Slijper’s two-legged goat - developmental plasticity

[Diderot]

In her treatise 'Developmental plasticity and the origin of species differences' (PDF), Mary Jane West-Eberhard argues 'that the origin of species differences, and of novel phenotypes in general, involves the reorganization of ancestral phenotypes (developmental recombination) followed by the genetic accommodation of change'.
As an example West-Eberhard writes about 'the famous two-legged goat described in 1942 by the Dutch morphologist Slijper'. 'Slijper’s two-legged goat was born with a congenital defect of the front legs so that it could not walk on all fours, and so it learned to walk and run by using its hind legs alone.' After its accidental death Slijper documented 'remarkable changes in muscle and bone, including striking changes in the bones of the hind legs; the leg muscles, including a greatly thickened and elongated gluteal tongue and an innovative arrangement of small tendons, a modified shape of the thoracic skeleton, and extensive modifications of the pelvis.'
According to West-Eberhard 'a very large body of evidence shows that phenotypic novelty is largely reorganizational rather than a product of innovative genes.' And it is 'genetic change that follows, and is directed by, the reorganized condition of the phenotype.'

My questions are:
1. What is doing the reorganization?
2. How is genetic change directed by the reorganized condition of the phenotype?

 

[Darwin123]

In her treatise 'Developmental plasticity and the origin of species differences' (PDF), Mary Jane West-Eberhard argues 'that the origin of species differences, and of novel phenotypes in general, involves the reorganization of ancestral phenotypes (developmental recombination) followed by the genetic accommodation of change'.
As an example West-Eberhard writes about 'the famous two-legged goat described in 1942 by the Dutch morphologist Slijper'. 'Slijper’s two-legged goat was born with a congenital defect of the front legs so that it could not walk on all fours, and so it learned to walk and run by using its hind legs alone.' After its accidental death Slijper documented 'remarkable changes in muscle and bone, including striking changes in the bones of the hind legs; the leg muscles, including a greatly thickened and elongated gluteal tongue and an innovative arrangement of small tendons, a modified shape of the thoracic skeleton, and extensive modifications of the pelvis.'
According to West-Eberhard 'a very large body of evidence shows that phenotypic novelty is largely reorganizational rather than a product of innovative genes.' And it is 'genetic change that follows, and is directed by, the reorganized condition of the phenotype.'

The claim is that most major changes in form are caused by changes in timing. The spatial and behavior organization of living things is to a large part determined by when chemical reactions occur relative to each other. How things connect together is determined by small changes in timing that accumulate.

The goat with two legs was not different from conception. The chemicals that made up the goat were not different. The same enzymes were present in this goat as in any other goat. The cellular structure of the goat was the same in this goat as in any other goat. Even the steps in development were probably the same. The differences in this goat were made by the timing in what happened, not in the list of what happened.

The individual cells in the front legs did not “know” they were supposed to make a front leg. Their programming, if there is any, told them what to do when they were in a limb bud. Turn left, turn right, divide, stop dividing, stick together, don’t stick together. A cell responds to its immediate environment at the moment that a gene expresses itself. So what mutations do is change the response in the immediate environment. So on a molecular level, the mutation was really about when something occurred. Not what occurred. This is reorganization, not novelty.

There was no gene for front legs that disappeared due to mutation. What probably happened is that the part of the gene that determines timing changed, not the part that codes for the enzyme. The genes that made the enzyme for bone growth did not turn on in the limb bud at the precise time necessary to grow the front limb. The genes that made enzymes for muscle growth in the limb bud probably did turn on, but the muscles attached to different tissues because there was no bone available.


http://www.stri.si.edu/sites/publications/PDFs/West_Eberhard_2005_PNAS_STRI.pdf
“In developmental recombination, phenotypic traits are expressed in new or distinctive combinations during ontogeny, or undergo correlated quantitative change in dimensions. In the most easily visualized examples, elements of the phenotype controlled by switches are turned off or on in novel combinations.”

My questions are:
1. What is doing the reorganization?

A so called allele has two parts: a section that codes for a particular protein and a section that determines when the protein is made. I will refer to the part with the sequence that determines the protein as the sequence. I will refer to the part that determines when that protein is made as the switch. The switch is turned on and off by certain proteins made nearby that are controlled by other genes.

The mutations that this person is talking about occur in the switch, not the sequence. The mutation causes a delay or a speed up in the time where the associated protein is made. The activity of the cell during development is determined by when that protein is made relative to when other proteins are made.

2. How is genetic change directed by the reorganized condition of the phenotype?

This is backwards. The phenotype is determined by the series of chemical events. The resulting phenotype is the consequence of the series of chemical events.

