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Revolutionary Biology
Evolution News and Views ^ | October 20, 2014 | Jonathan Wells

Posted on 10/21/2014 6:58:05 AM PDT by Heartlander

Revolutionary Biology

Jonathan Wells October 20, 2014 11:36 AM | Permalink

It is not surprising that for thousands of years people thought the Sun and stars revolve around the Earth. We see it with our own eyes every day and night. In 1543, however, Nicolaus Copernicus proposed that the Earth revolves around the Sun and thereby revolutionized our conception of the solar system and the universe. A century and a half later, Isaac Newton proposed laws of motion and gravitation to explain the behavior of all material bodies -- not only on the Earth but also in outer space -- in terms of material particles (mass) and force.

As telescopes improved and astronomers learned more about other planets and the stars, it became clear that the Earth -- in spatial terms -- is only an infinitesimal part of the universe. It is not surprising, then, that scientists now tend to regard the universe as the most general manifestation of natural laws, and life on Earth as a special case. In particular, most modern biologists tend to analyze living things as special cases (albeit very complex ones) of general laws that describe all phenomena in terms of material particles and forces.

Copernicus.jpg

Copernicus, De revolutionibus orbium coelestium (1543)

This mechanistic approach to living things fits well with René Descartes's 17th-century "machine metaphor," according to which animal bodies are machines composed of smaller machines. This metaphor still dominates much of modern biology. In 1998 Bruce Alberts, President of the U.S. National Academy of Sciences, wrote in the prestigious journal Cell that "the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines." The same issue of Cell carried articles about "chromatin-modifying machines," "chaperone machines," and "machines within machines." One article was titled "Mechanical Devices of the Spliceosome: Motors, Clocks, Springs, and Things."

Darwin and Design

In addition to working within the framework of the machine metaphor, most biologists also work within the materialistic framework of Charles Darwin's theory of evolution. According to Darwin, all living things are descendants of one or a few common ancestors that have been modified by unguided processes such as variations and natural selection. Adaptations that previous biologists had attributed to design, Darwin argued, were actually produced by natural selection, which operates without foresight or purpose. In 2007, Francisco Ayala wrote that "Darwin's greatest contribution to science" was "to explain the design of organisms, their complexity, diversity, and marvelous contrivances, as the result of natural processes," without the need for intelligence.

But Darwin did not know the mechanism of heredity or the origin of novel variations, so his theory was seriously incomplete. After 1900, Mendelian genetics seemed to remedy the first deficiency, and after 1953 DNA mutations seemed to remedy the second. The resulting Modern Synthesis combined Darwin's theory with the idea that organismal development is controlled by a genetic program written in DNA sequences, and that DNA mutations can change the program to generate the raw materials of evolution. According to molecular biologist Jacques Monod, "with that, and the understanding of the random physical basis of mutation that molecular biology has also provided, the mechanism of Darwinism is at last securely founded. And man has to understand that he is a mere accident." (Quoted in Horace Freeland Judson's 1979 book, The Eighth Day of Creation, p. 217.)

So in the context of Darwinian evolution and molecular biology, many biologists tend to regard the living organism as a special kind of machine -- that is, a computer, in which DNA sequences are the software. As Bill Gates put it in 1995, "DNA is like a computer program but far, far more advanced than any software ever created." In both the technical and popular literature, phrases such as "genetic program" and "DNA blueprint" have become commonplace. Francis Collins, Director of the Human Genome Project, wrote in his 2006 book The Language of God that DNA is an "amazing script, carrying within it all of the instructions for building a human being." (p. 2)

Yet combining Darwinian evolution with the notion of a genetic program leads to a paradox. Computers and computer programs (like machines in general) are made by intelligent agents, namely, human beings. Not surprisingly, proponents of intelligent design (ID) have argued that machine- and code-like aspects of living things point to the very design that Darwinian evolution tries to exclude. Thus Michael Behe points to a molecular machine, the bacterial flagellum, which does not function unless several dozen parts are already in place -- a feature characteristic of intelligent design. And Stephen Meyer points to complex and highly specified DNA sequences, which like computer software cannot arise by chance but point to an intelligent designer.

