Classify, you Yellow-y Slimy Mouldy maze solver!



Pysarum solving a maze[5]

Physarum polycephalum, I know you’re not one of those anti-membrane-bound-organelle things, in fact you eat bacteria. So heartfelt props on being a contributing member of the anti-prokaryotic league.

But lets not get too friendly. I have my issues with you. Lets start with yellow… it’s not your colour. Actually there is no colour that will match your unparalleled protist madness. (What is a protist anyway? We can’t figure out what a protist is other than eukaryotic.) Why are you galvanotactic[1]? How do you anticipate periodic events[8]? What does acceleration-stimulus even mean to you[2]? Do you really have to do some weirdly efficient shuttle-streaming motion shit[3]? Last I checked, your “many-headed slime” pseudonym didn’t make you suddenly grow even a single brain.

Though you look like a gross yellow pulsating blob, somehow move in the superbly mesmerizing ways of shuttle streaming. We have real limbs and nervous systems and muscles that work by the usual sliding filament method that aid in our motility while you go around doing some strange endoplasmic streaming that reverses direction periodically on the time scale of minutes by contractions of the actinomyosin system in a Ca++ dependent fashion[4] to generate contractile forces of up to 180g/cm2[3]. That’s like more than normal human blood pressure, which if you didn’t know, takes a lot to regulate. (Still only half giraffe blood pressure but they have already been dealt with in FU, Penguin). We tried to model your streaming with 12 parameters representing Ca++ and cAMP levels (and whatever else we could think of). We have some ideas about how you oscillate ATP and tension in phase and Ca+ and cAMP out of phase[9]. But in my opinion, you should stop working on your moves and start working on classing up you looks instead by being less yellow-y and less slimy and less mouldy, but I’m sure you think you’re beautiful on the inside or something. Well, we thought so too, till we started looking inside you and what we found was frankly disturbing. Apparently, this shuttle streaming lets you optimize networks of tubes to locations of food sources?

When we challenged you with different configurations of food sources, we found that you can come up with very efficient networks of tubes to connect them. We understand you want to keep your average degree of separation (AS) between two food sources to a minimum which can be achieved with some not-so-complicated logic that even we can wrap our brains around. But then you go and maximize your Fault tolerance (FT) to total tubular length (TL) ratio as well so that you can have the robust to injury while minimizing your tube length[6]. How can you solve the travelling salesman problem that something many PhD years have been spent on in a matter of hours? (OK fine. They are PhD years but the question is still valid.)

Anyway, I’m not buying it. If you are so great at coming up with efficient networks, why don’t you plan our cities for us? Oh, what is that? You tried it[7] and it’s too basic a problem for the great shuttle-streaming, efficient-network-solving, many-headed slime? Fuck you. (Because, like the rest of us, you have membrane bound organelles and all that jazz which makes conjugation hard and you have to exchange genetic material the normal eukaryotic way.) Doubt all the sequencing in the world is going to tell us how you do what you do but thought we’d try anyway.

All of this we might have been able to live with. But then you go all topology on our ass and solve mazes[5]. WHY? Do you think you’re Euler or something? You change your shape to cover the shortest distance between food sources no matter the obstacles we place in your path[5]. Seriously, is there no end to how you can belittle our intelligence?

So, in conclusion, please stop blowing our highly evolved thinking minds… Perhaps keep yourself busy trying to figure out how many possible mazes exist and then solving them all or some other such obscure classification theory problem. Also, while you are at it, we are very confused by what a protist is, so please let us know if you have any thoughts on that classification front as well.


