Saturday, September 29, 2012

47. What is Life?

Perhaps there is no clear dividing line between life and nonlife. Nevertheless, the emergence of what many of us intuitively understand to be life marked a major milestone in the evolution of complexity in our world. Here are some definitions of life:
But what is life? Like time, life is obvious to discern yet elusive to define. Although most biologists generally skirt the issue, we suggest that our very essence can be defined as follows: Life is an open, coherent, spacetime structure maintained far from thermodynamic equilibrium by a flow of energy through it – a carbon-based system operating in a water-based medium, with higher forms metabolizing oxygen (Eric Chaisson 2001).

Life does not exist in a vacuum but dwells in the very real difference between 5800 Kelvin incoming solar radiation and 2.7 Kelvin temperature of outer space. It is the gradient upon which life’s complexity feeds (Margulis & Sagan 2002).

A living organism is an organized unit, which can carry out metabolic reactions, defend itself against injury, respond to stimuli, and has the capacity to be at least a partner in reproduction (Daniel Koshland).

Life depends on the availability of free energy. Without an input of free energy or 'negative entropy' (see below), all processes would tend to take a system towards a state of entropic death. Intake of food keeps an organism alive by providing negative entropy. The complex molecules constituting food are full of free energy or negative entropy, which is derived ultimately from the Sun.

In 1943-1944 Schrödinger wrote a little book What is Life. This is how Roger Penrose described this book (in 1991):

… which, as I now realize, must surely rank among the most influential of scientific writings in this century. It represents a powerful attempt to comprehend some of the genuine mysteries of life, made by a physicist whose own deep insights had done so much to change the way in which we understand what the world is made of. … Indeed, many scientists who have made fundamental contributions in biology, such as J. B. S. Haldane and Francis Crick, have admitted to being strongly influenced by (although not always in complete agreement with) the broad-ranging ideas put forward here by this highly original and profoundly thoughtful physicist.

It is important to realize that when Schrödinger wrote the book, the atomic structure of DNA was not known (it was determined later by Watson and Crick). I quote Freeman Dyson (1985):

Schrödinger’s book was seminal because he knew how to ask the right questions. The basic questions which Schrödinger asked were the following: What is the physical structure of the molecules which are duplicated when chromosomes divide? How is the process of duplication to be understood? How do these molecules retain their individuality from generation to generation? How do they succeed in controlling the metabolism of cells? How do they create the organization that is visible in the structure and function of higher organisms? He did not answer these questions, but by asking them he set biology moving along the path which led to the epoch-making discoveries of the subsequent forty years: to the discovery of the double helix and the triplet code, to the precise analysis and wholesale synthesis of genes, and to the quantitative measurement of the evolutionary divergence of species.

How did Schrödinger define life? He avoided giving a direct definition, but highlighted an important property of life by invoking the idea of NEGATIVE ENTROPY. He characterized living matter as that which stays alive (‘evades the decay to equilibrium’) by feeding on negative entropy or negentropy.

How can entropy be negative? How does living matter feed on negentropy, and what is the source of this negentropy?

The answer to the latter question is that the Sun has been bombarding our ecosphere with low-entropy or ‘high-grade’ energy. Why ‘low-entropy’? Recall that differential entropy is defined as dS = dQ/T (cf. Part 6), and the average value of temperature T for the Sun is huge compared to that of the Earth. On entering our ecosphere, the energy of the photons coming from the Sun gets degraded to a large extent through the processes of ‘thermalization,’ namely dissipation into a state of much lower average temperature (and therefore a correspondingly high value for the entropy).

A small fraction of this energy, however, gets trapped as free energy. It is stored in our ecosphere in the form of simple or complex molecules. Some of the energy-rich simple molecules in which the free energy from the Sun gets stored are: H2S, FeS, H2, phosphate esters, HCN, pyrophosphates, and thioesters.

When food is consumed by a living organism, its processing by the organism builds up a high information content (negative entropy) for the organism. Boltzmann-Gibbs entropy S is the same as missing information I. This means that –S (negentropy) is the same as available information (cf. Part 22).

