ريتشارد دوكنز's Blog, page 572

Science And Stalin’s Crap Grab: Can Excrement Reveal The Secrets Of Our Personalities?

Health and Medicine





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Did Mao pass the poo test? CC BY-SA

“I am here to do more than eat and shit,” an irate Mao ZeDong shouted during his only meeting with Josef Stalin in Moscow, having been kept waiting for days. This was Stalin’s attempt to show him who was the real boss. Yet it transpires that he was far more interested in Mao’s inner workings than he let on.

World Health Orgaization Declares Zika Virus A Global Health Emergency

Health and Medicine





Photo credit:

Kateryna Kon/Shutterstock

The World Health Organization (WHO) declared the Zika virus an international health emergency on Monday, a rare move prompted by the “explosive” spread of the mosquito-borne virus. 

U.K. Scientists Given Green Light To Edit Human Embryos

Health and Medicine





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The embryos will be allowed to develop until it is made up of around 250 cells. Lukiyanova Natalia/frenta/Shutterstock

Scientists in the U.K. have been given the green light to edit human embryos. The decision will allow researchers to genetically modify early embryos and watch them develop for up to seven days, in a bid to figure out what influences miscarriages. The controversial procedure will be carried out at the Francis Crick Institute in London, and will work with up to 30 embryos to begin with, though there are hopes they could extend their research using more.

Answer Monday!

Fossil Friday

Last week, I told you that you’d all recognize this specimen once I told you what it was, and I stand by that. Meet Deinonychus.

Museum of Comparative Zoology, Harvard University

You don’t recognize the name? Or the skull? Well, do you recognize this foot?

Museum of Comparative Zoology, Harvard University

Or this movie star? But wait! That’s Velociraptor, you say? In the movie (and book) Jurassic Park, that’s how it was billed, but it turns out the velociraptors were really deinonychuses. Why? Well, we can yet again blame the confusing world of taxonomy. According to a 2008 article by Brian Switek:

While it did differ in important ways, Deinonychus can basically be thought of as a scaled-up version of Velociraptor, being almost twice as long and twice as tall as its Mongolian cousin… The genus changed how people thought about dinosaurs, suggesting that they were much more active and dynamic than had been supposed previously.

This new view of dinosaurs, in part, inspired the 1988 book Predatory Dinosaurs of the World by paleo-artist Gregory S. Paul. Not only was the volume chock-full of illustrations of feathered dinosaurs, but it also attempted to revise some dinosaur taxonomy. Paul noted the similarities between the skeletons of the Velociraptor from Mongolia and the Deinonychus skeletons from North America. They were so similar, in fact, that he decided to group the Deinonychus fossils under the name Velociraptor, as the older name took precedence according to the rules by which organisms are named.

Paleontologists did not agree with this change— Velociraptor was kept distinct from Deinonychus—but Paul’s book was a hit with the general public. And one of the people who read the book was author Michael Crichton. We know this because in the acknowledgements for his novel Jurassic Park, Crichton listed Paul as one of the people who inspired his vision for dinosaurs portrayed in the book, and he used the name Velociraptor to describe the large, sickle-clawed predators that disembowel so many humans in the fictional yarn. The same taxonomy was carried over into the film series, which ultimately made what would otherwise seem to be an abstruse scientific term a household name.

So, basically, Crichton was describing and envisioning Deinonychus while writing Jurassic Park, but he was under the impression that Deinonychus had been swallowed up by Velociraptor. (The names, that is, not the dinosaurs.) Are you following?

(And yes, we all know that no matter what they were called in the books and films, they should have had feathers. Hollywood owes us paleonerds a lot of feathers. But that’s a rant for another day.)

But wait, you cry! Stephanie, you said that there was a connection to last week’s fossil! Deinonychus is a dinosaur and last week you told us unequivocally that ichthyosaurs are not dinosaurs! So where’s the connection?

Well, golly. I didn’t say that the two fossils were closely related, did I? I just said that there was a connection. And here it’s a thematic connection, not a phylogenetic one. Look again at the original photo I shared on Friday.

