Posts Tagged ‘science’

Weird Science As Explained To Emmy The Dog

Sunday, March 27th, 2011

I have been reading “How to Teach Quantum Physics to your Dog” by Chad Orzel, because I love reading about quantum physics, relativity and the creation of universe, partly as I am a geek and also as I do not understand what is going on at all and reckon that sooner or later I will get there and I will have a Eureka moment.  This book is really quite light hearted, yet tackles many of the core underlying themes in modern physics, e.g. wave particle duality, Heisenberg’s Uncertainty Principle, Schrödinger’s Cat and the Quantum-Zeno Effect.  It is built off the back of his amazing blog – http://scienceblogs.com/principles/.

So while Chad was banging on about Heisenberg, he wrote:

“You can make the momentum change smaller by increasing the wavelength of the light (decreasing the momentum that the photon has available to give to the electron), but when you increase the wavelength, you decrease the resolution of the microscope, and lose information about the position.  If you want to know the position well, you need to use light with a short wavelength, which has a lot of momentum, and changes the electron’s momentum by a large amount.  You can’t determine the position precisely without losing information about the momentum, and vice versa.” [p48 from Chad Orzel's book]

It was then that I had one of those small moments of understanding where I felt that physics teachers have been deliberately misleading me, obfuscating and confusing me and making it all seem harder than it really is: wave-particle duality does not mean that light, matter etc is two things at once, which is how they explain it.  Rather this idea of duality is simply artifice to explain light’s properties mathematically and physically, i.e. a model to explain the behaviour of things in the universe.  Light is light, matter is matter, the lamp post outside my window is a real physical object and the sycamore on the green lives and so on.  However, the physics and so maths needed to explain the properties of these objects and how electrons and light work needs more than one theme to get it all sorted out.  So measurable stuff comprises a physical form (the particle bit) and energy (the wave bit), and we need both bits to sense things.  By the way, both of these are relative to other things, so it is really relative physicality and relative energy, hence I cannot feel something that is too small for me to sense.

This raises an interesting thought, being what happens if you have energyless particles and particleless energy.  Now modern physics says that even the lowest energy particles have velocity and so you cannot get a no-energy state.  But what if you can decouple energy and physicality?  If you could get these “things”, then you would not be able to measure them and so they become voids or “dark”.  Is this what dark energy and dark matter are? Formless energy and energyless form.  Humanity is not coded to be able to sense these, or even really to understand such things.  But what happens if that is what these missing bits are, i.e. 23% for dark matter and a whopping 72% for dark energy of mass-density of universe? Could you actually measure them rather than infer them – the only way to measure these two missing parts of the universe would be to give them back what they have lost, i.e. give energy to dark matter and form to dark energy, but would that actually be possible, or even for that matter a good thing.

Thinking about it why shouldn’t there be energy without a physical side and matter without an energy side.  Yes that’s not what we see/measure, but these are things you cannot measure or see, so why not?  In fact, it makes physical things more unique and basically says that there is something special about “normal” matter and energy as these are things where matter and energy are linked together rather than separated.  It is quite easy to envisage energy without shape as that is simply energy, i.e. just a wave and no particle bit, however how do you have matter that you cannot see as wouldn’t we just bump into it as we try and measure things.  Perhaps dark matter is shape than has folded in on itself until it is so infinitesimally small that you just cannot measure it and that there is something about adding energy that enables pre-matter to unfold and become detectable.  But now I am really lost in my own explanation.

Another thing that Chad Orzel writes about is why quantum mechanics does not work in the real world very often and that systems collapse into old-fashioned Newtonian mechanics.  This is one of the reasons most of us simple punters find quantum physics so complex as it does not marry up with our experience of the physical world, even if the maths works and so has allowed loads of new discoveries.  The theories, or philosophies, as to how the quantum world collapses when things are measured/observed includes theories like the Copenhagen Interpretation, Everett’s Many Worlds Ideas and Feynman’s Shut Up and Calculate Concept [actually not Feynman but David Mermin, but he's way less iconic].

I feel all these are too complex and perhaps too overthought and overwrought, i.e. everyone is simply trying to hard.  I think it is really just a matter of scale, so quantum theory works fine at a small level where there are very few components to a system.  However, as you scale up, you just need a new way of looking at things.  Nothing has changed with quantum physics as it still works at a micro level, but it just does not work on larger scales.  Different things need different ways of looking at it.

However, should you still want a mechanism for why it changes, here goes.  Everything can be described by a wave pattern using Schrödinger’s rules.  These are all different shapes and sizes, but everything big and everything small has a wave that describes them.  At a small scale where there are not many things about and the gaps between everything are relatively large, these waves have the space to take shape and grow to their full size, hence the properties of that wave become paramount in their behaviour.  So at this small scale and with little noise from other stuff kicking about, quantum physics and all those ideas work.  However, as you scale up, other waves start getting in the way, interfering with each other, changing the shapes of the waves, filling up the space with other waves and so preventing them fully expressing themselves.  In effect, quantum waves interfere with other quantum waves and they reduce their influence on their behaviour, so their impacts are nullified.  This means mathematically, there will be a point at which simply adding together quantum waves will cancel their individual effects and there will be no more measurable individual quantum effects anymore and classical mechanics takes centre stage.  I call this idea entanglement.

Size matters.  QED.

By the way, this means there are no parallel universes going on right now, ones where I am rich and famous or am the world’s greatest painter, and much of science fiction is well science fiction.  Sorry about that.

But it does mean that the sycamore tree on the green can exist even if no-one ever has observed it or a falling tree actually fall if not observed, because as all the individual waves of each particle entangle and interfere with each other they create existence, fixing things into space and time.  This philosophy and physics problem can be seen in works by George Berkeley or in physics forums, where a load of strange and complex answers are given.  Pragmatism should always rule over philosophy, as many things just are without being measured or proved; whether you can explain it is a different matter, but that does not stop it being so.

Axel’s Universe, And Some Thoughts On The Universe, Creation, Apples And Bits Of String

Wednesday, December 29th, 2010

Having re-thought the origin of species, I became ridiculously ambitious and decided to really go for it and started to tackle Life, The Universe and Everything…

I have come back to science after many years of ignoring it.  At the end of university, it just became something I could not wait to leave behind; it had become a rigid discipline that no longer held any joy.  However, I have continued to relish the heart of science – to wonder at the beauty of the wisteria as it flowers every year outside my back door and the snowdrops and daffodils as they poke out there noses from the hard ground in springtime.  These continue to give me a juvenile sense of frivolous delight and I wonder at the world.  Then on clear dark nights, I look into the heavens and see pinpricks of light and think about planets, stars and the universe and whether there is something out there and what am I actually looking at? 

Science is not just about data, calculations and formulae, but a delight in learning, in having those fleeting glimpses of understanding and the continued amazement in things – for example, while I understand the physics behind flight and density, I still shake my head in amazement when I see an aeroplane fly or a metal ship float on the high seas.  For me, science is not about answers, but about questions and more questions, then again about maybe just one more little question.  For me, there can never be an answer to everything nor the perfect universal equation, but only ever more whys, hows; forever to wonder.

So I have to apologise now for my thoughts as they contain no theories, no experiments, no maths, but are simply random musings, thought experiments, or perhaps even the ramblings of a madman.  Per my blog on evolution, I have written it in the personal form to distinguish it from real science, but perhaps some may find a kernel of reality in it.  These thoughts hold none of the discipline of true scientific thought and maybe are pure and simple nonsense that have been synthesised mistakenly in my mind from lingering memories of interesting and unusual pieces of science mixed in with some misread and misunderstood factoids.  Yet I have been puzzled by ideas of cosmology since my school years and have turned these over like precious stones ever since for over 30 years now.  Every so often, I pick up these gemstones delicately as they are important to me, turn them over, look at them again and put them down like curiosities.  They are like museum exhibits that you know are important but cannot fit them into any overall picture.  Well, I still cannot build them into any masterpiece that will explain the universe to me (or anyone else for that matter), but as they remain perplexing to me and seem to answer some niggles, I thought I would share them.

My journey begins with numbers and mathematics.  I have never been especially good at maths, but have always liked playing with numbers.  However, I struggled with higher maths, which has held back a lifelong fascination with physics, especially quantum physics and cosmology, as my mathematical skills never matched my inquisitiveness.

Numbers are symbols, a human artificial construct.  They make life easier.  So for example, we learn from early age what 0, 1, 2, 3 and so on are and perhaps marvel at a series like 1, 2, 4, 8, 16 etc. However, they are not necessarily complete and do not explain the world as it is, but rather serve to simplify the world around us into an easy and recognisable, universal symbolic language full of neat patterns and models.  But what if numbers are just what I have said pure artifice? A model, a methodology, that acts as the powerful lens through which we try and understand the universe, but nevertheless an artificial set of rules that is simple, communicable and versatile, yet still a human built, and a rather too convenient, model.  The teachers’ answer was always numbers are fundamental and pure, so just accept and get on with it.

