On Darwin and His Theory

Evolution is a word that can divide the world.  Its opponents often claim that all that lives today, in terms of species diversity, did so yesterday…all the way back to the ‘first’ yesterday, which some people claim was precisely 4004 B.C., when ‘God’ created everything essentially in a moment.  Bishop Ussher, of Ireland, published his ‘findings’ in 1650 and his ‘documentation’ is that most frequently referenced by opponents of evolution.  He has it down to the day, Oct. 23 of that year.  This is a problem when a researcher goes in with an ‘answer’ and is only looking for corroborating evidence, evidence which they will eventually find.  Science, through the study of evolution, has developed various specialized technologies and techniques to reach back in time and analyze the evidence at hand.  It has done this building on the work of those studying paleontology, microbiology, geology, chemistry, atmospheric chemistry; palynology, the study of pollen; astronomy and cosmology, quantum physics, stochastic methods developed around the hypothesis of a molecular clock which posits a rate of genetic change; and cladistics which assesses genetic lineages, the relationships between species and larger classification groups…scientists have collectively been dating ‘life’ back over Earth’s 4 billion years.  The creationist argument depends entirely upon belief, denies science and views evidence such as fossils simply as ‘puzzles’ God left to confuse us.…Others accept that lower species may have ‘evolved’, but Man, created in His image, is special, exceptional and exempt, a creation of God, fixed and forever.  Modern science does not give a pass to such claims of specialness seeking instead more direct evidence, making connections, following patterns, doing science….

The factors that define a species’ success are many and can change over time.  We must factor in other species with which they compete, as well as those with which they share supportive relationships and the physical conditions within which they live.  Species are limited and supported by their immediate environment and community.  Niches for any one species are limited.  A single species cannot reproduce outside of limits without threatening its own as well as the continuation of other species.  They exist in relationship, one with critical parameters, outside of which existence is unsupported.  Fitness varies, it is not just a matter of the biggest, strongest most aggressive succeeding, though those factors play a role…there is always an element of chance, of opportunity, gained or lost.  The extant conditions within which a species lives, its relationships with other species and within populations of its own, may favor other characteristics, such as the more social skills of cooperation, be they of root associations in plants or behaviors that support social bonding between animal individuals.  Darwin spent much of his adult life studying and writing on this topic, before he finally, formally, introduced it.  He was a scrupulous thinker, educated in christian fundamentals to live a life as a minister and man of God.  He was painfully aware of what the idea of evolution could mean to the church and for devout believers, of whom his wife was one, and it was important to him that this concept, which he was convinced of, be presented in a way that it could be accepted.  Others before him had proposed evolutionary ideas.  One important one was Charles’ grandfather, the respected physician, Erasmus Darwin, who influenced Charles, another was Jean Baptiste Lamarck, trained as a botanist who went on to become an expert in invertebrate biology.

Lamarck, through his study and the increasing fossil evidence of his time, the mineralized bones of creatures never before seen by humans, proposed the first full theory of evolution, which would become known as Lamarckism, writing that through inheritance organisms pass on the successful physical traits that they possess, traits which develop through use, over generations.  One of his ‘examples’ was that of the giraffe that he proposed lengthened it’s neck gradually by stretching to feed and then passing that trait on to its offspring.  Keep in mind that although Gregor Mendel had long earlier written up his ideas of inheritance and his early concept of genes, in his study of peas, his ideas had not been accepted or even very widely known.  Mendel’s work would wait until just before the 1900’s to be ‘discovered’.  Lamarckism would never become very widely accepted.  It had run head first into the dominant, christian thinking of the day, that all that is alive was a creation of God and had been here from the original creation, though some would later concede that there had been other smaller creation events, orchestrated by God. 

Another important figure in this was Alfred Russel Wallace, who independently arrived at the idea of ‘natural selection’, arguably before Darwin.  Wallace shared his early ideas in letters with Darwin who had been working on a fuller exposition of the idea for years, an idea he kept with very few exceptions, to himself.  Wallace came from a family without the means of Darwin’s, he had to work for a living, spending much of his time in the field making collections of specimen that could be sold back in Europe to a growing population of men of means and natural history museums.  (Darwin’s family was established, his grandfather Erasamus was a physician, and well to do and his father married into the wealthy Wedgwood family which built a fortune on its ceramics wares.) The more unusual, the more beautiful, the greater the price could be demanded…and Wallace was obsessed with the species of the Bird of Paradise species, of which he would ‘discover’, as a European, 5 of the 40 species, the Standard-Wing, named Semioptera wallacii after him, he considered his greatest discovery.

Opponents see the ‘hand of God’ and rail against science’s assertion, as they see it, that we descended from monkeys, a claim Darwin did not make (monkeys, chimps, apes and humans descended from independent ‘lines’ within the hominid group each following different genetic lines, patterns and strategies).  Religious fundamentalists tend to have a very limited view of the capacities and value of the natural world.  They claim that only god could have been so miraculously creative, that nature via random mutation and Darwin’s ‘natural selection’, acting to cull the weak from the strong, the survival of the fittest in a ‘dog eat dog world’, cannot be responsible. This phrase too of the endless violent struggle between species and individuals has always been misleading.  In our world dogs don’t normally eat dogs.  Dogs are social and work together in packs, they establish a social hierarchy, each with their roles, unless bred or trained by us to be vicious to one another.  Yes, in some species, there is a degree of ‘violence’ amongst the breeding population, but it is generally not fatal.  Dominance is established along with its hierarchy, in some cases and life goes on.  But even with dogs, the social order, the pack, is established and assures the survival of as many as possible.  It is a limited, but relatively successful strategy.  ‘Dogs’ might not be ‘failures’ as individuals without such a social order, but they certainly are more successful and longer lived because of it.  Darwin’s ideas have been taken and applied in ways he would never have approved of, unsubstantiated ways, some of which have been broadly adopted, such as the idea of ‘social Darwinism’, which supporters reference to forward their own agendas, in human competitions, in which one ‘team’, race, culture or country, is superior to another and is favored and thus justified in exerting its will, as if it were some preordained destiny and ‘natural order.  This, however, is a perversion of Darwin’s ideas.  (White supremacy and Hitler’s dominant Aryan race, the superiority of the Han in China…sadly, many other examples abound.)

