Friday, December 28, 2007

Top 10 Friday Beautiful Sciences of 2007

Everyone is making lists for 2007, and I thought I would too. Here's a list of my favourite Friday beautiful science posts of 2007. In particular, I'd like to take issue with Phil Plait's (of Bad Astronomy) statement:

Astronomy is arguably the most beautiful of the sciences. I’m biased, of course, but it’s nearly impossible to gaze upon a picture of a galaxy, a moon, a nebula, and not see in it something compellingly artistic. Sometimes it’s the color, sometimes the shape, and sometimes it’s the knowledge that we can understand the subject of the picture itself.
Many of the pictures I present are from biology, also a beautiful science. In no particular order, I present my top ten picks of Friday beautiful science:

Today's Friday Beautiful Science is a depiction of the tree of life, done as a sphere. Previously, I've discussed the limitations of depicting phylogeny on a standard tree, and suggested that doing it as a circle or a sphere would be more useful. Turns out I'm not the only one who thinks that. This is one particular 3-D visualization that I've taken from Tim Hughes at the University of Bergen (he has several others at his site). Yet other 2-dimensional visualizations can bee seen here.


This weeks Friday beautiful science comes from Eye of Science:
Scales from the skin of a shark. These sharply pointed placoid scales are also known as dermal teeth or denticles. They give the shark's skin the feel of sandpaper. The tip of each scale is made of dentine overlayed with dental enamel. The lower part of each scale, which anchors it into the skin, is made of bone. The scales disrupt turbulence over the skin, considerably reducing the drag on the shark as it swims. This design has been investigated by engineers for use on the surfaces of aircraft and boats. Coloured scanning electron micrograph, Magnification: x70.
Eye of Science is a:
two-person team of photographer and biologist,
our aim is to combine scientific exactness with aesthetic
appearances, and thereby help to bridge the gap
between the world of science and the world of art.


Today's Friday beautiful science comes from the lab of Julie Theriot. These are sped up movies of Listeria bacteria inside human cells. Listeria actually attaches to the actin filaments inside the cell, and uses the actin to force itself around through the cell (and to force its way into neighboring cells). On the left side of the human cell, you can see some bacteria stretching the cytoplasm. If there had been another human cell adjacent to this one, the Listeria cell likely would have punctured the membrane of the human cell, and moved directly into the adjacent human cell. Super cool.

From the Theriot lab website:
Listeria monocytogenes is a small rod shaped gram-positive bacterium that is ubiquitous in the environment, in the soil, on plants and animals. Listeriosis (the state of Listeria infection) is associated with eating of unpasteurized cheese or dairy products, or consumption of contaminated vegetables. Infection occurs primarily in newborns and infants, elderly or immunocompromised individuals, or pregnant women (mother is asymptomatic or has influenza-like syndrome, but the newborn can acquire it during birth, or infection can cause abortion or premature delivery). According to the CDC about 1500 cases are reported in the United States each year, mostly in the aforementioned high risk groups.

Listeria enters the host along with infected food. Most of the bacteria will be killed by acid in the stomach, but the surviving bacteria invade the cells of the intestinal tract, going from cell to cell and thereby spreading the infection laterally. Intracellular movement of the bacteria is essential for this lateral infection to occur, and Listeria has been described to move with a "comet-tail" or like an "actin rocket". The Theriot Laboratory is studying how Listeria moves within cells, and results of this research may someday be used to generate vaccines or other means to prevent infection by Listeria. Currently, the only preventive measures are thorough cooking and cleaning of food, as well as pasteurization of dairy products. Treatment of Listeriosis primarly depends on antibiotics.
Check out this part of Dr. Theriot's site for more cool movies.


This Friday's beautiful science is a photo of the surface of Europa taken by the Galileo probe in 1998. The American Museum of Natural History in New York is having a show of fantastic photos taken from various space probes. Michael Benson put the photographs together using raw data from NASA (many of the shots are composites). If you can get to New York, see the show (and please, comment on it here).

For those of us unable to make it to the show, Michael Benson has put together a book. I got it last week, it's fantastic. The photos are all stunning. The very few photos that I've seen that are better than the photos in his book are the very recently taken photos of the sun taken by Hinode, and of Saturn from Cassini.

