Feedback Solicitation – Page 5 – The Big Room (and the little things in it)

I Hate You, Carl Zimmer!

Carl Zimmer wrote a book. Of course, that’s no reason to hate him, and I don’t hate him for that.

His book is all about Escherichia coli (“E.coli”). The friggin’ “Microsoft” of the biotech world. Accursed E. coli, hogging up all the print space and protocol development and sucking up electricity for -80�F freezers. I mean, come on people! You could be doing transformation of B. subtilis and related organisms instead, which form nice, sturdy endospores which you can dry out and keep in an any cool, dry place, no -80�F freezer needed! Or you could use something like Agrobacterium tumefaciens, and as a bonus be able to then transfer your nice transformed genes into plants, too! But NOOOOOooo….it’s always “E.coli, E.coli, E.coli.” DAMN YOU, E.COLI!

Of course, none of that is Carl Zimmer’s fault, either, so this is also no reason to hate him.

Now, if his book was lousy, that MIGHT be a reason to hate him, but as far as I can tell there’s no reason to think the book is lousy, so this is no reason to hate him either. In fact, that’s kind of the problem.

No, the reason I Hate Carl Zimmer is that he’s written a book about friggin’, stage-hogging E.coli…and I want it. (Well, a copy of it anyway.) It sounds like a very interesting book. I feel like a Republican who wants a copy of “The Audacity of Hope”. Or a Democrat who wants to plan a vacation to visit the George W. Bush Presidential Library. The cognitive dissonance torments me, and it’s all Carl Zimmer’s fault! CURSE YOU CARL ZIMMER!

Okay, got that out of my system. A review might follow eventually if I manage to get a copy of the book. Meanwhile, for a change of pace, anybody want to hear about my Asterisk setup? Or should I just get back to the fermentation stuff?

P.S. Here’s a bit of trivia for you: “Frig” is apparently an old-English word meaning “to wiggle”…

Boosting fermentation with science

All right then – I’ve got five pounds of honey, a pound of frozen cherries, packets of a couple of different dried yeasts, miscellaneous other potential additives, two 2-gallon polyethylene terphthalate fermentation containers with screw-top lids and spigots, several feet of aquarium airline tubing and connectors, silicone sealant, and miscellaneous kitchen gadgets (including a hydrometer). Now it’s time to discuss what I’m about to do and fish for comments and criticisms before I jump into it.

My goal here with this brewing experiment is a quick primary fermentation. And to compare the results from two different yeast strains, uh, TWO goals, quick fermentation, yeast strain comparison, and fermentation container design. THREE goals. Quick fermentation, comparing yeast strains, fermentation container design, and to try to keep the yeast cultures from dying off too quickly during the fermentation. FOUR. Four goals…

In this post, I’ll stick to talking about what I’m putting into the brew and how I hypothesize my additives and process with speed the fermentation along and help keep a large portion of the yeast viable during the primary fermentation.

Actually, the health of the yeast populations and the speed of fermentation are overlapping goals; more cells remaining alive and healthy means more cells simultaneously chewing up sugars and spitting out ethanol for me, resulting (hypothetically) in faster primary fermentation. In this experiment, I’m going to be focussing on nutrients and spices that are reported to benefit yeast activity. Here’s the process I am currently planning to follow, focussing primarily on the fermentation-boosting parts:

I’ll boil the 5 pounds of honey with enough tap-water to make about 2 gallons of must, adding the frozen cherries sometime after the boil gets underway.

Fermentation boost: we have water so hard that you have to wear a helmet to take a shower. (Joke stolen from my Environnmental Chemistry instructor, so you can blame Dr. Rosentreter for that one). It’s loaded with Mg²⁺ and Ca²⁺, which seem to be able to help the yeast to produce ethanol faster and survive higher ethanol concentrations better[1][2] as well as just being general nutrients[4].

Two approximately �-liter amounts of the must will be put into clean glass quart bottles and used to develop the initial yeast culture for pitching (each one for a different strain of yeast).

Fermentation Boost: Growing up a large population of yeast from the dried yeast packets before pitching will give me a faster start. In addition, the large headspace and the use of cloth rather than plastic or rubber covering of the top will allow oxygen to get into the starter culture, helping it to develop more quickly and in a more healthy fashion (i.e. a larger proportion of healthy, viable cells).

Nitrogen supplementation: Capsules of arginine picked up cheap at a certain big-box store will be added to the yeast starter.