Darwin’s theory of Natural Selection guiding evolution, like any theory, represented his best understanding of the working of the evolutionary process at the time.  Evolutionary scientists to this day hail it as one of the most important theories of science to date, on par with Newton’s theories of motion and mechanics…and, like those theories, it is important to remember that they are incomplete, that they were our best understanding and can and have been improved or refined, not thrown out.  Their proven utility, their explanatory ‘power’ will not magically go away, but our understanding will continue to improve and with it will come other theories which supplement or adjust our previous theories.  It is a very complex universe and we are very small our perceptions limited.  Science continues onward, inexorably.

Darwin’s original theory has been augmented over time  incorporating into it Mendel’s ideas, our modern understanding of genetics and the ideas accrued over the last 150 years by researchers.  We view genes as the carriers of inheritance, that through their mixing which occurs within the processes of sexual reproduction, distinct individuals are formed.  He argued, without the capacity to fully understand how this could work, for a process of incremental mutation.  Added to this in more recent decades, are various forms of Horizontal Gene Transfer, HGT, in which a gene from one individual may be shared with those of an entirely different individual, even species, outside of sex, a process once described as ‘infection’.  A virus’ ability to infect and alter another organism’s DNA is relatively well understood today as is our understanding of how those changes can become permanent in that individual and passed on to its progeny.  Darwin saw gradual change of a species over time, expressed morphologically in the form of resultant individuals.  Through HGT significant changes can be interjected into a genetic line suddenly, though unpredictably.  These changes may be positive and result in a more successful individual, giving it a survival and reproductive edge and more offspring over time; be neutral and essentially held ‘dormant’ within an individual’s and its progeny’s DNA; or negative, unsupportable, and the individual and its progeny less likely to continue into successive generations.  This modified, blended theory, is known as ‘Neo-Darwinism’ and there are multiple versions of it with minor differences.  Neo-Darwinism is widely accepted as our best ‘idea’ of the process.  There are a growing number of evolutionary scientists, who are questioning its adequacy…not saying that it’s wrong, just incomplete, that something else is also at work here, playing an important role.

Evolution happens at a micro- and macro- level.  Microevolution refers to the change of gene frequency within a particular population of a species as it, for example, develops pesticide resistance over the course of a few generations, those more resistant surviving, reproducing and passing on to their young this genetic resistance.  This can happen relatively quickly, in a time frame observable to us in single celled organisms as well as those with a much more rapid reproductive cycle.  Such a change comes about because natural selection favored this gene; because a given population received new immigrants carrying the gene; because some nonresistant genes mutated into the resistant version; or because of ‘genetic drift’ from one generation to the next.  Macroevolution, on the other hand, operates over much longer time periods and refers to the appearance and development of new species, genera and families.  Macroevolution concerns the development of primitive angiosperms, flowering plants, how they arose from the flowerless, seed forming gymnosperms and those from even older seed forming ferns which followed the early true ferns which reproduced by spores…a process the surviving ferns today still follow. The process of natural selection operates at all levels.  We should ask ourselves, at whatever level evolution is functioning, is it fully explained by a process of random rolls of the genetic dice?

Natural Selection as a ‘Reductive’ Process and the Limitations of Random Mutation

The theory of ‘natural selection’ itself is not at issue.  The issue is whether it is reasonable to think that strictly random mutation is responsible for the appearance of life and its evolution into higher more complex forms.  Religions generally place this in the ‘hands’ of chosen gods.  Science has long ascribed this function to the process of mutation, with a more or less random and incremental change over time to any species’ genetics.  The ‘selection’ part of the process is itself ‘reductive’, reducing the diversity of a population by ‘favoring’ the more fit so that they may breed while the less fit does not, or does so in lesser numbers, changing a shifting base point.  Successful random mutation shifts this next ‘starting point’ incrementally, where the next mutation is as likely to be a step ‘forward’ in fitness as it is to be a step backward.  The ‘fitness’ of an individual would be determined by a complex mix of factors which includes its environment and all of the other members, species, that comprise its larger community.  Natural selection does not generate options directly, it selects from a ‘pool’ of individuals, mutations or innovations, those which are more fit, ‘choosing’ from what is available. What ‘succeeded’ in the past may not at some future date.  Evolutionary biologists have hypothesized that successful gene mutation and consequent changes to a species, proceeds at a calculable rate.  From this they have devised molecular ‘clocks’ which allow them to gauge the amount of change a species underwent to get to a given stage of evolution and their calculations can get quite specific.  Still evolution presumes that mutation is a random process…and fulfills this ‘demand’.  Those who study complex systems suggest that something else is at work here, that the process is not entirely ‘random’, that such changes are more ‘probabilistic’. 

This question has become increasingly hard to ignore as our understanding of genetics, the requirements for life and the mathematics of random mutation is proving, perhaps, insufficient to the task in its capacity to adequately explain how life has arrived at its current state in time.  Systems scientists argue that there is some positive ‘driver’, which in a sense ‘tunes’ the parameters within which these changes occur conserving time and materials by not pursuing every option.  Such a driver would tilt the genetic probabilities to produce those patterns with a higher rate of success, would be more creative, generative.  ‘Mistakes’ could still be produced, but every mistake possible, would not.  Physicists and systems scientists have been working out theories and hypotheses which argue that organisms and other ‘dissipative, out of equilibrium structures’ (such ‘structures’ include living organisms, but more on this later) tend toward self-organization and increasing complexity when supplied with adequate energy and the capacity to rid themselves of waste, to dissipate it.  Complexity, they argue, builds on itself and it does so in a more organized fashion than random mutation, beginning at each stage with what works, then moving on to the next level and, having done that, readjusting the ‘starting’ point for the ‘next’ move.  Evolutionary change is progressive and probabilistic.  Evolution tends toward self-organization and increasing complexity while niche and ‘need’ of the system ‘hold’ places for necessary, more basic and system supporting organisms, such as those which are central to maintaining a stable mix of atmospheric gases and others that can adequately break down dead organisms into their reusable constituent parts. Life they argue is intricately allied with chemistry and the idea that random mutation can account for the trillions and trillions and trillions of possibilities is simply not supportable.

