To
do anything requires energy. To specify what is done requires information"
- Seth Lloyd
In the first part I focused on information as fundamental to
the life process. Personal experience as a physician, personal observations of
nature and review of the literature gave direction to my thinking. Then I realized that I have to know the basic
theories of Information as a scientific discipline and started reading books on
this topic and related fields 1,2,3,4. The current essay is a review
of the scientific study of Information and how the concepts developed as part
of Information Theory (IT) can be applied to processing of information in
living organisms.
The mathematical theory of Information is based on the concept
of data. John Wheeler who coined the
term “it from bit” seems to suggest that the ultimate nature of physical
reality (“it”) is derived from Information, the “bit”.
There are
different definitions of the word “information” within the field of the
mathematical theory and its physical applications. When biological information
is added to the discussions, other scientific disciplines with their own
vocabularies need to be accommodated in this definition. Floridi2
has provided a conceptual map and definitions of terms to study the various
components of Information (Figure 1). I plan to use this map for the concepts
it provides and to relate these concepts to examples of information processing
in biological organisms.
Warren Weaver and Claude Shannon recognized three aspects of
information for scientific analysis. They are the technical problems (dealing
with quantification of information),
semantic problems (dealing with meaning
and “truth”) and “influential” problems (dealing with the effect of information on human behavior). They did not mention the
effect of information in biology as part of “influential” problems. Their own
focus was on the technical aspects.
According to the
Information Theory (IT), General Definition of Information states that an instance
of information is said to be present if, and only if, it consists of
well-formed, meaningful data. Information
theory deals with information based on the concept of data.
This mathematical theory of information as data is applicable to biological information also.
Figure 1 shows the various steps connecting data to meaningful information.
From life sciences point of view, meaningful information may be physiological
functions through its instructional pathway or knowledge through the semantic
pathway, although this dichotomy is conceptual only.
What is a datum? It
is defined as “lack of uniformity” or “a distinction that makes a difference”.
According to the Information Theory (IT), datum is when x and y are
uninterpreted variables and their relationship is one of “being distinct”.
Before a datum is interpreted by intelligent organisms, it is accessible
through inference, since it has to be there for the information to be possible.
As pointed out in part 1, before pure data gets interpreted or subjected to
cognition, it “is empirically inferred from and is required by experience,
since they are what has to be there in the world for our information to be
possible at all2”.
This basic intuitive sense of lack of uniformity is called
the dedomena in the IT. This is the
basis of lack of uniformity between two physical states (called signals) or between symbols made by these signals as perceived by intelligent organism.
This definition information as “well-formed, meaningful
data” allows application of IT to biological information also since information
depends on well formed data with a syntax and a meaning and data depend on the
occurrence of differences in the physical state. In what format, medium and
language, the data is encoded (electrical signals or genetic code) is not
relevant. Genetic code, three dimensional structure of a protein, hydrogen bond
are as good as Morse codes or digital codes (0 and 1). Principles of IT can be
applied to information processing in biology as has already been pointed out in
Part 1 (processing of TNF signaling in cells5,6)
It is important to point out that this definition of
information as data is too restrictive for use in biology, although the
concepts are useful for future research.
Now that we have defined the relationship between
Information and data, let us look at different types of data which give a piece
of information. According to IT, there are five categories of data. They are,
primary, secondary, meta, operational and derivative.
Primary data is seen in the form of 0’s and 1’s or a series
of numbers. In biology, codons may be considered as primary data. Any
biological switch such as receptors before attachment to its ligand can be
considered primary data. The all- or-none aspects of action potential can also
be considered as such. All of these are equivalent to the 0 or 1 positions in
IT. My guess is that when we go deeper and deeper to the molecular level in
biology, positive and negative charges carried on molecules may have to be
considered as the primary data.
Secondary data is the converse of primary; or the absence of
data. Absence of data is useful as a piece of information. Knockout mice are
examples of this idea. Misfolded proteins and missence mutations represent
secondary data. At the knowledge level, absence of anti-DNA antibody, in a
proper setting, excludes the diagnosis of SLE; or the absence of
anti-streptococcal antibody by any method rules out Acute Rheumatic Fever.
