Wednesday
Mar162011

Highlights du Science

Your Brain Could Be a Scientist, Even if You're Not One

I think we would be better served by making clear that scientific thinking is just thinking, and the sort of thing that everybody does all the time.
--Chad Orzel

As an astronomy educator/public-outreacher, this response to Neil DeGrasse-Tyson's (DGT, from now on--coined!) recent comments about the difficulty and unnaturalness of scientific thinking hit home (runs) for me. DGT said that scientific thinking was unnatural, implying that logic and analysis are modern impositions that require neurological rewiring. Untrue! says Orzel, and I agree. People are walking saying things like, "Math is hard," and, "Science is hard," and, "Science isn't my thing, yo," and, "I'm just an artsy person, lol," not seeing that, as Orzel says, "Science, stripped down to its essentials, is just a method for figuring things out: you look at some situation, come up with a possible explanation, and try it to see if it works...This does not require an arcane or complicated skill set." When people dismiss science and analysis as modes of thinking that are too difficult or foreign, they are a) wrong and insulting themselves, b) excusing themselves from learning how the world around them works, when that is not a good idea because the world around them is working, c) preventing themselves from appreciating not only scientific knowledge, but also their own minds, which are observation-taking, prediction-making  pattern-recognition machines figuratively chomping at the figurative bit, waiting for people to take their horsepower seriously.

Everybody Thinks Scientifically, Uncertain Principles by Chad Orzel

Sperm Whales: They Are Us

Subtle variations in sperm-whale calls suggest that individuals announce themselves with discrete personal identifier.

Unsurprisingly, a cafepress search for sperm whale t-shirts, from where this came, is "successful."
That would have made a better opening quote if sperm whales introduced themselves with "discreet" personal identifiers. "Click click click shoot click," as opposed to "click click click $%^@$% click." Anyway, the point is, Luke Rendell and his team found that the timing of a certain five-click sequence is slightly different for each individual whale in their study, suggesting that the sequences are unique to each individual, suggesting, though certainly not proving, that these sequences are identifiers (names! click click click Miley click) for each individual. A sperm whale's recognition that it is an individual, as well as recognition that others are individuals and that those distinctions warrant attention, is significant. Even characters in dystopian novels don't even recognize that, which is, I suppose, what makes them dystopian.

Sperm Whales May Have Names, Wired Science, by Brandom Kleim

Friday
Mar112011

The bacteria in your gut can affect the neurons in your head.

Earlier this week I heard Dr. Bill Goldman speak (Professor & Chair, Microbiology & Immunology, UNC Chapel Hill) about his new project with Yersinia pestis (caustive agent of plague). He was infecting mice with Y. pestis intranasally, in this method you place a drop of bacteria on the mouse's nose & the mouse breaths it in, and his lab found that the Y. pestis wasn’t alone in this infection! He found there were commensal bacteria, bacteria that have adapted to coexist in a symbiotic relationship with mammals (ie: gut bacteria), from the nose/pharynx that were traveling down into the lung with the Y. pestis, and these bacteria were effecting the severity of the Y. pestis infection! This inspired me to write a “commensal bacteria are special and very important to every aspect of your life” post. Unfortunately Dr. Goldman has not published his results yet, there are still tests to be done! But in the meantime I found a stellar article showing commensal gut microbiota, or gut bacteria, have an influence on neural development!

Earlier this year Rochellys Heijtz et al. published a paper that showcased the power of a great collaboration, the mixture of a gut homeostatis & regulation lab (Sven Pettersson’s lab) and a neuroscience lab (Hans Forssberg’s lab), titled Normal gut microbiota modulates brain development and behavior. It had been shown previously that development of the mammalian brain is susceptible to both internal & external environmental cues during gestation & development (aka perinatal life) - in fact multiple behavioral disorders (including autism & schizophrenia) have been linked to microbial pathogen infections during gestation. Blending methods & resources, these two labs found normal brain development & behavioral functions are effected in the absence of normal gut flora.