Take a human being.  Look at our DNA and its literal billions of base pairs (base pairs are the component ‘rungs’ of the DNA ‘ladder’).  If nature were truly random and an organism were simply the result of enough random combinations eventually being tried, then there have not been enough years in the universe to have stumbled upon the accident of this particular combination, even if each such combination required only one nano-second, one billionth of a second!!!  Conventional evolutionary thought describes a progression from less complex toward more complex species in continuous lineages, significant failures of which would mark the end of such a line.  This progression of speciation can be traced back all of the way to the ‘last universal common ancestor’, LUCA, that first organism or proto-organism from which all others can be traced, from which all others began their differentiation into unique lineages, presumably for multicellular organisms, the first true eukaryote.  The first eukaryote in a sense, set the genetic table for every organism to follow.  The line of descendency is common and shared and we can trace the changes and lineages back to that…at least theoretically.  The holes in the fossil record make this difficult. 

Perhaps the ‘biggest magic’ had already happened…before LUCA.  The formation of the living cell complete with its capacity to reproduce itself faithfully, accurately and consistently, the same cell which has come to differentiate and collect into complex living structures such as ourselves.  Our cells today share much with that original, LUCA.  All of the many millions of species since then share this common structure and have passed it on to every successive individual.  The differences are in specialization and a cell’s capacity to join in mutually supportive structures, ’communities of cells’, to form multi-celled organisms  This has required a very fine level of communication and coordination between cells.  Mutation or genetic change, has had to occur more at this ‘leading edge’ than at any basic structural level.  The eukaryotic cell of today is still readily identifiable as the same basic eukaryotic cell of a billion + years ago.  Speciation and radiation have been occurring, arguably, at an increasingly faster rate.  Each species has not had to ‘reinvent’ itself from scratch.  We have, with very tiny changes, been reassembling successful patterns of the past, incorporating smaller innovations.  

The structures of modern organisms are extremely complex and precisely organized, built up from cells  These changes, this evolution, has faithfully followed ancient patterns, making incremental changes, fine tuning and innovating in the creation of new species.  Mutation in such a complex process is extremely likely while its chance of producing success, with the necessary and precise changes to birth ever more ‘fit’ structures with the increasingly  complex functions of an evolving multi-celled organism, is extremely low.  Fidelity is essential for reproduction and the long term survival of a species.  Random change is not.  Random change of DNA, of the basic controls and limits on reproduction and life, present a tremendous risk.  Errors undoubtedly happen, but how likely is it that fit, successful organisms, can be built from that process alone?

In a human being we have 23 matching pairs of chromosomes.  Each chromosome is made up of a variable number of base pairs, pairs of nucleotides which include the coded four phosphate groups cytosine, guanine, adenine and thymine.  We have a total of better than 3 billion base pairs . 

[Now consider that many ‘simpler’ species have a vastly larger genome: the broad-footed salamander (65.5 billion bases), the African lungfish (132 billion) and the Paris japonica flower (149 billion). What ‘explains’ this huge difference? What is going on with DNA?…There is an ongoing ‘discussion’ questioning the role of DNA as the sole ‘recipe’, operator’s manual or ‘architectural set of plans’ for each living organism. DNA would seem to be inadequate in terms of its ability to explain all structures, their development, on going ‘maintenance’ as well as the internal functioning of of a cell and the larger organism. The precise role of much of it remains unattributable and would seem to be superfluous, though I doubt that it is. This begs the question of what exactly is it for? what is its role? because it definitely does have one in the creation of proteins and even function, as our own ‘tweaking’ has demonstrated, at least in part, of an organism?]

DNA is in ‘coded’ form so the precise pattern of those base pairs is essential to understanding it.  Shift this arrangement and the structures that constitute an individual can change.  Here is where the numbers, the probabilities, become impossibly large and incomprehensible.  

In humans, because science has identified the entire human genome, we know that we have 23 chromosomes of variable size.  In chromosome ‘1’ there are 249 million base pairs; in chromosome ‘2’, 243 million base pairs; chromosome ‘3’, 198 million; in ‘4’, 191 million; in ‘5’, 181 million; in ‘6’, 171 million; in ‘7’, 159 million; with a descending, but still huge number down to the smallest, chromosome ’21’, with ‘only’ 48 million base pairs (Our ‘sex’ determining X and Y chromosomes, are both larger than ’21’.)….(Please note that other organisms may have more chromosomes so chromosome number is not directly related to the complexity of an organism.) Now, multiply all of those numbers together to get the total number of possible combinations…each of which would have an equal likelihood of occurrence in a truly random process.  Now, multiply the number of base pairs in each chromosome times all of the others….To have a rough idea of the numbers involved multiply 100 million by itself 23 times.  This would be a conservative estimate.  That would yield the number 1 followed by 184 zeros!!!  This means that there is one chance out of 1¹⁸⁴ that our species chromosomes could have occurred.  In a single year there are a little more than 31.5 million seconds.  To carry out this random operation at the rate of a billion/second, would take 1, followed by 163 ‘0’s, years! Recall the the universe is estimated to be ‘only’ 13,800,000,000 years, or 1 followed by about 10 zeros! There is clearly something else at work here, ‘biasing’ this process, making the structures and organisms dependent upon them, more possible.

Of course, humans did not magically appear wholly formed from nothing, at least, science does not accept that it did so…nor did any other species occupying the world today.  Eukaryotes, all species above the level of a bacteria, the Prokaryotes and Archea, descended from a first innovative cell and have built on it in ever more complex ways.  The odds were still incredibly long against the creation of LUCA, but they were lower for it than the spontaneous ‘generation’ of a singular human individual.  

