Psience Quest

(2017-10-15, 12:00 AM)Steve001 Wrote: [ -> ]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/:

Quote:"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": 

Quote:"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.

(2017-10-15, 07:04 AM)nbtruthman Wrote: [ -> ]

Quote: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.

Quote: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:

Quote: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.

(2017-10-15, 01:56 AM)Michael Larkin Wrote: [ -> ]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:

...........................................................................
...........................................................................

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.

I'm about half way through the paper. So far there seems to be two main arguments:

(1) "....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." 

In other words, the entire intricate path of the evolution of the stimulation of gall production in plant hosts by random mutation + natural selection has to have been independently repeated tens of thousands of times in the tens of thousands of different gall-producing parasitic insect species. The likelihood of this approaches zero.

(2) "It must be further assumed that, in contrast to the animals, in the plant hosts
natural selection not only failed continually and totally to do anything against
the parasites – so far no clear signs of resistance – during all the eons of time,
but that the plants, in clear opposition and full defiance to natural selection, must
increasingly have invested much of their energy and substance to help the
parasites flourish, improve and strongly multiply in preparation for the next
rounds of infestations."

The parasitism of the production of insect-induced galls comes at high cost to the plants involved. The galls furnish virtually no compensating advantage to the plants involved. So there should have been strong selection pressure on them to develop defenses against gall production, but this has not happened. Natural selection didn't work, and it is supposed to be the universal god-like principle of evolution. In fact, natural selection seems to have operated in reverse on the part of the host plants, because plant mechanisms controlling local plant tissue and cell growth seem to have been modified exclusively for the insects' benefit. 

This empirically invalidates Darwinism, since Darwin himself said that his theory would be proven false if "it could be proved that parts of the structure of any one species had been formed for the exclusive good of another species. For natural selection will never produce in a being anything injurious to itself."
 

I don't see any answer to these arguments other than ad hoc speculations. For instance, for argument (1), maybe horizontal gene transfer or some other mechanism operated to spread the basic genetic changes in the parasitic insects' genomes, rather than requiring each species to evolve the modifications independently. For argument (2), maybe the basic design of the plant systems makes development of defenses more costly to the plants than the losses induced by growth of the galls. So in the tradeoff, it is less disadvantageous (that is, actually advantageous) to the plants to just allow parasitism by the gall insects. 

Of course, there is no evidence for either of these ad hoc speculations.  It would take a lot of new research to try to verify these speculations.

(2017-10-15, 04:20 PM)Steve001 Wrote: [ -> ]Disclaimer:
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.

I didn't cite the "Third Way" group suggesting that it supports ID, other than that they clearly recognize problems in the theory by their own statements. I pointed out how its approach to solve them won't work. 

(bolded): Assumes the point in contention, plus a little speculative hand-waving that doesn't engage the examples previously presented.

(2017-10-15, 05:17 PM)nbtruthman Wrote: [ -> ]I'm about half way through the paper. So far there seems to be two main arguments:

...Of course, there is no evidence for either of these ad hoc speculations.  It would take a lot of new research to try to verify these speculations.

Yup. You got it. I was surprised to find this article and that the arguments have been raging about galls since the 19th century -- and the arguments then on the part of Darwinists displayed the usual story telling abilities based around an irrational faith in the almost omnipotent natural selection. "Imagine this situation...then with a woulda coulda shoulda, hey presto, natural selection wins."

An infinitely flexible hypothesis that explains everything ends up explaining nothing.

That said, there must be some explanation for plant galls. Insisting it's all down to natural selection effectively stops further investigation that might cast some light on the true causes of evolution. That's the real tragedy of the situation.

(2017-10-15, 05:27 PM)nbtruthman Wrote: [ -> ]I didn't cite the "Third Way" group suggesting that it supports ID, other than that they clearly recognize problems in the theory by their own statements. I pointed out how its approach to solve them won't work. 

(bolded): Assumes the point in contention, plus a little speculative hand-waving that doesn't engage the examples previously presented.

You seem to not want to give a straight answer.

I know you didn't. I post part of their statement so it was clear to our resident creationist and any others that may show not to cite it.
For some that is the point of their contention and I don't know if it yours.


This whole purpose of this topic is to dispell TOE; why should any of the points be addressed further? Evolutionary biologists readily admit TOE is not a complete theory, but there is enough known to know is it a correct theory.

Michael,

I have just downloaded that PDF - so I'll see how I get on - my biology at a scale larger than a cell is rather weak!

This idea possibly relates to the puzzle as to why plants produce entheogens.

There is also the claim that many medicinal plants produce a mixture of chemicals that are more valuable medicinally than their individual components.

Both vaguely suggest that something has been done for the benefit of a different species.

I rather think arguments like this would not move sceptics, who manage to dodge (in their mind) even the raw maths of combinatorial explosion. Nevertheless, once you decide that evolution by natural selection is wrong/very incomplete, these offer possible starting points to a better theory.

David

Quote:I rather think arguments like this would not move sceptics, who manage to dodge (in their mind) even the raw maths of combinatorial explosion. Nevertheless, once you decide that evolution by natural selection is wrong/very incomplete, these offer possible starting points to a better theory.

