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Moving Beyond Darwin

Moving Beyond Darwin

MbddarwinThis essay was first published six years ago in a very obscure publication. Since it has only been read by at most half a dozen people, I have decided to post it here where we might make that up to the full dozen. It's about 6,000 words, and has nothing to do with games.

I have always had the unshakeable feeling that there was something wrong with our perceptions of evolution, but since biology has been my ‘neglected science’ until recently, I haven’t really been in a position to expand my viewpoint until now.  I once said that I felt the modern view of evolution explained matters of biology as well as Newtonian physics explained the physical world.  A good friend countered that, to a reasonable degree, Newtonian Physics was a good approximation for the physical world.  Two years later and I can confidently report that Newton fudged his results to get his version of gravity accepted by the orthodox scientific community.  It is fair to say that for terrestrial engineering, Newtonian gravity suffices. 

But in evolutionary biology, where the battleground is largely ideological and not pragmatic, rigid adherence to neo-Darwinian beliefs seems less acceptable.  Science, or at least the patient, agnostic investigation of what passes for reality (which is what I hope science represents), has very little to do with what the establishment sometimes attempts to pass off as truth.

So what am I about to say?  That Darwin was Wrong?  Of course not.  He was no more Wrong than he was Right.  He had an idea, a brilliantly insightful idea, certainly, and an idea that has helped many other people have brilliant ideas.  But Darwin’s idea no more perfectly explains biological life than Pythagorus or Euclid’s ideas perfectly explained mathematics.  It was the first step on a long road.  I’m going to tell you my current view of that road on the understanding that this is just my perspective.  Walk the same path and you may well see different things.  But this is what I see.

In the beginning…

We don’t know how life began.  We probably never will know.  Likewise, we will probably never know with any certainty if terrestrial life started in pools on Earth, in the black smokers of the deep oceans, on Mars, or in the deep voids of space (all of which have been suggested by various people at one time or another).  One thing I can say with confidence is that at this point in time, all these possibilities and more are at the very least plausible.  It is fair what Lynn Margulis says, however, that moving the origin of life off the planet doesn’t get us any closer to solving the question of how life started, but frankly what little evidence we have at this time no more points to Earth than it does to space.  The origin of life remains a question of faith.

However, it seems probable that the first step towards life was some kind of self-replicating chemical construct.  Once such a chemical existed it would only be a matter of time before all available raw materials in the putative primordial soup would be converted to this replicator.  Once you have self-replicating chemicals, the way is open for more efficient replicators to develop, and certainly as time goes by, these replicators have the opportunity to become more complex.  Ilya Prigogine, a Nobel prize winner who for once almost certainly did deserve praise, showed how increasing complexity was an almost inevitable by-product of dissipative systems (such as living organisms) which means essentially that whilst the rules of thermodynamics suggest everything will fall apart, life is playing by a subtly different set of rules.

So we have our so-called prebiotic replicator, and somehow, by some mechanism, we end up with a genetic code.  Probably a whole set of different genetic codes, actually, but somewhere down the line we get DNA and RNA and the raw materials of life as we claim to know it.  Most of this early view of life is undisputed in so much that no one has anything but broad guesses as to what could or might perhaps have happened.

MbddnarnaAnd here comes my first break with conventional thinking.  The establishment claims that whilst the creation of self-replicating molecules is monstrously unlikely there were enough random encounters between chemicals that it became highly likely, if not inevitable.  Fair enough, as a belief.  But one can hardly claim that such an approach is any more sound than claiming that God, Goddess, Whimsy or Magic caused the origin of these molecules, because either way the hypothesis is untestable and comes down to what you, the individual, choose to believe.

I personally believe that it makes no great shakes as to how we choose to see the ball being set in motion.  What’s far more interesting is the fact that we are here now and able to waste our time speculating about such things, if we choose to.

Unwitting Co-operation

MbdprotistaSomehow, we get to the earliest single celled organisms.  Whatever else we can say about them (and we can’t say much with any confidence) they were good custodians to the planet.  They looked after it for four billion years without batting an eyelid, because quite frankly, the first eyelid wouldn’t evolve for quite a while.

I suppose the conventional view of this time before multi-cellular life was a host of different competing organisms, savagely fighting for the available resources and with only the strongest surviving. 
Eventually the fist single celled organisms were so advanced that they became multi-cellular and took the battle onto a whole new playing field.

Nothing could be much further from the apparent truth of the matter.

Firstly, nothing short of Divine Intervention could have created the cells from which all multi-cellular life springs using only the Darwinian mechanisms of mutation and natural selection. Even the orthodox scientific community has been forced to concede this (although like all defeats, the news is slow in travelling).  The biological requirements for multi-cellular life are such that randomly shifting nucleotides is just not enough to make the leap.  Later, we will look at just what was required to make that advance possible at a cellular level, but first we have to look further afield.

Biologists, generally speaking have been reluctant to pay attention to the atmosphere, despite the fact that nearly all life depends on it as a complex conveyor belt of raw materials.  Interestingly, geological evidence suggests that the composition of the modern atmosphere is essentially the same as it has been since the early days of life.  The reason this is so interesting is that the composition of the atmosphere, whilst apparently stable, is a long, long way from equilibrium. 

