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, 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.

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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.

7 thoughts on “Firefox, Bacteria-snot, and job-hunting geologist”

  1. Looks like those are all the same entry-level “soil scientist” jobs at the USDA, unfortunately (~$30000/year is kinda feeble, especially for living in California…). Thanks for the pointer to the site though. I’m pretty sure is one of the sites she’s been watching for jobs, but if not I’ll point it out.

  2. Best of luck for you both. Hopefully something will turn up soon!

    On a completely different issue, based on your writing on geotagging, I’m purchasing a GPS system to do geotagging with. We’re spending a lot more time in the field collecting samples and I want to be able to pinpoint EXACTLY where we got them. It seems that geotagging is perfect for this, and along with photographing site details I can then return to those pictures to jog my memory as to physical conditions, positioning, and the like. Plus, I think it’ll look good in presentations.

    So … thanks!

  3. Wait…something I wrote here influenced someone in a positive way?

    Hang on a moment, I need to bask in my own ego for a moment….AHHHHHhhhhh…

    Okay, that’s better.

    One of the potential uses of that “geostring” tag format I’ve been playing with would be as part of a Genbank “source” field.

    Something I’ve thought would be interesting to do in my Copious Free Time™ (and my vast wealth, of course) would be to build up a geotagged culture collection of (in my case) food- and industrially-relevant microbes (i.e. lactic acid bacteria, Gluconobacter and Acetobacter strains, yeasts, mold varieties that produce useful products, etc.), and then try to correlate phenotypic variations with geographical information (typical soil types, presence of types of industrial activity, precipitation, etc.) to guide future bioprospecting site choices.

    More abstractly, comparing genetic identity between related organisms to geography to try to infer the path of their spread and mechanisms of transport.

    (If anyone reading this wants to hire me as a graduate student so I can dive into this, let me know…)

  4. I think that geotagging would be an integral part of all environmental metagenomic studies. I know that the TerraGenome project is currently underway, and we’re doing a fair degree of bacterial fingerprinting (T-RFLP) in our neck of the woods. Geotagging these fingerprints would be a great idea … especially if we plan to revisit them years down the line to look at any significant changes.

    Is there one particular GPS system you would recommend above all others?

  5. The question of which GPS I’d want is still a little up in the air since Magellan abandoned me. However, if someone told me they where going to buy me a new GPS, but I had to pick it NOW and agree to use it for the next year or longer, there are a couple of Garmin handhelds that I’d pick from.

    The eTrex “Legend” and “Vista” HCx and a few others support recording your track to a microSD card inside the unit. In these, it’s actually saving the tracks in the well-supported “GPX” format rather than Garmin’s proprietary (but documented!) format, so it should be easy to pull the card out and read the track into a wide variety of useful software. Since Garmin’s own format is documented and also pretty widely supported as a result this isn’t that big of a deal, but it saves you a conversion step.

    The only warning I’d give for Garmin units is that they have a seriously annoying but relatively minor (so long as you know about it) malfeature. Garmin units have the option to save a copy of the current track, which is nice if you’re visiting several places and only want to record where you walk around and not have one continuous track between everywhere. The problem is that Garmin assumes that the only reason you want to save a copy is to trace the path later, so they throw out all the timestamps, making the copies useless for geolocation later on. I really wish they’d fix that. Not a huge problem, since normally by default you just work with the current track in memory, which still has the timestamps.

    A less-versatile possibility would be a GPS and Camera containing smartphone. My wife’s G1 phone automagically geotags photos taken with it. The downside is that as far as I can tell you can’t really use it for mapping otherwise unless you’re in an area where the cellphone can download map tiles from Google (i.e. I don’t know of any offline map applications, currently). Still, if you take a picture of something you want to geolocate, you can extract the location from the EXIF headers of the picture later. (Another downside of this option is that the battery life of a dedicated handheld GPS is much better than that of a smartphone…)

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