On Plato, the Early Church, and Modern Science: An Eclectic Meditation

November 30, 2004 | Jean F. Drew

[PatrickHenry]

I'm not convinced the human genome is the longest.

From this site here:

But among multicellular species, the size of the genome does not correlate well with the complexity of the organism. The human genome contains 3 billion base pairs of DNA, about the same amount as frogs and sharks. But other genomes are much larger. A newt genome has about 15 billion base pairs of DNA, and a lily genome has almost 100 billion.

[betty boop]

Evolution merely means change (of allele frequencies to be more specific.)

But doesn't Darwinist theory say that natural selection is what promotes the "survival (and thus reproduction) of the fittest?" At the very least, it would appear that survival (reproduction) is the "end," goal, or point of the exercise, the "good" toward which nature "strives." (I used quotation marks to indicate figurative language, so don't go hoopy on me). Or are you suggesting that what evolution really means is "change for the sake of change -- no good changes, no bad changes; just changes, randomly produced?"

Forgive me, Doc, but this strikes me as totally mindless.

[js1138]

Again, I would have to argue that your interpretation of complexity is transactional. There is nothing inherently more complex about a human blueprint than that of a newt. It is the interaction between the blueprint and the supportive infrastructure that appears as complexity.

But the notion that tiny changes to the underlying blueprint can be read as profound differences in structure and complexity is an underlying assumption of Darwinian evolution.

[Doctor Stochastic]

"Survival of the adequate" would be a better description.

Evolution is the change in allele frequency. "Good" or "bad" in an evolutionary context usually refer to having more or fewer descendants.

[betty boop]

They would have been executed under Stalin whose regime was extremely anti-Darwin.

This is news to me, Doc. Got a cite?

Stalin executed two types of people: Kulaks and "intellectuals." Of the latter, one could be "in favor" one day, and "out of favor" the next. (The Kulak seems never to have been in favor....) Stalin resorted to a good purge every now and then -- terror being one of his tools of totalist control -- and I feel reasonably sure that whether someone was a Darwinist or not was not a selection criterion. Stalin was glad to execute victims of either persuasion. He executed Ervin Bauer in 1947 in a "routine" purge. Bauer was not a Darwinist (as far as i can tell).

As to whether Stalin was a "true Marxist," my impression is he served nothing -- no one and no idea -- except his own lust for power and the idea of his de facto "divinity."

[js1138]

Forgive me, Doc, but this strikes me as totally mindless.

I assume this offends your aesthetic and moral sense. I'm not exactly sure what kind of argument this is. Is it more pleasing to contemplate all the suffering in the animal world to be the result of a deliberate act of design?

Mind could be visible at some scales and not noticed at other scales. That gets back to emergent properties. What seems random at the quantum scale becomes order and predictibility at the macro scale. We do not know if there is a scale at which natural selection might appear to be the workings of a mind. Underlying randomness noes not preclude emerging order.

[js1138]

http://eserver.org/cyber/stalin.txt

[Doctor Stochastic]

Check out the Affair Lysenko. This is well known among biologists. Of course, the removal of Darwin from the biology and thus agriculture fields did help the Soviets set a record for crop failures.

[js1138]

http://www.haciendapub.com/article7.html

[D Edmund Joaquin]

I like your analogy, but isn't it strange, we always seem to have donkey carts mixed in with old Chevys, and Mazzeratis, let alone jets and beyond? Perhaps these are the transitionals that the evolutionists are seeking. Another problem too is that of the observer -- whereas one may perceive a "donkey cart", another, aware of other information in the cosmos, might well be in awe of a stealth fighter, which was mistaken for a donkey cart because the first observer had no idea of what he was seeing

As to consciousness, it's probably "outside the quantum" and can't be measured

[betty boop]

I assume this offends your aesthetic and moral sense....

No, that's not the offense, js1138. When I said that Doc's argument struck me as mindless, I meant exactly that. I thought it was irrational.

Doc seems to suggest that the failure of Soviet agriculture was due to Stalin's poor choice of a scientist. I gather Doc thinks that if Stalin had just gone with Darwin instead of Lysenko, Soviet agriculture would have thrived. [Maybe Lysenko would have, too. But he alas was also purged by Stalin....]