Museum of Comparative Zoology, Harvard University

What the heck are we looking at? It’s Deinonychus’s tail! If you look between the horizontal bands running down its length, you’ll spy the caudal (tail) vertebrae. That’s the link, you see, another animal with another cool backbone. And as you know, I love a good backbone. So what exactly are those horizontal bands running the length of Deinonychus’s tail? Well, we’re not 100% sure, but the best hypothesis is that they’re ossified tendons that would have stiffened the tail and provided balance while running and pivoting and scaring the bejeezus out of potential prey. The vertebrae themselves have really long processes on the top and bottom that run laterally down the tail, too, adding additional stiffness.

Congratulations to ... no one. So many of you got pieces and came close, but no one got it. I stumped you! WOO! I'm so proud of me. (: (Sidenote: someone did guess right on Facebook, but the unofficially official rule is that correct answers don’t count unless they're here on the blog. Sorry about that...but be sure to comment here!)

A final story before I go. I’ve told you before, I think, that I studied paleontology under the amazing Farish Jenkins. Farish studied under John Ostrom, who discovered Deinonychus in the 1960s when Farish was his student at Yale. In 1974, Farish was leading his own expedition in Montana, accompanied by his wife and some other paleontologists. He told my vertebrate paleontology class one day that his wife was taking her turn using a jackhammer to clear overburden (a fancy name for the rock that’s in the way of the rock you want) and bits of rock were flying. Farish was standing close by and picked up a piece of flyaway rock…only it wasn’t rock. He waved his arms furiously to try and get his wife’s attention. Finally, she saw him and shut off the jackhammer. What had Farish picked up? A piece of fossilized bone, of course. But not just any piece of fossilized bone. It was a piece of fossilized bone that turned out to belong to a Deinonychus—the very Deinonychus that is on display at Harvard to this day. Thank goodness Farish was such a keen observer—he didn’t miss a trick…or a fossil.

Are you a teacher and want to tell us about an amazing free resource ? Do you have an idea for a Misconception Monday or other type of post? Have a fossil to share ? See some good or bad examples of science communication lately? Drop me an  email  or shoot me a tweet @keeps3.

Robotic Comet Lander Philae Says Good-Bye

On a dark stretch of the chilly Comet 67P/Churyumov–Gerasimenko the lander Philae has begun a lonely and silent vigil. After it landed awkwardly and bounced across the comet’s surface on November 12, 2014, Philae operated for just under three days—its planned primary mission length—before running out of energy and falling into hibernation. As the comet approached the sun in 2015 and the solar-powered spacecraft was able to warm up and recharge its batteries, the European Space Agency (ESA) reestablished contact on June 13, but messages were sporadic and the craft went silent on July 9. After tireless attempts to regain contact with the first spacecraft to land on a comet, the ESA will officially end Philae’s mission this week. Rosetta, the probe that carried Philae to the comet, is still orbiting the body and will continue to collect data.

Losing contact with a spacecraft, be it a lander that ran out of energy or an orbiter that was intentionally crashed, is always bittersweet—and also expected—for the humans who build and operate it. “If you plan out your mission, you’re aware you only have certain given time to collect your data,” says Stephan Ulamec, the Philae lander manager for the Rosetta mission.

Philae has had a rocky life on Comet 67P. For a landing like Philae’s there was only so much planning the engineering team could do. Unlike for landers destined for Mars or the moon, Ulamec and his team did not know what Philae’s landing site would look like in advance and knew very little about the comet itself, because no previous spacecraft had ever imaged it up close. Mission planners had to wait until the Rosetta probe reached the comet and could send back surface images before they could begin to rapidly select a good landing site. Because of these constraints, rather than design the lander for the specific terrain, they had to pack it with redundancies and make it flexible enough to operate on a variety of possible topographies.

 

Space Graveyard 

Defunct spacecraft litter the solar system from decades of expired missions. Some of them are landers and impactors that studied the surface of our astronomical neighbors and eventually lost contact with Earth. Others are orbiters sent to various bodies that were intentionally deorbited and crashed after their missions were complete. Here we show the final resting sites for a selection of these dead or purposely terminated spacecraft. 

Graphic by Amanda Montañez

These redundancies were vital when Philae’s initial bounce across Comet 67P/C–G’s surface landed it in an inhospitable region of the comet, called Abydos. Without sunlight, Philae’s solar array could not collect enough light to keep the lander going. It was able to use its backup battery to operate for a few days, during which it took measurements of the comet’s composition, surface strength and magnetic properties while also snapping pictures and scanning the comet’s internal properties. In fact, it was able to complete roughly 80 percent of its primary science goals in its short operational life.

