Beyond Earth (ATWG) - Chapter 13 - Harnessing Bacterial Intelligence by Eshel Ben-Jacob

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Chapter 13

Harnessing Bacterial Intelligence: A Prerequisite for Human Habitation of Space

By Eshel Ben-Jacob

"Man, being the servant and interpreter of Nature, can do and understand so much and so much only as he has observed in fact or in thought of the course of nature. Beyond this he neither knows anything nor can do anything,"


Francis Bacon

Our Best Friends

Eons before we came into existence, bacteria inhabited the then hostile planet Earth. Being the first form of life here, they had to devise ways to counter the spontaneous course of increasing entropy and convert high-entropy, inorganic substances into low-entropy, organic molecules. Acting jointly, these tiny organisms also paved the way for other forms of life by changing its harsh conditions into the life-sustaining environment we know. With their impressive engineering skills, bacteria changed the atmosphere above us to be oxygen rich, and the water and soil to be loaded with nutrients, resulting in the Biosphere that supports all life on Earth (1-5).


Four billion years have passed, and the existence of higher organisms still depends on the unique bacterial know-how that converts between inanimate and living matter. With all our scientific knowledge and technological advances, the ways that bacteria act as Maxwell demons against the second law of thermodynamics is still a mystery. This makes bacteria our best friends on Earth, indispensable friends we simply cannot do without. If we seek a future for the human race in space, we must take bacteria along for the ride, as none other can prepare the setting for us. They will quickly learn how to thrive in any new environment, and make use of whatever it offers to synthesize life-sustaining organic molecules and to recycle waste products for further use.

Our Worst Enemies

But, as we know, the same best friends are also our worst enemies. In our rush to free the human race from deadly bacterial diseases, we created a major health problem worldwide: bacteria are becoming increasingly resistant to antibiotics. Unaware of bacteria's cooperative behavior and social intelligence, which allow them to learn from experience to solve new problems and then share their newly acquired skills, we recklessly used, and still use, antibiotics to fight them. As a result, we are now witnessing the resurgence of strains of disease-causing bacteria believed to have been vanquished long ago; only now they come armed with multiple drug resistance, and we can't invent new drugs fast enough.


And it gets worse when we venture beyond Earth. The very same conditions that suppress humans' immune systems and general well-being seem only to awaken bacteria to the challenge: they become smarter. Since bacteria are inevitable companions in human space exploration, as it is impossible to sterilize the crew and spacecraft, space programs dedicate much research effort to the effect of space flight on microorganisms and on host-microbe interactions. It turns out that exposure to microgravity and to a high level of radiation causes bacteria to undergo faster genetic alteration while adapting to new conditions. New pathogenic strains may develop that way, some of which could possibly be very different from any we have ever encountered on Earth, and for which we have no ready response. Bacteria can also cause much damage by ingesting electronic components and communication lines, blocking pipelines with stable biofilms, and producing toxins.


The New Strategy

If we want to survive the challenges that bacteria pose to our space voyages, we need to learn how to outsmart them, how to harness their adaptation capabilities to our benefit, and at the same time to tame those capabilities to reduce the health risk.

For this to happen, we must first understand that bacteria are not the simple, solitary creatures of limited capabilities they were long believed to be. These most fundamental of all organisms are smart, cooperative beasts that use advanced communication to lead complex social lives in colonies of enormous populations (4,6-17). They know how to glean information from the environment, talk with each other, distribute tasks, generate collective memory, and turn their colony into a massive "brain" that can process information, learn from past experience and might even create new genes to better cope with new challenges (18).

In this chapter, I will try to demonstrate how we can go about recruiting bacterial intelligence to our Space quest. I suggest sticking to a model that has already been proven to work once: let bacteria go there first to prepare the ground, and then go ourselves with them at our side. To prepare the pioneering troops, bacteria should go through a training program during which they will be exposed, here on Earth, to a variety of conditions they are likely to encounter in the new places we intend to inhabit. And if we gain understanding of how bacteria learn from experience to solve unfamiliar problems, we can even speed up the training process by boosting their intelligence in ways much like those we employ to improve our own intelligence.