The other thing about probabilities, that we should consider, is that such long odds, do not preclude the chance that any roll of the genetic dice could be successful.  It is possible to roll the human genome, though such an occurrence is vanishingly small, on the first roll.  If one were able to roll the genetic dice in the laboratory 1¹⁸⁴ times, we could expect to get the precise human genome, once, whether it came on the first roll, the last, or far more likely, somewhere in between.  Nature didn’t have to do this.  It produced simpler structures first, ‘proved’ them and then built off of them as a kind of template.  This was the major accomplishment in the evolution of life on Earth,  It took over 2 billion years to come up with that first eukaryotic cell!  All other life, which has followed, is built upon that first cell.  Once this pattern was set, evolution could advance at a much higher rate than would otherwise be expected, because there is some kind of ‘fidelity’, successful genetic patterns have a strong tendency to repeat.  Schrodinger’s concept of an ‘aperiodic crystal’, stable and deterministic as the guiding structure in heredity and evolution, a ‘base’ constant in life, guiding and shaping it, which later, Watson and Crick would substantiate with their discovery of DNA, is that ‘crystal’ around which life grows.  DNA does not reinvent itself with each new generation.  Cells, tissues, organs and the organisms themselves are susceptible to change, evolution.  Larger, more complex, organisms, must remain coherent, more finely ‘tuned’.  What remains most unchanged is that which is most basic.  All of the ‘parts’ of an organism must be functional if the larger, more complex organisms is to be so, but they will likely require some modification, some ‘customization’ to ‘work in a new organism.  The more complex the organism the more ‘highly tuned’ must be its collective parts.  A successful organism possesses these capacities to coordinate and regulate itself within its environment and the conditions that prevail inside it.

Given the fidelity with which chromosomal duplication occurs in the formation of an individual’s gametes during meiosis, sexual reproduction is not a random mixing of all of these base pairs, but a mixing of the parents intact contribution of each chromosome.  From each parent an offspring receives a gene responsible for a particular protein, structure or function within the forming organism.  Each was successful in this in its parent and so represents a success.  One of these is ‘expressed’ in the forming organism.  An organism utilizes these genes as wholes.  They are not themselves, randomized, mixed up and reformed…genes are ‘passed on’.  This reduces the chances for genetic failures.  Genes in the nucleus are copied faithfully.  Over the span of life’s roughly four billion years here, every species’ chromosomes had to be built up, from the first organisms.  Success on success.  Species developed in lineages over time, lineages we can trace back over many millions of years.  With high speed computers we are mapping out the incredibly ‘regular’ and diverse structures of DNA, reassessing the relationships between species.  These structures themselves and their closely correlated bodies are ‘assembled’ from their basic elemental parts.  This does not happen haphazardly.  

In chemistry we have come to understand that atoms and molecules have specific properties that give them specific affinities.  Their combinations are not random either and their occurrence can require specific conditions.  Molecules don’t just combine suddenly based on proximity and availability.  Organic chemistry, the formation of organic molecules, the component ‘parts’ necessary for an organism and life, are the same, only those necessary conditions are likely even more precise and limited.  Successful patterns build on themselves, they do not reform in random patterns.

Peptides are chain like organic molecules of up to 30 amino acid groups.  21 of these amino acids occur in humans.  There are not billions, millions, thousands or hundreds of these…only 30 of all of the possible combinations.  They all share a common basic structure defined by a unique side chain of molecules which give them different shapes and properties.  These form into longer chains with other peptides, each with a characteristic shape, to form Proteins with ever more complex, folded, 3-dimensional shapes.  Their shapes, component elements, charges, polarity and mass go to determining their functions and roles in an organism.  Proteins can contain literally thousands of linked amino acids.  The structures of amino acids, the peptides and proteins they are formed into, are highly specific, not some random assemblage of available molecules.  The simpler organic molecules that must be there to form these are not random either.  Many molecules may have the same ‘formula’, but be in different configurations, and thereby have different properties.  These are known as isomers and each possesses capacities unique from one another despite their shared constituent ‘parts’.  Again, none of this is random.  The success of any given organism is directly linked to its physical and chemical properties as a whole and in its parts.   Fitness is a performance measure which includes all of its properties.  We have had a tendency to think of fitness in humans in terms of physical size, strength and command, even charisma, but it includes all of our capacities, our intellect, compassion, courage, our ability to cooperate not just dominate…all play a role.  As we become more complex biologically, psychologically and sociologically, what defines our fitness, changes.

The point here is that this process has been more than a random one.  It is ‘biased’ toward complexity and life.  There is something behind the scene here at work and those studying complexity, systems, chaos and information theory are beginning to define this.  We know what we know, but.…

As people we tend to be linear, cause and effect, thinkers…we have more trouble envisioning a process wherein multiple factors combine in a difficult to define result.  Natural selection is the ‘choosing’ between those individuals most fit for survival from a field consisting of both successful ‘mutants’ and genetically consistent offspring…but are there factors which might be at play that bias, or direct, mutation?  Is it really just random?  The work of Ilya Prigogine, now corroborated and expanded by many others, describes a relationship between energy and the far out of equilibrium dissipative structures which it can create, energize and maintain.  Physicists and biologists are coming to see this dynamic relationship at the core of life.  Their work collectively shows how energy has a tendency to both ‘organize’, structure, matter and push it into ever more complex patterns.  At a quantum level physicists see matter, its atoms and molecules, as ‘informed’ energy.  This all suggests that there is a relationship between life, evolution and the flow of energy through it.  It supports the idea that change in the organization and complexity of such structures is a product of this throughput of energy.  In biology this then must combine with the genetic template of an organism’s DNA.  It is not one or the other, but a joining of the two.  DNA and the dynamic nature of life work in combination.  It makes no sense that DNA, a product of natural forces and change, would, in an organism, not be influenced by this flow of energy at work in each and every moment.