Which is, of course, totally bogus on the historical record. Soviet agriculture failed because Stalin decided to destroy the Kulaks, a small-propertied class of farmers (rather like those imagined in Thomas Jefferson's reveries], titled to land by ancestral birthright, from whose produce the Russian people had historically been able to feed itself more or less. Certainly the Kulaks and their families and communities had a certain independence from the common trend.

So Stalin wiped them out by the scores of millions. And then collectivized their lands. Marxist Planning was to substitute for long perduring, deep human connections with the soil, its own theory of rational agricultural planning and production -- all of which made possible by the destruction of every human community within its sway, and a way of life and livelihood to boot.

But hey! these are merely the eggs one has to break to make an omelette, you know. [No wonder Soviet agriculture failed....]

To the best of my knowledge (such as it is), up to its last gasp, the USSR was a net importer of the most basic foodstuffs, such as wheat.

If Stalin wanted a scientist to help him with such tedious business as feeding his people, then I don't see where Darwin would have been of much help. Stalin would have done better to (a) leave the Kulaks alone; and (b) check out the hybridization work first conducted by Mendel. But he was no "intellectual"; and I digress.

Had the Levises, Lewontins, and Chomsky's of our world lived during the Stalin era, I feel reasonably certain that they would sooner or later have been "purged," each and all of them. And any other suchlike ingrates.

js1138, I really liked this:

Underlying randomness noes not preclude emerging order.

To me it seems the single most fascinating prospect of science as it emerges today is the reconciliation of the perspectives of the microworld of quantum theory, the macroworld of Newtonian mechanics, and their common context in Einsteinian relativity theory and beyond.

And I also really liked this:

We do not know if there is a scale at which natural selection might appear to be the workings of a mind.

No, we don't. But that's what we're looking for.

[Matchett-PI]

"Now; to the charge that "there is no evidence for Macroevolution." Bull! This falls under the rubric of ignoring contradictory evidence. I'll post an excerpt from the U-Cal San Diego link I cited earlier. I quote as follows:" [snip]

"Evidence"???? Sheeeesh!!

February 10, 2002

Biologists are ecstatic. In "Genetic Archeology Uncovers Early Animal Evolution," biologists claim they “have uncovered the first genetic evidence that explains how large-scale alterations to body plans were accomplished during the early evolution of animals.”

Have they?

Making genetic modifications between fruit flies and brine shrimp, they found this “suppresses 100 percent of the limb development in the thoracic region of fruit flies, but only 15 percent in Artemia­would have allowed the crustacean-like ancestors of Artemia, with limbs on every segment, to lose their hind legs and diverge 400 million years ago into the six-legged insects.”

Because of this, macroevolution, overnight, has been solved, with one set of experiments!

The study seems to be aimed at “creationists” as this statement details:

“Creationists have argued that any big jump would result in a dead animal that wouldn't be able to perpetuate itself. And until now, no one's been able to demonstrate how you could do that at the genetic level with specific instructions in the genome."

Have they found the “big jump” or have they focused so narrowly on one part, that they hope non-thinking people will give up and go home?

How does changing legs equal the complete biochemical change between species?

How do they conclude these changes actually took place, outside their intelligently designed experimentation other than they may have?

How long would such a species survive with a defect of missing legs?

It seems the miracles of naturalists only happen under carefully controlled experimentation.

The article goes on to say the finds may contribute to “understanding human disease and genetic deformities.”

Ah, so genetic changes generally aren’t beneficial to an animal or human after all?

As usual, the obvious (i.e. reason, etc.) is left out of naturalistic “science.” ~ Darrick Dean @ Science Watch

[Matchett-PI]

"There is no "religious" attachment to the Theory of Evolution and "Darwinianism" only exists in the minds of creationists."

Some define faith as "belief that isn't based on evidence". Dawkins calls it the "principal vice of any religion"

[ Biblical] Christians realize that this definition of faith is a caricature. Instead of viewing faith as belief that is not based upon evidence, we view faith as that which is a pre-condition for gaining any other knowledge; faith itself is not irrational or unscientific, but that which must be in order to gain other knowledge through science and logic.

