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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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.

Continue reading "There will be brains"!

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"!

Science on Charlie Rose

Below is a video of James Watson and E.O. Wilson being interviewed by Charlie Rose. They discuss the influence of Charles Darwin on biology. Watson is a wanker, but his contribution to science is great, so I can listen to his perspective on that.




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Visualizing science

This article from the Boston Globe on opening up science* pointed me to some really exciting online resources that are free and open for anyone to access. Most interesting is the Journal of Visualized Experiments (JOVE). This site publishes videos of experimental protocols submitted by researchers. Each is reviewed by a panel of experts, so quality and relevance are ensured. The videos range from basic wet-lab techniques and equipment-care tips to highly specialized imaging and brain recording methods. It's all free and open from the start, you don't even need an account.

This is extremely useful for other scientists, particularly those attempting to learn a technique for the first time. It's also a great example of transparency and camaraderie within the scientific community - a group that unfortunately, faced with trickling grant money and declining job prospects, are often forced to be quite competitive and opportunistic.

I see sites like this, however, as really important for educational purposes, for getting the word out on what scientists do day to day. Videos are especially useful for this because they get around technical learning curves that prevent most from comprehending scientific journal articles. You don't need to have an extensive background knowledge to understand what a scientist did in the methods section of a scholarly paper if you can see it. Ever wanted to know how scientists image individual neurons within a living brain? How stem cells are collected and analyzed? Now you have videos with pretty pictures to watch.

Any effort to remove some of the secrecy and mystery associated with research, to help the public see that science isn't just for stuffy Ph.Ds and nerds, but rather, can be an interactive, dynamic, and open exchange of ideas among researchers and everyday people, is worthwhile and necessary for progress.

*I plan to comment more about the open science movement. The linked article discusses some of the reservations old guard scientists and journal publishers have about giving everyone access to their data (so read that too), along with several web 2.0-esque science resources new to the internet. I think it's an interesting generational issue, sort of the Napster debate of science.

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Aptostichus stephencolberti

Jason Bond, a biologist who recently named a spider species after Neil Young, has named a new spider after Steven Colbert. This adds to the list of things already bearing Colbert's name, including a bald eagle from the San Francisco Zoo. Colbert reacts, talks to Bond in the hilarious video clip below.




Here's another awesome trapdoor spider video.



Continue reading "Aptostichus stephencolberti"!

For Your Consideration: Media recommendations

Book

The Drunkard's Walk: How Randomness Rules Our Lives by Leonard Mlodinow. Mlodinow is a Caltech physicist and author of several popular science books, notably, Feynman's Rainbow and (with Steven Hawking) A Briefer History of Time. This new book explores probability in everyday life, emphasizing how humans misunderstand randomness. We (read: primates) are especially evolved to form patterns and associations, to build heuristics that confer us some ability to predict future events. In other words, we seek out non-randomness in the world, a quality that was helpful in a simpler time, before modern civilization, but one that can lead to bad probability judgments when applied to modern scenarios. I've only gotten a few chapters into this, but so far it's highly entertaining and informative.

Pastoralia by George Saunders, is a collections of short stories and a novella. As the book jacket notes, Saunders is an author in the tradition of Mark Twain, Thomas Pynchon, and Kurt Vonnegut, sharply satirical and smart. The title story, "Pastoralia" is a swift and punchy, but utterly disturbing riff on the absurdity of modern America. After reading this, I'm going back to get all of his other work.

Magazine

SEED Magazine has been around for a couple years, along with its blog network Scienceblogs (Something else I would recommend as a great place to read about science/politics/culture/etc). I've been a subscriber and reader online for a good chunk of that time. Their motto, "Science is Culture," reflects the focus on the confluence of science and society, what really interests me about the magazine. Great art design too.

Podcast

The Naked Scientists is a podcast by several young Cambridge, England researchers, distributed by the BBC. It covers a wide swath of popular science stories, from public health to space exploration. Each episode includes a review of the week's science news, Q&A with listener email, interviews with prominent researchers, and a "kitchen science" experiment reminiscent of Mr. Wizard. Add in a bit of cheeky Brit humor, and you've got a great show. What makes it really entertaining, in my opinion, is the hosts' enthusiasm for the subject matter and interest in promoting public scientific literacy. The science is presented in an accessible way, but it's never dumbed down.

Philosophy Bites is a great little podcast by two British authors. Each week they interview a philosopher on a specific topic - such as, for example, evil, forgiveness, infinity, and human rights. This week's episode discusses the paradox of tragedy - that is, how we seemingly take pleasure from tragic literature and film, even though such things are filled with pain and suffering. Most of these discussions are 10-30 minute segments, so it's easy to stay engaged.

Continue reading "For Your Consideration: Media recommendations"!

