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|Date: 2005/04/29 04:19:40, Link|
If you are about to die you have a freedom to take risks that you would not normally do.
A simple and obvious idea.
But if you are a species facing extinction and the risk is elective mutation then the combination is enough to destroy Darwins theory on the Origin of Species.
If a species facing extinction happens, because of its genetic heritage, to risk elective mutation it increases the chances of a change that will allow a successor. There are no costs, the species will be extinct anyway. The succesor will retain the risk taking genes. After enough extinction events most of the surviving species will have adopted risk taking at extinction. Once you know what to look for the evidence is easy to find. A bacterium that will live happily unchanged for thousands of years will increase its mutation rate a millionfold when threatened with extinction by an antibiotic.
The following article was submitted to the infidels web site, but apparently proved too much for their religious views.
The short disproof of the Darwinian theory of the origin of species.
The Darwinian theory of evolution is based on the idea of slow steady changes arising from accumulated mutations. It is slow because, according to the theory, mutation is disadvantageous. The only mutations occur as a result of unavoidable errors in transcribing genetic information.
The normal expression of the disadvantage of mutation is in terms of there being far more disadvantageous mutations than favourable ones. This is true but irrelevant. Note that company balance sheets do not show the number of items of expenditure and income, only the value. Small numbers of high value transactions have the same effect as large numbers of low value transactions. The correct value for mutation is obtained by considering all possible mutations and assigning them a probability and a cost (or benefit). The net cost (benefit) of mutation is the sum of the costs (benefits) multiplied by the probability that they will individually occur.
Costs are not fixed. Supply and demand applies. A mutation that conserves water is of little value in a lake, of great value in a desert and the value will change with the environment. Of more importance, a beneficial mutation increases the long term probability of an organism having descendants and is limited by the impossibility that the probability can exceed one; similarly a deleterious mutation decreases the long term probability of an organism having descendants and is limited by the impossibility of the probability being less than zero.
Over a time scale, usually taken as a generation, the numbers of a population vary. The ratio of the numbers in one generation to the numbers in the preceding generation is a reproduction ratio. If the environment of an organism changes sufficiently for the long term reproduction ration to fall below one then the population of the organism will become extinct and disappear. At any point where the reproduction ratio drops sufficiently to virtually ensure extinction the long term probability of the organism having descendants is essentially zero. Consequently, the cost of deleterious mutations, as a fraction of this must also be zero. The only mutations which contribute anything to the cost(benefit) calculation for mutation are the small proportion of beneficial mutations which return the reproduction ratio back above one. All other mutations have no net effect on the slide into extinction, they can only affect the speed at which this state is achieved.
Once the long term reproduction ratio of a population drops below one the organism is in a position where mutation has a net positive effect. It has literally nothing to lose and a slight possibility of survival to look forward to. When mutation is a net good then more mutation is better and increases the possibility of a favourable outcome. It follows that under these conditions any organism having any genetic disposition to respond to the significant drop in reproduction rate by increasing its rate of mutation will have a greater long term probability of having descendents. The tendency to mutate at incipient extinction is genetically favoured. The greater the extent to which mutation is increased and the greater the accuracy with which the condition is detected the greater the advantage for the organism.
The process of mutating at extinction has positive feedback, compound interest in economic terms. Once initiated it will increase as the more extreme exponents of the process gain ever increasing advantage from electing to mutate. The limits are a totally accurate recognition of the state where mutation is advantageous and whatever turns out to be the upper limit of the mutation rate that will still allow any form of survival of the organism. Until these limits are reached the mutations, and the new species resulting from these mutations will increase with time. Eventually the numbers can be expected to reach and exceed the numbers of new species produced by Darwinism.
The condition that the two mechanisms, Darwinism and mutation at extinction, have exchanged as the primary producer of new species is easily detected. Following the crossover the number of species will show an abrupt rate of increase in numbers as the increasing rate of the extinction mechanism becomes apparent. Species will increasingly be created in the brief windows of extinction giving a fossil record with far fewer intermediate forms than under Darwinism with massive increases in the variety of life forms following periods of mass extinction. Species like bacteria will respond almost instantaneously to life threatening pollution and chemical hazards. There will be a marked difference in the rate of evolution in hazardous environments, such as land compared with the more benign ocean environments. The need to accurately gauge the population increase and decrease will lead to complex behaviours sensitive to population numbers. Etc.
Recognise it? Darwinism has not been the major evolutionary mechanism producing new species for quite some time.
So there you have it. Yes Darwinism exists, yes it works to keep species well adapted, yes it occasionally produces a new species, and yes, if you look at a species it will normally be the only form of exolution on display. But in the brief
periods of extinction wild risk taking changes occur producing most of the new species.
This description only shows the what of the evolutionary process, not the how. I do have an outline of how I think it works but
a) I am not a trained biologist so my account will undoubtedly contain errors that would be siezed on as reasons for ignoring what I am saying.
b) There are some potentially very valuable medical uses of evolution and I would like to try for some retirement income. (offers from pharmaceutical or similar companies welcomed - state the percentage of the profits you are willing to let me have).
|Date: 2005/10/30 14:40:59, Link|
On overlooking the obvious
This is an outline of an article I am working on. I am sending/posting it to get feedback on the ideas and suggestions for alternative ways of making the proposed measurement.
As a gross simplification the process of evolution consists of an organism acquiring a change in its inheritance or genes and in consequence incurring changes in its characteristics and subsequently a variation in its prospects for flourishing in the environment.
A wide variety of things can produce changes in an organisms’ genes and for many, if not most, we have a detailed theory of the process in neo-Darwinism which covers all of the common changes that can arise from within the organism’s own genes. However, as well as an organism’s own genes it exists in an ocean of alternative genetic material, from fragments of dead organisms through pollens, viruses and bacterial plasmids to complete consumable organisms of different species. We know that there are some instances where an organism has acquired a gene or group of genes from another. The process is referred to as horizontal gene transfer. Two classic instances are the transmission of resistance to antibiotics and mitochondrial DNA. Concern over genetic engineering has brought further examples to light.
The processes of horizontal gene transfer and neo-Darwinism operate in very different ways and therefore each should leave its own distinctive signature on the pattern of new species found in the evolutionary landscape. So we will compare the two processes and look to see if there are any ways in which horizontal gene transfer could leave an identifiable signature on the new species and use this to see if there is a detectable component of horizontal gene transfer in the evolutionary record and, if so, estimate the proportion of evolution that could be attributable to it.
There is a problem that you encounter as soon as you attempt the calculation. This can be seen in the obvious case of the fossil record. A single gene contains a truly extraordinary amount of accumulated evolution. It takes hundreds of individual changes to make a gene sequence in a piece of DNA. Of greater importance are the innumerable alternatives and byways that produce DNA sequences that are not genes or are genes that kill the organism. The possibilities are so numerous that it is at present unknown just how any significant number of useful genes can be produced within the time life has been present on earth. Remember that until a gene is complete and activated there is no evolutionary pressure that can be brought to bear on it. There is an astronomical ratio between the number of neo-Darwinian changes required to bring about a given level of change in a species and the number of horizontal gene transfers to achieve a comparable effect. Neo-Darwinism could be expected to contribute an essentially continuous gradation between species whereas horizontal gene transfer would leave far fewer but much larger jumps in the fossil record. As Darwin himself noted, the fossil record does not match the neo-Darwinian prediction and continuous gradation from one species to another is not seen at all. A simple analysis of the fossil record would merely conclude that 100% of evolution was attributable to horizontal gene transfer. In this case we have instead a problem in identifying a signature of neo-Darwinism in the evolving species. Neo-Darwinian evolution occurs, there is ample evidence for that. Some unexplained factor is suppressing the expected pattern in the evolved species.
There is an alternative analysis that can be made that depends on a different characteristic of horizontal gene transfer. In neo-Darwinian evolution each organism experiences its own changes, good or bad. If one population has ten times as many members as another it will experience ten times as many mutations and have ten times as many new genetic variants on which natural selection can operate. A large population has many potentially useful variants, a small population can run out of genetic diversity leaving it vulnerable to extinction. Conversely in the case of horizontal gene transfer the organism fragments, pollens, viruses and plasmids occur in large numbers so that there is a huge pool of genetic material available to any taker, irrespective of the size of the population of the mutating species. A change large enough to lead to a new species will be far more likely for a very large population than a very small one for neo-Darwinism, but essentially equally likely for all population sizes for horizontal gene transfer. So an estimate of the significance of horizontal gene transfer can be made by looking at the evolutionary tree and computing the correlation between estimated population size at a point on the tree and the probability of there being one or more descendent species. However simple observation of the published trees indicates that the problem we had before is again apparent. The trees are replete with extensive outgrowths arising from source species originally present in very small numbers. The sum total of the entire populations of every single species that has given rise to a vertebrate descendant species is far less than that of many single celled species that over the same period and with the same evolutionary pressures have give rise to few if any descendant species. We find again that the problem in estimating our ratio is an almost total lack of the expected signature of the neo-Darwinian descendant species and are left with the same, peculiar, estimate that 100% of new species arise from horizontal gene transfer
An alternative way of determining the effect of numbers on probability of evolving that eliminates many variables is to take a well studied organism, like homo sapiens, and note that for every individual homo there are numerous accompanying parasites and symbiotic bacteria. Since these all have gone through the same evolutionary history the history can be largely discounted and the question becomes one of counting the number of new species of human flea, skin mite, athletes foot yeast, gut bacteria etc that have appeared in the last couple of million years while humans evolved from a Miocene ape. To the extent that the numbers of new species reflect their population sizes the process is neo-Darwinian. To the extent that the numbers of new species match the number of human species in the interval the process is horizontal gene transfer. The actual numbers are again and oddly essentially identical. The problem with this analysis is that the numbers clearly indicate that there is no tendency whatever for larger populations to be more likely to leave descendent species and again leads to the conclusion that virtually all change is horizontal gene transfer.
