Arguing Against Intelligent Design

[Biochemist]

A lot of emphasis has been given the "Cambrian Explosion" and for the most part rightly so. But I think it should be given a context that is more correct than explosion....

The real question is how many different animals were really distinct lines as in did all the Cambrian animals have one common ancestor or did the animals of the Cambrian have more than one protist ancestor? ...Either way the Cambrian "expansion" wasn't as fast as the word explosion would seem to indicate and the multiple body plans could be the result of multiple protist ancestors.

This is the one of the core issues. We have referenced the probabilistic issues associated with the "sudden" appearance of the 70 (or so) phyla before the "explosion" from the 3 phyla before the explosion several times. Depending when you start, the window of rapid appearance of new body plans ranges for 50 million to 200 million years. This may seems like a long time, but it is very difficult to hypothesize a mechanism to generate even a single new enzyme system de novo over 200 million years, unless we assume some very significant predisposition to decrease the probability from something on the order of 1 in 10^250 (a purely random association of DNA-driven amino acid sequencing) to some more "acceptable" number. The derivation of the probabilisitic issue was re-posted in this thread several times and again here:

 

http://hypography.com/forums/biology/5505-statistical-probability-issues-speciation.html

 

(by the way, a couple of folks have pointed out the errata in this monologue- ribosomes do not transcribe from DNA, they transcribe from m-RNA (oops); but the statistical numbers still hold)

 

I don't believe anyone has refuted the magnitude of the problem. And if we add to this issue the troublesome notion that there has been little expansion of the number of body plans (in fact, there has been a material contraction), this history is at odds with the presumptive model for speciation-via-mutation. More extant body plans should lead to more opportunities for mutation-generated body plans. In the ensuing 500 million years, we have not seen that evidence. Hence we had numerous body plans (e.g., phyla) show up in 200 million years, then none for 500+ million.

 

We could certainly assert that "something" happened that made the explosion of body plans "more likely" during that phase, but whatever it was has not happened since. This does not line up well with a mutative/selective model at all.

[Biochemist]

I invoke Lamarck because I see no way for transferring the phenotypical change you envisage to the genotype without acquired characteristics impacting on the genotype. That is certainly Lamarckian in principle if not in detail.

That is the way I read T-Bird's hypothesis as well.

[InfiniteNow]

ID "evolved" from this. I reject them all as really stupid, dangerous, and toxic:

 

 

YouTube - Creationists Pollute Young Minds at Museum on Nightline http://www.youtube.com/watch?v=9D8AeiAamjY

[Biochemist]

ID "evolved" from this. I reject them all as really stupid, dangerous, and toxic:

And I really appreciate your religious point of view on this.

[Biochemist]

One speculative theory for the Cambrian Explosion is connected to viral exchange. Virus can insert DNA into the DNA of a host cell. Rather than wait for a random mutation, a simple virus insertion scenario saves time allowing more options for any given time period.

This indeed is a proven mechanism. But it does not solve any questions related to the source of the gene that was extant in the virus. If the gene in the virus was not previously extant in some live phenotype, then it was never "selected". So this mechanism does not do anything to support or refute a mutative thesis.

[freeztar]

This indeed is a proven mechanism. But it does not solve any questions related to the source of the gene that was extant in the virus. If the gene in the virus was not previously extant in some live phenotype, then it was never "selected".

 

Why?

Because viruses are not "alive"?

 

Are you familiar with the RNA world hypothesis?

[mynah]

I invoke Lamarck because I see no way for transferring the phenotypical change you envisage to the genotype without acquired characteristics impacting on the genotype. That is certainly Lamarckian in principle if not in detail.

Genetic inheritance is essentially Mendelian, but epigenetic inheritance is, to a significant extent, Lamarckian.

[Thunderbird]

I invoke Lamarck because I see no way for transferring the phenotypical change you envisage to the genotype without acquired characteristics impacting on the genotype. That is certainly Lamarckian in principle if not in detail.

Further scientific investigation has revealed why, and now our nearly 150-year old evolutionary synthesis -- which has never had a coherent theory of form -- is about to get one.