Under harsh conditions, these versatile organisms work as a team and benefit from the power of cooperation. By acting jointly, they can live on any available source of energy and thermodynamic imbalances the environment offers, from deep inside the Earth's crust to nuclear reactors, and from freezing icebergs to sulfuric hot springs. Since we do not know to do the trick, we will need bacteria to operate as Maxwell demons at our service to sense the new conditions, perform their secret information processing to extract the biologically relevant information, and then to convert the local matter into breathable and edible substances for us.

The Engineering Skills Of Bacteria

The idea that bacteria act as unsophisticated, solitary creatures stems from years of laboratory experiments in which they are grown in Petri dishes in benign conditions. They can be tempted to reveal their tricks by, for example, growing them on nutrient-poor hard surfaces. The bacteria you see in fig. 1 coped with this situation by collectively producing a lubricating layer of fluid, which allowed them to swim on the hard surface. As they swim, the individual bacteria at the front push the layer forward so as to pave the way for the colony to expand. By carefully adjusting the lubricant viscosity, the bacteria stick together and keep the colony dense enough for protection (4,6,15-17).

Under conditions somewhat more favorable to motion, such as softer substrate, the bacteria engineer radically different classes of colony patterns. In this situation, the branches exhibit macroscopic chirality, always curling in the same direction (handedness). Accompanying the colonial structure is a designed genome change; the bacteria are now programmed to become much longer, which helps them to move in a coordinated motion within the branches (4,6,15-17).

To achieve even greater efficiency, bacteria invented the clever mechanism of chemotactic signaling, in which the individual bacteria send chemical messages to tell their peers in which directions to move. For example, when detecting a rich source of food they call their peers to join the meal by sending attractive chemotactic signals. On the other hand, bacteria that detect regions of low food or harmful chemical imbalances send out a repulsive chemical to signal the others to stay away (4,6,15-17).

Using these self-engineering strategies, the individual cells collectively manipulate the overall colony organization for the group benefit, as is reflected by the tantalizing colonial patterns shown in Fig.13.1. (Also see color section.)

Fig. 13.1: Cell Colony Organization

Patterns of Paenibacillus dendritiformis bacteria form when grown on nutrient-poor, hard substrate. Far from being shapes of mere aesthetic beauty, these colonial structures reflect the self-engineering skills of bacteria. The spreading patterns help the colony access more of the scarce food in the most efficient way under the given conditions. Ordinary branching pattern is shown on the left (a), and the chiral one (with broken left-right symmetry) is shown on the right (b). The top pictures show the colony patterns. Each colony is a few inches in size and has more bacteria than the number of people on Earth. The bottom pictures (c) and (d) show the individual bacteria (the small bars) at the branch tips with x500 magnification for (a) and (b) respectively.

Clearly, bacteria cannot contain in their genes the information for creating all the patterns they might need to survive in unexpected situations. Well, they don't need to; they only need to have coded genetic information to provide them with the strategic design principles and the tools for communication, for information processing, and for changing themselves accordingly. Using these tools, they can design new creative shapes (4,6,15-17).

Bacterial Communities

Bacterial engineering creativity is further manifested when forced to grow on very hard surfaces. The colony is now formed from new building blocks - the vortices shown in Fig. 13.2. It becomes much like multi-cellular organisms, with cell differentiation and distributed tasks.

Fig. 13.2: Bacterial Engineering Creativity

Patterns of the Paenibacillus vortex are formed during growth on very hard surface. In these colonies (a), foraging vortices of rotating bacteria shoot out to conquer the hard agar, lubricating the way for their followers. The dynamics is fascinating: a vortex (b) grows and moves, producing a trail of bacteria and being pushed forward by the very same bacteria left behind. At some point, the process stalls and this is the signal for the generation of a new vortex behind the original one; the latter leaves home (the trail) as a new entity toward the colonization of new territory.

In fact, bacteria can go a step higher and form a community (biofilm) of many cooperating colonies [8,9]. Each colony in the community acts as an organism that communicates with the other colonies for coordination and distribution of tasks, for the benefit of the community as a whole. To have an idea of the complexity involved, let us look at our oral cavity, which hosts a biofilm composed of hundreds colonies of different bacteria species, each consisting of tens of billions of bacteria.

