AN HYPOGENIC CAVE: VILLA LUZ

°

DID YOU SEE THE GOOGLE ADSENSE ADS ON THE RIGHT?

1) WHY DO WE DISCUSS HYPOGENIC CAVES

------------------------------------------------------

Two posts ago, we discussed bacteria in caves and I promised you more about them. Here it is.

In the last twenty years, cavers have discovered a few caves formed not by surface waters like the one we usually know but by gases and waters seeping from the deep volcanic parts of the earth crust. Often, these caves do not have any communication with the outside world, a fact which explain why we have not discovered them earlier. They are called "hypogenic caves".

The true wonder is that these caves are full of life, archaic life originating in long past geologic times when our atmosphere was not choked with oxygen. They are exactly what I need for my bactorgs.

In this post I will tell you more about two of them: Cueva de Villa Luz in Mexico ( an intermediate cave just at the border between hypogenic and normal caves) and Movile Cave ( a true hypogenic one) in Romania.

If you want to read a report on a fossilized hypogenic cave, do a Google search on "Grotte du chat, Daluis (in French)". Look also the sites devoted to Frasassi cave (Italy). Finally, look also at the many sites devoted to Lechuguilla cave, one of the most beautiful cave known to man. For Lechuguilla, I give you just the site of a short report on a trip in Lechuguilla by Michael Ray Taylor, a caver , professor, journalist and writer specializing in cave bacteria, if you are interested, you should read his book "Dark Life: Martian Nanobacteria, Rock-Eating Cave Bugs, and Other Extreme Organisms of Inner Earth and Outer Space (Scribner, 1999)". Please... do a search on Lechuguilla and on all the caves I have been mentioning... wonders are awaiting you, just a few clicks away.

2. CAVE LIVING BACTERIA AND CREEPY CRAWLIES
---------------------------------------------------------------

We will discuss two caves in which our bacteria are living; Villa Luz and Movile. The home of bactorgs in WE SHARE is inspired from them but needs a lot of modification to exist in Provence (different climate and geology) and fit my purpose (development of an eon-traversing bacterial community, communications with the outside).

2.1 CUEVA DE VILLA LUZ (TABASCO, MEXICO)

A transition between hypogenic and normal caves

Choking with sulfur oxide (H2S and CO2), having all its galleries coated with strongly acidic slime, a cave in south eastern Mexico is nevertheless teeming with life. Without any solar energy, any light or green plants, an alien food web has evolved in the Cueva de Villa Luz. An ideal set up for my bactorgs. Let's learn about this amazing ecosystem.

You see here a map of the cave.

(Image courtesy of Louise Hose). This map is taken from the following paper:

As you can see, it is not really a pure hypogenic cave (i.e. one having no communication with the outside, far from it. Instead, it has lost of outside communications: the resurgence and all the side entrance pits through which light, heat, gases and all sorts of animals may enter the cave. I see Villa Luz as an intermediate case; a transition between almost hypogenic in its farthest recesses and a normal cave near the resurgence. This is neat... In my novel, I need a way for a truly hypogenic bacterial community to communicate with the surface. Something like Villa Luz might fill the bill. Of course, I will have yet to invent a nice little twist to have it at a depth of about -600 meters.

Note: Villa Luz is a tropical cave warm and filled with life. My novel takes place in Provence... I will have to adjust for this... Provencal caves ar e almost alpinecaves. Life does not fill them.

Anyway, as a transition cave, Villa Luz has a lot to teach us about hypogenic ecosystems. Let's discover it.

THE VILLA LUZ ECOSYSTEM

As seen on the map, a river rich in H2S enters the cave in its more distal parts (left side) and H2S is also seeping from cracks in the soil connected to deep volcanic sources and pockets of gas. The river flows through the whole cave from left to right and exits through the entrance. On its way, it creates a series of small ponds. MAny fishes live in the ponds closest to the entrance (sardines, the Indian name of the cave is indeed "cueva de las sardinas"). This unusual abundance of life is easy to understand. These fishes eat all sort of living matter flowing out from the deeper recesses of the cave and transported by the river.

Indeed, the Cueva de Villa Luz's fishes are linked, as upper level predators, to a highly astonishing and extensive food web living in the dark in the ponds and passages farthest from the entrance. Thefood web members depend for energy not on photosynthesis from sunlight (there is none) but on an inorganic chemical process: oxidation of sulfur compounds.

When the explorer James Pisarowicz first entered Cueva de Villa Luz in 1987, he was flabbergasted by its "out of this world" geochemical features. The following description is modified from his paper: "Everywhere I saw yellow sulfur, white gypsum crystals, and colored slimes coating the walls. The "rotten egg" odor of hydrogen sulfide was almost unbearable. Hanging from the ceilings were strange stalactites that dripped sulfuric acid. Their examination showed later that they were massive colonies of sulfur-oxidizing micro-organisms. They looked really like rubbery stalactites made of mucus, so I dubbed them "snottites"...

You might have explored caves for years everywhere in the world, nothing prepares you for Villa Luz.

Indeed, as I have said before: it is hypogenic.

This means that it is not, like most caves carved out from entrance to bottom by carbonic acid, the compound that forms when rainwater picks up carbon dioxide from the air. In these normal” caves, the mild carbonic acid, the same we drink in beer and soda, seeps into the limestone cracks and, over geologic times, dissolves the rock and widen the caves forming the passages, pits and rooms we are used to see in caves.

