What Have I Been Doing?

Just what Have I been doing lately? I certainly wasn't posting on this blog, as is evident from the time stamp on my last post. I've been working on the high school science class demonstration I outlined in my last post, and doing a LOT of reading on neuron imaging, current injection and computational models (both theoretical and practical).

On the front of science demonstrations, I've made a lot of progress as far as pinning down protocols, and now am mainly just waiting for supplies to arrive so I can start testing the techniques and protocols I've conglomerated from resources online and the helpful posts of fellow biohackers on the Diybio google group. I've posted a first tested draft of a human DNA extraction protocol on this blog for the world to start perusing (if the world ever manages to find my blog), and it is workable if not incredibly coarse and still slightly unquantified (ran out of time to test the optimal amount of meat tenderizer protease for the mixture, and will probably need to see results in electrophoresis before I can really determine what ratio and conditions are optimal or even make a difference).

I spent five hours yesterday in the high school lab working on different scales of extraction and trying to coax the DNA I extracted into "spooling" onto a bamboo shoot (as is talked about here, here and just about everywhere else that uses a protocol like the one mine is based off). My conclusion is that either my stirring/enzyme use has somehow not yielded the structural form of DNA that their experiment yields (shearing or DNA structural proteins still coiling the DNA), or that human and animal DNA behaves differently at a macro level. My specialty isn't genetics so I consulted the diybio group, and their answer is "we haven't ever tried 'spooling' DNA". My conclusion is that spooling human DNA most likely isn't possible, and am going to use a centrifuge to pelletize the DNA im trying to extract.

So, yes, I bought my first piece of lab equipment yesterday. A Dremel 300 from a big box store for $49 US, and a Dremelfuge Rotor designed by Cathal Garvey and sold by Shapeways for a total of $58 US with shipping to the USA (not sure where it's coming from). It should arrive by 11/9. It promises to be a good investment, being able to develop (relatively safely; disclaimer: I'm not responsible if you get shot in the leg or eye by an errant centrifuge tube) just over 50,000Gs worth of force. That's as good as a high grade commercial centrifuge I'm told, and I'm excited to see how it works, and will post pictures, text and maybe even a video of it when it comes in.

In the realm of neuroscience I've been splitting my time between continuing to read about research methods in the realm of neuron imaging and current injection (reading what a neuron does, and making it do what I want it to do respectively), and the mathematical models that exist to describe both a single neuron and the computational nature of many neurons acting in concert.

In the realm of neuron imaging I have gone from reading about recording electrodes full circle back to the realm of fluorescence imaging techniques, this time in reference to voltage sensitive dye techniques, which are less complicated than the voltage sensitive proteins I had read about and possible mentioned earlier in the course of this blog.

Also, I'm trying to pin down and wrap my head around the nature of and the specifications of an electrode capable of injecting a current into a single neuron along the lines of those used in the Dynamic Gap technique, which I have been reading about quite enthusiastically. It sounds like the perfect technique for refining and modifying the single neuron model that I think badly needs attention.

And what better segue could I have asked for to talk about computational neuroscience, aka the art and math of figuring out what these neurons we're observing are doing to information? I've been mostly focused on the single neuron models such as Intercept-Fire, the Hodgekin-Huxley model, and the stochastic models derived from the H-H model. In order to look at system level models I'm going to have to have a good grasp on these first. I'm most definitely only doing research at this time, and to be honest am struggling with the math involved, as my last Calculus class was in my senior year of high school, and even then we didn't get very far in the book. So, right now I'm wrestling with the single neuron model, trying to work my way up, fighting on another front with the math involved with any of this. The single greatest resource I've found so far is a computational neuroscience textbook that I randomly found posted on a website in the .ch domain. I haven't had the time to figure out if it's a legally published copy or not, but it has most definitely been a god send for this scientist.

I apologize for the lack of links in the neuroscience part of this post, and will do a link update in the next few days, but I'm too lazy on my last day off to track down all the articles I've been reading. I did at least bother to find the link to the neuroscience textbook I've been reading, as it's sitting in the tab next to this one on my browser. You'll be hearing a lot more from me, and possibly even seeing me, in the coming weeks, as I ramp up my efforts on this science demo, and continue working on my neuroscience pursuits. Now:


Stand Back, I'm Going to Try Science.

Onward and Upward, Challenges and Chances

Well guys, I've done a lot more research and have been talking (and asking copious questions) on the diybio mailing list(google groups). It looks like I have my work cut out for me, and I'm going to have to study a good deal, but the plans for the lab are starting to come together.