The phenotype is effected by the genetic change indirectly. There could be a mutation that affects the sequence of amino acids that defines the protein. I think this is what the article means by novelty. However, it is more likely that a mutation affects when a particular protein is made. I think this is what the author thinks of as reorganization.

Whether the change occurs in the switch or the sequence, it is the series of events that is changed when the genes are changed. The resulting phenotype is the consequence of the series of events. If events occur in a different order, the anatomical form of the final animal is going to be in a different order.

Thin origami, not sculpture.
1) When a new form is made in origami, who is doing the reorganization?
2) How does someone direct the change in origami form?

Repeat with balloon animals.

 

[Diderot]

Mr. Darwin123, the front legs of the goat, or rather the lack thereof, are not worthy of your attention. Please direct your focus to the area of the hind legs. What is in need of explanation is ’the expression of a whole suite of correlated and adaptive changes in behavior, muscle, and bone.’
Slijper's goat developed into a 'new' coherent animal that in some respects looks more like a kangaroo than a goat. How do we explain this 'suite of correlated and adaptive changes'? How can the kangaroo-like development be explained considering the goat’s hereditary makeup?

 

[Darwin123]

Mr. Darwin123, the front legs of the goat, or rather the lack thereof, are not worthy of your attention. Please direct your focus to the area of the hind legs. What is in need of explanation is ’the expression of a whole suite of correlated and adaptive changes in behavior, muscle, and bone.’
Slijper's goat developed into a 'new' coherent animal that in some respects looks more like a kangaroo than a goat. How do we explain this 'suite of correlated and adaptive changes'? How can the kangaroo-like development be explained considering the goat’s hereditary makeup?

Part of the plasticity is "training". Organs like the brain and muscles accumulate experience.

A lot of this has to do with the goats brain. The brain with associated memory is an organ which evolved to give the organism plasticity. Some brains are ruled by instincts, which are specific behaviors that the animals inherits which don't involve learning. Some brains also have drives, which are specific behaviors that the animals develops which involves learning.

Goat's are very smart animals. The goat has a drive to move around. In the wild, it does a lot of climbing. Whenever it learns something that gives it mobility, the goat is rewarded. If it is forced to stand still, it suffers. Eventually, it learns what behaviors are necessary to get it prancing.

Note: I am not discounting heredity. The goat inherits a brain that can learn and drives which force it to do so. However, the resulting "learned behavior" may be very different from the learned behavior of other goats without the disability.

Muscles that get used more get larger. This is an inherited capability. The result would be muscles that had already developed will get stronger with use. If the goat learns to dance with its hind legs, then the muscles of the hind legs will get larger. This is a type of training.

As for prenatal changes in the hind legs, I don't know. However, you haven't provided any evidence that the hind legs of this goat are fundamentally different from the hind legs of any other goat. Your comparison of this goat to kangaroos is just an analogy. You could have equally compared the goat to a bird or any other bipedal animal.

Maybe the goat was born with the same hind legs as any other goat. In the adult, training muscle made the proportions of the muscles vary from other goats. However, the topology of the muscles was much the same. It's brain learned how to walk on two legs the same way that all animals learn to walk on two legs by trial and error. The circuitry of the brain was different, but because of learning.

Does the author of this article really make a comparison between this goat's morphology and the morphology of a kangaroo? Why not make the comparison between the legs of this goat and a bird? Birds, kangaroos and two legged goats hop.

Note that there are dogs that learn to walk on hind legs with no training from humans. Some individual dogs just like to walk on two legs. A lady that I met showed me her Yorkie. The Yorkie walked on hind legs. She swore that she never trained it to do so. It just liked to do so.

I walk on all fours sometimes. It is useful when I dropped something on the floor. There are people who can walk on their hands. The anatomy of the limbs involved have not changed dramatically. However, they have learned to do so.

Please note that memory is mediated by those genetic switches that I was talking about. Furthermore, both tissues that I have talked about, muscles and nerves, have prion proteins. Prions are proteins which can copy structures from other prion proteins. I conjecture that some of the ability of nerves and muscles to train may have something to do with the prions.

 

[Diderot]

The brain with associated memory is an organ which evolved to give the organism plasticity.

However smart goats may be, the novel phenotype induced by a correlated shift in morphology, as exhibited in Slijper’s goat, seems to be well out of grasp of the powers of the goat’s brain. A totally different explanation is in need here.

Muscles that get used more get larger. This is an inherited capability. The result would be muscles that had already developed will get stronger with use. If the goat learns to dance with its hind legs, then the muscles of the hind legs will get larger. This is a type of training.

I think it’s safe to assume that Mary Jane West-Eberhard (and Slijper) had good reasons to discard the possibility of ‘trained muscles’ when she wrote: “(…) the leg muscles, including a greatly thickened and elongated gluteal tongue and an innovative arrangement of small tendons (…)”.

