Scriptorium Scientifica

The colors of fall

2006-11-06T21:45:00.000-05:00

The leaves are falling off the trees pretty quickly here in New England, but only after putting on a fantastic color display this year. I haven't seen blazing foliage like that in a while.

But where do those colors come from? What causes that fiery display? As we all learned in high school biology class, the green we see in the leaves from spring through summer is caused by chlorophyll - the pigment that captures sunlight for photosynthesis. As the temperatures drop and the days get shorter, leaves stop producing chlorophyll. And here's the trick. The orange and yellow pigments, called carotenoids, are already there...the leaf produces them at the same time that it produces the chlorophyll, but they are masked by the intensity of the green coloring. Once the green is gone, the orange and yellow can show through.

As for the reds, they come from pigments called anthocyanins - and these are a little more mysterious. They are only produced in the fall, act as a kind of antifreeze and sunscreen for the leaves, and, interestingly enough, can be a sign of a tree in distress (a tree that turns red early is in some trouble).

In nature, you often find that brilliant colors are a signal for danger or distress. Me, I like to think of these colors as a sign that my favorite season is here.

[Read more at MSNBC.]

When astronomy meets...demolition?

2006-11-06T21:30:00.000-05:00

It can be a dangerous world, even if you don't go out your door. Late last month a cottage in western Germany was destroyed by a fire. What made this fire unusual is that it seems to have been caused by a meteroite. Authorities in Siegburg, Germany, baffeled as to how the fire could have started, turned to a nearby observatory for assistance. At the time of the fire, the earth was passing through a field of "meteoroid splinters." Witnesses who saw the fire also reported seeing a "blazing arc of light" in the night sky.

Most meteors don't make it thru the atmosphere, burning up long before reaching the ground. Seems this one didn't. The police think the meteor that destroyed the cottage was no bigger than 10 mm.

[Take a look at Reuters for the original story.]

Imagine all the people

2006-10-16T21:16:00.000-04:00

As I write this, the US population is on the verge of breaking 300 million. In fact, the Census Bureau estimates that we'll hit the magic number at 7:46 AM EDT tomorrow morning. The last time the country broke a hundred million mark, it was 1967. (That would be 7 years before I was born.)

While many are taking the opportunity to discuss America's consumption patters, resource usage, and immigration policies, an interesting article showed up on New Scientist today. What would happen to the environment, the world, if the human species just up and left? How long would the traces of human habitation last on the planet?

As you can imagine different aspects of the human footprint would disappear at different rates. It's actually a fascinating study in entropy (roughly, the tendency of a system to go to the least energetic state - to just fall apart - when there's no one to maintain it). There's a couple of ways of looking at this article. First, the glass-half-full argument: that in spite of how much we've done to the planet, none if it is totally irreversible, that if left to its own devices, nature will take care of her own. Then there's the glass-half-empty argument: that it would take 100s to thousands (in the case of nuclear waste, maybe even millions of years) to undo the damage we have done.

You can read into it what you want. Me, I like the idea that things can bounce back. But, if we were to turn everything off right now, would the environment, the ecology turn out exactly the same? No, of course not. The environment probably didn't return to an exact pre-Ice Age state after the glaciers melted, either. Once an ecology is altered, artificially or naturally, I imagine it's nearly impossible to return it to its native state. However, the resilience of nature is amazing. You can see it just by looking at a vacant urban lot, and see the grass, weeds, and trees taking it over. Nature will grow back where it can.

But that doesn't mean we shouldn't still be careful what we do.

[See New Scientist for the global exit story. To see how close the US is to the 300 million mark, see the Census Bureau's population clock. Most likely, by the time you read this, the zeros will have turned over. "Earth at Night" courtesy of NASA's Astronomy Picture of the Day.]

Nobel Prize updates - have you got your scorecard out?

2006-10-04T14:34:00.000-04:00

Since my last Nobel prize post, two more of the Nobel prizes for 2006 have been handed out.

On Tuesday, the Nobel Prize in Physics was awarded to John Mather and George Smoot for their efforts to peer into the earliest moments of the universe. Dr. Smoot should not be confused with Oliver Smoot, another MIT alum whose physical stature was the basis for the smoot, a somewhat non-standard unit of measurement.

Wednesday dawned with the announcement that Roger Kornberg had been awarded the Nobel Prize in Chemistry for his work on the mechanisms of genetic translation (the process by which our DNA is decoded into, well, us). Dr. Kornberg follows in the footsteps of his father, Arthur Kornberg, who took home the Nobel Prize in Medicine in 1959; they are the 6th father-and-son laureate pair in the history of the Nobel Prizes.

[More on the Nobel website.]

If Fluffy makes you sneeze...

2006-10-02T22:37:00.000-04:00

....then it's time to trade up to a hypoallergenic cat!

For those allergic cat lovers who can't be bothered with antihistamines or allergy injections -- and have about four grand kicking around -- science brings you a new kitty specifically bred to produce less of the protein that makes you red-eyed and and sniffly. The new kitties, created by a research firm called Allerca, were produced by the oldest form of genetic engineering in the book: selective breeding. By finding cats that naturally produce less of the protein (called Fel d1) and breeding them together, Allerca was eventually able to raise cats that don't raise the hackles of our immune systems.

Allerca first started taking orders for the sneeze-less felines back in 2004, and there's already a long waiting list.

[More on the BBC, or on the Allerca website.]

It's like the Oscars, but for academics

2006-10-02T22:01:00.000-04:00

The academic world is holding its collective breath, as we've entered the most exciting time of the year...Nobel season. Over the course of the next few days, the Nobel Institute will announce the winners of this year's Nobel Prizes. Awarded by Sweden's Nobel Institute, the Nobel Prizes have been awarded since 1901 for achievements in physics, chemistry, physiology or medicine, literature and for peace.

