Darwin Unhinged: The Bugs in Evolution

He is and I think it is justified. My only problem with him is that he tries to identify the designer in evolution as the God of the Scriptures. For many reasons I think that is unlikely. He doesn't recognize that there could be multiple designers (perhaps in the form of powerful spiritual entities nevertheless much lower in the hierarchy than God). Or other possibilities some of which we probably can't even imagine.

I have always had the same problem with Meyer and the discovery institute as well as some other issues which get included in their agendas. I have noticed that many of the paranormal researchers seem to distance themselves from ID and the DI. One conspicuous comment Stephen made in their chummy little chat was when he reacted to Shermers conflating ID with spoon bending (the paranormal) infering they had an alliance in debunking paramormal claims and ID was more on the level of the "real science" that Shermer defends.

https://theconversation.com/natural-gm-h...ion-159468

 Indeed, this premise forms the basis of much of our understanding of evolution. But we now know that this process is not sacrosanct and some of our most widely grown crops may be fiddling the system by supplementing their genetic information with stolen genetic secrets. Our new study, published in New Phytologist, shows that this does in fact happen in grasses.

Grasses aren’t the only culprits, however. Bacteria are the master criminals in this regard. They are able to freely absorb genetic information from their environment. This process is termed lateral or horizontal gene transfer, and is thought to play an important role in the spread of traits such as antibiotic resistance.

Although scientists originally thought this process was restricted to bacteria, it has since been documented in a broad range of animals and plants. Examples include aphids that can synthesise a red fungal pigment to avoid predation, mushrooms that have shared the genetic instructions to assemble psychoactive compounds, and whiteflies that have turned their host plants’ defences against them.

Go, go shrooms.  Make a better trip.


Genetic strategies -- have to come from mental activity at a species level.  Mind is active in evolution

I have always had the same problem with Meyer and the discovery institute as well as some other issues which get included in their agendas. I have noticed that many of the paranormal researchers seem to distance themselves from ID and the DI. One conspicuous comment Stephen made in their chummy little chat was when he reacted to Shermers conflating ID with spoon bending (the paranormal) infering they had an alliance in debunking paramormal claims and ID was more on the level of the "real science" that Shermer defends.

That's true about the dismissal of the paranormal by most leading ID scientists and advocates, despite the fact that they themselves are espousing a position on evolution that is just as heretical to the mainstream as is the paranormal. This is to say nothing about the numerous other issues where the DI scientists and other ID advocates mostly espouse very conservative religious and other views on social issues, that are abhorrent to many. 

And most parapsychologists and advocates of the paranormal in general think the same way about ID and dismiss it. It's like the blind men and the elephant - some think it is all legs, others the trunk, and so on.

Hardly anybody recognizes that both areas of this world and life in it are part of the overall reality, and that any theoretical system explaining this world has to include both "heresies".

https://theconversation.com/natural-gm-h...ion-159468

Go, go shrooms.  Make a better trip.


Genetic strategies -- have to come from mental activity at a species level.  Mind is active in evolution

Examine the implications. This could mean (for example) that the intricate irreducibly complex machine of the bacterial flagellum and its biological assembly system at some point existed as a design in the mind of something like the collective consciousness of some bacterial species. I find this to be mostly beyond belief, requiring a certain credulity. Of course, it can't absolutely be ruled out - we know too little about the nature of consciousness, for example.

Hardly anybody recognizes that both areas of this world and life in it are part of the overall reality, and that any theoretical system explaining this world has to include both "heresies".

Very well put.

Examine the implications. This could mean (for example) that the intricate irreducibly complex machine of the bacterial flagellum and its biological assembly system at some point existed as a design in the mind of something like the collective consciousness of some bacterial species. I find this to be mostly beyond belief, requiring a certain credulity. Of course, it can't absolutely be ruled out - we know too little about the nature of consciousness, for example.

I admit to drinking the kool-aid here.  I have thought in terms of the "collective mind" as an encompassing environment, just like a physical environment, for many years.

Examine the actual evidence for mind, as well.  The article points out that the process of directly "mining" useful meanings is observable in nature and the outcomes from application of meanings is obviously a powerful tool in adaptation.  It seems like there is a learning strategy built-in.  Useful functions in the environment are open to be copied.  Emerging from study are examples of earthy understanding by life about life's ability to obtain important "meanings".  Organisms consume ideas as much as food.

It is the imagination of life that opens the door to innovation and adaptation.  Living things find biological affordances due to these possibilities being detectable.  Plan and designs emerge from feedback, trial and error and active struggle.  The affordances shake-out and living things find them.