For instance, confidence in the law of non-contradiction could be said to be faith.

There is no direct way to prove the law of contradiction except that it must be presupposed in order to learn anything or differentiate anything from anything else.

Likewise, the principle of induction, which states that the future will be generally like the past, is what makes possible the formulation of scientific laws and theories.

We cannot test the truth of this principle scientifically, for we would be assuming the truth of induction to try and prove it.

We cannot test the truth of the principle logically, for logic has as its subject matter static propositions.

Thus, induction and the law of contradiction, two of the bedrocks upon which all the rest of Richard Dawkins' knowledge is based, are both things he must accept on faith. ~ Jonathan Barlow

[Matchett-PI]

"... it could be stated that the Catholic Church [put forth] no argument that God intervened in the material sense to create man, the intervention was a spiritual one."

Not so.

"....... Pope John Paul II, in a General Audience on 24 January 1986, addressed the issue and said that "The theory of natural evolution, understood in a sense that DOES NOT EXCLUDE divine causality, is not in principle opposed to the truth about the creation of the visible world, as presented in the Book of Genesis."

Conflicts between the truths of science and the truths of faith, in other words, are only apparent, never real, for both science and faith, the natural world accessible to reason, and the "world" of revelation accessible to faith, have the same author: God.

..Being all powerful, and having created EVERYTHING out of nothing...."

HERE

[Alamo-Girl]

Thank you for your reply, js1138. Again, I would have to argue that your interpretation of complexity is transactional. There is nothing inherently more complex about a human blueprint than that of a newt. It is the interaction between the blueprint and the supportive infrastructure that appears as complexity. But the notion that tiny changes to the underlying blueprint can be read as profound differences in structure and complexity is an underlying assumption of Darwinian evolution,

I do not define complexity in terms of a "transaction". Nor am I valuing the complexities or interpreting them beyond their definitions as described. But, by all means, see for yourself:

Here are the two basic types of complexity:

NECSI: Complex Systems

Complexity is ...[the abstract notion of complexity has been captured in many different ways. Most, if not all of these, are related to each other and they fall into two classes of definitions]:

1) ...the (minimal) length of a description of the system.

2) ...the (minimal) amount of time it takes to create the system.

The length of a description is measured in units of information. The former definition is closely related to Shannon information theory and algorithmic complexity, and the latter is related to computational complexity.

And here are the type of complexity I mentioned, their definitions and categories in which they seem to fit, to me:

Least Description

NIST: Kolmogorov Complexity

Definition: The minimum number of bits into which a string can be compressed without losing information. This is defined with respect to a fixed, but universal decompression scheme, given by a universal Turing machine.

Wikipedia: Cellular Automata (aka Self-Organizing Complexity)

A cellular automaton (plural: cellular automata) is a discrete model studied in computability theory and mathematics. It consists of an infinite, regular grid of cells, each in one of a finite number of states. The grid can be in any finite number of dimensions. Time is also discrete, and the state of a cell at time t is a function of the state of a finite number of cells called the neighborhood at time t-1. These neighbors are a selection of cells relative to some specified, and does not change (Though the cell itself may be in its neighborhood, it is not usually considered a neighbor). Every cell has the same rule for updating, based on the values in this neighbourhood. Each time the rules are applied to the whole grid a new generation is produced.

Adami: Physical Complexity

In this paper, we skirt the issue of structural and functional complexity by examining genomic complexity. It is tempting to believe that genomic complexity is mirrored in functional complexity and vice versa. Such an hypothesis, however, hinges upon both the aforementioned ambiguous definition of complexity and the obvious difficulty of matching genes with function. Several developments allow us to bring a new perspective to this old problem. On the one hand, genomic complexity can be defined in a consistent information-theoretic manner [the "physical" complexity (4)], which appears to encompass intuitive notions of complexity used in the analysis of genomic structure and organization (5). On the other hand, it has been shown that evolution can be observed in an artificial medium (6, 7), providing a unique glimpse at universal aspects of the evolutionary process in a computational world. In this system, the symbolic sequences subject to evolution are computer programs that have the ability to self-replicate via the execution of their own code. In this respect, they are computational analogs of catalytically active RNA sequences that serve as the templates of their own reproduction. In populations of such sequences that adapt to their world (inside of a computer's memory), noisy self-replication coupled with finite resources and an information-rich environment leads to a growth in sequence length as the digital organisms incorporate more and more information about their environment into their genome. Evolution in an information-poor landscape, on the contrary, leads to selection for replication only, and a shrinking genome size as in the experiments of Spiegelman and colleagues (8). These populations allow us to observe the growth of physical complexity explicitly, and also to distinguish distinct evolutionary pressures acting on the genome and analyze them in a mathematical framework.

