Wednesday, January 31, 2007

Petri dishes rule!

This post by Tara at scienceborgs is too cool to pass up. One of the commenters even produced the original reference:

Petri, R. J. 1887. "Eine kleine Modification des Koch'schen Plattenverfahrens." Centralblatt fur Bacteriologie und Parasitenkunde, Vol 1, pages 279 - 280 .

Now that is geekdom at its finest.

Can’t hack fashion? Try chemistry

A recent article in The Australian has pointed out that the minimum entry score for university science courses is lower than the minimum required marks for almost any other course.

“At the University of Technology, Sydney, the entry score for a science degree was 76.9, compared with 88 for fashion and textile design, 80.25 for sport and exercise management and 84.15 for an arts degree.”

The study cites a lack of prestige, higher course fees, and boring year 11 and 12 courses as contributing factors. For those American readers out there, entry scores in Australia are demand driven, so either all the high-scoring students are choosing to pursue careers outside of science, or nobody at all is interested in science. Thus science departments are letting anyone in off the streets to fill up classes.

Usually I’d slide a snide punchline in here, but this is so depressing that I can’t think one up.

I disagree with some of the proposed solutions, though.

In a follow up article, a professional scientist spokesman is quoted as saying, "There's a view among some kids at secondary school that science is nerdy. We've got to make it sexy.

Alternatively, we could point out to them that being sexy without knowing any science will turn you into a syphilis-addled teen parent. But maybe he was looking for a more positive spin.

Apparent Dip and Green Gabbro both contain posts about how to get more people interested in geology, and what we ought to be communicating to the public. Thermochronic seems to be pushing the inspiration angle, while Yami prefers to hold San Francisco hostage.

I think the inspiration angle has its problems. Let’s be honest folks. We spend most of out time looking at rocks. Or squeezing them. Or figuring out what they are made of. This is not the sort of inspirational topic that propelled the Greeks to create one of humanity’s most enduring mythologies. There is no ancient Sumarian deity who split the feldspars from the amphiboles or chewed the primordial muck to distinguish silt from clay. The wow factor of rocks is essentially zero.

I don’t fancy the fear factor either. Most people don’t really care if their hometown will get flattened once every 400 years, and there is enough irrational fear-mongering going around already, without us spoiling the party by pointing out threats that are actually real.

I reckon the best approach is to find a way to communicate how science works. The really great thing about geology is how we connect seemingly unrelated things to put together a story. For example:
If you find me an ancient hunk of hyaloclastic basalt (or low-grade metagabbro), a geochemist can tell you whether or not the shoreline near where that basalt erupted had a serious tsunami risk. And they can do it by measuring three elements that most people can’t even find on the periodic table: lanthanum, niobium, and uranium.

The reasoning is simple:
Niobium is compatible in titanium minerals, due to the similar ionic radius and the ability to charge-balance trivalent cations.
Titanium residues in magma formation form during the hydrous melting of the mantle.
Transporting water into the deep hot mantle requires a subducting oceanic plate.
Subduction zones are the main sites of tsunami-generating magnitude 9+ megathrusts.

And if that sort of connectivity between seemingly unrelated factoids isn’t cool, then maybe you should be selling houses or balancing ledgers. Or maybe I’m just a dork.

The story behind each line in the above argument is an entire geology class. Learning how to test and verify these outlandish ideas is how we learn about the natural world.

I think the big challenge is getting people interested in appreciating the power of the scientific method, and then teaching them how to apply it to things that interest them. And finally, if their natural inclinations don’t point them towards outcrops or osmium, we could just appeal to their pocketbooks:

“Some geologists have eclipsed dentists as the highest-paid graduates in Australia, scoring rock-solid wages of more than $80,000 a year”.
-The Australian 19/12/05

Tuesday, January 30, 2007

Buy me a burger and protest a cult

The stunt-loving zealots known as “People for the Ethical Treatment of Animals” have gotten feministe upset by using a stripper to promote their crusade. A number of her readers seem to wish there was a way of protesting the degradation of women without having to actually eat meat. At the same time, they don’t want their vegetarianism to get in the way of a protest that would dissuade PETA from subjugating women.

