DIY DNA Extraction

This is awesome

One summer years back I worked in a plant genetics lab doing something not completely unlike this to isolate DNA. I guess the main difference would be in the purity and integrity of the DNA collected - you certainly couldn't use this method to get analyzable samples. The kits we used in that lab contained lots of buffer solutions, enzymes, and other chemicals to break down the cell walls, remove the proteins, and precisely isolate the DNA. At the end, you get a few micrograms of the stuff. I'll stick with the stovetop method from now on. It's probably not hard to modify this to get DNA from other things - certainly other plants - but what about animals? You would have a hard time getting a big enough sample to collect a visible amount of DNA, and it might be more fragile. I've never done that, so I'm not sure how the procedure differs.

Maybe one day I'll be outside poking around in the dirt and come across some fossilized amber with a mosquito inside. I'll take it back to my kitchen, pull out the blood from the mosquito and...

DINO DNA!!
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The Year of Science

2009 is here, big and bold.

An alliance of scientific organizations has declared this the Year of Science. The ScienceInsider blog (which I would recommend for science policy news) of the AAAS has more information. The Coalition on the Public Understanding of Science is spearheading the outreach, organizing programs at science conferences, new websites for teachers, and other public programs. It's a nice idea. Whatever gets more people interested in this sort of thing, the better. I especially like the idea of providing people with simple, instructive content about the nature of the scientific process (particularly its iterative, ever-changing nature - something few people fully appreciate).



I recently read an article about the increasing disinterest in science seen among US students. As kids grow up, science is presented to them as less fun and more hard work. They lose the Mr. Wizard mentality, adopting a more cynical view. I think this in part explains why we are seeing fewer science degrees in the US, relative to other nations. People that don't find science interesting are more likely to distrust it. If something is viewed as closed off, obscure, or just hard, few will take the time to investigate it and this, over time, erodes the integrity of our science infrastructure. The public's perception of science is a lynchpin for future progress.



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Book Review - Descartes’ Error: Emotion, Reason, and the Human Brain

My lone class this term was a seminar of the psychology of emotions. We discussed classic and modern literature on evolutionary and mechanistic perspectives of emotions, mood, and feelings. Randy Nesse, a UM psychiatrist and researcher, was our instructor. It was a great class, full of students from varied departments and psychological areas. One of our final assignments was a book review. I read Descartes' Error: Emotion, Reason, and the Human Brain, by Antionio Damasio. Damasio is a renowned neurologist who has written extensively on the human mind, incorporating neuroscience, philosophy, and psychology. I thought I'd repost my brief essay on the book. It's below the fold.


In Descartes’ Error: Emotion, Reason, and the Human Brain, Antonio Damasio tears down the western philosophical view of mind/brain duality, and in it’s place substitutes a lovely body-minded conception of rationality, decision making, and emotion. At the heart of Damasio’s work is a single assertion: the human mind is not separable from the physiological mechanisms that constitute the human body. This, he declares (though somewhat anticlimatically) was Descartes’ error - the rarefaction of the most refined operations of the human mind into a metaphysical spirit, and the subsequent neglect of the importance of somatic processes to the human experience of the self. Damasio inserts emotions and feelings in the middle of the rational decision-making process. Furthermore, Damasio proposes the somatic-marker hypothesis, a synthesis of environment-body-brain-behavioral elements that leads to the distillation of human choice and rationality through experience of affective and bodily feedback. Damasio provides historical and personal patient accounts, exhaustive neurobiological evidence, and some convincing accounts of the importance of body-brain interactions for the generation of behavior. The book is organized into three parts that roughly follow the headings historical context, empirical evidence, and theoretical implications.