As for prenatal changes in the hind legs, I don't know. However, you haven't provided any evidence that the hind legs of this goat are fundamentally different from the hind legs of any other goat.

Don’t you consider the references presented in West-Eberhard’s treatise to be 'evidence'?

Does the author of this article really make a comparison between this goat's morphology and the morphology of a kangaroo? Why not make the comparison between the legs of this goat and a bird? Birds, kangaroos and two legged goats hop.

Have you not been able to find the kangaroo comparison? Allow me to assist you. West-Eberhard: “(..) Slijper, who noted that some of the novel morphological features of the two-legged goat resembled those of kangaroos and of other bipedal species such as orangutans “(p.6545)

I walk on all fours sometimes. It is useful when I dropped something on the floor. There are people who can walk on their hands. The anatomy of the limbs involved have not changed dramatically.

Well, I guess that’s a decisive difference with the topic at hand.

 

[Darwin123]

However smart goats may be, the novel phenotype induced by a correlated shift in morphology, as exhibited in Slijper’s goat, seems to be well out of grasp of the powers of the goat’s brain. A totally different explanation is in need here.

I think it’s safe to assume that Mary Jane West-Eberhard (and Slijper) had good reasons to discard the possibility of ‘trained muscles’ when she wrote: “(…) the leg muscles, including a greatly thickened and elongated gluteal tongue and an innovative arrangement of small tendons (…)”.
Don’t you consider the references presented in West-Eberhard’s treatise to be 'evidence'?

http://www.stri.si.edu/sites/publications/PDFs/West_Eberhard_2005_PNAS_STRI.pdf
Page 6545, Second column.
“Then, when it died an accidental death, Slijper dissected it and documented remarkable changes in muscle and bone, including striking changes in the bones of the hind legs; the leg muscles, including a greatly thickened and elongated gluteal tongue and an innovative arrangement of small tendons, a modified shape of the thoracic skeleton, and extensive
modifications of the pelvis (ref. 5, p. 53).
”

It doesn’t sound like anything is controlling it but the goat. It still sounds like intelligence, muscle training, and courage coming from the goat. Even the changes in the pelvic bones are part of its muscle training. Exercise changes the texture and even the shape of bone, especially when young. The direction of these changes is determined by the “free will” of the goat as an organized system.

Have you not been able to find the kangaroo comparison? Allow me to assist you. West-Eberhard: “(..) Slijper, who noted that some of the novel morphological features of the two-legged goat resembled those of kangaroos and of other bipedal species such as orangutans “(p.6545)

Well, I guess that’s a decisive difference with the topic at hand.

http://www.stri.si.edu/sites/publications/PDFs/West_Eberhard_2005_PNAS_STRI.pdf
Page 6545, Second column.
"Similar effects on behavior and morphology are quite common in quadripedal mammals, including primates, forced or trained to walk upright (ref. 5, p. 42, figure 3.12 on bipedal baboon; ref. 25; see also descriptions of a bipedal macaque in ref. 62 and a bipedal dog in ref. 63)."

Maybe it was the same dog?
I am going to use “free will” as an analog to plasticity. “Free will” is a concept used in moral and legal discussions. It is ambiguously defined. However, “free will” is sometimes used as a synonym for plasticity. In your post, “direction” seems to be a synonym for “coercion”. So let me say that the goat isn’t being “coerced” to walk on two legs. The organized system called Slijper’s goat is made a decision.

“Free well” describes the sequence of expression for some of the genes. The sequence of behavior, including thoughts, is determined by the sequence of certain genetic switches in the brain. The sequence that goes off varies considerably with the environment that the brain features. There is even some “randomness” caused by the motion of the individual molecules, which you mentioned before. Therefore, there is no way to predict with certainty how different goats will deal with the situation at birth. The sequence of switching aren’t controlled by “free choice”, they are the “free choice”. The expansion of muscles due to exercise is also caused by switches that go off in the brain. Transcription proteins, including neurohumors and hormones, switch genes “on” and “off”. However, these switches are triggered by certain behaviors determined by the brain, which also works by “switching”. I would rather not say that the switching controls the choice. I think it is more accurate to say that the sequence of switching is the choice.

The article is really interesting but not for the reasons that you are stating. What the article suggests is the "choices" made by the organism can produce changes comparable in size to some of the changes brought on by natural selection. Every genome carries a "wardrobe" of adaptations that it may or may not express in a certain environment. The "random" choice of what adaptation to "wear" may greatly influence natural selection itself.

