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.
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.
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 Potter'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
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