#1 on Google!

Over on scienceblogs.com’s The World’s Fair, the author has started an amusing meme.

It goes like this: the challenge is to find 5 sets of search terms for which your own blog or site is the #1 hit on a Google search. Note that it is acceptable to quote specific phrases but of course it’s more impressive if you don’t. Here are 8 that (as I type this) for which this blog is the #1 hit (links go to the blog address that is the hit):

There was at least one other which I’m having trouble remembering at the moment. Perhaps I’ll update later if I remember what it was.

Why I blog, and the Office of Technology Assessment

Via a post over on the Aetiology blog (and Retrospectacle) I happened upon a survey being taking about science blogging. It got me thinking a bit about why I’m doing this – aside from the masses of screaming groupies I have.

Aside from just being fun (I like to write), I set up this particular blog as a platform to practice communicating scientific topics. It’s a skill that really isn’t emphasized much in science education as far as I can tell, and regardless of where my career may go post-graduation I’m sure the ability to articulate scientific and technical topics will be beneficial to me.

In fact, I can see two different ways I could go with a career either during or after graduate school. Obviously, I could end up employed in a capacity where I’m officially “doing” science, which could be anything from “brewmeister” to curating a culture collection to academic research to being a lab grunt. I could also see myself pursuing a policy or science communication angle as well, though. This could be anything from Public Relations for a scientific or technical company to science writing to scientific advising…which brings me to the Office of Technology Assessment.

A post over on the “Denialism Blog” at Scienceblogs.com started a stream of “Bring Back the Office of Technology Assessment” posts around the net. Now, there’s a dream job. I would personally love to have a job like that. Make an enjoyable and comfortable living from whatever talent I have at explaining scientific and technical topics, and directly and substantially benefit my country in the process? Sign me up! Of course, even when the OTA existed, it only had a small number of employees, and presumably they were all Ph.D.’s with backgrounds in science and public policy, so the odds of me getting hired there (specifically) would probably be comparatively slim. Still, I can dream, and perhaps if we luck out and my wife (a Ph.D. Geologist with a background in borehole geophysics, petroleum geology, nuclear technology, and a variety of other areas – anybody out on the East coast in the general vicinity of Washington D.C. need anybody like that?…) and I have the opportunity to move somewhere with a good “science and public policy” graduate program I may have a chance.

My personal desires aside, though, if there’s one thing the people who are supposed to be running the country seem to really need, it’s rational science and technology information. Since the disbanding of the OTA we’ve had the DMCA and the costly and predictable abuses it brought (such as DMCA lawsuits over printer ink refills and replacement garage door openers), minimally-rational ideological fights over things like stem cell research and global climate change, panic and “security theater” over technically improbable-to-impossible “terrorist” threats (like the possibility that a terrorist will blow up a plane with a “liquid bomb” made of 4 ounces of baby food and shampoo, or “blow up” the fuel depot at JFK airport) (Mayor Bloomberg’s “STFU and GBTW” style of response to the panic was a glimmer of hope to me that there was some rationality left among my fellow human beings). I will refrain from picking on Ted “Series of Tubes” Stevens other than bringing this up as another example of lack of good information for policy-setting congresspeople. All this disruptive fuss, largely over ignorance and misunderstanding, which seems to be what the Office of Technology Assessment was intended to address. I would definitely agree that the OTA or something like it appears to be an urgent need – either that or Congress should quit playing around and just formally declare a science-boosting ‘War on Science’.

There are one or two things I’d like to figure out before I start mailing letters to congresspeople and presidential candidates though. For one thing – what would be the difference between the Congressional Research Service’s Resources, Science, and Industry division? Would one group be more focussed on specific policy implications while the other deals with “just the facts”? Also, the one legitimate-sounding complaint that I’ve seen in some of the newspaper articles on the subject is that it would often take longer to come out with a report on a subject than congress had (that is, congress would end up having to assemble a law and vote on it before the reports were completed). Should whatever takes the place of the OTA be re-designed to focus more on getting quicker answers? Like, maybe, hiring a bunch more people? Including, say, eager and capable grad-students…Okay, I’ll stop begging…

More to follow on this and related topics. Oh, and advice on successfully pursuing this type of career would be welcome.

What I Learned In School Today: Mortals have Limits, and Socrates was a jerk…

…Or at least, Plato’s accounts of him make him seem that way.

