Bringing Bicycles on Trains and Buses..the efficient way

I often find myself traveling, and I often find myself in need of a bicycle. I finally solved this problem by buying myself a folding bike a couple months ago, and I love it.

 But, the folks on the MegaBus won't let me bring a folding bike on their bus unless it is in a bag or a box. So... last weekend I went to an army surplus store in Chicago and bought a duffel bag that could hold the bike. It works, I can now comfortably carry it, but it does look a little funny.

Bringing Neuroscience to the Garage - The Interview

When I can spare the time, my favorite hobby is to go into the garage, put some music on, and work on my cars. I enjoy it so much, sometimes it has bothered me. If you should do what you love, and given a choice I would rather spend my time in the garage, why am I a neuroscientist? Shouldn't I be a mechanical engineer?

Upon reflection, I realized I do love neuroscience, but it is simply impossible to do bench level neuroscience at home. All of my previous homemade neuroscience has consisted of satirical or theoretical writing that did not require any equipment besides a brain and a labtop. So...for this year's Society for Neuroscience meeting, my close friend and colleague Greg Gage and I decided to attempt to do some amateur neuroscience on the cheap, within the budget of a middle class high school student.

If you have a labtop, an insect, and $100, can you record an action potential using components solely obtained from RadioShack and Ace Hardware? We tried to answer this. Greg spent his spare time the last two months working on the electronics, and I worked on the micromanipulator. We presented our work in progress at the Society for Neuroscience conference in Washington, D.C. last week, and the response was overwhelming. DrugMonkey, a blog journalist writer for ScienceBlogs, covered the event rather nicely for us. Educators heavily encouraged us to complete the project and begin delivering it to students. Wow!

I also contacted Kerri Smith, the podcast editor for Nature Magazine, who was attending the conference, and she interviewed us for the Nature Neuroscience Podcast. You can listen to the ~1 hour podcast highlighting research from the whole conference here, or if you just want to listen to our bit, that clip is here (also embedded above). Thanks Kerri!

Stayed tuned y'all; I am already working on prototype V. We are close to fully operational spike.

Organism of choice, but I am beginning to look into crayfish as well.

Prototype IV of the MicroManipulator: 3 degrees of freedom, but still contains a little wobble that new prototypes should fix.

Greg's two pole bandpass filter pass plus amplifier on a breadboard. He is looking into alternative low noise op amps that cost 1 -2 cents more, still within our budget.

Finishing our presentation the night before at the hotel bar. Our first reviewers were the barflies, and they gave us great advice on the presentation format. That's Greg on the left, me on the right.

Greg delivering our message of neuroscience liberation to our colleagues and converts.

******

Finally, if you came to my blog in search of satirical neuroscience, here are the links to pdf's of our group's (Greg, Hirak, and me) previous work.

SfN 2005 Stock Market Behavior Predicted by Rat Neurons
(satirical poke at overuse of correlation)

SfN 2006 How Many Neurons Must One Man Have, Before You Call Him a Man?

(educational/semi-serious thought experiment on long-term memory...the paper finally just came out; all figures hand drawn!)

SfN 2007 Cingular Theory of Unification: The Cingulate Cortex Does Everything
(satirical poke at overinterpretation of fMRI mapping data)
The work will appear in a German book, translated in German, in early 2009.
Gage G. Marzullo T. Parikh H. "Die Cinguläre Theorie der Vereinigung: Der Gyrus Cinguli ist Für Alle Geistigen Leistungen Zuständig." in the book "Braintertainment 2.0"
An abridged version also appeared in a recent issue of the Annals of Improbable Research, and you can watch a youtube version of the work.

Enjoy! We encourage any readers out there to tackle issues in their own science field through satire. Sometimes scientists take themselves too seriously in the importance of their results (I sometimes do this as well), and a good-humored joke can spark more serious discussion of the limitations of our tools and methods.

Rolling Your Own Gaskets

Yes. I am still working on Bopper trying to bring it back to life. The cylinder head is back on, and now I am trying to reassemble all the pieces to get her back on the road again.

