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kottke.org posts about biology

A biologist explains CRISPR to people at five different levels of knowledge

posted by Jason Kottke   May 26, 2017

For the second part of an ongoing series, Wired asked biologist Neville Sanjana to explain CRISPR to five people with different levels of knowledge: a 7-year-old, a high school student, a college student, a grad student, and an expert on CRISPR. As I began to watch, I thought he’d gone off the rails right away with the little kid, but as soon as they connected on a personal issue (allergies), you can see the bridge of understanding being constructed.

The first installment in the series featured a neuroscientist explaining connectomes to five people.

The Biodiversity Heritage Library on Flickr

posted by Jason Kottke   May 25, 2017

Biodiversity

Biodiversity

Biodiversity

Biodiversity

The Biodiversity Heritage Library maintains a huge trove of plant and animal drawings that they’ve put up on Flickr for free.

The Biodiversity Heritage Library (BHL) is a consortium of natural history and botanical libraries that cooperate to digitize the legacy literature of biodiversity held in their collections and to make that literature available for open access and responsible use as a part of a global “biodiversity commons.”

Over 110,000 images are available, organized into hundreds of albums. You could easily lose an entire afternoon in there.

P.S. While the Biodiversity Heritage Library doesn’t appear to be an official participant, Flickr’s The Commons project remains one of the under-appreciated gems of the Web.

The Earth’s five energy revolutions

posted by Jason Kottke   May 22, 2017

Five Energy Expansions

Since life first formed on Earth billions of years ago, the ability of organisms to use more powerful and efficient energy sources has been key in driving the diversity and complexity of life. According to this provocative piece in Nature by Olivia Judson, the history of life on Earth can be divided into five energetic epochs characterized by the following energy sources: geochemical energy, sunlight, oxygen, flesh and fire.

The first two were present at the start, but oxygen, flesh and fire are all consequences of evolutionary events. Since no category of energy source has disappeared, this has, over time, resulted in an expanding realm of the sources of energy available to living organisms and a concomitant increase in the diversity and complexity of ecosystems. These energy expansions have also mediated the transformation of key aspects of the planetary environment, which have in turn mediated the future course of evolutionary change. Using energy as a lens thus illuminates patterns in the entwined histories of life and Earth, and may also provide a framework for considering the potential trajectories of life-planet systems elsewhere.

Organisms formed on Earth and changed the planet, which led to the formation of new organisms more suited to the new environment. For instance, when a type of bacteria evolved to turn sunshine into oxygen, it completely changed the planet.

In the absence of a biotic source of oxygen, trace quantities of the gas can be generated abiotically: water molecules can be split by sunlight or radioactive decay. However, these abiotic processes are much less efficient than their biotic equivalent. Had cyanobacteria, or something like them, never evolved, oxygen would never have built up in the atmosphere of the Earth.

But build up it did. Between 2.45 and 2.32 Ga, significant quantities of oxygen began to accumulate in the air, an episode known as the Great Oxidation Event. Before the Great Oxidation, atmospheric oxygen levels were less than 10^-5 of the present atmospheric level of ~21%. By ~2 Ga, they had risen to perhaps 0.1-1% of the present atmospheric level. Although the subsequent history of oxygen is complex and many details are uncertain, Earth’s atmosphere has contained an appreciable level of the gas ever since. (Full oxygenation of the oceans, however, would not happen until around 1.8 billion years after the Great Oxidation.)

The original piece in Nature is fairly readable for a science journal, but this summary in The Atlantic is worth a look if you’re short on time or attention. (via @CharlesCMann)

Super cool time lapse video of cell division

posted by Jason Kottke   Mar 21, 2017

This is a stunning time lapse video of the cells in a tadpole egg dividing over a period of 33 hours. The filmmaker, Francis Chee, built a custom microscope and lighting system to capture the action.

I can say that it was done with a custom designed microscope based on the “infinity optical design” It is not available by any manufacturer. I built it. I used LEDs and relevant optics to light the egg. They too were custom designed by me. The whole microscope sits on anti-vibration table. I have to say that it doesn’t matter too much what microscope people use to perform this. There are countless other variables involved in performing this tricky shot, such as for example: the ambient temperature during shooting; the time at which the eggs were collected; the handling skills of the operator; the type of water used; lenses; quality of camera etc etc.

Chee says in the comments that he’s perfecting his technique and hopes to capture a complete egg-to-tadpole video in the near future. His other videos are worth a look too, like this mushroom time lapse and this gruesome video of a praying mantis eating a fly alive. (via colossal)

The rove beetle’s ability to mimic army ants independently evolved many times

posted by Jason Kottke   Mar 13, 2017

Rove Beetle Ant

Rove beetles have evolved the ability to look and smell enough like army ants that they can live amongst them. Until it’s dinner time.

