Science on the Edge

I thought that this article that appeared on the news page of the journal Science was an appropriate follow-up to my previous post. Bradley Byrne, a candidate running for the position of Governor of the great state of Alabama, is vehemently denying that he believes in Evolution after being "smeared" in a political ad that's been running for a few days now. The nerve! he responded by saying the following (among much more):

"As a Christian and as a public servant, I have never wavered in my belief that this world and everything in it is a masterpiece created by the hands of God," Byrne wrote. "As a member of the Alabama Board of Education, the record clearly shows that I fought to ensure the teaching of creationism in our school text books. Those who attack me have distorted, twisted and misrepresented my comments and are spewing utter lies to the people of this state." 
 
First, people need to get beyond the idea that somehow believing or not believing in evolution somehow affects his capability of running the state. Second, get in the real world - evolution is a "debate" (it's not really, we just have this inherent need to show two sides to an argument) between SCIENTISTS and crazy people...and since this is a "debate" about SCIENCE, the scientists win!

There isn't really much else to say...sometimes there is only the controversy we've created to seem fair and balanced. The evidence stands for itself...take away all the fossils, take away all the molecular genetic techniques, take away dating techniques, and there's still enough evidence to convince any rational person.

So, again, why should this even figure into a political campaign. The only way it should come in is to point out to the people that you are going to vote for someone who doesn't believe what is right in front of their face.

Just my opinion!

The brilliant man-genius behind xkcd brightened my day this morning with this lovely "comic", so I thought it would be only right to pass it on as it is relevant to the way we(well, not we as in Canadians, but oh well) think about science. Enjoy!

Anyone who has ever had to pick up pinecones and was violently poked in the process knows what a painful experience it can be. Instead of cursing to the heavens, you should blame dinosaurs for the pulsing pain in your hands or feet (I honestly don't even want to think about the excruciating experience of running barefoot and unwittingly stepping on a rogue pinecone).

While most modern conifers produce two distinct types of cones - slender male cones that house pollen, and bulky female cones which house seeds - most ancient cones were about the same size and shape. To answer why this situation might have arisen, Dr. Andrew Leslie of Yale University scoured the world's herbariums (like any good paleobotanist would) in search of fossilized cones. He measured the widths of 70 well-preserved specimens and compared them with the 200 or so living species of conifer. Unsurprisingly, his original observation stood up - female cones have indeed increased in size. But why?



To figure this out a number of factors had to be considered. First was what actually increased in size. Leslie found that it was actually the scales, which are used primarily for protective purposes, that increased dramatically in size. Second was when the shift in size happened. Interestingly, the shift seemed to begin right around the Jurassic period (199-145mya) when many of the largest herbivores (Diplodocus and Barapasaurus) walked the Earth. The long necks of these dinosaur species would have allowed them to graze much higher up on trees than an others before them, in turn putting female cones at risk.



While the pattern of the timing and physiologies of the cones are very striking, Leslie feels as though we shouldn't be so quick to discount small mammal and bird species that may have been inhabiting the upper canopies of these trees. The relatively poor recording of these species in the fossil record makes it a bit more difficult to figure out exactly what was going on in the trees themselves, but hopefully one day we will be able to figure this out!

A new study published in the Proceeding of the National Academy of Sciences seems to have made breakthroughs in the field of alcoholism and addiction research. A group from the Scripps Research Institute led by Dr. Juan Liu injected an RNA molecule into the amygdalas of a group of "alcoholic rats". These rats had been provided with all the free booze that any college attendee would be jealous of for a period of 3 weeks. After the amygdala injection treatment, the researchers found that the rats stopped drinking almost immediately and continued neglecting the alcohol for approximately one week.

The RNA molecule they injected blocks a gene that codes for the production of GABA receptors in the brain. These receptors normally signal emotional responses to certain stimuli. When the authors examined the brains of the rats the found a significant decrease in the presence of genes previously known to be linked with alcoholism in humans. The authors hope that this new RNA injection treatment which they are calling RNA interference may become a viable treatment for alcoholism in humans.

We used to think that "handedness" was a characteristic unique only to humans, but recent research is suggesting that it is present, and possibly even common, in other vertebrate groups. A recent publication in Biology Letters by a group of researchers from Macquarie University in Australia tested for the presence of handedness in 322 birds from 16 parrot species found in Australia. They found that in all but one species (the cockatiel) the eye the birds used to look at their food corresponded to the foot they used to pick it up, and that this relationship was carried on through their lives. In four of the species tested, near exclusivity in handedness (or footedness, I guess) was found, with the Sulfur-crested cockatoo still having no right-handed individuals to speak of. This suggests that the handedness characteristic has become fixed in these populations.