“Gage was no longer Gage”

Damasio opens with an account of legendary neurological patient Phineas Gage. Gage was a construction foreman who, durning an excavation explosion in 1848, was impaled through the left cheek with an iron rod. The rod exited through the top of Gage’s head, obliterating a large part of his frontal lobes in the process. Damasio outlines the subsequent treatment of Gage done by John Harlow, in which he documented Gage’s change from an even tempered, clever businessman to an indecisive, irrational, and profane social outcast. Deprived of his orbitofrontal and prefrontal cortices, Gage was never the same; though his other faculties remained unfazed, his decision making, rationality, and emotional expression were profoundly changed. Damasio, in collaboration with his wife Hanna, conducted detailed analysis of the Gage case, and through modern imaging techniques, were able to reconstruct Gage’s skull to infer the damage. Damasio goes on to describe several other historical cases of patients exhibiting Gage-like frontal lesions, as well as personal patients. Damasio’s work with frontal lesioned patients is thoughtfully retold, and it offers a clear insight into the formulation of his ideas about the mind. He develops, as the book progresses, a strong empirical foundation, one that later on, during discussion of his main thesis, the somatic-marker hypothesis, supplies needed authenticity.

In the middle chapters, Damasio outlines, in great detail, the physiology of bioregulatory, emotional, and decision-making events. He provides substantial neurobiological evidence of what he calls perceptual images. Damasio argues that thought is mostly made up of mental representations of knowledge about the world. These images are based on innate tendencies and those acquired though experience. Damasio argues that this coneption of thought, as a series of images, is how the brain produces an integrated mind out of “parcellated” activity. Emotion is integrated with factual information in the process of generating these images to express reasoning and decision making. These central chapters nearly wander too far into monotonous anatomical lecture, but Damasio is careful to reorient himself to one of his central theses: that emotions are an inextricable part of human decision making and rationality.


“To know but not to feel”

A key insight into Damasio’s views on emotion and reason came when he realized that these frontal lobe patients were affectively stunted. They appeared aware of the expected reaction to emotionally charged events, but were unable to express appropriate responses. They exhibited a cold cognition that Damasio related to impairment of their decision-making faculties. As he notes in chapter four “reduction in emotion may constitute an important source of irrational behavior” (pg. 53). Damasio argues that the incorporation of emotion into factual cognitive processes is essential for normal decision making, planning, and rationality.

In chapter seven, Damasio outlines his views on emotions and feelings. Notably, he distinguishes the two, the former very generally being a collection of dispositional changes in the brain/body prompted by certain mental content, the latter being the perception of those changes. This dichotomy is important, as it is in the frontal lesioned patients that emotional feeling is disrupted; they nearly never come to a perception of states of anger, fear, or joy, and this has an impact on their executive functioning. This distinction (one of function and physiology) may prove useful in experimental and clinical settings. In separating the emotion of anger from the feeling of anger, one may be able to parse apart how emotional disorders manifest and persist. Damasio further distinguishes primary emotions (Jamesian, based on ancient subcortical structures) from secondary emotions (built on top of primary emotions, utilizing the highly evolved somatosensory and prefrontal cortices - these are what might be considered “full” emotions, the products of cognitive appraisals and calculations). This discussion of emotional neurobiology illustrates an important application of Damasio’s work; he shows how an understanding of the brain is necessary for a full conception of higher-order cognitive function, and can provide substantial theoretical fuel for such a conception.

Damasio’s emphasis on the importance of subcortical emotional processing provides necessary context for his discussion of basic bioregulation mechanisms (chapter six). Damasio suggests that the bodily systems that control basic regulatory processes also support the production of emotions and feelings, and through their connections with the cortex, are implicated in all human behavior. To Damasio, we wear our evolutionary pedigree on our sleeves (or in our skulls, so to speak), and this provides the basic foundation for his primary theoretical contribution: the somatic-marker hypothesis.



“The organism has reasons that reason must know”

The somatic marker hypothesis is Damasio’s attempt to subvert traditional cognitive accounts of decison making, which posit top-down, “high reason” mechanisms that require logical calculation, conscious weight of costs and benefits, and full consideration of alternatives. Damasio acknowledges that those processes can and do occur, but more often, and perhaps more initially, reasoning comes out of the recall of stored bodily (somatic) feelings. When an event occurs, somatic feedback and a given response are associated with a perceptual image. During future, similar events, these representations are recalled, allowing the individual to narrow the choice of potential decision outcomes. In this way, Damasio intends somatic markers to be efficiency mechanisms; they free up attentional and memory resources so decisions can be made quickly. Damasio further argues that these representations are stored in the ventromedial prefrontal regions of the brain, and their absence in lesioned patients results in impairment of rational thought and decision making. The primary evidence for the importance of bodily feedback in decision making comes from skin conductance experiments, in which lesioned patients fail to exhibit normal physiological reactions to emotional stimuli. Damasio concludes that it is primarily a lack of incorporation of feedback from the body (not just the viscera, as William James contended, but also from the musculature and sensory systems) and affective information in the frontal lobes that disrupts a lesioned patient’s ability to formulate rational decisions, plan, and behave appropriately in social situations.