There is third way of estimating the ratio of neo-Darwinian evolution to horizontal gene transfer. We can look at the whole issue from a global perspective. Basically life involves taking energy from the sun and using it to create living organisms and support other organisms living on the first group and each other. The amount of sunlight does not vary by much. The proportion of the surface of the earth where life can occur does not vary by much. So the total amount of life should not vary by much. Since more than 99.9 % of living organisms are single celled the total number of living organisms should also not vary by much. There should be roughly the same number of organisms per planet now as there were three million years ago – give or take a factor of ten or so. The number of genes per organism also does not vary by much. There are organisms with a lot of genes but they appear in such small numbers compared with plankton, bacteria, yeasts and other single celled life that their contribution may be ignored in the global scheme of things. So although the number of species varies the total number of copies of all genes on the planet should be roughly constant and if they all change at a roughly constant rate the total number of new gene variants per year should be roughly constant over geological time. This leads to an expectation that the number of cases per year where enough variation is accumulated in a population to constitute a new species should be roughly constant for neo-Darwinian evolution and not dependent on the number of species forming populations at that time. If there are ten times as may species each gets, on average, a tenth of the available variation. Some success at last, this was true for the first three million years of biological history and we have a neo-Darwinian signature. The process of horizontal gene transfer follows a different rule as new species creation depends on the number of genes available in the global pool and number of species absorbing genes from the pool. This has an increasing growth and must, inevitably, eventually dominate over any constant process. This applies no matter how insignificant a proportion of genetic change is initially attributable to horizontal gene transfer. The observed distribution of number of species does in fact follow the expected curve where some species arise from an essentially constant process and some from an essentially exponential process starting from a lower base level. (plot a graph of return from 5% simple interest on $1000 plus .5% compound on $1 over 3000 years to see the resulting curve). The problem with the analysis is that almost all species arose after the exponential component became dominant and would have to be assumed to have been derived from horizontal gene transfer. We are still back to the nearly 100% of species arising from horizontal gene transfer.
To hark back to the second mode of estimate – there is a simple calculation that says that if 99.99 % of living organisms are single celled then 99.99% of copies of genes are in single celled organisms and 99.99% of the genes changed by neo-Darwinian processes are in single celled organisms so that 99.99% of populations that accumulate enough change to produce a new species will be single celled and 99.99% of new species arising under neo-Darwinism should be single celled. Put this down as another odd calculation that suggests that most multicellar life originated via horizontal gene transfer.
Let us try a fourth, and more direct approach. The human genome has been decoded, as has that of much of the immediately related primate species. Thus we can look at the actual genes that have changed in the process of evolving. For neo-Darwinism the process of obtaining a new gene is clear. A stretch of DNA acquires random changes until eventually it meets the criteria used by the cell chemistry for identifying it as a gene at which point it can produce a protein that will have an effect on the cell and the whole process of natural selection and gene-tuning can commence. Thus for any new gene the presence in several related species of a string of DNA that is not a gene and never has been a gene but has a 99% match to the sequence of the new gene will be a reliable indicator that the gene has originated by neo-Darwinian processes. Conversely the absence of such a DNA sequence or alternatively anything that positively identifies the gene as having come from somewhere external to the organism will identify the gene as having arrived through horizontal gene transfer. Once again, however, we get the “wrong” answer. The genes identifiable as new to the homo sapiens which have a corresponding non-gene found in any related species are, to put it mildly, rather thin on the ground. Worse still, over 200 new genes can be almost certainly identified as having originated in bacterial sources. We still deriving values of the ratio of neo-Darwinism to horizontal gene transfer with almost 100% horizontal gene transfer at least for the case of new genes.
Complete information on genetic sequences would allow the proportion of horizontal gene transfer to be estimated by checking which genes were duplicated in what species. In the case of neo-Darwinian evolution a gene can only appear in an initial species and species linearly descended from the initial species. In contrast a generally useful gene is likely to appear in a substantial number of unrelated species, especially following a widespread ecological crisis. All that is necessary is for the mutating organisms to be exposed to a donor species for the gene. There need be neither physical nor temporal proximity. Too few organisms have been sequenced for this approach to be applied with any accuracy although there are a few regulatory genes that have a suspicious distribution. In the case of the human genome the information is definite. It is impossible to reconcile the human gene pattern with a model of divergent human groups forming separately evolving groups. The discrepancy is so marked that some writers, whose commitment to neo-Darwinian orthodoxy appears almost religious, appear ready to claim that racial differences are merely a culturally determined illusion. The approach demonstrates only that there is a significant amount of horizontal gene transfer as a lot of data is required to distinguish the two cases of a gene being passed to all or most descendent species and all or most descendent species acquiring the same gene subsequent to speciation.
On to approach five. Let us look at what sort of genes are being created. Are there any distinctive characteristics that would identify a gene or a group of genes as having almost certainly either originated through neo-Darwinian processes or having been imported from an external source? In both cases the answer is "yes" although the characteristics are quite different. For genes produced through random permutations of DNA there is a very simple pattern to the length of the gene. If you step through a randomly produced gene, codon by codon, there is at each step a probability of encountering a “stop” marker that terminates the gene. The twenty-fifth codon of a gene can only exist if none of the preceding twenty-four codons was a terminator. This leads to an expectation that if you plot the numbers of new genes against the length you should get an exponentially decreasing curve with a gene of length one being the most common and anything above one hundred being extremely unlikely. This is, as one might by now have come to expect, never observed.
For genes acquired by horizontal gene transfer the identifying characteristic relates to the fact that most, if not all, new transferable genes originate in bacteria or other single celled organisms (largely a question of numbers). There is a problem in explaining any gene that has a function related to, say, bone formation, as bacteria do not have bones and the gene cannot have that function in the original organism. For horizontal gene transfer to be a workable form of evolution there would have to be genes that are dual function and serve one purpose in the original bacterium but some other, quite different, function in some other organism. Since it is highly improbable that a randomly generated string of DNA that happened to meet the criterion of being a gene would have any useful function at all the probability of such a gene having two totally different useful functions is grossly improbable. However there is at least one class of genes and their proteins which have exactly this peculiar property. Many bacteria respond to toxic levels of an element by chelating the offending atoms and excreting the chelate. Unlike bacteria, all higher level organisms have a significant trace element requirement. These trace elements are used in chelates and in some cases it is possible to work out how the whole process works. For example a bacterium occupying a niche at the edge of an underground clay pan will be exposed to very high levels of iron atoms with the proportion of ferrous to ferric varying with water flow. Such a bacterium will find considerable use for a chelate that will allow several atoms of either ferrous or ferric iron to be excreted. If, later, a species with internal fluids acquires this gene it has just obtained haemoglobin. A similar analysis can be done on other trace elements – the elements naturally occur somewhere in toxic quantities and the protein involved serves both to excrete the toxic element and also for some purely serendipitous function in the secondary organism. All this analysis takes us no further forward. We are left, again, with no clearly identifiable genes that look neo-Darwinian but at least some that look as if they arrived via horizontal gene transfer.
There is one other characteristic of horizontal gene transfer that might allow an estimate to be made of the extent to which it contributes to evolution. For this we need a little bit of theory that is not widely circulated. Neo-Darwinism contains a couple of principles stating that natural selection operates only on existing genetic variation and that an organism cannot affect its own evolution. These principles do not apply to evolution in general and serve only to delimit the forms of evolution that can be correctly described by neo-Darwinism. Natural selection can be a lengthy process and a genetic change can easily occur within or as a result of the selection process. Organisms can and do exhibit behaviour that affects the probability of genetic change. Indeed, in the two common cases of cancer and HIV, you personally may be aware of actions that you have taken or not taken with the specific intent of reducing the probability of that genetic change. With horizontal gene transfer the degree to which cellular mechanisms are involved make it impossible to ignore this factor in the way it is, for example, in the case of the radioactive decay of carbon 14 to nitrogen. To understand the implications we need only look at the simplest version of what I term the “abandon ship” effect.
Consider, for a moment, a hypothetical single celled organism living within some structure as a stromatolite or algal slime. Maintenance of the structure requires each organism to react in some way to the presence or absence, or for that matter health, of the surrounding organisms. For such an organism it is not stretching the bounds of possibility to imagine that the probability of acquiring a gene from the environment might increase under the stress arising from the death of several surrounding organisms. This condition is a very strongly self-reinforcing evolutionary adaptation and once established will persist. For an organism suffering very high losses and headed for extinction the normal rules about mutation do not apply. For normal mutation the majority of mutations are deleterious and attract a penalty derived from the large cost of death compared with non-mutation and survival and the benefits attract only a small advantage in being possibly slightly better at surviving compared with non-mutation. In the case of incipient extinction non-mutation leads to extinction and deleterious mutations attract only the negligible disadvantage of death slightly earlier than for non-mutation whereas the benefits can include the large one of survival. This resembles the situation where jumping off a ship in a storm is normally a suicidal idea, but following a call to abandon ship because the ship is sinking becomes an excellent stratagem as the small chance of survival is far greater than the zero chance of survival associated with going down with the ship. If all unmutated organisms of a species will die, and some mutated ones survive then mutation, whatever the risks, becomes advantageous. Our hypothetical organism can thus be seen to have achieved the status where it detects and responds to the condition that mutation is advantageous. Since it is advantageous the organism is more likely to produce a successor species which will also, since this is a heritable characteristic, behave similarly in the face of the population decline that heralds extinction. For the individual organism mutation is a hit-or-miss affair. However for the species the effect is very powerful. If there is an advantageous gene available anywhere in the environment, and this is very probable, then having every member of the population acquire a gene will inevitably result in some individuals acquiring the advantageous gene or genes and after the dust has settled the variant with the most useful of the advantageous genes will go on to become the preponderant representative of the successor species. Thus the innocuous individual characteristic “if surrounded by dead, acquire a gene” becomes scaled up in the broader case of the population to “in a crisis acquire the most useful available gene”. This has so great an evolutionary advantage that it does not take very many brushes with extinction for it to become a preponderant trait in all evolved species.