The impostors look and smell like army ants, march with the ants, and even groom the ants. But far from being altruistic nest-mates, these creatures are parasitic beetles, engaged in a game of deception. Through dramatic changes in body shape, behavior, and pheromone chemistry, the beetles gain their hostile hosts’ acceptance, duping the ants so they can feast on the colony brood.

As you can see in the photo above, the resemblance is strong…the beetle is in the foreground with the larger headed ant behind.

But that’s not even the most amazing part. A recent discovery has shown that rove beetles have evolved this capability at least a dozen separate times, suggesting that certain evolutionary possibilities are more likely than other in the presence of strong environmental factors and traits.

The ant-mimicking beetles all belong to the Staphylinidae, or rove beetles, but don’t mistake them for close relatives: the last common ancestor of the beetles in the study lived 105 million years ago, at about the time that humans split from mice. “What’s exceptional is that this convergent system is evolutionarily ancient,” says Parker. Although most other convergent systems, such as Darwin’s finches, three-spined stickleback, and African lake cichlid fish, are a few million years old at most, this newly discovered example extends back into the Early Cretaceous.

Given this great age, Parker and his co-author Munetoshi Maruyama of the Kyushu University Museum argue that their finding challenges Stephen J. Gould’s hypothesis that if time could be rewound and evolution allowed to replay again, very different forms of life would emerge. “The tape of life has been extremely predictable whenever rove beetles and army ants have come together,” says Parker. “It begs the question: why has evolution followed this path so many times?”

(via @stewartbrand)

John James Audubon’s five mystery birds

posted by Jason Kottke   Mar 07, 2017

Audubon mystery bird

Audubon mystery bird

Audubon mystery bird

Over a period of thirteen years beginning in the 1820s, John James Audubon painted 435 different species of American birds.1 When he was finished, the illustrations were compiled into The Birds of America, one of the most celebrated books in American naturalism. Curiously however, five of the birds Audubon painted have never been identified: Townsend’s Finch, Cuvier’s Kinglet, Carbonated Swamp Warbler, Small-headed Flycatcher and Blue Mountain Warbler.

These birds have never been positively identified, and no identical specimens have been confirmed since Audubon painted them. Ornithologists have suggested that they might be color mutations, surviving members of species that soon became extinct, or interspecies hybrids that occurred only once.

The specimen that Audubon used to paint Townsend’s Bunting is now in the Smithsonian Museum of Natural History, identified as Townsend’s Dickcissel, but no bird exactly like it has been reported, Dr. Olson, an authority on Audubon’s work, noted in an email. Ornithologists suggest that it is either a mutation of the Dickcissel or a hybrid of Dickcissel and Blue Grosbeak, she said.

And that’s not counting the ones he got wrong for other reasons:

And indeed, there are several birds painted and explained in Birds of America that are not, in fact, actual species. Some are immature birds mistaken for adults of a new species (the mighty “Washington’s Eagle” was, in all likelihood, an immature Bald Eagle). Some were female birds that didn’t look anything like their male partners (“Selby’s Flycatcher” was a female Hooded Warbler).

Audubon also painted six species of bird that have since become extinct: Carolina parakeet, passenger pigeon, Labrador duck, great auk, Eskimo curlew, and pinnated grouse. Here’s his portrait of the passenger pigeon:

Audubon Passenger Pigeon

There were an estimated 3 billion passenger pigeons in the world in the early 1800s — about one in every three birds in North America was a passenger pigeon at the time. Their flocks were so large, it took hours and even days for them to pass. Audubon himself observed in 1813:

I dismounted, seated myself on an eminence, and began to mark with my pencil, making a dot for every flock that passed. In a short time finding the task which I had undertaken impracticable, as the birds poured in in countless multitudes, I rose and, counting the dots then put down, found that 163 had been made in twenty-one minutes. I traveled on, and still met more the farther I proceeded. The air was literally filled with Pigeons; the light of noon-day was obscured as by an eclipse; the dung fell in spots, not unlike melting flakes of snow, and the continued buzz of wings had a tendency to lull my senses to repose… I cannot describe to you the extreme beauty of their aerial evolutions, when a hawk chanced to press upon the rear of the flock. At once, like a torrent, and with a noise like thunder, they rushed into a compact mass, pressing upon each other towards the center. In these almost solid masses, they darted forward in undulating and angular lines, descended and swept close over the earth with inconceivable velocity, mounted perpendicularly so as to resemble a vast column, and, when high, were seen wheeling and twisting within their continued lines, which then resembled the coils of a gigantic serpent… Before sunset I reached Louisville, distant from Hardensburgh fifty-five miles. The Pigeons were still passing in undiminished numbers and continued to do so for three days in succession.