 

It was thrilling and somewhat humbling to read developmental biologist Stuart Newman’s hypothesis of the evolutionary triumph of life as it self-organized half a billion years ago, using what he calls toolkit genes from single-celled highly plastic organisms to make a balletic leap into multicelluarity at the time of the Cambrian explosion when virtually all of today’s modern animal forms (35 phyla) first appeared, as evidenced in the fossil rock.

 

 

 

Invoking Larmark just confuses the mechanisms I'm attempting to address here.

 

 

 

The hypothesis is not about genetic changes..... for this scenario to be correct there has to be a prior genetic tool kit in place before archetypal forms that emerged in the Cambrian.

 

 

 

...So if you have cells with genes that evolved for single-cell functions, and you put the cells together into clusters, then those clusters of cells have physical properties -- including self-organizing properties – that individual cells never had. And then those cell clusters can make 40 or 50 different kinds of forms very rapidly by virtue of the physics mobilized by the existing gene products in the changed scale. They don’t need a lot of genetic changes to go from one form to another. And the forms produced in this way can become locked in later by natural selection.” -- Stuart Newman, is currently Professor of Cell Biology and Anatomy at New York Medical College in Vallhala, New York where he teaches and directs a research lab.

 

http://http://www.scoop.co.nz/stories/HL0804/S00103.htm

 

 

A simplified scenario

 

1.A Benthic microbial community mass,.. complex in chemical cellular relationships yet simple in an x-axis geometry.

 

2.These masses produce master cells enabling the community it reproduce as a stem cell reproduces. These archetypal cells are in place, the hierarchy of phenotype genotype is in place. This place however is only of the structural hierarchal level of the simple geometry of the x-axis.

 

 

3. The structural blueprint is emergent, this emergence however self-organizes within principles of geometric structural tensegrity on the extr-cellular level.

 

 

 

 

"A molecule of water does not form itself into waves and vortices. However, a mass consisting of trillions of water molecules does. You don't need new substances. It's just a matter of changing the scale and bringing new physical processes into play.Stuart Newman

This dynamic orienting structure of the cells that I describe initially formed geometrically top down, to the extracellular matrix, not from the bottom up of genetics.

 

 

 

 

Below is a description of this emergent structure that lies between the hierarchy of the body plan, and the intracellular genetics of the cell.

 

 

 

 

 

 

ULTIMATE COMPUTING

Stuart R. Hameroff

Department of Anesthesiology, University of Arizona

5.5.4 Geodesic Tensegrity Gels

 

 

Michigan State University have examined compressive and tensile properties of cytoplasm.

They find that semi-rigid microtubules are under compressive forces generated by interwoven contractile actin filaments. A balance between parallel compressive and tensile forces leads to a self-supporting property characterized by Buckminster Fuller (1975) as

"tensegrity." Tensegrity can provide cell support even if the rigid parallel element are not in direct contact. Tensegrity in the cytoskeleton might explain the self-supporting structural properties of cytoplasm in which the rigid parallel elements are not in direct contact.

 

Robert Jarosch (1986) has proposed that contractile actin winds and unwinds microtubules by a "torque drive," causing rotational oscillations and perhaps tuning and detuning of the microtubule system. Dynamic compression/tension may also be important in the regulation of membrane receptors whose mobility are limited by anchoring MT.

Conversely, contractile actin filaments can redistribute the receptors unless they ar restrained.

Dynamic tensegrity (Chapter 8) may be an important mechanism in many biological functions. In the cytoplasm, complex structures assemble, perform, and vanish into soluble

subunits.

1.5.1 Reaction Diffusion System

Winfree and Strogatz (1984) have studied the 3 dimensional behavior of reaction diffusion

systems. They find that reaction diffusion waves commonly appear as involute spirals or scrolls radiating from tiny rotating activity patterns called "organizing centers." The scrolls emanate from their central organizing axis which typically forms a closed ring or toroidal vortex. The origin of the waves is defined as a phase singularity whose immediate neighborhood is a rotating pattern of chemical activities, the pivot of the rotating spiral wave from which it radiates. The ostensibly flat spiral is actually a cross section of a three dimensional wave shaped like a scroll which emerges from a filament of singularity in 3

dimensions

Figure 1.10: Three dimensional computer simulation of a reaction-diffusion

system. A filamentous organizing center emanates "scroll ring" patterns. With

permission from Arthur Winfree.

