Biocomputers:
Learning From The Human Brain
Abstract
Molecular
computing (especially DNA computing) means, using bio-molecules as a support for
computations and devising computers. This
is in constrast to the current opposite directions of research, the classic one,
where computers are used in studying molecules (especially DNA), a field now
commonly termed the science of bioinformatics.
Using
DNA as a "'chip" or
support for computation is not a new idea, and has been speculated upon since
the 1950's.
DNA
computing is a domain of clear interdisciplinary work, and is definitely a field
in rising expansion. Biocomputing can be understood as the construction and use
of computers, which function like living organisms or contain biological
components, so called biocomputers.
Biocomputing
could, however, also be misunderstood as the use of computers in biological
research.
Introduction
Alternative
futurestic computing disciplines have been proposed, such as Optical,
and Quantum computing which are quite different models.
Biocomputers are different, for it use a massive parallel features given by the
DNA molecular reactions. Therefore, biocomputers have completely different
architecture from silicon computers, which we know and use.
The dream of computer scientists is to construct a computer that
resembles human beings. Accordingly, biocomputing could be understood as a new
technological continent that needs to be explored and thoroughly researched by
computer and biology scientists jointly.
What
is DNA?
DNA (Deoxyyribo Nucleic Acid) is the genetic material that stores information regarding its own replication and the order in which amino acids are to be joined to make protein.
RNA (Ribo Nucleic Acid) is another type of nucleic acid. An RNA molecule called massenger RNA (mRNA) is an intermediary in the process of protein synthesis, converting information from DNA regarding the amino acid sequence in aprotein.
Figure
(1)
The DNA structure shows how it stores information, as is required of the genetic material. DNA contains four types of nucleotides:
Two
with purine bases, Adenine (A)
and Guanine (G), which have adouble ring, and two with pyrimindine
bases, Thymine (T) and Cytosine (C), which
have a single ring.
Figure (2)
Figure (3)
Figure
(4)
The
DNA is a double helix with sugar- phosphate backbones on the outside, and paired
bases on the inside. A is Hydrogen-bonded to T and G is
hydrogen-bonded to C. The DNA double helix molecule resembles a twisted
ladder. The complementary base pairing dictates that the two strands of the
molecule are antiparallel.
Following
replication, there is usually an exact copy of the DNA double helix.
During
DNA replication each old DNA stand of the stand of the parent molecule serves as
tamplate for a new trand in daughter molecule.
The replication requires the following steps:
1- Unwinding: A special enzyme called helice unwinds the molecule by breaking the weak hydrogen bonds between
the paired bases.
2-
Complementary
base pairing: the process of complementary base pairing positions
new* complementary nucleotide.
3-
Joining:
the complementary nucleotides join to form new strands.
An enzyme complex called DNA polymerase with specific
function carries out the last tow steps.
Why
DNA Computers?
For the same reasons that DNA was selected for living organisms as a genetic material, its stability and predictability in reactions, the DNA molecule can also be used to encode and store databases.
The exploitation of DNA computation power to solve problems, has an very
imp0rtant motivation:
"Working with DNA molecules offers the chance to perform billions of operations simultaneously, compared with only few thoussands (or millions) of operations by the most advanced silicon computers".
A small flask can hold up to (210) strands of DNA, each
encoding a string of data in its sequence of nucleotides. The data can be
manipulated in variou ways by the molecular biology techniques:
Combining,
strands, splitting at well-defined points, copying them, extracting strands with
a given nucleotide equence...etc.
Although a single operation is still slow compared to silicon computers,
the operation however, is done on the entire DNA in the flsak at once.
Basic
Concepts of Biocomputing:
"A reflective and engineering paradigm concerned with the adaptive information processing system that develops their own algorithms in reponse to their environment ".
Regardless, it is wise to start with two basic principles:
"Information "and "control ", to construct a conceptual definiton based on them, through the interaction with other related basic science disciplines as illustrated. Figure (5)
Figure
(5)
The
relationships between these disciplines and the two basic principles could be
considered as bases of biocomputing, to provide nine entities as a result of the
synthesis of the six science disciplines, and the basic elements of biocomputing.