Here is where your article gets interesting.
On page 6546m first column,
“Recurrent phenotypes, similar or identical phenotypic traits with discontinuous phylogenetic distributions, are quite common in a wide diversity of taxa (5). Their similarity is sometimes attributed to parallel evolution, the independent origin of phenotypic similarity due to selection and adaptative change in similar environmental conditions.”

Scientists have been assuming certain variations are the result of variations in genetic sequence. There are many species that are said to have converged in some feature by natural selection. The author is suggesting that this is sometimes a mistake. Even the shape of a bone can be greatly modified by exercise, diet, and so forth. S

He also suggests that natural selection of genetic traits can sometimes be influenced by this “free choice”. This sounds like a generalization of the “Baldwin effect.”

To summarize: the only one directing the development of the hind legs is the goat. The sequence of genes controlling the hind legs provided the choices, but the epigenetic switch network made the final choice.

You didn't give enough credit to the goat. The goat, as a network of epigenetic switches, chose its path. In my value system, it chose well.

 

[Diderot]

Besides muscle training you offer ‘gene expression’, ‘epigenetic switches’ and ‘some randomness’ as an explanation for the correlated shift in morphology in Slijper’s goat. For reasons beyond my comprehension you equate 'gene expression' and 'epigenetic switches' with free choice, free will, courage, the goat as a whole, intelligence, only to take it all back and state that there really are no such metaphysical things. This juggling act with words has no explanatory value at all with regard to the correlated shift in morphology and merely illustrates the fact that in the Neo-Darwinian mindset there is no room for phenomena like 'free will' or ‘a goat’. Like Daniel Dennett said about organisms: ”(…) all that purposive hustle and bustle, and yet there’s nobody home.”. Since there is nobody home you should not say things like: "the only one directing the development of the hind legs is the goat" and offer it as a kind of explanation.

By the way, how about the ‘innovative arrangement of small tendons’, explicitly mentioned by West-Eberhard? Can this also be 'explained' by muscle training or ‘free will’ (which according to you really isn’t ‘free will’ but in fact a sequence of expression of genes)?

 

[Darwin123]

Besides muscle training you offer ‘gene expression’, ‘epigenetic switches’ and ‘some randomness’ as an explanation for the correlated shift in morphology in Slijper’s goat. For reasons beyond my comprehension you equate 'gene expression' and 'epigenetic switches' with free choice, free will, courage, the goat as a whole, intelligence, only to take it all back and state that there really are no such metaphysical things. This juggling act with words has no explanatory value at all with regard to the correlated shift in morphology and merely illustrates the fact that in the Neo-Darwinian mindset there is no room for phenomena like 'free will' or ‘a goat’. Like Daniel Dennett said about organisms: ”(…) all that purposive hustle and bustle, and yet there’s nobody home.”. Since there is nobody home you should not say things like: "the only one directing the development of the hind legs is the goat" and offer it as a kind of explanation.

By the way, how about the ‘innovative arrangement of small tendons’, explicitly mentioned by West-Eberhard? Can this also be 'explained' by muscle training or ‘free will’ (which according to you really isn’t ‘free will’ but in fact a sequence of expression of genes)?

My comments about the goat having free will were meant as a satyr -uhh- satire. I was using the animals "thought process" as an example of how epigenetic switches affect development in a big way.

Each of us has a little knowledge, or at least experience, with our own thoughts. We all know that our thoughts, by influencing choices, can often influence development. Let me point out that thoughts are really mediated by genetic switches that are turned on and off in the brain. Just like computers. Instead of solid state switches, the brain uses genetic switches. So when we way that the brain can innovate, we are really saying the some genetic switches can innovate.

I think that the patterns of epigenetic expression are in some ways analogous to thought. The whole is more than its parts. The individual parts don't think or plan.

Christopher Reeve started a rather intensive regime of exercise after he broke his neck. He tried exercises that have never been tried before. For example, he had his hands and feet tied to a motorized bicycle that moved his arms and legs in circles for at least an hour a day. He made up his exercise regime.

At the end of a few years, he could feel in his fingers. He could even move, just a little. Very little. This amazed scientists. This level of healing had been seen in salamanders, not mammals. His healing was “innovative”.

If you were a scientist investigating this, what would you look for? A difference in his Chakra or a difference in his behavior? I submit it was his behavior that made the crucial difference from other quadroplegics. Every quadroplegic has a Chakra but not every quadroplegic exercised this way.

I propose that there was no force fields involved that made his nerves like salamander nerves. There was no difference in heredity that made his nerves able to heal better than the nerves of other people. There were choices. He tried something and it worked a little. Now, more quadroplegics may try it. So in a way, natural selection is choosing for this exercise behavior.