If Philae had been able to anchor itself to its quickly selected landing spot, it might have stayed in touch with Earth for months, not days. Unfortunately, it was unable to secure itself to the comet’s surface on its initial touchdown. A combination of harpoons and thrusters attached to the lander that were designed to anchor it both failed; ice screws meant to drill into soft material could not penetrate the hard surface. Because of the comet’s extremely low gravity, after touching down it bounced to a less favorable location, and is thought to have come to rest shadowed from the sun, thereby unable to use its solar panels to recharge its batteries.

Serendipitously, the bounce helped reveal some details about the comet’s surface, which was initially expected to be relatively soft. “Many people were warning us that we would sink into the surface, like if you drop a stone into new-fallen snow,” Ulamec says. Instead, the fact that Philae bounced at all proved, surprisingly, that the comet’s surface was hard.

Losing contact with the lander does not disappoint Ulamec, considering how challenging the mission was and how much data Philae managed to collect despite its difficulties. “What was a bit disappointing was reaching contact again last summer and feeling there was a real chance at getting additional data,” Ulamec says. But saying good-bye to Philae had always been the plan. “The fact that we have a limited lifetime, that’s just how these missions have to be.”

Many times that limited lifetime is longer than anticipated. The NASA rover Opportunity, for instance, has explored Mars’s surface for the past 12 years whereas its initial life span was conservatively expected to be just 90 days. “The Energizer Bunny wouldn’t have lasted a day on Mars, yet this rover lasted over 4,000 days and it keeps going,” says John Callas, Mars Exploration Rover Project manager for Spirit and Opportunity. “This is like your 95-year-old grandmother playing a tough game of tennis every single day.”

Opportunity’s twin, Spirit, was also long-lived in comparison with Philae, but its ultimate demise was for similar reasons. After six years Spirit became mired in sand and could not position its solar panels toward the sun to collect enough energy to power its heaters so it survive the Martian winter.

After decades of probes launched to space on behalf of NASA, ESA and other international space agencies defunct spacecraft now dot the solar system, either drifting through space, in orbit or lying in rubble or at rest on the surfaces of planets, asteroids, comets and moons. “These vehicles are our proxies for exploration. We put them in these harsh environments and we send them on these one-way trips—we’re not bringing them home,” Callas says. These robotic vehicles deepen our understanding of the solar system by going where humans cannot. Although it is always sad to say good-bye, what they discovered endures and fuels future missions.

In the meantime the Rosetta probe is still going strong and will ideally enter a low orbit of the comet later this year. At that point, it should be able to get a visual of the lander on the comet. So although we may not be able to communicate with Philae, this likely is not the last we’ll see of the robotic explorer.

Antioxidant Use Still Small Mixed Bag

Are you gobbling up antioxidants as part of your diet and nutrition regimen? The benefits may be, well…

“It seems surprising, but even after several decades we don’t have a clear answer, there’s not, if there were really across-the-board powerful benefits we would have seen it, and that’s not the situation.”

Walter Willett. He chairs the Department of Nutrition at the Harvard T.H. Chan School of Public Health. He spoke at a January 15th forum on Cancer and Diet that wound up touching on diet and health in general.   

“The studies so far, randomized trials that have been done, don’t show much benefit. There was actually a surprising increase in lung cancer with beta-carotene, one of the antioxidants, in people who smoked and were heavy drinkers, although there was no increase in risk in people…who were generally pretty healthy to start with. So even the randomized trials give different answers…I think…that antioxidants are not a magic solution to cancer or other diseases, but there probably are some benefits. One example is that in a physicians health study randomized trial over 12 years, at the end of that period of time those taking beta-carotene had better cognitive function than people on placebo—a really interesting and potentially important finding.”

So antioxidants may provide some benefits to some people.  

“But even if there are, that’s only a small part of the changes that we need to make in diet and lifestyle to reduce our risk of cancers…there are so many other things that are quite well documented.”

The entire hour-long forum featuring Willett and other researchers discussing diet and health is archived online. Just google “Harvard public health forum”.