Ladies, there is a third way. Even if you don’t like eating meat yourselves, you can always buy a big, meaty lunch for one of your carnivorous friends whenever the PETA stunt brigade adopts a frat boy mentality. Write your protest message on your lunch date’s Big Mac wrapper, and mail it to the PETA fundraising address. And if you can’t find a meat-eating grad student, colleague, or buddy to buy this lunch for, I suppose that I could sacrifice my cardiovascular health for the good of the cause. Not that I’m trying to scam a feed or anything. I do have standards. Somewhere. They just don’t apply to food.

Rate your own carbonado news story

Nitrogen defects in diamond. a. is type Ib, b. is type IaA, c. is type IaB. We use FTIR to determine nitrogen aggregation state becasue our eyes aren't sharp enough to make out the balls and sticks unaided.

I had someone else come up to me and ask about my opinion of the carbonado news today. Strangely, they didn’t offer to plot any data or fight the Bruker for me (the software for our IR scope runs in the OS/2 operating system, and the most advanced portable media reader on that computer is a 3.5 inch diskette drive). So, for those of you who want to know how reliable the coverage is in your medium of choice, here is a simple formula to rate the coverage:

They simply rephrase the press release to remove any big words: 0
They say that diamond is usually made by compressing coal: -5
They make any other basic geologic error by trying to over simplify: -1
They use, and explain, the term carbonado: 1 (the scientific community doesn’t even have a rigorous definition, so we can’t really complain about the quality of the press’s descriptions)
They interview an author: 1
They interview an independent “expert,” whose comments show that he doesn’t have a clue about the subject matter and is simply trying not to say anything that might make him look silly: 1
They interview an independent expert who can actually contribute meaningfully: 3
They do their own independent reading and explanation: 5
They interview one of the authors of any of the papers referenced by Garai et al.: 5
They interview a referenced author who speaks knowledgably: 10
They get their independent source to talk about experimental design, and pitfalls therein: 15
They get an author and an independent source to debate methods and data, instead of interpretations and models: 20
They get all interviewees to discuss the ramifications of the paper without anyone flapping their arms: 25

So far, the biggest score I’ve seen is about a 5.

Thursday, January 25, 2007

Hand waving

I decided that I really wanted to get a picture of that comet, even though I don’t have a tripod. So I figured hey, why not at least try a 60 second hand-held shot? The first few attempts were hopeless, but by holding the camera on the top of a fencepost, with a wooden block to brace it against, I did manage to get a few shots where the comet is visible. This one only required a little bit of contrast correcting:

Wednesday, January 24, 2007

The speed of science: relativistic media vs. classical research

As mentioned previously, I will be writing a comment on a paper which failed to impress me. My general complaints are that I think it misrepresents the literature, fails to describe its samples and analyses well enough to allow an objective interpretation, and overstates the quality of the data. But outside the ivory tower, life goes on.

Despite any previous metaphors used in this blog to describe the comment and reply process, it is one of the more standard, classical ways of discussing scientific findings. When done well, it is measured, fair, and provides greater illumination of how different research groups approach problems and weigh various evidence for and against competing hypotheses.

At the other end of the spectrum of scientific discourse is sound-byte and press release science. As it happens, the paper on which we wish to comment is accompanied by two press releases, by the university and by the NSF.

I think it may be interesting to compare the progress of buzz and reportage to the rate of constructing a scientifically sound counter-argument. So here’s a timeline:

Dec 20
The Astrophysical Journal Letters publishes the Garai et al. paper on carbonado diamond, which I think is a poor research publication.

Jan (date unknown, but probably the 2nd)
American Mineralogist publishes a Kagi et al. paper on carbonado, which I think is a contender for the best paper on the subject in the last 5 years.

Jan 8
NSF press release issued about Garai et al. paper
Articles on Garai et al. ‘06:
Articles on Kagi et al. ‘07: (none)

Jan 9
Articles on Garai et al. ‘06:,2933,242575,00.html
Articles on Kagi et al. ‘07: (none)

Jan 10:
My postdoc adviser emails me the paper.

