Ten commandments in systems biology

Joseph X. Zhou — Wed, 03 Oct 2007 17:19:09 -0400

The 5th European Conference
on Complex System is holding in Dresden, Germany now. This is really
an emerging research area. The multiple para-sessions themselves show
how diverse and multi-disciplined it is. It includes:

Complex system method
Cognition
Networks
Social system
Biological system

Researchers not only from all countries
of Europe, but also from US, Canada, Japan ect.. The most inspiring experience of this
conference is that the traditional barriers among disciplines are
broken down. You can hear the hybrid system of brain tissue and
microelectronic chips, then system biology illustrated using the
virtual heart. It was followed by mathematical model of rhythmic
behavior in biological system, and a speaker from HP computer Lab
talked about social dynamics in cyberspace, mentioning the network
properties and quality control of Wikipedia etc.

Today's most heated topic is Prof.
Denis Nobel's talk about his revolutionary views about system
biology. When I talked with several people after his speech, they all
called it astonishing. He called his experience as ten commandments
in systems biology.

Commandment 1 (C1): Gene itself has no
functions.

It is actually the cooperation and
system of genes lead to the function of living things.

C2: Transmission of information is NOT
one-way

Traditionally we think that gene decide
protein -> pathway -> sub-cellular -> cell->tissue->
organ->body. it is totally wrong that we can start with gene,
proteins and then build everything. It is doomed to fail. Gene
expression is also decided by the cell culture and proteins to
translate them.

There is no magic gene/ genes to cause
Cancer, homosexuality, selfishness or high blood pressure. All
functions and malfunctions of human being in all level are system
properties emerging from the network and interaction of elements.

C3: DNA is not sole transmitter of
inheritance

It is quite anti-Darwinism and
pro-Lamarkism. But there are some scientific evidences for that. More
can seen in article:

Jane Qiu (2006), Unfinished symphony,
Nature, 441, 143-145

C4: Theory of biology Relativity

We need to understand the interactions
at all level to understand the real functions of living things. We
can not unlock nature's myth only from bottom-up strategy. That is,
we can not understand the organism only from gene level up to cell
level etc. We have to understand it from organ regulating cell or
even gene as well.

C5: Gen ontology will fail without
high-level insight

It is very mis-leading to find the
causes of cancer from the selection of genes without clear
understanding the physiology of cancer and evolution theory of
organs. Gene is called a blueprint of life. It is wrong. Gene is NOT
the book of life. If it is the book, it is the book with huge gap
which can not be read at all.

C6: There is not “genetic program”

gene itself is not a program of life,
it is only the database of life. There is NO program written in the
gene. The reading of this database come from the cell and protein to
transcript and translate them.

C7: There is no program at any other
level

Life is like a well-coordinated concert
but without conductor. Further reading
“The art of Gene”,
Enrico Coen ( Oxford Univ Press, 1999)

C8: No program from any level,
including brain

C9: Life is the self integrated
process, not an object or substance.

C10: There are many more to be
discovered, the theories of biology do NOT yet exist. Seeking
theory/ies is real challenge in system biology.

(Denis Biography from Wiki)

Denis Noble (born November 16, 1936) is
an eminent British biologist who held the Bourdon Sanderson Chair of
Cardiovascular Psychology at Oxford University from 1984-2004 and is
now Professor Emeritus and co-Director of Computational Physiology.
He is one of the pioneers of Systems Biology and developed the first
viable mathematical model of the working heart in 1960[1]. His
research focuses on using computer models of biological organs and
organ systems to interpret function from the molecular level to the
whole organism. Together with international collaborators, his team
has used supercomputers to create the first virtual organ, the
virtual heart.

Noble was educated at Emanuel School
and University College London (UCL)[1]. In 1958 he began his
investigations into the mechanisms of heartbeat. This led to two
seminal papers in Nature in 1960 giving the first proper simulation
of the heart. From this work it became clear that there was not a
single oscillator which controlled heartbeat, but rather this was an
emergent property of the feedback loops in the various channels.

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Ten commandments in systems biology