DaveRAFinn
Posts: 15
Joined: April 2005
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A heretical alternative, non-neo-Darwinian, theory of the evolution of new species.
Introductory Generalisations
Rats, so they say, desert sinking ships. The idea is plausible because going down to the bottom of the ocean is a fairly guaranteed way for a rat not to have any more descendants. Any instinct that resulted in a rat abandoning a ship about to sink would be favoured by an increased chance to breed new descendants who would, naturally, inherit that instinct. This does not only apply to rats. The cry of "abandon ship" is understood because the chances of survival, and therefore descendants, may be small in a stormy and possibly shark infested ocean, but they are infinitely greater than the zero chance associated with going down with the ship. So there is a natural selection for life with an instinct to abandon sinking ships. The genetic equivalent of this process is an organism that abandons a doomed species by indulging in a fit of mutation, probably by taking some genes from something else, and becoming a different species. Its chances of surviving in the ocean of life may be small but they are higher than if they joined the great family of extinct species. Any instinct to behave in this way would be rewarded by an increased chance of descendants. After many vicissitudes in which the instinct to abandon species had been rewarded it might be expected that many, if not most organisms had an instinct to abandon doomed species. For an organism to take control of its own evolution it need not know how it must change, it is sufficient that it know that it must change and alter its variability accordingly. This article is an exploration of that idea.
I wrote this article because I had occasion recently to investigate a phenomenon that resembled or was an odd example of evolution. To my surprise I found that there was a serious shortage of plausible explanations of how evolution actually works. Most of the readily available material is a variant on either the religious “’Daddy fix’ was a powerful incantation for the worshipper when a three year old, this looks like a powerful incantation, therefore it must be a version of ‘Daddy fix’” or the fatally flawed and easily disproved neo-Darwinian theory of origin of species. I have worked out the following version of evolution myself although the structure is simple and obvious so that it is probable that someone else somewhere else has come to similar conclusions. If so, their impact on the documented theory has been too small to show on my radar, but my apologies anyway for not mentioning them. My university studies were in philosophy and in real science, physics and chemistry not in biology. Whenever the data, logic and mathematics point in one direction and the conventional biological assumptions point in a different direction I have been prepared to ignore the conventional biological assumptions. Hence the heresies mentioned in the title. If, like many of the biologists I have encountered, all you wish to do is to find some reason, any reason, for ignoring the arguments and evidence against the conventional neo-Darwinian view then you will undoubtedly find something that can be interpreted as grounds for dismissing this article. You will probably save yourself (and me) time by not reading it. If you are not a biologist or are one of the exceptions and are prepared to recognise that something is awry with the conventional evolutionary theories you should find at least some of the following ideas interesting.
Evolution is about living things, organisms surviving in an environment. The organisms have characteristics which enable them to survive and reproduce in said environment. “Characteristics” is a general term and may refer to permanent and visible features like a colour or a tail but may also refer to totally different things such as behavioural features - nocturnal, migratory, and timid. The characteristics may always be shown in all members of a species or, like the migratory behaviour of locusts, only shown in some populations under specific environmental conditions, such as high or low moisture, temperature, acidity or salt level. The characteristics are encoded in a genetic structure that is inherited by their descendents, which therefore, in the same environment, have essentially the same innate characteristics. No specific relationship needs to be assumed between parts of the genetic description and the associated characteristics although it is worth emphasising that most characteristics depend on a specific pattern of several pieces of genetic information and may be affected by either omission of one part of the pattern or addition of a disruptive component to the pattern. There are numerous quibbles and qualifications that can be applied to the above simplified description, but, with one exception, they do not significantly affect the following argument so apply them, or not, as you please.
Evolution is the process where a change occurs in the genetic description of an organism with a consequent change in the characteristics of the organism and its interaction with the environment in such a way as to increase or decrease the average number of descendants of the organism as compared with the original unmodified organism. A repeated decrease will result in the extinction of the variant unless there is a change in the environment. A repeated increase will result in proliferation of the variant unless or until there is a change in the environment (which will eventually occur from the proliferation of the organism, if for no other reason). Note that nothing in this description assumes either a constant or a changing environment or that a change in the environment, if there is one, precedes or follows the genetic change. Evolutionary selection requires only that at some point there is a differential in the relative ability of variant forms of an organism to leave descendants. This is popularly known as survival of the fittest. There are numerous quibbles and qualifications that can be applied to the above description, but, with one exception, they do not significantly affect the following argument so apply them, or not, as you please.
Although my emphasis my be slightly different from usual there is not meant to be anything in the argument, so far, that in any way differs from conventional thinking. As I said, with one exception, if you want to add any quibbles or qualifications do so. The one exception concerns the use of adjectives to describe the genetic change. You may personally have a strong metaphysical conviction that the only changes of importance occur at full moon, or as a result of the effects of ionising radiation, or random copying errors or any of a thousand other conditions. However, there is nothing in the description of evolutionary selection that requires any such assumption and we will leave the decision as to which changes are important until after we have a way of evaluating that importance. In my opinion premature decisions on which changes should be studied are one of the commonest errors in evolutionary thinking.
Change
Genetic changes, like most changes, come in a wide range of magnitudes. Some genetic changes, such as the common single base pair change in an inactive part of a chromosome, have no effect whatever on the exhibited characteristics of an organism. At the other end of the scale there are changes like the formation of internal symbionts between two independent bacteria that give nucleated cells, mitochondria and chloroplasts, a level of change that occurs only about once in a billion years and can have major and permanent effects on evolution. In common with other changes, such as earthquakes, floods, meteorites, windfall financial gains and the like there is a general pattern that small changes are far more common than large ones. However the effect of a class of changes is the product of the probability of the changes and the magnitude of the individual changes, so that, although rare, the large events can often outweigh the more common small ones. A one in a thousand year flood causes more erosion than a thousand annual floods. A one in 100 million year meteorite causes far more destruction than 100 million years of small meteors and meteoric dust.