  1. Anderson JD. Galvanotaxis of slime mold. J Gen Physiol. 1951 Sep;35(1):1-16.
  2. Block I, Rabien H, Ivanova K. Involvement of the second messenger cAMP in gravity-signal transduction in Physarum. Adv Space Res. 1998;21(8-9):1311-4.
  3.  Kamiya N. Physical and Chemical basis for Cytoplasmic Streaming. Ann. Re.. Plant PhysioL 1981. 32:205-36.
  4. Kuroda R, Kuroda H. Relation of cytoplasmic calcium to contractility in Physarum polycephalum. J Cell Sci. 1982 Feb;53:37-48.
  5. Nakagaki T, Yamada H, Toth A. Maze-solving by an amoeboid organism. Nature. 2000 Sep 28;407(6803):470.
  6. Nakagaki T, Yamada H, Hara M. Smart network solutions in an amoeboid organism. Biophys Chem. 2004 Jan 1;107(1):1-5.
  7. Tero A, Takagi S, Saigusa T, Ito K, Bebber DP, Fricker MD, Yumiki K, Kobayashi R, Nakagaki T. Rules for biologically inspired adaptive network design. Science. 2010 Jan 22;327(5964):439-42. doi: 10.1126/science.1177894.
  8. Saigusa T1, Tero A, Nakagaki T, Kuramoto Y. Epub 2008 Jan 3. Amoebae anticipate periodic events. Phys Rev Lett. 2008 Jan 11;100(1):018101.
  9. Smith DA, Saldana R. Model of the Ca2+ oscillator for shuttle streaming in Physarum polycephalum. Biophys J. 1992 Feb;61(2):368-80.

Tiny prey stalking murderers!


Bdellvibrios growing inside a host cell (Sockett, 2009)

We were not ready for you. Not sure we ever would have been. We were looking to isolate bacteriophages that prey on gram negative bacteria like you. Instead we found these slower growing plaques on lawns of Pseudomonas that was you[10]. So what if you can bore into other bacteria, use their macromolecules and finally kill them to release more of yourselves. Virus do that. You’re a living, respiring cell. You should have stronger character! But I guess its hard to fit morality into a tiny cells like yours. Bdellovibrio, you’re just about the most diabolical bacteria ever.

Because your way of life was so strange and perverse to us, we studied your developmental stages. We recognize the little ‘attack’ cells (that move at an amazing 60 – 160 um/s in liquid) that you fashion yourselves into when you’re looking to bore into an unassuming fellow bacteria. But we also know that you can use slower guiding motility (15 – 20 um/s) on sold surfaces to find prey[4]. Some of your close deltaproteobacteria cousins (Myxobacteria) hunt in packs and secrete extracellular enzymes to digest prey. But you hunt alone and when you find prey, you invade their peptidoglycan layer[8]. We hear the host bacteria transcriptionally “screaming” by upregulating stress response genes and cell wall repair genes[3]. But we can do little else as we watch with horror as you form bdelloplasts of undivided filaments in the preiplasm of other gram-negative bacteria and suck out their bodily fluids, finally exit through a pore in the dead host membrane[2].

So, we sequenced your large genome and pretend we know a little more about you. You think you’re so cool because you’re an enigma wrapped in a puzzle. Tiny cells (.5um) with an unusually large genome (3,782,950 bp)? Live by preying on other bacterial cells and having ready access to their DNA but no evidence of horizontal gene transfer ? No ATP transport proteins to get energy from your prey? And no quorum sensing??[6] Are you fucking kidding me? Every other bacteria does it. And it would really benefit you to know how much prey is around. But no. You’re above that. You don’t even want to talk to each other, forget about other bacteria. I’ve never heard of a more self important pesky prokaryote!

And it turns out you can live and divide in a saprophytic cycle in a totally host-independent fashion[7]. At least viruses that prey on bacteria can’t divide outside them. You on the other hand, can do just fine even with out hosts. (Don’t even try and deny this. We found the full complement of genes that let you produce ATP through glycolysis and oxidative respiration[6].) So is this just some kind of extreme sport? That’s just ridiculous. In an attempt to diminish our awe for your ridiculous invincibility, we tried to find bacteriophages that would do to you what you do to other bacteria. And we did. Except, it turns out that once you’ve infected another bacteria, these phages have a hard time getting into you[11]. And no, preying on cells is not an acceptable way to evade phages. Fight your own battles. Grow a better cell wall or something. I know plenty of other bacteria that live inside other cells that don’t kill their hosts (I’ll introduce you to Wolbachia someday).

Also, what is the deal with odd number of progeny? How do you not understand the simple rules of bacterial fission? One cell divides to give 2 and two cells divide to give 4 and so on. Just because you developed some way to synchronously septate once you gorged yourselves on all the available cytosol doesn’t mean you can go around releasing odd numbers of offspring from a single infection of a cell[1]. Don’t think you can get away with it because you’re so tiny. It took us a while, but we got you on camera doing what you do best, murdering other gram-negative bacteria to release more of yourselves.

