Wonders of Nature Ending
ending of Wonders of Nature

 XIX. Nematocyst (The first animal weapon?)
А ныне завладел дикарь
Священной палицей Геракла,
И черная земля иссякла,
Неблагодарная, как встарь.

Osip Mandelstam, "The Zoo" (1916, 1935)

I am always amazed by the diabolical insiduousness of animal weaponry. For example, by the much hyped projectile tooth of a fish-hunting cone snail Conus catus that "injects venom into fish prey using a high-speed ballistic mechanism. " High speed it is not! This weapon may look impressive, but it is slow and it is a patent violation. Also, it is not too important in the grand scheme of things. There is a weapon that is much faster and much older, a weapon whose emergence marked one of the most important evolutionary events in the history of Kingdom Animalia, viz. the origin of Cnidaria (which include jellies, hydras, polyps, sea anaemonies, etc.) Cnidocysts in the stinging cell (cnidocytes) of the jellies are instantly recognizable deadly machines. Their design is beatiful, intricate, and extremely complex. Without these organelles, the jellies cannot hunt and they make an easy snack. Comb jellies have their weapons too (gluey lasso cells called colloblasts), but those are far, far less deadly. It is a lasso against a pistol. There is simply no comparison:

The “firing” sequence of nematocyst. On the far left is a nematocyst inside its cellular capsule. The cell’s thread is coiled under pressure and wrapped around a stinging barb. When potential prey makes contact, operculum flies open, the thread rapidly uncoils and a barb emerges. The barbs at the end of the nematocyst sticks into the polyp’s victim and injects poison. When subdued, the polyp’s tentacles move the prey toward its mouth and the nematocysts recoil back into their capsules. http://www.oceanservice.noaa.gov/education/kits/corals/media/supp_coral01b.html

...Cnidocytes are single cells which contain a subcellular organelle named cnidocyst. The cnidocysts are composed of a hollow coiled thread-like structure attached to the bulb-shaped nematocyst capsule body. The externally-oriented side of a cnidocyte cell also has a hair-like trigger on it, called the cnidocil. When the trigger is activated the cell "fires" - the shaft of the cnidocyst penetrates the target and the hollow thread is everted into the target organism body. This discharge is one of the fastest biological processes, takes no more than few microseconds and reaches accelerations of about 40,000 g [sic!]. Following penetration, the toxic content of the nematocyst is injected into the target organism. The rapid activity of the injected neurotoxins serves to immediately paralyze the mobile prey, thus allowing the sessile cnidarian to devour it. A single nematocyst has been shown to suffice in order to paralyze a small crustacean (Drosophila larva). A cubozoan Chironex Fleckeri is "claimed to be the most venomous marine animal known."

Coiled weapon, ready to kill

...The nematocyst capsule stores a large concentration of calcium ions, which are released from the capsule into the cytoplasm of the cnidocyte when the trigger is activated. This causes a large concentration gradient of calcium across the cnidocyte plasma membrane. The resulting osmotic pressure causes a rapid influx of water into the cell. This increase in water volume in the cytoplasm forces the coiled nematocyst to evert rapidly. In order to regulate their use, cnidocytes are connected as "batteries", containing several types of nematocytes connected to supporting cells and neurons. The supporting cells contain chemoreceptors, which together with the mechanoreceptor on the cnidocyte (cnidocil) allow only the right combination of stimuli (prey swimming, chemicals found in prey cuticle or skin, etc.) to cause the cnidocyst to discharge.(Wikipedia)

Flabellina rubrolineata uses bright color to advertize that it has cnidocytes stolen from the jellies: do not mess with me!

...[Beautifully colored, poisounous] sea slugs Aeolidiopsis ransoni and Flabellina rubrolineata have cnidosacs, one of the most remarkable examples of recycling in the animal kingdom. These slugs eat cnidarians and are then able to retain some of their stinging cells (nematocysts) in a functional state so that they are able to reuse them in their own defence. Glaucus atlanticus is a nudibranch that can severely sting humans. It is now thought that nematocysts reach a state of physical but not physiological maturity in the cnidarian. Usually, after some time, they then become part of the cnidarian's functional armoury. It is thought that the nematocysts which are captured and able to be used by the aeolids are those that are physically mature when eaten, but not yet physiologically mature. http://www.seaslugforum.net/factsheet.cfm?base=defcnid

I cannot imagine a jelly without their cnidocytes; it would be a suicide. It is their key adaptation and the source of their entire identity. So, it seems that the nematocytes should have evolved first in some kind of an organism and then defined their subsequent animal possessor as a cnidarian. Where did these deadly cnidocytes come from? Some worms have them, some Myxozoa also have them. The well-being of a huge number of soft-bodied animals totally depends on them. Given all that, where did this all-important adaptation come from? The short answer is, there are no good ideas. As is often the case when it comes to the emergence of the most important, unique adaptations, the talk about the "survival of the fittest" ceases and uncomfortable silence sets in. They have emerged... somehow... somewhere...

How? Where? There are some bravehearts that try answering these questions, but their solution is to point in the direction of unknown, extinct protists:

...Shostak hypothesizes that the cnidarian epithelium came from one group of animals and the interstitial cells (I-cells), the precursors of cnidocyst-producing cnidoblasts, came from another. His evidence is that: (1) The cnidarian epithelium and I-cells are autonomous and differ in their morphology, cellular dynamics, and the relationship of differentiation to proliferation. (2) Hydras and their planula larvae can be "cured" of I-cells and their derivatives, thereby creating "epithelial" animals that lack responsiveness but are able to survive. (3) I-cells can be successfully reintroduced into "epithelial" animals that lack responsiveness and that the reintroduction of I-cells into "epithelial" animals restores missing differentiated cell and organismic characteristics. http://www.devbio.com/article.php?ch=23&id=228

...Did cnidarian cnidocysts originate from cnidocyst-bearing protists living as symbiotic partners with an epithelial placula? If an increase in the fitness of symbiotic partners was "locked in" by an evolutionary stable strategy, co-evolution and compartmentalization could have led phyletically separate, eukaryotic symbionts to fuse and undergo nuclear merger. Traits originating in the symbiotic partners would have been brought to the "synthetic" organism and reworked through evolution into the development of an integrated organism. http://www.pitt.edu/~biohome/Dept/Frame/Faculty/shostakabstract.htm#283

Could it be that if we forget about the cnidocytes, the answer about cnidarian origin would be simpler to answer? That is not the case. The origin of Cnidarians has always been a mystery. A view is gaining popularity (following the recent analyses of Hox genes) that the cnidarians and other Radiata are, in fact, degenerate bilaterians who lost their germ(?) layer (becoming diploblastic) and bilateral symmetry. As you might have guessed, in such a case one needs to postulate that we (Eumetazoa) are a paedomorphic form of bilaterally symmetrical sponge larvae. Well, all I can say is that the difference between a sponge and a jelly is larger than that between a cave and a skyscraper. Jellies have eyes, muscles, nerves, guts and what not. How was this gigantic step forward made remains an unsolved problem.

...Some cnidarians, such as the sea anemone Nematostella vectensis, exhibit bilateral symmetry. It uses homologous genes to achieve bilateral symmetry: Multiple Hox genes are expressed in a staggered fashion along its primary body axis, and the transforming growth factor is expressed in an asymmetric fashion about its secondary body axis. These data suggest that bilateral symmetry arose before the evolutionary split of Cnidaria and Bilateria. http://www.sciencemag.org/cgi/content/short/304/5675/1335

...The studies of the development of Nematostella suggest that cnidarians evolved from bilaterians, secondarily losing bilateral and gaining radial symmetry. If we want to get a picture of what happened at the boundary between diploblasty and triploblasty, we need to go back to the sponges. They are classically considered to be simple metazoans, with no obvious symmetry. The homeobox complement of sponges [a cluster of development regulation genes] is limited to a few NK-like genes; no Hox or ParaHox gene has been found. It is tempting to place the genesis of the [homeobox] megacluster at the sponge-cnidarian divergence, right at the origin of bilaterality and triploblasty (assuming that cnidarians are regressive bilaterians and triploblasts). Sponge larvae are architecturally closer than adult sponges to other metazoans. One possibility is that other metazoans (including cnidarians) evolved from a neotenous larva of ancient sponges, and that sponges were, in fact, the simplest bilaterian metazoans, having a single or only a few Hox-like genes and several NK genes. This would imply that no basal non-bilaterian animals currently exist. Perhaps all extant animals are primitively triploblasts, with a few lineages that have secondarily lost bilaterality and germ layers, with only the forlorn placozoa as the very last holdout of the ancient diploblast line.

Will we ever find out who the jellies are and how did they get their sting?

Suggested reading
excellent review on physiology of nematocysts is given by G Kass-Simon and AA Scappaticci (2002)
Shostak, S. A symbiogenetic theory for the origins of cnidocysts in Cnidaria. Biosystems 29(1993)49-58
P. Holland, The Ups and Downs of a Sea Anemone, Science 304(2004)1255 - 1256.
UPD: interesting finding about cnidarian Hox genes (looks like these are not clustered like ours)

XX. Paramecium aurelia (The origin of criminality)

Так соборы кристаллов сверхжизненных
Добросовестный луч-паучок,
Распуская на ребра, их сызнова
Собирает в единый пучок.
Osip Mandelstam (1937)

In the last essay of this series, I return to the subject of weaponry. We have seen how deadly the stinging cells (cnidocytes) of the jellies might be. These cells kill by shooting a tethered poison dart that is tightly coiled inside a specialized inner pocket. The only worthy idea as to where such a deadly weapon might have come from was that it is stolen by the jellies from an extinct protist.

There are, in fact, protists that use somewhat similar types of weapons, albeit far less advanced. A stone knife may be regarded as the progenitor of a crossbow, although the transition required several technological revolutions, much tinkering, and a span of 100 kyr in order to complete. One of the protist favorite weapons is a long, thin ribbon that is tightly coiled within a specialized "organelle." The ribbon is released to ward off or kill the predator, or a competitor -- sometimes even a mate! In one case (see below), this release is triggered by the hormone adrenalin -- the same hormone that triggers bloody shoot-outs in Hollywood movies. Sometimes there are nasty proteins attached to this ribbons, to drive the message in.

Interestingly, in many cases these "organelles" are vestiges of symbiotic bacteria. In some cases, the "poison darts" are produced by live bacterial symbionts. The symbionts make the darts, and the protist uses them to kill or scare other protists. As for the bacteria, they have been using tubular structures (for instance, injectisomes of bubonic plague bacteria) in order to penetrate their victim's cell walls for ages; the penetration is followed by injection of cytotoxic proteins. The bacterial Cains were killing eukaryotic (and bacterial) Abels for millions of years before the protists learned from their endosymbionts how to use these tricks for defense and agression:

...A variety of deadly human diseases involve a particular infection mechanism, a needle-like structure that transfers proteins from the disease-causing bacterium to the host cell. The bacteria with such a structure, called an injectisome, cause bubonic plague, salmonellosis, typhoid fever and infantile diarrhea. Effectors transported via the injectisome disrupt the actin cytoskeleton of the host cell membrane. This system gives the bacteria the ability to evade phagocytosis, preventing an inflammatory response which leads to massive tissue colonization. http://www.world-science.net/ScienceNewsBriefs/050225_Bacteria's.htm

Did the symbiont bacteria invent their ribbons and syringe tubes? In one case, it has been conclusively demonstrated that the ribbons are made (by the bacteria) from the genes encoded in their plasmids and bacteriophages [bacterial "viruses"]; perhaps the ribbons served first as tail sheath proteins (?) of the phages. They were used by these phages and/or "selfish DNA" to get inside the bacteria. Amazing, isn't it?