Fermentation Boost: “Free Amino Nitrogen” is perhaps the most important bulk nutrient for yeast, and arginine seems to be the preferred amino acid source[3][4], presumably because it contains the most reduced nitrogen per molecule of the amino acids. I actually want to try to develop a process for using dry milk powder instead, but achieving sufficient hydrolysis of the milk proteins looks like it’s going to take some development on my part. For now I’ll “cheat” and use arginine instead.

Vitamin supplementation: A single well-crushed children’s “chewable vitamin” (“Flintstones�” or generic equivalent) will be added to each starter culture as well.

Fermentation Boost: Pantothenic Acid (Vitamin B5), Inositol, trace minerals, and small amounts of additional potassium and phosphate to supply vital nutrients to the yeast culture.[4]

Fermentation-enhancing spices: I will be adding ground ginger and cinnamon (actually cassia) to the must near the end of the boil.

Fermentation Boost: In addition to providing what I think will be excellent complementary flavors to the final product, it appears that even fairly large amounts of these two spices – among others – provide a boost to fermentation rate[5] (via Shirley O. Corriher’s “Cookwise”[6]) of Saccharomyces cerevisiae cultures. If I’m doing the conversions appropriately, the peak fermentation boost for ginger works out to something like 3 tbsp of ground ginger per liter, or something like (very roughly) 10 tablespoons per gallon. I don’t plan to add quite so much, but a couple of tablespoons of each spice in the two-gallon batch ought to provide some nice flavor while still hopefully providing a boost to the fermentation rate as well.

“Cinnamon”: In the US, the rust-colored stuff labelled “Cinnamon” is not, actually, cinnamon. True cinnamon (Cinnamomum zeylanicum)is actually tan in color. What you get in the US when you buy a bottle of “Ground Cinnamon” actually comes from Cassia (Cinnamomum aromaticum), a closely related plant. Realistically, as far as I have been able to find out so far, there’s not likely to be a huge difference in the active components or flavor. While I haven’t yet gotten my hands on a copy of the old article from Cereal Chemistry[5] mentioned above, I’d give good odds that the “cinnamon” used in the study was also actually cassia anyway.

There’s one more thing that I hypothesize would help promote my goals that could be added: small amounts of oxygen[7] (say, less than 13% O₂, or very roughly speaking, around half of the normal atmospheric concentration or less). However, I’m still trying to work out an easy way to achieve this automatically and am not yet ready to try it. Besides, this is already pretty poorly-designed for a “real” scientific experiment as it is, considering the number of variables that are really contained in this brewing process. Really, my hypothesis here boils down to a relatively vague “This mixture and process will allow me to finish the primary fermentation within a day or two of pitching”. If I ever have opportunity to do serious experimentation on this, it’ll require setting up a large number of separate fermentation reactions to assess the effects varying each individual set of hypothetically-fermentation-boosting additives. Hopefully one of these days things will settle down enough to let me try it.

If anybody sees anything stupid (or just interesting) up there, please say something…

[1] Dombek KM, Ingram LO: “Magnesium limitation and its role in apparent toxicity of ethanol during yeast fermentation.”; Appl Environ Microbiol. 1986 Nov;52(5):975-81.
[2] Nabais RC, S�-Correia I, Viegas CA, Novais JM: “Influence of Calcium Ion on Ethanol Tolerance of Saccharomyces bayanus and Alcoholic Fermentation by Yeasts.”; Appl Environ Microbiol. 1988 Oct;54(10):2439-2446.
[3] Carter BL, Halvorson HO: “Periodic changes in rate of amino acid uptake during yeast cell cycle.”; J Cell Biol. 1973 Aug;58(2):401-9.
[4] Fugelsang KC, Edwards CG: “Wine Microbiology – Practical Applications and Procedures (2nd Ed.)”; 2007; Springer Science+Business Media LLC; pp 15-18
[5] Wright WJ, Bice CW, Fogelberg JM: “The Effect of Spices on Yeast Fermentation.”; Cereal Chemistry. 1954 Mar;Vol.31,100-112
[6] Corriher, SO: “Cookwise”; 1997; HarperCollins Publishers, inc; New York; pp 69-70
[7] Nagodawithana TW, Castellano C, Steinkraus KH: “Effect of dissolved oxygen, temperature, initial cell count, and sugar concentration on the viability of Saccharomyces cerevisiae in rapid fermentations.”; Appl Microbiol. 1974 Sep;28(3):383-91.