With this theory under our belt we can identify two more characteristics of horizontal gene transfer that should be absent when neo-Darwinian evolution is responsible for new species. The first of these is a strong correlation between the appearance of new species, especially radically new species with the incidence of mass extinctions. Since it is the actual mass extinction that initiates the new species creation new and novel species will appear in the fossil record almost immediately following the extinction whereas for neo-Darwinism the only increase in the rate of species formation arises from the emptying out of ecological niches which will then be refilled at the same rate as the original colonisation of the niche and by a similar species to the original colonist of the niche. The neo-Darwinan effect is masked in this case but the plots of numbers of species against time do show a very rapid recovery in numbers following mass extinctions suggesting a high proportion of new species arising through horizontal gene transfer
The second characteristic derives from the basic "shape" of the evolutionary process. What is possible in the way of life forms is dictated by the laws of physics, chemistry and information. Evolution is a process of exploring the possibilities. With neo-Darwinism the current population of species has an envelope of variants which inexorably moves slowly out over the range of possible life forms. With horizontal gene transfer the process divides into two quite distinct phases, the static where there is no advantage in evolving and very little, if any, significant changes occur and "explosions" where there is an advantage to evolving and a species mutates rapidly creating a shell of new life forms all radiating away from the population that has encountered the "abandon ship" scenario. The two mechanisms differ considerably in the pattern of appearance of species when a new zone of possible life, such as land or flight is encountered. In neo-Darwinism the first land animal, for example must derive from a population of "almost land animals" as only small changes can occur. New species of land animals will drift slowly in, predominantly from the "almost land animals" until such time as the population of land animals reaches large numbers and can exhibit sufficient variation in its own right. In horizontal gene transfer the first land animal will arise as a result of a substantial random jump from a previous species and the "almost land animals" will not exist. The exigencies of the new environment will result in very rapid radiation out from the initial species until stable forms are found. Thus the ratio of neo-Darwinism to horizontal gene transfer can be estimated from the extent to which new classes of organisms appear as a slowly increasing number deriving from a similar precursor (neo-Darwinism) or as a significant number of species appearing almost simultaneously without any obvious precursor (horizontal gene transfer). The latter form would appear to be the dominant form.
Thus all attempts on estimating the ratio of neo-Darwinian species formation to horizontal gene transfer species formation have foundered, not on the difficulty of finding a signature of horizontal gene transfer but on a difficulty in finding a signature of neo-Darwinian species formation.
Which leads me to the title of the paper. Somebody somewhere must be overlooking something obvious. Maybe it is me, in which case I would be most interested in a analysis that shows why all these different methods of calculation should all fail and gave the same erroneous answer.
Alternatively, just possibly, everyone else is overlooking something obvious.
The logic for assuming that neo-Darwinism is responsible for all evolution of species was always of the smoking gun variety and might, just possibly, not be true.
|Date: 2005/11/03 13:36:11, Link|
As my readers may have inferred, I am also am not a biologist – my training was in physics, chemistry, mathematics and philosophy followed by a career with computers. After many years of noticing “experts” offering clearly unjustified and unsupported claims, followed some years later by the great “discovery” that the previous experts were wrong I decided to try prodding one of the stupidities to see if the process could be made more rapid.
One of the unfortunate facts of life is that a sentence that appears pellucid in the eye of the writer can become unrecognisable when processed by the reader. It also appears that there are some surprising misunderstandings about over both speciation and horizontal or lateral gene transfer. So, in an attempt to clear up some misunderstandings:
HGT is an abnormal transmission of an otherwise normal gene, not a characteristic of a gene that results in it being transmitted via HGT. Following an incident of HGT there are two evolutionary trees created by normal evolutionary inheritance and normal selection of the fittest, one for the donor species and one for the recipient species. The gene changes the characteristics of the organism exactly as for any other gene, the characteristics are selected exactly as for other genes, the gene is transmitted to the succeeding generation (if any) exactly as for any other gene. There is no way that the shape of evolutionary tree incorporating an HGT gene can be distinguished from one in which the gene arose through random mutation without making a reference to the second tree. However, where there is a large degree of HGT the same genes can appear in more than one place making it impossible to describe inheritance using a simple tree. This confused situation, or at least, something that looks exceptionally like it, is known to occur (e.g. plants, human races). The actual rate of duplication in the world may not be very large since bacteria are observed to create (and also lose) genes at a global rate of “several” per year, so the total number of genes in all phylogenetic trees could be substantially larger than the number of genes currently available in the bacterial pool with relatively few HGT duplicates. I will include a fuller description in later versions.
Simple consideration of the process suggests that speciation is normally a two stage process. Take an example of a recent new species that arguably appeared by purely neo-Darwinian evolution, the Colorado potato beetle. There is no doubt in this case that what initiated the speciation was the arrival in the parent species domain of a large new available food source. Once the new food source is adopted then all the minor differences between the previous foods and the new food drive normal neo-Darwinian evolution until, after a relatively short period, there are detectable differences between the beetles and you have a new species. This is not a normal situation and required (inadvertent) human intervention. In the wild an empty sustainable ecological niche will exist because there is some barrier to its exploitation. Minor variation will not breach this barrier. Some barrier chemical must be broken down, a material with novel properties acquired, some novel way of processing something in the environment, a replacement for something missing in the new environment etc. This requires a new gene and a single new gene may allow the barrier to be crossed resulting in a new occupied niche and a new species. Some barriers require multiple new genes. This is why the acquisition of new genes is of primary importance in the appearance of new species as opposed to the adaptation of a species to its environment. Theoretically a slowly changing environment could lead to a gradual drift to a new species but there are very few environmental changes that are gradual over time scales of even thousands of years. Many environmental changes, especially the arrival of a species from outside a region, occur within decades as in the case of the beetle above. Ask any farmer or horticulturist.
Theoretically the processes normally described in neo-Darwinism – radiation damage, transcription errors in duplicating DNA and the like can create, by chance, a useful new gene. Simple probability calculations, as the creationists are fond of pointing out, make this an extremely unlikely event. Furthermore, as I pointed out, new genes found in evolving species do not have the statistical characteristics that would be expected from such a process. While there are enough organisms over the whole planet for there to be some new genes produced by purely random shuffling of DNA even the current rate of observed new genes, which is "several" useful new genes per year globally is higher than simple theoretical calculations would suggest. A simple explanation of the very long early period of life where very little happened is just that at that point there were no efficient ways of creating new genes and consequently evolution was necessarily very slow. There is evidence that bacteria can affect the rate at which they mutate and under unusual conditions do create new genes at higher than their "resting rate". Creating a new gene is easy, simply splice a start, a middle and an end from three different genes together and there is a fair probability that the result will be a gene, and new. Something like this seems to be what actually happens. The differences in the statistics for neo-Darwinism and HGT arise not from any differences in what happens after the genetic change has happened – there is none, The differences arise because the large steps in evolution associated with novel genes are almost exclusively associated with HGT and the circumstances under which they occur are different and therefore the actual rate of evolution of any specific species will depend on different parameters in the two cases. Although there is no difference between the effect of a single new gene that arises within a neo-Darwinian environment and a single gene being imported via HGT only a small proportion of neo-Darwinian evolution comes into this category and consequently there are statistical measures.
C.J.O’Brien, If you and Henry are not biologists you may be able to appreciate the following argument. The global rate of gene production by all life in the world is in the range of “several” per year. Even in ordinary surface seawater there are more bacteria per litre than the total number of humans until very recent times, and there are (much) more than a trillion litres of surface water. The average rate of gene production within a species such as humans, which are (much) less than a trillionth of the total number of organisms in the world will be (much) less than a trillionth of that rate. Over the evolutionary period for humans, about 2 million years, the average number of genes produced within the human gene pool will be “several” times “(much) less than a trillionth” times “2 million”. This comes out, at best, as a few millionths of one gene, the rest of the genes will have to come from somewhere else. Biologists appear unable to do arithmetic on large numbers and seem to regard all numbers greater than a million as equally “a very big number” and are uniformly unable to follow the above logic.
With regard to C.J.O'Brien's point about precursors. The word “immediate” should have preceded precursor. Novel species do, of course, have precursors in the fossil record. My point concerned the case of a novel species, say, “novellus” in the fossil record. There is an assumed (since it is not in the fossil record) immediately preceding species “hypotheticus”. In the case of neo-Darwinian evolution the two species must be very similar and a second “novellus” species must be at least as likely to arise from one of the existing populations of “hypotheticus” as from the single population of “novellus”. In the case of predominantly HGT “hypotheticus” will be more dissimilar and subject to very much less frequent mutation. In this case the probability of a second HGT incident occurring and happening to match the effect of the first is relatively low so that new “novellus” will arise predominantly from the original. Thus for neo-Darwinism the first half dozen “novellus” species would tend to be physically separated but very similar whereas for HGT they would tend to be physically adjacent but more diverse. The species distribution naturally produced by consecutive large HGT steps cannot easily be reproduced by neo-Darwinism and does appear to occur. If it helps think of it as like the difference between the ways a weed mat like tradescantia spreads and a wind borne weed like a thistle spreads.
On the subject of the meathod of HGT. My argument does not depend on a specific means of transfer. HGT is known to occur from bacterial species to multicellular. The usual figure given for the difference between humans and chimpanzees is about 3%. This translates into roughly 600 genes. Of these over 200 can be shown unequivocally to have arrived by HGT from bacteria. (Look it up). Given the relative numbers of single celled life and multicellular life the expectation would have to be that almost all novel genes would originate in single celled life. All new genes that are datable in that they interact with some chemical that is only created by industrial man have been found in single celled life, usually bacteria. Thus only the (imperfectly understood) mechanism that is known to exist is required. As has been pointed out elsewhere there is no violation of any biochemical rules in allowing the possibility that a scavenging bacterium could acquire a gene from the detritus it was consuming. So transfer from species to species via bacteria is in general feasible. The most probable means of transfer is via disease as this often involves bacteria in the bodily fluids where any cell, including those involved in reproduction are accessible. As I pointed out, any organism that responds to the destruction of its ecological niche by acquiring new genes will be more likely to leave descendents that one which does not. The correlation of disease with lots of dead bodies is well documented. There is no need to postulate a new mechanism for the transfer – everything is descended from single celled organisms which could acquire genes so all that is required is a reason for this ability to be retained, which I have given.
