RSS 2.0 Feed

» Welcome Guest Log In :: Register

    
  Topic: Overlooking the Obvious, A statistical observation on evolution< Next Oldest | Next Newest >  
DaveRAFinn



Posts: 15
Joined: April 2005

(Permalink) Posted: Oct. 30 2005,14:40   

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.


Dave Finn
Cedar Ridge

  
Henry J



Posts: 4812
Joined: Mar. 2005

(Permalink) Posted: Oct. 31 2005,07:00   

Funny, I thought the "evolutionary tree" was the signature of common ancestry.

I'm not a biologist myself, but I'd think the signature of "100% HGT" would be a single species (i.e., no genetically isolated taxa at all) with lots of varieties that sort of blur into each other. Sort of like what we see in currently living sexual species (since that is basically a form of HGT).

Okay, now I'll just wait for a real biologist to comment on the posted article.

Henry

  
C.J.O'Brien



Posts: 395
Joined: Aug. 2005

(Permalink) Posted: Oct. 31 2005,07:54   

Quote
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.

There's a lot to cover in this post, but the tidbit here is not justified by the fossil record. There are no fossil specimens "appearing... without any obvious precursor," at least not since the Cambrian. Note that finely-graded transitionals between individual species is not expected given the "coarseness" of the fossil record, but between larger taxonomical classifications the fossil record does not contain lineages that "pop up" without a related, and older, lineage being present.
Further, and this regards the entire point being made, what is the mechanism for lateral transfer between multicellular species? The transfer of material between bacterial genomes is well-documented, but I do not know of gene transfer between "higher" organisms. (Aside from sexual reproduction, as Henry notes, but that is gene transfer within a single species.)
((I am not a biologist either.))

--------------
The is the beauty of being me- anything that any man does I can understand.
--Joe G

  
The Ghost of Paley



Posts: 1703
Joined: Oct. 2005

(Permalink) Posted: Nov. 01 2005,12:31   

Quote
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.


You can say that again. Evolutionism is an ontological theory stating that mind is subordinate to matter with the obvious implication the universe itself it fundamentally amoral. There is no evidence for this belief, abd a great deal of evidence against it, but it exists because evolutionists want to justify their immoral behavior.



Quote
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.


Of course! All of the excuses for why things aren't like the way Uncle Charles said they were supposed to be.

Quote
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.


Maybe this sort of thing is all there is, and all "evidence" for relationships among the different kinds our Father hath created are nothing but figments of febrile evolutionistic imaginations. It's just like seeing the virgin Mary in a peanut butter jar. If a man is determined to find a pattern, he does!



Quote
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.


Again, your like a mental patient seeing Mary in a peanut butter jar, and trying to eat all of the peanut butter that is not the Blessed Virgin as "proof" of his find!

Quote
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


In a moment of sanity, you admit it is all a crock. There is nothing there but peanut butter.

Quote
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.


Oh, where to begin. To claim that humans share an evolutionary history with fleas, mice, and gut bacteria, and Miocene apes is an egregious act of question-begging. Furthermore, you fail to take into account the massive difference in the level of complex specified information(CSI) contained in a human versus a bacterium. Even if one admits that bacteria evolved without intellgent design (This was already proven impossible by Dembski and Behe!;), to think that humans could is utterly absurd. Humans have a level of CSI that is almost immeasurable. How do you compare bacteria changing themselves with the aid of intellegent design (genetic engineering) with humans suddenly evolving complete with a moral sense and a knowledge of God without any intellegent input? The inanity of evolutionists never ceases to amaze me!


Quote
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.



Exactly how does horizontal gene transfer increase CSI? At least Neo-Darwinism provides a mechanism, albeit a crude one. Did everything evolve just randomly?


Quote
Alternatively, just possibly, everyone else is overlooking something obvious.



Yes, we have been made in the image of God, just as the Bible says. That is what explains the data and that is what you've all been overlooking.

--------------
Dey can't 'andle my riddim.

  
Weevil



Posts: 6
Joined: Sep. 2005

(Permalink) Posted: Nov. 02 2005,00:07   

Quote

humans suddenly evolving complete with a moral sense and a knowledge of God without any intellegent input?


Finally!  An admission that 'knowledge of God' came into being 'without -any- intellegent(sic) input'  :p

It's been guesswork and fantasy from the beginning then, has it?  Took you long enough to see it, didn't it?

I wondered about horizontal gene transfer in multicellular animals too.   I figured I'd let someone more eloquent have at it, that's quite a diatribe.  

Lesser of two weevils

  
Ved



Posts: 398
Joined: Oct. 2005

(Permalink) Posted: Nov. 02 2005,04:47   

Quote
... that bacteria evolved without intellgent design [...] was already proven impossible by Dembski and Behe!