Villa Luz like a few other caves in the world tells us a totally different geochemical story. These caves have not grown from mildly acidic waters coming from the surface. Instead, they have been, at least partially, carved by the strong sulphuric acid and chemical reactions made possible by the high sulfur content of the water rising from cracks in the soil connected to deep volcanic chambers in the earth crust.

Such hypogenic caves (i.e. formed from below) may, for millenia be carved by the acid coming from the deep earth’s crust without any connection to the outside world, no oxygen connection. They may exist as chambers totally isolated from outside and thus unknown to us.

Obviously, Villa Luz is not isolated... but one knows such an isolated hypogenic cave, called Movile Cave in Romania(we will study it in another post). Imagine an isolated cave, without any communication with the surface, filled with gases and strange animals, somewhere underground.

Now anhypogenic cave may not stay isolated forever. If there is deep water rising in the cave, it may slowly carve a way out and meet a surface cave. Then we will have a sulfurous spring somewhere.

Of course nothing precludes also such an isolated cave to encounter after many millenia a normal flow coming from the surface and having formed a normal cave. Then we have a mixed situation where some parts of the cave are hypogenic and other are formed from the surface. Villa Luz might be such a cave (or is it formed only by deep waters flowing out?).

On the map given above, you see a series of rooms and ponds going from the deepest parts to the entrance. The ones close to the entrance have obviously an atmosphere rich in oxygen (see the pits). Eexcept for the richer than usual life present in them, they have many characteristics of normal caves at these latitudes. As you travel deeper and deeper into the cave, you go into more and more strange passages, more and more characteristic of hypogenic caves: a choking atmosphere, drops of skin burning sulphuric acid, and most astonishingly, a teeming life.

Indeed, hypogenic sulfur-based caves are not formed solely by inorganic chemical reactions (rock dissolution by acid). They are also carved and, literally, made by the enormous quantity of microbial life forms they support. Basic in these life forms are the bacteria. They derive their energy from inorganic chemical reactions (literally, they are rock eaters). They metabolize the H2S dissolved in the water and use the oxygen from the CO2 in the cave's atmosphere to produce sulfuric acid, a strong acid indeed since it is the one used in car batteries.

Question: I am not at all clear about the last sentence. Where does this oxygen comes from in truly hypogenic caves, from CO2? Then where is CO2 coming from? I am just no enough of a chemist to know. What is a truly sensible reaction mechanism?

The sulfuric acid then reacts with the rocks. It does not completely dissolve it but converts limestone into gypsum (calcium sulfate) forming beautiful white crystalline structures (needles, trees…). Gypsum falls into the stream and, being very soluble in water, it is then transported out of the cave. With time, more limestone is transformed into gypsum and the cave widens.

Indeed, sulfur-eating bacteria form the basis of the ecosystem (food web) of Villa Luz. They oxidize sulfur to get the energy they need and use thus carbon dioxide, water, and sulfur as the basis for their life. These sulfur eating bacteria are not isolated. Other bacteria eat them. All together, bacteria form huge mats and biofilms (veils in water, mats on rocks, snottites). Small invertebrates (e.g. innumerable midges and worms) graze on these slimy mats. Spiders prey upon the bacteria eaters.

As we have said before, the most spectacular form of bacterial biofilm found in Villa Luz is made by “Snottites”, slimy, rubbery chandeliers hanging from the ceiling or the walls and made entirely from many species of coexisting bacteria and a a complex biofilm structuring material. Small worms and mites live within and on the snottites; spiders walk their nooks and crannies.

The fishes in the external ponds (Poecilia mexicana) eat midges and sulfur-oxidizing bacteria.

As you see from the maps, Villa Luz has many entrances through which skylight can come in and visiting bats can fly and prey upon the ecosystem. This certainly couples Villa Luz’s ecosystem to the outside world and makes the story of Villa Luz much more complex than the one of a purely hypogenic cave. Nevertheless, it clearly shows how a sulfur based, oxygen fearing ecosystem can develop in an hypogenic cave. I will need such a cave, truly hypogenic in some parts but communicating with the outside world in other.

This is all I want to tell you for now about Villa Luz. In the next post we will discuss another hypogenic cave, a much purer one, Movile cave in Romania.

THINKING, BACTERIAL STYLE: KOLTER AND HELLINGWERF

°
DID YOU SEE THE GOOGLE ADSENSE ADS ON THE RIGHT?

1) INTRODUCTION

Try a Google search on "intelligent bacteria", bacterial signalling, "quorum sensing", "bacterial neural networks" and even "bacterial evolutive learning" or "bacterial multi-cellularity"... You'll come up with papers by people like Bonnie Bassler, Eshel Ben Jacob, Klaas Hellingwerf, Claudio Aguilar, James Shapiro, and now, Saeed Tavazoie. What do these works all have in common?

They promote a view of bacterial colonies as super-organisms having sophisticated, computing behaviors and even some form of logical computation and elementary thinking (in the sense for instance of a loose artificial neural network). They even start to speak about learning in bacterial communities.

This is what this post is all about: in which sense can we say that a bacterial colony is a sort of elementary proto-brain, able to compute and learn?

Why are we interested in this? In the preceding posts, you met what I call" Andrones" and "Bactorgs".