Let me explain.  Imagine a chopping board.  Now looking at the chopping board, how many apples are there? None.  Now, place an apple on the board; how many apples are there? One.  Next, add another to give two, and another to give three.  Let us then assume that the universal apple has a mass of 100g, but we had here one apple of 95g, another of 110g and the final one at 103g; now how many apples are there on the board – 3 or 3.08 apples?  Next, take away the apples and ask yourself the question again – how many apples are there?  Is the answer now zero, three or infinity (a number equating to all the apples in the universe that we cannot necessarily see but know to exist in the past, present and future).  Well, it depends on how you look at the question, i.e. is it what you can see on the board, or in your mental kitchen, or the universe throughout time?  That is the crux of the scientific method – setting a framework to test a theory and collecting data within that experimental framework, but what if everything that is interesting was just off screen – like dark matter?  Finally, return the apples to the board and chop one in half and another into quarters and leave one alone; are there one, three or infinity apples?  So numbers simplify how we look at the apples, but they do not give us all the answers, and I really do not know the answer to that final question.  And where would we be as humans before we saw the first apples; would any apples have then existed?

Luckily, life is much simpler and we can make assumptions, since we can live very happily with the idea of there being as many apples as we see at any time within our own personal space, and who actually cares anyway whether there are more or less apples in existence.  Finally, those apples tasted really sweet as I picked them from our garden and, in my opinion, are far better than pears unless poached in red wine or saffron.  So we can make assumptions about life and get by really well without needing to know how many apples, pears or oranges there are now, have been or will be.

But perhaps our numbers are not always correct and as natural as we think them, as there are universal constants like π at 3.1416 and e at 2.7183, which would have been much simpler had they been round numbers that were easier to manipulate.  Also, numbers and constants change – feet and inches morph into metres and centimetres, while grams can be ounces or even cups and these change depending on which side of the Atlantic you live.  Even how we do maths changes and it was not until people started using base 10 that numbers became simpler to manipulate, resulting in a blossoming in theoretical maths.  Even without the ideas of relativity, time changes depending on where you live and what watch you are wearing and I, who do not wear a watch, have my own personal timescale which is particularly random and dependent on a car clock that is out of time by 22 minutes and widening!  So what is Axel’s time?

Then there are imaginary numbers that even characters in Alice in Wonderland would wonder at.  Yet √-1, complex numbers and other imaginary numbers are very real as they form the basis of semiconductors, digital communications and fluid dynamics inter alia, yet we cannot comprehend them and just must dream them.  So not all maths is touchable and pure.

So where does that leave us.  It leaves me perplexed and vexed.

Next, you have the theories of physics, the absolutes.  At school, I learnt of Newtonian mechanics and gravity, of apples that fall to the ground.  However, we then moved on to Einstein, only to discover that gravity does not exist, rather that mass distorts space-time and this deformation results in something we perceive as gravity.  However, we continue to talk and think of gravity, as well as to experience it day in-day out with windfall apples still falling to the ground and no visible sign of space-time becoming deformed in my back garden.  Einstein’s concepts of general relativity enable us to predict everything from big bang to black holes, as well as the expansion of the universe.  But Einstein also predicted dark energy that is pushing space apart, something which no-one has found, and nor does general relativity square up with gravity.  Have we, therefore, found the limit of Einstein’s laws of physics in much the same way that Newtonian physics ran out of gas and (going back a few paragraphs) is c really a constant at 299,792,458 m s-1 or can it change and flex in different parts of the universe or at different times in the development of our universe, and would it be the same in another universe or is it unique to where we exist?

For me, physics and my lack of maths throws up even more questions, but perhaps it can also free me up to think outside of a number system and speculate without the shackles of the scientific straightjacket and perhaps, to disagree with Stephen Hawking, philosophy is not quite dead and people outside of the scientific community can still be allowed to think: How did the universe start? Will the universe end? Is there a way to unify all basic theories of physics? Is light a wave or a particle? What is dark matter?

So I wander further in my mindscape and consider whether our numerical system is flawed.  Sometimes I think that perhaps numbers can be stretched and are flexible so perhaps you could have an imaginary thin 1, a fatter 1 and a high pitched or low pitched 1 and the same with 2, 3 and so on.  That would really cause issues for mathematicians and physicists, but would be a dream for accountants and investment bankers who would jump up and down with joy to know that the universal fudge factor was a real mathematical truth.  Perhaps that answers the question with my apples; each apple is a unit of 1 but that unit can be stretched and contracted, so it actually forms a bell curve around a mean and not just from a statistical perspective but in real universal laws?  How much havoc would that cause if numbers were not natural, unbending and stable but stretchy and creative rather than pure, simple and immutable, but imagine the impact that could have on almost all scientific theory, where the idea of standard deviation was not an error factor but simply a measure of stretchiness?  Perhaps, complex numbers hint that the universe is really a much more difficult question than we have the willingness to believe.

More importantly, I also think about nothing and I mean really nothing. We are taught that 0=0, 1=1, 2=2, 3=3, but what if this could be turned on its head?  Let us think about zero or nothing; these were concepts introduced into maths in ancient India and the Mayan kingdom, but are they real or simply an accounting tool and a mathematical convenience?  Let us think further about the two key numbers, zero and one.  Imagine that 0=1 rather than 0=0 and 1=1.  Why are these the two key numbers? Well, zero is where something does not exist and one encompasses all of something, e.g. every apple in the world (or universe), then all maths does is divide up the units between zero and one and call these numbers.

You can visualise this idea in a thought experiment: take a piece of string: at one end is 0 and the other is 1 and all the way between 0 and 1 are varying degrees of probability or improbability or points between 0 and 1 and so your number scale; now take the piece of string and curve it around so that you have a perfect circle with the 0 touching the 1; imagine they reform into a circle so that on one side of the join you have 0+∞ and on the other 1-∞ (where ∞ is an infinitesimally small amount); what is the number at the point where they touch? For me, I cannot get it out of my head that 0 and 1 must meld together, i.e. 0=1.  So there you have it, the start of the universe without complex maths, just a piece of string and some imagination.  Now this seems nonsense, but no more ridiculous than the √-1.

What would be the reality or consequence of this?  For most of us, not much in the same way as in our apple experiment when we have zero apples; we just buy some more or pick some from the tree, or simply do not care.  But for reality and the universe, perhaps it can answer some questions.  And going back to my thought experiment with the chopping board, you did not have no apples, but really just no visible apples within your observation matrix and apples still exist, i.e. it was not a case of zero, nothing, nada, but just not any in that place.  Therefore, zero, i.e. zero apples, is no more than an accounting convention, i.e. not any apples within my kitchen or personal inventory, rather than there being no apples at all. 

Whereas, at the beginning of the universe, there was nothing and I mean absolutely nothing.  As there was really absolutely completely nothing, you would be at that cusp point and immediately numbers would collapse and zero would really equal one, so at that point of absolute nothingness everything is created.  Think of it reverse, hold out your arms and collect all the mass, energy and dark energy and matter in the universe and bring it into the palm of your hand; now roll it into a ball and squeeze it tight to the size of a table tennis ball – it is a tad heavy but you can do it; now squash it even more down to the size of a water molecule, then an atom – it is really heavy now and quite unpredictable but squeeze even harder until you are at 0+∞mm in diameter.  What happens if you squish it down even more until it is nothing?  Where has all that mass and energy gone?  Are you a magician and it has gone forever or as I have predicted at absolute zero or nothingness everything is created, all matter, all energy, absolutely everything and it blossoms out as a big bang.  So there is no need for any external creators, no need for any complex higher physics, just simple number collapse.  I know that for superinflation to occur you might need a big bounce rather than a big bang, but I am talking about the ur-creation, the original start.  So there is no need for external creators, no external god question of who created god, just a simple fact, nothing simply does not exist, so immediately there must be everything.

Another question, then – what happens in the cosmic web in areas of empty space?  Are there parts of this emptiness that are actually voids and areas or pinpricks of absolute nothingness – if so, then whole new universes could bud out in these regions creating multi-verses.  Or perhaps areas of emptiness oscillate between 0 (pure absolute nothingness) and 1 (existence of everything), creating points that perhaps generate fleeting, massive amounts or smaller quantities of energy and matter (new universes ) that can push apart our universe like wedges driven into rock, but perhaps most of these new universes collapse under their own mass right back down to zero giving the appearance of a void again; effectively rocking from 0 to 1 at the number cusp point, yet still seeming to be nothingness from our position as an external viewer, because we can never see a new universe from where we are watching, nor can we see nearly nothing because we are not wired that way.

To find dark energy, therefore, maybe we should look for nothing rather than something?  I do not believe that nothing exists, so when I look up into the night sky I do not perceive empty voids but everything must be there, somewhere out of sight and out of mind.  Be a child again and think about the air – it is empty and clear, then later you learn it is full of invisible gases as well as bacteria and viruses and dust motes, the stuff of life; or remember the classic experiment with smoke to show Brownian motion where you must infer that there are invisible molecules buffeting the smoke around.  There is something in the void space and perhaps we are just trying too hard to fit it into our own paradigm of the universe and should just suspend our beliefs and dream again – perhaps it is other universes budding out of pinpricks of nothingness, which push out other universes in some never ending fractal pattern?

