The Biosphere
The biosphere was originally defined as the place on Earth's surface where life dwells. This seems a slightly
restrictive definition, though quite applicable in the light of available knowledge when the term was coined in
1875. I shall use a more natural definition - as that region of a planet where life grows. This includes the
surface of the land, the oceans and other water bodies and the subterranean caves and rocks in which
bacteria have been found to thrive several kilometres beneath the Earth's surface. It also includes the air,
including the clouds where certain bacteria apparently multiply and contribute to the seeding pf rain droplets.
Thus, the Earth's biosphere, as currently known, extends from about 5 km beneath the Earth's surface to the
top of the troposhere (that region of the Earth's atmosphere which animals breath and which contains the
Earth's weather systems) at 10-17 km above the Earth's surface. Life extends to the bottom of the deepest
ocean trenches (the Hadal Zone) of which the Marianas Trench is the deepest at about 11 km, and probably
some distance in the sediments and rocks beneath this. Thus the biosphere spans a hollow sphere from about
5-15 km depth to 10-15 km height (say 15-30 km in thickness). This is still quite thin in real terms.

The Gaia hypothesis states that: all organisms and their (inorganic) surroundings on Earth are closely
integrated to form a single and self-regulating complex system, which maintains the conditions for life on Earth.

One of the hallmarks of Nature is the complexity of living systems. For example, when we look inside an animal
body we find a complicated system of organs and tissues, coordinated by a myriad of hormones and nervous
pathways. Looking inside a single cell we find a phenomenal array of nano-machinery in which large molecules,
such as proteins, work together to sustain life, being coordinated by electrical waves within the cell and a
complex system of chemical messengers that pass signals from one part of the cell to another. What is also
apparent is the sensitivity of such systems, an animal has a rich variety of complex sense organs to detect and
analyse the patterns of energy in its environment, be they complex mixes of sounds, information encoded in
light or other forms of energy. As we have learned more about plants, and other living kingdoms, it has become
apparent that they too are very sophisticated and sensitive creatures, tuned to their environments in
astonishing ways. A single cell has a complex arrangement of receptors for detecting signals from nearby cells,
and neighbouring cells may be electrically coupled (via gap junctions) and cells respond to touch, light and
chemicals in their environment. Virtually all cellular organisms studied have internal clocks that reset
themselves according to external light-levels, temperature and other so-called zeitgebers (German for
'synchronisers'). These clocks enable living systems to operate in harmony with the natural rhythms of the
Earth.

Cycles of nature

What is not so obvious, from our anthropocentric point of view, is that living systems are well-organised on
much larger scales. For a long time it has been recognised that ecosystems respond and adapt as their
organisms respond to one-another and to non-biotic stimuli (temperature, light, etc.). It is surprising, therefore,
that the Gaia hypothesis, developed by James Lovelock and Lynn Margulis, encountered so much initial
resistance from the scientific community. Developed in the 1970s it was probably ahead of its time, but I
suspect that the problem is also to do with the limitations of human perception. It is easier for people to
understand that components of their own bodies closely interact - they have senses feeding back information
to their consciousness, and they are aware that their bodies are physically compact with all parts close
together. For centuries human beings regarded themselves as the pinnacle of evolution, the maximum of
complexity and order. It has become increasingly obvious, however, that ecosystems are indeed very
well-organised and that although organisms appear as individuals to our eyes, there are indeed strong
connections between them and between them and their inorganic environments. This has led many to question
the meaning of an 'individual'. Consider a colony of ants, which has been described as a 'superorganism'.

We now know that ecosystems are composed of 'circuits' in which material flows to be recycled by living
organisms. Nature is ever efficient. One classic example of such an 'integrated circuit' is the nitrogen-cycle.
In this cycle, nitrogen  is incorporated into living cells, as a key element and building block of proteins and
nucleotides and certain other vital molecules. The numbers in brackets refer to the oxidation state of the
nitrogen (for the chemists). When the nitrogen is oxidised, then its oxidation number increases, but when it is
reduced its oxidation state decreases. (Remember: OIL RIG - oxidation is loss of electrons, reduction is gain of
electrons).

  • Nitrogen is essential to all known forms of life on Earth. It is a key element and building block in nucleic
    acids, like DNA, and proteins (polymers of nitrogen-containing amino acids).

  • Excess nitrogen (generated from amino acid metabolism) is excreted (initially from the cells as
    ammonia, but in some organisms this is converted into urea, uric acid and/or other nitrogen-containing
    compounds prior to excretion, and turned back into ammonia by bacteria).

  • Organic nitrogen is also locked up in the tissues of dead organisms and bacteria are largely
    responsible for recycling this nitrogen, as part of the decay process, ultimately converting into a form
    that other organisms can assimilate again.

  • This process whereby bacteria convert organic nitrogen into ammonia is called ammonification and is
    an example of hydrolysis (requiring water as a reagent to break-up or lyse the organic molecules).
    Pseudomonas is an example of a bacterium that carries out such reactions as part of its metabolism.

  • Ammonia is toxic to most living cells and so they cannot assimilate ammonia. Fortunately, other bacteria
    can oxidise the nitrogen in ammonia into less toxic forms, as nitrite and nitrate. This is the process of
    nitrification. Nitrite is unstable and quickly metabolised/oxidised into nitrate.

  • Some nitrate is assimilated by plants, being absorbed by their roots and so converted back into organic
    nitrogen. However, in oxygen-poor soils and sediments, certain bacteria can use nitrate as an oxygen-
    source. In this process of respiration, the nitrogen in the nitrate is reduced, in a process called
    denitrification, which eventually produces elemental nitrogen gas.

  • Nitrogen fixation is the process whereby gaseous atmospheric nitrogen is converted back into organic
    nitrogen. Plants can not assimilate nitrogen directly, but some have symbiotic bacteria that perform this
    role, for example the rhizobacteria in the root nodules of legumes. Cyanobacteria are also major
    nitrogen-fixers.