Yet bacteria of all those colonies communicate for tropism in shared tasks, coordinated activities, and even exchange of relevant genetic bacterial information. For that to happen, cells should be able to talk and make sense of chemical messages they receive within a chattering of a huge crowd that is about thousand times larger than the number of people on Earth. In linguistic terms, the cells have multi-lingual skills, and each cell should be able to identify messages from its peers to the colony but at the same time also understand some of the messages from other colonies.

For that, bacteria have developed intricate chemical signaling mechanisms using a broad repertoire of biochemical messages - from simple molecules to "cassettes of genetic materials" (plasmids). More recently, it was realized that to conduct social life, bacteria use the chemical messages much like a language, including the semantic (the assignment of meaning or interpretation of messages) and pragmatic (conduction of a dialogue) levels of linguistics (15).

Learning From Bacterial Intelligent Mating

Bacterial communication methods have endured through evolution and are now crucial for the successful survivable of almost all organisms. For example, chemotactic signaling is the mechanism used for the wiring of our brain during its embryonic development. Sperm cells navigate towards the egg also using the methods of chemotactic signaling invented by bacteria. Even the pheromones used to attract partners and for mating have evolved from the pre-pheromones bacteria made for courtship before conjugation.

Some bacteria assume the role of Information Keepers for the well-being of the community. The stored information, say resistance to antibiotics, is given to other bacteria by mating (conjugation, which is direct injection of genetic material from the giving to the receiving cell). Prior to mating, the information-carrying cell sends courtship messages to make potential partners aware of the valuable load it carries (8). A bacterium in need of that information responds by sending pheromone-like peptides to declare its willingness to mate and what it can offer in return. Then, if the other cell accepts, it begins foreplay by emitting competence peptides to modify the membrane of the partner cell to form a pipe like segment. The latter is then used for direct injection of the genetic information. During this process, some valuable proteins and metabolic materials are given back in return for the information.

Bacterial Intelligence - A Metaphor Or Overlooked Reality

In fact, bacteria also invented the foundations of intelligence and sociality (5,15): to generate individual and group identity, to recognize the identity of other colonies, to make individual decisions, perform information processing, to conduct a dialogue for collective decision-making and to generate common memory to learn from past experience..48 The use of the term bacterial intelligence reflects the recognition that these features are the fundamental (primitive) elements of cognition that any living being must possess (15,19).

However, based on Gödel's theorem, it was suggested that for an organism to be intelligent the genome must function as a cybernetic system -perform information processing to solve problems and then change itself and even create new genes according to the outcome of the computation (18,19). Some special strains of ciliates provided direct proof that indeed the non-coding part of the genome (Junk DNA) can perform computer-like computations and also build new genes (20).

This daring idea about the cybernetic genome received strong support from the findings of the human genome project. I refer to the facts that our genome has only 30,000 genes while some bacteria strains have 8,000 genes, and that about 10% of our genes came almost unchanged from bacteria. These discoveries led the Celera team to exclaim in wonder: "Taken together, the new findings show the human genome to be far more than a mere sequence of biological code written on a twisted strand of DNA. It is a dynamic and vibrant ecosystem of its own, reminiscent of the thriving world of tiny Whos that Dr. Seuss' elephant, Horton, discovered on a speck of dust . . . One of the bigger surprises to come out of the new analysis, some of the "junk" DNA scattered throughout the genome that scientists had written off as genetic detritus apparently plays an important role after all."

Bacteria can perform the same "tricks," and more. A colony as a whole, by using its communication capabilities, the exchange of genetic messages and the internal information processing in each of its hundreds of billions of cells, acts as a massive brain (18). This colonial brain, with more-than-supercomputer capabilities, can generate new genes to allow the bacteria to cope with new environments.

Learning from Past Mistakes - Respect Your Enemy

Overlooking bacterial intelligence, we made a colossal mistake - the hasty use of antibiotics for people and especially in agriculture (16). Now we understand that by doing so we led to a surprising evolutionary phenomenon in the microbial world (18,21). New strains of more sophisticated bacteria are rapidly appearing. These new strains have multiple drug resistance and, moreover, can learn to develop resistance to new drugs at an alarming rate. In effect, what we did is to boost bacterial intelligence by forcing them to cooperate and challenging them with increasingly harder problems to solve (advanced drugs to cope with).