Well, a PHP example, anyway

Once I dove in and started messing around, I only had to fix two typos as the example I was working on seems to work correctly, at least to the extent that I’ve tested it. I now have what appears to be a working example of Geostring parsing in PHP. In this case, the example reads my feed from the Twitter website, sifts out any geostring tags it finds, then generates Google Maps links for each one found. As I write this, there are two geostring tags on that page, representing places (and times)
that I have actually been, and it seems to work.

You can take a look at the source code for the example here, or see it in action here.

Feel free to grab a copy to play with if you’d like (or write one yourself that isn’t so messy – hey, as someone who doesn’t consider himself a professional “coder”, I’m just happy that it did exactly what I wanted it to do on the first try…). You should only need to worry about two things – changing the $text_to_read, and whether or not your web server (or CLI) has fopen wrappers turned on so the script can read another web page if you use a web page as your text to parse rather than a local file.

Since generating a geostring tag is trivial, I didn’t bother trying to incorporate that into this example. If you want one, then here:

<?php
//generate a geostr tag with the most typical information only
//point not part of a track nor including heading or angle
$lat=44.027168;
$lon=-111.297892;
$elev=”1711.9m”; //could leave off the “m” and treat as float, since it defaults to “meters”
$timestamp=”20071125T123438-06″; //6 hours behind UTC

print(“geostr:$lat,$lon,$elev:$timestamp:geostr”);
//”full” version: print(“geostr:$lat,$lon,$elev:$timestamp,:,:geostr”);
//completely unnecessary, but legal
?>

As always, comments and suggestions are welcome.

Off-Topic and Back Again: “Framing”, Cluetrain Manifesto, and Twitter

“Framing” came up briefly on one of the other small independent blogs I follow. I’d link
to the post but it’s gone now. I sincerely hope its disappearance wasn’t related to the
comment I posted there, unless it was just because of the “don’t feed the trolls” part
of it – (in which case excuse me for a moment while I tell myself what an amazing fountain of useful advice I am and feel self-important for about 15 seconds before I return to reality…). I’m guessing the poster just decided he didn’t want to keep the post, but I won’t let that spoil my brief ego-feeding fantasy.

For those lucky enough to have missed it so far, here’s my flippant and extremely brief explanation
of my understanding of how the “framing” thing goes. An assistant professor of communications popped up among the science blogs one day with what seemed to begin as a couple of reminders of the obvious (mainly because it occasionally seems that people have forgotten). Namely, that if you want someone to understand what you are trying to communicate (particularly scientific matters) and agree with you, you are more likely to succeed if you can connect what you are discussing to something that your audience already cares about, and you are less likely to succeed if you are, shall we say, unfriendly to them as you present your subject.

From there, “framing” seems to have grown into something resembling the brand-name of some kind of mass-market “self-help” product line. Its primary proponent, from the distant vantage point
whence I occasionally catch a glimpse of the fight, starts to seem like the angry Vice President
of Communications for Science, Incorporated, whose office issues angry memos denouncing the insubordinate “screechy monkeys” who insist on deviating from the approved language when discussing Science, inc.’s Mission Statement. The fact that science is a conversation among people rather than a corporation probably explains why so much of the response has been not “Oh, crap, we’d better behave ourselves or we’ll get in trouble” but “Who the heck are you, and why are you telling me what I can say and how I can say it?” And that, I think, is all that needs to be said. (Anyone who stumbles upon my little blog and disagrees is welcome to say so in the comments.)

Actually, it’s probably more than needs to be said, and I wouldn’t have even mentioned it except that the problem of trying to apply this sort of approved “Command and Control” approach towards information in the Internet age reminded me of something else. The Cluetrain Manifesto was published so long ago that AOL was still considered a successful and valuable operation at the time, but it still seems to be relevant. (It’s free to read online – follow the link if you want to do so). At its core, its central thesis seems to be that the “Command and Control” approach to information management favored by corporate and political entities is effectively broken now because of the two-way communication made possible by a ubiquitous internet. In essence, “the market” is no longer made of isolated individuals passively sitting on the couch “consuming” the approved messages coming through the television, but a “conversation” of people who can easily tell the difference between a corporate “message” and authentic human conversation. Here’s a relevant passage:

“Imagine for a moment: millions of people sitting in their shuttered homes at night, bathed in that ghostly blue television aura. They’re passive, yeah, but more than that: they’re isolated from each other.

