Evolution is not 'just a theory'

Evolution is a theory. However, it is a theory in the full-bodied scientific sense. This means that it isn't simply a
philosophy dreamed up, but rather it is a rational theory based upon empirical evidence which is in full accordance
with the known laws of nature. It is also a testable theory - experiments and further observations can test and
verify many aspects of the theory and so far the theory of evolution has stood up to all empirical evidence and
experimentation, indeed it is fully supported by these observations. This places evolution on a par with the atomic
theory of matter, or the theory of relativity. Furthermore, evolution remains the only viable scientific theory capable
of explaining this vast body of empirical data.

Like any other scientific theory, the theory of evolution is dynamic. Although it has its main root in Darwin's theory
of natural selection, it is by no means Darwin's theory. Rather, it is a neo-Darwinian theory which is based upon a
much more extensive and modern set of evidence coupled with a more modern theoretical explanation in terms of
natural laws. Darwin did not get everything right, nor did he understand the whole theory as it stands today.
Furthermore, details regarding the mechanism of evolution are still being elucidated and the theory of evolution
will be further modified in future.

Evolution is inevitable

Simple logic demonstrates that evolution is not 'just a theory' but rather that it is inevitable. Evolution depends on
the imperfect transfer of information from generation to generation. The word 'genetic' originally referred simply to
the inherited attributes of an organism. The ancients observed that each type of organism breeds true - a dog
begets dogs, grass begets grass as each organism inherits certain genetic characteristics from its parents. The
ancients exploited this property in selective breeding, for example, to produce 'better' crop-plant varieties. We now
know that the vast bulk (though not all) of this inheritance is due to DNA (deoxribonucleic acid or deoxyribose
nucleic acid). DNA is an information storage molecule, and a very effective one at that. Checking estimates of the
size of the Internet, as of the time of writing in 2011, and bearing in mind that the tiny nucleus of a cell stores the
equivalent of a CD-ROM's worth of data, it can be shown that a memory stick (smart pen or flash drive) based on
DNA rather than silicon could easily store the entire Internet!

DNA is able to replicate, using itself as a template to copy or transcribe the information stored in it. In this way,
when a cell multiplies and produces copies of itself as two new daughter cells, its DNA is necessarily duplicated.
This is a lot of information to transcribe and no information-copying system can be perfect. The fidelity of an
information copying system is the accuracy with which it copies the original information. For example, the fidelity of
a hi-fi (high fidelity) record player is high, so that in copying the music to the electronics and on to the speakers,
few errors are introduced. However, sometimes, in even the highest fidelity system, errors are bound to happen. In
the case of DNA these errors represent various mutations which are passed down to offspring. It is often said that
most mutations are harmful to an organism, in fact they are not, most are neutral and have either no noticeable
effect or only a small effect.

Other information systems, in which many copies are made, mutate over time. Consider a Chinese whisper - as a
message travels down a chain of people, whispered from one person to the next, errors easily creep in, since
whispering is an error-prone replication mechanism. An example (taken from the external web site:
http://www.family-games-treasurehouse.com/chinese_whispers.html) is: 'The moon shines on a windswept beach
near the foggy sea.' After 6-10 copies the final message may become: 'Taboo shoes on a windy beach near the
forty trees', or 'Moonshine, sun and windy bees make a body free.' The remarkable thing about Chinese whispers
is that they usually do not end-up as meaningless sounds, but as meaningful words. Why is this? Surely mutations
are random? What happens is that even if one person hears garbage, their brains interpret best fitting words,
according to the rules of phonetics. The sound 'ees' may be interpreted as 'bees' or 'sees'. The censor of the
brain is guiding the mutation process. In nature, DNA mutates, but if this was totally unrestrained then the end
result would soon be garbage. Just as the brain selects meaningful words and sentences, so natural selection
selects and favours those mutations that are meaningful. Of course, the analogy is not perfect, but the principle is
the same - faulty information replication combined with a restraining principle that keeps the message making
some kind of sense cause evolution or progressive change in the information - evolution is inevitable! It can be no
other way - information is bound to drift in meaning over time, but is not as prone to reduce into random garbage
as one may suppose.

