Monday, January 30, 2006

Hot dogs as a microbicide

I just saw this on Science Blog : a common food preservative may be very powerful against the kind of bacterial infection which is so destructive to Cystic Fibrosis Sufferers. Mutations which cause CF in humans result in abnormally thick and acidic mucus. Bacteria such as Pseudomonas aeruginosa which can get in there are effectively shielded from the immune system by the mucus and their own deposits, which are referred to as alginate.

Now, in recent study of American CF patients, 84% of the Pseudomonas aeruginosa isolates themselves carried a mutation in the gene MucA. This mutation allows the bacteria to make more alginate, which in turn gives the mutant bacteria an improved shield against the immune system relative to the wild-type bugs. Here's where the story gets really cool- this same mutation makes the mutant bugs (which are frustratingly resistant to antibiotic or immune therapy) very sensitive to acidified sodium nitrite, a compound used as a preservative for hot dogs or bacon. So in principal this nitrite could be made into an aerosol and clear up the mutant bacteria; and other therapies could help get the rest.

The original reference is here.

For a description of recent work on saline washes as a way of getting the sticky mucus of CF sufferers out, see Aetiology.

Tuesday, January 24, 2006

It always rains on the fourth of July

Mars repeated weather

I came across this in the NASA/JPL web page and I thought it was pretty cool: there are places in Mars that have repeated, predictable weather patterns. These four photographs show a circular cloud appearing over the same terrain, near the Martian North pole, each Martian summer. Another example is here where a volcano gets a massive dust devil every year in the late Martian autumn. Here's the Mars Global Surveyor (MGS)report:

The wide angle cameras have shown us that Mars has fairly predictable weather, with some storms and cloud phenomena repeating every year, like clockwork. There are specific times of year and locations on Mars which have experienced the same dust storm patterns every Mars year since we began observing with the first MGS MOC approach image in July 1997.

Apparently Martian atmospherics are dominated by seasonal heating and local geological features, making for a much simpler picture than earth.


Is it fake? Is it real? Mathematics and digital images.

There's a very interesting article in todays New York Times about scientists and image editing software. Many of the most striking images, such as astronomy photographs, must be digitally enhanced even to be intelligible. But in the Photoshop world, it is very easy to beautify digital images beyond this in a way that leaves no visible trace-- in short, to fudge. However, since Photoshop is essentially a collection of math algorithms, the manipulations-- rotations, rubber stamps, contrast gradients-- can be detected by their mathematical signatures. The editors of the Journal of Cell Biology have been able to detect these little fudges, such as cutting out a background band or selective contrast enhancement. Even as outright deception by Photoshop appears to be very rare, fudging is suprisingly common. My brand of science is very visually driven so a great deal of attention, benign and otherwise, is lavished on the images.

A tangentially related problem was covered in a recent Slashdot thread, which describes researchers using digital analysis to authenticate a Rembrandt. Jumping the link to ZDNET blog , a quote from Dan Rockmore says it all:

"The fact that you can put everything on the computer means that everything is numbers," Rockmore says. "As soon as everything is numbers, it makes perfect sense to ask mathematical questions about what the numbers represent." If he's right — if computers can distinguish between artists more accurately than connoisseurs can — the art world is in for some high-stakes corrections."

The ZDnet article is really fascinating, and shows how this method was used to identify four different artists' hands in a large Renaissance painting. ZDnet also cites some pushback by art historians- for example, a Rembrandt might have eight layers of paint, so that a surface analysis might miss underlying information. I also know that in Renaissance workshops the master might put the finishing touches on a face blocked in by an apprentice. This mixed effort should look very confusing at the mathematical level.

UPDATE: But the final picture is so compelling! (Can't decide if this better suits scientists or Rembrandt.)

Meme: dusting off ancient history

Coturnix tagged me with this meme:

1. Go into your archives.
2. Find your 23rd post.
3. Post the fifth sentence (or closest to it).
4. Post the text of the sentence in your blog along with these instructions.
5. Tag five other people to do the same thing.

Well, the relevant sentence is pretty strange when taken out of context:

In most of the Forstenrieder Wald, the oaks are continually replaced and rather young looking.

