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kottke.org posts about science

Deforestation changing bird wing shapes

A recent study indicates that the wing shapes of North American birds are changing in response to deforestation.

He found that over half of the species he examined demonstrated changes over time with boreal birds developing more pointed wings and temperate birds developing rounder wings. These results support the hypothesis that habitat isolation is spurring evolutionary changes in birds.

Boreal forests have suffered severe deforestation over the past century, and so Desrochers had predicted that increased distances between habitat patches would select for more pointed wings in birds. Pointed wings are associated with more energy-efficient sustained flight.


Evidence of early human seafarers found

The discovery of stone tools that are possibly 130,000 years old on the island of Crete may indicate that humans were seafaring far earlier than is commonly believed.

Archaeologists and experts on early nautical history said the discovery appeared to show that these surprisingly ancient mariners had craft sturdier and more reliable than rafts. They also must have had the cognitive ability to conceive and carry out repeated water crossing over great distances in order to establish sustainable populations producing an abundance of stone artifacts.


Shaking cancer cells to death

Some scientists have developed a promising method for targeting and destroying individual cancer cells without harming the tissue around them. Tiny (like nano tiny) gold-plated iron-nickel discs are attached to cancer-seeking antibodies. The antibodies attach themselves to the cancer cells and when an alternating magnetic field is applied, the metal nano-discs vibrate and literally shake the cancer cells to death.

Since the antibodies are attracted only to brain cancer cells, the process leaves surrounding healthy cells unharmed. This makes them unlike traditional cancer treatment methods, such as chemotherapy and radiation, which negatively affect both cancer and normal healthy cells.

(thx, @richardjellis)


Black hole simulation

Were you to be close to a black hole, this program shows you what you might observe.

The optical appearance of the stellar sky for an observer in the vicinity of a black hole is dominated by bending of light, frequency shift, and magnification caused by gravitational lensing and aberration. Due to the finite apperture of an observer’s eye or a telescope, Fraunhofer diffraction has to be taken into account. Using todays high performance graphics hardware, we have developed a Qt application which enables the user to interactively explore the stellar sky in the vicinity of a Schwarzschild black hole. For that, we determine what an observer, who can either move quasistatically around the black hole or follow a timelike radial geodesic, would actually see.

For Linux and Windows only, although there are sample videos for non-downloaders or those on other machines.


Nature’s quantum computers

One of the big bummers about quantum computing is the cold temperatures required (hundreds of degrees below zero). However, a number of researchers believe that certain algae and bacteria perform quantum calculations at room temperature.

The evidence comes from a study of how energy travels across the light-harvesting molecules involved in photosynthesis. The work has culminated this week in the extraordinary announcement that these molecules in a marine alga may exploit quantum processes at room temperature to transfer energy without loss. Physicists had previously ruled out quantum processes, arguing that they could not persist for long enough at such temperatures to achieve anything useful.

(via mr)


Einstein’s 1905 chronology

In 1905, Einstein came up with the concept of special relativity, published his paper on the photoelectric effect, finished his doctoral dissertation, devised the E=mc^2 concept, published a paper on Brownian motion, was approved for his doctorate, and turned 26.

So……what have you guys been up to?


Life is but a holographic projection

An experiment to detect gravitational waves may indicate that our universe is a holographic projection.

If this doesn’t blow your socks off, then Hogan, who has just been appointed director of Fermilab’s Center for Particle Astrophysics, has an even bigger shock in store: “If the GEO600 result is what I suspect it is, then we are all living in a giant cosmic hologram.” […] Our everyday experience might itself be a holographic projection of physical processes that take place on a distant, 2D surface.

My socks have been blown so far off they are in a parallel universe. We might be living in the shadow of Flatland. Read the whole thing…it’s noodle-bending throughout. Reminds me of the discovery of cosmic background radiation. (via aegirthor)


Not your father’s evolution

Recent evidence of horizontal gene transfer โ€” in which genes are exchanged from other organisms, not from ancestors โ€” has some scientists thinking that the dominant form of evolution for most of the Earth’s history was between non-related organisms and not among ancestors.

In the past few years, a host of genome studies have demonstrated that DNA flows readily between the chromosomes of microbes and the external world. Typically around 10 per cent of the genes in many bacterial genomes seem to have been acquired from other organisms in this way, though the proportion can be several times that. So an individual microbe may have access to the genes found in the entire microbial population around it, including those of other microbe species. “It’s natural to wonder if the very concept of an organism in isolation is still valid at this level,” says Goldenfeld.

Read on for their hypothesis about how horizontal evolution drove innovation โ€” development of a universal genetic code and genetic innovation-sharing protocols โ€” in life forms early on in the Earth’s history. Fascinating.