The vast majority, 99 point something percent of genetic changes have no significant evolutionary impact. The change is an inactive part of a chromosome, or does not change the amino acid coded for, or the amino acid is not in the active zone of an enzyme or the change in an enzyme does not produce a change in the characteristics of the organism or the change in characteristics does not affect the reproductive success of the organism. In this case there is no selection function, no "survival of the fittest". There is a well-established theory of genetic drift using mathematical models from well researched subjects like thermodynamics. Changes of this sort are described in terms of random walks with chance determining the direction of change. There is an interesting theorem about random walks that says that if you draw a circle round your starting point you will eventually return to within the circle, eventually being longer as the size of the circle decreases. It is theoretically possible for numerous miniscule changes to accumulate to make a large one, but in the absence of any mechanism to coordinate the changes they just tend to cancel each other out and the overall rate at which change occurs is negligible. A million times zero is still zero so the chances of significant numbers of new species arising by genetic drift are negligible.
Of the remaining changes the vast majority, 99 point something percent, are only small changes. Typical genetic changes result in the replacement of one or possibly a few amino acids in a protein changing its shape making it slightly more or less effective, or by switching a common and rare amino acid making it easier or harder to produce. While there can occasionally be large changes in characteristics if a critical threshold is crossed the changes in an organism are normally also only small. Lots of small changes over time can accumulate so long as there is a natural selection function, like "survival of the fittest" to provide a trend to the change. There is a well established neo-Darwinian theory of small changes using mathematical models derived from linear programming and other branches of economics. For any given set of genes and environment there will be some variants on the genes that are better or worse than others in terms of enabling the organism with them to leave descendants. Preferential selection of the better variants eventually reaches the point where all individual variants are essentially equal to or worse than those possessed by the organism and the organism is optimally adapted to its environment. Given the complex relationships that exist between genes and characteristics there may be some other significantly better combination of genes but the tuning process terminates when a particular local optimum configuration is achieved. New species are only produced when a change in the environment changes the optimum at a rate that can be tracked by adaptation and this would appear, in practice, to be a relatively rare phenomenon. Furthermore however much you substitute one variant of a gene for another you will never get any radical change in the organism. No amount of allele substitution will change a cabbage into a cockroach. So few or none of the interesting genetic innovations can be expected to arise from small changes.
Natural selection of large changes
Now consider the big changes. While relatively few in number there are still plenty of them. The total evolutionary history of an organism has millions of one in a thousand year events, thousands of one in a million year events and even a few one in a billion year events. While the numbers may be small compared with other levels of change the total effect, frequency times size of change, is still substantial. Remember the effect of chloroplasts and mitochondria. Large changes typically occur when combinations of genes lead to new materials, such as chitin, new feedback mechanisms such as warm bloodedness, new tactics, such as phototropism or new instincts such as migration. Think of your own examples of large changes, the important point being that they exist, not what they are.
The first important feature of large changes is that the change itself represents a potential threat to the organism. Large changes are risky. Most aircraft accidents occur when the plane is in transition, taking off or landing. Birth and puberty are risky times for mammals. Event apparently purely beneficial changes, such as winning a large lottery or emigrating from a despotic country can ruin a life purely through an inability of the individual to handle the magnitude of the change. The effect of this additional risk is to split the natural selection function into two. Evolution by large change, if graphed as "progress" versus time gives a crenellated or zig-zag line with quite distinct vertical “change points” joined by horizontal “business as usual” segments. For the descendants of an organism to reach the present time in the process it must survive through both the horizontal and the vertical sections of the path, either section could be responsible for extinction. The problem conditions in the horizontal and vertical sections are quite different. There is therefore one selection process for the horizontal sections of the life history and another, quite different, for the vertical sections. The horizontal section is essentially the same as natural selection under neo-Darwinism. It basically selects for fitness, or ability to survive and reproduce, in the current environment. You will be familiar with it so we need not discuss it further.
The second, vertical, phase is the interesting one as it selects for the ability of an organism to handle a major change. The nature of the filter can be seen from a simple example. If an organism changes by doubling its size then the surface area increases fourfold and the mass eightfold. In order to survive the change the mechanisms that control the assembly of different types of tissue must each be keyed to something that will result in the appropriate dimensions and quantities of all tissues in the new organism, or it will fail to thrive. The condition being selected for is that the control mechanisms of the organism work not only for the current configuration of the organism but also for other configurations and for the transitions between them. The group of creatures with the best capability in surviving through radical reorganisation is probably the insects. They exist as eggs, larvae, pupae and adult with quite different appearance and physiology for the four stages and manage quite spectacular changes in form within each generation. As the well known experiments on fruit flies have demonstrated, this family of living things will produce relatively functional organisms in the face of quite major genetic changes that would totally disrupt other life forms. Insects do not often fail at the transitions and it is an indication of the importance of the second, “survival of those organisms able to change” selection mechanism that over half of all known species are insects.
The ability to change within a generation is relatively common. A very large proportion of living things have juvenile and adult forms that differ from each other by far more than the juvenile form differs from that of similar species or the adult form differs from the adult form of similar species. Insects, as mentioned, have extreme variation - caterpillars and larvae resemble other caterpillars and larvae -beetles, butterflies and moths resemble other beetles, butterflies and moths but there is little resemblance between the caterpillar or larvae and the adult beetle, butterfly or moth. Similarly an acorn is more similar to a chestnut than it is to an oak tree which is, in turn more similar to a chestnut tree than that tree is to its fruit. A human foetus living parasitically within the mothers’ womb is far more different from an adult human than an adult human is from a chimpanzee. The basic point here is that most species have the organisational flexibility to manage a structural change of a size adequate to get classified as a distinctly different species and do it within a single lifetime. Other writers have noted this flexibility and noted that it is clearly the result of a natural selection process. Flexibility in handling large changes is not a natural consequence of changes of neo-Darwinian magnitudes. The presence of this flexibility in life is an indication of how important large changes have been in shaping evolutionary history.