The awards were established in the will of Alfred Nobel, who, according to the Nobel Prize website, was "a scientist, inventor, entrepreneur, author and pacifist." He also happened to be the man who invented dynamite.

The will said, in part:

The whole of my remaining realizable estate shall be dealt with in the following way: the capital, invested in safe securities by my executors, shall constitute a fund, the interest on which shall be annually distributed in the form of prizes to those who, during the preceding year, shall have conferred the greatest benefit on mankind.

Nobel died in 1896, but the first award was not given until 1901. The reason? His family contested the will. Ahh, sweet litigation.

And how does one find out if they've won one of these coveted awards? In the US, it seems that one receives a phone call at home, very early in the morning. Still only half-awake, one picks up the phone, and wonders if the person on the other end is a crank caller with a bad Swedish accent. Then one receives several dozen other phone calls, usually from reporters who have also woken up at unreasonably early hours. And then one realizes, "Holy Crap, I'm a laureate! I'd better have some coffee!!"

As of this writing, only the prize for physiology or medicine has been awarded. The winners: a pair of researchers, Andrew Fire and Craig Mello, who discovered RNA interference (RNAi). This natural process effectively silences genes like the mute button on a stereo, and can be used both experimentally (to answer the question, "Hey, what happens when I turn this gene off?") and potentially therapeutically in diseases like cancer.

The unusual thing about this particular award is that it came so quickly. The researchers only published their seminal work on the subject 8 years ago. Nobel awardees (or laureates) typically don't receive awards until decades after the actual accomplishment for which they are nominated.

And now, for a shameless plug - the Nobels' lesser-known stepcousin, the IgNobel Prizes, will be awarded this Thursday night. Only slightly less prestigious (they can make or break careers, you know), the Igs honor those achievements which make people laugh, and then make people think. The awards, which are handed out by actual Nobel laureates (there are one or two of them just hanging around in Boston), are awarded in a ceremony with all appropriate pomp and circumstance. I can say that because I will be on stage helping herd the winners through the ceremony.

[For more on the prizes, check out the Nobel website or a recent story from Reuters. For more on the IgNobels, including how to get tickets or see the webcast, take a look at Improbable.com.]

El Nino? Ay caramba!

2006-09-18T21:07:00.000-04:00

Last week, the National Oceanic and Atmospheric Administration (NOAA) announced that a new El Nino event is building. The announcement was based on an increase in sea surface temperatures in the Pacific Ocean off the coast of South America...hallmark of a rising El Nino.

El Nino is part of a weather pattern called the Southern Oscillation, a see-saw of temperatures and air pressure between the eastern and western Pacific that can change the normal movement of moisture and wind across the ocean. El Nino (Spanish for "Christ child," a reference to the fact that it always arises late in the year) has a little sister called La Nina, which is characterized by lower-than-normal temperatures near South America.

Why is this a big deal? Because El Ninos can disrupt weather globally. El Ninos can make things wetter in North America, drier in South America and Australia, and can put a damper on hurricane formation in the Caribbean - like what might be happening this year.

The length of time El Ninos last can vary. This one is predicted to hold on until early next year. But then again, no one thought an El Nino was going to occur this year until the last few weeks.

[Check the NOAA website for more information on this El Nino event. To learn more about El Ninos in general, check out NOVA.]

Summer vacation is over...

2006-09-18T21:04:00.000-04:00

...and the Scriptorium is back. My apologies for the silence the last few months.

It's a planet! Wait, no it's not, but it is. Hold on, there are 12?

2006-08-18T15:09:00.000-04:00

Remember the mnemonic you learned as a kid so you could remember the names of the nine planets? It was probably one of these:

"My Very Eager Mother Just Served Us Nine Pickles."

"Mother Very Easily Made Jane Stop Using Nail Polish."

"My Very Enormous Monster Just Sucked Up Nine Planets."

Well, it's time to unlearn them, because the nine-planet solar system everyone thought was set in stone after the discovery of Pluto in the 1930s just got tossed. Welcome to the age of the 12-planet solar system, thanks to the new definition of "planet" proposed at a meeting of the International Astronomical Union. They also propose to create a new class of mini-planet called a "pluton."

With the new definition comes the following changes:

Pluto gets downgraded from planet to pluton
Charon, Pluto's moon (more on that in a second), gets bumped up to pluton designation
Ceres, a really big asteroid in the belt between Mars and Jupiter, bypasses pluton-ness and goes straight to planet
The large body discovered in 2003 beyond Pluto, which has the melodic name 2003UB313 (unofficially dubbed Xena by its discoverer), becomes the third member of the plutons.

Pluto and Charon are seeing the biggest change in the org chart of Solar System, Inc. Charon gets promoted to independent status - a moon no more - because it is so heavy that the center of gravity between it and Pluto is smack in between them (meaning they revolve around a point in space). Contrast this with the Earth and our moon, where the center of gravity of the two-body system is in the Earth itself (so that the moon actually revolves around us). Thus, Pluto and Charon become the solar system's first double planet.

There may be more plutons on the way; if the definition is approved, then a host of other bodies in the solar system, including other asteroids and maybe even other moons, will earn the title. Meaning we could potentially end up with a solar system with hundreds of such mini-planets. And some really long mnemonics to remember them.

Oh, and the main criterion for joining the planetary club? Roundness.

[Read on at New Scientist to learn about the debate over the definition of planet. And many thanks to my father-in-law for the mnemonics.]

