User talk:DavidRAFinn

External Gene Pool Evolution
"It is not the strongest of the species that survives, not the most intelligent, but the one most responsive to change." — attributed to Charles Darwin.

There is general agreement that the arrangement of species, both extant and extinct conforms to a tree corresponding to descent with modification. While this clearly implies some evolutionary mechanism any proposed explanation can only be adequate if it correctly predicts the statistical characteristics of the structure and nodes of the descent tree and of the resulting species and their genetic codes. Nodes, or branching points in the tree, correspond to points where there are novel characteristics or major changes in existing characteristics. Characteristics are based on genes and genetic mechanisms and nodes in the evolutionary tree will often, if not invariably, require the acquisition of genes and mechanisms that go with those characteristics. There is widespread dissatisfaction with orthodox Darwinian theory in that novel genes and genetic mechanisms are neither discussed nor explained. Estimates of expected rates for appearance of genes are phenomenally incorrect. It should be apparent that the single, most obvious, statistical characteristic of evolution, the remarkably small standard deviation in the number of genes in modern species, cannot be accounted for by Darwinian theory. This variance is far smaller than the range in mass, lifespan, number of offspring etc. the variance in number of genes is so small after 500 million years that it clearly implies a model in which new species arise from some orchestrated global process and Darwinian theory is neither orchestrated nor global.

A Taxonomy of evolutionary mechanisms
A general understanding of evolution is assisted by the realisation that evolution, the overall process, is like erosion, progress and life, a product of several distinct subsidiary mechanisms. A simple classification of evolutionary mechanisms can be made by starting with two distinctive features of evolution. The first feature is that evolution is a change and therefore shares one of the common characteristics of change: The bigger a change the rarer it is. The common mathematical form is logarithmic. There is a scale of size and for every step up the scale the frequency of incidents decreases by a constant ratio. This is essentially the same rule as for dice and coins – the number of runs of 16 sixes is one sixth of the number of runs of 15 sixes, the number of runs of 16 heads is half the number of runs of 15 heads. (Were Darwinian evolution the correct explanation of origin of species this rule could be expected to apply universally and the breakdown of this rule at the jump in frequency for the species change level is one of the statistical objections to general application of Darwinian theory.)

The second useful feature is that there is a characteristic time that is associated with a genetic change from when it arises until it has disappeared or has reached some stable proportion of the population – frequently 100%. The reverse rule applies in this case – the larger the change the shorter the time a selection process takes to resolve the change as retained or dropped. Although resolution times theoretically go out to infinity, for all practical purposes time scales are limited to less than a billion years. There is an even briefer limit as at any reproduction there is a possibility that the number of carriers of any variant genetic change may increase or decrease purely due to random fluctuations. This change in proportion can eliminate variations in a number of generations dependent only on population size and short enough to be the upper limit of time scales of interest. For a given species or population these factors can be laid out in a graph with time set against magnitude of change.

(Graph to be added) Graph shows typical time between changes and typical time to resolve plotted against magnitude of change (small to large) with a crossover point and the area of neutral change where the time to resolve does not increase as the magnitude decreases.

The crossover point where the interval between changes matches the resolution time is critical. If the resolution time is greater than the interval between changes there will be a pool of unresolved changes, if less there will be no such pool. This is like e-mails – if you get 10 messages a day and check your mail daily there will be a pool of messages which can be sorted by source, time, length subject etc; if you check the messages several times an hour there will be no pool and therefore no possibility of sorting the single isolated messages on any basis whatever. There are thus three regions of evolutionary processes. The most numerous cases of evolution involve the area under the straight line - neutral theory – there is a huge pool of genetic change where selection occurs through random processes similar to Brownian motion. The next most numerous involve Darwinian evolution where there is an optimal genome for a species with variation providing a surrounding halo from which a new optimum can be selected in the case of slow environment changes with the new optimum eventually acquiring a surrounding halo centred on the new optimum. Finally there is the least common case where the genome of the species does not contain any variation of the magnitude of interest. The species changes notable in the fossil record are well within this zone as the interval between them is typically a hundred thousand years or more and the resolution times are, notoriously, too small to be detected in the geological record. It is this last category of evolutionary change that is of interest here.