His personal choices were just a subset of the switching pattern of his genes. His choices did not change his genome. The genes provided the opportunity. However, his genome did not determine all the switching that went on.

http://www.urigeller.com/articles/weekly-news/sep-28-2002.htm
“After five years of frustratingly-slow progress, Reeve discovered a regimen of physical movements allied to mental exercises which began to rebuild the mangled neural pathways.
The recent revelation that he has regained feeling all over his body is a testament to the fantastic power of his therapy.”

http://www.thefreelibrary.com/SUPER...tures+Christopher+Reeve's+first...-a060568988
“SUPERMAN WALKS AGAIN; Family video captures Christopher Reeve's first tentative steps.”

 

[Diderot]

I think that the patterns of epigenetic expression are in some ways analogous to thought. The whole is more than its parts. The individual parts don't think or plan.

Here we are in perfect agreement. ‘The whole is more than its parts’, I remember you have written it before. I consider this to be profound wisdom and I couldn’t agree more. Are you perhaps familiar with the writings of Stephen L. Talbott? If you are interested you can find those here: http://natureinstitute.org/txt/st/ According to him the latest developments in science show that everything that takes place in the cell must be understood in the context of the whole; the cell. Talbot: ”We cannot reconstruct the pattern at any level of activity by starting from the parts and interactions at that level. There are always organizing principles that must be seen working from a larger whole into the parts.” Talbott is strongly adversed to ‘the habit of explaining the whole as the result of its parts’. He rejects both Intelligent Design and Neo-Darwinism.

Let me point out that thoughts are really mediated by genetic switches that are turned on and off in the brain. Just like computers.

You are not explaining thoughts as just a result of the parts, are you? You just stated: "The individual parts don't think or plan." Don’t forget about the whole!

 

[Darwin123]

Here we are in perfect agreement. ‘The whole is more than its parts’, I remember you have written it before. I consider this to be profound wisdom and I couldn’t agree more. Are you perhaps familiar with the writings of Stephen L. Talbott? If you are interested you can find those here: http://natureinstitute.org/txt/st/ According to him the latest developments in science show that everything that takes place in the cell must be understood in the context of the whole; the cell. Talbot: ”We cannot reconstruct the pattern at any level of activity by starting from the parts and interactions at that level. There are always organizing principles that must be seen working from a larger whole into the parts.” Talbott is strongly adversed to ‘the habit of explaining the whole as the result of its parts’. He rejects both Intelligent Design and Neo-Darwinism.
You are not explaining thoughts as just a result of the parts, are you? You just stated: "The individual parts don't think or plan." Don’t forget about the whole!

Maybe you misunderstand me. The whole can be greater than its parts. However, the whole must be consistent with its parts.

The arrangement of hind leg muscles were said to show "innovation". However, I read "innovation" different from you. I read "innovation" as "serendipity". The arrangement in the hind leg muscles was random. The "innovation" was in the way the goats nervous and endocrine systems used the "random" arrangement of muscles to walk.

Some environmental condition or genetic mutation caused the hind legs to disappear and caused a rearrangement of the hind leg muscles. There was no foresight or mercy in the process that altered this goat. However, the other systems in this animal had feedback loops to change both behavior and morphology to compensate for environmental conditions. Feed backs that occur in the brain are sometimes called "trial and error".

The goat was born a freak but learned to walk through trial and error. If it tried one way and felt extremely bad, it stopped. If it tried another way and felt better, it continued. This trial and error capability probably evolved so a four legged goat could climb hills. It did not evolve so that a two legged goat could move across a meadow. Some muscles, glands and nerves were probably stretched to the very limit of their capability.

If a different arrangement of hind leg muscles had come about, the goat may also have learned to walk. Or maybe not. Maybe a different arrangement of muscles would have been too hard. However, the goat with this arrangement of muscles learned by trial and error to walk on two legs with the muscles that it had been given "randomly". The director here is "trial and error".

Features that are "plastic" have a parameter that is adjusted to the environment. There are feedback loops that have evolved that change the parameter to somewhere in the range. Usually, these loops have evolved to help an organism survive over the range of environments experienced over the lifetime of its ancestors. However, there are some conditions that push these parameters to the limit of their ranges. It does not matter if these feedback loops had evolved to counter an entirely different type of environmental change.

Studying the individual parts is useful even though the whole is greater than the parts. The reason is that the whole is never free of the parts. Sliijper's necropsy of the goat revealed an unusual arrangement of hind leg muscles. The fact that the goat was able to use this unusual arrangement tells us something about the feed back systems inside the goat. The size of its muscles and the strength of its bones tell us about the limits of exercise in changing the morphology of animals. However, Slijper's study does not show that exercise has an unlimited ability to affect animals.

The parts have the same limits that they always had. The limits of the parts can be rearranged but not changed. The whole may have great limits because limits of the parts can be rearranged.