Not shown on the diagram are the various abiotic processes that also contribute to the nitrogen cycle. For
example, lightning can trigger nitrogen and oxygen to react, forming nitrogen oxides, which can combine with
water to form nitrous and nitric acids, which falls in rain and reacts with minerals to form nitrates. Human
activities have also had major effects, such as the presence of nitrogen oxide pollutants in fossil-fuel
emissions. The detailed biology and chemistry of the nitrogen cycle is  a very complex and fascinating topic,
and a future article on this topic is planned.

There are other elemental cycles operating in Nature, the most apparently significant of which are the carbon,
water and oxygen cycles, but there is also a sulphur cycle and even a mercury cycle. All these cycles heavily
involve living organisms which largely drive the cycles. Consider the oxygen cycle, it is well-established that
the primordial earth had very little elemental oxygen - oxygen is a very reactive element and in the hot
conditions of the early Earth reacted to form oxides, including water (most of which was probably later lost,
with new water arriving in impacting meteorites and comets). Photosynthetic bacteria, similar perhaps to
modern cyanobacteria, were probably the first to produce elemental oxygen in quantity, as a by-product of
photosynthesis. To most bacteria living on Earth at the time, and bacteria were probably the highest life-form
at this time, oxygen was poisonous. Many bacteria today still find oxygen toxic or poisonous and thrive in
anoxic sediments (such as in the mud beneath stagnant ponds). However, oxygen is a useful oxidant in the
energy-releasing biochemical reactions of
respiration, occurring inside cells, and so many bacteria became
not only resistant to oxygen, but began to depend upon it. Humans are ultimately descended from such
bacteria or similar organisms. [Note: I prefer to use the word bacteria in a descriptive and convenient, albeit
old-fashioned, way to include both the eubacteria (true bacteria) and the archaebacteria (archaea, not now
considered bacteria by many).]

Why is it that oxygen levels remain more-or-less constant? Well, they do change slowly over time, but when
oxygen levels in the atmosphere reach about 25%, lightning will probably cause spontaneous fires which
consume oxygen, lowering the level. What about the biotic oxygen cycle? Living organisms are critical for
producing and recycling oxygen, and must play a role in regulating oxygen levels, though it is not easy to
tease apart the importance of abiotic and biotic factors in regulating these cycles.
The boxes below give more information on free radicals, for those who wish to avoid the technical aspects of
the chemistry skip to 'Biogenic origins of bromine compounds' below:
Reactive radicals, especially chlorine and bromine radicals catalyse the destruction of atmospheric ozone.
Recall that a
catalyst accelerates the rate of a reaction (strictly accelerates its movement to equilibrium)
whilst remaining unconsumed by the reaction (though it does of course take part in the reaction). The
catalytic cycle for ozone depletion is summarised below, where X is any reactive radical species (e.g.
Br or Cl free radicals):
Biogenic origins of bromine compounds

Although stratospheric bromine is some 400 times less concentrated than atmospheric chlorine, a bromine molecule is
estimated to be 40-100 times more effective at catalysing ozone depletion. Most atmospheric chlorine is also
anthropogenic, so bromine is more important in natural ozone-regulation, from a Gaia perspective.

Both inorganic and biotic processes contribute to the pool of atmospheric halogens. About 35-54% of atmospheric methyl
bromide (MeBr or CH3Br) is anthropogenic, being produced by a range of processes such as soil fumigation, petroleum
processing and burning organic materials. Most of the rest is thought to be biogenic, some from natural forest fires, but
much being produced by oceanic algae, especially algae in the coastal zones (ref. 6) and polar regions, including Arctic
and Antarctic ice algae (ref. 7).

The function of MeBr synthesis in algae is unknown (and it occurs in both microscopic phytoplankton and larger
macroalgae or seaweeds) but the concentration outside the tissues far exceeds that inside, suggesting that it is either
rapidly excreted or synthesised at the algal surface. Algae have a varied chemistry processing compounds containing a
single carbon (1C or methyl compounds) and these compounds serve at least one function as
osmolytes. That is they
regulate water entry and exit into algal tissues by osmosis. Degradation of these osmolytes by bacteria produces
compounds like methylamine, methanethiol and DMS (dimethyl sulphide). Compounds like DMS add to the bracing smell
(and associated feeling) so characteristic of coasts. Bacteria that metabolise these 1C methyl compounds are called
methylotrophs (literally 'methyl eating') and they can also process MeBr and DMS (ref. 8). Algae have a phenomenal
ability to extract and concentrate the halogens iodine and bromine from sea water, which contains large amounts of these
halogens, but in very dilute solution. (Chlorine is of course much more plentiful in sea water as chloride salts).

Seasonal effects

The picture is complicated by seasonal fluctuations in these reactions, due to the severe seasons seen at the Earth's
Poles. During the long Polar Winters the air above the Poles cools dramatically. The sharp temperature gradient, moving
from warmer latitudes towards the Poles, generates a persistent winter air vortex above each Pole. Temperatures in these
polar vortices continues to drop, as the cold air becomes trapped inside and if these temperatures reach about -80C
(which they can do at both Poles, though more so in the southern Antarctic polar vortex) then special clouds form at high
altitudes, called
polar stratospheric clouds (PSC). These clouds form initially, not from water droplets, but as crystals
of frozen nitric acid (which later incorporates water ice). These ice crystals are thought to catalyse the breakdown of
CFCs (chlorofluorcarbons, anthropogenic ozone-depleting chemicals) and so generate chlorine molecules, which become
stored inside the ice clouds inside the vortex. These vortices act as
chlorine reservoirs.

When the Spring arrives, the vortices become disrupted by warmer air moving in, accompanied by dramatic temperature
increases. This suddenly releases the chlorine store they accumulated over winter and the sunlight photodissociates the
chlorine molecules into reactive chlorine radicals. The chlorine radicals catalyse the sudden depletion of ozone, causing
ozone dents or holes in the Spring.