The basic non-Darwinian mechanism
Since the genome of a species evolving in the third area of the graph contains no variations of the relevant magnitude there can be no selection from that source and any evolutionary selection must therefore involve an external source of genetic variation. This requirement leads to a totally different style of evolution from Darwinian as the organisms involved must take some action in order to access such external pools. The basic process can be seen in a well documented phenomenon. Following the introduction of a new antibiotic there is an interval before resistance to the antibiotic appears whereupon a large number of other bacterial species also exhibit the resistance. For the latter part of the process the external source of variation is obvious – it is the genome of the species first exhibiting resistance. The basic requirements for this evolutionary process to occur are: There must be an external source of variation which can be sampled with a probability, p, of a useful genetic variation. The number of individuals, n, participating in the sampling must be sufficient that n times p gives a number large enough to give propagation of descendants. There must be a trigger condition which allows the sampling, which is normally a deleterious process, to be initiated as a response.

Under these conditions a species or population that under stimulation exhibits the response behaviour of sampling will leave a line of descent which inherits the sampling behaviour. The better the instinct to sample, both in terms of an appropriate external source and in terms of appropriate times for exhibiting the behaviour the greater the probability of a succeeding line of descent. Thus this pattern satisfies the requirement that it naturally propagates through selection and inheritance.

The existence of an “instinct” of this sort to change may be more easily understood if you recognise that you have such instincts yourself. You instinctively understand the imperatives “run for your life” and “abandon ship”. The strength of these imperatives does not lie in their being strategies with a particularly good chance for survival – they are not. The strength arises from the alternative of not following the strategy having negligible prospects for survival.

The concept of accessing genes from outside the genome may be more easily appreciated if you remember that retroviruses, sex and bacterial lateral gene transfer all involve genetic material arriving at the outside of a cell and being transferred from there to the cells genetic code by a number of supporting genetic mechanisms. This is actually a fairly well established path.

Differences from Darwinian evolution
People familiar only with Darwinian ideas often have problems understanding non-Darwinian evolution through not realising the degree to which the assumptions of the two mechanisms differ. So a few points may need to be made to be stated explicitly:
 * - It should be remembered that in this evolutionary mechanism the changes are very rare and very large. Acquiring change from an external source typically involves the acquisition of complete genes and partial or complete genetic mechanisms. An estimate of the rarity can be made from the number of extant species and the low or zero difference the genes of a species from its nearest associated species. Over the entire evolutionary history of the earth the total number of cases where a novel gene has appeared within a species and conferred sufficient benefit to be retained in the line of descent is, at most, in the billions. The Darwinian level of allele change and the rules associated with that level are in this case irrelevant.

- Because the process involves a lottery in which only a relatively small proportion of the population emerge with a beneficial genetic change there is little possibility of successive changes, there is usually insufficient population and a recovery interval is essential. Thus the process involves separated saltatory events and not a continuous process. - Variation needs to be handled differently. In Darwinian evolution the only function of variation is to provide a halo of alternatives surrounding an “optimum” genetic configuration from which selection can occur. The actual source of changes is irrelevant, so long as adequate change is present. In external source evolution variation is accessed and therefore each form of variation needs to be treated differently as it will differ from others in both means of access and in probability of beneficial result under various different circumstances. - It needs to be emphasised that there is no survival of the individual fittest. The survivors are those that are fortunate in their probes into variation. There is no preceding individual idiosyncrasy that could be construed as “fitness” any more than there is for any other lottery. It is the genetic disposition to do the probes that is subject to the idea of “fittest” and this must be expressed in a population, not an individual, to be subject to selection. Consider the similar case of a lottery where a few individuals hold two tickets instead of one. These each have twice the chance of winning and therefore twice the “fitness”. However the most probable outcome is that the lottery will be won by one of the vastly more numerous single ticket holders. - Extreme care needs to be taken with the concept of randomness. The few definitions typically found in a dictionary do little justice to the extraordinary range of meanings often confused within this one portmanteaux word referring to the partial or total absence of a number of factors – pattern, predictability, control, purpose and intent. Within statistics it is technical term applying to a variety of statistical distributions. In Darwinian theory the dominant meaning, appropriate to naturally occurring accidental DNA base substitution, has to do with lack of predictability, control and purpose. In lotteries, including evolutionary ones, the random process occurs within the context of an overall system. A lottery is conducted for a purpose and one may ask of the random component of the process whether it has statistical or other parameters appropriate to the overall objective – Lotto, with different numbers and numbering of balls, is an excellent example. In this sense “random” does have purpose and control but involves unpredictability closely tied to a different probability distribution from “Darwinian random”.

