pelican, potential prey for the sharks. Would the sharks be more interested in the bundles or the swans, they wondered? While the methodology wasn’t exactly rigorous, the duo found that the local sharks seemed more interested in the bundles, even taking a bite or two out of them. While Hird noted that this simply could be because the bundles are an interesting new thing in their environment, the experiment showed that sharks may interact with floating bundles of cocaine, potentially getting high and transforming into “cocaine sharks.”

For fish, cocaine is an anesthetic

But what would a cocaine shark even look like? Cocaine acts on dopamine transporters in the brain, blocking the recycling of this “pleasure hormone” and allowing it to build up in synapses, producing feelings of euphoria and alertness but also potentially resulting in panic, hyperactivity, and even aggression when consumed in large amounts. Hird and Fanara dropped a bunch of dried fish powder into the water, suggesting that this tasty treat might mimic the effects of cocaine on sharks. Swimming through the fish powder, the sharks certainly got excited, but there’s no way to know if cocaine would create the same effect.

In the past, scientists actually have given cocaine to zebrafish, a popular animal model in research, and it didn’t seem to have much of an effect on their behavior. Throughout “Cocaine Sharks,” viewers were frequently shown a video of jumping, hyperactive salmon in a tank and told that they were high on cocaine. But this was misleading. The video was shot at a German fish farm where authorities subsequently found that the water tanks had been contaminated by a polluted stream nearby, distressing the fish. While they did find cocaine and other chemicals in the stream, cocaine was not present in the fishes’ habitat.

For the grand finalé of “Cocaine Sharks,” Hird and Fanara had a plane drop white bales full of fish powder into the water, causing quite a frenzy among the local sharks. Would a cascade of tightly wrapped cocaine bundles prompt similar excitement? It’s impossible to know for sure, but it’s probably unlikely considering there wouldn’t be anything sumptuous for the sharks to smell.

Hird and Fanara conclude “Cocaine Sharks” by calling attention to the sad fact that our oceans have become dumping grounds for all sorts of human-made chemicals, including illicit drugs, harming animals and ecosystems. They do not, however, conclude that “cocaine sharks” are real — probably because they aren’t. The amount of cocaine dropped off the Florida Keys isn’t enough to get the local wildlife hooked, nor do we even know that it would get them high. As reported by the Palm Beach Post, Florida International University PhD student Laura Garcia Barcia said, “A few studies done with cocaine shows that it affects fish really differently than it affects humans.” It acts as an anesthetic, not as a stimulant.

With “Cocaine Sharks,” the Discovery Channel has told yet another fishy tale.

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A Great Gray Owl is listening, always listening. Its head rotates to glean the source of a sound. Its ears are so acutely tuned, it can discern the faint footfall of a shrew in the forest, the wingbeat of a Canada Jay, the muffled rustle of a vole tunneling deep beneath the snow. It will fly to the spot, hover over it, head facing down toward the sound, then just before impact thrust its legs forward and punch through snow more than a foot and a half deep to seize its prey.

To be able to hunt by sound alone, owls need not only supersensitive ears but also the ability to locate the source of a faint noise in three‑dimensional space sometimes from a distance and sometimes through a thick layer of snow, soil, or leaves. The late Masakazu (Mark) Konishi tackled the problem of how an owl might do this.

Konishi died in 2020. A year later, on the anniversary of his birthday, a large group of researchers — peers and graduate students — gathered for a virtual celebration to honor the scientist and the man and to bring to light new research inspired by his work. The titles of the talks reflected the feeling of awe they shared with Konishi: “The Amazing Barn Owl Cochlea,” “The Owl’s Amazing Midbrain,” “The Amazing Nucleus Laminaris.”

When Konishi heard biologist Roger Payne report that a barn owl can catch a mouse relying only on sound, he wanted to understand exactly how a bird could do this. How can an owl track its prey in complete darkness? How can it work out exactly where a sound is coming from? What sort of brain circuitry allows for that? Konishi knew that facial disks helped in the task, and also the asymmetry of ears — at least in certain owl species.

