Darwin Unhinged: The Bugs in Evolution

Exactly - desire, intention and goal-oriented behavior become primary factors.  Switching away from my personal viewpoint and back to the current thinking of the folks involved with the third way:

1/ Darwinism, as espoused by C. Darwin incorporated Lamarckian elements.
2/ Regulation implies a target state to which positive and negative feedback is the primary means to maintaining stasis.  Epigenetics is a regulatory system and feedback is part of information theory as cybernetics.
3/ Darwin used the term induction as the effectual means for how the minds of animals changed aware behavior into instinct.  Note the following wording:

It seems to me that with Lamarckism it still boils down to proposing that organisms somehow incorporate a backward-mapping function (from needed physiological/behavioral changes to the required DNA changes for them), a huge and very difficult computational task. How do epigenetics and feedback accomplish this? Darwin apparently finally attributed the origin of instincts to group selection. This is interesting though it seems misfounded due to the extreme unlikelihood of just the right changes occurring randomly to the DNA encoding the incredibly complicated neural structure. The statistical problem seems much greater even than that with other less complicated parts of the animal body.

On bird beaks: epigenetics.

http://www.iflscience.com/plants-and-ani...igenetics/

Such repeated epigenetic adaptation of bird beaks to changing conditions doesn't seem to be anything but the turning on and off of certain existing genes or parts of existing genes in a heritable way. It doesn't alter the basic sequences of DNA in the genes; it doesn't seem to explain the origin of any of the genes. It doesn't explain the evolution of the bird beak structure and development in the first place. Epigenetics doesn't seem able to explain the creativity of macroevolution, just some microevolution.

Such repeated epigenetic adaptation of bird beaks to changing conditions doesn't seem to be anything but the turning on and off of certain existing genes or parts of existing genes in a heritable way. It doesn't alter the basic sequences of DNA in the genes; it doesn't seem to explain the origin of any of the genes. It doesn't explain the evolution of the bird beak structure and development in the first place. Epigenetics doesn't seem able to explain the creativity of macroevolution, just some microevolution.

I just posted it as an example of how evolutionists look at the same phenomena in different ways. I agree that, from the little I understand, epigenetics as proposed still falls short in explanatory power and, for me, the missing ingredient is still mind.

Let me see if I understand your position. You espouse the idea that information is the template matter follows for self assembly? To put it another way: Information pre-exists and matter follows those rules. Is this correct?

Of course.  That is how QM works.  Before manifestation as a single state - multiple information objects exist in superposition.

John Wheeler's -- It from Bit -- says it all.  

Following "rules" makes me squeamish.  My stance is: there are probabilities for physical event outcomes based on the equations vetted in physics.  AND there are probabilities for informational event outcomes based on the equations vetted in information theory.

Of course.  That is how QM works.  Before manifestation as a single state - multiple information objects exist in superposition.

John Wheeler's -- It from Bit -- says it all.  

Following "rules" makes me squeamish.  My stance is: there are probabilities for physical event outcomes based on the equations vetted in physics.  AND there are probabilities for informational event outcomes based on the equations vetted in information theory.

Ok, then I would say your next step is doing research; if not, then find scientists that are, because claiming doesn't prove a thing.

I was thinking of a structure which was of benefit only when complete - so that selection pressure couldn't assist during its development. But once it was complete, selection pressure could come into play.

If the structure is a copy of another structure with a simple modification or two, then that could happen by accident.

I don't think you can get a complex structure from scratch without positive pressures along the way.

You have to be careful that you don't think: nothing . . . nothing . . . not helpful . . . not helpful . . . bam! something really cool.

