Microbial Fuel Cell netcast…

It’s only my first attempt at anything like this, so constructive comments are welcome…

(Hopefully you can see the embedded audio player here…)For those of you just tuning in, this is a 90-second explanation of Why Microbial Fuel Cells work. A longer (though still simple) explanation can be found at a slightly older post here.[Update: this was featured in the November 6, 2007 broadcast! Hooray, I can now claim to be an international “radio personality”!]Presuming hosting this file doesn’t kill my bandwidth, I’ll leave it up here. BelowAbove, you should see an embedded flash player (assuming you have Macromedia® Flash® player installed) which you should be able to click on to start the audio. I’ll also place a direct download link below. It should be noted that like everything else on this blog (unless otherwise specified), this audio is also available under the Creative Commons non-commercial/attribution/share-alike license, so as long as you have no problem with the terms of that license you are welcome to copy, redistribute, put up on bittorrent, host a public performance, turn into an interpretative dance art project, or whatever else you might want to do with it so long as you give me credit for it, don’t use it for commercial purposes, and distribute any derivative works of it under the same terms.

You can download the audio directly from here – right-click on the link and select “save link as…”. Ogg Vorbis format available on request…

Electricity-breathing bacteria! (Microbial fuel cells)

I made a 90-second “pod”cast of why microbial fuel cells work. I don’t yet know if This Week in Science is or was interested in playing it. [Update: this was featured in the November 6, 2007 broadcast! Hooray!] Either way, once I find a way to make it available without killing my bandwidth I shall. I’ll probably do more of them – if nothing else I obviously need the practice.

It was oddly difficult getting myself to actually talk to the microphone – more so than actually publically speaking to real people. I’m not sure why. It strikes me as something I’ll get over quickly once I’ve done it a few times, and my voice won’t sound quite so bland in the future.

In any case, microbial fuel cells are possibly the topic that got me really interested in a college education in applied biotechnology. I’ve been meaning to do a post on why they work for a while, so here’s one, in somewhat more detail than the 90-second audio version.

First, some quick review: We all remember that atoms are made of positively-charged protons, uncharged neutrons, and negatively-charged electrons, right? Protons and usually neutrons in the middle, and electrons hovering around. When atoms chemically react with each other, they’re really just having a fight over who gets to keep the electrons. When the reaction is over, some kinds of atoms or groups of atoms will have gained at least partial custody of electrons that used to belong to some of the other atoms or groups of atoms. The ability of a kind of atom to take electrons away from other atoms is called “electronegativity”. The second most electronegative element in the universe just happens to be a major part of our atmosphere – Oxygen.

As bacteria break down food molecules to get biological energy, there are electrons left over along the way. The bacterial cells have specific carrier molecules that take these extra electrons away, where they can be later dumped elsewhere into any of a variety of other useful biological reactions that need them. The one we’re concerned with today is called the Electron Transport Chain.

In many bacteria, and in the mitochondria of plants, fungi, and animals, the Electron Transport Chain regenerates a huge amount of a cell’s biochemical energy. The extra electrons get sucked into the beginning of this chemical chain, and as they are pulled along, the force of this pull drives a process which regenerates the cells’ main energy-carrying molecule, called ATP. This process is “respiration”, and it’s also exactly the reason you need to breathe oxygen. Humans need so much energy just to remain alive that we couldn’t survive without the huge amount of extra energy that respiration provides.

What drives this whole chain is some chemical at the other end pulling the electrons out. In aerobic organisms, this is oxygen. Some bacteria can use other chemicals, like nitrates, sulfates, and ferric iron (yes, there are bacteria that can breathe rust…) None of these chemicals provide quite as much energy as oxygen does, but it’s better than nothing and gives bacteria that could be damaged by oxygen something to breathe.

Normally, this last step happens inside the cell, but some bacteria have ways of extending this last step so that the final hand-off of the electrons happens outside itself. Some bacteria even make electrically-conducting biological “nano-wires” that this can happen through. Others make “shuttle” molecules that can pick up electrons, dissolve out of the cell, hand off the electrons somewhere outside, and then dissolve back into the cell to pick up more.

