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Say Cheeeeese!!! February 24, 2010

Posted by ecogeeko10 in Biology, Genetics.
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So I’ve been noticing a recent trend in the scientific world lately. Researchers are getting better and better at figuring out the fine details of organisms that occurred many years ago. Take dinosaurs for, for example. It was once thought that all of these “terrible lizards” were only covered with scales. However, it wasn’t too long ago when paleontologists first began finding evidence that some species of dinosaurs actually had feathers. Not many people believed that we would ever get to figure out the actual colors of these feathers, but it turns out that this is also possible.

Historic Portraits

Jakob Vinther, a graduate student at Yale University was studying the ink sac of an ancient squid, when he discovered microscopic melanosomes in the fossil. Melanosomes are cellular organelles that contain melanin, which is a light-absorbing pigment that is found in certain animals such as birds. Once researchers heard about this discovery, they quickly began examining the fossil remains of other organisms such as Anchiornis huxleyi. We can now conclude that many dinosaurs like A. huxleyi were not necessarily dull and gray, but rather, they were quite colorful (see figure 1). The fact that this species of dinosaurs was so colorful could prove that feathers may have had multiple adaptive uses at that time. Not only were they good for warmth and flight (eventually), but they were instrumental display features. What dinosaur wouldn’t want to mate with such a beautifully adorned creature?  This was a very important discovery because it gives evolutionary biologists much more insight into the evolution of birds. We now have more evidence that birds did indeed evolve from theropod dinosaurs.


But wait!!! I’m not done!!!

It also turns out that we are able to take “snap-shots” of people who lived thousands of years ago! Just recently researchers were able to analyze the complete genome of a 4,000 year old Greenland resident—a Saqqaq. Simply by analyzing the DNA in this old man’s hair, geneticists were able to conclude that this man had brown eyes, dry ear wax, was genetically prone to have thicker hair (thicker than most Europeans and Africans), and yet he was also at risk of growing bald (see figure 2 for “snap-shot”).

What’s most important about this discovery, though, is that these findings help to shed new light on the settlement of North America. Apparently, through analyzing this man’s genome, researchers were able to determine that his closest living relatives were the Chukchis—who lived on the easternmost tip of Siberia. What’s interesting is that the Saqqaq man’s ancestors diverged from the Chukchis around 5,500 years ago and that helps geneticists to believe that this man’s ancestors must have traveled across the northern edges of North America to Greenland.


Saqqaq Man

Maxwell on Molecules February 22, 2010

Posted by isotopeeffect in Chemistry, Physics.
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This post continues the art theme, at least momentarily.

While refreshing my memory about the works of the Pre-Raphaelite Brotherhood I stumbled upon the rather excellent Victorian Web, a web site gathering links on areas of interest from that era ranging from fine art through science, from religion through economics, a veritable liberal arts goldmine.

There is plenty of material on the site to recommend itself under the heading of science, but I was particularly struck by an essay by James Clerk Maxwell entitled “Molecules”, first published in Nature in 1873.

Maxwell opens with a reference to the ancient Greeks, by distinguishing the philosophy of the atomists, represented by Democritus, from that of Socrates’ teacher Anaxagoras (a somewhat less well-known – because “wrong” – philosophy called Homoiomereia). Neither philosophical stance counts as what we would now call science; both are essentially entirely speculative in nature. Anaxagoras’ perspective was that substances are homogeneous and thus can be subdivided indefinitely without losing their character, while that of the atomists was that a limit would be reached where matter can no longer be so subdivided, but has been reduced to its fundamental units, atoms, objects which (literally) cannot be cut.

Of course, for all the ingenuity of the ancient Greeks they had no concept of molecules (their idea of “elements” more closely resembling our modern idea of “states of matter”), so jumping to a more modern concept, Maxwell quickly defines the molecule as the simplest unit of a particular substance that retains the composition of the whole before moving on to his main arguments.

Maxwell’s overall goal in this essay is to introduce the public to recent research in the field of molecular science, areas of study that we would nowadays call statistical thermodynamics and the kinetic-molecular theory of gases.