And all the arguments about no possible useful precursors are crap.

https://www.youtube.com/watch?v=BQJtV_YLuNE

~~ Paul

Why?
Why?
How about necessity to change? Intention and desire are loaded words. I would consider  lack of necessity ( survival advantage) is the reason mice did not grow back their tails.
A very recent article:

In Lamarckism, mutations are preserved based on beneficial acquired characteristics, which would require some way for bodies to identify which acquired traits are useful, reverse-engineer the genetic changes that would achieve them (which is basically impossible without huge computational resources because DNA is more of a recipe than a blueprint), then update gametes with these changes. The only mechanism found to even remotely furnish this capability is epigenetics, but epigenetic mechanisms only operate at the level of entire genes or long DNA sequences - no real creativity. With Lamarckism it has also sometimes been proposed that the required genetic changes can arise through some other mechanism than random mutation. This amounts to three or four amazing capabilities for which no mechanism has ever been proposed.

In Lamarckism, mutations are preserved based on beneficial acquired characteristics, which would require some way for bodies to identify which acquired traits are useful, reverse-engineer the genetic changes that would achieve them (which is basically impossible without huge computational resources because DNA is more of a recipe than a blueprint), then update gametes with these changes. The only mechanism found to even remotely furnish this capability is epigenetics, but epigenetic mechanisms only operate at the level of entire genes or long DNA sequences - no real creativity. With Lamarckism it has also sometimes been proposed that the required genetic changes can arise through some other mechanism than random mutation. This amounts to three or four amazing capabilities for which no mechanism has ever been proposed.

I am not qualified to expound on the subject - but I think you are not aware of the context of Bioinformatics.  DNA is just one part of an entire communication system.  No one part of bio-communication does it all; and any change to one means they may all are affected.  Epigenetic changes are defined as being outside of changes to DNA codon chemistry.  You will typically see me refer to DNA/RNA/Ribosomes as a grouping to designate the subject.  In my limited understanding, it is in the decoding process of RNA transcription and rDNA where epigenetics communicate with the functional channels that carry signals for protein building.

I read into your responses the materialist worldview where chemistry runs the show.  This is not the case, as communication runs the show and presents instructions.  The reverse engineering doesn't start with the mechanical "gears" - but with goal-oriented messages.  Messages are measured in information theory and in linguistics - neither which are covered in chemical bonding studies.  DNA is hardware beloved by materialistic contexts.  Behavior, symbolic representation and epigenetic signals are functional as software.

Mind makes a difference.  Selections made by minds change real-world probabilities, including adaptive behavior.

 Transformations of Lamarckism

From Subtle Fluids to Molecular Biology
Edited by Snait B. Gissis and Eva Jablonka 

“This book is long overdue. Lamarck and Lamarckian ideas were not only ignored but actively ridiculed during the second half of the 20th century. As the subtitle of this book indicates, some of the most cogent reasons for reassessing those ideas come from within the citadel of molecular biology itself. A great strength of the book is that it does not seek to reintroduce Lamarckian ideas as they were originally formulated; rather, the Lamarckian perspective is used to assess where the modern synthesis needs extending or even replacing. For any serious student of evolutionary biology, this work will be a bible for many years to come.”

—Denis Noble, FRS, Oxford University, author of The Music of Life 

In Lamarckism, mutations are preserved based on beneficial acquired characteristics, which would require some way for bodies to identify which acquired traits are useful, reverse-engineer the genetic changes that would achieve them (which is basically impossible without huge computational resources because DNA is more of a recipe than a blueprint), then update gametes with these changes. The only mechanism found to even remotely furnish this capability is epigenetics, but epigenetic mechanisms only operate at the level of entire genes or long DNA sequences - no real creativity. With Lamarckism it has also sometimes been proposed that the required genetic changes can arise through some other mechanism than random mutation. This amounts to three or four amazing capabilities for which no mechanism has ever been proposed.

Here is how plants do it. It would be reasonable that a similar mechanism plays a role in animals.

https://m.phys.org/news/2017-10-mechanis...otein.html

The Nat geo article may show epigenetics at work. 
Though I feel I will fail what I'm really attempting to demonstrate is there's no legitimate reason to interject a supernatural reason, consciousness... to explain the various ways species evolve.