Ghost of Paley, I am unsure where (or whether) to start with your illogical diatribe. Without any evidence you rudely attack me personally as having committed numerous intellectual sins which I assure you I have not committed. In particular I have never, at least in the last 40 years, assumed that anything statement has absolute certainty simply because someone made it. I regard the idea that documents "prove" anything as a useful legal convention. All are subject to interpretation – have you considered the possibility that the bible is a digitally encoded message for the 22nd century cunningly disguised as religious rubbish to ensure its transmission via the gullible? In any case it is a book assembled in Rome by a group of Romans to assist a Roman emperor, Augustus Caesar, establish a religion based in Rome. The sections of the bible used as the basis of the doctrine are largely those of a mentally unstable Roman soldier, notwithstanding the addition of large amounts of miscellaneous material of dubious authenticity from Greek, Hebrew and Egyptian sources. If that does not make it Caesar's then I will eat my hat (but not the one with the pretty blue pompom). As someone famous is reputed to have said "Render unto Caesar what is Caesar's and unto God what is God's". If you are trying to establish a claim for God being responsible for the life on earth you should not be quoting from Caesar's book.
|Date: 2005/11/04 10:51:51, Link|
Further answers to commentators.
Information on bacterial genes in the human genome can be found simply by using the two phrases "human genome" and "bacterial gene" in a search. It is a relatively recent outcome of the human genome project and is surprisingly underreported, I found it only because I was specifically looking for it. The other area of interest is the way in which the bacterial genes are identified as such. Documents in the area make it clear that recent bacterial genes are a normal feature of the genomes of "higher" forms of life.
The situation of the HGT genes showing up is arguably true. It is certainly true that there are inheritance trees that simply cannot be made to function because of the conflicting information available from adjacent related trees. The human genome cannot be resolved into the gene patterns resolve into a simple structure based on geographical separation and race. Because the writers on the subject are operating within an environment where assumption of neo-Darwinism is mandatory, if you wish to keep your job, they do not report on whether or not the observed pattern can be simply resolved on the assumption of HGT. My suspicion is that it can be, but I do not have the time, resources or energy to undertake the research myself.
Your calculation on rate of gene change is unfortunate. (I took first humanoid rather than preceding ape for the time interval, it is of little import, the answer comes out the same for one million or ten million years). Your calculation implicitly assumes that the modern human genome was present and could be used to determine which of the base pairs should change and in which way that should change. The whole point of natural evolution is that the future genomes are not pre-determined. There has to be sufficient genetic change to account for not only the actual change which did occur but also all the equally probable changes which did not occur. Unless you can think of some good reason why only the changes which did occur should occur you need to include other possible changes in your calculation and then the rate is (spectacularly) too low.
HGT is very different its operation from "traditional" genetic change. It is therefore essential that in discussing it you avoid taking assumptions from "traditional" theory without checking first that they apply in the HGT case. A surprising number do not, mostly because the "resource" for genetic change is an external pool and not the internal genome. For example you assume that the rate of HGT would depend on the number of places to mutate, because this is the case for neo-Darwianian mutation. A moments thought will convince you that for HGT the number of places to mutate in the recipient species can have no effect on mutation in the donor species and the number of changes involved in HGT is one, the insertion of a gene, so that the presence of 10, 100, 1000 or 10,000 possible insertion points will have no effect whatever on the rate of HGT, this is determined by the content of the pool of available genes and the rate at which the genes find their way through the various barriers that normally keep then out of the genome. This, incidentally, provides a check which you might care to make on my claims. For neo-Darwinian evolution the rate should depend on the length of the chromosomes, as you indicate and therefore the proportion of new species arising from neo-Darwinism vs HGT can be estimated by looking at species with particularly long or short DNA and comparing the extent to which they are associated with fast or slow evolution of species. Be my guest and try it, I would be interested to see what you come up with.
The point about the abandon ship analogy is not the matter of choice. The point is that in that situation, as in many others, the probabilities are different from "normal" and therefore the optimal strategies are different. Doing nothing is normally an option with considerable survival value. In the case of extinction this is not true. This is what I mean by the normal rules being different. Your statement that rates of mutation are basically constant is an oversimplification. For most forms of mutation this is essentially true, as long as a reasonable time frame is used. However HGT differs from most forms of mutation in being mediated. The incoming gene has to be passed through the outer cell wall, the nucleus wall and then be incorporated into the chromosomes. There is a lot of cell chemistry involved and this can be affected by temperature, acidity, salinity, magnetic or electric fields etc etc. The assumption of a uniform rate cannot be made in this case. The point of the argument is that if, as a result of some random mutation, an organism ends up with some coupling between some feature of the environment that correlates with extinction and the operation of the mechanisms involved in HGT which has the overall effect that the rate of HGT increases under extinction then this mutation will be selected for under normal rules of evolution. It is a way of being "fitter", it increases the probable number of descendants. This peculiar characteristic is naturally selected for the reasons I have given. This being so one may expect that an increasing proportion of new species will have inherited this characteristic. The process is similar to arguing that it is useful for a member of a species to be able to locate other members of its species and that therefore you would expect a substantial proportion of species to emit a chemical, audible or visible sign which other members of the species were equipped to detect and use to find each other. Those species with this characteristic can survive with more sparse populations than those that cannot therefore the mechanism is selected. The characteristic can be analysed in terms of its probable success as a strategy without any suggestion that there was any though that went into its adoption. Genetically encoded strategies are a legitimate form of inheritable characteristic, this is, after all, why evolution tends toward greater complexity. There is no suggestion that species are choosing to increase the rate of mutation in any stronger sense that one might say a seed chose to germinate. Simply that the mechanism is present purely because any organism with it will tend to leave more descendants than one without. I left neutral mutations out because they do not significantly affect the argument, and they are, in the case of the massive injection of genetic information in HGT, considerably rarer than for single changes with DNA normally discussed.
|Date: 2005/11/15 06:33:14, Link|
One of the main reasons that ID has a bad reputation is that the proponents confuse the concepts of intelligent creator and god. The two are quite distinct and indeed incompatible - an intelligent creator is, by definition, working within rules to achieve an effect, a god, presumably, is above rules and operates by whim.
An example of a scientific intelligent creator theory can be obtained by noting that any gravitationally dominated universe is unstable (see Einstein). A stable universe can only be obtained by use of a feedback system. One may offer the theory that since the universe is highly chaotic (in the technical sense), contains black holes (which affect curvature) and has intelligent life it has the necessary components of a feedback system (detector, amplifier, corrective effect) and may eventually acquire one once we have learnt how to play our part. The theory that the universe is optimised for this condition is an ID theory. It is testable - the optimisation can be checked and proved (or more probably disproved). Within any physical theory of this type the optimisation formula is the only representation of ID - essentially the formula is the ID, anything else is speculation and the ID would have a similar function to any other natural law. The only difference being that it is intentional in the sense that it is goal directed - the effect precedes the cause.
|Date: 2005/12/11 22:41:10, Link|
Natural variation within species is present at all times including such times (the majority) when speciation is not occurring within a given species. Therefore it is not presence or absence of natural variation that causes new species.
Natural variation occurs as a result of changes occurring within individual members of a species. Therefore the amount of natural variation occurring within a species is directly proportional to the number of members of that species.
The probability of any species giving rise to a descendent species is virtually independent of the population size. This can be seen from:
a) the fossil record
b) the evolutionary tree with estimated populations for each node
c) co-evolution of species with their far more numerous parasites, symbionts and pathogens.
From Lemma 2 and Lemma 3. There is no correlation between the amount of natural variation within a species and the probability that there will be a descendent species.
Note this lack of correlation applies over more than 24 orders of magnitude of population size and is therefore exquisitely precise.
Natural variation plays no part in the origin of species.
|Date: 2006/03/20 12:02:52, Link|
A heretical alternative, non-neo-Darwinian, theory of the evolution of new species.
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.
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.
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.
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.
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
|Date: 2006/03/20 12:08:08, Link|
Sorry, the tail end of the listing got dropped - here is the remainder.
Evolution is allowed to occur at radically different rates at different times.
There is a direction to evolution, although it is from disaster, not to anything.
The fallacy of the claim of neo-Darwinism as the origin of species
Neo-Darwinism is, for some reason, widely held up as a proven scientific explanation for the origin of all species, as opposed to merely being an observed evolutionary mechanism with a possible occasional ability to create a new species. The basic extrapolation from observed genetic changes to new species is totally fallacious as can be seen by applying the same logic to a different subject: Tides are a change in water level. Rain can be observed as a ubiquitous phenomenon. Following rain observation shows that puddles, rivers and lakes show changes in water level. The sea can be considered to be a sort of large lake and given enough time rain will therefore account for any nominated change in sea level. Therefore tides are caused by rain. ?? The disproof of a silly argument of this type is simple, one merely points out that there is no agreement or correlation between the type of change that would be expected from rain (very slow and uneven in rate) and the characteristics of tides, which occur in less than a day and are totally predictable so that I can get tide forecasts for Castlepoint with a simple web query. Exactly the same technique may be used for neo-Darwinism. The age of the earth is known, the rate of change of species may be estimated from observation of known species, either fossil or living and in neither case is it remotely near fast enough for the aggregate changes in evolution of, for example mammals or birds. Evolution has as its converse extinction, which rarely takes longer than a few hundred years so evolution of new species must occur in significantly less than this time, a conclusion amply confirmed by the fossil record. The most effective statistical objection, mentioned earlier, is that neo-Darwinism is based on random changes originating within the genes of the source species and as such the probability of sufficient change accruing to produce a new species must be directly proportional to the population size of the source species, since each member contributes its quota of changes. Nothing resembling this statistical characteristic is observed in the evolutionary record. Any student of evolution will be aware of other objections to this peculiar theory. The origin of species, as is admitted by intellectually honest biologists, must lie predominantly with some other mechanism.
Evolution occurs because some changes to the heredity of organisms make them more likely to leave descendants. Changes of different type and magnitude have different evolutionary logics. In particular changes of a magnitude great enough to be a challenge to the survival of the intact organism are associated with their own distinct “survival of the fittest” selection criterion quite different from that applying in the case of continued survival in the absence of large changes. Large changes select for organisms able to survive large changes. For organisms able to handle large changes an additional evolutionary mechanism becomes possible. Where an organism suffers a catastrophic change in its environment there are normally no available options within its immediately adjacent “gene space”, neo-Darwinian evolution having placed it at a local optimum. The nearest survivable point in “gene space” is at a distance that can only be bridged by a substantial gene acquisition. Any organism that happens to have a tendency under catastrophic conditions to incorporate foreign DNA, rather than eat it, will have a chance of bridging the gap to a survivable configuration and will therefore, on average, leave more descendants. Multiple catastrophic events over geological time reinforce and refine this tendency so that it eventually becomes the dominant species-producing evolutionary mechanism. Evolving is something organisms intermittently do, not something that happens to them. Heresy!
|Date: 2006/04/03 12:55:59, Link|
Here is my $0.02 worth.