Ah, hahahahahahha! Thanks for the hearty laugh! What a crock! Hey Paley, I just ran some calculations that prove god doesn't exist, so there!

  
DaveRAFinn



Posts: 15
Joined: April 2005

(Permalink) Posted: Nov. 03 2005,13:36   

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.

  
C.J.O'Brien



Posts: 395
Joined: Aug. 2005

(Permalink) Posted: Nov. 03 2005,14:31   

Quote
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.)

Better give me a link, because as far as I know, that is simply wildly untrue.

--------------
The is the beauty of being me- anything that any man does I can understand.
--Joe G

  
Henry J



Posts: 4812
Joined: Mar. 2005

(Permalink) Posted: Nov. 03 2005,16:43   

I'd think that extensive HGT would show up in comparisons of genetic sequences, since such would result in lots of genes that aren't directly related to genes in the close relatives of the species that got them via HGT.

As for the not enough time for new genes to form, I don't think so. As I recall, humans have around 4 billion base pairs, we seperated from chimps around 6 million years ago, and we have about 1% difference in base pairs in DNA that's common to both species (the other 2% difference is from DNA that isn't in common). 4 billion * 0.01 / 6 million gives about 7 base pair differences per year. Half of that due to changes in each species, so about 4 base pairs per year, or between 40 and 80 depending on average generation span. If I'm not mistaken that's fairly close to the expected mutation rate (over the entire genome) from a common ancestor 6 million years ago.

Henry

  
Swoosh



Posts: 42
Joined: Oct. 2005

(Permalink) Posted: Nov. 03 2005,23:07   

I'm not sure I understand this very well.  The idea is simple enough, and I get where you are trying to go with it.  But the whole thing is pretty large and rife with things that made me go, "huh?  Where did that data come from?"

I'm going to look at one section.  At first I was intriged by your abandon ship analogy, but upon reflection I don't quite see how it fits.  You seem to be saying that a population on the verge of disaster acquires mutations at a significantly higher rate.  But abandoning ship is a concious choice.  Mutations or HGT aren't something organisms opt for out of desperation.  They are a result of environmental factors which are largely out of control, and especially concious control, of the organism under consideration.  For any given population of, say, bacteria, things like risk and strategy are not really going to be a factor.  Are you really trying to say that bacteria reason?

As an aside, I admit that more and more these days humans are conciously tampering with their genomes.  But that's a special case.  And their ability to do so is directly related to their proliferation.  High technology requires high specialization, which in turn requires a huge population to support the specialists.  So at least in humans it would seem that the only reason they are able to opt for genetic tampering is precisely because there are so many of them around in the first place.  I have my doubts a tiny, nearly extinct human population would be able to decide, hey I think its high time for a boatload of tasty mutations right about now.

Okay, you say, the anology is not meant to be taken so literally.  Abandoning ship is just a way of looking at the effects--concious decisions aren't really at play here, its just an analogy.  But I still don't see how it could work.  Rates of mutation are basically constant.  Given that, isn't it the case that a population would have a mutation/HGT count directly proportional to the number of places available to mutate?  The more material there is to work with, the more mutations you'll see.  How does a smaller canvas in any way increase the options for the painter?  I don't get it.

You said, "For an organism suffering very high losses and headed for extinction the normal rules about mutation do not apply."

What what? Why not?  

And then, "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."

Isn't it pretty much understood in the community that the majority of mutations are neutral?  I'm too lazy to look up references, but this was my understanding.  Then, even if one grants that the majority of mutations are in fact very very bad, I don't see how this would be any benefit to populations on the verge of extinction.  And again, what would cause the numbers of mutations to suddenly increase, while simultaneously flipping survivability modes from "kill!" to "live long and prosper!"

There are a few questions for ya to chew on.  Depending on how it goes, there may be more later. :)

  
Henry J



Posts: 4812
Joined: Mar. 2005

(Permalink) Posted: Nov. 04 2005,06:17   

One thought on mutation rate going up under stress- cells generally have repair mechanisms to fix damage to DNA. I expect that probably reduces the mutation rate quite a bit from what it would be without those mechanisms. So if the repair mechanisms slow down or stop, the mutation rate goes up. And under stress, that repair mechanism might be one of the things impacted by the stress.

Henry

  
Ved



Posts: 398
Joined: Oct. 2005

(Permalink) Posted: Nov. 04 2005,09:45   

I could see there being some correlation between a species under "stress" and faster "mutation rates", but I don't think in this situation that this would mean that the mutations themselves would be happening more frequently. Instead, the results natural selection acting on the same number of mutations would have a greater affect in altering the form of that species.

If a species is threatened, in that it's population is being drastically reduced, obviously the circumstances of it's environment are exerting some very strong selection forces upon that species. These forces may be different than the forces that allowed the population to become large as well as refine that species to suit it's certain niche. The threatened species' environment may select to keep individuals that are different, that might be able to survive by finding another way to get by.