Here are the details:

...The six known species of the single-celled marine protist Euplotidium are distinguished from their relatives by a band of bumps on their surface, from which defensive ribbons shoot when the protist is approached by other, predatory protozoans. On close inspection, the bumps turn out to be bacteria that are "body-farmed" by Euplotidium to serve as a defense organ. Neither Euplotidium nor their bacterial bodyguards can live on their own, and so this life-form clearly evolved when one genome acquired the other. http://www.findarticles.com/p/articles/mi_m1134/is_10_111/ai_95357577

Euplotidium. The bumps are ectosymbiotic bacteria that shoot ribbons at unicellular predators.

...Epixenosomes ("external alien bodies") of ectosymbionts [bacteria living attached to the surface of a host cell] on ciliate Euplotidium defend their host against another ciliate predator, Litonotus lamella. These episymbionts are located on the surface of marine ciliates of the Euplotidium; they are closely related to bacteria Verrucomicrobia. Epixenosomes contain a basket built up of bundles of regularly arranged tubules whose inner and outer diameters (22 and 13 um, respectively) fall into the range reported for tubulin microtubules [these are bacterial tubulin-like proteins rather than common 24 nm diameter eukaryotic microtubules, see http://www.annalsnyas.org/cgi/content/abstract/503/1/515b] External signals of unknown origin are detected by membrane receptors which triggers the ejection of the tubulin ribbon. The ejection process is involved in defense. During the ejecting process, the extrusive apparatus unrolls from the inside and forms a hollow tube, about 40 um long. The most similar structures to the epixenosomal extrusive apparatus so far described are the R bodies of Caedibacter teniospiralis [see below], the bacterium that confers the killer trait to ciliate Paramecium aurelia. The extrusive apparatus of epixenosomes, however, is a far more complex structure. There are also eukaryotic organelles consisting of coiled ribbons that unroll from the inside during ejection; for example, the ejectisomes [see below] of cryptoprotists. http://www.pnas.org/cgi/content/abstract/97/4/1813

Paramecia that are mentioned in the previous paragraph are amazing protists. They typically have hundreds of bacterial or algal symbionts:

...Paramecia are aerobic ciliates from fresh water and brackish water habitats. Many of the paramecia brought in from nature are found to contain symbionts. Usually, there are hundreds and sometimes even thousands of symbionts per paramecium. Endosymbionts may be found in the micronucleus, macronucleus, perinuclear space and cytoplasm of paramecia [Like other ciliates Paramecium has two kinds of nuclei: a large macronucelus, and 1 to 80 smaller micronuclei. Micronuclei are thought to be essential for generating genetic variation during sexual reproduction] With respect to endosymbionts, Paramecium is by far the best-studied ciliate genus.

Paramecia with its food vacuoles stained red. The oral groove looks like a membrane flap folded over. At the end of the groove, cilia force food into the food vacuole as it forms. A lot of excellent color photos of Paramecia can be found on http://ebiomedia.com/gall/classics/Paramecium/paramecium2.html

...Paramecium bursaria is capable of farming certain algae within its own cytoplasm! It receives some of the products of the alga's photosynthesis in return for providing a home for the algal symbiont, Chlorella. http://ebiomedia.com/gall/classics/Paramecium/paramecium2.html

....Many of the symbionts of Paramecium confer on their hosts the ability to produce toxins capable of killing sensitive Paramecium strains of the same species and even of other species, if the toxins are liberated into the medium. The toxin producers are called "killers" and their victims "sensitives." If the toxins act only during the period of cell-to-cell contact at conjugation, the toxin producers are called "mate killers." Different killer stocks of Paramecium induce spinning, vacuolization, paralysis, formation of aboral humps, and rapid lysis.

A video sequence showing the murder of a "sensitive" cell is given on

...A feature unique to the killer symbionts of the genus Caedibacter [in Paramecia] is the ability to produce R bodies. R bodies (refractile bodies) are proteinaceous ribbons (10-20 um long, 0.5 um wide, and 13 um thick) rolled up inside the bacterial cell to form a hollow cylinder about 0.5 um in diameter and 0.5 um long. By appropriated triggers, such as low pH, they are induced to unroll. Before the release, the ribbons are rolled into tight coils. When released, they make a coiled tubular structure. http://www.pnas.org/cgi/content/abstract/80/1/250

...the genetic determinants of R bodies are plasmids or bacteriophages that have lost the ability to lyse their host cells. R bodies of some Caedibacter species are associated with phage capsids. The proteins of these R bodies and perhaps also the toxin are encoded on bacteriophage genomes. Only Caedibacter bearing phages or plasmids may confer the killer trait to their hosts.
see photos on

...The ejectosomes of cryptomonads occur in two sizes in the unicells: as small ones underneath the cell surface and as larger ones lining a cell invagination. Each ejectisome consists of two spiral ribbons under tension connected with each other. If the cells are irritated either by mechanical, chemical or light stress, they discharge their ejectisomes and the cells try to escape from the source of danger by jumping away in a zig-zag course. [Cryptomonads also have chloroplasts that they stole from red algae] http://fixedreference.org/en/20040424/wikipedia/Ejectisomes

This story illustrates the difficulty of tracing down the "invention." It is not easy to point out who invented what. The bacterial phages and/or plasmids stumbled upon coiled ribbons to get in and out of the bacterial cells. The bacteria learned how to resist these puncturing coils, but many protists did not. The ribbons are made by the bacteria and used by their symbiont hosts to kill or ward off "sensitive" protists. One of these protists or its bacterial symbionts or their phages/plasmids developed this strategy to perfection and the solution was stolen, via symbiosys with an (algal?) protist, by a proto-jelly who learned how to wield this weapon with deadly efficiency against larger prey. The jellies were in turn used by sea slugs who harvest and reuse their stinging cells. Perhaps "natural selection" played some role in all of these events, but the creative vehicle was serial symbiogenesis.

Is this how innovation typically occurs in Nature: through endless stealing and integration of the best solutions?

Suggested reading
G Petroni, S Springdagger , K-H Schleiferdagger , F Verni, G Rosati, Defensive extrusive ectosymbionts of Euplotidium (Ciliophora) that contain microtubule-like structures are bacteria related to Verrucomicrobia, PNAS 97(2000)1813-1817

Epilogue (What is Life?)

Я скажу тебе с последней
Все лишь бредни, шерри-бренди,
Ангел мой.

Osip Mandelstam (1931)

This post concludes the series on the "Wonders of Nature." Of course, I did not run out of wonders, but I ran out of time – and perhaps everyone’s patience too. After all, there are millions of species living on this planet, every single one of them a little wonder, and I cannot cover them all. I might yield to the temptation and add more "wonders," but more examples would not mean more understanding.

What was the point of these essays? Of course, it was asking a question. This particular question is nothing new. Almost 60 years ago, Erwin Shroedinger asked the very same question, "What is Life?" – in his famous book by the same name.

That book provided the major spur to molecular biology and the discovery of the double helix. Unfortunately, the book did not answer the question. Shroedinger was not the first and he will not be the last to ask this question and fail to provide an acceptable answer. I have heard many such answers in my time, and I cannot avoid making painful conclusions. The answers typically reflect the mentality of the one who answers and the state of contemporary science and technology rather than any deep insight into Life. To the 19th century materialists (Engels), Life was "a mode of motion of albuminous bodies" (the age of the microscope). In Shroedinger's time (the age of the x-ray tube) Life was an "aperiodic crystal" of some sort or the one "which avoids the decay into equilibrium." In the 1950s, Life was the way in which the code, the freshly discovered DNA, is translated into organism's morphology (the age of the type recorder). Presently, there are many computer-inspired definitions that are revolving about information processing (the age of the desktop). One typically gets something along the lines of "Life is actuation of the instructions encoded in genes" (Dulbecco) and a lot of vague talk about programming and self-correcting, self-improving codes. These abstractions culminate in a computer game or a mathematical model of dubious import that supposedly imitates Life. The holistic definitions with the ecological bent, in contrast, reflect the more recent rise of the web, and so do various network-inspired definitions (Kauffman, Conrad). The infamous Intelligent Design (in which Life is regarded as an erector set of ingeniously-designed molecular machines) is the reflection of our latest infatuation with nanotechnology. Anthropomorphic views of Life as an assembly of struggling individuals grimly intent on the survival of the fittest or equally poetic comparisons with the 20th century factories ("blue prints," "building blocks") tell more about us than they do about Life. The reductionist, over-detailed "scientific" definitions (the cells are built in such and such way) are missing the point altogether. One can provide the full list of DNA bases that make a man and still be clueless what man is or how to make one. The familiar lists of main attributes of Life that hop from one biology textbook to another (the matter/energy flow, self-reproduction, organization, adaptation) would have you to admit that snowflakes and eddies are alive. The latest craze is, of course, "complex systems." From that you get "non-reducibility" and "a material system is an organism if, and only if, it is closed to efficient causation" (Rosen). Tomorrow it will be something else.

There are other definitions of Life that are more on the philosophical side. Some say, for example, that living organisms are "autopoietic systems" (self-regulation, self-replication, etc.) Others (Wicken, Margulis) suggest that Life is a peculiar reaction to energy gradients. Like a convection flow which self-organizes into a complex honeycomb pattern between the hot and cold plates, Life "self-organizes into the patterns of increasing complexity." How does that happen exactly is not too clear, but it is a minor point. The third group of definitions stresses the organization and/or the autonomy in so many ways. One popular definition specifies that Life is what undergoes evolution by natural selection (Maynard Smith). In such a case, if you are skeptical about natural selection, you are not studying Life, and there is nothing to talk about, so you better keep mum. The milder version of this Machiavellian maxim is that Life is a system "capable of evolution." I discovered these amusing formulas in a book by Franklin Harold ("The Way of the Cell: Molecules, Organisms, and the Order of Life", Oxford U Press, 2005) that sums up many of such definitions in Chapters 2 and 10; you can peruse this book and see for yourself. It is a good book, although I am afraid it is not quite on the par with Shroedinger’s classic. Yet it integrates over a lot of material, and one can quickly review the ideas. Unfortunately, the net result of this review is zilch: a lot of clever metaphors, but no answer worth taking home.

All of these definitions, ingenious as they might be, are lacking in one important respect. I do not think that people who study Life or those who are fascinated by Life do so because it is an autopoietic system capable of evolution by natural selection, or a peculiar reaction to energy gradients, or the selfish genes battling each other, or a spatial arena for the survival of those of the fittest that are closed to efficient causation. I do not know anyone who got interested in the subject inspired by such concepts of Life. Furthermore, all of these definitions suffer from the lack of precision and the inability to compare directly with other implementations of life. It is tricky to generalize something that is utterly unique, like Life. If that is not enough, most of Life happened in the distant past, which would never be fully accessible. Even if we will find alien life elsewhere, it may not help us to understand the life on this planet. Life as we know it is ours only, it cannot be recreated elsewhere. We are stuck with what we have and we must make sense of it.

I believe that our fascination with Life has entirely different cause than "the energy flow" or "the organization of albuminous protoplasm." I suspect that deep down any biologist and biochemist, any scientist and any lay man already knows what Life is; the question is redundant. Every little kid knows the answer, and those few who don't quickly discover it for themselves on their first trip to a zoo or a museum. I also guessed the answer instantly when I found my first shellfish, on that fateful summer day 35 years ago. The answer is very simple and it is right before your eyes. The more you learn about Life and its inner workings, the more you get of this answer and the clearer its truth transpires. I wanted to remind you of that answer, the only correct answer, which you always knew anyway:

Life is a vast, ever-changing collection of oddities, miracles, and wonders.

Why? That is the real question. The answer will be long in coming.

Я скажу это начерно, шопотом
Потому что еще не пора:
Достигается потом и опытом
Безотчетного неба игра.