The origin of the changes.
Large changes normally require either radically new genes or a significant combination or interaction of genes, some or all of which may be part of the normal complement of the organism. Omission or suppression of genes from a genome is readily explained as there are a variety of transcription errors that can remove a gene from those available to an organism. However the acquisition of new genes is a different matter. Within neo-Darwinism changed genes normally arise as a result of mutation of a specific piece of DNA within a specific individual organism followed by propagation of the change through the population as a result of the advantageous nature of the variant. It is clearly theoretically possible for a new gene to arise as a result of random changes within the DNA of an organism, but this is an exceptionally improbable event. It is easy to demonstrate that acquisition of new genes is not, in general, the result of the same sort of mechanism that produces variant alleles of genes. Several of the more pertinent criticisms of the neo-Darwinian explanation of the origin of species are based on showing that the random production of new genes is far too infrequent a process to explain the current numbers of genes and the expected distribution from such a process does not match the observed distribution.
The clearest indicator that the neo-Darwinian process is not being followed lies in the rate at which new species form. It is surprisingly constant for all species. If you take your favourite version of the “evolutionary tree of life” and count the number of nodes from the original “first cell” through to different current life forms you find that the numbers are roughly comparable on the different paths. You can make a similar observation by noting that there are numerous cases where multiple species have long standing symbiotic or parasitic relationships that extend past species change. Birds, cats, rabbits and humans all have their own variants of lice, fleas and other, mostly microscopic, associates. Although these hangers-on are far more numerous than the hosts there is no corresponding proliferation in the numbers of their species. This relationship extends to bacterial diseases and symbionts many of which are specific to a very narrow range of hosts the members of which are outnumbered by the bacteria by extremely large factors.
The reason that this is surprising is that if new gene were to arise in a species by any process that involved an unusual event occurring within an individual member of the species then the number of such genes arising would tend to be in proportion to the number of members of the species. If each member of the population of a species contributes their own variants to the genome of the species then a populous species will have more variants than a scanty one. One would then expect the greater variance to be reflected in a greater probability of a species producing a descendant species and a lesser probability of the genetic line terminating in extinction. However, although population sizes of species vary by a spectacular factor of about a trillion trillion (10^24) there is no, or almost no, corresponding change in the rate of creation of descendant species. Most species have descended from a prior species with a population that is miniscule compared with that of the more populous bacteria. The numbers of members of different species varies by trillions so the number of variants of genes introduced by those members also varies by trillions. If you can change the amount of natural variation between species by a factor of a trillion and have no observable effect on the rate of species formation then natural variation cannot possibly be a major factor in species formation.
Some simple arithmetic provides an alternative way of viewing this issue. If one takes very approximate, rounded figures one can get a measure of the rate of new gene formation. The total number of useful new genes produced during evolution is (I did say very roughly) a few million species times a few tens of distinctive genes per species with an allowance of 99% having been lost to extinction – 10 billion or 10^10. The world population of organisms is a few times 10^30, mostly bacteria which have been around for a few billion years giving a total number of organism years of roughly 10^40. Thus the average gene production rate is about one new useful retained gene per 10^30 organism years. There are a many novel man-made chemicals that have been added to the environment and genes that interact with them tend to get noticed. Such genes, many of which are probably novel, are discovered at a rate in rough agreement with the 10^30 figure (a “few” per year). A very rough estimate can be made of the rate at which new useful genes should appear given the observed rate at which DNA mutates in living organisms. “New, useful” is not a very well defined concept, but I have seen guestimates on gene production that are not impossibly much less than the figure of 10^30 organism years per gene.
The difficulty with the theory comes when you attempt to apply this figure to actual cases. In the well documented case of human evolution from a Miocene ape the calculation of the expected time taken for a population of, at best, a few hundred thousand individuals to produce the observed few hundred new genes gives one hundred thousand million million times the age of the universe and this is an impossibly high figure. This figure is as wrong as measuring the thickness of a piece of kitchen cling film and getting the distance to Pluto. It is so wrong that there are no remotely plausible re-estimates or special assumptions that can make the calculation work. Changing the assumed gene production rate by even a factor of a thousand strains the match with observation. The sophisticated error correction mechanisms of advanced life is normally assumed to produce lower rates of change than for bacteria making it implausible that humans have a special, spectacularly, spectacularly, spectacularly high, rate of new gene production. Exactly the same problem applies, if anything more so, to all large predatory (and therefore rare) creatures. Some other explanation is required for the new genes.
The problem is one of distribution. We have enough genes, or at least, somewhere near to enough. Bacteria are the only organisms occurring in sufficient numbers for much creation and evaluation of novel DNA sequences by random processes and it is within bacteria that novel genes are found. However the greatest repositories for genes are the non-bacterial species. The obvious explanation is that there is that some form of lateral or horizontal transfer of genes going on. Lateral transfer of genes is a demonstrated and documented process so there is no real issue in assuming it occurs. There are a couple of additional pointers to it being present in evolution. The first is the substantial amount of parallel evolution. Although photosynthesising organisms represent a very early split from other life the plants duplicated a number of major changes, multicellular life, sexual behaviour, seasonal variation, immune systems and migration to land forms at similar times to the other branches of life suggesting a shared environment as a factor. The second pointer is that the production of new genes is a very inefficient process. Wherever new genes arise there must inevitably be large numbers of short, incomplete or dysfunctional genes for every gene of any use. For example in a random generation of a string of DNA each codon has roughly a 5% chance of terminating the gene (3 out of 64 codons are terminators). For each 100 codon gene, useful or not, you would expect about a hundred length 1 genes. This sort of genetic detritus is not found in any quantity anywhere with the possible exceptions of pathological cancers and stressed bacteria.