One computer to rule them all

This piece from Wired reeks of that pop-science sensationalism that I often find hard to stomach, but it's a cool idea, and they have flashy graphics! Wired is like the US Weekly (OK, maybe more like People) of science/tech magazines; it focuses on science that's hot, in the Paris Hilton sort of way (Last minute edit: NO, Paris Hilton is not hot, this is referring to her common catchphrase "That's Hot," which she uses to indicate something that is cool or trendy or expensive. Fans of the movie Mean Girls may also relate to the term "Fetch," as in, that piece of clothing is soo fetch! Clearly, these terms can be applied to science-y things as well, as in, "that particle accelerator is hot!.") But they also simplify it to such an extreme as to state it as fact, thus seemingly removing the need for critical thought or consideration. If one were to only read Wired, and never examine more serious science journalism (or, maybe-just-maybe, actual science papers!), one would come to believe that researchers are curing cancer, are communicating with aliens, or are, in the case of the highlighted article, building computers equal to the human brain. Such computers, or computer, singular, the One Computer that is a conglomerate of all the world's data-calculation machines, interconnected by the world wide web, can already do more calculations than your brain. By 2040, this net of computers will have the combined processing power of all the human brains in the world. Wired's conclusion is simple: computers are totally becoming smarter than humans, which is awesome! It's so simple!

w00t!

The article makes a simple analogy between a neuron (a nerve cell, as you might have heard it called) in the brain, and a transistor on a computer chip. The One Computer has many many many more transistors, or switches, than a single brain has neurons. But neurons are only part of the brain's processing story. It's the connections between neurons, or synapses, that matter for information processing, learning, and as a collective, thought. The synapse analog in the global computer is the hyperlink - a connection between webpages. Compared to the human brain, with roughly 100 trillion synapses, the One Computer falls short at 57 trillion hyperlinks. This is already half, sure, and is increasing exponentially, but I don't think the basic analogy holds up. In the brain, synapses, these neuron-neuron connections, are constantly changing, strengthening, weakening, decaying, shifting, and splitting. Their chemical makeup is also in constant flux; synapses are some of the most molecularly complicated cell interfaces around. When you learn something new, taking in and processing sensory information, it doesn't just run through a circuit of static nodes, like transistors and links, but the very nature of the cells change, in infinitely minute ways. This change occurs continuously, from the time your brain develops in the womb, to when you die. THAT's a lot of information, all locked up in one three-pound mass.

In order to form the equivalent connection on the internet, there would have to be a more (much more) fluid interface between nodes/machines/pages. The difference between the brain and a big computer is information density. We're talking millions of molecules - receptors, enzymes, signaling proteins, etc, moving, recycling, pulsating with life within a single synapse. If a computer system can ever approximate that sort of complexity at each of its connections, and do it on a mere few watts of power, I'll be impressed. What this Wired article fails to point out is that while we are busy congratulating ourselves for technological innovation, we forget that that innovation is plagiarized from the natural world. Something that's only been "online" for a couple billion years.

Okay, okay, I get it, that's not a "hot" message. Continue reading "One computer to rule them all"!

Check out this brain book

I'm reading Soul Made Flesh: The Discovery of the Brain--and How it Changed the World (buy it from Amazon), by Carl Zimmer. Zimmer is a science journalist and author, featured often in the New York Times and other newspapers, Discover, Scientific American, and other publications. He also has a blog, The Loom, and has written several books on eclectic science topics.

Soul Made Flesh is an account of the conceptual developments and discoveries of the past 2,000 years that led to our current understanding of the brain and nervous system, presented within their political and cultural context. From the start the focus is on Aristotle and the Four Humors, then Galen and Descartes. The meat of the book dwells on the Oxford circle in 17th century Britain. This group of natural philosophers included Robert Hooke, Christopher Wren, Robert Boyle, and Thomas Willis, with influences from Thomas Hobbes, among others. In the midst of English civil war, the fall of the monarchy at the hands of Oliver Cromwell, the eventual Restoration of royal rule, and many religious feuds, Oxford remained a bastion of scientific pursuit. Willis and the others performed countless dissections and experiments on the corpses of criminals (and dogs), leading to a detailed account of the anatomy of the nervous system and the first basic understanding of where human perception, thought, emotion, and intelligence reside. For nearly 1500 years before their discoveries, most people thought the heart was the center of human sensation and the soul was it's rational intellect. Aristotle's dogma loomed large over the Catholic church of Europe, and criticism of his Humors was serious business.