Andrones are interconnected sets of real neurons, living in a culture medium on top of a multi-electrode array connected to a computer. They learn to do what real neural networks do : to exchange electrical and chemical signals to produce quite complex behaviors (drawing something pleasant for us on a piece of paper, controlling the flight of a model plane, doing logical computations and so on...). These applications do really exist. Of course, they are still a bit rudimentary and need a lot of progress. Even so, the very fact of their existence is a testimony to the ingenuity of the researchers who designed them. It is one of the true adventures of modern experimental science and engineering. Just finding how to make these in vitro neurons to live, interconnect and learn is a first rate accomplishment

Yet, on a more theoretical viewpoint, Andrones are not so astonishing... They learn to compute. Well, after all, that's what neurons have evolved to do. They develop some form of rudimentary intelligence and are happy afterwards forever ... no big theoretical breakthrough...

Bactorgs are completely different. First they do not exist or are not yet really acknowledged. In "WE-SHARE" (as you will remember, this is the title of my novel), they are bacterial multi-species communities developing also a rudimentary form of thinking and learning (or perhaps, after all, not so rudimentary...).

Think twice,... "thinking bacteria"? I'll adopt a very limited definition of what thinking is but still, that's a big step to take. As you know, I want, all my premises to be very realistic scientifically speaking. So, I have better to document this point very carefully.

The first point I'll discuss is that, under certain conditions, a bacterial colony behaves, not as a collection of separated individuals, but as a coordinated whole, i.e. an integrated organism. This is clearly a prerequisite to act as a protobrain.

2) A BACTERIAL COLONY AS A MULTICELLULAR ORGANISM

It all starts with James Shapiro who, in a 1988 Scientific American paper, proposed that a bacterial colony was not to be seen as a collection of individual cells but as an integrated organism having its own unity and emergent behaviors not deducible from the comportments of the isolated bacteria. (see Sci. Am; 1988, 256; 82 - 89).

Read this paper, it is a must. Its idea was initially received with much skepticism...; usual is n'it? But paper after paper, many researchers elaborated upon and ten years later, Shapiro was able to put together a wonderful review paper on the progresses made during the first decade of live of the concept of "bacterial multicellular organism". It was found that several species were developing colonies acting as multicellular organisms having coordinated behaviors: development of structured colonies, swarming, metabolic cooperation and much more (see "Thinking about bacterial populations as multicellular organisms, Ann. Rev. of Microbiology, 1998, 104, 52-81).

It was also found that bacteria benefit from this multicellular organization by using cellular division of labor, accessing resources that cannot be effectively utilized by single cells and optimizing population survival by differentiating into distinct cell types.

Fast forward ten more years and, today, in 2008, bacterial multi-cellularity has become a very important way of thinking, an emerging paradigm. It has been found that cell to cell communication mechanisms (a.k.a. quorum sensing) is present in virtually all species. It has also been found that bacterial colonies grown under usual laboratory conditions (what we call now "domesticated cultures") present much less intercellular features than so called" wild colonies", grown in nature or in conditions emulating nature. In retrospect, this is no wonder, usual practice in microbiology does all it can to isolate cells and subcolonies. No wonder they loose intercellular communication and coordination.

The picture hereafter is taken (with permission) from a paper by Claudio Aguilar, Hera Vlamakis, Richard Losick and Roberto Kolter (from Harvard) (Thinking about bacillus subtilis as a multicellular organism published in Curr. Opinion Microbiol. 2007, 10(6): 638-643).

Claudio Aguilar ----------------------- Roberto Kolter

Their paper is a tribute to Shapiro and presents a recent summary of the field. On the left, you see three wild colonies showing clearly intricate structures. On the right, you see the corresponding "domesticated" cultures showing much less structure (they are mainly simple blobs...). If you want to study bacterial organisms, take a walk on the wild side...

So, wild colonies are multicellular and organized. If you need supplementary arguments think about Eshel Ben Jacob's work which we discussed in a previous post... wonderful multicellular structures. It is then normal to think that there are some computations done in the wild colonies to synchronize and maintaintheir structures and affect different roles to bacteria at different places.

Our second step is now to suggest that these multicellular organisms do not only compute but do it almost as neural networks. Ben Jacob, as we have seen, clearly suggests it. However, his arguments are indirect. Can we say something about the cellular or genetic mechanisms used by a single bacterium in these multicellular
organisms to do their bit of computation?

I will now discuss the work of Klaas Hellingwerf, the guy who has proposed to take seriously the analogy between ANNs and bacterial signalling networks.

A WARNING: Below, I will suppose that you have at least some general notions on artificial neural networks. Later, I will post a short primer on neural networks. Here I will just discuss how bacterial networks fit or do not fit the framework of neural networks. For more details, see later.

4) NEURAL NETWORKS ANALOGUES IN A SINGLE BACTERIUM?

As I promised you before, we will go now one step further in the direction of thinking bacteria. Meet Klaas Hellingwerf from Amsterdam University. He will tell us more about the computing mechanisms in a single bacterium. He studies the genetic and molecular processes used by bacteria to compute their decisions from what they sense about their environment and their internal states.

Klaas speaks somewhat metaphorically (or perhaps not so metaphorically) about "bacterial neural networks" and in 2002, he organized an European EURESCO conference on this theme in Obernai (France). The conference, attended by about 200 people elicited a wide interest in bacterial computations (interconnected phenomena of signaling, behavior and development) which has now become a big theme in microbiology with surveys published in some major journals.

See for instance an EMBO report by Susan Golden (Texas A&M) on this conference entitled "Think like a bacterium"... (EMBO reports Vol 4, N°1, 2003, pages 15-17).