The first part of Maxwell’s argument is the modern counterpart to the opinion of Lucretius that bodies are in ceaseless motion (on what we would now call the atomic scale), even when they appear to be at rest. Tracing a historical thread that runs through the “usual suspects” Boyle and Charles to Bernoulli, Clausius, Joule, and Boltzmann, not to mention Maxwell himself, Maxwell shows how once gas pressure is recognized as a product of atomic motion and collisions a theory can be built that allows us to calculate the speeds at which molecules move (“about seventeen miles per minute”), the average distance between molecules (“about the tenth part of the length of a wave of light”), and the number of collisions undergone per second (“hundreds of millions”).

The next section of the essay contrasts the “historical method”, in which the history of an individual is followed through time, with the “statistical method”, in which general results relating to groups or populations are obtained. This section is remarkable enough to quote at length:

“The equations of dynamics completely express the laws of the historical method as applied to matter, but the application of these equations implies a perfect knowledge of all the data. But the smallest portion of matter which we can subject to experiment consists of millions of molecules, not one of which ever becomes individually sensible to us. We cannot, therefore, ascertain the actual motion of any one of these molecules, so that we are obliged to abandon the strict historical method, and to adopt the statistical method of dealing with large groups of molecules.

“The data of the statistical method as applied to molecular science are the sums of large numbers of molecular quantities. In studying the relations between quantities of this kind, we meet with a new kind of regularity, the regularity of averages, which we can depend upon quite sufficiently for all practical purposes, but which can make no claim to that character of absolute precision which belongs to the laws of abstract dynamics.

“Thus molecular science teaches us that our experiments can never give us anything more than statistical information, and that no law deduced from them can pretend to absolute precision. But when we pass from the contemplation of our experiments to that of the molecules themselves, we leave the world of chance and change, and enter a region where everything is certain and immutable.

“The molecules are conformed to a constant type with a precision which is not to be found in the sensible properties of the bodies which they constitute. In the first place the mass of each individual molecule, and all its other properties, are absolutely unalterable. In the second place the properties of all molecules of the same kind are absolutely identical.”

Maxwell here points out the astonishing fact that molecules resemble one another in a manner very different from that in which, for example, apples or golf balls do; while the latter may be similar but for a nick or blemish, the former are (up to the point of being in different quantum states) completely identical in every respect.

The indistinguishability of atomic or molecular states has ramifications even Maxwell did not think of. In the world of quantum mechanics, the wavefunction of a system of particles must show a distinct symmetry with respect to the pairwise interchange of particle labels. For particles like electrons, for example, the requirement that the wavefunction be antisymmetric is known as the Pauli principle, which every chemistry student knows as the principle determining that an orbital can contain only two electrons. A slightly more elusive implication of the antisymmetry principle, however, is that if a helium atom is in the 1s2s state, we cannot say which of the two electrons is the 1s electron. In statistical thermodynamics, symmetry requirements impact which combinations of states can exist and lead to phenomena such as Bose-Einstein condensation (see here for NIST’s BEC site) and degeneracy pressure (the phenomenon that keeps white dwarf stars from collapsing).

Maxwell goes on to show that the identical nature of all molecules (or atoms) of a particular type is precisely that which allows us to use the methods of spectroscopy to make discoveries not only about samples in front of us in the laboratory but about any object in the universe from which light can be detected. Here’s Maxwell again:

“But in the heavens we discover by their light, and by their light alone, stars so distant from each other that no material thing can ever have passed from one to another, and yet this light, which is to us the sole evidence of the existence of these distant worlds, tells us also that each of them is built up of molecules of the same kinds as those which we find on earth. A molecule of hydrogen, for example, whether in Sirius or in Arcturus, executes its vibrations in precisely the same time.”

In this latter point, Maxwell is not quite right. Light from distant objects beyond our galaxy exhibits a redshift due to the velocity at which these objects are receding from us. (In their own reference frame, as Maxwell states, they emit radiation of the same frequency as molecules on Earth. ) There is an approximately linear correlation between recession velocity and distance which led Georges Lemaître to his theory that the universe that we now know evolved from a “primeval atom” (his term) in which all the mass-energy now present was compressed into a tiny volume, via a cosmic explosion now universally known as the Big Bang.

