Author: Epicanis

The Author is (currently) an autodidactic student of Industrial and Environmental microbiology, who is sick of people assuming all microbiology should be medical in nature, and who would really like to be allowed to go to graduate school one of these days now that he's finished his BS in Microbiology (with a bonus AS in Chemistry). He also enjoys exploring the Big Room (the one with the really high blue ceiling and big light that tracks from one side to the other every day) and looking at its contents from unusual mental angles.

Audio Geotagging

“Kimz” left a comment over on the blog’s “About” page asking about geotagging of audio, so I thought that was a good excuse to bring the topic back up here.

Even less audio (and video, for that matter) seems to get geotagged than pictures, and even though more photographs online are getting geotagged automatically by GPS-enabled cellphones, I still usually find myself disappointed when running into an interesting photograph online and finding no geographical information in the image telling me where it was taken.

I have the same kind of interest in where and when other kinds of recordings where made. I’m obviously not the only one: the Freesound project also maintains geographical information for some of the sound recordings they have. Unfortunately, although they SAY the recordings are “geotagged”, they’re not.

Take this sound sample, for example. It’s an ambient sound recording from the lobby of an office building, and you can see there’s a link to a map showing where the recording was made. However…if you download the actual sound file, there is not geographical information associated with it at all. If the geographical information is not directly attached to the file, then I maintain that the file is not “geotagged”.

Let’s say I work in a very odd sort of specialty shop, and one day we get in a shipment of inflatable anatomically-correct life-sized Australian marsupials. “Price-tag these”, the boss says. The next day someone asks the boss how much the inflatable male platypodes are. “Isn’t it on the price tag?” “There is no price tag!” When the boss chews me out for not doing my job, do you think I’ll be forgiven when I explain that I DID “price-tag” the shipment…by writing down the prices in a little notebook that I keep with me, separate from the actual merchandise? No? Then keeping the geographical information in a little database that your server keeps separate from the files isn’t “geotagging”, either!

I suppose the bizarre and potentially incoherent nature of that example just serves to illustrate my over-busy and under-slept state. Anyway, the point is that I’d love to see more geographically-tagged media, and I open up this post for discussion of how, why, and what to geotag. (For “How”, I would offer up my “Geostrings” proposal as an option that ought to be feasible for virtually any kind of media…).

If they ever get around to publishing “Mapping Hacks, Volume 2”, what should the entry for geotagging media include?

YOU DANG KIDS GET OFFA MY LAWN!

Looks like the truckloads of candy-seeking larvae are done finally. Wretched little urchins now get driven from block to block rather than walking the neighborhood like we did.

(It doesn’t actually bother me as much as that makes it sound, I just like having an excuse to say “wretched little urchins”…which reminds me – I have only about a month to get a cheerful flashing “Bah! Humbug!” sign built…)

The only thing that really annoyed me is the fact that having to be ready to be interrupted by another horde of costumed consumers meant I couldn’t really spend any of the evening getting into anything requiring any real attention…which means the 113g of CaCl2.2H2O I’ve got sitting here now to go with my Xanthan Gum has been left neglected, and I still don’t know if I can make Xanthan Gum gel into beads the way you can with sodium alginate. I figure it must be possible, given that both Xanthan gum and Alginate (among others) were all formed into little “bio-booger” beads using the same kind of process in the paper I discussed in Episode 2 of my little audio oggcast. Perhaps I’ll have time to find out tomorrow.

For now, it’s time for bed. Daylight Losings Time starts tonight, so if the critters allow me to actually sleep, I ought to be well rested to attempt some serious lake-spanking in the morning – there’s supposedly a resort on the shore of the lake that has a sushi bar, and the idea of being able to paddle out for sushi amuses me. It looks like it’s at least 9-10 miles away, though, so it’ll be a long trip if I attempt it. Hopefully I’ll have time left after that.

Also, the developer of the libdmtx datamatrix barcode encoder and decoder software posted a recent comment on my previous post about the software and its potential uses – looks like some interesting projects going on there, including one intended to generate ID cards that only legitimate authorities could read (so as to prevent identity theft).