What we have in polar springtime is an
ozone depletion event. In this article we are primarily concerned with the role of
bromine, as this is the major biogenic or naturally occurring halogen. However, stratospheric ozone depletion may be
caused mostly by anthropogenic bromine and also by volcanic eruptions (ref. M.L. 1) rather than by biogenic bromine.
Most biogenic bromine probably gets processed before it leaves the troposphere (though naturally produced methyl
bromide is more stable and could contribute to stratospheric ozone depletion). Bromine is chiefly responsible, however,
for destruction of ozone in the lowest few km of the troposphere. It is this
depletion of tropospheric ozone which is
important in protecting organisms from the toxic effects of ozone.

Accumulation of bromine in winter is likely driven by biological processes

During the Arctic Winter when sea ice accumulates, this ice becomes enriched in bromine compounds. These compounds
are thought to be produced by algae and further metabolised by bacteria, chiefly at the water/ice boundary. Winds will
carry these compounds further across the ice in windblown snow. Thus, over winter, bromine accumulates on the sea ice.

Accumulation of tropospheric ozone in polar regions in winter

The height of the troposphere (the tropopause or boundary between the troposphere and stratosphere) is much lower
over the polar regions and especially in winter. This causes more stratospheric ozone to enter the troposphere (are the
vortices important here?) and so ozone accumulates at low altitudes over polar regions in winter.

Ozone in the stratosphere may be a good thing, but low-altitude ozone is toxic. Indeed, anthropogenic emissions of ozone,
e.g. in car exhausts, helps catalyse the formation of smog in cities and is a major respiratory irritant thought likely
responsible for many thousands of deaths each year.

Ozone depletion events in spring

Thus, bromine accumulates on the surface of ice in winter and ozone accumulates at low altitudes. In the spring, sunlight
will thaw some of this sea ice, including any bromine deposits, especially on the surface. This results in a springtime
bromine explosion as bromine levels in the lower troposphere suddenly increase. Although high levels of bromine are
toxic, this bromine has one key advantage to life - it destroys the toxic ozone in the troposphere. Furthermore, since
bromine is a catalyst, it needs only be present in tiny (and so non-toxic) amounts in order to do this, and in real terms
bromine concentrations remain low, so life is protected. One of the products of this ozone destruction is the normal
allotrope of oxygen, O2, which will be recycled by the
oxygen-cycle.

What happens to the bromine?

Some of the bromine will eventually be returned to the sea in the bromine-cycle, e.g. by falling to the sea as
hydrobromic acid in rain. See the following external link for a good diagram and description of the
bromine-cycle:
http://www.people.fas.harvard.edu/~parrella/research.html.

Coupling between cycles

One of the key requirements for Gaia is that the geochemical cycles of Nature link together. There is no doubt that
biological activity drives these cycles and so maintains elements in the states required for life, e.g. by making nitrates
available to plants or removing toxic mercury and ozone. For the system as a whole to operate in an intelligent manner,
these various
cycles must link together. By intelligent we mean a system which processes information (inputs) and
generates the appropriate outputs and maintains a suitable balance by homeostasis.

The bromine explosions and ozone depletion events are good examples of how homeostasis is achieved by linking
together two cycles, the oxygen and bromine cycles, with atmospheric ozone and bromine levels fluctuating seasonally,
but remaining near to a homeostatic set-point over the millenia. In the normal usage of the word, these cycles maintain
the biosphere in an 'equilibrium'. However, this term has different meanings in science, in which equilibrium is usually
taken to be a state of reaction completion and in which life is viewed as a process 'out-of-equilibrium' or in 'disequilibrium'
maintained by a constant input of energy. We can think of such a disequilibrium as a kind of high-energy
quasi-equilibrium which can be maintained for a long time but not indefinitely. The Sun provides most of the energy
fueling the biosphere, and the Sun has a life-span of about 10 billion years, but will eventually cease to burn and Earth
will collapse into a lower-energy equilibrium state (indeed it may be incinerated!). In this view, the whole Universe can be
regarded as a temporary state of disequilibrium which began with the Big Bang.

That the cycles do link together in an intelligent way is irrefutable. What remains to satisfy the Gaia hypothesis fully is a
fuller quantitative analysis of how strongly these cycles couple together and so gain a measure of how intelligent the
system as a whole is. It should also be remembered that these cycles work over very long periods of time, which further
adds to the conceptual difficulty in evaluating their effectiveness.

These links are still not well understood, and this may well fuel much scepticism about Gaia. However, we only need to
look at Earth's nearest neighbours to see what happens when biological activity does not drive geochemical cycles, at
least not in any major way.

Modelling Gaia

Any scientific theory is only of value if it makes predictions which can be tested. The study of Gaia focuses in large part
on the atmosphere, since this is the primary life-support system of the Earth. Atmospheres are notoriously complex to
model mathematically, physically and chemically. However, as in any modeling process one starts with the simplest
possible model that captures the essence of a problem, then one tests its predictions and if there is a significant mismatch
between the model and our empirical observations of Nature then we refine the model, which usually means adding
another layer of complexity to it. This approach ensures that our model is no more complicated than it need to be to give
us the predictions we want and it also enables us to better understood atmospheric processes by evaluating which factors
are most important and which factors are minor. The success of much of modern science in modeling complex systems
relies on the fact that the major behaviour of a system can usually be modeled by incorporating relatively few components
or complexities.

One of the methods used to model such systems, and that used to model the bromine explosions (refs. 2-5) is the method
of cellular automata. A
cellular automaton is a numerical or computational model in which the system under study is
divided into a network of discrete units or 'cells' arranged on a regular grid (in any number of dimensions), for example
the troposphere over the Arctic could be divided into such a grid of cellular spaces. This saves on computation, since it is
not feasible to model every point or molecule in at atmosphere! The size of each cell is carefully chosen so as not to
introduce critical errors into the model - it needs to be small enough to be accurate but not so small as to waste
computation time. We start the model running with each cell in an initial state and then we advance time in discrete units,
for example days. At each time-point (e.g. day) we recalculate the parameters of interest in each spatial cell, for example
we calculate the BrO levels, based on how the cell interacts with its neighbours (i.e. whether BrO flows into or out of it).
We can define neighbouring cells to be those adjacent to the cell of interest or those within a specified distance. We might
look at the rate of generation and destruction of BrO in each cell, and also the extent of movement of BrO from one cell to
its neighbours. This method is an approximation, since all cells will be affecting their neighbours at all times, but so long
as the jump in time is not too great then the model will be accurate (and there are well-defined ways to estimate the sizes
of such errors).