Until 1944 most scientists were of the view that genetic information was carried by the proteins of the chromosome. Schrödinger’s book, apart from invoking negative entropy for the sustenance of life, introduced new concepts for the genetic code. It inspired Watson and Crick to investigate the gene, which led to their discovery of the double-helix structure of DNA. In their 1953 paper they wrote: ‘It has not escaped our notice that the specific pairing [of the two strands of DNA] we have postulated suggests a possible copying mechanism for genetic material.’ This sudden blaze of understanding laid bare the inside story of heredity, and of present-day life itself.

What is even more important, Schrödinger argued that life is not a mysterious or inexplicable phenomenon, as some people believe, but a scientifically comprehensible process like any other, ultimately explainable by the laws of physics and chemistry.

Saturday, September 22, 2012

46. Emergence of Autocatalytic Sets of Molecules

Life depends on molecules of RNA, DNA, proteins, polysaccharides, etc. How did such large molecules ('polymers') get synthesized spontaneously from their building blocks, namely nucleic acids, amino acids, sugars, etc.?

A polymer is a long molecule, the backbone of which usually comprises of a chain of covalently-bonded repeat units (monomers). There can be variations, either in that the bonding is not covalent everywhere, or in that not all subunits are identical. Examples of polymers and polymer solutions include plastics such as polystyrene and polyethylene, glues, fibres, resins, proteins, and polysaccharides like starch.

Short polymers can form spontaneously in Nature? Recall the lock-and-key mechanism I described in Part 44. Suppose a monomer has a shape and charge distribution such that another monomer can fit snugly into some part of it. There are random collisions among the monomers in a fluid medium, and usually they do not stick together, and simply bounce off after a collision. But once in a while the collision may be such that the two monomers have just the right orientation for a lock-and-key fitting. Then the chances of the two sticking together and forming a stable dimer are much larger.

Dimers can lead to trimers, and so on, resulting in polymers. But this can at best be a rather low-probability, and therefore very slow, process, and only short polymers can possibly form spontaneously in reasonable time.

Then how did very long polymers like RNA, DNA get formed? There had to be a mechanism for speeding up the rates of polymerization. The answer came from the emergence of autocatalytic sets of molecules.

Catalysis is a process that facilitates or speeds up a chemical reaction. Often a chemical process involves two or more intermediate reactions. A catalyst is a molecule that speeds up the production of an end product of the chemical process by participating in the intermediate reactions, but separating at the end of the chain of reactions, thus becoming available all over again for further catalysis. Often, a chemical reaction may almost never occur if no catalyst is present. Enzymes are examples of proteins that assist (i.e. catalyse) chemical reactions in biological systems.

Photosynthesis carried out by green plants in the presence of sunlight is another familiar example involving catalysis. Chlorophyll is the catalyst here. Through a number of intermediate reactions, the net reaction is as follows:

CO2 + H2  C6H12O6 + O2

That is, carbon dioxide combines with water to produce glucose and oxygen. This is the oxygen we breathe.

Autocatalytic sets of molecules are those which can catalyse the synthesis of themselves. Autocatalysis requires that a given 'factor' (say A) should be able to convert a substrate or precursor B into a new factor of the same type: A + B 2A + C. The idea of autocatalysis was introduced by Calvin (1969) as a mechanism for 'molecular selection', with implications for how life emerged on Earth.

Stuart Kauffman carried Calvin’s idea much further for explaining how long polymers like RNA could form spontaneously during the course of chemical evolution on our Earth. In the so-called primordial soup, namely a fluid in contact with rocks of various types, there existed small molecules of amino acids, nucleic acids, etc. Given enough time, some of them must have undergone random polymerization reactions of various types; i.e., short polymers got formed. It is entirely possible that at least some of these short polymers, with side chains and branches hanging around, acted as catalysts for facilitating the production of other molecules which may also be catalysts for another chemical reaction. Thus: A facilitates the production of B, and B does the same job for C, and so on. Given enough time, and a large enough pool containing all sorts of molecules, it is quite probable that at some stage a molecule, say Z, will get formed (aided by catalytic reactions of various types), which is a catalyst for the formation of the catalyst molecule A we started with.