100 years later, they were all dead. Which may have had at least one interesting consequence:

But the sad echo of the loss of passenger pigeons still reverberates today because its extinction probably exacerbated the proliferation of Lyme disease. When the passenger pigeons existed in large numbers, they subsisted primarily on acorns. However, since there are no pigeons to eat acorns, the populations of Eastern deer mice — the main reservoir of Lyme disease — exploded far beyond historic levels as they exploited this unexpected food bonanza.

  1. Interesting note: Audubon financed this project through a subscription plan. Each month or two, each subscriber would receive a set of five prints and the proceeds covered the costly printing process and Audubon’s nature travels.

Photos of evolution in action

posted by Jason Kottke   Jan 18, 2017

Southern Cassowary

For his new book, Evolution: A Visual Record, photographer Robert Clark has collected dozens of images that show the varying ways in which plants and animals have adapted to their changing surroundings.

Evidence of evolution is everywhere. Through 200 revelatory images, award-winning photographer Robert Clark makes one of the most important foundations of science clear and exciting to everyone. Evolution: A Visual Record transports readers from the near-mystical (human ancestors) to the historic (the famous ‘finches’ Darwin collected on the Galapagos Islands that spurred his theory); the recently understood (the link between dinosaurs and modern birds) to the simply astonishing.

The photo above is of a southern cassowary, a flightless bird that is particularly dinosaur-esque in stature and appearance.

Order from Chaos, a mesmerizing video of emergence

posted by Jason Kottke   Jan 03, 2017

French visual effects artist Maxime Causeret took a track from Max Cooper’s album Emergence and created these wonderful biologically inspired patterns and interactions.

Maxime also shows us a section of animated reaction-diffusion patterns, where simple chemical feedback mechanisms can yield complex flowing bands of colour — these forms of system were originally thought up by Alan Turing, and were part of the early seeds of the field of systems biology, which seeks to simulate life with computers, in order to better understand the systems producing the complexity we see in the living world. They were also the starting point of my main research area many years ago before I got lost in music! (where I began with the question of what patterns could be produced via reaction-diffusion forms of system as opposed to gene-regulatory network controlled patterning).

There’s a blue brain coral pattern at the 1:30 mark and a neuron-ish pattern at 2:30 that I wish would go on forever. Headphones recommended, psychoactive drugs optional. (via colossal)

Evolution at work: ivory poaching and tuskless elephants

posted by Jason Kottke   Nov 29, 2016

Tuskless Elephants

Poachers in Africa in search of the biggest ivory tusks have altered the gene pool of African elephants in the process.

In Gorongosa National Park in Mozambique, 90 per cent of elephants were slaughtered between 1977 and 1992, during the country’s civil war. Dr Poole said that because poachers disproportionately targeted tusked animals, almost half the females over 35 years of age have no tusks, and although poaching is now under control and the population is recovering well, they are passing the tuskless gene down to their daughters: 30 per cent of female elephants born since the end of the war also do not have tusks.

“Females who are tuskless are more likely to produce tuskless offspring,” she said.

(via mr)

Update: Vox has an interesting look at the growing trend of tuskless elephants.

The Foldscope: a paper microscope that costs $1

posted by Jason Kottke   Nov 01, 2016

Stanford biophysicist Manu Prakash is the inventor of the Foldscope, a small microscope that folds like origami, costs around a dollar, and provides “700 nanometer imaging”. Watch the video for examples — 700 nm is very small and the level of detail is incredible. Why do this? Prakash says:

It’s not just for scientists to figure out how the world works…We all start by being curious about the world. We are born with this and we really need to culture this, because fundamentally curiosity needs to be nurtured and kept alive forever.

You can read more about the Foldscope at the New Yorker or watch Prakash’s TED Talk.

He calls it the Foldscope, and it comes in a kit. (Mine arrived in a nine-by-twelve-inch envelope.) The paper is printed with botanical illustrations and perforated with several shapes, which can be punched out and, with a series of origami-style folds, woven together into a single unit. The end result is about the size of a bookmark. The lens — a speck of plastic, situated in the center — provides a hundred and forty times magnification. The kit includes a second lens, of higher magnification, and a set of stick-on magnets, which can be used to attach the Foldscope to a smartphone, allowing for easy recording of a sample with the phone’s camera. I put my kit together in fifteen minutes, and when I popped the lens into place it was with the satisfaction of spreading the wings of a paper crane.

You can’t currently buy a Foldscope but the website says that their Kickstarter campaign launches sometime this month, so stay tuned for that.

Update: You can now get your very own Foldscope on Kickstarter.