Also, probably more importantly, if the population of a once widespread species is drastically reduced, portions of that population will become isolated from each other, and then begin to drift apart genetically, because they cannot mix with their lost kin.

  
DaveRAFinn



Posts: 15
Joined: April 2005

(Permalink) Posted: Nov. 04 2005,10:51   

Further answers to commentators.

C.J.O'Brien

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.

Henry J

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.

Swoosh

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.

  
Swoosh



Posts: 42
Joined: Oct. 2005

(Permalink) Posted: Nov. 04 2005,13:57   

Quote
HGT is very different its operation from "traditional" genetic change.


Of course.  HGT is not a mutation in the pure sense of the word.  My bad.

Quote
This, incidentally, provides a check which you might care to make on my claims.


I'm terrible at word problems.  Math has never been my strong suit.  I'll leave the calculations for others for the time being.  That is, unless I am madly overtaken by the revolutionary fervor of your idea here, which, as yet, I am not.  

Quote
The point is that in that situation, as in many others, the probabilities are different from "normal" and therefore the optimal strategies are different.


But how different?  You are implying that the difference is total and complete.  My feeling is that on the whole, species under duress don't undergo a significant increase in mutation OR horizontal gene transfer.  But maybe they do.  I'm not aware of any experiments that show this either way.  Are you?

And what if its true?  My hunch is that is isn't, but who knows.  But even if its true, natural selection still operates on the altered organisms.  What gives HGT such a tremendous advantage over plain ol mutation?  In the one case, the mutation is random.  But then the HGT is also random.  Insert a random gene into a random organism.  I can't see any obvious reason why the organism should be majorly predisposed to benefit from the transfer.

Let's take a look an overview look at what you are saying.  Evolution by mutation is bogus.  Its impossible.  Neo-Darwinism is a red herring, and the scientific establishment suppresses dissent via subtle economic mechanisms.  Scientists are not encouraged to search for alternatives lest they be ostracized.  Dr. Jehosaphat will lose his job if he dissents from the mainstream view, etc.  

But wait!  Here you are presenting the Truth to the foolish neo-Darwists!  The Truth of the situation is that mutation cannot account for the diversity of life--evolution.  The Truth--TRUTH!--is that HGT is 100% responsible for it, and evolution is a lie.  This all sounds very familiar.

Maybe I don't know enough about HGT to fully appreciate your argument here.  I would be inclined to agree that HGT has some effect in the overall scheme of things.  But you've got a big hill to climb if you intend to persuade the community that its flatly impossible for mutations to play any role in the unfolding of the tree of life.

  
Henry J



Posts: 4812
Joined: Mar. 2005

(Permalink) Posted: Nov. 04 2005,14:34   

Here's a couple of threads on Panda's Thumb that talk about HGT, from July and August:

Quote
Carl Zimmer on "The Loom" describes recent work on the phylogenetic tree. Researchers have looked at vertical and horizontal transmission of genetic information in various bacteria.

Continued at Carl Zimmer: Tangling the tree

Quote
It has been over 30 years since the suggestion that horizontal gene transfer (HGT) may have been a factor in the evolution of life entered the literature. [...] Speculations that HGT may have been a bigger factor in the evolution of life was inviting because it offered broad explanations for a variety of biological phenomena that have interested and puzzled biologist for over the last century and a half.

Continued at The Last Universal Common Ancestor

Henry

  
Henry J



Posts: 4812
Joined: Mar. 2005

(Permalink) Posted: Nov. 04 2005,17:03   

Re "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."

Say what? Why does there have to be time for things that didn't happen?

Re "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."

How so? Each section of DNA would have been passed down (with occasional mutations) from some ancestor 6 million years (or whatever time period) to the descendants living today. That section of DNA would accumulate only the changes that happened to it; it wouldn't have to take the time to not accumulate the changes that didn't happen to it.

The genetic changes that stayed in the species were undoubtedly a tiny fraction of the changes that occurred - most mutations would have simply disappeared along the way. A few would presumably spread due to selection, and a few due to genetic drift.

Henry

  
Swoosh



Posts: 42
Joined: Oct. 2005

(Permalink) Posted: Nov. 04 2005,19:25   

Fascinating and informative read.  Thanks, Henry.

  
Pastor Bentonit



Posts: 16
Joined: Oct. 2005

(Permalink) Posted: Nov. 06 2005,20:50   

Yes, but have you also considered (super- and subscript notwithstanding, you´ll figure it out):

d(-S)=-mcuidxi-qAidxi+aFik2dVdt-bRdVdt

There´s more fun at www.crank.net.

  
  17 replies since Oct. 30 2005,14:40 < Next Oldest | Next Newest >  

    


Track this topic Email this topic Print this topic

[ Read the Board Rules ] | [Useful Links] | [Evolving Designs]