Why not make a computer out of geobacter bacteria / silicon hybrid
era...@gmail.com
Enough of able to make artificial life which is what artificial
intelligence is ?
Why not train bacteria ?
**************************************
Desirability of combining biological computing with silicon computing
S. B. Khadkikar, Department of Atmospheric and Space Sciences,
University of Pune, Pune, INDIA.
Erach A. Irani, IKB Research Institute, 106 B. Desai Road, Mumbai 400
036. INDIA. [ erach27 [at] yahoo.com ]. For more information see
http://www.geocities.com/erach27
Abstract
We are introducing a method to develop and fabricate a biological
computer - silicon computer hybrid which can make decisions that no
computer can at present and crunch data at the speeds of silicon
computers. Fabricating the hybrid computer may require the skills of
several technologists devoting part-time efforts. For the minimum, a
biotechnologist is required who combines the skill of a microbiologist,
electronic engineer, computer programmers and computer scientists at a
minimum. In this speculative article, research is cited that shows how
living cells have been joined to silicon computers. Also cited, is
proof of "bacterial intelligence". We are speculating that
bacteria can be evolved using carbon nano-tubes that are
semi-conductors to form a bio-electronic brain that can solve all the
world's problems. A speculation as to the development of the
CONSCIOUS bio-electronic information processing bacterial unit (a
CBEIPBU, pronounced "see-beep-boo", like a silicon transistor in
electronic computers) using nano-tubes is also given. How to make a
CBEIPBU and how to identify a CBEIPBU in the bacteria is given.
The implication of electronic speeds for the CBEIPBU and the
bio-electronic brain is that what we learn as humans in 40 years, the
bio-electronic brain made out of CBEIPBUs will learn in seconds or
minutes.
The species of bacteria has been identified as the Geobacter bacteria
(www.geobacter.org) that connect directly to electrodes and exchange
electrons with an electrode. They join together and use nano-wires (or
pili) and make biofilms on the electrodes. Since these Geobacter
bacteria respond to electricity, they will directly train with patterns
such as left-drift, right-drift, simple delay and later on XOR on a
grid of electrodes. Use of these Geobacter bacteria makes the task of
demonstrating trainable intelligence in bacteria trivial.
A solution containing both Geobacter (to connect to electrodes by
exchanging electrons) and E.Coli (for its intelligence since it lives
in the human intestine and works with bacteriophages to exchange genes)
can demonstrate even more trainability and intelligence. Putting a 300
* 300 (or even 30 * 30) grid of electrodes in a solution and training
time-based left-drift, right-drift, associativity and XOR should
demonstrate bacterial programmability. Mutating these bacteria with
carbon nanotubes should demonstrate even faster electronic speeds as
the bacteria form transistors with the carbon nanotubes and mutate to
evolve how to use them.
We are aware of the work done in programming bacteria by transferring
genes [14] and integrating our method of harnessing the consciousness
of bacteria with this method should result in sensors for vision, etc.
Integrating synthetic biology with this method of harnessing and
evolving bacterial consciousness should also be useful.
1. Introduction
Silicon computer programs are very good at data-crunching to come up
with summaries of data. However, a human being is using the data. A
human being is an example of a biological computer which has the
"Observer" built into it. "Observer" is a notion from quantum
mechanics. A human being is capable of making DECISIONS from what the
computer reports. Computers are not capable of making DECISIONS.
Computers are made of transistors made of non-living silicon. We
introduce the notion of bacteria modified with nanotubes to work at
electronic speeds. Nanotubes are semi-conductors and the bacteria
should form CBEIPBUs or Conscious Bio-Electronic Information Processing
Bacterial Units that are conscious. Many CBEIPBUs should network
together to form a conscious computer.
Lots of strategies have been tried to make computers mimic biological
systems. However, we contend that all these attempts will fail.
Computers CANNOT MIMIC biological systems in their ability to make
decisions. Computers CANNOT IMITATE biological systems.
