In systems where quantum mechanics applies, there may be limits to what can be known about the outcome. In some situations this can imply that a given set of preconditions can have more than one possible outcome, or that the outcome depends on the observer.

Now, those who say that life is an accident are generally determinists who see randomness at some point in natural history as the reason why life has turned out in the particular way that it has. In contrast to this view, those who say that at some point, or perhaps several points, in our natural history the turn of events has somehow been directed from an external source (or at least external to the neo-Darwinian paradigm) generally believe there is physical indeterminism at some point, in other words, an opening for that external source to have effect.  

Thus arguments about chance in evolution are often rather arguments about determinism, and this is then where the protagonist's real concern lies. Is there room for a purposeful divine will? Or are we merely mechanical resultants of prior causes that could not have happened other than the way they did in the particular instance of our history, and would not happen the same way again? From a determinist viewpoint, the random elements make our history accidental; the non-random elements make it inevitable; there is no room for anything else: we are passive. From the indeterminist viewpoint, while much is obviously determined and while random factors play a part, there is scope for optional alternative pathways, whether through action of divine intervention or human choice or some other external agency, meaning that our history is not entirely accidental. Examining questions of the role of chance in evolution leads some way into clarifying and answering the issue of determinism. Could the outcomes we see now have come about entirely by a series of chance events in the evolutionary process in the given time? If not, then an indeterminist interpretation is more promising, and a deterministic one seems unlikely.

Chance and Probability: Two questions

If we consider the neo-Darwinian paradigm, the first question then is this. Is evolution by chance likely to have happened the way it is thought to have happened, or unlikely?  Please bear in mind, problems with mutations being the main agent of change in living organisms is explored in the page on adaptation and mutation. If unlikely, our next question is this. Do the improbable factors of chance imply that neo-Darwinian theory is inadequate, or - as at least the more orthodox of its proponents believe - that it is valid, complete, sufficient and the trajectory of evolution up to humans was an accident that just happened to turn out that way?  The anthropic principle, that we only seem special because we happen to be the result of such a chance.

Then, with or without the neo-Darwinian paradigm, there are then two basic questions when it comes to the role of chance in the origin and diversification of life.  Firstly, what is the likelihood of life as we know it arising in our universe - or on our planet?  Secondly, the likelihood of any form of life happening at all anywhere, ever.

If we give the benefit of any doubt on cosmic and geological timescales such as to give more time for the processes of chance to work, is it feasible that there have been sufficient chance variations for the complexities of life as we know it to have evolved within a timeframe of a few billion years and in the range of terrestrial habitats?  Or of any such highly complex and intelligent life to have naturally so evolved?  Or is this impossible without something supernatural going on?

Then if life started, there follows the question: why should life forms continue?  How is it that there has always been a good-enough suitable environment around the corner?  Is this chance?  Or providence?

If we are dealing with random events, the answers have to be probabilistic. If we consider that genetic mutations more or less follow the pattern of a statistical random walk, where the favourable mutations must predominate over the unfavourable ones in the given time allowed. (although evidence suggests to the contrary).  Likewise other events associated with natural selection must be sufficiently frequent and favourable. So we have to demonstrate - as far as possible - whether in the given space and time frame (phase space), it is likely or not that a sufficient number of events occurred. 

In addition, the organisms may encounter various contingencies: misfortunes as well as fortune. Life on earth nearly ended in the Permian-Triassic extinction that killed the dinosaurs. Fortunately man-eating triffids did not evolve. For tentative beginnings of life at the start, continuation must have been even more precarious. Sudden chance variations of the habitat are a threat. Evolution would be best served by a stable but gradually changing environment. 

Viewpoints

Thus on the one hand there are arguments that would support the idea that mutations and the processes of evolution are frequent enough, so that life and humans could be an accidental result of the series of random contingencies and that neo-Darwinian theory gives a sufficient explanation.

The totality of the universe has an enormous number of physical states and permutations of these and even more so if we are in a multiverse of many universes or an eternal cycle of big bangs. A very large collection of permutations of factors would seem to increase the likelihood of something unusual happening where the beginnings of life of some kind might by a series of random coincidences exist.

Patterns of genetic structure are closely parallel to the patterns of species differences and could indicate an evolutionary processes of change containing accidental turns of events. The DNA of species A still alive today which is believed to be a precursors of more recently evolved species B usually relates to B's DNA in a way that makes sense to an evolutionary geneticist who has evidence of how mutations and variations in a genetic code can come about. Vestigial stretches of DNA as well as vestigial organs corroborate this. There is apparently supporting genetic evidence.

Organisms and ecosystems are diverse. There are now thought to be around 9 million species - all adapted to their habitat. This gives plenty of opportunity for evolution of new kinds.

On the other hand there are arguments that in spite of all this, the progress of the story of evolution at key points is extremely unlikely - almost impossible. The initial conditions of the earth, with water and the CHNOPS elements (carbon, hydrogen, nitrogen, oxygen, phosphorus and sulphur); the formation of the first biochemicals; self-replication; the persistence of life; the formation of cells with a cell membrane, eukaryotes and mitochondria were, among several others, all necessary steps in the apparent evolution of multicellular organisms. Yet each of these is remarkable, unusual and incredibly unlikely to have occurred fortuitously. There is chance, but if chance throughout, this includes a different kind of chance. There is something else going on, whether physical or metaphysical.

It is important to remember that the question of whether mutations were frequent enough for neo-Darwinian theory to give a feasible, sufficient and self-contained explanation is a factual one even if all the facts cannot be ascertained; but if any theory apparently has no need for factors external to it, it does not logically follow that there are none. Anomalies may turn up. Hence assertions about the neo-Darwinian paradigm accounting for all forms of lie, and its results being purely accidental, are an interpretation of the known facts and so contain an element of opinion or supposition.

Properly measuring chances and time requirements of mutation and survival in a given environment is thus not so easy, and most estimates so far have relied on partial guesswork. Fortunately it is now a closer possibility with recent techniques such as the development of pattern theory (Mumford, 2010). This enables one to look at how a genome coding some variation of phenotype matches and interacts with its physical dynamic environment.

The Drake Equation

This section will consider if the chance occurrences claimed by neo-Darwinian theory would be frequent enough for evolution to have occurred.  

