Evolution is relative

[Gottservant]

Hi there,

So someone I knew came up with an argument that you could use against the people who say "you don't understand Evolution".

The argument goes like this, Evolution happens in steps; the smaller those steps, the faster Evolution will take place; Evolution will happen faster because the steps needed to advent that "Evolution" are closer together.

For the sake of contrast, if you had to walk a hundred steps, you would walk a hundred steps quicker: if the steps you were taking were smaller (because they could be closer together, in principle).

 

[SkyWriting]

The argument goes like this, Evolution happens in steps; the smaller those steps, the faster Evolution will take place; Evolution will happen faster because the steps needed to advent that "Evolution" are closer together.For the sake of contrast, if you had to walk a hundred steps, you would walk a hundred steps quicker: if the steps you were taking were smaller (because they could be closer together, in principle).

That's is both correct and wrong. Evolution seems to follow an orderly process over time, but in many cases, because of "switch genes" a population can change dramatically in a few years. My personal conclusion is that God planned and executed every step.

Psalm 3:5
I lay down and slept; I woke again, for the Lord sustained me.

 

[Halbhh]

Hi there,

So someone I knew came up with an argument that you could use against the people who say "you don't understand Evolution".

The argument goes like this, Evolution happens in steps; the smaller those steps, the faster Evolution will take place; Evolution will happen faster because the steps needed to advent that "Evolution" are closer together.

For the sake of contrast, if you had to walk a hundred steps, you would walk a hundred steps quicker: if the steps you were taking were smaller (because they could be closer together, in principle).

It is an interesting thing to realize that the mainstream ideas of evolution fit perfectly to Genesis chapter 1 if we realize Genesis chapter 1 is a vision (see 1 Samuel 3:1 The boy Samuel ministered before the LORD under Eli. In those days the word of the LORD was rare; there were not many visions. about visions as a way God communicates key things to us).

A vision, given in images and also with some very brief narrations (in quotation marks in the Genesis chapter 1) -- thus in key ways similar to visions in general in the Bible, like the vision Peter got in Act chapter 10 -- mysterious scenes that the reciever cannot understand without some narration from God to aid them to have a partial understanding. God speaks during the vision so that the reciever of the vision understand something about it. Without His words, they often would understand nothing at all about the vision. The representative scenes in the vision aren't about trivial stuff, like mere history.

Never about mere time duration or trivial things.

But instead about profound things.

All that is was created so that our home, Earth, would be "very good" as a home for us.

 

[Gottservant]

Thanks for your replies guys - you honestly didn't bait me at all!

I think what I've realized is, even as a colloquial expression,, the fact that Evolution is rigorously propounded means that certain systemic truths remain relevant.

It's like Jesus talking about His Cross all the time, by the time He is there: He is ready not to budge an inch!

Thanks for your replies!

 

[stevevw]

Hi there,

So someone I knew came up with an argument that you could use against the people who say "you don't understand Evolution".

The argument goes like this, Evolution happens in steps; the smaller those steps, the faster Evolution will take place; Evolution will happen faster because the steps needed to advent that "Evolution" are closer together.

For the sake of contrast, if you had to walk a hundred steps, you would walk a hundred steps quicker: if the steps you were taking were smaller (because they could be closer together, in principle).

That would be assuming that the subsequent steps were the right ones at the right time each and every time and that the change brought by that step was fixed into the population. Otherwise, even if there are small steps it could be one small step forward 2 steps backwards, sideways, or upside down. Darwin said evolution should show

infinitely numerous transitional links between the many species

descent with slow modification through natural selection

Darwinian concept of natural selection as a process that acts on infinitesimally small differences, producing a gradual transformation of species.

But what we often see is stasis and the sudden appearance of well-defined creatures without any small graduations. As Darwin also said

"Firstly, why, if species have descended from other species by insensibly fine gradations, do we not everywhere see innumerable transitional forms? Why is not all nature in confusion instead of species being, as we see them, well defined?

 

[The Barbarian]

That would be assuming that the subsequent steps were the right ones at the right time each and every time and that the change brought by that step was fixed into the population.

No. What gave you that idea? Particularly with sexually-reproducing organisms, alleles get reassorted in reproduction and they can come about at different times.

Otherwise, even if there are small steps it could be one small step forward 2 steps backwards, sideways, or upside down. Darwin said evolution should show

infinitely numerous transitional links between the many species

In a finite universe, you won't see infinite anything. Nor does Darwinian theory predict this. However, YE creationist Kurt Wise acknowledges that the many, many transitional series in the fossil record are "very good evidence for macroevolutionary theory.

descent with slow modification through natural selection

Yes, that is an observed fact.

Darwinian concept of natural selection as a process that acts on infinitesimally small differences, producing a gradual transformation of species.

Sometimes. But often larger changes happen as well.

Would you like to learn about some of these?

But what we often see is stasis and the sudden appearance of well-defined creatures without any small graduations.

Sometimes. But the fossil record is still mostly incomplete. As YE creationist Kurt Wise acknowledges, there are now, many, many such transitional series in the fossil record.

As Darwin also said

"Firstly, why, if species have descended from other species by insensibly fine gradations, do we not everywhere see innumerable transitional forms? Why is not all nature in confusion instead of species being, as we see them, well defined?

There were none known when he presented the theory. However, as time went on, more and more of the predicted transitionals began to turn up, validating his prediction.

Would you like to learn about some of them?

 

[stevevw]

No. What gave you that idea? Particularly with sexually-reproducing organisms, alleles get reassorted in reproduction and they can come about at different times.

I thought according to evolution variation or new features comes from random mutations. So any creature transitioning to a new form will depend on random mutations that could be beneficial or more likely neutral and harmful. Add to this other conditions and processes that can affect the transitioning from one form to another and that no creature can mutate from one form to another in one go. Plus transitioning will more than likely involve a process where the morphing can go in a number of directions this would make it a hit and miss process.

In a finite universe, you won't see infinite anything. Nor does Darwinian theory predict this. However, YE creationist Kurt Wise acknowledges that the many, many transitional series in the fossil record is "very good evidence for macroevolutionary theory.

Then why does Darwin himself predict this? ie that the earth should be covered with infinitely fine graduations of creatures transitioning from one to another.

Sometimes. But often larger changes happen as well.

Would you like to learn about some of these?

Well yes, could you give examples of these larger changes and how they can happen.

Sometimes. But the fossil record is still mostly incomplete. As YE creationist Kurt Wise acknowledges, there are now, many, many such transitional series in the fossil record.

Such as.

There were none known when he presented the theory. However, as time went on, more and more of the predicted transitionals began to turn up, validating his prediction.

As far as I understand it around 95% of the tree of life displays HGT and is more like a forest than a tree with may trunks and interconnecting branches. This makes complex creatures more like a little bunch of twigs in some corner of a larger forest which hardly accounts for much of the overall pattern. Even so, research is showing that complex creatures display a great deal of HGT as well which makes it hard to form any tree and therefore transitional branching.

Would you like to learn about some of them?

Yes similar to the above can you provide some examples and explanation of how this can happen so that this can be supported rather than assuming that it happened.

Even if we do find transitions this does not mean that this happened through Darwinian evolution as I have mentioned before. If we take the Bird to Dino example which seems to be a popular one. There have been discoveries that undermine the straightforward story of transitions such as there being modern birds around with the Dino'.

But also that the complex body plans of birds such as their respiratory system and bone structure needed to such this and bird flight has not been found in any transitioning Dino nor can even be explained as to how it could happen without those transitions being non-beneficial and even causing the Dino not to survive.

 

[The Barbarian]

I thought according to evolution variation or new features comes from random mutations.

And natural selection. Which is why it's not random. Natural selection sorts things out to increase fitness in a population.

So any creature transitioning to a new form will depend on random mutations that could be beneficial or more likely neutral and harmful.

Which are sorted out by natural selection. Except for the neutral ones. Depending on the environment, neutral mutations may be very slightly beneficial, or very slightly harmful. So those tend to fluctuate in a population over time, as the environment changes slightly.

Add to this other conditions and processes that can affect the transitioning from one form to another

That's not a common thing. We have for example, more Hox genes in common with crayfish or sharks than ways by which we differ. The stuff that mediates overall development is remarkably stable.

and that no creature can mutate from one form to another in one go.

Creatures don't evolve. Populations do. This is the error that trips up a lot of creationists trying to understand how evolution works.

Plus transitioning will more than likely involve a process where the morphing can go in a number of directions this would make it a hit and miss process.

It's why you don't see new species popping up every day.

Barbarian observes:
In a finite universe, you won't see infinite anything. Nor does Darwinian theory predict this. However, YE creationist Kurt Wise acknowledges that the many, many transitional series in the fossil record is "very good evidence for macroevolutionary theory.

Then why does Darwin himself predict this? ie that the earth should be covered with infinitely fine graduations of creatures transitioning from one to another.

He seems to have been no mathematician. He had the same idea about time, until a geologist friend explained that "infinite" was not a realistic idea. But he meant "countless." Why don't we sees different species with all sorts of intermediate forms between them?

Well, in some cases we do. They are called "ring species" or "clines." Leopard frogs in the United States are like that; frogs from Minnesota and frogs from Louisiana can't interbreed. But they can each interbreed with frogs from intermediate places.

Herring gulls and lesser black-backed gulls form such a ring around the Arctic. The recently-evolved apple maggot flies form such a continuum with hawthorn maggot flies.

Mostly, though, natural selection tends to remove such links between species.

Well yes, could you give examples of these larger changes and how they can happen.

Sometimes. But the fossil record is still mostly incomplete. As YE creationist Kurt Wise acknowledges, there are now, many, many such transitional series in the fossil record.

Such as.