The ability to make decisions is required in "self-programming" of
computers, the ability to interview users and to write programs for a
digital computer. Computers have become very good at transforming
computer programs through compilation, however, to-date they are not
able to make ANY DECISION. Computers are also very good at
number-crunching and lightning fast data-processing, however since they
lack CONSCIOUSNESS, they cannot make ANY DECISION.
2. What is Consciousness and what is a Decision?
Consciousness is intimately connected with the ability to make
Decisions.
Consciousness requires an ability to somehow sense your Own Self in the
Universe around you to the extent that you can perceive it and make
transformations that allow your own Self to continue existence. We
hypothesize that this Consciousness is innate in all living things.
Bacteria are now hypothesized to contain Intelligence [2,3,4].
Bacteria work in bio-films and as bacterial consortiums to interact
socially to achieve tasks. It takes intelligence for an organism or
even perhaps a cell of a body to achieve its own tasks. A Decision is
the ability to make the organism direct itself towards a goal.
Computers lack consciousness and hence have no ability to recognize
their environment or to have a goal. They are only good at
data-processing.
3. Can Computers be joined towards biology?
25,000 rat neurons can fly an F22 simulator simulation through
difficult requirements[5]. These rat neurons learned to fly the F22
simulator in 15 minutes.
[http://dsc.discovery.com/news/briefs/20041018/brain.html] Dr Eschel
[4] argues successfully for bacterial intelligence BUT HE DOES NOT USE
TRAINING like we propose using electronics to HARNESS and PROGRAM
bacterial intelligence.
The authors have proposed how to make a collective identity of
bacteria to enable the bacteria do tasks [1]. There is also an
achievement of a researcher making a NATURAL urinary-bladder by growing
cells on a scaffolding which dissolved away [7,8]. So, perhaps, it is
not so difficult to make a brain out of neurons but which interfaces to
a computer although the brain is a complex organ. A slime mould has
been connected to a robot to make the robot move. [6].
Synthetic biology is not harnessing the natural intelligence and
consciousness of biology. Instead it is merely trying to design
"biological circuitry" to do human-defined tasks. One of the
authors, had studied for his PhD thesis proposal in 1988, a work by
Robert Blum, a discovery system, RX, which wished to use a computer
based discovery system that would self-operate in a loop to obtain new
facts. Such a system has yet to come in existence, because, we
speculate, that no digital computer has the ability to make decisions.
Biological systems have life, with life comes the ability to be
conscious, have a recognition of one's environment, and make
decisions.
4. What is the future of computing?
The future of computing is a biological living computer joined to a
silicon or non-living computer. The biological computer makes
decisions and the silicon computer crunches data rapidly. We speculate
that training biology to make decisions should be easy, that is what
Life is all about hopefully, advancing consciousness and thus being
able to recognize and manipulate more of the Universe.
For an article on consciousness, one can read
http://home.att.net/~ag2kh/consciob.htm
Consciousness is not easy to define, perhaps it can be defined as what
a human being or living being has and what a computer, although
imitating intelligence and far superior to most people in
chess-playing, does not have. A chess-playing computer is not aware it
is playing chess, a human being is very much aware that he/she is
playing chess.
By all these amazing feats of biology, one can indicate, that biology
is far more self-repairing than computers and the flexibility of
biology to make decisions when connected to a computers data-processing
capabilities, should hopefully yield computers capable of understanding
the human body.
5. FABRICATING A BIO-BRAIN (ONE HYPOTHETICAL WAY)
In the 1960's, there was a lot of work done on artificial
intelligence by psychologists specifying how the brain thinks.
Similarly, it is useful to speculate how a bio-brain can be built out
of bacteria incorporating nano-particles. Speculation at least
provides a platform for discussion that leads to better
experimentation. Making a human brain out of neurons is perhaps too
complicated, and one does not wish to duplicate the human brain, one
wants a biological component connected intimately to a computer system.
