dearies... this blog entry is dedicated to the one who made me very happy last nite/just now/ before 12 yesterday... anyway,when he read this... he will sure know y it is for him.... hehee....

anyway this is on wat my RJ for today is like... n i think this explains a lot of things.... alvin, u should read this sia... this is good stuff...

post url first: http://www.thymos.com/tat/biology.html

b4 posting, a little update.... did not slp last nite coz was rushing lab report... yes, i stayed up the whole of last nite coz wanna made my lab report perfect.... hehe... coz of a certain someone lar.... hehe.... then well... did not slp.... n kinda proud of myself.... hehe.... anyway, today had a really heavy lesson man... so many things to do n research on.... hiaz....

aft sch, met him n well... went to eat.... at jack's place... seems like that is goin to b our usual place liao.... haha.... anyway, kept the reciept as usual.... haha... donno y... everytime aft we eat he will pass me the reciept then i will keep them one.... hehe... then.... well for me n him to know.... n u guys don bother finding out.... ahahaha..... =P

so moving on.... here is the thhing that i wanna show u guys.... for u patient people.... or lazy to clikc on the url... ehhehehe....

Life has three dimensions. One is the evolutionary dimension: living organisms evolve over time. One is the reproduction dimension: living organisms are capable of reproducing. One is the metabolic dimension: living organisms change shape during their life.
Each dimension can be studied with the mathematical tools that Physics has traditionally employed to study matter. But it is apparent that traditional Physics cannot explain life. Life exhibits properties that rewrite Physics.
The Origin Of Self-organization: life as negative entropy
The paradox underlying natural selection (from the point of view of physicists) is that on one hand it proceeds in a blind and purpose-less way and on the other hand produces the illusion of more and more complex design. This continuous increase in information (i.e., the spontaneous emergence of order) seems to violate the second law of Thermodynamics, the law of entropy.
Ludwig von Bertalanffy borrowed the term "anamorphosis" from the biologist Woltereck to describe the natural trend towards emergent forms of increasing complexity.
Entropy is a measure of disorder and it can only increase, according to the second law of Thermodynamics. Information moves in the opposite direction.
Most things in this universe, if left alone, simply decay and disintegrate. Biological systems, instead, appear from nowhere, then organize themselves, then even grow!
This leads to the "two arrows of time": the behavior of physical systems pointing towards entropy increase and therefore disorder increase, and the behavior of biological systems pointing the other way by building increasingly complex structures of order.
When you drop a sugar cube in your coffee, it dissolves: while no physical law forbids the recomposition of the sugar cube, in practice it never occurs, and we intuitively know that it cannot occur. Order is destroyed and cannot be recreated. That's a manifestation of the second law of Thermodynamics. On the other hand, a teenager develops into an adult, and, while no biological law forbids it, and as much as they would like to, adults never regress to youth. This is a manifestation of the opposite arrow of time: order is created and cannot be undone.
Since organisms are made of chemicals, there is no reason why living systems should behave differently than physical systems. This is a paradox that puzzled not only biologists, but physicists too.
The Austrian physicist Erwin Schroedinger, one of the founders of Quantum Mechanics, first proposed the idea that biological organization is created and maintained at the expense of thermodynamic order. Life displays two fundamental processes: creating order from order (the progeny has the same order as the parent) and creating order from disorder (as every living system does at every metabolic step, eating and growing). Living systems seem to defy the second law of Thermodynamics. In reality, they live in a world of energy flux that does not conform to the closed-world assumptions of Thermodynamics. An organism stays alive in its highly organized state by absorbing energy from the environment and processing it to produce a lower entropy state within itself. "Living organisms feed upon negative entropy": they attract "negative entropy" in order to compensate for the entropy increase they create by living. Life is "negentropic". The existence of a living organism depends on increasing the entropy of the rest of the universe.
In 1974 the biologist (and Nobel prize winner) Albert Szent-Gyorgyi proposed to replace "negentropy" by the positive term "syntropy", to represent the "innate drive in living matter to perfect itself". This has a correspondent on the psychological level, "a drive towards synthesis, towards growth, towards wholeness and self-perfection".
Life as Non-equilibrium
In the 1960’s, the Belgian (but Russian-born) physicist Ilya Prigogine (who will later be awarded the Nobel prize for his work in Thermodynamics) had the fundamental intuition: living organisms function as dissipative structures, structures that form as patterns in the energy flow and that have the capacity for self-organization in the face of environmental fluctuations. In other words, they maintain their structure by continously dissipating energy. Such dissipative structures are permanently in states of non-equilibrium.