In case I am losing people’s attention, let me restate that as follows: if all life on earth was somehow made extinct, say by a drunken God, inadvertently pushing the biological self destruct button, the atmosphere would very rapidly change a very different mixture of gasses.  The only reason the atmosphere stays the way it appears to be is the action of the biosphere (and some related processes) constantly removing some gasses and pumping others into the air.

Mbdearth_1I won’t dwell on this for too long, because if you are interested you should go and read James Lovelock, who knows the material far better than I do and writes with both charm and insight.  The bottom line is that one thing that had to happen in the four billion years before multi cellular life began to flourish, was the establishment of a homeostatic control mechanism that could regulate the environment and keep it within tolestable limits.  Lovelock calls this mechanism Gaia.

The outspoken atheist Richard Dawkins calls Gaia “wrong and dangerously wrong”.  I find his attitude surprising and disappointing.  Homeostatic control mechanisms – such as that which keep your body at a constant temperature – certainly evolved in multi cellular life.  It is not at all clear to me why anyone should consider a large collection of unicellular lifeforms, to be subject to wholly different rules to multi-cellular life, except that the former has even more room to maneuver.

No one is claiming that the organisms that first came together to make Gaia were aware of how their co-operation was creating a stable environment for life.  It is merely the case that whatever helps life persist will in turn be encouraged to persist, just as implied by Darwinian natural selection.

And despite Dawkin’s protestations, the geological, atmospheric and biological evidence points unerringly towards Gaia.  Without it, even the small yet steady rise in our suns out put of radiation would have rendered the Earth a lifeless rock many aeons ago.  Without it, the build up of certain gasses would have made multi-cellular life impossible.  When Lovelock first proposed Gaia in the 70’s it was just an insightful hypothesis attempting to explain some pretty gigantic gaps in our knowledge.  Today, Gaia theory has gained a considerable degree of legitimacy.

I will take a moment to explain why this essay seems to be attacking Dawkins so resolutely. It is important to understand that the orthodox scientific community, being essentially a power block of old ideas, has surprisingly little variety in its perspective. Because of this, any one spokesman is as good as any other. Since Dawkins willingly accepts the mantle of what might be characterised as the current (or currently retiring) paradigm, I have no qualms at directing my criticisms towards him as a representative of that which will eventually pass into history. (This runs on Thomas Kuhn's proposition that all scientific paradigms eventually shift).

I should also say I have great respect for Dawkins' work; the idea  of ratcheted progress in evolution is a powerful explanatory  device, for instance. The problem in my view is his lack of  perspective. Dawkins himself admits he lacks a grounding in  philosophy, and this sadly lets him down. His concept of a meme is  a valuable metaphor, for instance, but when he writes about memes  he steps out of science and into philosophy, and his subsequent  attacks on religion are both intensely biased and quite  unreasonable.

The Earliest Communes

With Gaia in place – a huge selection of different organisms and processes that, through changes in population and similar mechanisms regulate the terrestrial environment – multi-cellular life was a possibility.  Animals, as we know them, require a high level of oxygen in the atmosphere to act as fuel for their high-octane metabolisms, but the oxygen could not be allowed to rise too high or everything not underwater would be wiped out in a spectacular conflagration the moment lightning first struck. (Oxygen is dangerous stuff - we forget this because we need a certain amount to fuel our bodies. But a culture of non-oxygen breathing creatures would probably be quite disturbed by our relationship with such a dangerous gas).

The stage was set.  But our actors were still just single cells. Hamlet one suspects would be less impressive if performed by bacteria.

SET, or Serial Endosymbiosis Theory, has struggled for acceptance for much the same reasons the Gaia theory has.  Anything that even remotely resembles holistic thinking has been anathema to the current paradigm.  However I am proud to report that all but one of SET’s claims has now been grudgingly accepted by the orthodox scientific community, and Margulis remains by her own admission stubbornly optimistic that its final (and from my perspective, least important) claim will eventually be vindicated.

It intrigues me, but does not surprise me, that Margulis has been involved in two of the scientific theories at the forefront of the new paradigm, Gaia theory and SET.  Call me a sexist if you will, but women strike me as far less likely to get trapped in the closed minded territorial tub-thumping of Neo-Darwinist fundamentalism.  I have high hopes that the near future will finally put pay to the hideous old boys club that served so effectively to keep women out of scientific research in the nineteenth century and before.

But what is SET, and why is it so important to multi cellular life?  In essence, what it claims is that the components of eukaryotic cell (those cells that make up multi-cellular life) are the product of symbiosis between single-cellular components that were to become the nucleus, the ribosomes and the mitochondria. They started out as single celled organisms in their own right and ended up inside the cells of modern life, possibly as a result of a failed attempt at digestion.

MbdeucellSET is practically unrefuted at this time (although the issue of whether flagella are also the result of endosymbiosis remains a live one).  Every cell in our bodies is the modern descendent of the earliest communes in existence, and just as Gaia represents macro-symbiosis, SET represents micro-symbiosis.  It is becoming more and more apparent that the history of life is not just the story of competition between differing life forms but also of co-operation.