Once such a loop closes on itself, it would head towards what we now call 'self-organized criticality' (SOC). There will be more production of A, which will lead to more production of B, and so on, finally reaching a 'critically stable' configuration.

The plausibility advantage of this scenario visualized by Kauffman is that there is no need to wait for random reactions. And once a threshold has been crossed, the system inches towards the edge of chaos and acquires robustness against destabilizing agencies.

Kauffman argued that this order, emerging out of molecular chaos, was akin to life: The system could consume (metabolize) raw materials, and grow into more and more complex molecules. It progressed into a situation where the forebears of DNA started appearing:

Once a set of autocatalytic reactions had established itself, it went on incrementally evolving into still more complex sets of molecules. Chance events and/or new external conditions resulted in the emergence of a slightly more complex version of, say, one of the molecules in the autocatalytic set. A further round of chemical Darwinism and evolution of a new set of autocatalytic set of molecules followed. And so on, till molecules as complex as RNA, DNA and proteins emerged on the scene, which have life-sustaining and life-propagating properties.

The question of the emergence of order and complexity in open systems was investigated in the 1970s by the Nobel Laureate Prigogine. An important feature of his work on open systems was that self-reinforcement or positive feedback is also needed for self-organization or pattern formation to occur. Only then can small chance events become magnified, sometimes taking the system to new valleys in phase space (basins of attraction). This ‘law of increasing returns’ or positive feedback, illustrated above by autocatalytic sets of reactions, can often lead to a multiplicity of qualitatively new outcomes. The actual outcome may depend on chance initial conditions, a feature characteristic of highly nonlinear systems.

Saturday, September 15, 2012

45. Chemical Adaptation and Chemical Evolution

Lipid bilayers and micelles are striking examples of chemical self-organization. The amount of information contained in such assemblies is very high. This information is distributed among the shapes of the component molecules, and in the interaction patterns among them.

The build up of such information involves a succession of stages: molecular recognition; self-assembly; self-organization; chemical adaptation; and chemical evolution. The first two were discussed in Part 44. Let us now focus on molecular self-organization, and chemical adaptation and evolution.

Jean-Marie Lehn is a pioneer in the fields of supramolecular chemistry and evolution of chemical complexity. He defined self-organization as the spontaneous but information-directed generation of organized functional structures in equilibrium conditions’. The necessary information (‘coding’) for self-organization is contained in the molecular-recognition and self-assembly proclivities of the component molecules (cf. Part 44). This coding also determines how the self-assembled edifice further self-organizes into a functional structure in equilibrium. For a survey of the various types of coding for self-organization, see, for example, my book Complexity Science.

Self-organization is a far more ubiquitous phenomenon than something at just the molecular level. Here are some examples:

  • A laser is a self-organized system. Under properly engineered conditions, photons spontaneously group themselves into a configuration in which they all move in phase, resulting in a powerful laser beam.
  • A hurricane is a self-organized system. The steady influx of energy from the Sun draws water from the oceans, as well as drives the winds. And mild tropical winds may grow into an organized configuration of a hurricane when some critical threshold is crossed.
  • A living cell is a self-organized system, which organizes itself all the time, depending on the environment.
  • An economy is a self-organizing system. The demand for goods and services, as also the demand for labour, constantly reorganizes the economy in a spontaneous way, without any central controlling authority.
Given a set of conditions, molecules in an open system tend to self-organize so as to minimize the overall free energy. This is chemical adaptation. Now suppose this set of conditions changes. This is very likely, in fact inevitable, because we are dealing with an open system. A further round of self-organization must occur, governed as always by the second law of thermodynamics for open systems. This is chemical evolution.