In fact, the empty space in space is not completely empty and stuff does just appear as if from no-where.  These are vacuum fluctuations where particles and fields appear spontaneously to be created out of nothing.  Hence, there really is no nothingness out there, simply spaces where there is not very much, but where energy and matter can spontaneously appear.  Perhaps that is what the cosmological constant really is – a background count of somethingness, a mysterious creative energy, that stops there being nothing, because nothing creates everything and you cannot have that happening too often, can we now; for my piece of string, it is as if the cusp point, the creation point, is constantly switching from 0=0 to 0=1 to 1=1 and back to 0=0, but instead of netting out to an answer of 0, there is always a remnant of energy that cannot be lost leaving the cosmological constant, effectively the background energy of failed creation events.  Now that means that even though everything was created in the single creation event at T=0 more energy is constantly being created than was possible ab initio and is actually increasing the energy within our universe, so forcing distant supernovas to expand at an ever increasing rate.

Perhaps all I am stating is a truism – we exist, we perceive ourselves as real, therefore the universe must have been created.  Truly, there is no nothing, no non-existence.

Interestingly, this idea of nothing as being not possible, Axel’s theory of the impossibility of impossibility, means that life in the universe had, also, to be created spontaneously straight away.  As the idea of creating life is impossible, it would have to occur immediately; however, can life start more than once in the same universe, now that is so very unlikely that it probably will not have occurred twice?  Does that mean that there are no other inhabited planets in this universe? No, it simply means that the spark of life occurred on creation, but how that has been distributed across the universe is a different question; I am merely saying that spark of life can perhaps only be created once per universe.

To sum up, there is no such thing as nothing, therefore at the point of completely and absolutely nothing, number systems collapse, 0=1 and the universe is created.  Thereafter, whenever there is nothing in existence, energy and matter will perhaps spontaneously be created as new universes (whether big or small), which may exist out of sight and out of mind, or might collapse back down to nothingness, but leaving a residue of energy that will increase the amount of energy in the universe.

Next I get lost in trying to unpick the standard model of everything

Towards An Updated Theory Of The Origin Of Species

Tuesday, December 28th, 2010

In my previous blog, I posted a stream of consciousness on evolution that suggested that perhaps evolutionary theory as currently presented was too simplistic and not necessarily a complete mechanism for the origin of species.  Therefore, I owe it to those who might happen upon that blog to propose an alternative idea.

There are at least two overarching competing forces ongoing to develop species on earth: one higher risk and one lower risk.  The higher risk process is random mutation and speciation (macroevolution), while on the other hand there is adaptation, which includes several processes including microevolution and lateral gene transfer.

Against this backdrop, life on earth follows at least three basic principles: (i) preservation of life on earth; (ii) conservation of the status quo rather than favouring radical change; (iii) relative efficiency (or laziness) of life that will co-opt good ideas as they arise.

By overlaying these forces and principles, you have constant competition between the process of mutational speciation and that of adaptation with limited speciation, i.e. between the higher risk and lower risk strategies.  However, as life and species become more interlocked and interdependent, the weight of the conservative and lazy principles of life becomes increasingly strong, which will work against mutational speciation, because it could destabilise the rest of life on earth, i.e. life normally selects naturally for the status quo and deselects for new species.  Furthermore, it appears that this conservative principle kicks in pretty quickly as microorganisms appear to almost always prefer adaptation, including lateral gene transfer, over speciation.  But why chose adaptation over speciation, because the status quo itself confers protective benefits to all current species on earth, whereas speciation results in the need to change the structure of a biological niche or life in general, which can be devastating for the rest if living species and resultsin a weak species without the protection conferred by the capability to adapt.

However, when new unoccupied niches become available, higher risk mutational speciation might become more attractive as opportunity outweighs inherent risks in generating new species and new ideas arising from genetic errors might prevail and can be tried out without the competitive pressure of life.  Therefore, new species might arise relatively quickly in these circumstances, as there is no negative pressure from the rest of life.  Such situations could occur at the start of life on earth, when life moved onto land or after mass extinctions, where opportunism reigns.  However, as life becomes established in a niche or set of niches, embedded life will act like a dead hand tending to prevent new ideas being tried out and so life will favour change via adaptation.  Generally completely new speciation is deselected as being normally negative for life.

However, a really radical new idea, like photosynthesis, can overcome this inherent conservatism and establish itself.  However, it has to be a crackingly good idea and not just a reinvention of the wheel, which will be prevented from establishing itself.  So in all these situations, life could be viewed to make a risk analysis, i.e. is it worth upsetting the status quo for this new idea? If not, then life works to squeeze it out, or if it is, then life will take the risk of potential extinctions for the future potential to increase the amount of DNA-RNA on earth.  So even though there is a background level of new potential species being created all the time, it is unlikely that many (or any) of these will establish themselves.

What I like about this theory is that you can see how a chaotic change in species can happen all the time, with even the amount of permitted speciation and adaptation being capable of variation as the situation and needs move around.  Also, it can explain why some species never disappear as it postulates that life only changes where and when changes are needed and better ideas arise, or when there is extinction in a niche, but for example no better solution to living in the hot springs at Rudeira has been found than stromatolites, so stromatolites it is then, but find a virgin untapped island like Galapagos then a finch can blossom out.  It also explains why changes in range and composition of species is a more normal response than speciation as life prefers to use what it already has got than go for radical new ideas.

[This is a raw idea so needs to be worked on by those better than me to articulate more succinctly and perhaps even build a model that could even be run on a computer to simulate the origin of species.  As for modelling, I envisage that whenever there is a change to the global environment (in its widest sense) species must consider whether it can adapt to these changes through behavioural changes, distribution changes, working together with other species, natural genetic variation, lateral gene transfer or finally speciation.  Or perhaps interested people could analyse competition and speciation by looking at what happens in the business world when new businesses are formed and new ideas are invented, and watch how these survive and/or are transferred through the economic community and/or how they compete and work together to maintain existing relationships rather than nurture new businesses that might alter the status quo.]

Axel’s Earth, Or Too Many Answers, But Not Enough Questions

Monday, December 27th, 2010

Recently, I was at the Sage in Gateshead listening to brass band music, and I did what I often do when listening to live music, I shut my eyes to listen to the sounds and I was struck again by how the music sounds different when your eyes are closed to when they are open.  It is the same when I am tasting spices or teas at Steenbergs – if you do it with your eyes closed, everything tastes different, perhaps clearer.  At home, we play a game with our children called “The Guessing Game”, where household items are put into cups and you then must smell or feel these and guess what they are, but with your eyes closed; it is really difficult to work things out when you are left without all your senses.  There is a lovely girl called Rosie, who our childrens’ childminder looks after; she is severely handicapped and cannot see or hear very well, so her body has compensated and her sense of smell is heightened and she can recognise people by their own distinctive smell when they come into the room.

But what does our world feel like and how does reality shape itself?  We sense the world with all our senses, perhaps using our sense of sight rather to the exclusion of everything else.  Our body sees, hears, smells, feels and tastes the world around us and uses these to build a picture in our brain of our own personal space.  It is, however, a model built from incomplete data mixed in with models of how that world should be constructed, a matrix.  For a start, our eyes provide a really incomplete picture of our world with a clear picture only coming from about 1 degree of visual angle at the retina’s centre and the rest is a fuzzy, pixilated image that is fed down your optic nerve to the brain, where the optic nerve itself creates a big blind spot in that data set.  The brain then interprets the data it has been given, mixing it in with memories and symbols of how things should look like, so the piano beside me should look like a black upright piano with white keys on it, the filing cabinet should be grey with sharp edges, but it does not expect a chocolate éclair to be flying in the corner of my vision, so hey presto that is exactly how my brain sees them, i.e. a black piano, grey filing cabinet and no random flying chocolate éclair (pity about the éclair, though).  Then feed into that the sound of the keyboard clattering away and the computer’s fan humming and you have my reality, my personal space, but which came first the idea of how it should all look or the sensual data to create that world?

Another thing that the brain is good at is changing features and zoning things out – when you return home after a time away, the house always feels strange with vaguely familiar smells hitting you, electrics humming constantly and somehow the house feels more cramped and darker with edges not quite where they should be, but soon the alien smell disappears and the familiar sensory shape of your house returns; your house has not changed but your brain as reasserted its model of how your house should look from its stored memories, so the characteristic smells and noises of the house slip again into the background, allowing your brain to focus only on changes to that model of normality.  An extreme example of this is perhaps our spice factory (Steenbergs) where everything smells intensely of spices, but I cannot smell them except after a long trip away as for my model of the world and my own personal space, these extreme aromas are normality.  It is, I suppose, a shortcut for the brain, allowing it to focus on the unfamiliar and changes to that model of reality, so serving as an efficient survival technique for most of us.

