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kottke.org posts about science

Discovered: a new form of life

NASA’s astrobiology announcement is that they’ve found a new kind of life that incorporates the normally toxic arsenic into its DNA.

Life like us uses a handful of basic elements in the majority of its biochemistry: carbon, hydrogen, oxygen, and nitrogen for the most part. But phosphorus is also a critical element in two major ways: it’s used as the backbone of the long, spiral-shaped DNA and RNA molecules (think of it as the winding support structure for a spiral staircase and you’ll get the picture), and it’s part of the energy transport mechanism for cells in the form of ATP (adenosine triphosphate). Without it, our cells would literally not be able to reproduce, and we’d be dead anyway if it were gone. There are many other ways phosphorus is used as well, including in cell membranes, bones, and so on. It’s a key element for all forms of life.

[…]

Amazingly, using radioisotope-tagged molecules containing arsenic, they were able to find that the microbes incorporated the arsenic into their very DNA! It’s hard to stress how shocking this is; as I understand it, saying something like that to a microbiologist without evidence would’ve had them slowly backing away from you and looking for weapons or an escape route.

I guessed wrong about what NASA was set to announce today, but the actual announcement is much more interesting than the mere discovery of extraterrestrial life. Aliens are inevitable β€” we’re going to find them sooner or later β€” but a new kind of DNA, that’s not something that happens every day. Exciting! (thx, jon)


Has NASA discovered extraterrestrial life?

Here’s a curious press release from NASA:

NASA will hold a news conference at 2 p.m. EST on Thursday, Dec. 2, to discuss an astrobiology finding that will impact the search for evidence of extraterrestrial life. Astrobiology is the study of the origin, evolution, distribution and future of life in the universe.

I did a little research on the news conference participants and found:

1. Pamela Conrad (a geobiologist) was the primary author of a 2009 paper on geology and life on Mars

2. Felisa Wolfe-Simon (an oceanographer) has written extensively on photosynthesis using arsenic recently (she worked on the team mentioned in this article)

3. Steven Benner (a biologist) is on the “Titan Team” at the Jet Propulsion Laboratory; they’re looking at Titan (Saturn’s largest moon) as an early-Earth-like chemical environment. This is likely related to the Cassini mission.

4. James Elser (an ecologist) is involved with a NASA-funded astrobiology program called Follow the Elements, which emphasizes looking at the chemistry of environments where life evolves (and not just looking at water or carbon or oxygen).

So, if I had to guess at what NASA is going to reveal on Thursday, I’d say that they’ve discovered arsenic on Titan and maybe even detected chemical evidence of bacteria utilizing it for photosynthesis (by following the elements). Or something like that. (thx, sippey)

Update: According to Alexis Madrigal, the answer to the hyperbolic question in the headline is “no”.

I’m sad to quell some of the @kottke-induced excitement about possible extraterrestrial life. I’ve seen the Science paper. It’s not that.


Stem cells to aid the blind

Clinical trials are about to begin where embryonic stem cells will be injected into the eyes of people with Stargardt’s macular degeneration.

Robert Lanza, the company’s chief scientific officer, said that the first patient could receive the stem cell transplants early in the new year and although the trial is designed primarily to assess safety, the first signs of visual improvement may be apparent within weeks. “Talking to the clinicians, we could see something in six weeks, that’s when we think we may see some improvements. It really depends on individual patients but that’s a reasonable time frame when something may start to happen,” Dr Lanza said.


On the merits of premature ejaculation

Evolutionary speaking, premature ejaculation may not be such a bad thing after all.

So given these basic biological facts, and assuming that ejaculation is not so premature that it occurs prior to intromission and sperm cells find themselves awkwardly outside of a woman’s reproductive tract flopping about like fish out of water, what, exactly, is so “premature” about premature ejaculation? In fact, all else being equal, in the ancestral past, wouldn’t there likely have been some reproductive advantages to ejaculating as quickly as possible during intravaginal intercourse-such as, oh, I don’t know, inseminating as many females as possible in as short a time frame as possible? or allowing our ancestors to focus on other adaptive behaviors aside from sex? or perhaps, under surreptitious mating conditions, doing the deed quickly and expeditiously without causing a big scene?

Still, for recreational sex, it blows. (As it were.)


When science goes backward

John Horgan argues that in some areas, science and technology are moving in the wrong direction. Among those areas are space colonization, the origin of life, and ending infectious disease.