Life maintains itself far from equilibrium: the form stays pretty much the same, while the material is constantly being replaced by new material, part of which comes from matter (food, air, water) and part of which comes from energy (sun). The flow of matter and energy "through" the body of the living organisms is what makes it possible for the organism to maintain a (relatively) stable form. In order to stay alive, they have to be always in this state far from equilibrium.
Equilibrium is death, non-equilibrium is life.
And here is the solution of the riddle. Equilibrium is the state of maximum entropy: uniform temperature and maximum disorder. A system that is not in equilibrium exhibits a variation of entropy which is the sum of the variations of entropy due to the internal source of entropy plus the variation of entropy due to the interaction with the external world. The former is positive, but the latter can equally be negative. Therefore total entropy can decrease.
An organism "lives" because it absorbs energy from the external world and processes it to generate an internal state of lower entropy. An organism "lives" as long as it can avoid falling in the equilibrium state.
(In a sense, organisms die because this process is not perfect: if our bodies could be made to keep their shape exactly the same, they would always remain far from the equilibrium and they would never die).
Thanks to the advent of non-equilibrium Thermodynamics, it is now possible to bridge Thermodynamics and evolutionary Biology. By focusing on entropy, structure and information, it is now possible to shed some light on the relationship between cosmological evolution and biological evolution. Biological phenomena can be viewed as governed by laws that are purely physical. This step might prove as powerful as the synthetic theory of evolution.
Prigogine’s non-equilibrium approach to evolution, i.e. that biological systems (from bacteria to entire ecological systems) are non-equilibrium systems, has become a powerful paradigm to study life in the context of Physics. Life is finally reduced to a natural phenomenon just like electromagnetism and gravity.
Bioenergetics
These ideas led to an approach to life, called "bioenergetics", which consists in applying thermodynamic concepts (energy, temperature, entropy and information) and non-equilibrium (or irreversible) Thermodynamics to biological structures.
The starting point, in the 1920s, was the biologist Alfred Lotka's assumption that ecosystems are networks of energy flows. Then, decades later, the brothers Howard and Eugene Odum devised a thermodynamic model for the development of the ecosystem. That became the route followed by an entire branch of Biology: looking for the thermodynamic principle that guides the development of ecosystems.
The thesis of the American biologist Harold Morowitz is that the flow of energy through a living system acts to organize the system: organization emerges spontaneously whenever energy flows through a system. The contradiction between the second law of Thermodynamics (the universe tends towards increasing disorder) and biological evolution (life tends towards increasing organization) is only apparent, because Thermodynamics applies to systems that are approaching equilibrium (either adiabatic, i.e. isolated, or isothermal), whereas natural systems are usually subject to flows of energy/matter to or from other systems.
First of all, life is the property of an ecological system, not of a single, individual, isolated organism. An isolated living organism is an oxymoron. Life of any organism depends on a flow of energy, and, ultimately, life "is" that flow of energy.
Morowitz has proven two theorems that analyze what happens during that flow of energy through the chemical systems that living organisms are made of: 1. those systems store energy in chemical bonds, i.e. their complexity steadily increases; and 2. those systems undergo chemical cycles of the kind that pervade the biosphere (e.g., the carbon cycle).
The flux of energy turns out to be the organizing factor in a dissipative system. When energy flows in a system from a higher kinetic temperature, the upper energy levels of the system become occupied and take a finite time to decay into thermal modes. During this period energy is stored at a higher free energy than at equilibrium state. Systems of complex structures can store large amounts of energy and achieve a high amount of internal order.
The cyclic nature of dissipative systems allows them to develop stability and structure within themselves.
The bottom line is that a dissipative system develops an internal order.
The Origin of Biological Information
A non-biological approach to life that has also yielded stunning results over the last few years is the one based on information and directly influenced by Cybernetics and Information Theory. Life is viewed as information capable of replicating and modifying itself.
The American anthropologist Gregory Bateson always believed that the substance of the biological world is "pattern" (not this or that chemical compost), a position that allowed him to seek a unified view of cognitive and biological (and cybernetic) phenomena. His definition of information stretched beyond mere computation: a bit of information is a difference that makes a difference. Thereby implying that, in order to be information, a pattern must affect something. (Also, information is not a thing, it is a relation).