Pools of variation and their access
It is not necessary for a pool of variation to exist physically for it to be usable by a population or species. The case of antibiotic resistance provides an example. The distributed search strategy used by bacteria, although more sophisticated, may be loosely described as one of cutting and pasting fragments of genes to make new ones. In this case the pool of change is the range of genetic material that can be created by such actions. Because chemicals come in families with significant similarities genes operating on the elements of the chemical family are likely to have similarities. So on exposure to a new member of the chemical family an organism is far more likely to arrive at a suitable novel gene from this process than from randomly changing base pairs. It is still not an especially productive process, the numbers required to bring probable successes often exceeds 1020 although much lower numbers apply to toxins like mercury. By the time a few million people have been given a new antibiotic an antidote gene becomes probable.

Under most environmental circumstances major genetic variation is highly unlikely to provide a benefit and quite likely to be detrimental so that such variation is normally undesirable. In consequence organisms have been selected for a variety of protective mechanisms that either reduce the natural rate of change or apply error correction procedures that counteract the effects. This situation makes it possible for most types of genetic variation to be actively increased in effective rate simply by temporarily disabling or modifying the protective and corrective mechanisms. While an organism may actively modify its genetic code this is not necessary for an increase, temporary incapacitation of existing correction mechanisms is sufficient.

There is a widespread misconception that the forms of gene exchange seen within bacteria do not occur at all, or only negligibly within more complex species. It should be noted that all advanced species must, of necessity, contain nutritious internal fluids for cells not directly able to access external sources of sustenance. These fluids, such as blood, are notoriously prone to colonisation by bacterial species, especially so under conditions of stress. Under the conditions under which active evolution becomes appropriate there will inevitably be bacterial species within the organism able to provide a pool of genetic variation. Since the cells of the organism are descended from bacterial cells which do have such mechanisms there is no requirement for a novel mechanism, only for a variant on an existing one. It should also be noted that immune systems of all types act as filters in that a bacterial species containing a novel gene is more likely to be present than one without. It is also of interest that the more recently a species has experienced significant change the wider the “hole” in the immune system that permits infection tends to be. Domestic species, selected from a series of “sports” are noted for their abnormal tendency to disease under stress.

Global Drivers
The condition that advanced species have a roughly uniform rate of gene acquisition can most easily be accounted for by the trigger factor in this form of evolution being global. A number of events, such as meteoritic impact and major periods of vulcanism are naturally global. However the pattern of gene acquisition suggests an alternative and more interesting essentially global driver. The bacterial “acquired resistance” mechanism can achieve this effect. Any reasonably large bacterial population trapped in some enclosed body of water accompanied by some toxin, internally or externally derived, will generate a genetic mechanism that converts the toxin to some other chemical. The individuals achieving this conversion will benefit even if the new chemical is as, or more, toxic since the initial toxin concentration will be low. Repeated iterations of the genetic search will eventually assemble a sequence of chemical transitions that start with the original toxin and end with a neutral or beneficial chemical. The sequence sugar – ethyl alcohol – acetic acid – etc is well known.