Check out the book here:


This is an image taken of a siphonophore taken from the Arctic in 2005. Stunning.


Here's an old shot (2005) from the Mars rover Spirit. It's photos like this why I got involved in science.


Today's Friday beautiful science comes from the book Evolution by Jean-Baptiste De Panafieu. As described:
Each chapter is made up of a short text that illuminates one theme of the evolutionary process-repetition, adaptation, polymorphism, sexual selection-and a series of exquisitely composed photographs of skeletons against a black background. Approximately three hundred photographs of whole skeletons or details have been made possible by the French National Museum of Natural History. The reader learns, by experiencing each text and photograph together, how the structure of every creature has been shaped by its environmental and genetic inheritance.
This one's on my Christmas list.

More photos below.


via Bad Astronomy, I bring you Iapetus. Again! Blow this image up, turn out the lights, and gaze at it on your screen. It's beautiful. (These images were taken by Cassini on Sep 10, 2007 - so they're really very new).

Update: Even more amazingness from Cassini:


Today's Friday beautiful science comes from the AKARI satellite, launched by the Japanese Space Agency. From their website:
The infrared astronomy satellite AKARI started the regular observations in May 2006. In the last one year, AKARI has carried out the All-Sky Survey observations to map the entire sky, as well as thousands of pointed observations of selected targets. Here we show the beautiful images constructed from the AKARI All-Sky Survey data; The entire sky in the mid-infrared light, the far-infrared image of the constellation Orion and the Milky Way, and the far-infrared image of the Cygnus-X region.
This photo is a composite of many thousands of images. The line running through the middle of the photo is the Milky Way.

Sadly, the satellite is nearly done its mission. It was designed to last for 550 days, and has nearly run out of liquid helium (which helps keep its sensors cool).

I'm pretty excited about this photo, and have already had a print made which I'll frame this weekend and hang in my living room. I hope you like it as much as I do.


Here's a video I've been dying to post since I first saw it a few months ago. Blogger now makes it easy to post videos that aren't on YouTube. The video function choked today, and I had to get put the video on Youtube.

As described on the Cornell Mushroom Blog:
Here’s something I know you’ve all been dying to see. A video of one of the most compellingly jaw-dropping spectacles in mycology, condensed from four days of electrifying footage. What you can’t see is the stink, the awesome stink associated with this event. It caused our noble departmental photographer, Kent Loeffler, to vent the noxious, carrion-like fumes into the fourth floor hallway outside my office. We have all suffered here in the service of science.

There are two fungi in this video. On your right, the common pinkish-stemmed Phallus ravenelii. On your left, the rarer, paler, netted stinkhorn, Dictyophora duplicata. Note also the guest appearance by Hubert the fly (aka “The Vector”) late in the video! Oh! the humanity.

To preemptively answer your insightful questions, let me clarify a few points. The stinkiness is part of the dispersal mechanism of the crafty stinkhorn. The green goop covering the heads is a spore slurry that stinks in a sultry way and attracts flies and such. Insects disperse the spores on their little feet. Why does the mushroom look this way? I can’t say, but I can assure you that you’re not the first to notice a certain resemblance. The stinkhorns belong to an order of fungi called the Phallales. They have been causing trouble for a long time, and first got their suggestive Latin name in 1564.
More cool time-lapse videos here.

via Small Things Considered.


Thursday, December 27, 2007

Jon Swift Best of 2007

Jon Swift has made a best of 2007 blog post. I'm delighted that he included my entry.

Thanks, Jon.


Saturday, December 22, 2007

Secular charity

One other issue that comes up this time of year is charitable giving, whether it be due to Christmas or the fact that the tax year is coming to a close. If I may be so bold, I'd like to suggest a few secular charities that are worthy of your support, and that my wife and I support:


I Support the Public Library of Science

PLoS. These people tirelessly support open-access of scientific research, both in their own journals and as public policy. That is, they support a model of publishing scientific results where all journals are open and available to scientists and the public at large without charge. Scientific publishing costs money and advocacy costs money, and they get this partly through donations and partly through charging the folks who are publishing their papers. Donate here. (Donate enough, and get this nifty coffee mug that will be the envy of your peers).