A couple months ago, during disassembly, when I removed the carburetor from the intake manifold, I noticed the cork gaskets from the rubber bottom of the carburetor were horribly rotted and needed to be replaced. Now that I am back to putting it all back together, when I went to Murray's  to get the gaskets, but they didn't have any for this specific Toyota 3AC engine. However.... they had rolls of gasket material, so I thought, "hey what the hell, I'll just cut my own; that's what most gearhead folks do anywhere on odd cars when you can't really find readily available replacement gaskets from the store."

Note; To non-gearheads out there, a gasket is a piece of rubber, cardboard, or cork that goes between two metal parts to complete a seal. Getting two parts of metal to seat perfectly against each other is very difficult, and every modern car engine uses gasket material between two metal parts to fill in any irregularities, so that a fluid-tight and gas-tight seal can be formed.

But how do I make my own gasket? I recalled the woodblock techniques from my high school art class. Cover the metal part with paint, and stamp the pattern on a piece of paper.

Then tape the painted gasket picture on a piece of gasket material, and use a fine #11 edge blade (re: scalpel) to cut out the gasket pattern.

Below you can see the cut out paper pattern on top, the homemade gasket in the middle, and, below that, the piece of rubber the gasket will attach to.

You can see the new gasket placed on the intake manifold of the car.
And coated with a high temperature resistant silicone sealant.
The thick rubber block between the carburetor and intake is installed...
Another handmade gasket is put on top of that, with more high temp sealant...
and viola! 
The carburetor is installed! Now to hook up that mess of vacuum and fuel lines...

From Genes to Social Behavior - A Meme Gone Out of Control

Those close to me know about the recent fiasco regarding the neuroscience program forcing my colleagues and I to retract an abstract we sent to the Society for Neuroscience meeting this year.

The abstract, entitled,"From cell fate to human fate decisions: the role of notch signaling in global conflicts," was a satirical poke at contemporary neuroscience by claiming that all human wars are the result of one gene, Notch, which is required for nervous system development. 

The point of the abstract was to point out how easy it is to exaggerate the importance of single proteins and genes in the function of the human mind. True, Notch definitely is responsible for human wars (because we wouldn't have functional brains without it), but a lot of other genes and factors, to understate it, are required as well.

And, true to form, look what appeared in the November 7th issue of Science Magazine in a article entitled "Genes and Social Behavior." The figure that explains it all. We should all stop working; it's all figured out.

Head Gasket Finally Replaced

With a screw driver I was able to scrape off the carbon deposits on the valves in question (see previous post). Then, with a combination of steel brushes, more screwdrivers, rags, and engine cleaners, I tried my best to remove the gasket material from the bottom of the cylinder head. I couldn't make it completely clean, but I made it as smooth as I could, and with a straight edge the bottom of the head did not seem warped.

So, Bopper, what failed on you almost five months ago in Southern Ohio, with me since averaging probably 3-6 hours a week working on you in any time since I could spare, is finally being replaced. It's time for your new head gasket!

As you can see in the picture and video below, I had previously exposed and cleaned the engine block and cylinder heads. I was worried that maybe a piston component had failed, but it appears not so.

And the culprit! Compare the old gasket to the new one, and notice the rip in the gasket between the #1 and #2 cylinder hole. I had a brief moment of minor annoyance when I saw that the gaskets were not exactly the same, but the two coolant pathways on the front of the old gasket don't lead to anything, as there no passage way for those holes on the head! See picture at top of post. 

I bought some special gasket sealant spray from the auto parts store that contains bits of copper to improve heat transfer, which made the gasket a very pretty burnt orange look (Hook 'em Horns!). The gasket slipped right on the top of the engine block. Like a glove.

I took one last look at the cylinder and piston heads, said "It was good knowing you, but hopefully we don't have to meet again for a very long time." I put the cylinder head on carefully (it's a bit heavy!), put the 10 bolts in the slots, and tightened each one down in the correct order, carefully eventually torquing them up to 50 lbs in 10 lb steps.

Now I only have to install the carburetor, distributer, timing belts, water pump..... Twill still be a while before she's fired up again.

Valve Damage Question

This was an e-mail I sent to some of my gearhead friends today regarding the repair of my 1981 Toyota Tercel "Bopper":

Hi all,

I am finally putting Bopper back together and am almost ready to put the head back on the engine. Turning the head upside down to clean off all the old baked-on gasket material, I noticed one of the valves, third from right in attached picture (with a closer view in another picture) has some weird precipitate on it.