We’ve been reading (as English translations) accounts of Socrates’ trial and related occurrences as written by Plato. It started off with a possibly fictional dialog before Socrates’ trial, between Socrates and some guy named Euthyphro, who is some kind of priest.

In short, they get to talking about why they are there at the court, and it turns out Euthyphro is there to accuse his own father, who has apparently committed what we in the modern U.S. would call “manslaughter”. Euthyphro’s father had caught a murderer, then tied him up and thrown him in a ditch while he sent somebody to ask the authorities what to do with the murderer. While waiting for the messenger to return with the answer, the murderer in the ditch had evidently died. Euthyphro says “piety” demands that his father be tried for the death of the murderer but complains that everybody seems to think that hauling his own father to court for this is “impious”. And now you have the backstory for a long, involved, and ultimately unsettled discussion of just what the heck “piety” is supposed to be.

That’s where you notice that Socrates is a sarcastic butthead who thinks he’s on a mission from The Gods™ to prove that everybody is an ignorant fool. He puts on a snide show, pretending that he expects Euthyphro will reveal The Secret Of What Piety Really Is (Socrates claims that the knowledge will be useful for his own defense at his trial later) all the while busily demonstrating that Euthyphro really can’t answer the question.

The argument dances around various definitions. They more or less settle on the notion that “piety” is something that pleases all of the Gods (and impiety, by definition, displeases all of the gods), and that The Gods™ love an action because it is pious rather than something being pious because it is loved by The Gods™. (There’s a bit of virtually Dickensian pedantry there involving whether something is “being carried” because someone is carrying it or whether people carry things because they are “being carried” objects.) I guess that means nobody would have to worry that they’d wake up one morning and discover that The Gods had decided on a whim that “piety” would mean raping puppies and eating babies for the next few days. They manage to reach agreement that “piety” has something to do with being like a servant to the gods, but are completely unable to come up with a definitive test by which they could define any particular act as “pious” or “impious”.

Euthyphro finally says (more or less) that hey, he’d love to stay and go around and around and around and around with this annoying little brain-teaser but he’s got places to be and things to do, and the dialog ends with one last bit of Socratic Sarcasm as Socrates wails about how he was hoping to show up at his trial and tell everyone he’d learned the divine secret of Piety from Euthyphro and therefore wouldn’t be accidentally corrupting the youth with his lack of wisdom any more…

I have to wonder if Plato wrote this dialog so that readers would understand why so many Athenians wanted to get rid of him…

Of course, as an (self-proclaimed) Applied Empirical Naturalist, I think they’re whole problem is that the knowledge they were seeking was defined as something that would only necessarily exist in the minds of Supernatural entities – since “piety” and “impiety” are entirely defined in terms of what The Gods thought, it’s not clear that “piety” can be known outside of the Invisible Giant People Up On Mount Olympus. Of course for Euthyphro, being a professional priest, admitting that he doesn’t – and maybe can’t – know what “piety” actually is and that he really has no clue what’s going on in the minds of The Gods would be a definite Career-Limiting Move, and Socrates doesn’t seem (to me) to actually care what it means so long as he gets to prove that Euthyphro doesn’t know either, so it’s no wonder that this point doesn’t come up.

I wasn’t kidding about the “thinks he’s on a mission from The Gods™ to prove that everybody is an ignorant fool” comment, either. In his “Apologia” (defense speech during his trial), as reported by Plato, Socrates describes how someone once went to the Oracle at Delphi and asked if anyone was wiser than Socrates, and was told that, no, nobody was wiser than Socrates. Socrates says he interprets this to mean that nobody is really wise and that this answer from the Oracle (who is just passing on messages from the Gods, after all) means that he has a sacred duty to go around demonstrating this fact – which is the basis of the famous “Nobody knows anything, but I know I don’t know anything, so I know more than anybody else” flippant description of this argument.

Oh, and one unrelated odd fact – the introduction to the translation says that Socrates is about 70 years old during this trial, but at one point during Socrates’ rambling defense speech he explains that he wouldn’t want to be like other people who show up in court and have their kids plead with the jury for mercy in order to avoid punishment. Socrates says he had three kids – one adolescent and two who are “children”. So, wait, he’s wandering around Athens unmarried, when suddenly he runs into some woman willing to shack up with a penniless, irritating old guy who’s almost sixty and they have three kids who survive childhood? What?