The co-operation of the separate organisms that make up eukaryotic cells provided the raw materials for life to 'go multi', so to speak. With function differentiated inside the cell, each cellular component could become more efficient at what it did, because it could rely on its allies to carry out those tasks that it wasn’t good at.  So mitochondria concentrate on being efficient at handing energy whilst the nucleus learns how to store protein designs safely, and to co-ordinate the construction of these proteins.

Now we have a stage, some actors and (for those who choose to believe in such things) a director.  All we are missing is a script.

The Impotence of Being Earliest

MbdprecambrianThe earliest multi-cellular fauna we know about are found preserved in Pre-cambrian strata and are known collectively as Ediacara. They appear essentially to be large, hollow pancakes, with very little differentiation.  We don’t know if their cells were eukaryotes (i.e. cellular communes) or not, but we do know that they didn’t last long, geologically speaking.  If they represent multi-cellular life’s first script, they are more an episode of Days of Our Lives than Hamlet.

A lot of questions remain unanswered about both this early experiment in Growing Big and the more successful experiment to follow.  I am particularly interested in how cell differentiation came about.  Without it, you couldn’t be made of bone, muscle, blood, brain and the other components that make up how you are.  Without differentiation, you would presumably be a hollow pancake just like the Ediacara.

In essence the problem is the issue of design.  There is little doubt that DNA represents the blueprint for all the proteins in an organism.  But one cannot build a house from a list of building materials.  A plan or design of some kind is required.  I am greatly troubled by my inability to find any evidence that the scientific community has taken this issue seriously.  They just seem to assume that the DNA does it somehow.  If this is the case – that the establishment view rest purely on assumption – then it is a deep embarrassment to a supposedly scientific perspective.

Informally, I was able to convince myself that it was theoretically possible for an organism’s design to spring from the result of a branching instruction, coded in the DNA implicitly.  But I could not find any evidence to support this hypothesis.  Indeed there is more evidence to support Rupert Sheldrake’s suggestion that an animals shape is controlled by morphic fields than to support the purely reductionistic approach.

Not that I am saying Sheldrake is right.  We just can’t be sure right now.  But as I once said to friend, his work is most valuable because he is asking the right questions.  Sheldrake, of course, has a very holistic perspective on biology, but many of his questions may have reductionistic answers. Indeed, elements of Sheldrake’s work appear to be explicable by epigenetic programming (a recently discovered Lamarlian inheritance mechanism).

Nonetheless, it is fair to say that Sheldrake was influential in reopening the issue of Lamarkian inheritance (the idea that changes to an organism can be passed to its offspring). In that area, his courage has been an asset to the research community, especially those outside of the narrow confines of the conventional thinking. There is now little doubt that there are Lamarkian inheritance mechanisms that supplement classical Mendellian inheritance and allow organisms a greater degree of adaptability to changes in local conditions on time scales too short for conventional evolutionary mechanisms to operate.

To return to the point in hand, it is not at all clear how organisms end up the shapes they do, and neither is it clear how the early cellular communes developed the ability to take on these shapes. The one thing that is clear is that as soon as life learnt how to do it, there was no turning back.

Lights! Cambrian! Explode!

MbdcambrianThe Cambrian explosion, as it is affectionately known, is the name for an extraordinary period of time roughly 545 million years ago. It is so named for the profusion of life that seemed to just explode onto the scene in what is (in geological terms) just a clock tick. Thanks to the infamous (to paleontologists at least) Burgess shale, we have a surprisingly detailed record of early multi-cellular life.

We will probably never know what bridges the gap between the first eukaryotic cells and the fauna found in the Burgess shale, but we can speculate. It fascinates me that there should be such variety of body plans in such a short period of geological time. It implies a rate of change vastly more rapid than any other that the fossil record points to.

Perhaps multi-cellular life occurred simultaneously from many different sources (which makes sense from the perspective of Formative Causation/morphic fields, but makes very little sense from an orthodox perspective). Perhaps the early co-ordination mechanisms were so sloppy that early organisms just couldn’t reproduce accurately, and random design was the order of the day. Perhaps some condition that triggered multi-cellular life somehow triggered the change in many different eukaryotic cells at the same time. We can only speculate.

When I first came to look at the Burgess shale, I had been told that there were a vast array of different body plans, far more than exist in the modern world, and this intrigued me, as I have always been suspicious of the apparent lack of variety in the general design of creatures. Why should bilateral symmetry be so universal, for example? (Bilateral symmetry essentially means that an organism has a line of symmetry from head to tail – which if you think about it is true of the vast majority of multi-cellular organisms that are capable of movement).

My most biologically literate friend suggested that bilateral symmetry might be an inevitable part of design for an organism that moves; ingest food at one end, excrete waste products from the other. Very convenient as you can then move towards food and away from your own waste. I would tend to agree with her, but since bilateral symmetry was already the norm by the time of the Cambrian explosion I have to be sceptical about this idea.

Given the rapidity at which bilateral symmetry became the norm (bearing in mind that there are many other ways of putting together a hypothetical organism, including radial symmetry such as in starfishes and asymmetric plans, as in plants) I have to question any appeal to Darwinian issues in the establishment of bilateral symmetry as a prevailing scheme. Dawkins might claim that bilateral symmetry represents such a good engineering solution that it was inevitable that it would predominate. But one has to ask how we know it represents such a good engineering solution, and Dawkins answer might be that it must be a good solution because it predominated so rapidly. Having reduced his reasoning to a mere tautology, we have no choice but to reject it, at least on scientific grounds.