Osip Mandelstam (1937)

PS: translation of the epigraph:
I will tell you with the utmost
All is folly - sherry-brandy, -
Angel mine.


Увы: ни музыки, ни славы!
Так от зари и до зари,
В силках науки и забавы
Томятся дети-дикари.

Osip Mandelstam, "Soccer" (1913)

These essays form a single narrative concerned with a bizarre phenomenon that we call Life and all these puzzling, wonderful creatures lurking around. The series addresses long-standing problems in evolutionary biology, the problems that I deem more important than ad hoc explanations for the variation of beaks in Galapagos finches. Among these key problems is eukaryogenesis, the origin of multicellularity, sex, and germ-soma division, the origin of crucial adaptations in animals, such as blood, skeleton, eyes, and nerves. I repeatedly juxtaposed animals and plants and discussed phototrophy and bioluminescence. I take fancy in the latter two issues, professionally as well.

As you might have noticed, "natural selection" has not been dismissed, but it was seldom relevant to the discussion. By contrast, symbiosis and lateral gene transfer have appeared many times in the series. I generally abstained from the broad-sweep theories of evolution, because I am sceptical of all such theories and even the possibility of such theories. Instead, I focussed on specific examples and evolutionary transitions. Actually, these are much more interesting and educational. This series is about questions rather than answers (not that such answers presently exist). Some of these essays might be excessively long. It is not easy to put an unsolved, important problem in a nutshell.

Keep in mind that I am not an evolutionary biologist; I am not even a biologist. I've been learning about these problems as I was writing about them; these are my notes.

There might be factual errors or incorrect interpretations given in the text. Please, do not hesitate to point these errors to me. It is also likely that I have omitted or overlooked some important developments that shed entirely new light on the problems discussed. I would appreciate if you straighten me up.

Post Scriptum

I would like to recommend a few popular books for those who are interested in the question, but lack grounding in biology and biochemistry. These are well written, relatively short books that are still on the shelfs of our bookstores. I'll revisit this list and add to it if I'll find more such books.

Unfortunately, most of the evolution biology textbooks aim either too low or too high. BTW, reading Ernst Mayr's (or Dawkin's) and Lynn Margulis' books back to back might be very entertaining. Her latest book has a perfect epigraph, from Darwin's "The Origin of Species" (1859): Any one whose disposition leads to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject my theory. And then she furnishes devastating criticism of neo-Darwinism. I cannot imagine what are they going do to a school teacher who would read aloud some of the more provocative passages from Margulis' book. The worst part of it is that she is the most influential evolution thinker in the US. You cannot declare her incompetent or crypto-Creationist. Here is the short list:

E Mayr, "What evolution is?"
L Margulis and D Sagan, "Acquiring Genomes" (her "Early Life" is a perfect companion)
FM Harold, "The Way of the Cell"
JB Carroll, "Endless Forms Most Beautiful" [the development biology (Devo part) is explained very poorly, but the Evo part is fine]
AH Knoll, "Life on a Young Planet"
N Lane, "Oxygen: the Molecule that Made the World"
I Fry, "The Emergence of Life on Earth: A Historical and Scientific Overview"
R Dawkins, "The Ancestor's Tale" (very broad scope, but a lot of factual errors)
D Grimaldi and MS Engel, "Evolution of the Insects" or AP Rasnitsyn and LJ Quicke, "History of Insects"


Я палочку возьму сухую,
Огонь добуду из нее,
Пускай уходит в ночь глухую
Мной всполошенное зверье!

Osip Mandelstam, "The Zoo" (1916, 1935)




Ripping yarns. 1. The fate worse than death

Barbarian, stay! that bloody stroke restrain;
The crime was common, common be the pain.
I can no more; by shame, by rage suppress'd,
Let tears, and burning blushes speak the rest.

Alexander Pope,
Eloisa to Abelard

I have two leftovers that did not make it into the "Wonders" series. These are tragic stories of arms races and sex. Evolutionary biologists are having hard time explaining sex. Perhaps all of the ideas currently in circulation are incorrect, but that does not really matter. Following and testing these ideas has already been rewarding because it stimulated re-examination of the familiar and the search for the exotic.

Castration of Uranus by his son, Chronus. The Furies were born from the spilt blood.

We have briefly discussed the famous Red Queen (RQ) hypothesis which posits that the advantage of sex (vs. asex) is in the reduction of parasite load on the host: the [host] organisms are running cyclic arms races with their parasites and the role of sex is to preserve genes which are currently disadvantageous, but which might become advantageous against the background of a likely future population of parasites. Parasites evolve quickly, due to their short lifespans. Two consecutive host generations might be faced with very different selective pressures. If this change is rapid enough, it might explain the persistence of sex.

I am very skeptical of the RQ hypothesis. For instance, many if not most of the parasites reproduce sexually. Who are THEY racing against? (it cannot be the slowly changing host) Furthermore, if a sexual host is not in the interest of the parasite, it would go to great lengths to create a situation in which asex is the only possible way of reproduction. How can this behavior be fitted into the RQ hypothesis? Parasites routinely interfere with the sex life of their hosts. The proverbial bacteria Wolbachia alters the sex of its host, the wasp (it prefers females). There are also numerous aquatic parasites that castrate their hosts, e.g., by sterilization of males. Castrated males are bigger and fatter: there is more food and shelter for the parasite.

...The harm parasites cause to their hosts is an unavoidable consequence of parasite reproduction with costs not only for the host but also for the parasite. Castrating parasites minimize their costs by reducing host fecundity [potential reproductive capacity], which minimizes the chances of killing both host and parasite prematurely. http://www.journals.uchicago.edu/cgi-bin/resolve?id=doi:10.1086/424606

It is a good strategy. The fact remains, though, that there are no known populations in which such parasitic castration resulted either in a switch to asex or clear preference for sex over asex. What should we make of such observations? Does these mean that the RQ hypothesis is correct? If it is correct, these observations confirm that even the greatly reduced chance for sexual reproduction is better than asex. If it is incorrect, the preference for sex has absolutely nothing to do with the parasitism. From the onset, many people have voiced such a concern about the RQ hypothesis: seemingly, it can rationalize any outcome.

...In the RQ theory, parasites should be under strong selection to be able to infect the most common local host genotypes. Hence, as a clonal mutant spreads in a sexual population, it should be selected against in direct proportion to its frequency. If infections are sufficiently virulent to compensate for the reproductive advantage of clonal females, then sexual females should be preserved in the short term. This leads to the expectation that asexual populations, where they exist, should be associated with a low risk of infection. However, the individual hosts from asexual populations should be easier to infect by local coevolving parasites than individuals from a sexual population. So, on one hand, sex should be associated with the relevant selection pressure (parasites); but, on the other hand, asexual populations are expected to have higher levels of infection (assuming all else equal). This kind reasoning has lead to the criticism that the parasite theory can predict any kind of association between parasites and host sex in the wild, thereby making the theory unfalsifiable.(Lively, 2001)

The evidence can always be turned both ways. More damning for the RQ hypothesis is that in the populations where both the sexual reproduction and the asexual cloning occur, no evidence has been produced, despite persistent search, that it is, specifically, the parasitism that maintains sex. In short, even such an extreme form of parasitism as sterilization of the host fails to produce clear-cut evidence for the RQ hypothesis.

Welcome to the exciting world of parasitic castration:

...Rhizocephalans are distant relatives of acorn and goose barnacles that parasitize on shrimp and crabs. The morphology and life cycle of rhizocephalans make these perhaps the most spectacular and unusual of parasitic organisms. Adult rhizocephalans possess no appendages and are anchored by a stalk from which roots proceed into host tissues. The larvae attaches to its host via its antennae. It metamorphoses into another form of larvae which form embryonic cells that are carried throughout the crab forming the root-like branches throughout the host called the sacculina interna. A large mass then forms and this contains the genital system which, when mature is called the sacculina externa. The motile larvae are released from this structure. These free-living stages are the only stages of the animal that has any hint of resemblance to nonparasitic barnacles. http://web.mala.bc.ca/goatert/PARASITE/PARRHBRN.HTM

...Branching roots of the parasite invade all tissues [of affected prawns] and absorb nutrients. Infection causes stunting of growth, modification of the secondary sexual characteristics and castration. Infected prawns usually die when the parasite has completed its life cycle. The disease usually occurs in low prevalences (< 5%), however, high prevalences (up to 47%) were found on some stocks of prawns in northern British Columbia. http://www.pac.dfo-mpo.gc.ca/sci/shelldis/pages/sylonsp_e.htm

In Taiwan, the infection rate of Sacculina spp. on crabs reaches 30-40%. In Mexico, this rate is as high as 52% (in a population of the blue crab, Callinectes sapidus Rathbun). The castration of crabs did not start yesterday, it was going on for millions of years:

...Examination of the sterna and abdomina of extinct crab, Tumidocarcinus giganteus Glaessner, from the Miocene (> 5 Myr ago) showed that some animals exhibited an abdomen that had the male characteristic of outline of the abdominal somites but the abdomen was abnormally broad. This remarkable morphology can be attributed to parasitic castration. The barnacle consumes the gonads, shutting down production of male hormones, so that the host crab is "feminized." http://www.zoeticzone.com/p/articles/mi_qa3790/is_200311/ai_n9307733/pg_6?pi=zoe

Many other aquatic parasites castrate their victims. E.g., trematode worms castrate their host snails (both females and males) to induce gigantism:

...The shells of [freshwater snails] Lymnaea truncatula infected with the larval stages of [sheep liver fluke] Fasciola hepatica are significantly longer than those of comparable uninfected controls. The dry tissue mass of infected snails is twice that of the controls. Castration was brought about 17-21 days after infection as a result of the direct consumption of the ovotestis [hermaphroditic gonad of the snail]. In a separate experiment it was demonstrated that a population of infected snails survived as long as a similar group of control snails. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=6892863&dopt=Abstract

There are even bacteria and unicels that castrate their hosts:

...Endoparasite bacteria Pasteuria ramosa castrate their host, the planktonic crustacean Daphnia magna. Both antagonists are resource-limited and there is resource competition among them. P. ramosa induces gigantism, which reduces host fecundity but assists parasite reproduction. The gigantism is beneficial only for the parasite. Hosts have evolved counter adaptations: the infected hosts have enhanced reproduction before castration that compromises parasite reproduction. http://www.journals.uchicago.edu/cgi-bin/resolve?id=doi:10.1086/424606

...The microsporidia are spore-forming unicels that lack mitochondria in all life cycle stages; they are completely dependent on the host cell for the supply of energy. All major groups of animals host microsporidia. They are especially common and important parasites of insects, crustaceans, and fish. Many species of microsporidia influence their hosts in various ways. Parasitic castration, gigantism, change of host sex are effects of microsporidian parasitism. In the most advanced cases of parasitism the microsporidium rules the host cell completely and controls its metabolism and reproduction. http://www.biol.lu.se/cellorgbiol/microsporidia/proj_descr.html

...Ciliate parasitic castrators in mayflies feed on hemolymph as well as gonadal and muscle tissue and fat bodies. http://www.findarticles.com/p/articles/mi_qa3845/is_200301/ai_n9304836

Et cetera, ad infinitum. Why are the species in which 50% of the males are castrated by a parasite still reproduce sexually? What is the advantage of sex for such maltreated hosts?

The recent studies by Lively on common freshwater snails, Potamopyrgus antipodarum, in New Zealand mountain lakes gives an interesting perspective on the sex-parasitism connection. A popular rendition of these studies (with many diagrams and figures) can be found on his web site: http://www.indiana.edu/~curtweb/Research/sex&recomb.html. I'd rather follow his 2001 paper which is much more tempered and cautious in tone than his initial 1995-1999 "optimistic" reports -- perhaps as the result of persistent criticism .