The Drake Equation, used by SETI (the Search for Extra-Terrestrial Intelligence project), estimates the probability that another intelligent civilisation capable of letting itself be known to us exists elsewhere in the Milky Way galaxy. SETI scans for new radio emissions and detects candidate habitable planets. It is closer to its goal, but there are some factors in the Drake Equation that are really unknown: the chance of life developing, even if conditions are right, and the likelihood of it evolving to a communicating, technology-enabled civilisation.

We can only estimate such factors through looking at the life forms we have now, and how they might have arisen, such as  random assembly of molecules in abiogenesis, or Darwinian natural selection.

From a historical viewpoint, there are then three distinct phases that underpin neo-Darwinian theory: firstly (1), the particular laws of physics in our universe that make life possible (which mean all possible laws if our universe is one of many in a multiverse); secondly (2), the origin of life: the transition from inert amino acids in say a "primordial soup" of organic and inorganic chemicals, to the stable self-replicating systems of life;  thirdly (3), the evolution of life to humans and other modern life forms; (or other dynamic relationship): i.e. what we are most familiar with under the heading of evolution. 

To examine the probability of advanced organisms arising only by the physical processes of evolution, one has to consider 1, 2 and 3, not just 3; all are necessary.  Without 2 there would not be 3 and without 1 there would not be 2. Events must have happened with a particular frequency and outcome for life such as we have today to arise.  We will consider the likelihood of the development of life by chance, including the processes of neo-Darwinism, in the framework of the Drake equation.

The particular laws of physics in our universe that make life possible.

 "Ye cannae change the laws of physics!" Scotty, in Star Trekkin', 1987, Rory Kehoe/The Firm

This section should start with the question: what is the likelihood that the universe exists? Within the generally accepted paradigm of cosmology, there are various theories as to what was before - or rather beyond - the Big Bang, and the matter is not settled.  The principal  group of theories says that our universe is one of many comprising the multiverse, each of which has its own physical laws. These theories are now hovering around the question of how such pre-universe situations came about. 

The existence and perpetuation of life requires that conditions such as temperature, moisture content, concentrations of carbon dioxide, oxygen and other elements were suitable.  More importantly, it requires that the universe which can somewhere contain these conditions exists in the first place. There are a number of fundamental constants such that the structure and composition and even the physical laws of the universe would have been very much altered had the value of one or more of these constants been different. This is what is referred to as fine tuning.

The precise value of the cosmological constant, a factor originally and reluctantly added into Einstein's general relativity equations, is an example. This constant has to be accurate to 120 decimal places. If you can imagine the whole universe as a large dial for "fine tuning" itself, then nudging the dial just 1mm at its circumference would put its value way out, and the universe would disintegrate or collapse almost instantly. The chemicals, reactions, temperatures distances and densities that life depends on would never have existed.

Other laws and constants of physics have to be exact, and one effect is to determine the proportion of cold dark matter (23%) and dark energy (73%) and light matter/energy (5%).  The normal "light matter" of the universe consisting of atoms and molecules, and so on, is actually only about 5% of the mass of our complete universe. The dark matter does not contain the atomic particles that enable ordered structures to exist; life forms within it are inconceivable. And if the proportions were different, life would not exist in the known universe. All of the independent fundamental constants have to be right.

Some say that among the many universes of M-theory (see Douglas, 2003), one that would generate life by chance is surely likely to exist. But if you add up all the fine tuning constants, that claim is severely weakened.

The question then arises: did our universe have to turn out as it did?  If the Big Bang were repeated, would it be the same? Slight random contingences caused particular outcomes - for example the Milky Way being the size and shape that it is. Either chance or predetermination play a part.

Carbon is an essential ingredient of all life "as we know it".  Only carbon can give rise to such a variety of organic chemicals: the ones on which cellular structures and ingredients depend.

Within large stars at a temperature of 100 million degrees C, an excited quantum state of carbon-12 - known as the Hoyle resonance - is formed from colliding helium atoms. A small percentage of this excited carbon-12 remains as the same carbon that gives such a vast variety of organic molecules. The formation of this carbon nucleus within the star depends on a precise balanced relation between the strong nuclear force pulling the nuclear particles together and the electrostatic force causing the positively charged particles to repel one another. The strength of this electrostatic force is governed by the fine structure constant. If it did not have the value that it does, there would be no carbon, and therefore no organisms such as seen on the earth.

The origin of life:  probability of living organisms

 "It's life, Jim. But not as we know it!" Spock, in Star Trekkin', 1987, Rory Kehoe/The Firm

These factors apply whatever galaxy is a candidate for hosting life. In addition to these fundamental prerequisites, one also has to consider the likelihood of suitable planets - such as earth.  In the framework of the Drake equation, this depends - for a given galaxy - on the rate of star formation, the fraction of stars with planetary systems, and the proportion of planets in a star’s habitable zone that have water.  There would also need a workable portion of the CHNOPS elements (carbon, hydrogen, nitrogen, oxygen, phosphorus and sulphur) for the protein-based life that we know to develop.

Biologists tend to believe that RNA rather than DNA held the first genetic code, and that RNA preceded proteins. Nearly all biochemical reactions are catalysed by enzymes.  Without enzymes, reactions would be slow or not happen, and the various alternative uncatalysed reactions would require a bigger range of media with different pH and temperatures to work effectively. RNA itself can act as an enzyme, and conceivably produce the first proteins - and some have speculated that RNA reproduced itself first, before structures built of proteins. However, the question then is what preceded RNA - how was that formed?  And how was the gulf between simple RNA and enzymatic synthesis of proteins made? These phases are an improbable leap.  (De Duve, 2005, Ch.7; Futuyma, 2005, Ch.5).

The famous Miller-Urey experiment in the 1950s found some amino acids and other compounds when they imitated what they believed to be the conditions of early earth in the laboratory (Miller & Urey, 1959).  With an atmosphere of water, methane, ammonia and hydrogen - but no oxygen, nitrogen or carbon dioxide - heated to boiling point and with sparks between electrodes, all in a flask, they produced amino acids glycine, alanine and others. Opinions have shifted on the make-up of the early atmosphere, but suggested then that sufficient building blocks of proteins could have arisen in this inorganic soup of suitable ingredients in the early earth. This has since proved unlikely.