Some owls, such as Great Horned Owls and Eastern Screech Owls, have ears placed at about the same level on both sides of their heads like most animals do. But others — barn owls, Northern Saw‑whet Owls, and Great Gray Owls — which rely heavily on sound for hunting, have one ear hole higher on one side of the head than the other. 

I once had the chance to see a Great Gray Owl up close, a resident male named Percy, at the Skansen Open-Air Museum in Stockholm, Sweden. The asymmetry of Percy’s ears is stunning. Beneath that mass of soft feathers, the left ear sits just below eye level, the right, slightly above. To accurately locate prey, Percy compares the sounds arriving at each ear, how loud they are, and which ear detects them first. Percy’s right ear is more sensitive to sounds coming from above the midline of his face, while the left ear is more sensitive to sounds coming from below. The difference in the time of arrival of sound waves between his two ears, known as the interaural time difference, helps Percy gauge the exact azimuth (or horizontal location) of a sound. The difference in loudness between his two ears helps him to determine the sound’s elevation. Where azimuth and elevation intersect is where he directs his strike. Species like Great Gray Owls, barn owls, and Northern Saw‑whet Owls can locate sounds within just two or three degrees.

There’s more to it. Tracking prey precisely takes two ears, and their asymmetrical arrangement helps. But in the end, it’s the brain that locates sounds in space in a most ingenious way.

By the time Konishi moved from Princeton to Caltech in 1975, he had 21 barn owls trained to strike at loudspeakers producing all kinds of sounds, including one owl named Roger, after Roger Payne. (It should be noted that Roger the owl turned out to be female; at one point, “he” laid an egg.) Roger starred in so many publications that the researchers celebrating Konishi thought he might be among the most famous published animals, rivaling Alex the African Gray Parrot, who, together with Harvard scientist Irene Pepperberg, taught the world so much about bird brains and intelligence.

Konishi’s research got a boost when a Caltech machinist famous for working on the Viking lander in the first Mars mission designed and built some fancy equipment for his owl studies — an ingenious light‑rail, arranged in a semicircle. Attached to the rail was a small remote control loudspeaker that could travel around the head of an owl at a constant distance in both horizontal and vertical directions. With the help of this space‑based gadget, Konishi and his doctoral student Eric Knudsen made a remarkable discovery. Certain auditory neurons in an owl’s brain respond only when a sound is coming from a particular location. By comparing the responses to sound by neurons in the cochlea of both ears, the brain builds a kind of multidimensional map of auditory space. This allows owls to fix the location of prey with speed and precision.

This was a surprise. Animals have brain maps for vision and touch, but these are built from visual images and touch receptors that map onto the brain through direct point‑to‑point projections. With ears, it’s entirely different. The brain compares information received from each ear about the timing and intensity of a sound and then translates the differences into a unified perception of a single sound issuing from a specific region of space. The resulting auditory map allows owls to “see” the world in two dimensions with their ears.

This proved to be a big leap toward understanding how the brain of any animal, including humans, learns to grasp its environment through sound. Think of it. Standing in a forest, you hear the crack of a falling branch or the rustle of a deer’s step in the dry leaves. Your brain calculates the time and intensity of sound to determine where it’s coming from. Owls do this task with incredible speed and accuracy. Each cochlea in the owl provides the brain with the precise timing of the sound reaching that ear within 20 microseconds. This determines how accurately the brain can calculate the interaural time difference, which in turn determines the accuracy of the localization of a sound in the azimuth. “The precision in microseconds provided by the owl cochlea is better than in any other animal that has been tested,” says Köppl. “We have big heads, so the interaural time differences are larger, making the task for cochlea and brain easier. In a nutshell, it is the combination of a small head and very precise localization that makes the owl unique.”