Southern Poverty Law Center
. My wife introduced me to these folks nearly 10 years ago. They're fantastic. They publicize hate-mongers and holocaust deniers. Nothing like shining a big light on big liars to get them to go back under the rocks the crawled out from. They also sue hate crime perpetrators out of existence. For example, when an Aryan Nations group attacked a mother and son and ran them off the road, the Souther Poverty Law Center helped the mother and son sue the group into bankruptcy. They do excellent education work as well. Support them here.


Medecins sans Frontières (Doctors without Borders). These folks started out as a group of Red Cross medical doctors who were upset with the policy of the Red Cross not to publicize what they see (the Red Cross policy is intended to secure access in situations where governments might be embarrassed of what is going on there). In addition to providing medical support in some of the most dangerous parts of the world, Medecins sans Frontières provide news agencies with information about the situation (for example, they've provided considerable information to news agencies about the crisis in Darfur). They're often the last group to leave an area that has become "too dangerous even for aid organizations". They do fantastic work. Donate here.


Friday, December 21, 2007

Medical myths

Medical myths exposed the Guardian! (I confess, I believed the last one):

Everyone must drink at least eight glasses of water a day

This advice is thought to have originated in 1945 from the Nutrition Council in the US, which suggested people needed to consume 2.5 litres of water a day. But Vreeman said the water contained in food, particularly fruit and vegetables, as well as in milk, juice, coffee and soft drinks, also counts towards the total.

We only use 10% of our brains

"The myth arose as early as 1907, propagated by multiple sources advocating the power of self-improvement and tapping into each person's unrealised latent abilities," say Vreeman and Carroll. "The many functions of the brain are highly localised, with different tasks allocated to different anatomical regions. Detailed probing of the brain has failed to identify the 'non-functioning' 90%."

Hair and fingernails continue to grow after death
According to Vreeman, the myth persists because of an optical illusion. "As the body's skin is drying out, soft tissue, especially skin, is retracting. The nails appear much more prominent as the skin dries out." The same is true, but less obvious, with hair. "As the skin is shrinking back, the hair looks more prominent or sticks up a bit." The actual growth of hair and nails requires a complex set of precisely regulated hormones, which do not continue after death.

Reading in dim light ruins your eyesight

Generations of parents have warned their children not to read in poor light, telling them that it could somehow damage their sight. Though dim lighting can cause stress in the eye, the important thing to remember, say the researchers, is that the effects are not permanent. "Suboptimal lighting can create a sensation of having difficulty in focusing. It also decreases the rate of blinking and leads to discomfort from drying. The important counterpoint is that these effects do not persist."

Shaving causes hair to grow back faster or coarser
This theory may go some way toward sustaining the multimillion-pound waxing industry. But it, too, is an optical illusion: when hair first grows after being shaved, it has a blunt edge on top, which gets worn away over time and results in the fine taper of long hair. Also, the sun naturally bleaches hair over time so hair that is newly emerged may seem darker but is, in fact, no darker than any other new hair growth.

Mobile phones are dangerous in hospitals
Early studies in the UK showed that mobile phones interfered with only 4% of devices and only at a distance of less than one metre. In a 2005 US study, 510 tests were carried out with 16 medical devices and six mobile phones - the incidence of clinically important interference was 1.2%. Conversely, a recent survey of anaesthetists found that the use of mobiles by doctors reduced the risk of medical error or injury from delays in communication between hospital staff.

Eating turkey makes you especially drowsy
Vreeman and Carroll admitted that even they initially believed this myth. Tryptophan, a chemical that is contained in turkey, can cause drowsiness but there isn't really very much of it in the bird. Chicken and ground beef contain about the same amount per gram while other protein sources such as pork and Swiss cheese contain more.

The real reason you might feel sleepy after a huge Christmas dinner is more straightforward: the vast amount of food diverts blood away from the brain and towards the stomach, which has the mammoth task of digesting the turkey, sausages, stuffing, vegetables and Christmas pudding.
Yep, turkey doesn't make you especially drowsy. I feel drowsy after Christmas dinners because I stuffed my face. (I'll try to be more careful this year, honest!)