They looked at germ-free (GF) mice, with no commensal bacteria, versus specific pathogen free (SPF) mice with a normal gut microbiota. These mice are raised in special plastic isolators to ensure proper growth conditions and are generally used for pathogenic research (it is very helpful to have a germ-free mouse during an infection when you’re looking for the effects of one specific pathogen).

They found GF mice had altered behavior, neurotransmitter turnover & expression of synaptic-related proteins. GF mice showed increased motor activity & reduced anxiety-like behavior in comparison with SPF mice – I would take this to mean that the mice are running around with no real objective (= bad), but I’m definitely taking creative liberty with some of these results. There was elevated levels of noradrenaline (NA), dopamine (DA) & serotonin (5-HT) turnover in the striatum (inner brain where the motor cortex hangs out). Briefly, these neurotransmitters are produced & released by neurons to communicate specific signals to adjacent neurons (Figure below). If there are alterations in neurotransmitter production this could decrease the life-span of the neurotransmitters & subsequently the efficacy of a neuronal synapse (the gap between neurons where neurotransmitters are released, responsible for communication between neurons). Specifically, they looked at the expression of synaptophysin, a synaptic vesicle glycoprotein that is a hallmark for synaptic vesicle maturation & synaptogenesis. Synaptic vesicle maturation is required for efficient release of neurotransmitters in the synapse. Therefore modulation of these proteins by the gut microbiota could lead to long-term modulation of synaptic development & transmission – this could affect motor control and anxiety-like behavior as an adult.

They hypothesize that their results suggest “ that during evolution, the colonization of gut microbiota has become integrated into the programming of brain development, affecting motor control & anxiety-like behavior” & they go on to speculate that these differences observed are mediated by signaling initiated soon after birth at a time when the newborn mice become exposed to gut microbiota.

When my boss teaches our immunology course he always stresses that you cannot look at single cells during an infection or during development & assume what ever you’re observing is the only thing happening – you always have to remember that we’re dealing with highly complex organisms and that you’re looking at 1 of billions of proteins in 1 of billions of complexes that affect 1 of billions of down stream events.

Studies like these always remind me to keep my eyes WIDE OPEN.

ResearchBlogging.org
Heijtz RD, Wang S, Anuar F, Qian Y, Björkholm B, Samuelsson A, Hibberd ML, Forssberg H, & Pettersson S (2011). Normal gut microbiota modulates brain development and behavior. Proceedings of the National Academy of Sciences of the United States of America, 108 (7), 3047-52 PMID: 21282636

Monday
Mar072011

Science Brief Today:

Life on other planets: Travelin' in on rocks.

Fossils of Cyanobacteria in CI1 Carbonaceous Meterorites: Implications to Life on Comets, Europa, and Enceladus

Richard B. Hoover, Ph.D.
NASA/Marshall Space Flight Center, Huntsville, AL

It's been in big in science news the last few days that esteemed & celebrated NASA scientist Dr. Richard Hoover has published a paper shows evidence that there might be extra-terrestrial cyanobacteria. This paper is published on the online Journal of Cosmology. I would advise everyone to take a brief moment & read the article. Also, the Editor-in-Chief of the Journal of Cosmology, Dr. Rudy Schild from the Center for Astrophysics at Harvard-Smithsonian, will be posting commentary from the scientific community addressing pertinent questions & concerns.

For those in the Atlanta area, Dr. Richard Hoover will be speaking at the Frontier in Microbial Biology Symposium at Emory University, May 13, 2011.

**EDIT** (3/8/11) If you follow the link to the article Journal of Cosmology has published 21 commentaries from the scientific community!

Fatal Laboratory-Acquired Infection with the Yersinia pestis (the causative agent of plague)

Do you guys remember when a Chicago professor died suddenly of the plague in September 2009? Briefly, a 60 year-old professor came into the doctor with fever, body aches, and a cough and 3 days later died of a chronic Yersinia pestis infection. Turns out he was working with a Y. pestis lab strain (attenuated) that was genetically modified to have a deficiency in iron uptake. Iron uptake is essential for infection of Y. pestis, therefore this strain could not cause disease. When they cultured the Y. pestis from his organs and inoculated mice this strain did not cause disease in the mice! After extensive genetic work they found that this professor had a genetic disorder that caused sequestration of iron in the liver and other organs. Therefore, the bacteria did not need to gather iron because his body was doing it for them. His genetic disorder literally complemented mutant bacteria.