P.S. Anybody know how to build a really good (but simple) ozone generator for sanitization purposes? Or the effective pore sizes of commonly available materials like plastic wrap? Or if a corporate entity can be a shareholder/partner in a Limited Liability Company?

Don’t forget to feed and walk your mitochondria

Yes, I’m still here – though I don’t know if any of YOU are.

The pay at my job is somewhat low for the skillset it requires, but makes up for that by having a very reasonable workload, a pleasant work environment, and certain perks – like access to the electronic journals that my employer subscribes to. I added an RSS feed from pubmed intended to cover my main interests – basically edible and industrial microbiology and biotechnology. Every day, a list of 300-600 or so new scientific articles pops up in my feedreader and I scan through the titles looking for anything interesting to me. Unintentionally, my selection appears to also result in quite a bit of diabetes, obesity, and sports medicine research. Lately I’ve taken a moderate interest in our own most blatantly bacterial components, the mitochondria.

Mitochondria are kind of like a nearly 2-billion-year-long case of typhus (or Rocky Mountain Spotted Fever, if you prefer). After infecting our ancestors (and now us) for so long, they’ve been reduced to dependency on living in our cells. Perhaps a bit like the progression from wolves to Chinese Crested dogs. On the other hand, having thoroughly domesticated them, we get a lot of use out of them, and couldn’t live without them. Their ability to harness the electron-sucking power of oxygen means we get almost 20 times more energy out of our food than we otherwise would, which is a good thing since biologically speaking, keeping the hideously complicated mess of biochemistry that makes up a human body takes a ridiculous amount of biochemical energy compared to that of normal organisms (i.e. prokaryotes).

Lately in the stream of new publications I’ve been seeing a number of papers suggesting that a lack of proper mitochondrial activity might be related to obesity and related problems (e.g. “metabolic syndrome”, type 2 diabetes and insulin resistance, obesity-related “inflammation”, and so on) and even some age-related problems, both physical and mental. There is some seriously interesting research going on into treatments to potentially stimulate mitochondrial activity and whether this might help solve a number of health problems.

So…take good care of your mitochondria. For the past couple of weeks I’ve been trying to pay special attention to properly feeding my mitochondria and making sure I take them for regular walks (and paddling trips and so on). It could, of course, be purely psychosomatic, but right now I feel better than James Brown…

There’s a fair amount of rational skepticism over using drugs or nutritional supplements to stimulate mitochondria, but here’s a tip that I suspect everyone’s doctor would accept: make sure you take your mitochondria for regular walks. Frequent exercise (particularly endurance exercise) seems to be a scientifically well-accepted way to induce production of more mitochondria.

But now I have to go to bed. My main complaint with work these days is that it eats up essentially my entire day, leaving me with just enough time for some household chores between getting up in the morning and going to bed in the evening. Not their fault I live almost and hour and a half from work, though (and at least the commute is through relatively low-traffic and scenic terrain.). Still, it makes it hard to get blog posts and podcasts done (episode 4, on the subject of “heat-fixing” of bacteria for microscopy – particularly Mycobacterium tuberculosis – will be out as soon as I can manage. Still pondering the subject of Episode 5. I’m saving the “Two Mass Spectrometers, High Performance Liquid Chromatography, and a Female Donkey” episode for later when I manage to surpass the “nearly 3” listeners that I seem to be stuck at…)

Stir-Fried Stochasticity Ep 03:”Los Angeles Sucks (water and oil)”…FINALLY up.

FINALLY – with this vowel movement I am finally over this recent bout of podstipation. Episode 3 of “Stir-Fried Stochasticity” is finally up. Today’s paper is:
Bowden G, Thatcher W, Stein RS, Hudnut KW, Peltzer G:”Tectonic Contraction across Los Angeles after Removal of Groundwater Pumping Effects”; Nature; 2001; vol412; pp812-815

You can download the audio or (if you are using a modern-enough web browser) listen to this episode directly here.

