Author Archives: George Johnson

Can GeoEngineering Beat Global Warming?

If the Paris accords fail, GeoEngineering may offer our last best hope for beating global warming… but there is much we do not yet know.

Atmospheric carbon dioxide levels are at a 2 million year high, with most of the rise since 1900. In response, global temperatures are rising rapidly. If nothing is done to reverse this trend, earth’s oceans are going to rise as polar ice melts and flood coastal cities like Miami. Drought and weather extremes will become commonplace.

FPO Fig 38.6, p808

The amount of CO2 in earth’s atmosphere, estimated in many different ways, shows little increase for the first 800 of the last thousand years. Over the last 200 years, however, levels have increased dramatically. Precise measurement at Mauna Loa Observatory, Hawaii indicate the steady rise continues unabalted today.

What should we do to reverse this trend? There are only two feasible solutions to global warming induced by the carbon dioxide released by humans into earth’s atmosphere. One is to reduce the amount of CO2 humans release. While attempts are being made to reduce car and power plant emissions, no serious impact has been achieved. Meeting in Paris last week, the nations of the world agreed to attempt better control of carbon emissions, setting long range targets focused on reducing the burning of coal and other fossil fuels. The goal: to reduce carbon emissions to keep the rise in global temperature  “well below 2 degrees C.”  No one knows if these promised efforts will succeed in meeting that ambitious goal, but the attempt is essential.

Discouragingly, even if the goal is met, the Paris target gets us only half-way there… which takes us to the other potential solution to global warming: GeoEngineering.  GeoEngineering is a  deliberate intervention to alter earth’s climate. Among a host of proposals, many impractical, two approaches are being evaluated seriously. One removes CO2 from the atmosphere by fertilizing earth’s oceans to induce massive photosynthesis, while the other injects sulfate aerosol into the atmosphere to reflects sunlight away.

Ocean Fertilization.  Removing the excess CO2 from earth’s  atmosphere is easier said than done. Attempts to store (sequester) atmospheric  CO2 in deep wells do not seem practical on a large scale. Where else might one put it? The most promising answer, oddly enough, is: back where it came from.

In 1988 Ocean ecologist John Martin famously said, “Give me half a tanker of iron and I’ll give you an ice age.” He was pointing out that earth’s oceans are rich in marine algae, their growth limited primarily by lack of iron (Fe). Adding iron to the upper ocean could trigger an algal “bloom,” its intense photosynthesis sequestering massive amounts of CO2 in organic matter that would then fall to the ocean’s bottom where it could no longer react with earth’s atmosphere. In essence, fertilizing the oceans with Fe would reverse man-made global warming, returning CO2 to the state from which the burning of fossil fuels had released it.

In the laboratory, experiments had suggested that every pound of iron added to ocean water could remove as much as 100,000 pounds of carbon from the air, so Martin’s quip was taken seriously. However, while exciting, Martin’s iron dump hypothesis is not an easy idea to test. In a series of small-scale tests of the idea, adding iron to sea waters always succeeded in drawing carbon from the atmosphere into the oceans (Figure 38.7) , although not as efficiently as in the laboratory.

FPO Fig 38.7, p808


12 small-scale ocean experiments have been carried out since 1988 (red dots on the map).

However, two potential problems were revealed by these early experiments: 1. Tiny xooplankton that live on the ocean’s surface eat much of the bloom of algae as soon as it forms, returning the CO2 back to the atmosphere; 2. Surface bacteria consume dead algae, and in doing so remove life-giving oxygen from the water. These two processes both assume the algae do not sink beneath the ocean surface, as Martin had claimed they would. Do they? In these studies, ocean currents have confused our ability to assess this critical question, but researchers in 2012 found a solution. In the Southern Ocean near Antarctica, currents swirl, forming stable eddies within which the necessary measurements could be made. If Martin is right, adding Fe to the ocean waters should produce an algal bloom within the eddy that would then fall downward into the deep ocean.

George's ship


To test this prediction, a businessman-turned-eco-warrior named Russ George added 100 tons of iron sulfate from a fishing boat into the ocean eddy, and then for a month measured organic carbon and chlorophyll in a 100 meters deep column of ocean water.

FPO Fig 38.7, p809

You can see in the graph what happened in the graph: a week after fertilization an algal bloom explodes within the eddy waters, reflected in rapidly rising levels of organic carbon. Another week later, the bloom reaches its maximum size, and then begins to fall as the algal mass sinks to the ocean bottom. Martin’s iron dump hypothesis is confirmed.

While this result is promising, ocean fertilization remains a highly controversial approach. Legal and ethical issues arise fom the fact that no one country owns the earth’s oceans (for example, George’s experiment, done without obtaining any international approvals, was greeted with outrage by many countries). The key problem is that the potential ecological impact of extensive and prolonged Fe fertilization is poorly characterized, and may be significant even if the Fe-induced algal blooms sink below 1000 m. It seems likely, for example, that Fe fertilization will promote growth of the bacteria responsible for nitrification in the oceans, and N2O is a much more powerful greenhouse gas than CO2. Simply said, there is a great deal we don’t know, making iron fertilization of earth’s oceans ecological risky until these matters are more clearly understood.

Sunlight Reflection.  A second geoengineering approach makes no attempt to reduce CO2 levels in the atmosphere. Instead, it turns the upper stratosphere into a mirror, reflecting the sun’s rays back into space. Despite rising CO2 levels, the world’s climate does not warm because light is not being absorbed by the CO2 molecules.

How to convert the stratosphere into such a mirror? Researchers propose to inject sulfate particles high up into the air; suspended in an aerosol, these particles act like countless tiny mirrors. Seen from space, the earth would look bright with reflected light.

Could this be done? Almost certainly. A few hundred thousand tons of aerosol would need to be added to the atmosphere annually, not a simple task but doable.

Would it work? Much of the support for the approach comes from computer climate-prediction models which have a record of uncertainty. The only way to know for sure will be to try it.

Like iron fertilization of earth’s oceans, using sulfate aerosols to reflect sunlight from earth’s atmosphere is a controversial approach because of the possibility of profound unintended ecological and climatic consequences. A recent event provides a picture of the sorts of things that might happen: On June 15, 1991 the top blew off Mount Pinjatubo in the Philippines, delivering 20 million tons of sulfur dioxide to the stratosphere.

FPO Fig 38.9, p809


As would be expected, earth experienced a general global cooling (about 0.9 degrees F) due to this stratospheric reflective veil of sulfate, but some regions experienced significant warming instead; a large portion of the earth experienced dought conditions in 1992, in patterns difficult to predict. The influence on agricultural photosynthesis was profound but patchy in ways not well understood.

There is a second problem with this approach, subtle but profound. It does nothing to slow or reverse the steady increase of CO2 in earth’s atmosphere. The ocean acidification that results from CO2 dissolving into seawater (CO2 + H2O = carbonic acid) continues unabated, with ecological impacts at least as unpredictable as those of ocean fertilization. Again, there is simply a great deal we do not know.  And there is this: increasing levels of atmospheric CO2 in the future, unreduced by this approach, will make abandoning the program of sulfate aerosol injection less and less possible as years go by, lest we cook the earth.

On balance, then: No clear solution provided by GeoEngineering, with what we now know.  Clearly, time to start learning more.