Metadata gives an indication of some other data, most often
primary data. They may describe properties or location or availability of
information, rather than describe the information itself. Environmental
information such as pH at which reactions occur and medium (aqueous or lipid)
in which reactions occur belong to this category. At a macro level,
environmental triggers for a disease belong to this category also.
Operational data is about the dynamics of the operation and
performance of the system itself. Efficiency of processing of information
leading to the effect may be altered by “noise” as described in Part 1 (TNF
signaling in the cell in the midst of noise) and competing metabolic pathway
may belong to this category.
Finally, Derivative data are indirect sources of
information. When data are used to search for clues and patterns of things
other than those directly addressed by data themselves, they are considered to
be derivative data. For example, a low potassium may be the data suggesting
that the glucocorticoid – glucocorticoid receptor pathway is underperforming or
overactive. Clinically, fatigue may be the indirect source of information about
the status of glucocorticoid metabolism.
Based on one or more of these types of data, information may
become available if they are well-constructed and have a meaning. This information
may be of one of two major categories – semantic or environmental. Semantic
information refers to content. This may be either instructional or statement of
a fact (factual, a truth). Factual, semantic content of information is of
paramount importance in the field of neurosciences and essential to human
communication, construction of knowledge, consciousness, thinking etc. Most of
what I wish to focus on is about the instructional nature of information.
Before we discuss
ideas related to instructional information, a word about environmental
information. As defined by IT theorists, environmental information points to
data which might be meaningful independent of an intelligent “producer” or
“informer” of the data. As an example, Floridi points to the rings in the trunk
of a tree which offers information about the age of the tree. If we accept this
definition in biology, nature is full of such information. I wonder whether we
may not need a different definition, because of the way genes (epigenetics),
immune system and metabolic systems work. There is primary data for the direct
response. But it is modified by environmental clues. In philosophy, such
information is grouped under “causes and conditions” for everything that
happens in this world. This should be called environmental information in
biology and neurosciences.
Well-formed, meaningful data give rise to semantic content
of information. Semantic information can be representing reality as is (as in finger patterns), can be for a specific purpose of reality ( as
in genetic code, commands) as instruction or about reality as in textbooks and maps. Instructional information
is not a description about a situation. It is meant to bring about a new state
of the system. According to the linguistic root of the word, Information, in forme is to bring about, to create.
This is the mode of information in all of basic biology. Genes bring about new
proteins. New proteins bring about new biochemical reactions. Biological
stimuli of all kinds bring about responses. All biological pieces of
information are instructional in nature.
Factual information about reality is the basis of knowledge
and communication, whether it is true information, misinformation or
disinformation. These are not the subjects of this essay.
Such compartmentalization is too restrictive for use in
biology. However, it provides a framework to study concepts related to
information and information processing in nature and in man-made environment.
Information and processing of information is at the core of
all of biology. For example, a recent issue of Science7 has several
essays on unsolved problems in cell biology. Almost every question deals with
the ability of single cells to sense information and respond. How does the cell
know where to position its proteins for efficient functioning? How does the
cell know to avoid or go towards tiny gradients of chemicals in their
environment? To behave appropriately in a multi-cellular organism, a single
cell has to know in which tissue it is. How do they “know”?
In the same issue there was another essay on the Unfolded
Protein Response8 and its role in homeostatic regulation. All
signaling proteins needed to communicate with the cells environment are
assembled and folded in the endoplasmic reticulum before they are secreted or
sent to the surface of the cell to receive signals from the environment. These
proteins are involved in receiving signals from the environment and direct the
cells to respond with migration, division, differentiation or death. All of these
functions (responses to stimuli) are information-based.
It is clear that information as data is inherent in every
step of genetics. DNA molecule contains the genetic code for all life forms.
DNA is made of nucleotides which consist of a sugar moiety, a phosphate
molecule and a base. This base may be one of four kinds – A, G, C and T. Gene
is a segment of the DNA molecule which carries information to make a functional
protein. Proteins are composed of amino acids and there are 20 amino acids.