The worms that grow their own food

posted by Jason Kottke   Oct 27, 2016

A species of worm in the north-east Atlantic has been observed farming. They plant grass seeds in their burrows and feed on the sprouts when they start growing.

Ragworms (Hediste diversicolor) were thought to consume the seeds of cordgrass, an abundant plant in the coastal habitats where they live. But the seeds have a tough husk, so it was a mystery how the worms could access the edible interior.

Zhenchang Zhu at the Royal Netherlands Institute for Sea Research in Yerseke and his team have now discovered the worms’ surprising trick: they bury the seeds and wait for them to germinate, later feeding on the juicy sprouting shoots.

I, for one, welcome our new farming worm overlords.

How the Cretaceous coastline of North America affects US presidential elections

posted by Jason Kottke   Oct 20, 2016

2012 Election Map

That’s a portion of the 2012 US Presidential election map of the southern states broken down by county: blue ones went Barack Obama’s way and counties in red voted for Mitt Romney.

But let’s go back to the Cretaceous Period, which lasted from 145 million years ago to 65 million years ago. Back then, the coastline of what is now North America looked like this:

Cretaceous Coast

Along that ancient coastline of a shallow sea, plankton with carbonate skeletons lived and died in massive numbers, accumulating into large chalk formations on the bottom of the sea. When the sea level dropped and the sea drained through the porous chalk, rich bands of soil were left right along the former coastline. When that area was settled and farmed in the 19th century, that rich soil was perfect for growing cotton. And cotton production was particularly profitable, so slaves were heavily used in those areas.

McClain, quoting from Booker T. Washington’s autobiography, Up From Slavery, points out: “The part of the country possessing this thick, dark and naturally rich soil was, of course, the part of the South where the slaves were most profitable, and consequently they were taken there in the largest numbers.” After the Civil War, a lot of former slaves stayed on this land, and while many migrated North, their families are still there.

The counties in which slave populations were highest before the Civil War are still home to large African American populations, which tend to vote for Democratic presidential candidates, even as the whiter counties around them vote for Republicans. The voting pattern of those counties on the map follows the Cretaceous coastline of 100 million years ago — the plankton fell, the cotton grew, the slaves bled into that rich soil, and their descendants later helped a black man reach the White House.

Zoomable tree of all life on Earth

posted by Jason Kottke   Oct 04, 2016

Zooming Tree Of Life

OneZoom is an interactive zoomable map of “the evolutionary relationships between the species on our planet”, aka tree of life. Browsing around is fun, but you’ll want to use the search function to find specific groups and animals, like mammals, humans, and mushrooms. The scale of this is amazing…there are dozens of levels of zoom. (via @pomeranian99)

Impressive insect camouflage

posted by Jason Kottke   Sep 16, 2016

Meet the lichen katydid. Hailing from the forests of Central and South America, this insect has evolved over the millennia to blend in amazingly well with the lichens that populate the forest.

The internet of trees: how trees talk to each other underground

posted by Jason Kottke   Sep 15, 2016

In June, ecologist Suzanne Simard gave a talk at TED about her 30 years of research into how trees talk to each other. Underneath the forest floor, there is a communications network on which trees — even those from different species — trade carbon with each other, send warnings, and trade messages. Simard described one of her first experiments (from the transcript):

I pulled on my white paper suit, I put on my respirator, and then I put the plastic bags over my trees. I got my giant syringes, and I injected the bags with my tracer isotope carbon dioxide gases, first the birch. I injected carbon-14, the radioactive gas, into the bag of birch. And then for fir, I injected the stable isotope carbon-13 carbon dioxide gas. I used two isotopes, because I was wondering whether there was two-way communication going on between these species.

The idea was to use the isotopes to track whether the trees were trading carbon when some of them were shaded and less able to make their own energy.

The evidence was clear. The C-13 and C-14 was showing me that paper birch and Douglas fir were in a lively two-way conversation. It turns out at that time of the year, in the summer, that birch was sending more carbon to fir than fir was sending back to birch, especially when the fir was shaded. And then in later experiments, we found the opposite, that fir was sending more carbon to birch than birch was sending to fir, and this was because the fir was still growing while the birch was leafless. So it turns out the two species were interdependent, like yin and yang.

Fascinating. German forester Peter Wohlleben came out with a book this week called The Hidden Life of Trees: What They Feel, How They Communicate (Simard contributed a note to the book). From a Guardian review:

Trees have friends, feel loneliness, scream with pain and communicate underground via the “woodwide web”. Some act as parents and good neighbours. Others do more than just throw shade — they’re brutal bullies to rival species. The young ones take risks with their drinking and leaf-dropping then remember the hard lessons from their mistakes. It’s a hard-knock life.