Amazing!

(original article published online in the weekly CDC MMWR)


Tuesday
Mar012011

MoND versus Dark Matter: Battle to the Death in Low Surface-Brightness Galaxies

Today, I decided to exercise my artistic skill and create a 12-layer .gif. This .gif, which you will see very soon, demonstrates the reason scientists have postulated the existence of dark matter.

See, in the solar system, the farther you get from the Sun (where most of the system's mass is concentrated), the slower the planets orbit, as they experience less gravitational pull from the Sun. The same should be true of galaxies, where the mass is concentrated in the center. If this were true, we would observe the work of art labeled as 'expected' in the .gif, where velocity goes down as distance goes up. However, that is not what we see. What we see is that orbital velocity pretty much stays the same as you get farther from the center of the galaxy.

So astronomers said, "Whoa. There is mass missing. This missing mass must not emit light, making it 'missing,' and it must be distributed away from the galactic center in order for it to have the gravitational influence we're seeing, namely making things far from the see-able mass rotate quickly." This, by the way, is a direct quote from all astronomers.

Anyway, here's the .gif:



Most astronomers, scientists in general, and the general public accept, and are even excited by, the existence of dark matter, not least because of its suave name.

But there is another idea that can explain a flat galactic rotation curve, and it has an unsuave name: MoND, or Modified Newtonian Dynamics. MoND introduces a new factor, "a_o," into the Universal Gravitational Equation, in the form of a/a_o.

In situations like the solar system's, where acceleration (a) due to gravity is relatively high, a>>a_o approaches a, and Newton's equations are a perfect approximation. But in situations like the galaxy's, where the distance from the central mass is large and the gravitational acceleration thus small, a_o>>a, and gravitational behavior totally changes.

So Stacy McGaugh of the University of Maryland decided to do something to help resolve this debate between the MoNDistas and the Dark Matternians.

The Baryonic Tully-Fischer Relation (BTRF) is an empirical relation between baryonic mass (which in this case mostly means not-dark, and includes both gas and stars) and rotational velocity. Mass is assumed to be proportional to luminosity, because the brighter a galaxy is, the more stars it has--but there are problems with the specifics of the proportionality, namely that there are large errors introduced by uncertainties in stellar evolution and the stellar mass function. Calculating the gas-mass of a galaxy is much easier, because the gas is made of neutral hydrogen atoms, and each atom always emits a photon at a specific wavelength and a specific brightness. So if we know what the total brightness is, we can calculate how many atoms it would take to make that brightness, and then we can use our knowledge of the periodic table to find out how much mass is in that many H atoms.

So what if there was a galaxy that was made mostly of gas, so that we could calculate its mass very precisely, without the confusion of a bunch of stars? That's what McGaugh did. He found 47 "late-type, low surface-brightness galaxies," calculated their masses, calculated the rotational velocity profile that the BTRF dictates the galaxy should have, and then compared the predictions of the BTRF to MoND's and dark-matter's predictions for this same amount of mass.


This figure shows the mass/velocity of the 47 galaxies as neon spaceships. As you can see, the spaceships hover close to the MoND prediction, whereas the dark matter prediction is cold and alone.

Now, the author is careful not to say that MoND is The True Theory. There are things we observe that MoND doesn't predict, predictions MoND makes that we don't observe. However, it is one of the few 'fringe' theories that has experienced any 'predictive success.'

While this paper neither proves MoND correct nor dark matter incorrect, it does say, "Look, MoND is doing something right, and dark matter is doing something wrong. Stand up and take notice, because these are actual data, and you can't ignore the problems they present for your model." This paper shows that Dark Matternians have some explaining to do, which will, in the end, either make their theory stronger or destroy it in a flaming burst of scientific mind-death.