Another related method that is used is
network theory. In network theory we divide the system into discrete 'lumps'. For
example, in a chemical reaction each lump could be a chemical species (e.g. Br, BrO, etc.) and these lumps are
connected by arrows that determine the rate of transfer of material (e.g. bromine atoms) from one state or lump to the
next in the sequence. It is important, in order to complete the calculations, to consider
conservation of material - in our
reaction bromine atoms are neither created nor destroyed, and so they are conserved, meaning that the total number of
bromine atoms remains constant. (Though we could add sinks and sources if we need to).

These numerical models simplify the equations, but the number of calculations is immense and computers must be used.
Mathematical skill is also required to understand, estimate and control the various possible sources of error.

For example, bromine explosions and their coupled ozone-depletion events have been modeled (see ref. 5) assuming a
constant number of bromine or BrO-emitting nodes over a circular area over the Arctic. The predictions of this model
match well the actual measurements showing the seasonal rise and fall of BrO levels as the strength of the BrO-emitting
nodes varies. However, this model does not produce the variability in BrO levels typically seen day-to-day in recorded
measurements. Adding the additional complexity of statistically varying the number of emission nodes over time
(according to a Gaussian distribution) produces more realistic variability. However, the main source of bromine is the
Arctic sea/ice boundary and this has been modeled more accurately as a wobbling ring centred over the Arctic, to better
model the Arctic basin and continental shelves and the seasonal fluctuations in sea ice. This model gives more accurate
predictions, matching past measurements which show the BrO levels as concentrating in a ring around the Arctic.

Other planets

Mars is generally a dead planet. That does not mean that no life exists there, but certainly there is not a great deal on the
surface, for Mars is almost entirely desert. There may be life on the valley floors, or in other regions beneath the soil
where there is liquid water, or indeed in subterranean rivers and caves. So what went wrong with Mars? Mars is much
smaller and lighter than the Earth and most of its primordial atmosphere has certainly escaped into outer space. The
Earth slowly leaks gases to outer space as some molecules acquire enough energy to escape Earth's gravitational field.
On a planet like Mars this process is much more rapid and so Mars today has a very thin atmosphere. There is plenty of
oxygen on Mars, but it is locked up as oxides, indeed oxides of iron (similar to rust) give Mars its reddish-brown
appearance. However, clouds of methane gas have been detected on Mars. These must come from reservoirs beneath
Mars' surface. This methane could be purely chemical in origin, though it could also be due to life beneath the surface,
perhaps some sort of bacteria operating a carbon or methane cycle. For whatever reason, Mars has failed to sustain a
complex biosphere like that on Earth and has tended toward an equilibrium state, with little atmosphere and water frozen
as permafrost beneath the surface and oxygen locked up in rocks.

Venus is quite another story. It has a very thick atmosphere, and certainly no likely living thing, especially not near the
surface with its soaring temperatures. Lacking a biological carbon-cycle, Venus' atmosphere has reached an equilibrium
of sorts with an atmosphere of mostly carbon dioxide! This in large part accounts for the surface temperatures of Venus
due to a run-away greenhouse effect, though water vapour may have driven this warming earlier on in the planet's
lifetime. The high temperatures maintain high carbon dioxide levels by breaking down carbonate rocks, releasing carbon
dioxide and the whole seems to have spiralled away in a positive-feedback cycle that raised the planet's temperature.
(Although positive feedback can occur in the normal cycles of living organisms, it usually represents a loss of control and
negative feedback is more characteristic of living systems).

Titan, Saturn's largest moon or satellite and a 'planet' in its own right by virtue of its size, as a final example is especially
interesting. It has lakes of liquid hydrocarbons and rocks of ice due to its very low surface temperatures. There is a
hydrocarbon-cycle operating on Titan, as it has a dense atmosphere of nitrogen with hydrocarbon clouds and
presumably some sort of hydrocarbon precipitation. There are no obvious signs of life there, though there may be a
sub-surface hydrocarbon ocean and/or a warmer subsurface ocean of liquid water. Could it be that this world's cycles are
biologically driven? The current opinion is that Titan has maintained a complex geosphere due partly to its very low
temperatures preserving its primordial atmosphere, much in the state that the prebiotic atmosphere of Earth may have
been. Also, it is maintained in disequilibrium by a source of energy due to tidal heating resulting from the massive tides
generated by Saturn. It is thought that the atmosphere and lakes of Titan are subject to considerable seasonal
fluctuations.

The value of the Gaia Hypothesis in the search for extraterrestrial life

One of the main aims of current astrobiology is to identify far-away planets that may likely harbour life simply by observing
the electromagnetic
spectra of these planets. By observing the range or spectrum of wavelengths of light reflected or
emitted by planets it is possible to determine many things, including the elements and compounds that constitute their
atmospheres, temperatures and rates of rotation. The hope is to detect the signatures of water and oxygen, combined
with a hospitable temperature. However much this may indicate habitability, discerning whether or not life has actually
evolved on such a world is another matter. Some believe that life is likely to evolve wherever it can if given long enough,
others are less certain of this. It may be that water and oxygen are part of complex cycles, driven, steered or regulated by
living processes, or they may be simply abiotic cycles (perhaps like the hydrocarbon cycle on Titan?). What we need are
better indicators of life, and it seems to me that one such possible indicator may be coordinated and periodic fluctuations
in atmospheric composition about a set-point. Supposing a planet was found that contained oxygen in its atmosphere.
Now supposing some of this is present as ozone and supposing observations could reveal seasonal and coupled
fluctuations in bromine and ozone levels in the polar regions. This is far more likely to indicate the presence of life in my
opinion, since it indicates a regulation of atmospheric content that is beneficial to life. Such indicators are not simple to
derive, but further research and modeling into Gaia and atmosphere dynamics might produce a set of such indicators.