If an organism's complexity is a reflection of the physical complexity of its genome (as we assume here), the latter is of prime importance in evolutionary theory. Physical complexity, roughly speaking, reflects the number of base pairs in a sequence that are functional. As is well known, equating genomic complexity with genome length in base pairs gives rise to a conundrum (known as the C-value paradox) because large variations in genomic complexity (in particular in eukaryotes) seem to bear little relation to the differences in organismic complexity (9). The C-value paradox is partly resolved by recognizing that not all of DNA is functional: that there is a neutral fraction that can vary from species to species. If we were able to monitor the non-neutral fraction, it is likely that a significant increase in this fraction could be observed throughout at least the early course of evolution. For the later period, in particular the later Phanerozoic Era, it is unlikely that the growth in complexity of genomes is due solely to innovations in which genes with novel functions arise de novo. Indeed, most of the enzyme activity classes in mammals, for example, are already present in prokaryotes (10). Rather, gene duplication events leading to repetitive DNA and subsequent diversification (11) as well as the evolution of gene regulation patterns appears to be a more likely scenario for this stage. Still, we believe that the Maxwell Demon mechanism described below is at work during all phases of evolution and provides the driving force toward ever increasing complexity in the natural world.

Least Time

NECSI: Functional Complexity

Given a system whose function we want to specify, for which the environmental (input) variables have a complexity of C(e), and the actions of the system have a complexity of C(a), then the complexity of specification of the function of the system is:

C(f)=C(a) 2 ^C(e)

Where complexity is defined as the logarithm (base 2) of the number of possibilities or, equivalently, the length of a description in bits. The proof follows from recognizing that a complete specification of the function is given by a table whose rows are the actions (C(a) bits) for each possible input, of which there are 2 ^C(e). Since no restriction has been assumed on the actions, all actions are possible and this is the minimal length description of the function. Note that this theorem applies to the complexity of description as defined by the observer, so that each of the quantities can be defined by the desires of the observer for descriptive accuracy. This theorem is known in the study of Boolean functions (binary functions of binary variables) but is not widely understood as a basic theorem in complex systems[15]. The implications of this theorem are widespread and significant to science and engineering.

Wikipedia: Irreducible Complexity

The term "irreducible complexity" is defined by Behe as:

"a single system which is composed of several interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning" (Michael Behe, Molecular Machines: Experimental Support for the Design Inference)

Believers in the intelligent design theory use this term to refer to biological systems and organs that could not have come about by a series of small changes. For such mechanisms or organs, anything less than their complete form would not work at all, or would in fact be a detriment to the organism, and would therefore never survive the process of natural selection. Proponents of intelligent design argue that while some complex systems and organs can be explained by evolution, organs and biological features which are irreducibly complex cannot be explained by current models, and that an intelligent designer must thus have created or guided life.

Specified Complexity

In his recent book The Fifth Miracle, Paul Davies suggests that any laws capable of explaining the origin of life must be radically different from scientific laws known to date. The problem, as he sees it, with currently known scientific laws, like the laws of chemistry and physics, is that they are not up to explaining the key feature of life that needs to be explained. That feature is specified complexity. Life is both complex and specified. The basic intuition here is straightforward. A single letter of the alphabet is specified without being complex (i.e., it conforms to an independently given pattern but is simple). A long sequence of random letters is complex without being specified (i.e., it requires a complicated instruction-set to characterize but conforms to no independently given pattern). A Shakespearean sonnet is both complex and specified...