This isn’t discussed at all, really, it just struck me as a really odd circumstance…

The Oldest Microbiology Book (that I own)

There’s this thing that some people do sometimes when they’ve been getting stressed out in one place for a while. I hadn’t done it in so long I can’t remember what it’s called. You know, where you Leave the area and then avoid it for a while. Oh, yes, that was it, a vacate-shun. Anyway, leaving the barren desert wastelands of the West, we headed east, and spent a few days admiring the area around the midpoint of the Appalachian Trail: Harpers Ferry, West Virginia. (Incidentally, I can recommend the “Angler’s Inn” Bed and Breakfast there, and the whole time there was incredibly delightful to me. I think I’d love to move to the area.).

I was delighted to note that there was an Old Book store in downtown Harpers Ferry. One thing about the Eastern US is that it’s been settled by book-using folks for somewhat longer than the West, so it would seem it’s easier to find really good Old Books. I found a publication of a 110-year-old microbiology book. In decent condition, for just over $20, no less! Not counting the (relatively modern) reprint of Micrographia that I picked up from a library sale, this makes it by far the oldest microbiology book I own now.

Oh, yes, did I mention I collect (casually) old books, especially old scientific and technical books?

The book in question, published in 1897, is “Story of Germ Life”, by Herbert William Conn. Not to be confused with Harold Joel Conn of “Conn’s Biological Stains” fame…who happens to be Herbert William Conn’s son. To be fair, the book *I* got was actually a republication from 1904, so only 103 years old…back when copyright was more rational (7 years, plus an OPTIONAL 7 more years. Thus explaining why my republication came out 7 years after the original.) It appears to have been part of a series called “Library of Valuable Knowledge”. The bookstore actually had another one of them, but I don’t remember what its topic was.

“Story of Germ Life” isn’t really a textbook so much as an overview of the subject of “Bacteriology” (as understood in 1897) for otherwise well-educated people – the kind of book I don’t think there are enough of these days. The Gutenbook project actually has a plain-text-only version of the book online here. Of course, then you miss out on the incredibly useful illustrations:

I always find it interesting to go back and see the earlier stages of scientific endeavors – especially as relates to my own interests. There always seem to be things that have since been forgotten, abandoned, or glossed over in them.

H.W. Conn seems to have been most interested in dairy microbiology, so there is a substantial amount of space devoted to it. I’ve heard of “blue milk” before (Yummy!….Pseudomonas?), but not Red or Yellow milk. He also devotes space to discussing the affect of “good” (and “bad”) bacterial cultures on butter, cream, and cheeses. I’m not even sure if butter is cultured these days, or if they just churn it up fresh and cold with minimal growth. Dangit, one of these days we’re just going to have to move somewhere we can keep a miniature dairy cow so I can do some experimentation with real unpasteurized fresh milk.

Bacterial phylogeny was so quaint back then. “Bacillus acidi lacti.” Ha! I love it. Interestingly, the term “Schizomycete” doesn’t appear anywhere in the text, though that may or may not be because it was considered unnecessarily technical for the intended audience. There’s actually very little about microbiological methods, too, which is the one major disappointment for me. Oh well, still interesting stuff. Conn actually mentions various “industrial” uses of bacteria including retting (soaking fibrous plants like flax or hemp so that bacteria eat the softer plant material to free the fibers), the roles of different bacterial cultures in curing tobacco, and even a fermentation in the production of opium (which Conn says is fungal rather than bacterial).

Also, much to my approval, the first 2/3 of the book is not about diseases. Only the last third of the book discusses “parasitic bacteria” and related topics. I leave you with this quote from the book’s 1897 Preface, which I think is still relevant today:

“Few people who read could be found to-day who have not some little idea of these organisms and their relation to disease. It is, however, unfortunately a fact that it is only their relation to disease which has been impressed upon the public. The very word bacteria, or microbe, conveys to most people an idea of evil. The last few years have above all things emphasized the importance of these organisms in many relations entirely independent of disease, but this side of the subject has not yet attracted very general attention, nor does it yet appeal to the reader with any special force. It is the purpose of the following pages to give a brief outline of our knowledge of bacteria and their importance in the world, including not only their well-known agency in causing disease, but their even greater importance as agents in other natural phenomena. It is hoped that the result may be to show that these organisms are to be regarded not primarily in the light of enemies, but as friends, and thus to correct some of the very general but erroneous idea concerning their relation to our life.” — April 1, 1897

The Gram Stain Post to End All Gram Stain Posts

Gram stain, Gram stain, Gram stain! Bah. I think it’s time Microbiology grew up and moved out of Medicine’s basement.