The Gestalt hypothesis and emergent cooperative behaviour

The Gestalt hypothesis, originally developed in psychology, states that: the whole is greater than the sum of its
parts
(when stated as a general principle). This notion is becoming increasingly important in many aspects of science,
particularly in the study of intelligent systems. Consider consciousness, for example, which is widely held to be an
emergent property due to the way brain cells interact with one-another. (Others consider consciousness to be a
fundamental property of matter in much the same way as mass and length, and just as fundamentally elusive to our
understanding). In the study of neural-networks, computer researchers and neurologists see more complex patterns
arising in such networks than could be easily predicted. Science has traditionally taken a reductionist approach, assuming
for convenience that the whole system is nothing but the sum of its parts. Whatever the flaws in reductionist thinking,
science is now beginning to put systems back together again and realising the truth of the Gestalt hypothesis. Examples
of emergent behaviour include social behaviour in microscopic algae, which can be modelled purely by assuming that
each individual unicellular alga is behaving in a
selfish manner. Thus, the laws of physics do indeed predict emergent
behaviour, but doing so is difficult and frequently requires computational models.

Animal societies, including primate societies, are now considered to have evolved as a result of selfish motives -
organisms sometimes need one-another but some will try to teach by gaining assistance without reciprocating, so a
general principle states: 'Scratch my back and I'll scratch yours.' The
Selfish Gene Theory takes things a step further
and says that
DNA is ultimately selfish and uses cells and organisms merely to replicate itself, because if it didn't it would
cease to exist. (Note that such 'selfishness' does not justify anti-social behaviour as 'selfish' commonly means.) The pros
and cons of such theories deserves a separate article, but in Gaia we can envisage organisms (or their genes) behaving
in a selfish manner and
complex patterns of useful behaviour arising from their interactions. Such systems require
mathematically complex models, as the interactions make the equations non-linear and very hard to understand
intuitively. For example, consider the motion of a pendulum. This motion is regular and quite easily described
mathematically. However, if you have two pendulums attached end-on-end in series, or an iron pendulum swinging above
two or more magnets, then their motions become extremely complex. Every time you start them running you would see a
different pattern of behaviour, as if their motion was unpredictable or chaotic. This is the essence of
Chaos Theory.
However, their motions are perfectly predictable mathematically, it's just that starting them from any two different positions
that differ by an imperceptible amount would result in massive differences in their motions - the system is very sensitive to
initial conditions. However, such systems, especially when made more complex, have certain stable states to which they
tend, called
attractors. In this way such systems can exhibit apparently very ordered and stable bahaviour. In very
complex systems this behaviour can be intelligent - disturb the system (but not too much!) and it will find a path back to its
attractor - it maintains itself in homeostasis.

The importance of life in geochemical cycles

Thus, it is quite natural to see intelligent behaviour emerge from complex systems, be it the cells in an organism's body,
the brain, an animal society, selfish genes interacting, or the Earth's biosphere. Considering the complexity of Earth's
biogeochemical cycles, we would
expect intelligent behaviour to emerge (and if it didn't we would probably not be here to
ponder it!). In this way the Gaia hypothesis is a very sound and reasonable hypothesis. What remains, as I have said, is
to work out all the 'circuits' and assess how intelligent they are. Intelligent systems could exist on a dead world, like
perhaps the geochemical cycles on Titan, but to sustain life those systems have to be more finely tuned and life seems
well placed to effect control over these processes. Research is continually turning up more roles for life in geochemical
cycles, and processes once thought to be totally abiotic are now understood to be effected by living things. For example,
bacteria accelerate rusting and the weathering of desert rocks. Many mineral deposits may have been formed, at least in
part, by microbial action. Bacteria are partly responsible for the formation of crude oil by the slow decomposition of plant
remains and many subterranean caves were probably etched by sulphuric acid secreted by bacteria (e.g. see Engel
et al.
2004).

Micro-organisms are implicated in regulating the salinity of Earth's oceans. Rivers constantly deliver salts, from eroded
rocks, into the sea, and yet salinity is maintained at a level suitable for life. Of course, physical processes alone might be
able to achieve a balance, with salt somehow being precipitated out of the water column and deposited, but life could be
and probably is also responsible. That isn't to say that the control systems cannot be broken. The Dead Sea has grown
saltier and saltier due to evaporation of water leaving salt behind and the lack of mixing with other bodies of water.
However, even in the Dead Sea live some bacteria live (but not much else, just a few other microbe types). In
hypersaline lakes like this, one of the bacteria types most frequently encountered are the Halobacteria. These
salt-loving bacteria (halophiles) actually
accelerate salt-crystal growth, acting as crystal nucleation sites. The bacteria
may become encased inside salt crystals, in which they can live for several years. This illustrates a possible
salt-regulatory mechanism, removing salt from solution.

The more geochemical processes have been elucidated, the greater the role of microorganisms in these processes has
been found to be. It is likely that more roles for life in geochemical cycles will become apparent in future.

What motivates organisms to work together to sustain an ecosystem?

Organisms exist, from a practical point of view, because otherwise they would not! This odd statement is actually the
essence of life and survival of the fittest, since forms that are not fit disappear whilst fitter forms persist. Of course it is not
so black and white, relative fitness is important, since organisms have a tendency to compete with one-another and the
fittest from what is available is generally the best suited for survival and so has a higher probability of outlasting the
others. Organisms can also avoid direct competition (and often do so) by occupying different ecological niches, that is by
doing different 'jobs' or utilising different food sources. By 'fitness' we really mean the ability to reproduce and so persist
over time. What does the persisting? On one level it is the DNA that is passed from generation to generation, but more
exactly it is the information that encodes the pattern of life that persists.

