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. We know that, proteins are produced by the flow of information from the aminoacide. The human brain and the neural sytem represent the multicellular exposure of the information flow. Life can be defined, as a chemical machine controlled by fuzzy control operations greatly resemble the computer operations. More exiting is the multi-biological activities, which are initiated from the mechanical structure of the biomolecules.

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. Therfore, it is incorrect to think of biocomputers as fifth generation computers. In fact, it is a technological contenet, exposing its enormous potentials. Biocomputing is one of the major scientific and technological diciplines in the 21st century.

 

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. The DNA replication refers to the process of copying a DNA molecule.

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:

One of the currently more acceptable definitions of the biocomputing is: 

"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.

 

The Ultimate Integration of  Biodevices: 

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. One bit of information corresponds to one pair of nucleotides (AT or GC). The density of integration in terms of molecular weight correspnds to "1 bit/10-21 gram�. It is worth emphasizing that all genetic informatiom of biology is determined by the sequence A, G, C and T in DNA. This means that, in man, there are some 5600000000 bit (base pairs) of such information.

 

 

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. The mechanism, which opens and closes the various kinds of channel, is called a "gate" and the portion, which detects the potential, or concentration is called the "sensor", but these terms have slightly different meanings from those found in electroins.  

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: The wiring of the sensory nervous system of mammals is at least approximately determined genetically, but this is further refined after birth by the environment. The actual structure of the brain is altered from the normal morphology simply as a consequence of the environmental manipulation.

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. On the other hand, it is clear living organims have very orderly structure.

For Example: The protiens produced by certain viruses can form a regular duodecahedron .How is such perfect geometrical information encoded in the genetic program? When the amino cid sequence of that protein I studied, it is found to have a repeating structure appropriate for such geometrical shape. The rules for such structure, as seen at the molecular level, are undoubtedly present at higher levels, for example; at the cellular level, as well.

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. Assuming that a person is awake for about 50 years during life time, the total volume of meaningful information received is only about 1010    bit's  (=amount of information stored in the human genome). The bulk of this informaion passes through the brain with only transient effects, but some information in short-term memory ha influence on planning and behaviour. Hanse marko in 1965, ued a sophisticaed mathematical model to show how short -term memory is connected to consciousness and long-term is related to the unconscious. These models are a source of insight into the bidirectional tranfer of information between any tow entities, which send and receive information.

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!