From Toward a Creationist Understanding of Transitional Forms
Kurt Wise
Darwin’s third expectation - of higher-taxon stratomorphic intermediates - has been confirmed by such examples as the mammal-like reptile groups31 between the reptiles and the mammals, and the phenacdontids32 between the horses and their presumed ancestors. Darwin’s fourth expectation - of stratomorphic series - has been confirmed by such examples as the early bird series,33 the tetrapod series,34,35 the whale series,36 the various mammal series of the Cenozoic37 (for example, the horse series, the camel series, the elephant series, the pig series, the titanothere series, etc.), the Cantius and
Plesiadapus primate series,38 and the hominid series.39 Evidence for not just one but for all three of the species level and above types of stratomorphic intermediates expected by macroevolutionary theory is surely strong evidence for macroevolutionary theory. Creationists therefore need to accept this fact. It certainly CANNOT said that traditional creation theory expected (predicted) any of these fossil finds.
https://creation.com/images/pdfs/tj/j09_2/j09_2_216-222.pdf

Keep in mind that Dr. Wise does not think evolution is what happened. He believes that someday, creationists will find a way to explain why the evidence indicates evolution, in a way that does not require evolution to have happened. He's just pointing out that what we have at present is "very good evidence for macroevolutionary theory.

As far as I understand it around 95% of the tree of life displays HGT and is more like a forest than a tree with may trunks and interconnecting branches.

The first person to notice that all living things fit nicely into a family tree (more of a bush, really) was Linnaeus. He didn't know about evolution and had no idea why it was so. Darwin showed why that is.
And then Genetics and the fossil record, and observed speciation, and biochemistry and many other things confirmed it.

Would you like to learn about some of them?

Yes similar to the above can you provide some examples and explanation of how this can happen so that this can be supported rather than assuming that it happened.

Let's consider the horse series. We start with a rather small, browsing forest creature, living on leaves, with a flexible spine, five toes, and rather ordinary teeth.

Shortly after Hyracotherium, the world got cooler and drier, and the forests retreated. And a variety of forms appeared, most of them more fit for living on grasslands and running. They diversified into a bush of different genera, one line of which led to the only surviving genus, equus. (modern horses)
Learn about it here:
Horse Evolution Over 55 Million Years

We have very good documentation of this lineage, because they tended to have very large populations, and lived where the chances of fossilization was relatively good.

Even if we do find transitions this does not mean that this happened through Darwinian evolution as I have mentioned before.

That's right. Observed Darwinian evolution shows us that. Darwin's prediction that random variation and natural selection leads to increased fitness has been repeatedly verified.

If we take the Bird to Dino example which seems to be a popular one. There have been discoveries that undermine the straightforward story of transitions

Nope. The more we find, the less room there is for dissent on that.

such as there being modern birds around with the Dino'.

Ah, the "if you're alive, your uncle must be dead" argument. It was never a very good one. Dinosaurs didn't all become birds. Only one lineage of them became birds. And that doesn't mean the rest of them had to die.

But also that the complex body plans of birds such as their respiratory system and bone structure needed to such this and bird flight has not been found in any transitioning Dino

You've been misled about that:

Integr Zool. 2006 Jun;1(2):80-5. doi: 10.1111/j.1749-4877.2006.00019.x.
Origin of postcranial skeletal pneumaticity in dinosaurs.
Wedel
Abstract
The sauropodomorph Thecodontosaurus caducus and theropod Coelophysis bauri are the earliest known dinosaurs with postcranial skeletal pneumaticity. In both taxa, postcranial pneumatic features are confined to the cervical vertebrae. This distribution of pneumaticity in the skeleton is most consistent with pneumatization by diverticula of cervical air sacs similar to those of birds. Other hypotheses, including pneumatization by diverticula of the lungs, larynx and trachea, or cranial air spaces, are less well-supported.

Bird-style pneumatized bones have been found in various species of dinosaurs. Because they lived in an era of rather low oxygen content, it was a bit of a mystery how they could have such active and energetic species like velociraptors. Turns out, it's because they had a much more efficient lung system than other animals. Birds just put it to a new use.

 

[stevevw]

And natural selection. Which is why it's not random. Natural selection sorts things out to increase fitness in a population.

Natural selection cannot create any variation itself. It can only selection pre-existing variations. The fitness levels depending on the environment. What may be deemed as an increase in fitness in one environment may actually be a disadvantage under the natural state. I.e. bacteria with antibiotic resistance or resistance to other normally detrimental conditions are only that way in that environment. Compared to the natural wild type they are less fit. So, in some ways Natural selection is blind in that it has no purpose apart from preserving something that works but not necessarily something that works the best.

Which are sorted out by natural selection. Except for the neutral ones. Depending on the environment, neutral mutations may be very slightly beneficial, or very slightly harmful. So those tend to fluctuate in a population over time, as the environment changes slightly.

Except as far as I have read slight mutations are more likely to be harmful and can be hard to weed out by selection.

That's not a common thing. We have, for example, more Hox genes in common with crayfish or sharks than ways by which we differ. The stuff that mediates overall development is remarkably stable.

Yet it seems that the basic body plans of most living things have been much the same from the beginning when they appeared. It seems all variation has been based on pre-existing body plans and has not really added much of anything new.

Creatures don't evolve. Populations do. This is the error that trips up a lot of creationists trying to understand how evolution works.
It's why you don't see new species popping up every day.

But should not we see evidence of the experimenting of different variations of features considering that mutations are random. For every feature selected for there had to have been 10 or more that proved non-beneficial. That’s unless a random mutation popped up the right feature first time every time for selection to choose.

Barbarian observes:
In a finite universe, you won't see infinite anything. Nor does Darwinian theory predict this. However, YE creationist Kurt Wise acknowledges that the many, many transitional series in the fossil record is "very good evidence for macroevolutionary theory.

He seems to have been no mathematician. He had the same idea about time, until a geologist friend explained that "infinite" was not a realistic idea. But he meant "countless." Why don't we sees different species with all sorts of intermediate forms between them?

Well, in some cases we do. They are called "ring species" or "clines." Leopard frogs in the United States are like that; frogs from Minnesota and frogs from Louisiana can't interbreed. But they can each interbreed with frogs from intermediate places.

Herring gulls and lesser black-backed gulls form such a ring around the Arctic. The recently-evolved apple maggot flies form such a continuum with hawthorn maggot flies.

Mostly, though, natural selection tends to remove such links between species.

I think he was meaning that because his theory predicted that creatures gradually changed in small steps that each and every creature would have many many transitions leading from one form to another. We can perhaps see half a dozen examples for some creatures at best, but I think Darwin was thinking countless as in 100’s for each. Like for example, the whale examples give a few examples from a dog-sized creature (Pakicetus) to say a Blue whale of around 100 feet and 170 plus tonnes. Without going into the all the different changes that need to happen if we just look at weight and size a few transitions are not going to do it. For the mother to be able to accommodate the birth of increasing size there would need to say at least 50 to 100 transitions or more other wise the baby could not pass through the birth canal.

Keep in mind that Dr. Wise does not think evolution is what happened. He believes that someday, creationists will find a way to explain why the evidence indicates evolution, in a way that does not require evolution to have happened. He's just pointing out that what we have at present is "very good evidence for macroevolutionary theory.

Seems like an interesting paper. I will have to spend some more time on it. There could be a number of different explanations. Also, just because the evidence points to macro evolution does not mean it happen by Darwinian evolution. As mentioned before there are many different mechanisms that have and are being discovered that can also cause evolutionary changes i.e. HGT, symbiosis, developmental processes such as developmental bias and plasticity and inclusive inheritance.

Also, what may be deemed as transitional may be natural variation within the same type of creature. The variation has a wide reach which can cover several different forms which have been determined as separate species when they were just a variation of the same species. It is the splitters and lumpers argument where some want to split everything into different species and others want to lump everything into fewer species.

A good example is the skulls at Dmanisi. Here several hominid skulls were found of the one species Homo Erectus where the variation was previously attributed to several other species in the past. So, the new discovery has knocked out several species Homo rudolfensis, Homo gautengensis, Homo ergaster and possibly Homo habilis and made them into the one species but with greater variation.
Skull of Homo erectus throws story of human evolution into disarray

If we begin to lump other species this way, we may end up with only a few species that have great variation. In that sense, it takes away the great morphing of life from one type of creature to another. It just means that only a few types of creatures were created, and they have produced a great amount of variation of pre-exiting genetic info that perhaps is switched on or activated through various processes. Mutations may just be one mechanism that activates this ability to produce a variation of the existing body plan.

The first person to notice that all living things fit nicely into a family tree (more of a bush, really) was Linnaeus. He didn't know about evolution and had no idea why it was so. Darwin showed why that is.
And then Genetics and the fossil record, and observed speciation, and biochemistry and many other things confirmed it.

But once again the tree is all about fitting a model to it. Plus finding that genes fit the evolutionary model still does not discount other methods that I have mentioned that will produce the same evidence. The only evidence this shows is that all living things are related through their genetic makeups. But this is also true for common design and for processes already mentioned like development where all the genetic info was installed into the original phylum and then evolved from this either by being switched on or off. This would also form a tree-like pattern.

From what I understand there is a lot of debate about molecular trees fitting the evolution model. The tree will depend on which set of data and creature/organism you want to look at and therefore many different trees can be made, and some do not fit the evolutionary tree that Darwin made.
Pattern pluralism and the Tree of Life hypothesis
Pattern pluralism and the Tree of Life hypothesis

If we lump creatures together like the homo erectus example above, then you begin to knock out transitional and branches and may end up with a few trunks with very little branches. If you look at micro organisms you come up with a different tree again, you begin to add many vertical branches. Considering these makeup most of life complex creatures would only represent a small twig in the overall tree and are not an accurate measure of the evolutionary pattern of life. ie

Today, biologists disagree on whether horizontal gene transfer plays the prominent role in evolution, or if it just adds noise and makes it difficult to pinpoint the complex branching of the tree of life. Some scientists think that horizontal gene transfer may accurately explain the evolution of the simple organisms such as bacteria, archaea and prokaryotes such as amoeba, but that complex animals evolve vertically. But considering that these simple organisms make up 90% of all species, and have been around for 3.8 billion years whereas multi-cellular organisms appeared just 630 million years ago, a linear tree of complex creatures would be more like a small offshoot of the overall web.
Read more at: https://phys.org/news/2009-01-darwin-tree-life-thicket.html#jCp

If we use microRNAs this will produce different trees again that links distant branches on the tree together and tears down closely related branches.
“I've looked at thousands of microRNA genes, and I can't find a single example that would support the traditional tree,” he says. The technique “just changes everything about our understanding of mammal evolution”.
Phylogeny: Rewriting evolution

If you begin to look at specific genes, then you start to link different creatures from distant branches in some cases and unlink closely related branches in others.