However, they could have arisen beyond the earth. Meteorites sometimes contain some of the carbon compounds necessary for life. For a period in geological chronology between the Earth's formation 4,600 million years ago (4.6 Gya) to about 3.9 Gya there was heavy meteorite bombardment, and the earliest life forms are believed to have arisen around 3.8 Gya. When researchers dissolved and purified fragments from the Murchison meteorite, found in Australia in 1969, their analysis showed that the meteorite contained chemicals with a role in RNA and DNA biochemistry, notably xanthine (a purine) and uracil (the ribonucleotide that complements DNA's thiamine in transcription). Furthermore, the carbon atoms in the two substances was in a heavy form that is extremely rare on Earth, showing that they must have originated in outer space. (Martins et al., 2008)

However, protein synthesis of particular relevant proteins containing a configuration of many amino acids is a big leap from bunches of a few amino acids or nucleotides lying around. Normally, enzymes are required to synthesis proteins from a pattern encoded in RNA.

The probability of the first proteins arising by chance has been compared to that of a team of n hardworking hypothetical chimpanzees with typewriters creating random texts, producing a Shakespeare sonnet. With 153  14-line sonnets and 27 possible characters (ignoring capital letters and punctuation) and averaging 41 characters per line, the team would write a sonnet in 27⁵³² / 153n which is  > 10⁶⁰⁰ different attempts. (The number of universes with distinct physical laws in the multi-universe hypothesis proposed by M-theorists is only 10⁵⁰⁰.

Several scientists, notably Francis Crick, Fred Hoyle and Chandra Wickramasinghe believe that the necessary complex molecules must have an extra-terrestrial origin, since it is just too unlikely for them to have come about here on earth.  Some have concluded that there must be a pre-existent intelligence which sent life to earth in order to perpetuate it.  Or that it arrived in some form from beyond our four-dimensional universe. Certain ingredients are not uncommon in outer space - e.g. the amino acids found in meteorites, and may even have preceded the solar system. The difficulty is in moving from these to the complex and reproducible life forms that contain so much more information than simple biochemicals.

 "But in that dawn of certainty, in what might have been a moment of satisfaction, we hit a difficulty that knocked the stuffing out of us. No matter how large the environment one considers, life cannot have had a random beginning... Just as the brain of Shakespeare was necessary to produce the famous plays, so prior information was necessary to produce a living cell. But information from where?" Hoyle and Wickramasinghe, 1981, p.148

"An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle." Francis Crick, 1982, p.88.

Some have speculated that this is some extra-terrestrial intelligence in this or some other universe must have deliberately freighted information in the form of a DNA or RNA molecule in order to instigate life on Earth. Their studies support the thesis that abiogenesis from chance alone is too improbable, and point to a prior intelligence; but if this is alien intelligent being(s), then what is their origin?  What is the source of their intelligence?

If life started, what is the chance that it continued?  Life consists of self-perpetuating systems. These are made of proteins, nucleotides and enzymes though other life-forms might be conceivable. DNA contains sophisticated programming for do-it-yourself genetic engineering including error detection and correction. What is the likelihood that the structures arising so far, contained inherently the machinery for evolution: a system of replication with perpetuation of information (e.g. genetic blueprint), growth and protection, and the long-term capability to adapt to a changing environment?  Why the drive to survive?  Did it just happen that some bunch of proteins became self-reproducing, and this never ever stopped?  Why didn't they just stay wherever they were and never get noticed?  This is remarkable and has to be an example of extreme luck right at the source of life if it evolved in this way.

Humans and other modern life forms

 "There is no gene for the human spirit." Gattaca, Andrew Niccol, 1997 Columbia Pictures.

Given that elementary life forms (replicating, growing/metabolising information-processing systems) are present, what is the likelihood that these have evolved in the manner ascribed by neo-Darwinian processes?  There are key stages that diversification of life on Earth is believed to have passed, from proto-bacteria, plants, oxygen, eukaryotes, higher plants, vertebrates, primates. Each involve leaps of apparent improbability.  In addition to that, life must have survived catastrophes such as asteroid bombardment, notably the one that appears to have demolished the dinosaurs 65 million years ago.

Mutations are many times more likely to be towards the harmful side than on the beneficial side (though the actual ratio varies greatly according to circumstances). Nearly all are not far from neutral in their affect, only slightly harmful or beneficial, and therefore not filtered out in later evolution, but mostly remaining redundant if the organism survives. The slightly beneficial may extend in the population and have a gradual influence. Cumulative good mutations are possible. For a new mutation to become predominant in a population, the majority of the rest of the population must reproduce less often (e.g. due to failure to survive to reproductive age, or sexual selection), or new and old populations become distinct through genetic drift. Usually this would mean a large number of generations and a large number of offspring from the favourable variant. Factors in and around the population have to be right for this to happen.  

Since most mutations are harmful or neutral, there must be sufficient numbers in the population to buffer their effect, such that the lucky one will have a chance. In any case a high  predominance of negative and neutral mutations is more likely to have a degenerate effect, especially if the mutation rate per generation is high.   

“Wildlife in the heavily contaminated Chernobyl zone sometimes appears to flourish, but the appearance is deceptive. …This zone is analogous to a ‘black hole’, in which there is accelerated genetic degeneration of large animals …. The Chernobyl zone is a micro-evolutionary ‘boiler’ where gene pools of living creatures are actively transforming, with unpredictable consequences. We ignore these findings at our peril.” Alexei Yablokov, quoted in Evans, 2011, p.32

Christian de Duve and Singularities

De Duve (2005) examines such crucial events in the "pathways of life".  These singularities were essential, yet only happened once. We have discussed some of them above.  He considers seven scenarios of how they may have occurred, ranging from deterministic inevitability through to intelligent design. These singularities are of particular interest to us here if there appears to be a chance that they may not have happened.

The stages considered include among others: biochemical origins and proto-metabolism, ATP, RNA, proton-motive machines, eukaryotes, mitochondria, oxygen and the genus Homo. And the singularity of the appearance of life itself (pp. 159 - 167).

