Darwin Unhinged: The Bugs in Evolution

Well shouldn't we consider first, if neutral mutations - which happen in a purely random way - can do anything significant, and if so how. I mean, the only thing that used to make Darwin's theory viable, was the assumption that each step in a chain of mutations could be independently beneficial. There doesn't seem much point in adding random (unselected) mutations because although some will happen, they hit a brick wall of combinatorial explosion.

David

I guess the just-so story has something like the following form: a component part of a needed new body subsystem just happens to appear by random mutation and just happens to be neutral (as many or most mutations aren't) - it surprisingly doesn't screw up some other system, and it spreads in the population. Like a mutation to build the "melon" in the front of the dolphin's head with the new tissue in just the right shape and location and having just the right sonic refraction coefficient at the right frequency needed to form an echolocation emitted pulse focusing "lens". It is now providentially waiting for the appearance of more parts. But wait, for this mutation to be truly neutral and not be selected against the new "proto melon" must not adversely affect the animal's hunting ability, reproduction, etc. even though it is a new structure built on the front of the animal's head with little functional advantage to compensate for its energy and other costs (since the other parts of the new subsystem aren't yet in place, like the necessary accompanying changes to the brain). Then another component of the new subsystem just happens to appear as another neutral random mutation and gets fixed in the genome in the population. Like a neural change in the incredibly complex brain structure to automatically adjust the emitted pulse rate in just the right way to accommodate different detected target distances, a precise neural change out of innumerable possible changes, which also has to take into account the effect of the new "proto melon" on the embryonic new system. And we have to consider how many generations it would take for this to happen somewhere in the relatively limited population.

Then another neuroanatomical change, this time for emitted pulse amplitude control. Here's a little detailed information about just this individual modification, which again requires complex changes in the brain designed to do precise things in real time during echolocation: 

In bats and technological sonars, the gain of the receiver is progressively increased with time after the transmission of a signal to compensate for acoustic propagation loss. The current understanding of dolphin echolocation indicates that automatic gain control is not a part of their sonar system. In order to test this understanding, we have performed field measurements of free-ranging echolocating dolphins. Here we show that dolphins do possess an automatic gain control mechanism, but that it is implemented in the transmission phase rather than the receiving phase of a sonar cycle. We find that the amplitude of the dolphins' echolocation signals are highly range dependent; this amplitude increases with increasing target range, R, in a 20log(R) fashion to compensate for propagation loss. If the echolocation target is a fish school with many sound scatterers, the echoes from the school will remain nearly constant with range as the dolphin closes in on it. This characteristic has the same effect as time-varying gain in bats and technological sonar when considered from a sonar system perspective. 

And then another of the needed highly complex changes to the neuroanatomy, like the precise brain neural net changes (out of the innumerable possible random mutations to the incredibly complex structure) needed to achieve target discrimination by analyzing the structure of the returned pulse echo, like determination of target size, shape, number, etc.. And another change and so on until all the component parts of the new subsystem are present. Voila - we've got the new echolocation system. But wait, until all these mutations form an integrated whole with major selection advantages to the animal, they can easily be degraded by other random mutations. But wait, in a lot of cases of the extreme body system adaptations of the cetaceans a number of such subsystems need to be developed and implemented simultaneously in order for the animal to remain viable. 

The fantastic improbability of such a story is obvious, but this is what Darwinists appear to be depending on to explain a large part of macroevolution by neutral mutation.

I guess the just-so story has something like the following form: a component part of a needed new body subsystem just happens to appear by random mutation and just happens to be neutral (as many or most mutations aren't) - it surprisingly doesn't screw up some other system, and it spreads in the population. Like a mutation to build the "melon" in the front of the dolphin's head with the new tissue in just the right shape and location and having just the right sonic refraction coefficient at the right frequency needed to form an echolocation emitted pulse focusing "lens". ...................

The fantastic improbability of such a story is obvious, but this is what Darwinists appear to be depending on to explain macroevolution by neutral mutation.

To be honest, I don't think there is a rational argument at the back of this. I mean each of these components is a complicated thing in itself - it must have many steps (e.g. point changes in DNA) which aren't selected for. Then when this potentially useful thing finally beats the sheer improbability of it appearing, it almost has to be detrimental. I mean,:

1)           How can a new protease (or the original one) be acceptable to the cell before the entire control mechanism associated with it is in place. The first cell to express this enzyme will eat itself!