UPDATE: Turns out that if the IAU accepts the new planetary definition, things could get really weird in the solar system, with our moon even eventually qualifying for planethood. Tune back in in about, oh, 5 billion years.

ANOTHER UPDATE: Scratch pluton, make that "dwarf planet." And it's 8, not 12.

Do these bacteria make my thighs look fat?

2006-06-19T22:07:00.000-04:00

Believe it or not, you have a bacterial infection in your intestines right now. And it's OK. We all have bacteria in our guts, ones that live with our bodies in a mutually beneficial (or "symbiotic") relationship. We provide a nice, safe, warm environment, and in return they help us digest our food. There are certain foods that we just couldn't digest without our helpful little microbes, and certain proteins, amino acids, and other nutrients we need that we would have a hard time absorbing if they weren't preprocessed.

Now it appears that they may also influence how well we absorb sugars and store them...and when we store sugars, we store them as fat. Researchers at Washington University inoculated germ-free mice with different microorganisms or a combination of microorganisms and measured how they digested their food. The mice given the combination of bugs digested the sugars within their feed more efficiently, but instead of burning them off, the mice stored them as fat, causing them to gain more weight.

The researchers look at the study as a "logical extension of the human genome project - one designed to define the microbial side of ourselves." They even managed to drop the word "microbiome." (Add that one to the list.)

The take home message? While dieting and exercise are still the best ways to lose and control weight, the bugs in your gut may have something to say about it. The researchers hypothesize that one day treatments that alter the microbial composition of our intestines could be a vital aspect of nutritional control.

[Many thanks to EurekAlert and LiveScience.]

Genetically carnivorous?

2006-06-19T21:30:00.000-04:00

Twin studies are often used to probe the relative contributions of nature and nurture - that is, heredity and environment - to behavioral and other traits. The results can be eerie at times; the popular and scientific literature are rife with descriptions of twins who are separated at birth and meet decades later to find that they have followed the exact same career paths, have the same likes and dislikes, and have similar personality traits.

How about food preferences? Researchers in England surveyed the parents of hundreds of sets of identical and fraternal to determine the heritability of food preference. The results? Kids are more likely to inherit a taste for fish or meat, while preferences for vegetables - and dessert(!?) - are more heavily influenced by availability and/or parental choice.

Does this mean we can breed out vegans?

Believe it or not, this research does have a good purpose. The leader of the research group, Professor Jane Wardle of the Health Behavior Unit at University College London, is keenly interested in what shapes children's food preferences so as to better understand why kids diets are so, well, bad. If you can mold their diet when they're young, maybe you can keep them from getting cancer and heart disease later.

[Check out Yahoo for more, but if you really want to get to the meat of the story, check out Prof. Wardle's UCL faculty page.]

Ropeless jump rope patented

2006-06-14T09:20:00.000-04:00

Yes, you read that correctly. A ropeless jump rope. As in a jump rope, sans rope. Which, in my mind, isn't really a jump rope, rope being the fundamental component, the very essence, of a jump rope. For at the core of a jump rope is, well, rope. That one can jump over. Thus, what we really have here is a pair weighted jump handles, which you can't really jump over.

Come to think of it, what it looks like we really have here is a pair of hollow donuts on sticks.

Coming next to a playground near you: hoopless hula hoop (aka hula dancing), square-free hopscotch, and dodge (same as dodgeball, but without the ball; you just throw yourself to the ground when someone on the other team waves their arms at you).

[Thank you Engadget and Globe and Mail! You can also view the patent, #7,037,243, on the USPTO website.]

The sleeping pill that puts you to sleep AND wakes you up

2006-06-13T22:33:00.000-04:00

Advertisements and PR for sleeping pills (and other medications, too) crack me up, like the one for Lunesta with the freaky glowing butterfly that floats into everyone's bedroom. (Word to the wise: if you're lying in bed and you see a radioactive moth hovering over your head, don't close your eyes. Swat that unholy thing and run.)

But the makers of Ambien seem to be experiencing some mixed PR of late. First came the stories that arrests for driving while under the influence of Ambien are on the rise. Most of the drivers arrested while sleeping behind the wheel didn't even realize they were driving.

You can tell just how powerful Ambien's wake up kick must be, because now there are a limited number of reports of coma patients being temporarily roused by the drug. Three men in England who had been diagnosed as being in a permanent vegetative state (PVS) started interacting with their environment or showed other improvements for short periods of time when given Ambien as part of a research study. The question remains whether the men were misdiagnosed to begin with; supposedly it is impossible to rouse patients in a true PVS by any means.

Ambien: Helps you get a full night's sleep, makes you sleepdrive, and can potentially wake the comatose. I think I'll stick with my long time favorite sleep aid.

[You can read more at New Scientist.]

Can you hear me now? Not if you're over 30.

2006-06-13T21:59:00.000-04:00

I love it when a technology gets turned on its head, but this one could cause some serious consternation among educational professionals. Some students apparently have started downloading a ringtone to their cell phones that is of such a high frequency that adult ears don't pick it up. Thus, if kids have this ringtone on their phones, teachers will never hear the constant beeping as they text message each other with the answers to that math quiz.

It's a simple byproduct of aging - as we get older, we lose the ability to pick up on high-frequency sounds.

The ironic thing? The ringtone is a spin-off of a technology designed to drive off teenagers loitering in front of shops without bothering the older, more genteel shopping clientele.

[Check out the New York Times for more.]

You can almost taste the sonar

2006-06-13T21:55:00.000-04:00

Let's go down the list of ways in which we've enhanced our senses. We have night vision goggles, as well as plain old eyeglasses like mine, for the eyes. There's even a bionic eye in the works. We have sensitive microphones and headphones/earbuds for the ears. There are guys out there with magnets in their fingertips that supposedly let them "feel" magnetic fields. Smell? Not so much done on this as far as I know, although if anyone knows of technological enhancements for the old schnoz, I'd love to hear about them.