The snails are either sexual (diploid) or asexual (triploid females). The asexual lines are derived from sympatric sexual females. There are lakes where there are only asexual snails and the lakes where both sexual and asexual snails coexist, but there are no lakes in which only sexual snails are present. The clonal diversity in these mixed populations is very high. The clones tend to be unique to a particular lake population, and they share alleles that are present in the local sexual population. In other words, they have emerged independently in many populations of snails.

In most of these populations, fewer than 5% of the individuals are infected by sterilizing trematodes (that infest all snails regardless of their sex), but in some lakes as high as 45-50% of the snails are infected. If one plots the prevalence of infection vs. the frequency of males, there is almost no correlation. Lively concludes (in this and his other studies) that coevolutionary interactions give the advantage to rare genotypes rather than sex as such; there are no data suggesting that sex in snails is maintained by the parasites. In fact, the introduction of two clonal lines in the mixed population invariably caused the extinction of the sexual snails. The parasites appear to be selecting for clonal diversity rather than sex. Genetic diversity, yes; the maintenance of sex, no. Of course, one can always retort that the RQ-active parasites were not the ones studied, but such refutations only entrench the view that the RQ theory is inherently unfalsifiable. All other experimental tests of the RQ theory have similarly faltered. The studies claimed to provide the "proof" of the RQ are hotly contested. The theory sounds great but it appears to be either incorrect or unfalsifiable. Lively suggests that RQ in concert with the purge of deleterious mutations (Muller's ratchet) might have explained the results, but verification of that is even more tricky than proving or disproving the RQ hypothesis alone.

What keeps sex going? Why are the parasites (if sex is a very good resistance strategy) not forcing asexuality on their hosts?

Suggested reading:
CM Lively, Trematode infection and the distribution and dynamics of pathogenetic snail populations. Parasitology 123 (2001) S19-26 (on
(Lively' web site http://www.indiana.edu/~curtweb/Research/sex&recomb.html has many more references)
Ebert, D., H.-J. Carius, T. J. Little, and E. Decaestecker. 2004. The evolution of virulence when parasites cause host castration and gigantism. Am. Nat. 164:S19-S32.

Ripping yarns. 2. Bad bugs

Marke but this flea, and marke in this,
How little that which thou deny'st me is.

John Donne,
The Flea

Perhaps insects supply more examples of bizarre sex than all other animals put together. Generally, males do not have happy, rewarding lives. The females are bigger, more aggressive, live longer, etc. There are females (e.g., of the mantids) that eat or behead their mates before, during, or immediately after the copulation (so-called sexual cannibalism); other females use their mates as a food supply for their brood. While such behavior is understandable (who needs a male after the insemination; there are always more around), I find cruelty to males despicable and unpardonable. It is also foolhardy: poor treatment of males can lead to their revolt and the reversal of fortunes. Cruelty begets cruelty. The boys can be every bit as mean as the girls, or worse...

...Recently, there has been a shift away from the view that the sexes share a common goal during reproduction and a move toward the concept that males and females are often in conflict over reproductive outcomes. Sexual conflict occurs because of the potentially different fitness optima for each sex resulting from copulation, such as conflicts over isogamous and anisogamous reproduction, copulation duration and mating frequency, and relative parental investment. Conflicts can also arise when copulation is costly to one partner (usually the female), because of adaptations in the male that are associated with sperm competition. Eg, female fruit flies are polyandrous and their mates transfer proteins within the ejaculate that act to disable and kill the sperm of rival males. Male success in sperm competition is, in part, determined by these proteins that are also toxic to the female and reduce female longevity and fitness. The resulting conflict has produced a rapid coevolutionary arms race between the sexes.

Beastly boys: bed bugs.

...[Traumatic] extragenital insemination (internal insemination without the involvement of the female's genitalia) is rare but taxonomically widespread in invertebrates. It has been described in two orders of insects (Hemiptera and Strepsiptera) of which the hemipteran family, the Cimicidae [bed bugs], are the most widely cited example. Copulation consists of abdominal wounding of the female by the introduction of a specialized male intromittent organ [paramere] through an external groove overlying the pleural membrane in the female's abdominal wall. The genital tract is not used for copulation but functions solely in egg laying. Once the intromittent organ pierces the body wall it enters a female paragenital organ containing haemocytes [called spermalege]. Sperm then migrate to the ovaries (where fertilization takes place) via the specialized structures.

...Male bedbugs produce an abdominal wound in females during mating. Do female bed bugs pay a cost for mating? Under controlled natural conditions, traumatic insemination was frequent and temporally restricted. Traumatic insemination results in (i) last-male sperm precedence, (ii) suboptimal remating frequencies for the maintenance of female fertility, and (iii) reduced longevity and reproductive success in females. The females did not receive indirect benefits from multiple mating. We conclude that traumatic insemination is probably a coercive male copulatory strategy that results in a sexual conflict of interests. http://www.pnas.org/cgi/content/full/98/10/5683

...The frequent wounding of female bedbugs during copulation has been shown to decrease their fitness, but how females have responded to this cost in evolutionary terms is unclear. The evolution of a unique anatomical structure found in female bedbugs, the spermalege, into which the male's intromittent organ passes during traumatic insemination, is a possible counteradaptation to harmful male traits. Several functions have been proposed for this organ, and we test two hypotheses related to its role in sexual conflict. We examine the hypotheses that the spermalege functions to (i) defend against pathogens introduced during traumatic insemination; and (ii) reduce the costs of wound healing during traumatic insemination. Our results support the 'defense against pathogens' hypothesis, suggesting that the evolution of this unique organ resulted, at least partly, from selection to reduce the costs of mating-associated infection. We found no evidence that the spermalege reduces the costs of wound healing. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14667353&dopt=Abstract

...Meanwhile, the reason why male bedbugs should have adopted such an unusual insemination technique in the first place remains a mystery. Molecular phylogeny of the bedbug family [may provide] clues as to how this extragenital system has developed from ancestors with a more conventional sex life. http://www.the-scientist.com/article/display/21635

Why do they follow such odd sex practices? How did the male bedbugs turn the table on their females?

Endless forms not too beautiful

Today I took my kid to Field Museum, Chicago. They've just finished their new palaeontology exhibit (completely remodeling the entire floor). I am very pleased with this new exhibit (especially with the Cambrian virtual aquarium). The only eyesore are the ghastly 1930s paintings of Charles Knight taken from the storage and displayed prominently on the walls. One of the new exhibits is on extinct North American sharks. Two of these, Helicorpion Ferrieri and Stethacanthus altonensis, were remarkable in their oddity. Each one presents a formidable puzzle involving their "teeth." These are perhaps among the most queer fish I've ever seen. The first puzzle is, how to put teeth on a shark? This one:

Helicorpion, Illinois, mid-Permian (250 Mya, Leonardian). Neither the position of the whorl teeth is known nor their function understood. These "reconstructions" are artist's imagination. Some other takes are on http://school.discovery.com/schooladventures/prehistoricsharks/gallery1.html
Some of these designs are clearly inspired by can openers and chain saws.

...Helicorpion comes from mid-Permian deposits in Russia, North America, Japan, and Australia. Curious spiral structures, some 10" across, were first thought to be the coiled shell of an ammonite. On closer inspection, it was discovered that they were a continuous whorl of teeth [!] or perhaps dermal denticles from some kind of shark. In short order, the creature was named Helicoprion and the game of trying to figure out how this structure might have fit onto a shark began in earnest. A Russian paleontologist A. P. Karpinski invested years of his life in futile attempts to restore the position of the whorl. Karpinski tried just about everything. He perched the whorl on top of the first dorsal fin, like some kind of bizarre windmill. He tried hanging it from the tip of the tail, coiled like a piglet's tail. He even placed the whorl on the tip of its nose, making the fish resemble a sinister swimming elephant. It is now generally agreed that the structure is a complex whorl composed of up to 180 teeth and must therefore have fit somehow into the mouth. Further specimens revealed that the teeth of Helicoprion most closely resembled those of a group of Paleozoic sharks known as edestoids. One of the best-known species, Edestus giganteus, was a 20' super-predator (about the same size of the modern white shark) with teeth that kept growing beyond the tip of its snout. The most likely orientation - based on the teeth of Edestus and related edestoid sharks - is that the teeth overhang from the lower jaw like the vertical blade of a circular saw, having coiled about themselves as new teeth were generated from behind. Perhaps Helicoprion used this buzz-saw arrangement to snag squid-like creatures with a sideways swipe of the head while swimming through a school of the soft-bodied molluscs. Helicoprion exemplifies some of the difficulties involved in reconstructing ancient creatures from only a few clues.

...Many isolated tooth whorls of HelicoprionHelicoprion</i> that shows the shark's lower jaw curling downward into a tooth-studded spiral. One could imagine that the shark uncoiled its jaw and lashed at prey with a sort of toothed whip. Another theory is that Helicoprion's tooth spiral mimicked coiled shellfish called ammonites in order to attract these ammonites, the shark's prey. "It seems more likely," Long writes, "that these sharks used the jagged tooth-whorls when charging into a school of fish or ammonites and thrashing about to snag prey on the projecting array of teeth." Another paleoichthyologist, R. Lund, pointed to the disproportionate size of the teeth making up the whorl, and the bases of the teeth being locked together during growth, a feature that prevented the shedding of the teeth. "Thus the smaller and older teeth are just shoved out and down, sort of like an ingrown toenail, only with teeth." Lund believes the spiral must have been proportional to the size of the jaw that supported it: "Any reconstruction of the fish itself must be big enough to accommodate, smoothly, a buzz-saw-like gadget that got up to three feet in diameter. This yields a fish of very impressive size as well as impressive dentures." http://www.findarticles.com/p/articles/mi_m1134/is_2_110/ai_71317744

Puzzle No. 2 is Stethacanthus altonensis, another shark that lived in the late Devonian and through the Carboniferous, about 320-375 Mya:

Other conceptual drawings can be found on http://www.hmnh.org/galleries/deadanimalblog/stethacanthus.jpg

...The body lacked scales except for those on the top of the head and the crest of the first dorsal fin of males.The pectoral whip was widened by proteinaceous rays for better control of maneuvering and they had an almost symmetrical high aspect ratio tail, which would make them good crusiers with significant maneuverability. (R. Lund)

...Stethacanthus was an odd, dogfish-sized shark. The brush-like dorsal fin with enlarged denticles on its flattened top and corresponding denticled patch on top of its head have generated much speculation about their possible function. http://www.ucl.ac.uk/lifesciences-faculty/imagedetails/shark_fossil.htm

...The top of this fin was covered in rough, tooth-shaped scales that match a patch of skin on the Stethacanthus' snout. Was this supposed to mimic a huge mouth and make the creature appear more frightening? Stethacanthus tended to patrol shallow coastal waters on the lookout for food. It ate small fish, crustaceans and cephalopods (eg goniatites). There's evidence Stethacanthus may have been migratory, returning to particular places to mate and give birth. http://www.bbc.co.uk/science/seamonsters/factfiles/stethacanthus.shtml

..Dozens of highly imaginative ideas have been advanced to 'explain' the function of Stethacanthus' bizarre headgear. One suggestion is that the paired structures might have mimicked the jaws of some creature much too big to mess with, thereby discouraging would-be piscivores from attempting to dine on Stethacanthus fillets. Another, somewhat more whimsical notion, is that - by craning its neck and arching its back - Stethacanthus might actually have clamped onto the belly of a larger marine animal and hitched a ride. According to R. Lund, the brush structure does not appear to have been very mobile. Neither of the above proposals, however, explains why only male Stethacanthus are so endowed.It seems far more likely that the dorsal brush and cranial bristles of Stethacanthus played some role in their courtship rituals. Perhaps the brush was a symbol of virility, like the antlers of deer stags, enabling Stethacanthus females to have chosen the best, most genetically fit male with whom to mate. Or perhaps the brush and bristles were used during male-to-male pushing matches, enabling the combatants to grapple together as they tested each other's strength in competition for access to mating grounds or sexually receptive females, by pushing (like modern bannerfish). If, like modern sharks, Stethacanthus relied on forward motion to ventilate its gills, the weaker combatant in such matches would become breathless fairly quickly, and be forced to concede victory. http://www.elasmo-research.org/education/evolution/golden_age.htm

In short, nobody has a clear idea how did these sharks look like and what was the function of their weird "teeth"? What was it?