Coywolves In Our Backyards

Wolves of the Northeast deep woods have interbred with western coyotes, and the hybrid coywolves now thrive among us

I have never seen a wolf or coyote, outside of a zoo. An urban college professor, I have lived for the last 45 years in suburban Saint Louis. A red fox family once graced our subdivision for a few years, but never a coyote “yip” or wolf “howl” have I heard in our well-groomed neighborhood, no wild fur have I seen.

Until last month. Driving along a city street passing through a patch of woods not one hundred yards from a traffic light intersection, I saw something my eyes had a hard time believing. Dashing from the trees to my right and across the street in front of my car was a coyote, a really big one! Its tail streaming behind, it soon vanished into the patch of forest to my left, a brief apparition that engraved itself on my memory.

At least I thought it was a coyote. Big, though, for a coyote, heavy set rather than slender. Too small to be a wolf like those I had seen at the zoo, so probably not a wolf. Not a dog, either – of that I was certain. While it was the size and build of a really big German Shepard dog, there was no escaping the appearance — the long red-grey fur of its coat and its full furry tail – of a coyote.

What I had seen, it now appears, was a coywolf.

Grey wolf – coyote hybrids don’t happen

wolf     Four species of the genus Canis live in North America: coyotes and three kinds of wolves (grey, eastern, and red).  Grey wolves like the one in the photo are the most ancient of the four species, diverging from the other three 1-2 million years ago. Coyotes diverged from eastern and red wolves much more recently (150,000 – 300,000 years ago); as a consequence, coyotes are quite a bit closer genetically to these two wolf species than they are to the grey wolf.

Because of the great genetic distance between them, hybrids between coyotes and grey wolves are extremely rare. Several hybrids have been produced in captivity using artificial insemination, but in the wild hybrids simply don’t happen.

The Coywolf

coyote     So what is it that I saw? Too small for a coyote (as in the photo), and, besides, coyotes have never been common so far east as Missouri. However, it seems things have been changing. The trigger has been civilization. Over 400 years of clearing forests for farming in eastern North America and the hunting of wolves that has accompanied this clearing has led to a drastic population decline in eastern wolves. Like a falling chain of dominos, this decline has led to a chain of consequences, each triggering the next. The steep reduction in numbers of eastern wolves opened the door to an invasion of coyotes, moving into the wolves’ fast-emptying ecological niche from the coyote’s prairie homeland to the west. The dearth of available wolf mates facilitated the mating of the remaining eastern wolves with their new coyote neighbors.

Biologists think the initial hybrids were produced among dwindling wolf populations in southern Ontario, Canada, perhaps a century ago. As decades went by, the dogs that accompanied the farmers were added, like seasoning, to the genetic mix. Because of their genetic similarity, the wolf-coyote-dog hybrids were vigorous and successful – more successful, it turns out, than either parent species in the rapidly-changing environments of the ever-more-densely-populated northeast.

coywolf     The coyote-eastern wolf hybrid has been formally labeled the “eastern coyote,” but the name has not stuck, as the new beast is a long way from a coyote. The hybrid animals now numbers in the millions and are found throughout eastern Canada, in every eastern state north of Virginia, and as far west as Missouri. A study last year of the genetic makeup of 437 of these hybrids living in ten north-eastern states and Ontario revealed DNA which on average is 64% coyote, 26% wolf, and 10% feral dog. The resulting critter is informally but widely known as a coywolf.

Is the Coywolf a species?

So what are we to make of the coywolf? Should we think of it as true species, a fifth American member of the genus Canid? Many argue “no,” that the coywolf is just a transient, an accident of circumstance that will not persist. Continued mating with feral dogs will inexorably dilute the mix, these naysayers claim. If its genetic makeup is not constant, how can it be thought of as a species, they question. Other biologists disagree with them, pointing out that the anatomy and genetic makeup of coywolves is quite different from that of wolf, dog or coyote, and that there is little evidence of continued admixture of coywolves with dogs. All over the northeast, the coywolves look the same, and coywolves are now common in places where wolves and coyotes are not found (like Saint Louis). Isn’t that enough to qualify as a species?

Any high school student taking biology will be familiar with the biological species concept, which defines species as groups that are genetically sequestered – that is, that do not interbreed with other species. By this definition, coywolves are not a true species, as they freely interbreed with dogs (and presumably with wolves and coyotes). But by this same definition, wolves and coyotes are not true species either – after all, it was their interbreeding that produced the coywolves in the first place!

So there is lots of room to disagree. On balance, I don’t see a problem with accepting coywolves as a provisional species, a functional biological unit. Linnaeus knew little about the breeding behavior of the species he named. He looked for characteristic differences shared by all members – a way to identify an individual as a member of a group. I am happy to live by that limited definition. What I saw was — a coywolf.

Living amongst us

The coywolf I saw bounding across the road didn’t seem to be having any problem living in the middle of the Saint Louis suburbs. He knew how to cross the street in traffic, how to keep out of sight during the day, and big as he was, he certainly wasn’t having any trouble finding things to eat.

Screen Shot 2015-11-08 at 11.21.04 PM            What does an urban coywolf eat? Fast of foot and with big jaws, catching squirrels presents no problem (the squirrels in my yard as dumb enough even the dogs catch them). Pets also prove tempting targets. Studies of coywolf droppings reveal many cats are eaten. Adult Coywolves weigh in at about 55 pounds (25kg), twice the size of a coyote and strong enough to take down a small deer. With the population explosion of urban deer, coywolves may provide an ecological counterweight, keeping the numbers of deer down. Unlike wolves, coywolves like hunting in open terrain. They now live in a vast area east of the prairies where coyotes have never lived and where wolves have long since been exterminated. Now common in rural areas, they also populate the suburbs, and are even urban, living in big cities like Boston and Washington — New York City is said to harbor a population of some 20!

Those who study coywolves say their cries are a mixture of their ancestors’ cries. They start off with the deep-pitched howl of a wolf, sliding into the higher-pitched yipping of a coyote. I have not heard this cry in Saint Louis. But now, of an evening, I find myself listening.

e-Cigarettes: Legal Enslavement In the Name of Health

# e-cigarettes, fashionable among teens, are nicotine delivery tubes that financially chain teens to Big Tobacco

A new fad among American teens is the “smokeless” electronic cigarette, or e-cigarette. A tube made to look like a rather large cigarette, an e-cigarette contains no tobacco, delivering to the smoker a measured dose of nicotine within water vapor. Because no tars are introduced into the lung, e-cigarettes do not cause lung cancer. I read an editorial in the New York Times today about e-cigarettes that alarmed me to such a degree I had to write about it. A columnist I respect named Joe Nocera wrote strongly criticizing those who “demonize” e-cigarettes. While admitting in passing that “nicotine addicts smokers,” he points out that it is the tars in tobacco smoke that damage DNA and so cause lung cancer. Nicotine does not cause cancer. How can anyone object to e-cigarettes instead of cigarettes, he asks, as “there is no doubt the switch could save lives.”

That argument, which sounds so reasonable, makes the hair on the back of my neck stand on end. It is a classic bait-and-switch: waving health as a flag, it in fact endorses addiction for profit. The switch, you see, lies in the unstated assumption that only those already addicted to cigarettes will smoke e-cigarettes. Nocera’s claim that opposition to e-cigarettes “is costing lives” is only true given that assumption. A false assumption.