MbdtasmanianwolfI have met the same argument when dealing with convergent evolution in other places. The Tasmanian wolf is almost identical in design to other canines, including the domestic dog. And yet the Tasmanian wolf is a marsupial, genetically removed from dogs and their kind by such a huge degree that they are effectively not related at all. (And there are many other examples of convergent evolution, such as ichthyosaurus and dolphins). The conventional attitude seems to be that there must be a limited number of solutions to the problems of animal design and hence it is not surprising that many animals find the same solution. This is not wholly implausible, but it is entirely unsupported by any specific evidence. One might just as well say that Goddess/God/Aliens designed the genetic code to produce such similar animals for some spiritual purpose. It argument would hold about the same weight.

Someone once said to me, as I was arguing that there were important questions to be resolved regarding convergent evolution: “But convergent evolution does happen.” This is a wonderful statement, because it seems to miss the point entirely. Of course it happens. We can see that it happens. But that doesn’t put us any closer to understanding why it happens.

I have no solution to this question of bilateral symmetry, although I feel it is of some considerable relevance. If the common assumption about body designs resulting directly from DNA is validated at some future point, perhaps it will be revealed that bilateral symmetry is the most information efficient way of designing an organism that is going to move. Who can tell? For now, the issue is an open one.

The importance of the Cambrian explosion, in my opinion, is twofold. Firstly, the person who discovered the soft-bodied fauna completely missed their relevance and tried instead to classify them in terms of modern animals. One can hardly blame him. He was unable, as so many scientists are, to see his find in any terms other than those he had been taught and had lived with comfortably for so long. What a mental breakthrough it must have been to suddenly realise that what he had discovered was something that completely overturned conventional thinking on life! The Burgess shale represents a wonderful illustration of how excessive belief in currently orthodox ideas can block the acceptance of ideas that more accurately model what we choose to call reality.

Secondly, the Burgess shale represents reasonably convincing evidence that the classical Darwinian perspective of survival of the fittest is erroneous. Why? Because no-one, not even the most learned biologist, could look at the fossils of the Cambrian explosion and say with any confidence which species were destined to evolve into modern life, and which were destined for extinction.

Experts have been able to identify which species were the likely ancestors of modern life, and they look no better adapted to their environment, or superior in any other sense, to many of the other forms around at the same time. Indeed, only the tiniest fraction of the body plans around in Cambrian times survived to the modern day. And as far as we can tell, more by luck than by superior design.

The message from the Burgess shale appears to be quite straightforward. Evolution is not a record of progress (as was believed for quite some time – and indeed, is still believed in some camps) but a record of the adaptations made by various creatures to survive at various times, and who survived to the present day in part by a whole lot of luck.

Stephen Jay Gould talks of the Wheel of Fortune as a metaphor for the way that many species become extinct – extinction by lottery. Whilst some are no doubt made extinct by competition from better adapted organisms, the vast majority die out for no reason other than random chance. With this in mind, any idea of evolution as a line with single celled organisms at the bottom and man at the top (the so called "ladder of progress") is insane and ridiculous. Our position is no more privileged than any other life form around at the moment. Our chief difference seems to be that we have evolved a sense of arrogance far outstripping the rest of nature.

Where Did All the Giants Go?

MbdmegladonI find it curious that all the truly gigantic animals have become extinct. Whale sharks and blue whales aside, modern life is practically miniaturized compared to the standards of the Mesozoic (crudely, the Dinosaur Era). We all know the Big Lad dinosaurs like tyrannosaurus rex, and apatosaurus (brontosaurus), but if you have a good look around you’ll find huge birds, giant snakes and enormous sharks have all gone by the wayside. (Megladon, a shark the size of a whale, makes the great white shark look like an anchovy by comparison).

All extinct.

Now you may wish to claim that these animals were just not efficient, or that they were out-competed or something similar. But the fact is, the environmental conditions than existed in the Mesozoic were essentially identical to modern conditions. And these creatures existed for millions of years, with substantially no changes at all if the fossil record can be believed.
Megladon teeth, for example, are one of the most abundant fossils around.

I would hazard a guess that the reason that there are no giant creatures around at the moment does not represent the superiority of ‘smaller’ animals, but merely the prevailing trend for the current conditions. People often forget that the environment that an organism adapts to is made up not only of the inanimate, but of all the animals that co-exist with it. It seems plausible to me that the web of Mesozoic life supported these giant predators, whereas our current days where speed rather than size seems to be more important cannot support such enormous animals.

But times will change. At some point, the playing field will shift again and no-one can say what will predominate when it does. This is one of the great messages of evolution, that what dominates now will likely be extinct at some future point.

MbdammoniteTake one of my personal favourite animals, the ammonite. These nautilus-like creatures dominated the oceans in the Mesozoic, but when the Cretaceous came to an end, they, like the dinosaurs, were wiped out. I have seen no better explanation for the extinction of these shelled creatures beyond bad luck. The asteroid impact at the end of the Cretaceous (an event for which the geological evidence is largely in support of – the iridium deposits found in post-Cretaceous strata lack any other reasonable explanation) may well have been the cause of the mass extinction that robbed the world of the dinosaurs and the ammonite.