The Monthly, Maclean’s, and Scribd all have excerpts of Wohlleben’s book if you’re interested.

Update: See also this episode of Radiolab, From Tree to Shining Tree. (via @Chan_ing)

Watch time lapse videos of bacteria evolving drug resistance

posted by Jason Kottke   Sep 09, 2016

Researchers at Harvard have come up with a novel way of studying how bacteria evolve to become drug resistant. They set up a large petri dish about the same shape as a football field with no antibiotics in the end zones and increasingly higher doses of antibiotics toward the center. They placed some bacteria in both end zones and filmed the results as the bacteria worked its way toward the center of the field, evolving drug resistance as it went. Ed Yong explains:

What you’re seeing in the movie is a vivid depiction of a very real problem. Disease-causing bacteria and other microbes are increasingly evolving to resist our drugs; by 2050, these impervious infections could potentially kill ten million people a year. The problem of drug-resistant infections is terrifying but also abstract; by their nature, microbes are invisible to the naked eye, and the process by which they defy our drugs is even harder to visualise.

But now you can: just watch that video again. You’re seeing evolution in action. You’re watching living things facing down new challenges, dying, competing, thriving, invading, and adapting — all in a two-minute movie.

Watch the video…it’s wild. What’s most interesting — or scary as hell — is that once the drug resistance gets going, it builds up a pretty good momentum. There’s a pause at the first boundary as the evolutionary process blindly hammers away at the problem, but after the bacteria “learn” drug resistance, the further barriers are breached much more quickly, even before the previous zones are fully populated.

Scientists discover giraffes are actually four separate species

posted by Jason Kottke   Sep 09, 2016

Giraffe Species

Suddenly, there are four species of giraffe now. Previously there was only one. Scientists have analyzed the genetic code of hundreds of giraffes in Africa and found much variation in their DNA, enough to split one species into four.

Some of the differences were as large or larger than the differences between brown bears and polar bears.

Despite their similar appearances, members of the different species don’t appear to mate with each other. It’s amazing that scientists didn’t know this until now.

The biggest war in animal history

posted by Jason Kottke   Aug 10, 2016

According to theoretical biologist Suzanne Sadedin, the biggest war in animal history (humans included) is happening right now.

Once upon a time there was a tiny brown ant who lived by a swamp at the end of the Paraná River in Argentina. Her name, Linepithema humile, literally means “humble” or “weak”. Some time during the late 1800s, an adventurous L. humile crept away from the swamp where giant river otter played and capybaras cavorted.

She stowed away on a boat that sailed to New Orleans. And she went to war.

Update: And bang, here’s the supporting science in the form of a 2010 study.

Here, we perform inter-continental behavioral analyses among supercolonies in North America, Europe, Asia, Hawaii, New Zealand and Australia and show that these far-flung supercolonies also recognize and accept each other as if members of a single, globally distributed supercolony. Furthermore, populations also possess similar genetic and chemical profiles. However, these ants do show aggression toward ants from South Africa and the smaller secondary colonies that occur in Hawaii and California. Thus, the largest and most dominant introduced populations are likely descended from the same ancestral colony and, despite having been established more than 100 years ago, have diverged very little. This apparent evolutionary stasis is surprising because, in other species, some of the most rapid rates of evolutionary change have occurred in introduced populations. Given the spatial extent of the Argentine ant society we report here, there can be little doubt that this intercontinental supercolony represents the most populous known animal society.

The “25 years and beyond” section of the Facebook product roadmap contains a single word, unlined twice in red ink: ants. Can ants be trained to look at ads though?

Update: Radiolab also did a segment on these ants. (via @minwoolee)

Update: Wow, the Argentine ant is having a bit of a moment…I didn’t expect this to be my most updated post of the week. Annalee Newitz just dropped a long article about their world domination: Meet the worst ants in the world.

UC Berkeley environmental scientist Neil Tsutsui helmed an effort to sequence the genome of L. humile, in part to find out where the invading group had originated. He and an international team of colleagues published the results of their analysis in 2011. They compared the genomes of Argentine ants in California to those of native populations, and Tsutsui told Ars that they were initially surprised by the results. “I was expecting Buenos Aires to be the source, but it was actually a city upstream called Rosario,” he said. “It turns out that in the late 19th century, when the ants were moving around, Rosario was actually a bigger shipping port than Buenos Aires. So it made more sense as a source for introduced populations.”

Genetic evidence supports the idea that the ants made their way from Port Rosario all across the globe. Subsequent sightings of the ants in the United States show that they also hitched rides on trains from New Orleans, ultimately arriving in California in 1904. Trucks probably transported them throughout the state. But how could such fragile creatures survive these journeys in giant machines and go on to found insectile empires? With their countless queens and nomadic lifestyle, they turned out to be the ultimate adapters.