Screen Shot 2015-11-03 at 4.41.04 PM


Each day, thousands of teens and young adults who do not smoke cigarettes light up their first e-cigarette. Their friends are doing it, they have been told that there is no danger to their health, and Big Tobacco has made smoking e-cigarettes seem cool. So where’s the harm?

The harm is chemical enslavement. An e-cigarette is a nicotine delivery vehicle, nothing more and nothing less. Smoking one delivers a measured amount of nicotine to your lungs. The problem? Nicotine is a highly addictive drug. Many if not most of those teens experimenting with e cigarettes will become addicted, just as smokers do, and for exactly the same reason.

Many are going to find, when they try to quit, that they can’t. Addicted to the nicotine delivered in e-cigarette “smoke,” they simply will find it too difficult to overcome the habit. Most studies indicate a cigarette-smoking ‘quitting’ success rate — at least two year’s abstinence — of about 20 percent. Think about it: that’s an 80% addiction rate to nicotine.

The chemical nature of nicotine addiction is a tragedy but not a mystery. Scientists understand nicotine addiction quite well. Individual nicotine molecules attached themselves to a key protein on the surface of brain nerve cells that act to “fine tune” the sensitivity of a wide variety of other brain activities to chemical signals within the brain. Adjusting particular sensitivities up or down to slow some activities, speed others, this protein is responsible for overall coordination of the brain’s activities.

By artificially stimulating the system normally used by the brain to coordinate its many activities, nicotine alters the pattern of release by nerve cells of many chemical signals, called neurotransmitters— like turning up the setting on a TV remote that controls many television sets. As a result, changes in level of activity occur in a wide variety of nerve pathways within the brain. These changes are responsible for the profound effect smoking has on the brain’s activities.

Addiction occurs because the nervous system responds piecemeal to nicotine’s fiddling with its central control. The brain attempts to “turn the volume back down” by readjusting the sensitivities of each kind of activity to its signals individually, eventually restoring an appropriate balance of activities. Unfortunately, these readjustments may occur after only a few e-cigarettes.
Now what happens if you stop smoking e-cigarettes? Everything is out of whack! The newly coordinated system now requires nicotine to achieve an appropriate balance of nerve pathway activities. The body’s physiological response is profound and unavoidable. You are addicted to nicotine. There is no way to prevent this addiction with willpower, any more than willpower can stop a bullet when playing Russian roulette with a loaded gun. If you smoke e-cigarettes for long, you will become addicted.

e-cigarette smokerWhen a teen starts smoking e-cigarettes, he or she is signing on to contribute significant amounts of money to the tobacco industry for years to come. No wonder the tobacco industry promotes e-cigarettes. Instead of curing your nicotine addiction, they chain you to it.

So what do I think should be done about e-cigarettes? I think we must address the assumption implicit in Joe Nocera’s argument: while allowing adult smokers to switch to e-cigarettes, the federal government should restrict their availability to teens. We have just this restriction with alcohol, not a perfect protection (which of us didn’t manage to sneak a beer as a teen) but on the whole very successful. No one likes government intrusion into our private lives, but surely restricting availability to teens is preferable to their financial enslavement by Big Tobacco. In effect, they are selling cigarettes to our kids without the need to produce tobacco – they won’t sell them the more deadly product so long as they still make the same money. What they are selling – what they have always been selling – is addiction. For those they have already ensnared, e-cigarettes make sense. Selling them to anyone else should be a crime.

Does Life Exist on Other Worlds?

SETI (the Search for Extra-Terrestrial Intelligence) has a new lease on life – and a Goldilocks planet to listen at.

Screen Shot 2015-07-28 at 3.56.52 PMEighteen years ago this month, the film CONTACT was released, exploring the possibility of contact with life on other stars. The central idea of the film was to listen: Radio signals can travel through space, and those reaching earth might carry signals from other civilizations living on planets orbiting distant stars. While the film was fiction (based on a thoughtful book by astronomer Carl Sagan), the search was — and is — not.

The Search for Extraterrestrial Intelligence, or SETI, was originated in 1960 by the then-young astronomer Frank Drake. He was working at the new Green Bank 26-meter radio observatory dish in West Virginia, and was able to beg 150 hours of observation time from its (I-suspect-amused) director to point the telescope at two nearby stars, Tau Ceti and Epsilon Eridani, and scan for radio signals. He didn’t hear any, but it was the birth of a search that is ongoing, and that this week gained a huge new push.

images-2But before leaping to this exciting development, it is worth taking a moment to look back. Drake was not the first to speculate about life elsewhere. In the nineteenth century it was commonly speculated that life might exist on the moon.  In 1865 the French novelist Jules Verne described moon men in From Earth to the Moon.  We now know that life never evolved there.  Life did, however, reach the moon in 1969.  The planet from which life came can be seen in the photograph to the left, rising above the distant hills in the moon’s twilight.

How about life elsewhere in our solar system? Ever since the erroneous reports of canals on Mars by nineteenth century astronomers, it has been speculated that life in some form might Unknown-1exist there. In the mid-1970s the first of many space probes landed on the martian surface to explore for life. Extensive tests were done on soil samples, but no evidence of life was found. Nor has any direct evidence of life been found by the trusty little rovers NASA has had sniffing around the martian landscape in recent years.  Like the teasing suggestion of watery seas, all we have are insubstantial hints.

Nor is Mars the only place in our solar system with conditions that might foster the evolution of life.  Europa, a large moon of Jupiter, is a far more promising candidate. Europa is covered with ice, and photos taken in close orbit in the winter of 1998, like the one shown here, reveal seas of liquid water beneath a thin skin of ice. imagesAdditional satellite photos taken in 1999 suggest that a few miles under the ice lies a liquid ocean of water larger than earth’s, warmed by the push and pull of the gravitational attraction of Jupiter’s many large satellite moons. The conditions on Europa now are far less hostile to life than the conditions that existed in the oceans of the primitive earth. In coming decades, satellite missions are scheduled to explore this ocean for life.

Might life exist on other solar systems in distant galaxies?  The nearest galaxy to ours is a spiral galaxy called Andromeda.  It contains millions of stars, many of them resembling our own sun. The universe contains over 200 billion such galaxies, with 1020 (100,000,000,000,000,000,000) stars similar to our sun.  We don’t know how many of these stars have planets, but it seems increasingly likely that many do.  The first was discovered in 1995 orbiting the star 51 Pegasi, about 50 light-years from earth. Its discovery ignited a storm of discovery that is still growing. Since the launch of NASA’s Kepler planet-hunting spacecraft in 2009, 4,675 distant planets have been detected, and the list continues to grow. Astronomers now believe that at least 10% of all stars are orbited by potentially habitable Earth-size planets.

Is it likely that any of these far planets harbor life?  What would the distant planets have to be like?  The life forms that evolved on earth closely reflect the nature of this planet (water rich) and its history (oxygen gas becoming common in the atmosphere only later).  If the earth were farther from the sun, it would be colder and chemical processes would be much slower.  Water, for example, would be a solid, and many carbon compounds would be brittle.  If instead the earth were closer to the sun, it would be warmer, chemical bonds would be less stable, water would be a gas, and few carbon compounds (carbon is the basis of all life here on Earth) would be stable enough to persist.  The evolution of a carbon-based life form is probably possible only within the narrow range of temperatures that exist on earth, which is directly related to its distance from the star it orbits, the sun.