Sometimes I have a very vivid imagination.

I was visualising this scene as the "sceptics, who manage to dodge (in their mind) even the raw maths", pictured as walking through heavy gunfire across a battlefield. In their own mind they are happy to have somehow magically dodged all the bullets and continue their path unscathed. What they haven't noticed is that their body fell in the first few steps, and now they are just a spirit walking invisibly in another world ... but soon there will be a bright light appearing in the distance ...


Apologies for the diversion from serious discussion

(2017-10-15, 06:42 PM)Steve001 Wrote: [ -> ]You seem to not want to give a straight answer.

I know you didn't. I post part of their statement so it was clear to our resident creationist and any others that may show not to cite it.
For some that is the point of their contention and I don't know if it yours.


This whole purpose of this topic is to dispell TOE; why should any of the points be addressed further? Evolutionary biologists readily admit TOE is not a complete theory, but there is enough known to know is it a correct theory.

Somewhat against my better instincts, I will respond to this. Some people can't get it into their minds that there aren't just biblical creationists on the one hand, and on the other, those who think evolution is a genuine phenomenon attributable to RM + NS, with no gradations between.

The best evidence shows that evolution has occurred: the fossil record alone confirms that. But what the fossil record doesn't confirm is that natural selection, working on random and minuscule mutations, gradually generates cumulative macroevolutionary change.

The most marked evidence against Darwinism is the fact that macroevolutionary changes appear in relatively short periods of time with very little, if any, evidence of gradualism: witness  the several different "explosions", such as the Cambrian (in which most of today's known animal phyla made their appearance), and those subsequent to that, such as the mammalian, avian, and angiosperm radiations in plants, all of which seem to have happened relatively quickly.

I mean, at the time Darwin wrote, it was possible, because of the then paucity of the fossil record, to posit that eventually lots of intermediate forms would be found to confirm the theory. But now, over 150 years after the Origin was published, they still haven't been found despite enormous efforts. Every now and then some rare fossil is found that is posited to be a "missing link", but apart from that, bupkis. If gradualism were true, fossiliferous strata should have by now provided ample evidence of intermediary forms.

The overwhelming evidence against RM + NS being the primary driving force of evolution is as plain as plain can be. No one is denying that RM and NS actually occur, but they can only account for microevolutionary changes: at best from one species within the same genus to another, but not for gross, macroevolutionary changes.

A better evolutionary theory than Darwinism would have to account for the empirical evidence found in the fossil record; would have to explain in some plausible way why we don't find gradualism, but rather periodic and rapid increases in complexity, as if there are sudden injections of information from time to time. As it is, however, all the Darwinists have been able to come up with are the ad-hoc hand-wavings of narrative spinners. The fact that they expect Joe Public to swallow these narratives, nay, try to label anyone who doesn't as a creationist loon, only emphasises their desperation.

Whence come periodic injections of information? If one can't have a purposeless gradualism because the empirical evidence flat out proves one wrong, then what can one have? How can one come up with plausible and completely blind mechanisms that account for the generation of new information in living beings that causes them to evolve? RM + NS is the only explanation people have so far been able to come up with, and it's woefully inadequate. The only reason it blunders on, zombie-like, is its superficial claim to plausibility because RM and NS do actually occur, albeit don't provide adequate explanation for macroevolutionary change.

The only other line of thought we've been able to posit so far is based on the known creative powers of conscious intelligence, of some sort, being in operation. If anyone could come up with a way of circumventing that conclusion without imperious and dismissive hand-waving, then I'd be prepared to examine the evidence. The third-way people don't seem to me to have an answer; I applaud their willingness to think out of the Darwinian box and take on board relatively recent discoveries in epigenetics, horizontal gene transfer, Margulian symbiosis, and so on, but they still haven't been able to crack the crucial question of whence comes new information enabling macroevolution to occur. They're still skirting around that question, still desperately trying to salvage some kind of role for blind process.

I've mainly touched on the fossil evidence, but there's also the combinatorial issues, problems such as those discussed in the article on galls, not to mention the challenge of abiogenesis. It seems to me that Darwin came up with the only half-way plausible blind mechanism for evolution, but that time has proven it utterly incapable of explaining how macroevolution can have occurred.

Make no mistake, I and many other people are 100% sold on the idea that evolution has, and continues to, happen. It's just that we don't buy into Darwinism being the only explanation in town. The only thing we can think of that provides an explanation would seem to have to involve some kind of intelligent input. Maybe that's just a testament to our inability to come up with a purely naturalistic alternative, but if that's our failing, it's also the failing of Darwinists, who also haven't been able to come up with anything better than Darwinism.

Can I ask a completely ignorant question?

Is it possible to take a concrete example - for example the development of a particular biological structure - and make an estimate of the time that would be required for it to develop by random mutation, unassisted by any natural selection pressure, and then to compare that with the time actually taken, as estimated from the fossil record? Obviously the first estimate would depend on assumptions about population size and mutation rates and so on.

Or is the argument a purely qualitative one?