Che Guevara and Lionel Messi are also from Rosario and have taken over the world in their own way. (via @tcarmody)

Body of Theseus

posted by Jason Kottke   Jun 29, 2016

How old are different parts of our bodies? Does anything stick around the entire time? The hair on our bodies lasts only a few years. Fingernails are fully replaced every six months. Your skin lasts 2-4 weeks. Even your blood and bones regenerate every so often. There’s at least one part of your body with lasts the whole time you’re alive, which I found somewhat surprising. See the ship of Theseus paradox.

The ship wherein Theseus and the youth of Athens returned from Crete had thirty oars, and was preserved by the Athenians down even to the time of Demetrius Phalereus, for they took away the old planks as they decayed, putting in new and stronger timber in their places, in so much that this ship became a standing example among the philosophers, for the logical question of things that grow; one side holding that the ship remained the same, and the other contending that it was not the same.

How do we know the lifespans of different cells in the body? Carbon-14 levels from nuclear testing done in the 50s and 60s.

Analysis of growth rings from pine trees in Sweden shows that the proliferation of atomic tests in the 1950s and 1960s led to an explosion in levels of atmospheric carbon 14. Now, Jonas Frisen and colleagues at the Karolinska Institute in Stockholm have taken advantage of this spike in C14 to devise a method to date the birth of human cells. Because this test can be used retrospectively, unlike many of the current methods used to detect cell proliferation, and because it does not require the ingestion of a radioactive or chemical tracer, the method can be readily applied to both in vivo and postmortem samples of human tissues.

Increasing the efficiency of photosynthesis

posted by Jason Kottke   Mar 28, 2016

Stewart Brand wrote a summary of a seminar given by Jane Langdale about how the efficiency of photosynthesis might be improved for some of the world’s plants, particularly rice.

Most plants use what’s called C3 photosynthesis to produce sugars and starch, but the process is not very efficient. Some plants, like corn and sugarcane, have evolved the capability to produce sugars and starch using the much more efficient C4 photosynthesis process. So if you could modify rice to use C4 instead of C3, yields would increase dramatically.

Rice is a C3 plant — which happens to be the staple food for half the world. If it can be converted to C4 photosynthesis, its yield would increase by 50% while using half the water. It would also be drought-resistant and need far less fertilizer.

You can read more about the efforts in developing C4 photosynthesis in Technology Review.

CRISPR, a cheap and accurate copy/paste for DNA

posted by Jason Kottke   Nov 13, 2015

Michael Specter has a truly fascinating piece in the New Yorker about CRISPR, a relatively new genetic tool for editing genes that geneticists are very excited about.

With CRISPR, scientists can change, delete, and replace genes in any animal, including us. Working mostly with mice, researchers have already deployed the tool to correct the genetic errors responsible for sickle-cell anemia, muscular dystrophy, and the fundamental defect associated with cystic fibrosis. One group has replaced a mutation that causes cataracts; another has destroyed receptors that H.I.V. uses to infiltrate our immune system.

The story has everything: the cheap copy/paste of DNA, easily editable mice, pig Hitler, “destroyer of worlds” overtones, and an incredible tale of science that could actually revolutionize (or ruin, depending on who you talk to) the world. I was shocked at how easy it is to do genetic research nowadays.

Ordering the genetic parts required to tailor DNA isn’t as easy as buying a pair of shoes from Zappos, but it seems to be headed in that direction. Yan turned on the computer at his lab station and navigated to an order form for a company called Integrated DNA Technologies, which synthesizes biological parts. “It takes orders online, so if I want a particular sequence I can have it here in a day or two,” he said. That is not unusual. Researchers can now order online almost any biological component, including DNA, RNA, and the chemicals necessary to use them. One can buy the parts required to assemble a working version of the polio virus (it’s been done) or genes that, when put together properly, can make feces smell like wintergreen. In Cambridge, I.D.T. often makes same-day deliveries. Another organization, Addgene, was established, more than a decade ago, as a nonprofit repository that houses tens of thousands of ready-made sequences, including nearly every guide used to edit genes with CRISPR. When researchers at the Broad, and at many other institutions, create a new guide, they typically donate a copy to Addgene.

And CRISPR in particular has quickened the pace. A scientist studying lung cancer mutations said of her research:

“In the past, this would have taken the field a decade, and would have required a consortium,” Platt said. “With CRISPR, it took me four months to do it by myself.”

Also recommended: Radiolab’s podcast on CRISPR from back in June.