The ammonites gave way to the fishes. Not because the fish were superior, but because the ammonites were unlucky. That seems to be the way it goes.

This leads to the concept of punctuated equilibrium, the theory proposed by Gould and Eldredge which suggests that rather than a steady, continuous process, evolution is marked by periods of stasis (in which very little evolutionary change occurs) followed by sudden periods of change. Animals alive today owe their survival only in part to superior adaptation, and to a very great degree to being damned lucky.

After much investigation, I can only conclude that Gould and Eldredge have hit the nail on the head. At this point in time, the only arguments against punctuated equilibrium that I have heard result from trying to use classical evolutionary reasoning to explain something that now seems far more complex than simple Darwinian reasoning can deal with.

For example, a sensible complaint is that punctuated equilibrium implies evolution only takes place at certain points in time, whereas as we understand the Darwinian methods, it should be taking place constantly. This is a reasonable point to raise, and like many reasonable questions it exposes the problems in orthodox thinking.

Darwinian thinking goes something like this: organisms mutate, superior organisms thrive, inferior organisms die. Hence, evolution constantly improves organisms, adapting them to their environment. This view in the extreme is what is known as adaptionism.

However, let us take task with the first point, that organisms mutate. I am prepared to accept that there are indeed methods by which changes to organisms occur (after all, evolution is dead in the water without it). But despite the common claim, no evidence exists that new genetic variation occurs spontaneously. Although we have seen natural selection at work in our time, we have only seem selection work on genetic features that were already present.

MbdblackmothFor example, many people know about the moth that, with the advent of the industrial revolution, began to be increasingly found ‘dressed’ in black rather than its natural beige. The black moths could hide on the soot-caked trees and walls of the post-industrial world better than the beige moths, and hence had a selective advantage. However, the genes for the black colour were already present in the moth. The genes did not evolve in our time.

Indeed, there is a substantial problem with evolution by mutation, in that 99% of mutations (or more) are detrimental to an organism’s chances of survival. Most mutants die. The orthodox scientific community responds by claiming that, yes, most mutants die, but over the time scales of evolution enough mutants occur that a small number are ‘fitter’ and hence survive. There is nothing wrong with this argument, but there is no evidence for it.

Conversely, there is evidence that natural selection actually slows the rate of change in genetic material. This apparently contradictory claim was first suggested by Kimura, and has since been demonstrated to be factual. The rate of change of nucleotides in the parts of DNA which are not expressed (intron DNA) compared to those parts that are involved in coding proteins used by the animals (exon DNA) is radically different: and it is the introns ("junk DNA") which changes faster.

It actually makes a lot of sense. If most mutations are detrimental, then most changes to exon DNA will cause the creature to be inferior and hence to be less competitive than its non-mutant peers. Conversely, changes to introns produce no effect to the individual creature and hence the rate of change of sequences in intron DNA can be much faster than in exons where the watchdog of natural selection limits the amount that the code can change. It is called the Neutral theory of genetic change, and it has been broadly validated by research.

In fact, I even have a hypothesis as to what the ‘purpose’ of intron DNA might be. Viruses occasionally copy sections of DNA to different parts. Often these changes are dangerous or fatal, but at times the substitution effectively codes for a new and exciting protein. This may well have happened recently (geologically speaking) with the Antarctic cod. Genetic evidence suggests that its ‘anti-freeze’ glycoprotein occurred as a result of a transposition of intron DNA into an exon. Given that intron DNA can mutate far faster than exon DNA, it seems plausible to me that evolutionary novelty might happen as a result of intron DNA’s freedom to mutate. I call this the Cut and Paste hypothesis, but at the moment I have no way to test it. If this hypothesis is true, intron DNA is a requirement for genetic novelty.

Moving back to the central issue of punctuated equilibrium, I do not find it at all hard to accept that evolutionary change is ‘stifled’ during long periods of history. This is, after all, exactly what is shown in the fossil record. Some scientists explain the same evidence by saying that there are many other animals, but they just aren’t recorded in the fossil record. (This is a bit like saying that the accused’s finger prints are not found at the crime scene because the accused never touched anything). There are going to be gaps in the fossil record, that is unavoidable, but one cannot deny that many animals span a vast period of billions of years in the fossil record.

MbdcretaceousmammalsOne can suppose that once a set of organisms have evolved into a reasonably stable set, the ‘room to maneuvre’ is so low that change can only happen on the most gradual of time frames. However, after a mass extinction, a whole new set of rules apply. The extinction of the dinosaurs and their kin made way for mammals to have a shot at being the top predators. Throughout the Mesozoic they had been tiny little scavengers, eking out an existence in between the lumbering thunder lizards. At the end of the Cretaceous, the rules changed and mammals got their turn at bat. Presumably, somewhere down the line, something will take out the mammals and give some other type of animal a chance.

It occurred to me, as I was devising the Cut and Paste hypothesis, that after a mass extinction, the pressure of natural selection should actually be reduced. With the well established predators gone (dependent as they are on the food web underneath them), organisms that previously would have been too poorly adapted to survive suddenly have a chance to show their stuff. Dawkins’ metaphorical ratchet is off, and for a brief period of time animals have far greater freedom to change.