So the parts are still useful. The better the electronic flip-flops, the greater the potential of the computer. It is still useful to design better flip-flops. However, piling flip-flops on top of each other doesn't make a computer.

One thing that article of yours does is show us the limits of some assumptions in neo-Darwinian theory. For instance, there is an assumption sometimes made that saltations (i.e., extreme mutations) never contribute to evolutionary change. The assumption is that saltations usually die, or at least their offspring dies. However, plasticity makes this condition a bit weaker.

Slatations can survive for generations using plasticity. Saltation die young, except if they find a way to survive by trial and error. Saltations never leave progeny, except if they find new ways to mate.

I would be interested if this goat left any progeny. Not only for the question of whether its phenotype could be inherited. Usually, I would not expect a two legged goat to mate with other goats. My assumption would have been that such a goat is immobile. Therefore, all its genes would die with it, not just the mutated gene. However, this goat could have mated with lots of other goats before it died. Therefore, it could have had offspring both with and without the mutated gene.

In any case, the walking behavior that it learned gave it a small chance of passing on its genes. In that way, the plasticity of the goat could affect evolution. Not by directly changing the genome, but by giving the genes an increased probability of survival.

 

[Diderot]

The arrangement of hind leg muscles were said to show "innovation". However, I read "innovation" different from you. I read "innovation" as "serendipity". The arrangement in the hind leg muscles was random. The "innovation" was in the way the goats nervous and endocrine systems used the "random" arrangement of muscles to walk.

So your explanation boils down to ‘randomness’. West-Eberhard (W.E.) does not agree with you: “Even though the event that caused these changes was random with respect to adaptation, the phenotypic result was not a random variant. Rather, it was an adaptive accommodation of a random input, the result of pushing to extremes developmental plasticity in behavior, muscle, and bone that had already been subjected to a long history of selection and adaptive evolution.”
In her opinion randomness as an explanation is ruled out, because too many similar cases like Slijper’s goat have been documented. W.E.: “Similar effects on behavior and morphology are quite common in quadripedal mammals, including primates, forced or trained to walk upright (…). These observations raise the possibility that the two-legged-goat effect, or ‘‘phenotypic accommodation’’ has played a role in the evolution of bipedal locomotion in vertebrates, including humans, as suggested by Slijper (…)”. (p. 6545, second column)
This lays the fundament for her idea: “Here, I argue that the origin of species differences, and of novel phenotypes in general, involves the reorganization of ancestral phenotypes (developmental recombination) followed by the genetic accommodation of change. “(p. 6543, first column)
Calling developmental recombination ‘not random’ is an obvious deflection from the Neo-Darwinian doctrine, because the prescribed 'explaining from the parts' would compel her to say it is all random; like you just did. I think it is quite clear that she is suggesting that there is a ‘phenotype’ (a whole / 'the goat') who has the power to induce and direct non-random developmental recombination.
I would like to add two more quotes by W.E. from her book ‘Developmental Plasticity and Evolution’ (Oxford UP, 2003):
”Phenotypic plasticity enables organisms to develop functional phenotypes despite variation and environmental change via phenotypic accommodation -- adaptive mutual adjustment among variable parts during development without genetic change“.( p. 51.)
“Responsive phenotype structure is the primary source of novel phenotypes.“( p. 503)

Maybe you misunderstand me. The whole can be greater than its parts. However, the whole must be consistent with its parts.

Indeed I misunderstood you. Now it is clear. You don’t adhere any power to the whole (W.E. would say: 'the phenotype'). The whole may be greater than its parts, but it is totally passive and cannot do anything and it that sense it does not exist. In fact ‘there is nobody home’.

 

[Darwin123]

So your explanation boils down to ‘randomness’. West-Eberhard (W.E.) does not agree with you: “Even though the event that caused these changes was random with respect to adaptation, the phenotypic result was not a random variant. Rather, it was an adaptive accommodation of a random input, the result of pushing to extremes developmental plasticity in behavior, muscle, and bone that had already been subjected to a long history of selection and adaptive evolution.”
In her opinion randomness as an explanation is ruled out, because too many similar cases like Slijper’s goat have been documented. W.E.: “Similar effects on behavior and morphology are quite common in quadripedal mammals, including primates, forced or trained to walk upright (…). These observations raise the possibility that the two-legged-goat effect, or ‘‘phenotypic accommodation’’ has played a role in the evolution of bipedal locomotion in vertebrates, including humans, as suggested by Slijper (…)”. (p. 6545, second column)
This lays the fundament for her idea: “Here, I argue that the origin of species differences, and of novel phenotypes in general, involves the reorganization of ancestral phenotypes (developmental recombination) followed by the genetic accommodation of change. “(p. 6543, first column)

I agree with her 100%. She said, "The event that caused these changes was random with respect to the adaptation." Whether it was a genetic mutation or some trauma in the prenatal environment, the probability of the change occurring was completely independent of the survival of the organism. There is no correlation between the survival of the organism or its chance to procreate.