Lateral Transfer of Genes.
A few notes to clear up common misunderstandings. I have used the terminology “lateral transfer of genes” rather than the more common “lateral gene transfer” as it is clear that the latter phrase is nearly as effective as religion and sex in suppressing any form of rational thought. There are no such things as lateral genes. It is the lateral transfer of an otherwise normal gene that is being discussed. There is nothing special about the gene itself, it is inherited normally and forms a normal phylogenetic tree just like any other gene. It is just that when you get down to the earliest common ancestor carrying the gene in a phylogenetic tree you have not got to the first occurrence of the gene, that occurrence is outside the specific tree you are looking at. If, as is, however, all too often the case, you cannot identify a single plausible earliest common ancestor then you quite probably have a case of two, or more, transfers of the same gene from outside the tree. Although widespread lateral transfer of genes may be distinguished from creation of genes within a genome by the statistical characteristics of the genes, the only way to demonstrate lateral transfer of a specific gene is by showing the existence of that gene in a distantly related species and showing that the gene is not present in any hypothetical common ancestor.
Lateral transfer is a relatively infrequent occurrence. For the well documented case of humans if all the new genes arrived by lateral transfer the rate is only about one gene per ten thousand years. Since the more obvious vectors for genes such as retroviruses, bacterial plasmids and pollens, are all capable of transferring multiple genes one is probably looking at a rate nearer to once per hundred thousand years. The process does not need to be frequent. Remember from the earlier calculations that a single gene is equivalent to about 10^30 organism years of evolution. This is a phenomenal amount of evolutionary experimentation compressed into a small package. A huge average rate of evolution can be achieved by a very infrequent addition of new genes. There is no need for a lengthy accumulation of small changes. Considered purely as a method of achieving an organic change for subsequent natural selection it wins hands down for speed and convenience. There is an additional advantage; the process is far less risky than random mutation. The new gene is an addition so no existing genes are damaged by acquisition of the external gene. A new gene is almost certainly functional, the dysfunctional genes having been filtered out in the source species. It is also not particularly likely to be immediately pathological as the source species thrived while containing it. For random mutation there are risks to the organism from both the process that produces the gene by scrambling the existing genetic code and from the effect the gene has on the exhibited characteristics of the organism. For lateral transfer of genes the predominant risks to the organism lie only in the effect the gene has on the exhibited characteristics of the organism.
The most important difference between gene transfer and internal genetic mutation is not, however, the utterly different statistical characteristics it is the fact that it is a mediated process. In normal neo-Darwinian mutation the organism has no influence on when or whether a change occurs in its DNA. There are corrective mechanisms that may correct a change or alleviate the effects of the change but the actual change is not in any way under the control of the organism. In gene transfer the incoming gene has to pass through the external cell wall, the nuclear wall and be integrated into the host DNA. All the steps in the process, as well as possible steps not taken, like digesting the incoming gene as food, are part of the active cellular operations of the organism. The process is, in principle and probably in fact, under the control of the organism. This point is important since, as you may remember, the relative equality of evolution rate of different size populations shows that the acquisition of genes is not something dependent on population numbers. Gene transfer is not just an improbable event that would be more likely if the population were more numerous. The relative equality of the rate of speciation of different sized populations is most easily explained by assuming that the gene transfer is dependent on some specific but rare condition in the environment.
The statistical point may be illustrated with an idealised example. We take a unit of population of sufficient size to acquire a new gene by whatever mechanism is relevant in some unit of time. We may reflect different population sizes by taking 20 such populations, 15 of species A, 4 of species B and 1 of species C. Note that in the real world the differences in population size, even with bacteria excluded, are billions to 1, not 15 to 1.
Case 1: Assuming the change is merely improbable. After our period of time each population has acquired its new gene and there will be 15 mutants A1 to A15 each of which has a different gene. Similarly for B1 to B4 and C1. In the following natural selection the probability of the 15 A variants containing a mutant with favourable characteristics leading to survival of a new species is clearly larger than for either the four B variants or the single C variant.
Case 2: Assuming the change involves a new gene being transferred from a small pool of genes (say 1 to 6) that happen to be readily available in the environment at some specific time when the conditions for gene transfer occur. After our period of time each of the A populations will have mutants A1 to A6, each B population the mutants B1 to B6 and the C population will produce mutants C1 to C6. There are more individuals of each of the variants of A than of B or C but the actual number of variants is the same. In the following natural selection the probability of any of the species containing a favourable characteristic leading to a new species is equal for A, B and C.
Conditional transfer of genes.
So what sort of conditions might arise every hundred thousand years or so that might reasonably be associated with a session of lateral transfer of genes? This is easy. The environment is not constant. The physical environment changes due to climatic, geological and astronomical mechanisms. In addition organisms are not isolated and face both competition and predation form other organisms. Many organisms are also dependent on other organisms to provide food or other life support. All these other organisms are evolving and present further changes in the environment. The effect is to make evolution obligate. If an organism does not evolve it will become extinct. Changes of sufficient magnitude to make species extinct are relatively rare and do fit into the hundred thousand year or so bracket. We know about extinction. Lots of species have been observed to go extinct, admittedly often with human help, but this often extends only to the introduction of a predator, parasite or competing species. The time scale is short, rarely more than two hundred years and sometimes far less. In the campaign that bald eagles were becoming extinct and something should be done the assumed time scale was not the next hundred thousand years. Preventing extinction requires immediate action. The choice normally facing a population of a species is evolve or become extinct. With extinction taking only centuries evolution must take less. Controlled lateral transfer of genes is one of the few mechanisms that can produce substantial species change in the required timescale. The fossil record confirms the short time scale, in chalk which is almost 100% fossil and makes an almost day by day record there are no examples of any population of a species taking a geologically perceptible time to evolve.