Sure, the Gram stain[1] has its uses, but the procedure is grossly over-hyped. “[…]the most important stain in microbiology[…]”[2]! “[…]it is almost essential in identifying an unknown bacterium to know first whether it is Gram-positive or Gram-negative.”![3] “The Gram Stain reaction is an especially useful differentiating characteristic.[…]The Gram reaction turns out to be a property of fundamental importance for classifying bacteria phylogenetically as well as taxonomically.”![4] “[…]differentiates bacteria into two fundamental varieties of cells.”![5] “The Key to Microbiology“![6] [emphasis added…]

Bah! Sure, the Gram stain has its uses, but the hype it gets (even 125 years after its invention) is ridiculous. It’s worse than Harry Potter!

You really want to know what the Gram reaction tells you? Really? Okay, here it is:

A “Gram Positive” reaction tells you that your cells have relatively thick and intact cell walls

A “Gram Negative” reaction tells you that they don’t.

That’s it. That’s about all you can reliably infer from the Gram stain.

Previously, I put up a post describing what was my understanding of the conventional view of why the Gram stain works. Today, I’ll give you a much more detailed – and more correct – explanation of why it works as well as what its real significance is to identification of microbes. But first, a brief one-paragraph rant on why I think the Gram stain has such a hold on microbiology teaching.

I blame the fact that microbiology education is still largely in the shadow of medical technology education. When you artificially exclude the 99+% of organisms that aren’t associated with human diseases, the tiny number left do, indeed, seem to largely separate into two phylogenetic categories. Judging by what I’ve encountered thus far, it seems you get a lot of Proteobacteria (especially ?-Proteobacteria, like E.coli), which are “Gram-negative”. You also get a lot of Firmicutes (Bacillus, Streptococcus, Staphylococcus, etc.), and a couple of scattered Actinobacteria (Mycobacterium, for tuberculosis and leprosy, Corynebacterium for diptheria…). Both of these are considered “Gram-positive” (although if you use the standard procedure these days, the Mycobacteria may show no reaction at all). That’s, what, 3 phyla out of about 25 eubacterial and archael phyla? If we throw in Syphilis and Chlamydia, that’s still only 20% or so of the currently recognized prokaryotic phyla. If your microbiology classes assume everybody is training to be a medical technologist or clinical microbiologist, then the Gram stain becomes inflated in importance.

Enough of that – here’s a quick review of how the Gram stain works. Solutions of “Crystal Violet” (a purple dye) and Iodine are applied to cells fixed to a slide, where they soak in and precipitate in the cells. A “decolorizer” (usually ethanol) is applied to see if it will wash this dye precipitate out of the cells. A different, lighter-colored dye (such as safranin) is added so that the cells which DO have their dye washed out can be seen as well. In the end, “Gram positive” cells are a dark purple from the crystal violet/iodine that was not washed away, and “Gram negative” cells are not dark purple. (Usually they are pink, from the safranin, assuming that’s the dye used as the counterstain.)

Note that this does not differentiate cells into “two fundamental types” as is often claimed. You actually get four types: Groups of cells that are normally always “Gram positive”, Groups of cells that are normally always “Gram negative”, Groups of cells that are normally sometimes “Gram positive” and sometimes “Gram negative” (“Indeterminate”, or as I like to call it, “Gram-biguous”), and groups of cells that are normally NEITHER Gram-positive nor Gram-negative, like Mycoplasma, which aren’t dyed at all by the process. Incidentally, phylogenetically speaking, Mycoplasma is one of the “Gram positive” Firmicutes, just like Bacillus and Staphylococcus.

It’s kind of interesting to me that the Gram stain reaction has been such a mystery up until a century after its invention. What is it that makes “Gram positive” cells retain the dye while “Gram negative” ones don’t? Along the way, it seems like nearly every part of the bacterial cell was hypothesized to be the reason for the Gram reaction – lipids, carbohydrates, nucleic acids, “Magnesium ribonucleates”, and so forth. Davies et al, 1983, includes a table listing many of these and referencing historical papers making the claims. The fact that the reaction had something to do with the cell wall seems to go back quite a while, though the “Magnesium ribonucleates” idea doesn’t seem to have been entirely abandoned until the mid-1960’s[7]. It was also hypothesized that the “Gram positive” cells simply absorb more dye and therefore take longer to “decolorize”.