At its center, Damasio’s idea is a simple one: the body provides vital information that the brain uses to form a perception of the world and to behave in adaptive ways. His argument for the inclusion of emotional processing into a “neurobiology of rationality” is strong, and particularly useful for experimental and theoretical conceptions of the phenomena. The somatic marker hypothesis, while potentially overly complex and biased for negative environmental situations, is notable because it focuses on a holistic, “body-minded” view of human behavior. This is something, Damasio notes, modern cognitive scientists should be keenly aware of.

Damasio successfully pulls the human soul and mind back into the body, and illustrates how in no way does this relocation simplify or diminish it. Damasio’s book is a lucid explanation of what it is to be a human, in all our “fragility, finiteness, uniqueness, and complexity” (pg. 252). We should learn from Descartes’ error, and strive to see each other as what we are, firmly embedded within ourselves.

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There will be brains

Tomorrow, I'm off to Washington, D.C. for the annual Society for Neuroscience meeting. This conference is huge - 30,000+ attendees. My lab has a few posters, listed here. I hope to post highlights of interesting stuff I see, maybe even some photos. I went to SfN two years ago, and one of the greatest parts is the vendor exhibit. They reserve one hangar-size room for biotech, imaging, publishing, etc companies to set up booths and hawk products. These booths are just like those you might find at other conferences (like the Consumer Electronic Show, for example), but instead of big HD TV displays and video games, they have hi-tech microscopes, pipetters, and analysis software. Anyone can browse the goods, and there is a ton of free stuff. I'm hoping for a plush rat and a squishy brain stress ball. There are also scores of free publications, and, as usual, candy, to go around.

There's science to be seen, sure, but conferences are really just big parties. Academic meetings are infamous for illicit hookups and other decadence among Ph.Ds. I probably won't post on what I see of those (at least not pictures). I like D.C., and I expect the city to have a certain energy given the recentness of the election. The G20 summit is also going on, so if I see Angela Merkel, I'll be sure to give her a shoulder rub.

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Update: I know, bad blogger. A dearth of updates the past couple weeks. The conference was fun, but uneventful science-wise. I saw a bunch of posters, met some people, and explored Washington. The past couple weeks have been super busy. I had a presentation, a paper, and a lot of experimental work to do. At any rate, that is subsiding, and I am preparing to leave work for a brief holiday vacation. Hopefully that will mean more blogging.

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Civic scientists

Sunday I wrote about the need for government to embrace science once again for prudent policy, and for scientists and lay persons to stand up in science advocacy. In today's issue of the Journal of Neuroscience, there is a special commentary from Dr. David P. Friedman, a professor of Physiology and Pharmacology at Wake Forest University. He is last year's winner of the Society for Neuroscience's Science Educator Award, here offering a perspective on the importance of science education and outreach. Specifically, Friedman emphasizes the need for universities and other institutions to provide educational support to pre-college children, where anti-science groups often run smear campaigns unopposed. Also important is better science communication to the mainstream media and further utilization of the internet, through blogs, and other outlets.

This is what we need. Anti-intellectualism runs deep in this country. Nicholas Kristof, writing in Sunday's New York Times, discusses this idea further. Reinserting science into the public consciousness will not be done in one grand gesture, it will require a grassroots, bottom-up change.
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The term civic scientist was coined by Neal Lane, former director of the National Science Foundation. I like it. Continue reading "Civic scientists"!

Science and Politics - Let's get it on

Science's influence on society is immeasurable. Medicine, technology, engineering, telecommunications, and education, owe their modern existence to systematic observation and experimentation - the scientific method. Whether or not you care at all about it, science has had a direct and profound impact on your quality of life, health, communication, and entertainment. For these reasons, and zillions of others, science matters.