2)           Any visible change on body shape - such as the 'melon' - will presumable reduce that creature's sexual attractiveness.

There seem to be two arguments that are swapped about as necessary. One is the argument that evolution avoids combinatorial explosion because each step is selected for. The other is to argue that you don't need natural selection for long periods of evolutionary change - but that is inconsistent with the maths of combinatorial explosions.

When an ID enthusiast performed a combinatorial calculation, I used to automatically think they were making the fallacy of forgetting the power of step by step selection. Whether they were or not, the proposal by mainstream science that meaningful evolution can happen without selection seems totally bizarre.

I mean at one point Paul wrote

No one is suggesting that it's only due to neutral mutations.

This seems to be heart of the issue - you have two theories of evolution and each clearly cannot work, so what benefit is there in using both?

David

 I mean each of these components is a complicated thing in itself - it must have many steps (e.g. point changes in DNA) which aren't selected for. Then when this potentially useful thing finally beats the sheer improbability of it appearing, it almost has to be detrimental. I mean,:

1)           How can a new protease (or the original one) be acceptable to the cell before the entire control mechanism associated with it is in place. The first cell to express this enzyme will eat itself!

2)           Any visible change on body shape - such as the 'melon' - will presumable reduce that creature's sexual attractiveness.

True. The suggested scenario was oversimplified. This just makes the whole thing even more fantastically improbable.

Well shouldn't we consider first, if neutral mutations - which happen in a purely random way - can do anything significant, and if so how. I mean, the only thing that used to make Darwin's theory viable, was the assumption that each step in a chain of mutations could be independently beneficial. There doesn't seem much point in adding random (unselected) mutations because although some will happen, they hit a brick wall of combinatorial explosion.

Each step doesn't have to be beneficial. It only needs not to be deadly. The combinatorial explosion problem comes into play if you have some goal in mind. Then, indeed, random mutations are unlikely to meet that goal. But there is no goal. We could just have well been significantly different.

~~ Paul

1)           How can a new protease (or the original one) be acceptable to the cell before the entire control mechanism associated with it is in place. The first cell to express this enzyme will eat itself!

You're thinking of it happening all-of-a-piece. There could be 100 intermediate stages where the mechanisms have different functions, some possibly not even particularly useful.

I think people are having a hard time dumping the idea that there is a target that evolution has to match by turning the current organism into the new organism in one fell swoop.

~~ Paul

Each step doesn't have to be beneficial. It only needs not to be deadly. The combinatorial explosion problem comes into play if you have some goal in mind. Then, indeed, random mutations are unlikely to meet that goal. But there is no goal. We could just have well been significantly different.

~~ Paul

It would be interesting to see, rather than handwaving referrals to the power of neutral evolution which of course has absolutely no target, no direction or purpose, instead a specific detailed scenario for the origin of some actual body system, for instance the cetacean echolocation system or one of the other complex body and neural adaptations. 

The just so story certainly gets intricate and complicated. Apparently the neutral model goes something like this: Let's say a random neutral mutation occurs that just happens to be a part of some possible mechanism that just might be useful to the organism some time in the future if circumstances change in some way (becoming combined with certain specific additional neutral changes, environmental change in a particular direction and/or isolation of a small population group, etc.). This neutral mutation drifts since there is no selection for fitness and despite that just happens to become fixed in the population, which takes time. This is along with multitudes of other neutral mutations the vast majority of which have no possible future use. 

And then a second neutral mutation has to come along that will, by some fortuitous means not yet understood when combined with the first and some as yet unspecified number of future random mutations, produce some new complex mechanism or structure that wasn’t there before. At most of the steps of this process the complex too has to get fixed while drifting. Becoming fixed is rare. Usually, it will be lost or degraded. This process takes even more time. And all the while none of the changes can get lost or disrupted or we’re back to square one. Wash rinse repeat. And as we add more mutations to the scenario the odds that the prior ones get disrupted in some way go up - after all, there’s no selection to favor them. It’s just pure dumb luck. Blind search at its finest. 

Of course, it's possible for some in this series of mutations to have some sort of alternate positively selectable functions, rather than being neutral or deleterious, but the likelihood of that is even lower. 