See also another report published in "Molecular microbiology (2003, 47(2), 583-593" by Judith Armitage, Professor of biology at Oxford and some co-authors. This report is entitled"Thinking and decision making, bacterial style".

These reports show that some form of crude "bacterial thinking" (I mean "thinking as it is done in an artificial neural network" - see Rumelhart PDPs or Mc Culloch and Pitts) , is now a serious scientific subject and no longer exclusively the stuff of science fiction.

What is thus Hellingwerf's argument? I will summarize it from one of his papers entitled "Bacterial observations: a rudimentary form of intelligence" (Trends in microbiol., 13, 4, 2005, 152 - 158).

He starts by saying: "Until very recently, bacteria were considered too small to be little more than bags of enzymes unable to realize complex processes like signal transduction, association, gene expression, response to various stimuli, intra and extra-cellular communication. This is no longer so. We know now that even a single bacterium has many regulating mechanisms and can use them to express genetically the required chemical components for each of the above processes at specific times and places."

Then his argument goes a little bit like this: "Most notably, signal transduction can take an (extra) cellular signal S of a chemical or physical nature (e.g. light or perhaps electricity or electromagnetic waves) and convert it into a different form called response R (for instance a transduction of light into a given concentration of some protein which, then, can affect gene expression or enzyme activity and lead to specific behaviors (e.g. chemotaxis, phototaxis, swimming)." The figure below is modified from his paper, see above, and gives a schematic representation of a typical S-R system.

Legend: A two component S-R system in a bacterium. S is a sensory molecule in the membrane of a bacterium (blue rectangle). It has an input site (a) and a transmitter site (b). The input is activated by binding a signal molecule (1). Because of this activation, the transmitter side phosphorylates (takes a P from ATP). The receiver domain (c) of the corresponding (called cognate by biochemists and having compatible stereochemistry and chemical properties) response regulator (R) transfers the phosphoryl group from S (3). The output site (d) of R become activated and changes genetic expression in the bacteria

What is this? Just a genetic embodiment of the familiar S-R (stimulus response) generic model of biological signal processing! Several genetic S-R systems may be present in a single bacterium, all different but operating in parallel on various signals to produce various responses. These mechanisms form what we may call a "genetic network of signal processing".

Neuronal networks are also signal processing networks. Klaas proposes that the S-R networks of bacteria may abstractly be considered as functional equivalents of simple neuronal networks (i.e. accomplish the same kind of abstract computational algorithms but of course with different mechanisms and signals). To be considered as functionally equivalent to a neuronal network, Klaas says that our bacterial network must satisfy four properties:

- There must be many parallel S-R mechanisms (pathways) and these pathways must be branched (e.g. an individual S-R mechanism may have several inputs coming from the environment or from other S-R mechanisms and several outputs going into effectors or to other S-R mechanisms.). Neural networks do this because signals have multiple pathways and do many computations in parallel. A bacterium does this since it has several messaging pathways like the one illustrated above in parallel. Remark that traditional computers are not parallel and thus do not fit the paradigm. It is possible of course to simulate a parallel network on a serial computer but not in real time.

- These S-R pathways must execute logical operations. Computational nodes must combine the signals from two or more previous elements, compute an output depending on all the incoming signals and pass the result to another node. The result must be able to be represented approximatively by a mathematical or logical function (E.g.: and, or, not...). Klaas does argue that bacteria do this because their signaling systems combine inputs from different sources. Non linearity is essential.

- There must be some auto amplification mechanisms (feedback). This is a very important property which means that a computing node (e.g. an enzyme) acts as a non linear function of an input. The reason for this requirement is that it is very important for a neuron to have an output which is a non linear (for instance, a sigmoid) function of a combination of its inputs. The logical, classification and learning properties of an artificial neuron depends critically on this sigmoid-like output (treshold behavior, back propagation).

Bacteria may do that quite easily. Suppose that a signal is used to generate a small amount of a given chemical. If this chemical is auto-catalysed (as it is the case for many genetic expressions). The response chemical will use cellular resources to synthesize itself more and more leading to an enormous increase in its concentration (the sigmoid response). Thus as soon as a threshold is reached, the autocatalysis mechanism sets in and the sigmoid response is reached. If it is very strong and quick, it may even be seen as an all or none response (Boolean response, see René Thomas and kinetic logic in Google).

- There must be some significant amount of cross-talk between mechanisms. This is where the difficulty lies for a single bacterium. This means that parallel chain reactions of signal response must exchange signals so that the way one chain operates change the ways the other run. Again this is essential in artificial neural networks if we want them to have interesting behaviors like distributed processing and coding, associative memory, generalization, graceful degradation or complex classification. Klaas says that there is some scarce evidence for crosstalk among signaling pathways in a single bacterium. Yet, today, the operative word is "scarce".

Based on existing detailed experimental work, he then suggests that the bacteria Sacharomyces Cerevisiae presents these four features. However, he insists that evidence for crosstalk is still quite small.

The figure hereafter shows his view of such a S-R network in a single bacterium. Each circle in the upper membrane shows a molecule receiving an input S (a chemical, a light signal, an electrical signal, an electromagnetic radiation and as we will see later even a sound wave) .

Then the red arrows show the internal pathway from the various S to various R (blue nodes are intermediate chemicals. Responses are gene expression, membrane processes activation, flagellar movement and the like. You can see the multi-input, multi-output feature. The green circles show the auto amplification of some chemicals; the blue interrupted lines show the putative cross talk interactions still to investigate. Clearly this is a neural network analogue.