We build models of our space.  We are taught models for our world.  These influence how we see everything and how we react to the data that our body senses.  We feel really uncomfortable when data or situations occur that do not fit within these preset paradigms, and most people chose to ignore or even to force reality to fit into the models of their reality at all costs rather than admit what they see before their senses – it really cannot be a chocolate éclair floating in my kitchen so I must be mad, but what if it was really and truly so?  We chose denial over reappraisal of our human created models.  Would you notice a really good value bottle of wine if it was sitting on the supermarket shelves squeezed between two types of washing powder?  Could you taste the difference or pick out the flavours in three drinks – all diluted apple juice, but if one was green, one was yellow and one was orange or would you try and name one apple, one lemon and one orange?

But there are different ways of interpreting everything and all may be possible, even probable, and some alternative ways of conceiving the world may be just as good as others; for example, in Britain, we live in a secular but predominantly Christian country with a royal family but a largely fair democracy where the rule of law functions, property is respected and freedom is honoured.  It is a decent, sensible society, but it is a no more correct model for society than were we to become a republic and follow the American legal system or an Islamic state or a totalitarian Communist state or follow the ways of the San people of the Kalahari Desert – all are valid ways of modelling society.  We have our own views on which is best or better based on our own moral framework, but that is really only because we have been living in that type of country all our lives and have been learning about it through the education system, the media and general living and it fits nice and snug like an old, familiar overcoat.  It must be really exciting when new ideas initially come onto the scene and seem to offer a valid alternative to the political status quo, so all the more disappointing that human nature usually simply moulds and squeezes these new ideas into its standard socio-political models, so for example Marxism was warped and became no better than traditional political systems and was certainly very poor at organising an economy and protecting human rights.  I will perhaps return later to the idea of how we model our societies.

But I wondered whether, with this idea of preconceptions niggling at my brain, if I relooked at some theoretical science, I could come up with a different way of modelling the data and information provided.  So being overambitious, I decided to start with one of the unassailable icons of modern scientific thinking, evolution.  I liked the idea of evolution as it caused quite a stir when it first came out, since it did the unthinkable in that it challenged and then changed a world model, which, when you rethink about the reaction to it, explains and justifies the seemingly extreme reactions of general society and the religious community to the concept of evolution as it violated a standard human model, i.e. God made man, which appears in all religions from Christianity and Islam through to Hinduism and the beliefs of the Bashongo tribe in Africa.  As an aside, the fact that humans (and probably all species) use models to organise the world in their minds is why climate change evokes such anger and scepticism, because it challenges another fundamental model for organising modern societies, i.e. the concept that economic and technological progress is good and that man’s impact on the world is basically benign, if not an improvement on nature.  Once again, perhaps I will address that on another occasion.

Evolution is basically an hypothesis that all species that exist today came from species that existed in the past forming a tree of life and that the key process whereby the genetic traits within today’s species have been selected is via a process of adaptation and natural selection driven by the biological environment, where better genetic attributes survive over time and are positively selected for by the impact of the physical and biological environment – the concept of “survival of the fittest” – and speciation (or new species) results over time through this mechanism of evolution.  There is, also, an underlying feeling of beneficial progress with branches of the tree of life branching ever onwards with today’s species being the pinnacle of evolutionary achievement, as well as there being an overall sense of logic to evolution, as if it were overseen by an ethereal, non-existent blind watchmaker.  And it does work to explain how Homo sapiens evolved from apes and marsupials and placental mammals share a common ancestor.  So evolution is a powerful and elegant hypothesis for the origin of species.

However, I think evolution is perhaps too grandiose, too definitive and too progressive, coming nowadays with far too much emotional baggage attached to it.  So let me propose a more mundane, fuzzier and conservative model, something less elegant, more real and excitingly chaotic – a ramshackle shanty town of life rather than the pristine, but sterile, new town of high rise blocks and concrete.

Firstly, let us consider life or at least the purpose of life.  Some time ago in the depths of time, RNA and DNA started replicating.  It is a truly unique, amazing and wondrous thing that ability to replicate and the desire to create complex and orderly chemical and physical structures repetitively over time.  Since then, the purpose of life has been to sustain that replication of RNA and DNA on the planet.  Genetic material is not really concerned about the outward appearance of species containing replicating DNA-RNA, rather it simply wants it to continue existing and that is the underlying purpose of all life – nothing high minded, nothing existential or religious – simply pure maintenance of a bunch of sugars that replicate.  From the viewpoint of DNA-RNA, quantity is, therefore, more important that quality and it views the influenza virus as highly as the blue whale and marine annelids with as much pride as the human being.  This is one of the first concepts that is perhaps at issue with evolution, as evolution sets great store in the cumulative momentum of speciation with current species, especially Homo sapiens, being the pinnacle of life, as if life marches ever onwards always improving; however, life is more basic than that, life is simply about maintaining life.  Is our understanding of evolution really viewed through the eyes of the western, educated intelligentsia and simply a scientific replacement of the religious story of creation – evolution created the plants and animals of the earth and then on the last day evolution made humans (in his likeness)? 

Secondly, life is not inherently progressive.  In fact, it is rather like all the species on the earth and is at its core conservative, and risk averse.  Life would perhaps prefer to take a snapshot of all species as they exist today and maintain that as it is until oblivion, since the way we all interact as species, busying away in our little biological niches, doing our own special things, supports and maintains all the earth’s biological, environmental and physical systems as they are today; that is effectively the concept of Gaia.  To me, this is one of the amazing things of life – Why is there so little speciation when we have so much genetic variation around within species themselves?  Why are new species only quite rarely generated?  Why are there living fossils still around now like Platynereis, a marine annelid from 600 million years ago and possessing a proto-brain, or stromatolites of blue-green cyanobacteria that can be traced to fossils from 2.7 billion years ago and maybe even to 3.4 billion years ago? Therefore, this regressive force means there is a large conservative drag acting on the tree of life, working against novel ideas and new species as these could result in destabilising all other species on our planet, upsetting biological and environmental systems.  Returning to this regressive idea of life, the species on earth today are no better or interesting from the viewpoint of DNA-RNA than those during the Jurassic Period, we just want to believe they are.  I will concede, however, that we are perhaps more suited and better adapted to the current environment and set of species than those existing before, but conversely we would not have survived very long in the environmental conditions on earth some 3.1 – 3.6 billion years ago when bacteria first started living on earth, but perhaps we (current life on earth) might in any case have moulded the environment in part to suit us.  Also, why evolve with all the risk involved if you can adapt without creating new species, so life chooses adaptation first, while will co-opt genetic changes either if the change is small and so the risks low (microevolution/genetic drift) or if the change is significant and worth the damage it might cause, i.e. high risk/high return (e.g. photosynthesis, multicellular organisms etc).

Thirdly, life is inherently lazy (or efficient).  Therefore, where it can borrow really good ideas that have arisen elsewhere, it will do its utmost to co-opt that new technology for itself rather than seek to reinvent the genetic wheel; after all, this is the lower risk strategy.  So bacteria swap genes around as if they lived in a genetic world wide web (lateral gene transfer), and multicellular organisms absorbed archae that photosynthesised and respired to gives us the modern organelles, chloroplasts and mitochondria, and life seems to work together as communities of species that interact, where plants gives us oxygen, which animals respire and birds and insects pollinate plants, and animals eat the plants and foods with microorganisms breaking down dead matter and so on and so on into greater detail.  Should we really consider life at a larger scale as communities of species that change and adapt over time rather than focus on the detail of species by species analysis?  Is it these communities of species that matter?

So that is the essential backdrop to the way I envisage life – life is about sustaining life in the form of replicating DNA-RNA, life is conservative rather than naturally progressive and life will borrow good ideas wherever it can.  Finally, our concept of speciation and so “the tree of life” might be too simplistic and perhaps human-centric, as the swapping of genes between monocellular organisms (and sometimes even with multicellular organisms) might mean that we do not have just the one parental line, or at least microorganisms might be more incestuous in their family trees, and so most species on earth might not have neat family trees with everything flowing logically down from single ancestral points.  These concepts all mediate against the central position for evolution as the mechanism that drives life on earth.

But then the question remains, if not evolution, then how come we have arrived at the species on the planet today with all that variety, beauty, specialisation and then us with our supreme mental ability, human beings as the pinnacle of life?

The answer is that genetic material has developed a number of survival mechanisms to ensure that it is sustained over time, because physical, chemical, environmental and biological conditions on earth do change which means that life cannot remain static as this would militate against the first rule of life – that life needs to be maintained.  What might impact the survival of life?  Well, the environment changes (oxygen and carbon dioxide go up and down, for example), meteorites hit the earth, the sun’s heat and light levels change, genetic coding goes awry and new species are created.  So DNA-RNA needs to have some survival tactics to address these potential threats to its survival.