It turns out that “Gram-positive” cells actually don’t, necessarily, take up more dye than Gram negative ones. This was tested by taking a set concentration of bacterial cells and adding them to a set concentration of dye. After letting them soak, the samples were centrifuged to remove the bacteria, and the amount of dye found to be missing from the liquid was taken as the amount absorbed by the cells. They found that some Gram negative cells actually took up more dye than the Gram positives did. So much for that idea.[8]

Even relatively recently, I’ve seen it written that the bacterial cell wall, specifically, is what holds onto the stain, but even that turns out not to be true. Although the cell wall is the structure that seems to be responsible for the Gram reaction, in the late 1950’s it was demonstrated that it was not actually the staining of the cell wall that caused the reaction, but rather the ability of the cell wall to keep the decolorizer out of the cell.[9]

Apparently, the Crystal Violet/Iodine complex itself doesn’t even play a vital role. The complex apparently dissolves again more or less instantly as soon as the decolorizer touches it[10], and it’s even possible to differentiate “Gram positive” and “Gram negative” with simple stains like methylene blue or malachite green, if you’re clever about it[11]. The latter authors set up a clever test with crushed cell material, dye, and paper chromatography. They had the decolorizer soak into the paper, past a spot where dye-soaked cell material from Gram-positive and Gram-negative cells was placed, and watched for obvious differences in the amount of time it took the dye to be carried out by the decolorizer. Incidentally, my quick examination of this paper makes it look like cheaper 100% isopropyl alcohol (“rubbing alcohol”) might be slightly better than the standard 95% ethanol for Gram stains.


So, here we are at 1970 or so, and we already know that the Gram reaction is entirely based on how well the cell wall structure prevents organic solvents (like ethanol) from soaking into the cell to dissolve the dye complex. Yes, the mystery of why the Gram stain works in normal cells was largely solved by the Nixon era.
A few corners of the mystery remained, though. Why do “old” cultures of “Gram positive” cells often end up staining “Gram negative”, for example? Why do some kinds of cells seem to be sometimes Gram positive and sometimes Gram negative in the same culture? What, exactly, is really happening to the cell, deep down, during the staining process?

In 1983, the Gram Stain made the great technological leap into the 1930’s, when a variation of the technique was devised which allowed the Gram Stain to be observed by electron microscopy[12]. Using a funky platinum compound in place of iodine, the electron microscope reveals exactly where the dye complex is at any particular stage of the Gram stain process. Using this technique, it was possible to see how the decolorizer disrupts the outer membrane of classically-Gram-negative organisms and to see that the decolorizer potentially damages the cell wall and interior membrane, possibly allowing cell material to leak out (or decolorizer to get in and dissolve the dye complex). It was also seen that the dye complex permeates the entire cell, not just the cell wall.[13]

If you’ve been wondering about the sometimes-Gram-positive-sometimes-Gram-negative cells, the same technique was also used to investigate this. As suspected, it turns out that the “old cultures become Gram negative” problem is due to the cell walls breaking down as the culture ages. Bacteria are continuously, simultaneously, building up and tearing down their cell walls, in order to be able to grow and divide. As nutrients run out, the bacteria run out of material to rebuild cell walls, while the cell-wall degrading enzymes keep on chugging. Breaks in the cell wall occur, and through these breaks the decolorizer can get in and rapidly dissolve the dye. Actinobacteria can have a similar problem, but rather than only being in “old” cultures, apparently weaknesses appear briefly during cell division, and if a particular cell happens to be at this stage of growth when you stick it on a slide, heat-fix, and Gram stain it, the weakness at the septum where the division is occuring can crack and allow the decolorizer in, resulting in a “Gram negative” response even while surrounding cells of the same kind might still be “Gram positive”.[14]