Cytoplasmic microtubules and centrioles are organizing centers which could behave like

the singularities described by Winfree and Strogatz. Dynamic activities of the cytoskeleton may release diffusing waves of calcium ions which can alter the nature of surrounding cytoplasm by sol-gel transformations (Chapter 5). Coding by microtubule associated proteins (MAPs) and other factors could result in reaction-diffusion patterns specific to the dynamic state of the organizing center. Such patterns could suffice as short term memory in cells ranging from simple protozoa to human brain neurons. Another type of interactive,

3 dimensional pattern with interesting properties is the hologram.

http://http://www.theenginesofevolution.com/GeodesicTensegrity.pdf

 

 

 

I was surprised and delighted to see the one overall structure that I observed in the artifact corresponded exactly to a fractal pattern on the cellular level.

 

 

 

 

He also says what DPMs were made of. They were gene products (proteins) but also networks of physical processes that shaped and patterned organisms using adhesion, polarization, viscoelasticity, etc. DPM elements also combined with one another to make oscillations and segmentation, as well as morphogens from secreted multicellular molecules.

The morphogens then traveled through the organism to create organismal forms. Newman says the survival of cell types later became a matter for selection.

[Thunderbird]

From my paper....The following process will attempt to show how multi-cellular life forms can emerge all at once, into rings of higher order, from an assemblage point of spontaneous organization.

This point being a dissipative structure that starts by recapitulating pre-existing organizational phases of its environment, These points on instabilities begin as layers of oolitic spheres bound in a chemical cellular community matrix along an X-axis as a microbial mat. This mat begins to form protuberances upward into the water column. in so begins to be reformed within the cycles of the shallow sea. A these protuberance grow, the waves and tides act as a construction mechanism. These cycles build a concentric wheel or bagel configuration that contains an enfolded pattern that represents the ebb and flow of waves and tides. This embryonic form emerging as a self-constructed, self-contained micro-environment. a central aperture and connects the internal environment with external dynamics (cyclical flow of waves and tides) .

 

 

 

These construction are not simply a spiral that spins in the same direction, but are formed by turning back on itself in a cycle of recursion. This recursive structures having been patterned after the ebb and flow of tide and wave pulses. This cycle recorded in concentric layers of enfolded oolitic spheres connected by filaments of cyanobacteria providing a micro-environment for more complex eukaryote cell that had attained a critical amount of genetic variables adapted over billions of years in a Varity of conditions, environments and symbiotic relationships. They are in essence the stem cells for animals that are about to form nonlinearly. Once the form reaches a critical mass it becomes stationary and is reformed into an egg shaped vessel. The wave pulse then becomes internalized bringing the inner clockwork pattern into a dynamic synchronicity with the macro-environment at large. These layers form a symmetrical pattern of embedded concentric channels that unite at a central basin. Seawater is directed into right and left apertures that have opened into logarithmic spirals. This energetic form being shaped by the balance between internal structure and external flow. This recursive logarithmic structure appears to be key initiating an internal autopoitic system. In essence an over all structural pattern emerges as a fractal of the cellular level components as the chemically based cellular community conforms to the internal fluid cycles.

 

 

Another key in the self-making ability of the embryonic material that forms these structures is in it's ability to shape-shift around the tendency of a fluid to seek an ordered path though and around a medium. This medium having a fine balance of cohesion and plasticity.

The next key is in the mineral content of the spheres. Aragonite, this form of calcium carbonate has properties that promote microbial growth and acts as a mineral substrate for initiating an autopoetic biochemical cycle. This mineral has been discovered to be a fundamental element in maintaining an autopoetic system in coral reefs and closed artificial systems such as salt water aquariums.