Quoting Maxwell again:

“Natural causes, as we know, are at work, which tend to modify, if they do not at length destroy, all the arrangements and dimensions of the earth and the whole solar system. But though in the course of ages catastrophes have occurred and may yet occur in the heavens, though ancient systems may be dissolved and new systems evolved out of their ruins, the molecules out of which these systems are built — the foundation stones of the material universe — remain unbroken and unworn.”

To revise Maxwell, our current understanding is that atoms (specifically, hydrogen atoms) did not exist until about 400,000 years after the Big Bang. Before that, there was too much energy present in the compact early universe for atoms to be stable, so any atoms formed would instantly ionize. Traveling further back in time, a few minutes after the Big Bang energy was so concentrated that protons and neutrons themselves could not exist; the tiny universe was an extremely hot “quark soup”. In the first microsecond after the Big Bang quarks themselves were not stable. An enhanced understanding of what happened in those first few instants after the Big Bang is a research goal of the Large Hadron Collider.

It is an interesting irony that in this essay Maxwell seems to so strongly espouse a “particulate” picture of the universe. Most physics students first meet Maxwell through his famous equations describing the behavior of electromagnetic fields. The modern descendents of Maxwell’s work are the various forms of quantum field theory that describe the universe in a manner in which “particles” are viewed as excited states of a quantum field, an entity that spreads throughout space. Perhaps the followers of Anaxagoras were not entirely wrong.

CLASH! When art & science meet… February 22, 2010

Posted by Dr. O in Biology, Environment/Conservation, Uncategorized.
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While this post is slightly off the beaten path of scientific findings…one of my other interests is to examine how science infiltrates and influences other walks of life.  One of my favorite things to witness is when art and culture run head on into science.

I figured I’d blog about this after reading a short news piece on the fashion designer, Vivienne Westwood.  She is known for her punky, off-the-wall fashion loved by millions, but recently she was stated as saying, “I hope people stop buying my clothes!” after a recent fashion show.  Why, you may ask?  Turns out Westwood is a huge fan of the environment and has somewhat recently become more and more impassioned about climate change.  She realizes the huge carbon footprint that comes at the expense of consumerism and has thus turned her catwalk into a crusade on eco-consciousness to educate people about current environmental policy.  She recently designed a t-shirt to bring attention to global warming and released the sale of it just before the climate talks in Copenhagen earlier this year. She remains a supporter of REDD+ (Reducing Emissions from Deforestation and Degradation).

Vivienne Westwood's REDD+ t-shirt

In the world of music, Sting (former front man of The Police) and his wife, Trudie Styler,  have been an ardent supporter of the Rainforest Action Network and is joined from the film world by Leonardo DiCaprio and his efforts to maintain biodiversity.  In the realm of literature, Michael Pollan, author of The Omnivore’s Dilemma (the current book choice for Marian University’s “senior seminar”), has brought attention to millions about the way we eat and the way the production of food influences our lives both in health and in environmental sustainability.

But how science has influenced art and culture can be witnessed throughout history.  Leonardo da Vinci was both brilliantly left- AND right-brained.  He was not only a magnificent painter ( he painted the most recognizable painting, the Mona Lisa,  as well as The Last Supper, and more science-y Vitruvian Man) but also a brilliant scientist and inventor.  He conceptualized the first helicopter, thought about early solar cells to capture solar energy, and mused about plate tectonics!  He often wrote  the details of his inventions backwards to prevent theft.  His ideas were only discernible by holding the blueprints up to a mirror.  His detailed and beautiful artwork was obviously improved by his attention to details of anatomy…of which he explored on real life cadavers with early medical doctors.

Vitruvian Man

da Vinci's helicopter

da Vinci's anatomical drawings

But other artists and designers have explored the clash of art and science over the years.  One of my favorite artists, Frida Kahlo, was almost killed in a bus accident as a young girl.  Her back was broken, pelvis and legs shattered, and she was left bed-ridden for years.  She never properly healed from her injuries and lived in constant pain.  This theme of pain and medical intervention wove itself into her works as well as her love for the natural beauty of her native land of Mexico.