My normal position on scientific subjects is attempting to explain why the silly idea is silly. e.g. Planting by the phase of the moon makes no sense because a) if you calculate the forces involved they are far too small and b) if it really did have an effect then you would expect at least some flowering plants to have synchronised their flowering and seed production with the phase of the moon. I am familiar with and can and do work pro-science.
On the subject of ToE I find myself in the opposite role
in that what I observe in the world does not at all agree with what I expect from what I understand of evolutionary theory. In principle this might be because of a deficiency in my understanding of evolution, as many, especially lay, versions of theories contain serious logical errors (I have yet to encounter a lay version of black hole theory that is not logically inconsistent). So,if nothing else, an understanding of the queries being made tells you something about the quality of the teaching. However, when I raise my concerns there are three principle responses in order of frequency:
a) abuse, I must be stupid not to see the received wisdom. I must be an IDer (I'm an atheist for Murphy's sake) etc.
b) an attack on my point of view based on some minor essentially irrelevant detail. On the receiving end the impression one gets is that the post has been made as "here is something that can be interpreted as an error, therefore everything the guy says can be ignored".
c) a reasoned criticism of an incorrect point of view that I am totally unable to account for as a possible interpretation of what I have written, followed by an explanation of a related issue which is often very similar to what I though I was saying in the first place.
There is something wrong with the communication process on ToE. Frankly I can get better engagement with visiting Jehova's Witless (although they do not like the idea that the bible as a compendium assembled by Caesar's committee to support Caesar's views an giving special prominence to one of Caesar's citizens (Paul) constitutes something of Caesar's not God's and promptly leave). I grant that there are a number of silly ideas based on religion or simple misunderstanding. However there are a number of serious issues in ToE where the response resembles pseudoscience rather than science. This is not just a personal opinion, refer to works on philosophy of science for similar, authoritative views.
An example of this suspect response can be seen in discussing the fossil record. There is a major problem classical ToE in that the fossil record exhibits a very noticeable granularity and species changes below a fairly large threshold simply do not appear, even in materials like chalk which preserve an almost day-by-day record. I have yet to see any pro-neo-Darwinist discuss this subject without, within one paragraph, referring to the issue as "missing fossils" and changing the subject to the totally different one of whether there are series of fossils and whether the gaps in the series can be explained. You can actually see the mental blinkers going on.
So some of us "kooks" out here do believe in science, logic and basing theories on data. We think we have an obligation to attempt to enlighten those who are unable to understand and follow the basic principles of science. This is especially true when, as appears to be the case, the majority of workers in a supposedly scientific subject come into that category.
|Date: 2006/04/03 16:46:47, Link|
Shi is, I think incorrect in describing his data as the best fact disproving Darwinism.
First you have to define Darwinism. If you take it as including the general ideas around the "central dogma", random changes in the individual DNA of organisms resulting in variant alleles that subsequently get selected according to the tendency of the possessor to leave more descendants then there are several candidates for facts disproving Darwinism.
The basic process in evolution is going from one species to zero, one or more successor species. The mechanism that achieves this inevitably leaves some statistical signature in the distribution of genetic information and species. Shi is correct in observing that a distribution found does not match that expected under neo-Darwinism.
I still think the best example of a mismatch between theory and observation in distribution lies in the relationship between a new species and the number of members in the parent or source species. If one million rabbits can produce one new species in one million years then one hundred populations of a hundred rabbits should produce one hundred new species in the same time. All different because it takes several genetic changes to get enough change for a new species and the number of combinations of changes possible vastly exceeds the number of rabbits (or any other species). The statistical effect is to make it far more likely for a numerous species to leave a descendant species than a scanty species. The expected distribution of species for neo-Darwinism would have almost all new species having as their predecessor one of the most populous species in the previous round of evolution. If, however, you assume that the major genetic changes originated outside the genome and were transferred by some form of lateral gene transfer then the number of possible successor species is limited to those that can be formed using new genes available in the environment and that may well be a fairly small number. In this case, as long as there are more of a species than available genes the actual number of individuals in the species is irrelevant and the new species may form with equal probability from and size of source species. There is no doubt that the second scenario is a far better statistical fit.
As I have pointed out before, there are lots of statistical indications suggesting that new species formation is predominantly a matter of gene transfer and the observed natural variation just a red herring.
|Date: 2006/04/05 13:56:34, Link|
Chris Hyland - you did not read my note carefully enough. My comment applied specifically to what is being taught. Several sources, including Wikipedia, specifically state "evolution is a change in the relative frequency of alleles". As a statement about evolution it is clearly false. As a statement about current evolutionary theory it is, at best, seriously misleading. It is probably true that all textbook examples of present day evolution are examples of changes in relative frequency of alleles. Antibiotic resistance provides clearer examples of evolution but the process does not conform to neo-Darwinian principles and they are therefore not used as examples.
Henry - you are quite right about evolutionary theory and probability. Mathematical probability theory does exist and is a well defined subject. I suggest you acquire some familiarity with it should you feel any urge to do any real science. The word "random" does appear in evolutionary theory and therefore probability theory does apply. If the chances of getting a six on a throw of a dice is one in 6 then, on average if you throw the dice six times you will get one six, if you throw it six hundred times you will on average get 100 sixes, not as you believe only one. Evolutionary theory states that beneficial changes arise through rare chance events. It also states, as you note, that the fewer the number of chance events the greater the change of a random beneficial outcome. This illogical conclusion is sufficient to get evolutionary theory classified where it belongs, with astrology, iridology etc. Sorry, if the options are believing 2+2=4 or neo-Darwinism I will always opt for the former. Until such time as someone can explain evolutionary theory in a way that is not incompatible with mathematics I am not going to believe it.
|Date: 2006/04/05 17:37:09, Link|
One of the issues I have a problem with is the US paranoia about Creationism. Locally (New Zealand) it is not a burning issue - sure we have a few Creationists and other oddballs, but they do not form a significant or powerful lobby so there no for/against evolution battlefield. I am not coming from anywhere near a creationist viewpoint and keep running into someone else's war. My instinctive reaction is to take sides against anyone who says " if you are not for us you are against us" whatever the issue.
One way of looking at what I am saying is to consider the "aha" factor. An example, when we move to our current rural location we planted some walnut trees. These do not like standing water round the roots so we planted them on the ridgeline, thinking, we thought at the time reasonably, that since water flows downhill the location would be reasonably well drained. We now know otherwise. The reason the ridgeline is the ridgeline is that is where the particularly gooey, sticky, water retaining clay was, everything else washed away. "Aha".
I enjoy reading science subjects because I like the "aha" of finding out how something counterintuitive actually works. Alone amongst the reasonably solid sciences is evolution which never gives me an "aha" feeling. The process remains just as counterintuitive no matter how much I read and I am never able to say "that is how you calculate the correct answer". It can't be just my intuition because I have done some quantum mechanics and there is nothing to beat that for counterintuitive effects but I still get "aha" from it. Furthermore nobody ever publishes an example of the correct calculations. It is always "once upon a time" or "given enough time" or something else sufficiently vague to prevent numerical analysis. The argument that further study will make things clearer only works if some progress can be felt - astrologers and other crackpots all insist that their subject can only be really understood by initiates.
Anyway, as a result of planting trees I got to notice a strange phenomenon that resembled "saltation" to use your term. So I thought about it. I eventually came up with my own version of evolution, seriously different from neo-Darwinism but perfectly consistent mathematically and biochemically. This theory does give me "aha" feelings. This theory does give me correct calculations. So I say to some biologists "excuse me, but are you sure you have got it right, this approach seems to work better?" And I get accused immediately of being stupid religious crank who has not learnt or understood his lessons correctly.
Brief summary of alternative theory.
a) Although mutation is generally detrimental when an organism is far enough from a survivable equilibrium the potential advantages of mutation get to outweigh the disadvantages, a fatal mutation does not matter if you are going to die anyway. You can obtain confirmation of this point by checking the published liturature - seriously stressed bacteria increase their rate of mutation, selectively.
b) Lateral gene transfer is an especially efficient way of getting additional mutation in a short time scale. The potential advantage of getting a gene from something that thrives in the environment is significant and the worst of the bad mutations have already been filtered out. Mostly it is one #### of a lot of evolution in one convenient package so any organism that does it under the same conditions as the bacteria increase their mutation rate will tend to, on average, leave more descendants.
c) The process is self reinforcing in that any organism that is particularly good at recognising the right conditions and reacting to them will tend to leave more descendants that an indifferent player.
d) It works for all species as they are descended from bacteria which had the mechanism and still retain, albeit sometimes intermittent, contact between all their cells and the bacteria which produce bacterial plasmids.
Now, what is stupid or religious about that?
|Date: 2007/08/21 05:33:53, Link|
Caution, the following argument assumes at least some slight familiarity with logic. For example, given the following syllogism, you should no difficulty in recognising it as being logically faulty:
All Darwinian evolutionists are mammals.
All donkeys are mammals.
Therefore all Darwinian evolutionists are donkeys.
Many Creationist arguments only gain plausibility because of major deficiencies in evolutionary theory. Remove the deficiencies and their arguments lose plausibility.
There is one common logical error in many presentations of evolutionary theory, and this proposal is directed to that specific error. With a bit of cleaning up the argument can be expressed as:
The patterns of inheritance among fossils and between species shows that species have been produced by an evolutionary mechanism.
Individual variation plus natural selection gives an evolutionary mechanism.
Therefore the evolutionary mechanism that produces species is the evolutionary mechanism formed by individual variation plus natural selection.
The astute reader will recognise this as being a simple variant of the illogical argument with which I introduced this discussion. Indeed many of the more careful of the writers on evolution are careful to avoid this faulty argument. However many accounts of evolution, and much of the discussion in forums like this appear to assume the two evolutionary mechanisms are the same. This is strange since natural variation plus natural selection has been fairly fully explored as neo-Darwinism and is predominantly a fairly slow, gradual, reversible change in the proportions of alleles within populations of species and the evolutionary process that produces new species appears to be an irreversible, saltatory process that adds genes to a genome.