Let's consider the horse series. We start with a rather small, browsing forest creature, living on leaves, with a flexible spine, five toes, and rather ordinary teeth.

Shortly after Hyracotherium, the world got cooler and drier, and the forests retreated. And a variety of forms appeared, most of them more fit for living on grasslands and running. They diversified into a bush of different genera, one line of which led to the only surviving genus, equus. (modern horses)
Learn about it here:
Horse Evolution Over 55 Million Years

We have very good documentation of this lineage, because they tended to have very large populations, and lived where the chances of fossilization was relatively good.

No one is disputing that there have been transitions and evolution. But even the original horse form was similar in form to modern day horses. We see some transitioning, but this is usually either the loss of features and the reusing of existing features in different ways. There is nothing new. In other words, all the ‘genetic info was there from the beginning and is just being tapped into and used or reused. As the saying goes natural selection is good at explaining the survival of the fittest but not the arrival of the fittest.

 

[stevevw]

Stevevw says
Even if we do find transitions this does not mean that this happened through Darwinian evolution as I have mentioned before.
The Barbarian says
That's right. Observed Darwinian evolution shows us that. Darwin's prediction that random variation and natural selection leads to increased fitness has been repeatedly verified.

Not necessarily, these are assumptions that have been made. There are other methods where new variation can be produced. Natural selection is given more creative ability than it really has. As noted by a section taken from an article about Darwin’s theory as it stands up to modern day findings some have become fixated on a gradualist view which incorporates a gene-centric and adaptative approach.

Darwin emphasized that evolution works with slight incremental and accumulating variation. This view makes genetic changes to be slight and has caused explanations to be focused on finding many small genetic changes which have been impossible to verify. It seems the modern synthesis is limited in its explanation and takes a rigid and narrow view at what may influence and cause living things to change.

The EES is more inclusive and based on constructive processes such as in development but also includes ecology that has an influence on evolution and takes a systems approach that considers all the possible factors of influence that the MS tends to either neglect or reject. Part of the EES explanation is a revised role of natural selection where it is not as dominant role in directing evolution, but rather other processes such as through development and self-organising abilities are more responsible.

Sorry for the extended reference but posting only part of this would not give the entire explanation and leave it out of context.

The formalized core of the MS theory was—and still is—population genetics [35], a mathematical account of gene frequency dynamics in populations of organisms. The empirical basis and key concern of the population genetic approach is the measurement of trait variability in populations, and its intended explananda are adaptive variation, speciation and calculations of fitness. The flurry of fitness landscapes based on ever more nuanced algorithms is indicative of this received approach.


Whereas the MS theory and its various amendments concentrate on genetic and adaptive variation in populations, the extended framework emphasizes the role of constructive processes, ecological interactions and systems dynamics in the evolution of organismal complexity as well as its social and cultural conditions. Single-level and unilinear causation is replaced by multilevel and reciprocal causation. Among other consequences, the extended framework overcomes many of the limitations of traditional gene-centric explanation and entails a revised understanding of the role of natural selection in the evolutionary process.


But it has become habitual in evolutionary biology to take population genetics as the privileged type of explanation of all evolutionary phenomena, thereby negating the fact that, on the one hand, not all of its predictions can be confirmed under all circumstances, and, on the other hand, a wealth of evolutionary phenomena remains excluded. For instance, the theory largely avoids the question of how the complex organizations of organismal structure, physiology, development or behaviour—whose variation it describes—actually arise in evolution, and it also provides no adequate means for including factors that are not part of the population genetic framework, such as developmental, systems theoretical, ecological or cultural influences.


Criticisms of the shortcomings of the MS framework have a long history. One of them concerns the profoundly gradualist conception the MS has inherited from the Darwinian account of evolution. Darwin saw slight, incremental and accumulating variation as the essential prerequisite without which ‘my theory would absolutely break down. Subsequently, the perceived necessity of a slow and continuous flux of variation seemed to have been supported by innumerable studies that demonstrate corresponding behaviours of character variation in natural populations or under artificial selection regimes. The notion of slight successive variation was further reinforced by the molecular conception of genetic variation. When mutation of individual genes or even smaller entities of DNA is taken as the predominant source of variation, it seemed inevitable that phenotypic modifications should be small, because larger changes were deemed to be disruptive and unlikely to produce adaptive outcomes. The supposed randomness of genetic variation further contributed to this view.


Today, all of these cherished opinions have to be revised, not least in the light of genomics, which evokes a distinctly non-gradualist picture [40]. In addition, it is necessary to realize that all models of gradual variation are based on empirical measurements of precisely this kind of change and to the exclusion of other forms of variation. If cases of gradual variation are chosen and quantified, and theoretical models are derived from them, it should not be unexpected that it is gradual variation that will be explained.


Connected with the gradualist requirement of the MS theory is the deeply entrenched notion of adaptation. Again, we are confronted with a feature of the classical theory that has been criticized repeatedly in the past, both on empirical and theoretical grounds [30,41] but also on the basis of modern results of genetics [22]. Whereas different forms of adaptationism can be discerned, for instance in the British and the American research traditions [30], the notion most frequently encountered is still that of a collection of features that make up the organism, each one individually adapted to performing a function in the way best suited for the organism's survival, a picture that has been described as ‘bundles of discrete adaptations.’


This view was neither eliminated by Dobzhansky's alternative view, in which he interpreted populations as states of relative adaptedness [30], nor by the demonstration of the frequent occurrence of non-adaptive traits. Already in the late 1970s, Gould & Lewontin [41] described the adherence to pervasive adaptationism as an ‘old habit,’ but despite extensive learned discussions of the subject that habit has not receded.


Natural selection, the cornerstone of the MS theory so intimately linked to both gradualism and adaptationism, has itself been the subject of a fair share of critical debate. In this case, it is not so much the principle itself that is contested, but the uniqueness of the causal agency that has been ascribed to it. Are all features of biological organisms necessarily the result of natural selection, and is it the only factor in the evolutionary process that provides directionality to organismal change? Numerous authors have challenged the pervasiveness of natural selection as a unique ‘force’ of evolution, whereas others have questioned whether the individual is the sole and appropriate ‘target’ of selection or whether other levels of selection at supra- and infra-individual levels also need to be included in selectionist scenarios [42–44]. Again we are confronted with a classical criticism that stood at the centre of multiple debates in the past [42], but the issue is as unresolved as ever.


Finally, it is apparent that nearly all of the relevant predictions that derive from the MS theory are based on genetic principles and gene determinist convictions. Although the long-held belief that genes are the unique determinants of biological form in development and evolution has been challenged by an extensive number of commentators [21,23,45–48], the genetic program idea underlying MS theory has remained unaltered. This is also true with regard to the mechanisms of transgenerational inheritance. The proposition of uniquely genetic inheritance has been falsified multiple times [3], but the gene-centric position remains constitutive of the MS. The contemporary version of this position, gene regulatory network evolution, really represents only an extension of the ‘gene-determines-phenotype’ view.


The limitations of the MS theory are not only highlighted by the criticisms directed against several of its traditional tenets but also by the failure to address some of the most important phenomena of organismal evolution. The question, for instance, of how complex phenotypic organizations arise in evolution is sidestepped by the population theoretical account, as is the reciprocal influence of these features of higher levels of organization on the evolutionary process. Indeed, the MS theory lacks a theory of organization that can account for the characteristic features of phenotypic evolution, such as novelty, modularity, homology, homoplasy or the origin of lineage-defining body plans. As will be shown below, evo-devo, niche construction, systems biology and other areas harbour the capacity to address at least certain aspects of these topics where the classical theory fails.


Even though only the most prominent issues were mentioned here, this brief overview indicates that the problem agenda associated with the MS theory is extensive. The fact, often mentioned by defenders of the orthodoxy, that these issues have been raised before, does not alleviate the problems. Rather, the current evolutionary paradigm is still dominated by the very same basic assumptions that marked the origin of the synthesis approach. Despite the fact that substantial challenges to these positions have arisen in the past decades from a host of different areas of biology, they have rarely resulted in alternative proposals. Gould's 2002 comprehensive treatment of the history of evolutionary debate [42], for instance, takes up most of the criticisms and suggests alternate concepts, but it does not actually offer an alternative overall structure of evolutionary theory as its title suggests.


All the extensive discussions, led over decades, seem not to have altered the preponderant stance to hold on to the classical prerequisites of gradualism, adaptationism, selectionism and gene-centrism. The predictions that follow from the MS framework continue to be based on these prerequisites and ignore all predictions derived from alternative models. Hence, the claim of continuous incorporation of new conceptual components by the MS theory is misleading.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5566817

 

[The Barbarian]

Barbarian observes:
That's right. Observed Darwinian evolution shows us that. Darwin's prediction that random variation and natural selection leads to increased fitness has been repeatedly verified.

Not necessarily, these are assumptions that have been made.

It's a prediction that has been experimentally verified, and directly observed in nature.

There are other methods where new variation can be produced.

Of course. Variation occurs randomly. Fitness increases by natural selection.

Natural selection is given more creative ability than it really has.

So far, no one has been able to show that anything else works. So that's not a good assumption.

As noted by a section taken from an article about Darwin’s theory as it stands up to modern day findings some have become fixated on a gradualist view which incorporates a gene-centric and adaptative approach.

Not surprising, since that's what we see in nature.

Darwin emphasized that evolution works with slight incremental and accumulating variation.

That's usually what we see, but occasionally, there can be a saltation that results in greater changes. This was suggested by Darwinians like Huxley, even in Darwin's time.

This view makes genetic changes to be slight and has caused explanations to be focused on finding many small genetic changes which have been impossible to verify.

That would require an exhaustive census of a population, and very close monitoring of the population. Not surprisingly, when this was done on Daphne Major, the accumulation of small genetic changes was observed:

The Grants have focused their research on the medium ground finch, Geospiza fortis, on the small island of Daphne Major. Daphne Major serves as an ideal site for research because the finches have few predators or competitors. (The only other finch on the island is the cactus finch.) The major factor influencing survival of the medium ground finch is the weather, and thus the availability of food. The medium ground finch has a stubby beak and eats mostly seeds. Medium ground finches are variable in size and shape, which makes them a good subject for a study of evolution.