 After all, evolution is studying events that happened thousands and even millions of years ago. But there is a significant statistical increase in the number of transferred genes present today in grass species with rhizomes – modified roots that allow plants to propagate themselves asexually (a process in which part of a plant can be used to generate a new plant). The transfer of DNA into the rhizome could be facilitated via direct contact between species underground, possible through root fusion. Interestingly, scientists have recently observed DNA moving between tobacco plants that have been grafted together, further supporting this hypothesis.

Any foreign DNA transferred into the rhizome would then be replicated in all the cells in the daughter clone that arises from this tissue as the plant reproduces asexually. This foreign DNA would subsequently make its way into the germline (cells that pass on their genetic material to offspring) and future generations when the daughter clone flowers and produces seed.

The results of this study show that grasses have been genetically engineering themselves.

I know it is not usual to say that what plants do - is mind - but when seen from the objective view of science, plants use coded information  And use it in a way that appends internal information functions to external information objects.  Understanding is this binding of in/out relationship.   Making affordances your own and grasping their potential usefulness is the definition of understanding.

I admit to drinking the kool-aid here.  I have thought in terms of the "collective mind" as an encompassing environment, just like a physical environment, for many years.

Examine the actual evidence for mind, as well.  The article points out that the process of directly "mining" useful meanings is observable in nature and the outcomes from application of meanings is obviously a powerful tool in adaptation.  It seems like there is a learning strategy built-in.  Useful functions in the environment are open to be copied.  Emerging from study are examples of earthy understanding by life about life's ability to obtain important "meanings".  Organisms consume ideas as much as food.

It is the imagination of life that opens the door to innovation and adaptation.  Living things find biological affordances due to these possibilities being detectable.  Plan and designs emerge from feedback, trial and error and active struggle.  The affordances shake-out and living things find them.

I don't think this rather vague conceptualizing can adequately address the real problem of biological design. An example is the intricate, extemely complicated interconnected irreducibly complex design of the arthropod, which appeared suddenly at the beginning of the Cambrian period at the beginning of what has come to be called the Cambrian Explosion. The only thing which we know of that can produce such designed systems of systems is focused conscious intelligence. The following is taken from an earlier post of mine:

It might be instructive to consider in moderate detail one of the major accomplishments of macro-evolution that ID contends must have been due to some form of outside intelligence. This might give some clues as to what level of intelligence, creativity and foresight can be attributed to whatever this designing source was, which then might constitute a clue as to the probable nature of this intelligence. 


This survey into a little of the nitty gritty detail gives some idea of the magnitude of the biological design problem:

One example would be the phylum Arthropoda (present insects, spiders, crustaceans, etc.), which inexplicably to Darwinism appeared suddenly (as evolution goes) over a period of 10 million years or so at the beginning of the Cambrian period over 500 million years ago. This event was the sudden appearance of most of the complex animal body plans, and has been called the Cambrian Explosion. Like the other body plans, the body plan of the arthropods appeared with absolutely no simpler (developmental) pre-arthropods in the Precambrian, whereas neo-Darwinism predicts that there must have been a very long period of gradual development via RM + NS. Absolutely nothing of this supposed evolutionary history containing intermediate stages of design has been found in 150 years of digging, despite the presence of many sedimentary deposits that should have contained fossiliferous traces of this evolution.

This body plan which appeared far too quickly to be explainable by RM + NS (or by some previously unrecognized primitive cognizing by primitive life forms) consists of a very complex interconnected system of organ systems  consisting of multitudes of specialized tissues and cell types all working together in many specialized different biological mechanisms.

The major systems are the exoskeletal system, the muscular system, the respiratory system, the digestive system, the circulatory system, the reproductive system, and the nervous system. There are others also, like the secretory glandular and excretory systems.

The following capsule descriptions are of the sea-living forms that initially populated the Cambrian period.

The exoskeleton is a structure composed of several layers combining chitin and calcium carbonate. Since this is rigid, a molting subsystem had to also be incorporated to allow for growth. The exoskeleton is divided into plates over the body and through a series of cylinders around the appendages. At the joints between the plates and cylinders the exoskeleton is thin and flexible because it lacks the exocuticle and because it has to be folded.

The muscles, which attach to the inside of the exoskeleton, act together as an intricate lever system, a lever system as is also true in vertebrates.

The digestive system consists of a foregut, midgut region, and hindgut. In general, the midgut region is the principal site of enzyme production (which of course requires specialized cell types and corresponding tissues), and absorption of digested food. The enzymes may pass forward into the front part of the gut.

The respiratory system of the aquatic arthropods uses gills, which are outgrowths of the skin, which are covered by a thin gas-permeable layer of exoskeleton.