Extreme handedness situations like those found in these parrot populations are some of the only known cases outside of humans (we have about a 90:10 ratio). Some of the previous research done in this research area has shown that handedness in humans reflects the use of one brain hemisphere over the other, a behaviour that scientists call "laterality". The presence in animal species for one limb over the other suggests that an animal's brain function may also be lateralised, with one side of the brain dominating control of certain functional tasks (like picking up food). The researchers believe that the hemisphere of the brain associated with food selection may also be the hemisphere associated with the determination of handedness. It is interesting to note that juvenile parrots will experiment with each foot before settling on one, much like what human children do.

A recent report in the Proceedings of the Royal Society is attempting to explain how 50 million or so birds take to the skies for their annual migrations. Dr. Jakob Mueller and his colleagues trapped individuals from 14 separate European blackcap (Sylvia atricapilla) populations. These small warblers spend their summers in northern Europe and migrate during the winter to southern Europe and northern Africa. When they migrate, the typically diurnal species has no problem flying through the night to get to their destination quickly. This type of "non-typical" behaviour is very common with migrating bird species, with many species changing their activity patterns, social behaviour, diets, and even their physiology.

What the authors did next was search for the gene which was controlling this restless nocturnal behaviour. They targeted four genes and found that one, ADCYAP1, seemed to be responsible for this change in behaviour with a longer form of the gene coding for increased restlessness. They found that the gene codes for a protein, PACAP, which plays a major role in melatonin secretion, metabolism, and feeding patterns. The modification of levels of this protein could be serving as a preparatory mechanism for the long flights that the birds take on during migration.

A number of ornithologists are hailing this paper as a landmark discovery in the field and feel that its implications will be far-reaching. In addition, because DNA sequences that are conserved across species were analyzed, the implications could be stretched to other migratory species. 

What is a food bubble and why should we care? That is the question posed in an article by Alison George on the New Scientist website a couple of days ago. A food bubble is created when populations inflate food production through the unsustainable use of land and/or water resources. And the bursting of food bubbles is something that should concern us all, according to the founder and president of the Earthwatch Institute and the Earth Policy Institute, Lester Brown.

This, in theory, is something that everyone should be familiar with, but unfortunately many of us are not. It's hard enough for us to picture the amount of water we are removing from a visible source, like a lake or river, let alone an underground aquifer. In many regions around the world, food bubbles are getting precariously close to bursting. I won't get into the details here as I think the article puts it perfectly, however, I will echo the final section...what can I/we do about it?

While recycling, being energy conscious, and buying your food locally and organically can all make a difference if we band together, the solution recommended by the authors, and one that is becoming more and more prominent, is to get politically active (and I would add socially active as well). One of the benefits (in theory) of living in a democratic society is that you get a say. I know that my "activity" has diminished over the past few months for various reasons, but this article is just the kick in the pants I needed. I will be back to posting on websites and blogs that I like, sending letters and emails to people in positions of power, and spreading the knowledge to my friends and family.

The last few days have been full of famous birthdays (as Google so conveniently alerts me with their fancy search doodles) - Jules Verne, Thomas Edison, and now Charles Darwin have all celebrated their birthdays (born in 1828, 1847, and 1809 respectively).



“Ignorance more frequently begets confidence than does knowledge: it is those who know little, not those who know much, who so positively assert that this or that problem will never be solved by science.”

-Charles Darwin

I think that happy moments like this always deserve a mention. A new addition to the slowly recovering mountain gorilla (Gorilla beringei beringei) came in the rare form of twins (reported by The Gorilla Organization). The pair, only the fifth known occurrence in the Rwandan population, were born on February 3rd to a gorilla fondly known as Kabatwa (check out the picture below). This population, the Virunga population, continues to slowly rise in numbers and is currently thought to be approximately 480 (with the other group, the Bwindi population, is estimated to be 302, bringing the total to around 780). No word as of yet as to the names of the new twins.

Stories like this really piss me off! On February 3rd the Indian High Court threw out a case filed by PIL (Public Interest Litigation) seeking action against bogus astrologers, tantriks, vaastu shastra practitioners, tarot card readers, reiki practitioners, and similar occupations. In a land rich with mysticism where millions of people make important life decisions based on the alignment of the stars, it would not be too surprising to find out that many people consider astrology a science. No, the surprising part is that the courts do too! Precedent was set in 2004, when the High Court concluded that astrology was to be considered a "Science" like biology, physics, or chemistry. In fact, they had the balls to suggest that universities should consider introducing the subject into their curriculum (we know that class wouldn't have a laboratory component!). But in all seriousness, if India wants to be considered a superpower in the scientific community stuff like this cannot be happening, or they are bound to end up like the U.S. with its Creationism-Intelligent Design-Evolution "debates". Save yourself some money and a trip to your friendly neighbourhood astrologer's office and just buy a $1 mad lib book and fill in some words about your future...it would be just as accurate!