This brings us to archaea and some eukaryotes (i.e. yeasts). Yeasts stain “Gram positive” normally. Although their cell walls are completely different chemically than bacterial cell walls, they are quite thick (microbially speaking). Poor, neglected Archaea seem to be all over the place in terms of Gram reaction. Since their Gram reaction doesn’t tend to correlate to any particular phylogenetic grouping[15], it seems nobody really pays much attention to their Gram stain reaction. On the other hand, and on the subject of “Gram-biguity”, I thought the investigation of Methanospirillum hungatei[16] was interesting. M.hungatei is an archaen that grows in chains. When Gram-stained, the cells on the ends of the chains are “Gram positive”, while the others have no Gram reaction at all. It turns out that the chains are covered by a sheath, and the only contact with the outside world is through thick “plugs” in the cells at the ends of the chains. These “plugs” act like thick cell walls, allowing the Gram stain dye material to soak in but excluding the decolorizer, while the sheath keeps the rest of the cells from soaking up any stain at all.

There you have it – a relatively detailed history and explanation for the Gram stain, and you didn’t even have to get through some obnoxious paywall to read it. Aren’t you lucky?

Comments, suggestions, and corrections, as always, are welcome.

[1] Gram, HC.”Ueber die isolirte Faerbung der Schizomyceten in Schnitt-und Trockenpraeparaten.” Fortschitte der Medicin. 1884 Vol. 2, pp 185-189.

[2] Popescu A, Doyle RJ. “The Gram stain after more than a century.” Biotech Histochem. 1996 May;71(3):145-51.

[3] Brock TD, Madigan MT, Martinko JM, Parker J. “Biology of Microorganisms (7th Edition).” 1994. Prentice Hall, Englewood Cliffs, NJ pg. 46

[4] ibid, pg. 715

[5] Beveridge TJ.”Use of the gram stain in microbiology.” Biotech Histochem. 2001 May;76(3):111-8.

[6] McClelland, Rosemary. “Gram’s stain: The key to microbiology – isolate identification method – Tutorial” Retrieved 20070810 from http://findarticles.com/p/articles/mi_m3230/is_4_33/ai_74268506/print

[7] Normore WM, Umbreit WW.”Ribonucleates and the Gram stain.” J Bacteriol. 1965 Nov;90(5):1500.


[9] BARTHOLOMEW JW, FINKELSTEIN H.”Relationship of cell wall staining to gram differentiation.” J Bacteriol. 1958 Jan;75(1):77-84.


[11] Bartholomew JW, Cromwell T, Gan R.”Analysis of the Mechanism of Gram Differentiation by Use of a Filter-Paper
Chromatographic Technique.” J Bacteriol. 1965 Sep;90(3):766-77.

[12] Davies JA, Anderson GK, Beveridge TJ, Clark HC.”Chemical mechanism of the Gram stain and synthesis of a new electron-opaque marker for electron microscopy which replaces the iodine mordant of the stain.” J Bacteriol. 1983 Nov;156(2):837-45.

[13] Beveridge TJ, Davies JA.”Cellular responses of Bacillus subtilis and Escherichia coli to the Gram stain.” J Bacteriol. 1983 Nov;156(2):846-58.

[14] Beveridge TJ. “Mechanism of Gram Variability in Select Bacteria.” J Bacteriol. 1990 Mar;172(3):1609-20.

[15] Beveridge TJ, Schultze-Lam S. “The response of selected members of the archaea to the gram stain.” Microbiology. 1996 Oct;142 ( Pt 10):2887-95. (Abstract)

[16] Beveridge TJ, Sprott GD, Whippey P. “Ultrastructure, inferred porosity, and gram-staining character of Methanospirillum hungatei filament termini describe a unique cell permeability for this archaeobacterium.” J Bacteriol. 1991 Jan;173(1):130-40.

A Government “War on Science” is GREAT for this country!

They say that politics and controversial statements are ways to encourage traffic on a blog, so here’s some. Comments welcome, of course.

I have cause to celebrate the future potential for science in the U.S. Here’s a bit of simple history (Update – added the “War on Poverty” to the list 20070810):

1964: Lyndon Baines Johnson declares a “War on Poverty” Today: the gap between the Rich and the Poor in the US is widening and economic mobility is stagnant.

1971: President Nixon declares a “War on Drugs”. Today: “Drugs” are widely used, even among kids, who appear to be losing their fear of drugs. Market innovations (blatantly illegal and of questionable morality, but innovations nonetheless) such as crack cocaine, MDMA (“ecstasy”), and “ice” (crystal meth) seem to be in the news a lot. People growing illegal plants in their closets and basements or brewing up complex chemical stimulants in the backs of minivans seems to be an almost daily topic of the news.