The first event that the Grants saw affect the food supply was a drought that occurred in 1977. For 551 days the islands received no rain. Plants withered and finches grew hungry. The tiny seeds the medium ground finches were accustomed to eating grew scarce. Medium ground finches with larger beaks could take advantage of alternate food sources because they could crack open larger seeds. The smaller-beaked birds couldn't do this, so they died of starvation.


In 1978 the Grants returned to Daphne Major to document the effect of the drought on the next generation of medium ground finches. They measured the offspring and compared their beak size to that of the previous (pre-drought) generations. They found the offsprings' beaks to be 3 to 4% larger than their grandparents'. The Grants had documented natural selection in action.


While beak size is clearly related to feeding strategies, it is also related to reproduction. Female finches tend to mate with males that have the same size beaks. These factors together can add to the development of new species.


The Grants return each year to Daphne Major to observe and measure finches. They have been collecting data on the finches for over 25 years and have witnessed natural selection operating in different ways under different circumstances.
Evolution: Natural Selection in Real Time

It seems the modern synthesis is limited in its explanation and takes a rigid and narrow view at what may influence and cause living things to change.[/quote[

There certainly may be other factors. But so far, nothing that doesn't fit a Darwinian framework.

The EES is more inclusive and based on constructive processes such as in development but also includes ecology that has an influence on evolution

That's a Darwinian principle; fitness only counts in terms of environment. Of course a changing environment will influence evolution. Darwin established that from the start.

and takes a systems approach

I have a master's degree in systems, with my work in biological systems. Tell me what tools you've used to look at this problem.

that considers all the possible factors of influence that the MS tends to either neglect or reject.

Which factors are those?

Part of the EES explanation is a revised role of natural selection where it is not as dominant role in directing evolution,

What, specifically, do you think is directing evolution?

[quote[but rather other processes such as through development and self-organising abilities are more responsible.

The field of evolutionary development seems to be rather Darwinian to me. How do you suppose it's not? Evo-devo seems inherently "gene-centric" to me.

Sorry for the extended reference but posting only part of this would not give the entire explanation and leave it out of context.

No problem...

(material in post above)

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5566817

There don't seem to be that many advocates of the strict adaptionist approach, these days. Gould's advocacy of the role of contingency in evolution seems to have won out, and this is not a recent thing. There were arguments about this much earlier:

Darwinism vs. Evo-Devo; a 19th Century Debate
https://www.pitt.edu/~jhs/articles/darwinism_vs_evo_devo.pdf

 

[The Barbarian]

Barbarian observes:
And natural selection. Which is why it's not random. Natural selection sorts things out to increase fitness in a population.

Natural selection cannot create any variation itself.

Yep. It's just a sorting mechanism that increases fitness.

The fitness levels depending on the environment.

Which is why natural selection will change when the environment changes. It's a Darwinian principle; "fitness only counts in terms of the environment."

What may be deemed as an increase in fitness in one environment may actually be a disadvantage under the natural state

So Darwin wrote.

So, in some ways Natural selection is blind in that it has no purpose apart from preserving something that works but not necessarily something that works the best.

Right. Evolution is not about perfection. It's about fitness.

Except as far as I have read slight mutations are more likely to be harmful and can be hard to weed out by selection.

The vast majority of mutations don't do much of anything. Some are harmful, and a few are useful. But probably, no mutation is absolutely neutral. They might be very slightly harmful or very slightly useful in specific instances, and whenever they don't have much effect on the likelihood of an organism living long enough to reproduce, they tend to persist in a population. Of course, neutral mutations, just by chance will eventually either be eliminated or fixed in a population. But as you suggest, that may take a long time.

Yet it seems that the basic body plans of most living things have been much the same from the beginning when they appeared.

Chordates seem to have rather radically changed over time. In this case, it seems to have been by neotony, the retention of the mobile larval form in mature adults. Motility has a definite advantage over more primitive chordates like ascidians.

It seems all variation has been based on pre-existing body plans and has not really added much of anything new.

Well, that's an animal-centric idea. In animals, there seems to have been early on, a major change that led to HOX genes, one consequence of which is a conservative basic body plan. Genetic evidence shows that it happened in sponges:

Curr Biol. 2007 Apr 17;17(8):706-10
The NK homeobox gene cluster predates the origin of Hox genes.
Larroux C1, Fahey B, Degnan SM, Adamski M, Rokhsar DS, Degnan BM.

Abstract
Hox and other Antennapedia (ANTP)-like homeobox gene subclasses - ParaHox, EHGbox, and NK-like - contribute to key developmental events in bilaterians [1-4]. Evidence of physical clustering of ANTP genes in multiple animal genomes [4-9] suggests that all four subclasses arose via sequential cis-duplication events. Here, we show that Hox genes' origin occurred after the divergence of sponge and eumetazoan lineages and occurred concomitantly with a major evolutionary transition in animal body-plan complexity. By using whole genome information from the demosponge Amphimedon queenslandica, we provide the first conclusive evidence that the earliest metazoans possessed multiple NK-like genes but no Hox, ParaHox, or EHGbox genes. Six of the eight NK-like genes present in the Amphimedon genome are clustered within 71 kb in an order akin to bilaterian NK clusters. We infer that the NK cluster in the last common ancestor to sponges, cnidarians, and bilaterians consisted of at least five genes. It appears that the ProtoHox gene originated from within this ancestral cluster after the divergence of sponge and eumetazoan lineages. The maintenance of the NK cluster in sponges and bilaterians for greater than 550 million years is likely to reflect regulatory constraints inherent to the organization of this ancient cluster.

But should not we see evidence of the experimenting of different variations of features considering that mutations are random. For every feature selected for there had to have been 10 or more that proved non-beneficial. That’s unless a random mutation popped up the right feature first time every time for selection to choose.

Yes. Which is what we see. Barry Hall's work with E. coli showed just that happening. Lots of variation, but only some of it actually was beneficial. And those were most numerous. And subsequent evolution worked on those forms.

I think he was meaning that because his theory predicted that creatures gradually changed in small steps that each and every creature would have many many transitions leading from one form to another. We can perhaps see half a dozen examples for some creatures at best, but I think Darwin was thinking countless as in 100’s for each. Like for example, the whale examples give a few examples from a dog-sized creature (Pakicetus) to say a Blue whale of around 100 feet and 170 plus tonnes.

As time goes on, we see more and more of them. The transition from nostrils to blowhole, for example, is nicely gradual, even with a few dozen examples.

Without going into the all the different changes that need to happen if we just look at weight and size a few transitions are not going to do it. For the mother to be able to accommodate the birth of increasing size there would need to say at least 50 to 100 transitions or more other wise the baby could not pass through the birth canal.

Let's say five million years, strong selection for increased size, and a population of a million individuals. Say 20 years to maturity. If there was only one mutation per individual, (and you and I would have a dozen or so) that would be 250,000,000 mutations. Seems like enough for something as simple as mere increase in size.

Seems like an interesting paper. I will have to spend some more time on it. There could be a number of different explanations. Also, just because the evidence points to macro evolution does not mean it happen by Darwinian evolution. As mentioned before there are many different mechanisms that have and are being discovered that can also cause evolutionary changes i.e. HGT, symbiosis, developmental processes such as developmental bias and plasticity and inclusive inheritance.

How do you think these things are unable to come about by Darwinian processes?

Also, what may be deemed as transitional may be natural variation within the same type of creature.

You couldn't have transitionals if it was not.

The variation has a wide reach which can cover several different forms which have been determined as separate species when they were just a variation of the same species.

This was Darwin's point. He noticed that "species" was hard to define, specifically because transitional features are "in-between." We have all sorts of disagreement on how much variation is required to define a species.

A good example is the skulls at Dmanisi. Here several hominid skulls were found of the one species Homo Erectus where the variation was previously attributed to several other species in the past. So, the new discovery has knocked out several species Homo rudolfensis, Homo gautengensis, Homo ergaster and possibly Homo habilis and made them into the one species but with greater variation.
Skull of Homo erectus throws story of human evolution into disarray

https://www.theguardian.com/science/2013/oct/17/skull-homo-erectus-human-evolution

Yep.

If we begin to lump other species this way, we may end up with only a few species that have great variation. In that sense, it takes away the great morphing of life from one type of creature to another.

Don't see how. If we change our naming, it doesn't really change reality.

More later.

 

[stevevw]

Barbarian observes:
That's right. Observed Darwinian evolution shows us that. Darwin's prediction that random variation and natural selection leads to increased fitness has been repeatedly verified.

It's a prediction that has been experimentally verified, and directly observed in nature.

Can you give some examples for both please.

Of course. Variation occurs randomly. Fitness increases by natural selection.

My point was not all variation happens randomly. It is only because some take a narrow view of how life can evolve by only using the Darwinian evolution that they think variations occur randomly to justify the relevance of natural selection and give it prominence as that is what is claimed to direct the appearance of life. But this is an assumption based on having a narrow view and excluding alternative processes like I have mentioned in the EES.

So far, no one has been able to show that anything else works. So that's not a good assumption.

Of course they have been able to show other methods work that either diminish or bypass natural selection altogether. What about the processes I have been posting about like developmental bias, plasticity, niche construction and inheritance beyond genes to begin with? Then add HGT and symbiosis.

The point is natural selection acts on the variation it is given. Natural selection is only given an elevated position because some people believe that variation can only come from a random process and therefore will need sorting. But what about variation that comes from a non-random source. Variation that comes from a non-random source is mostly non-random because it is meant to happen. It stems from a part of something that is designed to provide living things with what they need and therefore is already selected to be of benefit. This diminishes and even eliminates the role of natural selection. I have already supplied support for this in the papers I posted. But here are some examples

In addition, in the EES, development assumes a constructive role, natural selection is not the only way that variation in populations can be modified, causation does not run solely in one direction from the external environment to populations and, instead of a single inheritance mechanism, several modes of transmission exist between generations.