Moreover, the set of changing conditions, i.e. the changing environment experienced by the molecules, need not necessarily be that external to the set of molecules. Even internal changes in the molecular system present a changed environment to every member of the set. And molecular configurations are changing all the time. Thus, chemical adaptation and evolution occur in an open system of molecules (including our ecosystem) all the time.

One can draw analogies with Darwinian evolution to see if ‘natural selection’ (i.e. molecular selection) and ‘survival of the fittest’ also occur in chemical evolution. The answer is ‘yes’ because, when the resources are limited, there is competition among the alternative molecular-reaction pathways, and only the fittest pathways can survive so far as consumption of precursor molecules and energy-rich molecules is concerned.

Such considerations aroused special interest for explaining the origin of life-sustaining molecules. Some pioneering work in this direction was done by Melvin Calvin (1969), who introduced the idea of autocatalysis as a mechanism for molecular selection. I shall consider autocatalysis in the next post.

To sum up, the lock-and-key idea explained in Part 44 is crucial for explaining the evolution of molecules and molecular assemblies of increasing complexity in Nature. Two molecules may ordinarily interact only weakly, but a snug fitting of portions of the two molecules can lead to a much stronger degree of cohesion between them, because they ‘touch’ or attract each other at many points.

Another crucial factor for the chemical evolution of complexity is the reversibility of the non-covalent bonding between molecules; reversibility is the key to self-assembly. And once a stable self-assembly has got created (through molecular trial and error), generally there is no ‘looking back'. The overall large cohesive energy has a stabilizing effect.

But there can still be a looking forward: If the environment changes, the self-assembled system can respond (i.e. adapt) by again exploiting the reversible nature of its non-covalent interactions. This is chemical evolution. As we shall see in due course, chemical evolution has led to biological evolution. And evolution and emergence are the hallmarks of complexity.

I conclude this post by mentioning vesicles, which provide a good, even dramatic, example of self-organization in nonliving complex systems. Vesicles are spherical supramolecular assemblies separating an aqueous interior volume from an external solvent by means of one or more lipid bilayers. Vesicles can form naturally, or they can be prepared artificially. The later are known as liposomes.

Given the right conditions, lipids can self-assemble into giant vesicles the size of biological cells. The basic driving force for their self-assembly is the hydrophobic interaction. As vividly described by Menger & Gabrielson (1995), vesicles can mimic the living cell in many ways, even though they are not living entities:
When a giant vesicle, which happens to have a smaller vesicle inside it, is exposed to octyl glucoside, the smaller vesicle can pass through the outer membrane into the external medium (‘birthing’). The resulting injury to the membrane of the host vesicle heals immediately. Addition of cholic acid, on the other hand, induces a feeding frenzy in which a vesicle grows rapidly as it consumes its smaller neighbours. After the food is gone, the giant vesicle then self-destructs (a case of ‘birth, growth, and death’). Such lifelike morphological changes were obtained by using commercially available chemicals; thus these processes should be assigned to organic chemistry, and not to biology or even biochemistry.

Saturday, September 8, 2012

44. Of Locks and Keys in the World of Molecular Self-Assembly

The big question is: How could the very long molecules like RNA and DNA get created on their own? I begin answering this question by first introducing the basics of molecular self-assembly and chemical evolution.

The lowering of free energy at the atomic or molecular scale occurs as follows: If two atoms are close to each other, they will bond together to form a molecule if the molecule has a lower free energy than that of the two separate atoms.

Next, let us consider the possible bonding among molecules to form still larger assemblies (or ‘supramolecular aggregates’). Things get more interesting now. The important concept of MOLECULAR RECOGNITION becomes operative here: Those types of molecules are likely to form assemblies or aggregates which have a certain degree of mutual complementarity.

There are two types of complementarity to consider: That of lock-and-key-like shapes, and that of complementary charge distributions (remember, positive charge attracts negative charge). These complementarities, if present, enable portions of two molecules to fit snugly into each other, thus lowering the overall potential energy, and thence the free energy, by a fairly large amount. This is a more stable configuration because thermal fluctuations or other perturbations are less likely to knock the snugly-fitting (and therefore more tightly bonded) molecules apart. This is the essence of chemical self-assembly in Nature.