The first is simply the maintenance of the status quo, that inherently conservative streak in nature, with most genetic material simply copying itself and replicating clonally and largely correctly.  The second trick of DNA-RNA is the rapid, continuous replication of genetic material, enlisting that most basic survival technique of safety in numbers, so the more you replicate and the faster you do it, the more chance there is of some genetic material surviving.  The third method encompasses a broader set of mechanisms and this is what I call adaptation, which includes within it the idea of evolution itself.

So let us look again at this idea of adaptation in some more detail – if life is conservative, why does it need to adapt?  There are various reasons, including responses to environmental change, errors arising in the genetic material and competing bits of genetic material, as well as to increase the chances of survival through, for example, exploiting randomly generated improvements in genetic material thrown up by natural variation in DNA-RNA or adapting to unexploited niches and to generate greater robutsness in a genotype.  Why would life want to exploit more niches?  It is a case of the more the merrier, so it wants as much genetic material out there as possible, so that means it will try and adapt to fit into every niche that it finds available.

Now, some will say that sounds a bit like good old-fashioned evolution, but no it is different and I will explain why.  Evolution involves species and the adaptation of species followed by natural selection moulded by the earth’s environment in its widest sense, i.e. including all physical, chemical and biological drivers.  In fact, adaptation may involve no genetic change or might involve swapping genetic material around rather than from any form of natural selection, hence it is less constrained by the idea of species.  Adaptation occurs through a number of possible mechanisms, including (but not limited to) the following changes some of which have no genetic impact at all: (i) behavioural changes; (ii) range changes; (iii) mutuality and community building; (iv) lateral gene transfer; (v) genetic variation within species (akin to evolution but on a micro scale); and (vi) random speciation. 

Of these, genetic variation within species might include the idea of evolution, but it perhaps only occurs on a very detailed and micro-evolutionary scale, while random speciation occurs all the time but most newly created random species simply never come to life or fail to have any impact and fizzle out very quickly as a good idea, but arising at the wrong time and/or place, plus life tends to protect itself against these changes (by competition/natural selection), as they are often profound and could destabilise the rest of life on earth.  For example, the development of early forms of photosynthesis increased the levels of oxygen in the atmosphere and increased the amount of carbon fixed as sugars, all of which was hugely destructive to the rest of life on earth; this resulted in most of life becoming extinct about 2.4 billion years ago in the Great Oxygen Event – oxygen killed off anaerobic life and the reduced atmospheric carbon dioxide significantly lowered global temperatures killing off other forms of respiration.  In fact, I am arguing that species will seek to adapt to as many niches as possible within a community’s own natural genetic pool, while simultaneously trying to minimise the amount of speciation that actually occurs.

Some examples of how adaptation might work in practice could include [this is the more sciency bit in the blog]:

(i)  Behavioural changes: classic examples of behavioural responses to environmental change include population movement to find new and more amenable habitats, including the migration of birds, fish and reindeer, or changing to a dormant state, including aestivation, hibernation and the formation of seeds and spores.  A good example of simply moving when a change arises is in the Bering Sea, which was one of the richest seabed ecosystems in the world, however climate change has seen a rise of 3oC in temperature and is driving a change in species composition (this can be used as an example for (ii) Range changes below), in particular pelagic fish are entering the Bering sea driving out bottom dwellers and so their predators are moving northwards with them, i.e. eider ducks, walruses and gray whales (Grebmeier et al, 2006).  These are really cases of “can the species move to a more conducive environment for its niche needs or can it become dormant and wait like Walt Disney for a better time?”  There is very little evidence for evolutionary driven behavioural responses arising out of environmental changes (Lowe et al, 2010), indeed it is suggested that insect species biorhythms (e.g. photoperiodism) must be capable of adjustment as species have simply altered latitudes as the environment changes (Coope, 1979).

(ii)  Range changes: in a study of North American tree taxa after the end of the last ice age, it was found that distribution shifts in tree types was individual, “with large variations between species in rate, time and direction of spread”, which showed that there were no species specific responses driven by climate change, i.e. the trees act as individuals with no discernible species driven trend (Davies, 1983).  Similarly, the fossil record for trees indicates that forest communities are just temporary distributions of similar trees with no discernible coordinated trend, hence there is no evidence that “modern forest communities evolved together”.  There is a similar lack of evolutionary evidence for animals, with North American mammals being unchanged for hundreds of thousands of years from an evolutionary perspective even if there have been major changes in distribution, as well as similar results for insects where it is concluded that insect fossils from the last 1.6 million years are identical to species living today and insect fossils from 5.7 million years ago fall outside the range of natural variation but are almost identical to current living insects that they may be ancestral to current living species or the result of small shifts in genetic variation (Coope, 1979).

(iii)  Mutuality: all species work together in a massive mutually supporting and interconnected matrix for life, but could this matrix be self perpetuating and cohesive and work to maintain the status quo as much as possible.  For me, I speculate in my mind that this is what occurred with chloroplasts and mitochondria, where in the past sometime, the original bacteria perhaps lived closely with another microorganism in a mutually supporting symbiosis and then perhaps via straight absorption or through transfer of sufficient of the useful DNA into the symbiont via straight uptake of DNA (or other form of recombination), these bacteria became organelles.  I know that sounds very casual and easy, but it did need only to happen once and this form of attempted transfer happens all the time for small stretches of DNA and usually fails for longer stretches, but perhaps just once.  Then having happened, it would have opened the door for such opportunism that it would have been a case of first mover advantage and no alternatives would have the chance of getting an evolutionary look in (especially if you take into account that it would perhaps be another billion years before the next time this might occur). 

Anyway, I said this section would have some science rather than mind games, so let us think about microbialites.  These are prokaryotic communities of bacteria than form communities with a physical structure created out of biofilms.  They are usually found in relatively extreme conditions suggesting that these bacterial communities formed out of mutuality, where each bacterial species offers something to the community enhancing the whole and so militating against a selfish, unitary life; also, perhaps these communities could have been more prevalent, however more complex forms of eukaryotic life might have more successfully taken over those biological niches, so closing out those environments from other microbialitic communities continuing to exist.  These are very diverse and complex mutual societies of bacteria centred around cyanobacteria (probably the origin of the proto-prokaryote for chloroplasts), so, for example, in a study on modern Rudeira stromatolites, there are a number of species of cyanobacteria (mainly Leptolyngbya and Pseudoananabaenaceae) as well as a wide range of over 95 different non-cyanobacteria, including isolates from bacterial genera Actinobacteria, Arthrobacter, Bacillus, Firmicutes, , Proteobacteria and Sporosarcina  Overall, there was more diversity in the non-cyanobacteria and more cohesion in the cyanobacteria, with no Archael bacteria found.  (Santos et al, 2010).

(iv)  Lateral gene transfer or direct transfer of genes: while bacterial are generally clonal in the way in which genetic material is transferred, with most transferred via asexual cell division, genetic material can also be exchanged by conjugation, transduction and transformation, which are the movement of DNA by direct contact between bacteria or via encapsulation by a virus or simply the direct uptake of naked DNA.  Additional important wrinkles include that much of the transfer might be mediated through plasmids or bacterial viruses and that only a small portion of genetic material is transferred “sexually” for bacteria.  This transfer of genetic material between bacteria actually works against speciation in bacteria as it means that bacteria remain more genetically cohesive over time than evolution would demand; furthermore, more genetic material is transferred between bacteria than is caused by mutation, suggesting that (a) these transfers of material are more important for bacteria than mutation followed by natural selection, and (b) life (or at least bacterial life) is efficient (or lazy) and will share a good genetic idea widely through “sexual” transfer rather than be selfish and create a new species, i.e. contrary to the mechanism of evolution.  In fact, it is suggested by Lawrence and Retchless that a new bacterial species takes a long time to develop and it occurs gene by gene rather than with one mutation, i.e. as step-wise speciation (Lawrence & Retchless, 2010).  Perhaps direct gene transfer, also, occurs in multicellular organisms where viral and endogenous retroviral DNA are the remnants of such transfers?

(v)  Genetic variation within species (and microevolution): the classic example of this is industrial melanism in the peppered moth which displays genetic drift over time for dark and light bodied moths (Wikipedia, 2010, Peppered Moth Evolution).  The allele for dark bodied moths is dominant over the light coloured moth.  Prior to the industrial Revolution in Britain, the light grey form of the moth was prevalent, then during the Industrial Revolution, the light lichens that the moth hid on died off and the trees became darkened with soot and the dark bodied peppered moth prevailed.  With the cleaning up of the air via Clean Air Acts in Britain, the lichens have grown again, trees have become lighter in colour and the recessive light bodied moth has become more prevalent.  The evolutionary mechanism for this is that birds eat the peppered moth and colouration acts as camouflage for the moth while it rests on trees, so the colour of moth that is best hidden will be selected for (Wikipedia, 2010, Peppered Moth Evolution).   While I argue that this is simply genetic variation within a species group for adaptation and survival, others argue that this is evolution in progress; I guess we are splitting hairs over what is a species, but nevertheless this perhaps only works at the micro scale.