Of course, calculating the improbability of this sort of causal chain for an actual complex mechanism that came about has to consider the vastly greater probability of neutral mutations that add up to nothing, ones that drift and peter out, and detrimental mutations that get weeded out by selection. Then figure in the likelihood that the new machinery that somehow came about against all the odds is the particular machinery that was needed for the actual adaptive path that the organism followed. If it is claimed there could have been other adaptive paths leading to the fully aquatic lifestyle that was the actual historical direction of adaptation (other ways of engineering the body and brain for echolocation, feeding, swimming, breathing, diving, reproduction, etc.) please specify them. What the animal has now seems pretty optimal.   

Actually the scenario is even more unlikely, because often several additional bodily mechanisms and/or structures were needed at the same time for the animal to remain viable. 

Evolutionists sure do call upon some incredible serendipity. Too good to be true? Not for Darwinists.

David Berlinski on the neutral theory, with his usual dry wit:

"The publication in 1983 of Motoo Kimura’s The Neutral Theory of Molecular Evolution consolidated ideas that Kimura had introduced in the late 1960s. On the molecular level, evolution is entirely stochastic, and if it proceeds at all, it proceeds by drift along a leaves-and-current model. Kimura’s theories left the emergence of complex biological structures an enigma, but they played an important role in the local economy of belief. They allowed biologists to affirm that they welcomed responsible criticism."
 

Kimura's theories have been extended, but Berlinski's comment still applies.

James Shapiro – Molecular Biologist:

“There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject.”

It would be interesting to see, rather than handwaving referrals to the power of neutral evolution which of course has absolutely no target, no direction or purpose, instead a specific detailed scenario for the origin of some actual body system, for instance the cetacean echolocation system or one of the other complex body and neural adaptations. 

The just so story certainly gets intricate and complicated. Apparently the neutral model goes something like this: Let's say a random neutral mutation occurs that just happens to be a part of some possible mechanism that just might be useful to the organism some time in the future if circumstances change in some way (becoming combined with certain specific additional neutral changes, environmental change in a particular direction and/or isolation of a small population group, etc.). This neutral mutation drifts since there is no selection for fitness and happens to become fixed in the population, which takes time. This is along with multitudes of other neutral mutations the vast majority of which have no possible future use. 

And then a second neutral mutation has to come along that will, by some fortuitous means not yet understood when combined with the first and some as yet unspecified number of future random mutations, produce some new complex mechanism or structure that wasn’t there before. At most of the steps of this process the complex too has to get fixed while drifting. Becoming fixed is rare. Usually, it will be lost. This process takes even more time. And all the while none of the changes can get lost or disrupted or we’re back to square one. Wash rinse repeat. And as we add more mutations to the scenario the odds that the prior ones get disrupted in some way go up - after all, there’s no selection to favor them. It’s just pure dumb luck. Blind search at its finest. 

Of course, it's possible for some in this series of mutations to have some sort of alternate positively selectable functions, rather than being neutral or deleterious, but the likelihood of that is even lower. 

Of course, calculating the improbability of this sort of causal chain for an actual complex mechanism that came about has to consider the vastly greater probability of neutral mutations that add up to nothing, and detrimental mutations that get weeded out by selection. Then figure in the likelihood that the new machinery is the particular machinery that was needed for the actual adaptive path that the organism followed. If it is claimed there could have been other adaptive paths leading to the fully aquatic lifestyle that was the actual historical direction of adaptation (other ways of engineering the body and brain for echolocation, feeding, swimming, breathing, diving, reproduction, etc.) please specify them. What the animal has now seems pretty optimal.   

Actually the scenario is even more unlikely, because often several additional bodily mechanisms and/or structures were needed at the same time for the animal to remain viable. 

Evolutionists sure do call upon some incredible serendipity. Too good to be true? Not for Darwinists.

David Berlinski on the neutral theory, with his usual dry wit:



James Shapiro – Molecular Biologist:

What alternative(s) can you provide to the standard of evolutionary theory?

To introduce a new argument about the bugs in Darwinian evolution, I've just come across a very interesting scholarly article by Wolf-Ekkehard Lönnig which can be downloaded in PDF format here.