How does the scientific community explain specified complexity? Usually via an evolutionary algorithm. By an evolutionary algorithm I mean any algorithm that generates contingency via some chance process and then sifts the so-generated contingency via some law-like process. The Darwinian mutation-selection mechanism, neural nets, and genetic algorithms all fall within this broad definition of evolutionary algorithms. Now the problem with invoking evolutionary algorithms to explain specified complexity at the origin of life is absence of any identifiable evolutionary algorithm that might account for it. Once life has started and self-replication has begun, the Darwinian mechanism is usually invoked to explain the specified complexity of living things.

But what is the relevant evolutionary algorithm that drives chemical evolution? No convincing answer has been given to date. To be sure, one can hope that an evolutionary algorithm that generates specified complexity at the origin of life exists and remains to be discovered. Manfred Eigen, for instance, writes, "Our task is to find an algorithm, a natural law that leads to the origin of information," where by "information" I understand him to mean specified complexity. But if some evolutionary algorithm can be found to account for the origin of life, it would not be a radically new law in Davies's sense. Rather, it would be a special case of a known process.

Principia Cybernetica: Metatransition (a kind of punctuated equilibrium)

Consider a system S of any kind. Suppose that there is a way to make some number of copies from it, possibly with variations. Suppose that these systems are united into a new system S' which has the systems of the S type as its subsystems, and includes also an additional mechanism which controls the behavior and production of the S-subsystems. Then we call S' a metasystem with respect to S, and the creation of S' a metasystem transition. As a result of consecutive metasystem transitions a multilevel structure of control arises, which allows complicated forms of behavior.

[Alamo-Girl]

Another problem too is that of the observer -- whereas one may perceive a "donkey cart", another, aware of other information in the cosmos, might well be in awe of a stealth fighter, which was mistaken for a donkey cart because the first observer had no idea of what he was seeing.

Indeed. Great catch. Thanks for the post!

[Doctor Stochastic]

Note that Stalin (and Lenin before him) could have used either Witte's or Stolypin's reforms. Either would have produced enough food to avoid the starvation of Kulaks. See Crankshaw's "Shadow of the Winter Palace" for some history.

[D Edmund Joaquin]

I always thought a good short story could be written about Einstein's wife. Everybody is in awe of his genius and she sits there puzzled, thinking this guy? lol, We can call it, Everybody loves Albert

[Alamo-Girl]

Thank you so much for including me in your discussion on the assertion that evolution merely means change, i.e. that "higher" or "lower" are purely subjective terms not biology.

I can believe that biologists - and particularly evolutionary biologists – didn’t much care about complexity (please refer to the definitions at post 875.)

But mathematicians care a great deal about such things. Evolution makes no sense unless the observed complexity of living organisms can be explained.

As Marcel-Paul Schützenberger described, the biologists themselves opened the door to potentially fatal scrutiny of the theory when they invited the mathematicians to the table.

Interview with Schützenberger

The participation of mathemeticians in the overall assessment of evolutionary thought has been encouraged by the biologists themselves, if only because they presented such an irresistible target. Richard Dawkins, for example, has been fatally attracted to arguments that would appear to hinge on concepts drawn from mathematics and from the computer sciences, the technical stuff imposed on innocent readers with all of his comic authority. Mathematicians are, in any case, epistemological zealots. It is normal for them to bring their critical scruples to the foundations of other disciplines. And finally, it is worth observing that the great turbid wave of cybernetics has carried mathematicians from their normal mid-ocean haunts to the far shores of evolutionary biology. There up ahead, Rene Thom and Ilya Prigogine may be observed paddling sedately toward dry land, members of the Santa Fe Institute thrashing in their wake. Stuart Kauffman is among them. An interesting case, a physician half in love with mathematical logic, burdened now and forever by having received a Papal Kiss from Murray Gell-Mann. This ecumenical movement has endeavored to apply the concepts of mathematics to the fundamental problems of evolution -- the interpretation of functional complexity, for example.

Again, I assert that to deny there is a "higher" or "lower" structure of natural living organisms over time is to deny complexity altogether and casts evolutionary biology as a laughable ideology under color of science.

[Alamo-Girl]

LOLOLOL! I'd love to read it, too!