(vi)  Speciation: what are species firstly?  We define the world in a very human-centric fashion and view species of organisms that can successfully reproduce and those that are different species as those that cannot successfully reproduce.  However, for microorganisms they tend to take longer to speciate than multicellular organisms, being more interested in keeping their genetic material cohesive and shareable as keeping a wide range of gene apps (genetic applications) available for use is a good defensive mechanism.  So microorganisms only become “species” slowly by excluding genetic material on a gene by gene basis, with the rest of the genome potentially remaining shareable.  Perhaps more complex organisms lost this ability for widely perimissive genetic variability when they decided to aggregate, so you can imagine (for example) that multicellular organisms need most of the genome to be similar to be able to repoduce successfully (or perhaps it is the other way around and that it needs to be the 5% of differentiated DNA that must be the same).  Anyway, mutations happen all the time with most of these falling into the camp of  genetic variability, however new species might form all the time, but being a high risk route for the origin of species and one that does not confer the benefits of protection from adaptability most species either never come to life or disappear quickly, having never managed to establish themselves; many mutations will be a case of wrong time, wrong place rather than never being of any use, e.g. being capable of photosynthesing is not a useful trait if you are a bacteria that lives in the earth’s crust.  Furthermore, I speculate that speciation is a negative action from life’s perspective, as it tends to weaken an organism’s chances of survival, i.e. it is negative for natural selection, because (i) it takes a geneotype out of its natural niche that it has been developed for, so it will be more (not less) exposed to the negative forces of life (natural selection?); (ii) new species lack the robustness of genetic variation conferred by variation in its former gene pool and so needs time to create a new one, compensating for any weak attributes brought into the new niche (but which may have been positives in the previous biological niche); (iii) it lacks the protection provided by the interlocking relationships provided by the web of life and so will need to develop new mutual relationships.  As a result, most new species will wither away, but adaptive radiation can occur rapidly, where either new species are ecologically protected (e.g. in isolated communities or after extinctions) or the new species has created some positive attribute (perhaps very rare, such as the ability to photosynthesise or create multicellular organisms).  However, speciation is not normally positive for the new species.

These adaptive response mechanisms explain why species on earth do not vary as much over time as evolution would suggest – how often have we seen actual evolution occurring with changes in the earth’s environment? The species that actually exist at a particular time and place simply modify their behaviour to adapt to changes or move around to find alternative environmental niches that suit them better or work together with other species as a community better to survive any changes or even swap genetic material around via lateral gene transfer.  These actions do not necessarily result in a change in core genetics nor do they necessarily result in a need to drive through adaptive gene selection, for example if global temperature rises and water levels fall, plant species existing in a region will simply change their relative composition in that forest or grassland community; if there is a forest fire, plants and animals will return and perhaps will configure themselves differently to before, but essentially it will be the same bunch of species rather than any wholesale change having needed to occur.  I understand that under certain circumstances different results might occur, however this is usually only in isolated places where special conditions apply, so Darwin’s finches might be an interesting exception rather than the general rule; so for a fire on an island, the pool of available plant species might be limited to one or two survivors and then these might be able to adapt and speciate.

An even neater reaction or strategy to change is that employed by bacteria, being lateral gene transfer.  For me, microorganisms are a clever solution to life – simple, focused and reactive, where they can undergo asexual reproduction, as well as pull in genetic material from elsewhere in the bacterial world to suit particular environmental or physical needs via an ersatz “sexual” reproduction; they function like stripped down life, carrying around only the genetic information that they need to continue and increase the amount of DNA-RNA in the world, then drawing on genetic applications from other places as they might require them.  Similarly, they respond to environmental change through adaptation, increasing or decreasing their relative populations within the bacterial community as needs be.  No need to evolve and no need to push for speciation, with a tendency towards genetic cohesiveness over time rather than diversity.  Hence, bacteria and viruses perhaps, also, function more as communities of genetic material rather than species per se and we should look at and study them as such.  In fact, the idea of species implies that a species can only successfully reproduce within that species, however, as already discussed, bacteria are more promiscuous than that; perhaps multicellular organisms would be also but cannot due to their complexity, so the existence of ring species of salamanders show that while two distant species might not be able to reproduce successfully, were you to go along the ring of species, each adjacent species can reproduce successfully and so theoretically you could transfer a genetic trait along the line, albeit in a complex way.  Are we perhaps too focused on the differences between species but should look at our similarities? For example, bird flu and swine flu can move between those species to humans as from a viral perspective we all seem similar in the same way that people in Britain call trees trees, but our ancestors and agricultural people in other parts of the world would say “that sycamore” on the green rather than “that tree”, i.e. we lump together trees generically now rather than by species!

Bacteria and viruses, also, raise another interesting point about genetic progress, being mediocrity.  One of the presumptions of evolution is the survival of the fittest and the development over time of the best alternatives for working in a particular niche.  In reality, the evidence everywhere is that life favours mediocrity first, then specialisation later or not at all, as mediocrity (or generalisation) enables species to work with each other in maintaining the status quo, the interlocking and mutual matrix of life.  A good example is influenza, where although we have had concerns recently about killer flu viruses, the key factor about flu is that is works with human beings, so it wants to infect them, but it does not want to kill off its hosts as then it could not reproduce.  In effect, a killer flu virus would be useless for the virus itself, so while it might start out strong, it will select for weaker forms over time, so ensuring mutuality.  Of course, there are situations of killer viruses, however they are rare and usually select themselves out by being very difficult to transfer, e.g. even cholera dies very quickly when exposed to air and does not travel long distance in water, hence it only really effects people very close to the source of contamination (or HIV can be used as an example as it is difficult to transmit except directly via blood).  Another example would be lions, which sit at the top of the food chain, but actually do not need to feed regularly, and out of practicality and laziness, they tend to capture the weaker targets, so actually helping to improve the stock of their targets rather than destroy them; if they killed everything all the time and destroyed the fittest targets out of sport, they would soon have no food chain to be the kings of.  Specialisation works against the concept of survival as the more specialist you become the more exposed that species is to even slight changes in its biological niche, so slow-moving, turkey-sized birds without wings quickly became an easy foodstuff for humans and dodos became as dead as the metaphorical dodo, while pandas in the wild survive more and more by a thinner thread.

Similarly, reverting to Darwin’s finches, perhaps they succeeded on Galapagos because the original finch was a mediocre generalist, then later over time they specialised.  If the original finch had been adapted to a really specific niche, then it might have died off immediately it arrived on virgin Galapagos.  All current species derive from mediocre, generalist forebears, as specialists tend to be weaker in evolutionary time and true specialists will die out immediately a niche changes.  Therefore, trace back a few generations in most species living now and you will find a dull, boring generalist that has expanded into a niche or several niches; this is the key to the genetic development of species, the steady march of the bulk, mundane and mediocre species rather than the ever improvement on the genetics of specialists, i.e. species are the wood and you need to find the trees – which generalist will be the next successful specialist?

This is controversial as the colour and interest in species on earth tends to be the quirky and evolutionarily redundant species, with people looking over and ignoring the boring and mundane, e.g. bacteria, insects and slime moulds.  However, perhaps that is a mistake and we could reduce the number of species we worry about by focusing on strong generalist species rather than worrying about keeping every special and interesting genotype.

So in this hypothesis, where does standard evolutionary theory sit? It still occurs, but it is not the central driver for the development of life.  Generalist species adapt through shifting their natural genetic variation within a species or pulling in different genetic material via lateral gene transfer, then, if these changes stick, over time genetic traits that favour occupying these new or wider niches might be favoured and so genetic makeup might drift from the current norm in space and time.  However, in most cases, this is not permanent and if the niche environment falls back to its previous make-up then the core species make-up might drift back to close to its previous norm.  This genetic ebb and flow might be the mechanism for microevolution.  In fact, this genetic variation is key for the survival of species as it provides a species with a bank of potential genetic variations on which to draw when conditions change, whether these are endogenous as in multi-cellular species or exogenous for micro-organisms, which seem to use them like genetic applications in a world wide gene-web from which to pull in new coding as needed via lateral gene transfer, hence I query whether it is really evolution as envisaged by Darwin.  Interestingly, I mention the idea of space-time and it is interesting whether we should really conceive of life in a quantum way rather than our usual Darwinian way of thinking, i.e. life is determined by probabilities and is fractal by nature – (a) like big bang for the universe, were you to start the clock of life on earth again, wouldn’t you get a different answer at today’s date and time for how the community of life would look; (b) is there a complete range of possible future forms of life on earth and what life you find and how you articulate and model those discoveries depends on the observer and that observer’s own particular space and time matrix; (c) similarly, don’t fields of probability determine the range of possible historic species that existed and only when you find/observe particular species do they effectively come into reality (via fossil discoveries, for example).  So life is less neat and more chaotic than we want it to be.