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In the Beginning….

Much has changed over the Earth’s existence.  Earth has been here the equivalent of 225 million human generations, yet the first hominid, an identifiable human ancestor, has been found to be only 4.4 million years old, or there about, so we’ve actually only been here roughly 200,000 generations, less than 1/1000 of the existence of the Earth.  The question is how did we get from a lifeless molten Earth, with a minimal and toxic atmosphere, to the world today?  Through chance and random mutation? The magical hand of god?  Or, are their physical and chemical processes at work here driving it all toward some unknowable, probabilistic end?

It was not just life that had to arise and develop, not even just the simpler organic compounds and molecules that constitute even the simplest of organisms, no, in the beginning not even the elements we describe in the periodic table existed.  The earliest stages of the universes’ expansion and development is believed to have been a very rapid, inflationary process, mind bogglingly so, measured in tiny fractions of a second.  The creation of most other elements has occurred within the furnaces of stars as they formed and ‘burned’ for billions of years, each unique, a process that continues to this day, new elements being ‘fused’ within the nuclear furnaces of the stars at temperatures of several hundred millions of degrees centigrade and fantastic pressures impossible to duplicate in an Earth bound lab.  Elements, the basic stuff of atoms, ‘react’ with others only under the proper conditions combining to form molecules, more or less stable composites of atoms.  Each molecule has a particular chemical structure, properties and capacities which dispose them toward reactions and the formation of very particular molecules, or not.  The formation of molecules did not proceed uniformly across the universe, it is still occurring.   Each such combination, reaction, requires very specific conditions, within very precise ranges.  They occur locally.  The stuff of stars can be chemically ‘fingerprinted’, measured spectroscopically, and the lineage of stars traced back in time to earlier stars and regions of space.  Elemental carbon itself formed originally within the core of stars, more massive than our sun, in order to reach the pressures and temperatures necessary to fuse helium atoms.  Our own sun is still fusing hydrogen, the most common element in the universe, into helium.  Organic, carbon based molecules, require carbon.  These simplest of organic molecules then began to form ever more complex products, precursor molecules, forming within tight temperature limits, many perhaps unique to Earth, though that is difficult to claim in such an extraordinarily large universe.  None of these could have occurred in open space.  Many, if not all, of ‘our’ organic molecules are believed to be unique to Earth with its particular composition, its water and atmosphere, its range of temperatures.  And form they did.  

The Earth and its Conditions

The Earth has been following its particular orbit for 4.5 billion years, if you count the time before gravity eventually pulled all of the ‘loose’ matter into itself that once formed a ‘cloud’ around the young Sun.  Earth spins on its axis like a, figure skater having pulled her arms in, producing our days and nights.  Our orbit around the Sun, moving in a limited, patterned, predictable way, has set the amount of energy the planet receives, consistent through out its orbit and from year to year, tilted on its axis as a result of a massive asteroid collision, that gave us the moon, and maybe most importantly, varying seasons.  Were it not for such a collision we would have a single static ‘season’, or nearly so.  Each day would follow much more like the previous.  The concept of a year, without seasons, would be more of a detail of astronomical trivia than one of experience.  How would you mark it?….There are far longer cycles related to the combined movement of the other planets, their gravitational effects, particularly those of massive Jupiter and Saturn, which effect the ‘shape’ of our orbital path and our distance from the sun, our ‘wooble’ as we spin on that axis and even the tilt of that axis itself, all predictable, all effecting the large cycle of our daily pattern of insolation or received solar radiation…you know, light.  These produce very long cycles in Earth’s conditions leading to Ice Ages and the changing extremes of climate as they switch between southern and northern hemispheres even a slight shifting of length of seasons, none of these changes perceptible over a human lifetime.  Cycles measured in thousands of years.

Take all of the different ‘elements’ in play on one of our solar system’s planets and then add the empowering energy each receives as it orbits the Sun.  The radiant energy we receive is in direct relationship to our distance from the Sun, the radius of our orbit.  The further you are from the source, the sun, the less energy you receive.  Move twice the distance away and you receive one quarter of the energy.  Half your distance and you receive 4 times the energy.  I discussed some of this earlier, that life can only exist within relatively narrow parameters.  Too much sun light and the temperatures on Earth would rapidly escalate to levels that would evaporate all liquid water and life as we know it would cease…cool it too much and water would ‘freeze’ into its solid form, ice, and life would cease.  Here on Earth we are ‘bathed’ in a continuous flow of energy from the Sun.  We live in a ‘Goldilocks’ world, in which all parts of the environment are ‘just right’…only we didn’t ‘find ourselves here’, we, life, has evolved here.  We ‘fit’ here.

The Sun warms the Earth’s surface unevenly because of Earth’s curvature and its ‘tilted’ axis about which it spins producing our cycle of days, our revolution around the sun, the quirk of its seasons.  Much of the radiant energy Earth receives is converted to heat as it strikes matter, the surfaces of its land, water, even the organisms here and the dust suspended in air.  Immediately this heat begins to disperse around the Earth, moving from the warmer equatorial region, which receives more, to cooler areas toward the poles, through our atmosphere and oceans, producing their currents and winds in somewhat stable patterns, forming a dynamic system of weather around the globe, weather that keeps much of the Earth’s surface and oceans within ‘livable’ limits.  Other photons that arrive from the Sun strike plants and their energy is ‘converted’ into chemical structures, sugars, within the plants they can use to fuel themselves, enabling their metabolic processes which produce compounds from cellulose, to proteins, to lipids and more complex sugars.  Animals then eat plants or other animals, that eat plants, and utilize the chemical energy stored in their structures to power their own.  The entire system of living organisms, woven into ‘nature’, self supporting, mutualistic, consumptive and evolutionary, incredibly and intimately complex, each individual nested in relationships with all others.