Since the old head gasket had failed and coolant was leaking into the cylinders, I am thinking that this is some weird antifreeze byproduct on the valve. It's very hard to get off.

I don't want to replace the valves, I want to finish this job and start driving Bopper again, but the question is, does this raise any alarm bells for y'all? I was just going to try to clean it as best I can and then put the head back on.  Have any of you seen this before?

Thanks,

Tim

And my mentor gearhead guru Mark's response: 

"It looks like carbon deposits to me.  As long as the valves are seating properly and there isn't carbon build up on the valve stem it should be fine.  The valve might run hotter than the others but that usually is only a problem on air cooled engines w/sodium valves.  Just make sure you scrape off as much of the old head gasket as possible and wipe down with acetone before putting the new gasket on.  And make sure the #1 piston is at TDC.  And follow the torque order..."

Thanks Mark! Anyone on the interwebs have any suggestion as well?

Pop Art Means Cutting Edge Neuroscience

In the latest issue of Science Magazine, a group of Israeli scientists recorded neurons of the hippocampus in humans with microelectrodes as part of  an epilepsy surgery. As the single neurons were recorded, the patients were played videos from various pop culture sources. After the movies were played, the subjects were then asked to recall what they saw. As you can see in the movie below, the sample neuron fires whenever Tom Cruise is shown, and, later, when the patient freely recalls what he saw on the TV, notice the neuron fires again approximately 1-2 seconds before the patient says "Tom Cruise." 

The video is amazing for its sheer pop art meets neuroscience combination. I thought it could be in a museum as an experimental modern art piece. But that aside, the big science ramification is that, perhaps, this neuron is where "the memory" of Tom Cruise resides. It also probably encodes more than Tom Cruise (as you can see in its sporadic response to other images), and whether it is truly where the memory trace exists can only be shown by either deactivating that neuron with GABA agonists / cooling, which is only done in animal models, or by stimulating that neuron and then asking if the patient immediately thinks of Tom Cruise. Even then, the neuron may still only be the "librarian" of the memory, and not the actual storage. Perhaps the brain doesn't make such distinctions in its storage mechanisms. 

These are tough problems to solve, but ultimately the most fascinating. I consider it even more interesting than the "C-word" problem. Oh brain oh brain, how ever do you store declarative memory?

Tour de Troit 2008

Last Saturday my friends and I went on a 42 mile bike ride through Detroit as part of an annual revitalization event. I had two bikes: I let my girlfriend take my mountain bike, and I rode in my folding bike. Folding bikes are not designed to go on long trips (they have small wheels and low gear ratios), but I felt I was in enough shape to handle the stairmaster that is the single speed. You have to pedal very very fast just to keep pace with the regular bikes.

The trip began at the old Michigan Central Station, a beautiful abandoned building that was in an odd part of town even when it was newly constructed. It will never be torn down and will forever remain perpetually mired in aborted renovation plans.

Not all the of the living things on the bicycles were human.

After a late start (10:30 AM) we were off, and we went directly towards downtown Detroit. You can see the route map and area highlight list below (courtesy of the Wheelhouse).

There were about 1100 bikers, but we were all appropriately spread out that only rarely did it become uncomfortably crowded.

In the video below, notice the iconic steam rising from the manhole covers as we pass Woodward avenue. If you look very closely as we make our left turn you can also see the Spirit of Detroit Statue.

 

After a brief tour of the downtown Detroit we then drove through the old neighborhoods on Detroit's Northwest side of town. There were only 2 other people with folding bikes out of the 1100 people, and people we would pass in the neighborhoods would always call out(especially the kids), "Whoah..that bike is cool! It looks like a scooter!" When Miss Trigger rode it, the effect was even more so.

In the final part of the trip, we headed south on grand river avenue for 10 miles back into corktown. I thought this was rather curious, but Miss Trigger told me the neighborhoods around that area are pretty bad. The police escort actually stopped the whole biking group two or three times on the road to keep us all clustered together. Whether that was to make the police force's job easier or keep us safe, or both, I don't know.