—Steve Mirsky

(The above text is a transcript of this podcast)

Scientists get ‘gene editing’ go-ahead

UK scientists have been given the go-ahead by the fertility regulator to genetically modify human embryos.

It is the first time a country has considered the DNA-altering technique in embryos and approved it.

The research will take place at the Francis Crick Institute in London and aims to provide a deeper understanding of the earliest moments of human life.

It will be illegal for the scientists to implant the modified embryos into a woman.

But the field is attracting controversy over concerns it is opening the door to designer – or GM – babies.

DNA is the blueprint of life – the instructions for building the human body. Gene editing allows the precise manipulation of DNA.

In a world-first last year, scientists in China announced they had carried out gene editing in human embryos to correct a gene that causes a blood disorder.

Prof Robin Lovell-Badge, a scientific advisor to the UK’s fertility regulator, told the BBC: “China has guidelines, but it is often unclear exactly what they are until you’ve done it and stepped over an unclear boundary.

“This is the first time it has gone through a properly regulatory system and been approved.”

Groundbreaking

The experiments will take place in the first seven days after fertilisation.

During this time we go from a fertilised egg to a structure called a blastocyst, containing 200-300 cells.

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Can We Decipher the Language of the Brain?

Understanding how brains work is one of the greatest scientific challenges of our times, but despite the impression sometimes given in the popular press, researchers are still a long way from some basic levels of understanding. A project recently funded by the Obama administration's BRAIN (Brain Research through Advancing Innovative Neurotechnologies) initiative is one of several approaches promising to deliver novel insights by developing new tools that involves a marriage of nanotechnology and optics.

There are close to 100 billion neurons in the human brain. Researchers know a lot about how these individual cells behave, primarily through “electrophysiology,” which involves sticking fine electrodes into cells to record their electrical activity. We also know a fair amount about the gross organization of the brain into partially specialized anatomical regions, thanks to whole-brain imaging technologies like functional magnetic resonance imaging (fMRI), which measure how blood oxygen levels change as regions that work harder demand more oxygen to fuel metabolism. We know little, however, about how the brain is organized into distributed “circuits” that underlie faculties like, memory or perception. And we know even less about how, or even if, cells are arranged into “local processors” that might act as components in such networks.

We also lack knowledge regarding the “code” large numbers of cells use to communicate and interact. This is crucial, because mental phenomena likely emerge from the simultaneous activity of many thousands, or millions, of interacting neurons. In other words, neuroscientists have yet to decipher the “language” of the brain. “The first phase is learning what the brain's natural language is. If your resolution [in a hypothetical language detector] is too coarse, so you're averaging over paragraphs, or chapters, you can't hear individual words or discern letters,” says physicist Michael Roukes of the California Institute of Technology, one of the authors of the “Brain Activity Map” (BAM) paper published in 2012 in Neuron that inspired the BRAIN Initiative. “Once we have that, we could talk to the brain in complete sentences.”

This is the gap BRAIN aims to address. Launched in 2014 with an initial pot of more than $100 million, the idea is to encourage the development of new technologies for interacting with massively greater numbers of neurons than has previously been possible. The hope is that once researchers understand how the brain works (with cellular detail but across the whole brain) they'll have better understanding of neurodegenerative diseases, like Alzheimer's and psychiatric disorders like schizophrenia or depression.

Today’s state-of-the-art technology in the field is optical imaging, mainly using calcium indicators—fluorescent proteins introduced into cells via genetic tweaks, which emit light in response to the calcium level changes caused by neurons firing. These signals are recorded using special microscopes that produce light, as the indicators need to absorb photons in order to then emit these light particles. This can be combined with optogenetics, a technique that genetically modifies cells so they can be activated using light, allowing researchers to both observe and control neural activity.

Some incredible advances have already been made using these tools. For example, researchers at the Howard Hughes Medical Institute’s Janelia Farm Research Campus, led by Misha Ahrens, published a study in 2013 in Nature Methods in which they recorded activity from almost all of the neurons of zebra fish larvae brains. Zebra fish larvae are used because they are easily genetically tweaked, small and, crucially, transparent. The researchers refined a technique called light-sheet microscopy, which uses lasers to produce planes of light that illuminate the brain one cross-section at a time. The fish were genetically engineered with calcium indicators so the researchers were able to generate two-dimensional pictures of neural activity, which they then stacked into three-dimensional images, capturing 90 percent of the activity of the zebra fish’s 100,000 brain cells.