And here’s a finding to drop the jaw. José Luis Peña, a neuroscientist at the Albert Einstein College of Medicine, and his collaborators have discovered that the sound localization system in a barn owl’s brain performs sophisticated mathematical computations to execute this pinpointing of prey. The space‑specific neurons in the owl’s specialized auditory brain do advanced math when they transmit their information, not just adding and multiplying incoming signals but averaging them and using a statistical method called “Bayesian inference,” which involves updating as more information becomes available.

All of this calculating in less than the blink of an eye. I know, it’s mind‑blowing.

This article The wizardly owl brain uses “Bayesian inference” to find prey is featured on Big Think.

Just like you can’t judge a book by its cover, you can’t judge a dog by its breed. A canine’s behavior is far more influenced by environment and upbringing, according to a 2022 study published in the journal Science.

The finding comes courtesy of a Herculean effort by researchers associated with The Broad Institute at Harvard and MIT, the University of Massachusetts, and Arizona State University. Lead author Kathleen Morrill, a PhD student studying the genomics of behavior in dogs, and her numerous co-researchers surveyed owners of 18,385 purebred and mixed-breed dogs and genotyped 2,155 dogs as part of the citizen science project Darwin’s Ark.

For the project, participants were given a battery of surveys to fill out about their dogs. They then received a DNA kit to swab their pup’s saliva and send it back to the lab for genetic testing. The information was collated into a large database that was freely shared with researchers around the world. In return, curious dog owners were sent a genetic and breed profile of their dogs.

(Full disclosure: My wife and I participated in Darwin’s Ark with our mixed-breed rescue pup, Okabena. The genetic results we received scientifically confirmed that she is the cutest puppy in the whole world.)

With the copious data provided to them by citizen scientists, Morrill and her team discerned a number of fascinating findings, but the biggest was this: “Breed offers little predictive value for individuals, explaining just 9% of variation in behavior.”

In other words, a breed is far more defined by how a dog looks, and has little to do with how an individual dog behaves. “Although breed may affect the likelihood of a particular behavior to occur, breed alone is not, contrary to popular belief, informative enough to predict an individual’s disposition,” the authors wrote.

The researchers broke down dog behavior into eight categories: comfort level around humans, ease of stimulation or excitement, affinity toward toys, response to human training, how easily the dog is provoked by a frightening stimulus, comfort level around other dogs, engagement with the environment, and desire to be close to humans.

Of these behavioral traits, response to human training (also known as biddability) and toy affinity were most linked with breed, but the associations were slight. Biddability was very common among Border Collies and Australian Shepherds, while toy affinity was common among Border Collies and German Shepherds.

A dog’s age was a much better predictor of behavior. Older dogs, for example, were less excitable and less toy-driven than younger pups.

Modern dog breeds really only go back about 160 years, “a blink in evolutionary history compared with the origin of dogs more than 10,000 years ago,” the researchers described. So it makes sense that breed wouldn’t explain a dog’s behavior to a significant degree.

Hunting through the thousands of canine genomes on file, the researchers found eleven genetic regions associated with various behaviors, ranging from howling frequency to human sociability. Genes in these regions varied widely within breeds, providing further evidence that breed is only marginally linked to behavior.

The study’s findings call into question laws that target specific, supposedly “dangerous,” breeds. More than 900 cities in the U.S. currently have some form of breed-specific legislation.

This article Why you can’t judge a dog by its breed is featured on Big Think.

Quantum physics governs the world of the very small and that of the very cold. Your dog cannot quantum-tunnel her way through the fence, nor will you see your cat exhibit wave-like properties. But physics is funny, and it is continually surprising us. Quantum physics is starting to show up in unexpected places. Indeed, it is at work in animals, plants, and our own bodies. 