Vegetative state not so vegetative

Using brain scanning equipment and a cleverly designed interrogation technique, scientists have been able to ask questions of so-called vegetative patients; one of them even answered yes or no questions:

Several times when Subject 23 was asked to imagine playing tennis, Monti said, the region of the brain most closely associated with complex motor planning became highly active, and stayed active for 30 seconds after researchers prompted such imagery by saying “tennis.”

Similarly, when researchers asked the patient to imagine walking through the house where he grew up and then said the word “navigate,” Subject No. 23 responded with bursts of activity in the region of the brain involved in constructing and navigating a mental map.

The young, French-speaking man was the only subject who was then trained to answer simple yes or no questions โ€” whether his father’s name was Paul (yes) or Alexander (no), whether he had siblings and how many โ€” using the imagery technique he had already learned.

Checking the patient’s responses for accuracy and comparing them to the yes-no brain responses of a group of healthy volunteers, researchers discerned that Subject No. 23 was not only still “in there,” but capable of purposeful thought and communication.


Richard Feynman Explains Magnets, Sort of

I really can’t do a good job, any job, of explaining magnetic force in terms of something else you’re more familiar with, because I don’t understand it in terms of anything else you’re more familiar with.

This is why science is so maddening for some and so great for others.


Pokemon for the real world

Kids can remember hundreds of Pokemon characters but very few animals. The solution? The Phylomon Project is an open source initiative aiming to make Pokemon-type cards for actual animals.

Update: Xeko is an “eco-adventure game” that features Pokemon-like cards for hundreds of real animals. (thx, josh)


How wolves became dogs

In an excerpt from his recent book, The Greatest Show on Earth, Richard Dawkins writes about how wolves evolved into dogs first through self-domestication and then through domestication by humans.

We can imagine wild wolves scavenging on a rubbish tip on the edge of a village. Most of them, fearful of men throwing stones and spears, have a very long flight distance. They sprint for the safety of the forest as soon as a human appears in the distance. But a few individuals, by genetic chance, happen to have a slightly shorter flight distance than the average. Their readiness to take slight risks โ€” they are brave, shall we say, but not foolhardy โ€” gains them more food than their more risk-averse rivals. As the generations go by, natural selection favours a shorter and shorter flight distance, until just before it reaches the point where the wolves really are endangered by stonethrowing humans. The optimum flight distance has shifted because of the newly available food source.

(via @linklog)


The orchid hypothesis

David Dobbs tells us about a new theory in genetics called the orchid hypothesis that suggests that the genes that underlie some of the most troubling human behaviors โ€” violence, depression, anxiety โ€” can, in combination with the right environment, also be responsible for our best behaviors.

Most of us have genes that make us as hardy as dandelions: able to take root and survive almost anywhere. A few of us, however, are more like the orchid: fragile and fickle, but capable of blooming spectacularly if given greenhouse care. So holds a provocative new theory of genetics, which asserts that the very genes that give us the most trouble as a species, causing behaviors that are self-destructive and antisocial, also underlie humankind’s phenomenal adaptability and evolutionary success. With a bad environment and poor parenting, orchid children can end up depressed, drug-addicted, or in jail โ€” but with the right environment and good parenting, they can grow up to be society’s most creative, successful, and happy people.

From start to finish, this is one of the most interesting things I’ve read in weeks.


The gravity of the solar system

Today on xkcd, an illustration showing the gravity wells of our solar system’s planets and some of their moons.

Gravity wells

Two of Mars’ tiny moons barely have any gravity at all:

You could escape Deimos with a bike and a ramp. A thrown baseball could escape Phobos.

That’s great, but you forgot Pluto!


The physics of space battles

The logistics of fighting wars in space is a little different than the movies have lead us to believe.

For the same reason that we have Space Shuttle launch delays, we’ll be able to tell exactly what trajectories our enemies could take between planets: the launch window. At any given point in time, there are only so many routes from here to Mars that will leave our imperialist forces enough fuel and energy to put down the colonists’ revolt.


Hubble goes deep

In 2004, the Hubble Space Telescope took an image called the Hubble Ultra Deep Field; basically astronomers pointed the Hubble toward an “empty” part of space and took a long-exposure shot in the visible spectrum. What they found were thousands of far away galaxies from early in the development of the universe. Now the Hubble has peered even deeper into the universe in near-infrared and captured this image:

Hubble IR Deep Field

Each one of those little specks is an entire galaxy, some only 600 million years old. Here’s a zoomed-in section:

Hubble IR Deep Field


The parachute physics of hungry whales

How did whales get so big eating such tiny creatures? And why aren’t they bigger? Carl Zimmer explains.