Overall, we need to view a species as a fuzzier less exact category; a bell curve of genetic material that varies significantly, with the breadth of the curve itself being an important indicator of the viability of a certain species, so a very thin pointy curve denotes a very delicate species that will become extinct quickly with any environmental changes, whereas a broad bell curve enables a species to draw on a wide range of potential genetic applications and so adapt to environmental changes without resulting in a collapse in species range.  Only relatively rarely does adaptive gene selection become permanent and a new species is born, since having a wide range of genetic variants within one set of interbreeding species is a better survival technique, whereas a tightly knit gene pool is severely limiting.  Then as environmental changes occur that species’ genetic bell curve might centre on a different variant that is more adapted to these new conditions, however were the conditions to change back to the original state, then the bell curve might fall back to almost where the original bell curve was but not exactly the same place, because of the fractal nature of life.  If all the environmental changes were one directional, the bell curve might be moved several times in one direction, resulting in the original genotype no longer being accessible within the pool of natural variation and so in effect a new species has occurred, but not because of some great evolutionary plan, but simply because life is fractal and it cannot shift the bell curve back to encompass the original genotype.  However, it also means that were the original conditions to reappear, when the “new variant species” sought to adapt and searched for a suitable genotype it would choose a different choice from the original starting position and that choice may not be as good a genetic choice, i.e. you do not always get the best answer to the current need for an adaptation, just a decent answer from the current gene pool.  This results in a randomness to life and a fractal pattern for speciation.  The cumulative impact of these small adaptive movements in individual species’ bell curves might result in much of the micro-variation of complex life on earth.  Is this how evolution works, i.e. on a micro scale and for multicellular organisms only?  Perhaps lateral gene transfer would occur if possible, but the sheer complexity of larger, complex beings precludes regular successful transfer of genetic material into complex species; however, pieces of viral DNA have entered the human genome and remained there as endogenous retroviruses, coding for key proteins in human placental development, e.g. for syncytin 1 and syncytin 2, as well as for human Y chromosomal development; in fact more of human DNA is directly viral (9% for endogenous retroviruses and 34% for retrotransposons) than for actual human genes (1.5% only)(i).

In addition, major changes to genetic make-up occur all the time by chance; most of these are unviable and so never survive and others are dead ends that simply never continue in existence for very long; however, some ideas stick around, most of which muddle along without much impact, while some ideas have resulted in major species’ shift because the error in the DNA-RNA creates a new and revolutionary way of organising life.  This is macroevolution driven by mutation and speciation; this is, however, really high risk as most spontaneous speciation results in unviable organisms that cannot replicate or are weak and so die off quickly or because they do not confer any greater benefit than an incumbent and so will be driven out, similar in a way to new businesses that might offer a better, say, operating system but cannot remove the main incumbent, Microsoft, which has the advantage of being the dominant incumbent.  For example, the ability to photosynthesise enabled species to live in the high carbon dioxide world and nutrient declining world around 4 billion years ago, but eventually as the new technology became perfected and as an unfortunate side effect, it caused massive species collapse as oxygen poisoned most living species and carbon dioxide levels collapsed.  This evolutionary change happened successfully only the once, but are newer, better versions of photosynthesis created all the time but can never ever get a look in.  Other key genetic changes that have occurred include: the ability to respire and so utilise the carbon stored as sugar together with using up the oxygen, the ability for single celled organisms to live symbiotically within other cells and the ability for cells to aggregate together for their mutual benefit and create multi-cellular organisms.  These changes run against the wishes of the generally conservative dead hand of life that dislikes change; in fact, life is perhaps correct because each of these changes caused major havoc to life on earth, resulting in turmoil amongst species existing at the time, causing huge species die off.

Arguably, this is what is happening now.  Humankind, a relatively weak and mediocre, immature ape, has evolved in such a way that it can adapt its and other species’ behaviour, range and mutuality through learning, communication and changing the physical, chemical and biological environment through adapting and “evolving” outside the biological world in the abstract world of thoughts and ideas.  This new form of change through knowledge rather than genetic adaptation is causing destructive changes to the environment similar to that wrought by the initial ur-photosynthesising microbe, hence changing the environment and driving species’ collapse; humanity overall is destabilising one of the key crutches of life, i.e. maintenance of the status quo.

There is one final situation where you get rapid change and that is another key driver for life – opportunism.  As I have said, life tends to be conservative, but there are times when due to external changes opportunity knocks and life adapts rapidly; this occurs when biological niches become available, for example after photosynthesis caused species collapse there would have been ample opportunity for newly available niches to be filled after the former occupant died out, or when mitochondria started respiring and eating sugar this would have created new niches or when the dinosaur population collapsed at the end of the Mesozoic era some 65 million years ago, the small and mundane mammals (who were also perhaps a natural variant on reptiles) were able to blossom out into available niches, at the same time as those inconsequential, and clumsy, flying reptiles that had split from dinosaurs or another reptile species around 65 million years ago were able to conquer the skies and become birds, and similarly when the first breeding pair of finches landed on Galapagos, they would have found loads of opportunity to spread out.  Some scientists have postulated that opportunity frees up species from the laws of natural selection, which fits in with my ideas neatly (Yoder et al, 2010), but are really situations where new ideas are given the time to become more robust species and establish themselves without the negative selection pressures imposed by the rest of life on novelty – life hates change.

These rare circumstances are amazing and result in great variety and stunning beauty, but I argue they are not the norm, but one of the rare and unusual responses by DNA-RNA to the maintenance of life on earth.  Evolution occurs on the one hand, but on the other it is perhaps not the primary driver of life on earth on a daily basis, even if it is a very enticing and exciting sideshow – it is like human life on earth where our primary role is reproduction and nurturing new life, but all the colour and excitement of the Premier League is much more fun, even if over geological time it is completely irrelevant.

I would, also, like to return to the idea of lateral gene transfer and mutuality.  I wonder whether this mechanism is more prevalent than we sometimes think.  Imagine a bacterium that lives on earth at the same time that photosynthesis arose; the increase in levels of oxygen is trying to kill me off as a species; there are 3 responses to this: (a) become extinct; (b) develop aerobic respiration; (c) work mutually with these ur-chloroplasts and incorporate them over time into my cells.  This latter idea of mutuality is similar to in the business world where, when new technology arises, you go bust, or fall behind your competitors or bring it into your business; therefore, perhaps the process of working with chloroplasts and mitochondria is an adaptive development arising out of mutuality and could occur more easily than we have previously considered.  As mentioned earlier, there is evidence that suggests that some of the genetic coding in the human genome is simply coding brought into it via retroviruses with some of it potentially being very useful – is this evidence of mutuality having occurred even in Homo sapiens?

Much has been written on evolution and how it creates through natural selection the beautiful diversity of life on earth.  Suffice to say, evolution does happen and it works as an hypothesis to explain how finches differentiated on the Galapagos Islands and how Homo sapiens developed from the ape family tree some 4 to 8 million years ago, but I do not believe that it explains how, or even why, most of life on earth is at is.  There are just so many unsolved questions, for example: How and why do microorganisms adapt and change over time using lateral gene transfer? Why, even after we had thought them extinct, do coelacanths and tadpole shrimps still exist (unchanged for at least 25 million years and 220 million years respectively)?  How and why did chloroplasts and mitochondria end up in the cells of other species?  How do the populations of trees in forests shift over time if they change individually rather than in a coordinated, evolutionary response to external changes? Why do “old” species like archaebacteria or amphibians or reptiles still exist if mammals are “more advanced”?  Or to repose Charles Lyell’s question to Charles Darwin in 1856 why do fossils for types of mollusc in the British fossil record abruptly disappear only to reappear 2 million years later unchanged? 

However, a broader, fuzzier and less neat mechanism that starts with the premise that the make-up of life on earth is driven by a different theory of life, where life is a conservative rather than radical and where various possible types of adaptation arise chaotically and continuously work to maintain the status quo of current life on earth, with evolution being only one of the possible mechanisms for change and perhaps limited to complex multi-cellular organisms.  It is a more chaotic mechanism where adaptation might normally occur through behavioural changes, range changes and altering interconnecting mutual relationships between species, supplemented by genetic adaptations such as lateral gene transfer, or general genetic variation within species, and more rarely by random mutation but with no external influence from natural selective forces.  Furthermore, adaptation and change should perhaps be seen more holistically, as how communities of life shift with changes to it rather than following the evolutionary progress of individual lines of species.

It is, also, a mechanism that recognises that life on earth is perhaps made up of the stories of the more mundane and mediocre species that continue their march hidden in the background, but whose genetic material is stable and cohesive and will later form the basis of new specialisations.  It is these boring creatures that should be celebrated, so true life is less colourful, less quirky and less cuddly and photogenic than science would sometimes have us all believe (but there ain’t no money or television in that story!). 

I apologise for my ramblings, and I am not sure this stream of consciousness on evolutionary theory is at all sharp enough, so I will summarise in the following blog with a mechanism that might work.

Notes:

(i)  It mainly appears to be retroviruses that have inserted themselves into mammalian genomes, however bornavirus DNA has also been found in human DNA, so lateral gene transfer might occur throughout multicellular species even if at a lower rate than in microorganisms.