Since these events only happened once in evolution, if there was a chance that the event might not have occurred, the course of evolution could have been radically different or more likely stopped. The capture of the first mitochondrion, the key to the eukaryotic cell and of the future evolution of larger organisms with a higher energy requirement is an example; and comparative genomics indicate that this only happened once (Lang, 1999).

Irreducible Complexity

Irreducible complexity (IC) is a structure, or process comprising a number of linked and essential components that could not conceivably have evolved by step by step gradualism, each component is essential such that they must have arisen together: the precursors don't have a function alone such as would give a selection advantage. If all components evolve simultaneously, even though they may for a time have been latent and non-functional, multiplies the improbability that the functioning whole arose by chance. It really does more than this, because the odds of two (or more) streams of development independently happening in the same organism at the same time are much greater than them appearing separately in different organisms in the population whose descendants might never meet.

A mousetrap consists of a base, a spring, a hammer; a trigger (bent to put cheese on).  For mutations to arise to give all four components, the improbability of each one is multiplied. There is no selective advantage for the householder with three-quarters of a mouse trap over the one with none in their battle for survival against the mouse. 

 Darwin himself had said: "IF it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case. No doubt many organs exist of which we do not know the transitional grades, ...  We should be extremely cautious in concluding that an organ could not have been formed by transitional gradations of some kind." Darwin (1859, Ch.VI).

The concept of IC was put forward as an argument by several other key figures last century. Biochemist Michael Behe (1996) gave it the name. He employed seven chapters of examples where he saw irreducible complexity as a serious stumbling block for the standard theory of gradualist evolution. In all of these examples the parts must have arisen together for their function to have worked.

There have been objections: that Behe omitted to consider some contemporary studies, and that for some structures once thought to be examples of IC (e.g. the mammalian middle ear), a precursor has since been discovered (e.g. reptilian jaw bones). There has been much research since, especially in the genetics of these cases, but some examples still have parts that cannot be explained.  The examples of the eye, blood clotting, and the cilium and flagellum are largely derived from Behe (1996).  

The Eye   

The eye was a challenge to Darwin: how could a complex organ, a set of interacting parts, each with their own function, evolve gradually?  "Reason tells me, that if numerous gradations from a simple and imperfect eye to one complex and perfect can be shown to exist, each grade being useful to its possessor, as is certain the case; if further, the eye ever varies and the variations be inherited, as is likewise certainly the case; and if such variations should be useful to any animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, should not be considered as subversive of the theory." (Darwin, 1859, Ch. VI).  

 Magritte - Le Faux Miroir

Nilsson and Pelger (1994) estimated the time taken for a flat patch of light-sensitive cells sandwiched between a transparent protective layer and a layer of dark pigment, to evolve into the focussed lens eye through continuous small improvements of design. They said 1829 steps of 1% would be needed for this and conclude that it would only take around 364,000 generations - or years if average generation is one year. Their model does not assume any simultaneous parallel changes as suggested by cases of irreducible complexity, but linear gradual evolution, and this seems to be a valid assumption for the changes they describe as development of any of the key parts could improve overall function. The formula they employed for their calculation applies only to the model of continuous substantive variation of existing structures (taken from Falconer, 1989). The coefficient of variation (V = the ratio of standard deviation to the mean in a population of phenotypes) is given a value (0.01). Even if this value is over-optimistic and over-estimates the rate of change by a factor of 100, if their model is otherwise valid, then this evolution would still be in a feasible time frame of the millions of years of the fossil record.

However, this model applies only to the anatomical development of the eye itself. As Behe explains, the biochemical process of translating light to nerve impulses involves a sequence of several steps which must be reset to an initial state ready to repeat that process. Some of these steps must be exremely rapid, almost instant. And there must somehow be a link between the chemistry that detects the impact of a photon, and the very different set of chemical reactions that produce a nerve impulse. This is rather like the puzzle where you have to go from say BOAT to CREW, one letter at a time. The evolution of such a system calls for discrete changes, not the continuous variations in the possible anatomical development. To develop this gradually, using chance processes is extremely improbable, even if one or two of the words happen to be lying around.

The biochemical chain begins when the rhodopsin cofactor 11-cis-retinal (produced from vitamin A) changes conformation to trans-retinal when hit by a photon. Via metarhodopsin II, transducin, phosphodiesterase, GDP and GTP, the cGMP (cyclic guanosine monophosphate) level falls, closing the ion channel and disallowing Na+ and Ca++ ions to cross the plasma membrane of the photoreceptor thus producing a potential difference which becomes an electrical impulse in the neuron of the optic nerve. This process must then be reset. The calcium stimulates generation of guanylate cyclase which increases the level of cGMP which reopens the ion channel, while another group of reactions inhibit the local production of transducin. At the same time, transretinal changes to trans-retinol and then to 11-cis-retinol which changes to 11-cis-retinal, ready for another photon.  Each of these reactions is catalyzed by an enzyme.

All this, which is a simplification anyway, shows the elaborate sophisticated processes necessary for what one might at first imagine to be a simple operation. Critics of irreducible complexity say that these chemicals must have been hanging around there anyway, functioning for a different purpose. One or two of them perhaps. But most are specifically tailored for the job in hand; retinal and rhodopsin are not used for anything else in animals.

Morphological change to the modern camera-type eye may have been feasible; but it is hard to see how the biochemical mechanism could have arisen through gradual, functional steps.  

Blood Clotting

Similarly, blood clotting involves a sequence of biochemical processes which I will summarise to show the elaborate cascade that links the detection of the need for a clot to its construction.

Firstly, primary haemostasis is brought about by damage to the inner wall (endothelium) of a blood vessel causing platelets to alter their surface to stick to the damaged surface. Platelet activation is triggered by ADP and the von Willebrand factor, and they then stick to the collagen layer under the broken endothelium, to form a clump to stop up the wound.  With the help of calcium ions, phospholipids gather to stick onto the surface of the clump of platelets. The platelets release thromboxin A2 (TXA2) which activates more platelets at the site of injury.

In secondary haemostasis there are two pathways:-

• The extrinsic pathwaystarts with the tissue factor which is secreted from certain types of damaged cells "extrinsic to" or outside the blood vessels. This combines with convertin (Factor VII) and activates the Stuart factor (or Stuart-Prower factor or Factor X).