With (planet or other heavenly body) in its (number) house this month, this would be the (adjective) time for (activity). If you had been hoping to (vague activity that someone is always thinking of doing) this month, as (planet or other heavenly body) approaches (another planet or heavenly body). This will also bring about feelings of (some nice descriptive, bubbly word), but also (kind of the opposite word, but not enough to make you not feel awesome), providing you with the perfect opportunity for (love/romance/advancement at work/taking a trip you always wanted/etc...). You may also find that (insert vague reference that points to you maybe finding love or winning the lottery or getting a raise).

Continue ad nauseum...literally.

Niko Tinbergen was a famed ethologist, ornithologist, Nazi prisoner-of-war, Nobel Prize Winner (with Konrad Lorenz and Karl von Frisch), professor, wildlife filmmaker, and one of the greatest naturalists to have ever walked the Earth (well he probably would have done less walking and more observing). His main focus was concentrated on the individual and social behaviour patterns observed in nature, something which he studied in a variety of animals ranging from wasps to birds to fish.



A photo of Niko Tinbergen (left) and his colleague and nobel prize co-winner Konrad Lorenz (right)

"The test I did next was again quite simple. If a wasp used landmarks it should be possible to do more than merely disturb her by throwing her beacons all over the place; I ought to be able to mislead her, to make her go to the wrong place, by moving the whole constellation of her landmarks over a certain distance. I did this at a few nests that were situated on bare sandy soil and that had only a few, but conspicuous, objects nearby, such as twigs, or tufts of grass. After the owner of such a nest was gone, I moved these two or three objects a foot to the south-west, roughly at right angles to the expected line of approach. The result was as I had hoped for and expected, and yet I could not help being surprised as well as delighted: each wasp missed her own nest, and alighted at exactly the spot where the nest ‘ought’ to be according to the landmarks’ new positions! I could vary my tests by very cautiously shooing the wasp away, then moving the beacons a foot in another direction, and allowing the wasp to alight again. In whatever position I put the beacons, the wasp would follow them. At the end of such a series of tests I replaced the landmarks in their original position, and this finally enabled the wasp to return to her home. Thus the tests always had a happy ending—for both of us. This was no pure altruism on my part—I could now use the wasp for another test if I wished.
 
When engaged in such work, it is always worth observing oneself as well as the animals, and to do it as critically and as detachedly as possible—which, of course, is a tall order. I have often wondered why the outcome of such a test delighted me so much. A rationalist would probably like to assume that it was the increased predictability resulting from the test. This was a factor of considerable importance, I am sure. But a more important factor still (not only to me, but to many other people I have watched in this situation) is of a less dignified type: people enjoy, they relish the satisfaction of their desire for power. The truth of this was obvious, for instance, in people who enjoyed seeing the wasps being misled without caring much for the intellectual question whether they used landmarks or not. I am further convinced that even the joy of gaining insight was not often very pure either; it was mixed with pride at having had success with the tests."

As I mentioned in an earlier post, Michael Pollan is one of my favorite writers. His books (The Botany of Desire: A Plant's-Eye View of the World, The Omnivore's Dilemma: A History of Four Foods, and In Defense of Food: An Eater's Manifesto) are some of the most accessible and interesting books out there on the topics of food and agriculture. In addition he recently consulted and co-starred in Food, Inc., writes for the New York Times, and has given talks for TED talks, the Long Now Foundation, and FORAtv (some links are at the bottom of the page). The following is an excerpt from The Omnivore's Dilemma...

"When you think about it, it is odd that something as important to our health and general well-being as food is so often sold strictly on the basis of price. Look at any supermarket ad in the newspaper and all you will find in it are quantities–pounds and dollars; qualities of any kind are nowhere to be found. The value of relationship marketing is that it allows many kinds of information besides price to travel up and down the food chain: stories as well as numbers, qualities as well as quantities, values rather than “value.” And as soon as that happens, people begin to make different kinds of buying decisions, motivated by criteria other than price. But instead of stories about how it was produced accompanying our food, we get bar codes–as illegible as the industrial food chain itself, and a fair symbol of its almost total opacity.