The size of the earth has also played an important role in favoring life, because it has permitted a gaseous atmosphere.  If the earth were smaller, it would not have a sufficient gravitational pull to hold an atmosphere, and it would be cold and lifeless.  If it were larger, it might hold such a dense atmosphere that all solar radiation would be absorbed before it reached the perpetually cold surface of the earth. To harbor life, it thus seems a planet would have to be what is referred to as a “Goldilocks” planet (like the fairy tale of Goldilocks and the three bears : “Not too hot, not too cold…”).

How many far planets are roughly the same size as earth, and the same distance from their sun?  All we have been able to do so far is guess.  If only 1 in 10,000 of these planets is the right size and at the right distance from its star to duplicate the conditions in which life originated on earth, the “life experiment” will have been repeated 1015 times (that is, a million billion times). We don’t KNOW, of course, if it has been repeated at all.

Kepler 452b earth-like planet
Until this month. On Thursday July 23, astronomers announced they have found a Goldilocks planet, orbiting a star 1,400 light-years from Earth. Labeled Kepler 452b, it circles a star very much like our sun, taking only 20 days longer to get around than Earth does. Temperatures on Kepler 452b would be similar to lukewarm water – not unlike the tropics on Earth. Its mass seems to be about five times that of Earth, meaning there is a good chance it is rocky like Earth, and not gaseous like Neptune. To be sure of this, astronomers will have to measure its mass more precisely, and that means observing the wobble of the star as it is tugged by the planet’s gravity – something we cannot yet measure at such a distance.

If so many planets in the universe may harbor life, how might we look for it? Radio and television signals can easily travel between the stars. Indeed, every radio and television program ever broadcast on earth will eventually reach the stars, although as a very weak signal. Elvis Presley’s appearance on the Ed Sullivan show in 1957 reached the nearest star Zeta Herculis after travelling 31 light years.  If they were to respond, we might expect to hear from them in four years.

UnknownWe will be listening. And THAT’S the huge new push for SETI announced this month! On July 20, Russian Internet billionaire Yuri Milner announced he would spend $100 million in the next decade to search for signals from alien civilizations. Because of the high cost of observation time on huge radio-telescopes, SETI has until now been forced to limit its search to a few radio frequencies deemed most likely for alien messages. With the funding provided by Milner, the search will be able to purchase ample time on some of the world’s biggest radio telescopes. Scanning the 1,000 closest stars with new multi-channel spectrum analysis techniques, SETI will be able to simultaneously monitor, for ten years, the millions of channels over the entire range of clear radio frequencies that reach the earth from space.

It does not seem likely to me that we are alone.  Our own galaxy, a small spiral galaxy called the Milky Way, contains many millions of stars.  Looking up on a clear night, I find it impossible not to ask myself, “On planets orbiting how many of these stars is someone studying the stars and speculating on my existence?”

Of course, with 1015 worlds on which life might have emerged, it seems to me we should have heard from someone by now… In a wonderful Calvin & Hobbs cartoon, Calvin says “I was reading about how countless species are being pushed toward extinction by man’s destruction of forests.” He goes on in the next frame to say “Sometimes I think the surest sign that intelligent life exists elsewhere in the universe is that none of it has tried to contact us.” As our rapidly-warming world listens to the stars, I can only hope that Calvin is being too cynical, that we will wise up and stop destroying our planet, so we will have something worthwhile to say to whoever out there might be trying to communicate with us.

How to Kill a Dinosaur

As JURASSIC WORLD roars in theaters, scientists again debate whether dinosaurs were killed by an asteroid or by volcanos

Screen Shot 2015-07-06 at 2.12.03 PMThe current film hit Jurassic World, like the three dinosaur thrillers before it, involves killing a lot of dinosaurs running amuck on an isolated island. Ignoring Lewis Carroll’s warning to “shun the frumious Bandersnatch,” scientists on the island have genetically engineered dinosaur DNA to create really scary critters, who of course get loose and begin eating people. How do the folk in these movies kill the dinosaurs? They shoot them, blow them up, electrocute them – almost anything a kid would dream up playing with toy dinosaurs on the kitchen floor.

Oddly enough, the key dramatic question driving the action in all of these films – how to kill a dinosaur – has become a very lively topic of argument among scientists in the last few months. There was a day – last year, say – when we thought we knew how all the dinosaurs died. Killed by a meteor impact, right? Now… maybe not. Another candidate for Dino Killer, long discounted, has returned to the list of possibilities. How it has done so is a story too good not to explore, so lets have a look:

The event we are talking about – the extinction of the dinosaurs – took place at the end of the Cretaceous, 65 million years ago. Not only did all dinosaurs disappear, but so did flying reptiles (pterosaurs)but not birds, swimming reptiles (ichyosaurs and plesiosaurs) but not fish, all ammonites (a very diverse group of marine animals), all marine forams (the White Cliffs of Dover are made of foram shells)   — in fact, everything in the sea with a shell became extinct, and everything large on land except plants. Whatever killed the dinosaurs did a very thorough job of killing.

Needless-to-say, people have wondered what happened. When you discount the “crazy” theories (dinosaurs were hunted to extinction by cavemen, mammals ate all the dinosaur eggs, a dino virus did them in, etc), there are only three theories in serious contention.

Failure to Adapt. During the Cretaceous period, earth’s climate gradually grew cooler. This theory proposes that dinosaurs were unable to adapt to a cooler earth, and gradually died out. The problem with the theory is that the change in the fossil record is far more abrupt than the climate change, a few hundred thousand years at most, and probably far less. If you look at a specific place – say the Hell Creek dinosaur bed in Alberta – there is no change in dinosaur diversity right up to the very end of the Cretaceous – then no dinosaurs at all. So this theory is rejected by the data. While a drastic change in the environment surely has something to do with the dinosaur death, that change was not gradual.

Death from Space. If you look at old rock, there is a clay layer that formed at the end of the Cretaceous. In 1978 Paleontologist Walter Alverez set out to look carefully at this band to see if the tiny sea shells of this clay were of uniform age – a technical point, but of interest to him. To date the calcium carbonate of the shells, he needed a constant reference point. He chose the element iridium, common in meteorites (500 parts per billion) but very rare in the earth’s crust (only 0.03 parts per billion). Everything went pretty much as expected until Alverez’s measurements reached a thin, dark line in the center of the clay layer: the iridium in this narrow band of rock was 450 parts per million! Puzzled, he took this alarming data to his father Luis, a Nobel Prize winner and so no slouch at sorting out scientific puzzles. The Alverez brothers looked at other rock samples. Wherever on earth the samples came from, rocks sampled from the boundary layer marking the end of the Cretaceous contained iridium, lots of it, while no other rocks did. The boundary layer rock also contained shocked quartz grains of a sort found only at nuclear test sites and meteor craters like the one below.

meteor crater 2

Their conclusion: the iridium found in the boundary layer is extraterrestrial, and came from the only place in our solar system where there is a lot of iridium – a meteor. To get enough iridium, they calculated the meteor that hit the earth would have to have been some 10 km in diameter, so big that it would have created a 185 mile diameter crater! In 1990 a candidate crater was impact site mapfound, at Chicxulub (“dragon’s tail”), off the north coast of Yucatan, Mexico. The crater was big enough (110+ miles in diameter) and the right age (just 32,000 years before the end of the Cretaceous). A blast of the size such an impact would have created could easily have had enormous environmental impact all over the world, enough to kill dinosaurs. And the impact happened just when all the dinosaurs disappeared. For the last 35 years, this asteroid theory of dinosaur extinction has been the winner, widely accepted as proven.