The primary assumption in neoDarwinian theory was not violated here. The mutation is the change in base sequence of DNA or whatever subsystem of heridedity. The probability of the change in base sequence of DNA was completely independent of the survival of the goat.

There is a secondary assumption in neoDarwinian theory that the phenotype is strictly determined by the base sequence of DNA. By "secondary", I mean that no one actually states it as a hypothesis. However, the mathematics and computations made by neoDarwinian theory often include this hypothesis. The evidence of this hypothesis is somewhat weak. It probably is good as an approximation most of the time, but it is easy to think of exceptions.

The very existence of plasticity shows that the phenotype is NOT precisely determined by the genome alone. If the phenotype were precisely determined by the genome alone, then the morphology of the organism would be the same regardless of the environment. Obviously, some parameters can vary.

The morphology of the goat in the later stages of development were not random with respect to the survival and reproduction of the goat. In the embryo, muscles attach to any bone that they come into contact with. Obviously, if a bone is gone they will attach to some other bone. Once born, the goat tries things for the stimulus. The exercise it does makes whatever muscles that work grow. Motion that gives it pleasure are likely to be learned. The final morphology of a goat can vary quite a lot from other goats with the same genome.

Even the differences between identical twins violates the secondary hypothesis of neoDarwinism. Identical twins are never truly identical, though they have an identical base sequence in DNA. I submit that the final differences between "identical" twins are not random with respect to the survival of the twins. Every variation in environment, prenatal and post natal, contributes to the differences between the twins.

Calling developmental recombination ‘not random’ is an obvious deflection from the Neo-Darwinian doctrine, because the prescribed 'explaining from the parts' would compel her to say it is all random; like you just did. I think it is quite clear that she is suggesting that there is a ‘phenotype’ (a whole / 'the goat') who has the power to induce and direct non-random developmental recombination.
I would like to add two more quotes by W.E. from her book ‘Developmental Plasticity and Evolution’ (Oxford UP, 2003):
”Phenotypic plasticity enables organisms to develop functional phenotypes despite variation and environmental change via phenotypic accommodation -- adaptive mutual adjustment among variable parts during development without genetic change“.( p. 51.)
“Responsive phenotype structure is the primary source of novel phenotypes.“( p. 503)

1) What did I say that is different?

Maybe I didn't understand your question. You originally asked what directs the construction of the new phenotype. I provided two examples of what can direct a phenotype: brain learning and muscle conditioning. There must be others, but I suggested two. You said that I was wrong. You seem to be claiming that learning and conditioning do not change the phenotype.

Exercise and learning rearrange the sequence of genetic expression. I remember studies of birds learning songs where it was shown that remembering a song changes the sequence of expression of the genes (not the sequence of base pairs). Similarly, processes that grow muscles involve changing the sequence of expression in genes. Some of this is caused by hormones made by glands, which themselves are timed by the sequence of expression in genes. So learning and exercise both "reprogram" expression.

There probably are others, but I was just providing two that I hypothesize were important in Slijper's goat.

2) Why do you think that learning and conditioning are not included in what W. E. means?

I know about "genetic recombination" in organisms. However, I have never read the phrase "developmental recombination" before. I assumed that it simply meant a rearrangement of the sequence of genetic expression, rather than a rearrangement of base sequence pairs.

3) What does the phrase "developmental recombination" mean to you?

Indeed I misunderstood you. Now it is clear. You don’t adhere any power to the whole (W.E. would say: 'the phenotype'). The whole may be greater than its parts, but it is totally passive and cannot do anything and it that sense it does not exist. In fact ‘there is nobody home’.

I never said that the whole was passive. I am quite comfortable with the idea that the whole is making decisions based on feedback that it gets on the macroscopic scale. However, the whole can not know anything about what happens on the microscopic scale. The goat did not choose where each molecule in its muscles go. It tried to move certain muscles, and the muscles in those areas grew. Maybe the muscles already had a funny arrangement compared to the muscles in other goats. However, the motion of the goat with respect to those muscles was novel. The goat tried them in a certain way and they worked.

There is nobody home on the molecular length scale. However, the phenotype exists on a macroscopic scale. On the molecular length scales, the motion is random with respect to the survival of the whole organism. The molecule knows nothing.