Now, we can make a microbial fuel cell. An electrode is put where the bacteria are growing – without oxygen – and a wire runs from this, out of the area where the bacteria are and to another electrode which is exposed to oxygen. It’s like an electric snorkel for bacteria. From the electrode and through the wire, the oxygen sucks electrons away from the bacteria. An electrical device stuck between the ends of the wire can use this energy exactly the same way that it could use the energy from electrons being sucked from one end of a battery to another.

Interestingly, the common “simple stain” Methylene Blue can also act as an artificial “shuttle” molecule. When reduced (carrying extra electrons) methylene blue is actually colorless, and I would swear I’ve seen protocols somewhere that use this to measure just how active a yeast culture is, and one of the demonstration microbial fuel cell setups actually uses a culture of yeast in methylene blue rather than a microbe that can naturally breath through electrodes.

By the way, if you thought you could tell a human from a realistic humanoid robot bent on world domination by the fact that only humans eat, I’ve got bad news for you. One interesting application of microbial fuel cells is Gastrobots. Literally, robots with digestive systems, where bacteria breaking down the contents of the “stomach” act as a microbial fuel cell to power the robot.

I hope you find this explanation useful and interesting. If you have (or even if you haven’t) please let me know. I can’t necessarily tell if I’m doing anybody any good without feedback!

Stir-fried random…

Just a few brief random comments for the moment:

  • Am I the only one who is already completely sick and tired of the word “spooky”?
  • I think I’ve figured out what Descartes’ problem is. He’s gone on this meditation where he’s convinced himself that as far as he knows, nothing exists…except for himself. I think what happens next is that he gets horribly lonely, so when he realizes that his thoughts also exist with him, that’s when he developed that unwholesome passion for them and inability to bear leaving them that I’d previously mentioned. “But what kind of thing am I? I’m a thing that thinks. A thinking thing is what I am. But what kind of thing is that? Oh, yeah, I already said, it’s a thinking thing. Did I mention I was a thinking thing that thinks thoughts?….”. Okay, Descartes, we got it the first time…
  • One of my fellow “college science bloggers whose obscurity currently keeps them low in the vote totals” actually has a pretty neat blog. The Biourbanist focusses on features and attributes of urban areas. Well worth adding to your RSS feeds, I think. After you’ve already voted for me, of course…
  • I am currently attempting to put together my first netcast, in which I shall attempt to crunch an explanation of why microbial fuel cells work, in a form hopefully comprehensible to anyone with a good junior-high-school science education (or a mediocre high-school education, which is probably sadly more common), that fits into 90 seconds. Wish me luck.

More to follow…
UPDATE: Got the “pod”/netcast done – a real blog post on the subject of Microbial Fuel Cells to go with it may be found here tomorrow (Tuesday, October 16th) sometime, so long as nothing unexpected happens…

Saturday Night Meta-Blogging

I’d like to thank (profusely and repeatedly) everyone who has been coming to check out my blog via the College Blogging Scholarship site. Whether you’re deciding to vote for me or not, I hope you’ll keep coming back.

First, the bad news. We all know how this goes: the finalists are announced, and they all go ask all their friends and associates to vote for them, and to pass on the message to go vote for them. When someone, given the “Go vote for Sean” (or whoever) message, lands on the voting page, they’re confronted by a list of 19 other blogs besides the one they went there to vote for. How many of them REALLY think “Gosh, I should probably check out all of the other blogs to see which one really deserves my vote!”. The vast majority, I’m sure we all realize, just click on whoever they came to vote for and leave. Obviously whoever has the largest network of affiliated bloggers to send out repeated “vote for my buddy” posts every day has a huge advantage. Checking my server logs, I see that this is definitely true. (I’m lookin’ at YOU, scienceblogs.com! Unfair? No, actually, not at all. Jealous? You bet your sweet bippy I’m jealous!)

Since the start of the competition, I’ve gotten a total of 465 unique visits referred from the scholarship finalists announcement page. At present, there are 19,740 votes that have been cast – so less than 2.5% of the voters have bothered to check out the other blogs.