2001: President George W. Bush declares a “War on Terror”. Today: A majority of Americans feel that there is a greater threat of terrorism than before, which seems to be true, at least as far as “Jihadist” terrorists go, if the declassified portions of the government report paint an accurate picture of the situation. Heck, when the president invaded Iraq in 2003, major terrorist organizations didn’t even seem to be there. And now, it seems like EVERYONE we’re fighting in Iraq is Al Qaeda, and we’re treated to frequent vague but earnest-sounding warnings of impending terroristic doom.

Given these historical precedents, if there really is a government-run War on Science, then we’re in for a huge increase in scientific activity here.

I’m picturing a virtual underground Scientific Renaissance, where, like much of the late 1700’s and 1800’s, “citizen science” becomes a fashionable pursuit. People secretly building science labs in their basements and attics and performing legitimate, useful scientific research in them. Kids hanging out in abandoned parking lots at night, doing complex calculus problems in chalk on the ground and experimenting with broadcast power. Anonymous rebel scientists developing methods to cheaply and effectively convert lawn clippings into fuel ethanol and plastic grocery bags and soda bottles into biodiesel. Ignorant politicians assume home biology labs are marijuana-growing operations, that home chemistry labs are making methamphetamines, and that home physics labs are building radioactive “dirty bombs”. A multibillion-dollar new agency, the Science Enforcement Agency is hastily assembled and laws are badly written to restrict scientific activity to carefully-regulated government-controlled settings only.

Public science devolves into (when Republicans are in control) attempts to “debunk” global warming and evolution, “cure” homosexuality, develop ridiculously expensive military-grade weaponry, and silly projects that just plain won’t work but happen to be run by buddies of a senator or (when Democrats are in control) multimillion dollar projects to study “self-esteem”, research on “psychic powers”, development of homeopathic “medicine”, and silly projects that just plain won’t work but happen to be run by buddies of a senator. Disgusted underground scientists are only egged on by this state of affairs.

Within a few years, a cautious exchange of money in a public restroom will buy disease-curing doses of novel, effective, but non-FDA-approved antibiotics that cure drug-resistant Staphylococcus aureus or Tuberculosis. A backyard moonshiner-like biotech lab somewhere in the rural west secretly sets aside part of their flock of chickens, genetically engineering them to produce HIV vaccines with billions of dollars in “street” value. Someone with a closet chemistry lab develops an illicit catalyst that facilitates hydrolysis of water to produce hydrogen with no more energy input than ordinary body heat, while another develops an illegal strain of cyanobacteria that turns atmospheric carbon dioxide into a plastic substance which can either be used for building or is easily converted to biodiesel at such a rate that the developer has to rapidly build a huge, secret underground complex to hide the vast quantities of material produced overnight….

In the end, as always, government goes utterly insane and bankrupts themselves (more, I mean) trying to stamp out Illegal Science, but in the meantime, anyone who’s scientifically inclined ends up making a fortune. On the other hand, the efforts drive a lot of the science out of the country and Mexico becomes the new world superpower with their fleet of antigravity flying armored space cars, zap death ray guns, and clusters of quantum-supercomputers. (Note to self: get back to learning to speak Spanish!). This doesn’t really slow the flow of science into the US, though, and “science tourists” can sneak to Mexico to undergo age-reversing and/or intelligence-boosting medical treatments or to obtain cures for cancer or obesity that actually work. People end up in jail for recovering from leukemia or losing weight.

Meanwhile, on a more personal note, people like me who actually think doing science is fun get a few publications in underground science-journal ‘zines, spend a few years developing something useful, make a huge pile of money, and then retire before The Man catches up to us, to live a life of luxury somewhere. Maybe living in a giant mansion in Mexico between stints as lab techs for Mexican scientists once in a while, done just for fun and extra pocket-money…

It’ll be glorious. So – write your legislators today, and tell them we NEED the “War on Science”. For the Children.

(My political opinion? Lets just say that my political fantasy right now is that the 2008 presidential race will come down to a run-off between a Bloomberg/Paul ticket and a Gravel/Kucinich ticket….)

There, is THAT enough controversy to get some new traffic here?…

Curse you, public library!