 

[Darwin123]

So your explanation boils down to ‘randomness’. West-Eberhard (W.E.) does not agree with you: “Even though the event that caused these changes was random with respect to adaptation, the phenotypic result was not a random variant. Rather, it was an adaptive accommodation of a random input, the result of pushing to extremes developmental plasticity in behavior, muscle, and bone that had already been subjected to a long history of selection and adaptive evolution.”
...
Indeed I misunderstood you. Now it is clear. You don’t adhere any power to the whole (W.E. would say: 'the phenotype'). The whole may be greater than its parts, but it is totally passive and cannot do anything and it that sense it does not exist. In fact ‘there is nobody home’.

The author of that article agrees with me there. At least, that is how I read it. If I am wrong, then perhaps you could tell me what she actually meant. Explain to me what she meant by "feed back loop."

I am not sure that you are reading that article the way the author intended it. When the author talks about feed back loops, she is talking about macroscopic phenomena that emerge from microscopically random events. She says again and again that the event that caused these changes are "random". The feed back loops are what make the phenotype not random.

She is claiming that these feedback loops can cause large changes that are biased in favor of the survival of the organism. She is not saying that the molecules can do anything independent of these feed back loops. Perhaps you could give me your own example of a feed back loop, as you understand them.

I believe that the author would agree with me that exercise and learning change the phenotype. Here are some links connecting gene expression to the behavior of the organism as a whole.

Birds “learn” songs by changing their gene expression. he change their gene expression by singing. This is what I call a feed-back loop.

Brain learning involves feed back loops. Here are some links concerning bird songs and gene expression.

http://en.wikipedia.org/wiki/Bird_vocalization
“ Several other studies have looked at seasonal changes in the morphology of brain structures within the song system and have found that these changes (adult neurogenesis, gene expression) are dictated by photoperiod, hormonal changes and behavior.
The gene FOXP2, defects of which affect both speech production and comprehension of language in humans, becomes highly expressed in Area X during periods of vocal plasticity in both juvenile Zebra Finches and adult canaries.”

http://www.pnas.org/content/97/7/2965.full
“Along the same lines, the IEGs studied thus far do not appear to be induced in the SS of awake birds by acoustic stimuli (14–17), even by the tutor song (as Bolhuis et al. report for the first time in ref. 18), but are strongly activated in SS nuclei when the bird sings (39, 40). Of course, specific genes that are responsive to acoustic stimulation in the SS may yet be identified; a song playback-induced increase in the high vocal center (HVC) of a DNA-binding protein linked to many activity-induced genes, phosphorylated CREB (cAMP response element binding protein), hints at this possibility (41). Moreover, a lack of gene expression does not necessarily indicate a lack of neuronal excitation.”Muscles “learn” too, mostly by changing gene expression.
http://www.hindawi.com/journals/jnume/2012/960363/
“Exposure to exercise stress initiates adaptation in gene expression, cellular protective mechanisms, and remodelling, which help protect muscle during subsequent bouts of exercise [49].”

http://www.ncbi.nlm.nih.gov/pubmed/20739716
“This study examined alterations in skeletal-muscle growth and atrophy-related molecular events after a single bout of moderate-intensity endurance exercise. … This study provides the groundwork for future investigations designed to optimize the metabolic conditions necessary to positively influence the cellular mechanisms specific to skeletal-muscle protein turnover during recovery from endurance exercise.”

http://www.jappl.org/content/104/2/371.full
Effects of resistance exercise with and without creatine supplementation on gene expression and cell signaling in human skeletal muscle
…
In conclusion, 5 days of creatine supplementation do not enhance anabolic signaling but increase the expression of certain targeted genes.” Here is W.E. reviewing another book that I strongly recommend. I bought “Evolution in Four Dimensions” and read it very carefully. I would take some of the conclusions with a grain of salt. However, the authors present their book as merely showing milestones in what is turning into “a new synthesis.”

It isn’t entirely clear to me the differences between Jablonka’s theories and hers. However, there is clear agreement that the expression of genes in different forms is one important “director” in development.

If you read her review, you will see that she doesn’t think “anybody is home” on a microscopic level. She basically agrees that the molecules do their thing with short range interactions that are basically mindless.

http://www.stri.si.edu/sites/publications/PDFs/West_Eberhard_2007_BP_STRI.pdf
“Evolution in Four Dimensions, by Eva Jablonka and Marion Lamb, is a disarmingly good-humored book that challenges the overly gene-centered ‘Neo-Darwinian’ (mid-20th-Century-Synthesis) view of evolution via selection on phenotypes affected by random changes in DNA.
…
Given that reinforcement learning is extremely widespread in animals, including in unicellular species and others that lack cross-generational transmission of learned traits, the evolutionary effect of learning for the origins of novelty is probably great, and its evolutionary effect is probably usually via genetic rather than via nongenetic inheritance.”