Volcanoes. There has however, in the background, been another theory that refuses to go away. To get our hands around it, it is useful to step back a minute. There have been five mass extinction events in the history of life on earth. The most extensive 5 extinctionsoccurred at the end of the Permian 252 million years ago when 90% of marine species on the planet were destroyed. Two mass extinctions, at the end of the Permian and the end of the Triassic, occurred at about the same time as massive volcanism. The
volcanic activity photogreatest volcanic outbursts in earth’s history, they covered Siberia with a blanket of lava miles thick bigger than the area of Western Europe, and much of the floor of the North Atlantic. Might these fiery events have led to mass extinctions? To find out, geochemists measure the age of the old lava, using the slow but steady radioactive decay of uranium-238 to lead-206 in tiny zircon crystals created by the eruptions. New, very precise measurements of the volcanic rocks date them bang-on with the mass extinctions: the Siberian lava is 252.3 million years old, and the Permian extinction took place 251.9 years ago. 50 million years later, lava gushed from the seams of the supercontinent Pangaea as it broke apart, creating the Palisades across from New York City – whose age has recently been measured as matching the date of the mass extinction at the end of the Triassic.

So what has this got to do with the dinosaurs? You got it – there was another massive volcanic event that occurred in west India 65 million years ago at the end of the Cretaceous – the same time the dinosaurs went extinct. Called the Deccan (Sanskrit for Southern) Traps (Dutch for staircase), the lava flows cover 2 million square kilometers! As you can see in the photo, the layers of lava from successive eruptions do indeed look like a staircase. Until recently, it was thought that the volcanic activity occurred over a protracted photo of Deccan traps

period of half a million years, way too slow a change to have removed the dinosaurs. New more accurate lava dating, announced only last month, changes that conclusion. It now appears that most of the lava erupted in less than a million years. When? As you can see in the graph below, just before 65 million years ago. Just when the dinosaurs made their exit. A “smoking gun” indeed.

map of Deccan Traps

So, two rival theories. The volcano theory has the advantage that it can be put to work explaining three mass extinctions. Could asteroid impacts also explain other mass extinctions? Two candidates come quickly to mind: the 62-mile-wide Manicouagan crater in Quebec should have been big enough to wipe out a third of life on earth, but when dated had no discernable effect on biodiversity. Nor did the huge meteor that created a 90 km crater under Chesapeake Bay 35 million years ago. Other than at the end of the Cretaceous, there are no asteroids at mass-extinction boundaries. One point for the volcano guys.

The dinosaurs were not the only groups to go extinct at the end of the Cretaceous. Everything in the sea with a shell also disappeared. Its easy to explain this with volcanic eruptions – injection of massive amounts of sulfur into earth’s atmosphere would lead to world-wide acid rain (sulfuric acid, no less!) and acidification of the world’s oceans. Calcium carbonate dissolves in acidic water. There go the shells of ammonites and forams. Can asteroid impact match this? Not well. In a bit of a stretch, it is conceivable that the intense heat of the shock wave could have caused O2 and N2 to combine to form nitric acid, acidifying the oceans that way. A bit far-fetched. On balance, another point for the volcano guys.

So who wins? There is no way to choose, really. Both asteroid impact and volcanic eruption events occurred at the time the dinosaurs disappeared. Imagine someone shot at the same time in head and heart by two assailants. Who killed him? Either bullet would do the job. You pays your money, you takes your choice.

Ballpark Physics

Xavier Scruggs, a terrific batter recently brought up from the minors, has never hit a major league home run, for reasons that have a lot to do with physics

As Major League Baseball warms up for its mid-season All Star Game on July 14, my attention turns to the ball field. In part this is because I live in Saint Louis, and here we love our Cardinals. Also because I love the science of baseball, and the maturing of the season has by now begun to reveal this year’s masters at ballpark physics. And success in baseball is all about physics. Nowhere is this more true than in the ultimate baseball act, hitting a home run.

oblong Scruggs

The batter above is Xavier Scruggs, novice first baseman for the Saint Louis Cardinals. You see him in the act of hitting a baseball, something he is very good at doing: His batting average since being called up from the minors a month ago is .375; in his last two starts he has gone 6 for 8 with 4 RBI. But he has not hit a single home run. So Scruggs sits on the bench a lot, while other first basemen play who can hit one out of the park at least occasionally.

So why is it so hard to hit a home run? To sort this out, imagine you are at the plate in Xavier’s shoes, your muscles tensed with anticipation, holding a 42 inch wooden bat while you wait for the precise instant to swing at a 3 inch, 5 ounce cowhide-wrapped ball hurtling toward you at over 90 miles per hour. At this speed, it will take a little less than four-tenths of a second for the ball to travel the 60 feet, 6 inches from the pitcher’s mound to home plate.

This famous diagram, by Robert Adair of Yale University, lays out your challenge clearly. In that brief interval, if you decide to swing the bat, and have the good fortune to hit the ball, you will be carrying out a physics experiment on the transformation of energy. As you can imagine, there is a lot of energy invested in a baseball travelling 90 miles per hour. This energy of motion is called kinetic energy by scientists, and it’s easy to appreciate its raw power. Not so evident is the latent power in the muscles of the batter awaiting the pitch. Like coiled springs, their energy is ready to be put into action. This stored energy is called potential energy by scientists, energy ready to be put to work swinging the bat. The more potential energy the batter’s muscles release, the faster the speed of the bat through the swing.

Obviously there is a lot of energy at play here. The batter has converted a considerable amount of potential energy from his arm and shoulder muscles to the kinetic energy of the swinging bat. Similarly, the pitcher has converted potential energy from his throwing arm to the kinetic energy of the speeding baseball. What happens in the instant when the ball hits the bat is the difference between a home run, a fly ball, and the single or double “hit” Scruggs is so good at getting.

A lot of scientists’ time has been devoted to understanding that brief 1/1,000th of a second, the measured duration of the collision of a pitched baseball on a swinging bat.

The Sports Biomechanics Laboratory at the Davis campus of the University of California has for decades carried out detailed examinations of the scientific principles governing baseball. Many of the researchers in the Lab are graduate and undergraduate students in biomedical engineering. The student researchers have learned a lot about what it takes to hit a home run. The on-the-field mechanics of baseball: how pitchers throw, how batters swing — are examined through equations that attempt to simulate what happens when bat meets ball. When a simulation seems to take the laws of physics into account properly, it is then checked by direct measurements to see how well the simulation predicts what actually happens.

First lets look at how the ball is thrown. Three variables turn out to be of particular importance:

  • Ball velocity. Not surprisingly, balls that are pitched faster travel off the bat further. Much of the kinetic energy of the ball is returned to it by the bat, as kinetic energy of motion in the opposite direction.
  • Spin. However, even more important is the spin of the pitched ball. Conventional wisdom says a hitter can drive a fastball farther than a curveball the fastball travels some 42 meters per second, the curve ball only 35 meters per second, so the fastball has much more kinetic energy to contribute to the ball’s flight, imagesthey say. Not so, it turns out. A curveball is thrown with topspin, so the top of the ball rotates in the direction of the pitch. Being hit by the bat throws the ball into reverse, giving it backspin and thus lift to carry it further. A fastball is thrown with backspin; it spins the other way when hit, and so has less lift and sinks sooner.
  • Ball elasticity. When the ball is deformed by its collision with the bat, it tends to bounce back. The more elastic the ball, the more of its kinetic energy is returned by the bat. The cork core of a baseball is wound tightly with yarn to make it bouncy. If the yarn is wound tighter, a more “lively” ball results, one that travels further off the bat.