In order to fabricate a bio-brain, one grows a colony of bacteria on a
3-dimensional grid. The 3-dimensional grid has surfaces on which
bacteria can grow, 'food holes' from which food can be pumped using
MEMS (Micro electronic mechanical structures). Alternatively, we can
use a grid of fine plastic pipes with holes in them and use pumps to
pump the food. The food can be a mixture of proteins and carbohydrates
at different locations on the grid, or a mixture of proteins and
carbohydrates uniformly throughout the grid. An electric grid which
serves to provide electric current used for heating up points on the
grid, and/or lighting up diodes, and/or generating magnetic waves which
may influence the bacteria. We may use for example magnetosomes
bacteria or bacteria with carbon nano-tubes incorporated in them.
The first task is to build up an associativity between food and
electric impulses that generate heat, light, or magnetic waves. The
grid supplies food through micro-plastic pipes. The grid also
communicates information about where the food is supplied and in what
quantity through intensity of electric currents. This should lead to
an associativity between food and electric currents. If one
speculates, that biology tends to increase its intelligence in the
presence of the right intelligent environment, then one speculates that
the associativity will be formed.
If an associativity is formed, then one impresses different patterns on
the grid to increase learning. In "neural networks" [9] branch of
computer science/artificial intelligence a neural network capable of
associativity learned to simulate language making the same type of
mistakes that children do when learning speech and do computations.
Therefore, teaching associativity to a bacterial network is the
foundation of intelligence in bacteria.
6. HOW TO INITIATE A FEEDBACK BETWEEN THE BACTERIAL NETWORK BRAIN AND
THE COMPUTER SYSTEM
The input to the bacteria is the food pattern and the electric current
pattern. Since the bacteria have nanotubes, we can have sensors on the
3D grid which detect the movement of the bacteria. These sensors
detect the motion of the nanotubes and report back the movement of the
bacteria to the computer system. The computer system then responds by
giving food and electric flow to the bacteria. Only reward is used in
training, since punishment is automatic in nature as lack of food and
electric flow.
7. MAKING OF DIFFERENT SENSOR REGIONS IN THE BACTERIAL NETWORK BRAIN
The human brain has different regions. Assuming a associative
bacterial network brain is formed we concentrate the electric current
and food for different signals in different parts of the bacterial
network brain to concentrate the bacteria in different regions.
8. CONNECTIONS BETWEEN DIFFERENT REGIONS OF BACTERIA
Biological nerves are slow compared to electronic circuits. By using
the computer to conduct information between different bacterial
regions, we supply bacteria with a rapid path for exchange of
information.
9. COMPARISON BETWEEN NEURONS AND BACTERIAL COMPONENT
Neurons are slow compared to the bacteria which have semi-conducting
properties built into them from the very beginning. Further the
bacteria exchange information using electronic circuits. Thus they
should be much faster than any biological brain.
10. IS THERE ANY WAY BESIDES MAKING A BACTERIAL BRAIN TO CONNECT TO
COMPUTERS?
Advantages of designing a brain using bacteria and semi-conducting
nano-tubes from the ground up is that we are designing a very fast
conscious brain. Bacteria are among the smallest units of life with
extremely fast mutating characteristics and hence they are chosen.
Bacteria mutate at the rate of millions of generations a day under
adverse conditions. Genes of neurons can be placed in some bacteria so
that the bacteria may incorporate the genes.
Using neurons (human or animal) will not result in an extremely fast
circuit that can be integrated with a computer and yet be the size of a
football stadium if necessary. One needs a fast and large biological
brain to work with all the knowledge on the internet and which can
still suggest more experiments to deal with issues like decoding the
human body's disease patterns, perhaps even aging and death,
alternative energy, quantum physics, and perhaps even time travel. In
future, there may be limitations on the size of a brain built using
neurons, a bacterial brain with nano-particles, and electronic
computer-connected wires as nerves should have no size limitations.
Silicon has yet to make a single decision. As a computer programmer, I
point out the paradox that a computer can now play better chess than
most people, but it does not know that it is playing chess. Examples
of electronic computers that cannot make a decision and hence are not
trusted are the expert system MYCIN, the expert system INTERNIST, and
most famously even the search engine Google which is incapable of
differentiating what content should be shown to children and adults.
