Prepared July, 2010


       

In Celebration of Psalm Nineteen:
God's handiwork in Creation

Chapter 8
Remarks on Evolution

UNDER CONSTRUCTION

Evolution and Creation
A "Cross-grained" Approach
   
For more than a century, those who believe in evolution by purely natural means have invoked "science" for proof of their belief. In fact, this belief is the opposite of science. It is an irrational disregard for any rational discourse, however strong, that points to evidence for design or purpose in creation.

In response to this irrational disregard, many who believe in the Biblical statements about creation view evolution as a discredited theory.

The truth of the matter is somewhere between these extremes, but irrational beliefs of scientists and creationists alike virtually ensure that the subject of evolution will never get a reasoned, logical, scientific treatment. This chapter presents my own views of a rational middle course.

A near-universal disregard for evidence of design or purpose in nature flourished among scientists almost immediately upon the publication of Darwin's Origin of Species in 1859. A scan of the scientific writings of the time gives striking evidence for this sudden change in viewpoint, leading to Lydia Miller's lament in 1869[FOOTNOTE: Lydia Miller was the widow of Hugh Miller, a well-known geologist of the mid-1800s. Hugh Miller authored a number of popular accounts of geology, always presented with a high regard for the accuracy and divine inspiration of the Biblical Creation accounts. See Testimony of the Rocks and other of his books available on-line in the Golden Age of Geology Library]:

“I must confess that I was at first startled and alarmed by rumours of changes and discoveries which, I was told, were to overturn at once the science of geology as hitherto received, and all the evidences which had been drawn from it in favour of revealed religion. Though well persuaded that at all times, and by the most unexpected methods, the Most High is able to assert Himself, the proneness of man to make use of every unoccupied position in order to maintain his independence of his Maker seemed about to gain new vigour by acquiring a fresh vantage-ground. The old cry of the eternity of matter, and the 'all things remain as they were from the beginning until now,' rung in my ears. God with us, in the world of science henceforth to be no more! The very evidences of His being seemed about to be removed into a more distant and dimmer region, and a dreary swamp of infidelity spread onwards and backwards throughout the past eternity.”
Lydia Miller in Sketchbook of Popular Geology [1869], p.xxx

Scientists of the day seized on Darwin's work as a life preserver that did away
, once and for all, with any need to further consider design arguments. In their view, William Paley's famous Watchmaker arguments for the evidence of design in nature were finally dispensed with. Proponents of such arguments were labelled "cross-grained geniuses." Whole political and philosophical systems -- indeed the very viability of atheism -- have since then been based on this "scientific evidence" and on the conclusion that they can dispense with a God because they "have no need for that hypothesis.[FOOTNOTE: Attributed to LaPlace.]"

The 1879 lecture, Darwin vs. Galiani, by Prof. Emil Du Bois-Reymond (University of Berlin), which rejects any admission of purpose or design in the natural world, is an  articulate (and readable -- I recommend it highly) example of this point of view, concluding:

The possibility, however remote, of ... everywhere setting up blind necessity in the place of final causes, is to be regarded as one of the greatest advances ever made in the world of thought.... That he has in some measure diminished that torture of the mind which tries to understand the universe, will be Charles Darwin's highest title to fame so long as there exists a philosophic student of nature.
Emil Du Bois-Reymond,  Darwin vs. Galiani
.
This dismissive viewpoint is reflected in virtually all discussions of evolution today. John Theodore Merz (1907), citing this lecture, said it this way:

That which puzzles the spectator of [Paley's] watch, as it does the spectator of every organism, is the apparent design and purpose, without which neither could be conceived to have been formed. Here, then, the idea that it was a process of natural choice, of automatic adjustment, which produced the apparent end and purpose at the moment when the structure itself was produced, came as a great relief. It explained [without explaining! dcb] how it comes about that nature, even with unloaded dice, so often -- yet not always -- throws doublets.