This, for me, is quite a compelling argument towards punctuated equilibrium. Because when we look through the fossil record we find rapid change in the animals recorded in the fossils only in two types of place: one, at the boundary points representing mass extinctions (where the rules of the game were suddenly changed), and two, at the Cambrian explosion (where the rules of the game were being made up as life went along).

Changes do occur in between these times, stasis is not total, after all, and evolution still works in the long stretches of time in between. But the most radical changes to life happen in the wake of the mass extinctions, when life has a chance to make up a whole new set of rules. In our case, we’ve come into the game at a time when giant animals are no longer as effective as once they were. Who knows what the life that follows us will find?

MbdjupiterAs a final point before I put punctuated equilibrium to one side, it is worth understanding that if major changes in life can only come about by mass extinctions, then we may owe our much-vaunted intelligence in part to the fortuitous position of Jupiter and the asteroid belt, the arrangement of which causes asteroids to be thrown repeatedly into the path of the Earth. Perhaps this arrangement constitutes an ‘evolutionary pump’, shaking up the status quo frequently enough for evolution to achieve far more than it could in a state of constant stasis.

Then again, if it wasn’t for Jupiter drawing away many of the comets from the Oort cloud from the Earth’s surface, we might have impacts so frequently that life would never actually get much of an opportunity to recover from the devastation and we might have no multi-cellular life at all. We can only speculate.

And so… the Present

And so I have followed evolution from its shaky beginnings, through its questionable middles and now to its uncertain present. There are many questions that remain to be answered – more than I can adequately elucidate in a single essay. However, from careful analysis of the competing views I can only conclude the following:

Evolution consists of a large number of tools, of which mutation and natural selection represent only one perspective.

As well as the classical Darwinian and Mendellian processes, contingency seems to be a major theme of evolution, and life seems to utilize a high degree of symbiosis on both a macro and micro scale, as well as utilising other mechanisms, such as epigenetic inheritance, which we have only just begun to investigate.

It is far too premature to assume that we have found even a fraction of the answers to the questions that Darwin first raised.

I will leave you with one final thought. If you are not yet convinced of the importance of symbiosis to the history of life, consider that mammals are only able to give birth to live young by virtue of a viral invader which has integrated itself into our genetic make up. When you see a foetus develop, it is surrounded by little viral allies which do not harm the developing organism but rather have made live young a possibility by breaking the ties with the embryology of the past.

MbdmeerkatsCompetition may be part of life, but it is not the whole of life. Dawkins’ “selfish gene” metaphor may be a useful tool for allowing us to reason outside of the narrow confines of humanocentric thinking, but it does not follow that selfishness is the guaranteed norm. Indeed, without symbiosis, multi-cellular life simply could not exist. And I cannot help but find it ironic that whichever way you look at the “selfish gene”, life breeds out pure selfishness: any creature which cares only for itself must surely die out. Dawkins may see an organism sacrificing itself for the survival of its young as selfishness, but from the point of view of the organism I can see only altruism. An individual gene, after all, codes only for a protien and is scarcely in a position to do anything but persist if it happens to be useful.

In this, as in so many things, it comes down to which metaphors you wish to use, and how you wish to look at the problem. I now look on the current world genome – the complete set of all the different genes in use by organisms today – as a record of those genes which helped propagate life up to this point. Some of those genes may have principally benefited just an individual organism, and some may have contributed to wider mechanisms. But ultimately, all we can say about the genes in the world today is that they made it here somehow.

And what more can you say about humans other than that, somehow, we made it here.


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ooh my god, i tried.
looks like someone got a little intimidated by danc's long winded nintendo post :P (j/k)

That is an awful bit of muddle-headed thinking that manages to be confused about virtually every concept in evolutionary biology. The origin of life, for a scientist
attempting to create a theory, is NEVER a question of faith: it's a question of using the best-known theory that accords with the presently-known evidence, and that is a testable hypothesis. And it goes downhill from there, managing to misunderstand thermodynamics (Life is able to create complexity in exactly the same way that a star is able to create complexity - by the
application of massive amounts of energy. There's no "special rules" for life.) through to punctuated equalibrium (which is based around small populations, NOT sudden bursts in the general population). He even manages to get the weather in the Mesozoic period wrong.

Bunk, stuff and nonsense. You'd be better off reading the articles about evolution on Wikipedia.

Ouch! :) Well, I suppose I open myself up for such criticism when I republish old material like this.

Anyone have a less bellicose reaction? Anything constructive to offer? I'm not really interested in going to war with anyone over this, but I was hoping for a chat. Have I picked a topic for which it is not possible to have a friendly discussion?

i apologise if my spontaneous comment may have come off as hostle, disruptive, or too rash for jest. i really enjoy your blogs and don't want to pollute your blog with unwanted comments. it wasn't a topic of interest for me, if i were more mindful i would have just moved on.


"it's a question of using the best-known theory that accords with the presently-known evidence, and that is a testable hypothesis."