It comes from This post where I talk about the beautiful oak trees in my neighborhood in the south of Munich. I have to say, I love Bavaria in a way that only California can eclipse.

I had forgotten how bloggy I was in the old days!

I will try to update with people to tag later...

Sunday, January 22, 2006

Ears that breathe

The Scientific American Editor's blog has a very nice summary of some recent ideas about the transition from living in the sea to living in land . The bones of the inner ear of terrestrials, for example, may have been derived from a breathing hole that initially allowed clean water to be pumped over the gills independently of the mouth. (Nearer to my own work, the swim bladders of fishes were adapted to generate terrestrial lungs, and they have a whole slew of molecular similarities to our airbags.)

UPDATE: the lung/swimbladder story is not as simple as I thought. Apparently both structures emerged multiple times during fish evolution, and the current similarity is an example of convergent evolution. Hat tip to Lloyd .

In summary, a whole lot of body structures had to get refitted for this transition to happen. The post has very nice explanations, and lots of links!

Thursday, January 19, 2006

Stardust returns

Astrobiology magazine has a nice writeup about the initial assessment of the Stardust mission, which returned safely to earth last Sunday. The spacecraft had very large panels, coated with aerogel, which were hoped to capture particles from a comet's tail. Upon landing the scientists opened up the panels, and confirmed that about a million such particles were brought back. Very cool.

Lab humor doesn't translate

There's a funny letter to Nature this morning about whimsical names for genes, as chosen by bench scientists, which don't play well in a clinical setting. Just off the top of my head, I could say that bazooka, gurken, pokemon (now under copyright challenge) or sonic hedgehog are cute when descibing a fly, but don't sound quite right when you're doing genetic counseling.

But the biggest such unpalatable genetic term wasn't even intentional: CATCH-22, for 'cardiac anomaly, T-cell deficit, clefting and hypocalcaemia' associated with Chromosome 22 deletions.

Wednesday, January 18, 2006

Diversify your reading!

Professor Steve Jones in Connected complains that science writers need to broaden their horizons. Glancing this week through newspapers in English, French and German, he sees the same major science stories appearing again and again. He also makes the very interesting observation that the primary research in many cases originated in Nature , by most measures the world's premiere general science journal:

A glance at this week's newspapers and popular science magazines shows just how wide a range there is: global warming killing off frogs, new methods for generating stem cells, plants that make methane, and what space dust might tell us about the origin of the Universe.Those stories are interesting, varied and up-to-date; but they all share a hidden thread that links - or entangles - everyone who writes about science, for each of them first appeared in Nature.

Jones goes through a list of a huge trove of sources for interesting science available on the web: the Public Library of Science, the free side of highwire press (note: link was dead at the time of writing), and Google scholar. I would add to this list Wikipedia or Google itself.

While of course there are many sources (and "science" sections of newspapers are frequently just dumps of the AP wire) I think that Nature really does deserve special reading attention. For me, Nature is a brand name telling me that what's inside is very interesting to many people and has also been carefully reviewed. (the same goes for Science). As I often post well outside my expertise, I rely on the editors that the main premise of the paper I'm reading is at least self-consistent. It takes long enough to understand the stuff! And Google Scholar can turn up a lot of dodgy stuff especially with specialized searches.

With that said, right this second I'm reading in PLoS about goldfish longevity and its relevance to humans. Very, very cool.

Sunday, January 15, 2006

The evolutionary value of laughter

Maggie Witlin at the beta of SEED magazine (the one swallowing up science bloggers) has an excellent article on the practical side of humor . Laughing probably comes in two distinct flavors. "Emotional" laughter appears to be very ancient-- preceeding even language-- because apes will also make a distinct pant-grunt when they tickle each other. This ancient form might be a way of communicating safety or group cohesion. The other types of laughter, called "conscious laughter"-- anything from nervous laughing to Dr. Evil's cackle--involve different areas of the brain and might have a completely different evolutionary function.

Friday, January 13, 2006

Did viruses "invent" DNA?

All modern cells are built with very similar components: A wall to keep everything in, DNA which stores the genome, and RNA and protein which take care of the mechanics and metabolism. These components are heavily interdependent, and it is actually something of a puzzle how the modern cell emerged from the prebiotic chemistry of early earth. (See Wikipedia here ).