We once thought that biological systems are too warm, too wet, and too chaotic for quantum physics to play any part in how they work. But it now seems that life is employing feats of quantum physics every day in messy, real-world systems, including quantum tunneling, wave-particle duality, and even entanglement. To see how it all works, we can start by looking right inside our own noses. 

The quantum nose

The human nose can distinguish over one trillion smells. But how exactly the sense of smell works is still a mystery. When a molecule referred to as an odorant enters our nose, it binds to receptors. Initially, the prevailing theory held that these receptors used the shape of the odorants to differentiate smells. The so-called lock and key model suggests that when an odorant finds the right receptor, it fits into it and triggers a specific smell. But the lock and key model ran into trouble when tested. Subjects were able to tell two scents apart, even when the odorant molecules were identical in shape. Some other process must be at work.

Another, still controversial, model suggests that our noses are sensitive to the vibrations within odorant molecules. These vibrations occur when individual atoms within the molecule oscillate back and forth with respect to one another, as if they were loaded onto tiny springs. When an odorant settles into a receptor, the energy of its vibrations causes an electron to quantum tunnel to another location in the receptor. 

The shape and vibrational models can be combined. In the so-called swipe card model, our noses are sensitive to both the shape of and vibrations within an odorant. 

A new model, labeled the luminescence hypothesis, proposes still another step. Once the electron tunnels to a new position within the receptor, it loses its energy. As it does, the hypothesis proposes, the electron emits photons. Our noses detect these photons, and this helps us distinguish smells. Interestingly, the authors of this hypothesis suggest that it might help explain why some people with COVID lose their sense of smell.

Entangled navigation

Every year, Arctic terns set off on a migration that takes them around the world. They travel from Greenland to the Weddell Sea off Antarctica — a journey of 90,000 kilometers, all without the help of Google Maps. Birds have an uncanny ability to navigate. They can find the right direction of travel despite changes in weather, and at all hours of the day or night. Scientists believe this is possible because birds can sense the Earth’s magnetic field, allowing them to precisely align their position on the globe.

It appears to work something like this: Normally, two electrons can occupy an orbital, one with spin up, and one with spin down. But occasionally, something, such as a high-energy photon, can knock a single electron off a molecule, transferring it to another molecule. Both the giving and receiving molecules are now radicals — that is, molecules with an unpaired electron within one of their orbitals.

Radicals are very reactive, but what’s more, when they are created in this way, they become entangled with one another, forming what’s known as a radical pair. These pairs are created in proteins called cryptochromes within birds’ eyes. This radical pair will oscillate back and forth remarkably quickly between having spins aligned or anti-aligned with one another. Spin is spin angular momentum, which gives the molecule a magnetic moment. Because of this, the amount of time these molecules spend in each aligned or anti-aligned state is very sensitive to external magnetic fields, so sensitive, in fact, that birds can detect changes thousands of times less than the strength of Earth’s magnetic field.

Quantum evolution

Quantum mechanics might also play a part in evolution. DNA has four bases, called A (adenine), C (cytosine), G (guanine), and T (thymine). The “shapes” of these bases make it so that A always bonds to T, and G to C. During replication, an enzyme “unzips” the DNA strand from top to bottom. Both sides of this unzipped DNA can now be built into identical DNA strands, matching A to C and G to T.

Bases are held via hydrogen bonds, where a hydrogen atom attracts a negatively charged molecule, sort of like a magnet. Rather than sharing electrons, these bonds stick electrostatically together. As the DNA is unzipped, occasionally the hydrogen nucleus (a proton) can quantum tunnel to the opposite side of the unzipped DNA. When this happens, it creates a tautomer. A tautomer is another version of a molecule with the same chemical formula but a different shape, and hence, different connectivity.

Tautomers that survive long enough in the duplication process can cause the wrong bases to pair with one another. At first, it was believed that tautomers didn’t survive long enough to last through the entire replication process. But recently, scientists found that these tautomeres can survive through DNA replication and cause a mutation — and over time, may influence the course of evolution.