• The intrinsic pathway starts with the Hageman factor (Factor XII), and is stimulated by exposure of the collagen layer, normally shielded from blood plasma. The Hageman factor interacts with the protein HMK (high molecular weight kallikrein factor or high molecular weight kininogen, or Fitzgerald factor) to convert inactive prekallikrein (Fletcher factor) to the active kallikrein. The activated Hageman factor and HMK then activate PTA (plasma thromboplastin antecedent or Factor XI) which then, with convertin (Factor VII) activates the Christmas factor (IX).  Activated Christmas factor helped by the antihaemophilic factor (VIII) change the Stuart factor (X) to its active form.

The Stuart factor is the start of the common pathwaythat is part of the extrinsic and intrinsic pathways. It activates proaccelerin (Factor V) allowing prothrombin (Factor II) to become thrombin.  Fibrinogen (Factor I) which circulates in solution in the blood is split by thrombin to form fibrin  the sticky fibres that make the mesh framework of the blood clot. The fibrin stabilising factor (XIII) then does as its name suggests.

Extra feedback loops and interactions reinforce the process. Both pathways are needed in the human to form a rapid and reliable blood clot.

This complex set of reactions starting with the detection of damage and ending with a mesh of fibrin threads traps red corpuscles and more platelets to form the mature clot.  Behe (1996) claimed that the elaborate sequence of about 20 biochemical reactions in these cascades are such that they will not work if any of several of the steps is missed out. (A few can be omitted, but the clotting is less efficient.) This is demonstrated by the various disease conditions where there is a deficiency in one of the factors. Also experiments - particularly on the common pathway - have shown that where genes for particular factors have been removed the system fails. Therefore we are left with the question of how the essential elements of this biochemical process could have evolved together, and the probability of them doing so by chance.

Because some of the factors in the blood clotting cascades are genetically similar (serine proteases) some believe that they evolved from proteins hanging around in the organism already.  Patthy (1990) concludes:

"The data suggest that the blood coagulation and complement cascades are descendants of an ancestral defence system that served the dual role of immobilization and destruction of invading bacteria and the prevention of loss of body fluids. The enzymes of the fibrinolytic, tissue-remodelling cascades form a distinct group, more closely related to the proteases of the digestive tract ... Molecular evolution of these enzymes therefore suggests that they are descendants of an ancestral protease responsible for degradation of extracellular proteins." Patthy, 1990, p.153

This is still a mystery. There are many vertebrates with somewhat simpler coagulation pathways. But  the main components of the cascade between detection of the need for a clot and the clot itself would be needed before the process could work. You can't walk across a bridge if a chunk of it is missing; the whole bridge has to be constructed before it is usable. 

The cilium and the flagellum motor

The cilium and flagellum have sophisticated (though different) mechanisms for moving. The cilium employs a leverage mechanism; the flagellum a rotating motor. Both use several accurately constructed components.  In challenging these examples of irreducible complexity, it has been claimed that the required proteins were hanging around anyway, but it stretches the imagination to see how all of these were already available in the cell previously.

Cilia themselves are long thin tubes, consisting of a nine double fibres (microtubules) in a ring, covered with a membrane that is continuous with the cell membrane. The cilium also has two microtubules in the centre. The tubulin molecules are made of segments that dock on top of ones below them.  A flexible protein strap called nexin connects each microtubule to its neighbour. Another protein, called dynein, also links the microtubules and this one is capable of bending, transforming electro-chemical energy into motor energy. When the dynein is energised with ATP, it pushes the adjacent microtubule down, to an extent limited by the nexin, so that the pair of microtubules bend.

All these components are necessary for cilia to move effectively. If any one of the proteins that form it is removed experimentally, it does not work. In addition to the structure, biochemical sequences are necessary to provide the ATP at an appropriate time for the cilia to function.  As with the mousetrap analogy, the chance is very low that these components are all there by chance.

The flagellum is a different structure but with a similar function of propulsion of the cell through a fluid. It is even more remarkable. Flagella move together like synchronised swimming, and respond to navigational signals within the cell. 

The flagellum acts rather like a helical propeller, being connected directly to a rotary motor. Now the axle of the motor, or the flagellum itself must be separate from the cell wall, but not risk any breach of it.  Like a water-resistant electric motor, this motor has seven essential parts: a rotor, axle, bushing (for strength and ease of movement), a seal (so that water outside doesn't get in, and lubrication inside doesn't get out), an armature, and a means of creating a force between the rotor and a stator such that the rotor rotates (magnetic force for the electric motor), and a controlled energy supply. All of these seven parts are necessary in the bacterial flagellum motor.

The motor rotates by using the ion potential (H+ or Na+) across a plasma membrane.  This in itself is part of a complex process. It rotates at variable speeds of up to 20,000 rpm, at energy consumption of only around 10-16 W and with energy conversion efficiency close to 100%.  And it can switch between forward and reverse directions in mid-rotation.  

The flagellum and motor self-assemble from about 25 or more proteins. It is interesting that assembly occurs in an order that is optimum for building the structure, and not necessarily the order one might expect if this repeats the sequence of development one would assume from a Darwinian hypothesis.

All the parts work together as one unit. Studies analysed diffraction data from X-ray crystallography equipment and a synchrotron to observe the 3-D arrangement and the motion of individual atoms to understand the dynamics or structure of these protein nano-machines.

The flagellum itself is built from a helix of bundles of protein proto-filaments. A mere 0.8 Angstrom difference in L type and R type filaments determine the helical structure and enables rapid change of rotation direction. These structures in the flagellum are not ones that just happen to suit their needs. They are specifically and optimally shaped for their role in the whole structure.  
Schematic Diagram of Flagellar Motor - NanoNet

“The atoms constituting proteins do fluctuate but the average positions of individual atoms are very precisely determined with an accuracy of sub-angstrom level. That is why individual proteins can properly identify partner molecules to bind and get assembled into the higher order structures of living organisms. The fluctuations of protein structure, that’s what makes living organisms function in such sophisticated and well regulated ways. I am willing to dedicate my entire life to the hard work unveiling the mysterious world of protein structure and function.” Namba,  2003.