Data supporting a fringe theory will force the dominant theory to explain itself, to alter itself to fit the data or, if that is not possible, to cease and desist. I like it when the underdog undermines the dominant paradigm. And, as a side note, I like to think the underdog is the correct dog. In the end, though, I will cheer for whatever idea actually lines up with the way those crazy galaxies are spinning.

Reference

ResearchBlogging.org
Stacy McGaugh (2011). A Novel Test of the Modified Newtonian Dynamics with Gas Rich Galaxies Physical Review Letters

Friday
Feb252011

Science Highlights (mostly having to do with robots)

Robots think about thinking

"Then 'we removed a leg,' and over time the robot's self-image changed and learned how to move without it."
--Hod Lipson, Cornell University



I quote the above quote because it reminds me of Brooke's dog, Gonzo, who is missing a leg and has, like (apparently) a robot, adapted to life as an adorable tripod. Researchers at Cornell University have begun to create robots that are capable of metacognition (or proto-metacognition, as I think is a more accurate term), because "the greatest challenge for robots today is figuring out how to adapt to new situations." And here I thought it was figuring out how to overthrow our puny society. Anyway, here's an example of an experiment: They created a robot with two brains. The first brain was presented with moving red and blue dots and had to learn that blue dots led to rewards (seek!) and red dots led to punishment (evade!). The second brain just watched. And then when the second brain was presented with the same stimuli, but was rewarded for seeking red dots and punished for touching red dots, ITS BRAIN INTERPRETED RED AS BLUE AND BLUE AS RED SO THAT ITS OLD BEHAVIORAL MODEL STILL WORKED. Also one time a researcher removed a robot's limb, and it got phantom limb syndrome. FYI.

Choi, Charles. "Automaton, Know Thyself: Robots Become Self-Aware." Scientific American. 24 Feb 2011.

I'm not going to make a joke involving the phrase "Elementary, my dear Watson"

"You may want to ask how to prepare sushi. Watson can't answer that."
--Nico Schlaefer, grad student who gave Watson an algorithm



In case you live in a cave that doesn't have a satellite dish attached to its outer rocks, I'll begin this highlight by informing you that a robot played Jeopardy. Like many people, you may at first say, "Big deal, man. If I had a bunch of Wikipediae in my brain, I could win Jeopardy too," but if you said that, you would be missing the point. The point is not that Watson can find a fact in his big-ass brain and then spit it back at Alex Trebek, but that he can figure out what fact he needs to find. While it is simple for a human to interpret language in the form of questions, it is no small task for a robot. Think about what Google does--it doesn't interpret your query for you. It just takes your key words and phrases and searches to see if those words also appear on a web page or two or ten thousand. But Watson, in order to win Jeopardy, had to be able to transpose phrases, translate idioms, and decipher puns. As Schlaefer put it, "Take the Jeopardy! clue: 'This company acquired Sun Microsystems.' Passages in original sources may say, 'Oracle paid $7 billion for Sun.' A human knows Oracle acquired Sun, but it's not obvious to Watson that paying money means acquiring something. The answer may be there in an obscure way or [might] occur only once." Check out this interview with Schlaefer.

Frenkel, Karen. "Schooling the Jeopardy! Champ: Far from Elementary." Science. 25 February 2011: Vol. 331 no. 6020 p. 99.





An Extra Phantom Limb
(I don't know why this is italicized, but I can't make it stop, not even using HTML--SORRY)

"It is also conceivable that people with demanding work situations could benefit [from] an extra arm."
--Henrik Ehrsson, two-armed researcher 

Though it sounds absurd, two guys named Guterstam and Ehrsson could easily convince you that
a) you have three arms
b) you can feel them tickling your third arm with a brush
c) your third arm is in danger of being stabbed with a knife, which will hurt your third arm.

And all they have to do is place a rubber arm next to one of yours and cover your upper body with a sheet so that you can't see whether it's connected to you or not. I can't really say anything else about this because I'm still learning how to type with 15 fingers.


Harmon, Katherine. "Researchers convince people they have three arms--then threaten one with a knife." Scientific American. 23 Feb 2011.