This cardinal mistake will inspire us to elevate bacterial cooperation and boost their intelligence when they are tricked into functioning for our benefit. At the same time, we can also learn from this mistake to tame bacteria and limit the risks posed by them during space exploration.

Taming the Bacteria

Studies show that bacteria fare well aboard spaceships. In microgravity, bacteria's growth rate increases and large, stable multi-colonial biofilms are formed. The combination of microgravity and strong radiation seems to elevate bacteria's intelligence and creativity.

Another expression of bacterial increased creativity is the heightened resistance to antibiotics (22,23). The nature of this mechanism of resistance is unknown to us, but we can deduce that it is specially designed to fit space flight conditions, as resistance is quickly lost upon return to Earth. Hence it is reasonable to expect that the acquired resistance is not just a result of a higher rate of random mutations, but rather the outcome of adaptive self-improvement processes.

Bacterial increased resistance, together with human immune suppression, is one of the more severe risks faced in space. Only by understanding the foundations of bacterial intelligence we will be able to outsmart them and protect our health. For example, we should not wait for resistant strains to appear following the use of antibiotics and then try to develop new antibiotic drugs to replace the old ones; it may be too late! Instead, we should use the old war strategy of cutting the enemy communication lines, or even confuse it by sending wrong messages. Doing so, we will render the bacteria more vulnerable to the antibiotic drugs, which will allow us to use lower doses. At the same time, in the absence of communication, the bacteria will not be able to process information for the redevelopment of new resistant strains.

A simple and direct way to interfere with communication could be by blocking the receivers (membrane receptors) they use for reading the incoming chemical messages. Or we can block the transmitters (membrane channels) used by the bacteria for broadcasting the chemical messages.

Once we learn to talk bacteria language (identify the different molecules that convey different messages), we can turn to more efficient and elegant tricks. For example, we could paralyze the bacteria by spreading the message "let's sporulate." Or we could drive them to engage in purposeless group sex rather than go about their routine tasks and protect their colony. This would be done by exposure to a "love potion" concocted from both "male pheromones" secreted by bacteria on the look for partners to transfer genetic information to and "female pheromones" broadcast by bacteria seeking conjugation with a bearer of needed information.

These are just two of the many creative ways we can scheme to use bacteria's intelligence against them. However, for this to happen we must first learn to decode the chemical messages that bacteria are using.

Keeping Our Immune System in Shape

While bacteria flourish in space, human physiology and general well-being decline. Human immune suppression in space was first observed in the 1960s and 70s during the Apollo missions. Notably, 15 of 29 Apollo astronauts reported a bacterial or viral infection during a mission, immediately after, or within 1 week of landing back on Earth. In 1991, experiments on STS-40, the first US space shuttle mission dedicated to medical research, identified T-cells as the particular components of immune function that were compromised (23,24). Most of us are aware of the important role of the immune system in protecting us against external invaders - microbes and viruses. Less appreciated is the immune system's role in maintaining the synchronization and harmony between our different cell types, each with its own self-identity and specific tasks. Coordination and enforcement of disciplined behavior

To perform these roles, the immune system developed advanced modes of communication between the immune cells and the other cells of our body. Much like in bacterial colonies but in a far more advanced manner, the communication is used to glean information about the state of the body and assaults by intruders, to perform distributed information processing, learn from past experience to solve newly encountered problems, and to generate an inner common self-identity of our body.

Studies on human physiology in space show that normal cells behave differently than they do on earth. This can cause the immune system to be confused about the identities of our own cells during voyages to space. The result can be devastating; it will trigger the autoimmune system to attack various internal organs, giving rise to avalanches of known and new autoimmune disorder. At the same time, weakening of the immune system can severely reduced its ability to identify abnormal cells. The outcome of this malfunctioning will be an alarming increased rate of emergence of malignant cells that will be misidentified and missed by the immune system, leading to bursts of multiple tumors.