I would appreciate any constructive or at least mildly witty feedback – please post in the comments below…

A brief update, and reminder that I’m a nerd

Episode 3 of Stir-Fried Stochasticity should be recorded and posted soon. I had intended to already have it done, but there have been…delays.

Most recently, I had to drop everything to take care of the Minister of Chew Toys here at the Asylum for the Sufficiently Nerdy. Cornelia (our dog) came down with her yearly sudden, extremely messy and foul diarrhea problem. After getting everything cleaned up, and a minimally-sleepful night of getting up every few hours to let the dog out to emit foul-smelling material and disgusting noises, I got her to the vet this morning and came home with the usual prescription for Metronidazole and special food. If previous years are any indication, the symptoms should be over by tomorrow.

But, even as I cleaned up the foul mess that greeted me when I got home, I found myself wondering if the slimy material was being produced by the dog or by whatever bug was causing the problem. (Despite Episode 2 of Stir-Fried Stochasticity, I did NOT consider whether it could be turned into a food additive. Even I have my limits…) And, despite not wanting to be anywhere near the mess I was cleaning up, I found myself wishing I had a microscope.

And today, after the veterinarian took a look at a sample under the microscope (and let me look, too), and tentatively suggested infection by a Clostridium species, I found myself wondering if I could culture it, obtain a phage that infects the bacteria, generate and purify a huge sample of the phage, and then save it for next year and try to treat next year’s infection with it. And then I thought “Hey, if I also culture up the bacteria to produce a lot of that slimy stuff and purify it, I could make phage-containing bio-boogers (go back and listen to Episode 2 if you don’t know what I mean), which might be more effective!” on the assumption that the bacteria in question might also secrete enzymes to break down the slime that I’m assuming it produces, thus releasing the phage particles around the active bacteria…

And then I realized that if I had the equipment, supplies, and time right now (and was willing to deal with regulatory hassles involved in playing with Potentially Pathogenic Prokaryotes), I would probably actually follow through and try it…though I’d probably stop short of actually testing the treatment on my dog without some sort of approval and supervision by a real veterinarian. Even now I’m resisting a slight urge to save a small dried “sample” (which would be full of long-lasting spores that I would probably be able to culture later). Don’t worry, it’s not hard to resist…the point is just that the temptation is actually there.

I still insist I have very little interest in medical microbiology. Really.

At least I know that between potential digestive-tract phage therapy and probiotics, if we end up having to move back to where we came from for financial reasons, I might at least find a place for some graduate work in the “poop group” (sic) at my previous college institution if nothing else.

Meanwhile – Episode 3 is coming, honest! It’s a rather small but dense paper that explains how it’s hard to monitor the tectonic activity in the Los Angeles area because Los Angeles sucks. I’m hoping to get that recorded this weekend, along with the other mass of stuff I need to do.

Any words of encouragement and/or threats (or other useful or allegedly witty comments) may be posted below in the meantime.

Stir-Fried Stochasticity Ep.02: “Bio-Boogers”

A slime-covered handAfter getting rave reviews from nearly four people for the pilot episode, I’m hopeful that Episode Two will be even better. (Seriously – I don’t think more than a handful of people even know this project is going on, but the few people who’ve listened and commented to me have been very encouraging so far.)

You can listen to and/or download the audio directly in either they shiny new spiffy Ogg Vorbis format or old-school .mp3 by clicking right here. As always, I’d very much appreciate comments, suggestions, questions, amusing limericks on the subject of the paper, etc. – feel free to post below, or you can email me at the usual location: epicanis+sf at bigroom.org.

This episode’s paper: Ding WK,Shah NP:”Effect of Various Encapsulating Materials on the Stability of Probiotic Bacteria”;2009;J. Food Sci.;vol.74 #2; pp M100-M107. Enjoy!

“Stir-Fried Stochasticity” podcast: pilot episode

Cornelia the Happy Mutt with a tennis ballI’m still not sure I know why I have a desire to push recordings of my voice onto a more or less innocent worldwide population, but I do. And now I have a real theme to wrap an attempt at a podcast (or as I prefer – “oggcast”) around: scientific papers.