Scaling laws and the speed of animals

posted by Jason Kottke   Oct 19, 2015

Animal Speed Scaling

A recent paper found that the time it takes for an animal to move the length of its own body is largely independent of mass. This appears to hold from tiny bacteria on up to whales — that’s more than 20 orders of magnitude of mass. The paper’s argument as to why this happens relies on scaling laws. Alex Klotz explains.

A well-known example is the Square-Cube Law, dating back to Galileo and described quite well in the Haldane essay, On Being the Right Size. The Square-Cube Law essentially states that if something, be it a chair or a person or whatever, were made twice as tall, twice as wide, and twice as deep, its volume and mass would increase by a factor of eight, but its ability to support that mass, its cross sectional area, would only increase by a factor of four. This means as things get bigger, their own weight becomes more significant compared to their strength (ants can carry 50 times their own weight, squirrels can run up trees, and humans can do pullups).

Another example is terminal velocity: the drag force depends on the cross-sectional area, which (assuming a spherical cow) goes as the square of radius (or the two-thirds power of mass), while the weight depends on the volume, proportional to the cube of radius or the first power of mass. As Haldane graphically puts it

“You can drop a mouse down a thousand-yard mine shaft; and, on arriving at the bottom, it gets a slight shock and walks away, provided that the ground is fairly soft. A rat is killed, a man is broken, a horse splashes.”

Scaling laws also come into play in determining the limits of the size of animals: The Biology of B-Movie Monsters.

When the Incredible Shrinking Man stops shrinking, he is about an inch tall, down by a factor of about 70 in linear dimensions. Thus, the surface area of his body, through which he loses heat, has decreased by a factor of 70 x 70 or about 5,000 times, but the mass of his body, which generates the heat, has decreased by 70 x 70 x 70 or 350,000 times. He’s clearly going to have a hard time maintaining his body temperature (even though his clothes are now conveniently shrinking with him) unless his metabolic rate increases drastically.

Luckily, his lung area has only decreased by 5,000-fold, so he can get the relatively larger supply of oxygen he needs, but he’s going to have to supply his body with much more fuel; like a shrew, he’ll probably have to eat his own weight daily just to stay alive. He’ll also have to give up sleeping and eat 24 hours a day or risk starving before he wakes up in the morning (unless he can learn the trick used by hummingbirds of lowering their body temperatures while they sleep).

Mother Nature invented the gear

posted by Jason Kottke   Sep 23, 2015

Nature Gears

Scientists have discovered that an insect has evolved something like a gearbox to coordinate its leg movements while jumping. That’s right, nature invented mechanical gears before man got around to it.

The gears in the Issus hind-leg bear remarkable engineering resemblance to those found on every bicycle and inside every car gear-box.

Each gear tooth has a rounded corner at the point it connects to the gear strip; a feature identical to man-made gears such as bike gears — essentially a shock-absorbing mechanism to stop teeth from shearing off.

The gear teeth on the opposing hind-legs lock together like those in a car gear-box, ensuring almost complete synchronicity in leg movement — the legs always move within 30 ‘microseconds’ of each other, with one microsecond equal to a millionth of a second.

This is critical for the powerful jumps that are this insect’s primary mode of transport, as even minuscule discrepancies in synchronisation between the velocities of its legs at the point of propulsion would result in “yaw rotation” — causing the Issus to spin hopelessly out of control.

“This precise synchronisation would be impossible to achieve through a nervous system, as neural impulses would take far too long for the extraordinarily tight coordination required,” said lead author Professor Malcolm Burrows, from Cambridge’s Department of Zoology.

Tree of 40 Fruit

posted by Jason Kottke   Jul 24, 2015

Artist Sam Van Aken is using grafting to create trees that bear 40 different kinds of fruit. National Geographic recently featured Van Aken’s Tree of 40 Fruit project:

The grafting process involves slicing a bit of a branch with a bud from a tree of one of the varieties and inserting it into a slit in a branch on the “working tree,” then wrapping the wound with tape until it heals and the bud starts to grow into a new branch. Over several years he adds slices of branches from other varieties to the working tree. In the spring the “Tree of 40 Fruit” has blossoms in many hues of pink and purple, and in the summer it begins to bear the fruits in sequence — Van Aken says it’s both a work of art and a time line of the varieties’ blossoming and fruiting. He’s created more than a dozen of the trees that have been planted at sites such as museums around the U.S., which he sees as a way to spread diversity on a small scale.

(via colossal)

Copy and paste, but for DNA

posted by Jason Kottke   Jul 22, 2015

No hunger. No pollution. No disease. Wired’s Amy Maxmen welcomes you to the age of copy and paste DNA editing and the end of life as we know it.