Much of our food system depends on our not knowing much about it, beyond the price disclosed by the checkout scanner; cheapness and ignorance are mutually reinforcing. And it’s a short way from not knowing who’s at the other end of your food chain to not caring–to the carelessness of both producers and consumers that characterizes our economy today. Of course, the global economy couldn’t very well function without this wall of ignorance and the indifference it breeds. This is why the American food industry and its international counterparts fight to keep their products from telling even the simplest stories–”dolphin safe,” “humanely slaughtered,” etc.–about how they were produced. The more knowledge people have about the way their food is produced, the more likely it is that their values–and not just “value”–will inform their purchasing decisions."



As promised...links!

FORAtv Slow Food Nation (some amazing people in this one -Wendell Berry, Carlo Petrini, Vandana Shiva, Eric Schlosser, Alice Waters, and Michael Pollan) Part 1 and Part 2.

Michael Pollan's Website


A talk at Google

...insert obligatory "my English prof is making me do this paraphrase assignment" here...

Anyone that knows me could tell you that I have a great interest in food crop production. I have worked doing research on fruit crops in the Okanagan Valley for Agriculture and Agri-Food Canada and am planning on going back to do more research this summer, and I love the books of Michael Pollan, Jared Diamond, and Wendell Barry. Of particular interest to me is how we are going to deal with the ever-rising world population. The obvious answer is "just move the food around....we are already making enough!" But we couldn't possibly do that could we? So instead, science and brilliant scientists are attempting to answer the foreboding Malthusian wave. I have written papers for classes before on GM crops looking at their benefits and disadvantages, but I decided for this class paper to look at the development of transgenic C4 rice. While the advancements that were so promising early on seemed to have cooled off, a recent influx of papers synthesizing a lot of the information that we had with some of the new molecular and genetic research over the past few years seems to be occurring. The paragraph I am attempting comes from a review paper published in Plant Physiology online in October 2010 and in print in January 2011. Here is a link to the paper (as it is open access!)

The ultimate goal of photosynthesis is the fixation of carbon dioxide through the utilization of the enzyme RuBisCO (Ribulose-1,5-bisphosphate carboxylase oxygenase). However, RuBisCO is extremely inefficient in carrying out this process under normal atmospheric conditions. Under optimal conditions, RuBisCO catalyzes the carboxylation reaction of one molecule of ribulose-1,5-bisphosphate (RuBP) into two molecules of 3-phosphoglycerate; however, as the Earth's atmosphere has an approximate O2:CO2 ratio of 20:1, the oxygenation reaction in which one molecule of RuBP is converted into one molecule of 3-phosphoglycerate and one molecule of 2-phosphoglycolate is predominant. In order to recover the carbon atoms tied up in the 2-phosphoglycolate molecule, a relatively useless and somewhat toxic (in high enough concentrations) compound, a salvage pathway called photorespiration needs to be employed which consequently wastes valuable ATP  (Anderson, 1971). The ultimate result of this process when coupled with other environmental factors like drought and raised temperatures is a decreased photosynthetic efficiency (Ehleringer et al., 1991). In looking at the specific evolutionary history of RuBisCO, it is easy to see how this situation may have evolved as three billion years ago, when this enzyme was first thought to have evolved, the atmospheric concentration of CO2 was high and O2 was low. Over time, it seems as though this original arrangement was unable to be changed nor was another carboxylase able to be substituted. Despite this, some plants have evolved various coping mechanisms including the C4 and CAM photosynthetic pathways.

More on this topic to come as I write my paper...

The Raffles' pitcher plant (Nepenthes rafflesiana) is a strange plant. For years it baffled scientists by its apparent incompetence at catching insects, the primary activity by which the carnivorous pitcher plants obtain their food. Recent research however is pointing to a different source of sustenance...bat guano! This particular species differs from its relatives in that it possesses a long and narrow pitcher, with no apparent scent or pattern for attracting insects. Normally, pitcher plants employ enticing aromas, ultraviolet decorations, and delicious nectar to attract insects which promptly slip into the small leaflike cups (the pitchers) and drown in a pool of digestive fluids allowing the plant to obtain otherwise absent nutrients.

On a research expedition in the jungles of Borneo, lead scientist Ulmar Grafe and some students came across a bat roosting in the pitcher of one of these plants. The dismissed it as happenstance until Grafe read a paper describing the apparent lack of insect-killing ability of this particular plant. Over a period of 7 weeks, Grafe and his team made countless pitcher plant patrols and discovered that nearly 25% of the plants they found had bats roosting in them, more specifically Hardwicke's wooly bats (Kerivoula hardwickii). These bats are usually less than 4 cm long, making them the perfect size for the pitchers of these plants.