Now imagine another magic wire strung from house to house, hooking all these poor bastards up. They’re still watching the same old crap. Then, during the touching love scene, some joker lobs an off-color aside � and everybody hears it. Whoa! What was that? People are rolling on the floor laughing. And it begins to happen so often, it gets abbreviated: ROTFL. The audience is suddenly connected to itself.

What was once The Show, the hypnotic focus and tee-vee advertising carrier wave, becomes in the context of the Internet a sort of reverse new-media McGuffin � an excuse to get together rather than an excuse not to. Think of Joel and the ‘bots on Mystery Science Theater 3000. The point is not to watch the film, but to outdo each other making fun of it.”

And now we take one more step towards on-topicness: One current set of the metaphorical wires described in that passage is Twitter. Twitter is kind of like a gigantic lobby at a convention center where some huge conference is going on. The lobby is filled with little groups of people, collectively discussing with each other all kinds of little thoughts, observations, and events that each person there has encountered. You can easily wander through the lobby for hours, listening for snippets of conversation that relate to your own interests. Sure, being a raw, natural, human group of discussions, Sturgeon’s Law (“90% of Everything is Crap”) is in full effect. Sometimes literally: On Twitter I’m tracking the term “brewing” which seems to pick up more metaphorical uses of the word than literal, and a recent “Tweet” that popped up was somebody commenting that someone didn’t flush the toilet (“someone’s been brewing up a 1.6 gallon pot of turd stew.”)

So why bother? Because I think the remaining 10% has enough potential value to make a little mental effort to sift through the stream of messages worthwhile. I’d say a majority of the messages that come through are related to events happening at that moment. Twitter seems to get a lot of use as a back-channel for commenting on things that are happening, and for organizing impromptu gatherings. In most of these cases I think location information would be a valuable addition…and now I’m finally back to “on-topic”.

I think it’d be exceedingly nifty to be able to map Twitter messages in real-time. If I can convince anyone else that my “geostrings” idea is worth using, and then if one were to track “geostr”, any “tweet” with parseable location information would automatically show up. A small tag containing precise location information would make it possible for your computer automatically alert you if a post was describing something anywhere near where you are. Imagine the case of posts like “I just saw a tornado touch down, I’m going down to the basement now”. Or, say, “Who wants to try the homebrew I’m about to bottle?”

Example code in Javascript and PHP for picking out and parsing geostrings to follow soon. I’ll get back to yeast again shortly thereafter, though.

What really counts as a “microbe”?

Just a brief pre-post before the main one I’ve got brewing now (which will be posted either later today or tomorrow).

A tapeworm: Since when does 30-36 feet long count as 'micro'??? Microbiology is the dominating topic of this particular blog, but I don’t think I’ve ever addressed what I consider to really count as “micro”biology. This isn’t necessarily an obvious topic. My old “Microbiology” book from 8 years ago, plus the textbook from last year’s “Pathogenic Microbiology” class both contained large sections discussing organisms that are visible without a microscope. Heck, the “Pathogenic Microbiology” text even had a whole section on spider and insect bites. And, tapeworms? Since when is “over 30 feet long” considered “micro”? As I like to say: It’s time for Microbiology to grow up and move out of Medicine’s basement.

So: Here are the defining features of what I consider to be a “microbe”, at least for purposes of what I tend to discuss here on the blog:

Obvious: the organism cannot be effectively examined visually without a microscope and individual organisms can virtually never be observed by the “naked eye”.
In nature, a full normal population of a microbe can and will develop from a single live cell, and isolated individual cells are reasonably commonly observed.
Microbes do not “eat”.

It’s that last point that prompted me to write this post, mainly because it’s such an important part of why microbes work and how they affect their surroundings, especially when it comes to food microbes. What I mean by “do not eat” is that they are incapable of taking large (microbially speaking) chunks of material into themselves to use. Any cell nutrient for a microbe must be in the form of small molecules, like sugars, small peptides or individual amino acids, and so on that can be easily transported across the cell membranes and through the cell wall where applicable.

The importance of this is that for a microbe to grow on a complicated substance like meat or bread (for example), they have to excrete specialized enzymes that break down the substances out in the environment into simpler components like sugars or small peptides. If a microbe cannot secrete a protein-digesting “protease” enzyme, it can be surrounded by tasty, nutritious proteins and still starve to death. If a microbe can’t secrete an amylase (starch-digesting) enzyme, it doesn’t matter that starch is made of nice yummy glucose molecules because they’re all wadded up into long chains of starch that the microbe can’t get at.