Now, the good news: This is actually much higher than I would have guessed. Given the comparative obscurity of my blog (at the moment), the fact that more than one in fifty voters have at least looked over the first page of my blog makes me very happy. So, again, thanks, and I hope you’ll keep coming back.

In other news, Josh Charles of “[website]$sudo life” suggests that my post suggesting a “War on Science” could be a good thing for science would make a good basis for an entertaining spoof documentary. I’m kind of liking that idea…

Enough of that for now, though. I’ll be getting back to my science communication, amateur science, and microbiology roots in the next few posts. Stay tuned…

“Dog Philosophy”

But first, a quick request for information for anyone who happens by: where you live, what is the job market like for Ph.D. Geologists (with a background in stratigraphy, mining, and petroleum, among other things) and what kind of opportunities for non-medical biotechnology graduate programs are in your local colleges?

(And a quick side-question: is it obvious to most people that you get extra information if you hover over or click on things that look like this? I’ve never formally checked the usability of this trick for normal people…)

No login required to answer – they’ll appear as soon as I’ve filtered out any spam. Okay, on with the meat of this post.

In case anyone’s wondering what the “Epicanis” handle is all about: it’s a pun on the concept of “Dog Philosophy”, based on the name of the famous Greek philosopher “Epicurus” and the word “Canis”. Yes, I know, “Canis” is Latin, not Greek, but I figured “Epicanis” would be more a more recognizeable pun to most people than “Epicynus”.

Properly defining “Dog Philosophy” involves a joke which necessarily incorporates mild profanity and adult situations. In case any of the readers are of more delicate sensibilities, I present instead a more matter-of-fact (but sadly less funny) version.

Plato once famously wrote that dogs were philosophers. Like all philosophers that I know of, dogs consider the nature of what is real (metaphysics). To the dog, everything that exists external to the dog can be assigned to one of four categories:

  • Food
  • Toys
  • Companions
  • and

  • Everything Else, which is generally useless except as a surface for territory marking

You may wonder what that has to do with “Applied Empirical Naturalism” or science blogging.

The explanation is simple: science is fundamentally a method for examining the natural world to determine how and why it works. That’s what I like about science. One can find novel or unexpected applications of any system or thing by learning how and why they work, or in other words, it’s a method for, among other things, taking things from the “useless” category to one of the “useful” categories. Finding ways to make otherwise-useless things beneficially useful for people strikes me as a particularly rewarding purpose in life.

In addition to wanting to make the world a better place, I’m also kind to puppies and kittens and I think people should be nicer to one another.

(This shameless display of sympathy-solicitation has been brought to you by my participation in the following competition:)

Calling on the entire internet to study for a Philosophy exam…

I’ll probably do two posts today, but only because this one is a preview and an attempt to gather opinions…

I find writing helps me think, and we’ve got a Philosophy exam day after tomorrow. We’ve got a “study sheet” with eight concepts and fourteen potential essay questions that might come up on the exam. Is anyone reading this particularly interested in any of these (some of these have been addressed in earlier posts, but here’s the whole list)?

Concepts: “valid argument”, “sound argument”, “a priori knowledge”, “a posteriori knowledge”, “epistemology”, “metaphysics”, “doctrine of recollection”, “Objective reality/formal reality”

Essay topics (in short):