Now consider how the ball is hit. Again, three variables have been found to be of prime importance:

  • Bat speed. More than any other variable, the speed with which the hitter swings the bat determines how far the hit ball will travel. As a general rule, increasing the bat velocity of an average home run swing (30 meters per second) by one meter per second increases the distance of the hit five meters.
  • Bat position on ball. For optimal range, the bat should not contact the ball squarely, but rather 2.65 cm below center. This undercut imparts backspin, creating lift that causes the ball to travel further.
  • Ball position on bat. The impact of the ball causes the 42 inch wooden bat to vibrate, like plucking a tightly drawn string. This is important, because every vibration of the bat draws energy away from the ball, reducing its speed as it leaves the bat. Each bat vibrates at several low and high frequencies at once, like the harmonics of a violin string. Striking the bat at “nodes” where a frequency produces no vibrations avoids this loss of energy. The optimal position is about 6 inches from the tip. Interestingly, the shape of the shaft and handle makes no difference whatever — by the time the vibration reaches there, the ball has already left the bat.

Screen Shot 2015-07-01 at 10.51.37 AM

Because of the enormous kinetic energy invested in the baseball when a big league pitcher throws a 90 mph fast ball, to hit a home run Xavier Scruggs must act very fast, and very precisely. He has less than a quarter second to see the pitch, judge its speed and location, decide what to do, and then start to swing. The bat must meet the ball within an eighth of an inch of dead center to avoid a foul ball, at precisely the right millisecond to generate the correct arc to send it out of the park. A home run by Xavier, should he hit one, is all about precision in the application of energy. See? Ballpark physics doesn’t have to be boring…

Can CRISPR Eliminate Malaria?

Eliminating malaria may soon be possible, spreading resistance genes among mosquito populations in a chain reaction driven by CRISPR

One of the nightmares associated with genetically modified (GM) crops has been the worry that a genetic change engineered in the laboratory might somehow “escape” from a target crop and spread like fire through natural populations, with unknown and uncontrollable consequences. “Don’t fool with Mother Nature,” they warn – and they are not smiling.

            Over the last year, their nightmare has come one step closer to reality – and, paradoxically, humanity may be greatly enriched by that step. The step involves CRISPR, a precise and easy-to-use gene editing system that was the subject of a recent BiologyWriter article, Editing Your Genes with CRISPR.  One of the ways bacteria protect themselves from viruses is to store fragments of viral DNA, and cut up any sequences that exactly match the fragments. Researchers have recently learned how to substitute other DNA sequences for the viral ones, so that the cutter will target these new sequences instead — using this approach, called CRISPR, researchers can target any gene for cutting. If the researchers also at the same time supply a new sequence to the cell’s gene repair system, the cell will incorporate this new DNA to repair the cut area. Presto! You have changed one gene sequence to another… AND, if you do these edits in cells that give rise to sperm or eggs, the changes you have made will be inherited by future generations.

This is all in the lab, of course. Released outdoors, modified animals or plants would not take over wild populations, for the simple reason that most modifications do not improve an organism’s ability to survive and reproduce. In a sexually-reproducing diploid species like us, a gene has a 50% chance of being inherited by each parent, so that without improved survival, its frequency doesn’t change from one generation to the next. Every beginning biology student learns this as the Hardy-Weinberg rule.

But what if you stacked the deck? If the gene is passed on MORE than half the time, it could quickly increase in frequency within a population, couldn’t it? This sort of bias, called “gene drive” by professional biologists, doesn’t happen often in nature — but might it be possible to find a way to do it?

Yep. In 2003 British geneticist Austin Burt suggested a thought experiment: use target-specific DNA-cutting enzymes (called endonucleases) to attack mosquito genes necessary for transmitting the malarial parasite. Because the DNA-cutting enzyme would act on both chromosomes, the effect would be to change the 50% chance of the change being inherited to 100%. In effect, Burt said, the targeted nature of the nuclease attack would DRIVE the gene change through the population.

mosquito photo


            In 2015 Burt’s theoretical idea of an endonuclease drive was put to the test in Panama, and succeeded in reducing wild populations of dengue fever-carrying Aedes aegypti mosquitos 93%. Gene drives really work, just as Burt said they would

Enter CRISPR, which allows a particular gene sequence to be replaced by a new one devise in the laboratory. What if that new sequence was a two-part cassette that included not only the gene to be replaced, but also a copy of the CRISPR sequence? Do you see? A gamete with this cassette in its DNA will act in a fertilized egg on the DNA of the gamete contributed by the other parent, so that BOTH of an offspring’s chromosome sets now contain the cassette, and all of that individual’s offspring will bear the “new gene plus CRISPR” cassette. In future, every individual mated by any of these offspring will suffer the same fate, as will all of their offspring — a chain reaction!

Now imagine again Burt’s proposal of a gene drive for mosquitos. DNA researchers in the laboratory could insert into a mosquito a DNA cassette containing both CRISPR and a gene preventing transmission of the malarial parasite, directing CRISPR to cut the original but not the edited version of the gene. Released outdoors, this mosquito would mate with a wild individual, their offspring inheriting one wild and one laboratory copy of the parasite transmission gene. 50% transmission, right? But now CRISPR attacks the normal wild copy, inserting in its place the edited version + CRISPR. And so it begins: A CRISPR-driven chain reaction.

gene drive diagram

When tested in fruit flies in early 2015, this sort of CRISPR-driven chain reaction proved to be more than just an interesting possibility – it really works! In fact, it is shockingly efficient as a gene drive. Using a CRISPR drive cassette, researchers at UC San Diego “drove” a recessive mutation that blocks pigmentation of fruit flies from a 50% chance of being inherited to 97%!

Geneticists are already busy at work building a “Burt” laboratory mosquito with a CRISPR cassette containing the genes necessary to block parasite-transmission. Using this CRISPR gene drive, geneticists hope to be able to drive the parasite resistance genes into and through wild mosquito populations, and so eliminate malaria. Over half a million people die every year from malaria, so what these researchers are trying to do is no small thing — and think of the range of other diseases that could be conquered using a similar approach.

A little scary, though. CRISPR gene drives would allow any scientist to spread nearly any gene alteration through nearly any sexually reproducing population. Humans don’t reproduce as rapidly as mosquitos, of course, so it would take hundreds of years for a CRISPR-driven change to spread through human populations. And yet in 2015 we hear of a Chinese researcher using CRISPR to modify the genomes of nonviable human embryos.

Surely some sorts of safeguards are in order. This autumn The US National Academy of Science and the National Academy of Medicine are convening researchers and other experts “to explore the scientific, ethical, and policy issues associated with human gene-editing research.” While the potential for future good is great, decisions about when and how to use CRISPR gene drives should be made collectively. If we are going to fool with Mother Nature, we should do it carefully.

The Silence of the UFOs

There have been 90,000 reports of UFOs, now mapped. What is a scientist to make of UFO sightings by reasonable people?