And that, finally, is important because it brings up issues of growing multiple microbes together to accomplish something. Sake, for example, is made by fermenting rice, but rice is made primarily of starch. Saccharomyces yeasts don’t make amylases, so in order to make sake, you also have to add a kind of mold (Aspergillus oryzae, one of the types of white-mold-with-little-black-specks that you may see growing on the bread you’ve left sitting around for too long). A. oryzae is also a microbe and therefore can’t “eat”, but it does produce amylase. Since the amylase is breaking down the starches outside of the cells, this means the released glucose is also available for the yeast to use.

Admittedly, my definition above isn’t perfect. On the one hand, it leaves out protozoa (like amoebae and the well-known Paramecium, both of which actually do take in “chunks” of food, but both of which most people would normally consider to be “microbes”. It also leaves IN things like mushrooms, which are not usually thought of as being “microbes” by people who aren’t microbiologists. And, of course, it leaves me with no excuse not to go and learn something about eukaryotic (“plant”) algae (as opposed to bacteria-algae, a.k.a. cyanobacteria) and diatoms. Suggestions for updating my definition may be left in the comments…

Just something that came up while I was assembling what will be the next post. Stay tuned.

New toy: “Twitter”

Wow – Celestron takes 8 business days to get me a terse one-sentence answer. BigC responds in one. Impressive. Apparently their technical people are all at trade-shows at the moment so my bigger question will have to wait until they get back, but they were at least able to answer my question about their “tabletop” digital microscopes magnification (answer: the “600x” really is optical magnification, not digital.)

Another digital microscopy WANT/DO NOT WANT post to follow when I get the followup reply. Meanwhile, after hearing about it on the This Week in Tech podcast for a while, I finally talked myself into signing up to play with the coincidentally named Twitter system.

It sounds like a really stupid idea – “Oh, goodie, now I can broadcast ‘text messages’ no more than 140 characters long about trivial events in my life to the whole world! Whoopee!” “Wow! I can find out when random strangers are drinking coffee AS IT HAPPENS!” Thrills! Excitement! Adventure!…

On the other hand, having the messaging system watch for particular words might be a handy way of monitoring current events. Plus, there seems to be a lot of potential for fun, off-the-wall uses, even if many of them are kind of silly.

It DOES seem like kind of an ideal context to play with that “geostrings” concept I’ve been toying with. A terse, easily-machine-parsed format for geotag data that can fit into a “twitter” post and still leave room for a sentence or two to go with the geographic information seems like it might be useful. If you’re so incredibly bored that you want to see some examples, you can check out my own Twitter posts, several of which I’ve embedded geostrings into.

Do Not Want: Celestron LDM

Back in Idaho for the moment. The trip was somewhat exhausting, but I thought a followup to The previous post on the Celestron LDM microscope was in order, as I finally got a reply back after almost two weeks.

(20080329:Quick update. I am surprised to see this post is getting more interest that I’d anticipated. I’ve added a brief summary to the end of the post to help clarify my opinion since it seems people may be interested.)

I had asked them if it was possible to replace the objective lenses (so as to be able to use an oil-immersion lens to get 1000X magnification – pretty much a neccessity for decent bacteriological work – such as examining yogurt cultures) and whether the camera could be swapped for a regular eyepiece. Larger yeast cells used in brewing might be okay in 400X, but even there it’d be nice to be able to zoom in adequately to get better detail – like watching conjugation or budding of yeast cells.

The answer:

“The answer is ‘no’ to both because of the sizes, etc. are specific to this unit.”
Email ID: ZZR-372549
Department: Technical Support
Priority:
Status: Closed

I guess there’s no point in asking about getting a darkfield condenser for it. On the plus side, they did actually give me a reply at least.

I’ve got to say I’m seriously disappointed that Celestron has evidently intentionally engineered this microscope product (and their other offerings as well, perhaps?) to Not Play Well With Others. Why else go to the trouble and additional expense of coming up with your own special specifications for the parts when standard parts are readily available?

This seems especially absurd in a product aimed at science enthusiasts, who strike me as very likely to be strongly aligned with the “Maker” attitude…at least if they’re any good at Science Enthusiasm. I think the “if you can’t open it, you don’t own it” concept meshes very well with the investigative attitude necessary for science. So, we want “internet”, and they give us “AOL” instead. A sad, sad fate for an otherwise great concept, and on this basis I must render a verdict of “Do Not Want”.