Most mutations are harmful. Most organisms are reasonably well adapted to their environment, a natural consequence of neo-Darwinian evolution, and a divergence from their adaptations, particularly a large one, is far more likely to “detune” the adaptation than confer a benefit. Even in the case where the environment has changed and the organism is no longer attuned to the environment there are a lot of dimensions in which change can occur and in most of them a change is unlikely to have any useful effect that compensates for the change in the environment. The harmfulness of mutation is widely and incorrectly assumed to make deliberate mutation a self-defeating process. This is not always true. The harm done by mutation is the product of the damage from a genetic change multiplied by the probability of it occurring. Similarly the benefit of mutation is the gain from a genetic change multiplied by the probability of it occurring. Although the arithmetic normally comes out against mutation there is at least one unusual situation where the arithmetic comes out the other way round. In the case of a species in decline to extinction the calculation goes like this: Most of the mutations are harmful but the damage is zero, the organism was going die and become extinct anyway. One or two mutations are beneficial and change the organism sufficiently to allow survival. The benefit in these few cases is immense. Overall result for mutation in this special case, a few mutations with a positive benefit to the organism’s descendants minus a host of mutations with no additional extra damage to the organism’s descendants – positive.
So how plausible is it that there could be an evolutionary adaptation that changed the rate of change in response to circumstances? You will be familiar with the sexual display mechanisms, especially of birds like the peacock. With only a minor change in viewpoint these can be interpreted as evolutionary mechanisms. Genetic drift ensures that there are a large number of ways in which an individual may vary slightly from the norm of the population. So any population can be considered as having a central core of “normal” individuals surrounded by a corona or fringe of variants differing from the norm. Mild forms of natural selection will tend to prune individuals from the corona. They are too far from the optimum to which the species has become tuned. Under these conditions a simple survival strategy is to be as normal as possible. On rare occasions the environment will change so that the core of the population is no longer at the optimum whereupon natural selection will be more extreme and will eliminate the central “normal” part of the population leaving only part of the corona, that nearest the new optimum configuration, as survivors. Under these conditions a simple survival strategy is to be part of the corona. While the ideal is to be in the “preferred” part of the corona it is sufficient to be in the corona to increase the survival chances from zero to the average for the corona. The combined strategy for handling the two cases is to look at the median or “ideal” individual. If they are doing well, mate into that part of the population, if they are doing badly mate into the corona. To implement the strategy all a hen has to do is to go to the prime, central, displaying male and count the number of competitors. If there are many then the central part of the population is doing well so go with the norm, if few then the central part of the population is failing, go with the screwball. These are just the simple messages given by financial advisors – “invest in what succeeds” and “in times of uncertainty diversify you investments”.
Sexual selection is not required for an evolutionary strategy. So long as a species has some means of determining the health of the species then it can respond to an environmental disaster by increasing the rate of mutation by any available technique. A significant proportion of bacteria and other single celled organisms form temporary of permanent structured aggregates such as stromatolites, slimes and fruiting bodies. For these structures the replication and behaviour of individuals is influenced by the number of proximate fellow organisms. There is no absurdity in assuming that an organism might exhibit different characteristics if most of the proximate organisms are dying from that which it would exhibit in the case that they were alive, indeed it would be strange if they did not. This is all that is required for active, elective evolution to become a normal part of an organism’s life. As we have pointed out before, in the occasional situation where an organism is exposed to an environmental change of a magnitude that threatens the existence of the species the greater the diversity of the species the greater the probability of there being a variant sufficiently different to survive under the changed conditions. Under these conditions an organism that has an instinct to respond to the evidence of the catastrophic threat by increasing its rate of genetic change will thereby increase its variability and the chances that it will leave some form of descendant. The descendants will, as in the case of other instincts, inherit this tendency to respond to a catastrophic change in this way. It will not take many catastrophic changes for this mode of response to become dominant since those species unable to respond with a change in mutation rate will suffer a relatively lower probability of leaving descendants. To go back to an earlier point, organisms are selected for on their ability to handle large changes and one aspect of handling a change is being able to exert a level of control over where and when the changes occur.
Elective Genetic Change
For elective genetic change to work each species has to have at least one condition which it can recognise as the signal to mutate. There are well known responses, such as the adrenaline response in mammals and the fruiting response in trees where an individual member of a species behaves in an unusual and extreme way in response to an extreme individual threat to that member of the species. The mutation response is a similar response, more like that of locusts and desert plants, where all or most members of a population of a species behave in an unusual or extreme way in response a change in the environment. In many cases the trigger in the environment will be the presence of large numbers of dead of the species. Sentient species are well known to recognise their own dead and avoid places where they may be found. Many other species are known to produce “warning” chemicals when they are damaged or under threat of death. More research would need to be done to confirm the point. The basic argument is that the required response is not significantly different from responses known to exist and the relative lack of documentation on such responses can, arguably, be attributed to the relative infrequency the process. The mechanism would only be observed in the relatively rare circumstance of conditions so extreme that the probability of mutation increases the chance of descendants over that expected from enduring the conditions.
The evolutionary process operates at two levels. For species with very large populations relatively simple methods of gene modification, analogous to those encountered within neo-Darwinism can provide an adequate supply of novel genetic variants. As the population numbers decrease the species must increasingly rely on the genetic variation available in other species and browse the global gene pool to obtain the required variation. The process is in some ways analogous to the division between plants and animals. Plants capture the diffuse energy from sunlight and make it available in the relatively condensed form of sugars, starches and oils. Animals use the condensed form of the sunlight energy to support a very much more active lifestyle than the plants although they are, in a sense, fuelled by sunlight. The source of evolution is essentially random changes in DNA but by making use of the genetic information already filtered by bacteria and other life a “gene browsing” organism can maintain a far more active evolutionary life than is possible on the raw genetic change. All that is required is the ability to tell when such gene acquisition is likely to be beneficial in leaving descendants and that ability itself is subject to direct evolutionary selection. Those organisms that browse genes at the right time leave more descendants than those that do not.