For a proposal as to how the flagellum may have evolved, see Liu and Ochman, 2007. There are close similarities with the Type-III Secretory System (T3SS) found in some bacteria, notably Yersinia pestis, the agent of bubonic plague which injects toxins into eukaryotic cells with a mechanism employing proton-motive force just as the flagellum motor does. This also has several components precisely arranged, and though they are similar and may well be related, the origin of such structures remains a mystery. Darwinian explanations are not feasible.

Mitochondrial Symbiosis and the Eukaryotic Cell

The eukaryotic cell was essential for multi-cellular organisms with a greater energy consumption. This is possible through respiration specialisation of the mitochondria. These organelles are relatively self-contained, having their own genome. Comparison of sequences of various mitochondrial and prokaryotic genomes confirms that the mitochondrial genome originated from a eubacterial ancestor - as first proposed by Lynn Margolis - but raises questions about the evolutionary antecedents of the mitochondrial proteome (Gray et al., 2001). This symbiosis gave an enormous breakthrough in energy efficiency for power and growth, and evolution could not have occurred at the rate it apparently since did without it. (De Duve, 2005)

Likewise chloroplasts are believed (in neo-Darwinian theory) to have originated externally (about 3 Gya), and without them we would not have had sufficient photosynthesis to give the oxygen-rich atmosphere on which most species depend. Higher life forms depend not just on the arrival on the scene - by chance or otherwise - of one organism or genome, but two.

The Krebs cycle, which takes place within the mitochondria, is itself remarkable. This is the set of biochemical reactions that release energy in the form of ATP energy carriers for use by an organism. Behe (1996) explains the synthesis of AMP as an example of irreducible complexity. (The Krebs cycle involves ADP and ATP, and may have been originally synthesised by phosphorylation of AMP.)  [AMP, ADP and ATP are adenosine mono-phosphate, diphosphate and triphosphate.]

The move from prokaryotic to eukaryotic cell structure involves a number of other changes that work together in its total system dynamic: cell membrane, new specialised organelles, mitosis. See De Duve (2005) for further discussion on the advances of the eukaryotic cell.

Human Mind and Consciousness

Humans are said to have several distinctive interconnected characteristics that have been absent or almost absent in other species. Some claim that these have arisen by chance as a by-product of increased brain capacity, even if their current extent is not needed for survival.

Self-awareness of self-consciousness: if self-consciousness evolved, then how and why?  Is it really a survival advantage for the organism to be aware of itself, as long as the organism reacts well to its environment and reproduces? Is consciousness a stage in the natural trajectory of evolution; an inevitable consequence of a critical mass of neurological complexity?  If so, with a different set of chance contingencies to the ones our natural history has endured, would beings similar to humans have arisen? Lee Cronin at Glasgow University is researching life-systems built of metals and produced a “metal cell” which perchance will evolve into a robot.  It seems that “higher” animals, pets to porpoises, have intelligence that seems to some degree self-conscious. Against this, is the argument that human consciousness is on a totally new level that does much more than could be expected from chance variation and selection.

Language, singing and music, aesthetic expression and sensibility: some regard these as more complex developments from earlier forms that serve group cohesion: warning, hunting and mating signals and recreational expressions, that may had become over-elaborate as a consequence of a much larger and more complex brain. But for others, the aesthetic expression is much more than functional, and is a physical expression of spiritual meaning.

Mental tools, conceptualisation and the ability to discover the nature of the universe: Are these merely an extension of physical tools and skills to manipulate the environment?

Altruism: the usual view from the Darwinian perspective (not to be confused with "social Darwinism"), is that altruistic tendencies gave a survival advantage to the group. In many circumstances they do. Captain Oates sacrificed his life to help the group survive (even though he was unlikely to survive anyway and they didn't quite make it). But people do occasionally lay down their lives for others out of empathy and compassion in situations where a self-centred approach would fare them better.

Free will: is claimed to be an illusion; but is it? Brain scans show electrical activity during the information processing involved in decision-making. But human reflection and conscience tell us that alternative choices are possible.

Moral instinct: gives humans values that are unrelated to the issue of survival and oblige them to constrain behaviour that would otherwise assist survival (Collins, 2007). This is a paradox that evolution cannot explain.

The urge to ask “why?”, and the inbuilt sense that there is a purpose and significance to things. Why should an object that evolved somewhere in the universe simply as a result of a series of circumstantial contingencies and chance seek to know the significance of that universe and its place within it?

And some would add a propensity to destroy its own species and habitat.

These features are universal among all human societies, though some are more prominent than others in different cultures at various historical periods. They seem to have emerged and flourish to a level that is well above what is necessary for simple survival. Are they not more than side effects of having by chance reached a critical mass of neural connections, information processing and communication?

"Our activities in each area (human knowledge, morality and sense of beauty) certainly derive in important ways from our biological nature, but that once having emerged they cannot ... be analysed in biological or evolutionary terms." O'Hear, 1997, p.vii

Quantum Mechanics

Several functions in biology are quantum phenomena best described by quantum mechanics. The effect of the photon on 11-cis-retinal is an example. Neural processes in brain activity may involve quantum processes and some researchers are investigating quantum computing or information processes in this context.  Quantum processing is extremely fast.  Quantum mechanics underlies the nature of molecular shapes and bonding, metabolic energy exchanges, diffusion rates and many biological interactions. As Schrodinger pointed out, the genetic coding system is a discrete digital system, as is the quantum world; and they should have some common principles in the way they process information.

Some researchers in quantum mechanics have been exploring whether quantum phenomena may be at the root of the origin of life - the original RNA; structure and metabolic processes of early life forms; photosynthesis, rapid processing in the brain, and consciousness itself. 

Such quantum events need a space and a sufficient period when they can operate while keeping the delicate relationship between the components of the wave function (coherence) before being disturbed by the surrounding environment (decoherence).  The phenomena of entanglement and superposition mean that it is possible for quantum information processing to occur within biological cells and tissues, giving an enormous advantage of speed and processing power compared to classical information processing.