Some strange ideas die hard; others seem immortal, alive in our minds, immune to logic or the criticism of wise elders. Flying saucers are an idea like that. Nowadays we call Unidentified Flying Objects, or UFOs. When I was a child, a lot of years ago, reports of flying saucers routinely made the news. They still do. Investigations by the government and by private individuals are announced from time to time, but have never led to conclusive proof that UFOs do, or don’t, exist.

UFO map

I am reminded of this forcefully with the recent publication of a map locating UFO sightings in the United States since 1905 – over 90,000 of them! Can so many people be flat wrong? Not surprisingly, reports of sightings tend to be located on the map most frequently where the most people are – and occur EVERYWHERE that people are. On the map, the size of a circle indicates how many different people reported seeing a particular UFO. The large circle over Chicago, for example, refers to the night of October 31, 2004, when 77 people scattered about the metro area reported seeing a formation of flying fireballs, travelling as triangles, then in straight lines, then again as triangles. 77 puzzled people – not all of them can be crazy, can they?

As a scientist, I am sure that the only way to resolve the issue of UFO sightings is to examine individual cases in detail. I was not in Chicago in October, 2004. I WAS, however, in the general area of another of the large circles where many people reported seeing a UFO. I am referring to the sighting of a UFO in central Illinois early one January morning fifteen years ago.

This particular UFO flew over Melvin Noll’s miniature golf course about 4 a.m., the morning of January 4, 2000. Flew is perhaps too strong a word. It wasn’t moving fast at all. Floated might be more like it. Melvin says he saw rows of windows. “It was all lighted up and so low that someone could have waved at me out the windows.”

Melvin, after digesting this unusual sight for a few minutes, lit out for the local police station at Highland, Illinois. The dispatcher called the police in Lebanon — it was headed that way — and they saw it too. Later, as it moved west, so did other police. In addition to Melvin Noll, four Metro East police officers filed reports of seeing the object in the sky as it passed Lebanon, Shiloh, Millstadt, and Dupo. At least two civilians also reported seeing the object as they drove to work early that morning.

I can think of three ways to account for Melvin’s UFO:

First, its all some sort of joke or hysteria, and there was in fact nothing real floating over Melvin and his miniature golf course. This doesn’t seem to me a likely explanation. Four independent police reports are no casual bit of nonsense, no encounter of the “after the bar closed” kind. Police are high quality observers, neither delusional nor fanciful. And the police that saw the UFO did not think it a joke. Indeed, two of the officers contacted the National UFO Reporting Center in Seattle the morning after the sighting.

Second, Melvin’s UFO might be some sort of novel military craft, not known to the general public. The police witnesses told reporters the object resembled a drawing of a “stealth blimp” that appeared recently in Popular Mechanics magazine. Was it an experimental military aircraft? There is no radar track to confirm or disprove — the air traffic control tower at Scott Air Force Base was shut down at the time. The government denies all knowledge of any such craft. Still, this is where I would bet my money.

Third, Melvin’s UFO might be a UFO. All those windows and brilliant glaring lights don’t sound like any blimp I ever heard of. How could a blimp generate enough power? But if it wasn’t a blimp, what was it? Sherlock Holmes said that when you have eliminated the impossible, what remains, however improbable, must be true. I suspect Homes would vote for the UFO.

My UFO path

A particularly interesting thing about Melvin’s UFO becomes clear if you plot the five confirmed reports of police sightings on a map. The sightings move south and west on a slow swooping curve aimed right at — St. Louis! The thought of just what in St. Louis is attracting UFOs beggars the imagination.

So, bottom line, are there UFOs? As a scientist I don’t accept UFOs as anything more than highly unlikely – but I see no reason to rule them out of the real world, consigning them to fantasy like Santa Clause and jackalopes. Said simply, there are very real limits to what we know, to what science is able to understand. Seems to me it’s a mistake to simply ignore 90,000 people, many of them sensible, reasonable folks. Better to skeptically reserve judgement.

I live quite comfortably in a world where reasonable people see UFOs. UFO sightings are sort of like background noise, constantly reminding us of the limits of what we know. I would miss them if UFOs were to be proven imaginary after all. I can no more imagine a world without UFOs than one without Santa. If there were one, I suspect it would be a drab grey place, with no “X files,” no “MEN IN BLACK,” no “INDEPENDENCE DAY.” I wouldn’t want to live there.

A Sense of Where You Are

This year’s physiology Nobel explains how LeBron James is able to sink a jump shot without looking at the basket.

LeBron James close-upIt is June of 2015 and you are watching the NBA championship game. LeBron James has the ball and is moving past the basket, closely guarded. Without looking back, he unexpectedly tosses the ball back over his shoulder. The ball rises up in a tight arc   and drops smoothly right through the net, behind James, who is still moving away from the basket. Two more points among the thirty he scores that night.

But wait a minute. LeBron James wasn’t even looking at the basket! How did he DO that? To those who watch a lot of basketball, the shot does not come as a great surprise. The over-the-shoulder basket was a specialty of Bill Russell, a great of a past generation, and of Bill Bradley, one of the most accurate of all shooters from out on the floor in the days before you got three points for doing it. When Bradley was interviewed about his over-the-shoulder shot by a neophyte reporter writing his first article for the New Yorker, the reporter wrote that Bradley tossed a ball over his shoulder and into the basket while he was talking and looking the reporter in the eye. The reporter retrieved the ball and handed it back to him. “When you have played basketball for a while, you don’t need to look at the basket when you are in close like this,” he said, throwing it over his shoulder again and right through the hoop. “You develop a sense of where you are.”

A sense of where you are. That is what LeBron James had that June night. But still – how did he DO that? Interestingly, the scientists who answered that question were awarded the Nobel Prize in Physiology this year for sorting this mystery out.

Like many Nobel prize stories, this one starts a long time ago — in 1948, when an experimental psychologist in London named Ed Tolman began studying how animals learn to navigate. He came to the conclusion that animals form some sort of cognitive “map” in their brain that allows them to move sensibly through their environment. No idea, of course, of what a cognitive map might look like, or where it might be located in the brain. The prevailing view among behavioral psychologists was that Tolman was being overly simplistic, and that his so-called “map” was not a thing, but rather a gestalt resulting from a complex web of sensory and motor neural relationships. Tolman’s “map,” in their view, was a metaphor.

There the problem sat until a young researcher, John O’Keefe, began to study animal behavior in the late 1960s. Experimental neurobiology was exploding with new approaches, and he was one of the first investigators to record the activities of single cells in the brain. Working carefully, O’Keefe was able to implant a tiny electrode into a single cell within the brain of a rat and record when that cell emitted a signal (in researcher parlance, the cell is said to have “fired”). He chose cells in the hippocampus, a small region of the brain that appears to be involved with balance, and after inserting the electrode let the experimental rat run about in a box. As the rat ran around exploring the box, O’Keefe recorded exactly where the rat went, and when the cell fired. The firing pattern was unlike anything he might have expected! Individual cells fired only when the rat was at a particular place on the floor of the box, and nowhere else. Different hippocampus cells fired at different places in the cells

O’Keefe called the individual hippocampus cells “place cells” and concluded that an animal’s memory of a place is stored as a specific combination of place cells in the hippocampus. Tolman’s map was real after all. For his discovery of place cells, O’Keefe was awarded half of this year’s Nobel Prize in Physiology.