My favorite picture is the one below of Greg, happy and relaxed on a nice Saturday bike ride, with a wonderful view of an iconic image, unfortunately, of Detroit's negative population growth: the abandoned burned out building in the background.

The "bad ass" bike of the day award goes to the dude below. What is it even called?

The tour ended soon after that, and after packing the bikes up we had some lunch in Mexican town, drove back to Ann Arbor, and I promptly passed out for two hours. 

Continued Search for Optimal Rocket Motor #2

Who knew designing rocket motors from scratch would take so long? But..I finally think I am ready for a compression test next week with the full load cell test stand. I was originally using Elmer's Glue as a binder, but further tests revealed the Elmer's glue actually substantially inhibited the combustion and ignition (motors took forever to ignite, and then burn at a low rate for a minute or so...way too long when I want a burn of at max 2 seconds). I speculate that since Elmer's glue is water-based, it is somehow degrading the propellant.

I thus moved to an organic binder, a nasty smelling contact cement I bought at the local hardware store that is  used to apply linoleum to floors. The movie below shows a mixture of 25 g pyrodex, 3/4 ounce of the binder, and 10 g sodium bicarbonate (baking soda). After baking in the oven at 200 degrees for about a week, it was sufficiently dry to do a burn test. It took 5/6 of a second to burn (measured via the video time), which may be short enough to provide a good level of thrust for the rocket but long enough that the risk of overpressurization is low. Last night I gave myself a headache making some more motors (that binder glue is nasty), but stayed tuned for next week when fellow gearhead and garage guru Dr. Mark Lehmkuhle comes to Ann Arbor for a week! We'll finally get that static test up and running with the new motors!

The first and last day of graduate school

I began graduate school on August 16th, 2001. After a year of rotations, I joined Daryl Kipke's Neural Engineering Lab at the University of Michigan, and six years later, I graduated with my PhD. In total, from the time I began graduate school to the time I "completed all requirements," was seven years. Exactly seven years. As in I turned everything into the Rackham graduate school on August 15th, 2008. Why did it take so long? Now that is a long conversation my friend.

On my first day of graduate school, I woke up in Ann Arbor in my new apartment, had a cup of coffee, and walked the 2.5 miles to the Krause Natural Sciences Building on central campus to attend the "boot camp" for neuroscience students where we learned basic techniques in neurobiology. I remember being a bit tired that day because I had stayed up late the previous night writing songs with my roommate Eric. I was single at the time, not tied down to much of anything, and unknowing what the future held.  The out of focus* photograph below shows that first morning.

Seven years later to the day, on August 15th, 2008, I got up in the morning, went to Expresso Royale for a cup of  coffee spiked with a shot of expresso (graduate school having increased my tolerance for caffeine), then biked the 1.5 miles to my lab in the Lurie Biomedical Engineering Building on North Campus. I grabbed the last two dissertation forms from my advisor, printed out a revised table of contents, and then biked from north campus to central campus to pay a $70 binder's fee to the University of Michigan. I then turned all the final paperwork in to the administrative staff at Rackham graduate school. The last person between me and my PhD told me she really liked the dedication to my grandfather at the beginning of my dissertation and the Henry David Thoreau quote at the end of my dissertation (it's funny as I think she is the only one who noticed those two things...none of my faculty advisors commented on them). She then printed out a "fulfilled all requirements" paper for me, and told me I was done. 

That was that. I wanted to hug her. Happiness. I stood there awkwardly for a few minutes overcome with emotion, and she rightly noticed it and shook my hand saying "Congratulations." I walked out of that building in the early afternoon and the day had never looked so beautiful. I had to go back to lab to help a labmate with a experiment, and here you can see me on my last day of graduate school looking over a surgical prep.

Then, the day after graduate school, I found myself a victim of eternal recurrence, sitting in a high school classroom. 

Would I do it all over again? I am happy having studied and continuing to study neuroscience, but I probably would have taken more engineering classes in undergrad. It would have made graduate school a helluva lot easier given the nature of my dissertation. The only "what if?" on my mind is whether I should have gotten a materials science or aeronautical engineering degree instead. Would I be, to phrase Maslow's hierarchy of needs, more "self-actualized?" I imagine everybody has such thoughts. Scaled Composites is hiring....sometimes late at night I playfully let my mind wander, and I imagine just hopping in my car, driving out to California, and knocking on their door.