Richard Dawkins, in his compelling book, 'The Selfish Gene', explains how it is the gene, or unit of inheritance that
persists and so the organism is effectively merely a vehicle for these genes. In molecular biology, a gene is defined as a
sequence of DNA that codes for one functional building block of life, usually a polypeptide or protein. In actual fact the
original definition of 'gene' was simply: the unit of inheritance. Now we know that most (though not all) inheritance is
through the DNA (there are some examples of other forms of inheritance). A gene will succeed if it finds ways of
preserving and so replicating itself. To be more precise, it is the information carried by the gene that matters, and so
when a gene exists as many copies then they all have equal importance and if one gene copy dies to ensure that two
others survive, then the gene has a winning strategy. This is the genetic basis of kin selection - the tendency for an
organism to risk its life to save those who are closely genetically related to it. A mother may be prepared to die to save
her children, or a warrior to save his tribe. Our colony of ants behave as a 'superorganism' because the workers are
sisters, and so closely related genetically and kin selection is strong in this case.

Gaia is often seen as the complex behaviour that manifests when organisms strive for selfish purposes. Hence, a school
of fish may show apparent social behaviour, moving as a single entity to evade predators, but in truth each is using its
colleagues to shield itself, and yet this strategy potentially benefits them all. Social behaviour also manifests in colonies of
single-celled organisms that individually follow a selfish course of behaviour.
Insect societies are so well integrated
because the workers are all sisters, and so much more closely related than human beings are within a typical social
group. Hence, an ant, or a bee, is very likely to have many genes in common with her sisters and will more willingly
sacrifice herself to protect them. (However, there is still rivalry and sometimes selfishness even in insect societies). More
specifically, social behaviour evolves not so much because individual organisms strive to selfish ends, but because their
genes do! Even genes form cooperative associations, so again it is not so much individual genes that are selfish, but
patterns of genes, that is: information itself!

The key point is that life is all about preserving information. Of course that information changes over time, enabling
evolution, but nevertheless it is the tendency for that information to persist in whatever form is relevant that characterises
life. If this information was erased, then life would cease. Life is all about information storage and processing. Each cell
has inner biochemical and electrical circuits that receive and process information from the environment and attempt to
compute an appropriate output. The brain of an animal is also a computer. On the cellular, tissue, organ and organism
levels, life is a computational device. Why then should we be so surprised to learn that ecosystems, natural cycles and
even the whole biosphere also function much like computers? The validity of the Gaia hypothesis seems to me a natural
expectation from what we know of living systems.
Similar reactions occur for chlorine and methylhalides (methylchlorine, methylbromine):
References and Bibliography

1. A.S. Engel, L.A. Stern and P.C. Bennett, 2004. Microbial contributions to cave formation: New insights into
sulfuric acid speleogenesis.
Geology, 32: 369–372.

2. M. Ludin, 2010(a). Study of the fundamental physical principles in atmospheric modeling based on identification of
atmosphere - climate control factors: part 1, bromine explosion at the polar arctic sunrise. [
http://arxiv.org/abs/0712.
2723] [http://arxiv.org/ftp/arxiv/papers/0712/0712.2723.pdf]

3. M. Ludin, 2010(b). Study of the fundamental physical principles in atmospheric modeling based on identification of
atmosphere - climate control factors: part 2, Gaia paradigm, a biotic origin of the polar sunrise arctic bromine explosion.
[
http://arxiv.org/ftp/arxiv/papers/0812/070812.4797.pdf]

4. M. Ludin, 2010(c). Study of the fundamental physical principles in atmospheric modeling based on identification of
atmosphere - climate control factors: part 3, enforced development of the Earth's atmosphere, physical and
transcendental divisions, physical division: ozone-oxygen transformation in the early atmosphere. [
http://arxiv.
org/ftp/arxiv/papers/1007/1007.4866.pdf]

5. M. Ludin, 2010(d). Study of the fundamental physical principles in atmospheric modeling based on identification of
atmosphere - climate control factors: part 4, stochastic cellular automata simulations of the arctic bromine explosion.
[link?]

6. S. Soemundsdbttir and P. A. Matrai, 1998. Biological production of methyl bromide by cultures of marine
phytoplankton. Lmnol Oceanogr , 43: 8I-87.

7. W.G. Sturges, C.W. Sullivan, R.C. Schnell, L.E. Heidt and W.H. Pollock, 1992. Bromoalkane production by Antarctic
ice algae. Tellus 45B: 120-126.

8. S.E. Hoeft, D.R. Rogers and P.T. Visscher, 2000. Metabolism of methyl bromide and dimethyl sulfide by marine
bacteria isolated from coastal and open waters. Aquat. Microb. Ecol., 21: 221-230.
Reactive free radicals, such as these, catalyse the destruction of ozone in the atmosphere.
Fragile Ecosystems?

Another aspect of Gaia concerns the fragility of the Earth. The way in which ecosystems consist of many parts that
interact to achieve a complex balance has led to some regarding ecosystems as fragile. This is both true and false,
depending on one's perspective. Certainly, as we have seen, it is easy to destroy a forest or poison grassland or in other
ways reduce biodiversity. In this respect ecosystems are fragile in that they are
sensitive, they respond to changes and
so change themselves. However, the biosphere itself is remarkably robust, it has persisted for some 2-3 billion years on
earth and survived mass-extinction events, such as the Permian-Triassic extinction event, some 250 million years ago,
which destroyed an estimated 96% of marine species and 70% of land-dwelling species! Nevertheless, life on Earth
made a full recovery, but was irreversibly changed. The vast majority of species known to science are now extinct. Thus,
when you hear people say, 'Life is fragile', remember that the life of an individual might be, even whole species come and
go, but life itself has persisted on Earth for aeons, continuing the same chemical chain-reaction, which began when that
first spark of life ignited. Thus, Life,
per se, is actually very robust. People should be concerned, however, for the
environment and what they do to it, since the human race will most likely die-out before life on Earth does, and a change
in environment could trigger that extinction. (The exception might be if humans one day colonise the stars, but that's
another story!)