It's well known that Darwin said: If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find no such case.

However, what's somewhat less well known is this statement of Darwin's: If it could be proved that any part of the structure of any one species had been formed for the exclusive good of another species, it would annihilate my theory, for such could not have been produced through natural selection.

The article concerns plant galls, produced by many thousands of species of insect -- in, for example, the orders hymenoptera (ants and wasps), diptera (two-winged flies), coleoptera (beetles), etc -- and in some cases other organisms such as mites and nematodes. with insects, the large majority of galls provide exclusive benefit for the insect, with none at all for the plant. In fact, the effect on the plant is deleterious and therefore couldn't have been selected for.

A gall provides food, shelter and a favourable microenvironment for the insect or its grub, but makes the plant less fit for survival: indeed, severe cases of infestation have the name of a disease: cecidiosis (after cecidium, the Latin name for a gall).

I think it's important not to confuse the situation with the effects of many disease organisms, which can cause the host organism to produce various kinds of defence structures (e.g the rashes of chicken pox). What produces the galls isn't the host organism's defence mechanism, but ultimately the insect itself's effect on the plant to foster exclusively the insect's own well-being. Galls, in and of themselves, aren't fatal for the plant except perhaps when present in very large numbers, but any galls at all are definitely deleterious because the insect is commandeering plant resources that otherwise could be used to further the plant's own well-being; infected plants do less well when compared to uninfected ones.

Nor is the situation quite like that in viruses, which inject their DNA into the host's genome and commandeer the latter's DNA machinery to reproduce themselves: the host doesn't produce any new structure (check Darwin's statement again -- it specifically refers to this). The only thing produced is viral material; the host doesn't construct anything new to further the aims of the virus. Rather, the virus simply takes advantage of structure that is already there, viz., the host genome and its cellular machinery, to generate more viral material.

Besides, the host does mount an attack on the virus, whereas the gall is not at all a defence against the offending insect; quite on the contrary, it offers a safe haven for its offspring, which will grow up to infect others of the plant's species, affecting their well-being too. Galls are of a specific size, shape, and layered construction, and may even develop exit plugs for the developing insect grubs that can only be opened from the inside.

The article is packed with detailed information that explicitly challenges Darwinism, and I won't go any further at this point except to post a few acerbic quotes from it:

...let’s analyze Mayr’s line of argumentation in detail:

“Why ... should a plant make the gall such a perfect domicile for an insect that is its enemy? Actually we are dealing here with two selection pressures.

Are there really “…two selection pressures” involved, which are in competition with each other running at different speeds? The doubtful basis for this statement is the imaginary conviction of many evolutionary biologists that "natural selection comes close to omnipotence"...

According to Charles Darwin, natural selection displays, in fact, limitless power and virtually godlike abilities for the origin of life’s “endless forms most beautiful”, saying (1859, p. 84):


“It may be said that natural selection is daily and hourly scrutinising, throughout the world, every variation, even the slightest; rejecting that which is bad, preserving and adding up all that is good; silently and insensibly working, whenever and wherever opportunity offers, at the improvement of each organic being in relation to its organic and inorganic conditions of life. We see nothing of these slow changes in progress, until the hand of time has marked the long lapse of ages, and then so imperfect is our view into long past geological ages, that we only see that the forms of life are now different from what they formerly were.”

(1859, p. 469, 1872, p 412) What limit can be put to this power, acting during long ages and rigidly scrutinising the whole constitution, structure, and habits of each creature,—favouring the good and rejecting the bad? I can see no limit to this power, in slowly and beautifully adapting each form to the most complex relations of life.

...Let’s now contrast this somehow deceptively beautiful and alluring language of the delusion of the omnipotence of natural selection with the sobering facts nature.