According to pro-evolution philosophers Massimo Pigliucci and Maarten Boudry, "creationists and their modern heirs of the Intelligent Design movement have been eager to exploit mechanical metaphors for their own purposes." So "if we want to keep Intelligent Design out of the classroom, not only do we have to exclude the 'theory' from the biology curriculum, but we also have to be weary [sic] of using scientific metaphors that bolster design-like misconceptions about living systems." Pigliucci and Boudry conclude that since "machine/information metaphors have been grist to the mill of ID creationism, fostering design intuitions and other misconceptions about living systems, we think it is time to dispense with them altogether."

But there are better reasons to dispense with the machine metaphor (and Pigliucci and Boudry mention some). Although the mechanistic approach has borne some fruit in biological research, the truth is that living things are very different from machines.

The End of the Machine Metaphor

A century after Newton's mechanical picture of the universe captured the scientific imagination, philosopher Immanuel Kant pointed out that living things -- which he called "organized beings" -- cannot be understood mechanistically. A machine is organized from the outside in by an external agent, but a living thing organizes itself from the inside out. "An organized being is then not a mere machine, for that has merely moving power, but it possesses in itself formative power of a self-propagating kind which it communicates to its materials though they have it not of themselves; it organizes them." So organisms cannot be understood by analogy to any natural causality we know. Instead, we must conceive of them as having an "internal purposiveness." In an organized being, "every part is reciprocally end and means. In it nothing is vain, without purpose, or to be ascribed to a blind mechanism of nature." (§65, §66)

According to Kant, the idea that organisms are internally purposive is a "regulative principle" that governs our thinking. In order to understand organisms properly, we cannot help but think of them in terms of purpose and design (and modern biologists, in spite of Darwin, habitually talk about organisms in such terms). But Kant did not claim that his description applied to the actual "thing in itself," which for him was unknowable -- a philosophical position that has been influential but controversial. The important point here is that he recognized that organisms cannot be understood as machines.

There is now growing criticism of the machine metaphor among biologists and philosophers of biology. According to Keith Baverstock, "a rapidly accruing body of evidence challenges the DNA centric dogmas that dominate evolution and cell regulation, both of which are predicated on the machine metaphor." Daniel Nicholson writes that "despite some interesting similarities, organisms and machines are fundamentally different kinds of systems... the former are intrinsically purposive whereas the latter are extrinsically purposive." Thus the machine metaphor "fails to provide an appropriate theoretical understanding of what living systems are." According to Ann Gauger, "the machine metaphor fails," in part, because organisms are "causally circular beings." Not only do new cells require existing cells, but also in many cases the biosynthetic pathway of a molecule requires the very molecule that is being synthesized. Stephen Talbott bluntly calls biology's refusal to disown the machine metaphor "an inexcusable mistake" that "has gripped the scientific community for decades, severely perverting biological understanding."

Yet going beyond a mechanistic approach to living things will not be easy. After all, the world of Newtonian mechanics seems so... well, natural. But just as relativity and quantum physics demonstrated that Newtonian mechanics is a special case from the cosmic and atomic perspectives, so a revolution in biology is now demonstrating that Newtonian mechanics is a special case from the organismal perspective as well. All three revolutions reveal that Newton's laws are only a subset of the laws governing phenomena in nature, which is much richer (and stranger) than is dreamt of in a mechanistic approach.

Revolutionary Biology

To overcome the limitations of the mechanistic approach to living things, Nicolas Rashevsky developed what he called "relational biology" in the 1950s. Instead of starting by analyzing the molecular constituents of a cell, Rashevsky focused on the organization of relations in a cell. Rashevsky's student Robert Rosen developed relational biology with the help of "category theory," a mathematical approach introduced in the 1940s by Samuel Eilenberg and Saunders MacLane. Relational biology has been further developed by Ion Baianu, Andrée Ehresmann and Jean-Paul Vanbremeersch, Paul Kainen, Aloisius Louie, and Richard Sternberg.

According to Rosen, relational biology is revolutionary because it describes living things in terms of laws that are not found in the inanimate universe. No longer is the organism a special case of universal natural laws; instead, the organism is the general case and the inanimate universe is a special case, because the latter embodies only a subset of the laws that apply in living things. As Rosen put it:

Organisms, far from being a special case, an embodiment of more general principles or laws we believe we already know, are indications that these laws themselves are profoundly incomplete. The universe described by these laws is an extremely impoverished, nongeneric one... In short, far from being a special case of these laws, and reducible to them, biology provides the most spectacular examples of their inadequacy. The alternative is... a more generic view of the scientific world itself, in which it is the mechanistic laws that are the special cases. [Essays on Life Itself, pp. 33-34]

Does this mean that we now understand life? Of course not, any more than we understood the universe after 1543. But the radical change in perspective provided by relational biology -- like the change in perspective provided by Copernicus -- at least opens the door to more fruitful exploration.