The more of you tiny non-HGTing fuckers we find, we shudder to think that why you haven’t taken over the gram-negative bacterial world[8]… yet. And in this post-species age that you and your prokaryotic cousins have very quickly ushered in, we gave up on naming you all and just call you Bdellovibrio and like organisms (BALOs). So we continue to study you, and knock out genes to see how you manage to be so amazingly efficient at sucking the life out of other cells. We learn about your type IV pilli that you use for infection[5]. We learn about how the motor flagella necessary for your life cycle[2]. We pretend we want to use the knowledge of your plundering pilli and muderous motors to kill other bacteria[12] but in reality, we are just unable to fathom how and why you do what you do.

You fast-swimming, cellwall-boring, bdelloplast forming tiny little freaks, I’m on to you. So don’t give me that shit of how your discovery was serendipitous. You (and all your prokaryotic friends) are just out to blow our lowly eukaryotic brains.


  1. Fenton AK, Kanna M, Woods RD, Aizawa SI, Sockett RE. Shadowing the actions of a predator: backlit fluorescent microscopy reveals synchronous nonbinary septation of predatory Bdellovibrio inside prey and exit through discrete bdelloplast pores. J Bacteriol. 2010 Dec;192(24):6329-35.
  2. Flannagan RS, Valvano MA, Koval SF. Downregulation of the motA gene delays the escape of the obligate predator Bdellovibrio bacteriovorus 109J from bdelloplasts of bacterial prey cells. Microbiology. 2004 Mar;150(Pt 3):649-56.
  3. Lambert C, Ivanov P, Sockett RE. A transcriptional “Scream” early response of E. coli prey to predatory invasion by Bdellovibrio. Curr Microbiol. 2010 Jun;60(6):419-27.
  4. Lambert C, Fenton AK, Hobley L, Sockett RE. Predatory Bdellovibrio bacteria use gliding motility to scout for prey on surfaces. J Bacteriol. 2011 Jun;193(12):3139-41. Epub 2011 Apr 22.
  5. Mahmoud KK, Koval SF. Characterization of type IV pili in the life cycle of the predator bacterium Bdellovibrio. Microbiology. 2010 Apr;156(Pt 4):1040-51. Epub 2010 Jan 7.
  6. Rendulic S, Jagtap P, Rosinus A, Eppinger M, Baar C, Lanz C, Keller H, Lambert C, Evans KJ, Goesmann A, Meyer F, Sockett RE, Schuster SC. A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective. Science. 2004 Jan 30;303(5658):689-92.
  7. Seidler RJ, Starr MP. Isolation and characterization of host-independent Bdellovibrios. J Bacteriol. 1969 Nov;100(2):769-85.
  8. Sockett RE. Predatory lifestyle of Bdellovibrio bacteriovorus. Annu Rev Microbiol. 2009;63:523-39. Review.
  9. Starr MP, Baigent NL. J Bacteriol. Parasitic interaction of Bdellovibrio bacteriovorus with other bacteria. 1966 May;91(5):2006-17.
  10. Stolp H, Starr MP. Bdellovibrio bacteriovorus gen. et sp. n., a predatory, ectoparasitic, and bacteriolytic microorganism. Antonie Van Leeuwenhoek. 1963;29:217-48.
  11. Varon M, Levisohn R. Three-membered parasitic system: a bacteriophage, Bdellovibrio bacteriovorus, and Escherichia coli. J Virol. 1972 Mar;9(3):519-25.
  12. Wolfe AJ. Sighting the alien within: a new look at Bdellovibrio. J Bacteriol. 2010 Dec;192(24):6327-8. Epub 2010 Oct 15.

Bacteria of the world unite, you have nothing to lose but your energy!


Stop the light pollution!