In this perspective, developmental bias and plasticity assume central roles as generators of novel and coordinated phenotypic variation by conferring directionality on the selective processes.
Why an extended evolutionary synthesis is necessary

In other words, developmental bias and plasticity can direct what natural selection can and cannot do and in some cases bypass natural selection altogether to provide well suited and integrated variations. You need to read the entire section to understand exactly why but it is to do with the way developmental processes work in which certain forms are produced over others and therefore are already pre-determined as most suitable. Also, the way in which living things are connected and in tune with their environment which allows them to receive and give feedback and change accordingly in form that will suit the particular circumstances. Because these variations are usually in tune with a creature situation, they are already well suited to what they need and therefore not randomly produced or need sifting through selection.

Not surprising, since that's what we see in nature.

The evidence seems to actually contradict this and that is the whole point of the EES. To say that is what we see in nature is to dismiss a lot of scientific research that contradicts the gradualist, gene centric and adaptive view. Some of this support is what I posted above which explains how not all variation stems from random mutations and selection which are based on the gene centric view. If natural selection is minimised and bypassed, then so is adaptive evolution.

Some variations just happen and is not a result of adaptation but a consequence of development. A bit like the arches and Spandrels argument from Gould and Lewontin. Arches may be needed to hold up the roof, but spandrels are just the extended design of arches and therefore have no benefit for fitness and survival. Large change can happen suddenly through development in regulatory genes and not as a consequence of adaptive gradual adaptive evolution (Cambrian Explosion). The evidence for this is growing and I think you need to read the papers to fully appreciate the evidence for this. This can probably be summed up with these quotes for the following papers

Whereas the MS theory and its various amendments concentrate on genetic and adaptive variation in populations, the extended framework emphasizes the role of constructive processes, ecological interactions and systems dynamics in the evolution of organismal complexity as well as its social and cultural conditions. Single-level and unilinear causation is replaced by multilevel and reciprocal causation. Among other consequences, the extended framework overcomes many of the limitations of traditional gene-centric explanation and entails a revised understanding of the role of natural selection in the evolutionary process.
Why an extended evolutionary synthesis is necessary. - PubMed - NCBI

EES difference to the MS
strikingly different novel phenotypes can occur, either through mutation of a major regulatory control gene expressed in a tissue-specific manner, or through facilitated variation
About the EES – Extended Evolutionary Synthesis

That would require an exhaustive census of a population, and very close monitoring of the population. Not surprisingly, when this was done on Daphne Major, the accumulation of small genetic changes was observed:

This does not mean that this was caused by Darwin’s evolutionary process. As noted, development allows for the regulation of genes to switch on and off its components to vary shape and size. There is a fair amount of plasticity available to varying forms as well which is a response to environmental pressures. But isn’t it a strange coincident that many birds were able to just happen to evolve the ideal beak in a number of different environmental situations or was there some connection between what the birds were experiencing and the influence this had on their physical features?

There certainly may be other factors. But so far, nothing that doesn't fit a Darwinian framework.

I cannot see how you can say this when there is so much evidence such as in the EES that contradicts this. The very idea of the EES is to show that the Darwinian framework is inadequate and too narrow for accounting and explaining what we have seen and discovered especially in the light of the other modern sciences such as genomics, development, embryology, ecology and social science.

That's a Darwinian principle; fitness only counts in terms of environment. Of course, a changing environment will influence evolution. Darwin established that from the start.

Yes but Darwin saw the change coming through random mutations acting on genomes and natural selection sifting variations which were a limited view. We now know there are a number of other processes that are involved in how variations are formed. Ecology is used in a different meaning as far as the EES is concerned. Whereas Darwinian evolution creatures are adapted to environments under the EES creatures can change the environment to better suit them and avoid gene change to survive. So rather than be adapted to environments they adapt environments to them.

The environment can also effect phenotypic change through a direct effect on tissues and cells rather than from an internal process of mutational change of genes. So, it is a two-way influence rather than a single process programming gene to change phenotypes. Some influence also comes from the cultural and social conditions created that can affect evolvability. The standard theory has a limited view on what contributes to change and is being outdated whereas the EES is more inclusive and can account for what we are finding.

I have a master's degree in systems, with my work in biological systems. Tell me what tools you've used to look at this problem.

As with systems there can be a number of influences that need to be considered to understand the whole system. Despite some saying that the Modern synthesis includes a wider range of influences most still focus purely on gene (allele) change through mutation and natural selection. Most supporters of the EES point out this gene centric and adaptive approach does not include other factors that affect phenotypic change and evolvability as mentioned in this post. Because of this the EES takes a systems theory approach by including all the possible influences of evolutionary change. This can be summed up below

As a consequence, unlike the MS, the EES includes a constructive component. Instead of chance variation in DNA composition, evolving developmental interactions account for the specificities of phenotypic construction. This interpretation is also based on a fundamentally different account of the role of genes in development and evolution. In the EES, genes are not causally privileged as programs or blueprints that control and dictate phenotypic outcomes but are rather parts of the systemic dynamics of interactions that mobilize self-organizing processes in the evolution of development and entire life cycles.
Why an extended evolutionary synthesis is necessary

Which factors are those?

The EES mentions that there are several processes that can dictate what natural selection can and cannot do and are therefore causes and drivers of evolution such as

What, specifically, do you think is directing evolution?

Influences like developmental bias, plasticity, niche construction, inheritance beyond genes all cause and direct evolution. These can have an influence on how and when natural selection can influence change and can be summed up with the following.

The extended evolutionary synthesis perspective
too much causal significance is afforded to genes and selection, and not enough to the developmental processes that create novel variants, contribute to heredity, generate adaptive fit, and thereby direct the course of evolution.


So in other words they are saying too much emphasis is being placed on the adaptive view of evolution through gene change and natural selection and that there are other forces that cause and direct evolution which occur through other processes such as.


In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism–environment complementarity.

the diversity of organismal form is only partly a consequence of natural selection—the particular evolutionary trajectories taken also depend on features of development. Some work on developmental bias suggests that phenotypic variation can be channelled and directed towards functional types by the processes of development [27,28].


The pathways of inheritance that derive from a parental phenotype (‘parental effects’) have a number of evolutionary consequences similar to those of plasticity, cultural inheritance and niche construction [67]. For example, non-genetic inheritance can bias the expression and retention of environmentally induced phenotypes, thereby influencing the rate and direction of evolution [68].
http://rspb.royalsocietypublishing.org/content/282/1813/20151019

The field of evolutionary development seems to be rather Darwinian to me. How do you suppose it's not? Evo-devo seems inherently "gene-centric" to me.

It is different to Darwin’s main tenets of evolution theory in that development processes can produce biased variations as opposed to random variations with Darwin’s theory of random mutations. Darwin’s theory requires random variations for natural selection to work on. If the variation is fixed to one outcome that is already well suited, then what is selection going to work on. Biased variations point to pre-determined changes that would be more associated with design than a random and blind process like Darwin’s evolution.

Also, developmental plasticity will not involve genes, so it cannot be gene centric at least initially. The variation is often well suited and therefore does not need to be sifted through selection. But these are only part of the processes that the EES mentions. Niche construction does not involve genes, and inheritance beyond genes is the same and more about self-organising abilities that will improve evolvability.

The point is not that evolution does not involve gene change, but that Darwin’s theory focuses exclusively on gene change as being the only method for phenotypic variation. Whereas there are other influences as already mentioned that are causes of evolution already mentioned that Darwin’s theory excludes which need to be considered to get the whole picture of what is going on.

There don't seem to be that many advocates of the strict adaptionist approach, these days.

Whenever I read articles about evolution or speak to people on this forum and others, they still seem to talk about everything in terms of natural selection and population genetics. Explaining how features and behaviour came about in adaptive terms for the survival of species i.e. the gazelles run fast to escape the lion, apes walk upright to get a better view through the grasses, humans cooperate to avoid conflict to survive etc. Evolution by natural selection is an easy concept to hold even for lay people and this is cemented by scientists like Dawkins who praise the power of selection and the adaptive view.

 

[The Barbarian]

Can you give some examples for both please.

Sure. A culture of bacteria was observed to evolve a new, irreducibly-complex enzyme system in a few months. The observation showed that many mutations occurred in this time, most of them not adaptive. The few adaptive ones persisted and produced bacteria more fit for that environment.
REGULATION OF NEWLY EVOLVED ENZYMES. I. SELECTION OF A NOVEL LACTASE REGULATED BY LACTOSE IN ESCHERICHIA COLI

Barry G. Hall and Daniel L. Hartl

Genetics March 1, 1974 vol. 76 no. 3 391-400

A population of lizards, removed to an island with a new environment, evolved stronger jaws and a new digestive organ in a few decades.
In 1971, biologists moved five adult pairs of Italian wall lizards from their home island of Pod Kopiste, in the South Adriatic Sea, to the neighboring island of Pod Mrcaru. Now, an international team of researchers has shown that introducing these small, green-backed lizards, Podarcis sicula, to a new environment caused them to undergo rapid and large-scale evolutionary changes.
Lizards Undergo Rapid Evolution After Introduction To A New Home

My point was not all variation happens randomly.

That's natural selection. Perhaps you're confusing individuals with populations. Populations evolve. Individuals do not. Mutations happen randomly. Luria and Delbruck got their Nobel for demonstrating this fact.

On the other hand, there are epigenetic changes, but so far, no one's shown that such changes persist more than a generation or so.

It is only because some take a narrow view of how life can evolve by only using the Darwinian evolution that they think variations occur randomly to justify the relevance of natural selection and give it prominence as that is what is claimed to direct the appearance of life. But this is an assumption based on having a narrow view and excluding alternative processes like I have mentioned in the EES.

It might be useful to find a mechanism for those. It would go a long way to showing that they exist.

Of course they have been able to show other methods work that either diminish or bypass natural selection altogether. What about the processes I have been posting about like developmental bias, plasticity, niche construction and inheritance beyond genes to begin with? Then add HGT and symbiosis.

Perhaps you could demonstrate the mechanism for these, and how you think they aren't possible under natural selection. Symbiosis, for example, obviously occurs by Darwinian processes.

The point is natural selection acts on the variation it is given.

Darwin's point, in fact. It's a basic part of Darwinian theory.

Natural selection is only given an elevated position because some people believe that variation can only come from a random process and therefore will need sorting.