Plants with a PhD 

Plants and bacteria that utilize photosynthesis use the quantum nature of light to convert sunlight into energy using quantum coherence. When sunlight hits a plant, chlorophyll molecules within the leaf absorb photons of specific colors, and these photons excite an electron within the chlorophyll. That energy then moves from the chlorophyll molecules to a structure called the reaction center, where it is converted into chemical energy stored for the plant’s use.

But the path from chlorophyll to the reaction center is not direct, nor is it easy to find. The energy has to reach its destination fast, otherwise it will be lost as heat. To ease this challenge, the plant uses a clever trick called quantum coherence. Instead of taking one path and hoping this is the way to reach the reaction center, the electron uses its wave-like nature and takes all available paths at once, finding the reaction center every time. Quantum coherence is closely related to quantum entanglement, which is also shown to give plants a boost in efficiency.

This article Quantum biology: Your nose and house plant are experts at particle physics is featured on Big Think.

The average dog breed is highly inbred, with a genotypic profile that you might expect if two siblings mated, according to research published in 2021 that was conducted by scientists at the University of California-Davis School of Veterinary Medicine. As you might have guessed, this is not at all good for pups’ health.

The researchers, led by animal geneticist Dr. Danika Bannasch, determined the level of inbreeding for 227 different breeds using Wisdom Health Genetics’ DNA testing dataset of 49,378 dogs. The results show that the “majority of dog breeds display high levels of inbreeding well above what would be considered safe for either humans or wild animal populations.”

Just 11 of the 227 analyzed breeds had an inbreeding score of 0.125 or less, equivalent to a cross between two half-siblings. The vast majority scored above 0.25, a value you would expect if two siblings or a parent and offspring reproduced.

The researchers then paired this inbreeding information with pet insurance data from the company Agria, which provided the rate of nonroutine veterinary care events per 10,000 dog-years for each breed. With these figures, Bannasch and her colleagues calculated that, on average, purebred dogs require 24.4% more nonroutine vet visits than mixed-breed dogs. These are visits for injuries, diseases, or other unexpected maladies.

Canine health: a mixed tale

Not all dog breeds are alike in terms of health, however. Tamaskan Dogs, Barbets, Australian Labradoodles, Danish-Swedish Farmdogs, Mudis, and Koolies were some of the least inbred, and they had rates of vet care comparable to mixed-breed dogs. Border Terriers, Chow Chows, Pomeranians, Samoyeds, Shiba Inus, Collies, English setters, and Siberian Huskies also maintained decent health, despite being more inbred.

Dogs with brachycephaly — a facial feature characterized by short, stubby noses which makes it difficult to breathe — were some of the most inbred and required lots of veterinary attention — 44.6% more than a mixed breed dog. Bulldogs and Pugs fall into this category.

Larger inbred breeds like Mastiffs and Rottweilers also suffered from more health problems on average, particularly owing to their immense size. Labradors and Golden Retrievers, consistently two of the most popular dog breeds in the U.S. (if not the world), also were highly inbred and needed more vet care than average. Retrievers commonly fall victim to painful hip issues and are stricken with cancer at disturbingly high rates.

Make no mistake, humans are to blame for our furry friends’ genetic infirmities. Most modern dog breeds were established in just the past 200 years through rampant inbreeding to achieve desired looks and demeanors. In this vain pursuit, dogs’ health regularly fell by the wayside.

“Careful management of breeding populations to avoid additional loss of existing genetic diversity, through breeder education and monitoring of inbreeding levels enabled by direct genotyping technologies, is essential,” the researchers urge. “In the few breeds with low inbreeding levels, every effort should be made to maintain the genetic diversity that is present.”

Prospective pet owners also have a say in this matter. They can choose to adopt healthier breeds or seek out mutts from their local shelters and dog rescue agencies.

This article Most dog breeds are dangerously inbred is featured on Big Think.