Find me a version of this product – from any vendor – which can accept standard oculars and objective lenses and I’ll sell blood plasma and beg on the street to raise money for it. (If nothing else, it’d give me an excuse to finally start up the “science begging” blog-post series I’ve been threatening for a while now…) Of course, it’d be nice to have an ordinary “real” microscope, too…this blog still doesn’t have enough pictures.
(P.S. Dear Celestron: although I doubt anybody at Celestron will ever even see my obscure blog, and in that respect my previous post’s comment about sending me one to review was just a joke. Despite this, I was sincere, so in the unlikely event that someone out there sees this post and has the authority and inclination to do so, feel free to send me one to review anyway. And a pony.)

SUMMARY (in my opinion):
Good:

VERY nice, highly desirable concept overall.
Self-contained, platform-neutral design, should work with anything that can support SD cards or USB Storage devices.
Potentially a nice field microscope? (Probably not hard to hack together a battery pack that could be used in place of the AC adapter)

Bad:

Does NOT appear suitable for bacteriological or similarly high-magnification applications
Non-standard components prevent upgrades.
Non-standard components mean vendor lock-in problems (if Celestron gets tired of making replacement parts and some kid scratches your objective lenses or cracks the viewscreen, you’re out of luck.)
Digital camera and viewscreen appear to be integral, so if the camera or viewscreen dies I’d guess the whole device becomes a useless lump.

My recommendations for Celestron or other microscope manufacturers (should any of them care about the opinion of some nerd on some obscure blog like this one):

Please, please use standard parts wherever possible – it makes your device a much safer bet for anyone thinking ahead towards possible upgrades or replacement parts.
Don’t ignore bacteriological applications.
Easily replaceable parts make for graceful failures. For example, if the camera on this model could be swapped for an ordinary ocular, the microscope would at least be usable while the camera portion was being sent in for repair or replacement.

All this week: A topic important to secular and religious people alike

It’s not midnight here yet, I’m still on time!

Hello, “Just Science 2008” subscribers and everyone else. My life is insane at the moment but dagnabbit I’m going to do my best to get at least one post up on a scientific topic every day from today (Monday, February 4th) until Friday…

Today’s post is in the form of a gedanken experiment.

First, imagine the following:

Some “entities” existing somewhere

It doesn’t matter what “entities” you are imagining, whether they are products in a market setting, or data structures in a computer program, or topics of discussion on a news broadcast. All that matters is that there can be more than one of them.

A mechanism by which these “entities” are copied (and, optionally, also sometimes removed)

Products are manufactured or recalled, data structures can be copied or deleted, additional news anchors can be added to comment on a topic or conversely may shut up about them…

At least one mechanism by which changes can occur between or during copies

Product designs can be changed, a computer program may consult a “random number” generator and use it to make small changes in the data structure, scriptwriters may alter the news anchor’s teleprompter messages…

Some aspect of the “entities” that affects the rate at which they are copied (and/or, optionally, removed).

Demand by buyers in the market results in ramping-up of production, a computer program may perform some test or comparison of a data structure and use the result to determine how many copies of it to make (or whether or not to delete it), news topics that result in more people watching are repeated more often while those that people tune out from are dropped from the schedule…

What happens to this group of “entities” over time should be obvious. Taking the example of products in a market, producers introduce a variety of products (the group of “entities” in this example) and buyers examine their characteristics and, based on which ones they like, buy some of them. The producers observe which kinds of products are selling more and make more of those, while reducing or outright eliminating the production of those that aren’t selling well. Over time, a few of the kinds of products in this group which best fit the preferences of the buyers and the ability of the producers to make them. These products will dominate the market until the preferences of the buyers or the ability of the producers to produce them change [example: a shortage in the price of a particular material needed for a popular product].

You have most likely observed this process in the “news topic” context yourself, where it tends to happen much faster as “cheap and easy” news stories are happily picked up by news agencies to broadcast until people get sick of them and tune out.

This can all, hopefully, be understood as a purely logical outcome – a conclusion that universally and necessarily follows from the premises given. There should be nothing supernatural or even surprising here, is there?

So, now that you understand why and how evolution works (if you didn’t before), I can move on. (Incidentally, the part of the example above that describes a computerized system is actually referred to as a “genetic algorithm”.)