Articles on Garai et al. ‘06:
Articles on Kagi et al. ‘07: (none)

Jan 11:
Articles on Garai et al. ‘06:
Articles on Kagi et al. ‘07: (none)

Jan 12:
Articles on Garai et al. ‘06:
Articles on Kagi et al. ‘07: (none)

Jan 13:
Articles on Garai et al. ‘06:
Articles on Kagi et al. ‘07: (none)

Jan 14:
Articles on Garai et al. ‘06:
Articles on Kagi et al. ‘07: (none)

Jan 15:
I get back from summer holiday, check my mail, read paper. Scratch head, read again, explode. Scrape self off ceiling, email postdoc advisors and PhD advisor to see if they are interested in co-authoring a comment (My PhD was on carbonado diamond). I start digging back through papers I haven’t looked at for 6 years.
Articles on Garai et al. ‘06:
Articles on Kagi et al. ‘07: (none)

Jan 16-19:
Post doc advisors get on board, I chat with one of them, we map out a general plan, start looking for the software/ archived files we need. I learn that Statview hasn’t been sold since 2002, start thinking up workarounds.
Articles on Garai et al. ‘06:
Articles on Kagi et al. ‘07: (none)

Jan 20-21:
Go through paper (over weekend) with attention to detail, start categorizing things I don’t like by relevance, type of issue, dubiousness of claim, etc.
Articles on Garai et al. ‘06:
Articles on Kagi et al. ‘07: (none)

Jan 22-present
Finally get some obscure articles from Geoscience Australia (not in our library) to confirm selective referencing, crash IR scope computer trying to remember how the OS/2 operating system works, get PhD supervisor interested, get swamped with work for visiting scientists.
Articles on Garai et al. ‘06:
Articles on Kagi et al. ‘07: (none)

Draw your own conclusions.

Tuesday, January 23, 2007

Chasing a comet

Last night I went out to spot the McNaught comet around sunset. Some friends, Mrs. Lemming, and I had failed to spot it the previous night, so I ran up Mt. Painter just in time to catch a beautiful sunset.

As the sunset progressed, I managed to get a picture with both the moon and Venus in the same frame, but the comet was still not visible.

Finally, the comet appeared. By then it was dark enough that my attempts at hand-held shots were pretty poor, but the darker the sky got, the more spectacular the comet became, until by 10 the tail was a huge fountain of light. Too bad I don’t own a tripod.

Thursday, January 18, 2007

Comment and Reply

The evolution of animal behavior can be a surprisingly conservative process. Even though the habitat, niche, and social organization of a creature may change as it evolves, certain core behaviors are often retained.

One example of this is the fecal throwing habits of monkeys. Bereft of dangerous claws, poison, or hooves, monkeys have been forced to defend themselves by slinging their own poo at perceived enemies. Despite tens of millions of years of evolutionary divergence, the adaptation of culture, and the invention of the scientific method, researchers do exactly the same thing. Only they call it “Comment and reply”.

There are two criteria that must be met before a researcher engages in this undignified activity.

First, he must identify a paper that, despite appearing to be the summation of a scientific research project, is in fact a huge, steaming pile of shit.

Second, he must fee that this paper was either hurled at him directly by a rival team, or else tossed close enough that the smell distracts him from the dispassionate pursuit of knowledge.

When an aggrieved scientist feels that these two criteria have been met, he then squeezes out his own steaming turd, and fires it off at the editor of the offending paper. That editor takes the crap, examines it with the help of a reviewer, and passes it on to the original authors.

Those authors in turn drop a load in response to the comment, called a reply. The comment and reply are then generally published, side by side, in the journal that ran the original paper.

Usually that is all that happens, aside from the odd snide letter to the editor. Rarely, one side or the other will capitulate, and plate the opposing side’s poop with gold. And every now and again, a real shitfight results, with claims and counter arguments splattering against each other for years to come.

I am about to start putting together my first comment. Hopefully the level of discourse will be higher than that in this explanation.

Tuesday, January 16, 2007

The second day back

The second day back after a holiday is way more trying than the first.

On the first day back, I generally expect it to be a bit of a shock, and work accordingly. On the first day back, the goal is to simply make it through a normal day without screwing anything up. All the tricky stuff is left for the second day.

So it is that second day back that requires trying to make up for all the time away. For me, that meant doing a month’s worth of deferred maintenance on the ICP- changing the cones and both lens stacks.

Yesterday, I was content to just get it up and running. It was only going at about 98% of our preferred minimal sensitivity, but that was close enough for the first day back. So I waited until today to tear everything apart and reassemble it. And when I did, I found that I only had 8% of the minimum sensitivity.