At this point I will introduce a speculation, it is one of those things that if it is not true it is such a good algorithm it should be true. The raw genetic code, as it appears in the famous double helix does not unpack directly to a usable string of RNA. Scattered through the encoded string, rather like advertisements on TV, are intrusions which must be removed before the actual “real program” can be obtained. One of the ways in which a mutation of a gene can be achieved is by changing the rules for removing these introns so that either part of the real sequence is removed as if it were an intron or an intron is left in and the amino acids which it encodes are included in the resultant protein. There are cases where genes appear to have been modified in this way. The process also allows a very effective way of implementing elective gene creation. For a bacterium in a hostile environment it could temporarily change its framing rules and see if any of its genes operated better under the new framing. If so, the organism would revert to normal framing, so that it may continue to live, and having identified the portion of its DNA which is most likely to produce a useful new gene, make a copy of that part and make extensive mutations to that copy. This process is far more likely to produce a useful gene than random variation. An alternative way in which an organism might have a mechanism for creating genes it for it to take advantage of the fact that the most efficient way of creating a brand new gene is to take the beginning and end of an existing gene and splice into the middle a string of random, “noise” DNA. The basic point here is that there are simple ways an organism can increase its genetic variation in a controlled way and, for a species as numerous as a typical bacteria, a simple increase in diversity may well be adequate for the organism to have a few members of the population escape a lethal environmental trap and leave a few, admittedly rather different, descendants to carry on the family line. Over longer time frames an increase in mutation rate can be achieved simply by disabling the genetic error-correction mechanisms but it is the essence of most environmental disasters that the threat is immediate and the necessary response must be rapid.
One can infer a hierarchy of genetic responses to an environmental disaster:
First, exercise normally unused genes. This is not really an option for bacteria as they carry little genetic baggage and the overhead of unused genes normally results in their fairly rapid elimination. Indeed the bacterial practice of repeated reinvention and forgetting of the wheel is probably a significant factor in the proliferation of genes.
Second, scan the environment for available novel genes. Here the most obvious source, which is known to work and is used efficiently in the case of antibiotic resistance, is the bacterial plasmid. The same mechanism can apply to both single celled and multicellular organisms as the multicellular organisms are all descended from bacteria, which have the mechanism, and will have retained it since organisms that can evolve rapidly in response to environmental disasters leave more descendants than those that have lost that ability. Complex organisms have a plethora of associated bacteria some of which, even if only intermittently (diseases), circulate in their bodily fluids providing the necessary cellular access to plasmids.
Third, attempt to manufacture genes relevant to the environmental problem. This is really only a productive option for bacterial species. Where a group of cells in a higher organism undergo genetic change in response to a high incidence of adjacent dead cells the usual result appears to be a cancer rather than anything useful.
The conclusion is that although the hierarchy of evolutionary responses is similar for all forms of life the preferred or predominant mechanisms are different for bacteria and higher species and natural selection will tend to reinforce the use of the most effective mechanisms for the particular species.
Serendipity
A fact that has major implications for elective evolution via lateral transfer of genes is that there is a very significant probability that a gene that an organism acquires from a neighbouring bacterium will have a relevance to the survivability of the acquiring organism. There are several mechanisms that lead to this consequence. The simplest is the response to toxic ions, such as those of heavy metals. When these materials find their way into the environment and from there into the living cell the simplest way of dealing with them, from a bacterial point of view, is to chelate them and excrete the chelate. This solution is very simple as a chelate is simply an organic framework with a hole with the right size and ion distribution to preferentially hold any of the target ion that happens to enter it. Once the gene for one such chelate is available it becomes quite probable that a quite modest amount of genetic fiddling will produce another that works for a new toxic ion. The initial burst of genetic variation need not produce a good chelate, only one that works at all. Something is better than nothing. Once a chelate that works at all has been created normal neo-Darwinian evolution will tune it until it becomes a good chelate and very efficient at allowing the toxin to be excreted. The owner of the new gene will now thrive in the previously toxic environment. Since toxic ions tend to be toxic to all life forms the new gene will almost certainly provide the same benefit to any other bacterium, or for that matter, non-bacterial life. However, for non-bacterial life forms there is a possibility of a quite different outcome. Haemoglobin provides a good example. The original toxic problem, still found today in clay pans, is a high level of iron ions that vary between ferrous and ferric forms depending on rainfall (high water levels keep air out giving ferrous ions, low later levels let air back in and oxidise the ions to ferric). The optimal solution, achieved by neo-Darwinian evolution, is a chelate that will accept either a ferrous or a ferric ion. This works for the bacterium, and, given the levels of iron present, a chelate that can hold several atoms is even better. The serendipitous consequence is that for any multicellular organism with internal fluids, like a sea squirt, the acquisition by elective lateral gene transfer of the gene leads to excretion of iron chelate not only into the external environment but also into its internal fluids. The chemistry of iron being what it is the multicellular organism has acquired an oxygen reservoir giving it additional options as to the places it can survive. Subsequent natural selection then reinforces the secondary use of the chelate to the point where it is still used even in situations where there is a shortage of iron atoms. A quick look through the trace element requirements of complex living organisms shows that, almost without exception, the trace element is one that is both toxic and occurring naturally somewhere in the world in toxic quantities. The element is often in short supply in the current environment – an unlikely arrangement under neo-Darwinian evolution which would tend to select away from dependence on a rare element.