How about taste? Well, how would you like to taste the fact that you're about to walk into a wall? For some 30 years the Institute for Human and Machine Cognition has been working the BrainPort - a neural tongue interface. It works like this: the device has a grid of 144 electrodes that sit on your tongue and send impulses through the sensitive nerve endings that you usually use for taste. The result? Your sensory perception is augmented by whatever sensing technology (sonar, radar, IR, etc.) is hooked to the system. The US Navy is supposedly interested in a sonar version for divers, but apparently the visually impaired can also use the system to "see" their surroundings.

[Thanks to Engadget for bringing this to light. Apparently, they like'd it so much they've written about it twice, unless there are 2 different BrainPorts floating around out there.]

Little kids as scientists, scientists as little kids

2006-05-14T21:30:00.000-04:00

My wife likes to point out that our nearly-2-year-old son is the ultimate scientist...something that could be said of all young children. Starting with nothing but boundless curiosity and awe, they are able, with time, to figure out what this world around them is and how it works. You can see it in their eyes as they soak up every bit of information around them.

So you can see why the following made me both nod and chuckle:

"Over the past ten years, developmental psychologists have increasingly used the model of scientific theory change to characterize cognitive development. I have called this idea the "theory theory. It has been consistently productive in explaining the child's developing understanding of the mind and the world. ... The analogy to science has two aspects. First, children's knowledge is structured in a theory-like way, and second, that knowledge changes in a way that is analogous to theory change in science.

"This theory formation system may have evolved specifically to allow human children to learn. Human beings' evolutionary advantage stems from our ability to adapt our behavior to a very wide variety of environments. In turn, this depends on our ability to learn swiftly and efficiently about the particular physical and social environment we grow up in. Their long, protected immaturity gives human children an opportunity to infer the particular structure of the world around them. The powerful and flexible theory formation abilities we see in childhood may have evolved to make this learning possible. In this view, science takes advantage of these basic abilities in a more socially organized way and applies them to new types of problems and domains. Science is thus a kind of epiphenomenon of cognitive development. It is not that children are little scientists but that scientists are big children."

As you might imagine, I added the emphasizing bold and italics. It makes me wonder if Shakespeare had it wrong, that "second childishness" doesn't mark the seventh age of man, but the beginnings of graduate school.

[Many thanks to my ever-vigilant father-in-law for sending this in, via National Review Online. For the whole article, go down to your local library and look up: A. Gopnik (2000). Explanation as orgasm and the drive for causal understanding: The evolution, function and phenomenology of the theory-formation system. In F. Keil & R. Wilson (Eds.) Cognition and explanation. Cambridge, Mass: MIT Press.]

Getting in touch with your -ome

2006-05-01T15:55:00.000-04:00

Since the human genome project was completed (a feat that, according to some, was actually accomplished 3 times), the sound "-ome" has been emanating softly from laboratories around the globe. But it has nothing to do with meditation and everything to do with, well, everything.

The suffix "-ome" (a corruption of Greek, Latin, or English, depending on who you ask) refers to the organization of complete collections of aspects or features of biology, such as genes (the genome), proteins (the proteome), and so on. Each covers the total catalog of that particular feature for some point of reference, like the dog genome or the transcriptome of a white blood cells, and can form the basis for its own field of study (hence genomics and proteomics). This is the realm of computational biology and bioinformatics, where researchers can produce thousands or millions of data points per experiment, and where biologists spend large amounts of time in the presence of specialists from such fields as mathematics and theoretical physics, fields long used to crunching lots and lots of numbers.

So how many "-omes" are there? Well the list is big, and seemingly getting bigger all the time. Every branch of the biological sciences seems to have its own set of "-omes" nowadays, with more being proposed all the time. The ones I hear about most often are:

Genome (the total catalog of genes within a cell or organism; studied via genomics)
Proteome (the total catalog of proteins within a cell or organism; studied via proteomics)
Transcriptome (the total catalog of RNA transcripts produced by the genes within a cell or organism)
Kinome (the total catalog of kinases within a cell or organism)
Reglome (the total catalog of genes controlled or influenced by a particular pathway, gene, or protein within a cell or organism)
Metabolome (the total catalog of metabolites within a cell or organism; studied via metabolomics)
Interactome (the total catalog of gene or protein interactions within a cell or organism)

And while the proliferation of "-omes" strikes some as a little silly or even dangerous (and it does lead me to ask, do we have to redefine economics?), I actually find it refreshing because it really does signal a sea change in ways of thinking about biology. Each -omic field take a large scale, integrated view of an aspect of biology. And the field of bioinformatics exists today to integrate data from different "-omes" (usually genomics and proteomics these days) into a clearer, holistics picture of what makes the total biology of a cell or organisms. I guess you could call that the bioinforome.

A holistic biology. Sounds pretty zen. Ommmmmm.........

[Credit for the photo of the worm protein interactome goes to Harvard Medical School. Wikipedia also has quite a bit to say on the subject of "-omes"...take a look here and here. Oh, and apparently "comics" doesn't count as an "omic" science.]

Learning from our myrmecological brethren

2006-04-25T13:23:00.000-04:00

This morning, my thoughts turned to one of my earlier posts as I read the following passage in today's New York Times :

And scientists, if you wonder why the public doesn't like you, read one of your papers. Scientific language is necessary. But so is speaking plainly. And if you have something funny, or human, to tell, that won't undermine your work. But it may bring it to a wider audience.