The pioneering work of the ecologist Ramon Margalef in the 1960's set the stage. He viewed an ecosystem as a cybernetic system driven by the second law of Thermodynamics. Succession (the process of replacing old species with new species in an ecosystem) is then a self-organizing process, one whereby an element of the system is replaced with a new element so as to store more information at less energetic cost.
For example, Kuppers found an elegant way to reconcile the paradox of increasing information. Life is biological information, and the origin of life is the origin of biological information. Information has different aspects: syntactic (as in information theory), semantic (function and meaning of information for an organism's survival), and pragmatic (following Von Weiszacker, "information is only that which produces information"). Since evolution depends on the semantic aspect of information, there is no contradiction with the second law of Thermodynamics, which only deals with the structural aspect of matter (i.e., the syntactic aspect of information). The origin of syntactic information relates to the prebiotic synthesis of biological macromolecules. The origin of semantic information relates to the self-organization of macromolecules.
The American biologist Christopher Langton has emphasized that living organisms use information, besides matter and energy, in order to grow and reproduce. In living systems the manipulation of information prevails over the manipulation of energy. Life depends on a balance of information: too little information is not enough to produce life, too much can actually be too difficult to deal with. Life is due to a reasonable amount of information that can move and be stored. Life happens at the edge of chaos. Ultimately, life is a property of the organization of matter.
As the Canadian biologist Lionel Johnson put it, the biosystem can be compared to an information processor, whose job is to continuously extract, store and transmit information. Two fundamental and opposed forces compete, one leading towards increased uniformity (and lower information) over "ecological" time and one leading towards increased diversity (and greater information) over "evolutionary" time. This results in a hierarchy of living organisms, which has at the top the one species that developed the best strategy of energy extraction and storage, the highest resource utilization and the least dissipation (this is a reworking of a principle due to Alfred Lotka in the Twenties). Extracting information requires an energy flow, which in turns causes production of entropy. This can also be viewed from the point of view of communication: dissipative structures can exist only if there is communication among their components, whether in the form of genetic code (communication over stime) or societies (communication over space). The biosystem is, ultimately, an information processor and a communication network.
At the same time, the Hungarian chemist Tibor Ganti views life as the combination of of two systems: metabolism and information control. The simplest form of life, in practice, is the "chemoton": an autocatalytic cycle coupled with an information molecule. Tibor's living organism, therefore, looks more like a computer than a program, because it includes the "hardware". Life without the hardware is not life, it is just the process that generates life. It also takes that "information molecule" to have life.
Lives
The distinguished British biologist John Maynard Smith defined progress in evolution as an increase in information transmitted from one generation to another.
The key to evolution is heredity: the way information is stored, transmitted and translated. Evolution of life as we know it relies on information transmission. And information transmission depends on replication of structures.
The authors believe that evolution was somewhat accelerated, and changed in character, by and because of dramatic changes in the nature of biological replicators, or in the way information is transmitted by biological replicators. New kinds of coding methods made possible new kinds of organisms.
Today, replication is achieved via genes, that utilize the genetic code. The authors argue that this is only the latest step in a story that started with the earliest, rudimentary replicators, the first genes.
The first major breakthrough in evolution, the first major change in the technique of replication, was the appearance of chromosomes: when one gene is replicated, all are. A second major change came with the transition from the solitary work of RNA to the dual cooperation of DNA and proteins: it meant the shift from a unitary source of replication to a division of labour. Metabolism was born out of that division of labour and was facilitated by the chemical phenomenon of autocatalysis. Autocatalysis allows for self-maintenance, growth and reproduction. Growth is autocatalysis.
Early, monocellular organisms (prokaryotes) evolved into multicellular organisms (eukaryotes). The new mechanism that arose was gene regulation: the code didn't simply specify instructions to build the organism, but also how cells contributed to the organism. Asexual cloning was eventually was made obsolete by sex, and sex again changed the rules of the game by shuffling the genetic information before transmitting it. Protists split into animals, plants, fungi, that have different information-transmission techniques.
Individuals formed colonies, that developed other means of transmitting information, namely "culture; and finally socail behavior led to language, and language is a form of information transmission itself.