To investigate further, the team glued tiny transmitters to the backs of 17 bats and tracked where they slept each night. They found that the bats all slept in Raffles' pitcher plant cups, often times with mother and either a son or daughter, if present. Looking at the size and shape of the pitcher, one or two bats are capable of fitting perfectly, just above the digestive fluid. Interestingly, the bats wedge themselves in head-first, although they undoubtedly make the obligatory flip to the right-way-up before going to the bathroom.

Analysis of the plants showed that leaves adjacent to the pitchers in which bats were known to have slept had 13% greater nitrogen content than those adjacent to pitchers without bat occupancy. The researchers tested leaf blades for a nitrogen isotope found in the carnivorous bats, and therefore their poop, and discovered that nearly 1/3 of the nitrogen in those leaves came from the bat guano. Researchers in the field seem excited about the findings and are extremely interested in finding out if this is a case of coevolution or if more pairings occur.

I know that I will be sure to keep my eye out for these awesome plants when I am trekking through the jungles of Borneo next spring!

If the name Peter Atkins doesn't sound familiar, you should check your chemistry textbooks because there is a good chance he had a hand in writing them.  He is a world-renowned chemist, a well-known atheist, and a member of both the Oxford University Scientific Society and the The Reason Project. Putting aside his countless textbook contributions, his best work probably comes in his books directed to the public including The Creation, Creation Revisited, Galileo's Finger: The Ten Great Ideas of Science, and The Four Laws That Drive The Universe. The majority of his works deal with creation, thermodynamics, energy, and change, all displaying his wit and superb penchant for writing. The following are two excerpts from his wonderful book Creation Revisited.

"When we have dealt with the values of the fundamental constants by seeing that they are unavoidably so, and have dismissed them as irrelevant, we shall have arrived at complete understanding. Fundamental science then can rest. We are almost there. Complete knowledge is just within our grasp. Comprehension is moving across the face of the Earth, like the sunrise."

I though it would be fitting to have my first quote from one of my favorite Science writers of all time, Richard Dawkins. His elegance and intellect is always immediately apparent when you open one of his books, and his contributions to Science, and especially the field of Evolutionary Biology, can be matched only by a select few. 

After sleeping through a hundred million centuries we have finally opened our eyes on a sumptuous planet, sparkling with color, bountiful with life. Within decades we must close our eyes again. Isn't it a noble, an enlightened way of spending our brief time in the sun, to work at understanding the universe and how we have come to wake up in it? This is how I answer when I am asked — as I am surprisingly often — why I bother to get up in the mornings.

These inspiring words are an excerpt from Chapter 1, "The Anaesthetic of Familiarity", of his excellent book Unweaving the Rainbow (1998). A longer excerpt from this chapter is available on the Richard Dawkins Foundation site linked here. If you haven't checked out his books, you really should...and you can expect that this post will not be the last time I will mention his works. 

Who would have thought you could learn so much from tree rings...well, dendrochronologists I suppose, but who else? A very cool new study just recently published in Science has linked changing climate to the fall of the Roman Empire and a number of other historical events. The group, led by paleoclimatologist Ulf Büntgen, used 7284 oak samples from France and Germany, and 1500 stone pine and larch samples from high altitude regions of Austria to generate two sets of climate data for comparison.

In order to do this, they compared climate and weather records from the past 200 years with living tree ring data. This allowed them to observe how various temperature and moisture regimes affected tree ring growth. They then compared this data with timbers from historical buildings, preserved pieces of wood from bogs and rivers, and wood from archaeological sites to push back their timeline even further. When all of this data was combined they had a continuous records of the weather in France and Germany spanning more than 2500 years.

What they found was very interesting. They saw patterns which related times of social stability prosperity, like the rise of the Roman Empire between 300 B.C.E. and 200 C.E., with warm and wet summers ideal for agriculture. Similarly, these same climate patterns seem to be present in tree ring data corresponding with the height of medieval success in the region. And it was not just times of prosperity and success that were related to significant tree ring patterning. Times of turmoil and catastrophe were also readily observable in the data sets. For example, the period of widespread famine and plague starting around 1300 C.E. that wiped out half of the people in Europe within half a century was correlated with an extremely cold winter followed by consecutive wet and warm summers. Similarly, the period right before the Barbarian invasions and the eventual fall of the Western Roman Empire was characterized by extensive drought and poor agricultural conditions.

In addition to their climatological findings, they also noted some significant social findings in which wood cutting could be related to swings in social and economic activity for the region.

**The image used is an illustration of the Black Death as depicted in the Toggenburg Bible (1441)**