Imagine, if you will, what it’s like to be an average cat. You live with your owner on the fourth floor of an apartment building and, like so many of your fellow felines with exposure to the outside world, you have a fierce case of wanderlust. But until your owner gets home, you can do little more than sit on a sunlit windowsill, press your nose against the glass, and peer wantingly at the neighborhood below. You are beholden to someone who chooses to spend most of the day separated from you. No wonder your species is so notoriously moody.

In most parts of the world, you’d be stuck at home until someone comes and lets you out. But in certain European countries, human residents have built outdoor climbing aids, called cat ladders, to help their feline friends come and go as they please.

A cat-ladder reaching almost to the roof. (BRIGITTE SCHUSTER/CC BY-SA-NC 4.0)

Homemade cat ladders are as architecturally eclectic as they are charming. Many are simple and economical: a teetering plank between balconies; spindly pegs ascending a vertical drain pipe; a slatted wooden bridge laid diagonally from the branch of a climbable tree to a higher windowsill. Some are precarious, scaffolding-like structures of wood and metal that zigzag up multiple stories. Still others span intimidatingly wide gaps between roofs and apartment buildings, dozens of feet off the ground. At least one lucky cat has its own spiral staircase with a small perching platform on top.

Despite their whimsical photogeneity, cat ladders haven’t yet been thoroughly documented. The graphic designer and writer Brigitte Schuster aims to change that. She had spotted the occasional cat ladder in her native Germany, but it wasn’t until she moved to Bern, Switzerland, six years ago that she realized how popular they were. She’s since taken hundreds of photographs of cat ladders around the Swiss capital, compiling them in a book analyzing the structures from sociological, architectural, and aesthetic perspectives. Swiss Cat Ladders will be published by Schuster’s book imprint, Brigitte Schuster Éditeur, in German and English in fall 2019.

Cat stairs with a dwelling place for the cat and possibly other animals. (BRIGITTE SCHUSTER/CC BY-SA-NC 4.0)

Cats are the most common household pet in Switzerland, and also in Germany, Austria, and the Netherlands—all countries, Schuster says, where cat ladders are staples of urban and suburban environments. But a country that loves cats isn’t necessarily one that embraces cat ladders.

There aren’t cat ladders in the United States, where many states have so-called leash laws that forbid the animals from being off-leash outdoors, and where city dwellers have built screened-in “catios.” Russia, which ranks highest in Europe in both cat ownership and household cat population, doesn’t have cat ladders. In Istanbul, hundreds of thousands of stray cats—some feral, some cuddly, all ownerless—roam and scale the city without the help of ladders designed specifically for them. A recent documentary, Kedi, tells the story of seven such cats, for whom every climbable structure is a “cat ladder.”

“I was questioning if cats really need these cat ladders, or if humans impose the cat ladders on their cats because they find them practical,” Schuster says. Her question appears backed up by traditional feline lore: If cats always land on their feet (and have nine lives), why do they need cat ladders? Couldn’t someone just open the window for their dearest feline and let her find her way to the ground, even if doing so requires an acrobatic leap?

“Cats do need them!” says Dennis C. Turner, a veteran cat behaviorist who’s considered, by his estimate, one of the world’s “four or five foremost cat experts.” “They’re very important. But they’re rarely mentioned in books about how to properly house cats.”

The cat must climb upwards, over several roofs, using two cat ladders. (BRIGITTE SCHUSTER/CC BY-SA-NC 4.0)

Turner points to two reasons why cats need cat ladders: their physical safety and their mental well-being. Contrary to popular belief, cats don’t always land on their feet—the innate “cat-righting reflex” only works up to 30 meters, Turner says—and even when they do, their daredevil leaps can result in injuries as severe as torn ligaments, ruptured tendons, and broken legs.