So Luria and Delbruck showed in their work.

But what about variation that comes from a non-random source. Variation that comes from a non-random source is mostly non-random

I would have thought it would be entirely non-random. But variation in a population is random only if it has no effect on fitness. Otherwise, it's directed by natural selection, which is inherently non-random.

because it is meant to happen.

Show us that. Michael Denton has such beliefs, imagining a teleological universe, in which things are meant to be. And yet, he is quite comfortable with natural selection, assuming the universe is front-loaded so that things meant to be happen entirely by natural processes. So perhaps it's not necessary for you to seek another mechanism for your beliefs.

It stems from a part of something that is designed to provide living things with what they need and therefore is already selected to be of benefit. This diminishes and even eliminates the role of natural selection. I have already supplied support for this in the papers I posted. But here are some examples

In addition, in the EES, development assumes a constructive role, natural selection is not the only way that variation in populations can be modified, causation does not run solely in one direction from the external environment to populations and, instead of a single inheritance mechanism, several modes of transmission exist between generations.

I marked the key word here. Assumptions are always better if they are supported by real data. BTW, even Darwin noted that selection is not one-way. Environment pushes on populations, and they often push back, modifying the environment. That's not a new idea.

Some variations just happen and is not a result of adaptation but a consequence of development.

It's merely random mutation. Directly observed to be so.

Large change can happen suddenly through development in regulatory genes and not as a consequence of adaptive gradual adaptive evolution (Cambrian Explosion).

The Cambrian explosion seems to have been largely due to the evolution of completely scleritized bodies, allowing a rapid diversity in life styles.

There certainly should be more to evolution than the Modern Synthesis. Neutralist theories and punctuated equilibrium have already become part of Darwnian theory. But assumptions of teleological processes will still need some support in the real world.

This does not mean that this was caused by Darwin’s evolutionary process. As noted, development allows for the regulation of genes to switch on and off its components to vary shape and size.

And your position is that random mutation and natural selection could not produce such a feature?

There is a fair amount of plasticity available to varying forms as well which is a response to environmental pressures. But isn’t it a strange coincident that many birds were able to just happen to evolve the ideal beak in a number of different environmental situations or was there some connection between what the birds were experiencing and the influence this had on their physical features?

The Grants, studying a population of finches on Daphne Major, found that yes, the environment did determine the size and shape of beaks.

I cannot see how you can say this when there is so much evidence such as in the EES that contradicts this.

Gould didn't think so. He considered himself an "orthodox Darwinian." Of course, Darwinian theory has been repeatedly modified. First by genetics, then by neutralist theories, then by punctuated equilibrium, and again by evolutionary development.

Which of Darwin's five points do you think were refuted by any of that?

Whereas Darwinian evolution creatures are adapted to environments under the EES creatures can change the environment to better suit them and avoid gene change to survive. So rather than be adapted to environments they adapt environments to them.

Darwin described exactly that in his work on earthworms and their effect on soil.

The environment can also effect phenotypic change through a direct effect on tissues and cells rather than from an internal process of mutational change of genes.

Show us a heritable example of that. It seems you're putting a great deal of faith into the EES, which is real, but not the teleological end you seem to think it is.

As a consequence, unlike the MS, the EES includes a constructive component. Instead of chance variation in DNA composition, evolving developmental interactions account for the specificities of phenotypic construction. This interpretation is also based on a fundamentally different account of the role of genes in development and evolution. In the EES, genes are not causally privileged as programs or blueprints that control and dictate phenotypic outcomes but are rather parts of the systemic dynamics of interactions that mobilize self-organizing processes in the evolution of development and entire life cycles.

Show us those.



[/quote]

 

[stevevw]

Sure. A culture of bacteria was observed to evolve a new, irreducibly-complex enzyme system in a few months. The observation showed that many mutations occurred in this time, most of them not adaptive. The few adaptive ones persisted and produced bacteria more fit for that environment.
REGULATION OF NEWLY EVOLVED ENZYMES. I. SELECTION OF A NOVEL LACTASE REGULATED BY LACTOSE IN ESCHERICHIA COLI

Barry G. Hall and Daniel L. Hartl

Genetics March 1, 1974 vol. 76 no. 3 391-400

From what I understand with experiments like this they are really only talking about what I have already mentioned that this is activating a pre-existing and inbuilt ability for organisms to be able to adapt to new environments. The ability for bacteria to regulate lactose was activated or reactivated in this case. This is similar to examples of antibiotic resistance in bacteria. The mutations are classed as adaptive mutations (directed mutations) which were directed towards a certain outcome and not the result of Darwinian evolution.

This is similar to how development only produces certain outcomes with variation rather than a number of outcomes that would be expected with Darwinian evolution that is random and blind. If the outcome presented is restricted to one choice and is directed towards that one choice, then this can hardly be classed as Darwinian. The problem is some confuse this as Darwinian. Even the author acknowledges this about directed mutations.

Hall summarizes adaptive mutations well when he writes:

Adaptive mutations differ from growth-dependent mutations in two key respects. First, adaptive mutations occur in nondividing or slowly dividing cells which are under selection for a particular phenotype, whereas growth-dependent mutations occur in dividing cells that are not under strong selection. Second, adaptive mutations produce only those phenotypes which allow the cells to grow, whereas growth-dependent mutations occur randomly with respect to their effects on fitness.
Adaptive Mutagenesis at ebgR Is Regulated by PhoPQ

A population of lizards, removed to an island with a new environment, evolved stronger jaws and a new digestive organ in a few decades.

Once again this seems like all that is happening is like the finches being studies that changes in head size and shape are more to do with developmental processes. This is what people term micro evolution where there is a natural ability for creatures to vary but only up to a certain limit. The environmental pressure of the new environment had an effect on the creature and this, in turn, activated a change that responded to those pressures that produced the exact changes needed.

It was not a case that random mutations throwing up many different variations and natural selection eventually finding one that was of benefit and weeded out all those that were not. Developmental mechanisms made specific changes to vary the Lizards form to meet those environmental pressures. When the lizards are trying to eat tougher vegetation, its body is affected through the cells and tissues and this, in turn, will activate the genetic changes associated with the area that is under pressure and make those changes. The new environment can influence changes in form by the new conditions that are placed upon it.

For example, a plant placed in a new environment can form because of the different makeup of the environment such as the soil and surrounding environments and other plants.

We know that in the case of the fruit fly, Drosophila melanogaster, where the same kind of experiments were done, that epigenetic inheritance at the level of the chromatin binding proteins is involved14,15. What this means is that epigenetic variation within a cell, can lead to a positively reinforced response (which is developmentally selected), and then this response can be inherited by a new generation of cells or organisms (even if they are multicellular organisms).
Epigenetic inheritance in evolution: an interview with Eva Jablonka – Extended Evolutionary Synthesis

strikingly different novel phenotypes can occur, either through mutation of a major regulatory control gene expressed in a tissue-specific manner, or through facilitated variation
Developmental Bias and Evolution: A Regulatory Network Perspective

In modern-day organisms, there is significant plasticity. You don't have to go back 600 million years to see that. If you take a plant and put it in different soil or a different environment, it can look entirely different.
The Origin of Form Was Abrupt Not Gradual - Archaeology Magazine Archive

As a consequence, the EES predicts that organisms will sometimes have the potential to develop well-integrated, functional variants when they encounter new conditions, which contrasts with the traditional assumption of no relationship between adaptive demand and the supply of phenotypic variation [5,122]. For example, phenotypic plasticity and non-genetic inheritance contributed to the adaptation of the house finch to cold climates during its North American range expansion ([68]; see [27,28,49,101,105,107] for further examples).
https://royalsocietypublishing.org/doi/full/10.1098/rspb.2015.1019#ref-68

That's natural selection. Perhaps you're confusing individuals with populations. Populations evolve. Individuals do not. Mutations happen randomly. Luria and Delbruck got their Nobel for demonstrating this fact.

No I am talking about the mechanism that produces the variation in the first place for natural selection to act on. Yes, random mutations are one mechanism for producing some variations. Because they are random, they can be good bad or neutral, so this is where natural selection comes in and is supposed to weed out the bad to leave rare good mutations. But this can be hit and miss.

There are other mechanisms besides random mutations that produce variations that are not random. Some of those mechanisms such as in development and niche construction produce well suited and integrated variations and therefore don't need to be naturally selected because they have selected themselves in the sense that this was the only best option or the chosen option by the creature themselves.

On the other hand, there are epigenetic changes, but so far, no one's shown that such changes persist more than a generation or so.

According to the articles I am citing they do, and this is part of the new research that is challenging Darwinian evolution as being the cause of all change. Epigenetics is just one aspect of this. When taken all together there is a raft of influences that cause and direct evolution.

It might be useful to find a mechanism for those. It would go a long way to showing that they exist.

I don't understand what you mean by showing they exist and finding the mechanisms. The papers show that these extra mechanisms such as developmental bias and plasticity, niche construction, and extra genetic inheritance do exist. I have been providing this support, but it is being overlooked.

Perhaps you could demonstrate the mechanism for these, and how you think they aren't possible under natural selection. Symbiosis, for example, obviously occurs by Darwinian processes.

As far as I understand symbiosis does not work on Darwinian processes alone and in fact has been used to dispute Darwinian evolution as a means of change without the need for random mutations and Natural selection by one of the pioneers of symbiosis Lyn Margulis. Symbiosis is sort of like one living organism cohabitating with another so that a new form of life is produced.

Lynn Margulis: Symbiosis Is The Driver of Evolution
The dominant theory of evolution (often called Neo-Darwinism) holds that new species arise through the gradual accumulation of random mutations, which are either favoured or weeded out by natural selection. To Margulis, random mutation and natural selection are just cogs in the gears of evolution; the big leaps forward result from mergers between different kinds of organisms, what she calls Symbiogenesis.
http://www.everythingology.com/lynn-margulis-symbiosis-is-the-driver-of-evolution/

As far as the other processes are concerned, I have already explained and linked articles on these and how they can produce variations besides random mutations and natural selection. For example, developmental bias is not random and produces variation. That variation is biased and only produces what is needed and therefore does not need to be naturally selected. Plasticity can produce phenotypic change initially without changing genes so there is no random mutation going on because there is no genetic variation associated. The change can be environmentally induced and therefore can be well suited and integrated variation. This variation does not need to be naturally selected as well.