In cells, DNA encodes proteins and RNA molecules, which together form the building blocks of cells. Proteins are
composed of 20 or so different types of amino acid and long chains of these amino acids fold together to form a
polypeptide and one or more polypeptides fold together to form a protein. To a large extent this folding is  
automatic - different amino acids have different types of chemical attraction for one another and also different
shapes. The end result is that the amino acid sequence determines the final shape of the protein, for example, the
protein may be a helix, or a rod, or two balls joined by a flexible hinge, or barrel with a channel running down the
middle of it. The point is that some parts of proteins are more important than others. One protein may operate like
mechanical scissors - certain molecules may fit inside the 'active site' and be cut in two. Clearly changing the
active site may change what the scissors can cut - their shape or 'sharpness' may become altered, indeed it is
easy to blunt a pair of scissors. However, damage to areas other than the blades may be less likely to prevent the
scissors working well. This makes proteins quite resistant to mutations, which may tweak the protein rather than
radically altering it - proteins are flexible and adaptable. Some proteins may even perform auxiliary functions
additional to their main function, and even if an important protein is lost, others may be able to compensate to
some degree. Some proteins may even have non-critical functions, or perhaps no function at all (though if a cell
can find a function for what proteins it has then it will do so or it may switch off the manufacture of a non-functional
protein, either completely or partially, so as not to waste resources in making it. There are many possibilities - cells
are flexible and adaptable. Also, cells often copy genes, so if one copy mutates and becomes dysfunctional, then
the cell is still viable as it maintains a good copy. The faulty copy will continue to mutate and may become a useful
protein that does something altogether different, or it may add to the cell's inherited junk DNA. The point is, that
cells are quite tolerant of mutations and so able to evolve over time.
How can the more complex evolve from the more simple?

Example 1: The bacterial flagellum

When one sees the complex protein-based machinery of even a relatively simple cell, then it is natural to wonder
who such systems might have evolved. A good example is the
bacterial flagellum. A series of proteins work
together to form an efficient engine that enables many bacteria to swim. This rotor includes an electric motor and
a set of wheels that drive a helical 'propeller' shaft.
Gram_negative_bacterial_flagellum
Not all bacteria have flagella - some, including mutants, may live perfectly well without them, but clearly they
can be useful. Some bacteria also possess other locomotory systems, which are generally less efficient or
much slower than the flagella motor, but nevertheless quite useful - any means of getting about is an
advantage! Let us conduct a thought experiment. Many proteins fold to form barrel-like pores, in which a
channel passes through the middle of the protein. Many proteins are also incorporated into the cell
membrane. Some of these membrane proteins form channels that allow useful chemicals, for example ions
like Na+, to enter or leave a cell.

Imagine a series of channel proteins, like the one below, spanning the cell membrane. Each protein has
three channels in this instance, and these channels rotate clockwise as they wind through the protein from
outside the cell to inside the cell.
Imagine that sodium ions, Na+, can fit inside these channels and enter the cell, diffusing into the cell from
salty sea water outside the cell, along a concentration gradient. Outside the cell, in the surrounding sea
water, Na+ will be moving about at random, in random directions and with random velocity, due to their
thermal motion. Once they enter the channel, however, their movement is confined. The ions may knock
against the walls of the channel, but they are guided through the channel, spiralling clockwise as they go.
Now we have gone from random motion to a clockwise motion that has been imparted to the ions, giving
them net angular momentum. Now, since angular momentum is conserved, the ions will tend to push the
protein channel anticlockwise. Since our protein channels are floating in the liquid semi-crystal mosaic of
the phospholipid membrane, they are free to rotate anticlockwise.

Now, imagine several such channels at one end of a cell, all rotating anticlockwise. The cell body will
counteract this motion and tend to rotate clockwise. If the cell is corkscrew-shaped, as are many bacteria,
then this will tend to drive the cell along in one direction (forwards or backwards). As it stands, this mode
of locomotion is not very efficient, but it could cause slow gliding of cells, much like the gliding seen in
many bacteria.