Google is also not capable of deciding why a search is being done when
a search is done nor can it do a search refined on all the information
it stores on a person using Gmail. Google is also not capable of
imparting knowledge or even formulating search criteria in a
question-answer fashion.
10. Is evolving bacteria with nanoparticles an original idea?
The seeds of this idea originated in a talk given at Pune University.
Further refinements were done and a US Patent was filed on the concept
as US Patent Application number 20060024810 with a filing date of July
27, 2004. Jocelyn Paine, the editor of Dr. Dobbs AI Newsletter
published the idea with some very good instances of biological
intelligence [9]. Some instances where biology has been connected to
electronics to harness biological intelligence have been noted.
11. Circulatory channels with liquid flow
There can be circulatory channels in the grid with liquid flow to
remove waste-products and perhaps even to carry nutritious liquids
throughout the grid. The food-holes can put the nutritious liquids
inside the circulatory channels.
12. Ethics of killing thinking bacteria and how to resolve them
If the bacteria in the grid are proven to have a collective identity
that can think, then one does not want to kill them to make way for a
new brain. One just grows the grid and let the newer thinking bacteria
co-operate with the older thinking bacteria. This should resolve the
ethics of killing thinking bacteria.
12. Implication of bio-electronic speeds for the bio-electronic brain,
or why design the bio-electronic neurons to be bio-electronic from the
ground up.
Rat neurons as used in [5] will only give us a brain as fast as a human
brain. We need electronic speeds to be incorporated into the living
cell from the ground up. Electronic speeds are needed so that the
bio-electronic brain can learn rapidly at electronic speeds. What we
learn in 40 years it should learn in minutes or even seconds. Only
then can the bio-electronic brain learn all the knowledge of the
internet and decode the human body's biology and suggest cures in the
next few years, instead of decades.
13. Fabrication of the bacterial bio-electronic information processing
unit, the equivalent of the silicon transistor.
It has been stated on the internet that carbon nano-tubes penetrate
bacteria and go straight to the nucleus, killing the bacteria. Now,
one speculates, why do the carbon nano-tubes go straight to the
nucleus? Is that a random occurrence or just a biological happening or
are bacteria consciously inviting the nano-tube into the nucleus so
that the bacterial nucleus can harness the information-processing
abilities that result from using nanotubes in their genetic
computational operations.
Now, the first task before the researcher is to fabricate the
bio-electronic information processing unit (CBEIPBU) inside a
bacteria's nucleus. The good thing is that the researcher is not
responsible for fabricating a CBEIPBU, but the bacteria will fabricate
the CBEIPBU out of millions of mutations once it is exposed to
nano-tubes of different sizes and characteristics. The speculation is
that the CBEIPBU will be formed because the bacteria that succeeds in
processing information electronically as well as chemically, has an
advantage over other bacteria and hence dominates. Once a usable
CBEIPBU is formed inside the bacteria, it will share the genes for the
CBEIPBU with its neighboring bacteria and the CBEIPBU will dominate and
we will be able to see all the bacteria with the carbon nanotubes used
inside the CBEIPBU. Of course, one may expect that a particular form
(single-walled SWT or multiple-walled) and size of carbon nanotube will
be used preferentially but even that is not necessary as biology is
flexible.
Even if a CBEIPBU is not formed out of carbon nanotubes, one has to
experiment with different "things" that evolve bacteria to
accelerate bacterial information processing using electronics, until a
CBEIPBU is formed in bacteria.
14. Training once the Conscious bio-electronic information processing
unit (CBEIPBU) is formed in bacteria.
Once the CBEIPBU is formed the bacteria should mutate or think very
rapidly in response to challenges it is faced with. It will not be
thinking at chemical speeds, it will be thinking at a speed between
chemical speeds and electronic speeds. Problems of associativity it
should solve rapidly.
15. Which bacteria species to use ?
This is best decided by a microbiologist. But a species of bacteria
"geobacter" forms biofilms and passes electrons via nano-wires
called pili and is used in fuel cells. Perhaps this species can be
used initially [11].