My purpose in starting with this is because it really and truly is fundamental to the topic that I expect to spend most of this week posting about, and which has been of vital importance to human culture and intellectual development for thousands of years. This most important subject involves such notable figures as Charles Darwin,St. Thomas Aquinas, Noted American Science-guy Benjamin Franklin, New England Puritan Cotton Mather and Quaker William Penn ,Hardcore Catholics like Pope John Paul II, Hardcore Athiests like PZ Myers, even famous religious figures like Jesus.

I refer, of course, to wine (and beer and other examples of ethanol production).

Okay, here’s the background: I just graduated with my B.S. in Microbiology, and I’ve got this whole “Hillbilly Biotech”/”Do-it-yourself”/”Practical Science” kind of thing going on in my interests. That being the case, I wondered what it would take to isolate, culture, and maintain my own yeast (and bacteria – more on that later) stocks from the environment rather than buying “canned” cultures – or at least play with the “canned” yeasts to create my own stocks. As I was poking around, though, I kept running into the same attitudes – namely that it’s “too hard” to do this, and although there are a number of people who advocate re-culturing canned commercial yeasts for a short time to save money, none of them think it’s feasible to do this for more than a couple of generations, at which point we are assured that you have to go buy it again or else “mutations” will inevitably appear and scary and mysterious “off-flavors” will result and the brewing police will come and throw you in jail for deviating from the archetype of whatever pre-defined style of wine or beer you’re trying to make. Or something like that. In any case, it’s because of this fear of “mutations” that I am starting out with this “evolution”-related post: in biological evolution, various forms of alterations in the genetic material are the “changes before or during copying” in the gedanken experiment above.

I didn’t buy it when people were telling me that it was “too hard” to learn how my computer works so that I could run Linux and should instead leave deciding what my computer should do to the “professionals”, and I’m not buying the same argument about commercial yeasts, either. If I felt that way, I might as well leave the rest of the complex technology of brewing to the “professionals” too, and consign myself to “Lite Beer” and “Thunderbird” for the rest of my life.

I’ve been spending much of the last few weeks perusing books, online articles, and scientific papers on subjects related to brewing in general and brewing yeasts in particular, and this should form the bulk of this week’s post topics, of not well beyond this week. Tomorrow I intend to start in on the actual process of culturing yeasts. Meanwhile, feel free to correct my no doubt horribly over-simplified explanation of evolutionary processes in the comments.

My “geostrings” project, and coming attractions.

I have set up a more permanent “page” for my little project to come up with a way to embed geotags in things like mp3, Ogg/Vorbis, video files, text documents, image formats besides jpeg and geotiff, and so forth. I’ve got a definition of the format and a basic description of the parsing algorithm for it up there. Embedding and decoding examples and so forth will follow soon, though I’m hoping for some comments before I get too deep into assuming I’ve got the format finalized.

Meanwhile, I’ve signed on for this year’s “Just Science” week, So I’ve got to get together at least five consecutive days worth of science posts to go up between February 4th and 8th. Fortunately, I think I can fill most if not all of it with the brewing science (and yeast culture in particular) stuff I’ve been researching. I’d still like to get my hands on at least one more paper which isn’t readily available to me (Gasent-Ram�rez JM, Castrej�n F, Querol A, Ram�n D, Ben�tez T.: “Genomic stability of Saccharomyces cerevisiae baker’s yeasts.”; Syst Appl Microbiol. 1999 Sep;22(3):329-40.) but I do have quite a few others that I’m going over.

“Hooray for me!” or “About Friggin’ Time!”, take your pick.

Still traveling, and don’t currently have an especially good internet connection at the moment. More substantial posts to follow soon, honest, but in the meantime:

The college doesn’t wipe out my login for another week or so, so I was able to get logged into my registration information page. It still lists me as a “Senior”. However, when I have it generate an “Unofficial Transcript” for me, it now has the following before the class listings:

Degree: ASSOCIATE OF SCIENCE CORE CERTIFIED Date: 12/21/07
Major: CHEMISTRY
Degree: BACHELOR OF SCIENCE Date: 12/21/07
Major: MICROBIOLOGY

They don’t send out the actual pieces of paper until March, I’m told, so this is the first direct confirmation I’ve seen that indeed I can not continue to use “but I’m just an undergrad” as a disclaimer in my posts.

Now I just need to decide whether to go to grad school or just become a wealthy industrialist…