Each of these steps "invented" a new way of coding, storing and transmitting information.
The primacy of energy flows
In the beginning was energy, matter came later.
The American physicist Ronald Fox showed how, from the beginning, it was energy flows (lightning, volcanic heat) that allowed for the manufacture of unlikely molecules like aminoacids that are the foundations of life.
The emphasis shifts to polymers: organisms use energy to excite monomers until they start creating polymers spontaneously. The organism reaches a state in which polymers help produce (synthesize) polymers.
Fox speculates that organisms used an abundant natural source of energy (phosphate bond energy), that was created during the "iron catastrophe". That new flow of energy created a new kind of matter. Phosphate is still a key component of energy transactions in living molecules.
Biological evolution was subsequently driven by energy regulation and storage.
Fox uses nonlinear thermodynamics and therefore chaos theory to show how complex structures can then spontaneously emerge.
The nervous system makes sense in this scenario because it provides a biological advantage: it allows the organism to rapidly simulate the outcome of nonlinear events, that are, by their own nature, very hard to predict. Rapid simulation is the only way that the organism can predict what will happen and therefore essential to survival.
All based on the simple idea that whatever happened was driven by flows of energy.
The Irreversibility of Life
Not everybody agrees with Prigogine’s view of living systems as dissipative structures and with Schroedinger's view of life as "negentropic".
A law known as "Dollo's law" states the irreversibility of biological evolution: evolution never repeats itself. Darwin's natural selection does not necessarily prescribe progress or regression, does not imply a direction of evolution in time, it only states an environmental constraint. Indirectly, Dollo's law does: it prescribes a trend towards more and more complex, and more and more ordered, living structures. Dollo's law expresses the visible fact that reproduction, ontogeny and phylogeny are biological organizations whose behavior is irreversible: both during growth and during evolution, entropy of biological information constantly increases. We evolved from bacteria to humans, we grew from children to adults.
The goal of the unified theory of evolution put forth in the Eighties by the biologist Daniel Brooks and the philosopher E.O. Wiley is to integrate this law with natural selection.
Unlike Prigogine, Wiley and Brooks believe that biological systems are inherently different from dissipative structures. Biological systems, unlike physical systems, owe their order and organization to their genetic information, which is peculiar in that it is encoded and hereditary. Dissipation in biological systems is not limited to energy but also involves information, because of the genetic code, which is transmitted to subsequent generations. Organisms simply live and die, they don’t evolve. What evolves is the historic sequence of organisms, which depends on genetic code. The genetic code must therefore be put at the center of any theory of evolution.
Unlike most theories of information, that use information to denote the degree to which external forces create structure within a system, Brooks-Wiley's information resides within the system and is material, it has a physical interpretation. It resides in molecular structure as potential for specifying homeostatic and ontogenetic processes. As the organism absorbs energy from the environment, this potential is actualized and is "converted" into structure.
What they set out to prove (following Lotka's original intuition and exploiting Layzer's ideas) is that evolution is a particular case of the second law of Thermodynamics, that Dollo's law is the biological manifestation of that second law. Biological order is simply a direct consequence of that law. The creation of new species is made necessary by the second law and is a "sudden" phenomenon similar to phase changes in Physics. Phylogenetic branching is an inevitable increase in informational entropy.
In this scenario, the interaction between species and the environment is not as important in molding evolution: natural selection mainly acts as a pruning factor.
Over short time intervals, biological systems do behave like dissipative structures. But over longer time intervals, they behave like expanding phase space systems (as proved by Layzer). Their relevant phase space is genetic, an ever increasing genetic phase space.
The Brooks-Wiley theory is darwinian in nature, as it subscribes to the basic tenet that evolution is due to variation and selection, but, in addition, it also allows the possibility for evolution to occur without any environmental pressure.
A Hierarchy of Lives

so ahem... for those who skip all the above n came here... all i can say is that either u guys r impatient people or juz smart enough to read the summary.... all the crap is saying.... that there is no such thing as perfect balance.... coz if u r balanced or perfect... then u haf died.... ahaha... cool rite.... no wonder i live wif imperfection perfectly... haha....

note to him: don blame urself for things that has happened.... in the end, it will only affect me... n not u.... u juz play a part.... n i am not upset or watsoever bout wat will happen.... don really care too... so u also don haf to... hehe... relax.... relax.... n let me handle all the rest.... hehe.... muackz....