Self-assembly of supramolecular aggregates is like crystal growth, except that the end product carries a lot more information; i.e., it is more complex.

The role of molecular complementarity was discovered by the Nobel Laureate Paul Ehrlich. As a student he was working on the newly discovered aniline dyes, which he used for staining biological cells. He found that each dye stained only a particular type of tissue or a specific species of bacteria, and not others. What happens is that the dye molecule moves around in the solution till it finds a 'binding site' nicely fitting (complementing) the shape of one of its side chains, like a key fitting its own lock. For better binding the complementarity of such a ‘lock’ and ‘key’ should be not only spatial, but also electrostatic; otherwise the 'specificity' is not very strong: Not only the two shapes should be complementary, even the regions of positive excess charge on one molecule should be complementary to regions of negative excess charge on the other molecule.

Here are some examples of spatial and charge complementarity in Nature:

  • The complementarity between the active site of an enzyme and the substrate of the enzyme.
  • The well-known ‘base-pair complementarity’ between DNA strands (cf. Part 43).
  • Self-assembly of viruses and subcellular organelles.
  • Receptors located on the surface of cells only binding to a very limited number of substrates (often only one). The receptor is typically much more complicated (larger) than the substrate (hormone) that binds to it.
Let us remind ourselves that supramolecular aggregates, normally formed under near-ambient conditions, do not usually involve the strong covalent interaction. Instead, they are governed by weak, i.e. noncovalent or secondary, interactions (van der Waals; weak-Coulomb; hydrogen bond; hydrophobic; etc.). This means two things:

(i) The aggregates are stable if the ambient conditions do not change too much.

(ii) If the conditions change, the bonds in a supramolecular assembly at or near room temperature can get readily broken and re-formed, until the system has found its new stable configuration. Near-reversibility of bonding is a very important feature of self-assembly through molecular recognition.

Biological and other 'soft' materials can self-assemble into a variety of shapes, and over a whole range of length scales. There is usually some amount of water present, and the most important factors mediating molecular self-assembly are the hydrogen bond and the hydrophobic interaction.

We owe our lives to the hydrogen bond. Life and its evolution depend on the hydrogen bond. This bond is much weaker than the covalent bond, and yet strong enough to sustain self-assembled biological structures, enabling them to withstand reasonably well the disintegrating influences of thermal fluctuations and other perturbations. Hydrogen bonding, and the associated hydrophobic interaction, has the right kind of strength to enable superstructures to self-assemble without the need for irreversible chemical reactions. And yet, under appropriate conditions, there is a strong element of reversibility associated with these weak interactions, enabling the spontaneous making and breaking of assemblies until the lowest-free-energy configurations (lock-and-key arrangements) have been attained.

Incidentally, self-assembly per se is a far more ubiquitous phenomenon than just molecular self-assembly. Some examples are: crystals; liquid crystals; bacterial colonies; beehives; ant colonies; schools of fish; weather patterns; even galaxies.

Self-assembly may be either static or dynamic. The former occurs in systems which are in local or global equilibrium, and which do not dissipate energy (e.g. crystals). Dynamic self-assembly is more relevant from the point of view of evolution of complexity, and always involves dissipation of energy. Here are some examples: oscillating and reaction-diffusion reactions; weather patterns; galaxies.

I conclude by considering the example of the tobacco mosaic virus (TMV) to illustrate the hazy, perhaps nonexistent, line between life and nonlife. Any virus (including TMV) typically has an RNA core and a protein coating. It is possible to separate these two components, and purify and store them in the laboratory. At any later time the components can be mixed and incubated, and the TMV gets reconstituted by self-assembly. The reconstituted TMV thus not only comes back to ‘life,’ it can even reproduce itself if placed on a tobacco leaf!

Watch this video for an example of the importance of complementary molecular shapes.