You evolved this cute little system to measure local cell density involving a small extracellular molecule that all individuals in a population produce and sense. While we higher eukaryotes go around being all greedy and selfish, you figured out a way to communicate and cooperate with your fellow prokaryotes. Don’t look so delighted with yourself. Let me remind you, its just evolution and evolution is easier than revolution. So while the workers of the world unite, you little bacterial fuckers go around coordinating your behavior by producing molecules for the common public good, like Simpsons paradox is not a paradox to you[1]. And to that I say CONJUGATE YOU!

Vibrio fischeri, as the poster bacterium for quorum sensing, you’re number 1 on this shit-list. Your luciferase operon is the paradigm for quorum sensing. The operon that consists of the LuxI gene that produces acyl-homoserine lactone (AHL) that is exported out of the cell. This molecule induces the regulator LuxR that in turn induces the lux operon. You know the operon I’m talking about: luxICDABE. At first glance, this is just an innocent feed forward loop that we all use as on/off switches for cellular functioning[2]. But then you went and made it all fancy by having genes like flavin-dependent monooxygenase luciferase that can catalyze the oxidation of reduced riboflavin and a long-chain aliphatic aldehyde to produce light. Let me point out that you spend all this energy (115 kcal/mol) on reduction to produce the FMNH2 molecule and 2 NADHs which you then oxidize to produce light at 490nm wavelength giving you only 59 kcal/mol[5]. Somehow, this obvious waste of energy does not deter you. And you produce 1000 photons per second per bacterium[8]??? I’ve spent many a ~10 mins in a dark room with you, waiting for my eyes to acclimatize so I may witness your luminous highness. You know what, it ain’t worth it!

I may have even been able to live with your seemingly wasteful production of light if it were just for for an artistic outlet. But we know that you go around recruiting squids and fish (and who knows what else that lurk in the deep dark depths of the ocean) to your little rave parties. I can imagine the conversation now: “What up Euprymna scolopes! It must be hard being a tiny squid with all these predators around. We can help. We can trick your immune system into letting us hang out and luminess in your invaginated epithelial crypts of an organ that you make specifically to house us. It’s for your antipredatory behavior… we can counterilluminate so that you are camouflaged. We get nothing out of this. We’re doing this totally selflessly.”[3] Prokaryotic selfless behavior! Like that happens. And as always, in an attempt to humble your great prokaryotic ego (only paralleled by your sheer number in the world), I would like to draw your attention to other organisms that do the same thing with no help from you. Dinoflagellates, cnidarians, fungi, shrimps and fireflies, to name a few[8]. And some of them, like the dinoflagellates use this super power for cool things with it like to populate the Bioluminescent Bay that we humans can enjoy.

We have only begin to uncover the range of mechanisms you use to regulate this quorum-sensing. There are multiple autoinducer circuits that control different behaviors. They can act in parallel or by competition through phosphorelation and kinase pathways[7]. And just when we thought we eukaryotes were special for having regulatory micro RNAs, we find that you use ‘small regulatory RNAs’ to even more sensitively react to the concentrations of inducers[4]. And so we continue to study you with a deep fear and disgust of what we may find in your chemical vocabulary. I know you think Bonnie Bassler et. al. <3 you and sing the praises of your intricately regulated social interactions. But the truth is, my quorum-sensing light-producing cooperatively-benefiting little conjugating friends, you and your quorum sensing unions are just keeping more brilliant scientists from doing important things like curing cancer. I hope you’re happy.

Oh right. You like cancer. Your Agrobacterium cousins use quorum-sensing to form tumors on plant roots in which they can have huge orgies to exchange DNA[10]. I’m sure that’s a totally selfless relationship as well. Since most of your cousins can produce some version of these AHL communication molecules, there’s the inter-species communications machinery issue. Must I even mention the large conjugating orgies across species and genus boundaries that you can initiate though quorum-sensing? But just when I thought you were just trying to have a free HGT party I find out that you all engage in some strange form of warfare in which you try to intercept communications of other populations. You can secrete enzymes that make AHLs of another species inactive. You produce competing receptors to titrate the AHLs in the environment[9]. Your obvious disregard for your fellow prokaryotes disgusts me. I hope you annihilate yourselves by ensuring mutual communication destruction!