There’s a saying Turner often repeats during interviews and public lectures: “Once an outdoor cat, always an outdoor cat.” That is, if a kitten was born outside and spent its first weeks outdoors, it should be kept as a cat with outdoor access for the rest of its life. Outdoor cats held “captive” indoors, Turner says, will invariably develop behavioral problems, including urine marking and scratching furniture and drapes. For people in urban areas who live in apartments, or even in two-story houses, cat ladders (plus cat doors) are the easiest way to let cats come and go.

For those who might find the notion of an outdoor cat objectionable, Turner isn’t against keeping cats exclusively indoors—“I wouldn’t do it myself,” he says, “but that’s personal”—as long as two rules are fulfilled: They’ve never been outside and their home indoors is physically and mentally stimulating, with scratching posts, elevated perches, sunny views, and so on.

This cat ladder zigs and zags. (BRIGITTE SCHUSTER/CC BY-SA-NC 4.0)

Not all cats immediately take to their ladders like catnip. There’s a learning curve. Schuster says that some cat owners will put food on different steps to lure their pets out, in a form of positive reinforcement. “Cats only learn when they want to learn,” Turner says. “Punishment never works with them, but positive reinforcement does.”

In the preface of Schuster’s book, Turner writes, “I personally think that all ladders indicate a willingness to house the cats properly and respect the animals’ needs.” A home with a cat ladder is a home that knows and respects the needs of the cats who live there.

“If it fits, I sits” is an oft-memed saying associated with images of cats sitting snugly inside boxes, baskets, bowls, and other containers. Cats’ relationship with cat ladders might be described thusly: “If it’s mine, I climb.”

This article The Swiss city that’s full of cat ladders is featured on Big Think.

Despite its humble and extremely literal name, the last eukaryotic common ancestor (better known as LECA) is a single-celled trailblazer. This organism figuratively stepped outside the primordial pool to begin the transition from simple to complex life. 

From the Greek eu (“well” or “good”) and karyon (“kernel” or “nut”), eukaryotes have well-defined, DNA-containing nuclei enclosed within a membrane, along with other complex organelles that bacteria and other prokaryotes lack. Scientists consider LECA the first crown eukaryote — that is, the first organism that has all the distinguishing characteristics of eukaryotes. LECA evolved from stem-eukaryotes, which have some, but not all, of the characteristic eukaryotic morphology and physiology.

The eukaryotic gap

The evolution of eukaryotes led to extraordinary levels of complexity and biodiversity on Earth. Eukaryotes gave us everything from mushrooms and swordfish to baboons and Venus fly traps, leaving a deep mark on the planet’s ecology. But eukaryotic dominance did not happen overnight.

Scientific estimates confidently position LECA’s first appearance to approximately 1.6 billion years ago. However, LECA and its descendants do not show up as dominant members of the world’s biota until 900 million years ago. There is a gap of 600 million to 800 million years in which scientists acknowledge the presence of eukaryotes, but struggle to find evidence of thriving populations. It still stands as one of science’s most captivating unsolved puzzles.

Seeking answers, scientists from the Australian National University (ANU) delved into the eukaryotic lineage. They discovered intriguing evidence suggesting how LECA’s ancestors — our oldest semi-eukaryotic forebears — might have adapted to their environments before LECA could thrive. By analyzing ancient rocks that once formed the ocean floor, the researchers unveiled compelling evidence of the world inhabited by LECA’s ancestors. Along the way, the researchers propose a dramatic telling of the early competition that led to our own existence, and that of all complex life on Earth. The scientists published their results in Nature.

Fatty rocks

Scientists use two distinct approaches to identify eukaryotes. The first method involves searching for body fossils — namely, fossilized evidence of unique eukaryotic features such as specific cell surface structures and cell wall ornamentation. The second method looks for biomarkers, specifically hydrocarbon fossils derived from lipids. In particular, they look for crown sterols, a group of lipids like cholesterol that are unique to major lineages of eukaryotes. By mapping the signal of crown sterols, researchers have constructed a coherent picture of eukaryotic evolution over the past 800 million years, one that aligns with the fossil record. 