The author, James Gorman, uses the article to rejoice in the lighthearted way myrmecologist Walter Tschinkel sprinkles personal and sometimes humorous asides through his recently publish book, The Fire Ants, bringing a more human touch to the world of research.

Having spent my share of time speciating mosquitoes and identifying microscopic crustaceans in my research days, I can relate to how mindnumbing the grunt work of science can sometimes be...but that's part of the personal side of science, along moments of lab humor/silliness, celebration of "Eureka!" moments, lamentations over experiments that just refuse to work, and personal interactions with other scientists that sometimes leave us all scratching our heads. And while I hope that Gorman is being a little flip with his call for scientific journals to include interludes or asides with their articles (there is a proper time and place after all), it is worth remembering that there are ways we science writers can build humanity into our stories without watering them down, filling them with mush, or resorting to sensationalism.

(Oh, and in case you're wondering what the heck myrmecology is...)

Sweet sixteen

2006-04-24T21:30:00.000-04:00

On April 24, 1990, astronomy took a great leap forward with the launch of the Hubble Space Telescope. Operated by the Space Telescope Science Institute and NASA, the telescope was named for Edwin Hubble, a pioneering astronomer and one of the first to realize the true vastness of the universe. His work led to the formulation of Hubble's Law, which states that the father away a galaxy is from Earth, the faster it is racing away...first evidence of the expansion of the universe.

(Incidentally, that last link will take you to the announcement of the most recent estimate of the age of the universe - about 13.7 billion years. Take that, Archbishop Ussher!)

The telescope has more than lived up to the exploratory spirit of its namesake. It has returned some of the most astonishing and fascinating pictures of stars, nebulae, galaxies, and other inhabitants of the universe. It has provided us with the first optical proof of the existence of black holes. It has helped unravel some of the diverse and complex processes that drive the birth and death of stars.

And it has peered farther than ever before, both into the distance and into time. For the Hubble Ultra Deep Field survey, the telescope photographed a set of structures more than 13 billion light-years away; because a light-year is the distance traveled by light in one year, these pictures give us a view of a small slice of the universe as it looked more than 13 billion years ago.

Happy 16th birthday, Hubble. Let's hope they can keep you going.

[Photo courtesy of NASA.]

In terms of quality...

2006-04-24T20:37:00.000-04:00

...blogging while tired probably isn't as bad as blogging while drunk or stressed, and is probably less evident when it happens, too.

But it wouldn't even be an issue if my son hadn't decided to get up at 5:00 this morning.

A singular moment

2006-04-11T13:01:00.000-04:00

I know I missed this, and probably a great many of you did as well. But if you were up in the wee hours last Wednesday (April 5) and looked at your clock, perhaps you saw this:

01:02:03 04/05/06

That would have been the time and date at two minutes and three seconds past one o'clock in the morning.

And to think, we all had 24 chances to experience this moment....

[Many thanks to my father-in-law for alerting me to this, and my apologies for not reading it until a week later.]

I love a researcher who can speak English

2006-04-07T21:38:00.000-04:00

[Note to all the knee-jerk reactionaries out there - I am not referring to foreign scientists. Swallow your hypersensitive wrath and read on.]

I attended a seminar on stem cell research for reporters and writers a couple of days ago. Great talks, learned a great deal, and by the end of the day I could almost see stem cells floating in the air in front of me.

But what struck me the most was not the talk of nuclear cloning techniques or the ethics of therapeutic or research cloning. No, it was the speakers themselves and how they spoke to the audience. The best speakers were by far the oldest researchers, the ones who had been in the business for at least 20 years. They knew how to speak to the audience in plain language and as educated lay people.

The worst speaker of the day was the youngest. He was precise, direct, and brilliant, but got bogged down in the minutiae of his work. No one in the room needed to know about the structure of the transfection cassette he used to insert GFP into the ES cells harvested from his chimeric blastocysts. Nor did anyone understand it. Nor, frankly, did anyone care; such information was beyond the needs of that audience.

Now, this shouldn't be surprising, as with age comes understanding, experience, and an increased ability to read your audience. But it does raise an interesting idea. As I've said before, researchers need to be able to talk about what they do for it to mean anything to anyone. But why should it only be the most senior researchers that can do this?

Is it time for graduate and postgraduate programs to integrate media training/coaching into their curricula? Not for the benefit of reporters, really, but to equip students and postdocs to relate to the rest of us what makes their work important. After all we are paying for it. But more importantly, the public needs to be better informed to be able to debate the societal merits and pitfalls of scientific breakthroughs.

And how can we do that if scientists can't tell us in plain English what they do?

Off topic: When Gospel imitates art

2006-04-07T21:08:00.000-04:00

Few of you know this, but when I'm not writing about science I dabble in biblical archeology and religious history - the last refuges of the lapsed Catholic. So I've been really excited reading about the discovery and translation of the lost Gospel of Judas. This gnostic work (a 3rd century Coptic translation of a 1st or 2nd century Greek text) recasts the relationship between Jesus and his biblical betrayer, Judas, portraying Judas as Jesus's closest confidant and willing participant in the events leading up to the Crucifixion.

What I find ironic here is that Martin Scorcese's controversial The Last Temptation of Christ portrayed Judas in just this way.

While most biblical scholars are either a) excited to get another view on the earliest history of Christianity and the various forms it took, or b) don't think it will have any effect on current thinking in the Roman Catholic or Orthodox churches, I have to ask: What does are the implications for the Papacy and the leadership structure of the Catholic Church, which draw their authority from the leadership of the apostle Peter, if Judas was the real successor to Jesus's teachings?

And now back to the regular theme of our forum....