It seems that the scientists after the 1859 publication of Origin of Species were repelled by the arguments for design that dominated the first half of the nineteenth century, particularly by the early systematic geologists[FOOTNOTE: Perhaps the arch-typical example of this was the series of books originally published in the 1830s,  called The Bridgewater Treatises on the Power, Wisdom, and Goodness of God, As Manifested in the Creation, written by prominent scientists, which developed various scientific topics under that heading], and they saw in Charles Darwin's book the opportunity to throw off that oppressive mantle decisively, despite any and all evidence for design and purpose that might appear. In fact, Darwin's relief of the "torture of the mind" was more by way of a papal dispensation than a rational explanation. The way it appears from Prof. Du Bois-Reymond's lecture, rational science of the day was grasping for an excuse to reject the implications of design and teleology in the vast complexity of living species, and they seized on Darwin's arguments by eager consensus. He summarizes:

Leaving out of the account a few cross-grained geniuses, whose lamentations we can disregard and pass to the order of the day, it is on all sides admitted that the old ground was untenable, and that in the place of Cuvier's and Agassiz's series of creations must be substituted Mr, Darwin's doctrine of descent[FOOTNOTE: Wiliam Paley, Georges Cuvier and Louis Agassiz were prominent proponents of design in the early- to mid-1800s. Others included: Hugh Miller, Edward Hitchcock,  and James Dana. See the Golden Age of Geology for books by these and other 19th Century Scientists.].
Emil Du Bois-Reymond, ibid.

Well, I guess I am cross-grained -- genius or not.
   
What's wrong with the Consensus?

As reflected in the the 1879 lecture
Darwin vs. Galiani, consensus among most scientists is that Darwin's work implies evolution by purely natural means; that is, the view that all species of life arose exclusively by natural processes. This has been the prevalent view of most scientists (except for the "cross-grained geniuses") ever since the consensus formed shortly after the appearance of Darwin's book; indeed, whole philosophical, political and scientific disciplines have been based on this view.

Thus, as the lecture implies, these scientists conclude that nature, contrary to all experience in other scientific disciplines, "throws doubles" at an extra-ordinary rate -- a rate that would convince an observer in any other context that (quoting Fred Hoyle) "
the facts suggest that a super intellect has monkeyed with physics, as well as with chemistry and biology, and that there are no blind forces worth speaking about in nature." Some scientists attribute this proclivity for nature to throw doubles to a characteristic of nature called "emergence," which is explored in a recent book by
Robert M. Hazen, Genesis: The Scientific Quest for Life's Origins (2007). In my view the concept of emergence is a purely after-the-fact, non-scientific "explanation" which has no predictive power whatever, and is only contrived to evade the obvious conclusion of design aforethought. I would welcome experimental evidence that contradicts my view -- some specific, physically testable, reproducible evidence with predictive power -- that such a concept exists.

One great failing of the scientists of the late 1800s is that they did not -- indeed could not -- know about the vast complexity of life itself. One wonders whether these scientists would have so easily popularized their naturalistic views if this true complexity had been known at the time (indeed, the full complexity is not even known today). Early remarks on the origin of life by Ernst Haeckel and other prominent scientists at first took a very dismissive view about life -- attributing the "life force" to the jelly-like amorphous protoplasm. The consensus implied in the 1879 lecture grew out of this simplistic view, which even so was quickly modified as scientific evidence for deep complexity of the protoplasm became known. But even the most insightful understanding of life's complexity in the late 1800s missed the truth by factors of many millions.

Secular scientists are so vested in this early concensus that there is literally no evidence to the contrary that could change their viewpoint. This is the reason why intelligent design arguments will never have a mark on the scientific consensus. Scientists are deaf and blind to any contrary evidence. Thus the belief in natural evolution is "non-falsifiable" in the sense that Karl Popper asserted (before he modified his views somewhat).

In summary, evolution by purely natural means is a prevalent dogma in science which, in circular fashion invokes "science" for proof, disregarding any contrary evidence by fiat. In fact, this belief is the opposite of science. It is an irrational disregard for any rational discourse, however strong, that points to evidence for design or purpose in creation.



This wholesale and unequivocal embrace of natural evolution by the scientific community means in practice that no evidence, however compelling, will dissuade adherents from their secular dogma. Evidence of intelligent design will never be accepted. It is not a matter of scientific reason, it is an a-priori assumption.