Decades ago antibiotics, vaccines, pesticides, water chlorination and other public health measures were vanquishing diseases such as malaria, yellow fever, polio, whooping cough, tuberculosis and smallpox, particularly in First World nations. In The Coming Plague: Newly Emerging Diseases in a World out of Balance (Penguin, 1995), the journalist Laurie Garrett noted that in 1967 U.S. Surgeon General William Stewart said that it was “time to close the books on infectious diseases” (Garrett’s words) and shift resources toward non-infectious killers such as cancer and heart disease. The global eradication of smallpox in 1979 seemed to fulfill Stewart’s vision. Hopes for the end of infectious disease were soon crushed, however, by the emergence of AIDS, mutant flu viruses and antibiotic-resistant forms of old killers such as tuberculosis.


Mutations in genes and text not dissimilar

In a post called Mutated Manuscripts: The Evolution of Genes and Texts, Sam Arbesman compares genetic mutations with textual mutations caused by humans.

While fun to chronicle such similarities, these similarities can also be exploited in the same way. Mutational differences between DNA sequences can be used to understand the evolutionary history of a population, or even a group of species. And so too with variants of the same manuscript. A famous example of this is from a 1998 research article in the journal Nature that quantitatively studied the differences between the 80 surviving versions of Geoffrey Chaucer’s The Canterbury Tales. By subjecting the variants to a battery of genetic analyses, the researchers were able to better understand the contents of the ancestral version, Chaucer’s own copy!


Do animals think?

And if so, then what? Do animals feel? Do they have souls? This article is a nice overview of what we know about the thoughts and feelings of non-human animals.

But one by one, the berms we’ve built between ourselves and the beasts are being washed away. Humans are the only animals that use tools, we used to say. But what about the birds and apes that we now know do as well? Humans are the only ones who are empathic and generous, then. But what about the monkeys that practice charity and the elephants that mourn their dead? Humans are the only ones who experience joy and a knowledge of the future. But what about the U.K. study just last month showing that pigs raised in comfortable environments exhibit optimism, moving expectantly toward a new sound instead of retreating warily from it? And as for humans as the only beasts with language? Kanzi himself could tell you that’s not true.

All of that is forcing us to look at animals in a new way. With his 1975 book Animal Liberation, bioethicist Peter Singer of Princeton University launched what became known as the animal-rights movement. The ability to suffer, he argued, is a great cross-species leveler, and we should not inflict pain on or cause fear in an animal that we wouldn’t want to experience ourselves. This idea has never met with universal agreement, but new studies are giving it more legitimacy than ever. It’s not enough to study an animal’s brain, scientists now say; we need to know its mind.


Liquid magic

Under certain circumstances, you can mix liquids of different colors, then unmix them, and not violate the second law of thermodynamics.

(via fine structure)


LHC generates a mini Big Bang

By smashing together lead ions instead of protons, researchers at the Large Hadron Collider have produced a “mini-Big Bang”.

The collisions obtained were able to generate the highest temperatures and densities ever produced in an experiment. “This process took place in a safe, controlled environment, generating incredibly hot and dense sub-atomic fireballs with temperatures of over ten trillion degrees, a million times hotter than the centre of the Sun.

“At these temperatures even protons and neutrons, which make up the nuclei of atoms, melt resulting in a hot dense soup of quarks and gluons known as a quark-gluon plasma.” Quarks and gluons are sub-atomic particles β€” some of the building blocks of matter. In the state known as quark-gluon plasma, they are freed of their attraction to one another. This plasma is believed to have existed just after the Big Bang.


Seawater antennas

The US Navy is looking for a way to replace bulky antennas on warships with antennas made from seawater.

What they came up with is little more than an electromagnetic ring and a water pump. The ring, called a current probe, creates a magnetic field through which the pump shoots a steam of seawater (the salt is a key ingredient, as the tech relies on the magnetic induction properties of sodium chloride). By controlling the height and width of the, the operator can manipulate the frequency at which the antenna transmits and receives. An 80-foot-high stream can transmit and receive anywhere from 2 to 400 mHz, though much smaller streams can be used for varying other frequencies, ranging from HF through VHF to UHF.

Wow. (via bldgblog)


Conjoined twins…with a twist

Tatiana and Krista Hogan are conjoined twins who not only share a bit each other’s skulls but also parts of their brains. So are they two people with two brains & personalities or one person with one brain and two (split) personalities?