Of interest is the case where an intermediate is highly toxic. In this case the sequence can be repunctuated as a sequence for creation of a toxin and sequence to provide immunity. This pattern lends itself naturally to chemical warfare and any bearer of the sequences that escapes can, individually or collectively, apply this chemical weaponry to anything it encounters. Given the ubiquity of bacterial species and the degree of gene transfer it follows that most species are, sooner or later, likely to encounter the particular chemical attack, or some variant of it, and in consequence gain a genetic mechanism to deal with it. Note that the global trigger is the pattern of chemical attack irrespective of the species that is, in any particular instance, applying it. In this model the drivers are families of toxins and ubiquity of use, especially by bacteria, leads to similar numbers of genetic search responses by affected species and consequently similar numbers of genes. This process also has the benefit of explaining the presence of novel fragments of genetic mechanisms within bacterial plasmids and also the common pattern where intermediates in biological processes can be toxic when it might have been expected that an incomplete biological mechanism producing a toxin would exit from the gene pool once the toxin was produced.

Consequences of the mechanism
An interesting feature of this form of evolution is that the most significant evolutionary consequences are usually side effects of the genetic evolutionary algorithms. Bacterial plasmids and other sources of genetic material contain multiple genes. Consequently any organism obtaining genes useful against toxins by invoking lateral gene transfer will inevitably gain extra genes which are, at best, an overhead and may well be disadvantageous. The optimum strategy for dealing with these additional genes depends on population size. Those species sufficiently numerous to have access to the bacterial gene forming mechanism can afford to drop genes, for them new genes are readily obtained. For less populous species it is more advantageous to retain the genes, which may later prove useful, but prevent them being expressed. This selects for mechanisms which control appropriate expression of genes.

Novel genetic mechanisms can thus occasionally result from the process of adding a number of genes and fractional genetic mechanisms from an external source into the larger similar gene pool held by such less populous species. A common consequence of such mechanism creation is contention between the new mechanism and existing mechanisms using the same genes or related interacting proteins and products. Gaining the benefit from the novel genetic mechanism is therefore dependent on the organism having internal control structures that will separate the incompatible mechanisms in space and/or time. There are a variety of ways of arranging spatial separation. It can be done with chemistry using aqueous, fatty or lipids liquid environments. Within a cell separation occurs with nucleus and mitochondria/chloroplasts. For more complex organisms there are differentiated organs and in the extreme case symbiosis to achieve space separation. Temporal separation can be achieved with either biological cycles or development paths. The importance of these mechanisms to achieve separation within evolution has been recognised although researching them within a Darwinian context has provided few insights.

The genetic mechanisms, or groups of genetic mechanisms, that result first in the acquisition of novel genes and genetic mechanisms and secondly in configuration of the organism to gain the advantages of the new genes and mechanisms are both selected because possession in the members of a species results in some descendants that can carry on the genetic heritage. These mechanisms and their operation can be considered quite independently of any specific species that may be carrying them at any particular point in time. This is, in a sense, selfish gene theory extended to genetic mechanisms as it always should have been. However it should be noted that the first group of mechanisms, relating to acquisition of genes, is normally beneficial only at the transitions and is likely to be deleterious, if expressed, at any other time. Indeed a case can be made for inappropriate expression of the mechanism being a factor in many cancers. Conversely the second group, relating to the capability of reorganising the organism can be seen in normal operation in development, metamorphosis and the ability of severely disrupted organisms to maintain some form of life.

Development of individuals
Individual members of modern advanced species within their lifetimes go through a sequence of changes involving differences which are far greater than the difference between the adult and adults of related species. The concept of a development path as temporal separation of incompatible genetic mechanisms accounts for some of the more distinctive features. If a stage is being added to a development path the point at which it can be added with least disruption to the organism is as the final development. The preference for this position accounts for the phenomenon of "ontogeny recapitulates phylogeny". The pattern is not, of course, exact – insertion can occur at any point in the development path and the earlier stages of development occur in a richer mix of genetic mechanisms than was present in the earlier organism whose adult stage resembles the particular development stage. It is noteworthy that in the case of an insertion early in the sequence there is likely to be severe disruption of later development stages. There are two major symptoms of this occurrence. Firstly the adult of the new species is notably different from its predecessor. Secondly there are normally several possible reorganisations of the later stages of development that still leave viable organisms so that any reasonably large population evolving in this way will emerge with several distinct species none of which can be regarded as being prior to any others. This is, of course, exactly the pattern seen in the fossil record.