The gene is made of a code consisting of a unique
combination of the three nucleotides mentioned earlier. This is called the
codon. Since there are 4 nucloetides it is possible to get 64 different
possible combinations of three-letter codons. One of the combinations acts as a
start signal and three as stop signal and all others code for the 20
aminoacids. Redundancy is built in.
In the double-stranded DNA, A always combines with C and G
always combines with T. Indeed these proportions between A and C, and G and T gave
a clue to the structure of DNA.The genetic code has to be transcribed first in
the form of RNA, in which a mirror image of a single strand of DNA forms with C
wherever A was and vice versa. The sugar is of a different variety. RNA gets
translated into the a chain of amino acids ( 2 dimensional) which are then
assembled into proteins with a 3-dimensional structure. This 3 dimensional structure and the
locations of energy-bonds are important elements in receptor- substrate
interactions and proper interpretation of the message.
Information carried by genes is more than semantic
information. In essence, gene carries information for a purpose. It is
instructional for the development and functions of the organism. “Biological
information …… is procedural: it is information for something, not about
something”.
Let us look at brain, mind and their functions. Neuroscience
is about information processing. The nervous system consists of a network of
cells and its extensions that manage information about the organism’s internal
milieu to maintain homeostasis (such as temperature control) and about the
environment to increase the chances for survival and reproduction. Even a
unicellular organism has to receive signals from both internal and external
environments and respond. Information-processing network is a complicated
structure in multi-cellular organisms. It has a portion to deal with signals
from outside, a system to deal with signals from inside and systems with
ability to receive, store, recall these stimuli and respond. The entire system
is based on neurotransmitter chemicals and electrochemical signals. When
neurotransmitters bind to receptors, pores (called ion channels) open in the
membrane, through which charged particles can flow. This electrochemical phenomenon carries
information for excitation or inhibition of the neuron receiving the signal.
The electrochemical signals carried along axons are called action potentials.
They are signals with Boolean function (all or none) and the frequency of these
action potentials carries information.
We know now that thinking, feeling, remembering, recalling
involve networks in the CNS. Anatomical correlates of various cognitive
functions are known. Even forbidden territories such as self and consciousness
are under scrutiny 9,10. How simple electrochemical phenomena give
rise to complex mental functions such as these is a mystery to be solved.
When I try to think of human consciousness and my own sense
of “background awareness” as part of my daily meditations, I see several levels
of information. The word awareness implies awareness about something. In deep
sleep and in coma due to whatever reason, there is no general background
awareness. Therefore, there can be no sense of “I”. Under the influence of some
drugs and intoxicants, prolonged starvation and prolonged isolation, one is
awake and aware but the awareness is different10. This awareness
gives an altered sense of an “I”. The pure, basic awareness of someone waking
up from normal sleep is not there. With injury to the brain from trauma or infection,
there may be different levels of wakefulness, alertness and awareness. Some may
be aware but not able to respond. It appears that at some basic level of
awareness, the person will have a sense of “I”. For example, when someone is
waking up from deep sleep or from anesthesia, and during deep meditation there
is a moment when the person is aware of “life” and being alive without the
details of his/her individuality. This is called the “transient I” or Pure
Awareness by oriental mystics.
When you are fully aware, your mid is full of thoughts. Your
“I” is fully active. Without that basic pure awareness you cannot be aware of
your awareness. It is on that basic awareness, all perceptions are received,
feelings are felt, concepts are formed, ownership is created, memory is formed,
stored and recalled, will to act is generated and imaginations take flight
from. Thus an “I” is created.
The main point is that all of these are about information
being passed on, received and acted upon. Information is at the core of all
philosophical discussions of the nature of human consciousness. What gives
continuity to the individual from birth to death is information about oneself even
when the structures undergo change and parts get replaced.
What is surprising is that even single particles of colloid
suspended in a liquid seem to be “aware” of their presence and location! By
immersing a nanometer size colloid particle and trapping it in the focal spot
of a laser and monitoring the Brownian fluctuations, Franosch et al11
have shown that the observed changes in the spectral density are due to the
colloid’s self-interaction in response to the environment.