Adding to the conundrum, of course, are their linked brains, and the mysterious hints of what passes between them. The family regularly sees evidence of it. The way their heads are joined, they have markedly different fields of view. One child will look at a toy or a cup. The other can reach across and grab it, even though her own eyes couldn’t possibly see its location. “They share thoughts, too,” says Louise. “Nobody will be saying anything,” adds Simms, “and Tati will just pipe up and say, ‘Stop that!’ And she’ll smack her sister.” While their verbal development is delayed, it continues to get better. Their sentences are two or three words at most so far, and their enunciation is at first difficult to understand. Both the family, and researchers, anxiously await the children’s explanation for what they are experiencing.


What’s it like on the International Space Station?

For one thing, sleeping is more troublesome than you’d think, considering the remote location:

The onslaught of apparent days and nights would play havoc with astronauts’ body clocks, so a shutters-down and bedtime schedule is imposed by mission controllers. Each of the crew has a closet-like cabin where they can hook a sleeping bag to the wall and settle down for the night. Some strap pillows to their heads to make it feel more like lying down. The lights don’t go out completely, though. People dozing in orbit see streaks and bursts of bright colour caused by high-energy cosmic rays painlessly slamming into their retinas. Fans and air filters add to the distractions, so some astronauts wear ear plugs to block out the constant hum.

Unsurprisingly, falling asleep can take some getting used to. Just as you are nodding off, you can feel as though you’ve fallen off a 10-storey building. People who look half asleep will suddenly throw their heads back with a start and fling out their arms. It gets easier with time. One Russian crew member is renowned for doing without a sleeping bag and falling asleep wherever he ends the day. Anyone still awake after bedtime would see his snoozing form drift by, slowly bouncing off the walls, his course set by the air currents that gently pushed and pulled him.

Whoa! The whole thing is worth a read.


The world’s most famous brain

Lovely long piece in the November issue of Esquire about the brain of Henry Molaison, who you may have previously heard of as Patient H.M., aka the man who lacked the ability to remember anything for more than a couple of minutes. His brain has now been sliced into thin slices in an effort to construct a map of the human brain accurate to neuron-level.

Corkin first met Henry at Brenda Milner’s lab in Montreal in 1962, and over the years, as the mining of his mind has continued, she’s witnessed firsthand how Henry continues to give up riches, broadening our understanding of how memory works. But she’s also keenly aware of Henry’s enduring mysteries, has documented things about him that nobody can quite explain, not yet.

For example, Henry’s inability to recall postoperative episodes, an amnesia that was once thought to be complete, has revealed itself over the years to have some puzzling exceptions. Certain things have managed, somehow, to make their way through, to stick and become memories. Henry knows a president was assassinated in Dallas, though Kennedy’s motorcade didn’t leave Love Field until more than a decade after Henry left my grandfather’s operating room. Henry can hear the incomplete name of an icon β€” “Bob Dy …” β€” and complete it, even though in 1953 Robert Zimmerman was just a twelve-year-old chafing against the dead-end monotony of small-town Minnesota. Henry can tell you that Archie Bunker’s son-in-law is named Meathead.

How is this possible?

The piece is written by the grandson of the doctor who removed a portion of Molaison’s brain in an effort to cure his epilepsy.


The physics of everyday life

Christoph Niemann hits another one out of the park with an illustrated look at the how physics governs everything we do in life.

Niemann's laws of physics

I loved his idea for calorie-neutral foods:

All you need is to freeze a pint of ice cream to -3706 F. The energy it will take your system to bring the ice cream up to a digestible temperature is roughly 1,000 calories, neatly burning away all those carbohydrates from the fat and sugar. The only snag is the Third Law of Thermodynamics, which says it’s impossible to go below -459 F. Bummer.


Butter greases the cognitive skids

After Seth Roberts started eating half a stick of butter every day, his speed in solving simple arithmetic problems increased by 30 milliseconds. Flaxseed oil also seemed to help.

This isn’t animal fat versus no animal fat. Before I was eating lots of butter, I was eating lots of pork fat. It’s one type of animal fat versus another type. Nor is it another example of modern processing = unhealthy. Compared to pork fat, butter is recent.

But watching the video of the talk, it’s unclear what’s actually being measured here…it could be that the butter is making his fingers faster at pushing the buttons. Or look at the graph…might a single line that indicates steady improvement over the course of the year also fit the data?


Finding the resolution of the universe

Researchers at Fermilab are building a holometer, the most precise clock ever, which will attempt to determine if the 3-D aspect of the universe is a hologram.

Black hole physics, in which space and time become compressed, provides a basis for math showing that the third dimension may not exist at all. In this two-dimensional cartoon of a universe, what we perceive as a third dimension would actually be a projection of time intertwined with depth. If this is true, the illusion can only be maintained until equipment becomes sensitive enough to find its limits. “You can’t perceive it because nothing ever travels faster than light,” says Hogan. “This holographic view is how the universe would look if you sat on a photon.”


The Great Egg Race

The Great Egg Race was a late-70s/early-80s BBC TV show that was a kind of Junkyard Wars on a smaller and more nerdy scale. The first episode shows a number of people attempting to build small egg carrying cars powered by rubber band.

I love this stuff. I had a physics teacher in high school who presented us with a number of these challenges throughout the school year. There was the strong toothpick bridge (someone basically cheated and made a glue bridge with embedded toothpicks) and the rolling object (it had to go down a short ramp and stop on a mark about 10 feet away), but my favorites were the mouse trap-powered car and the egg drop.

The winning mouse trap car was made with a lot of assistance from the student’s father, who owned a machine shop. It was light but solid with precisely machined plastic wheels and a precisely machined axle and travelled probably twice as far as any of the other cars, which were generally built with whatever crappy off-the-shelf components could be scrounged from the local five-and-dime. I spent three satisfying late nights building my car and came in pretty close to last.

The egg drop challenge involved constructing a landing pad no taller than 12 inches for an unboiled egg. Competitors dropped their eggs from successively greater heights until the egg broke. The two winning landing pads were successful at the greatest height that our small school could muster…out a window at the top of the football field stands, probably about 35 or 40 feet tall. One was a huge box full of wool and other soft materials that could have successfully cushioned an egg dropped from the top of the Sears Tower. The other winner was a tupperware bowl full of stale popcorn that your humble blogger grabbed off the counter the morning of the challenge after completely forgetting about it over the weekend. No one was more surprised than I to discover that popcorn is an ideal egg cushioning material…not that I let on. :)


Lots of big machines to make a tiny Sun

The Big Picture has a selection of photos of the National Ignition Facility which I’ve written about previously.

“Creating a miniature star on Earth” is the goal of the National Ignition Facility (NIF), home to the world’s largest and highest-energy laser in Livermore, California. On September 29th, 2010, the NIF completed its first integrated ignition experiment, where it focused its 192 lasers on a small cylinder housing a tiny frozen capsule containing hydrogen fuel, briefly bombarding it with 1 megajoule of laser energy. The experiment was the latest in a series of tests leading to a hoped-for “ignition”, where the nuclei of the atoms of the fuel inside the target capsule are made to fuse together releasing tremendous energy β€” potentially more energy than was put in to start the initial reaction, becoming a valuable power source.

The NIF and the LHC are this generation’s Apollo program.


Gliese 581g, we hardly knew ye

That habitable exoplanet discovery? Maybe not.

Astronomer Francesco Pepe of the Geneva Observatory in Switzerland, who spoke Oct. 11 at an International Astronomical Union symposium on planetary systems, reported a new analysis using only HARPS data, but adding an extra 60 data points to the observations published in 2008. He and his colleagues could find no trace of the planet.


The physics of Angry Birds

Using motion tracking software, Rhett Allain finds out if the flight of the slingshotted Angry Birds adheres to the laws of physics.

The only force acting on the bird (if the bird is not moving too fast) would be the gravitational force from the Earth. This is where I see lots of intro-student mistakes. They tend to want to put some force in the horizontal direction because the bird is moving that way. DON’T do that. That is what Aristotle would have you believe, but you don’t want to be in his club. There is no horizontal force in this case β€” no air resistance.

He also determines the height of the red bird: about 2.3 feet tall. The big red bird must be at least double that.


Old Weather

Using journals kept aboard ships and the sweat of volunteers (that’s *you*), Old Weather is attempting to compile a more accurate look at our planet’s recent climate.

Help scientists recover worldwide weather observations made by Royal Navy ships around the time of World War I. These transcriptions will contribute to climate model projections and improve a database of weather extremes. Historians will use your work to track past ship movements and the stories of the people on board.


Western, Educated, Industrialised, Rich and Democratic

…aka WEIRD. The majority of the subjects in behavioral science testing are WEIRD people, who make up only a small percentage of the global population. You can see where this would be a problem.

In the “ultimatum game”, for example, people are given $100 and told to offer some of it to someone else; if the other person accepts, each keeps their portion, but if they reject the offer, nobody gets anything. On average, Americans offer just under half, which seems to say much about human notions of fairness, or the fear of making an insultingly low offer. But many cultures behave differently; the Machiguenga of Peru prefer to keep more cash or, if on the other side of the deal, to accept whatever is offered. Another example: speakers of the Mayan language of Tzeltal are among several more likely to describe things as east or west of each other, not on the left or right. Academics would bristle, the researchers note, if journals were renamed with titles such as Journal of Personality and Social Psychology of American Undergraduate Psychology Students. But perhaps they should be.

(via russell davies)


Potential Earth-like exoplanet discovered

A team of scientists has discovered a potentially habitable planet located about 20 light years from Earth.

The paper reports the discovery of two new planets around the nearby red dwarf star Gliese 581. This brings the total number of known planets around this star to six, the most yet discovered in a planetary system other than our own solar system. Like our solar system, the planets around Gliese 581 have nearly circular orbits.

The most interesting of the two new planets is Gliese 581g, with a mass three to four times that of the Earth and an orbital period of just under 37 days. Its mass indicates that it is probably a rocky planet with a definite surface and that it has enough gravity to hold on to an atmosphere, according to Vogt.

Gliese 581, located 20 light years away from Earth in the constellation Libra, has a somewhat checkered history of habitable-planet claims. Two previously detected planets in the system lie at the edges of the habitable zone, one on the hot side (planet c) and one on the cold side (planet d). While some astronomers still think planet d may be habitable if it has a thick atmosphere with a strong greenhouse effect to warm it up, others are skeptical. The newly discovered planet g, however, lies right in the middle of the habitable zone.

Sam Arbesman’s prediction of May 2011 might have been too conservative. And 20 light years…that means we could send a signal there, and if someone of sufficient technological capability is there and listening, we could hear something back within our lifetime. Contact! (thx, jimray)


New Apollo 11 footage

Due to the Moon’s relative position in the sky as Neil Armstrong started his moonwalk, Australia was able to capture the first few minutes of his descent down the ladder before NASA was able to find a signal. But it was lost until recently; the restored footage will be shown next week at an event in Sydney.


On scientific journalism

This is a blog post that links to a news website article about a scientific paper. The pullquote explains it so I don’t have to bother:

In this paragraph I will state the main claim that the research makes, making appropriate use of “scare quotes” to ensure that it’s clear that I have no opinion about this research whatsoever.

In this paragraph I will briefly (because no paragraph should be more than one line) state which existing scientific ideas this new research “challenges”.

If the research is about a potential cure, or a solution to a problem, this paragraph will describe how it will raise hopes for a group of sufferers or victims.

And then I’ll make a little joke about one of the study’s possible conclusions. (via someone who actually found the thing and sent it on to this lazy “curator”)


Putting your hand in the Large Hadron Collider

Several physicists weigh in on what would happen if you were to place your hand in the proton stream of the Large Hadron Collider at CERN.

There’s not a definite answer…the responses range from “nothing” to “you’d die for sure, instantly”.


Parting the Red Sea, a scientific explanation

Using computer modeling of a process called wind setdown, researchers have come up with a plausible scientific explanation of the Biblical parting of the Red Sea.

This animation shows how a strong east wind over the Nile Delta could have pushed water back into ancient waterways after blowing for about nine hours, exposing mud flats and possibly providing an overland escape route similar to the biblical account of the Red Sea parting.


Thermos to the Moon

Have you ever thought about a rocket as a giant flying Thermos bottle? You will now:

Lovely bit of production there as well. (via russell davies)


Bouncing baby bombs

This little guy is a newborn uncontrolled nuclear fisson reaction. You know, an atomic bomb.

Atom bomb born

This is from a NY Times photo slideshow of atomic bomb explosions. Check out the school bus sequence starting at slide #14.


When will the first Earth-like planet be discovered?

Using the properties of previously discovered exoplanets (that is, planets outside of our solar system) and their dates of discovery, Sam Arbesman and Greg Laughlin predict that the discovery of the first Earth-like exoplanet will likely occur in early May 2011.

Of course, it’s a bit more complicated than that, but here’s an overview of what we did. Using the properties of previously discovered exoplanets, we developed a simple metric of habitability for each planet that uses its mass and temperature to rate it on a scale of 0 to 1, where 1 is Earth-like, and 0 is so very not Earth-like. Plotting these values over time and taking the upper envelope yields a nice march towards habitability.

The authors don’t address this directly in their paper, but I wondered what the Moore’s Law for planetary discovery might be β€” e.g. every X years (or months?), the habitability of the most habitable planet discovered doubles. So I emailed Sam Arbesman and he said that his quick back of the envelope calculation would be “half a month or so”…which is an astounding pace.