RNA was likely to be among the very first of the modern cell components to emerge, because RNAs can do the jobs of genome storage (now done mainly by DNA) and enzymatic action (now done mainly by protein) whereas the other components cannot. Proteins might have come second, and DNA last. So how did DNA take over the job of genome storage?

This week's Nature has an amazing suggestion: DNA was "invented" by viruses as a way of evading the defenses of ancient cells. Ancient viruses, as with the ones today, could only make copies of themselves by succesfully infecting a host. So they become engines of innovation, thinking of every possible dodge to get inside the host cell. In an early, RNA-protein world, there would not be enzymes to degrade DNA, so a virus encoded by DNA would have a big survival advantage.

There are some clues from comparative genomics that the DNA world developed in pieces. The means of interpreting DNA genes (transcription, translation) are very similar among all the major domains of life, suggesting that these tools were present in the common ancestor of all present-day cells. In contrast, the means of handling and copying DNA vary quite a bit. DNA polymerases (the copying enzymes) in the various domains of life are in each case more closely related to viral proteins than to comparable proteins from the other domains of life. This suggests a scenario in which a clever parasite brings along DNA plus the means of copying it-- a different parasite for bacteria, archaea, eukaryotes-- and hijacks the cell's existing interpretation equipment. The merger of virus plus RNA/protein cell then created the modern cell.

With this topic it is important to realize that the ideas are very speculative. The attraction of this idea- that the parasite-prey relationship is a very old evolutionary engine- actually also makes trouble because modern day parasites and prey, especially in the microbial world, actually exchange whole chemical modules. Thus it remains very very hard to state what came first.

The original article (Biochimie) is here. An argument about DNA emerging in stages (TIGS) is here .

Thursday, January 12, 2006

Human ancestors hunted by Eagles?

Tuang Child, Australopithecus africanus

A replica of the Tuang child find, image taken from Skulls unlimited

One of the very early Australopithecus africanus finds is the so-called Tuang child, which was discovered in a limestone cavern along with the bones of many other mammals including baboons and antelope. Because of the heap of bones, it was hypothesized that the Tuang child was the victim of a predator and ended up in the heap with all the other prey. The early money was on a leopard or hyena, but a theory which has been around for quite a while is that a predatory bird, such as the crowned hawk-eagle (which can prey on animals up to 30 kg; the Tuang child was probably about 20 kg) was the predator in question. The first argument in favor of a bird was based on the mix of prey present in the bone heap, with small animals predominating as might be expected for a bird that has to fly off.

A second line of argument (for example here ) favors predatory birds based on the pattern of bone damage to the Tuang skull. Leopards and their ilk do a lot of gnawing, but birds are limited to what they can slice open with their beaks (which is still an awful lot- they brain a lot of their prey via the palate, leaving the postcranial skull alone). The authors of this theory propose looking at the long bones of the various mammalsin the Tuang assemblage, because birds will slice the ends off to get at the marrow while hyenas can just crush them.

The news this week is now (also at afarensis ) is that the bones of the eye sockets of the Tuang child find have radial scratches of the sort that a bird's talons would leave. Birds will strike a treeborne monkey and puncture the skull, and then wait for the animal to die before hauling it off. Sounds like a shark's method.

I just finished reading the Hobbit to the boys. Wouldn't want to have been one of those goblins.

Saturn, its rings, and ring shadow

From NASA's image of the day page:

Saturn with its rings and ring shadow

Wednesday, January 11, 2006

Home experiments for kids

The Telegraph has a short article on some science-based experiments you can do at home with your kids. There's a trick to sticking a skewer all the way through a balloon..

Sunday, January 08, 2006

Let c=cinnamon

Brad deLong offers a modest proposal to triple the amount cinnamon in all recipes. This is followed by a lengthy and very geeky comments section. deLong theorizes that the level of cinnamon reccomended in older recipes was determined by the price, not taste.