Kahlo self-portrait depicting her braces and spinal rod insertions

Self-portrait depicting bed-ridden contemplation of death, nature, etc

double self-portrait depicting emotions from the "heart" concerning love, native culture, consciousness, etc

Kahlo's love of her natural surroundings is portrayed in her art

Kahlo felt a groundedness in the cycle of life & death in nature

I have also enjoyed more recent fashion work by the designer, Alexander McQueen.  From his human ribcage-inspired  (as well as faux alligator skin-inspired) Samsonite suitcase, to his beautiful nature-inspired clothing.  He seems to be inspired by pieces of nature from oysters to butterflies to birds and even diatoms! Check out the comparisons below:

Ribcage-inspired suitcase

Oyster-inspired dress

REAL oyster

Parrot-inspired dress

REAL parrot

More avian-inspired dresses

More avian-inspired dresses

Butterfly-inspired dress

REAL Monarch butterflies

Diatom-inspired dresses

Diatom-inspired dresses

REAL diatoms

Anyone else want to comment about neat clashes of science and art?

How old is old? February 17, 2010

Posted by Dr. O in Biology, Evolution, Genetics.
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A short pictorial of the age of the earth both geologically and biotic-ly!

Age of the Earth: 4.5-4.6 billion years old

More info on this here.

Geological time frames

Age of bacteria, protists, & plants

Visit and ancient plant garden here.

Age of animal life: Ancient to Modern

More about the Cambrian Explosion of animals.

Age of Animals

And have a look at your ancient cousins!  What traits do you share with them?

Here we show biochemical evidence of evolutionary ancestral traits shared in the amino acid sequence of hemoglobin.

Evolution of hemoglobin

Link to hemoglobin information.

Willpower and the Brain February 12, 2010

Posted by Colleen in Behavior, Biology, Evolution, Neuroscience.
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It feels like we’re rapidly passing through February, which means March, as well as my spring break Marine Biology trip to Pensacola is quickly approaching. I’m hoping that the weather will be warm because I’d really like to spend some time relaxing on the beach. Naturally, that means breaking out the swimsuits and trying to watch what I eat to be in top shape. Many of my friends are in the same situation and are on diets in order to lose that pesky 5 pounds. We all seem to struggle with making good choices though (why, oh why, can’t I say no to chocolate?). It all leaves me wondering where my willpower went.

The science of will power

The other day while doing some other homework, I came across a radio story on NPR called “Willpower and the ‘Slacker’ Brain”. I had learned in psychology that the brain can memorize about 7 numbers at a time, which is why we’re generally pretty good at remembering people’s phone numbers (most of the time). In this particular study, they had people memorize numbers; some had to memorize a small series of numbers, like two, and others had to memorize a larger series of  numbers, like 7. They were then sent to another room to recite their numbers, but along the way were interrupted and offered a snack: either chocolate  cake or fruit salad. Most people who memorized a large number would take the cake and those with a small number would take the fruit. Apparently, the more you have on your mind, the more likely you are to choose something that you want emotionally rather than what makes logical sense. (Listen to the story to hear the whole study.)

So maybe that’s why I don’t always make the best food choices… I’ve got too much on my mind to think logically.

The Full Story Behind Antioxidants February 12, 2010

Posted by zach in Biology, Chemistry, Exercise, Health, Nutrition, Physiology.
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A recent article out of Kansas State University by Steven Copp shows that antioxidants may not be everything the media has hyped them up to be in being able to increase muscle performance.  Their data shows that in certain cases when people supplement antioxidants they can actually impair muscle function. While antioxidants at certain dosages may be considered an ergogenic aid, there has been a large amount of media hype which has attributed to their recent growth.

Copp found that antioxidants can have an effect on the blood flow in the muscles.  This is possible by antioxidants decreasing the concentration of oxidants in our body.  This all sounds good, but hydrogen peroxide which is naturally occurring pro-oxidant in our body is a vasodilator. In short when you supplement large quantities of antioxidants you are drastically decreasing oxidant concentration in your body, this in turn can cause your veins to constrict from a lack of vasodilators, which limits the amount of oxygen to your muscles.  This effect can lead to changes in key signaling mechanisms that can also have adverse effects on functioning muscles.