Finally imagine that the cell is secreting another protein, which spontaneously forms a helix (as many
proteins do). Should one of these proteins become chemically bound to our rotating channel, then it will
act as a propeller and allow a cell of any shape to swim through the water, assuming enough motors exist
to exert sufficient force. What we have now is a simple bacterial flagella. Add to this a protein inside the
cell that switches the motor on or off and an adapter protein which already interacts with sensory systems
to interact with this switch and our cell now has a very useful piece of kit, which is, of course, subject to
further refinements. Indeed, we have an electric rotor. In bacteria the flagella rotates and this rotation is in
fact driven by the movement of ions across it, such as Na+ in halophiles, or H+ in other bacteria.

Now, I am not saying that this is indeed how flagella evolved or that this is how they work. In fact several
different mechanisms have been proposed for
flagella rotation. Movement of ions through protein
channels are indeed involved in torque (rotary force) generation in bacterial flagella. Regardless of the
actual feasibility of my thought experiment, understand the bottom line - the molecules that make up cells
are physical entities that interact with their environment, often with 'unforseeable' consequences, but the
cell will make use of these interactions if it can. A good example are the slime jets in gliding cyanobacteria.
These mechanisms may have simply been used initially to secrete slime, but due to the helical
arrangement of molecules in the cell wall (a common configuration in many bacteria) secretion of slime at
one end causes the cell to rotate and so glide along in a corkscrew motion. (
Click to download a pdf which
discusses bacterial locomotion in more detail). What such thought experiments tell us is that we can
indeed build complex systems from simple components by evolutionary means.
Example 2: Evolution of the eye

Another object of wonder to those who ponder how evolution could possibly occur, is the eye. The
apparent complexity of this system and its fine-tuning makes it hard to see how it could have evolved. It
seems as if altering any of its components slightly more often than not damages its performance.
(However, as many people will testify, imperfect vision is better than no vision). So, let us see whether a
thought experiment can build-up an eye step by step.

Most, if not all, living cells are sensitive to light. In many cases there is no known use for this ability, for
example white blood cells respond to light, but there is no known example of how they use this in their
daily functions. All living cells are capacitors - they store electric charge. This is a property of the cell
membrane and the tendency for various factors to result in a difference in electric charge across the cell
membrane. This is important in sensing the environment, as many sensory functions release some of this
small charge, generating electric currents that act as signals to other parts of the cell and possibly to
neighbouring cells. Many organic molecules inside cells absorb electromagnetic radiation, and some
absorb visible light. These molecules are naturally coloured pigments called chromophores. These
molecules arise frequently in organic chemistry and have a number of diverse functions in cells. When a
chromophore absorbs a photon of light, it becomes energised. This energy can be transferred to other
molecules, triggering a cascade of chemical reactions which may even lead to a release of some of teh
stored electric charge in the cell capacitor. Some single celled organisms do just this and are able to
sense and respond to light in this way.

In some organisms, cells in the body wall of the animal may respond to light. This response may be
generic, with all cells responding, or it may be that some cells are more sensitive to light than others and
have become specialised photoreceptors. Cells in the surface of an animal are usually electrically
connected together, so if one cell responds to light then it may pass the signal to neighbouring cells. The
sensory cells may also be nerve cells and then an electrical signal will pass along their 'wires' (axons) to
other parts of the nervous system. In some cases, such specialised photoreceptors, connected to the
nervous system, occur dispersed throughout the body wall, but they may be more frequent where they
are most useful - in the head end. This is the situation with the earthworm.

Now, furthering ordering can produce tight arrays of photoreceptors. It can be useful to have one or more
such array on either side of the head, forming one or more pairs of eyes. By pairing the arrays in this
manner, the direction the light is coming from can be more easily determined. The efficiency of these
arrays will be increased further if they form the lining of pockets - protrusions of the cell wall, which may
protrude inwards - now we have simple eyes! Having the arrays arranged in partial spheres in this way,
increases their ability to determine the direction that light is coming from more accurately. Many animals
have eyes of this type. At this stage, it may even be possible to form a crude visual image.