Controversially, one may note that many development stages are triggered by chemicals circulating in the internal fluids and that it is, in principle, possible for sufficient cells in an organism to acquire novel genes that they can initiate a partial or complete novel development stage without the need for a delay until the next generation. One could propose puberty as an example of a fossil species change. This would account for the total absence of intermediate fossil forms. This is also consistent with the observation that the closest approximations to intermediate fossils more closely resemble individuals distorted by disease (which they would effectively be).

The origin of sex
The extreme form of spatial separation of incompatible genetic mechanisms occurs with obligate symbionts where the genetic mechanisms are in different but linked species. A common form of this relationship has a bacterial species bound to a more advanced species. This composite is sensitive to toxin attack since loss of either component is fatal and the bacterial component, being constrained in location tends to be less numerous than many other bacterial species. However toxins frequently reappear in new guises and are often similar to previous threats. Consequently there will be occasions where the advanced species has retained a gene or genetic mechanism than can manage a toxic threat where the bacterial component lacks access. This situation can be mitigated if the advanced species makes its entire genome, rather than the subset of a plasmid, available to its associated bacterial species. This allows effective transfer of the useful genetic material to the bacteria and in consequence those species that do make their genome available have an increased chance of survival and therefore the behaviour will become established.

The genetic material provided in this way forms a pool of genetic change available to any species capable of accessing it. This pool has an important characteristic. So long as a species has a reasonable facility in managing duplicate genes, and it will need at least some facility in order to reproduce, the closer a recipient species is to the donor species the fewer different and therefore potentially disruptive genes there will be. Thus species accessing this pool will have a higher chance of a successful genetic transition if they preferentially access the genetic material of a related species. The closer the relationship the lower the chance of disruption. The extreme case being access of material from the same species where the potential disruption from unknown genes is essentially zero. This condition then allows the mechanism to be used to gain relatively safe access to variants of genes, alleles. Thus sexual genetic transfer becomes established as an economical form of gene exchange.

Conclusions
The mechanism of natural active selection from an external source of genetic variation provides an alternative to the Darwinian model. The characteristics of evolution are radically different to those in Darwinism. Overall the statistical characteristics of the evolutionary history and of the distribution of genes conform to active external selection far better than passive internal selection.

Authors note
I have spent some time exploring the evolutionary model I have described and have found it effective and powerful. As a test of its predictive powers I used an example from human evolution. Since splitting from the main ape lineage humans have acquired several hundred new genes and a remarkable number of similarities to marine mammals. Following the aquatic ape theory on can look at an atlas and from departure and arrival locations infer a probable litoral environment for evolution of the North East coast of Africa. This environment is protected by one of the best known environmental change indicator species – coral. If humans obtained genes from bacteria in their environment then at this point corals, being sensitive to environmental effects, could be expected to also gain some of the same genes from the same bacteria. Since corals actually do have a significant number of the genes found in humans but not other apes I am reasonably sure that any scientific study of the origin of species will be constrained to a model similar to that I have sketched.

If someone has the resources they may like to investigate another prediction. Enzymes enfold atoms of various elements. A surprising proportion of elements appear in proteins in this way. There are a few elements, natively toxic, which have rarely been concentrated to the toxic levels under which mineral deposits appear. Boron, for example, is a possible candidate. It may be possible to trace the ancestry of genes involving such elements and date the appearance of the gene in the genetic descent. There should be a significant correlation with either the appearance of the relevant mineral deposit or its subsequent (partial) erosion.

Finally, many of the ideas in this article are anathema to Darwinists so this article is more likely to be trashed than improved. If you find it intact and are interested I suggest you make a copy for reference.

Dave R A Finn