Klaas ends up by proposing that, if we can make some experimental progress to demonstrate cross talk in a single bacterium, we will be entitled to see signal processing in a single bacterium as an analogue to a simple neural network. So, speaking metaphorically a bacterium will do neural computations, i.e. "think" if we adopt a crude operational definition of thinking as “doing what artificial neurons networks do”.

4) A NETWORK VIEW BASED, NOT ON A SINGLE BACTERIUM BUT ON A COLONY

I personally do not believe that seeing a single bacterium as analogue to a neural network is really mandatory. I think that what might be important is that the bacterium can process information in one or several coupled S-R networks doing logical operations with or without crosstalk. That seems to be experimentally demonstrated. Then, a single bacterium is more like a simplified neuron, what I would like to call a “proto-neuron” or a set of proto-neurons in parallel (each S-R mechanism being one) without much crosstalk.

Then consider a set of several millions (or billions) of bacteria (proto-neurons) and suppose they exchange signals between them. If the signals have some specificity (What John Holland calls tagged signals: a signal carries with it a part which tells which receivers can receive it, so there is communication specificity). Then various bacteria are sensitive to different signals and process them differently. You may thus consider that the signals diffuse in the medium but that a given bacteria receives only some of them. It selects its signals. If, in your mind, you link then by an arrow the bacteria which are able to exchange a signal, you see a network developing. The connections are not hardwired like those between neurons (axons, dendrites) but much more labile and dependent on who emits what and who receives what. Here is your cross talk, outside the bacteria... at the community level.

The result looks much like a simplified collective brain (a proto-collective brain) analog to those described for ants or termites. What I envision is thus this: one or several proto-neurons per bacterium; exchange of many different signals between neurons (ex: tagged by intensity or by chemical nature or by association of different signals); receptivity of different bacteria or sets of bacteria to different signals (and thus development of an implicit network with cross talk at the level of a set of sets of bacteria.

There is no reason why such a collective brain made of tens of billions of bacteria could not be, on its own evolutionary time scale, as powerful as the collective brain of a colony of ants. Of course, I have replaced Klaas's cross talk in a bacterium by cross talk between bacteria. So, I have now to look if this hypothesis makes sense.

It is time to meet somebody else who study just that: networks of bacteria talking together in a common language (i.e. exchanging signals). You will meet Bonnie Bassler, from Princeton (Princeton) who studies this language. I'll also introduce you to Ricard Solé from Barcelona who defined "Fluid Neural Networks', the kind of tool we might just need to simulate our colonies on a computer . I will also introduce a theoretical framework one of my students and I have described and which is called "Metadynamics". Here is the title of our paper you will find on that site:
I realize that until now, most of my posts have been a bit superficial and introductory. They also have been experimentally oriented and not theoretical. I'll have to equilibrate that somewhat. Do not forget: as a great engineer once said (Th. von Karman), " There is nothing more practical than a good theory".

CAVE BACTERIA: A PRIMER ON MOVILE AND VILLA LUZ

°
DID YOU SEE THE GOOGLE ADSENSE ADS ON THE RIGHT?

1) WHY DO I NEED BOTH ANDRONES AND BACTORGS IN "WE SHARE"?
-------------------------------------------------------------------------------------

Hi everybody, I hope that, by now, you're more than slightly interested in intelligent cultures of neurons and thinking bacteria, i.e. as I call them in my novel, "Andrones" and "Bactorgs". As you know, Andrones live in a lab but Bactorgs live in a deep cave. Building on what we discussed before, this post will thus be devoted to one subject:

bacteria in caves

but before, in this introduction, I'd like to discuss a question which has been nagging me for some time:

• I have to deal with Andrones (cultured neural networks) and bactorgs (bacterial organisms). That's a lot of science to cover. Life would be simpler for me if I could focus on only one of these, neurons or bacteria. Why do I need both?

Well, in the novel, I need a lot of interactions (sometimes, almost linguistic) between humans and bacteria. For that, I need a chain of plausible mechanisms and events allowing these distant species to communicate and the best way I found was to have andrones as messengers between bactorgs and humans.

Andrones will be contaminated by bacteria and viruses sent by the bactorgs and this will influence their behaviour. On one hand, andrones will have learned from us how to communicate with humans (i.e. exchanging simple messages). On the other hand, bactorgs will be able to receive chemicals and perhaps electrical messages from andrones, interpret them and react accordingly. Putting the two together, bactorgs will influence the messages andrones send to us... We will be able to communicate bidirectionally... for the best and for the worst.

Now let's come to the main subject of this post: bacteria living in caves.

2) CAVE BACTERIA: STRANGE METABOLISMS AND ECOSYSTEMS
------------------------------------------------------------------------------

We will now discover that our bactorgs have to live in caves and you will meet now the researchers whom I call the "Ladies of the Dark". Four scientists specialized in cave geology and bacteria: Louise Hose, Penny Boston, Diana Northup and Annette Summers Engel.




Penny Boston (University of New Mexico)

















Annette Summers Engel
(U. of Louisiana)









Diana Northup (U. of New Mexico)













Louise Hose (University of Texas) and National Karst Research Center












Question: First things first, why do my bactorgs have to live in caves?