  1. Chuang JS, Rivoire O, Leibler S. Simpson’s paradox in a synthetic microbial system. Science. 2009 Jan 9;323(5911):272-5.
  2. Engebrecht J, Silverman M. Identification of genes and gene products necessary for bacterial bioluminescence. Proc Natl Acad Sci U S A. 1984 Jul;81(13):4154-8.
  3. McFall-Ngai M. Host-microbe symbiosis: the squid-Vibrio association–a naturally occurring, experimental model of animal/bacterial partnerships. Adv Exp Med Biol. 2008;635:102-12.
  4. Tu KC, Long T, Svenningsen SL, Wingreen NS, Bassler BL. Negative feedback loops involving small regulatory RNAs precisely control the Vibrio harveyi quorum-sensing response. Mol Cell. 2010 Feb 26;37(4):567-79.
  5. Tu SC, Mager HI. Biochemistry of bacterial bioluminescence. Photochem Photobiol. 1995 Oct;62(4):615-24.
  6. Visick KL, Ruby EG. Vibrio fischeri and its host: it takes two to tango. Curr Opin Microbiol. 2006 Dec;9(6):632-8. Epub 2006 Oct 16.
  7. Waters CM, Bassler BL. Quorum sensing: cell-to-cell communication in bacteria. Annu Rev Cell Dev Biol. 2005;21:319-46.
  8. Widder EA. Bioluminescence in the ocean: origins of biological, chemical, and ecological diversity. Science. 2010 May 7;328(5979):704-8.
  9. Zhang LH, Dong YH. Quorum sensing and signal interference: diverse implications. Mol Microbiol. 2004 Sep;53(6):1563-71.
  10. Zhu J, Oger PM, Schrammeijer B, Hooykaas PJ, Farrand SK, Winans SC. The bases of crown gall tumorigenesis. J Bacteriol. 2000 Jul;182(14):3885-95.

Too insecure to stay with the name Micrococ(k)us?


You don't look like a conan to me. (Gross, 2007)

Even though you look more like the Micrococcus who you were named for in 1956, your 16S ribosomal sequences beg to differ and place you closer to Thermus. So we even gave you your own genus in the 80s: Deinococcus[2] and made you the first card-carrying member of i-can-survive-high-amounts-of-radiation club[7]. But that wasn’t enough for you. You wanted to be called “Conan” after some higher eukaryotic barbarian. We say NO! Go find your own pulp-fiction characters. And so as a protest, I assume, you go look all gram-negative with your cell envelope and your outer membranes (I ask you, do you really need 6 layers?) but you stain gram positive[12] … like gram staining isn’t bloody confusing enough. And what is it with you microbes and your need to be in the spotlight? You get your share of attention showered on you, being a POLYextremophile and all. You even get mentioned in Craig Venter’s TED talk. Before you go around telling the world how Craig Venter “optically mapped” you[11], let me tell you: he didn’t choose you because you are so good at fixing DNA breaks. He wants to USE you. And he will own your ass soon (if he doesn’t already). But whatever, live in your little desiccated reality.

I get it. Your life was hard. You’ve had to deal with desiccation (allegedly). So you rolled in tetracocci and got thick peptidoglycan skins. But your DNA was still just the fragile DNA (thankfully, the phosphorus backboned kind, unlike some others we know) that we all have and desiccation can cause double stranded breaks in DNA. So you decided to go one step further and figure out how to fix broken DNA. And while evolving to protect your DNA from desiccation, you just happened to render yourself also immune to high levels of radiation. Right. Likely story. I don’t mean to steal your thunder or anything, Sir Deinococcus, but the cyanobacterium Chroococcidiopsis can withstand high levels of ionizing radiation too[1] and they live on the underside of quartz stones. In the Atacama desert. AND can photosynthesize[9]. Who’s extreme now, bitch? (Yes Chroococcidiopsis, I know you exist, I’ll get to you too sometime.)