[If you get the National Geographic Channel, check out the documentary on this new text.]

Is it food or fuel?

2006-04-03T22:13:00.000-04:00

Bio-oil is one of many alternative fuels being developed to reduce our dependence on oil. But it didn't start out that way.

The stuff can be made from just about any organic material (also known as biomass) - wood chips, corn stalks, agricultural waste, etc. The US grows enough biomass to replace at least a third of its annual petroleum use. Starting with bio-oil instead of crude, fuel producers can make syngas (a synthetic alternative to crude oil) and, from there, further process it into automotive diesel.

Not bad when you consider that rapid thermal processing, the process used to convert biomass into bio-oil, was originally marketed as a way to make foods taste better. Reminds me of an old Saturday Night Live skit.

[For more, take a look at Wired.]

Copper never looked so good

2006-04-03T21:37:00.000-04:00

You know all those pennies gathering dusk on your bedside table? Well, you may have a new use for them. Researchers in the UK have found that they may have some value in preventing the spread of the flu. When placed on surfaces made of pure copper, samples of type A influenza viruses (the type that includes the much hyped H5N1 "bird flu") dramatically decline and are 99.99% eliminated within 6 hours. In contrast, virus populations on stainless steel surfaces decline by only 50% in the same amount of time.

The point? Surface contamination can be a significant factor in the spread of disease. The use of copper on communal surfaces (e.g., counters, tables, door frames) could help reduce disease transmission.

Metals have long been used for the treatment or prevention of infectious disease. For many decades, both before and after the rise of antibiotics, syphilis was treated primarily with mercury. Colloidal silver (silver dissolved in water) supposedly has some antimicrobial properties. However, as one former Senate candidate found, long term use can turn your skin blue.

[Many thanks to ScienceDaily]

Rejoice, Ye Beerlovers! The Wonders of Science Are With You!

2006-03-06T22:38:00.000-05:00

Step aside, red wine. Sit down, moderate exercise. And get behind me, low-cholesterol diet. I have a new weapon in my battle against heart disease. And no, it's not chocolate. It's beer.

According to a research team at Innsbruck Medical University in Austria, beer has an anti-inflammatory effect (think aspirin or Tylenol) that "may have a beneficial effect on coronary heart disease." Don't worry, teetotalers...this effect seems to be independent of alcohol content, which means nonalcoholic beers have these benefits, too.

And the joy doesn't stop there! Apparently beer also has anticancer properties and, in contradiction to the conventional wisdom, is not fattening. Researchers at Okayama University in Japan believe that an as-yet-unidentified compound(s) in beer (specifically lager and stout) may prevent cancer-causing DNA damage. (Keep in mind, though, that high alcohol consumption may be responsible for as much as 6 percent of cancers in the West.) AND, according to the ever unbiased British Beer and Pub Association (BBPA), beer has fewer calories than wine, milk, or orange juice. Why the beer belly, then? The BBPA says: Don't blame your hoppy friend, blame the pizza you're washing down with beer.

How do I know all this to be true? Because it just so happens that beer makes me more clever, too.

[Links lead to associated stories at The Register. And while you're at it, learn a little bit about the adventure of homebrewing at Homebrew Odyssey.]

Update 3/27/06: An anonymous commenter has suggested that I should "report (for sake of intellectual honesty and for completeness) that the anti-inflammatory effects of beer (particularly the interferon inhibition) has not been verified via a randomized control trial and does not necessarily improve healthcare outcomes (with regard to anti-inflammatory effect)."

For the record, I don't think any of these beer stories are worth their weight in hops. But it does go to show that if you want to believe something, the "facts" are only a Google search away.

Chocolate - the Elixir of Youth?

2006-03-02T20:31:00.000-05:00

It's been a good week for chocolate...well, for chocolate eaters, really. First came the news from a Dutch study that regularly consuming cocoa can halve the risk of dying (from a heart attack, I think; we all know what the real risk of dying is!). Then a group of New Zelanders announced that a glass of chocolate milk after taking a stroll may help one live a longer, healthier life.

But don't go knocking the corner store over for their stock of Hershey's just yet. Both studies were focused on the health of seniors and on ways to help reduce the impact of aging. Plus, both were advocating the use of chocolate in moderation (a word unfamiliar to many of us in the West). Keep in mind that turning to a diet of Mars bars can help boost the risks of type 2 diabetes and obesity. And at least from what I read, neither research group accounted for lifestyle factors outside the scope of the study. If it turns out that they happened to recruit a pack of retired marathon runners, then the results may not really apply to the rest of us.

But all that being said, I'm going to have some chocolate milk.

[Read more at New Scientist and ScienceDaily.]

Update 3/7/06: Apparently chocolate - or fudge, anyway - also has educational value, as a tool for teaching geology students about the properties of lava. (Seems scotch and rum are geologically educational, too.) Had I known that, I would have paid more attention in Geology 101!

Blog News: I've been a bad blogger....

2006-02-28T09:43:00.000-05:00

Gentle Readers:

You may have noticed that the rate of postings has declined precipitously of late. Believe me, it's not for lack of love, but for lack of time. I've recently taken on a substantial freelance project, which is cutting into my valuable blogging time.

But fear not! Once I discover the secret to omnipotence (which, according to my calculations, seems to have something to do with this odd concept called "work-life balance"...sounds French to me), I'll be back on the blogwagon with a vengeance. Until then, though, you'll have to make due with only the occasional post.

For the moment, I leave you with some words of wisdom from Dilbert.

TiVo in the brain?