Bactorgs are the real heroes in the novel. They represent the main scientific breakthrough, the discovery of a thinking proto-brain , a non human organism, who is at the same time an ecosystem and an individual (parts of it are disposable and serve as food for other or for its slave animals, part of it, the core ones are its brain and memory. As you will read someday, it is bactorgs who feel threatened by us and by changes in their environment, react by wreaking havoc everywhere in Provence, reach a truce with us and finally set up a difficult but cooperative peace treaty with humans.

But where on earth could such a community reside, unknown to us for eons and still reaching a high state of genetic development?

As far as the thriller aspect of WE SHARE is concerned, this is nice because, as a caver myself, I know that a lot of drama and adventures may be built around caving expeditions. Good material for a thriller. Moreover, we know for a fact that there are bacteria underground,at least up to seven kilometers deep in earth's crust. It has been said that the total mass and diversity of this deep underground life far exceeds our small... surface life.

Even better, close to us, at depths of a few hundred meters, bacterial communities have been found in some caves by our ladies of the dark (and other people too of course but I epitomize these four). These communities thrive in unbelievable conditions: no oxygen but sulfur, methane and CO2; very acidic environment (strong Ph below 1 ... acidic indeed, absolutely corrosive), choking with H2S. These caves have developed complete ecosystems based on bacteria. Worms, spiders, scorpions, centipedes, mites and many other species eat the bacteria and have adapted to the dark and lack of oxygen and light. This is the stuff of nightmares. Good for a novel, specially if the bacterial community is at the same time a thinking bactorg and the primary source of food for the ecosystem which it also enslaves.


Cave bacteria: There in the dark, they form enormous bacterial mats, multi-species slime biofilms making sulfuric acid to carve the cave walls and find their food which is simply the rock itself. Each biofilm is a community and contains many sub-colonies and species, all interacting.

Here are our families and towns of bactorgs. They grow and they provide food for all sorts of insects and animals feeding on them and forming a complete and strange ecosystem without oxygen, originating from the distant past (millions of years ago) when our atmosphere was not oxygen-based but methane and sulfur based. They have adapted to support modern (but strange and changed) insects. Don't get me wrong, I am not inventing here, these ecosystems do really exist (more about it later)!

Question: In "WE SHARE", I will have to invent ways in which such communities maintain their genetic diversity and innovation potential. We know that, in the lab, bacterial colonies grow, become senescent and die. How can we invent a plausible mechanism in order for our bactorgs to avoid this and stay alive as evolving communities for millions of years. How to avoid accumulation of genetic errors, ecosystem tiredness and, to put it bluntly, if they evolve some form of rudimentary consciousness, why don't they get bored to death?

So, here are our Bactorgs, deep in some caves in Provence. As I told you, they are modeled on the bacterial communities existing in two really existing caves Movile cave in Romania and Cueva de Villa Luz in Mexico. The next post will be devoted to these caves. For the moment let's see what our bactorgs will do in them.

Note: in addition to living in these caves, bactorgs will not be isolated. They will communicate with bacteria living in the small cracks of the Provence karst between caves, and even with bacteria in the earth crust and in the surface soil. We might even envision a bacterial super-organism covering the earth....

They will also infect and thus influence (enslave...?) all sorts of insects and animals, some of them (bats, birds, rats, spiders and even humans) living in the outside world. Through them, they will learn about the outside world and act upon it.

How will we observe our bactorgs? By looking at their effects upon infected animals and humans. How will they communicate with us? By infecting the Andrones cultured in an underground laboratory in Provence (You won't believe me but there is really such a lab in Provence - Look "Laboratoire souterrain à bas bruit" or "LSBB, Rustrel" on the web).

Bacterial and virus messengers from the bactorgs will enter the andrones through the micropipets used for chemical stimulations (See last post on Ben Jacob's work). They will then influence the behavior of the andrones and also learn from them. Bactorgs-controlled bacteria will be our interface with the bactorgs communities.

So, that's why I need caves, bactorgs and andrones in my novel. In other posts, we will have to learn a lot more about cave bacteria, their ecosystems and metabolisms. This is where we will meet our "Ladies of the Dark".

As I told you before, Louise Hose (National Karst Research Center, US), Penny Boston and Diane Northup (University of New Mexico) and Annette Summers Engel (Louisiana State University, Baton Rouge) are geologists and microbiologists. They spend a lot of time looking at bacteria in caves. They abseil down deep vertical pits, they crawl in the dark, they swim in underground rivers and they enter chambers in which you have to wear masks to breathe and be careful that droplets of sulfuric acid will not burn you to the bones.

They dare to crawl in bacterial mats and be covered with bugs of all sorts. But they are not only daring explorers. They are first class scientists, studying deeply the geology and ecology of the caves they explore. They do all sorts of geological and biological experiments, for instance, genetic studies and DNA decoding.. I tell you, they are real life adventurers, close to my heart.

They found an amazing diversity of life down there.This is all I need in my novel to make an enthralling world for the bactorgs to live in and for the humans who will enter the cave to experience true wonder. Later we will discuss the works of our ladies of the dark in far more details. Let's just see now three illustrations

This is a set of ...what they call "snottites",yes... like" snot" from your nose ...They are not stalactites of calcite but slimy, flexible biofilms made of billions of bacteria of various species intermixed with gypsum and the extracellular proteine matrix forming the material support of a biofilm. Snottites make drops of concentrated sulfuric acid (look at their bottom) which dissolve the walls of the cave to provide the nutrients needed by the bacteria living on the walls.