 "The power of quantum superpositions is that the system can explore many alternative pathways simultaneously, thereby potentially shortcutting the transition time by a large factor. Because life is a highly unusual state of matter, its formation from an initial state is presumably extremely improbable. Quantum mechanics provides a way to drastically shorten the odds and fast-track matter to life by exploiting the parallel processing possibilities of superpositions.  ...   It may even be 'steered' towards life by the inverse-Zeno effect. But this implies the environment somehow favours life - that life is 'built into' nature in a preordained manner. So an element of teleology remains" Davies, 2008, p. 11

Theology

"The old alliance is broken. Man finally knows that he is alone in the indifferent immensity of the Universe from where he emerged by chance. No more that he has a destiny; his duty is written nowhere.  It is up to him to choose between the kingdom of light and the kingdom of darkness." 
[The latter phrase is a reference to Manicheism.] Jacques Monod, 1970, pp.224-225.

 “Today, we are learning the language in which God created life. We are gaining ever more awe for the complexity, the beauty, and the wonder of God’s most divine and sacred gift.” Bill Clinton, announcing the success of the Human Genome Project, 26 June 2000.

For orthodox followers of the neo-Darwinian paradigm such as Jacques Monod (1970) chance is "pure chance" and leaves no room for external or divine intervention; life has turned out haphazardly and fortuitously and we humans happen to be here, so should make the most of our lucky existence; one of zillions of possible scenarios that might have happened in the cosmos by chance alone. They also usually conclude that there is no purpose, although even if current reality is a result of chance, it does not follow that it is without purpose. 

These protagonists have a monist view at the outset; the monist view being a materialist one.  Dualists see reality as made up of two domains: physical and spiritual/ideal. There are also those who refuse to make any distinction between these domains. Each has corresponding explanations for the living world.  These philosophies result in different views on the nature and implications of chance.

The monist view attempts to demystify or deny mystery. But mystery defiantly remains at the heart of the story of life. Simply denying it, rather than appreciating it, is pointless.  For these scientists who say our particular characteristics happened by accident alone, and conclude that there's no room left for God, this is always a self-fulfilling prophecy of a materialist - or rather physicalist - viewpoint, and preconceptions of living things as mechanical structures. Physicalism  (Neurath, 1931) is the view that all things have only physical properties, and that all sciences can be unified under common universal principles and (like logical positivism of which it is a reformulation) that anything metaphysical that cannot be verified empirically is to be rejected.  The term naturalism has become more current in recent years and refers to the same philosophy.

Their argument goes:

•  All things are part of a total unified self-sufficient physical system.

• The concept of God is not a part of such a system. 

• Therefore God is absent.

But God (or metaphysics, or mystery) is only absent from the premise of their mental argument. Physicalism is insufficient to account for what happens at the material level and the level of human subjective experience.

Indeterminate chance and random quantum events do leave room for metaphysical or divine intervention. At this level the inevitability and predictability of outcomes from known causes by the principles of classical mechanics do not apply. Mechanistic explanations are not quite sufficient.  Living things - or at least humans - are more than the sum of their parts (Canguilhem, 1977).

Ideas on the location and timing of such interventions among creationists, theistic evolutionists and proponents of intelligent design. For all of these, even if life did develop partly or completely by neo-Darwinian evolutionary processes, then to invoke chance as the sole source of change is untenable. For creationists, chance is not a decisive source of change and plays a minor role; the fact that it cannot account for key stages in diversification of life supports the arguments of all those who see God's wisdom in nature.

Among believers, there is something in the discovered universe that resonates with the God of experience, of majesty, love and power, in spite of the fact that there are what seem to us to be imperfections. There is also a dimension of beauty here that evokes respect and amazement. The fact that the Universe has existed and developed to make this life possible is something that cannot be put into words or equations; to realise we are a significant part of something vastly more than we can imagine, is a reflection of our relationship with God. The role of chance in the diverse multiplicity of life points to something much more profound than random accident.  An infinite number of permutations would still not enable it to happen.

Conclusions

 "To conclude, therefore, let no man upon a weak conceit of sobriety or an ill-applied moderation think or maintain that a man can search too far, or be too well studied in the book of God's word, or in the book of God's works, divinity or philosophy; but rather let men endeavor an endless progress or proficiency in both; only let men beware that they apply both to charity, and not to swelling; to use, and not to ostentation; and again, that they do not unwisely mingle or confound these learnings together." Francis Bacon: Advancement of Learning, I (3)

This review of the role of chance in the theory of evolution has shown there are key points of transition in natural history of very high improbability or impossibility. These points have provoked research and explorations that go beyond chance events: quantum mechanics, extraterrestrial origins, other universes, teleological causation, in areas where chance is inadequate as an explanation for the emergence and divergence of life.

The claim of Jacques Monod and others is that in an infinite or almost infinite universe, the extraordinary is nothing special, because it is bound to happen sooner or later. Chance and biophysical mechanisms account for the totality of life. But there are too many improbabilities in the development of life in the evolutionary framework as well as the beginning. The extensive and extreme complexity of nature just doesn't fit the consumerist brand of neo-Darwinian science packed as a product sufficient for all requirements. It is quite clear that at several stages, life could not have come about and progressed by chance alone, even though chance may be involved to some degree. The argument doesn't hold water.

Most neo-Darwinists conclude that life is a meaningless accident. But singularities define meaning - they demonstrate a matrix of value: statistical, informational and existential significance. Existence itself has value - it is illogical to try to claim that if the cosmos is a quirk fluctuation that just happened it is of no value. Significance cannot be encapsulated, branded or patented. It cannot be (pre-)defined, because that would be to limit it. It calls for an open-minded attitude of appreciation. The singularity of human subjectivity enables meaning in the universe. For Christians, the Cross represents a single moment to which everything else is related and from which the utmost significance can be claimed.

If humans can make a connection with God - the source of meaning, and can discover the universe is something significant, they are more than just a continuation of previous life forms.  Humans discover significance as well as facts, and therefore are themselves significant.

References

John D Barrow, 1990, The World Within the World. Oxford: Oxford University Press.

John Beatty, 2010, "Reconsidering the importance of chance variation", in Massimo Pigliucci and Gerd B Muller, Evolution: The Extended Synthesis, Cambridge, MA: The MIT Press.

Michael J. Behe, 1996, Darwin's Black Box,  New York: The Free Press.