2006-02-13T22:30:00.000-05:00

It's a whole new way of looking at the "rat race." Rats, while resting after performing a task like running a maze, run the entire experience backwards in their brains in a kind of instant replay. The process, researchers at MIT hypothesize, may help solidify memory and promote learning.

Does the same happen in humans? Likely. (Anyone want to volunteer to run back and forth in a maze with food at either end after having their brains wired up?) The findings may relate to the association of action and reward, and even add weight to the idea that rest after performing a task can facilitate the process of learning from experience.

In an interesting side note, they study may also help explain why hyperactive children can sometimes have learning problems - they don't get enough down time to process what they've learned.

[Read more at New Scientist]

Happy Birthday, Charlie!

2006-02-13T20:32:00.000-05:00

Sunday marked the 197th birthday of Charles Darwin, author of On the Origin of Species by Means of Natural Selection, or The Preservation of Favoured Races in the Struggle for Life (aka The Origin of Species) and (along with Alfred Wallace) one of the founding fathers of the theory of evolution. A day of celebration for scientists, yes, but for churches?

According to the New York Times, ministers around the country held services yesterday commemorating Darwin's birthday. Their respective churches were participating in Evolution Sunday, a nationwide event aimed at making the point that science does not undermine faith. That the fundamentalist voices supporting creationism and its kissing cousin, intelligent design, and who proclaim that Christians and others must choose between religion and science are misleading.

Good on 'em. I have long held that one can foster both spiritual faith and scientific understanding simultaneously, that each should hold sway in their own realm. A favorite example of mine in support of this idea comes from - of all places - the Bible. "Give unto Caesar what is Caesar's, and give unto God what is God's." (Mark 12:17) Can we replace "Caesar" with "Darwin?"

I see no reason why not. While some scientists find no room in their worldview for religion, others find their belief strengthened by their scientific inquiries, that what they see and learn enhances the world's mystery. In a remarkable irony, as his thoughts on natural selection crystallized, Darwin was drawn away from religious faith, while Wallace became ever more convinced in the existence of a higher intelligence. Maybe this, at some level, is where intelligent design comes from, an extreme extension of science informing faith. In my mind, the crucial question is whether one can find the balance between both types of knowledge, the secular and the spiritual.

[Learn more about Evolution Sunday on the website of the Clergy Letter Project, an academic and clerical response to efforts to discredit the teaching of evolution in public schools.]

Update 2/28/06: And good on William Broad at the New York Times for pointing out that those on both sides - secular and religious - who claim that their's is the "true faith" may be guilty of the highest forms of arrogance and hubris. [Note - let me know if the link doesn't work and I will reprint the article in a separate post.]

From Jaws to jaw lines: when evolution diverges

2006-02-09T21:14:00.000-05:00

The shark - a favorite scourge of the beach and the movie theater - has a "sixth sense," an ability to detect weak electrical fields in its environment. This sense evolved to navigate (potentially be detecting slight variations in the earth's magnetic field) and to help track prey, allowing the shark to seek out the weak electrical signals produced by the nerves of fish. Researchers at the University of Florida believe that the cells that make up the electricity sensing organs - electroreceptors - in a shark's head develop using the same genes that oversee the development of facial features in humans.

Interesting, because developmental biologists believe that all primitive vertebrates had the ability to sense electricity. But while marine mammals and fish retained the ability, terrestrial animals have lost it over time.

Which makes sense - given that air is not a great conductor of electricity . As one of the researchers said, "When it happens, it's called a lightening bolt, and you don't need special receptors to sense it."

[More on Yahoo!]

The Biology of Partisanship

2006-02-01T09:53:00.000-05:00

What with the Alito confirmation and the State of the Union Address, I thought it timely to point out a report released last week showing that both Democrats and Republicans are remarkably adept at ignoring facts that contradict their philosophies. The researchers, based at Emory University, monitored brain activity in members of both political parties while asking them to ponder information from the 2004 Presidential election that threatened their preferred candidate.

In short, brain circuits that control reasoning shut down, and circuits involved in emotional control and reward lit up. The pattern was consistent and, ironically, bipartisan - both Republicans and Democrats "consistently denied obvious contradictions for their own candidate but detected contradictions in the opposing candidate."

So what in the brain, biologically speaking, drives partisan preference? How do we choose one side and stick to it? And I'm not just talking about politics - Red Sox vs. Yankees, Mac vs. Windows, Coke vs. Pepsi, anything that involves a strong, unshakeable preference I imagine would fall under the same category. What has more influence, nature or nurture (yes, I have to open that can of worms)? Are Democrats more left brain, Republicans more right brain? (And are anarchists schizophrenic?)

[See Slashdot and LiveScience for more.]

Blog news: Tweaking the name

2006-02-01T09:11:00.000-05:00

A loyal reader (if I can actually have one at this point) has brought it to my attention that my Latin is a little off. The name of the blog, Scriptorum Scientifica, was meant to roughly translate to "Room of Writings Regarding Science" or, even more roughly, "Scientific Writing Room." As it stands, it translates to "Scientific [things] by Writers." Therefore, to remain honest and to keep from offending any classical scholars reading this, I've changed the name of the blog to Scriptorium Scientifica. To prevent a logistical nightmare, though, the Web and news feed addresses will remain the same.

My apologies.

Climbing the Cat's Tree

2006-01-25T21:29:00.000-05:00

The "kitty kat" is, by far, one of my son's favorite animals. But whence come our fluffy, fickle friends (evolutionarily, that is)? And their larger, less cuddly cousins like the puma or lion, for that matter?

A team of researchers at the National Cancer Institute may have put the question to rest (or at least given it a cat nap). After analyzing DNA from all 37 living cat species, the team has constructed a family tree for the family Felidae, rooted in a single species living in Asia 11 million years ago. From there, the cats spread across the world in at least 10 intercontinental migrations, with changes in sea level giving evolution a nudge. (See the original abstract in the journal Science.)