  • Describing the “Socratic Method” and contrasting it with the sophist method.
  • Discuss some of the Socratic philosophical positions that might call into question the view that what is right for a person is whatever that person believes is right.
  • Discuss Socrates’ claims that evil harms the evildoer and that “the unexamined life is not worth living”, and whether or not he’s justified in these claims
  • Critically discuss Socrates’ claim (at his trial) that he could not have been knowingly and willingly corrupting the youth
  • Discuss Socrates’ arguments in the “Apology” that death is not something to be feared
  • Discuss the “Learner’s Paradox” in the “Meno” (roughly – is it possible to “learn” something without being “taught”, and if so, how can this be?)
  • What was the point of the “slave boy” portion of the “Meno” (Socrates’ attempts to demonstrate that someone who doesn’t understand Geometry can come to have knowledge of geometry without being taught.)
  • Discuss Meno’s definition of “virtue” and Socrates’ objection to it
  • Discuss the distinction (in the “Meno”) between “true knowledge” and “opinion”, and how it relates to the question of whether virtue can be taught
  • From “Euthyphro”, discuss the issues around whether or not whether something is “pious” because The Gods love it, or if The Gods love it because it is “pious”.
  • State clearly and describe Descartes’ three levels of doubt
  • Discuss Descartes’ contention in the first Meditation that he cannot know if he is not dreaming
  • Discuss The Cogito (“I think, therefore I am” and why Descrates couldn’t instead say (for example) “I walk, therefore I am”
  • Discuss: “I hear a noise, I feel heat. These things are false since I am asleep. Yet I certainly do seem to see, hear, and feel warmth. This cannot be false.” (A quote from our translation of Descartes’…)

That’s what we’ve been given to work with. What are the odds that any of that is interesting to any of you? If so, please comment (no login required, and go ahead and put a fake email address in the comment form if it bothers you – as long as it doesn’t appear to be spam I’ll post it.). Come on, you’ll be doing me a favor, and you’ll automatically sound like a genius because we’re discussing philosophy.

Followup post later today…

I’m an interdisciplinary nerd…

Oh woe! Oh woe! Last time I checked, I was dead last on the College Scholarship Blogging Competition! Now, as I’ve mentioned elsewhere, I may be a cynic but I’m an optimistic cynic, and therefore think that surely if I apply my full mighty nerd powers, I can figure out what’s wrong and fix it.

First, what is going wrong? I thought for a while, and came up with a few possibilities:

  • God Hates Me
  • God Loves Me And Wants Me To Win, But Doesn’t Exist And Therefore This Does Me No Good
  • The divine is not involved, but there is a conspiracy against me involving the CIA, the NSA, the BATF, The Teamsters, the Freemasons, and the World Aquaculture Society.
  • Blatant Age Discrimination by a bunch of dang whippersnappers (Git offa my lawn!)
  • Dang Yankees
  • Perhaps my young and under-promoted blog is simply still too obscure and not well enough established to have the large number of connections that older and better-promoted blogs have, and this is just a natural result of more popular blogs being able to get their “vote for me” message out to more people, who in normal human fashion will vote for the blog with which they are most familiar.
  • (Hey, I was brainstorming, so even crazy ideas like this were considered…)
    Then, finally, the problem became obvious to me:

  • It’s too much work to vote for me

It’s so obvious now! Hordes of adoring fans are coming out of the metaphorical woodwork and going to vote for me, but are becoming exhausted and collapsing before they manage to find my name, buried near the bottom of the list of 20 different blogs!

You may not realize this, but I’m back in college because I’m trying to start my life over. I may be microbial biotechnology nerd now, but in my former life, I was a professional computer nerd for 15 years. My amazing nerd powers are therefore being applied to solve this problem (see also the update at the end of this post):

There – one click on the image (aw, look, Cornelia wants you to vote for me!), click the confirm button that pops up, and you’ve voted for me. Problem solved. When clicked and confirmed, a new window should open and you should see the current standings. If you are presented instead with an unselected voting form, it didn’t work – let me know. Now go! Go, my fellow conspirators! Click us to victory!

But seriously – I may yet come up with a way to gain enough fame quickly enough to have a shot at the prize, but right now I’m in last friggin’ place…which means I’m free! I don’t have to worry at all about “oh, gosh, if I do that will I lose the crucial vote that loses me first place?!?!?” and I can pretty much do whatever I want, within the bounds of ethics and legality, and it’ll make no difference. Therefore, I want to point something out:

Down at the bottom of this post, you’ll see that this material is made available under a Creative Commons license. Basically, as long as you’re not a commercial venture and you give me credit, you’re allowed to take and use anything you like from here, including taking and remixing the one-click-vote thing there. And, yes, this explicitly applies to my competition (Money or no money, I really can’t imagine how a scholarship competition counts as “commercial”.)