Now we must fast-forward to the 1990s. Tolman’s exciting finding had sparked a large number of scientists to study how place cells create a map of the environment within the brain. Among them was a young couple, Edvard and May-Britt Moser, PhD students at the University of Oslo in Norway. Completing their degrees, they went to O’Keefe’s lab as post-docs, but after only a few months accepted a job offer at a small university in northern Norway. Away they went – but O’Keefe has lit a fuse in their imaginations.

Setting up their own small lab in a basement, they set out to address a simple question about O’Keefe’s hippocampus maps: might the firing of place cells be triggered by activity outside the hippocampus? A simple question, it led right off an intellectual cliff. At first, studies of cells in a structure adjacent to the hippocampus seemed to show place cells similar to those discovered by O’Keefe in the hippocampus. Then the young investigators did something only young investigators tend to do – they thought “outside the box.”

grid cellsThe way the Mosers changed the standard O’Keefe experiment was the way an inquisitive child might – they made a bigger box. Allowed to run about in this far larger environment, the firing of the place cells they had found showed an astonishing pattern: Individual cells were active in multiple places! These firing locations were not at all random – instead, a cell’s firing locations form the nodes of a grid, interlacing hexagons like the chambers of a beehive. In recognition of this repeating pattern, the Mosers called these cells “grid cells.” For their discovery of grid cells, they share the other half of this year’s Nobel Prize in Physiology.

This was a very exciting result, as a grid system allows the brain to measure how far a body moves, and so put scale to the place map in the hippocampus. Here’s how (you will need to look at the diagram to get this): Imagine the firing pattern of a particular grid cell is the orange grid of circles on the diagram. The pattern of orange circles forms a hexagon. mapping movementNow imagine a second grid cell has a firing pattern represented by the green circles, and a third grid cell a pattern represented by the blue circles. Now look what happens when the animal moves from where it is on top of the orange node, travelling towards the lower left: the green grid cells fire, then the blue grid cells. This gives the brain information about direction, speed, and distance! As the rat moves, the grid cell system is constantly updating the place map of the hippocampus with information about distance and direction of movement.

It is important to remember that humans are not rats. Often experiments carried out on rats produce results that differ from what happens when the same experiment is carried out in humans. Who says a human like LeBron locates himself in space the same way a rats does? Actually, it seems likely. Human grid cells were reported in 2013, and while the experiments are more indirect (you can’t go around inserting electrodes into someone’s brain and ask the person to walk around while you record), human grid cells seem to work just like rat grid cells.

            So that’s how LeBron James does it. He’s got great grid cells!

Editing Your Genes with CRISPR

With a new easy-to-use tool called CRISPR, researchers are now able to edit our genes, a prospect both promising and a little scary.

photo for CRTISPR articleWhat is CRISPR, and how does it work? Lets start with the cute monkey you see on this page. He is a gene pioneer. Last year his genes and those of a twin brother were deliberately manipulated by Chinese researcher Yingxu Huang. Two of the monkey’s genes were targeted by Huang, one regulating the monkey’s metabolism and the other involved in its immune system. For each gene, Huang replaced the normal monkey sequence with one he had manufactured in the lab. The healthy but slightly puzzled monkey you see here was the result. Now an integral part of his chromosomes, the Huang versions of the two genes will be inherited by all of his offspring. The ability to reach in and “edit” the genes of a primate — man or monkey — is astonishing, undreamed of until pioneering advances announced only two years earlier.

So how did Huang pull this off?  By using a recently-discovered, powerful tool for editing genes called CRISPR. This awful name, which we will explain in a moment, reflects the history of the tool’s discovery. Like many important scientific advances, CRISPR’s discovery was unexpected. The story starts several decades ago, with work being done in a quite different scientific area. In 1987 Japanese biologists were using the powerful new gene sequencing technologies to study the DNA sequences of bacteria. One of the researchers observed an odd repeating pattern within the DNA sequence at one end of a bacterial gene: A sequence of several dozen DNA bases was followed by the same sequence in reverse, then 30 seemingly random bases of “spacer” DNA. This 3-part pattern was repeated, with different sequences of the random spacer DNA, again and again.  What grabbed the researcher’s attention was the DNA sequence repeated in reverse. Why of interest? Because RNA molecules copied from a DNA sequence repeated in reverse (called palindromes) fold back on themselves. This looped RNA can then binds to proteins, something single-stranded RNA cannot do. The loop’s sequence of nucleotides determines to which protein it attaches. It seemed to the researcher that these gene clusters were somehow designed to interact with a protein.

What protein? When the palindromes discovered by the Japanese researcher were examined by other researchers, the protein was identified: the RNA loops bind to a DNA-cutting enzyme called Cas9. The result?  A DNA-chopper that can link to a “spacer” RNA sequence. Not very exciting, right?

The next step in this journey of discovery was not taken for more than a dozen years, until 2005, when genome sequence comparisons made from data bases stored on the internet revealed that the 30-base spacer DNA sequences originally identified by the Japanese researcher, thought to be random, actually were not random at all — they matched DNA sequences found in the genomes of viruses that infect and kill bacteria. The researcher had, without intending to, discovered a weapon bacteria use to fight viruses! How does this work? First the “spacer” RNA binds invading virus DNA of matching sequence, then the Cas9 DNA-cutting enzyme attached to the loop cuts up the virus DNA!

Now, quickly, came the key advance that will affect all of us. In June of 2012, researchers Jennifer Doudna and Emmanuelle Charpentier, using now-standard gene engineering approaches, showed that any 30-base sequence can be substituted for the spacer sequence. Why is this the key advance? Because it allows the researcher to target any gene for modification or destruction! What was an arcane research finding became, with one stroke, a powerful tool.

This tool, called CRISPR (the initials of a very awkward name: “Clustered Regularly Interspersed Short Palindromic Repeats”), powerful and easy to use, is rapidly altering the scientific landscape. One example: In 2014 AIDS researchers used CRISPR to protect against infection by HIV, the virus that causes AIDS. Every AIDS infection begins with the entry of an HIV particle into a human cell, an entry which requires a door, a cell membrane protein called CCR5. CRISPR can be used to disable CCR5 and thus block this door. In a test of this approach, individuals with their CCR5 gene destroyed by CRISPR resisted HIV infection. Indeed, in one of six patients tested, the HIV virus vanished altogether. An AIDS cure?
Importantly, genes can be edited as well as disabled. Cells constantly “proofread” their DNA, inspecting the genes for damage. If a DNA break like that caused by Cas9 is encountered before the chromosome replicates, the cell immediately attempts to correct the problem: its proof-reading enzymes chop out the damaged gene, so it can be replaced with a newly-made sequence copied from the gene’s twin found on the cell’s companion chromosome.  It is during this replacement process that gene engineers edit the gene: the Cas9-treated cell is flooded with lab-manufactured copies of the gene sequence intended by the researcher to replace the Cas9-targeted one. Inundated with these copies, the cell inserts one of them into the gap, instead of the sequence copied from the companion chromosome. The result is an “edited” gene!

The future of CRSPR research is exciting – but also a little scary. In 2015 Chinese researchers, following up on the work with monkeys, attempted to make inheritable DNA changes in human embryos. While unsuccessful, this alarming attempt emphasizes the need for caution as the use of the CRISPR tool becomes widespread. Dr Doudna and other researchers have called for a moratorium on attempts to create altered human babies. What do you think?