Metal vs. Life. (1) Eating uranium, breathing rust

An alien organism that "eats" metal (e.g., the spaceship) is the staple of SF. There are, of course, many variants of the gloomy plot: say, a pacifist that unleashes steel-eating bacteria on the world's armies to promote universal happiness. Another such staple is the story of ironclad robots that revolt, savagely kill their humans masters, and live happily ever after.

I do not know much about our chances to be done in by these ungrateful robots, but I do not envy their future. It is not going to be happily ever after. A piece of metal is an invitation to lunch; that is why metallic substances are so rare here on Earth. The relentless onslaught of oxygen, water, and bacteria is unstoppable. Yes, the bacteria. One seldom hears about metal-eating bacteria because their biochemistry is the poorest understood of any of the major metabolic pathways in the microbial world. But bacteria that like metals and metal ions do exist, and they have been hungry for billions of years. They want their metal, and they want it badly. They've been pushed aside by other bacteria, but if the opportunity presents itself they would not miss it.

Dinnertime for thiobacillus. The main course: stainless steel.

First, there are iron/manganese oxidizers, most of which are chemoautotrophs (that is, they make their own organics out of atmospheric CO2; they need only inorganics). The most notorious of these is a sulfate reducer Gallionella that likes austenitic stainless steel. It reduces sulfate to H2S which reacts with the steel to produces metal sulfides. Actually, it is a double act. Aerobic bacteria near the outer surface of the biofilm consume O2 and create anaerobic conditions for these sulfate reducers. Other bacteria, e.g. Thiobacillus thiooxidans and Acidothiobacillus, make sulfuric acid that dissolves metals. They can live in pH 0 sulfuric acid. Ohio River carries 100 million tons of 98% H2SO4 per year made by such bacteria from the thiosulfate in mine deposits. And that's just the beginning.

...In presence of O2, aerobic bacteria like Thiobacillus thioparus, and Thiobacillus concretivorus, that are widely present in the environment, are the common corrosion-causing factors. Without O2, anaerobic bacteria, especially Desulfovibrio and Desulfotomaculum, are common [agents of corrosion]. Desulfovibrio salixigens requires sea water, but D. vulgaris and D. desulfuricans can grow in both fresh and salt water.

...Ferrobacillus ferrooxidans oxidizes iron(II) to iron(III) oxides and iron hydroxides. It only grows in very acidic habitats, pH<3 [Coca Cola is pH=2 - S.] Found with Thiobacillus thiooxidans that produces sulfuric acid. Ferrobacillus lives off the pH gradient created by acidic pH. This maintains very high proton gradient. As H+ flows in, ATP is made. The bacterium needs to get rid of H+ inside the cell, to keep internal pH at 7. So it uses iron(II) as electron donor to O2, combines it with H+ to form water, and gets rid of the extra protons. Iron functions as electron supplier to maintain the proton gradient. http://www.sp.uconn.edu/~terry/229sp03/lectures/autotrophs.html

Leptothrix and Gallionella do the same trick. And they have to be fast and eat a lot:

...The organisms must compete with the abiotic oxidation of iron because the purely chemical oxidation of ferrous iron occurs relatively rapidly. Because very little energy is generated in the oxidation of ferrous to ferric iron, these bacteria must oxidize large amounts of iron in order to grow... http://www.esr.pdx.edu/pub/biology/limnology/limn-12.htm

There are bugs that like jet fuel and steel!

...Cladosporium resinae and Pseudomonas aeruginosa are commonly present in jet fuel. They live in the water-fuel interface of the water droplets, form dark black/brown/green, gel-like mats, and cause microbial corrosion to plastic and rubber parts of the aircraft fuel system by consuming them, and to the metal parts by the means of their acidic metabolic products. http://en.wikipedia.org/wiki/Microbial_corrosion

That's the oxidizers. There are also metal reducers. These guys are so hungry for metals that they would eat uranium and plutonium! They are anaerobic, gram-negative sulfur-reducing bacteria that metabolize the organics by reducing metal ions, such as iron(II), uranium(VI), and plutonium, and use iron(III) oxide (rust) as terminal electron receptor, just like we use O2: they "breath" rust. The two best studied of these oddball bacteria are Geobacter sulfurreducens and Geobacter metallireducens. Not only these bacteria "eat" metal ions opportunistically; they actively look for these in their environment and then destroy them:

...The first Geobacter species was isolated from the Potomac River, just down stream from Washington D.C. in 1987. Geobacter metallireducens oxidizes organic compounds to CO2 with iron oxides as the electron acceptor. G. species provide a model for important iron transformations on modern earth and may explain the massive accumulation of magnetite in ancient iron formations. http://www.geobacter.org/about.html [it may explain the origin of certain types of Archean iron ore-S.]

...G. metallireducens uses a sensor to 'sniff out'soluble metal ions. If metal is not nearby, G. metallireducens grows flagella—whip-like cellular propellers—to find new energy sources. i>G. metallireducens specifically expresses flagella and pili only when grown on insoluble Fe(III) or Mn(IV) oxide, and is chemotactic towards Fe(II) and Mn(II) under these conditions. It senses when soluble electron acceptors are depleted and then synthesizes the appropriate appendages to permit it to search for, and establish contact with, insoluble Fe(III) or Mn(IV) oxide.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11961561&dopt=Abstract and http://www.genomenewsnetwork.org/articles/04_02/geobacter.shtml

...US DOE researchers used G. sulfurreducens to reduce uranium in the groundwater at Rifle Mill [nearby aquifers are heavily polluted by U(VI) leaching from this uranium mine in Western Colorado] by over 70-90%.
http://www.geobacter.org/publications/11520973.pdf See also here and here.

Geobacter has 100+ types of fairly unusual multihaeme cytochromes that it uses for metal reduction; it is highly specialized for reduction of metals. Apparently, it is closely related to S-reducing deltaproteobacteria (http://www.geobacter.org/publications/8636045.pdf). How, when, and why did such bacteria learn the trick of reducing iron and heavy metals and using rust for respiration is not known.

I think that this suffices to make my point. It takes Life to fight Life. The robots do not stand a chance, so they better give up on their rebellious thoughts right now. The bugs already know how deal with them, all that they are lacking is the incentive. I cannot imagine anything we can do, global nuclear war including, that can terminate Life on this planet. The bugs that thrive on plutonium, jet fuel, and stainless steel have been long waiting for their finest hour.

Metal vs. Life (2) Gold digging

Gold. People like gold. Where is it from?

There are traces of Au(III) cations in the rocks, the sea water, and the sediment, but where gold nuggets come from? There are two types of gold: lode (primary) and placer (secondary). There are three major hypotheses for load gold origin: geothermal, magma cooling, metamorphic. The fact remains that the largest known deposit, the Witwatersrand Basin in South Africa, from which 40% (sic!) of all gold mined during recorded history originates is secondary (see http://www.sciencemag.org/cgi/content/full/297/5588/1815). Australian Gold Rush was also about placer deposits. Where these gold nuggets come from? Here is the possible answer:

F. Reith, S. L. Rogers, D. C. McPhail, D. Webb, Biomineralization of Gold: Biofilms on Bacterioform Gold, Science 313 (2006) 233-236
Bacterial biofilms are associated with secondary gold grains from two sites in Australia. 16S ribosomal DNA clones of the genus Ralstonia that bear 99% similarity to the bacterium Ralstonia metallidurans — shown to precipitate gold from aqueous gold(III) tetrachloride — were present on all DNA-positive gold grains but were not detected in the surrounding soils. These results provide evidence for the bacterial contribution to the authigenic formation of secondary bacterioform gold grains and nuggets.

...Researchers had long suspected that bacteria help create the flecks and nuggets of "secondary" gold that prospectors pan from streams and miners dig from certain long-buried gold deposits. At microscopic scales, secondary gold can strikingly resemble mounds of bacteria, as if microbes had encased themselves in the metal. And in the lab, some bacteria defend themselves against toxic dissolved gold by turning it into the metallic form...At two Australian sites, grains of secondary gold where collected from soils that lie over rock whose gold leaches up into the soil. On the nearly pure gold grains, they found striking examples of "bacterioform" gold overlain by biofilms of bacteria and their exuded slime. Genetic analysis showed that the bacteria belonged to as many as 30 species, most of which could not be found in the surrounding soil. The most pervasive species was genetically nearly identical to the bacterium Ralstonia metallidurans, a microbe well-known for its ability to precipitate some heavy metals from solution in the lab. Reith and colleagues showed that R. metallidurans can also precipitate gold.

R. metallidurans is a marvel of nature that thrives in acutely toxic heavy metal loaded environments (mM's of metal cations!)

...Ralstonia metallidurans is a natural isolate that was found in the sediments of a Belgian zinc metallurgical plant. This bacteria is resistant against a large number of heavy metals including Ag(I), Cd(II), Co(II), Cu(II), Hg(II), Ni(II), Pb(II), Tl(I) and Zn(II)...metal-resistant Ralstonia, through evolution, are particularly well adapted to the harsh environments typically created by extreme anthropogenic situations...Ralstonia is better able to withstand high concentrations of heavy metals than any other organism. 13% of all genes in Rme encode transport proteins. Nearly one-third of the transporters identified (32%) appear to function in inorganic ion transport with three-quarters of these acting on cations. For every kind of resistance mechanism, the R. metallidurans genome ranked first for the variety of gene or gene cluster versions. The main illustration of this fact is the family of three component efflux of toxic compounds: most of the genomes contain 0 to 4 versions of this gene family: there are 12 of them in R. The genome of this bacterium contains also 8 P-type ATPase involved in metal efflux specialized in lead, cadmium, thallium and/or copper efflux, and several others mechanisms involved in metal processing. There are also new proteins (mostly encoded by the large plasmids) that were, up to now, never described in other bacteria.

The evolution of such detoxifiers is an enigma, but lateral gene swapping apprears to be the main mechanism for acquiring this trait. See

Could it be that the ultimate cause of "gold fever" is the excretion activity of a strange microbe? That would be the ultimate vindication of Sigmund Freud:

...all the interest which the child has had in feces is transferred in the adult on to another material which is set above almost everything else, gold. In dreams in folklore, gold is seen in the most unambiguous way to be a symbol of feces. "Dreams in folklore" (Freud and Oppenheim, 1911) http://nyfreudian.org/abstracts_16_12.html

The gold stands for feces because it is bacterial excrement.

Plants & animals: encounters of the second kind

Von Münchhausen vindicated

(1) Plants living on animals (Epizoic plants)

...Large leaf-feeding weevils of subgenus Symbiopholus, and other weevils and beetles, all inhabiting fairly high moss forests in New Guinea carry small gardens on their backs. The association involves symbiosis, with the weevils providing a favourable environment for the plants, and the plants endowing the weevils with a protective resemblance toscryptogram-covered parts of plants, or with chemical protection.

...the weevil Gymnopholus lichenifer has back that is typically covered with a community of living lichens. The lichens function as camouflage for the beetle, and they support a diverse group of nematodes, rotifers, psocids and mites (Richardson, 1974).