Budget wise, I'm looking at about a hundred dollars a month in financial resources. I'll post a work up on the money side in detail once more details are available to me, as I'm not sure what qualities of equipment I'm going to need, or what I'll be able to improvise. With that said, I should have a fully functioning neurobiology lab in a year on the outside. More on this later.

Right now the bulk of my time is spent catching up my knowledge of research methods to my theoretical understanding. I've decided there are a few main avenues I need to pursue in the short term.

One is general knowledge of neuroscience. My sources of information have primarily been books aimed at giving a practicing clinician background knowledge on the fine workings of the brain. This is because up until about a year ago I was planning on getting my M.D. in psychiatry and going into research from there. Now, I've obviously become absorbed in pure research. Because of this my knowledge of brain chemistry is quite advanced, but my electrophysiology and macro scale anatomy is quite lacking.

The next is a need to be able to understand complex biology protocols. I've done some basic labs in the little bit of college I've had so far but it wasn't at nearly the level that I need to be operating at.

Along with this is the need to get a grasp on the general research methods of biology and specifically those which apply to neuroscience. My focuses for right now are reading everything I can about advanced microscopy and the optics and electronic/physical principles behind them, electrical sensor arrays and the electrical engineering behind them and cell culturing and manipulation techniques such as microfluidics.

An interesting non-neuroscience development in that I am going to be proposing a diybio genetics demonstration to a high school science teacher co-worker of my mom. I heard in passing that the teacher was planning on doing a tissue collection on her students and sending it in to be sequenced and analyzed by the Human Genome Project. While this is a great and innovative idea, I thought it would also be cool for the kids to be able to tangibly see and manipulate DNA as well. To any biohacker this immediately screams a coarse strawberry DNA extraction. I've put together the materials list, protocol, and some interesting background information that can be presented during the demo in the hopes that she will at least use the material and, ideally, allow me to conduct the demo under her supervision. My meeting is set for tomorrow, and you can bet that I'll post more when I know more.

That's about it for this missive from the lab in potentia, so I'll leave you with a few more links, this time basic background and technique articles.

Principles of Microscopy, an article by a professor of cell biology and molecular genetics explaining the principles behind visible light, fluorescence, confocal, and phase contrast microscopy.

Basic Microfluidic Concepts, an article on the University of Washington faculty pages site about the basic concepts behind microfluidics, as well as some numeric analysis of those principles.

Bonus: The beginners Strawberry DNA Extraction, from the University of Utah. Not really a protocol so much as a recipe (there's even meat tenderizer!), it's a great way to show kids and your friends the wonders of science.

What is this? ...or... The fouding of a blog.

You may find yourself on this page wondering why in the world there is only one post. What is the purpose of this person sending text out into the internet, what do they want, what do they do? I created this blog as a way to chronicle my work on several projects I'm getting started, as well as a platform to post articles online.

And what is this work you ask? I'm into diybio and neuroscience. Really into it. I think a fun afternoon is reading about fMRI and the creation of a culture of cells of C. elegans from embryonic stem cells so that I can research how their neurons work (if you can't tell, thats been my afternoon). Furthermore, I'm so much of a mad man that I not only want to read about these procedures and wait patiently until I'm able to go back to college and work in a professional lab, I want to be able to do this in my home. Obviously I'm not going to be shelling mouse brains into tupperware or some other sort of frankenstein nightmare, I have a code of ethics and a mind for safety. But, my goal is to find a way to, while following standard ethical guidelines and safety regulations, create a lab environment in my home where I can do these sort of things.

That will probably be the first formal post on here, an article detailing my plan to make this happen. As anybody with half a brain will be able to tell, this isn't going to happen overnight and a lot of planning, preparation, leg work and experimentation is going to have to go into this. I've been thinking about this specifically for a couple of months now, and I think I've developed some good ideas as to how to make this happen.

Depending on how often I find myself itching to publish over the next few weeks, you can expect to be able to  find anything from posts of links I've found interesting, thoughts and ideas I want to get on record, or background on myself and what I'm planning to do.

To start you off with some actual content instead of this meta-content I've written so far, here's some of the articles I've read in the past few days:
Circuit Neuroscience, The Road Ahead(pdf)
Neural Circuits (preview page of a book on Neuroscience on the NLM site)
Abstract of a Nature article on a novel way to use florescent attached proteins to detect voltage levels in a neuron
WormBook A novel way of culturing nematode worm neurons to facilitate their study. (I could see this being paired with the florescent work above to make an observation setup)
As well as a slew of wikipedia articles branching off of the Neuroscience category.

I don't have a large presence on the internet but you can contact me by commenting here or by emailing me at the link provided in the "About Me" section. I'm also trying to start posting to the diybio global mailing list, available on google groups or linked to by the Diybio local page.