Niche construction allows living things to control evolution and how they vary. This also is not produced by random mutations and natural selection is either minimized or bypassed because the variations produced are exactly what is needed by the creature involved because they are the ones generating the conditions that produce those variations. The same for the variations produced by inheritance beyond genes such as by epigenetic and other influences from the way creatures create cultural and social environments that contribute to evolvability.

Here are some quotes from the articles I have posted that specify that random mutation is not the only way living things can generate variation and that natural selection can be either dictated by other influences in what it can and cannot do or is bypassed altogether. You will have to read the articles to understand this in more detail.

Developmental processes play important evolutionary roles as causes of novel, potentially beneficial, phenotypic variants, the differential fitness of those variants, and/or their inheritance (i.e. all three of Lewontin's [98] conditions for evolution by natural selection). Thus, the burden of creativity in evolution (i.e. the generation of adaptation) does not rest on selection alone [12,19,25,27,60,64,73,99–101].

The above quote is stating that development processes can produce variations that result in the same variants that evolution by natural selection is supposed to produce. Therefore developmental processes can be a substitute for evolution by natural selection.

The evolutionary significance of niche construction stems from: (i) organisms modify environmental states in non-random ways, thereby imposing a systematic bias on the selection pressures they generate; (iv) the complementarity of organisms and their environments can be enhanced through niche construction (modifying environments to suit organisms), not just through natural selection

the EES recognizes processes that bias the outcome of natural selection, specifically developmental bias and niche construction. All processes that generate phenotypic variation, including developmental plasticity and some forms of inclusive inheritance, are potential sources of bias. A broadened conception of inheritance encompasses genetic, epigenetic and ecological (including cultural) inheritance.

The most striking and contentious difference from the original MS concerns the relative significance of natural selection versus generative variation in evolution, one of the oldest controversies in evolutionary biology (e.g. [116,117]). In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism–environment complementarity.

The EES proposes that variation is more predictable and selection pressures less exogenous than hitherto thought.

Among other consequences, the extended framework overcomes many of the limitations of traditional gene-centric explanation and entails a revised understanding of the role of natural selection in the evolutionary process.

Particular forms of phenotypic change are taken as the result of internal generative conditions rather than external pruning. Thus, a significant amount of explanatory weight is shifted from external conditions to the internal properties of evolving populations. In addition, natural selection may be ‘bypassed’ by environmental induction, causing potentially adaptive developmental variation in many individuals of a population at once and long before natural selection may become effective.

Evolution is a process of the introduction, inheritance and reproductive sorting of variation in a hierarchy of reproducing entities, and today we know that important differential effects arise not only from biased reproductive sorting (selection), but from biases in the introduction of variation (mutational and developmental biases), and biases in inheritance (e.g., biased gene conversion). Natural selection cannot account generally for the course of evolution, due to the influence of neutral evolution and of these other factors.

The EES is thus characterized by the central role of the organism in the evolutionary process, and by the view that the direction of evolution does not depend on selection alone and need not start with mutation.

The EES challenges the standard evolutionary theory (SET). The above can be summed up with a quote from one of the papers which highlights the different positions each take.

too much causal significance is afforded to genes and selection, and not enough to the developmental processes that create novel variants, contribute to heredity, generate adaptive fit, and thereby direct the course of evolution.

Darwin's point, in fact. It's a basic part of Darwinian theory.

Yes but as opposed to the variation needing to be sifted out from other non-beneficial variation which is what natural selection does the variations produced by some of the EES processes such as developmental bias or plasticity can be beneficial and be the only variation presented to natural selection. If this is the case, then natural selection has little work to do and is in fact relegated to a minor role or no role at all.

 

[The Barbarian]

From what I understand with experiments like this they are really only talking about what I have already mentioned that this is activating a pre-existing and inbuilt ability for organisms to be able to adapt to new environments. The ability for bacteria to regulate lactose was activated or reactivated in this case. This is similar to examples of antibiotic resistance in bacteria. The mutations are classed as adaptive mutations (directed mutations) which were directed towards a certain outcome and not the result of Darwinian evolution.

No, that's wrong. The new enzyme wasn't created de novo, but was a modification of an existing enzyme. There was no "reactivation"; the enzyme gradually became efficient at catalyzing the substrate over a period of and countless mutations, only a few of which led to the new enzyme.

This is similar to how development only produces certain outcomes with variation rather than a number of outcomes that would be expected

The bacteria, for example, had a huge number of outcomes, only a few of which survived, due to natural selection.

with Darwinian evolution that is random and blind.

Darwin's great discovery was that it isn't random.

If the outcome presented is restricted to one choice and is directed towards that one choice, then this can hardly be classed as Darwinian.

It wasn't. But some are more fit than others. That's the one that eventually evolved. Was it constrained to a specific path? No. This is why the genes in different taxa may do the same things, but do it in entirely different ways. Would you like to see some examples?

Adaptive mutations differ from growth-dependent mutations in two key respects. First, adaptive mutations

occur in nondividing or slowly dividing cells which are under selection for a particular phenotype, whereas growth-dependent mutations occur in dividing cells that are not under strong selection. Second, adaptive mutations produce only those phenotypes which allow the cells to grow, whereas growth-dependent mutations occur randomly with respect to their effects on fitness.

Adaptive Mutagenesis at ebgR Is Regulated by PhoPQ

This doesn't seem to be what you think it is. From the paper:
The process or processes that produce adaptive mutations are not well understood. The most widely used system, reversion of the F′-borne lacI33 frameshift mutation during selection for growth on lactose, led to the conclusion that genes whose products are involved in recombination are necessary for adaptive mutagenesis (1, 15). That conclusion has been cast into doubt by the finding that when the lacI33 frameshift allele is located on the chromosome, rather than on the F′ episome, adaptive reversion is not affected by lesions in recombination genes (4).

Once again this seems like all that is happening is like the finches being studies that changes in head size and shape are more to do with developmental processes. This is what people term micro evolution where there is a natural ability for creatures to vary but only up to a certain limit.

Can you show us an organism that is at that limit, and can vary no more?

It was not a case that random mutations throwing up many different variations and natural selection eventually finding one that was of benefit and weeded out all those that were not.

Show us your evidence for that.

Developmental mechanisms made specific changes to vary the Lizards form to meet those environmental pressures.

Show us those mechanisms.

When the lizards are trying to eat tougher vegetation, its body is affected through the cells and tissues and this, in turn, will activate the genetic changes associated with the area that is under pressure and make those changes.

Starvation, for example. Selective pressure is indeed what made those changes. But show us your evidence that the only changes in the population were adaptive ones. When we observe this sort of thing, as the Grants did on Daphne Major, various changes occured, but only those with the advantageous variations lived long enough to reproduce.

The new environment can influence changes in form by the new conditions that are placed upon it.

So Darwin showed us.

For example, a plant placed in a new environment can form because of the different makeup of the environment such as the soil and surrounding environments and other plants.

Which is most often, the same as changes in human physiology, depending on altitude.

No I am talking about the mechanism that produces the variation in the first place for natural selection to act on. Yes, random mutations are one mechanism for producing some variations. Because they are random, they can be good bad or neutral, so this is where natural selection comes in and is supposed to weed out the bad to leave rare good mutations. But this can be hit and miss.

As the Grants demonstrated, this works very well.

As far as I understand symbiosis does not work on Darwinian processes alone and in fact has been used to dispute Darwinian evolution as a means of change without the need for random mutations and Natural selection by one of the pioneers of symbiosis Lyn Margulis. Symbiosis is sort of like one living organism cohabitating with another so that a new form of life is produced.

It's not a crazy idea; eukaryotes are symbiotic organisms. But natural selection mediates that process; it's been directly observed:

Trends In Cell Biology
Volume 5, Issue 3, March 1995, Pages 137-140
Bacterial endosymbiosis in amoebae
Kwang W.Jeon
Abstract
The large, free-living amoebae are inherently phagocytic. They capture, ingest and digest microbes within their phagolysosomes, including those that survive in other cells. One exception is an unidentified strain of Gram-negative, rod-shaped bacteria that spontaneously infected the D strain of Amoeba proteus and came to survive inside them. These bacteria established a stable symbiotic relationship with amoebae that has resulted in phenotypic modulation of the host and mutual dependence for survival.

 

[stevevw]

Darwin's point, in fact. It's a basic part of Darwinian theory.

Yes but as opposed to the variation needing to be sifted out from other non-beneficial variation which is what natural selection does the variations produced by some of the EES processes such as developmental bias or plasticity can be beneficial and be the only variation presented to natural selection. If this is the case, then natural selection has little work to do and is in fact relegated to a minor role or no role at all.

Show us that. Michael Denton has such beliefs, imagining a teleological universe, in which things are meant to be. And yet, he is quite comfortable with natural selection, assuming the universe is front-loaded so that things meant to be happen entirely by natural processes. So perhaps it's not necessary for you to seek another mechanism for your beliefs.

The EES processes are not about fitting anything to a belief and in fact, I would say most who support this are non-believers in God. Rather they are scientists in a number of fields who have been pointing out the inadequacy of the Standard theory for years and are using some evidence that has been around for some time and other new understandings to come up with a concept that fits what we see much better.

It is not about teleological processes. When I say meant to be, I mean these influences are part of how living things are made. It is inevitable and the outcomes are predictable in that they will produce certain outcomes rather than random and blind ones. You could say that this is Gods way of helping living things to adapt to planet earth in that there had to be some way for living things to change with the changing environments otherwise they would not survive.

Living things have mechanisms they were designed with that can produce the changes they need. Just like the laws of physics are designed to keep the cosmos in order or earth stable and able to recover from environmental setbacks. You either believe that somehow these mechanisms came from no intelligible source and just happened to fall into place and enable life and existence to function the way it does or that there is some design behind things. That design is being hijacked and interpreted as naturalistic and random processes that can happen without the need for God by a worldview of evolution.