One other important point is that information processing requires
energy. Therefore, information-processing is subject to thermodynamic laws both
in the physical and in the biological world. Physicists have been discussing for
several decades that information may be a third fundamental unit , after matter
and energy. More recently, Stuart Umpleby, a Systems Scientist has attempted to
bring these three concepts together although our knowledge about units of
information is not as rich as on physical objects12. More recently
Bremermann has suggested a triangular relationship between matter, energy and
information at an atomic level 13. By combining the relationship
between matter and energy with the relationship between energy and information
he has shown a new relationship between matter and information. Indeed
Bremermman has calculated a constant (1047 bits/gm/sec) a boundary
beyond which the flow of data (information) cannot be improved physically. It
is the limit at which symbols can be processed by matter.
Biology is all about chemistry. Chemistry is all about
atoms, molecules and electrons. Electrons are “quantum mechanical beasts at
heart”. Chemistry in biology is also
based on principles and laws of physical
chemistry. Will it be a surprise to see quantum play a part in biology? As
pointed out in part 1, some work is already being done in this area and there are
several books relating life processes to
quantum biology14,15.
Now it is time to
venture into borderline territory of metaphysics. Physics is theory of phenomena and metaphysics is about what might lie
behind these phenomena. Information is about the physics and the chemistry of
nature, about life and about consciousness, and therefore of life and the roots
of phenomena. The field of information may be the bridge between biology,
physics and metaphysics.
This is why I defined Information as potential for a future
event, physical or biological, inherent in Nature. Matter and energy are involved and the event
takes place in space and time when causes and conditions are present.
Life as we know it and consciousness as we know it were
inherently possible for them to appear, however low the probability was at an
earlier time. (I did not use the words “in the beginning”) As chaotic as the
Universe seems to be for this world to appear and life to evolve and as
complicated and delicate as life is, they were inherently possible from the
onset however improbable the chances were. Without bits of information inherent
in primordial matter under “causes and conditions”, how could life have
appeared? This sounds like a
tautological argument. Even so, this view is more likely to be acceptable to
those who dislike the cold, logical, materialistic explanation of the Universe.
Information has to be recognized as a fundamental unit of
Nature to explain the visible universe, including its living matter, all of
which are made of matter and energy unfolding under appropriate conditions, in
space and time.
1.
Gleick J. The Information. New York: Pantheon
Books, 2011.
2.
Floridi F. Information – A Very Short
Introduction Oxford University Press. 2011
3.
Wheeler, J A and Ford K. Geon, Black Holes and
Quantum foam: A Life in Physics. New York: Norton, 1998.
4.
Pierce JR. An Introduction to Information
Theory. 2nd edDover Publications New York.1980
5.
Thomas PJ
Every bit counts. Science 334: 321-322, 2011
6.
Cheong R, Rhee A, Wang CJ, Nemenman I and Levchencko
A. Information transduction capacity of
noisy biochemical signaling networks.
Science 334: 354 - 358, 2011
7.
Science November 25, 2011
8.
Walter P, Ron D. The unfolded protein response:
From stress pathway to homeostasis regulation.
Science 334:1081-1086, 2011
9.
Meeks TW, Jeste DV. Neurobiology of Wisdom. Arch
gen Psychiatry 66: 355-365, 2009
10.
Blakemore S. Consciousness – An Introduction.
Oxford university Press. 2004
11. Franosch
T, Grimm
M, Belushkin
M, Mor
FM, Foffi
G, Forró
L, Jeney
S. Resonances arising from
hydrodynamic memory in Brownian motion.Nature 478: 85-88, 2011
12.
Umpleby SA. Physical relationships among Matter,
Energy and Information. Systems and Behavioral Science 24:369, 2007
13.
Bremermann H.J. Quantum noise and information.
Fifth Berkeley Symposium on Mathematical Statistics and probability.
Berkeley,CA. University of California Press 1965
14.
Allemann
R, Scrutton N. Quantum tunneling in enzyme-catalyzed reactions. RSC Publishing,
Cambridge, UK 2009
15.
Abbott D, Davies P C w, Pati AK. Quantum aspects
of life. Imperial College Press, London. UK 2008