The issue can be settled as there are at least two very distinctive features of the two mechanisms which make it clear that there are two different mechanisms, which cannot be identified as variants of a single mechanism. The first is the appearance of major new families of organisms, such as insects. The neo-Darwinistic mechanisms must proceed according to the sequence:
The appearance of one or a few individuals forming a new family
Proliferation of the species represented by the individual/group.
Divergence of the species.
The actual fossil record in every case indicates a different sequence:
The appearance numerous wildly diverse species in a new family.
Selection of the most promising species within the new family
Divergence from this selection.
It is easy to come up with a natural evolutionary mechanism that will give year zero diversity for a new branch of the evolutionary tree. It is not possible to modify the neo-Darwinian mechanism to achieve such year zero diversity.
The second difference is a simple case of statistics. Consider three populations of a species, one with a thousand members, one with a million and one with a billion. Whatever mechanisms one assumes for natural individual variation it is obvious that however many genetic variants arise within a thousand individuals in a year the number will be a thousand times greater for a population of a million and a million times as great for a population of a billion. Moreover variants do not last forever and usually eventually become predominant or dropped. If it takes a thousand years to resolve a gene as dominant/lost in a population it will typically take 2 thousand years for a population of a million and 3 thousand for a population of a billion ? so variant genes hang about for longer in large populations. Also, for any characteristic of the species a population of a thousand will have most of its members near the average with only a few individuals found at two standard deviations from the norm. The population of a million will have a few thousand members at two standard deviations from the norm and even a few at four standard deviations. The population of a billion will have a few million at two standard deviations, a few thousand at four standard deviations and even a few at six standard deviations. This comparison can be extended out to species with populations of trillions of trillions.
In the event of a change in the environment which of these populations will be most likely to have a variant group able to survive in the new conditions? Obviously the larger population ? it covers a far greater ?gene space?. This gives a definitive statistical test for evolutionary mechanisms based on individual variation. For any reasonably large sample of species produced by individual variation (and we have a sample in the millions) when, for each species, you look at the immediately preceding species in the evolutionary sequence it will, on average, be one of the most numerous species of its cohort. The actual pattern produced by the natural species-producing mechanism could hardly be more different ? hardly any species are directly descended from any of the most populous thousand species and the majority are descended from a species not even in the most populous million of species. This bit of statistics makes it absolutely certain that the majority of species are not produced by any evolutionary mechanism using natural individual variation as its source of genetic change. Basically neo-Darwinism is a lottery with the individual as the ticket, and observation shows that far too many species are winning descendant species than is accounted for by their ticketholding.
So this is my simple proposal:
Stop making the daft claim that all species are produced by neo-Darwinian evolution ? hardly any are. Research and write up both mechanisms and make it clear which mechanism has what effect (to a first approximation neo-Darwinism is alleles and tuning, the other is gene addition and new species formation). You are left with an evolutionary theory without the gaping holes by which Creationists obtain credibility.
From the point of view of most of my readers there will be one significant objection to this proposal. Few, if any, of you will have the slightest idea how the second evolutionary mechanism works. Be brave, have a go at working out how the second mechanism works. There may even be more than one answer. Some comments from my own analysis: First the good news, it is actually a simple mechanism that can be reasonably easily seen, demonstrated and understood. You quite probably already know all that is necessary to understand it. It provides natural explanations for most of the problem areas in evolution and the arithmetic gives the correct answers. Second, the bad news, it has, apart from being a natural evolutionary mechanism, absolutely no resemblance whatsoever to neo-Darwinism. This is hardly surprising as the driving source of genetic change is not, and cannot be, individual variation. This means that if you maintain a ?drowning man? grip on examples, principles and rules which work for (but only for) neo-Darwinian evolutionary mechanisms then you will have extreme difficulty in understanding the species producing mechanism.
If you can?t find an answer, or wish to check if yours is the same as mine, check out www.nsof.co.nz.
|Date: 2007/11/15 16:24:37, Link|
A Layman’s Guide to Evolution
Evolution is an essential, natural process like photosynthesis, eating and reproducing.
Organisms that fail to adapt to changing circumstances become as extinct as those that fail to fund sustenance or fail to reproduce.
There are three and only three conditions required for active goal-directed evolution:
1) There must be, at the time of evolution, a perceptible local indication of the advantageous direction to evolution that can act as a stimulus.
2) There must be a possible response behavior by the organism that will move its genome in the beneficial direction.
3) The circumstances must occur with sufficient frequency for those organisms with the appropriate response to the stimulus to be preferentially successful.
There are several natural situations where these conditions are met.
The most important, and most easily understood, arises as a result of changes in the environment.
Where there are two species in the same environment, one of which is thriving and the other failing there is a perceptible direction for the failing species. The success of the thriving species is a consequence of it having a genome more suited to the environment and therefore movement by the failing organism toward the genome of the thriving species is likely to be beneficial. Note that it will frequently be true that a thriving organism has a genetic mechanism to neutralise a local toxin or release a local resource.
There is a mechanism, lateral gene transfer, by which a failing species can acquire portions of the genome of a successful species. (This is known to be predominantly a behavior of stressed species and thriving species are frequently profligate in genetic material).
This situation arises with sufficient frequency for the required stimulus response mechanisms to be reinforced.
Evolution of species is the consequence of numerous environmental changes which disturb the relative ranking of species and are followed by attempts by those species placed at the bottom of the heap to reposition themselves by acquisition of the genetic quirks that have placed those currently at the top of the heap in that position. Hence the general trend toward complexity.
Neo-Darwinism is unnecessary and irrelevant.
If you have doubts about this look at the data, go and check the distribution of genes. A particularly interesting example concerns those genes acquired by humans since they diverged from the other ape families. According to neo-Darwinian theory these should be found only in humans whereas many are also found elsewhere, especially in coral. And if you are puzzled why it is coral with these genes go and read up aquatic ape theory and note that coral is an indicator species for climate change.
Sounds good to me.
|Date: 2009/06/16 03:36:49, Link|
An Evolutionist’s Guide to Some Darwinian Errors and Misconceptions
This one is for those that can see the evidence for evolution but cannot swallow the Darwinian myth. Were Darwinism a real scientific theory that explained the origin of species the numerical predictions would match measurement. One of the few relatively unambiguous measured quantities for a species is its gene count. From the known rate of “random” genetic change it is possible to estimate the average rate at which novel useful genes should appear in the world, but no published estimate comes close to the observed and necessary rate of several per year. Worse, for a theory based on “random” change, these novel genes are known almost exclusively from the miniscule proportion of living things comprising the “advanced” species. Darwinism provides no clue how organisms with a couple of thousand genes and a few hundred genetic mechanisms evolved into a wide range of complex organisms with a few tens of thousands of genes and a few thousand genetic mechanisms at a rate that is astoundingly consistent in the face of factors like plant/animal, tropical/polar, marine/terrestrial and above all population size. It is a stunningly non-random distribution with individual species accumulating genes at rates many trillion times higher than the already suspiciously high average.
In the absence of a usable numeric formulation of evolution the Darwinists have been forced back on word based descriptions. This results in misconceptions arising from different meanings of words. Is a tiger a cat? The answer depends on which meaning of the word “cat” is being used. Many, if not most, words have a number of significantly different meanings. In real science a definition is a pointer to a theoretical term in a mathematical model and the model defines the meaning. Depending on your viewpoint Darwinism is either a con or a farce depending on misleading meanings of words and hidden changes in meanings of words.
So for evolution:
A species has predecessor and successor species that, of necessity, have somewhat different genetic messages in their DNA.
There is, in some sense of the word, “variation”.
Genes and genetic mechanisms do not come with instructions so there is a large element of trial and error in determining viable changes.
The process is, in some sense of the word, “random”.
Not all variants from a species survive.
There is, in some sense of the word “selection”.
The process conforms to the scientific laws of nature.
It is, in some sense of the word “natural”.
Darwinists say – look we have a theory of evolution based on random variation and natural selection. What more could one want? The answer, apart from accurate predictions, is that one could ask for the meanings of the words in Darwinism to be appropriate to the meanings in evolution. Have they got the meanings of those four words right? The answers are: No, No, No and No. This is a good starting point for exposing Darwinism as in the description “random variation, natural selection” each word encapsulates at least one piece of misinformation.
Darwinists would have you believe that evolution and biology were matters of genes. In reality a gene is actually only a component, like a transistor, resistor of capacitor. Evolution and biology are mostly matters of genetic mechanisms – a set of genes interacting to achieve a function similar to that of an electronic circuit. Only rarely does a single gene serve a purpose without support from other genes. Evolution covers all the processes that result in new genes, transmission and collection of genes, their assembly into genetic mechanisms, and the adjustment of those mechanisms to the requirements of living in a particular environment. There are many processes that affect one or more of the steps in assembling, tuning and deleting genetic mechanisms.
Variation is a collective term for all the variety of processes that modify a genetic message and the genes and genetic mechanisms. It covers a range from common radiation damage and transcription errors through to complex interactions like retroviruses and exceptionally rare phenomenon like acquisition of mitochondria and chloroplasts. The effects of radiation damage are different for external radiation and decay of a carbon 14 atom in a stretch of DNA. This tells you nothing about other forms of variation. There is a slightly different bias in transcription errors between bacterial and non bacterial species that allows the probable source of a novel gene to be distinguished. This tells you nothing about other forms of variation. The rate of transmission of AIDS depends on sexual preferences. This tells you nothing about other forms of variation. And so on. The word “variation” behaves like “product” for which totally different rules apply to mines, foundries, orchards and airlines. Apart from changing the genetic message there is nothing significant in common between forms of variation. They all have their own rules and characteristics. They vary widely in every characteristic and the type and magnitude of the change to the affected species.
Evolution meaning: A ratbag collection of phenomena with the only common factor a change in the genetic message.
Darwinist meaning: The small subset of common changes that essentially correspond to changes in the tuning of existing genetic mechanisms.