Unfortunately, public perception of the importance of science has significantly diminished over the past decade, particularly in the United States. There are myriad reasons for this, but a large share of the burden may lie with scientists themselves. Sure, the Bush administration has done their best to discredit and make irrelevant science for eight years, and religious conservatives have waged the so called "war on science" for even longer. Those factors matter, a lot, but I think a large portion of the blame lies within the scientific community and people that call themselves science advocates. As a bunch, I think we've become complacent, satisfied to remain within our own tiny spheres of influence. We run experiments, publish papers, give talks, and maybe even blog, but at the same time, we allow the constant denigration of our craft - within government, among the media, and at the hands of anti-science groups. This passivity has become all too common; scientists are quick to spout their misgivings about the state of research in America, when provoked (for taped interview, say), but self-motivated outrage at their own cheapened status is seldom seen.

That is not to say that the devaluation of science in America was caused by inaction among scientists. This is hardly the case, but I think this anti-science society persists in part because scientists as a group, and any science friendlies among the public, have not spoken up loudly and angrily enough. When the government rejects thousands of research studies from 50 years of investigation, and denies anthropogenic global warming, for example, the science-friendly public should have stood up, shouting and calling their congresspersons. We shouldn't have allowed this to pass, letting the big bad government rework reality as they pleased. We all share the blame for the current predicament, and so we all share responsibility to fix it.

We need to return (were we ever there?) to the days when science was the first and last resort of public policy. When we need answers, we should look to the research, examine the data. Health care, energy, immigration, foreign policy, *the economy*, and many other hot-button political issues are directly informed and influenced by knowledge gleaned from scientific research. This isn't just about some "elitist," academic pursuit of knowledge (though there's nothing wrong with that!), this is about coming to real-world solutions for current imperative issues.

So we are now past the blame game, past pointing fingers, past all those hand-wringing cliches. There are real crises in the world that need fixing NOW, and science can help. There may not be much time to begin fostering trust and excitement in science among the public, and enacting science-based policy. Sarah Palin and Bobby Jindal, two unabashedly anti-science politicians, are among those that may challenge the future. We have in front of us an opportunity, the chance to take advantage of a science friendly administration to reinstate science as the driving force behind prudent government.

Consider the multifaceted nature of your world. Consider the influences on your everyday life, where many disparate ideas coalesce into what you call society. For each of us, this world has its vital and precious parts. Let's keep it all intact. Continue reading "Science and Politics - Let's get it on"!

Visualizing the election results: now and then

After an busy week, in school and in politics, I return with some interesting figures of the breakdown of Tuesday's voting. The New York Times has an interactive electoral map that compares voting patterns this year with the previous four presidential elections. As you might expect, compared to 2004, the country swung heavily Democratic, even within states McCain won.



In this picture, blue areas represent counties that voted more Democratic than in 2004, whereas red areas are counties that went more Republican. You see a lot of blue, indicating a general increase in Democratic voting percentages across the country, except for parts of some southern states. Notably, you see a lot of blue in the Rocky Mountains, along the southern border, and among the northern plains states.

One might draw the conclusion from this map that the country has renounced conservatism and embraced liberal Democrats once more, underscoring Obama's mandate to change the country. Well, for some perspective, consider this year's election in comparison to 1992, when Bill Clinton defeated George H.W. Bush.


The 1996 map is similar.

Our heavily Democratic 2008 voting bloc was considerably more Republican than it was sixteen years ago. What do we glean from comparing these maps? The country remains much more conservative even now than it was in the 1990's. The Democratic shift is relative, and reflects just how strong Christian conservative turn out was in '00 and '04. With practical issues like the economy on voters minds, they worried less about abortion, but the gap in social issues remains sharp (sadly evidenced by the passage of gay marriage bans in several states).

Eight years of the Bush administration may have soured voters on George W. Bush, but it certainly didn't eliminate Republican support. What does this mean for Obama's presidency? Bipartisanship is key. Given that Democrats now control the executive and legislative branches, it will be interesting to see how they will get things done without alienating 46% of the country.

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