The nature of complexity building and  pattern

Stuart Kauffman studies complex systems, their patterns, the relationships between the various parts of natural and man-made systems, positive and negative feedback loops, creating algorithms, elaborate mathematical models which describe/predict/retrodict them.  Among other scientists, he argues that chemical and biological complexity arises naturally in a universe which tends toward self-organization when matter is energized.  Structure and pattern arise naturally, structure that then influences what follows as it reinforces and builds upon itself.  This is a dynamic, ongoing process, though not one that follows a specific and deterministic path, or fixed ‘recipe’, but one which is more probabilistic, more ‘likely’ given what has preceded it.  Complexity building on successful forms and functions, combining and coordinating them, innovating as needed to balance out, fulfilling niches and roles, adapting, refining.  

Organisms are highly organized, intricate, structures.  Structure is easy to recognize in the way that it stands out from its less structured, more randomized surroundings, it punctuates the more randomized ‘space’.  Structures can be characterized by their own internal patterns and by the patterns created through their relationship and proximity to other such ‘structures’.  These structures exist on a continuum of complexity from very simple and more likely predominant structures to more complex and less common structures, a chunk of basalt or a freshwater lake and the far less common Rainbow Trout. Complexity is in relationship to its overall population, its frequency of occurrence.  Structures can be solid, liquid or gaseous or more complex blends of these.  Living structures, organisms, exist on a higher plane of complexity, of a different type. They possess shared forms at a micro and macro level, while possessing individual or discrete qualities.  Their lineage, descendancy, their connection may be quite distant, in terms of generations, but still as organisms they are relatively closely ‘related’ in terms of their structure, material, energy, ‘behavior’ in comparison to ‘non-organismic structures, but even there, if you look closely enough, are shared patterns.  Similar forms exist where more of these elements are closely shared. 

These ‘systems’ are all dynamic, not static, and tend toward cycles, individuals responding to others and their conditions.  Within these processes and cycles a system has the opportunity and time for adaptations, response to changes in its world, to bring the system ‘back’ into stability.  This acts to continuously change the conditions and parameters for individuals, populations, local communities and entire species, adapting, utilizing their available genetic assets, making supportive processes more likely to continue to occur while tending away from those that aren’t.  The maladapted, the destructive, will tend to pull a system out of balance, but only to a point, the point where the system can no longer support them and their population ‘crashes’ quickly or over the course of generations.  Changes are made along lineages, generation to generation, each individual having a limited ability to adapt.  As any individual ages, its ability to reproduce declining, it loses its utility in the larger dynamic.  Still later, it becomes increasingly over mature and less effective in staving off its own inevitable decline.  Possibility lies with youth.  Stability lies with maturity and the precedent it set at birth and development.  The tendency toward health, organization and complexity is more fully manifest in the longer processes of evolution, as opportunities for further speciation become available, the structures and functions of existing species expand positively to fill them, building on past pattern and successes.  An existing individual, being more fixed in time serves the purpose of the moment, not the system wide need for the future.  Random mutations may occur at some very low rate, but would tend to negate each other without this template built from past success.  Successful adaptation occurs not just in changes of morphology, but internally in the function and the biochemical systems that regulate its function.  

Hormones and catalysts are essential factors in the ongoing development and metabolism of organisms, a great many of which are shared between species, with particular refinements here and there.  It is these shared patterns between species that make the study of biology even possible.  Organisms are not just random disparate chemical experiments, they are highly tuned and regulated systems which have achieved many efficiencies within their bodies in ways that are not reproducible in any lab.  This ability to organize and coordinate, with this degree of precision, and in such a manner, nearly perfectly synchronized with an individual’s need from moment to moment, is a master work of synthesis and coordination, shared between all organisms.

It is the animating energy that flows through organisms, its many structures and functional systems, reinforcing these same patterns that enables any given individual to continue living in a coherent way.  Patterns, which are condensed down into spore, then egg and sperm, made manifest in the development of each individual from zygote to adult organism, the coded form in some essential way still whole, conductive and expressive as energy and nutrients follow the embedded pattern in the unfolding of another individual.  There are two scales of action here, the individual and the species, caught momentarily on its evolutionary path, a bit of music, in a minimalist piece, that if we had so much more time we could follow and come to understand.

Hormones and catalysts appear to coordinate everything within an individual organism, but what coordinates them?  What sets their limits in such a dynamic system, activates and deactivates them…so precisely?   If an individual’s body is the instrument, catalysts act as keys that when pressed, form notes.  Hormones help set the tempo, but somewhere else lies the music, determining the length of each note, its intensity, and sets the tempo for the entire piece.  And it does this somehow through its own patterns which determine the energy coursing through it bringing it to life.  All of these ‘pieces’ must be coordinated to resonate truly and when it does it draws what it needs, self-regulating to the extent that it remains vital and healthy, becoming fully manifest, retaining its identity and form for as long as it can meet its own minimum standards, which in a piece of such complexity, can be quite high.  The music of an organism contains many sub-systems each which must be well integrated within our bodies.  Pressing the ‘keys’ of such an instrument requires energy and demands choice.  Catalysts permit the notes to be played.  Without them no force alone would succeed.  Certain molecules act to ‘catalyze’ certain reactions below the existing thresholds that we would expect in the absence of the catalyst.  Within an organism, by catalyze, I mean make a bit of music, a chemical reaction, more probable by reducing the energy requirement, allowing a measure of ‘control’, of limitation, so that all reactions do not happen chaotically or catastrophically, in a single moment.  Lower the concentration of an enzyme, a needed molecule, change the conditions within the organism, and the outcome changes, including its rate of reaction and the ‘products’ created!  Just as music requires a pattern of notes be played, ‘expressed’ in a very particular way.