This picture is really a snapshot of a small part of a bactorg in its everyday work! Snottites are found in the Villa Luz cave in Mexico. (Photo copyrighted in 2002 by K. Ingham, reproduced with permission)

And another photo...

Down this passage of Villa Luz, the explorers say that there are whole mats of "red goo", a mix of clay decay products, bacteria and rare earth elements. What is the strange metabolism which produced this? Another snapshot on bactorgs. (Photo copyrighted in 2002 by K. Ingham, reproduced with permission)




In the novel, as you know now, bactorgs will have to establish ecological relations with insects and other animals which will use them as a food source (primary trivial ecological role of bactorgs). Bactorgs will also have a second activity: to influence the behaviors of their enslaved insects and other animals (including humans) in subtle ways (close to what is called "enslavement of insects" by ants in ants communities and ants collective brains).


We'll discuss all that and the works of E.O. Wilson on collective brains in ants societies later. For now, just look at the photo hereafter: a snottite enmeshed in a spider's web. You might by now have already guessed: spiders like cavers ( and just like me) just love to be in the dark suspended to little wires... spiders will play an important role in "WE SHARE".


A snottite enmeshed in a spider's web. (Note: they have other photos of insects and midges crawling on snottites).

Not for the squeamish, the fear factor might be high, but for the biologically minded it is pure beauty. (Photo copyrighted in 2002 by K. Ingham, reproduced with permission)





Here is the link of the site you may use as a starting point to enquire about cave bacteria
They call themselves adequately the SLIME group, slime standing for The Subsurface LIfe in Mineral Environment team. Cute...

Enough for today, It's late, the cat is not complaining but I am. The next post will again be devoted to thinking bacteria and later I will tell you more about Villa Luz and Movile.

Let's end up with two little jokes about cavers:
- How do you recognize a good caver? Because he (she) is alive.
- And a more mathematical one: In his (her) life, a caver enters a cave N times and gets out of it alive N-1 times.

THINKING BACTERIAL OR NEURONAL STYLE: BEN JACOB?

°
DID YOU SEE THE GOOGLE ADSENSE ADS ON THE RIGHT?

1) A REMINDER ON BACTERIA, NEURONS AND THINKING
----------------------------------------------------------------------

As you know from my first post, my novel entitled"WE SHR", a mispelling for "WE SHARE", presents the adventures of what I call Bactorgs, bacterial colonies having social and intelligent behaviors (e.g. Weiss's work). It also present Andrones, cultured neural networks showing also social and intelligent behaviors (e.g. Potter's work). Finally, and "audaciously", the novel will discuss scientific theories about and computational models of these systems.

Why "audaciously": because there is a rule in novel writing; every time you insert an equation or a hard scientific reasoning, your audience decreases by 50%¨. By that account, the "WE SHARE" audience should be at the 0.00000001 level or perhaps worse. My goal is to make science pleasant. We'll see if I succeed.

So, we need to discuss thinking in bacteria, thinking in cultured neuronal networks and models of these systems. Unexpected as it once seemed to me, there is a researcher working, at a very high level, on these three subjects. Meet Eshel Ben Jacob. We will first discuss its work on bacteria. Then we'll see what he did on neurons and, later on in another post, his modeling work.





2) BEN JACOB'S WORK ON BACTERIAL COLONIES (MY BACTORGS)
--------------------------------------------------------------------------------

Seen from my point of view, Eshel is a first class "Jack of all trades". He is at Tel Aviv University where he does world class work in Physics and Biophysics. He is a deep thinker and works on many subjects. As you may guess, the ones which interest us at the moment are bacterial cultures.

• Eshel demonstrated that , when challenged to grow in difficult conditions, bacterial colonies respond by adopting very sophisticated spatial growing patterns optimizing their food intake. He challenges them to grow in conditions of limited nutrients or against antibiotics or with spatial obstacles and they respond by devising clever growing spatial patterns (mostly spatially organized fractals). Probably, bacterial colonies need to do some colony-level computation to do that.
  
• Here is the title of a paper, Eshel published in the journal "Trends in microbiology" . This paper was the most downloaded paper from that journal in 2004. You'll find it on Eshel's site (see later). Read it and think twice: It's not Sci Fi but hard, respectable and respected science

Can you believe this title? Eshel argues that his experiments and those of other show that bacteria have developed sophisticated communication capabilities (quorum sensing, chemicals and plasmid exchanges) which they use to reach a high level linguistic communication ability between themselves (shared interpretation of messages, dialogs and meaning-based communication allowing intentional (??) behavior, decision making, recognition and identification of other colonies, ... all Eshel's own words).

This may be called "bacterial social intelligence..." what else?

How can I extrapolate for "WE SHARE"?

It seems to me that the development of Eshel's idea requires going beyond communication to move into the realm of inheritable colonial memory and commonly shared genomic context. What I need is a computer or a Turing machine based on a bacterial colony (see later my discussion of issues like collective brains, fluid neural networks and amorphous computing).

Eshel Goes further. I do not understand him yet but he seems to imply that the limitations of Turing machines may be overcome by bacterial colonies. I do not claim to understand this or even to admit that they are limitations to Turing machines?

Here is a picture of two of Eshel's colonies. He argues that such fractal shapes cannot be generated by chance. He also suggests that they express some computational parallel algorithm at work. I agree, clearly, Mandelbrot is at work here. (With permission from Eshel Ben Jacob)





Remark however, that generating such shapes might, computationally speaking, be easier than expected and may need only much simpler algorithms than what you would think at first sight. For instance, I have myself shown that a drop of glue squeezed between two plates of glass which are then separated slowly, form on each plate a fractal tree which is determined not by intricate algorithms but simply by the speed of separation of the plates and the surface tension, adherence and flow properties of the glue. No complex algorithm is involved to generate this kind of complex fractal patterns but only a few parameters and some rules and physical laws.