OK, I’ll admit it. Back then, we thought you were so cool. So, we sequenced you and found some 2 large circular chromosomes, some HGT, some strange genes and more mundane genes[12]. We ran gels of your DNA before and after radiation and found that you could indeed fix broken DNA[5]. We even used the (at the time) hot new microarray technology to figure out what genes you were turning on to fix your DNA and found genes of unknown function: ddrA, ddrB, ddrC, ddrD, pprA[15]. And then we tried to characterize the protein products of these genes. And what we ended up with can be summarized in one meaningless sentence: “It is currently difficult to predict which mechanism(s) will be most important in radioresistance, or even whether all of the contributing mechanisms have been discovered.” I guess what I’m trying to say is we got precious little from that academic relationship. We did figure out that just having multiple copies of the genome does not by itself repair the 1000s of double stranded breaks inflicted on your genome with our high power γ-rays. We deduced this from the fact that normal bacteria often have 4 copies in a cell and they can’t fix shit when faced with 10000 Gray[2]. Oh, but don’t worry, we noticed the Manganese(II) you keep around[4]. Maybe it scavenges the reactive oxygen species (ROS) that would otherwise damage vital proteins[3] or maybe it just leads to the condensation of the genome so that the severed genomic pieces stay close to their actual neighbors[10]. We will let you know when we figure it out. Meanwhile, you go on fixing your double stranded breaks in a (partially) Rec-A depended fashion[14], like all the other run-of-the-mill, ordinary, banal, average conjugating bacteria everywhere.

Lets face it. You’re so 2001, when your genome came out and everyone thought you were the shit. There was even some debate about if you came from outer-space[13]. Frankly, I don’t really care right now, as long as you just go out (or back) into space (we know you can survive there[6]) and promise never to come back or show your brilliant little ionizing-radiation-resistant ass to me ever again. Conjugate you! (Ha! You aren’t fucking resistant to that! Wait, are you?)


  1. Billi D, Friedmann EI, Hofer KG, Caiola MG, Ocampo-Friedmann R. Ionizing-radiation resistance in the desiccation-tolerant cyanobacterium Chroococcidiopsis. Appl Environ Microbiol. 2000 Apr;66(4):1489-92.
  2. Cox MM, Battista JR. Deinococcus radiodurans – the consummate survivor. Nat Rev Microbiol. 2005 Nov;3(11):882-92.
  3. Daly MJ, Gaidamakova EK, Matrosova VY, Kiang JG, Fukumoto R, Lee DY, Wehr NB, Viteri GA, Berlett BS, Levine RL. Small-molecule antioxidant proteome-shields in Deinococcus radiodurans. PLoS One. 2010 Sep 3;5(9):e12570.
  4. Daly MJ, Gaidamakova EK, Matrosova VY, Vasilenko A, Zhai M, Venkateswaran A, Hess M, Omelchenko MV, Kostandarithes HM, Makarova KS, Wackett LP, Fredrickson JK, Ghosal D. Accumulation of Mn(II) in Deinococcus radiodurans facilitates gamma-radiation resistance. Science. 2004 Nov 5;306(5698):1025-8. Epub 2004 Sep 30.
  5. Daly MJ, Ouyang L, Fuchs P, Minton KW. In vivo damage and recA-dependent repair of plasmid and chromosomal DNA in the radiation-resistant bacterium Deinococcus radiodurans. J Bacteriol. 1994 Jun;176(12):3508-17.
  6. Dartnell LR, Hunter SJ, Lovell KV, Coates AJ, Ward JM. Low-temperature ionizing radiation resistance of Deinococcus radiodurans and Antarctic Dry Valley bacteria. Astrobiology. 2010 Sep;10(7):717-32.
  7. Dean CJ, Feldschreiber P, Lett JT. Repair of x-ray damage to the deoxyribonucleic acid in Micrococcus radiodurans. Nature. 1966 Jan 1;209(5018):49-52.
  8. Gross L. Paradox resolved? The strange case of the radiation-resistant bacteria. PLoS Biol. 2007 Apr;5(4):e108. Epub 2007 Mar 20.
  9. Lacap DC, Warren-Rhodes KA, McKay CP, Pointing SB. Cyanobacteria and chloroflexi-dominated hypolithic colonization of quartz at the hyper-arid core of the Atacama Desert, Chile. Extremophiles. 2010 Nov 11. [Epub ahead of print]
  10. Levin-Zaidman S, Englander J, Shimoni E, Sharma AK, Minton KW, Minsky A. Ringlike structure of the Deinococcus radiodurans genome: a key to radioresistance? Science. 2003 Jan 10;299(5604):254-6.
  11. Lin J, Qi R, Aston C, Jing J, Anantharaman TS, Mishra B, White O, Daly MJ, Minton KW, Venter JC, Schwartz DC. Whole-genome shotgun optical mapping of Deinococcus radiodurans. Science. 1999 Sep 3;285(5433):1558-62.
  12. Makarova KS, Aravind L, Wolf YI, Tatusov RL, Minton KW, Koonin EV, Daly MJ. Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol Mol Biol Rev. 2001 Mar;65(1):44-79.
  13. Pavlov AK, Kalinin VL, Konstantinov AN, Shelegedin VN, Pavlov AA. Was Earth ever infected by martian biota? Clues from radioresistant bacteria. Astrobiology. 2006 Dec;6(6):911-8.
  14. Repar J, Cvjetan S, Slade D, Radman M, Zahradka D, Zahradka K. RecA protein assures fidelity of DNA repair and genome stability in Deinococcus radiodurans. DNA Repair (Amst). 2010 Nov 10;9(11):1151-61.
  15. Tanaka M, Earl AM, Howell HA, Park MJ, Eisen JA, Peterson SN, Battista JR. Analysis of Deinococcus radiodurans’s transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance. Genetics. 2004 Sep;168(1):21-33.