Some further reading

[If I have missed out any references this is purely my error and is inadvertent and the result of resreaching this on my own and without anyone to check, challenge and criticise and so I would welcome the change to correct those omissions and apologies for my mistake and any potential offence caused.]

Bennett, K. (2010) The chaos theory of evolution, New Scientist, 18 October 2010, [Available from the Internet at http://www.newscientist.com/article/mg20827821.000-the-chaos-theory-of-evolution.html]

Davis, M.B. (1983) Quaternary History of deciduous forests of Eastern North America and Europe, Annals of the Missouri Botanical Garden, 70: 550-563, 1983 [Available from the Internet at http://biostor.org/reference/12744]

Coope, G. R. (1979) Late Cenozoic Fossil Coleoptera: Evolution, Biogeography, and Ecology, Annual Review of Ecology and Systematics, vol 10 p247 [Available from the Internet at http://www.annualreviews.org/doi/pdf/10.1146/annurev.es.10.110179.001335]

Grebmeier, J. M., Overland, J. E., Moore, S. E., Farley, E. V., Carmack, E. C., Cooper, L. W., Frey, K. E., Helle, J. H., McLaughlin, F. A., McNutt, S. L. (2006) A major ecosystem shift in the Northern Bering Sea, Science, 10 March 2006,  311, 1461 – 1464 [Available from the Internet at http://www.sciencemag.org/]

Lawrence, J.G., Retchless, A.C. (2010) The myth of bacterial species and speciation, Biology & Philosophy, Vol 25: 4 pp 569 – 588, September 2010 [Available from the Internet at http://www.metapress.com]

Lowe, K., FitzGibbon, S., Seebacher, F., Wilson, R.S (2010) Physiological and behavioural response to seasonal changes in environmental temperature in the Australian spiny crayfish Euastacus sulcatus, Journal of Comparative Physiology, 2010, 180: 5, 653 – 660 [Available from the Internet at http://www.springerlink.com/]

Santos, F., Peňa, A., Nogales, B., Soria-Soria, E., del Cura, A. G., González-Martín, J. A., Antón, J (2009) Bacterial diversity in dry modern freshwater stromatolites from Rudeira Pools Natural Park, Spain, Systematic and Applied Microbiology, 33 (2010), 209 – 221 [Available from the Internet at http://www.sciencedirect.com]

Wikipedia (2010) Peppered moth evolution [Available from the Internet at http://en.wikipedia.org/wiki/Peppered_moth_evolution]

Yoder, J. B., Clancet, E., Des Roches, S., Eastman, J. M., Gentry, L., Godsoe, W., Hagey, T. J., Jochimsen, D., Oswald, B. P., Robertson, J., Sarver, B. A. J., Schenks, J. J., Spear, S. F., Harmon, L. J. (2010) Ecological opportunity and the origin of adaptive radiations, The Journal of Evolutionary Biology, 23 (2010), 1581 – 1596 [Available from the Internet at http://onlinelibrary.wiley.com/]

Two Thoughts On Nature After A Walk In North Yorkshire

Sunday, May 16th, 2010

I walked along the River Ure last night.  It was sunny and warm, albeit with a slightly brisk wind towards the south east.  I was amazed that no-one else was out walking along the embankments – there are about 5,000 locally – but I guess that the draw of “Over The Rainbow” on the box was too interesting for nature.

What struck me was two things – firstly, the birds were so busy and noisy; and secondly, the colours. 

As for the birds, there’s a song thrush nesting in the chimney of our neighbour and she sings away early in the morning and in the evening, jamming away with a free flowing tune.  Blackbirds could be seen scruffling around in the leaves and debris below trees and in the hedgerows.  Ducks were busy on the water and several drakes were fighting while flying vertically up from the river, while house martins were flying in flocks of 5 or 6 in strict formation like Red Arrows planes (on reflection, I wonder whether they were sand martins).  Peewits landed in a newly sown field and start poking their black beaks into the soil, hunting for food.

Then there were the colours of the birds, as well as the bright blue sky.  Also, the colours of the plants – to a background of a wide variety of verdant greens, there were the white blossoms of cherry trees, apple trees and horse chestnut trees (I looked at the horse chestnut flowers and they had streaks of pink coursing through the petals), with the bright yellows of rape, brooms and dandelions.  I stooped to pick a seed head from a dandelion and blew 10 times to set all the seeds floating into the wind to start new generations of dandelions – this was done near to where the Battle of Boroughbridge was fought many, many years ago.

It made me think of two things. 

Firstly, how amazing nature is.  It just gets on with life and has worked out such an intricate way of enabling genetic material to pass from generation to generation, ranging from the clever floating seed heads of dandelions to the complex fighting of the drakes, and the beautiful temptations of the horse chestnut flowers luring in the busy bees to pollinate them.  Science is amazing and genes will continue to be transferred by a full range of complex mechanisms whatever we humans get up to.  I am in awe of nature, constantly amazed by its secrets; it has excited me since I was a small kid and it still fascinates me, as well as making me smile.

Secondly, I thought about dinosaurs.  I realised my views of dinosaurs were defined by big fossils in the Science Museum and films like Jurassic Park, Godzilla and Walking With Dinosaurs.  They have made me think of big animals, slow animals, a mute colourless world, deep throated calls and slow lumbering beasts.  But I reckon that’s all wrong – a paradigm shifted.  I reckon that the world of the dinosaurs was bright and colourful, full of high pitched chattering, buzzing insects and busy small animals scurrying around and living their lives.  I know that scientists have started imagining dinosaurs with feathers and colour, but I think that’s not going far enough.  The problem is that the big animals are the ones that leave a trail through geological time in the form of fossils, while the small bugs that dominate our world then and now leave no trail across the aeons.  There are next to no records of bacteria, viruses, moulds or other monocellular creatures and few records of insects and other bugs.

We have that problem even now, in that we see the world from a big mammalian perspective, whereas we don’t rule this world – it’s a world of bacteria, fungi, viruses, insects, spiders, plants and birds, as well as the bigger animals like mammals, reptiles and amphibians.  I realise that deep down I must actually miss the world of microbiology that I studied at Edinburgh University, of those weird bacteria and viruses that transfer their genes horizontally and vertically.  I really am just a science geek that went out into the real world, escaping the lab.

However, we would do well to remember that we are but curiosities to the rest of earth’s life – largely irrelevant.

Update:  I did the walk again today, but back to front and without the sun in my eyes, and they are definitely sand martins as I could see them flying in and out of their burrows in the riverbank opposite the Ings.

Pale Blue Dot

Sunday, April 11th, 2010

Sometimes you read something that says things so much more clearly and beautifully than one could ever hope to do oneself.  And I have recently read one of those – it comes from Richard Dawkins‘ brilliant anthology of science writing called “The Oxford Book of Modern Science Writing” and it’s a passage by Carl Sagan called “Pale Blue Dot” from “Pale Blue Dot: A Vision of the Human Future in Space”. 

For me, it sums up so much better than I can ever explain why I think that we should all come from the stewardship angle regarding our relationship with the earth and nature rather than to exploit it for the here and now.  It comes from a deeply-held philosophy that stems from earth as my home and everyone else’s home, as well as the home of all creatures and plants and microbes past, present and future.  We are but briefly passing through for the tinest fraction of time and we must be careful of our impact as the world is a unique, beautiful and very blue place in a universe full of cold, dark, black and dead nothingness.

“Look again at that dot.  That’s here.  That’s home.  That’s us.  On it everyone you love, everyone you know, everyone you have ever heard of, every human being who ever was, lived out their lives.  The aggregate of our joy and suffering, thousands of confident religions, ideologies, and economic doctrines, every hunter and forager, every hero and coward, every creator and destroyer of civilization, every king and peasant, every young couple in love, every mother and father, hopeful child, inventor and explorer, every teacher of morals, every corrupt politician, every “superstar”, ”supreme leader”, every saint and sinner in the history of our species lived there – on a mote of dust suspended in a sunbeam.

“The Earth is a very small stage in a vast cosmic arena.  Think of the rivers of blood spilled by all those generals and emperors so that, in glory and triumph, they could become the momentary masters of a fraction of a dot.  Think of the endless cruelties visited by the inhabitants of one corner of this pixel on the scarcely distinguishable inhabitants of some other corner, how frequent their misunderstandings, how eager they are to kill one another, how fervent their hatreds.

“Our posturings, our imagined self-importance, the delusion that we have some privileged position in the Universe, are challenged by this point of pale light.  Our planet is a lonely speck in the great enveloping cosmic dark.  In our obscurity, in all its vastness, there is no hint that help will come from elsewhere to save us from ourselves.

“The Earth is the only world known so far to harbor life.  There is nowhere else, at least in the near future, to which our species could migrate.  Visit, yes.  Settle, not yet.  Like it or not, for the moment the Earth is where we make our stand.

“It has been said that astronomy is a humbling and character-building experience.  There is perhaps no better demonstration of the folly of human conceits than this distant image of our tiny world.  To me, it underscores our responsibility to deal more kindly with one another, and to preserve and cherish the pale blue dot, the only home we’ve ever known.”