I marked the key word here. Assumptions are always better if they are supported by real data. BTW, even Darwin noted that selection is not one-way. Environment pushes on populations, and they often push back, modifying the environment. That's not a new idea.

The use of the word assumes in the quote above is not meaning that the EES proposes something without proof. It is used in the context of taking up a position such as the soldier assumes the position of defence. So, they are saying in the EES development assumes a constructive role as opposed to a programmed role. I do not think we need to assume that development cannot construct change, it is one of the biggest constructors of physical forms.

Though Darwinian evolution acknowledges some of these influences that are being rehashed or introduced the theory diminishes their importance and the impact they have on causing and directing evolution. Taken in isolation they each contributes a certain aspect of the EES but together these influences add up to a substantial shift in perspective in how evolution works.

So, what the EES is saying is that variations can happen besides Darwinian evolution. The cause of variations does not just go one way from the external environment acting on populations in changing alleles, but inheritable change can also happen with several other methods. These are also taken into consideration rather than the single method proposed by Darwinian evolution. I don't think I need to cover those other processes as they havee been mentioned before in my posts.

It's merely random mutation. Directly observed to be so.

What about the processes like developmental bias and plasticity, niche construction and the extra hereditary influences? Theey also produce variation except they are non-random.

The Cambrian explosion seems to have been largely due to the evolution of completely scleritized bodies, allowing a rapid diversity in life styles.

There certainly should be more to evolution than the Modern Synthesis. Neutralist theories and punctuated equilibrium have already become part of Darwnian theory. But assumptions of teleological processes will still need some support in the real world.

I think naturalist theories like punctuated equilibrium are more of an assumption anyway that need more support. They have been invented to address the findings in the fossil record rather than actually providing any evidence of how large evolutionary change can suddenly happen.

This is where processes covered in the EES have better explanatory power with ideas such as evolutionary developmental biology which can account for large and sudden changes in phenotypes through the regulation of control genes. If all the genetic info and instructions is already there then it is just a case of restructuring things so that large change can happen during development by switching on or off components/modules of genes.

Recent work in developmental biology has identified dynamical and physical mechanisms of tissue morphogenesis that may underlie abrupt morphological transitions during evolution. Consequently, consideration of mechanisms of phylogenetic change that have been found in reality to be non-gradual is increasingly common in the field of evolutionary developmental biology, particularly in studies of the origin of morphological novelty. A description of such mechanisms can be found in the multi-authored volume Origination of Organismal Form (MIT Press; 2003).

And your position is that random mutation and natural selection could not produce such a feature?

I think what is being interpreted as random mutations is actually more like directed mutations. A change in the existing genetic info that was triggered by environmental pressures which responded with the right sort of changes. Natural selection may have still played a role but perrhaps a deminished role because the variations were already well suited.

The problem I see is that the changes happened quickly and they produced the right sort of variation many times over which seems too good to be true for a random process that will only produce beneficial variations on very rare occassions. Something had to help produce the right variations at the right time and in the right place and be strong enough to be picked up by selection. Rare and slight random mutations cannot do this.

The Grants, studying a population of finches on Daphne Major, found that yes, the environment did determine the size and shape of beaks.

This is in line with the EES

Show us a heritable example of that. It seems you're putting a great deal of faith into the EES, which is real, but not the teleological end you seem to think it is.

Show us those.

It is not a matter of faith becuase the processes the EES talk about are verifiable such as through development. I only summize as other do with theistic evolution that this is Gods way of helping living things live and survive on the planet. I just happen to think it makes more sense than Darwinian evolution alone becuase it fits the evidence better which does not have to be something that is based on faith as non religious scientists are the ones who are coming up with the EES. It just happens to fit with something that God would do in equipping living things with a sure fire way of being able to adapt on earth which is always changing rather than a hit and miss pprocess.

Many of the processes produce heritable changes other than through random mutational variation and natural selection. For example

We know that in the case of the fruit fly, Drosophila melanogaster, where the same kind of experiments were done, that epigenetic inheritance at the level of the chromatin binding proteins is involved14,15. What this means is that epigenetic variation within a cell, can lead to a positively reinforced response (which is developmentally selected), and then this response can be inherited by a new generation of cells or organisms (even if they are multicellular organisms).
http://extendedevolutionarysynthesis.com/epigenetic-inheritance-evolution-interview-eva-jablonka/

Developmental processes play important evolutionary roles as causes of novel, potentially beneficial, phenotypic variants, the differential fitness of those variants, and/or their inheritance (i.e. all three of Lewontin's [98] conditions for evolution by natural selection). Thus, the burden of creativity in evolution (i.e. the generation of adaptation) does not rest on selection alone [12,19,25,27,60,64,73,99–101].


the EES recognizes processes that bias the outcome of natural selection, specifically developmental bias and niche construction. All processes that generate phenotypic variation, including developmental plasticity and some forms of inclusive inheritance, are potential sources of bias. A broadened conception of inheritance encompasses genetic, epigenetic and ecological (including cultural) inheritance.

So as you can see the vriations produced by the processes talked about in the EES not only can come from other sources besides randm mutations and can control what natural selection can and cannot do but also can be inherited by the next generation.

 

[The Barbarian]

Yes but as opposed to the variation needing to be sifted out from other non-beneficial variation which is what natural selection does the variations produced by some of the EES processes such as developmental bias or plasticity can be beneficial and be the only variation presented to natural selection.

As you saw, that's not what happened with Dr. Hall's bacteria.

If this is the case, then natural selection has little work to do and is in fact relegated to a minor role or no role at all.

To verify this belief, one would have to do what the Grants did, and see what was going on in the population, tracking all the mutations going on. That's hard. Hall was able to do it, because bacterial cultures are easier to track. But it's almost certain that he didn't catch all the mutations. Not surprisingly, he found (as Luria and Delbruck discovered much earlier) that favorable mutations don't arrive in response to need.

The EES processes are not about fitting anything to a belief

It is not about teleological processes.

Let's see...

Living things have mechanisms they were designed with that can produce the changes they need.

You don't think design is a teleological process? What do you think "teleological" means?

Just like the laws of physics are designed to keep the cosmos in order or earth stable and able to recover from environmental setbacks.

Only a very, very tiny portion of the cosmos is suitable for life in any way. Moreover, the history of the Earth has shown disastrous changes that wiped out huge parts of the biosphere. A suitably large hit by an asteroid would put an end to almost all living things on Earth, probably sparing only bacteria and archaea deep underground or at geothermal vents in the ocean.

You either believe that somehow these mechanisms came from no intelligible source

God created the universe with rules that lead to life and to us. He says that time and chance happen to all, but even so, He can use chance to effect His purposes as easily as He can use necessity.

That design is being hijacked and interpreted as naturalistic and random processes that can happen without the need for God by a worldview of evolution.

"Design" is an unnecessary assumption. God has no need to figure out things. It's true that one can study life without regard to God. For whatever reason, He did not leave a logically certain evidence of His hand in creation. But that doesn't mean He doesn't exist any more than the fact that plumbing can work without considering God means that it denies God.

Though Darwinian evolution acknowledges some of these influences that are being rehashed or introduced the theory diminishes their importance and the impact they have on causing and directing evolution.

It comes down to evidence. Observations of real populations shows Darwinian processes. Epigenetics and other non-Darwinian processes exist, but they seem to be relatively uncommon. And there's no evidence that they can't evolve by Darwinian means.

Taken in isolation they each contributes a certain aspect of the EES but together these influences add up to a substantial shift in perspective in how evolution works.

I think naturalist theories like punctuated equilibrium are more of an assumption anyway that need more support.

Theories, in science are accepted when they are able to explain the evidence in a parsimonious way; and there is much observational support for PE. It explains, for example, Mayr's observation that aberrant species are found in out-of-the-way places. Observation shows that a well-fitted population in a relatively stable environment has little evolutionary change, but the same population, moved to a new environment, shows considerable evolutionary change in a relatively short time. Darwin discussed this, but didn't seem to realize that it probably was responsible for most speciation.

They have been invented to address the findings in the fossil record rather than actually providing any evidence of how large evolutionary change can suddenly happen.

Actually, this has been repeatedly observed. The evolution of lizards in the Adriatic is an example.

I think what is being interpreted as random mutations is actually more like directed mutations.

The Luria–Delbrück experiment (1943) (also called the Fluctuation Test) demonstrates that in bacteria, genetic mutations arise in the absence of selection, rather than being a response to selection. Therefore, Darwin's theory of natural selection acting on random mutations applies to bacteria as well as to more complex organisms. Max Delbrück and Salvador Luria won the 1969 Nobel Prize in Physiology or Medicine in part for this work.
Luria–Delbrück experiment - Wikipedia

EES has been much less successful in explaining the direction of evolution than has been evolutionary development, which has proven to be a powerful way of analyzing phylogenies and evolutionary change across many phyla.

There is certainly something to the notion that populations don't just fit to environments; often they significantly change environments. And epigenetic change does happen.

Genetic assimilation does not contradict Darwinian processes:
Hsp90 as a capacitor for morphological evolution

• Suzanne L. Rutherford
• & Susan Lindquist

Nature volume 396, pages 336–342 (26 November 1998)
Abstract
The heat-shock protein Hsp90 supports diverse but specific signal transducers and lies at the interface of several developmental pathways. We report here that when Drosophila Hsp90 is mutant or pharmacologically impaired, phenotypic variation affecting nearly any adult structure is produced, with specific variants depending on the genetic background and occurring both in laboratory strains and in wild populations. Multiple, previously silent, genetic determinants produced these variants and, when enriched by selection, they rapidly became independent of the Hsp90 mutation. Therefore, widespread variation affecting morphogenic pathways exists in nature, but is usually silent; Hsp90 buffers this variation, allowing it to accumulate under neutral conditions. When Hsp90 buffering is compromised, for example by temperature, cryptic variants are expressed and selection can lead to the continued expression of these traits, even when Hsp90 function is restored. This provides a plausible mechanism for promoting evolutionary change in otherwise entrenched developmental processes.

 

[Gottservant]

most of this conversation is over my head...

needless to say "evolution being relative" means

absolution of design is impossible

why?

because design can be compared with design, evolution cannot be compared with evolution!

 

[The Barbarian]

absolution of design is impossible

What did design do to need absolution?