A second mechanism that affects the probability of transferred genes being useful in the adopting organism relates to toxic organic waste. Bacteria are simple creatures living, for the most part, in or adjacent to what are, compared to the size of the bacterium, relatively large bodies of water. Waste products are not normally a problem, they are simply discarded into the environment, just like many municipal sewerage systems. However, like the sewerage systems, sometimes the environment is not as accommodating as all that and the waste products build up to the point where they become a problem to the organism producing it. Consider the production of wine and yoghurt in which fermentation ceases when the waste products of yeasts get high enough to affect the process – even though the organisms’ waste products are what we want. Every now and again a bacterium will find itself in a pond of a size where one of its waste products builds up to uncomfortable levels. The evolutionary response to this is to attempt to acquire or create a gene that will allow the toxin to be rendered harmless, and it will sometimes be successful. Once this happens the organism will be in possession of a body chemistry that produces a toxin and a gene that allows it to avoid the consequences of that toxin, in short it has a chemical or biological weapon. Use of this weapon in a “toxic bloom” fashion may be advantageous to the organism and if so normal neo-Darwinian evolution will optimise this weapon and make repeated use of it a danger to other organisms. Other organisms will naturally exhibit an evolutionary response to this toxin resulting in wholesale exchange of genes that counter the toxin by converting it to some other chemical. There are three possibilities. The new chemical may be harmless, in which case the sequence stops. The new chemical may be toxic in quantity itself, in which case there will eventually be another round of chemical warfare. Or, occasionally the new chemical will be beneficial to some or many organisms. In this latter case there will be sets of genes available via bacterial plasmid or other genetic sources which create, from naturally occurring precursors in the cell, via toxic intermediaries, biologically useful chemicals. For an organism with an environmental problem the acquisition of such a set of genes may well confer a change adequate to allow survival. Again it is a configuration unlikely under neo-Darwinian evolution where selection would tend to tune against the toxic intermediary and therefore leave a low probability of the succeeding biochemical step arising.
Possibly the most important effect of adding new genes to an organism lies in the collective interactions of the chemicals produced as a result of the genes. There is the obvious point that some mechanisms, such as the clotting of blood, require a number of components to be present before the consequences occur. In these cases the addition of a gene may complete a process and thereafter the combination of genes has a joint effect and natural selection will operate on the group. Any loss of any component would make the organism less competent at leaving descendants. Once formed, any useful group of genes will tend to persist as a group. A more important consequence arises because the chemical systems of an organism are not independent and a change in one part of an organisms’ chemistry will often have an effect on another. The result of such interactions is to couple different parts of the organism so that a change in one area of its life has consequences in another. A change in the light or temperature may affect the movement or growth of the organism. These interactions may allow the organism to implement an algorithm or strategy that allows it to survive under conditions where it could not before. The characteristic of a genetically controlled strategy is that the functionality of the strategy can be evaluated quite independently of any particular implementation of it. For example, if there is some variable attribute of the environment that is valuable to an organism moving through the environment there is a simple algorithm that will attain the best of the immediate supply, move faster on the side of the organism that has less of the desired attribute. The algorithm works equally well for plants with phototropism, bugs looking for moisture and moths following a scent trail. It is a sort of genetically encoded wisdom about how the world works and does not require any specific genetic coding to work, indeed in some cases, such as the general solution for sparsely spread animals looking for mates – one issues a signal and the other homes in on it – it is essential that the genetic implementations of the algorithms are different. I am not aware of any general taxonomy of genetically implemented algorithms or strategies (a web search returns no hits) but these algorithms unquestionably exist and greatly affect the ability of the organism possessing them to survive and leave descendants.
To leave descendants an organism must be able to tap into a source of energy, otherwise it will become inert and lifeless. To leave descendants it must be able to reproduce because there will always be losses to accidents and accumulated damage from the ravages of time. To leave descendants it must be able to change because the world it lives in is changing and its competitors, symbionts and predators are changing and without change the organism will garner a steadily decreasing fraction of the resources in the environment. In all of these endeavours the acquisition of genetically encoded wisdom as control mechanisms, reactions and instincts give the organism an advantage in survival and leaving descendants. Once acquired the algorithms will persist as algorithms, because it is as algorithms that they provide the knowledge of how to survive and as algorithms they will be tuned by neo-Darwinian evolution until they accurately guide the organism through the exigencies of life. The evolutionary response, that when total disaster strikes the acquisition of genetic variability is the best way to allow descendants, is an example of a genetically encoded algorithm. It is not clear when the first implementation of the algorithm occurred but it could easily have been as early as the first structured bacteria several billion years ago. What is clear is the time when it became sufficiently well tuned and prevalent to become the predominant mechanism for the evolution of species. For neo-Darwinian evolution the rate at which new genes arise depends only on the aggregate kilometres of DNA and the errors occurring within it so the rate of new species formation using those genes is essentially constant whether there are a hundred species or a million species. With the evolution response the new species arise from combinations and re-arrangements of genes as species encounter environmental disasters and for this form of new species formation the rate is exponential. Any exponential process, however insignificant it may be initially, will eventually exceed any linear process. You may confirm this by with a spreadsheet by comparing simple interest with a normal rate of interest and initial capital and compound interest formulae with very small interest rate and very small initial capital and doing this over very long times. When you have found the point of crossover graph the sum of the interest from the two processes. The pre-Cambrian explosion of species is obviously, from the shape of the curve of the number of species, the point at which an exponential evolutionary mechanism caught up with and exceeded a linear evolutionary mechanism. The statistical characteristics of the mechanisms leave little doubt that the dominant earlier mechanism was neo-Darwinian, the dominant later mechanism an evolutionary response.
Incompleteness.