Stop showing off and just use the more stable backbone!


Fat-As(s) GFAJ-1 cells high on arsenic. (Wolfe-Simon et. al., 2010)

So you can apparently substitute arsenic for phosphorous[11]. Yes, we can’t even tell the difference between the two. In our defence, they are both elements of Group 15 and are only very slightly different in electronegativity and size (~0.02 nm). Our enzymes work hard to harvest the little phosphorous we can find and in their enthusiasm, end up being unable to distinguish arsenic from phosphorous. And so, while arsenic is still toxic to us because, for example, it has a high affinity for the dihydrolipoyl groups on our Pyruvate dehydrogenase, you somehow figured out not only how to protect the thiols on your metabolic enzymes from forming crippling chelate complexes with arsenic ions but also how to make the chemical backbones of your macromolecules out of arsenic instead of the universally accepted element, phosphorus. Great job! What do you want us to do about it? Give you a Nobel prize in bio-fucking-chemistry?

But before you go around asking to be knighted, let me bring your attention to a couple of things. I’ll have you know that we have figured out very cool ways to test for arsenic. James Marsh developed the Marsh test in 1836 to test for arsenic poisoning[8]. (It kills us, you know, and in case you didn’t notice, it was a popular murder tool at the time, which I’m sure you had something to do with.) An italian guy, Bartolomeo Gosio, in 1890, figured out that he could use certain fungi to achieve the volatilization of Arsenous oxide to a garlic-odoured gas on the suspected materials[1]. He even got this gas, trimethylarsine, named after himself as Gosio gas. Yes, your name starts with a G too but it’s not called GFAJ-1 gas is it? Do I hear you asking if we can tell between arsenic and phosphorous? Well, it turns out we can! How the fuck else do you think peer review works??? NanoSIMS is not only a nicer set of letters than GFAJ, but it is a new kind of secondary ion mass spectrometer that can measure trace elemental concentrations with a resolution of < 50 nm. (These scientists even come up with pop culture reference names for their equipment like MADONNA: MAinz Dust Observatory for the detection of Nanoscale Nuclear Anomalies. Does GFAJ-1 even stand for anything?) This ion microprobe can be used to spatially determine the composition of a material for up to 6 different elements or isotopes[6]. So not only can we tell our P from our As but we have come a long way in just 300 years and now even use arsenic for the greater good like curing cancer[9].