76th Skeptics' Circle

The 76th Skeptics' Circle is up at Aardvarchaeology. Go check it out.


Friday beautiful science


Today's Friday beautiful science comes from the Sandia National Labs. It's a simulation of the meteorite impact in Russia in the early part of the 20th century. This new simulation allows all kinds of predictions about the size and shape of the impacting object, and allows us to predict the frequency of such events:

The stunning amount of forest devastation at Tunguska a century ago in Siberia may have been caused by an asteroid only a fraction as large as previously published estimates, Sandia National Laboratories supercomputer simulations suggest.

“The asteroid that caused the extensive damage was much smaller than we had thought,” says Sandia principal investigator Mark Boslough of the impact that occurred June 30, 1908. “That such a small object can do this kind of destruction suggests that smaller asteroids are something to consider. Their smaller size indicates such collisions are not as improbable as we had believed.”

Because smaller asteroids approach Earth statistically more frequently than larger ones, he says, “We should be making more efforts at detecting the smaller ones than we have till now.”

The new simulation — which more closely matches the widely known facts of destruction than earlier models — shows that the center of mass of an asteroid exploding above the ground is transported downward at speeds faster than sound. It takes the form of a high-temperature jet of expanding gas called a fireball.
Head on over there. There are all kinds of movies to watch, and their detailed description is pretty fun.


Wednesday, December 19, 2007

For the geek in your life.

It's down to the wire for last minute Christmas shopping. I have a few recommendations for you, if you're like me and have let things go to the last minute. In the beautiful coffee-table science book category we have:

Fantastic evo/devo photos. This is one I put on my own Christmas list, and hope to find under the tree on Tuesday:


This is one that we have at home already. Beautiful, though a tiny bit dated (there are so many space probes putting out even better photos, but these photos are well worth having at home):


A photo from this book has found its way into my Friday beautiful science series. Also on my Christmas list, and I'm sure the nerd in your life would enjoy it too.


In the "neat scienceish category":

This book chronicles the life of a very high-functioning autistic synesthetic man. That is, he sees colors and textures when he thinks of numbers, allowing him to do some pretty fantastic mental math feats. While the book could have used pretty substantial editing (it's an autobiography, and like many books in the genre, he has a hard time seeing what will be interesting to readers about his life), it's still a really neat read. Cool to climb into the head of someone who thinks very differently from me (and yet on some levels, not so different).


I've only just started reading Vaccine by Arthur Allen. It's very well written, and presents aspects of the history of vaccinology that I wasn't aware of. He also lays out the book as his own personal effort to educate himself on the good and bad of vaccines. Well written, and in the parts that I can evaluate, the accuracy is very good. I'd recommend this book to anyone, science geek or no.


And finally, this book by Carl Zimmer isn't out yet, but if it's anything like his blogging and newspaper articles, this will be a fantastic book. This book is written about my favourite bacterium, Escherichia coli. Should be a fun read, but I won't say any more as I haven't seen it yet.

Good luck getting your last minute shopping in.


Do sciences start first as "proto-sciences"?

A quote from The Design Matrix:

I should make it explicitly clear from the start that I did not write this book to help those seeking to change the way we teach science to our kids. I do not argue that design deserves to be known as science. At best, Intelligent Design may only be a nascent proto-science [my bold] and thus does not belong in the public school curriculum.
Proto. i.e. primordial. Primordial science. He makes it sound like sciences evolve from being "proto-sciences" to being real sciences. Did molecular biology start out this way? Were Watson and Crick just a couple of guys talking out of their butts for years prior to discovering the structure of DNA? Were Meselson and Stahl pushing to have the method of DNA replication taught in schools for decades prior to their actual discovery? Did Hamilton Smith talk about restriction enzymes in Sunday School 20 years prior to his discovery?

The answer to all these questions is no. New sciences don't evolve out of philosophy or religious studies or a bunch of guys in a garage shooting the shit for decades. New sciences evolve out of old sciences. New experiments done using novel techniques that get at new answers. Molecular biology evolved out of biology and chemistry and physics. Synthetic biology is evolving out of genomics and molecular biology. These are people who are working *hard* to do experiments.