...An Epizoic Bryophyte and Algae Growing on the lizard C. cristatus in Mexican Rain Forest; S. Rob Gradstein, Clementina Equihua Biotropica, 27 (1995) 265. The authors found liverwort species T. obtusangula growing on the head of the lizard C. cristatus, protecting the head from overheating and the elements.

Can the origin of fur be in the epizoic symbiosis (wigs)?

(2) Warm-blooded flowering plants. Another, ancient way of attracting insects.

...The dead-horse arum of Corsica (Helicodiceros muscivorus) belongs to the group of several-hundred plant species scattered among some 10 families that can rev up their body temperature. That heat can launch strong odors. All the plant tissues so far found to warm themselves have reproductive functions. They tend toward large blooms, which have a low surface-to-volume ratio favoring heat retention. In many of these blooms, the female organs mature before the male parts, requiring the plant to briefly kidnap pollinators to make its pollination system work. When the plant first blooms, the finger radiates heat, which sends out strong aromas of oligosulfides. Female blowflies swarm over the bloom. This stench represents step 1 in an entrapment scheme, attracting blowflies as a nursery for their eggs. The flies crawl down into the pocket where the spathe narrows to surround the base of the finger. That pocket contains a band of male florets above a band of female florets. Spines and filaments at the entrance to the pocket imprison the flies.

...During the 1st day the arum blooms, female florets have matured enough to receive pollen, but male florets aren't releasing it. The flies, however, may carry pollen they picked up from a previous adventure in another, earlier-blooming plant. As the flies scramble around in the pocket, trying to escape, they dust that pollen onto female florets. By the next day, the female organs have lost their receptivity, but the male parts have matured. The trapped insects then pick up pollen. The blockade of spines withers, so the flies can at last squeeze up out of the pocket. They then carry the new pollen to the next arum, should they fall for the same trick again.

...P. selloum manages something more sophisticated: It regulates its heat generation to keep its flower temperature between about 30°C and 36°C, staying in this range even at 4°C. Most of the plant's heat comes from a band of tiny, sterile male flowers located between the fertile male and female flowers on the bloom's fingerlike projection. This philodendron lures insects inside. The philodendron's spathe closes over scarab beetles for 12 hours. Yet the beetles remain for some 22 hours: they mate, feed, and brush pollen onto female flowers. At the end of the beetles' stay, they pick up pollen from just-matured male flowers and fly off to another bloom.

...The eastern skunk cabbage (Symplocarpus foetidus) also keeps warm, independent of air temperature. Its bloom can melt holes in the snow. Skunk cabbages can bloom inside a snowbank and create their own ice caves. In experiments at air temperatures around 15°C, the inner core averaged some 9° higher. When the air temperature dropped to –15°C though, the fingerlike projections reached temperatures 30° higher than the air. "Some mammals can't even do that well." Mammalian mitochondria blast out heat relying on uncoupling proteins, UCPs. Similar chemistry was observed in potatoes (adaptation to cold). The slow-heat burns of arums are due to alternative oxidase or AOX that occurs only in plant mitochondria. The UCPs and AOX function simultaneously.

...The majority of the plants known to generate heat sprout from ancient lineages at the base of the botanical family tree. Self-heating may have been an early innovation that arose soon after the invention of flowering. Heat generation has turned up in plants of the most ancient lineages: the magnolias, Dutchman's pipes, star anises, custard apples, and water lilies. The trait also show up in a few lineages of moderately recent origin, such as the arums and the palms; the highest branch up is the Asian sacred lotus. The trait's absence among the newest plant families suggests that its value has declined as modern plants developed.

...Biologists first proposed that heat helps spread the plants' insect-attracting odors. The recent finding suggests that heat might make a plant more closely resemble a dead animal because microbial processes in a carcass raise its temperature. Heating an artificially scented plant restored a fading bloom's capacity to lure insects into its pocket. Another idea is that some plants keep the heat on after trapping insects in their chambers, so heat itself might serve as a reward for certain pollinators, letting the beetles cluster around, saving energy by drawing on the plant's warmth for their nighttime activities (sex). The next evening, when the bloom cools, the beetles fly off. The heat-generating flowers are like nightclubs for beetles. During evolution, a floral innovation may have supplanted the nightclub concept. A flower that offers just a sip of nectar or a pollen snack and then sends the pollinator on its way will probably spread its pollen over many more partners than will a plant that traps insects for a whole night.

Wow, what an idea...

First flowering plants->imitation of carcasses including warmth -> attracting and retaining insects -> heated nightclubs. The development cancelled by evolution of pleasingly smelling nectars -> investment not into heat but rather into nutrients for the pollinators.

Monterey aquarium revisited

All of the beasts are native to Monterey bay, CA. This year's catch includes

Sea pen (Ptilosarcus gurneyi)

Sea pen is not a single animal; it is an usual colony, even for colonial polyps. As far as I know, this type of organization is unique to sea pens and pansies: A single idividual is a root that supports ALL (thousands of) others colonists. For this essential service it gets lion's share of the catch, just like the CEO's of our corporations. Also, this individual alone decides where the entire colony goes; it is "in charge." Why is this type of organization so rare in Nature?

...sea pens are composed of polyps, each with 8 tentacles, that are specialized to specific functions: a single polyp develops into a rigid, erect stalk (the rachis) and loses its tentacles, forming a bulbous "root" or peduncle at its base. Other polyps branch out from this central stalk, forming water intake structures (siphonozooids), feeding structures (autozooids) with nematocysts, and reproductive structures. The entire colony is fortified by calcium carbonate in the form of spicules and a central axial rod. Using their root-like peduncles to anchor themselves in sandy or muddy substrate, the exposed portion of sea pens may rise up to 2 metres in some species, such as the tall sea pen (Funiculina quadrangularis). Sea pens are sometimes brightly coloured; the orange sea pen (Ptilosarcus gurneyi) is a notable example. Sea pens prefer deeper waters where turbulence is less likely to uproot them. Some species may inhabit depths of 2,000 metres or more. While generally sessile animals, sea pens are able to relocate and re-anchor themselves if need be. They position themselves favourably in the path of currents, ensuring a steady flow of plankton, the sea pens' chief source of food. http://en.wikipedia.org/wiki/Sea_pen

Sea lemon (a nice looking nudibranch) and hare (Aplysia californica, a sea slug with rabbit ears)

see also http://www.seaslugforum.net/factsheet.cfm?base=aplycali
I once cought two hares in Santa Cruz (Natural Bridges park) doing "it" the hermaphrodite style. My wife still shudders from this memory. For some reason, sea hares, like planaria flatworms, are the darlings of neuroscientists. Perhaps sea lemons are also good for something...

Ocean Sunfish (Mola mola)

Easily the oddest bony fish I've ever seen. Some photos are here
http://www.oceanlight.com/spotlight.php?img=06452 (breaching)
http://www.amonline.net.au/fishes/fishfacts/fish/molalav.htm (larva)

...The ocean sunfish, Mola mola, is the largest bony fish in the world. It is a unique pelagic fish, and specimens of ocean sunfish have been observed up to 3.3 m in length and weighing up to 2,300 kg. It feeds on jellyfish and other soft bodied zooplankton, as well as small fish. It has a rounded 'tail' known as a clavus instead of a caudal fin.

...Molas are often spotted floating sideways on the sea surface. Some observers have seen sea birds such as gulls picking ectoparasites off basking ocean sunfish. Others have seen mola flip over onto its other side after the gull has picked off its parasites, giving the bird a chance to have more food, and the mola a chance to have the bugs picked off of its body. Breaching has also been observed. This is when ocean sunfish jump out of the water as whales would. They are reported to jump up to ten feet out of the water. This is probably done to dislodge the large number of parasites on their body.

...Mola steers with its ability to spit strong jets of water out of its mouth or gills. It usually lets the current carry it. Its thick, leathery hide protects it because it is made up of collagen fibers up to 6" thick protecting it from the stinging jellyfish, which it eats. The ocean sunfish's unique ability to suck and spit water with its mouth helps it while feeding. The mola sometimes spits jets of water in the sand to search for food. It also sucks and spits jellies to tear them apart and make them easier to consume with its small mouth. The ocean sunfish has also reportedly used its ability to spit water out of its gills to squirt sea birds, which sometimes land on the mola's side while it is basking.

...The short, broad clavus is formed by extensions of dorsal and anal fin rays. It is wavy, with eight to nine ossicles and 12 fin rays. The ocean sunfish has rough, sandpapery skin covered with mucus. Because of its very short and stiff body, it has no more than 16 vertebra, and the spinal cord is under 15 mm long. A specimen of 200 kg may have a brain no bigger than a nut. The fish's unusual shape results from its unique development, in which the tail does not grow with the rest of the body. As the rest of the body grows to the enormous adult size, it 'wraps around' where the tail would normally be, giving the squared, 'cut-off' shape of the tail. Its fry resemble miniature pufferfish, having spines, a hint at the species' place in the evolutionary tree. The ocean sunfish uses its dorsal and anal fins to "scull." This behavior is described as a way to propel the fish, allowing it to swim forward by moving its dorsal and anal fins from side to side.

The largest fish in the sea spits upon everybody, likes to bask in the sun, has one of the smallest brains and next to no spine...odd, isn't it?

Geoduck clam (Panopea abrupta), Atlantic islandica, and the secret of long and happy life


...Geoduck the largest burrowing clam in the world, weighing in at an average of 0.5 - 1.5 kg at maturity, but specimens weighing over 7.5 kg and as much as 2 m in length are common. It has a life expectancy of about 146 years, with the oldest recorded at over 160 years. This makes the Geoduck one of the longest living animals. A geoduck sucks plankton down through its long siphon, filters them for food and ejects its refuse out through a separate hole in the siphon. Adult geoducks have few natural predators, which may also contribute to their longevity. It may also be the result of low wear and tear. A female geoduck produces about 5e9 eggs in her lifespan.

...On the other side of the Pacific, Crenomytilus grayanus from Peter the Great Bay is reported to have the greatest lifespan encountered among mollusks from the USSR, 150 years. The diminutive Tindaria callistiformis grows extremely slowly in the cold dark world it inhabits, attaining a size of only 8.4 mm in 100 years. The Ocean Quahog, Arctica islandica, currently holds the longevity record for bivalves as well as for all non-colonial invertebrates, and may, in fact, be the longest-lived animal. Individuals dredged from the middle Atlantic continental shelf often show over 150 annual growth increments. One specimen had 220. The longest-lived animal on earth may be a bivalve! http://www.conchologistsofamerica.org/articles/y1989/8903_jones.asp

...The ocean quahog A. islandica is among the longest-lived and slowest growing of marine bivalves with maximum ages >300 years. The animals exhibit a unique behaviour of self-induced metabolic reduction, by seemingly at random burrowing under to anoxic sediment layers. The time burrowed represents a period of deliberate metabolic reduction with heart rates suppressed to 10% of normoxic levels. Living at a much “slower” pace increases individual life span and therewith the chances to participate in yet more reproduction events. Chronic anoxic/oxic exposure fosters the extreme stress resistance in A. islandica. It is the only animal known to deliberately induce a torpor-like state that does not serve to escape adverse conditions (like hibernation in snails and frogs) but, presumably, to prolong individual life span. http://web.awi-bremerhaven.de/Publications/Phi2006a_abstract.html

The secret of the long life is spending most of it in a state of self-induced torpor in order to enjoy more "reproduction events."

Now you know.

Evolution and Bible literalism.