The nine synthesized entities that can cosntitute biocomputing are:
1-Biophilosophy
2-Information
principles
3-Bioinformation
4-Molecular
computing
5-Neurocomputing
6-Advanced
biotechnology
7-Information
biotechnology
8-Biocomputing
devices
9-Biocomputing
philosophies
Figure
(6) illustrates the metabolic activity of the "living computer" called
the human cerebrum.
Photo Gallery |
Cerebral cortical activity and increases in blood of the left hemisphere. The shaded areas indicate blood flow increases of 20% or more: (a) during speech; (b) during silent reading; (c) during silent counting; (d) during visual tracking of a moving object. The brain areas indicated with numbers are as follows: 1 prefrontal area; 2 motor association area; 3 motor area (mouth and tongue); 4 primary somatosensory area; 5 Broca�s area ( motor area involved in speech); 6 primary auditory area of the temporal lobe; 7 primary and secondary visual areas; 8 motor cortex; 9 motor cortex of frontal lobe near the region controlling eye movements |
Figure
(6)
The
collabration of various areas of the brain, as indicated by their simultaneous
increases in blood flow, is shown during many cognitive functions such as:
hearing, seeing and speaking. Although the neurons of the brain
can be viewed as individual devices, each neuron can be viewed as containing
many biodevices.[Ingvar etal,
1977]
Devices
and Circuits of Bioenergetics:
Living organism is like an energy and information processing
apparatus with the ability to self
replicate.
Silicon computer can process energy
and information because the devices and circuits, which supply energy, come from
external sources. In the living cell, various forms of energy are converted
within the cell itself and utilized for various purposes.
A "flow diagram" of information and energy can be drawn in the
thermodynamics of circuit networks, which views the energy and information of
living organims as a unified flow diagram from the perspective of irreversibble
thermodynamics (oster etal, 1980), both the devices and the flow of information
are treated as analogous to electrical circuits.
However, living organisms consist of biodevices, which are completely
different from those of resistors and copper wires. Therefore, it is very
interesting to invistigate the special features, of living organisms from the
perespective of the "H/W" of the individual devices.
All
of the devices needed to sustain life are found in miniscule bacteria measuring
less than 1Nm across (10-6).
Even the relatively large (macromolecule) like the protiens and nucleic acids, which are the main biodevices, which have diameters of the order of 10 -8 meter (figure 7)
Figure
(7)
The
density of integration in living 3-D biodedevices is some (10-6 --10-12)
times greater than that possible in current silicon based computer technology.
In
biodevices, the central memory "device" is the
DNA molecule.
Analoge-Digital
Converter Using Biodevice:
The energy and information that enter the cell (concentrations of substances, memberane potentials, light, and so on) are largely Analog data. But the high-level information processing by living organisms is more accurately and more conveniently carried out if the data are converted into digital form, (either as the base pairs of DNA or neuronal impulses). Therefore, among the various information processing devices in living cells, there exist Analog-Digital convertors of minute dimensions, [Yasou Kagawa 1991]. Figure (8) and Figure (9) show a channel, which opens depending upon voltage changes, and a channel, which opens depending upon the presence of a specific substance.
Figure (8)
Figure
(9)
If the membrane potential or the concentration of transmitter substance
(both of which are analog values) reaches a certain value, the structure of the
membrane channel changes and ions can flow into the cell according to the
electrochemical potential difference on the two sides of the membrane.
The electrostatic potential or concentration, which is the trigger for
opening and closing the channel, is called the "trigger�
and the mechanism by which an analog value is converted into a digital value.
It is worth noting that the fine structure of these channels is already
known in details at the molecular level. For any sensory organ, stimuli bring
about physico-chemical changes in the cell membrane at the sensory receptor
membrane.
In most cases, those changes are analogical and in direct proportion to
the strength of the stimulus (i.e, corresponding to the total of applied physico-chemical
energy). However, in the CNS analog sensory nerves, the information is converted
to a pulse -digitized to a "0"or "1". This is known as "coding".
The information concerning the senory stimulus, (regardless whether it
was originally light, sound, chemical potential or mechanical changes), is
represented as a frequency of mechanical impulses.