According to the scientists, this pattern occurs when the whales lunge into a cloud of krill and drop open their jaws. Pleats under the lower jaw open up, engulfing huge amounts of water. The whale slows down because of the drag. It behaves, in other words, a lot like a parachute. […] It’s a lot of water, the scientists have found: in one lunge, a fin whale can momentarily double its weight.

The scaling stuff later on in the article is especially interesting. See also The Biology of B-Movie Monsters.


How the H1N1 vaccine is made

The most striking feature of the H1N1 flu vaccine manufacturing process is the 1,200,000,000 chicken eggs required to make the 3 billion doses of vaccine that may be required worldwide. There are entire chicken farms in the US and around the world dedicated to producing eggs for the purpose of incubating influenza viruses for use in vaccines. No wonder it takes six months from start to finish. But we’ll get to that in a minute.

The most commonly used process for manufacturing an influenza vaccine was developed in the 1940s โ€” one of its co-inventors was Jonas Salk, who would go on to develop the polio vaccine โ€” and has remained basically unchanged since then. The process is coordinated by the World Health Organization and begins with the detection of a new virus (or rather one that differs significantly from those already going around); in this instance, the Pandemic H1N1/09 virus. Once the pandemic strain has been identified and isolated, it is mixed with a standard laboratory virus through a technique called genetic reassortment, the purpose of which is to create a hybrid virus (also called the “reference virus strain”) with the pandemic strain’s surface antigens and the lab strain’s core components (which allows the virus to grow really well in chicken eggs). Then the hybrid is tested to make sure that it grows well, is safe, and produces the proper antigen response. This takes about six to nine weeks.

[Quick definitional pause. Antigen: “An antigen is any substance that causes your immune system to produce antibodies against it. An antigen may be a foreign substance from the environment such as chemicals, bacteria, viruses, or pollen. An antigen may also be formed within the body, as with bacterial toxins or tissue cells.” So, when the H1N1 vaccine gets inside your body, the pandemic strain’s surface antigens will produce antibodies against it.]

At roughly the same time, a parallel effort to produce what are referred to as reference reagents is undertaken. The deliverable here is a standardized kit provided to vaccine manufacturers so that they can test how much virus they are making and how effective it is. This process serves to standardize vaccine doses across manufacturers and takes four months to complete. WHO notes that this part of the process is “often a bottleneck to the overall timeline for manufacturers to generate the vaccine”.

Once the reference virus strain is produced, it is sent to pharmaceutical companies (Novartis, Sanofi Pasteur, etc.) for large-scale production of the vaccine. The companies fine-tune the virus to increase yields and produce seed virus banks that will be used in the bulk production.

And this is where the 1.2 billion chicken eggs come in. A portion of the seed virus is injected into each 9- to 12-day old fertilized egg. The virus incubates in the egg white for two to three days and is then separated from the egg.

Vaccine eggs

For the shot vaccine, the virus is sterilized so that it won’t make anyone sick. This is the magic part of the vaccine: it’s got the pandemic virus antigens that make your body produce the antibodies to fight the virus but the virus is inactive so it won’t make you ill. For the nasal spray vaccine, the virus is left alive and attenuated to survive only in the nose and not the warmer lungs; it’ll infect you enough to produce antibodies but not enough to make you sick. Either way, the surface antigens are separated out and purified to produce the active ingredient in the vaccine. Each batch of antigen takes about two weeks to produce. With enough laboratory space and chicken eggs, the companies can crank out an infinite amount of purified antigens, but those resources are limited in practice.

[Side note. You may have noticed that the H1N1 vaccine has been difficult to find in some places around the US. The vaccine manufacturers have said that the Pandemic H1N1/09 virus when combined with the standard laboratory virus does not grow as fast in the eggs as they anticipated. The batches of antigens from each egg have been smaller than expected, up to five or even ten times smaller in some cases. Hence the slow rollout of the vaccine.]

The purified antigen is then tested against the aforementioned reference reagents once they are ready. The antigen is diluted to the required concentration and placed into properly labelled vials or syringes. Further testing is performed to make sure the vaccine won’t make anyone ill, to confirm the correct concentration, and for general safety. At this point clinical testing in humans is required in western Europe but not in the United States. Finally, each company’s vaccine has to be approved by the appropriate regulatory body in each country โ€” that’s the FDA in the case of the US โ€” and then the vaccine is distributed to medical facilities around the country.

Sources and more information: WHO, WHO, WHO, WHO, CDC, Time, Washington Post, The Big Picture, Influenza Report, NPR, Wikipedia, Wikipedia, Wikipedia, Wikipedia.

Update: Included in a recent 60 Minutes segment on the H1N1 vaccine is a look at the manufacturing process. (thx, @briandigital)


What will the LHC find?

With regard to the Large Hadron Collider, the Higgs boson gets all the press but other potential discoveries could be more exciting and easier to detect.

However, if the theorists are right, before it ever finds the Higgs, the LHC will see the first outline of something far bigger: the grand, overarching theory known as supersymmetry. SUSY, as it is endearingly called, is a daring theory that doubles the number of particles needed to explain the world. And it could be just what particle physicists need to set them on the path to fresh enlightenment.

If you haven’t been keeping up with particle physics for the past few years (as I haven’t), this will bring you up to speed a bit.


Nathan Myhrvold, cookbook author

Nathan Myhrvold, ex-Microsoftie and founder of an invention company called Intellectual Ventures, is also really interested in food, so much so that he’s writing a monster cookbook (currently ~1500 pages) about the science of cooking.

In another discovery of culinary heat transfer physics, Dr. Myhrvold said the bulbous shape and black color of Weber grills were wrong. To achieve an even cooking temperature across the cooking grate, the inside of the grill should be vertical and shiny to reflect the heat. That can be fixed by adding an aluminum insert to the grill. “So we have directions for that,” Dr. Myhrvold said.

You may remember reading about Myhrvold and IV in Malcolm Gladwell’s piece on the nature of invention last year.


Water on the Moon

NASA announced that it has found pretty hard evidence of significant amounts of water on the Moon.

“We are ecstatic,” said Anthony Colaprete, LCROSS project scientist and principal investigator at NASA’s Ames Research Center in Moffett Field, Calif. “Multiple lines of evidence show water was present in both the high angle vapor plume and the ejecta curtain created by the LCROSS Centaur impact. The concentration and distribution of water and other substances requires further analysis, but it is safe to say Cabeus holds water.”

I don’t have to tell you about the implications here. Just think of how much you could sell authentic Moon bottled water for.


Slow motion water drops

When you shoot video of water drops falling into a puddle in super slow motion, it turns out that they bounce in really interesting ways.

(via 3qd)


SuperFreakonomics not so super

In a New Yorker book review this week, Elizabeth Kolbert tears Levitt and Dubner a new one over the geoengineering chapter of SuperFreakonomics, calling the pair’s thinking on the issue “horseshit”.

Given their emphasis on cold, hard numbers, it’s noteworthy that Levitt and Dubner ignore what are, by now, whole libraries’ worth of data on global warming. Indeed, just about everything they have to say on the topic is, factually speaking, wrong. Among the many matters they misrepresent are: the significance of carbon emissions as a climate-forcing agent, the mechanics of climate modelling, the temperature record of the past decade, and the climate history of the past several hundred thousand years.


Hacking the senses

Researchers have been able to create new human senses of a sort…and to cross-pollinate two different senses in order to, for example, see with your tongue.

With Arnoldussen behind me carrying the laptop, I walked around the Wicab offices. I managed to avoid most walls and desks, scanning my head from side to side slowly to give myself a wider field of view, like radar. Thinking back on it, I don’t remember the feeling of the electrodes on my tongue at all during my walkabout. What I remember are pictures: high-contrast images of cubicle walls and office doors, as though I’d seen them with my eyes.

I am reminded of magnetic fingers and the boy who sees through echolocation. I wouldn’t mind a sense of maps that worked via smell…follow the cinnamon scent to your destination or some such.


Natural nuclear reactors

Several naturally occurring nuclear reactors have been discovered in Gabon, Africa. Groundwater flooding deposits of uranium ore made the reaction possible.

The natural nuclear reactor formed when a uranium-rich mineral deposit became inundated with groundwater that acted as a neutron moderator, and a nuclear chain reaction took place. The heat generated from the nuclear fission caused the groundwater to boil away, which slowed or stopped the reaction. After cooling of the mineral deposit, short-lived fission product poisons decayed, the water returned and the reaction started again. These fission reactions were sustained for hundreds of thousands of years, until a chain reaction could no longer be supported. Fission of uranium normally produces five known isotopes of the fission-product gas xenon; all five have been found trapped in the remnants of the natural reactor, in varying concentrations. The concentrations of xenon isotopes, found trapped in mineral formations 2 billion years later, make it possible to calculate the specific time intervals of reactor operation: approximately 2 hours and 30 minutes

Nice try Fermi, but Mother Nature got there first.