Myself, I have not yet gotten gingerbread to taste gingery, even after tripling the dry ginger and shaving in fresh. A topic obviously crying out for investigation

Saturday, January 07, 2006

A genetic taxonomy of cats

Carl Zimmer at The Loom talks about new work in the evolution of the cat family. The mighty sequencers used in the genomics efforts have been used to compare large amounts of sequence from many different cats. They take this purely genetic tree and try to propose how the modern cats emerged, taking into account divergences and migrations.

Carl points out that some of the highest profile paelontololgy results are coming out of genetics labs. (At least one expert that Carl consults is not too happy that they didn't try to relate the genetics to the fossil evidence).

In the comments section the issue is raised that even distantly related cats can interbreed. This is a topic I've been meaning to learn about myself-- that the base definition that two animals are of different species when they cannot mate must be supplemented with lots of shades of grey.

For more information about how sequence data are transforming paleontology, take a look at this list of newspaper articles from the great news aggregator SnowDeal.

Friday, January 06, 2006

Revised, older dates for Croatian Neanderthal fossils

It is known that Neanderthals co-existed with anatomically modern humans for some time in Europe, but the length of time during which the two populations might have interacted has been poorly defined. Neanderthal fossils found in Vindija Cave, Croatia had earlier been identified as the youngest of European Neanderthal finds at 28000 years ago.

A new paper appearing in this week's PNAS revists the dating of these fossils, still using C-14.The results suggest the fossils are about 4000 years older than was thought, that is, at least 33000 years old. This, combined with some revisions of modern Homo sapiens tools, tends to put an upper limit on how long or extensive the contact between the two species was. In their discussion the authors emphasize that there are just not many fossils of either kind available between 40000 and 30000 years ago.

UPDATE: A very good writeup at John Hawks. Apparently the younger dates obtained before from these fossils were due to contamination problems. Careful, careful, careful.....

Thursday, January 05, 2006

Human genomics at The Economist

Apparently the print edition of the Dec 24 Economist had a whole series of articles on human evolution and current human genomic research. The editor's note is here but the individual articles seem to be for pay.

I'll have to go get a print copy..

Stem cell scandal: Hwang risked his employees as well

William Saletan at Slate has a very good discussion of the implosion of the stem cell claims from Hwang Woo-Suk's laboratory. :Hwang claimed that large numbers of stem cells were prepared, at good efficiency, from oocytes freely donated (at personal risk) by human women. Good efficiency was a huge deal, because it means reduced risk to future women.
It turns out that pretty much everything in that claim-- except the risk and the women-- is false. An especially heartbreaking twist is that he in fact he exposed women under his administrative control to much, much higher risks than he admitted.

Here's Saletan:
A scientific panel investigating his 2005 study announced that he'd lied about the number of eggs as well as their sources. Hwang said he'd used 185 eggs. A former colleague said he'd used as many as 1,100. Maybe Hwang's 2004 study, in which he claimed to have gotten one stem-cell line from 248 eggs, was a fraud like his 2005 study. Maybe the cost-benefit ratio wasn't 248 eggs to one stem-cell line. Maybe it was 1,100 to zero.

And there is a claim from at least one female junior scientist in her lab that he pressured her to donate. Wow.

Freedom for plumbers

Via Wonkette, a court in Maryland ruled that it's not illegal to moon your neighbors.

Plumbers everywhere sigh in relief.

UPDATE: Check out Zoe Brain for gendered approaches to anatomy.

Wednesday, January 04, 2006

Tangled Bank #44 up at afarensis

The Tangled Bank Carnival of science-writing is up at afarensis . Have a look!

Mozart's skull confirmed?

Austrian scientists have been doing DNA tests on a skull sitting in a Salzburg museum to see if it really belongs to Mozart. Mozart was buried in a grave with 4 or 5 other bodies, but a gravedigger later went and got a skull which then ended up in the collection of a museum in Salzburg, Austria. This skull shows evidence of head injury , so if it really is Mozart's, then it could explain the headaches the musician suffered in his last year of life. Mozart's final illness went pretty fast, raising the question of foul play .

The new DNA tests compare DNA from the skull to DNA from the bones of known relatives, whose graves were identified in 2004. The results of the DNA testing will be televised at the end of this week.