To prevent these frightening prospects we must rely on the bacteria to help keep our immune system in shape. More specifically, they are needed to maintain its self-awareness, the abilities to tell self from non-self and its intelligence from decaying. The radical idea is to keep training the immune system by a designed continuous exposure of crew members to a wide variety of different bacteria, as opposed to the current attempts to keep the conditions as sterile as possible. This counter-intuitive idea stems from our cognitive perspective of the immune system and the lesson learned from bacteria: to boost a system's intelligence, it has to be challenged with problems to solve and learn from experience.

Tricking Bacteria to Work Harder

Having dealt with the destructive aspects of bacteria, we can now consider how to exploit their constructive capabilities. As an example, let us take Geobacter, microbes that like to dwell where there is plenty of iron and no oxygen. They also have the interesting ability to transfer electrons into metal, that is, to produce electricity while processing waste. These bacteria have even been shown to be able to generate electricity by decomposing body waste. Obviously, building bacterial power plants that can both convert wastes to usable materials and at the same time produce electric power is almost like a dream come true. However, letting the bacteria do the magic at a pace that suites their needs is far too slow for ours.

We cannot force the bacteria to work harder, but we can use their own intelligence in order to trick them into doing so. Suppose we'd like the bacteria to produce some particular enzymes at a higher rate (e.g. needed to decompose pop, process sugar into alcohol or any other need) or some human hormones (e.g. insulin) or any other useful material. We can prepare a plasmid (a cassette of genetic information that is used in genetic engineering) that includes both the genes for production of the material we'd like the bacteria to make for us, and genes for resistance to a specific antibiotic. Now, if we expose the bacteria to this antibiotic they will make many copies of the plasmid to protect themselves from the antibiotic and as a byproduct they will also make the substance we want. This illustrates how we can use bacterial skills to work for us once we understand the essence of bacterial intelligence.

Bacteria Training Program

As mentioned earlier, bacteria have a proven ability to make a hostile environment into a habitable one planet Earth. Sine the way they did it is still a mystery to us, let us send bacteria first to the new habitats to prepare the ground, and then afterwards go ourselves with them at our side.

To prepare the pioneering bacteria troops for the voyage, they should go through a training program during which they will be exposed, here on Earth, to a variety of conditions that they are likely to encounter in the new places we intend to inhabit. Armed with the new understanding how bacteria learn from experience to solve unfamiliar problems, we can plan an efficient training program much like the methods we would employ to improve our own problem solving skills - exposure of the bacteria to a sequence of varying conditions at increasing levels of difficulties. Moreover, we can apply what we learned from the mistake we made in the past that caused the rapid evolution of antibiotic resistant strains of bacteria to speed up the training program. For example, we can expose the bacteria to non-lethal levels of antibiotics during the training program to elevate the cooperation, "motivation," and "team spirit" of those pioneers.

Sending Bacteria to Pave The Way

The idea is to train and send three different families of new bacterial strains, or strains that will function as specialized of task forces to achieve three missions:

  • (1)Bacteria that will work with us inside the settlement bubble. These bacteria will be used for recycling, for the production of new materials from substances to be brought from the external environment, for supporting the life of other organisms, and to keep our immune system in shape and all other functions bacteria do to sustain life on Earth.
  • (2) Bacteria that will be spread outside the bubble as our pioneering troops to start changing the environment and to learn how to use the available substances and energy sources for life inside the bubble.
  • (3) Bacteria that will form a giant biofilm interfaced within the bubble wall. What I have in mind is a cyborg bubble built of several layers of materials and several different layers of bacteria. The bacteria will thus function as Maxwell demons, using their secret skills and knowledge for proper exchange of materials, energy, and bioinformation between the bubble and the environment.

The parts and tools for building the bubble will be sent alongside the bacteria. It will be built on site, and then the bacteria and the bubble itself will co-evolve to form a new gentler biosphere for us and other organisms to move into. I would like to conclude with another quote from Francis Bacon (could he have had Space travel in mind?) "It would be an unsound fancy and self-contradictory to expect that things which have never yet been done can be done except by means which never have yet been tried."