For an encyclopedia article on natural selection, I stated, among other things:

...Dobzhansky’s 1937 work Genetics and the Origin of Species is generally viewed as the crystallization point for the origin and growth of the modern synthesis or neo-Darwinian theory of evolution (Lönnig, 1999a). There is hardly a better example to illustrate the key message (and, at the same time, the weaknesses) of the modern theory of natural selection than the following quotation from this pioneering work of Dobzhansky (p. 149):

With consummate mastery Darwin shows natural selection to be a direct consequence of the appallingly great reproductive powers of living beings. A single individual of the fungus Lycoperdon bovista produces 7 x 1011 spores; Sisymbrium sophia and Nicotiana tabacum, respectively, 730,000 and 360,000 seed; salmon, 28,000,000 eggs per season; and the American oyster up to 114,000,000 eggs in a single spawning. Even the slowest breeding forms produce more offspring than can survive if the population is to remain numerically stationary. Death and destruction of a majority of the individuals produced undoubtedly takes place. If, then, the population is composed of a mixture of hereditary types, some of which are more and others less well adapted to the environment, a greater proportion of the former than of the latter would be expected to survive. In modern language this means that, among the survivors, a greater frequency of carriers of certain genes or chromosome structures would be present than among the ancestors...

For agreement on and further documentation of the principle of natural selection, see the group of authors cited above, beginning with Bell (1997). However, in the 1950s, French biologists, such as Cuénot, Tétry, and Chauvin, who did not follow the modern synthesis, raised the following objection to this kind of reasoning (according to Litynski, 1961, p. 63):
Out of 120,000 fertilized eggs of the green frog only two individuals survive. Are we to conclude that these two frogs out of 120,000 were selected by nature because they were the fittest ones; or rather - as Cuenot said - that natural selection is nothing but blind mortality which selects nothing at all?

Similar questions may be raised for the 700 billion spores of Lycoperdon, the 114 million eggs multiplied with the number of spawning seasons of the American oyster, for the 28 million eggs of salmon and so on. King Solomon wrote around 1000 BC: "I returned, and saw under the sun, that the race is not to the swift, nor the battle to the strong,...but time and chance happeneth to all of them" (KJV 1611).

If only a few out of millions and even billions of individuals are to survive and reproduce, then there is some difficulty believing that it should really be the fittest who would do so. Strongly different abilities and varying environmental conditions can turn up during different phases of ontogenesis. Hiding places of predator and prey, the distances between them, local differences of biotopes and geographical circumstances, weather conditions and microclimates all belong to the repertoire of infinitely varying parameters. Coincidences, accidents, and chance occurrences are strongly significant in the lives of all individuals and species. Moreover, the effects of modifications, which are nonheritable by definition, may be much more powerful than the effects of mutations which have only "slight or even invisible effects on the phenotype" (Mayr 1970, p. 169, similarly 1976/1997; see also Dawkins, 1995, 1998), specifying that kind of mutational effects most strongly favored for natural selection and evolution by the neo-Darwinian school. Confronting the enormous numbers of descendants and the neverending changes of various environmental parameters, it seems to be much more probable that instead of the very rare "fittest" of the mutants or recombinants, the average ones will survive and reproduce.

...Applied to the topic of plant galls and evolution, we can conclude that:

Natural selection – which was thought to be “daily and hourly scrutinising, throughout the world, every variation, even the slightest; rejecting that which is bad, preserving and adding up all that is good” – not only failed miserably and totally in all the thousands of affected plant host species, but also – against all expectations and predictions – would have been entirely efficacious, successful and victorious exclusively in the ca. 132,930 different galling insect species.

...Thus, natural selection does definitely not come “close to omnipotence”. Instead of selection reflecting "both the beauty and the brilliance in its omnipotence to explain the myriad observations of life", it has shown its total inefficiency and utter impotence to explain the myriad research results pertaining not only to plant galls but also innumerable further biological phenomena...

...Darwin had provided the basic idea of continuous evolution more than 150 years ago by postulating:

“innumerable slight variations”, “extremely slight variations” and “infinitesimally small inherited variations” (he also spoke of “infinitesimally small changes”, “infinitesimally slight variations” and “slow degrees”) and hence imagined “steps not greater than those separating fine varieties”,”insensibly fine steps” and “insensibly fine gradations”, “for natural selection can act only by taking advantage of slight successive variations; she can never take a leap, but must advance by the shortest and slowest steps” or “the transition [between species] could, according to my theory, be effected only by numberless small gradations” (emphasis added, see http://darwin-online.org.uk/).