Where does this leave intelligent design? Alive and well.

In his just-published book Being As Communion: A Metaphysics of Information, William Dembski defines intelligent design as "the study of patterns (hence 'design') in nature that give empirical evidence of resulting from teleology (hence 'intelligent')." (p. 58) But this definition does not limit ID to tracing teleology back to an external agent.

For Aristotle, "design" meant "a principle of movement in something other than the thing moved," while "nature" meant "a principle in the thing itself." But for Aristotle the "principle" in each case was teleological, so he was distinguishing between external and internal teleology. Materialism strips nature of internal teleology and treats organisms as machines, leaving only external teleology. For Dembski, ID is not limited to external teleology, but (like Aristotle's metaphysics) encompasses internal teleology as well. When ID advocates look at life mechanistically, they do so "as a temporary measure, as part of a reductio ad absurdum argument, to refute materialism. Once materialism is refuted, however, intelligent design is able to leave a mechanistic understanding of life behind, looking at life as it is." (p. 62)

And for Dembski, life -- indeed, the entire cosmos -- is fundamentally informational. He defines information as realizing some possibilities by ruling out others. Since matter only exists in the form of material objects -- that is, as particular realizations out of many possibilities -- information is ontologically prior to matter. Thus "information should properly be regarded as the prime entity and object of science, displacing matter from its current position of eminence... Materialists see the natural world as matter all the way down. Information realists, like me, see the natural world as information all the way down." (p. 91)

What is the source of the information in nature? Darwinian evolution attributes it to natural selection, but Dembski demonstrates that natural selection is really "an information redistributor rather than an information generator or creator ... On materialist principles, intelligence is not real but an epiphenomenon of underlying material processes. But if intelligence is real and has inherent causal powers, it can do more than merely redistribute information -- it can also create it." (p. 185) Indeed, "the defining property of intelligence is its ability to create information," and "intelligence is the ultimate source of information." (pp. 186, 187)

Furthermore, Dembski writes, "Because information is produced as some possibilities are realized to the exclusion of others, information is fundamentally relational: the possibilities associated with information exist only in relation to other possibilities." (p. 29) Thus "informational realism... is a relational ontology." (p. 197) Like relational biology, informational realism regards relations among objects as more fundamental than the objects themselves.

Informational realism and relational biology, unlike the machine metaphor and materialistic evolution, can conceptualize organisms as they really are. Instead of evolutionary biology, we now have revolutionary biology.



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To: Heartlander

Evolution occurs in populations and often is in reaction to the environment. Mutations are infrequently the basis for speciation or population change unless they are frequently occurring mutations. More frequently existing alleles are selected for among the diversity within the population by giving reproductive to individuals possessing that characteristic. So, it really isn’t all that random. Only genetic drift is in part random. Survival is the product of evolution and that isn’t random.


21 posted on 10/21/2014 11:34:15 AM PDT by JimSEA
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To: JimSEA

I did not say random (although mutation is random WRT fitness) - I said evolution cannot have a goal – is unguided and blind. What’s up with the song and dance routine?


22 posted on 10/21/2014 11:48:48 AM PDT by Heartlander (Prediction: Increasingly, logic will be seen as a covert form of theism. - Denyse OÂ’Leary)
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To: Heartlander
There is a reason why evolution occurs, it is guided by the environment and survivability. Thus, it's not random and unguided. Mutations are random but their persistence in the organism isn't random. Most mutations are decidedly unhelpful or fatal and are out of the sets of alleles and are not heritable. It is an article of faith among creationists and intelligent design believers that evolution is all chaos and random chance which is simply not true.

Also, when I want to illustrate something I often search YouTube to find the explanation I'm looking for. Here is an article from New Scientist on the flagellum or rather a whole range of such appendages..

23 posted on 10/21/2014 12:11:45 PM PDT by JimSEA
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To: JimSEA
I know how evolution works – I don’t need YouTube – I’ve read many books on the topic from Dawkins, Dennett, Futuyma, et al… (Did not buy any of Dawkins or Dennett books – I would read them at the coffee shop / book store. I would not give them my money)

So are you stating that you believe God guided evolution to create humans through the environment?