The trouble with changing everything at once is that it required going back in incrementally reverting, to locate the problem. So I pulled all the nice, shiny clean bits out, replacing them with the mangy ones that I had just removed. After that process, I managed to get back up to 30% of minimum. And this was the same configuration that gave me 98% yesterday.

So I banged my head on the wall, cried, and screamed at it. No change. Eventually, after a talk with my boss, I went outside and checked all the external bits- things completely unrelated to the maintenance that I did. And sure enough, one of the roughing pumps was down. The circuit breaker must have thrown when I pumped down after the first lens change. If only one pump dies, the vacuum degrades enough in the source to squelch the signal, but not enough to show up on the gauges. So it turns out that after tearing everything apart twice, all I had to do was reset a circuit breaker, and give it a few hours to pump down. I got everything fixed and checked out just in time to confirm that the scientist booked on the machine had given up and gone home for the day.

At least I got back to where I started.

Monday, January 15, 2007

Blog Love

I'd like to introduce a new geo blog, Apparent Dip. He's a geochemist, an error propogation nazi, he autoposts earthquakes, he's funny, he has a catchy title, and he likes me. What more could a blogger ask for?

Sunday, January 14, 2007

The perfect scientist is still a monkey

Over at Retrospectacle, Shelley Batts has posted a poignant story of love, loss, and labwork, and how they can interact in unpredictable ways. A possible contributor to her scientific troubles was the iconic image of a scientist- the ├╝berscientist as an implacable machine of discovery, dispassionately and efficiently wresting the secrets of nature from the void of the unknown.

The worship of this mythic scientist archetype- logical, knowing, and ruthlessly efficient- is no great surprise. After all, the practice of science requires us to separate data from interpretation, assumptions from observation, and model from process. It is no great mental leap to assume that scientists who analyze and compartmentalize their work for a living ought to be able to apply the same methodology to the rest of their lives. But this is not the case.

Back in the good old days of sailing ships, typhoid, and phlogiston, it was thought that as God’s final creation on the planet, it was our duty to figure out the rest of his week-long make-work project. By knowing the world, we would know the mind of The Lord, bringing us closer to truth, perfection, and divine tranquility.

As the pursuit of knowledge progressed, the sails, phlogiston, and typhoid all got flushed into the toilet of science history. Many scientists claim to have consigned the monotheistic deity to the same fate, but their approach to science belies this claim. For they still labor under the assumption that the universe is a soluble puzzle, a divine creation that can be unlocked through the pious application of the scientific method.

For the most part, the leap of faith that assumes science can work has been remarkably successful. We have discovered a mind-bogglingly large amount of stuff about the universe this way, so it is perilously easy to not only make the antiquated assumption that science will work, but to also that scientists are designed to figure out these secrets. Nothing could be farther from the truth.

The greatest science brains are not actually designed at all. They are, rather, the accidental products of hundreds of millions of years of worm, fish, and mammalian mutation, and the fact that they can program computers and spike solutions in addition to selecting and acquiring food, shelter, and mates is nothing short of miraculous.

Just consider: Even though crows, apes, parrots, dolphins, and octopus can all learn tool use- in the hundreds of millions of species-years that these tool-users have been cruising the planet, it is only recently that scientifically capable humans have actually evolved. And even though the fossil record shows that anatomically modern humans have been around for 195,000 years, we have only been doing science for less than 2 percent of that time.

So enjoy the miracle of scientific thinking, but don’t push your luck. The hypothetical ├╝berscientist archetype may be able to compartmentalize emotional suffering and scientific problems by throwing himself into cutting edge research or other activities as a distraction from the emotional pain. On the time scale of a single class or a degree course, a student even might be able to post good scores by doing this. But as Dr. Shellie posted last year, success on the career and semester timescales are not necessarily related. So here are two basic tips for not letting primal needs disrupt labwork.

1. Do not engage in high-risk, high-consequence activities (including labwork) as a method of distracting yourself from something that is bothersome or hurtful. As a coping mechanism, it is about as helpful as drinking whiskey, and it greatly increases the chance of mishaps. If you’re upset, sort yourself out first, then come back to lab. Or if you must hide in your work, do something where mistakes are reversible and non-hazardous. If you MUST go in and do the world’s trickiest procedure in humanity’s least replaceable sample, at least have a chat with your friendly neighborhood busdriver/officemate/techo beforehand to get your problem off your chest, instead of sucking it up and hoping you make it through the day.