‘in a very particular way’, so too does an organism.  An organism is much more than a given biological structure, containing appropriate nutrient levels.  It is an individual blend, beautiful and recognizable to us, its patterns familiar and animate, its structure completed in its living, not a thing, but a process existing in time, in shared time, if it is to be known to us. Because of this we have trouble hanging on to, understanding, what an organism is.  We get confused, distracted, by its physical body and tend to reduce it to that when we consider them.  We have trouble ‘placing’ them in time and see them in moments often outside of their requisite relationships, those relationships which are every bit as essential to their existence as are their own tissues and organs. Relationships that extend across time.  Each organisms is ‘related’ to those that preceded them, as will be those that follow.  Individuals and populations, communities are in this way connected to, dependent upon, others.  This pattern is consistent and exists between all living organisms, the innovations and links shared, even those that live in isolation as mature organisms…none are ultimately alone, even after their death and their ‘gift’ in the process of being passed on.  This makes sense in that each one follows from the other, the process, the ‘rules of life and evolution’ being the same.

Amongst these ‘products’, of catalyzed reactions, are the building blocks of proteins which serve multiple essential roles in organisms, structurally, functionally, as in the form of enzymes, those protein molecules serving to catalyze further reactions making the process of self-catalysis possible.  In the open environment, outside of organisms, reactions tend to be ‘simpler’.  When you step the complexity level of the environment up, the products, themselves become more complex, eventually resulting in what we may recognize as ‘organisms’.  The products produced within a given organism are unique to it, with increased complexity and specificity.  This does not mean that all components, all molecules, within a given organism are of the same level of complexity, they exist across a range, each higher level, supported and ‘created’ by those below, all necessary.

At each level in this process of creating compounds and organic molecules, even of inorganic compounds, energy is a necessity, a high enough quality and quantity of it, not just the dispersed, randomized energy of low levels of heat that permeate the universe.  Heat activates matter, increases the kinetic energy of atoms and molecules, causing them to move about with greater velocity, making them more reactive…but organisms are far more complex than a pot of boiling water and the flame that drives it…but even that pot of boiling water produces patterns, convective ‘cells’ of water, changing phase from liquid to gas, in recognizable patterns.  Patterns permeate the entire universe driven by energy.  The molecules that make up liquids and gases are in perpetual randomized motion.  Even the subatomic particles of solids continue to move well below our ability to perceive them.  Reaction rates diminish as temperature drops, the kinetic motion of liquids and gases slowing progressively, all of the way down to absolute zero, 0º kelvin, which is equivalent to –273.15°C or –459.67°F.  Theoretically, there is zero possibility of a lower temperature.  Movement cannot be slowed beyond this point.  This is the ultimate stillness of the subatomic particles.  Deep space, is not quite that cold, it measures 2.75º Kelvin, ever so slightly above it, still retaining residual ’heat’, left over from the ‘Big Bang’, the theoretical initial formation/expansion of this universe, which is ever so slowly still cooling. Not much can happen chemically in space without the addition of energy. (This is not entirely true. Open space is ‘full’ of so called dark matter and dark energy, a topic that is still relatively poorly understood beyond the ‘need’ for them when scientists attempt to make sense of the universe as a whole. This is a topic I will not approach. Understand though that there is more dark matter and dark energy than there is that is directly observable by us with our present understanding and technologies.)

Ambient temperature accounts for much of the random motion of atoms and molecules, how these respond is based on their structure and properties.  Sunlight, in the form of photons, is a very high quality of energy until it degrades into heat, but before that, it can ‘fill a room with light’ reflecting off of objects and, arriving at the receptors in our eyes, powering reactions, transmitted along our optic nerve to our brains, which can form a mental image of our surrounding world enabling us to understand it and function in a responsive manner.  Photons, produced by the countless stars of the universe, pass ‘intact’ through endless distances of space until they strike an object and are absorbed by transforming it in the process with a resultant degradation to heat…unless it is simply reflected or refracted by that contact and sent on its way redirected.  Other photons striking the green, chlorophyll rich tissues of photosynthetic plants, are harvested and used to drive reactions that form simple carbohydrates from the water and CO₂ in plant tissues.  The energy held within these chemical bonds are later utilized to power the creation of other compounds and cells in such a way as to grow and power themselves, or are consumed by other organisms, to permit those organisms that don’t photosynthesize, to grow, maintain themselves and reproduce.  Humans have learned to select those plants and animals which produce what we need most effectively, such as the carbohydrate rich organs of potatoes and proteins and fats from domesticated livestock.

Time is another necessary aspect of living organisms, their lives follow predictable, probabilistic, patterns over time.  An organism does not live out its entire life in a single instant…nor can it live forever (Although in geologic or more broadly universal terms, our lives are but an instant).  Organisms takes in and utilizes energy at a more or less set rate over the course of their lives, with adjustments based on individual metabolic demands to keep them within functional limits, so that they can stave off premature collapse of their systems…death.  The reactions within an organism are not random, but are themselves probabilistic, within limits.  Pushed beyond those limits, the system begins to break down.  Under utilized, the throughput of energy is decreased and an organism will fail to meet its minimum needs. Its cells, tissues and organs will degrade, atrophy, its structure fail to develop fully, its potential, be unrealized.  The individual’s growth and development require energy throughput.  Through use, the flow of energy helps shape and determine the individual, literally.  Each system, or individual, has an ideal structure which requires energy in order to both attain and maintain.  Health then allows for the organism to attain its ideal form.  Compromise health and the individual is an indicator of its internal fitness, its function.  Genetics and supportive resources are not the only determinants.  Use and stress play a role, which together, with energetic support, combine to create an individual’s ideal form.  Put these out of balance and the structure of the organism is compromised.

Earth has an ample source of photons from our Sun.  In fact the base level of energy it provides, goes to determining the precise functioning and structures of living organisms. This consistent supply of photons powers all of the processes that support living organisms, both through the physical warming of the Earth itself and via its driving of photosynthesis upon which modern life depends. The sun sets the energy ‘bar’ for all of life here.