THE  "CROSS-GRAINED" APPROACH

My own "cross-grained approach" which I outline in this chapter, is the position that is developed in this website. It is that in his works of creation, God used natural processes whenever natural processes ccould achieve the desired end result. This is a self-limitation that God has imposed on his own creative work, out of regard for the integrity of the silent speech that he has built into the natural world -- the speech which proclaims his glory and handiwork. God used direct, fiat creation only when natural processes cannot do the job.

I view that the task of science is to discover the limits of natural processes and the capacity for natural variation in species, using scientific and mathematical methods and experiments. The objective of science is to break down complexity into discrete components that can be demonstrated in the laboratory. Because of the vast complexity of nature, this is an exciting and never-ending quest, involves ingenious applications of imagination and method, and leads to great truths and insights. The past century -- and especially recent decades -- has witnessed many marvelous examples of this ingenuity, and there is no end in sight.

The claim that God is dispensible in the drama of creation -- "there is no need of that hypothesis" -- is an assumption that speaks to the ignorance and willful blindness of the claimant, and is a profoundly unscientific, irrational statement. As a metaphysical point of view, it is no more or less valid than belief in a personal creator, and neither belief or disbelief in it  should be relevant in any truly scientific expression.




fractal

Introduction. In the earlier chapters, little has been said about evolution. Still, it is obvious that the Creation Narrative implies that underlying it all is a vast enterprise of change and development. The question is: how does such implied change relate to natural evolution?

In a recent book review, I asserted that there are three great books on evolution (I would now say there are four), but that the last has not yet been written. This chapter is not that book (I don't have the necessary expertise), but it is perhaps a summary of some of the content that such a book would include.


Some Great Recent Books on Evolution
   
1. Richard Dawkins, The Greatest Show on Earth: The Evidence for Evolution, Free Press [2009].
2. Sean B. Carroll, Endless Forms Most Beautiful: The New Science of Evo Devo, W.W. Norton [2005].
3. Jerry A. Coyne, Why Evolution is True, Viking Penguin [2009].
4. Fourth book not yet written --
"a treatment of the different mechanisms of evolution, their implications for diversification of species, and the extent to which each mechanism is directed by environmental pressure or other forces. This book would also include a discussion of the way that different species control either for or against genetic change, and how these mechanisms promote or limit speciation. To give a hint of what such a book might say: I can see a distinction between random changes in the genome (due perhaps to radiation damage or to transcription errors), changes due to a built-in flexibility in gene expression (the action of the development genes, for example), and de-novo changes due to the creation of entirely new genes or gene packages. The problem that arises when the different mechanisms of evolution are overlooked is specious arguments that take examples from one sort of evolution to 'prove' an entirely different sort."



I. Experimental Support for Evolution.

The word Evolution as used here, means change in a living species that occurs as a result of purely natural processes and is preserved in its genetic material[FOOTNOTE: As will be remarked later, the "genetic material" may be more than the DNA; it may also include information implicitly contained in various molecules that accompany the DNA during cell division or sexual reproduction].
Evolutionary change does occur, and it can be demonstrated in the laboratory and in everyday life. At this point, we will consider only the most obvious examples of evolution. Later we will also consider the different kinds of evolution.

    A. Examples in Viruses. Every year the genetic make-up of the flu virus changes, and this is why the flu vaccine has to be modified each year. This is perhaps the most obvious evidence that living species do undergo change and that the change modifies the viral genetic material. This change is abundantly evident to anyone who cares to look.

Viruses are not strictly "living" since they cannot reproduce without a live host, but they are particularly useful in evolution research because the genome is so small (Figure 1) that it is possible in principle to determine the precise changes -- down to the exact nucleotides in the DNA/RNA; the precise amino acid, folding and functional changes in the proteins; and an exact enumeration of any novel genes and their evolutionary pathways. Furthermore, viruses do not have the "cloud" of information  that surrounds the genetic code in bacteria and eukaryotes in the form of pre-established organic molecules that control gene expression: the viruses are pure DNA or RNA plus a few specific proteins used in packaging, and nothing else.

Genome Size
Figure 1
Comparison of Genome Size
   
Viruses are the only biological entities that consist almost exclusively of DNA (or RNA), plus non-genetic sheething material. All other "living" species accompany the DNA with other molecules that may (in principle) convey some amount of genetic information -- such as the initial conditions that control how the daughter cell begins its metabolism (or cell division in the case of multi-cellular species). This information is carried in the cell contents that pass on to the daughter products during reproduction.