2. If you’re doing labwork, and you do make a minor mistake, stop. Obviously some protocols, especially in biology, can’t just be stopped in the middle and put on a shelf. But the most common cause of medium and large screwups in lab that I see- both by myself and by other people- is when people make a trivial error, and then compound it either by rushing to make up lost time, or by getting distracted by the mishap and losing focus. If you mess up, stop ASAP. Get out of lab, have a cup of tea, relax, and then go back to sort out the problem.

Friday, January 12, 2007

A Cunning Australian Orca

One of the highlights of my recent summer holiday was the Eden Killer Whale Museum. Eden is located on Twofold Bay, the southeastern-most deepwater harbour on mainland Australia. Eden was the base for shore-based open-boat whaling from 1828-1928. This is the sort of whaling where, when a shore-based lookout spotted a whale, the whalers would row out in longboats, harpoon the whale, get towed around until the whale tired, and then finish it off. In the early 20th century, however, the Eden whaling operations became unique, in that humans were not the only ones hunting the whales.

My brother and I posing with the skeleton of a whale-hunting orca

The Eden whalers developed a whale-hunting relationship with a pod of killer whales, which allowed them to continue shore based whaling until the development of factory whaling in the mid-20's.

Alternatively, a pod of killer whales domesticated the Eden whalemen, in order to provide easy dinners.

According to the museum (which contains several grainy pre-war photos of orcas cruising alongside whale boats and rorqual carcasses), the killer whales would find a baleen whale, chase it into Twofold Bay, and then alert the whalers. These humans would then harpoon the whale, and the orcas would expedite the whale killing process by hanging onto the harpoon hawser to increase drag and rolling the harpooned whales to prevent them from sounding.

Once the whale was killed, the orcas would eat the tongue (Baleen whales have very large tongues), and leave the carcass for the whalers to extract blubber from.

While this story falls squarely into the “stranger than fiction” department, the cool thing for me was the paleontological evidence. Two years after the last whale was taken, the body of one of the whale-hunting orcas washed up in the bay. The remains were processed, and the skeleton is now on display in the museum, where my brother and I found it.

The coolest feature is hard to see in the photo above, but thankfully Tim Cole and Nick Hodge have a better image on Nick’s blog. As seen in some of these pictures, the first six teeth on the whale’s lower left jaw have been worn down to the gum line. The seventh tooth (and to a lesser extent, the eighth and ninth) has a clean, rounded notch, which is consistent with the expected wear from a harpoon hawser or other medium-weight rope. So the skeletal evidence actually supports the historical reports of orcas towing boats or joining in on a Nantucket sleigh ride.

If anyone else out there knows of cleverer symbiotic behavior between non-domestic species, I’d love to hear it.

Wednesday, January 10, 2007

Birthday meme

Via Yami, data from Wikipedia

Born on my birthday:

  • Grigori Rasputin

  • George Foreman

  • Nicolas Steno

Died on my Birthday:

  • Carolus Linnaeus

  • Gabrielle "Coco" Chanel

  • William F. Cody

Happened on my Birthday:

  • 49 BC - Julius Caesar crosses the Rubicon, signaling the start of civil war.

  • 1776 - Thomas Paine publishes Common Sense.

  • 1861 - American Civil War: Florida secedes from the US.

In the Faulkland Islands, today is Margaret Thatcher day.

Tuesday, January 09, 2007

Wondering where Cassini got that funny ringtone?

The Tidbinbilla Deep Space Tracking Centre, which NASA uses to communicate with space probes when California and Spain are on the wrong sides of the planet, is located in a quiet agricultural valley drought-stricken wasteland about 30 km southwest of Canberra. It’s a fairly out-of-the way place, with little to offer other than a wildlife reserve, some burned-out pine plantations, and a few overgrazed paddocks. As a result, I hadn’t been out that way for a while.

This afternoon, however, after showing my visiting brother and his girlfriend around the nature reserve, I noticed a new sign on the space center access road. It turns out it wasn’t ET phoning home after all. It was just Bruce Yobbo calling in his takeaway. And the face on Mars was just a drunk guy checking in with his wife on his camera phone.