The problem is, spontaneous beneficial mutations that spread virally across a population are not "testable" per se, or reproducible in a lab. It is the best-fit hypothesis so far, but it's not something that can be tested yet. Natural selection can be verified, but inventing new genetic features is in fact a matter of faith to at least a small degree. It does require some leaps of faith to accept it - it seems like the logical solution, but until we find a way to test it we can't know. Now, keep in mind, pointing out that evolution is flawed does not in any way give credence to Intelligent Design, which requires several larger leaps of faith to accept. Evolution is by no means a perfect theory, but that does not enhance the status of the wishful thinking that is ID.

Additionally, while the Wikipedia is a good primer, it isn't the best source for in-depth fact finding. The Wikipedia makes for a good jump-off point, but it is not, of course, the last word on any topic.

C - Don't worry, I didn't find your post hostile! I know this piece is borderline unreadible. :) I had hoped to rewrite the key points into something shorter, but then I discovered that it had been so long since I'd read the half a dozen source books that I just couldn't face it. :)

James - your comment makes me see Ian's in a different light. Of course, the keyword 'faith' makes it look like I might be touting Intelligent Design... this probably set up a hostile reaction at that point.

It's a common facet of philosophy of science essays (and this is far from a sterling example) that they compare certain scientific models to belief in God et al. The violent reactions some scientists have to these comparisons is another reason why I believe philosophy of science would be a good thing to teach in schools.

I'd recommend to you The Beak of the Finch (, which discusses evolution in the populations of modern Galapagos finches. There is continuous evolution, but since it lacks any particular direction, the result is simply jitter around the mean. If there were a major change in environment, then you would see a major morphologic shift, ala punctuated equilibrium, but what would have changed was not the conditions of evolution, but the conditions of the environment.

As to large bodied critters, large creatures in general have an advantage in being less subject to direct predation, hence they would tend to arise in any long-term stable environment. However, large body size generally requires a reletively large resource territory, and thus large creatures are more sensitive to environmental changes which may subdivide their territories below their minimum requirements.

Finally, while I am a religious person, I hesitate to fill voids in data with the divine. If data appears to fill that void, where does that leave the divine?

Thanks so much for your comment, Evangolis!

Your explanation in regard of large creatures makes a lot of sense to me - although for a large oceanic animal like megladon, subdividing of territory seems harder to achieve. Reduction in overall resource supply is perhaps a more tenable theory in this case.

Although this essay is rather flippant in its use of religious terminology, I don't actually suggest filling gaps in data with the divine, per se - my mention of Divine Intervention was intended to contrast the insufficiency of strict Darwinian theory in the field of the origin of animal cells. I believe the realm of science (the testable) and the realm of religion (ethics and metaphysics) do not significantly overlap. I am prone to quote Einstein in this regard: "Science without religion is lame, religion without science is blind."

I will be sure to check out the book you recommend! Thanks once again!

Suyi: thanks so much for this! I had been thinking about taking this link off the sidebar - it's a very old article and very sloppily written - but this more than justifies it remaining! :)

An even older response to excessive focus on the agon of evolution... Neat. And written in *1902* as well. By Kropotkin. It's just too good to be true. :) I shall have to snag a copy of that. Thanks again!

You use words like "Somehow, We don't know, and probably". These are the words of someone who is under the religion of modern/secular humanism (i.e. Darwinism). You reject that which you cannot explain. I am not talking about just the sovereignty of God in creation, but the documentation of that creation given to Moses by God. Creation is the only sect to record how life came about. If you say it was written by man without witness, then be prepared to throw away the theory of evolution. Evolution has never been witnessed. The beginning of the world was only witnessed by God, though believeably manifested to Moses, but is revealed in the order of the universe by creation creating and rebirthing every second of everyday. You can get nothing in this universe without creation. Macro-Evolution, species leeping species, has never been witnessed and there is no manifestation of it in this time and space. I pray for your understanding, not for my benefit but for your own understanding and salvation. God Bless!

Chris: Thanks for commenting! While I agree with you on a couple of points - that you can get nothing in this universe without resorting to metaphysics, and that "species leaping species" has not been directly witnessed, I don't agree with your other points, which depend upon your own particular metaphysical choices. But I assure you, I am not much of a Darwinist or Neo-Darwinist, and believe these theories need considerable revision and improvement.

God's message to Christians was to go out into the world and to love one another as Jesus loved everyone. Were he around in physical form today, I do not believe he would consider this issue to be of any importance whatsoever. I call upon anyone who considers themselves to be a Christian to not worry about the ideas that scientists amuse themselves with and instead focus on doing good in the world around them.

Best wishes!

These might also be stimulating:
Darwin's Lost Theory of Love by David Loye

"Kropotkin Was No Crackpot." Bully For Brontosaurus (1991). Stephen Jay Gould.

(cribbed from The Trouble with Music, Mat Callahan)

Thanks for the continuing contributions, Suyi! I very much enjoyed Mutual Aid, which I read late last year.

I'm pretty sure I've already read Bully for Brontosaurus... I made my way through a lot of Gould collections when I lived in London. I would like to get my own copies, though.

The David Loye book is new to me, though - definitely worth checking out.

Thanks again!

Earlyish in the piece you lament the lack of connection between dna and actual products. I'd point you to Godel Escher Bach (,_Escher,_Bach ). He discusses internal data vs external data (the message vs the container), specifically as a leadup to discribing how dna/rna blur the line.