You could write a book on the peculiar meanings that have, at one time or another, been ascribed to this word. The word is so frequently misunderstood that it should be avoided, as it is in most sciences. A favourite trick of Darwinists is to introduce “random” under one, often unconventional, definition and then reuse it with a different meaning. Start with a dictionary. There are two families of meanings for the word “random” - colloquial and technical. For the purposes of science the situation is simplified. The test for correctness of a scientific theory is agreement between theory and prediction/measurement. For each meaning of the word “random” in your dictionary ask the question “How would I use this definition of ‘random’ to obtain a predicted value which could be checked against observation?”. Only the statistical meanings of “random” pass this test. This is not to deny the usefulness of other meanings, only to say that if you wish to use one of the colloquial or philosophical meanings of “random” it is preferable to use a different word or phrase that exactly and unambiguously encapsulates the particular intended meaning. Better still if the meaning can be tied to a body of science. There is a characteristic of evolution that an arbitrarily small variation early in an evolutionary sequence may lead to arbitrarily large consequences in descendant species and their companion species. The technical term “Chaotic” may be used to express this far more clearly than “random” and has the advantage of tying the intended meaning to established Chaos Theory.
The real problem with “random” lies a little deeper. If you are familiar with statistical theory you will be aware that there are two different contexts for discussing randomness which have slightly different formulae. In the context of evolution the distinction is crucial to an understanding although Darwinists carefully avoid making it. The distinction can be seen clearly in examples like Lotto where bets are placed on combinations of numbered balls and the game battleships where one attempts to identify and sink an opponent’s ships placed on a grid. In these cases there is an objective that can only be achieved through a randomised process. Predictability would defeat the objective. However in each case there is a party to the transaction who has control over it and has the power vary the rules for the randomising process. In this case the randomness is encapsulated within a set of rules. In contrast the raw form of randomness seen in radioactive decay and noise in communication where the rate and type of random activity is dictated by laws of nature. It is the fact that the owner of a random process can have exact knowledge of the random process which must otherwise be inferred that leads to the slightly different statistical formulae. It is in the interests of a Lotto operator that the biggest prize is usually but not always won leading to jackpots and they will occasionally change the options offered to achieve this. It is the aim of a “battleship” player to locate the enemy units and if they suspect their search algorithm is becoming stylised to their opponent’s advantage they may change it. The difference between the two cases may be summarised by the possibility of asking the question of a random process “Are the parameters of the random process appropriate to an objective or should they be changed?”. If change is possible then it is an encapsulated random process. If it is not possible then it is a raw random process.
Darwinists persist in regarding all random processes as raw although it is abundantly clear that certain crucial changes are encapsulated. The best documented cases come from antibiotic research. Bacteria exposed to antibiotics, or any other toxic material, have an increased rate of variation. Note first that the increase in variation is determined by the genetic mechanisms in the bacterium, not external circumstances. It is the bacterium that determines when the increase occurs and when it ceases. There is a balance between the advantages and disadvantages of increased variation and it is the bacterium that determines the actual rate. The factor that unequivocally marks the process as encapsulated randomness is the particular type of variation that increases. A typical population size and a specific increase in rate gives a number of random probes that can be made into a pool of genetic variation. For different forms of genetic variation there are differences in the proportion of beneficial variations. The only forms of variation for which bacteria increase rate are those for which the expected number of probes required for location of a beneficial variation is less than the number available to the species exposed to the toxic material. If the odds against a useful beneficial variation are a trillion to one and a population of bacteria increases their rate of mutation to the point where there are a few trillion probes they will succeed in finding a mutation that allows the species to continue. The overall outcome is almost totally predictable. The particular genetic solution found is not predictable, the particular individuals who will gain a genetic solution are unpredictable, but the fact that some individuals of the species will gain a genetic solution is predictable. This is a managed random process, not a raw one. Functionally it is a distributed genetic search engine (DGSE). There are several different DGSE’s mining different strata of genetic variation. Actual genetic search engines tend to be more sophisticated than this simple description suggests. It is these genetic mechanisms, the “Googles” of the evolutionary world, that Darwinists do not want to know about and do not want you to know about. It is these mechanisms that allow species to “cherry pick” a far higher proportion of helpful mutations than would be expected from a raw random process.
Evolution meaning: Any of a wide variety defined situations, encapsulated or raw, where a probability can be assessed.
Darwinist meaning: Any meaning that avoids discussion of distributed genetic search engines, or, if possible, any other probability calculations.
Who can argue with Natural? There are several different takes on the word. One refers to ordinary common situations. Another refers to compliance with laws of nature. A third distinguishes between human activity and the natural environment in which it occurs. Geologists fell into this trap with Uniformitarianism – the idea that all geology could be explained through processes visible today. It soon became apparent to them that rare processes like ice-ages and large meteorite impacts had to be factored in. These are processes and situations that, because of their rarity, are seen, in one sense of the word, as “unnatural”. Every thing alive today has an evolutionary chain of descent going back billions of years to the earliest forms of life. As everyone knows a chain is only as strong as its weakest link(s). These weakest links are the points at which the species changes and they are rare. The time scale is tens of thousands of years. In that time scale there can be fairly extreme variations in nature. The correct use of “natural” includes the rare, one in ten-thousand year phenomena, the Darwinian use of “natural” considers only the everyday phenomena. There are no grounds for the Darwinist assumption that observation of day-to-day changes will identify the dominant factors in one in ten thousand year phenomena.
Evolution meaning: Referring to any of a wide range of circumstances that occur in an evolutionary timescale.
Darwinist meaning: Referring to only those circumstances that occur commonly within a narrow range of time and location.
When you select a sports team, jury, present for a child or whatever you end up with a team, jury, present for a child or whatever. The process which determines which members of a species leaves descendants and which do not leave descendants can and sometimes does end up with none. One of the most distinctive features of the fossil record is that the first examples of a new species are almost always roughly contemporary with the last of the predecessor species. In these cases no members of the extinct species was selected to leave descendants of that species. The descendants, forming the new species, were filtered out using a different measure, although still a “natural” one. The deficiencies of the concept of selection have been noted and many accounts of evolution correctly point out that the essential issue is the differential probability of successor individuals with the individual’s genetic heritage. The simple model of selection has to modified not only by radical changes in environment but also by peculiarities of genetic transmission like selfish genes (or more correctly genetic mechanisms) and the group selection shown in social insects and distributed genetic search engines (DGSEs). Note carefully that in the case of a DGSE it is not the species that is selected, it becomes extinct. It is not the individuals that are successful, they are basically determined by a lottery. What is selected is the genetic mechanism that leads to a new species carrying on the genetic line and containing the evolutionary genetic mechanism.
Evolution meaning: The filtering arising from any differential reproductive success of any pattern of genetic mechanisms at any point in the evolutionary process.
Darwinist meaning: The filtering arising from the differential reproductive success of specific variant individuals within a narrowly defined environment.
There are other areas where Darwinists use language misleadingly.
Survival of the fittest
Anyone who has followed the Darwinist debates will be aware of the empty circularity of the term “fittest”. Some of the objections to the concept of “fittest” have been mentioned under “selection”. There are other objections to the term.
One of the most important is that under conditions of extreme “selection” where only a variant of a species can survive “fittest” is determined by the ability of the individuals in the species to access appropriate sources of genetic change and also to remain functional during and after the associated physiological changes associated with the genetic change. Over the totality of evolution there is extreme filtering for species that can manage such changes without disruption. The changes that some insects go through within a lifetime – egg, larva, pupa, adult – are far greater than are normally found in the progression of a species to its successor. Darwin noted this “It is not the strongest of the species that survives, nor the most intelligent that survives. It is the one that is the most adaptable to change.” Distributed genetic search engines involving lateral gene transfer can assemble novel genetic mechanisms that radically alter the individuals’ physiology and only those species with internal control mechanisms that can survive such radical overhaul will leave descendants.
A second major criticism of the implications of the term “fittest” is that all species, especially plants, are more affected by excesses or deficiencies of critical chemicals, especially water than by any other environmental factor, such as predators. It is very clear in the case of bacteria, but over all of evolution a better case can be made for the driving environmental changes being essentially chemical in nature than for the “athletic” changes suggested by “fittest”.
Given Long Enough
All theories involving randomness and combinations have a theorem that states that if a combination of circumstances is possible then given enough time it will occur. These are theoretical curiosities of no practical importance. If you stir some milk or sugar into your coffee then the molecules of milk or sugar get randomly distributed in the coffee. One of the possible random distributions has every molecule back where it started, and this is a physically possible state since it is what you started with. However it is possible to calculate how long it would be before such a rearrangement could be expected. The answer is many, many trillions times the age of the universe. In practice it never occurs. Air has 20% oxygen molecules randomly distributed so it is possible by chance to breathe a lungful of pure oxygen – so long as you keep breathing for many, many trillions of times the age of the universe. In practice it never occurs. There are not that many distinct genes, most are duplicated among many species. New ones occur only a few times per year. So one can calculate how long it would take for humans to acquire those genes that distinguish them from other apes. Humans were about a trillionth of a trillionth of the world’s population of organisms so the expected time is in the range of a trillion, trillion years. The universe is only about 13 billion years old. Yes it is true that given enough time humans could have evolved from a miocene ape by Darwinian evolution. Since the time required is impossibly long it is equally true that in practice that could not have occurred and some other explanation is required.
The basic error contained in arguments based on “long enough” is the assumption that if some amount of time; four billion years of evolution, 650 million since the Cambrian “explosion”, or 65 million since dinosaurs is all the time available; then it must be “enough”. There is no upper limit to the numbers that can be written in front to the word “years”. There are plenty of combinatorial phenomena for which the universe is simply too small and too short lived for them ever to occur. The argument relies on the times seeming unimaginable to an audience. In fact 650 million is not a particularly large number, it is about the number of bytes on a CD and far less than on a DVD, it is less than the population of China or India and far less than the wealth, measured in dollars, of the richest people in most countries.
No direction to evolution
There is a Darwinian claim that there is no direction to evolution. In just about any other field a direction is associated with a scale. There are local and global directions. This is reflected in pairs of words like strategy and tactics. There is no global direction to evolution in that there is no script or controlling “force” that pushes evolution into a specific direction. However local directions are a different matter. The most obvious and significant examples of a local direction arises when an environment changes. The effect of a change in environment does not usually affect all the species in the environment equally. A situation can arise, and often does, that there a few, possibly only one, species that thrives in the changed environment because they or it possesses a genetic mechanism that manages the deleterious effects of the change. In this case the other, failing, species have a definite direction to their evolution. If they too had the genetic mechanism they too would be more likely to survive. As everyone should be aware, in an environment changed by addition of an antibiotic that also contains a species that does have a genetic mechanism giving immunity from the specific antibiotic, those bacterial species that do not have those mechanisms respond by acquiring the mechanism. Although the actual process is relatively complex it is a simple case of a directional stimulus and a response (involving a distributed search engine) that moves the species in the locally indicated direction.