I finally got annoyed at press-release-based science stories one too many times, and thought to myself “why does almost nobody who does these stories at least cite the dang thing so I can go look it up and see what’s really in it, if they can’t be bothered to actually read and report on it themselves rather than just the press-release?” The story in question was the recent one about how babies understand dog-language (or something like that). Since I consider the dog to be a philosophical role-model, I wanted to read the actual paper and see if it was as silly as the headlines made it sound or (as I suspected) less flashy but more solid…but even “Science Daily” didn’t cite it.

Finally talking myself out of putting off doing audio recording, I tracked down the original paper, read it, and whipped out a rough show discussing what I found in the paper. I had fun doing it, so I’d like to turn it into a series.

I’ve put up a utilitarian page at http://bigroom.org/stirfry with both a built-in <audio> tag interface and direct-download links for both Ogg Vorbis and MP3 versions.

I’m still deciding exactly how I’m going to decide on the papers to cover – should I pick obscure, forgotten ones that almost nobody else would ever read again without me stumbling on them and talking about them? Classic papers? Papers related to recent news stories like this one? All of the above? Depending on how long I end up trying to make the episodes, perhaps starting with some kind of scientific question and then reporting on a selection of papers I dig up to address the question, or just a selection of papers on the same subject? I’ve already gotten a request for an episode on the theme of prokaryotic extracellular polysaccharides…

The rate at which I can convince myself to try to crank these out (and improve their quality) is directly proportional to how much interest there might be out there in them, so please don’t hesitate to let me know if you think this might be interesting. Please don’t let me slack off! Also, feel free to correct me if I’m wrong about anything I mention in the show or the attached show notes.

If you don’t want to comment here, you can also email me at epicanis at bigroom.org.

Thank you, and good night…

A secret message for Climate-Change Skeptics..

SHHH!!!! SHUT UP, MAN, YOU’RE GONNA BLOW IT!

I admittedly find it hard to believe that such a large proportion of scientists in any field, climatology or otherwise, could actually conspire together to pull off this big of a hoax when at all other times they’re competing pretty intensely against each other for funding and attention. Heck, most of us mad scientistsGrumpy Visionaries would sooner give up our armies of Atomic Robot Zombie Clones than share credit for scientific discoveries. Still, I’m just cynical enough to believe that it’s not impossible. Even if it’s true, though, I don’t care, because something unprecedented and very important is happening right now, and there’s no way we’re likely to ever have this chance again.

To those of you reading this who agree that something needs to be done about “Climydia” (hat-tip – if I wore a hat – to Justin Jackson of “This Week in Science” for this neologism; a combination of “Climate” and “Chlamydia”, if it’s not obvious, making “Global Warming” a metaphorical embarassing but hopefully curable disease): you can stop reading now. I agree. We must do something about it. It is a serious problem and needs to be corrected. The rest of this post is for those who don’t agree. Go ahead and click away. Don’t worry, I’ll tell the deniers off, you can go read something else now. Thanks.

Continue reading A secret message for Climate-Change Skeptics..

Firefox, Bacteria-snot, and job-hunting geologist

'Human Statue' striking a constipated looking pose on a toiletI have to say that suffering through periods of chronic blogstipation is seriously annoying.

There have been a number of things I’ve been wanting to post about, but I’ve been way too loaded down to have time to sit down and compose them. Therefore, lest anyone think I’ve abandoned bigroom.org, I’ll throw a few of them out here in shortened form.