Intelligent design has none of this. cdesign proponentsists don't propose experiments. They don't do experiments. They don't answer anything. They write books. That's it. At best, creationism intelligent design is a sloppy, poorly thought out philosophy. It is not science. It is not a "proto-science".


Evolution unmasked!

Gil Dodgen, creationist cdesign proponentist public intellectual, unmasks evolution for what it is:

So, are those of us with no formal academic background in evolutionary biology (or, poor me, with no college academic background outside of foreign language, literature, and music) automatically disqualified from making challenges and asking hard questions? Some would say yes; I say no. Spotting a con game is not all that difficult.
A con game. Really. A con game so big that effectively all active biologists are involved in it.

This is really what it comes down to. The only way evolution could be blatantly and flagrantly wrong... the only way that scientists could be so completely wrong on this while the folks at Uncommon Descent get it right... the only way that there could be so many home schoolers who "know" that creationism is wrong while scientists are teaching evolution... is if there were a conspiracy to hide the truth. For creationism intelligent design to be right
and evolution to be wrong, scientists would have to be involved in a truly massive coverup. A con game as Mr. Dodgen asserts.

Who's involved in this massive con game? Most of the members of the National Academies of Science, one would presume, as they've produced several documents endorsing evolution as the best description of the origin of species. Most biologists working under the NIH are involved in this conspiracy of conspiracies (approximately 18,000 working at the NIH, probably ten times that number funded by that NIH at external sites). All of these bright and talented people are involved in a coverup so massive that only common sense can reveal (as one of Mr. Dodgen's commenters reveals):
Common sense is still common sense, regardless if you’ve been indoctrinated into materialism or not.
Common sense. The same common sense that tells me that the earth is flat (otherwise we'd fall off!), that the moon is the size of my thumb (after all, I hold my hand up, and I can block it from view) and that the sun orbits the earth (I see it move through the sky during the day after all).

This common sense is what tells us that evolution is a con game. Good job, Mr. Dodgen. Nicely done.


Tuesday, December 18, 2007

Wasting time before the holidays

This Traveler IQ
challenge is brought to you by the Web's Original Travel Blog

I scored an travel IQ of 113 with 381720 points. How did you do?


Saturday, December 15, 2007

The Design of Life - by William Dembski


Friday, December 14, 2007

Intelligent design is *not* creationism.

Or, in the words of William Dembski, world-famous intelligent design proponent:

Interviewer: Does your research conclude that God is the Intelligent Designer?

Dembski: I believe God created the world for a purpose. The Designer of intelligent design is, ultimately, the Christian God.
Ouch. Dr. Dembski, isn't there a commandment in there that you've been breaking? Cause you told me it wasn't about religion...
Interviewer: Who is your target audience?

Dembski: I don’t want to give the impression that it’s not a demanding book, but the book works at several levels.
You mean it's a hymnal *and* a theology textbook coloring book?
Interviewer: How will your research affect the world of science?

Dembski: It’s going to change the national conversation. I don’t see how you can read this book, if you’ve not been indoctrinated with Darwin’s theory, and go back to the evolutionary fold.
Really? It'll change your life? Well, if you fail to change minds, it'll only be because the world is already indoctrinated. It couldn't possibly be because you're dead ass wrong... [/sarcasm]

enormous hat tip: ERV


Friday beautiful science

Today's Friday beautiful science is a 3-D image taken by the JAXA moon satellite that I'm clearly so enamored of. The photos are taken using 2 cameras aboard the satellite that are angled differently at the surface of the moon, and they have a resolution of 10m.

Clearly, another fantastic photo of the surface of the moon.


Wednesday, December 12, 2007

Ok, so maybe this is me...



Monday, December 10, 2007

Science Debate!

Via Mark at Denialism:

We must adapt to the fact that over the last few decades it has become critical that our politicians and policymakers understand science and implement policy that is consistent with scientific facts. And it is past time that we made science enough of a priority to merit a presidential debate on science. The need is clear, these days policymakers must be able to respond in an informed fashion to new technologies, new scientific findings, and potential disasters (such as climate change). Despite the need for a scientifically-literate political leadership, we have a president who says the jury is still out on evolution, who promotes failed abstinence-only sex education programs, and refuses to make any substantive changes to address global warming.