With all this being said it’s not that you should stop eating antioxidant rich foods.   Researchers are still looking at the full physiological effect of antioxidants on exercise training.  What the researchers are saying is you have to consider your antioxidant pro-oxidant balance.  Next time you are at the store and see antioxidant supplements claiming to have extraordinary effects, you may want to look at the science behind what you are buying before you buy a supplement that has a null effect on your muscle performance.

Full article on Science Daily

Antioxidants at work

Photosynthesis and Quantum Coherence February 9, 2010

Posted by isotopeeffect in Biology, Chemistry, Physics.
Tags: ,

A recent paper in Nature by Gregory Engel and co-workers presents direct evidence from two-dimensional Fourier Transform electronic spectroscopy that quantum coherence plays a role in energy transport within the Fenna-Matthews-Olson bacteriochlorophyll complex. Popular accounts of the research appear in various venues such as Wired magazine and The Scientist.

So what does that mean?

Photosynthetic light-harvesting is an incredibly efficient process, which seems at odds with the great complexity of the chain of molecules involved. The “wire” along which the excitation energy signal travels is sensitive to the precise geometric relationship between orbitals on all the molecules in the chain between the light-harvesting antenna protein and the reaction center, which in turn is sensitive to thermal agitations at the operating temperature of the photosynthetic system.

Past work on attempting to understand these processes has focused on semiclassical models involving (classical) “hopping” of energy between individual excited (quantum) states. The new experiment is a laser “pump-probe” measurement using ultrafast (sub-picosecond) laser pulses to excite one part of the system and detect changes remote from the original excitation. The key finding is the existence of “quantum beats”, correlations in phase between the wavefunction on one part of the system and another separated from it by a distance of thousands of atoms. These are illustrated below.

So, what’s the significance of all this?

The “beats” imply that the energy transport is wavelike, in other words truly quantum-mechanical (or “coherent”). The quantum state enveloping the whole photosynthetic system allows energy transport to occur along a superposition of multiple pathways, ensuring that the energy reaches its destination efficiently, with some degree of protection from the randomizing effects of thermal jostling. The energy travels along all possible pathways, so whatever the circumstances it travels along the “best” pathway (as well as all the others).

This is a remarkable result given the large size of the photosynthetic system. Such quantum effects are not observed in the macroscopic world, where “decoherence” scrambles the phase of the wavefunction, considerably impairing our ability to be in two places at once.

Full disclosure: I was first alerted to this paper via the blog Cosmic Variance (direct link via image above), where you can also see video of Drew Brees throwing a football at an archery target with rather disturbing accuracy.

Building upon the earlier critical point of water post…sort of February 8, 2010

Posted by Dr. O in Uncategorized.

An interesting article regarding the phenomenon of ice nucleation recently published in Science.  Ice nucleation usually requires a “seed” of impurity around which to form, if there is no impurity, water can be supercooled and stay liquid far beyond normal freezing temperatures.  As most of us know, water molecules are polar, and thus, can be encouraged to “line up” according to charge and snap into rigid ice formation…and here’s where electric fields become important in influencing the behavior of water.

Excerpt: “A watched pot never boils, but an electrically charged pot sometimes freezes. A study in the Feb. 5 Science reports that water can freeze at different temperatures depending on whether the surface it rests on is positively or negatively charged. Under certain conditions, water can even freeze as it heats up.”

Definitely an article worth checking out!

Dolphins and Bats… are they really THAT different? February 8, 2010

Posted by ecogeeko10 in Behavior, Biology, Evolution, Genetics.
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Hey fellow molecular genetics/behavioral ecology students (i.e. Kyle)! Remember when we were discussing how bats and dolphins independently developed similar abilities to use echolocation after diverging from their last common ancestor (which was a looooong time ago)??? Well anyways… Recent (I mean REALLY recent) studies are showing that they might be sharing more than what was once thought!

The evolutionary genetics of hearing

It has been assumed that it was different mutations of different genes that resulted in the “coincidental convergence” of certain traits in different species (I can write sentences like these because this is a blog). However, two studies (here and here) that were published in the January 26th issues of Current Biology suggest that the evolution of echolocation in bats and dolphins were brought about by identical genetic changes.