Another important roll of the oolites is in their ability to act as a dynamic scaffolding. As the aragonite spheres dissolve though chemical and mechanical forces, a synergy unfolds throughout the emerging structure, As the oolites shrink they become point attractors among the eukaryote cells, that have now adopted the fluid energetic pattern left by the cyanobacteria filaments. As the oolites lose mass they induce the production of new filaments that emerge from the outer cellular membranes of the eukaryotes. Anchoring proteins extend through the plasma membrane to link to the emerging cytoskeleton structure. Simply put, as the temporary oolitic scaffolding deconstructs, it constructs it's permanent replacement. These Anchoring-type junctions not only hold cells together but provide tissues with structural cohesion. These junctions are produced more abundantly in tissues that are subject to higher mechanical stress such as the outer skin and heart. Connective tissues begin forming flexible geodesic scaffolding by drawing in and connecting to points in space where the oolites have now vacated. These connecting points form the extracellular matrix, meanwhile the bilateral apertures acts as a cycle attractor spiraling inward keeping a central tension as the embryo loses mass and takes shape, simultaneously providing a flow of renewing sea water though the recursive system as it pulses in time with wave cycles. The central apertures begins to coil in slack in the form of a layered network of connected cells. This dense mass of wound together cells will form heart tissue. This tension that connects eukaryote cells in a medium of cohesion is called (tensegrity). Tensegrity results in a crystallization of connections in the architecture of the emerging organism, enabling the individual cell though it's own intracellular matrix to respond to a potential fitness space. This crystallization of the recursive dynamic structure might well result in an "algorithmic self-assembly" of genetic probabilities.

 

 

 

 

 

 

 

 

 

 

 

Figure 1.10: Three dimensional computer simulation of a reaction-diffusion system. A filamentous organizing center emanates "scroll ring" patterns. With permission from Arthur Winfree.

 

Cytoplasmic microtubules and centrioles are organizing centers which could behave like the singularities described by Winfree and Strogatz. Dynamic activities of the cytoskeleton may release diffusing waves of calcium ions which can alter the nature of surrounding cytoplasm by sol-gel transformations (Chapter 5). Coding by microtubule associated proteins (MAPs) and other factors could result in reaction-diffusion patterns specific to the dynamic state of the organizing center. Such patterns could suffice as short term memory in cells ranging from simple protozoa to human brain neurons. Another type of interactive, 3 dimensional pattern with interesting properties is the hologram.Stuart R. Hameroff

[Biochemist]

Why?

Because viruses are not "alive"?

No. In a speciation-by-mutation model, irrespective of whether a gene is transferred by a virus, by an episome (bacteria to bacteria) or by a standard meiosis/mitosis process, the gene still would have to be "selected". This means that a series of "mutations" occur that creates the gene. The gene gets expressed in phenotype. The phenotype advantages the species, and the gene then propagates because the phenotypic advantage results in (usually) numerical advantages for that phenotype in the population. That gene could then be "picked up" by a virus, but it still would have had to go through a vetting process to get selected. If a gene shows up that was never previously selected, that event is at odds with the reigning speciation-by-mutation hypothesis.

[Biochemist]

From my paper....The following process will attempt to show how multi-cellular life forms can emerge all at once, into rings of higher order, from an assemblage point of spontaneous organization.

I am sorry, but I still don't get this T-bird.

 

I am open to a new hypothesis about how single cells organize into multicellular organisms. But we also have to objectively deal with the fact that the extant multi-cellular organisms have different genomes, not just different multicellular organizations. The metaphor above for a swirling water vortex is inapplicable, because the chemical structure of water does not change when it "organizes" into a vortex.

 

In contrast, each species has unique genetic markers. As Eco said above, if the "organizing" process that you describe results in an inheritable coding structure in the genome, this is suggesting that a change in form or behavior drive a change in th genome. This is the step that looks Lamarckian.

[Thunderbird]

I am sorry, but I still don't get this T-bird.

 

I am open to a new hypothesis about how single cells organize into multicellular organisms. But we also have to objectively deal with the fact that the extant multi-cellular organisms have different genomes, not just different multicellular organizations. The metaphor above for a swirling water vortex is inapplicable, because the chemical structure of water does not change when it "organizes" into a vortex.

 

In contrast, each species has unique genetic markers. As Eco said above, if the "organizing" process that you describe results in an inheritable coding structure in the genome, this is suggesting that a change in form or behavior drive a change in th genome. This is the step that looks Lamarckian.

I believe you may be stuck with the Idea that is not mine, what you keep referring to as a change in genetics has nothing to do with what I showing you here.

 

Let me be clear This has nothing to do with genetic change.

I’ll use an analogy...

 

Imagine an orchestra with all the players present, phenotypes, genotypes, they all play very well.

 

Everything I have presented is about the conductor of the song the genes expressing what is already there, natural selection kicks in after all the complex instruments are already playing.