Each individual organism operates with a high degree of autonomy, regulating its own internal systems in a manner informed continuously each moment of its life.  Organisms are ‘wholes’.  In a sense, they are their own little world, intact, highly structured systems, nested within the larger community and world.  They are capable of reproducing themselves within the larger system their existence, contributing to the conditions and well being of the wider community upon which they themselves depend.  While animals consume individual other organisms necessarily, they do so within limits and in such a way that the larger system stays within a range, in a state of dynamic balance.  Organisms are a direct byproduct of the energies and systems extant on Earth. The relationship of all organisms and the Earth itself is an interdependent one, how could it be any other way? each supporting the other, even in the process of consuming the other. The end goal is not the individual, but the health and evolution of the system itself. Over the course of millions and billions of years organisms have evolved in this manner.  They have ‘learned’ this, structuring themselves in such a way that assures their continuing existence.

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Matter builds into ever more complex forms over time…extremely long periods of time.  What it becomes is dependent upon what it is. Matter evolves as do organisms in particular lineages, the past effecting future possibilities. The chemistry and physics of organisms are not something entirely separate from that of more stable minerals and compounds…these forces and cycles didn’t have to be ‘reinvented’ to allow for organisms.  Organisms are more complex, operating within the prescribed limits of out of equilibrium, dissipative systems, while simpler matter, such as a lump of coal or iron, operate at or closer to thermodynamic equilibrium, and because of this, they are much more stable over long periods of time and are not dependent on a steady, measured throughput of energy.  These other materials are more stable structures, and tend to stay as they are…though when energy is applied in the form of an electrical charge, heat or even light, if the conditions are right, those simpler compounds may still be transformed into other, possible forms. Whereas far out of equilibrium, dissipative structures are dynamic, responsive and a direct and continuous ‘expression’ of the flow of energy through them.  Without the energy, they do not exist. This pattern exists as an integral feature of nature, pushing it to more structured, organized states, increasingly complex, in those cases in which it is possible…and nature, has very particular favored patterns.  If life were to evolve on another planet would it be recognizable? It would follow the same general ‘laws’, but would it have made the same ‘choices’?  Could it evolve elsewhere built around other basic forms, different molecules, forming different compounds, forming different cells or wholly different structures?  That remains impossible to say. 

Organisms, on whatever they planet they may evolve, will always exhibit a great degree of coherence, their state an expression of their dynamic in any given moment, communicating continuously internally and with their environment, responsive within limits, limits which can evolve over time and generations. Their relationships to one another will remain tight and recognizable.  It is in the nature of their base materials and the energies involved that they be so.  Such ‘structures’ in this sense have learned this and express it through themselves morphologically and functionally.

As humans we have developed a very particular and limited understanding of ‘learning’.  We have developed the capacity for ‘abstract’ thought and can think about things that are not readily observable in ways that are removed from our experience and can thus explain a larger ‘problem’ or one ‘hidden’ from our direct observation.  Like the objects we may build, we ‘inform’ them with our understanding in terms of their aesthetic design as well as in their engineering, we too shape their capacities, as does nature…but nature doesn’t ever do a radically different redesign…it must work with available structures those that reference the oldest recognizable forms up to and including the most recent developments.  Every object, every organism is informed, executed, to follow particular patterns, patterns that are relatively limited and stable, consistent over long periods of time. Many exist as balanced or very near equilibrium structures, like mineral crystals and remain largely unchanged for millions of years, while other structures exist farther out of balance and require a greater input of energy to maintain their balance…these are subject to evolution, their future success or failure less determined. Nature ‘learns’ what works or fails when the changes are too great…it evolves taking ‘full’ steps, leaps from functional whole to functional whole, the unviable half step not an option.  Conscious or not this is ‘learning’…it is progressive and accumulative, ‘knowledge’ is accrued and applied.  Any way of learning, of informing or restructuring is valid.  Nature is self-organizing and its complexity is increasing.  Arguably the universe is learning while continuously reinventing itself.  We ourselves are a small piece of the process, intermediate, a side product, one with some capacity of self-awareness and reflection.  We are not a random event, but a part of an ongoing process, perhaps in the ongoing ‘awakening’ of the universe itself…it’s impossible to say.

This informed ‘recycling’ and restructuring of energized matter tends toward more refined, well tuned structures and forms.  While conditions remain stable so does the range and form of such structures…they also remain responsive to changes of all types.  Larger changes, greater opportunities, yield more and more widely varying options.  In a tightly knit, highly refined and balanced system, variants will become less and less significant and the entire ‘system’ will tend toward stability within those limits.  In a sense change, evolution, is a response to ‘stress’. This plays out in the real world over time as long as energy can flow more or less uninterrupted through the many systems.  Historically biomass has increased along with organization and complexity.  The fossil record shows this beyond doubt and evolution continues.  While energy moves toward randomness, increasing entropy, it produces ever more complex and diverse organic structures, organisms, which exist in more complicated and nested relationships.  Life is a product of this movement of energy, the ‘work’ that it does over time.

Mechanical complexity, the technology, physical structures and machines that we humans build, confers a degree of ‘fussiness’, or susceptibility to failure that will manifest as these systems ‘age’, wear down and degrade. Such systems tend to work within a relatively narrow range of parameters.  As our creations they lack the capacities of self-regulation and maintenance living organisms possess and so must be cared for by us, but even they wear down and provide for the possibility of an ‘evolving’ technology and the ‘improvements’ that it might bring.  But this is not the only difference because our built creations lie outside the larger cycles of earth and nature and our ‘dead’ are not easily brought back into the natural cycling of materials which are more directly of this earth.  The increased complexity in structure of organisms tends to increase the supporting forces of relationship states both internally within the individual and externally, between individuals, other members of their species, other species and the broader system of conditions  which apply across a given environment.  Complexity tends to increase adding to itself while linking organisms in ever more stabilizing relationships.  This is not the same for our own technologies.  Much of our creation lies outside of this living system and can in fact threaten its existence.  Is it too much to ask of a society to build in such a away that recognizes the natural forces at work within the larger earth system? We, today, see ourselves as independent individuals that live outside of nature, a nature that serves as our toy-box and storehouse intended simply to serve our own purposes.  We have much to learn.