I confess my grip of molecular biology lets me down, but he has significant references that can probably illuminate more than I ever could.

On the issue of bilateral symmetry, another interesting thing is the sexual selection involved - most species prefer partners who are symmetrical. The explanation I have read suggests that this is a good indicator of health and good quality genetic material, because it is much harder to produce symmetry than to wreck it (disease, injury and mutation can all destroy symmetry, for example).

Oh, wait - one more thing: On cooperation.

There are lots of studies on how virii become less dangerous over time. It's not hard to see how not killing your host can let the virus live longer and spread further, and the only thing better than not killing your host is helping your host (I don't know of any studies where virii actually went from parasitic to symbiotic, but I'll bet it's happened).

Jules: thanks for the comments! I wrote this piece *ages* ago, and it's full of minor problems. I've read most of Godel Escher Bach: Eternal Golden Braid... I haven't seen anything that bears on this directly in the book, but I wouldn't be surprised if there was.

Recent research has shown up another role for DNA, namely in the form of molecular switches. This gives three components to DNA - genes (data), switches (code) and introns ("research and development"). The addition of this element provides a plausible basis for an explanation of shape - we probably won't see such a hypothesis put forward, though, as most reductionists have already concluded this is the situation without devising a test for the hypothesis. :)

As for bilateral symmetry, I balk at explanations in terms of the gene-centric view. Sure, we can say that symmetry is a good indicator of genetics - but no organism knows this, and without a theory of how behaviour is encoded in genes such an explanation is utterly speculative. Here's an alternative explanation:

1. Animals learn what other animals of their kind look like from experience.
2. Assuming shape is the result of the control of cell division by switches, symmetric patterns are naturally preferred as asymmetric patterns (a) would require twice the instructions and (b) would rarely if ever provide an advantage and so would not be selected for.
3. Thus animals prefer symmetric partners because these most represent the "perfect" form suggested by and derived from prior experience.

This hypothesis can even be tested, although it requires one to collect a freak show of asymmetric animals to do so! :)

A gene-centric hypothesis is also possible, but I don't know how we would test such a claim while the gap between genes and behaviour remains so wide. It seems clear that some behaviours are inherited, but no-one is close to joining the dots as to *how* as far as I can tell. Neither the neurology nor the molecular genetics are yet in place.

And thanks for the info about viruses adapting towards co-operation - intuitively, this seems likely, it's great to hear there are studies to support this.

Congratulations for slugging through this monster of a post! It's far from my best work, but I leave it around because it occasionally attracts some interesting commentary, such as yours.

Best wishes!

"Dawkins may see an organism sacrificing itself for the survival of its young as selfishness, but from the point of view of the organism I can see only altruism"

That's pretty much what Dawkins says as well. His fundamental thesis in "The Selfish Gene" is not that genetics makes organisms fundamentally selfish; it's that the gene itself is fundamentally selfish and will promote altruism among its survival machine (organism in common parlance) when it serves its interests. (All emotional language in the preceding paragraph being understood to be purely metaphorical, as genes can't be considered "wanting" something so much as existing).

James: thanks for the comment! Yes, I think that Dawkins' ideas regarding the gene-centric view are perfectly valid, it's just unfortunate that by using the term "selfish" he invites common misconceptions. Such is the challenge of popular science - to find ways to simply the complex that are not prone to abuse and miscomprehension!

I prefer to avoid "selfish" in the context of genes because of the risk of misunderstanding. Rather, I would say that 'what is useful persists', to the benefit of the organism, the ecology or the gene, for the most part - beneficial traits persist better than detrimental ones, for fairly self-evident reasons. ;)

Best wishes!

I like it. Yeah, you're right, it does basically look like it's dancing around trying to promote Intelligent Design, but that's not what you're trying to do. I had to stop and re-read stuff again because I wasn't exactly sure what you were trying to say.

But I like it. It's a fun post.


Spot on! If these are your own original thoughts, I'm impressed.

(Sorry to be a few years late to the party!)

Single-celled organisms were followed by multi-celled organisms. This in itself is a huge leap. There is no reason at all (except for explanations indistinguishable from magic) that "tissue" should spontaneously arise from free-floating cells.

Tissue is followed by "organs", that is, specialized tissue that arises from specialized cells that somehow decided to get together to support an overall orchestrated, but specific, function. This function partially supports the life of the organism, but not entirely. Multiple organs, each with a distinct function, are needed to support the organism as a whole. I'm not sure which is more surprising, that any specialized organ came into existence at all, or that fact that you need multiple specialized organs to support the life of the whole organism. No organ, by itself, can support the organism. Yes, there is an organizing principle at work here -- a design.

Specialized cell types, specialized tissue types, specialized organs, specialized body plans ... orthodox evolutionary theory does not in any way explain (except by way of explanations which are indistinguishable from magic) how these hierarchical structures came to be.

Thinking in new ways in this area is of fundamental importance. Keep up your independent thinking!

EndoplasmicMessenger: this piece is ancient now, and is both too long and too woolly; I feel my grasp of the subject has moved on considerably since this piece. I keep thinking about taking it down, but I never quite manage it. :)

And yes, these were my original thoughts on the topic, however muddled.

Thanks for commenting!

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