I’ll even go one step further: if any of you other finalists happen to see this and would like to use this on your own blog, let me know and I’ll send you a version tweaked to vote for you blog instead of mine. I’ll even try to help you get it inserted into your blog if you’d like. All I ask is that you mention and link to my blog somewhere in one of your posts. Obviously I’d prefer something complimentary, but if you feel the urge to write “I hear that Sean at The Big Room rapes puppies, eats babies, and has an unnatural attraction for maple trees”, what the heck, as long as there’s a link…

What do you think? Good idea? Bad idea?
UPDATE: Dangit, I swear it looked like it was working yesterday, but the ‘one-click’ (plus confirmation) thing is unexplainably just not getting the vote in, though everything else was working correctly. For the moment, I’ve reverted to having the link bring up the official vote form in a separate window…

The offer to make it available to others still stands, however, if anyone’s interested. I’ll re-revise this post if I figure out how to get it working.

Yatta! I Fail to Reject the Null-Scholarship!

(Oops, got so excited I got carried away with the title. Fixed now.)

I am thrilled to notice this morning that I am in the running for the College Blogging Scholarship, honestly, if this even attracts a larger population of active readers, I’ll consider that alone an excellent “Runner-Up” prize.

Not that the scholarship money wouldn’t be much appreciated…but more about that later.

For the moment though: Hello, current and new readers, to the internet’s self-proclaimed foremost authority on Expired JellO, among other things. I suppose that since I’m asking people to vote for me, I should probably give a quick description of myself and this blog. I’ll keep it short for the moment:

My actual name is Sean Clark; the explanation for the “Epicanis” handle deserves a post of its own. I am a “non-traditional” student at Idaho State University, working on finishing my long-overdue B.S. in Microbiology. This is actually the 5th college institution I’ve attended. It’s not that I’ve been kicked out of the others or anything, just that I keep having to move and start over. I’m finally in one place here long enough to actually finish the degree. Where I end up doing my graduate work depends on where (and if) we end up moving next year – I’ll post about this if anybody’s interested.

My primary interest is in “applied” microbiology, particularly non-medical biotechnology. I’ve been convinced for many years that non-medical applications of microbial biotechnology are underappreciated and somewhat neglected, and I’d rather people not have to get sick before they can benefit from whatever I might come up with…

Incidentally, Hillary Clinton agrees with me (“we should increase investments in non-health applications of bio-technology” – see paragraph 23). Whether that helps or harms my position no doubt depends on your political opinions, but still, I appreciate that someone with some kind of official authority agrees with me. And, hey, maybe this means I’ll be able to find a decent job during or after graduate school. Anybody think the Office of Technology Assessment will be hiring again soon?…

This blog itself is primarily concerned with sharing some of my education, and science in particular, as an exercise in communicating science. I, for one, think I’ve gotten better as the blog has progressed.

A couple of important points: This is a blog, not a magazine: participation is encouraged. If nothing else, the voting for the scholarship looks like it goes on for a couple of weeks, so if you are thinking to yourself “Gosh, I’d vote for you, but you don’t talk enough about X” or “you talk too much about Y” or “I hate the background color of the webpage” or whatever, now’s your chance to speak up. You do not need to be logged in to comment (but I do screen comments, so spammers: you’re wasting both your time and mine), so please do. Also consider subscribing to the RSS feed, found in the upper-right area of the page.

I try to update at least a couple of times each week, though lately I’ve managed to maintain a nearly daily pace. Participation helps here, as comments from readers helps me come up with additional topics to post on. I’m getting a lot of enjoyment out of blogging, so I’ll post as often as I reasonably can…

One last quick note on using this blog: I try to put title tags on most special bits of posts, like images and links. And…bits of text like this, which you might think of as “inline footnotes”. If you hover over anything with that thick-dotted-underline, you should see some additional information. As of a week or two ago, if you click on them, the entire extra text will pop up in a separate box where you can read it all, assuming you don’t have javascript turned off. I haven’t yet gotten around to going back and doing this to the previous bits like this, but I will eventually.