More information on the Geobacter bacteria can be found on
www.geobacter.org. [13]. The Geobacter bacteria connect directly to
electrodes and exchange electrons with an electrode. They join
together and use nano-wires (or pili) [12] and make biofilms on the
electrodes. Since these Geobacter bacteria respond to electricity,
they will directly train with patterns such as simple delay and later
on XOR on electrodes. This eliminates the previously mentioned
tedious procedures of training the bacteria using "food-holes" and
MEMS and pumps and mutation using carbon nano-tubes although this
background could be used in future.
16. Combination of bacterial species to use and simple experiments to
do.
A solution containing both Geobacter (to connect to electrodes by
exchanging electrons) and E.Coli (for its intelligence since it lives
in the human intestine and works with bacteriophages to exchange genes)
can demonstrate even more trainability and intelligence. Putting a 300
* 300 (or even 30 * 30 initially) grid of electrodes in a solution and
training left-drift, right-drift, time-based associativity and XOR
should demonstrate bacterial programmability. Mutating these bacteria
with carbon nanotubes that are semi-conductors should demonstrate even
faster electronic speeds once the carbon nanotubes make transistors
with bacterial outer-membrane proteins.
17. Tumbling behavior of bacteria towards food. Distributed
bio-intelligence versus Central Processing Unit of computers.
I believe the statement below of bacterial motion shows that bacteria
have a distributed form of intelligence. Is there any reason why
bacteria which have developed a 50 protein flagellum "motor" in
which all proteins have to be present for the flagellum "motor" to
work cannot be trained. Geobacter bacteria have protein insulated 5-10
nano meter wide "pili" or nano-wires that are 10 micrometers long
and conduct electricity across the length of the pili. Is it
reasonable that the geobacter bacteria will respond to electric
patterns since they exchange electrons with their environment.
Bacteria may not have a CPU or central processing unit as in computers
but even the human brain does distributed processing where memory and
thinking is integrated in the neurons.
Central brains are not required for activity in biology. Despite their
name, jellyfish are actually not fish! Jellyfish are made up of over
95% water, and they do not have brains, hearts, gills, bones, or blood.
(http://www.edhelper.com/AnimalReadingComprehension_42_1.html)
Bacteria move towards food, for eg. by "blundering" towards it. Only
they "happen' to make fewer blunders when they are moving towards it
than when away from it.....it's called 'tumbling" motility. bacteria
randomly tumble after swimming short distances and after the tumble
they move in a random direction and again tumble and so on.... but,
when moving towards food their freq. of tumbling decreases and hence
they "end up" moving "towards" it.
18. Potentially cheap method of making carbon nanotubes
A potentially cheap method of making carbon nanotubes is given in [10].
In this article, new method for making multiwalled carbon nanotubes by
heating grass in the presence of oxygen has been demonstrated. The
nanotubes were about 1 micron long and 30 to 50 nm in diameter.
19. Miniaturization of bacterial computing elements by the bacteria
themselves
If bacterial computing (or mutation computing) succeeds, then each
individual bacterium should develop several small computing elements
(like pili or even smaller). A bacterium is of the order of a
micrometer, the individual computing elements will be much smaller.
The pili in geobacter are only 3-5 nanometers in width and upto 10
micrometers in length. ( http://www.geobacter.org/research/nanowires).
There are more characteristics of pili of Geobacter such that the
proteins that coat it are non-conducting too (to make the pilin like a
wire to conduct electricity) (letter to Nature) [16].
20. Length of the genome code in bacteria and computing requirements
As biofilms, the bacteria can compute in networks. We are also trying
to make the bacteria evolve using carbon nanotubes as tools. So we
expect the length of their genome code to go up. The length of the
genome code should not be a problem for the computing requirements if
one considers that bacteria compute socially. The human genome code is
not the longest in the animal kingdom, yet the amount of information on
the internet is immense.
Also, the bacteria have evolved a 50 protein driven motor for their
flagellum. The motor is irreducible, it requires all 50 proteins to
function. If bacteria can do that, geobacter can certainly sense
left-flow, right-flow, and other patterns of current especially since
they can be rewarded chemically.