I do not wish to get bogged down in the politics of the global warming debate, nor do I wish to argue with those who are
convinced that human beings have had and will likely have zero negative impact on the Earth's ability to sustain life. I will
simply state a few facts. Although the Earth's atmosphere is often quoted as 350 km or more in depth, most of this
consists of very rarified ionised gases. The bulk of the atmosphere that is of use to life is the troposphere, which contains
all the Earth's weather systems and the stratosphere above it which contains the shielding ozone-layer. The troposphere
varies in depth from about 10 to 17 km, a modest walk in distance. However, the drop in air pressure and density with
height means that an altitude in excess of as little as 2.5 km can readily cause altitude sickness. To be blunt,
the Earth's
atmosphere is thin
! There really is not a lot of it! It is only the continual recycling of that atmosphere by inorganic and
more critically organic processes that maintains it in a composition suitable to animal life. Dry land occupies some 30% of
the Earth's surface and much of this has seen deforestation and urbanisation, coupled with urban pollution and potential
damage to the capacity of the Earth to recycle its atmosphere. On Earth today we also see massive pollution and
ecological damage to marine habitats, especially those near the coast, which are the most nutrient rich and hence the
most important to the biosphere. It does not require a leap of faith to realise that humankind needs to be concerned
about its treatment of the biosphere and to realise the prudence of reducing emissions and ecological damage even
before the scientific analysis is complete! Of course the Earth has suffered severe climate and atmospheric changes in
the past, including global pollution from super-volcanic eruptions, but note that these events are typically accompanied
by mass extinctions and the fossil record tells us that large animals, like human beings, are often the most prone to such
extinctions. The pertinent question is not, 'Will human activity destroy life on Earth?', but rather, 'Will humankind survive?'

Conclusion

The Gaia hypothesis states that: all organisms and their (inorganic) surroundings on Earth are closely integrated to form
a single and self-regulating complex system, which maintains the conditions for life on Earth.

We have seen that organisms and their environments (organic and inorganic) are indeed closely integrated, this is the
basis of ecology. We have seen that the cycles of Nature are interlinked, and may have global consequences. We have
also seen how these cycles maintain conditions on Earth for life as we know it. What then remains to be demonstrated in
order to validate the Gaia hypothesis? In a sense, the hypothesis is already established as true. However, there is still
some uncertainty about the 'strength' of Gaia. More research is needed to answer questions like: To what extent can life
alter environmental conditions to make them favourable for itself? How would cycles, such as the nitrogen cycle, differ in
the absence of life? In other words we need a better understanding of the amount life contributes to regulating the
environment so we can draw up better developmental models of planetary systems in a) the presence of and b) the
absence of life. We also need a better understanding of the biochemical processes that affect the environment, for
example, a thorough understanding of how microbes metabolise bromine, crude oil and the various minerals whose
deposits are so valuable to us. Such knowledge would enable us to better understand how humans are affecting the
Earth's biosphere and resolve such issues as the consequences of anthropogenic carbon dioxide emissions. It would
also help us to better model alien planets and so refine our search for extraterrestrial life. Finally, but by no means least,
such studies have intrinsic scientific value in their own right.
The Philosophy of Gaia - Emergent Complexity

Complex systems, such as the Earth's biosphere can be
described as a higher level of physics which emerges from the
standard accepted basic laws of physics. It is becoming
increasingly apparent that physical laws, by which I mean the
fundamental rules of nature rather than our mathematical
models of these phenomona, result from symmetries 9or
broken symmetries) inherent in nature. In other words we are
describing patterns, and these patterns contain information.
For example, if in a chequer pattern, like on a chess board,
the squares are 3cm across, then this is a rule or law that
describes one attribute of this pattern. Whether or not these
natural laws are exact or approximate is another matter, and
this enters the debate on whether the Universe is fundamently
detrministic or non-deterministic, and is a matter we plan to
address in a future article on Cronodon. patterns encode
information (or is it the other way around?). Information
systems, natural or artificial, frequently display a curious
phenomenon - emergent behaviour; in that complex
interconnected systems such as neural networks or the
Internet, display behaviour that would have been difficult to
predict from elementary physical principles (at least without a
sophisticated computer simulation). That is they demonstrate
c
ollective behaviour that is greater than the sum of their parts.
Of course, this behaviour is indeed the result of basic physical
laws, or patterns, but the equations become too complex for
intuitive predictions to be made and so computers are needed
to carry out simulations. (Another example is the swelling of
old stars when they reach the
red giant phase: this can not be
explained intuitively by any single factor, but is due to the
interplay of several factors and is predicted by computer
simulations based on the basic laws of physics).

Mathematical fractals are a good illustration of how simple
equations (simple rules) can produce order from apparent
chaos. In fractals, a starting value is entered into the equation
to generate a new value to enter into the same equation. This
iterative feedback means that intricate solutions emerge, with
slight changes in the initial value often causing considerable
differences in the final fractal, making their final shapes
unpredictable without accurate computation!
Many believe that consciousness is another such metaphysical phenomenon, emerging as a higher physics from the
collective behaviour of neurones abiding by the basic laws of physics. Certainly biology, chemistry and physics today are
full of examples of how such complex behaviour or higher-order complexity arises from the way many 'particles' interact.
Personally, I think that consciousness is an odd case, in that nothing we currently know of in all the laws of physics can
predict or explain consciousness. Even creating a sophisticated neural network which behaved like a human mind would
not establish whether or not that network was self-aware; there is just something about consciousness which science has
so far been unable to get a handle on. It is not surprising, therefore, that some people are tempted to think of the Earth
as an integrated living 'organism' of sorts, which some consider to be conscious. Now we have really entered the realm of
metaphysics, that is philosophy beyond accepted physics, as consciousness currently does. My personal view is that the
Earth might or might not be a conscious entity (I don't think science can have an informed opinion on such matters), but
that the Gaia hypothesis in no way requires this. Rather Gaia requires the Earth to respond like an intelligent system, that
is all. Thus, sceptics who argue against Gaia on the ground that it invokes metaphysics beyond the realms of science are
mistaken. We also have to remember that the connections between neurones in the brain, although similar, are not the
same as connections between organisms in an ecosystem, nor the same as connections between organelles in a cell,
even if certain common patterns occur. Only in the case of the brain do we know that consciousness occurs, from our
own personal experiences, as for the rest we simply don't know. Remember, the organisms partaking in the biosphere do
not voluntarily keep the Earth's ecosystems in balance, they have no such intent, but rather they achieve this aim as an
inevitable and physical consequence of the way they interact with one-another and with their inorganic environments.
A 3D mathematical fractal of the Julia type, generated as
a 3D slice through a 4D fractal based on the 4D
hyperspace cosine function. Is this order from chaos or
chaos from order? Can you spot the asymmetries in this
fractal? (Click image to enlarge). This one makes me
think of growing crystals. A pattern such as this is
generated from precise mathematical rules, and yet it
gives rise to an approximate order, similar in many ways
to the kind of patterns we see in natural systems.
Intelligent Circuits?