1. Meeting of the opposites
My dictionary defines "evolution" as "a process in which something passes by degrees to a different stage" and "a process of change in a certain direction." Thus defined evolution is very common. It may be evolution of Life or evolution of inventions. It may be evolution of planets or evolution of texts. These examples may look eclectic and yet the more one examines such examples, the more commonalties one observes. There is a pattern there, but most people are reluctant to recognize these similarities. Nothing illustrates this thesis better than the unending conflict between the "evolutionists" and Bible literalists (specifically, fundamentalist and evangelical Protestants) in the US. If you listen to their bitter feud, it may appear that there is an unbridgeable gap between the two camps. In fact, these two sides have the same problem in common that goes to the very foundation of their respective worldviews.

This common problem is the reconstruction of multiply and faultily copied information written in the form of linear code and writing the history of how this information have changed over long stretches of time. The root cause of this problems is, of course, the inaccessibility of the past and hence the reliance on untrustworthy, fragmented, contradictory records. In one case, the information exists as a sequence of DNA bases in a genome, or a stratified, patchy fossil record. In the other case, the information exists as a scriptio continua sequence of letters in the New Testament (NT) of Our Lord Jesus Christ [originally written in Greek]. The NT has uncertain origin (that is presumably traceable to the irretrievably lost witness accounts) and it has been copied and re-copied countless times by scribes, both before and after the NT canon was formed in the 4th century. The NT has been preserved in more manuscripts (ms) than any other ancient work, having 5,700 Greek ms dating from the 3rd century to the 16th century; the fragments of the NT exist that are dated by 140 AD. Iliad is extant in 650 ms; Euripides' tragedies exist in 330 ms. The copying of the genome [the NT] was imperfect and multiple mutations [variants] have crept in. Some authors give a conservative estimate of 150,000 variants, some give a more realistic estimate of 400,000 variants. Both of these numbers are greater than the number of words in the NT. The King James Bible which is the bedrock of American literalists was based on a Greek NT codex, Textus Receptus, that was compiled by Stephanus in 1550. It integrated over 25 Greek ms that were available to him and his predecessors. In 1707, John Mills examined 100 Greek ms and compiled the first list of 30,000 variants. As more ms became available, the list rapidly expanded.

For Bible literalists, this multitude of variants presents a formidable problem. Here is a typical self-image of a Bible literalist:

...taking the Bible literally is to read and understand the Bible in the normal, historical and grammatical context in which it was written. Where the Bible describes history, we are to understand that the history being described is a true record of the events that happened... That is not to say that the Bible is absent any symbolism, poetic language and allegory, or that the biblical writers never spoke figuratively at times. The issue is that those must be understood with a proper approach to Bible study, which would include taking into consideration the historical and social context, as well as any grammatical and syntactical nuances of the original, biblical languages... We believe God’s Word, with the appropriate application of biblical study, reveals doctrine, teaching, and principles that transcend both time and culture, that can be literally believed by any of God’s people in any social setting, and during any time in history. http://www.fredsbibletalk.com/qa004.html

Bible literalism (Sola scriptura) was one of the major themes of the Reformation: the Bible should be interpreted literally, as this would enable lay readers to free themselves from papal rule and lead to a truer, personal understanding of God's will. This doctrine is far from being natural or self-evident theologically, and it emerged quite late and then only as a result of a specific historical setting. Most Christians are not Bible literalists and never were. For Roman Catholics and Orthodox Christians, the certainty about revealed truths stems equally from the Scripture and church traditions. Many of mainline Protestant denominations in the US are not Bible literalists either: Methodists , Presbyterians, Episcopalians, and Evangelical Lutherans do not teach the doctrine of Bible inerrancy. For fundamentalist and evangelical Protestants who do teach such a doctrine, literal reading of the Scripture requires securing the knowledge that the text of the Bible is not corrupt. In order to understand the Bible literally, one has to have the correct text of the NT as it was revealed to and by the first Jesus' disciples. The suspect text that we currently have should be replaced by, using the evolutionary language, the Last Common Ancestor of all NT ms. Hence there is a movement ("NT textual criticism") aiming to discover this original NT, purge it from the distortions, and reconstruct the true words of the apostles:

...Nothing short of a continuous miracle could have brought the text of the inspired writers down to us without alteration or corruption, and Divine Providence did not will such a miracle. [Our] task is to sort through the variants and establish a "critical text" that is intended to represent the original by best explaining the state of all extant witnesses. http://www.theopedia.com/New_Testament_Textual_Criticism

The standard Nestle-Aland edition of NT Graece echoes this noble sentiment:

...NT Graece seeks to provide the reader with the critical appreciation of the whole textual tradition... It should naturally be understood that this text is a working text; it is not to be considered as definitive, but as a stimulus to further efforts towards redefining and verifying the text of the NT... Editorial methodology proceeds essentially by constructing a stemma [cladogram-S.] to demonstrate the mutual relationships of its extant ms, and then reconstructing the original text on the basis of insights gained from a complete view of the history of the text (distinguishing daughter manuscripts from their parent exemplars, and eliminating them from further consideration). But the construction of such a stemma for the NT text is inconceivable either now or in the foreseeable future, not only because the number of witnesses to the NT text is incomparably large, but also because of basic factors characteristic of the transmission of the NT text. Due to the constant change of relationships among ms, each NT text requires its own individual treatment with a fresh consideration of not only the external but of the internal factors as well. (to appreciate the difficulty of this task, examine a few simulated "codices" in English given on http://www.earlham.edu/~seidti/iam/exercise.html)

The monumental task of NT textual criticism mirrors, to an astonishing degree of similarity, the task before the evolutionary biologists: locating the mutations and variations in the genomes, reconstructing the phylogeny, and going all the way back to the Last Common Ancestor of all Life. The methods used to obtain the cladograms, the nature of the "mutations," and the methods used for their identification are rather similar to those used in molecular phylogeny, genetics, and evolutionary biology. A little change in the vocabulary, and the switch from one field to another is effortless. Most of the quotations given in the next post were taken from various Bible study and NT textual criticism sites.

What is obvious from this reading is that Bible literalists would greatly profit from wider adoption of mathematical and statistical methods of evolutionary biology and genetics. Conversely, the tricks developed by the NT scholars might turn out to be useful for the evolutionary biologists. If only the two sides would stop their ridiculous "fight" and listen to each other, they might end up talking the same language...

2. The Live Journal
The search for the true Bible and the search for the true tree of Life are the two sides of the same pursuit. I do not think that such a viewpoint is far stretched. Take a closer look and judge for yourself.

He that is without sin among you, let him first cast a stone at her (John 8:7). This popular story is an example of inadvertent addition to the Gospels, due to a transmission error.

The uncertain beginnings (the Last Common Ancestor)

The formation of the Christian Canon is as mysterious as the origin of Life. There is no factual proof that the written Gospels existed before 125 AD (see the commonly given arguments on http://www.holysmoke.org/hs00/the-nt.htm). In the beginning, there was Logos, but shortly thereafter there was a lot of hearsay, confusion, tale telling, and distortion.

...The dominant view among critical scholars, the Two-Source Hypothesis, is that both 'Matthew' and 'Luke' drew significantly upon the Gospel of Mark and another common source, known as the "Q Source." Most Q scholars believe that it was a single written document, while a few contest that "Q" was actually a number of documents or oral traditions. No information about its author, if it existed, can be obtained from the resources currently available, and, indeed, little or any direct biographical information about their authors is assumed to be traceable. Many books of the NT, especially the Gospel of Mark and the book of Revelation, are written in relatively poor Greek. Relative exceptions to this include the gospels of Luke and John and the Acts of the Apostles, the latter probably written or edited by the same person who wrote or edited Luke. http://en.wikipedia.org/wiki/New_Testament

...There was a long dark 'tunnel period' between the writings of the NT and these being treated as Holy Writ. Between 70 and 150 AD, Christian writings were not seen as 'Scripture', but 'guides to Christian living' so there was no difficulty in making changes. The first earliest papyri dated 140 AD but it has only 6 verses of John. The first complete ms of the NT are 4th century (Codices Sinaiticus and Vaticanus). All NT writings were written in Greek - not the language that Palestinian Jews [the apostles] would have used. Moreover, major tampering with the text occurred in this 'tunnel period.' The differences between the Byzantine, Alexandrian, and Caesarean texts show copyists changed the text (e.g. Acts 2:17 in the Western text). [Heretic] Marcion, in the mid-2nd century, expunged his copies of the Gospel of Luke of all references to the Jewish background of Jesus. Origen condemned Christians for "their depraved audacity" in changing the text of the NT (the 3d century) and St. Jerome wrote of "numerous errors" which had arisen in the texts through attempted harmonizing [see below]. Even in the 4th century Codex Sinaiticus had been altered by at least three different scribes.

...About 150 AD, the church began to distinguish between the books that could and could not be read in the church; the basis of recognition was the belief it had been written by an apostle or personal disciple; they should also conform to the orthodox teaching. The church did not have any uniform agreement, though. It was not until the mid-4th century that there was agreement; the 27 books appear in the proceedings of the Synod of Laodicea and the Synod of Carthage. The 'Syrian' church of South India still does not recognize 4 books. The Ethiopian church has additional 8 books. http://jeromekahn123.tripod.com/newtestament/id16.html

Variants and the NT manuscripts (ms): how many?

...there are 3000+ continuous-text Greek ms of the NT. Between 85% and 90% of these are in minuscule script; the remaining 10-15% (uncials and papyri) are in uncial script [capital letters only]. http://www.skypoint.com/~waltzmn/intro.html

...In 1707 John Mill listed 30,000 variants in the different Greek NT texts (based on ca. 100 ms + citations of the NT by early church fathers). Currently, there are 200,000 to 400,000 recognized textual variants among 5700+ ms of the NT. The differences between the Textus Receptus [on which King James Bible is based] and texts based on the best Greek witnesses number about 5,000 variants. In other words, over 98% of the time, the Textus Receptus and the standard critical editions agree. [the difference between the human and chimp genomes is also 2% - S.] http://www.theopedia.com/New_Testament_Textual_Criticismhttp://www.theopedia.com/New_Testament_Textual_Criticism

Stabilization of the genome: the invention of the press

...Erasmus prepared the first printed Greek NT published in 1516. He had only 5-6 Greek manuscripts, none of them earlier than the 10th century AD. His 4th edition in 1537 contains his definitive text. The next important step was taken by Stephanus, whose version was based upon the work of Ximenes and Erasmus and had marginal readings from 15 new Greek ms. The 1550 edition of Stephanus, Textus Receptus, was used by the translators of the King James Bible.

Common ancestry and clades [stemmas]

...NT ms can be classified according to certain major families (types). A family type is the name given to a group of texts with a common ancestor. These texts are discerned through the deviations common to a group of manuscripts. For example, some scribal errors made in copying the text in Alexandria were perpetuated in later reproductions of that text type. Classification according to "text type" is the basic point of departure in the actual work of textual reconstruction. For example, one reading of a text that represents a good family type may provide more support for the original text than a dozen readings from a poor family type. These text types are not represented by entire manuscripts but often only segments of them. The modern practice of copying an entire ms at once was seldom followed in antiquity. Four main family "types" of texts have been sufficiently defined in biblical scholarship. http://www.theopedia.com/New_Testament_Textual_Criticism

Evolution of the genome

(a) Transmission mistakes: mutations, deletions, insertions, transpositions, junk DNA

Most of the copying mistakes listed below are instantly recognizable: these are typical point mutations and mistakes in DNA replication. The dynamics of mutagenesis is also familiar. E.g., several orthographic mistakes slowly accumulate in one segment of the continuous code, then the scribe tries to make sense of the meaningless passage and changes it. The main function of these unintentional variants (as is the case with neutral mutations in genetics) is that these serve as tracers useful for finding stemmatic (that is, cladistic) relations between the ms.