As remarkable as this achievement was, it shares a limitation with all “free-space” optical techniques that direct external light into the brain: light only penetrates so far into nontransparent tissue. Using two-photon microscopy, which uses high-wavelength light, the deepest tissue that can be imaged is two millimeters. This limits the regions that can be studied in animals where the outer structure, the cortex, is thicker than that. One of the core efforts of the BRAIN Initiative will be to push these limits. “People can use three-photon imaging to get deeper,” says neuroscientist Rafael Yuste of Columbia University, who pioneered calcium imaging and was a co-author of the BAM paper. The technology is now capable of penetrating three millimeters into tissue, he says. (Higher wavelength light penetrates further, but has less energy, so more photons are needed to illuminate the indicators.)

An alternative approach is being taken by a multidisciplinary collaboration of research groups, led by Roukes. Funded by a recent BRAIN grant, his team plans to combine optical methods with nanotechnology to produce nanoscale implants that are inserted into the brain but which interact with cells optically, at depths light can't otherwise reach. “With optical techniques where you're doing standoff sensing, as you go deeper, you lose resolution; the other paradigm is to implant things in the brain,” Roukes says. “Extremely narrow wires can be implanted slowly and tolerated, as long as you don't displace too much tissue.”

They call the technology “integrated neurophotonics.” The needles, or “shanks,” are studded with “emitter” and “detector” pixels, and optical waveguides (essentially tiny optic fibers) route light to the emitters, which use diffraction to send cell-size light beams into the brain. In effect, an optical imager is placed inside the brain. “It's an amalgamation of many different building blocks that applies photonic chip technology to functional brain imaging,” Roukes says. “It's exciting to think about how to use all these bricks to build a different kind of cathedral than has ever been created before.”

One of the project's early aims is to record from every neuron in a one-millimeter3 volume of tissue. “We can't understand the entire brain in one fell swoop, we've got to find some pared-down problems,” Roukes says. “The question is: Can we identify some sort of regional processor in the brain that we could understand deeply in the next 10 years?” There are small structures in the cortex called “cortical columns” where internal connections are dense and outward connections are sparse, making them likely candidates for being local processors. In mice these are one millimeter wide, with a one-millimeter3 volume containing around 100,000 cells—in other words, an ideal early target for study.

Roukes's group is also pushing conventional electrical probes to their limit. They have built nanorobes with needles of similar width to cells (around 20 micrometers), studded with nanoelectrodes, which poke into the space between cells. But because the distance over which electrodes can pick out signals from single cells amidst the cacophony of activity is limited, each electrode only allows researchers to record from, on average, one or two cells.

Such probes can currently record from around 1000 neurons. Scaling that up to 100,000 is “an engineering and financial problem” Roukes says, but this would have to be distributed across the brain, because recording every cell in one millimeter3 of tissue would involve around 70,000 electrodes, a level of intrusion far too likely to disturb cell function and damage tissue. Photonic probes might solve this problem. “The distance over which you can resolve individual neurons is much longer for optical than electrical interrogation,” Roukes says. “We can pick up 20 to 50 neurons, so we need fewer recording sites, which means we can space things out and make it less perturbative; that's why this approach looks very promising.”

The approach could bring the goal of recording from every cell in a millimeter3 volume in reach within two years. And if one probe can interact with 100,000 cells, 10 could interface with a million—the ultimate target of the project. All of which could potentially be done deeper inside the brain than is currently possible using free-space optics, and with less damage (and recording from many more neurons) than using “endoscope”-type methods for pushing microscopes deep into brains.

Everything is being developed in partnership with a manufacturing foundry, so the technology could be easily mass-produced and made available to the research community. Initial testing will be performed in mice but one of the project's neuroscientists, Andreas Tolias at Baylor College of Medicine in Houston also works with nonhuman primates, and plans to ultimately conduct tests in monkeys.