Tonight’s post will be an eclectic one…

I made the mistake today of heading for what passes for a “large city” in my local area in a general need to go somewhere besides my house and the college. I figured I could browse the local discount bookstore and see if they had anything interesting.

I happened to notice a sign advertising a book sale at the local library.

Why did they have to do this to me? Have they no decency? Have they no shame? Have they no MERCY?

As I previously mentioned, I actually do collect old science (and medical) books. Unfortunately, I ended up walking out of the library with a whole mess of microbiology books (and one Botany book that I picked up just because it was old – 1930’s). Fortunately, they were cheap.
I was just perusing one of the books I picked up: an old “Bacteriology” book[1] from the late 1940’s. It’s fascinating and instructive to see what scientists used to believe was true and what observations led them to believe it.

The introductory chapters of the book include a discussion of taxonomy and the place of “Schizomycetes” (meaning bacteria that aren’t photosynthetic) in the overall scheme of things. There’s a discussion that, given what information was available at the time, is perfectly reasonable and explains why bacteria are “plants”, just like other fungi (Fungi, you see, are just plants that aren’t photosynthetic – or so they explain). The author gives a classification scheme for plants that divide them into three categories, which roughly equate to “normal” plants (with stems and leaves), moss-type plants, and plants that don’t have roots, leaves, stems, or flowers. This latter category he broke into two sub-categories – Algae (including “Blue-green” algae, which we now know are actually bacteria) and Fungi. “Bacteria” are listed as one of the categories of Fungi.

The discussion justifying this categorization makes some interesting claims – some of which are startling to me. The author claims that some bacteria – “Acetobacter xylinum” have cell-walls that consist of cellulose, just like plants. (Actually, it would appear this bacterium does make cellulose, though I don’t think it’s actually a component of the cell wall – this is a standard “Gram-negative” type ?-proteobacterium). I had no idea up to this point that there were cellulose-producing bacteria. Interestingly, the author also states

“Some bacteria are said to possess cell walls of chitin, a distinctly animal substance which is the material of horn, hair, hoof, and insect shell”

which is completely wrong on every count except for the part about insect shells. (Horn, hair, and hoof (and fingernail) material is Keratin, which is a type of tough protein. Chitin is actually a polysaccharide…and it is what most fungal cell walls are made of.There are some interesting statements in the section on microscopy as well. The author claims:

“There seems no doubt that the gram-positive material in bacteria is ribonucleic acid. Bartholomew and Umbreit[2] have shown that it can be removed by soaking the gram-positive cells in sodium choleate. It may be replaced by treating them with magnesium ribonucleate. Normally gram-negative species will not accept the applied coating. The specificity of these reactions is shown by the fact that an enzyme, ribonuclease, will remove the gram-positive character (ribonucleic acid) of the cells very quickly.”

What the heck?… Now I have an urge to see if I can sneak a culture of some kind of Bacillus and some RNAse and see how much of this explanation actually matches observation. (Perhaps I can dig up Bartholomew and Umbreit’s paper as well). The author also mentions that nobody has managed to get a good image of a bacterial nucleus, either, which of course is because they don’t actually have one…
One other thing I’d never heard of: Proton Microscopy. According to the author, this technique, apparently first implemented in France in 1948, could theoretically give substantially better resolution than electron microscopy.

Some quick poking around seems to show that this is partly true, and there actually are proton microscopes that get used for some kinds of studies. However, protons are a heck of a lot harder to “focus” and they don’t seem to have caught on for microbiological work. They do evidently have some useful properties for doing analysis of what specific elements are in a sample, though[3].

I noticed some other apparent differences in style between the older textbooks and current ones, but I’ll save that for another time.

I will also at some point go back and re-write the Schizomycete article to include some of the information I’ve picked up in the last couple of weeks. Meanwhile – one more day of “Just Science” week! Looks like I should survive it after all.

[1] – Frobisher, Martin Jr. “Fundamentals of Bacteriology (Fourth Edition)”, 1949, W.B Saunders Company, Philadelphia
[2] Bartholemew JW, Umbreit WW, “Ribonucleic Acid and the Gram Stain”, J. Bacteriol. 1946, 48:567
[3] “Microscopy with Protons” http://www.innovationmagazine.com/innovation/volumes/v7n1/coverstory3.shtml (visited 2007-02-10)