...Typical errors: Errors Caused by Sight, Permutation, Haplography and Dittography [see below], Errors Caused by Faulty Hearing, Errors Caused by Memory Lapse, Substitution of Synonyms, Variations in Sequence, Transposition of Letters, Assimilation of Wording, Errors Caused by Poor Judgment, Spelling and Grammar Changes, Harmonistic Alterations, Corrections, Conflations, Doctrinal Alterations
[multiple examples of these errors are given on http://www.earlham.edu/~seidti/iam]

...many mistakes were caused by misreading that resulted in omissions, repetitions and transpositions of letters, words and even whole lines. For instance, eye-skipping occasioned by the same ending (as in Luke 12:8-9 and John 17:15) sometimes resulted in the deletion of a repetition.

...If the eye skipped over a word, letter, word or line(s), the error is 'haplography' ("single writing"). If it was a case of seeing something twice, the error is termed 'dittography' ("double writing"). One example of this can be found in 1 Thess 2:7 - the difference between 'we were gentle' and 'we were babes,' is whether one or 2 n’s belong in the Greek. In Matt 27:17, the insertion of 'Jesus' before 'Barabbas' in some ms may arise through repetition (dittography) of the last two letters of the Greek word 'for you' which in fact was the regular abbreviation for 'Jesus'. In contrast to this, it may in fact be a case of haplography where 'Jesus' has been omitted.

...A cause for another type of error was simply the copyist mishearing; if a letter was being dictated it would be inevitable that a scribe would mishear things; such a situation appears to have arisen in Rom 5:1 - 'we have peace' and 'let us have peace' which sounded the same in first century Greek.

...A copyist might misinterpret the abbreviations that were often used, especially for 'God' and 'Christ' which were frequently abbreviated. The variants found in 1 Tim 3:16 undoubtedly involved this point. [Typical examples: "Spirit" (PNEUMA) misread as "drink" (POMA), "Lord" (KURIW) misread as "time" (KAIRW)]

...On occasion a copyist would have to divide a word; as Greek uncials were written continuously, without a break, a scribe introducing his own word divisions would have to decide upon the position of the word-break. It is was not always clear where a sentence ended; Rom 9:5 is a good example of this and is important as it may be a rare occasion of when Paul appears to call Christ 'God'.

...Liturgical instructions also appear to have been added in some cases, e.g. Acts 8:37 which most likely reflects the baptismal confession in the church of the second century copyist. 1 Cor 4:6 is a good example of the errors that could arise when notes were added in the margin or under the text; the phrase 'to live according to the scripture' is literally 'not above what is written'; it is suspected that a copyist made an error in the first verses of 1 Cor 4, then made a note for the next copyist not to repeat this error, but instead, the next copyist not only did this, but also included the instruction which had been left for him. http://jeromekahn123.tripod.com/newtestament/id16.html

(b) Intentional variants: improving on the Gospels (editing the genome, purging the mutations)

The NT is based on witness accounts that sometimes contradict each other and quite often are less than clear. Many scribes tried to harmonize and refine the Gospels. The early Christians routinely changed the text as they saw fit. Later copyists made changes to remove what appeared to be a contradiction, to expand upon something that they felt was important, to change the meaning in order to suit their own viewpoint, or to clarify the meaning. Some of these changes matter: the contested verses involve the guilt of the Jews and ordination of women (see below). These are not minor, unimportant issues. There are at least 40 such loci in the NT. There were also theological/doctrinal (antiadoptionist, antidocetic, antiseparationist) alternations that might not matter presently, but those mattered a lot in the past, especially in Byzantium.

...On occasions the copyist might make changes to supply a more familiar word, e.g. the unusual verb in Mark 6:20 when Herod was 'perplexed' was changed in later version to 'did'. Clarification of a verse can be seen by Mark 14:12 'lest...it be forgiven them' becomes in certain ms 'their sins should be forgiven them'. In John 5:3b-4 , there is an insertion to explain the conversation that follows. When Matt (27:9) quotes an Old Testament passage which is mostly from Zechariah but it is attributed to Jeremiah, some ms show that a copyist has attempted to remove this. In Mark 1:2, two statements are brought together, one from Isaiah and the other from Malachi, but Mark attributes both to Isaiah; again some ms omit 'Isaiah' to try and remove this error.

...some copyists felt it would be useful to add further details, the two thieves being crucified with Christ were given names in Mark 15:27. In Matt 24:36 Jesus states that even the Son did not know when the parousia was to occur and some copyists felt this impugned Jesus' omniscience, and in some ms 'nor the Son' is missing.

...It is suspected a copyist's marginal protest note has been included in Luke 16:16-18. In v.16 Jesus states that the law and the prophets were only until John, and in v.18, Jesus forbids divorce (against the Deut 24:1-2 ruling), but in v.17 he states that not one dot of the law will pass away; some feel a marginal protest against 16:16 (and possibly v.18) by a Jewish-Christian copyist has been incorporated into the text and hence the contradiction.

...The view of the copyist towards Jesus' status was often reflected. In John 1:18 'the only Son' becomes 'the only God' in some ms; therefore the Christology of the copyist sometimes led to changes being made on occasion. Heb 1:8 has two different renderings and one of these has the Son being addressed as 'God'.

... [The last 12 verses of the Gospel of Mark are a late addition. The orignal ending is either lost or the ending was intentionally abrupt] One of the most significant additions to NT writing is Mark 16:9-20; here the abrupt ending of Mark has been continued to include post-resurrection appearances by Jesus to his disciples.

Are the variants important?

I do think so, especially if one is a Bible literalist. Some of the best known passages in the NT appear to be "mutations." Here are some examples from Ehrman's book:

The story of an adulterous woman and Jesus: Let the one who is without sin among you be the first to cast a stone at her…Go and sin no more (John 7.53-8:12) This famous story appears only in the Gospel of John; it is not found in the oldest and best Greek ms and its style and vocabulary resemble neither the rest of the Gospel nor other gospels. The passage is considered to be a later addition, perhaps due to the accidental incorporation of a marginal note that reported oral tradition. See more detail on http://www.bible.org/page.asp?page_id=2365

The version of Lord's Prayer in Luke 11:2-4 is much shorter than its usual version in Matthew 6. The scribes were not able to restrain themselves from harmonizing and they extended Luke by copying from Matthew 6:9-13.

…The personal view of the copyist could sometimes result in word changes that drastically altered the meaning of the sentence. In the Western text, the Jews 'act evilly' when crucifying Jesus, but in the Codex Vaticanus, the Jews merely act 'in ignorance'. In Acts 2:17 when Peter explains about the prophecy of Joel - that the spirit would be poured out on all flesh - the Codex Bezae has the noun for flesh in the plural to stress that this promise was for all nations and peoples, and not just the Jews. http://jeromekahn123.tripod.com/newtestament/id16.html

Yet another anti-Jewish alternation: Jesus' prayer Father, forgive them, for they do not know what they are doing (Luke 23:33-34) is missing from the earliest Greek witness [papyrus P75 from 200 AD] and several other Greek ms of the 4th century. It might also be an addition. See more on http://www.majoritytext.org/archive/fall02/newsletter3.htm

The case against the ordination of women rests on several passages including As in all the churches of the saints, let the women be silent, For it is not permissible for them to speak, but to be in subjection, just as the law says… (1 Cor, 14:33-35). A similar passage in 1 Tim. 2:11-15 was written by a second-generation follower in Paul's name, but 1 Cor. 14 letter is attributed to Paul himself. In three early Greek and Latin ms these verses [seemingly out of context in either one of these ms] appear after verse 40. It is assumed by many scholars that a marginal note to 1 Tim. 2 was accidentally incorporated into 1 Cor. 14.

Methodological problems and heterodoxy

Think of any ongoing controversy in evolutionary biology and you would find its nearly exact equivalent in the NT textual criticism. The similarities are so striking that just a few examples would do:

...How do we decide which reading is original? Scholars have given many names to their answers, and they apply them in different ways. But fundamentally they use two tools: "Internal Evidence" and "External Evidence." Internal evidence (sometimes called "Transcriptional Probability" or the like) is based on logic: "Which reading best explains the others?" It asks questions like, "Is there an easy way for this reading to have been converted into that one?" External evidence is based on the ms. It looks for the reading based on the "best," earliest, or most manuscripts. http://www.skypoint.com/~waltzmn/intro.html

…[Retrograde evolution, anti-gradualism:] One of the curiosities of textual criticism is its assumption of continuous processes: It is usually assumed that a text, once it started in a direction, just kept going in that direction. So the Alexandrian text just kept getting shorter, the Byzantine smoother, etc. This notion contradicts most theories of the text. They assume that most major variants arose before the ms era. It is quite likely that the history of ms is not a continuous process, but rather a complex history of destruction and reconstruction -- of copies getting gradually worse with each generation and then periodically being subjected to a systematic improvement. http://www.skypoint.com/~waltzmn/Destruct.html

[Enthusiasm vs. skepticism concerning the certainty of cladistic, aka stemmatic, analyses:]
... rational eclecticism has taken us as far as we can possibly get without an explicit history of the text. Recent advances in computer technology, especially among computational biologists, have finally made it possible to apply stemmatics [cladistics] on the scale of a ms tradition as complex as the NT to produce that history of the text. http://rosetta.reltech.org/TC/TC-links.html
For a skeptical take on the same issue see http://www.skypoint.com/~waltzmn/Mathematics.html#QuantMeth

[Difficulties of introducing uniform data bases, accepted protocols, and using mathematical methods in general]

Et cetera, ad nauseum.


As seen from the above, the rapidly expanding field of NT textual criticism, which is an important component of Bible literalism, faces rather similar problems to those familiar from the evolutionary biology and genetics. There are two immediate consequences. First, adopting each other's best methods would help both sides; this is especially true for NT scholars, who seldom implement cladistic and statistical methods. The same goes for wider use of data bases, which is another weak point of NT studies. Second, it appears that many concepts of evolutionary biology can be very well illustrated using the checkered history of Greek NT as an example. I do not think that there could be any objection from fundamentalist and evangelical Protestants to using the Scripture for teaching (illustrating) biology. Finally, I have a strange thought that I cannot easily expunge from my mind: the parallels between the evolution of the genome and the text of NT are so striking that one is tempted to ask: Why do we regard one specific example of such an evolution as "Life" and yet deny this qualifier to another, very similar example. If inexact replication, the flow of information, exploring new niches (vellum, papyrus, printing press), adaptation (e.g., via translation), etc. are the attributes of Life then the Scripture is quite alive. In Nature, the DNA commands its own transcription and replication and it defines the phenotype of the organism, yet it wholly depends on the enzymes (that it itself encodes); the Scripture does the same for the community of believers and it critically depends on the faith and the commitment of the brethren (that it itself fosters).

Is the New Testament alive? Is it, literally, a "Live Journal" of Jesus' disciples?

Suggested reading
BD Ehrman, "Misquoting Jesus" (HarperSanfrancisco, 2005)
see a review on
B Metzger, "The Text of the New Testament: Its Transmission, Corruption, and Restoration," (New York and Oxford: Oxford University Press, 1968).
Online Encyclopedia of NT Textual Criticism on
There are several pioneers in using graph theory and cladistic analysis in the NT studies (taken from http://www.skypoint.com/~waltzmn/Mathematics.html) It seems that they presently are were computational biology was 30-40 years ago:
E. C. Colwell & E. W. Tune: "Method in Establishing Quantitative Relationships Between Text-Types of New Testament Manuscripts"
Pickering & Hodges: "The Implications of Statistical Probability for the History of the Text"
L. K. Loimaranta: "The Gospel of Matthew: Is a Shorter Text preferable to a Longer One? A Statistical Approach"
G. P. Farthing: "Using Probability Theory as a Key to Unlock Textual History"