The
Future of Biodevices:
The activity of living organims consists of the conversion of energy and
the transmission and processing of information. As is also apparent from the
direct relashionship with thermodynamics "entropy", the
amount of information is inseparable from the value of energy metabolism.
Indeed,
great advances have already been made in the theoretical understanding of
information processing systems and energy conversion systems in terms of network
thermodynamics.
In
the pursuit of the analogy between the computer and living information
processing systems, it is essential to give due convension systems, which
mobilize informations. However, in the light of the fact that most biological
"devices" are principally "Protiens
" and have ATP (Adenoione TriPhosphate) as
their source of energy, they are fundamentally different from LSI chips, which
demand external energy source to drive their electrical circuitry. This is a
significant advantage for organic information systems to have over inorganic
systems. In contrast, the greatest defect of biochemical devices is their
instability, but even this problem has been resolved by using heat-resistant
bacteria. Already, the gene responsible has been isolated and
analyzed [kagawa teal. 1984], and the protein engineering technique
required for producing protein for desired effects are already well known [ulmer,
1983].
Finally,
the slowness of information transfer in living organisms, have been resolved by
a combination of transistors and Biodevices. Already many successes in
exploiting the specifity of Biodevices, and successes in converting them into
electrical signal have been reported since 1983 [karube etal, 1987,Tahata,
1983]. Since the mid 90's until now, great developments have been achieved in
extremely sensitive biosensors to complex biodevices capable of carrying out
process, which are only achieved in the biological world.
Information
Processing in Biological Organisms:
It is very important to consider the significance of "developmental
biology" from the perspective of biocomputing.
Both livng organims and computers are information machines, which operate
on the basis of internally stored programs, but the differences between these
systems are also quite large:
-In the cae of living organisms, self-asembly following an internal program occurs and the nervous system and brain formed in
this way
function as an "autonomous information machine�.
-Tradittional
computers must be "driven" from the outside.
-The
nervous system of living organisms has somehow incorporated within it, rules on
how to function.
-It
was this aspect of living system, which has drawn the attention, and curiosity
of computer scientists for obvious reaons.
In
biological entities for which there is no external blueprint, the deign plan is
entirely internal and is thought to undergo changes both in the evolution of
species and in the development of individuals.
For
example:
It
is also thought that non-genetic factors play an extremely
large role in the working of the mind and the development of intelligence in
man. It will remain difficult to obtain a true understanding of human
intelligence until we know how much by the physico-chemical environment, and how
much by cultural and pychological factors.
Life
Seen As Computer:
Certainly, there are similarities between computers and living organisms,
but the outstanding question for biologists is:
How does the genetic information, which is the program contained within
living organims, actually control behavior?
It
is very difficult to draw a straight line from genes to behaviour, and it is
know that amere micron (10-6 meter) of genetic information in
"e.coli" contains code for chemical reaction which have more than
4000 individual steps. Moreoverm, owing to feedback mechanisms,
Still
more complex relations are implied. In computer language it is as if the living
cell were not supply machine, but worked in respone to demand.
For
Example:
In general, when trying to clarify the ways in which living organism
computer, we encounter tow major problems:
1-How
genes constrruct living organisms.
2-How
dose behaviour emerges from the neuron network, which has been constructed by
the gene.
There
are two noteworthy methods to deal with thee biological design problem:
1-Phyically detroy one of the component parts.
(For example, a portion of the neuronal wiring or cells of a part of the growing
embryo can be selectively destroyed by laser).
2-Inducing mutations, to alter the original genetic plan. Both methods have their advantages and disadvantages. Living
organisms, even if they canbe validered as "biocomputers", are opportunistic in nature and have bottom-up, not top-down, control
structures. Indeed, this is the fundamental perspective hared by mot molecular biologist_(a faith that elucidation of
molecular details will lead to fundanental insights into the control of the living systems) and ultimately insights into how to
construct a biocomputer.
Memory
and Consciousness:
The
limit on the input of sensory information to human beings is approximately 107
bits\sec. The number of meaningful duta which can be brought to consciousness,
stored in the memory and later influence behaviour is only 10-50 bits\sec.