First, a public service announcement: HTML 5 is not just about turning the internet into Television. I keep seeing articles about “HTML5” and they all seem to focus obsessively on the <video> tag. The same is largely true of articles about the recent Firefox 3.5 browser release, since arguably the biggest feature of the new version is HTML5 support. Although there are quite a few other new features, the main one I wanted to briefly remind everyone of is that there’s also an <audio> tag. I think audio is important, because it’s a lot simpler for people to generate audio for the web than to produce a video. Also, the “Vorbis” audio codec is a definite step up in quality from the de-facto “mp3” codec. The latest Opera, Google Chrome, and Firefox browsers all support the <audio> tag with “Ogg Vorbis” files. Apple’s Safari browser doesn’t by default, but that’s easily fixed. If you install the free QuickTime® component from Xiph, it teaches QuickTime about Ogg files, allowing you to watch and listen to the same HTML5 audio and video that everyone else (aside from Microsoft, as usual) can. It apparently also allows you to create Ogg files through QuickTime, so you can make your own content available for everyone else to watch and hear if you want to.

If you’ve seen some of my earlier map-and-pictures posts, you can probably guess that I’m also interested in the new geolocation feature. As far as I can tell, it’s currently natively implemented in the new Firefox, but will be showing up in Safari, Opera, and Chrome (at least) in the relatively near future. My only real complaint is that right now Firefox can only get the location through Google via your current IP address, and that isn’t at all accurate (when it works correctly, the precision is limited to “somewhere around this city” – when it doesn’t, where it thinks you are depends entirely on whose network your internet connection comes from.) It’s still baffling to me why they didn’t include a simple “manual entry” option for geolocation. Anyway, I’ve not had time to dig into this either, so enough said about that. For now.

And now a question of science and microbiology enthusiasts who may read this – I may soon, finally, be able to buy a microscope. Any recommendations on where to get one? The only “special” features that I really want (and can afford) would be a sufficiently bright light source and ability to swap in a darkfield condenser from time to time.

Penultimately, bacteria snot Xanthan Gum is hereby declared my Favorite Food Additive of the Month. It turned out to do exactly what I hoped it would do in the lemon-ginger ice cream I made a couple of weeks ago. I must play with this delightful edible substance more.

Finally, is anybody in California actually hiring geologists? As if marrying me wasn’t proof enough of insanity, my wife really wants to move back there. We can’t stay here forever in Southeast Texas on just my meager academic staff salary, as nice as the job itself is, and although for months she’s been firing off applications all over the country (and even a few beyond the borders) she’d really prefer to take her geophysics experience and PhD in Geology from UC Davis back to California. Although I’m personally a bit less enthusiastic about the idea, the possibility of getting into UC Davis’ Fermentation Science or Food Science graduate programs definitely has some appeal. Plus, I’d be able to listen to This Week In Science live while it’s being broadcast.

Lava is Nifty, but Magellan Sucks

A dead Magellan brand handheld GPS unitHere’s a “fun” situation: take a Magellan-brand handheld GPS unit with a fresh set of batteries on a 10.2 mile hike over very rough terrain, having it record a track so that all the nifty pictures along the hike can be geolocated and the course of the hike can be mapped later. After a gruelling 8 hour trek, tell the unit to save the track. Watch in annoyance as it starts to save to the SD card but then complains “EXTREME LOW BATTERY – SHUTTING DOWN”. Just annoyance though – previously when it has done this, it merely loses the last few minutes of track, and you can replace the batteries and re-do the save when it comes back up. Except this time, when instead of actually shutting down it seems to restart itself, complain of “Low Battery”. Then throw a fit when I try to get the fool thing to actually shut down, watching in horror as it restarts itself a few times for no good reason before finally fading out. Then replacing the batteries and screaming with rage when the unit comes up with the same messages it did the very first time it was turned on…despite somehow keeping a copy of the “Points of Interest” I’d put in before, it has eaten not only all of my settings but also the entire friggin’ 10.2 mile track that I was trying to save!

Moral of the story: Magellan=BAD. Between bad hardware and the newer participant-hostile “consume-only” business model they’ve gone to with the new “Triton” line, I wouldn’t recommend them to anyone (unless I secretly hated them.)

So, I decided to cool off by hacking into NASA’s feed to one of the Mars Rovers to have it take a picture for me:

You don’t believe that I really hacked NASA, do you…well, read on:

Continue reading Lava is Nifty, but Magellan Sucks