I am not qualified to expound on the subject - but I think you are not aware of the context of Bioinformatics.  DNA is just one part of an entire communication system.  No one part of bio-communication does it all; and any change to one means they may all are affected.  Epigenetic changes are defined as being outside of changes to DNA codon chemistry.  You will typically see me refer to DNA/RNA/Ribosomes as a grouping to designate the subject.  In my limited understanding, it is in the decoding process of RNA transcription and rDNA where epigenetics communicate with the functional channels that carry signals for protein building.

I read into your responses the materialist worldview where chemistry runs the show.  This is not the case, as communication runs the show and presents instructions.  The reverse engineering doesn't start with the mechanical "gears" - but with goal-oriented messages.  Messages are measured in information theory and in linguistics - neither which are covered in chemical bonding studies.  DNA is hardware beloved by materialistic contexts.  Behavior, symbolic representation and epigenetic signals are functional as software.

Mind makes a difference.  Selections made by minds change real-world probabilities, including adaptive behavior.

The "Weismann barrier" is the fundamental barrier to information transfer from phenotype back to into genotype, or in other words, significant hereditary information moves only from germline cells to somatic cells not the reverse. Significantly, creatively, violating this principle means the impossible requirements for both a reverse-engineering calculation from needed body/behavioral change to the corresponding required DNA changes plus an actual physical mechanism for the results of the calculation to be somehow transformed into the actual DNA changes in gametes.

From a review of Transformations of Lamarckism, at https://dash.harvard.edu/bitstream/handl...sequence=1 :

"None of the contributors to ToL defend the kind of hereditary mechanism rejected by Weismann but
some expand Lamarckian inheritance to include all forms of ‘soft inheritance.’ Gissis and Jablonka (#10,
105) adopt Mayr’s definition of soft inheritance as “a gradual change of the genetic material itself, either by
use or disuse, or by some internal progressive tendencies, or through the direct effect of the environment,”
although it is clear that they do not limit the concept to ‘gradual’ changes. Soft inheritance is an elastic
concept but includes mechanisms of cellular epigenetic inheritance such as DNA methylation, self-sustaining
regulatory loops, structural templating, and RNA interference (Jablonka #21).....It seems a matter of personal
preference whether these mechanisms are seen as Lamarckian."

I don't think any of the newly understood mechanisms of "soft inheritance" (including horizontal gene transfer) break the Weismann barrier or incorporate the kind of creativity observed in actual macroevolution. It seems to me that to be credible the "new Lamarckians" would need to show in detail how these "soft inheritance" mechanisms can creatively invent intricate complicated self referent irreducibly complex biological machines like the bacterial flagellum. There seems to be an irreducible requirement for the operation of mind, not mechanism. 

Perhaps we agree on this, but disagree on what the nature of that mind must be. 

It's interesting that there isn't such a drastic separation between somatic cells and gametes in plants, so that there can be apparent violations of the Weismann barrier in plants (as opposed to animals). At  http://www.frozenevolution.com/weismann-barrier: 

"Because a flower can be formed in a plant through differentiation from somatic tissues, acquired traits can be inherited in plants. For example, if cells better adapted to growth in a certain temperature regime come, in time, to predominate in the tissues of woody species, this property can be transferred to further generations through the seeds from flowers formed by differentiation of these tissues . However, it should be recalled that this is not Lamarckian evolution, as adaptation of cells to a certain temperature regime did not occur through adaptive mutations, which would occur as a reaction to conditions or to the behaviour of the organism, but through the Darwinistic mechanism of survival of those tissue cells (or branches of the tree) that are best adapted to the local environment as a consequence of a random change, somatic mutation, somatic recombination or epigenetic change."    

Note that "random change, somatic mutation, somatic recombination or epigenetic change" are all random with respect to fitness.