Building the cat family tree has been a perplexing problem, as dated cat fossils are few and far between and many of the modern cat species diverged very recently. The research team got around these issues by using information from the sex (X and Y) chromosomes and mitochondrial DNA (often used for calibrating evolutionary clocks) to measure how related different species of cat are and when the different branches on the evolutionary tree split off from each other.

So where does this put the "kitty kat?" The household cat is the youngest member of the family, emerging 6.2 to 6.7 million years ago, with domestication probably occurring within the last several thousand years (the oldest known pet cat was found two years ago in a 9,500 year-old burial site in Cyprus). The team plans to next investigate the time and location of the cat's domestication.

Additional links:
New Scientist
Nat'l Geographic

Would you like some cheese with that w(h)ine?

2006-01-22T14:10:00.000-05:00

Perhaps cheese and wine don't go so well together. New Scientist recently reported on a study suggesting that cheese suppresses the flavors and aromas in wine...all of them, in fact, except for buttery aroma, which itself is a component of cheese. The study authors, who recruited trained wine tasters as test subjects (and presumably threw a big ol' wine and cheese party; I wonder where they get their funding?), hypothesize that cheese proteins may bind the flavor molecules in the wine, or that the fat in the cheese may coat the mouth. Whatever the answer, my wife has her own opinon on the matter: "Science be damned, I'll trust my tastebuds."

An interesting factoid

2006-01-21T01:00:00.000-05:00

Carolus Linnaeus, the 18th century Swede who - building on the work of John Ray and his concept of the "species" - gave us the beginnings of our modern system of biological classificaion, got his start studying the sexual organs of plants. His classification scheme was founded in comparative studies of the size, shape, and numbers of pistils and stamens in flowering plants. According to Daniel Boorstein's The Discoverers, Linnaeus was one of the more controversial researchers in the modest times of the mid-1700s, something of a Freud for the botanical world. (I think of him as more of a Kinsey.)

We don't need another hero...do we?

2006-01-20T22:16:00.000-05:00

In a recent New York Times article (1/1/06) , John Horgan opened up the middle-aged (if not old) question, "Will there be another Einstein?" The question itself was natural, given that previous day had marked the end of the 100th anniversary of Einstein's miracle year and the World Year of Physics 2005. Horgan points to one answer put forth by author and biographer James Glieck - "there are so many brilliant physicists alive today that it has become harder for any individual to stand apart...our perception of Einstein as a towering figure is, well, relative." But overall, Horgan believes, Einstein was a product of "time and temperament," the like of which won't be seen again.

This is not to say that science has, of late, lacked its towering figures. Horgan limited his musings to the world of physics - one which, his own sources admit, is becoming ever more esoteric. (I like to think of myself as being mildly intelligent, but when I try to read the physics articles in Scientific American, I get lost after the 2nd or 3rd paragraph.) James Watson and Francis Crick, Stephan Jay Gould, Richard Dawkins, Stephen Hawking, and Richard Feynmann are the names that immediately come by mind as some of the towers of late 20th/early 21st century science. We recently have seen the downfall of another such figure: Hwang Woo-suk, who, while not idolized in the West, had achieved almost rock-star status in the Far East.

I think Horgan asked the wrong question. I would ask, Do we need another Einstein, another scientist of such fame and moral regard? Given the struggles of American scientific education, a role model for budding young scientists, one who can get them jazzed up about science is certainly needed. Horgan, I think, points out one of the main problems: "[It] may be that science as a whole has lost its moral sheen. We are more aware than ever of the downside of scientific advances...." But not only this, we are more apt to point out the downsides before the good sides. We lost trust in our politicians and governmental institutions following the Vietnam War; that mistrust has bled over to many aspects of our culture, including our perceptions of science (particularly federally funded science). Thus the proponents of creationism and intelligent design are given greater voice.

I would like to raise another point...that scientists have forgotten how to talk to people. Einstein, Dawkins, Gould - each of them has/had a gift for communicating what they do so that the educated layperson could get it. Perhaps this was always a rare gift, but it seems be ever rarer, particularly as science has become ever more specialized and subspecialized. I had a professor in public health school, Dr. Schiff, whose understood this problem keenly, though he expressed it in a limited way. During graduate student seminars, he would occasionally ask what I called the Schiff Question: "You are at a school of public health. What does your research have to do with public health?" Nine times out of 10, the student would look up from their presentation on malaria genetics or viral replication, dumbfounded. They couldn't answer because they couldn't see or express the larger context of what they were doing. I find this to be disturbingly common in the biomedical world; I can only imagine what things are like in physics or chemistry!

But I digress. Do we need another Einstein? Perhaps. We need a figure (or figures) who can help bring trust back to the people who pay for the majority of experiments, who can speak with a moral voice on the good and bad of how scientific knowledge is applied. (And I remind you, scientific knowledge - data - in and of itself is amoral and agnostic...it's the means by which it is obtained, the spirit in which it is sought, and the manner in which it is applied that need to be examined.)

But we need more than that...we need an education system that prepares people to understand at least the basis of science, to understand how science integrates with their lives. The Register recently ran an item on a poll that asked what people think Jesus would have on his iPod. I tell you, if people could channel that energy into thinking about how the samples returned by the Stardust spacecraft are directly related to us (we are, after all, made from the same stuff as the rest of the solar system), we'd already have a much friendlier climate for science in this country.

And we need a training system that reminds scientists that they have to be able to tell people about what they do if they ever want to regain the trust they have lost.