The Gaia hypothesis requires that the levels of elements significant to life are regulated by the interplay of
living and abiotic (inorganic) mechanisms. When we look at a human body, for example, its internal
environment is carefully regulated and allowed to oscillate within narrow limits. For example, core body
temperature is maintained at about 37C, the set-point and will usually oscillate only fractions of a degree
either side of this (though the set-point is raised during fever). This careful regulation of the body's systems is
termed
homeostasis and the study of control systems is called cybernetics. For homeostasis to work the
body needs sensors that detect changes, e.g. temperature sensors in the brain, and it needs a way of
sending signals from one part of the body to another, which it does via hormones and the nervous system.
One common feature of these control circuits is
feedback, especially negative feedback, but also
sometimes
positive feedback. As an example, consider regulation of blood sugar levels. When you eat a
meal, especially a sweet meal, sugar enters the bloodstream from the gut and your blood sugar levels
increase. Cells in the pancreas act as sensors, detecting this increase, and then certain cells of the pancreas
release a chemical message into the bloodstream, as the hormone insulin. Insulin instructs muscle, fat and
liver cells to take up more glucose, lowering the blood sugar level. If the blood sugar falls below the set-point
then sensors will again detect this and another hormone, glucagon, will be released to cause blood sugar
levels to rise (by triggering liver cells to release glucose). This is an example of negative feedback: the
sensors constantly monitor changes in blood sugar levels, so that the effects of the control system feedback
information to the sensors. It is negative feedback because the action is taken to counter the sensed change
- if blood sugar rises, action is taken to lower it. It is also illustrates another common feature of control
systems - antagonistic effectors, that is the components that effect change (e.g. the hormones insulin and
glucagon) oppose one-another.

Elemental cycles also incorporate feedback. This feedback largely resides in the living organisms which
respond to environmental changes. A simple example we see regularly are algal blooms. When run-off from
agricultural land, rich in artificial fertilisers, enters the sea or a lake or pond, the algae that thrive on these
nutrients respond by feeding and growing and their population blooms. Unfortunately, they can take-up all the
oxygen in the water (by respiration) and so kill fish and other animals, but ultimately they bring about a
resetting of nitrogen and phosphorous levels by recycling these nutrients. This phenomenon of algal
blooming is called eutrophication (or hypertrophication).


Example of a regulated cycle: bromine explosions and ozone-depletion events

Chlorine and bromine are the main chemicals causing ozone depletion, resulting in the formation of ozone
dents and holes over the Earth's poles. Almost all of the chlorine and half the bromine are anthropogenic.
Some are also produced by natural phenomena, such as forest fires and reactions in the sea, such as those
catalysed by algae.

In Spring (i.e. dawn) in the Arctic there is a transient increase in bromine free radicals in the atmosphere.
These radicals are extremely reactive and react with oxygen to form BrO (another radical) and other reactive
molecules. BrO catalyses the destruction of ozone (it is an ozone sink) in this case in the troposphere. The
troposphere is that part of Earth's atmosphere which extends from the ground to about 15 km and is where
earth's weather occurs. Above this is the stratosphere, where ozone is formed by the impact of cosmic and
solar rays on the atmosphere. Ozone in the stratosphere is beneficial to life, since it screens out harmful UV
radiation, but ozone in the troposphere is generally harmful, since it is toxic. (Refs. 2-5).

A free radical is a chemical species with one or more unpaired
electrons and they are usually highly reactive
since electrons prefer to be in pairs. (The O2 molecule is a biradical, with two unpaired electrons in its ground
state, but is not especially reactive other than that oxygen is a reactive element because of its high
electronegativity).

Free radicals of halogens, like bromine and chlorine, can form in the atmosphere when a source of high
energy (such as lightning) excites the diatomic Br2 or Cl2 molecules, resulting in bond breakage by
homolytic fission. In these diatomic molecules two atoms are held together by a single covalent bond,
which consists of a shared pair of electrons. Homolytic fission is 'even' bond breakage which results in each
resultant atom receiving one of the two electrons and so each Br atom now has an unpaired electron (often
indicated by a dot to one side of the Br symbol).
Trefoil
Cyanobacteria link
Pea-flowers like this trefoil are important in
meadow-land, being legumes they have
symbiotic rhizobacteria living in nodules in their
roots and these bacteria fix elemental nitrogen
into forms that the plant can use. In the old
practise of leaving a field to rest as fallow,
plants like these help regenerate soil fertility by
enriching the soil with usable nitrogen.

To learn more about these and related
legumes, see
meadow flowers.
Cyanobacteria are also important
nitrogen-fixers. Soil recently flooded by
rivers is rich in cyanobacteria, which
enrich the usable nitrogen in the soil,
acting like natural fertiliser. This is one of
the chief reasons why floodplains make
such good arable land.