And just in case you go around saying “at least I did it without higher conciousness and support of the academy”, let me introduce you to brake fern Pteris vittata which can hyperaccumulate arsenic from the soil. It uses its phosphate transporters in its roots to uptake arsenic ions, reduces arsenate to arsenite if needed and then accumulates the anions primarily in its fronds (up to 27,000 mg As/kg dry weight)[10]. Ferns may have xylem and phloem (and unlike you, know what fronds are) but don’t even have flowers or seeds! So no, they don’t do it because it’s a challenging academic endeavour. And then there are also these other microbes that are so exclusive that they don’t even bother coming up with douchey acronyms like GFAJ-1. Like Ectothiorhodospira-like and Oscillatoria-like bacteria that can grow by anoxygenic photosynthesis using arsenic(III) as a sole electron donor. These amazing bacteria apparently do not posses a Arsenite oxidase but instead use their Arsenate reductase in reverse to oxidise the oxyanions arsenic(III) to arsenic(V), an electrochemical potential of 139mV[4]. I hear that they live quite close to you[5]. How many of your mechanisms to tolerate the toxicity of arsenic did you steal from these hard-working photoautotrophs that have evolved these Arsenate reductase and other arsenic processing genes meticulously from ancient times, long before you even thought about HGT-ing things from them? But you probably already knew about these neighbours and have something to do with why the age of their Arsenate reductase being currently contested by Schoepp-Cothenet et. al.[7] who you brainwashed with your visions of grandeur or threatened to poisoned with your arsenic backbones.

So, maybe you are an evil alien as some people report. Or maybe just you’re fat because you accumulate the arsenic(V) in your Poly-β-hydroxybutyrate rich vacuole-like regions and have cell body image issues (Figure 1 C/D, Wolfe-Simon et. al., 2010). Either way, stop showing off and just use the more stable and time-tested backbone. Do I need to point out that the symbol for arsenic is As, only one letter away from ASS? CONJUGATE YOU GFAJ-1 ASS!!!!


  1. Bentley R, Chasteen TG. Microbial methylation of metalloids: arsenic, antimony, and bismuth. Microbiol Mol Biol Rev. 2002 Jun;66(2):250-71.
  2. Carter DE, Aposhian HV, Gandolfi AJ. The metabolism of inorganic arsenic oxides, gallium arsenide, and arsine: a toxicochemical review. Toxicol Appl Pharmacol. 2003 Dec 15;193(3):309-34.
  3. Henry B.F. Dixon. The Biochemical Action of Arsonic Acids Especially As Phosphate Analogues. Advances in Inorganic Chemistry Volume 44, 1996, Pages 191-227.
  4. Kulp TR, Hoeft SE, Asao M, Madigan MT, Hollibaugh JT, Fisher JC, Stolz JF, Culbertson CW, Miller LG, Oremland RS. Arsenic(III) fuels anoxygenic photosynthesis in hot spring biofilms from Mono Lake, California. Science. 2008 Aug 15;321(5891):967-70.
  5. Oremland RS, Stolz JF, Hollibaugh JT. The microbial arsenic cycle in Mono Lake, California. FEMS Microbiol Ecol. 2004 Apr 1;48(1):15-27.
  6. P. Hoppe. NanoSIMS: A new tool in cosmochemistry . Applied Surface Science. 252 (2006) 7102–7106.
  7. Schoepp-Cothenet B, Duval S, Santini JM, Nitschke W. Comment on “Arsenic (III) fuels anoxygenic photosynthesis in hot spring biofilms from Mono Lake, California”. Science. 2009 Jan 30;323(5914):583.
  8. Spring RJ. The electrolytic test for detection of arsenic alone and in the presence of other metals. Talanta. 1982 Oct;29(10):883-5.
  9. Sumi D, Shinkai Y, Kumagai Y. Signal transduction pathways and transcription factors triggered by arsenic trioxide in leukemia cells. Toxicol Appl Pharmacol. 2010 May 1;244(3):385-92. Epub 2010 Mar 1.
  10. Wang J, Zhao FJ, Meharg AA, Raab A, Feldmann J, McGrath SP. Mechanisms of arsenic hyperaccumulation in Pteris vittata. Uptake kinetics, interactions with phosphate, and arsenic speciation. Plant Physiol. 2002 Nov;130(3):1552-61.
  11. Wolfe-Simon F, Blum JS, Kulp TR, Gordon GW, Hoeft SE, Pett-Ridge J, Stolz JF, Webb SM, Weber PK, Davies PC, Anbar AD, Oremland RS. A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science. 2010 Dec 2. [Epub ahead of print]


Get every new post delivered to your Inbox.

%d bloggers like this: