"WE SHARE": THINKING OR INTELLIGENT BACTERIA, , NEURONS AND CAVES

PHOTORHABDUS: A LUMINESCENT HUMAN PATHOGEN

2008-09-03T10:24:00.001-07:00

1. INTRODUCTION: A BIT OF SCIENCE FICTION," PHOTL++", A BACTERIA MAKING EYES GLOW AND THEN ROT...!

DID YOU SEE THE GOOGLE ADSENSE ADS ON THE RIGHT?

In "We Share", the novel on bacteria I am writing, the cave-living colony of bacteria which I call a bactorg will feel threatened by changes in its environment. To defend itself, it will launch a series of attacks on humans and animals outside the cave.

This will be seen initially as a bioterrorist attack. Soon, considering the variety of viruses and bacteria used and their complete strangeness, the scientists in the novel will understand that there is more at work than just "plain", human-invented bioterrorism... Indeed, they will be confronted with attacks devised by an organism, the bactorg, which has acquired, over its millions of years, a total mastery of cellular bioengineering at the evolutionary time scale.

It has built all sorts of strange bacterial and viral mutants and has enslaved many insects and higher animals. It is a frightful enemy. However, it is a bit naïve too, It does not really know the world outside the cave and does not really understand what we are or what are the constraints of massive terrestrial and airborne bioterrorism agents dissemination.

To build my directory of potential bactorg weapons, I have thus, at this stage, to find in the literature on "bacterial emerging pathogens", "viruses" and "bacterial curiosa", a set of dramatic infections using insects and animal vectors, bacterial and viral pathogens. I need my pathogens to induce nightmarish (yet plausible) illnesses. It is also mandatory that they use advanced and original signalling and logical processing methods, they need to be intelligent weapons.

I have thus to select carefully my pathogens for scientific interest and drama potential.

In this post, I'll present one of my favourites "Photarhabdus luminescent". In the novel, I modify it of course to amplify its effects and I call it PhotL++.

The real PhotL it is a bacteria living in nematodes (small worms) which infect the guts of many insects. The nematodes release the bacteria into the insect blood circulation and then the bacteria kill the insect. From my point of view, the real PhotL it has three interesting characteristics:

It is the only terrestrial bacteria which is luminescent... the question is why ??? This will be a big question in "WE SHARE"
Until recently, it was known to infect only insects but it is now emerging as a human pathogen.
It secretes many powerful toxins and also antibiotics

Just extrapolating a little bit, I will thus invent "PhotL++", a nicely dramatic mutant.

PhotL++ causes awful abscesses in humans and make them glow in the dark. It also attacks the eyes creating strong conjunctivitis and keratitis (inflammations of the conjunctiva -the outermost layer of the eye and the inner surface of the eyelids- and the cornea). The inflammated eyes present first an abundant, opaque purulent discharge and tears. Then they become red and glowing in the dark (very bright green light). Finally, they rot and the brain is attacked; the infected animal or person dies. Is that sufficiently awful? I guess so. As you will see, temporal lobe epilepsy is high drama stuff.

I will add one more twist: the emission of photoluminescence by PhotL++ will be influenced by electromagnetic radiations which can make its intensity pulsate

(I have a literature reference proposing this, see later).

Moreover, a PhotL colony will use its light signal to coordinate its actions and those of its symbiont, the nematode.

But enough on science fiction. When I had my initial nightmare about luminous bacteria, I was quite excited, here was an ideal weapon... Imagine, your eyes glowing in the dark, pulsating and then rotting...

Then I went hunting for it in the real world (I mean on the WEB) and as usual, I was flabbergasted... Reality is almost always better than fiction... My brainchild was almost existing. The real PhotL is known as Photorhabdus luminescent. In the following sections, I will just present the facts about it... just plain facts.

2. PHOTORHABDUS LUMINESCENT, THE FACTS

Meet Nick Waterfield, from Bath University, a microbiologist studying phosphorhabdus and many other microbes (sorry for the distorsion of the photo, for some reason, I can't get it right).

One of its many ideas is that insects are a neglected field of study when it comes to microbiology. They are an enormous reservoir, harboring many potentially harmful species. Their immune systems is, strangely enough (at least to me), quite close to ours. So the bacteria which have adapted to them have just small evolutionary steps to take to get their metaphorical teeth into us. So Nick's idea is that we should study more closely the bacteria infecting insects and that's what he does.
What follows is closely inspired from a text on his website on one of his pet subject, Photorhabdus (PhotL). It is the only known terrestrial bioluminescent bacterium. It is a pathogen of insects. It lives in the gut of a nematode. An ideal candidate for the "WE SHARE" casting.

Click here to have a link to Nick's site.

2.1 THE LIFE OF PHOTL: Infective young nematodes carrying PhotL search in the soil for their insect prey until they encounter one (often a larva). Then, they scratch their way into the insect's blood circulation and "vomit" up Photorhabdus into the blood where it secretes toxins and virulence factors that rapidly kill the insect.

Studies on the insecticidal-complex produced by PhotL have revealed that several extracellular macromolecules such as proteases, lipases and broad-spectrum antibiotics confer its insecticidal ability which is wide ranged (PhotL is proposed as a pesticide but that raises important security concerns. Its killing ability is wide ranging and it might very well kill useful insects). Imagine a few mutations and we have a fearful human pathogen.

The bacteria replicate rapidly and convert the insect tissues into more bacteria that serve as a food source for the nematodes which may then reproduce. It is around the time of insect death (when the food source will soon be exhausted... and signalling of that fact needed) that the bioluminescence of the insect corpse due to the bacteria can be seen. This will be important. Hereafter a couple of photo from Nick's site: on the left, two insect larvas glowing a little bit before being destroyed by the bacteria. On the left, a larva exploding and ejecting its full load of nematodes. (courtesy of Dr. Nick Waterfield, Bath University)

A load of bacteria in an insect, just below the collagen outside sheat.

2.2 RELATION OF PHOTL AND YERSINIA PESTIS (the black plague microbe): More stuff for nightmares, lateral transfer of genetic material between Photorhabdus and Yersinia has been demonstrated and is probably a result from their common association with insects as bacterial pathogens .

The association with yersinia pestis opens up interesting avenues for my novel. A few centuries ago (in 1720), there was a famous black plague epidemics in Provence, just where I need it. Yersinia and PhotL were there and were associated. Could they have been incorporated as part of the multispecies, underground Provencal bactorg community at that time? Could they then have been kept dormant until now for two centuries and then suddenly reactivated and released outside the cave as an answer to some quorum sensing set of signals from the outside eenvironment having suddenly reached the bactorg after the earthquake?

Remark: However note that the black plague has recently been the subject of alternative theories attributing its origin to other causes like anthrax or a virus like ebola…?

2.3 BIOLUMINESCENCE IN PHOTL:Bioluminescence is the production of visible light by a chemical reaction in a living organism (see the photo above). Bioluminescence is rarely reported in clinical bacteriology laboratories because bacterial bioluminescence is seen primarily in marine species. Some fishes indeed have an organ in which they grow a large colony of resident luminescent bacteria which provide them with a powerful light useful to attract preys or mates. But what could be the usefulness of light in a bacterium living in the gut of a worm inside an insect? Photorhabdus are the only terrestrial bacteria known to exhibit this property.A useful signalling system?

A culture of PhotL growing and swarming on an agar plate. It emits a faint light visible in the dark. Do you remember the fractal shapes of bacterial growth we saw when we discussed Eshel Ben Jacob's work? I think that this might be another example of it. Do these cultures grow in difficult conditions? Can we experiment on them by modulating their growth conditions like Eshel did? Will we observe nice fractals?

WHY DO PHOTL EMIT LIGHT? Energetically speaking, bioluminescence is a costly process, difficult to justify on an evolutionary basis if it has no clear role. Current theories include some unknown biochemical role or even that it is a lure to tempt fresh insect victims into range. I do not very much believe in them.

When the insect resources have been exhausted, the bacteria provide the nematode with an unknown "food signal" which switches them into a developmental state known as an infective juvenile. At this point they re-package the bacteria before bursting from the insect corpse in search of fresh victims. Could light play a role? A remark: Worms with enough food cease to emit light.

2.4 PHOTORHABDUS, AN EMERGING HUMAN PATHOGEN

Photorhabdus has never been isolated as free living in the environment. However, recent cases of human infections due quite plausibly to Photorhabdus have been reported in the US, Australia and Nepal. Many other cases might be misdiagnosed due to the failure of laboratories to recognise this unexpected pathogen.

Let us describe a clinical case (reported by Dr. Gerrard, Gold Coast Hospital, Queensland, Australia).

a 29-year-old woman with an intensely painful and swollen right foot (3). Two days before presentation, she had cleared debris and weeds from her country property while barefoot. She was started on oral amoxicillin-clavulanic acid in the emergency department, but by the next day her foot had become even more swollen, erythematous, and painful. She was admitted to the hospital and started on intravenous antistaphylococcal (flucloxacillin) antibiotics. Abscess before and after treatment with antibiotics... (courtesy of Dr. Gerrard)

Despite treatment, a local abscess formed. This was incised, and pus was sent to the laboratory for culture. Three days later, a gram-negative rod was isolated in pure culture. The Vitek GNI card identified the organism as Flavobacterium sp. It took them a lot of ingenuity to identify Phot L as the culprit, Thanks to them...

Another case (Dr Alice Weisfeld, Microbiology Specialists Incorporated, Houston, Texas )
A 54-year-old male presented to the emergency department of a local Houston hospital during July 2003. He was a ranch hand who believed that he was bitten by a spider on his left
breast. He presented with multiple carbuncles on his left chest wall and multiple pustular nodular lesions over his extremities. The patient, who has a family history of diabetes, had a blood sugar level of 400 on admission. His temperature was 101°F, his blood pressure was 135/70, his respiratory rate was 20, and his pulse was 60. Culture of the left-breast abscess showed moderate numbers of methicillin-resistant Staphylococcus aureus and an unremarkable gram-negative rod identified by a MicroScan Neg Urine Combo Panel Type 34 on the MicroScan WalkAway (Dade Behring, Inc., MicroScan Division, West Sacramento, CA) as Pseudomonas oryzihabitans. An identical gram-negative rod was isolated from four of four blood culture bottles from two separate venipunctures. However, it was identified on the same system as Providencia rustigianii.
Both isolates were sent to a local reference laboratory (Microbiology Specialists Incorporated). Each isolate produced two colony types, which exhibited annular hemolysis and swarming on blood agar (Fig. 1 and 2). Annular hemolysis is unusual in that there is no hemolysis immediately around the colony but there is a thin line (about 2 mm wide) of hemolysis about 12 mm from the edge of the colony. Each isolate was oxidase negative, catalase positive, and motile, with a nondiffusible yellow to dirty-brown pigment. Neither isolate reduced nitrate to nitrite, but both fermented glucose (Table 1). The isolate was finally identified as Photorhabdus asymbiotica (formerly Xenorhabdus luminescens) on the basis of weak bioluminescence when tryptic soy agar slants grown at either 25°C or 35°C were observed in the dark.

The organism identifications were subsequently confirmed by the Centers for Disease Control and Prevention (Atlanta, US) using conventional biochemicals (1) and a number of other rapid identification systems.

Source of infection: The source of human infection is not yet known, although an invertebrate vector(why not a spider bite, which would be nice for we SHARE in which spiders play a big role) is suspected. Indeed, cases occur indeed in warm wet months, usually after rain storms, and the victims are often people working in the outdoors. Moreover, the abscesses appear on feet and legs.

REmark that with th eclimate change in Some parts of Provence, the climate there is becoming dryer in summer but winters are warmer and wetter, ideal for PhotL...?

CONCLUSION: PHotL associated with severe soft tissue and systemic infections, and is now considered as “emerging human pathogen”.

ANGEL GLOW: Notice that some people believe that PhotL was the cause of a phenomenon called "angel glow", soldiers wounds glowing in the dark which were observed in people lying on the ground for days during the war of independence in the US. The soldiers with glowing wounds were recovering better, hence the name.
The hypothesis is that PhotL was infecting them by contact with the soil (either due to nematodes or free living bacteria). They were killing other bacteria with their antibiotics, hence the better survival probability. At that time, they were not pathogenic for humans... things change.

All together, I have an ideal scheme for my glowing wounds, I have just to suppose that PhotL is now pathogenic for humans, that it attacks not only the legs but also the eyes and that in its final stage, it infects the brain and kill people... a piece of cake.

A last twist I promised you: Why does the light emission from PHOTL++ pulsate?

Glowing rotting eyes are nice but in addition, in "WE SHARE", the light intensity is always changing.

Admittedly, PhotL does not do that. Why does PHOTL++ do it? The real reason is because it is nice. The second reason is that it allows PhotL to modulate its signal and make it more complex... Advanced signalling... more sophisticated language!

How does it do it? Consider the following reference:

Electromagnetic field effect on luminescent bacteria Berzhanskaya and al. IEEE transactions on Magnetics Vol 31, Issue 6, Nov. 1996 - pp. 4274-4275
Abstract: The effects of electromagnetic fields with frequencies varying from 36 to 55GHZ on the bioluminescent activity of bacteria were investigated. EMFs resulted in a decrease of bioluminescence which depended on frequency. The time of adaptation of cells to the EMF was longer than the intrinsic temporal constants of the bioluminescent signals. The effect was non thermal. Magnetic storms resulted in an increase of bioluminescence.

That's a good start. I'll leave you on this.

A NOTE ON THE USE OF PhotL as a biopesticide (see before), cf the following paper:

Biosafety concerns on the use of Photorhabdus luminescens as biopesticide: experimental evidence of mortality in egg parasitoid Trichogramma spp. Sharad Mohan1,* and Naved Sabir - CURRENT SCIENCE, VOL. 89, NO. 7, 10 OCTOBER 2005

Photorhabdus luminescens exhibit biopesticidal potential against important pests, independent of its host nematode. Indeed, it secretes powerful toxins and large spectrum antibiotics. The question is: can it also attack useful non-targeted organisms? The authors have tested this. They tested the bio-ecological compatibility of PhotL in vitro, against the common biocontrol (and thus useful) agent Trichogramma living as parasites inside the eggs of the rice grain moth, Corcyra cephalonica. Most Corcyra egg-shells became flaccid and there was significant reduction of up to 84% in the emergence of Trichogramma adults. The nematode carrying the bacterium within its gut had no effect on the emergence. This result points to the bio-ecological hazards of indiscriminate use of P. luminescens as a biopesticide. Due to its wide host range, the use of P. luminescens in a pest management programme must be questionned until it is proven safe for non-target organisms

EXTRAPOLATION FOR "WE SHARE": I might decide that PhotL has been used as a pesticide in Provence. Unknown to us, PhotL has been transformed by the insects they invaded which were containing other bacteria transmitted to them by the bactorg (remember what I call enslaving).
They've become PhotL++ and they carry death with them.They are thus there in the soil in large quantities but do not attack humans. Then some signal (probably transmitted by a phage) from the bactorg reaches them and they become active...
PhotL++ uses light as a modulated signal to control it sexpansion. But its light generation mechanism is receptive to EMF influence. In the cave, this was making no harm, EM fields were too weak. But outside, they receive EM radiations from the NSA-like site in the legion camp. It disorganizes them completely and they can't control themselves anymore... a recipe for disaster.

That's it folks?. Have a good night.

BACTERIALLY SPEAKING: BONNIE BASSLER

2008-07-23T01:35:00.000-07:00

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DID YOU SEE THE GOOGLE ADSENSE ADS ON THE RIGHT?

1. BONNIE BASSLER AND THE LANGUAGES OF BACTERIA

One of my problems when starting to think about bactorgs was to assess the plausibility of the science basis for that extrapolation. I wanted thus to look at what well respected, first class scientists were thinking about multicellular bacterial colonies and chemical signalling. Then I started reading the works of people like Hellingwerf, Kolter and Ben Jacob. Assessing their ideas the best I could and seeing where they were leading, I soon realized that here was a burgeoning yet important bud of science. The idea of communication and signalling in bacteria was rapidly becoming and is now a new paradigm.Today, you will meet another of these first class scientists studying "bacterial chat"...

Bonnie Bassler is a professor of microbiology in Princeton. She was the recipient of a Mac Arthur "Genius" award and is a member of the US National Academy of Sciences. She is thus a mainstream scientist and, from what I can see on the web, she is also a very energetic and kind person.

Her research is focused on disentangling the mechanisms of signalling and communication in bacteria. She started by looking at quorum sensing as classically defined and now proceeds to more advanced signalling (interspecies, with eukariots..). Clearly she goes a long way to reveal the mechanisms underlying the phospho-neural networks suggested by Hellingwerf. I have read as carefully as I can a few of her papers, She writes superbly. In this post, I will look in detail at one of the papers from her group (for more details, see the web page of Bonnie's lab in Princeton.

The paper I am referring to is by Stephan Schauder and Bonnie Bassler. It has been published in "Genes & Dev. 2001 15: 1468-1480". Download the PDF by clicking here.

Lets start with the title..... provocative but well supported by facts
Bacteria speaking.... a flavor of Bactorgs isn'it? Let's look at it more closely.

2) THE LANGUAGE OF BACTERIA
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Bonnie and Stephan discuss in detail many bacterial behaviors which lead them to believe that bacteria have sophisticated communication abilities. They also go at great lengths to explain the molecular and genetic mechanisms used by the bacteria to implement these communication capabilities.

The mechanisms they describe are very compatible with the ideas of Hellingwerf (see a previous post).. My goal in the current post is to see if we can look at the genetic regulations they describe in bacteria as analogs to neural networks susceptible to learn by evolving (i.e. in evolutionary time, not during the life of a bacterium).

However, Bonnie and Stephan say nothing about learning or adapting. More about that later when we will discuss a recent paper by Saeed Tavazoie and his associates. First let's look if we really have networks. This is the goal of the current post. Later we will see if these networks may adapt and learn.

I am not a cellular biologist nor a chemist. Thus I am not primarily interested in the chemical details of the various mechanisms nor in the exact nature of the various chemicals and genes involved. Moreover, even if I were, I would not understand these details. In what follows, I will just insist on the essentials: what are the behaviors and the general features of the mechanisms involved.

I have not tried to write a summary of Bassler and Schauder's paper. It is so well written that I would have made a abd job of it. Instead, I have collected some of their sentences in a series of excerpts. I have sometimes slightly modified them to suppress technical details and lists of references. I also changed a few words. I believe that I have not destroyed the meaning they intended to convey. I refer you to the original paper for further details.

You will find my modified excerpts in a sequence of blue panels hereafter. I link these panels by a few lines of text to tell you what I infer from them. I have also redrawn and slightly modified their figures. I believe that my panels and figures give to non specialists like myself a nice view of the current state of the art on bactorgs internal mechanisms. Try to imagine what we will know in ten years.

An introduction to quorum sensing:

Bonnie and Stephan start by summarizing what is quorum sensing:

THE LESSONS FOR WE SHARE: coordinated control of genetic expression in a multicellular community, control of many global behaviors, intra and interspecies communication, communication with eukaryotic cells, fight of other species against quorum sensing bacteria. All the basics I need for my Bactorgs are there.

Then Bonnie and Stephan give us a view of the early stages of the research on quorum sensing:

Thus, the evolutionary, functional importance of quorum sensing in V. Fischeri is clearly stated: to avoid the metabolical cost of producing light when it would be ineffective and only produce light it when it brings to the bacteria the clear advantage of protection in the host. It is also important to note that far from being limited to this species, quorum sensing is now known to be widely used by bacteria. It is clear from the beginning that if quorum sensing brings with it a large evolutionry advantage, it must have evolved in many bacterial species.

A network view of the basic mechanism of quorum sensing:

Here is a figure showing you the mechanism of quorum sensing in V fischeri.

LEGEND: The quorum sensing system of Gram negative bacteria. The LuxI protein makes the autoinducers (green pentagons) which then diffuse freely outside. Each bacterium doing the same, the concentration of external autoinducer is a measure of the size of the population(quorum). When the autoinducer concentration is high, it binds to a cognate receptor LuxR (cognate means having the same form and ad hoc characteristics to bind specifically to the molecule it receives). This is quorum sensing.
The complex auto inducer-Lux R then binds at target gene promoters and activate their effect (transcription) which has behavioral consequences.

The Lux-I Lux-R-gene expression pathway indicated here is just an example of the neural network-like pathways we discussed when we saw the work of Hellingwerf. If a bacterium has several quorum sensing pathways like the one above and if they share signals and communicate together, we have an Hellingwerf neural network analogue.

Quorum sensing in Gram positive bacteria

V fischeri is a Gram negative bacteria. As you know, Gram positive and negative bacteria have very different membrane properties (if you don't know this, look in Wikipedia). Hence the mechanism of quorum sensing in gram positive bacteria has to be a little bit different. However, it tells us very much the same story: signal, quorum, high density detection, gene activation. This confirms that quorum sensing gives an important evolutionary advantage to the bacteria using it. Indeed, it exists in almost all bacteria. Each species devised its own way to implement it (convergent evolution). Here is the mechanism in Gram positive bacteria.
Legend: A precursor peptide (the linked red pentagons) is produced by expressing a precursor locus on a gene. It is modified and an ATP-binding cassette (ABC) exporter secretes the end product peptide autoinducer (single red pentagons). It accumulates as a function of the size of the population. At high density (quorum sensing), the autoinducer is detected by a two component S-R system (acronym meaning signal –regulator or signal –response, take your pick).
As the name implies, this signal transduction system has two parts. A sensor protein (the little black bar S) recognizes and autophosphorylates (p) at a specific site (H). The phosphoryl group is transferred to a cognate response or regulator protein R which is then phosphorylated (D). The phosphorylated D binds to specific promoter genes (targets) to modulate the expression of the regulated genes.

Again, the similarity with Hellingwer's views are striking

Going further than the basic mechanisms: layered networks

Remember what Klaas Hellingwerf told us: in a single bacterium, several mechanisms are linked together to form a complex signal processing network, what he calls by analogy a phospho-neural network... Bassler and Schauder tell us very much the same story. Read the following excerpt:

They describe what is the beginning of a network: sequential steps, response to several signals (here from various species and even eukariots...), behavioral complexity. Bacteria can think in the same primitive sense that simple artificial neural network (Mc Culloch Pitts or PDP) can think (admittedly a rather limited definition of thinking but, as a starting point, it is not bad!). To read more about Mc Culloch and Pitts neuronal networks, click here, to know more about neural networks using Rumelhart's PDP approach, click here).

Remark that, like in Hellingwer's paper, thet do not say a lot about "crosstalk".

Speaking with prokariot and eukariot friends and foes: interspecies communication

One more step: it is nice to speak with your own kind but life is more complex than that. You need to dialog with ennemies and potential friends from other species (bacteria or eukariots). For instance, in a biofilm, many species of bacteria coexist. They cooperate or compete. They have to exchange all sort of signals like "I am a friend, I can give you this.." or "Beware, I can kill you.., look at this toxin". How do our bacteria achieve this?
Remark that they describe an exchange of signals at the community level or even among species. Moreover,their signals are what I called "tagged" a specific signal can only be seen by the bacteria having the proper receptors for it. It is all I required to build a "fluid neural network" or a "collective ant-like brain".

Here is a view of the mechanism, Bonnie and Stephan propose for V. harveyi. We will see the answer to the mystery question (see end of the blue panel) just afterwards.

Legend: The hybrid quorum sensing circuit of V. harveyi. .Elements characteristic of both Gram-negative and Gram-positive bacterial quorum sensing systems are combined.
An acyl-HSL autoinducer (AI-1, green pentagons) is produced by the activity of LuxLM. This is typical of Gram negative circuits. A second autoinducer (AI-2, red pentagons) is synthesized by the enzyme LuxS. AI-2 is proposed to be a furanone. Both autoinducers accumulate as a function of cell density. The sensor for AI-1 is LuxN, and two proteins, LuxP and LuxQ, function together to detect AI-2.
LuxN and LuxQ are regulator proteins that transduce information to a shared integrator protein called LuxU. LuxU sends the signal to the response regulator protein LuxO. The mechanism of signal transduction is a phosphorelay (denoted P). LuxO controls the transcription of a putative repressor protein (denoted X), and a transcriptional activator protein called LuxR is also required for expression of the luciferase structural operon (luxCDABE). The conserved phosphorylation sites on the two-component proteins are indicated as H (histidine) and D (aspartate).

This become more complex. I do not pretend to understand all of this but the message is clear: we see emerging a network associating the red and green messages. The node LuxU has all the connection characteristics of a two input logic processing node in a neural network. The exact nature of the computation done by that circuit is still a bit unclear.

Remember the pathways in Hellingwerf's paper. Some of them were associating several signals at some logical computing non linear nodes. Here they are.

Bonnie has thus found the perfect test system: V. harveyi. Why did this bacterium evolve such a complex network? How do other bacteria do? Here is what Bonnie says: A NOTE: Remark that, for "WE SHARE", another point should be developed: communication in biofilms. I will have to study a paper by Nadell and colleagues entitled "The evolution of quorum sensing in biofilms" (PLOS biology, January 2008, vol 6, Issue 1, p. 171 - 179). This is for another post.

A special case: communication with higher species

And finally, communication with higher species! Remember, bactorgs will infect humans and animals in order to defend themwelves against what they perceive as threats. However, the spectrum of infection will be wide, from lethal (no discussion between species) up to soft attacks, subtle influences on the brain (mainly the temporal lobe) and the reward/penalty system, lethal attacks, compromises and truces. This will need sophisticated two way communication between bacteria and higher species. Am I entitled to extrapolate in that direction?

Another reason for communications with the so-called higher species: I told you that, during their eons of evolution, bactorgs have enslaved many insects and small mammals just like the collective brains of ants and termites enslave some aphids. Bactorgs will use their slaves as messengers, weapons and spies in the outside world. Again, this will need a two way communication system between bacteria and the so-called higher species.

So, what does Bonnie tell us about communication with higher species?

First from higher species to bacteria:

And now from bacteria to their competitors (other bacteria) or to their hosts and preys (higher animals);Here are a few examples of bacterial strategies
What about eukariots
NOTE: I will have to write a post on toxin-antitoxin plasmid addiction systems (they are called "addiction modules", to see a paper on them, click here).

NOTE: One more points to look at: prisonners dilemma in bacteria (they have been documented in viruses...?) and more generally cheaters. I think that this might develop as an important theme in" WE SHARE".

Conclusion of the Schauder - Bassler paper

Really, I have all I need to say that Bactorgs are a valid hard sci fi extrapolation of what is currently known about bacterial multicellular systems. Considering that this kind of research is about ten years old, I feel entitled to extrapolate quite a bit. In WE SHARE, bactorgs will be alive, fit and kicking, thinking and speaking.

Here is the conclusion of Bonnie and Stephan's paper
Bonnie and one of her colleagues, Richard Losick, have written a more complete review of bacterial languages. It is mind boggling. I invite you to read it(it is in "Cell 125, April 21, 2006", click here to get it). I will certainly come back to it later, for the moment, the above excerpts should give you the essentials of what I think is needed to justify the bactorg idea. Here is a photo of the title of Bassler's and Losick review... You see, bacterial languages are with us to stay. Bactorgs are not unplausible. It is just a matter of knowing where I can place the limit.
A FEW MORE NOTES: I have now to make a list of all the extrapolations I envision for bactorgs in "WE SHARE". I have also to read more about Ben Jacob's work who studies isolated but wild cultures and put forward some highly speculative hypotheses about advanced communication and intelligence in bacteria. I have to make a synthesis of Hellingwerf, Bassler and Ben Jacob's work. What could be the language underlying Ben Jacob's organizations? Do we find fractal organizations in wild colonies and in biofilms? What is the true extent of the meanings conveyed by bacterial languages?

A NOTE ABOUT SIMULATING BACTERIAL COLONIES: Last but not least, at least from my own viewpoint as a researcher: over the last few years, I have developed a graphical modelling language for general kinetic systems at a population level (not at what is called an agent or individual-based level). I call my language "Kinetic Graphs or KG". I have implemented KG in a simulation package called 20 SIM which is a standard in electrical and mechanical engineering. I have adapted the 20-SIM graphical language which is called "bond graphs" to kinetic systems.
When, above, I said "generic" I was meaning that kinetic models are used in fields as diverse as chemistry, biology, ecology and even in resource modelling in management. My language, being generic, covers all these cases and I have developed demonstrators in each. I have taught KG at several universities (Technion Haifa, Ecole Polytechnique Fédérale de Lausanne, University of Lille and Kings College London).
I think that it is a very good language (but I am not neutral), forcing you to be accurate and rigorous while staying very intuitive and simple. Yet, as a generic language, it is not specifically optimised for genetic regulation although it may cover it. I think that, for circuits like those described above, it could be very nice and I intend to publish at some stage a few posts on it.

Just one more point on KG: They may, under some constraints, cover the case of networks which change their connections due to adaptation or learning. This is not easily done by other methods. Considering adaptive evolutionary learning in bacterial communities (Tavazoie, paper), we are led to networks like those described above but more complex and with adaptive connections. It could be a nice feature to have in modeling bacterial communication.

I am going to bed, I wish you a happy time.

Jack

HYPOGENIC CAVES IN PROVENCE: BIGOT

2008-07-22T02:18:00.001-07:00

DID YOU SEE THE GOOGFLE ADSENSE ADS ON THE RIGHT?

1) BACTORGS HAVE TO LIVE SOMEWHERE
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In the last post, you learned about the hypogenic caves of Movile and Villa Luz which are home to enormous biofilms containing hundreds of species of exotic bacteria eating rocks and producing sulphuric acid. These caves contain also "out of this world" ecosystems feeding on these bacteria. With their spiders, worms, scorpions and many other, they form a nice set up for my bactorgs.

Now the next question is:
This post tells you all about the reasons underlying that choice.

2) PROVENCE, THE IDEAL LOCATION FOR "WE SHARE"
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My novel will describe events taking place in the part of Provence named "Alps of high Provence", near the towns of Apt and Forcalquier, a transition area between the provençal plain near Marseilles-Aix and the high Alps of the Mont Blanc.

I want to locate the novel there for personal reasons because this is my favorite area in the world, the one I know best, the one in which I have been caving for the last thirty years, the one in which people are so kind to me.

I want my reader to experience its lavender fields, its hills lined with mountain oaks, its quiet, three hundreds years old, small villages perched on top of the hills, its springs and fountains, its serene way of life, the warmth of the day and the coolness of the night when the crickets sing their song. Let's also not forget the cold "rosé" wine, the goat cheese and the olives...

2.1 A few photos of the Apt area

Just to introduce you to the area, you will find hereafter a few photos. To see more, do a Google image search on keywords like "Banon, Oppedette, Forcalquier, Montagne de Lure, Mont Ventoux, Dignes, Gap, Sisteron". Try a Google Earth 3D view. You'll be rewarded by peace, beauty and pleasure.

First a general map: on the map, the area we are discovering is centered in one square centimeter around the town of Apt.Let's see now a view of the nature there. For France, it is a quite unpopulated area but not a wild one,by far. It is a peaceful union of man and nature. You can see a lavender field on the left side, wheat fields, hills, oak forests where boars and deers are roaming. Human life is hard, simple and still far from the unbearable pressures of the consumption society (but perhaps, not for long anymore).

It is time to go underground. Let's do some caving. In this area, we know about two hundred caves, ten of them going to depths of about minus 600 to 700 meters. Local cavers discover new caves and kilometers of passages every year. These are predominantly vertical caves with series of huge pits (the longer one being more than 150 meters deep). Hereafter a photo I took of my son going down one of these pits. It was taken in the Aven ( cave in provençal) of Jean Bernard near Apt and Sault in the summer of 1995. It gives you a feel for what is caving there.

Now, what about "surface life"?

Here is an old village called Saignon, five milles from Apt (look at the map again). it was built in 1500 on top of a hill to protect its inhabitants from the religious wars of that time.

And a close view of the lavender field which you saw above in the general picture.

You can't feel them of course but when I see this picture, I experience the smell, the tiredness of the day spent in the caves, the excitement to get there, the hot sun, the sound of the crickets, the burning hope for a glass of white or rosé whine in the nearest village, I tell you... this is, life at its best!

Now, a medieval passage in a nearby town (Sisteron). By the way such a passage, between houses and covered by stones, is called an "Androne" in Provençal. Does it ring a bell (anything in common with my neuronal cultures)?
From the above pictures, you might get the feeling that life is tough and austere in these high lands,... far from it. Here are a few proofs: goat cheese (the locally famous Banon), wine (the world famous Luberon wines), fruits and little terraces where, in quiet evenings, you can just enjoy life at its best.

2.2 The Apt area, more than just a nice place

Its nice to locate my plot there but I told you before that I wanted my novel to be realistic, I want not only my science to be as exact as possible but also other aspects like geography, ecology, human life and economy. If I want the reader to discover and enjoy the true Provence, I cannot invent an artificial one well suited to my purposes. I have to make my plot to fit naturally in the real Provence.This is a tough order; it means that in an area of about one hundred square kilometers, I must have several very specific features:

° First, I need an area suitable for quite advanced caving.

From what I have told you, you already know that the Apt area fits the bill but let me give some more details.

Look at a map of Southern France. Near Avignon, between Forcalquier, the Montagne de Lure, the valley of the Jabron, the Ventoux mountain, and the towns of Sault and Apt lies an area called the "Pays de Giono" or in English, the "country of Giono" (Giono is one of the main French writers who placed almost all his novels in this area). It is a country of rude living , big skies and green hills. People are friendly but reserved and cautious. Their life has many joys but little comfort.

The city of Apt lies just at the border of the "Pays de Giono". The caving part of the "pays de Giono" has the geologic structure illustrated below. There is a limestone layer (see "massif calcaire karstifié" in the figure). It is 600 to 1000 meters deep. Through it, run many predominantly vertical caves (the black jagged lines). Under this limestone layer, there is a layer of molasse and marne in which water cannot penetrate.

The water from all the caves is thus collected naturally into a series of collector, underground rivers. You can see one of them in the figure. They flow at the boundary between the limestone and marne layers. Cavers have been able to penetrate many of these caves and they have reached a few collector rivers at depth from -600m to -700m. The names of the most impressive caves are the Caladaïre, Jean Nouveau, Autran, Le Souffleur d'Albion.

As you can see, on the right side of the figure, the layer of molasses forces the water to come up and in fact, all the rivers join in a single vertical resurgence which comes out at only one point, the world famous “Fontaine de Vaucluse”, made unforgettable by Petrarque's poems and one of the biggest perennial springs in the world. Many divers (human and robotic) have tried, (currently without success) to reach the bottom of the Fontaine hoping to visit the deepest horizontal parts.

In addition to these caves which have a normal speleogenesis from surface water, the area contains also several sulfur and geothermal springs and, probably, a few fossil hypogenic caves (in what is known as the gorges d’Oppedette (the Oppedette canyon) near the city of Apt and nearby in the cave of Daluy).

Note: a fossil hypogenic cave is a cave of hypogenic origin which, during its evolution has been traversed by an exogenic cave (carved by surface waters). After eons of isolation, the hypogenic cave has thus came in communication with the atmosphere. Oxygen has completely destroyed its hypogenic ecosystem but fossil remains of the wall carving by bacteria and sulphuric acid can still be seen. It is what we have in Provence.

Extrapolations for WE SHARE

Thus the Apt area has all I need to suppose that unknown to everybody, a truly hypogenic cave is developing somewhere in the limestone, at a depth of about -600 meters below the surface, traversed only by a small flow coming from the surface and another one coming from the volcanic depths. The small surface flow allowed some invertebrates and insects to crawl in the cave and a Movile-like ecology developed a million year ago. Its bacterial communities are at least a million year old. During that time, they evolved and became Bactorgs (see previous posts)

I will also suppose that contacts were established by the bactorgs with larger insects and mammals which swam or crawled through some side exits of the flow. Bactorgs will be able to influence the behavior of these larger animals and domesticate some of them. Finally, through the domestication of these insects and rodents, bactorgs will be able to control the release of viruses and well choosen bacteria for which their slaves act as reservoirs.

When the story begins, an earthquake has widened the cracks between the hypogenic cave and a normal cave. The Bactorg ecology is perturbed and the hypogenic ecosystem defends itself by launching bacterial and virus attacks on the outside world. Much of the events described in the beginning of the thriller are just due to this defense reaction. Of course humans will react and organize a caving expedition into the Bactorg domain.

° This, I need a caving area which can plausibly harbor an active hypogenic cave.

This is not a small point: after all, we know only about ten of them in the world. For weeks, I did not dare to check on that point but finally I did it. A Google search on "hypogenic caves and Provence" got me absolutely flabbergasted. Here they were...! Just where I needed them. Of course, they were not active or alive like Movile, I would have known about them. They were hidden, fossil caves; hypogenic bubbles in the karst opened to the surface many thousand years ago but still showing remains of their hypogenic stages. To read a paper in English about hypogenic caves in Provence, click here (paper by Audra, Bigot and Mocochain in "Speleogenesis and evolution of karst aquifers")

For the last twenty years, my absolutely favourite village in the world has been Oppedette. It has only fifty inhabitants and the nearest town, Apt, is half an hour away. For a densely populated country like France it is quite isolated. For twenty years, I have each year spent months in Oppedette, living, sharing and speaking with the village people. Three hundred meters from the village there is a nice gorge, not like the Verdon or the Grand Canyon of course but still..., very impressive and at a more human scale (200 meters deep, six kilometers long). I have spent hundredths of hours exploring it and abseiling down all its rocks and cliffs. Will I tell you one day about Max Fayet, a retired flutist and now the greatest expert on the Oppedette's gorges. At 80, Max is walking everyday more than seven miles in its nooks and crannies to rescue lost hikers?

Here is a view of the village (about thirty houses) at the entrance of the gorges. Sure, it is not the Verdon or the Grand Canyon, but try to go down and visit every part to find hidden caves and passages. It took me many months..

The village:

The gorge: it starts just thirty meters after the village and runs like that for five millesThere, smack in the middle of the gorges, it exists a natural excavation called the "Chaire à Prêcher"). Jean Yves Bigot, a local geologist, studied it closely and found many traces of hypogenesis. Right where I wanted them to be.

He published his findings on the web (click here to see a map of hydrothermal caves in France). I got in touch with him and he told me that sulfur springs were quite common in the area. He told me also that some geothermal springs were not far apart (in a village called Greoux)... The Area near Oppedette had thus everything I wanted. A few post before, I gave you the address of a site he has developed on hypogenic caves. Here is another one, be sure to look at it (Daluis, grotte du chat).

° One more thing and not a small one: For the novel, I need a large underground laboratory...

At some stage, my bactorgs (underground Movile-like bacterial biofilms) will have to meet andrones (real in vivo cultured neuronal networks) living in a high security laboratory. These two guys do thus live far apart. A plausible way for them to meet is in a large, underground laboratory, nearby thehypogenic cave, five hundred meters deep and where scientists are conducting almost secret experiments on andrones and on many other subjects (geomagnetism, zero magnetic field biology...).

You will not believe me but such a lab exists: five milles miles down the road from Oppedette. It is called the "Laboratoire souterrain à bas bruit", or in English, the "Low noise underground laboratory". Years ago, the French army had its main launching site for nuclear missiles right near Oppedette. They had something like thirty underground silos with a missile in each. All the silos were linked to an underground command post, at seven hundred meters below the surface of the hills, wiht kilometers of passages in which electric trains linked the many command and logistic rooms.

When the French dismantled their nuclear force, the underground headquarter was taken over by the CNRS (French center for Scientific research) and transformed into a large underground laboratory which provides one of the most noise free environment all over the earth (no vibrations, no sound, no electromagnetic perturbations). It is where my andrones will live and be infected by the bactorgs messengers living just outside in the caves.

Do a Google search on "LSBB "laboratoire souterrain à bas bruit - Rustrel"(click here to visit the site of the lab). Here are a couple of images from the site of the primary school at Rustrel who, astonishingly went in to visit... (see their site by clicking here)

First a photo of the entrance of the lab; from there a two miles long passage goes deep into the mountain. The deepest part is seven hundred meters below the top of the mountain. In the vicinity, there are no industries, no towns, no large roads, no electronic installations. Almost no noise of every kind. Hence the name.Now, a photo of the main gallery going down to the labs. You can see the small electric train transporting the researchers.

A third picture: down the gallery shown above, the train lead to several rooms isolated from the outside by an armored door, a concrete wall two meters thick and a wall of steel several centimeters thick. Remember, they were part of the command and control post for the nuclear force, built to stand a nuclear bomb. Now they are laboratories in which you are almost vibration, noise and radiation free and ... secret work can be done there. Here is where my andrones will live. Cross the wall of the lab and you have limestone cracks communicating directly with the caves of the area, the ones in which bactorgs live...Two more pictures from a not so distant past... the nuclear cold war. The missiles were placed underground also but near the surface and all around the control center within about a ten miles radius. Each missile was in a silo and the nuclear heads were regularly transported from silos to silos on specially built roads. Everybody could see them. Goats were just liking it.

First the top of a missile silo a bit scary isn' it. No problem, these silos have all been destroyed in 1999.

Then a picture showing a nuclear head lowered down in a silo where the missile is already awaiting for it. Can you believe that such photos can be found on the web?

And finally, the one I find really nightmarish, a nuclear head transported on an army truck going openly on a public road, between the lavender fields. You could see it and hear your heart missed a beat or two. This leads us far from goat cheese and Rosé wine.

° One more thing I need: a trigger event for a bactorg-driven epidemic.

First and foremost, I need an earthquake. Fine: Provence is one of the most seismic areas of France. They don't have big quakes but lot of small ones. That's OK for me. I prefer small ones. They go unnoticed by humans but may cause large changes in the underground. They will open new cracks and perturb the bactorgs without humans noticing it. A large quake would not fit my bill.

Here is the distribution of small seismic events in Provence (Richter scale below 4.5) over the last twenty years. The region we are interested in is below Sisteron (see the blue oval).

One consequence of the earthquake will be the opening of a crack between a normal cave and the hypogenic cave which, for a million year, has adjusted to a strong level of isolation. Oxygen will flood in. The atmosphere and equilibrium of the bactorgs will be changed.. They will feel attacked and thay will have to react.

Another consequence of the quake will be the availability of a new food source to the bactorgs. The earthquake will open another crack through which methane and CO2 will flow in enormous quantities. There will be an exponential growth of some parts of the bactorgs (methane and CO2 eaters). Again perturbation and reaction! Bactorgs will start a war upon the outside world to defend their peace and serenity. They will send many kinds of viruses and harmful bacteria, strange epidemics will develop. Who can blame them?

How can this enormous food income take place? A man made catastrophe obviously!

You will not believe me but it's all there. Sadly enough, Oppedette has all the potential I need for a first class drama. Look again at the pictures I showed you before: peace, serenity, calm and joy... Wrong, totally wrong: you already know that nuclear missiles were there... a recipe for catastrophe. Imagine an underground radioactive leak, thirty years ago, initiating a mutation wave in the bactorgs? Why not? Two such leaks occurred just last week in France (July 2008, Tricastin and Roman, not far from Provence).

More plausibly..., I have spoken with the people in the area and I asked them to show me where sulfurous springs existed. I put them on the map. They were delineating several paths. One of them led me to a village I loved, Saint Maime , where my mother in law lives and where I have spent my holidays for the last thirty years. What was this path pointing at. ... To a catastrophe waiting to happen. Here is a photo showing it.The main picture show an area not far from Oppedette, about ten miles down the road in the direction of Manosque. It is a nice valley in the Luberon and it shows very much the same scenery than those you saw before. But it is disrupted by large clearings. What are they? Not wheat or lavander fields but the outside signs of an important industrial underground activity.

This is a picture of the exploitation site of a company called GEOMETHANE. Twenty years ago, it was called GEOSEL. (SEL = SALT in French). They were injecting water in large, natural underground chambers filled wit salt. The water was dissolving the salt. Then the water was ejected under pressure and was transporting the salt outside. Obviously, after a while, the pockets of salt emptied. GEOSEL found a new use for the remaining large cavities: gas storage. Today, they store methane and they could store CO2 if needed. They just had to rename themselves from GEOSEL to GEOMETHANE.

Obviously it created a big stir in the nearby villages. Not everybody was happy to sit on millions of cubic meters of explosive methane transported from and to Marseilles by a pipe line. Obviously, there are strong security requirements but still, here is a catastrophe waiting to happen (what we, in Europe, call a SEVESO site, click here for informations about SEVESO sites).

Of course; For WE SHARE, I do not need an explosion destroying fifty square kilometers and seven villages. In my novel, I want to be much more subtle, at least in the initial phases of the catastrophe. I'll just imagine an earthquake opening a communication between these methane stores and the bactorgs cave near Rustrel along the line of sulfurous springs I have delineated. An enormous food intake for the bacteria, their explosive growth, their reactions...

The details of one of the storage pits are shown in the inset. In fact, they are much deeper than you might think and are located at depths from 90 to 1300 meters deep, just the right depths for my purposes. To give you the sheer size of the possible catastrophe, let me give you a few numbers taken from the GEOMETHANE site. Am I reading them correctly...300 M Ncubic meters. What the hell is this?
What can be the consequences of such an input of methane on the bactorgs... That's for you to ponder. Let me give you a nice little sentence from their official site...,

"These installations are located in sensitive areas of the "Parc Naturel Régional du Lubéron" and received special attention as regards environmental protection, in close co-operation with the Parc authorities and the local communities. " Nice to know

I might be wrong but to me, it is just a typical piece of marketing nonsense and human hubris. Look their site at GEOSTOCK GROUP.

So the area I love best in the world has all I need for my novel, the best and the worst!

° a geology suitable for hypogenic caves,
° an underground lab,
° earthquakes,
° industrial storage of bacterial food.

° And a final fact: I am not that original, in my plot, like in everyone these days, I need the military (however, I think I found a fresh angle on them). And I have to confess I like some of them, I myself spent five years working with the Belgian army where I had a lot of contact with the French Foreign Legion. I want a Legion battalion in the plot because they are partly belonging to the establishment (which I do not like very much) and partly independent of it (in many aspects of their professional life, they establish and follow their own rules).

In "WE SHARE", the legion will have a security department, in charge of supervising scientific battles against terrorism. They will then be charged by the authorities to conduct the struggle against the epidemics but will make many mistakes and learn from them. They will then cooperate with the civilian scientists who will explore the hypogenic cave.

Obviously, you already know what I am going to tell you. At about six miles from Oppedette, there is a big legion camp with an engineering battalion and a small NSA-like listening center. It is the 2nd Regiment Etranger du Génie (quartier Marechal Koenig). Its people are experts on mountain combat (and thus I may suppose that they are knowledgeable about caving). Close to the quartier Koenig, there is really a site brimming with antennas. They won't tell me what it is but I suppose it is their listening center. This is what I will suppose. I will have a bioterrorist study group residing in the Legion camp. They will be in charge of tackling the "WE SHAR outbreak. Here is the site of the Second Régiment Etranger de Génie

Hereafter, a photo of a legion platoon marching near the entrance of the Koenig camp in St Christol, right in the middle of the plateau d'Albion, eight miles from Oppedette. The security site brimming with antennas is about five hundred meters behind the camp. You can see two antennas on the right.

Bye Bye now, I am a bit tired.. This post is a bit on the longish side, it took me a whole day to write it but I just couldn't stop... There were so many things I wanted to tell you about this place.

By the way, I feel a bit guilty to bring catastrophes, even imaginary ones, to the Pays de Giono. I hope my novel will also convey its peacefulness and soft but wild beauty.

Jack

AN HYPOGENIC CAVE: MOVILE

2008-07-20T02:47:00.000-07:00

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DID YOU SEE THE GOOGLE ADSENSE ADS ON THE RIGHT?

1) MORE ON HYPOGENIC CAVES
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In the preceding post, I introduced you to hypogenic caves and we discussed Villa Luz, a cave with mixed hypogenic and surface features. Here we will look at a much more hypogenic cave which developed an ecosystem almost completely preserved from outside influence for about 500 millions years. The hypogenic cave I'll invent in "WE SHARE" will be a mix of Movile and Villa Luz but at a much deeper level (minus 600 meters) compatible with the geology of the area where I locate it and with my taste for vertical caving adventures..

2) MOVILE: AN ALMOST OXYGEN FREE ECOSYSTEM
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The Movile cave is situated in Romania near the Black Sea. Its formation and isolation from the external world were made possible by the local geologic features (I believe its limestone layer is somewhat embedded in a clay layer with a very peculiar phreatic level but I lack details on this).

Movile is an active hypogenic cave, carved by sulphuric acid like Villa Luz. However, opposed to Villa Luz, it has been almost totally isolated from the surface since at least half a million years. The processes of rock carving by bacteria and establishment of an isolated ecosystem are thus much purer than in Villa Luz where surface and hypogenic features interfere strongly.

Movile is host to an endemic invertebrate fauna which is probably quite unique (it should be carefully compared to the one in Villa Luz but I do not know of any such comparison). It has adapted, like Villa Luz but much more completely, to the lack of light and oxygen and feeds on the bacteria which themselves feed on minerals dissolved in the water.

The Movile ecosystem is thus autarcic, without any input of solar energy (compare withVilla Luz). The Movilians use only chemical autotrophy (synthesis of organic molecules from inert minerals).

Here you see a vertical section of the Movile cave (sorry, it is in French but easily understandable: grotte = cave, cloche = bell, lac= lake, niveau de la mer = sea level)

You see a vertical entrance pit made by the people who found the cave and closed by doors isolating the cave from the outside atmosphere. (Movile was initially found by a geologic survey team digging there just by chance). When going down that pit, you first enter an upper level of dry galleries. A second short pit opens on a second set of rooms, filled with water at sea level and forming a sequence of gas filled bells and ponds (see the levels of oxygen, methane, nitrogen and H2s indicated in the figure).

It is where we encounter the Movile life (see the interrupted line indicating the biofilm or bacterial veil floating on the water). At the bottom of this level (see on the left) , deep water is entering the cave through a vertical water filled pit where water rich in H2S is coming from deep down (as I understand, it is a sort of geothermal spring ?).

Look now at the bells. In their water, bacteria oxidize H2S brought in by the geothermal springs and which is thus abundant in both the water and the atmosphere of the bells. Bacteria use this energy to synthesize their organic molecules from the CO2 which is also present in the cave. This is described in the following figure (sorry but right now, it is still in French, question: where does the CO2 come from):These autotrophic (i.e. rock eating) bacteria serve as food source for other bacteria and fungi organized in filaments and floating in the water. They are heterotroph (they can only eat organic matter and thus they eat lower, autotroph, living beings, i.e. the bacteria). These filamentous bacteria form biofilms (filamentous, slimy veils floating on the surface of the little ponds) and serve as food for small herbivores.

On top of the bacterial veil, terrestrial herbivores (e.g. isopods, collemboles, pseudo-scorpions) live and graze They are themselves eaten by carnivorous species (e.g. spiders, centipedes…). Below the bacterial veil, worms, crustaceans and snails graze also on the bacterial veil and are preys for leeches and other animals. All these animals were trapped half a million years ago and have adapted to their conditions. They display regressive evolution which suppressed their eyes and color pigments. Moreover, they survive without oxygen. Hereafter you see a few of them

A Movile eyeless spider

A Movile eyeless scorpioThe Movile ecosystem contains 36 terrestrial insect species. Twenty six of them are totally new to science. The density of insects is unbelievable. For instance, more than 1500 collemboles were numbered per square meter of bacterial veil and numerous spiders were observed ( the spiders are known as "Alisco Cristiani"). They have lost their eyes in regressive evolution. This spider species gives us an important clue: his nearest relatives live in the Canary islands. This points toward a specific point: except for bacteria, the Movile fauna seems to originate at a time when Europe’s climate was tropical. These eons of isolation have caused a lot of regressive evolution.

I cannot resist, I have to give you another picture of the eyeless Movile spider, beautiful and frightening, crawling on a gypsum crystal near the bacterial veil:

The aquatic species of Movile are less "out of this worldish". They live in the first ten centimeters under the surface. At this small depth, there is still sufficient oxygen diffusing from the small oxygen content in the air bell. These species had thus to adapt less than the terrestrial ones who were choking in H2S and living in the dark. About 25% of them are new (compare with the terrestrial species where this ratio is about 75%). This suggest that in the past, it was more difficult to crawl in the cave through narrow crevasses than to swim in it through the sumps which, then, linked the cave and the nearby sea or lakes.

According to geologists, the underground network of the Movile bells was created five millions year ago when the black sea emptied itself into the Mediterranean sea. Water and gases from the magma would then have invaded the original cavities and started to carve it more and more. Even today, it exists in the area some sulphurous lakes and swamps with water much like the one of Movile (e.g. lake Kara Oban).

3) Extrapolation: the Bactorg cave
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Hereafter, a rough picture of the cave I envision for my bactorgs to live in. An hypogenic cave has been fed for millions of years by water from a deep water rise. It was almost isolated from the surface. At the surface level, another cave was carved by surface waters but was not connected to the hypogenic cave except fror a small unknown connecting flow at a depth of minus 600 meters. When the novel starts, the passage between the hypogenic and the surface cave has just been opened by a minor earthquake. This perturbates the ecosystem of the bactorgs in the hypogenic cave and triggers all the events described in the novel.

End of this post, time to sleep, Don't dream about eyeless spiders crawling in the dark.

AN HYPOGENIC CAVE: VILLA LUZ

2008-05-21T02:02:00.000-07:00

DID YOU SEE THE GOOGLE ADSENSE ADS ON THE RIGHT?

1) WHY DO WE DISCUSS HYPOGENIC CAVES

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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
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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

2008-05-14T08:36:00.000-07:00

°
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

2008-05-13T07:36:00.000-07:00

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

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

2008-05-13T07:01:00.001-07:00

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DID YOU SEE THE GOOGLE ADSENSE ADS ON THE RIGHT?

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

THINKING BACTERIA AND NEURONS: WEISS AND POTTER

2008-05-13T06:57:00.000-07:00

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DID YOU SEE THE GOOGLE ADSENSE ADS ON THE RIGHT?

1) WHY THIS BLOG?
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You are a scientist, an engineer, a student of science and engineering or finally a layman interested in these subjects. You do not dislike "Sci FI" but you are choosy about it..

I hope that this blog will interest you! I write it for you. What's my goal?

I see myself as a young guy (65). I am an avid vertical caver (spelunker ??) and a university professor and mainly researcher in biomedical engineering and mathematical modeling in biology. I work in France (Ecole Centrale, Lille), in London (City University, Kings College and University College) and in Switzerland (Federal Polytechnic School, Lausanne).

At the moment, I am embarking on the writing of a science-based thriller happening in Provence (France). The novel is entitled "WE SHR", a mispelling for "WE SHARE". I give you my title here for further reference but, to maintain the suspense, I won't explain it here .... In "WE SHARE", two of the "good guys" are what I call "Andrones" and "Bactorgs".

What are ANDRONES?

Andrones (from androids and neurones) are cultured networks of living real neurons. An androne is made of a few tens of thousands neurons and associated cells living in a set of dishes in a laboratory and fed by appropriate nutrients.

What are BACTORGS?

Bactorgs are bacterial multi-species colonies. Their name, inspired from Cyborgs, is a shortcut for " bacterial organisms". They are living in a deep cave, somewhere in Provence, in a oxygen-deprived, sulfur based atmosphere! They nevertheless have contacts with the outside world (guess how? I will not reveal it now).

Andrones and Bactorgs develop some form of rudimentary (or perhaps not so rudimentary) intelligence... They have elementary moods and emotions. They have a memory... and perhaps (I have not yet discovered it) some rough elementary consciousness and a culture. They certainly have multiple adventures. All this may seem a bit preposterous but, as I will explain at full length in this blog, every of these features will just be an extrapolation of some facts or hypotheses which have been published in respected scientific journals by well known scientists.

Of course in the novel, I have humans characters too. At the first level, they play the main roles and I try to make them very real people with problems, strengths, weaknesses, questions, interests, emotions and so on. However, if you look at a deeper level, they are a bit secondary... At this deeper level, what is truly essential is the presence and behaviors of Andrones and Bactorgs...

A bit far fetched, well, perhaps not so much... You'll see!

"WE SHARE", a thriller which will be deeply based on existing science!

The main characteristic of my novel is that it will be written for thriller-loving scientists and engineers. I intend to justify and explain all the events described in "WE SHARE" by presenting and explaining the relevant science in supplementary chapters or excerpts. Science itself will be seen as a rational and positive factor, not one to be presented lightly or feared like in the works of some other authors. Of course, the use of science by humans may be bad or some harmful consequences may develop but the pursuit of science will be a beacon in the night, perhaps the only one.

So, hypotheses will be pondered, mechanisms detailed, extrapolations justified etc. It will be a novel for scientists, engineers, students and interested laymen more than for a larger audience. I hope it will be extremely hard Sci Fi but Sci Fi nevertheless. Some points will just be extrapolations and dreams.

Obviously, I'm not omniscient, so, I need your help with the science... a lot of help and this blog is the place where I require it from you.

I'll present my understanding of (or lack of... ) all the scientific papers which I find so inspiring. They are many questions and bones of contention. There are many things I simply do not know or misunderstand. Read my posts and see if you are interested in sending me your comments. Let's start some discussions.

Apologies are due..., I am new to blogging and, there also, I still have many things to learn, mainly on how to design fancy posts. Moreover, English is not my native language... I'm only a plain French speaking guy but in a couple of years, I intend to publish the novel as a series on the web simultaneously in French and English.

Which scientific topics will we be discussing?
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On top of the adventures of human characters, we will be discussing subjects in biology and bioengineering related to bacteria, viruses and neurons. We will deal with mathematical modeling, complexity theory and computers. Here is a shortlist of some subjects we will be discussing:

cultured neural networks, competition and cooperation in bacteria, bacterial signaling, social life in bacteria, cave dwelling bacteria, intelligence in bacteria, bacteria as (very) early prototypes of neurons, mitochondria and endogenesis, stem cells and neurogenesis, interaction between brains and bacteria, chaos in biological simulations, dynamic mathematical models, metadynamical models, agent models, synchronization, self organized criticality, edge of chaos, ... and many other.

If you are familiar with some of these subjects, keep reading. You might be surprised of the relationships with all the other. You're intrigued but not familiar with these themes... well, keep reading too, you might become fascinated.

For the cognoscenti, here are a few names of people whose work will be discussed (not an exhaustive list indeed):

Steve Potter (GATECH, Neural cultures), Ron Weiss (Princeton, Synthetic biology), Eshel Ben Jacob (Tel Aviv, bacteria and neural networks separately), Saeed Tavazoie (Pavlovian bacteria), Henry Markram (Lausanne, brain modeling), Craig Venter (CVRI, bioengineering), Bonnie Bassler (Princeton, quorum sensing and bacterial signaling), Klaas Hellingwerf (Amsterdam, bacteria as rudimentary neurons...), Per Bak (self organized criticality), Alan Perelson (metadynamics), Edelman (consciousness), E. O. Wilson (collective brains), Stuart Kaufman (SFRI, order in chaos), James Lovelock (the father of GAIA), Annette Summers Engel, Louise Hose, Diana Northup, Penny Boston (cave geologist and biologists) and many other...

DOES IT WET YOUR APPETITE?

Some words of caution to end up this introduction:

In this blog and in my novel, science and engineering are good guys, not bad guys like in too many thrillers intended for the large public in the US. We will be 180° opposite to these kind of approaches. I will not build on people's irrational fears. Science will be seen positively and explained in detail. Most extrapolations will be plausible and justified. Some people will use science in bad ways but science itself will be a positive force.
My distant ideal would be to follow in Greg Bear's steps (Darwin's radio) whose science was reviewed in depth in a six pages article in "Nature" which recommended the work as a superb novel with outstanding science ideas... Not bad for a non scientific author!
The sociology and economy of science and ethical questions like animal experiments or patenting genes or organisms will be discussed occasionally but only in the framework of what scientists consider a normal ethical approach to science. This will not be a place for fighting against science but for discussing it in an open minded way.

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In the next few posts, I will introduce a few people and their works. Later, I'll discuss these works in detail. Right now, let us start with a first contact with a couple of works which set the ground for what Bactorgs and Andrones are all about.
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2) A FIRST STEP TOWARD BACTORGS: WEISS'S BACTERIAL PROGRAMMING
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Thus, as I have told you, "Bactorgs" are bacterial multi-cellular organisms (this is a verified fact of science: bacterial colonies behave as multicellular organisms) gone intelligent up to a point (this is an extrapolation, how intelligent...). So, a first thing I have to look at is what is known currently on intelligence in bacteria.. a tall order.

Let's take a first step: a lot of (perhaps all of... Turing's thesis) intelligence is computing, So, what about computing in bacteria?

What do some modern scientists do with cells? How can they modify them to give them computing abilities?

So, one of my my starting point will be "synthetic biology": a name coined by Tom Knight from MIT to denote the building by engineers of artificial cells from basic biological bricks. What can we do in synthetic biology? For instance can we convince bacteria to do some useful computations by inserting the appropriate genes in their genomes? Meet Ron Weiss...

It is seven in the morning. Ron, a professor in Princeton University, is busy programming real bacteria to do his own bidding. YES, you have well understood... programming bacteria in a Petri dish,... live ones, not computer models.

He is inserting genes which, when expressed, program the microbes to behave as he wants in response to stimuli from their surroundings. For instance, he can make them draw patterns in red and green in their Petri dishes or do boolean logic computations using as input variables the presence or absence of selected chemicals in the environment of the bacteria.

Using the bacteria to detect toxic products in the environment or to produce worthy chemicals at our command is just around the corner (i.e. in ten years). This is an example of a new field of study called "synthetic biology" defined by Tom Knight and, like the bacteria themselves, it is in full bloom at the moment. Both man-made and naturally occurring bacterial computing will be one of our main themes in this blog and in the novel.

If you already knew about this, you may not feel too excited but otherwise, frankly, aren't you flabbergasted?

Here are a few examples of patterns drawn by millions of bacteria in Ron's lab. The bright spots are disks emitting a substance to which the bacteria respond by flashing a light of a different color depending on the substance concentration. The concentration of the emitted substance decreases with the distance from the emitting disk and the color of the bacterial response depends on the local concentration. Hence the patterns...
(Image courtesy from Ron Weiss, Princeton University)

To know more about Ron Weiss's work, click here: "Ron Weiss's lab.

Weiss's work and WE SHARE: the lesson

As far as WE SHARE is concerned, the general lesson to be drawn from Ron's work is that a bacterial genome may be programmed to do logical computations. If Ron can do it (i.e. if synthetic biology can do it), evolution has probably done it too. This is the general hypothesis I presented before. Thus, naturally occuring bacterial colonies will compute logical functions useful to them.

NOTE: I think that Weiss and his colleagues have programmed an eukaryot cell to be a universal logic computer for all combinatorial (not sequential) Boolean functions of up to five variables. Transpose that in bacteria, extrapolate a little bit, add memory, go from combinatorial to sequential functions (add feedback) and here you are... the general finite automaton or even approximate Turing Machine I told you about...

3) A FIRST STEP TOWARD ANDRONES: POTTER'S CULTURED NETWORKS

As you now know, in" WE SHARE", I also have Andrones, i.e. cultured neural networks gone a long way on their road to intelligence. So, what do we know about cultured networks of real neurons. Meet Steve Potter.

In Atlanta, Steve, a professor at GA TECH, is hard at work teaching a few thousand neurons living in a Petri Dish to draw nice pictures. He calls them a cultured neuronal network.

To do that, he isolated them from a fish or rat brain. Then he gave them the proper conditions to live and re-connect between themselves on a nutrient medium in a Petri dish. The bottom of the Petri dish was a multi-electrode array and the neurons connected themselves to the electrodes. Then he wired the electrodes to a computer and from there to a robotic arm drawing a picture on a sheet of paper.

Potter ans his colleagues succeeded in establishing a two way communication between the computer and the cultured network. Using this, he can reward or punish histhe neurons networks by sending appropriate electrical pulses. Progressively, hecan make them draw something close to what he wants or finds aesthetically pleasing. The cultured network learns...

Consider the implications for art, philosophy, brains and humans. They call their project "MEART" (for MEA = multi-electrodes arrays) but I very much prefer their initial name for it. At that time, they were using neurons taken from fishes and growing on a silicon chip, hence the "Fish and Chips" project....

When I read about this, I could not believe my eyes: real living isolated neurons, connecting, learning (i.e. modifying their connection patterns) to do something we want... Consider the science application: better understanding of what it means to learn in terms of changes in the connection pattern of the network , the stimuli to which they respond by changing the pattern and the dynamics of these changes. A window on brain learning mechanisms!

Consider the practical applications... for instance, a cultured network learning how to control a drone (they are not far from it, perhaps ten years, they've a cultured network controlling simple manoeuvers of simulated plane in a flight simulation program)! I told you, mind blowing and so cute!

Look at a first picture of their work.

On the left side, a culture of real world neurons in a Petri dish... cutesy , don't you think?
On the right a close view of some of the neurons growing on the dish. Note that the bottom of the dish is the multi-electrodes array which can transmit and receive signals to and from the cultured neural network. (Image courtesy from S. Potter, GA Tech)

And a second image:

On the left, a view of the robotic arm during an art show in Moscow, the neural brain was in Atlanta and the signals were transmitted both ways between Moscow and Atlanta by Internet.

On the right, some drawings. You might not be impressed at first sight. This is not Cezanne or Van Gogh, just a few thousands neuronal cells drawing on their own. When you think about it, it's another ballgame... texture, forms, trackings, colours... This is a totally different world view. It is is of course just the starting point of their work but it, once and forever, changes what we means by the very basis of what we call "art". It moves the focus from semantics to "being a visual animal" and getting" brain internal rewards" from the perception of pure form and color shapes without any interpretation. Where exactly does the art sensation lies. In your wallets (art collectors)..., in your emotional and semantic cortex or primarily in your visual relays (geniculate corpus or the primary visual areas...)? This is one of the works which, in the last few years, made me feel pure joy (no kidding)! What do you feel and think? (Image courtesy from Steve Potter, GA Tech)

And a third picture, a pragmatic one: It is very nice to feel joy and aesthetic vibrations but will MEART sell...? Yes, they did it.

This is one of the four MEART paintings which was sold to the MEIAC (Spanish Museu Ibero Americano de Arte Comtemporanea) for their permanent collection.
(Image courtesy from S. Potter,
GA Tech)

If you are not impressed, what can you still hope from life? And that's just their beginning point.

Steve and his colleagues did a lot more: controlling robots, disentangling the pulse spikes their cultures use for learning, and last but not least, succeeding in making their little guys (cultured networks) survive and learn for up to two years. Such a long time... and a first step toward long life... (extrapolate).
To know more about Steve Potter's work and lab, click on the following link: "Steve Pott er's Neurolab".

Potter's work and WE SHARE: the lesson

Clearly, Potter's cultured networks are a good basis for Andrones. They demonstrate neuronal processing in a culture and some elementary form of learning. Add memory, diversification in subnetworks with different cells and processing capabilities (e.g. reticulate cells, cortical cells, sensory cells, motor cells and so on). Do not forget glial cells and perhaps stem cells. Stimulate them not only electrically but also chemically, learn more about reward-penalty mechanisms and you have a well behaved Androne.

4) Conclusion of this first post; Where do I stand now?

I see Weiss's and Potter's works as strong signs that, someday, Bactorgs will be discovered in the real world and Andrones made by us will exist. This is the basis on which I felt the irresistible impulse to write a novel about them. Of course, in this post, I have just scratched the surface of these concepts. In the following ones, I will go into more details on every point discussed above.

It's about time to end up this post. My cat Touti ( pronounce "Tootee", French short name for "Tout-en-poil", meaning "completely made of hairs") is complaining that it is time to go to bed. The next posts will be on a few more examples of works used as inspirations for my novel:

- Eshel Ben Jacob's work on intelligent and social bacteria (and also on neuron networks)

- The works of Klaas Hellingwerf and Bonnie Bassler on signaling and "thinking" in bacteria.

- Saeed Tavazoie's paper on associative learning in bacteria.

- Theodore Berger's work on neural prostheses.

In that introductory set of posts, some supplementary ones will be devoted to modeling biological sets of cells on the computer.

- I'll present some work by people from Simon Levin's circle and, very modestly, some of the works from my own very small circle.

Finally, I've told you that I am a caver and that my Bactorgs live in caves. I will thus present what is known about astonishing cave bacteria who thrives not on oxygen but on sulphur, CO2 and rock. These pre-oxygen but still living communities are found in a few caves (e.g.: Movile, Villa Luz, Frasassi and Lechuguilla).
They support whole, non oxygen-based ecologies with worms, spiders, insects... In these slimy caves, bacteria produce sulphuric acid (pH = 1) which dissolve the rock. The atmosphere is choked with deadly (for us) H2S. This is a totally weird environment. This is where my Bactorgs live and have lived for millions of year.

Extrapolation: envision a thinking bacterial community acting as a multicellular being which is renewing itself, avoiding degeneration and senescence (How?) and evolving during all that time. How can it avoid boredom, get constant impulses to renew itself? My answers: by developing ways to contact the outside world (see alter), by living on the edge of chaos and in a state of self organized criticality (see complex system theory and Per Bak's work with deep regrets for his untimely death) and perhaps by developing a Zen attitude to life.

I'll thus also present briefly what cave geologists and microbiologists like Diane Northup, Penny Boston, Louise Hose and other have done to study these caves, namely Movile Cave in Romania, Villa Luz and Lechuguilla in America and Mexico and Frasassi in Italia

A last post in this introductory series will be devoted to Craig Venter's claim of having built the first "Man made " bacteria. I have very mixed feelings about this work (not about its result but about its patenting, commercial and marketing aspects) but it should be acknowledged as a great work. If it is true (which I believe) it is a landmark.

A THOUGHT FOR THE NIGHT:

We live in exciting times (scientifically at least, perhaps not from a human point of view: economically driven society, ecological irresponsability, short view imposed by our political systems driven by economic interests) and we start growing old when our regrets dominate our hopes and projects. Do not let that happen to you.

Next time you sleep, have wonderful dreams. By the way, one of the modes of interactions of bactorgs with humans and andrones will be to influence their dreams , yes, andrones and bactorgs dream...

Jacques