The circulatory system: this is an open system consisting of a dorsal (upper) heart and a system of arteries. The arteries deliver blood into tissue spaces (hemocoels), from which it eventually drains back to a large pericardial sinus surrounding the heart. A varying number of paired openings (ostia) are located along the length of the heart and permit blood to flow in when the valves are open. When the heart is contracting, closed valves prohibit the blood from flowing back and force it into the arteries of the tissues, from which it flows to other hemocoels. In the larger crustaceans, the blood then passes through the gills (where it becomes oxygenated) on its return to the heart. The blood of crustaceans contains the blue, oxygen-carrying pigment hemocyanin.

The arthropod nervous system including sensory organs consists of a dorsal brain and a ventral (underside), ganglionated longitudinal nerve cord (primitively paired in the early Cambrian forms) from which lateral nerves extend in each body segment. The sensory nerve endings are lodged in cuticular hairs (setae), peglike projections, cones, pits, or slits, which may occur in large numbers on antennae, mouthparts, joints, and leg tips. Some of the very first arthropods (related to trilobites) had complex compound eyes consisting of an intricate arrangement of separate lensed phoreceptors combined with associated image forming and motion detecting neural structures. Compound eyes are extremely effective in detecting motion. 

It should be noted that the compound eye is a very complex subsystem in itself consisting of an intricate array of lensed photosensors all connected together by optical nerves leading to a neural processing center able to detect shapes, motion and other characteristics of the composite image, and then decide whether friend or foe or food, etc.

The reproductive system: the two sexes are separate in arthropods; i.e., there are both male and female individuals. The paired sex organs, or gonads, of each sex are connected directly to ducts that open onto the ventral surface of the trunk.

I don't think this rather vague conceptualizing can adequately address the real problem of biological design. 

Surely, my rambling leave a vague pathway.  But, the fact that recent literature is strongly tracking the search for direct perception and for the detection of meaning by the minds of organisms.  Evolution means change and the change that counts is adaptation.  New ways of dealing with both inner and outer environments are promoted as functional abilities.  The interface between learning and heritable instincts is being carefully observed and measurable process models are being discovered.  Mind is at the heart of creativity.

The issue is not a metaphysical or philosophical one.  The nuts and bolts of how design processes work are not magical.

The chemistry for how bio-information molecules has made incredible progress in recent decades.  The newly discovered bio-informational objects are still being discovered.  The transition of DNA and genes- from being magic chemicals - is fast fading and research on the logical operations of biological communication are in full swing.

The research is methodically following the creation of information structures, just like a chemist creates useful reagents.  Please note that these papers are all current.

 Increase in Mutual Information During Interaction with the Environment Contributes to Perception

 Perception and motor interaction with physical surroundings can be analyzed by the
changes in probability laws governing two possible outcomes of neuronal activity, namely the
presence or absence of spikes (binary states). Perception and motor interaction with the physical
environment are partly accounted for by a reduction in entropy within the probability distributions of
binary states of neurons in distributed neural circuits, given the knowledge about the characteristics
of stimuli in physical surroundings........ 
5. Summary
In the beginning, we introduced three main principles of environmental psychology, namely:
(i) Perception is direct; (ii) perception is for action; and (iii) perception is of affordances [5]. In this
article, we used the information theoretic approach to provide a deeper understanding of the last
two principles. We argued that there are robust increases in mutual information between successive
circuits across the brain during an interaction with the environment, which is due to the increase in
joint probability distributions of binary states of neurons, given the knowledge about sensory stimuli
and motor tasks

 https://www.mdpi.com/1099-4300/21/4/365

 Abstract

James J. Gibson, the founder of ecological psychology, introduced a radical empiricist approach to perception and action centered on direct perception in naturalistic environments that was counter to popular representational views of his time. This direct perception approach and the associated introduction of the affordance concept have been extremely influential in several fields of study. 

https://journals.sagepub.com/doi/10.1177/1745691619868207

 What remains largely unknown is, therefore, how the physical geometry of an object perceived and used for specific goals determines fingertip placement, a question connected to the notion of affordances first formulated by Gibson [8]. In his view, affordances should be considered properties reflecting the potential relationship between a subject and relevant aspects of the environment. As Gibson [8] explained, “…to see things is to see how to get about them and what to do or not to do with them.” In other words, the relevant aspects of the world are those used to guide actions.

Although affordances have been studied in the context of reaching and grasping movements [9]–[18], how they interact with the end-goal of the action to determine a functional structure for reach-to-grasp movements before contact is made and the position that fingertips are placed on an object remain to be clarified.

https://journals.plos.org/plosone/articl...ne.0025203

https://twitter.com/discoverycsc/status/...36910?s=21