There may or may not be cells or secreted material covering the sensory cells - after all, biological tissues
tend to be translucent and light can easily penetrate overlying tissues over short distances. Of course,
the laws of physics dictate that if the light passes through overlying tissues that it will be refracted - the
tissues may act as a crude lens, focusing the light to some degree and thus increasing the sensitivity of
the eye and its ability to more accurately determine the direction of the light source. In brittle-stars and
trilobites, the calcium carbonate skeleton overlying the sensory cells of the eyes became transparent -
growing as regular calcite crystals. In the human eye, the cornea and fluids within the eye constitute the
main lens for focusing - the lens proper adds adjustable fine focus.

So you see, organisms alive today exhibit all conceivable stages in the evolution of the eye (a fact which
is being forgotten since not many scientists even study classical zoology any more).
Irreducible complexity?

One of the more rational theories put forward against evolution is the idea of irreducible complexity. This
theory essentially says that the evolution of complex systems is irreversible - take away part of the
mammalian eye, such as removing the lens, and the eye cannot function and such an individual would not
survive long in a natural environment. How then, it is argued, can the eye have evolved in the first place if
it had to go through so many steps whilst in a non-functional state?

The first flaw in this argument is that any visual acuity is better than none. Partially sighted people, and
even people registered blind will testify to the fact that they can often make some use of what residual
vision they have. Now, if such visually impaired beings existed at a time when no organism had modern
vision - such as in worms evolving in the sea, then if their rivals were totally blind those with some degree
of vision would quite possibly be at an advantage and this could be selected for. Indeed, many organisms
exist today with crude forms of vision, some of them can only perceive changes in light and dark. Such
organisms may exist in environments where vision is not useful, such as in dark caves, and so may have
lost their vision by evolutionary degeneration - mutations occurred which impaired their vision without
reducing their odds of survival in such an environment (indeed they may be at an advantage since they
need not waste resources building eyes and eyes can be easily damaged). Others, however, are
descendants of those organisms who never advanced their vision any further and yet they survive quite
well because of the niche they occupy. (An organism's niche is essentially its 'job' or the mode of
existence by which it sustains itself). Evolving an enhanced structure allows organisms to occupy new
niches, such as the evolution of more water-proof skins which would have allowed early
amphibians/reptiles to travel further from water and colonise new areas. However, a water-tight skin is of
little use to a worm that remains all the time in water. Evolution is not really about making organisms
'better' rather it is about allowing life to exploit many different niches and so create a more stable
ecosystem.

Also, one has to consider the whole organism as a package. An eagle has far superior vision to a human
being, but humans survive perfectly well without such enhanced vision - again they occupy different
niches. An elephant has a far superior sense of smell to a human, and it uses this to detect predators
from afar. This would possibly have been useful to early humans, but then they were well armed so they
had less need to move out of the way of predators who might encounter arrows and thrown spears before
getting close enough to strike.

The easiest way to see the flaws in the theory of irreducible complexity is by analogy. Think of a city. A
city is much like an organism - it is a complex body of interconnected systems. Now cut the electricity
supply to the city, permanently, or permanently cut off its water supply. Clearly chaos will follow and many
people will probably die. It is however, obviously false to argue that, therefore there could never have
been an ancestral city that lacked piped water or electricity! The fact is that when a complex system
discovers a new innovation, then it becomes dependent upon it, whilst enhancing its function. Modern
cities are far larger and more powerful than their ancestors, but they are more dependent on critical
technological systems. Similarly, mammals have very effective blood circulatory systems which carry
oxygen and nutrients to their cells and carry wastes away from their cells. Stop the heart beating and the
animal ceases to function within seconds and its cells will die in a matter of minutes to days. However,
some organisms never evolved blood circulatory systems and so never became dependent upon them.
Flat worms, for example, absorb oxygen across their body wall and being flat helps them do this (by
minimising diffusion distances from body wall to inner parts, since diffusion is fast over short distances but
very slow over large distances). Mammals are able to achieve much greater body sizes than flat worms, in
part because of their enhanced circulatory system, which they depend upon. Note, that it is wrong to think
of the mammal as a 'superior' organism to a flat worm, since both have survived for a very long time, but
because each can do things the other cannot, both survive in different niches.
Bacterium swimming
Above: a computer model of a bacterium swimming - hydrodynamic forces bundle together the
flagella at one pole of the cell, propelling the cell along.
Evolutionary Theory
Modularity - making the most of what you have