Note that this is not a peculiarly bacterial phenomenon. Advanced species of necessity have internal fluids to provide the necessaries of life to internal cells. Since these fluids are nutritious they periodically get bacterial populations. This leaves all cells of an individual of the advanced species with the same access to genetic material from another species that is enjoyed by bacteria in the case of antibiotic resistance transfer. Since advanced species are descended from bacteria with the ability to acquire genetic material there is the expectation that such a useful ability would be retained. The distribution of genes between species makes it abundantly clear that this is actually the case. The number of unfamiliar genes in a bacterial species that evades an immune system is so low that a DGSE operating in this area can be successful with very small populations – in the range of thousands.
There is an obvious objection to Darwinism that the bigger the evolutionary change the less plausible the Darwinian explanations become. Many are laughable. A Darwinist response is to claim that there is no fundamental difference between micro evolution (which works) and macro evolution (which does not). The argument is ridiculous – there is no specific sum of money at which one becomes rich therefore there is no difference between rich and poor? Any plausibility of the case depends on the differences in the characteristics of the evolving species – the phenotype. Butterflies and their caterpillars have the same DNA differently expressed. Small changes in genes can radically affect gene expression and the consequent external form of an organism. There is no natural boundary to the size of changes to the phenotype.
At the level of the genes there are two quite different distinctions that can be drawn although the boundaries are similar. Firstly one can note the difference between changes in an organism that arise from adjustments made to a genetic mechanism and those arising from the acquisition, by any means, of a novel genetic mechanism. A bacterium that is antibiotic resistant because of a novel genetic mechanism looks identical to one without the mechanism but the bacterium is significantly different. At the genetic level one can therefore define micro evolution as that involving variation within an existing genetic repertoire and macro evolution as that involving changes to the number of genetic mechanisms in the repertoire.
A more enlightening distinction is based on the extremely wide variation in different types of genetic change. For any given type of genetic change within any given size of population there are two time scales. The first concerns the rate at which potentially useful mutations arrive in the population. The second concerns the typical time scale taken for a novel mutation to be resolved and become either rejected or common in the population. Very small changes, like allele changes occur very frequently and usually confer small advantages that typically take many generations for the small selective advantage to achieve resolution. Conversely very large changes, like the addition or loss of a genetic mechanism, occur very rarely but confer a large selective advantage that often takes only one generation to achieve resolution. In the former situation the arrival interval is less than resolution time and the population will contain a diversity of mutations in the process of resolution. In the latter case the population will usually contain none of the mutation variants and each change will be resolved individually as they occur. A central feature of Darwinian theory is that a change in environment changes the relative advantages of variants essentially resorting their respective advantages. This can only happen for those mutations for which arrival times are less than resolution times. It is not possible to usefully sort nothing, or one single item. This divides the mutations into two classes, sortable and non-sortable. For sortable variants there is a greater possibility of advantage if there is a wide spread in characteristics. For non-sortable variants there is a greater possibility of advantage if the incidence of the changes is synchronised with the environmental change. Thus one can use a definition where micro evolution involves smaller changes that are not synchronised with environmental change and macro evolution involves larger changes that are synchronised with the environmental change.
Evolution is about changes in the proportions of alleles.
There is a type of logical argument called “reductio ad absurdum” in which an assumption is demolished by demonstrating that an impossible conclusion would follow were it true. This is the absurdum. The number of genes in advanced species is tens of thousands more than in earliest life. The substitution of one allele of a gene by another only alters the effect of that gene, it does not change the number of genes (or even of genetic mechanisms). The logical conclusion from the initial assumptions of Darwinian evolution, as supported by the data is that a number can be made bigger by adding zero a vary large number of times. It is difficult to see how anyone could rationally support this absurdity. An irrational determination to believe in the adequacy of Darwinism is apparently stronger than any propensity for logical thought. Anyone familiar with conservation principles will see the error. If some characteristic is conserved under a transformation then any multiple of that transformation will also conserve the characteristic. For those small variations that involve only the tuning of an already existing genetic mechanism by replacing one allele of a gene with another the Darwinist model of evolution works well. It is about the only type of evolution for which it works at all. However the number of genes and genetic mechanisms is conserved in an allele substitution. The difference between a bacterium and a human is not that the genetic mechanisms from the bacterium have been tuned differently. There are thousands of extra genes. There are thousands of extra genetic mechanisms (individual genes often appear in more than one genetic mechanism). It is these extra genes and genetic mechanisms that make the difference. You can no more add a genetic mechanism by varying alleles than you can convert “the quick brown fox jumped over the lazy dog” to Shakespeare’s Macbeth by varying the font of the characters. The variations in species arising from allele substitution may be interesting in their own right but they cannot contribute to the explanation of an increase in the number of genes and genetic mechanisms. There is one advantage of this statement. If you find it as a functional assertion in a textbook or article then you know the author is unable to think rationally about the subject. This means that you are going to have to check everything they say against a more reliable source. You can chuck the book/article in the rubbish bin in perfect safety.
The unspoken false assumption
At the time of Darwin geologists were cracking down on extravagant explanations of geological formations in terms of peculiar catastrophes by adopting the principle of Uniformitarianism – that only mechanisms observable today could be used in geological explanations. The principle did not survive as it became clear that there were epochs where conditions were substantially different and factors like ice ages and large meteoric impact, not seen today, needed to be included. At the time, and reasonably, Darwin assumed that the types of variation and selection observed today were typical of all epochs in the past. Although unstated, this remains an assumption of Darwinism. However, given the statistical mismatch between Darwinian mechanisms and the characteristics revealed in the fossil record and current day distributions of species, genetic mechanisms and genes it is an assumption that is clearly questionable.
In any selection process any small scale culling will favour individuals close to an optimum and will tend to produce convergence to a norm. Conversely large scale culling eliminates the population at the previous norm and the only favoured individuals are far from the norm and this tends to produce divergence. The logic of convergent evolution is different to that of divergent evolution. This distinction provides a simple basis for their being epochs in which the evolutionary patterns differ.
Darwinism has several other cases of words being used to mislead. However the above notes cover some of the most important ones. There are two interesting issues to be settled. Can evolution of species be explained without DGSEs or something essentially the same? Can Darwinism be extended to include DGSE’s or anything essentially the same?
Are DGSE’s necessary in an evolutionary theory?
The average rate at which raw random changes occur in DNA is known. Calculation shows that advanced species have too few members for the required numbers of genes and genetic mechanisms to arise by chance. DGSEs can assemble the genes in bacteria and transfer them to advanced species at the required rates.
Darwinian evolution works best for large numbers of a species spread over a variegated environment where different variants can be concentrated and accumulated in separate locations. This can produce novel species – a well known example being the Colorado Potato Beetle. In such cases, the original species, being numerous and well distributed will normally survive and be coexistant, as is true for the Potato Beetle. For DGSEs the maximum effect occurs when all members of the species are active, that is when the species is approaching extinction. In this case the new species will usually appear in place of the original species. The fossil record has the DGSE pattern as predominant.
Where a population of a species exercising a DGSE is significantly more numerous than is required to locate a genetic solution to an environmental threat it is possible for multiple solutions to be found before the first individuals with a solution come to predominate in the population. The effect is particularly noticeable for a DGSE assembling a genetic mechanism. This situation appears in the fossil record as an essentially instantaneous appearance of several different but related novel species. There are many cases of this pattern in the fossil record. Darwinism requires a first member species which subsequently diverges. This requires the absurd assumption that in every single case there was an unusual set of circumstances that resulted in none of the steps required by Darwinism appearing in the fossil record. While the deficiencies of the fossil record could conceal a few such sequences it is a ridiculous improbability to assume that all could happen to be thus concealed.
Execution of DGSE’s involving lateral gene transfer leaves a totally different distribution of genes from that expected from Darwinism. In Darwinism every instance of a gene appearing in two or more species should be traceable back to a common ancestor. DGSEs tend to transfer genes from common bacterial species to any other species sharing the environment and in difficulties. Once transferred the inheritance path of a gene does follow Darwinian inheritance rules. The actual distribution of genes does not conform to the Darwinian expectation but appears to be what would be expected from DGSE’s.
Last, a major statistical hurdle for any theory of evolution. For any proposed source of genetic novelty there will be a tendency for more numerous populations to get more of it. It is like a lottery, more tickets, more chances of a prize. There are lots of factors that could affect the rate at which a species evolved. As mentioned, obvious factors include plant/animal, marine/land, tropical/arctic, hunter/hunted. At the current time, after 4 billion years of evolution, the number of genes in the majority of advanced species from any source fall into a very narrow band indeed. Most have acquired between 15,000 and 30,000 genes in the last 600 million years. This is a variance of less than 25% in the average rate. Any theory based, as is Darwinism, on raw random processes will predict a vastly greater spread. There are plausible DGSE mechanisms that can yield such uniformity.
Can DGSEs be fitted into Darwinism
The answer has to be no. There are all the technical difficulties associated with the differences in the required meanings for the fundamental concepts. The following issues would need to be addressed:
Source of genetic change: Predominantly internal/predominantly external
Rate of genetic change: Continuous/saltatory
Unit of change: Allele/genetic mechanism
Typical size of change: Very small/very wide range
Environmental change: Gradual/abrupt
Direction to evolution: None/a major driver
Direction to change: Reversible/irreversible
Control of genetic change: None, a selection criterion
Time for new species: Many generations/at most one
Extinction: Incidental/coupled and matched
Individuals varying: One/several
However the greatest incompatibility is philosophical. Darwinism has all species (with the occasional exception made for, of course, humans) as unwitting victims of random events, over which they have no control, which shape their evolutionary path in an arbitrary way. The addition of DGSEs radically changes the model as evolution becomes something, like eating and reproducing, that organisms do, albeit only vary rarely. Evolution becomes part of the genetic repertoire of species not something external.
So a new theory of the origin of species is required. The great advantage of building in DGSEs is that the numbers come out right and most those “mysteries” cease to be mysteries and have simple logical explanations.