40 bits\sec of information can be input during reading, and 20-bits\sec
outputs during a piano recital.
One of the major motives for
biocomputing today is the following question:
1-What
is a man and how he thinks and uses hi biological senses?
2-I
it posible to simulate his brain and nervous system as a biocomputer?
These and more philosophical questions
still undergoing internsive interdisciplinary research works [].
3-Biocomputing
Vs silicon computer:
DNA computing has advantages compared with most
advanced silicon-
based supercomputer.
Silicon-based Super-Computers |
DNA-based Computers |
Every bit needs (1012) nanometer2 of storage on tape. |
Stores information with density of (1)bit / (nanometer)3. |
1012 operations / second. |
1020 operations / second. |
Needs 1 jule of energy to perform 109 operations. |
Only 1 joule is required to perform (2*1019) ligation (*) operation. |
* Ligation: Binding molecules together to repair breaks. |
Coding
& Decoding System Using Triplet Bases:
- The base domain of DNA strands
may have one of foure possible bases (A, T, G or C).
- One silicon-based computer, if
symbols are represented by (8) bits we get (256) symbols.
- One DNA based computer, if
symbols are represented by (8) bits basis we get (65538) different symbols.
- Using 3 base-DNA-symbols, the English alphabets can be represented as in the following tabel. Each character has a unique
triplet base.
# |
Char
|
TRIPLT
|
COMPLEMENT
|
1 |
A |
TTT |
AAA |
2 |
B |
TTC |
AAG |
3 |
C |
TTA |
AAT |
4 |
D |
TTG |
AAC |
5 |
E |
CTT |
GAA |
6 |
F |
CTC |
GAG |
7 |
G |
CTA |
GAT |
8 |
H |
CTG |
GAC |
9 |
I |
ATT |
TAA |
10 |
J |
ACA |
TGT |
11 |
K |
ATA |
TAT |
12 |
L |
ACG |
TGC |
13 |
M |
GTT |
CAA |
14 |
N |
GTC |
CAG |
15 |
O |
GTA |
CAT |
16 |
P |
GTG |
CAC |
17 |
Q |
TCT |
AGA |
18 |
R |
TCC |
AGG |
19 |
S |
TCA |
AGT |
20 |
T |
TCG |
AGC |
21 |
U |
CCT |
GGA |
22 |
V |
CCC |
GGG |
23 |
W |
CCA |
GGT |
24 |
X |
CCG |
GGC |
25 |
Y |
GCT |
CGA |
26 |
Z |
ACC |
TGG |
What
Should be Done:
1- This new paradigm must be constructed on top of current science and
technology .No one can starts from scratch.
2- As long as it takes to reach the ultimate goal, there are always results that could be reached before reaching the final
conquest .It is an open-ended research venture.
3- Both cientists and engineers must be basically and equally concarned with
research concepts.
4- Research concepts must be strongly related with the presective future goals and with difficulties caused by current
tecnological drawbacks.
5- Most importantly, teams of qualified graduates must be prepared through oriented academic schemes to achieve new
revolutionary educational society amalgamated by futuristic information technology to free the crippled minds and sytem
from its "manic
depressive syndrome" State.
Evaluating Biocomputing
Sound and consistent futuristic oriented science policy is desperately needed to plan and supervise efforts to secure aplace in
the race to research and develop, within suitable environments for biocomputing applications, and to measure its advancement
paces and its influence on other science and technology running simultaneously:
1- Get a clear idea about the joint international efforts in science and
echnology.
2-A through study of concepts of human genome and its importance.
3-A
dvanttages and disadvantages of big science projects .
4- the influence of research and developments upon the cientific advancement and
human ethical performance.
5- the fading gap between computers and living organisms- namely the human brane.
6- observing the effects of biocomputing on the world in general.
Last
Words:
Is
it posible to construct a biocomputer capable to function as the human brane
does? When? How?
As
for how.... ... ... How about the
inspection of how the brain really works!!
Biostorage device is good step to start with.
Human
beings do forget, but biostorage do not!