Most of the men of the Oxford group are known today for other work (e.g., Boyle, of Boyle's Law fame. Remember high-school chemistry?), or not known at all, but they are largely responsible for giving brain science (and in some ways, science in general) a systematic framework. It's true, though, that most were polymaths, dabbling in alchemy/chemistry, medicine, physics, astronomy, and other fields. Willis, the unofficial leader of the group, specifically published detailed drawings of the nerves, muscles, and brain, and is partly responsible for the idea of blood circulation. He was also the first psychiatrist, unknowingly diagnosing disorders like bipolar, depression, schizophrenia, and Alzheimer's centuries before they were fully understood. Most of this seems to be forgotten today. You might have heard of Boyle, or Hooke and Hobbes, but you probably don't know Willis. Ask any medical or neuroscience graduate student, however, and they will be able to credit Willis with at least one thing: the Circle of Willis.

The Circle of Willis is a ring of blood vessels that runs along the underside of the brain and brainstem, supplying it with blood. Oh, how many times I drew this picture during neuroanatomy last Spring. This is all that Willis gets, his name associated with a few (very important) blood vessels. It's a raw deal, if you ask me.

I'm two-thirds into this book at the moment - still in the 17th century - so I've yet to get to the more modern work of 19th century anatomists and the rise of the neuron in the 20th century - topics I'm more familiar with. So far this is a very nice account of the conceptual revolution underlying the shift away from a dualist perspective on the brain/mind that dates back to the ancient Greeks. The Oxford circle, though deeply religious themselves, moved understanding of human consciousness away from the sort of mystical soul-talk of the Middle Ages, and into the head. The cultural significance of this shift was huge, and Zimmer spends a lot of time discussing the persistent ideological struggles in Britain and elsewhere.

This obviously isn't just a neuroscience book. If you are interested in understanding how radical ideas develop within a cultural and political context, this offers an interesting perspective. Other late Renaissance philosophers and scientists, like Galileo, revolutionized their fields amidst similar tumult. There are also plenty of good bits on England early in it's colonial period, something most history classes seem to gloss over. Sometimes in the middle of the book, which I just read through, the chapters meander, and you're not sure who's book this is, who Zimmer is focusing on. I think that underscores the point, however, that big changes in the way people view themselves and their world, like the shift from a metaphysical mind to one made of matter, require a lot of time and a lot of people working to drive that change.

Continue reading "Check out this brain book"!

Cells and Easter wrap up

On this day in which the American death count in Iraq passed 4,000, I offer a visual distraction. Check out this video from Harvard and the Howard Hughes Medical Institute. It's a handsome depiction of some basic cellular processes.



In reality, the action of these molecules isn't so graceful; at that atomic level, movement is messy, frenetic, and quite random. An accurate depiction would have made for a seizure-inducing video, so we'll let that one slide. The specific physics don't really matter, just keep in mind that most of those processes are going on in your body trillions of times a second. There are a bunch of other videos on YouTube of course, but also here.

Yesterday was Easter Sunday. Not unlike any other Sunday for me; I watched Food Network over breakfast, went to lab, blogged about cereal. I also ventured to Best Buy to return a wireless-internet router, only to arrive at an empty parking lot. Best Buy gave their employees the day off to hunt eggs and eat chocolate bunnies, it would seem. This was irksome, sure, but luckily the adjacent Borders was open. I bought two books (that I have no time to read).

More disturbing was the "CNN Presents: The Mystery of Jesus" special I viewed when I got back. In an attempt to delve into the controversial history of the life of Jesus, CNN interviewed several religious scholars on his prophetic exploits. What is pretty certain are the main biographical elements like his place of birth, teaching, and crucifixion. What of the rest, such as the purported miracles and resurrection? Well CNN took a less than critical line on these events, concluding that "science can't account for them" but never questioning that they happened in the first place. (Just like science can't account for, ahem, the Easter Bunny?) The lone source material for all of this deep inquiry - the four gospels of the Bible. No mention of the myriad other accounts of Jesus' life, nor the contradictions implicit within the New Testament. To put a big disturbing cherry on top, CNN gets Liam Neeson to narrate. He might as well have been proselytizing the midi-chlorians.

Oh, I'd hate to end on such a cynical note. Here's another video (cell wars).

Continue reading "Cells and Easter wrap up"!

Publication (hopefully) forthcoming

In college, I spent a year in a lab researching effects of caffeine in rats. I also helped write the manuscript based on that work. It was fun, and good experience. Now, we are in the throes of the publication process. The manuscript has been submitted, returned, revised, and is now ready for resubmission. Early next week, the graduate student I worked with will send it on to the journal Pharmacology, Biochemistry, and Behavior. How exciting!

It's a nervous situation, though, because there is no guarantee they will accept this time either. We've addressed the original reviewer comments, hopefully adequately, but there is always more that could have been done.

If it's accepted, fantastic. Having a journal publication this early is still fairly uncommon. I'm afraid that if it is accepted, I will become uncontrollably excited. Seriously, I may paper the walls of my apartment in reprints. Continue reading "Publication (hopefully) forthcoming"!