BTW, despite reading The Making of the Atomic Bomb (twice!), I can’t recall hearing this pair of anecdotes before:

Due to a mistranslation, Soviet reports on Enrico Fermi claimed that his work was performed in a converted “pumpkin field” instead of a “squash court”, squash being an offshoot of hard racquets.

When the first self-sustained nuclear chain reaction was achieved, a coded phone call was made by one of the physicists, Arthur Compton, to James Conant, chairman of the National Defense Research Committee. The conversation was in impromptu code:

Compton: The Italian navigator has landed in the New World.
Conant: How were the natives?
Compton: Very friendly.

Pumpkin field, tube alloy, the Italian navigator, the Manhattan Project…the building of the atomic bomb had no shortage of fanciful language.

Update: BLDGBLOG did a post on fossil reactors recently, which is probably where I got the link above in the first place.


The history of inoculation

The process of inoculation against diseases like smallpox has been known for at least 1200 years. An 8th-century Indian book contains a how-to chapter on smallpox inoculations. Chinese use of the technique dates back to the first millennium as well. The technique was imported to Europe via the Ottoman Empire in 1721 and reached America at about the same time.

The practice is documented in America as early as 1721, when Zabdiel Boylston, at the urging of Cotton Mather, successfully inoculated two slaves and his own son. Mather, a prominent Boston minister, had heard a description of the African practice of inoculation from his Sudanese slave, Onesimus, in 1706, but had been previously unable to convince local physicians to attempt the procedure. Following this initial success, Boylston began performing inoculations throughout Boston, despite much controversy and at least one attempt upon his life. The effectiveness of the procedure was proven when, of the nearly three hundred people Boylston inoculated during the outbreak, only six died, whereas the mortality rate among those who contracted the disease naturally was one in six.

In a criticism of inoculation that would not seem so out of place regarding vaccination today, Voltaire takes his countrymen to task for not inoculating their children.

It is inadvertently affirmed in the Christian countries of Europe that the English are fools and madmen. Fools, because they give their children the small-pox to prevent their catching it; and madmen, because they wantonly communicate a certain and dreadful distemper to their children, merely to prevent an uncertain evil. The English, on the other side, call the rest of the Europeans cowardly and unnatural. Cowardly, because they are afraid of putting their children to a little pain; unnatural, because they expose them to die one time or other of the small-pox. But that the reader may be able to judge whether the English or those who differ from them in opinion are in the right, here follows the history of the famed innoculation, which is mentioned with so much dread in France.


Toddler science

Once a month, Maggie Koerth-Baker will answer a science question from a toddler. First up: Do turtles have eyelashes?


Seven questions that keep physicists up at night

At a recent conference, a group of physicists talked about the biggest answered (and perhaps unanswerable) questions in physics. Three of the questions are:

What is everything made of?
Will string theory ever be proved correct?
How far can physics take us?


Killer vaccines and the killers who kill with them

Wired has a long piece by Amy Wallace about the anti-science anti-vaccine crowd.

Ah, risk. It is the idea that fuels the anti-vaccine movement โ€” that parents should be allowed to opt out, because it is their right to evaluate risk for their own children. It is also the idea that underlies the CDC’s vaccination schedule โ€” that the risk to public health is too great to allow individuals, one by one, to make decisions that will impact their communities. (The concept of herd immunity is key here: It holds that, in diseases passed from person to person, it is more difficult to maintain a chain of infection when large numbers of a population are immune.)

Update: I am on Team Tom Scocca on this issue:

Anti-vaccine activists are degenerate idiots who deserve to get polio and live out their days in iron lungs while Child Protective Services takes away their children to be properly raised. Or tetanus. Get lockjaw and shut up and die. What’s the point of living in 21st-century America if not to avoid dying of stupid, easily preventable disease?

And Slate has an article about the effects of unvaccinated children on those with weak immune systems.

Ordinarily I wouldn’t question others’ parenting choices. But the problem is literally one of live or don’t live. While that parent chose not to vaccinate her child for what she likely considers well-founded reasons, she is putting other children at risk. In this instance, the child at risk was my son. He has leukemia.

(thx, cedar)

Update: Ben Goldacre on anti-vaccine scares as a cultural thing, not a science thing:

There’s something very interesting about vaccine scares. These are cultural products. They’re not about evidence. If vaccine scares were about genuine scientific evidence showing that a vaccine caused a disease, then the vaccine scares would happen all around the world at exactly the same time, because information can disseminate itself around the world very rapidly these days. But what you find is that vaccine scares actually respect cultural and national boundaries.

(via lined and unlined)


What the brain looks like

100 years of visualizing the brain, from the discovery of neurons in the 19th century to MRI investigations in the 1990s.

1899 neurons