*****Fin*****

*Note: The out of focus picture of my first day of graduate school above was taken with a Kodak DC4800 3.1 MB digital camera (the out of focus is my fault). In 2001 consumer digital cameras were still very novel, and I was the only one of my friends and colleagues who had one. I had received it as a graduation gift from my parents for my B.S. in Biochemistry. It was a decent camera, but at the time it was about $500-$700. Nowadays a camera of similar features and quality would probably sell at the drug store for $50.

Continued Search for Optimal Rocket Motor

I've taken up amateur rocket construction as a hobby in the past year, and my current struggle is designing a rocket motor that 1) doesn't burn too fast, overpressurize, and blow up, and 2) that doesn't burn so slow that the thrust isn't sufficient for leaving the Earthly plane.

I thought I was rather sophisticated with my load cell set up.

But my motors are not at the stage yet where I need my static test stand (which I spent the last few months idly working on) to record the thrust time profiles. Rather I need to spend more time playing with ratios of gunpowder, baking soda, and glue, so as to finally get a motor that burns for about two seconds. After that I will record the thrust with the static test stand and start scaling the recipe for bigger rockets. See video below.

Codicil: Coming back Home, 9000 miles and 19 States

I have been in graduate school too long, and I have become too comfortable with the free lifestyle it offers. After defending my dissertation, I felt a sense of wanderlust I had never felt before. I literally couldn't stand to look at a computer screen, to walk down Beal Street to my lab, or walk down South University to Panchero's to eat my typical burrito. It was just too much of the same of the same of the same every day.

The mind turns inward in graduate school. I became so immersed in my own black hole of thought that I forgot there is a world beyond the same streets I walk every day. It sounds trite. It is trite. It is true. America has plenty of beautiful places and fascinating cites; I don’t think I’ll ever fully explore them all.

But, after traveling around this country, I still find myself wanting to stay in Ann Arbor. My friends have criticized me for becoming too comfortable in grad school and Ann Arbor, and that I risk becoming stagnant (if not already). I’ve always felt rather odd regarding this criticism. One of the joys of graduate school, beyond becoming an independent scientist, is that I have seen the world: most of the United States, Egypt, New Zealand, China, India, Dubai, Europe multiple times, Mexico multiple times, Puerto Rico, etc.... I do not feel the need to leave Ann Arbor to find a new place, as I travel one week a month on average anyway. I enjoy, at the end of things, always coming back to Ann Arbor. And now that I am graduated and have my PhD, I am viewing this town as my home rather than as a place I am simply staying on a long-term visit. Tim, born in the Midwest, staying in the Midwest.

The road trip ended symbolically with my flight back from New York City. From the unpretentious Bopper taking me around the west coast, I rolled back to Detroit in first class, surrounded by suits. After landing and waiting for a special lady to pick me up at the airport, I idled with psychedelic visions of the walkway to Terminal C in my mind.

Encore: New York City pt IV -Summertime

With the arrival of Saturday, Thad was off work, so I suggested we go back to Williamsburg to lounge around on a generally nice hot Brooklyn Day. We sat at the Verb Cafe again, I tried to edit my manuscripts, Thad tried to read the New York Times, but it wasn't happening. Thad found it hard to concentrate and relax with all the people around, and I was a little bit hung over from the night before when we went out until 4 AM in the morning. So... we just chatted and watched the stick figure people.

Since it was a hot day, the fire department had opened up the fire hydrants for people to run through. Not many of the hipsters took advantage of them, but their dogs certainly did.

Bedford Avenue was closed off to traffic, and the streets were full of people enjoying themselves. Having been to New York, Chicago, and Pittsburgh in the period of the last three weeks, I am shocked by how beautiful the woman are in cities compared to Ann Arbor. Now Ann Arbor, like any college town, has plenty of pretty gals. But in urban centers, I don't know, women just seem incredibly more stunning than in rural middle America. I hypothesize such dense beauty is due to a number of factors: 1) the women in cities are generally in better shape since they walk a lot, 2) they are generally better dressed or dressed more exotically with the "newest" fashions that are pleasing to the eye due to the novelty, 3) some probably actually are models, 4) cities also have more a diverse population, so there is more of an "exotic" effect and 5) The simplest explanation: there are more women around, so the chance of seeing bombshells is higher. I don't have any pictures of the angels, unfortunately, as I often feel uncomfortable taking pictures of strangers without their permission.