However, for each of these postulated “insensibly fine steps”, each of the “numberless small gradations” etc. the following rule has unanimously been established by population genetics:

“Even a new mutation that is slightly favorable will usually be lost in the first few generations after it appears in the population, a victim of genetic drift. If a new mutation has a selective advantage of S in the heterozygote in which it appears, then the chance is only 2S that the mutation will ever succeed in taking over the population. So a mutation that is 1 percent better in fitness than the standard allele in the population will be lost 98 percent of the time by genetic drift.”

So, let’s keep in mind that for each of the “extremely slight variations”, each of the “steps not greater than those separating fine varieties” a mutation 1 percent better in fitness than the standard allele has to occur at least 50 times (in many cases even much more often) to have a chance to succeed in taking over a population. As for the additional remote possibility of the origin of new genes and protein folds, see, for example, Ax (2017).

Hence, in each and every case of all the different some 132,930 independently arisen galling insects species, correspondingly literally thousands of supposed long evolutionary gall histories must be postulated, all by “uncountable successive small microevolutionary steps”, “infinitesimally small inherited variations” etc. – and each of the necessary mutations had to occur separately of each other at least some 50 times on average to have a chance to succeed in a given population.


In other words: for the evolution of complex galls over innumerable intermediary links by the supposed micro-mutations “with slight or even invisible effects on the phenotype” (Mayr) in the genomes of the insects, it has to be assumed that these steps must have been successful not just once, but in each case of the individually evolving galling insect species and corresponding gall phenomena even tens of thousands of times, i.e. for each further infinitesimally small step in millions of years, eventually resulting in the present phenomena of elaborate plant galls.

I'll leave it there for now. I may have more to say in due course as I'm only about half way through this longish article. Meanwhile, I'd be interested to read any comments.

What alternative(s) can you provide to the standard of evolutionary theory?

I see it this way. It's necessarily lengthy. Intelligent design primarily makes the case that intelligence must be a major causative agent in macroevolution, that reductive materialism especially in the form of neo-Darwinism can't suffice to explain it. In doing this, it doesn't have to and doesn't try to come up with another mechanism with a specification or description of what the intelligent agent(s) are or were. It is sufficient to demonstrate that intelligent agents are the only known, observed, source of the sort of organized complexity in the form of intricate machines that macroevolution seems to have produced in greatly magnified biological ways especially as irreducibly complex machines. This of course also applies even more strongly to the origin of life problem. 

It may (or may not) be possible to determine the exact mechanism the designer used to do the designing, and the nature of the designer. But we don't have to be able to answer these questions to know that the object in question was indeed designed.

From https://evolutionnews.org/2015/11/whats_the_mecha/:

"The insistence on providing a mechanism is following a particular view of science known as methodological naturalism, or methodological materialism. This view of science claims that science must limit itself to strictly materialistic causes to explain all phenomena in nature, even things like the origin of the universe, the origin of life, and the origin and causes of human consciousness."

"We cannot directly observe the cause of the origin of life or repeat the events we study in the history of life, but we can infer what cause is most likely to be responsible, as Stephen Meyer likes to say, “from our repeated and uniform experience.”  In our experience the only thing capable of causing the origin of digital code or functional information or causal circularity is intelligence and we know that the origin of life and the origin of animal life, for example, required the production of just such things in living systems....The theory of intelligent design does not propose a mechanism (a strictly or necessarily materialistic cause (required by methodological materialism)) for the origin of biological information. Rather, it proposes an intelligent or mental cause. In so doing, it does exactly what we want a good historical scientific theory to do. It proposes a cause that is known from our uniform and repeated experience (to borrow a phrase) to have the power to produce the effect in question, which in this case, is functional information in living systems."

Some biologists and evolutionists recognize the problems with modern neo-Darwinism and think they have found a way to extend the theory to solve them. They think that the many additional mechanisms beyond random mutations creating genetic variation that have been discovered can save the theory. For instance there is a group called the "Third Way": 

"Neo-Darwinism ignores important rapid evolutionary processes such as symbiogenesis, horizontal DNA transfer, action of mobile DNA and epigenetic modifications. The DNA record does not support the assertion that small random mutations are the main source of new and useful variations. We now know that the many different processes of variation involve well regulated cell action on DNA molecules.....Genomes merge, shrink and grow, acquire new DNA components, and modify their structures by well-documented cellular and biochemical processes."