Extending it to humans won't be simple, however. “There's all sorts of issues with translating this to humans,” Roukes says. “At no time soon will that be possible.” Firstly, optogenetics involves genetic modification, and people are understandably hesitant to modify their genes. Also, the long-term biological compatibility of the implants in higher mammals is uncertain, especially as brains jostle as we move and breathe. “Most of the challenges will probably be around getting these shanks in without acute or chronic immune response,” says biophysicist Adam Cohen of Harvard University. “And without affecting circulation, popping blood vessels or having problems when the animal moves.” Then there's the matter of a surgical procedure to open the skull.

An alternative that might eventually be applied to humans is “neural dust.” Engineer and neuroscientist Jose Carmena of the University of California, Berkeley, and his colleagues, are thinking about nanoscale sensors incorporating wireless communications technology. “The idea is to build small sensors that record activity from local neighborhoods and transmit information wirelessly from deep in the brain,” Yuste says. “It's a third angle that's further in the future.”

Meanwhile, nanophotonics will benefit from related advances, such as better indicators. “All the details in the timing of individual spikes is what tells us what the brain is doing,” Roukes says. “And calcium reporters are slow, so they smear out some of this activity and lose information.” Voltage indicators are faster and record the neural signal researchers are most interested in, but they produce weaker and noisier signals. There are also indicators that report different types of activity—like other chemicals, neurotransmitters and even the actual physical force of moving parts of cells.  “The brain is a complex chemical system and [the] techniques for optical interactions over large volumes would be applicable to many different indicators,” says Cohen, who mainly works on developing such tools.

The potential applications are numerous and profound. “These tools will let us start to understand how complex behaviors arise from the ensemble of single-cell activity patterns,” Cohen says. “One might also use it to explore which areas are dysregulated in diseases and how those patterns lead to symptoms of the disease.” Brain–machine interfaces and neural prosthetics are other areas that will benefit. “This could address visual prosthetics for people who can't have retinal implants because the optic nerve is damaged,” Roukes says. “We could do direct interrogation and patterned stimulation of the visual cortex.”

Which of the approaches turns out to be most useful isn't the important question. A combination will likely be the ultimate answer. “There's a wide array of technologies on the table, and they're not mutually exclusive,” Yuste says. “This is not winner-take-all.”

 

New Weapon to Fight Zika: The Mosquito

Photo credit: Cristiano Burmester for The New York Times

By Andrew Pollack

Every weekday at 7 a.m., a van drives slowly through the southeastern Brazilian city of Piracicaba carrying a precious cargo — mosquitoes. More than 100,000 of them are dumped from plastic containers out the van’s window, and they fly off to find mates.

But these are not ordinary mosquitoes. They have been genetically engineered to pass a lethal gene to their offspring, which die before they can reach adulthood. In small tests, this approach has lowered mosquito populations by 80 percent or more.

The biotech bugs could become one of the newest weapons in the perennial battle between humans and mosquitoes, which kill hundreds of thousands of people a year by transmitting malaria, dengue fever and other devastating diseases and have been called the deadliest animal in the world.

“When it comes to killing humans, no other animal even comes close,” Bill Gates, whose foundation fights disease globally, has written.

The battle has abruptly become more pressing by what the World Health Organization has called the “explosive” spread of the mosquito-borne Zika virus through Brazil and other parts of Latin America. Experts say that new methods are needed because the standard practices — using insecticides and removing the standing water where mosquitoes breed — have not proved sufficient.

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Shifting Colors Of An Octopus May Hint At A Rich, Nasty Social Life

Photo credit: David Scheel/Current Biology

By Nell Greenfieldboyce

Some octopuses intimidate their neighbors by turning black, standing tall and looming over them threateningly, like an eight-armed Dracula.

That’s according to a study published Thursday that helps show that octopuses aren’t loners, contrary to what scientists long thought; some of the invertebrates have an exciting social life.

The study, in the journal Current Biology, focuses on one species, known as Octopus tetricus — the gloomy octopus — which gathers to munch on tasty scallops in the shallows of Jervis Bay, Australia.

“There can be over a dozen octopuses or more at this site,” says David Scheel of Alaska Pacific University. “Generally, during the Australian summer there are more and we see a lot of activity then.”

A local diver, Matthew Lawrence, first noticed there was a lot of octopus interaction going on there. His observations piqued the interest of Scheel, who is a marine biologist, and Peter Godfrey-Smith, a philosopher who had been thinking about octopus consciousness.

The research team eventually recorded 52 hours of underwater video, showing 186 octopus interactions.

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