This is, of course, an incomplete theory. There are gaps, like the role of viruses and the detail on the biochemistry of an evolutionary response. There questions like the degree to which bacteria are able to call on the retained genes of the higher organisms in order to obtain a genetic solution to an environmental problem that has been previously encountered and survived. I have attempted to sketch the outline of how I see evolution working with different mechanisms working at different levels and different times. As it stands it has the advantage that linear and exponential processes fit into linear and exponential data. The absence of mysterious transitional forms of species is explained, they never existed anyway. The similar rates at which different species evolve is comprehensible and some mysteries of co-evolution are explained – the two strands occurred simultaneously in response to the same environmental event. The explosions of new species following disasters like large meteoric impact or extensive pollution from volcanic outpourings are exactly as expected. In short, it is a far better fit to the data than neo-Darwinism.
A sketch of the theoretical framework.
Evolution involves inherited changes to genetic code. Rules of evolution depend on the size of the change. There are three distinct zones for genetic change dictated by the size of the change.
For very small or negligible changes.
The typical genetic change is a single base change in either a non coding part of the DNA or in the portion of a gene that codes for parts of a protein away from the active surfaces. There is normally no visible change in the expressed characteristics of the organism. Change occurs within an individual and propagates by normal sexual or asexual rules of inheritance. There is no genetic advantage and consequently no selection pressure. Change occurs by random drift analogous to diffusion of Brownian motion with no external conditions affecting the process.
For small changes.
The typical genetic change is a change in the coding part of the DNA that changes the effectiveness of a protein or its conditions of expression, ease of expression or stability. The changes in the expressed characteristics are typically small dimensional changes in organ or general size, change in colour or texture or in sensitivity to diet or environment. Change occurs within an individual and propagates by normal sexual or asexual rules of inheritance. The variances have small effects on the ability of an organism to survive and leave descendents. Variant alleles of genes that result in an increase in descendants for organisms expressing the variant become predominant. The species tends to a set of variants of its genes that are optimal for the environment.
For large changes
The typical genetic change is either a novel gene providing some significant new functionality or, more commonly, a combination of genes that jointly provide some significant new functionality or implement a version of a useful algorithm or control mechanism. The changes in the expressed characteristics are of a level typically shown between juvenile and adult forms of species. Biological mechanisms that facilitate and control the changes are selected. Eventually increased mutation rates occur in response to the extreme stress associated with a change in the environment that is likely to, and usually does, lead to extinction. The predominant form of mutation is lateral gene transfer, as this gives the greatest change in characteristics within the typically short time frame available and does so without a catastrophic associated risk. A general increase in gene modification also occurs but the effect is only significant for large bacterial populations. The rapid rate of mutation continues until either a survivable mutation is achieved or extinction intervenes. Changes have large effects on an organism in two ways. Both the ability of an organism to survive and leave descendants in a changed environment and the ability of the organism to make and survive the large changes are affected. There are two distinct selection criteria with totally different selection effects.
Heresies
Evolutionary theory has been shaped by the influence of opposing religious, metaphysical and superstitious ideas. The effects are far greater than in most other sciences, especially the physical sciences. The resulting distortions have been so great that serious doubts have been raised about whether it qualifies as a science at all. An obvious example of the distortions lies in the premature adoption of principles of evolution. Principles should follow, not precede, precise, confirmed mathematical models. The consequence is that the adopted principles are, to a significant extent, false and misleading. The issue of the extent to which an organism has any influence on its own evolutionary path is a key example. There are many ideologies that have the idea of life following some defined or preordained path. There are others that have an idea of a struggle for progress toward some ideal. In the conflict with these ideas evolutionists have stated their position in the form of a principle, that an organism does not in any sense follow a script or make decisions on its evolutionary path. To quote from an evolution source “Random changes (not related to the needs of the organism” occur in the genetic information”. This goes too far and throws the baby out with the bathwater.
What is biologically possible is determined by the laws of physics, chemistry, mathematics and information theory. Evolution is a process that explores the possibilities. The biologically possible is a complex multidimensional landscape with many complex patterns of hills and valleys. It may be true that there are certain patterns of life that will almost inevitably be found, whatever the course of evolution and patterns of life that, although possible, are so isolated from other patterns that they will never be found. This does not affect the logic of the search any more than the presence or absence of a hidden bomb affects the search strategy of a bomb squad. Evolution is always a selection process occurring in the present. Future prospects and the distant evolutionary landscape are an incalculable mystery to an evolving organism. The next evolutionary challenge is as unpredictable as the weather, literally so since many challenges arise from the weather. However the local evolutionary landscape is not hidden. Natural selection is a process that responds to the local landscape of the biologically possible by taking a species toward a local optimum. A species away from the local optimum will find part of the population “fitter” than the others and that portion will leave more descendants moving the centre of the species closer to the optimum. A species at the optimum will have random divergences in a fringe that is culled as less “fit” than the optimum and therefore having fewer descendants. The slope and curvature of the local evolutionary environment can be visible to an organism and it is theoretically possible for it to have instincts or genetic algorithms that result in it making genetic changes, such as increasing its rate of mutation, constructing or selecting genes, that are appropriate in the local evolutionary environment and lead to a greater tendency to leave descendants.
Once you allow the possibility that an organism may respond to the local environmental landscape then a substantial number of other assumptions fall also.
Many of these assumptions are already questioned, but some neo-Darwinists will cleave to all. As can be seen, there is no scientific grounds for these assumptions but for those who hold them dear and will deliberately disbelieve anything that challenges those assumptions here is a list of some of the most important challenges:
Change is considered to occur at all magnitudes, not just small and very small.
Genetic change is allowed to occur in response to an environmental change.
Genetic change is allowed from internal or external sources.
Changes involving combinations of genes are regarded as important.
Simultaneous parallel evolution of members of a population is allowed.
Evolution of a new species can occur within one generation of a species.
Evolution is allowed to occur at radically different rates a
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