 

This song starts with a chaotic composer. The principles are all there but you are still looking at the notes like they can make a composition and not looking at the conductor .

 

Since there is no signal composer it is more like a Jazz session.

 

 

 

Quote:

...So if you have cells with genes that evolved for single-cell functions, and you put the cells together into clusters, then those clusters of cells have physical properties -- including self-organizing properties – that individual cells never had. And then those cell clusters can make 40 or 50 different kinds of forms very rapidly by virtue of the physics mobilized by the existing gene products in the changed scale. They don’t need a lot of genetic changes to go from one form to another. And the forms produced in this way can become locked in later by natural selection.” -- Stuart Newman, is currently Professor of Cell Biology and Anatomy at New York Medical College in Vallhala, New York where he teaches and directs a research lab.

[Thunderbird]

These forms are geometric expressions first... genetic expression secondly.

 

 

 

 

 

 

[Thunderbird]

 

In contrast, each species has unique genetic markers. As Eco said above, if the "organizing" process that you describe results in an inheritable coding structure in the genome, this is suggesting that a change in form or behavior drive a change in th genome. This is the step that looks Lamarckian.

 

And the First Animal on Earth Was a ... - Hypography - Science for everyone

 

 

Comb Jelly

A new study mapping the evolutionary history of animals indicates that Earth's first animal--a mysterious creature whose characteristics can only be inferred from fossils and studies of living animals--was probably significantly more complex than previously believed.

 

This is one example posted in the news section of an ever growing trend there was no single simple animal at the base of the Darwinian tree of life, but rather a plethora of separate morphological forms emerging from one archetypal cell.

[freeztar]

Also from that article:

 

...the sponge [may have] evolved its simple form from more complex creatures--a possibility that underscores the fact that "evolution is not necessarily just a march towards increased complexity," says Dunn. "This scenario would provide a particularly dramatic example of that principle."

[Thunderbird]

The author here is Maxson J. McDowell a Micro-biologist turned Jungain psychologists, here he makes the distiction between Lamark, Darwin and the principles of self-organization that I am attempting address.

 

 

 

One line of evidence concerns the machinery of inheritance. I have only about 32,000 different genes (Baltimore 20001) while a bacterium has 3 to 5,000. But my anatomy is astronomically more complex than that of a bacterium. It has been estimated that the human body contains about 5x1025 bits of information in the arrangement of its molecules while the human genome contains less than 109 bits of information (Calow 1976, pp. 101-3). Again the disparity is of astronomical proportions. These numbers prove that my genes must be used economically. They must code for processes which enable my structure to evolve, but they are too few to form a 'blueprint', or image, of my final structure. My body's structure is emergent, that is, my body self-organizes with minimal guidance from the genes.

 

 

 

 

 

http://http://cc.msnscache.com/cache.aspx?q=73062817596814&mkt=en-US&lang=en-US&w=1e47834e&FORM=CVRE

 

 

A

geometrical principle

Jung (1938/68, para. 155) said that the archetype-as-such:

 

might perhaps be compared to the axial system of a crystal, which ... determines only the stereometric structure but not the concrete form of the crystal ... [Amongst different crystals of the same substance] the only thing that remains constant is the axial system, or rather, the invariable geometric proportions underlying it. The same is true of the archetype. In principle it can be named and has an invariable nucleus of meaning - but always only in principle, never as regards its concrete manifestation [or image].

 

Thus Jung said that an archetype-as-such is like a geometrical principle.

 

Pythagoras' principle may serve as an example: for any right-angled triangle a2 = b2 + c2, where a is the length of the hypotenuse and b and c are the lengths of the other two sides. The geometrical principle (archetype-as-such) is always and everywhere true. A particular right-angled triangle, however, whether it be formed in stone, or on paper, or in the cerebral cortex, is located in time and space; it corresponds to an archetypal image.

 

Jung's idea had great explanatory power but it was confused by the suggestion, which he made in the same passage, that an archetype-as-such is inherited. A principle is not inherited, nor does it evolve. It is inherent to our universe.

It is clear from Jung's writing (1936/68, para. 99; 1943/66, para. 109) that he did not understand the mechanism of evolution, nor the mechanism of inheritance. Jung's understanding was sometimes based on Lamarck rather than Darwin and Mendel. Jung said that an archetypal form of behaviour would, if it were rehearsed often enough, be inherited. We now know that only genes are inherited and that genes are not altered by behaviour but by random mutation. An individual whose behaviour is, by chance, better-adapted reproduces more and so perpetuates his or her own genes.