UPDATE, Jan 11: It's a bust- the DNA tests were ambiguous

CS Monitor top 10 web pages

Jim Regan at the CS Monitor lists his favorite web finds of 2005. I really enjoy his taste in sites-- for example The Theban Mapping Project is an interactive look at the vast archeological digs in the Valley of the Kings in Egypt. He has a few other really enjoyable ones. A great time sink!

Tuesday, January 03, 2006

Crashing to earth-- and surviving

Astrobiology magazine points out a fascinating side-effect of the the Space Shuttle Columbia tragedy. As the space shuttle broke up, its entire cargo, including scientific experiments, fell to Earth. During the recovery search, it was discovered that a colony of C. elegans roundworms which had been on board the shuttle actually survived the fall to earth despite travelling at anywhere from 600-1000 km/hours and a calculated impact velocity of 45 m/s.
The C. elegans had been growing inside sealed cannisters designed to later be incorporated into a long-term automated spaceborne experiment. They were effectively embedded in a soft gel.(In earth-based laboratories they grow on top of bacterial plates, eating the bacteria.) But the cannisters were not at all designed for impact.

Apparently the worms did not get extremely hot. The inner linings, made of polystyrene (melting point about 80 degrees C), were not damaged, and in any case earthbound C.elegans die above about 40 degrees C.

The first potential significance of this is that even multicellular organisms could possibly survive planetary impact. Space probes sent from earth should be well sterilized to prevent forward contamination of outside bodies; but also, allowing spacecraft to break up in the atmosphere of other planets may not be sufficient to kill everything on board.

A more speculative possibility is that natural objects such as meteorites could transfer multi-cellular organims between worlds. For example, as the authors point out,
(free abstract with link to pdf) the Martian metorite ALH84001 (his friends call him AL) was also not heated past about 40 degrees. Of course, once you've survived impact you'd need to survive whatever you landed in. The main danger to the current C.elegans was that their culture plates were being overgrown by (terrestrial?) mold.

UPDATE: Of all people, the hilarious David Sedaris had already written about these worms. In his short story "Can of Worms" in the collection Dress your family... , he overhears about the space worms and wonders about their perspective. You can hear an audio version of the story here at This American Life.

Monday, January 02, 2006

Are humans the point of evolution?

--The title of this post should be, "Are intelligent beings necessary?" or some such; see Ruse's title.
-- Via Three-toed sloth , a whole conference on complexity and evolution, and a book (reviewed by Cosma) about how the complexity of life on Earth might have been stabilized ("fixed") during natural selection. Clearly there's more going on here than I first appreciated, though I remain close to Gould.

Here's the original post:

Michael Ruse has a wonderfully written essay at Philosophy of Biology about the idea that humans are the pinnacle of evolution. A suprising (to me) number of thinkers, believe that a very common result of natural selection is an increase in complexity; and that, by extension, that Homo Sapiens or in any case a social, intelligent, environment-altering lifeform, is essentially inevitable. Here is E.O. Wilson as quoted by Ruse:

“the overall average across the history of life has moved from the simple and few to the more complex and numerous. During the past billion years, animals as a whole evolved upward in body size, feeding and defensive techniques, brain and behavioral complexity, social organization, and precision of environmental control – in each case farther from the nonliving state than their simpler antecedents did.”

A slightly less emphatic statement of the same idea comes from Conway Morris's notion of a sort of quantization of niches. For example, marsupials and placental mammals both gave rise to very similar-looking predators. Somehow intelligence and culture have beckoned in our era, the Cenozoic; thus Humans. (If not humans, then a cultural animal arising from a different lineage. Ninja turtles, anyone?)

Ruse himself does not come down with an opinion, so let me supply one: the law of natural selection by itself does not specify what will improve survival. (Ruse metntions this point, citing Stephen Gould, in his essay, then strangely abandons it at at the end). Thus, at the most basic level- given life on a World X would it *necessarily* become complex over time, I have to answer, emphatically, no, not necessarily. Whether the range of niches supplied by Cenozoic-era Earth led to an evolutionary gradient which our primate ancestors filled (with us) is speculative to the point of being a bit weird. Even the softer version of Wilson that simple "tends to" give rise to complex with time just does not feel written in stone to me.