Issues like Gellman's complexity, crypticity and depth are playing a role here (estimating the complexity of the algorithms needed to coordinate such a growth). That's food enough for another post.

I will soon re-read Eshel's papers. This is not always easy going and I'll write some more posts about it later. Anyway, here is a cornerstone of WE SHARE: a respectable scientific paper discussing bacterial intelligence, social life and colonial memory. Those are the three pillars on which, in my novel, I build my underground bacterial colonies, the Bactorgs. A bit of extrapolation and you have great perspectives. Actually, you do not have to really extrapolate. Eshel's paper is better than Sci Fi.

Here is a link to this paper on Eshel's site: Ben jacob's Trends in microbiology 2004 paper.
And here is a link To Eshel's site itself: Eshel's site.

3) BEN JACOB'S WORK ON CULTURED NEURONS NETWORKS (MY ANDRONES):
-----------------------------------------------------------------------------------------------

Independently of his work on bacteria, Eshel works also on multi-electrodes arrays and cultured networks (remember Potter's work discussed in my first post). So, he is a precursor, not only of bactorgs but also of Andrones.

His work is complementary to Potter's work. Potter has extremely sophisticated, closed loop, two way electrical communication and learning in a long term neuronal culture but he has no way to communicate chemically with his cultures.

That might be a problem since a lot of reward and penalty in the brain is probably done chemically (neuro-transmitters, endorphins, cannabinoids ...). Eshel developed a way to have his cultured network on the electrode array stimulated at selected points by chosen chemicals. Every year people discover new chemical neurotransmitters and find new roles for them, see for instance the recent discoveries on NO and now the new hypothesis on the role of chimiokines.

There is clearly now a need to combine Potter's and Ben Jacob's work.

Here is a picture which tells you all you need to know for now about Eshel's work.


In the upper panel, you see an MEA and its cultured network (1). Then a micropipet (2) used for local chemical stimulation at selected locations (probably mounted on some kind of stereotactic equipment. Potentials are recorded and sent to a computer (3). The volume of the stimulating droplets are controlled by a second micrometer and a syringe.

In the lower panel, we show the MEA (dots and black lines), its cultured network (cells on the blue plate) and on top, the translucent micropipet placed above one of the recording electrodes. For stimulation, Ben Jacob currently uses picrotoxin (an inhibitory antagonist, i.e. a substance relieving the inhibition of excitation felt by some neurons) and show that this stimulation makes it possible to imprint multiple memories in the form of collective modes of neuronal firing and that these memories persist for days. Memories.... an important element of what Andrones need! (With permission from Eshel Ben JAcob)

4) EXTRAPOLATING POTTER'S AND BEN JACOB'S WORK FOR WE SHR
------------------------------------------------------------------------------------

Let us consider the implications of coupling Potter's and Ben Jacob's works: chemical and electrical stimulation, long term culture, two way electrical communication for adaptive embodied behavior. Let's extrapolate a little bit.

Why not add some neurogenesis ability to cultured neuronal cultures (controlling stem cells is another hobby of Potter)? Why not also control and direct axonal growth?

Why not have multi-culture networks on the same or on different interconnected plates. A bit of cortical cells, a bit of hippothalamus, a bit of hippocampal and so on, all and each growing their own kind of connections and interconnecting between themselves?

(Note; there is a paper which I am, right now, unable to quote exactly which describes the guidance of axons by external stimulators along long distance (several millimeters ) lines. We could use such systems to interconnect separate subcultures together i.e. to build andrones as multi-cultures having specific global connection patterns.

What you get is then close to what I envision for what I call an "Androne", the neural culture hero in my novel. It lives on a set of MEA and Petri dishes and has all the features I've just listed + a few others.

NOTE: Just to tell you that, in the novel, the researcher developing Andrones has discovered a library of electrical signals and chemicals to communicate with them, make them learn, store and retrieve memories and so on... My Andrones will perhaps feel elementary emotions and perhaps some form of elementary consciousness (after all, it is probably a graded property). Is it too far fetched? What do you think? Compare with current models of pre-consciousness like Edelman's robots?

5) CONCLUSION
--------------------

All that to tell you that you have just met Eshel, one of my heroes. As Einstein said, you define a scientist by what he does. You have to admit Eshel does a lot and every bit of his work is minted in originality . Here we have just scratched the surface. Go diving deep in his site (see before)!

Again time to sleep, My cat Touti is meowing and that's the signal. In the next post, you'll meet some other people:

• Klaas Hellingwerf from Amsterdam who sees bacteria as proto-neurons and has organized the first European community sponsored workshop and research program on this theme.
• Bonnie Bassler who studies the languages bacteria use to speak between themselves ( in a given species and among species).

Together, they make an impressive case for the idea that bacteria have some elementary thinking ability (thinking being defined conservatively but operationally by what Mc Culloch and Pitts models can do..., a limited form of thinking admittedly but not a bad one as a starting point).

And as usual, a thought for the night:

To define art, don't ask what you can still add in a picture but what you can still erase...

Don't dream about Andrones and Bactorgs or, like me, just a little bit.

Jacques