24 posted on 10/21/2014 1:19:10 PM PDT by Heartlander (Prediction: Increasingly, logic will be seen as a covert form of theism. - Denyse OÂ’Leary)
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To: Heartlander

That’s a shame, the article is rather good. You seem to be saying that books, articles, presentations on the theory of evolution and basic biology are worthless? You’re missing out by not having an understanding of much of the world around you and you are telling me that nothing I can say could possibly get you to be interested in much of the world around you. That’s not an attack on you, I’m just saying we have entirely too few things in common to converse as I’m an old man set in his ways as much as you seem set in yours.


25 posted on 10/21/2014 2:18:55 PM PDT by JimSEA
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To: JimSEA
Give me a break Jim – I watched your first video – now did you read Behe’s article? I ask because you don’t seem to understand ID at all – you’ve mischaracterized it many times. At least I actually understand evolution.

Now back to the question, are you stating that you believe God guided evolution to create humans through the environment?

26 posted on 10/21/2014 2:38:12 PM PDT by Heartlander (Prediction: Increasingly, logic will be seen as a covert form of theism. - Denyse OÂ’Leary)
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To: Heartlander

Evolution by its very definition isn’t guided or managed expect by nature, biological processes and laws. I’ve read Behe’s articles and watched his presentations. I haven’t read his book nor am I likely to read it. He has an intelligent creator engineering proteins in the cell where a comprehensible alternative exists. Somehow the more we learn, the fewer instances of “irreducible complexity” we are faced with. When I was in high school, Crick and Watson had just figured out the structure of DNA, continental drift was highly controversial and the functioning of plate tectonics was unknown.

Particularly what I saw in ore body geology fit so well with the conclusions of tectonics in mountain and continental formation - structural geology. Biology has resulted in medicine and treatments that were just plain absent when I was born. I find the scope of change quite overwhelming but at the same time understandable where one directs their interest.

I’m looking forward to many more discoveries and understandings in whatever few years I’ve left.


27 posted on 10/21/2014 3:08:56 PM PDT by JimSEA
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To: JimSEA
I’m looking forward to many more discoveries and understandings in whatever few years I’ve left.

Good luck with that... I am not old and set in my ways - the irony being one of us is static living fossil - and the other is still evolving...

28 posted on 10/21/2014 3:32:02 PM PDT by Heartlander (Prediction: Increasingly, logic will be seen as a covert form of theism. - Denyse OÂ’Leary)
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To: Heartlander

If only us living fossils could be seen for what we are, successful populations of of which other populations have physically become isolated and in their new environment or due to small numbers have evolved new species. See the mantis shrimp, horsetail, hedgehog, etc. Or perhaps there are Lazarus species where very similar creatures (but the same in appearance only) have evolved more than once. Lots of speculation here bur a difficulty in doing more exact identities is the lack of ancient DNA. Of course, an Asian mussel will be different in allele frequency at least to a Mediterranean mussel.


29 posted on 10/21/2014 4:30:06 PM PDT by JimSEA
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To: JimSEA
Enjoy your niche...
[Darwin's] alternative to intelligent design was design by the completely mindless process of natural selection, according to which organisms possessing variations that enhance survival or reproduction replace those less suitably endowed, which therefore survive or reproduce in lesser degree. This process cannot have a goal, any more than erosion has the goal of forming canyons, for the future cannot cause material events in the present. Thus the concepts of goals or purposes have no place in biology... (p. 282)

This experiment conveys the essence of natural selection: it is a completely mindless process without forethought or goal. (p. 285)
The textbook Evolution, by Douglas J. Futuyma

---

Darwin showed that material causes are a sufficient explanation not only for physical phenomena, as Descartes and Newton had shown, but also for biological phenomena with all their seeming evidence of design and purpose. By coupling undirected, purposeless variation to the blind, uncaring process of natural selection, Darwin made theological or spiritual explanations of the life processes superfluous.
-Douglas Futuyma's Evolutionary Biology p. 5
..and try to live consistent in your stasis.
30 posted on 10/21/2014 5:03:33 PM PDT by Heartlander (Prediction: Increasingly, logic will be seen as a covert form of theism. - Denyse OÂ’Leary)
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