Georges Canguilhem, 1977, Ideology and Rationality in the History of the Life Sciences, trans. Arthur Goldhammer  Cambridge, Mass.: MIT Press, 1988. (Originally published as: Idéologie et rationalité dans l’histoire des sciences de la vie (1977) Editions Vrin.)

Francis S Collins, 2007, The Language of God: A scientist presents evidence for belief, New York: Free Press.

Francis Crick, 1981, Life Itself: Its Origin and Nature,  London: MacDonald, 1982

Paul C W Davies, 2008, A Quantum Origin of Life?, in Quantum Aspects of Life, Ed. Derek Abbott, P C W Davies, A K Pati,  London: Imperial College press.

Michael Douglas, 2003, "The statistics of string / M theory vacua", Journal of High Energy Physics 0305, 46 (2003). See also Ashok and M. Douglas, 2004, "Counting flux vacua", Journal of High Energy Physics  0401, 060 (2004).  These explain the workings behind the "10500 universes of 11-dimensional M-theory.

Christian de Duve, 2005, Singularities: Landmarks on the Pathways of Life,  Cambridge: Cambridge University Press

Patrick Evans, 2011, ‘Wildlife in the Dead Zone’, Geographical, Vol.83, No.4, April 2011, 29-32. See also Alexei Yablokov, 2009, Chernobyl: Consequences of the Catastrophe for People and the Environment.

Douglas Falconer, 1989, Introduction to Quantitative Genetics, 3rd Edition, (1st edition published 1960),  A standard textbook and reference on quantitative genetics; it emphasises an analysis of variance method.  

Douglas Futuyma,  2009, Evolution, 2nd Edition, Sunderland, MA: Sinauer Associates. (1st edition,  2005).

Stephen Jay Gould, 1989, Wonderful Life: The Burgess Shale and the Nature of History,  New York: Norton & Co.

Michael W Gray,  Gertraud Burger, and B Franz Lang, 2001, 'The origin and early evolution of mitochondria ',  Genome Biology 2001; 2(6): reviews1018.1–reviews1018.5.  See also B Franz Lang et al, 1999, ‘Mitochondrial Genome Evolution and the Origin of Eukaryotes‘, Annual Review of Genetics, 33:351-397.

Fred Hoyle, N.C. Wickramasinghe, 1981, Evolution from Space: A Theory of Cosmic Creationism, New York: Simon and Schuster

Stuart A. Kauffmann, 1993, The Origins of Order: Self-Organisation and Selection in Evolution, Oxford: Oxford University Press. 

B Franz Lang, Michael Gray, Gertraud Burger, 1999, 'Mitochondrial Genome Evolution and the Origin of Eukaryotes',  Annual Reviews of Genetics, 33: 351-97

Wen-Hsiung Li, 2006, Molecular Evolution. Sunderland, MA: Sinauer Associates.  A standard textbook; well up-to-date and comprehensive in range of topics.

Renyi Liu and Howard Ochman, 2007, Stepwise formation of the bacterial flagellar system, Proceedings of the National Academy of Sciences, 104 (17): 7116-7121

Zita Martins, Oliver Botta, Marilyn L. Fogel Mark A. Sephton, Daniel P. Glavin, Jonathan S. Watson, Jason P. Dworkin, Alan W. Schwartz, Pascale Ehrenfreund, 2008,.Extraterrestrial nucleobases in the Murchison meteorite,  Earth and Planetary Science Letters. 15 June 2008.  13/06/2008 Cornell Uni. Library. (PDF) https://astrobiology.nasa.gov/articles/extraterrestrial-nucleobases-in-the-murchison-meteorite/  [retrieved 24 Mar 2011].

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Eng.trans. Chance And Necessity, London: Fontana, and Harmondsworth: Penguin.  

David Mumford and Agnes Desolneux, 2010,  Pattern Theory: the Stochastic Analysis of Real World Signals, Natick, Massachusetts: A K Peters.

Keiichi Namba, 2003, Revealing the mystery of the bacterial flagellum: — A self-assembling nanomachine with fine switching capability, Osaka: Japan Nanonet Bulletin, 11 (5th February 2004) (Issued in Japanese: March 25, 2003). https://www.nanonet.go.jp/english/mailmag/2004/011a.html

D. E. Nilsson and S. Pelger, 1994, "A pessimistic estimate of the time required for an eye to evolve", Proceedings of the Royal Society B, 256: 53-58.

Anthony O'Hear, 1997, Beyond Evolution: Human Nature and the Limits of Evolutionary Explanation, Oxford: Clarendon Press.  Anthony O'Hear is a philosopher and classicist gives a thorough survey of the issues of human knowledge, morality, aesthetics.

L. Patthy, 1990, "Evolution of blood coagulation and fibrinolysis", Blood Coagulation and Fibrinolysis, 1(2): 153-66.  

David M. Raup, 1991, Extinction: bad genes or bad luck?, New York, Norton & Co.,

James Shapiro, 2001, "A 21st Century View of Evolution", Proceedings of the 4th International Conference on Biological Physics, Kyoto, Japan, July 30 - August 3, 2001, Chicago: University of Chicago Press. Considers design principles and computational engineering within the genome to be largely responsible for evolutionary change, as opposed to variation as a random walk. 

Erwin Schrödinger, 1944, What is Life, Lectures at Trinity College Dublin. Available at: https://whatislife.stanford.edu/LoCo_files/What-is-Life.pdf  accessed 24/07/2011 also reprinted in What is Life with Mind and Matter and Autobiographical Sketches, Cambridge University Press, 1992.

Gerald L. Schroeder, 2009, God According to God, New York: Harper Collins. Recommended.

Claude Shannon, 1948, A Mathematical Theory of Communication, Bell Systems Technical Journal, 27: (3):379-423 and (4):623-656.

F. J. K. Soontiëns, 1991, Evolution: Teleology or Chance, Journal for General Philosophy of Science, 22 (1):133-141.

Douglas F. Watson, 1st April 2011, "On the Anthropic Principle in the Multiverse: Addressing Provability and Tautology.",  Vanderbilt University.arXiv:1103.6044 [physics.pop-ph] Note the publication date!  A satire on typical arguments of this kind.

Chandra Wickramasinghe, 2011, "Alien Invasion: Did Life on Earth Originate from Outer Space?"  Fortean Times,  No. 277, July 2011.