 

 

 

 

Dynamic systems

While a triangle is static, the personality is a dynamic system. Here I discuss several dynamic systems which are more transparent than the personality. I use these systems not as analogies but to explain a homology, a single property which is true of all dynamic systems.

 

 

A stream

 

 

Imagine a mountain stream. It is a dynamic system because it only exists while energy flows through it, in this case the water's kinetic energy. Sometimes the stream forms a whirlpool and sometimes it takes the serpentine form (the latter is seen most clearly in an aerial photograph of a river delta). Each of these forms represents a pre-existing mathematical principle or possibility, characteristic of rivers and streams everywhere. A whirlpool is not caused by the bed of the stream because it may also form in the ocean or in the atmosphere. Even the stars of a galaxy sometimes form a whirlpool (Hildebrandt & Tromba 1996, pp. 12-13, 246). A stream organizes itself but the ways it can do so are constrained: only certain pre-determined forms are possible.

 

The whirlpool is robust or homoeostatic. It is called a stable attractor (Kauffman 1995, p. 187) because it is a stable form into which a dynamic system is attracted. Imagine a whirlpool around the drain in your tub. Interrupt the whirlpool by putting your hand in it and the water continues to drain, but not as a whirlpool. Remove your hand and the whirlpool reforms. Besides the whirlpool and the serpentine form, there are many other forms that a stream could assume but most of them are unstable. Whatever form the stream is placed into, it slides spontaneously into one of its few stable attractors and remains there.

 

 

 

A living creature

 

 

In biology we can trace the evolution of a dynamic system. Evidence comes both from the fossil record and from existing plants and animals. Because it only exists while energy flows through it a living creature is a dynamic system1. Like the evolution of a mountain stream, the evolution of a living creature leads to forms which represent principles of organization. This is proven by convergence in evolution. The snake is an example. Not all snakes are related because, at different times, several different groups of reptiles evolved the snake-form (Zug 1993, p. 119). It is an adaptation for penetrating through narrow apertures. A snake-like body-form also evolved independently in earthworms, in fish (the eel) and in mammals (the ferret). Thus the snake body-form is a principle of organization which has been rediscovered again and again by evolution. The wing is another example. It evolved independently in insects, reptiles, birds, and mammals. Holland (1995, pp. 27-8; 1998, pp. 229-31) discussed a further example, the principle of the camera-eye, which was discovered independently in the evolution of vertebrates and of squids and octopuses.

 

Holland is perhaps the foremost authority on the mathematics of self-organization and emergence. He warned against teleology. Different organisms do not evolve along convergent lines in order to attain the same end-point. Evolution is by chance.

 

Convergence refers to the similarity of agents occupying similar niches. With some knowledge of the niche, we can say something of the form of the agent that will occupy it (Holland, 1995, p. 169).

 

That is to say, given the air as an ecological niche, we can predict that many of the life-forms which colonize that niche will develop wings. Wings, therefore, are a pre-existing (predictable) principle.

 

In a dynamic system a principle of organization is not a static form like a triangle. Rather it is a dynamic, an ordered way for energy to flow. The whirlpool orders the energy of a stream, the snake- form organizes sinuous movement, the wing-form organizes flight, and the camera-eye organizes light to form an image.

 

The snake, the wing, the camera-eye, and many other examples of convergence prove that evolution fulfills pre-existing principles of organization. That the same possibilities are realized again and again at different times also proves that the total number of such principles is limited. Principles of organization are specific, unchanging, and limited in number.

 

You may object that there is no principle of organization, only an interaction between components the outcome of which is determined by their properties and by inherent constraints. Thus in the evolution of birds the properties of bone, muscle, feather, air and gravity interacted according to inherent constraints and the wing emerged from these interactions. But this objection misses the point. Insects and birds evolved independently. In the insect different components with different properties interacted under different constraints to evolve the same structure, the wing. The number of ways in which such components might interact is very large. Most of the structures formed, however, would not be functional. The few structures which could potentially function in movement represent the pre- existing principles of organization. These include wings, legs, the snake-form, tail-and-fin, and several others.