I don't think efforts like this can work to save neo-Darwinism, because they merely expand the number of ways, the number of reductive materialist mechanisms, that generate genetic variation that is mainly still random with respect to fitness. Epigenetics is one exception, but it operates primarily at the level of whole genes or at least of long strings of DNA. It doesn't seem to be able to create much, or explain how it evolves in the first place.

Other suggestions that the intracellular machinery somehow incorporates mechanisms that "purposefully" modify parts of the genome especially developmental pathways in just the right ways needed in response to particular stresses, etc. just push the problem down the road a little. Then it has to be explained how such what must be very intricate mechanisms originally came about, and so on. More importantly, they assume what is in question, that mechanical mechanisms however complicated can themselves create complicated integrated mechanisms, especially irreducibly complex ones.

I see it this way. It's necessarily lengthy. Intelligent design primarily makes the case that intelligence must be a major causative agent in macroevolution, that reductive materialism especially in the form of neo-Darwinism can't suffice to explain it. In doing this, it doesn't have to and doesn't try to come up with another mechanism with a specification or description of what the intelligent agent(s) are or were. It is sufficient to demonstrate that intelligent agents are the only known, observed, source of the sort of organized complexity in the form of intricate machines that macroevolution seems to have produced in greatly magnified biological ways especially as irreducibly complex machines. This of course also applies even more strongly to the origin of life problem. 

It may (or may not) be possible to determine the exact mechanism the designer used to do the designing, and the nature of the designer. But we don't have to be able to answer these questions to know that the object in question was indeed designed.

From https://evolutionnews.org/2015/11/whats_the_mecha/:

The above ain't science. It's fanciful religious thinking disguised as such and compelling only to those of such a mind.
Show direct evidence of God. You might wonder why I emphasized God? I did so because ID is the direct rebranding of creationism.

Some biologists and evolutionists recognize the problems with modern neo-Darwinism and think they have found a way to extend the theory to solve them. They think that the many additional mechanisms beyond random mutations creating genetic variation that have been discovered can save the theory. For instance there is a group called the "Third Way": 



I don't think efforts like this can work to save neo-Darwinism, because they merely expand the number of ways, the number of reductive materialist mechanisms, that generate genetic variation that is mainly still random with respect to fitness. Epigenetics is one exception, but it operates primarily at the level of whole genes or at least of long strings of DNA. It doesn't seem to be able to create much, or explain how it evolves in the first place.

Other suggestions that the intracellular machinery somehow incorporates mechanisms that "purposefully" modify parts of the genome especially developmental pathways in just the right ways needed in response to particular stresses, etc. just push the problem down the road a little. Then it has to be explained how such what must be very intricate mechanisms originally came about, and so on. More importantly, they assume what is in question, that mechanical mechanisms however complicated can themselves create complicated integrated mechanisms, especially irreducibly complex ones.

Disclaimer:

It has come to our attention that THE THIRD WAY web site is wrongly being referenced by proponents of Intelligent Design and creationist ideas as support for their arguments. We intend to make it clear that the website and scientists listed on the web site do not support or subscribe to any proposals that resort to inscrutable divine forces or supernatural intervention, whether they are called Creationism, Intelligent Design, or anything else.

With all you written in this post it's still not fundamentally clear why you think species do not evolve? It sees there are deeper reasons than TOE's lack of explanatory mechanisms.

Read on if you like.



The third way is science. But the point is still missed it seems by you. That point being, life evolves into various species whether precise mechanisms are known or not. Another point that missed is but is stressed ad nauseum is evolution doesn't make changes with intent or a goal but it must. Changes occur because the system of DNA replication is not 100% perfect. Occasionally something goes wrong and DNA makes a protein that causes harm or DNA does not produce a protein at all and the animal with that defect does not live to reproduce or if it does passes on a protein that makes it difficult for future generations to do so and after awhile that defect is lost. How many times has that occurred we do not know; we only see the successes. There are times that DNA does make a protein that confers an advantage for example. There's a specie of beetle with red and black markings. One day a beetle is born with more red markings than black. The beetle with more red markings did not get eaten and is able to pass on this new trait through multiple matings. After awhile more are born with this trait and survive longer that those with less; longer still and this trait becomes so dominate you have all red beetles and a new sub-species. If this beetle were to find a different habitat by accident it would adapt evolve into a completely new species.