Genome editing started with just a few big labs putting in lots of effort, trying something 1,000 times for one or two successes. Now it’s something that someone with a BS and a couple thousand dollars’ worth of equipment can do. What was impractical is now almost everyday. That’s a big deal.

[I recently listened to Radiolab’s show on Crispr. Recommended. -jkottke]

Bacterial handprint

posted by Jason Kottke   Jun 08, 2015

Tasha Sturm, a lab technician at Cabrillo College, had her 8-year-old son put his handprint on a prepared petri dish and then incubated it for several days. This was the result:

Bacteria Handprint

If you’ll excuse me, I have to go wash my hands about 4,000 times. Bacteria is cooooool though:

Bacteria Handprint Closeup

(via colossal)

Superwolves, pizzly bears, emerging hybrid species, and climate change

posted by Jason Kottke   Jun 04, 2015

Because of climate change and other activities caused by humans (invasive species, habitat loss), hybridization of species is resulting in things like super-sized coyotes, pizzly bears (grizzly/polar bear hybrids), and other animals that may not be ideally suited to survive.

Some scientists and conservationists see the coywolf as a nightmare of the Anthropocene — a poster child of mongrelization as plants and animals reshuffle in response to habitat loss, climate change and invasive species. Golden-winged warblers increasingly cross with blue-winged warblers in the U.S. Northeast and eastern Canada. Southern flying squirrels hybridize with northern flying squirrels as the southern species presses northward in Ontario. Polar bears mate with grizzlies in the Canadian Arctic along the Beaufort Sea to produce “pizzly bears.”

All of this interbreeding upsets the conventional notion of species as discrete, inviolable entities. Moreover, some scientists and conservationists warn that hybridization will degrade biodiversity as unusual species are lost to genetic homogenization.

Partly scientists fear hybrids will be less fit than organisms that have evolved in place over eons. And often that is true, but the problem solves itself over time as hybrids lose out in the competitive race for survival.

Teaching evolution to religious students

posted by Jason Kottke   Mar 27, 2015

James Krupa teaches a mandatory biology class at the University of Kentucky and some students have a difficult time because Krupa refuses to shy away from evolution.

Rarely do I have a Kentucky student who learned about human evolution in high school biology. Those who did usually attended high schools in large urban centers like Louisville or Lexington. Given how easily it can provoke parents, the teaching of human evolution is a rarity in high school, so much so in Kentucky that it startled me when I first arrived.

The story of our evolutionary history captivates many of my students, while infuriating some. During one lecture, a student stood up in the back row and shouted the length of the auditorium that Darwin denounced evolution on his deathbed — a myth intentionally spread by creationists. The student then made it known that everything I was teaching was a lie and stomped out of the auditorium, slamming the door behind him. A few years later during the same lecture, another student also shouted out from the back row that I was lying. She said that no transitional fossil forms had ever been found — despite my having shared images of many transitional forms during the semester. Many of her fellow students were shocked by her combativeness, particularly when she stormed out, also slamming the door behind her. Most semesters, a significant number of students abruptly leave as soon as they realize the topic is human evolution.

I personally don’t understand the compatibility of evolutionary biology and Christianity Krupa emphasizes in his class, but I guess it helps to meet people halfway?

God, Darwin, and biology class

posted by Jason Kottke   Oct 01, 2014

Every year, evolutionary biologist and professor David Barash gives his students The Talk about how evolution and religion do and do not get along.

It’s irresponsible to teach biology without evolution, and yet many students worry about reconciling their beliefs with evolutionary science. Just as many Americans don’t grasp the fact that evolution is not merely a “theory,” but the underpinning of all biological science, a substantial minority of my students are troubled to discover that their beliefs conflict with the course material.

Until recently, I had pretty much ignored such discomfort, assuming that it was their problem, not mine. Teaching biology without evolution would be like teaching chemistry without molecules, or physics without mass and energy. But instead of students’ growing more comfortable with the tension between evolution and religion over time, the opposite seems to have happened. Thus, The Talk.

This is the sort of thing Barash talks about:

The more we know of evolution, the more unavoidable is the conclusion that living things, including human beings, are produced by a natural, totally amoral process, with no indication of a benevolent, controlling creator.

(via @TomJunod)

A Disappearing Planet

posted by Jason Kottke   Jul 15, 2014

From ProPublica, an alarming series of graphs and charts on animal extinction: A Disappearing Planet.

Animal species are going extinct anywhere from 100 to 1,000 times the rates that would be expected under natural conditions. According to Elizabeth Kolbert’s The Sixth Extinction and other recent studies, the increase results from a variety of human-caused effects including climate change, habitat destruction, and species displacement. Today’s extinction rates rival those during the mass extinction event that wiped out the dinosaurs 65 million years ago.

(via @SrikarDR)