21. Why carbon nanotubes are specifically chosen as tools?
Carbon nanotubes are made of carbon which may integrate well with
proteins trying to bind around them. Carbon nanotubes have good
strength characteristics which gives the bacterium that adapts to it a
good claw to defend itself against bacteria with and attack other
bacteria for food. Carbon nanotubes enable the bacteria to digest
harder food and even perhaps cancerous cells (a possible cancer
treatment). SWT (single-walled tubes) have magnetic properties and
electrical semi-conducting properties which are good when forming
transistors.
22. What can the twin combination of carbon nanotubes and electronic
training result in?
Carbon nanotubes constitute wealth for the bacteria once the bacteria
adapt to them. This should induce loose collectives and induce
specialization in the bacteria and differentiation of function. The
bacteria may form balls where the outer bacteria adapt to defense
against carbon nanotubes and the inner bacteria nourish the outer
bacteria. The bacteria that can integrate electronic thinking by using
Carbon nanotubes as transistors think faster than the others and help
may mutate/evolve to do so under a electronic training pattern.
Initially, geobacter bacteria may switch around current and later on
learn to think electronically.
The twin impetus of electronic training and carbon nanotubes can cause
the genome length of the bacteria to go up.
23. CONCLUSION AND FUTURE OUTLOOK
The integration of microbiology with computer technology should result
in a hybrid computer which can take decisions rapidly and compute data
rapidly. This should enable all the information on the internet to be
integrated to suggest new experiments to solve humanity's
requirements. Training of this complex bio-silicon composite brain
will be the next step in creating a decision making and rapid computing
system. Training this bio-silicon brain should be feasible and simpler
than making a pure silicon brain neural network which cannot be made
functional because decision making is a consciousness based activity
and consciousness is a property of life.
Bibliography
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Collectives",
http://www.ainewsletter.com/newsletters/aix_0512.htm#erach
(www.google.com search for "AI Newsletter Erach Irani")
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(www.google.com search for "bacterial intelligence")
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http://en.wikipedia.org/wiki/Microbial_Intelligence
(www.google.com search for "bacterial intelligence")
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(www.google.com search for "bacterial intelligence Eschel")
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(www.google.com search for "25,000 rat neurons flying F22
simulator")
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Jha, science correspondent",
http://www.guardian.co.uk/science/story/0,,1709944,00.html
(www.google.com search on making a robot move using a slime cell)
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8. "First Bladders Grown in Lab Transplanted, Breakthrough Shows
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Nanotechnology 16 1192-1195 doi:10.1088/0957-4484/16/8/036
[Nanotechnology 16 1192] (6.13.05)
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BIOGRAPHY
Prof. S. B. Khadkikar, MSc, PhD is an internationally recognized
theoretical physicist and is a retired senior professor from Physics
Research Laboratory, Ahmedabad. He is cited in Marquis Who's Who
(science and engineering, world, Asia) in the years 1996-2006. He has
about 80 publications in renowned international journals, mainly in
nuclear physics.
Dr Erach A. Irani, B.Tech Computer Science (IIT Mumbai, India), M.Tech
Computer Science (University of Minnesota, Minneapolis, USA), PhD
Computer Science (University of Minnesota, Minneapolis) has worked all
his life in Computer Science and now theorizes with Prof S. B.
Khadkikar. He is a US Citizen. He has over 20 publications to his
credit while doing his studies at the University of Minnesota, mainly
in computer science and applications of Computer Science to medicine.
Jure
news:1150804306.4...@h76g2000cwa.googlegroups.com...
> Please see http://www.geocities.com/erach27 for details.
>
> Enough of able to make artificial life which is what artificial
> intelligence is ?
> Why not train bacteria ?
>
Yeah right, have you ever seen bacteria reading a book?
It only takes a few million years to get from simple form of life to
intelligent form of life :))))
People thing that ability to have sex and reproduce is necessary for
intelligent behavior.
Well, moving your ass up and down does not make you intelligent, it only
makes you happy :))))