References

Additional relevant publications, pictures of bacterial colonies and video clips of bacterial movements can be found at my Home page http://star.tau.ac.il/~eshel/

  • (1) Lovelock, J. (1995) Gaia: A new look at Life on Earth Oxford University Press.
  • (2) Margulies, L. and Dolan, M.F. (2002) Early life: Evolution on the Precambrian Earth Jones and Bartlett
  • (3) Liebes, S., Sahtouris, E., Swimme, and Liebes, S. (1998) A Walk Through Time: From Stardust to Us Wiley
  • (4) Ben-Jacob, E. (2003) Bacterial self-organization: co-enhancement of complexification and adaptability in a dynamic environment. Phil. Trans. R. Soc. Lond. A361, 1283-1312,
  • (5) Ben Jacob, E., Shapira, Y. and Tauber, A.I. (2006) Seeking the foundations of cognition in bacteria: From Schrödinger's negative entropy to latent information Physica A vol. 359 ; 495-524
  • (6) Ben-Jacob, E. et al. (1994) Generic modeling of cooperative growth patterns in bacterial colonies. Nature 368, 46-49
  • (7) Shapiro, J.A. and Dworkin, M. (1997) Bacteria as Multicellular Organisms, Oxford University Press
  • (8) Wirth, R. et al.. (1996) The Role of Pheromones in Bacterial Interactions. Trends Microbiol. 4, 96-103
  • (9) Rosenberg, E. (Ed.) (1999) Microbial ecology and infectious disease, ASM Press Washington DC
  • (10) Velicer, G.J. et al (2000) Developmental cheating in the social bacterium Myxococcus xanthus. Nature 404, 598-601
  • (11) Crespi, B.J. (2001) The evolution of social behavior in microorganisms. TrendsEcol. Evol. 16, 178-183
  • (12) Bassler, B.L. (2002) Small talk: cell-to-cell communication in bacteria. Cell 109, 421-424
  • (13) Kolenbrander, P.E. et al (2002) Communication among oral bacteria. Microbiol. Mol. Biol. Rev. 66, 486-505
  • (14) Velicer, G.J. (2003) Social strife in the microbial world. Trends Microbiol. 7, 330-337
  • (15) Ben Jacob, E. et al (2004) Bacterial Linguistic Communication and Social Intelligence Trends in Microbiology 12 (8) 366-372
  • (16) Ben Jacob, E., Aharonov, Y. and Shapira, Y. (2005) Bacteria harnessing complexity Biofilms
  • (17) Ben Jacob, E. and Levine, H. (2006) Self engineering capabilities of bacteria Interface.Published online. Rsif
  • (18) Ben-Jacob, E. (1998) Bacterial wisdom, Godel's theorem and creative genomic webs. Physica A 248, 57-76
  • (19) Ben Jacob, E. and Shapira, Y. (2004) Meaning-Based Natural Intelligence vs. Information-Based Artificial Intelligence. The Cradle of Creativity Edited by H. Nen Nun, Saarei Tzedk Jerusalem
  • (20) Landweber, L.F. and Kari, L. (1999) The evolution of cellular computing: nature's solution to a computational problem, Biosystems 52, 3-13
  • (21) Shapiro, J.A. (1992) Natural genetic engineering in evolution. Genetica 86, 99-111
  • (22) Todd, P.(1989) Gravity-Dependent Phenomena at the Scale of a Single Cell. American Society for Gravitational and Space Biology. 2:95-113,
  • (23) Cioletti, L.A.; Pierson, D.L.; Mishra, S.K. (1991) Microbial Growth and Physiology in Space: A Review. SAE Technical Paper Series No. 911512.
  • (23) Nicogossian, A.E.; Huntoon, C.L.; Pool, S.L., eds. (1994) Space Physiology and Medicine, 3rd Edition. Philadelphia, PA: Lea & Ferbiger,
  • (24) Konstantinova, I.V.; Rykova, M.P.; Lesnyak, A.T.; Antropova, E.A.(1993) Immune Changes During Long- Duration Missions. J Leukocyte Biol 54: 189-201,
  • (25) Tauber,A. I. (1994) The immune Self: Theory or Metaphor? Cambridge University Press

About the Author

Extracted from the book Beyond Earth - The Future of Humans in Space edited by Bob Krone ©2006 Apogee Books ISBN 978-1-894959-41-4

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