So, again, welcome. Comments, questions, and suggestions will help me improve the blog, and are therefore strongly encouraged. Oh, yes, and please vote for me. Otherwise, I’m going to have to resort to selling blood plasma and begging outside of scientific conferences. Thanks.

If I Win It…

One topic that I have hoped to emphasize much more on this blog is amateur science, and in particular (given my educational background) amateur Microbiology.

Don’t be dissuaded by my use of the word “amateur” here. I don’t mean “not really” science (i.e. the microbiological equivalent of the “baking soda volcano”). Rather, here I’m using “amateur” in its proper etymological sense – science done for the love of it. I don’t just mean my brief series of experiments on the toxicology of expired JellO®. I mean actual microbiology with potential practical application as well as educational value. Unfortunately, there are a few bits of equipment for this that I can’t reasonably cobble together out of spare parts or repurposed household appliances. A microscope, for instance. Or a dry-ice maker.

Being a full-time college student, I’m poor, and can’t afford a microscope. A decent ordinary “brightfield” microscope appears to cost about $400. Bonus materials like a “darkfield” condensor are extra, unless I think I can rig up an equivalent on my own. A nicer digital camera to take pictures with to share with you, my loyal reader(s) would add some more to the cost. Even in the case of equipment and supplies improvised from more ordinary and readily-available materials (pressure-cooker=”autoclave”), there is still a cost. Woe unto me, what shall I do?!?!?

For the moment, I shall revert to the time-honored traditions of “begging” and “hoping”…

You see, there appears to be a scholarship available for bloggers who are full-time college students. Why, what a coincidence! I blog…and I’m a full-time college student! What luck!

There appears to be a US$10,000 (that’s almost 10000 CANADIAN dollars!). It’s not explicitly stated but last year they also had $1,000 “runner-up” awards as well. Here, then, is my pledge to you all.

Should I be selected as a finalist for this scholarship competition, I will eat 2-year-old JellO! Furthermore, if I were to actually be selected to win a $1000 scholarship, I will buy a real microscope and be able to blog my microbiology experiments and studies much more vividly. I will also blog the design and construction of my own amateur microbiology lab, to the extent that I can afford. (Well, I was ALSO going to do this anyway, but with a scholarship I’d actually be able to start doing it…)

Were I to be selected to win the full $10,000 scholarship I propose to go absolutely Nucking Futs, with a microscope, a nice new digital camera, dry-ice maker and plenty of CO2, perhaps some dedicated hosting for this blog, and a complete collection of useful microbiology equipment (mostly improvised still, but that’s half of the education right there…). Furthermore, should my readers demand it, I might even be persuaded to drink a cup of fresh Lysogeny Broth!

Come on, who needs this money and attention more – me, or some wealthy (compared to me) graduate student over on scienceblogs.com? I bet none of them would eat 2-year-old JellO or drink E.coli Chow for it, would they?

10 Finalists are to be announced October 7th, from what I understand…wish me [good] luck…
UPDATE: I made the finals, though my fame doesn’t seem to be carrying along a rose-petal-strewn path to victory yet…

I am decidedly indecisive tonight…

I actually have a number of potential blog topics lined up now, and I can’t decide which one to do next…

  • “What I Learned In School Today: The Burden of Proof for Art Historians is Somewhat Lower Than For ‘Harder’ Sciences” (the Trois-Freres “Sorcerer”)
  • “What I Learned In School Today: Socrates Thinks Shrinkwrap Licenses Are Good”
  • Why Microbial Fuel Cells Work
  • What’s a “Clone Library”? (Since I’m trying to make one…)
  • Attention Getting Ploys for the Blog (should I promise to drink a cup of Lysogeny Broth when I reach 25 active readers?…)
  • What I Would Do With “Blogging Scholarship” Money (build my Hillbilly Biotech lab, and blog it.)
  • The Office of Technology Assessment Is Not Enough (arrogant amateur policy thoughts…)
  • What I Want To Be When I “Grow Up” (in a manner of speaking).

Anything in particular interest any of you regular or accidental (e.g. Google®-searchers) readers?

And, yes, I will follow through with the Lime JellO® experiment as promised soon.