A nice young woman had brought a barrel of sidewalk chalk, and she and her toddler were drawing pictures on the road. I asked if the chalk could be shared, and she happily gave me some of the chalk to draw with. I am, and will continue to be, a notoriously bad drawer, and so I drew the only things I know how to draw: a model of the neocortex column and a spaceship.

Following the walking tour of Williamsburg, we biked to Manhattan to see the Metropolitan Museum of Modern Art (see post on MOMA here) and visit central park. On the way, I saw a taxi garage, a lovely taxi garage, with plants everywhere hanging from the ceiling.

And then we went to central park. Central park was full of its typical melange of people: troupes of gay men in roller states dancing to music in makeshift rinks, groups of young black kids playing African-inspired percussion instruments, break dancers, lovers, bikers, and the like. I took a brief nap in one of the fields, and then we began to motor on to make it to our Mets game. Thad and I were talking as we were walking our bikes through a crowd on our way out, when a big black guy told us to stop and walk around a touch football game. We had screwed up the last play. I'm sorry, Puff Daddy. He was playing some touch football with his kids, and that was his bodyguard who had told us to watch where we were going.

I actually thought it pretty cool that the hip hop star could enjoy a day in central park like the rest of us, with minimal entourage (one dude), and no one would bother him.

We had tickets to the Mets game, but we had lounged too long in Central Park, so there wasn't enough time to bike out to Queens to make it to Shea Stadium. So...we had to break our own rule of not taking the subway anywhere on this trip. We were those guys, bringing our bikes on the subway.

We actually didn't even make it to the game until the 6th inning, but it didn't really matter because the game went out to 14 innings anyway. Twas the Mets versus St. Louis, and St. Louis ultimately won 10-8. When we left the game (saying goodbye to Shea Stadium as this is the last season before it is demolished), we biked down Northern Blvd all the way from Flushing back to Long Island City before we headed south down to Bushwick. We were exhausted from the near 20 miles of biking we had done that day and crashed out at home.

The next day had some rather nasty weather, but we tried to make it to a free concert in Brooklyn. Unfortunately, it was packed beyond capacity, so we met one of my old friends from Ann Arbor for dinner, and we spent the reminder of the night playing dominoes.

I got up up at 9 AM the next morning to get my cab for my 11 AM flight back to Detroit. Now, since I was rolling first class, I thought LaGuardia would run as fast as Detroit Metro (10 minutes tops to go through check in and security in first class lines), but I was wrong. It took 45 minutes to check 5 people in. The staff at the airport were overworked from the previous day of bad weather, the airport was full of people who had stayed through all night, and everyone was generally pissed off and not very helpful. Due to the huge lines, blast, I missed the flight! I had to arrange for another flight the next morning, 6 AM.

What a drag. I was ready to go home, and I had to get back to work anyway to work on my dissertation revisions and manuscripts. But, like staying at a party two hours longer than you want to, even though you liked the party, I had another day in New York City. I spent most of it in an internet cafe working on a manuscript that was due in two days. Some of the local hipsters would come in and out, and I particularly noticed this one gal who came in with her Boston Terrier. I normally hate these dogs..so yappy and alien looking, but this one was incredibly well behaved while its owner was surfing the net. I asked the cute gal if I could take a picture of her and her dog, and she laughed and said it was fine. I also enjoyed how her shirt was a shirt in name only.

And Yes, I was actually working, not just taking pictures of pretty girls with their dogs (see Hirak! I told you so).

I worked until about 9:30 PM, then took the L train back to Thad's place. I had to get up at 3:45 AM to catch my cab at 4 AM to the airport, so we chatted only briefly before I packed up and tried to sleep for a few hours before heading out of New York City to go back home, the great American exploration coming to a satisfying close.

Coming Up: Codicil: Coming back Home, 9000 miles and 19 States