For more, go to Science Debate 2008.


Monday, December 3, 2007

The Parable of the Ichthropic Principle

I found this while scanning the internets, and thought I would share:

The Parable of the Ichthropic Principle

Sixty meters underground, a river used to run through the limestone of the Mexican state of Oaxaca. Because the limestone was uneven in density and porosity, the river carved an irregular channel, widening and contracting. Eventually, over a very long period of time, the surface of the land above underwent changes resulting from diminished rainfall. As the volume of water draining through the underground river decreased, the channel it had carved became a cave. Nonetheless, a trickle of rain still flowed through cracks and crevices, enough to maintain stable pools of fresh water in the lightless depths.

In one such pool lived a small school of fish of the family Characidae. Characids are an adaptable group, occupying many ecological niches of the planet Earth. The characids of this geologically isolated pool had several distinctive adaptations, the most unusual being that they were eyeless. Thus we can identify them henceforth as blind cave fish. Lacking sight, the blind cave fish were well equipped to detect vibrations of any sort through the sensory cells of their lateral lines, which was how they foraged for food as well as how they located each other for mating purposes. Fortunately, water is a superb transmitter of vibrations. Greater self-awareness would not have been adaptive in the bleak conditions of their pool, but if they'd possessed it, they would have had no reason to suppose that any other characids inhabited any other pool in this or any other cave, or indeed that any other pool in any other cave was inhabitable.

The blind cave fish had two rigid requirements for survival--oxygen and food. The oxygen in the pool was maintained at roughly the level they required by the dependable trickle of rain which replenished the loss of water through the porous limestone bed of the pool. Also, the water was cold--a constant forty-one degrees Fahrenheit--which of course allowed maximal oxygenation. Although the fish had no "knowledge" of it, a grave danger to their survival existed in two kinds of pollution: nitrates from their own metabolic waste products, and gradual mineralization from the influx of acid rain water seeping through the soil. Periodically, however, drenching storms would flood the land, refilling the underground river channel and flushing the pool. Most of the blind cave fish would be swept away to an uncertain fate, but enough would survive to rebuild their population. Even the most catastrophic flushing would not decimate them, since their eggs, which were adhesive, were always laid in protected chinks and cracks. Had the floor of the pool been smooth, or had the flooding carried other menaces into their cave, no doubt the blind cave fish couldn't have thrived as they did. It should be noted that the thick layers of rock above, which shielded them from hot sunlight, also shielded them from ultra-violet and other forms of radiation that might have threatened their survival.

The blind cave fish were dependent for their nutrition on another intricate and improbable set of circumstances. Since no light whatsoever penetrated the cavern, no photosynthesizing plants or algae could flourish. Nonetheless, populations of microbes and nearly microscopic arthropods shared the pool. These were the food source upon which the blind cave fish depended, though they supplemented their diet by scavenging the corpses of their own dead. In turn the arthropods and microbes were dependent on bat droppings for 100% of their nutrients. The bats, in huge numbers, infested a large dry cavern of the same cave. The only above-water outlet from their cavern to the fresh air above passed through the grotto of the pool, the ceiling of which was too encrusted with stalactites to attract bats to nest. Thus the quantity of guano the bats dropped in flight was always enough to sustain the pool's organisms yet never enough to poison the water.

The blind cave fish were by far the largest and most metabolically active of these aquatic creatures. Having neither predators nor competition, they had ample reason to be happy with their lives--that is, had they had enough self-awareness to exhibit happiness--since each and every condition of their environment seemed specifically suitable to their needs, while any variation of those conditions would have made their life impossible. Indeed, the conditions in which they subsisted were so random yet so improbably assembled that it must have seemed to the fish--again granting them the self-awareness to consider probabilities--that the pool had been designed to provide for their existence.

Allowing them just a bit more rationality than they truly possessed, logic would surely have suggested to the blind cave fish that where there is design, there must be a designer. No matter how much intellect we attribute to our three-inch long albino eyeless characids, however, it's clear they had no means of fathoming the nature of the designer, unless it were itself an inscrutable but omnipotent blind cave fish.