According to Yang Liu et al, dolphins and bats developed the ability to echolocate because they both experienced similar mutations in their prestin genes. Prestin, which can be thought of as being amplifiers in the inner ear, were mutated in a way so that these species of animals could have a refined sensitivity and selectivity for certain “echolocate-able” frequencies. The evidence shows that these changes in prestin were selected for, so it is likely that they are critical for the evolution of echolocation in animals. The scientists are still working on why this may be.

The researchers were sure to point out, though, that there are still differences in how bats and dolphins echolocate. Dolphins can use echolocation at a range of >100 meters, while bats have a range of only ~3 meters. It is also worth noting that sound travels much faster in water. Therefore, bats and dolphins have had to adapt these differences in order to be successful in their unique environment.

A dolphin/bat superhero.....COOLAnd yes, that is an illustration of a bat/dolphin superhero…. it’s well known for its echolocation superpowers….

Early computers February 8, 2010

Posted by isotopeeffect in Math.
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What did early computers look like?

Well, they looked a bit like this.

From around the beginning of the eighteenth century, when laborious numerical calculations began to be a regular part of scientific activity particularly in fields such as navigation and astronomy, the need arose for a person or group of persons to carry out these calculations carefully and as far as possible without error. Over time, this became a respected and important job.

A recent book by David Alan Grier – whose grandmother was one of these “human computers” – documents this history.

Brute-force numerical solution of equations is required when an analytical solution is not possible. An example of such a case is the “three-body problem” in mechanics, in which the trajectories of a group of objects (such as planets interacting through gravitational forces) cannot be solved analytically if the number of objects is greater than two. Although Edmund Halley had already predicted (in 1705, using Newtonian calculus) the return of the comet named after him, a much more accurate calculation was carried out in 1757 by Clairaut, Lalande, and Lepaute, who broke the orbit down into a series of small steps and incorporated the comet’s gravitational interactions with the orbits of the then-known major planets Jupiter and Saturn. (The primary source of error in their calculations would have been the neglect of the gravitational effects of Uranus and Neptune, which were unknown at the time.) This is one of the earliest known examples of parallel computing, still used today to make large numerically complex problems tractable in a reasonable amount of time by distributing the effort over multiple “computational nodes”.

Initially the profession of “computer” was mainly the province of men, and largely closed to women (although Lepaute was female), but over time this situation gradually changed. The Harvard astronomer Edward Charles Pickering (known, for example, for the “Pickering series” due to ionized helium, first observed in the spectrum of the hot O-type star ζ Puppis) employed a group of computers known as “Pickering’s Harem”, one of whom, Henrietta Swan Leavitt, went on to discover the relationship between the period and luminosity of Cepheid variables, without which work Edwin Hubble would not have been able to find the linear relationship between galactic redshift and distance that led to the understanding that we live in an expanding universe.

The prevalence of women in Pickering’s group was most likely a consequence of Harvard’s pay scale at the time, in which women were remunerated at half the standard rate for men.

The last days of the human computer came at the time of the Manhattan Project, where the complex calculations involved in the design of the atomic bomb were mostly accomplished by hand (carried out by the scientists’ wives, an interesting window into the gender hierarchy of intellectual work at the time). The ever-puckish Richard Feynman, who was responsible for overseeing the laboratory of human computers and who with Nicholas Metropolis was charged with installation of the first electronic computers using IBM punch cards, staged a showdown between human computers and punchcard-programmed machines. For two days the humans held their own; on the third day, the humans began to slow down, and the tireless machines pulled ahead.

There is an intriguing postscript to the era of human computers. The first six people charged with setting up programs on the ENIAC, one of the world’s first general-purpose computers (that is, not set up to solve a single, specific problem), were drawn from the job marketplace of human computers, and thus the world’s first professional computer programmers were women, specifically Kay McNulty, Betty Snyder, Marlyn Wescoff, Ruth Lichterman, Betty Jean Jennings, and Fran Bilas.

There’s a review of the Grier book here, and a very nice Scientific American article on the subject of the origins of computing here.