However, prior to 800 million years ago, biomarkers contradict fossil evidence. Eukaryotic body fossils exist, but detection methods fail to identify crown sterols. This apparent mismatch of signals persists across a period of over half a billion years, and it remains unexplained.

To address this gap, the authors proposed an untested hypothesis: Ecosystems were dominated by eukaryotic stem-groups that lacked a complete sterol biosynthetic pathway but possessed the eukaryotic body form. In other words, the eukaryotic fossils found during the period when the signature eukaryotic lipids were undetectable might represent a type of stem-eukaryote. They exhibited a eukaryotic body type but did not yet produce these distinctive lipids.

To pursue this hypothesis, the ANU researchers revisited a 30-year-old concept first suggested by Nobel laureate Konrad Bloch. Along the metabolic pathway that creates crown sterol molecules, eukaryotes form a number of intermediate compounds. Bloch thought these intermediates (“protosteroids”) might have been the final lipids produced by ancient organisms. The ANU scientists proposed the same.

Using advanced techniques unavailable in Bloch’s time, the ANU team began searching for these protosteroids. They found that the protosteroids were ubiquitous, showing up in rock samples from ecosystems around the world, the oldest of which was 1.64 billion years old. Due to their unique lipid profile, the scientists named the organisms “protosterol biota.” While their exact size remains uncertain, the scientists speculate that they may have acted as the world’s earliest predators, possibly hunting bacteria.

Crown eukaryotes vs. protosterol biota

The discovery of protosterol biota allowed the researchers to put forth a theory describing the fate of eukaryotic life between 1.6 billion and 800 million years ago — that is, the time in between LECA’s appearance and the first period when scientists have evidence that eukaryotic life thrived. As it turns out, the Earth between 1.6 billion and 800 million years ago was a less hospitable place for crown eukaryotes.

Eukaryotic lipid demand is metabolically expensive and requires a lot of oxygen. But crown sterols are useful molecules, as they protect cells against dehydration and make them more tolerant to extreme cold and heat. Therefore, on the Earth of 1.6 billion years ago, crown eukaryotes were well positioned to occupy environments characterized by frequent dehydration and rehydration, elevated UV radiation, and daily temperature swings. However, these environments do not preserve the types of signals that researchers have been looking for, fossilized or otherwise, and this might explain the mysterious lack of eukaryotes in the biological record.

While crown eukaryotes were doing well on land, they were much less suited to thrive in the oceans. Anoxic surface waters and low atmospheric oxygen levels posed challenges for these oxygen-hungry organisms. Protosterol biota, on the other hand, thrived in oxygen-deprived oceans thanks to their less metabolically demanding biosynthetic pathways. However, protosterols did not equip them to inhabit extreme environments like the crown group eukaryotes.

This dichotomy led to a parallel existence spanning several hundred million years, with crown eukaryotes found mainly on land and protosterol biota mainly in the oceans.

Eukaryotic conquest

Fast-forward to the Tonian period (1 billion to 720 million years ago), when atmospheric oxygen levels rose and nutrient supply to the oceans increased. With oxygen to spare, crown eukaryotes were no longer confined to Earth’s most extreme environments. They ventured into the oceans and slowly began to outcompete their protosterol-bearing ancestors. Extreme weather events like glaciations and intense global heat further highlighted the advantages of the crown eukaryotes while dooming the suddenly maladapted protosterol biota.

With Earth finally more hospitable to crown eukaryotes, they began to expand, and this is about the time the molecular and fossil evidence begin to coincide. LECA’s crown eukaryotic descendants went on to become the most modern and intricate life forms, including humans. The authors characterized this period as “one of the most profound ecological transitions in the evolution of complex life.”

This article “Protosterol biota” may explain one mysterious gap in the evolution of complex life is featured on Big Think.