       B. Examples in Bacteria. One might say that bacteria are designed to facilitate changes in their genetic make-up. One biologist, Lynn Margulis, argued that the concept of species is not really appropriate for bacteria, because there is so much genetic variation[FOOTNOTE: Lynn Margulis, Five Kingdoms, p.54; also Kingdoms and Domains, p. 49, "Because bacteria that differ in nearly every measurable trait can receive and permanently incorporate any number of genes from each other or from the environment, ... the concept of 'species' applicable to named eukaryotes, seems inappropriate for the Prokarya. Because prokaryotes can change their genetic properties so quickly and easily, we agree... We doubt that bacteria ever evolved to form permanent species characteristic of all Eukarya. A certain flexibility must be tolerated in any bacterial taxonomic scheme." For further information, see Chapter IX Microbial Exchange of Genetic Material of Dr. Ronald E. Hurlbert's on-line Microbiology text.]. I disagree somewhat, because species still tend to remain as the same species after such variation.

These genetic changes are often beneficial to the bacteria, such as changes that build up resistance to infection, or that adapt to a changing environment, food sources, etc. Of course many, perhaps most, changes are harmful, but then the descendents of bacteria that experience harmful changes tend to die out, just as the descendents of bacteria that experience useful changes tend to flourish. So this asymmetry in the consequences of change is a powerful force that suppresses harmful changes and amplifies beneficial changes (from the point of view of the bacteria, of course). This is perhaps the most important way that evolutionary change, which may appear random, can lead to great benefit: bad changes get slapped down, while good changes prosper.


Here is where bacteria benefit from another feature: their high rate of reproduction.  It has been said that if all of the descendents of a single e-coli bacterium -- a common species that lives in the digestive tracts of humans and many other animals -- survived for a day, they would cover the earth a foot deep. Clearly the vast majority die quickly (providing food for other e-coli), which amplifies the effects of evolutionary change.

One feature of bacteria is that the genetic code mingles with the general cell contents so that the genetic material contained in food can become incorporated with its own genetic material, resulting in change, a process that is called Bacterial Transformation. Viruses take advantage of this to inject their own DNA into the bacterial DNA and then use the bacteria's own genetic machinery to duplicate the virus. Occasionally, snips of the bacterial DNA also find their way into the viruses thus produced.

Bacteria also have a specific sex mechanism to exchange genetic material called Bacterial Conjugation (Figure 2). This conjugation can occur between widely different species, and even between bacteria and eukaryotes.


Bacterial Conjugation
Figure 2
Bacterial Conjugation


These mechanisms for gene transfer are frequently used in laboratories to engineer disease resistant or herbicide resistant species.

So... evolution does occur in bacteria, and it responds to environmental pressure in the way that one might expect, developing such things as resistent bacteria. Because the bacteria can reproduce rapidly, these changes can take place rapidly, but there is also the possibility for more radical changes that take place on much longer time scales.

Bacterial transformation and conjugation involve the re-arrangement of existing genetic material.  Careful experimentation could determine the exact nature of this form of evolution -- are new genes created, or are existing genes modified? Are genes spliced or split up? How are the DNA sequences re-arranged? Does random mutation, the occurrence of transcription error, or flexibility in gene expression enter into the changes?

This form of natural evolution certainly exists and can be studied -- probably exhaustively -- by direct laboratory experimentation. This is completely valid form of evolution and evolutionary research.


The Lenski Evolution Experiment

  In his recent book The Greatest Show on Earth, Richard Dawkins cites a long-term e-coli experiment as "distressing to creationists ... a beautiful demonstration of evolution in action, something it is hard to laugh off...."[FOOTNOTE: See Dawkin's description of the experiment at pp.116ff.]. The experiment (still in progress), begun in 1988 had been in progress for around 33,127 generations when, in 2008, the survivability of one strain of e-coli suddenly "shot up sixfold." An evolutionary advance in survival is clearly indicated, which Dr. Dawkins took as an unqualified endorsement in support of natural evolution.

What was going on? Apparently the e-coli that had been feeding on glucose suddenly changed to use citrate for food, which e-coli cannot normally use in the presence of oxygen. Over the course of the experiment a number of changes had occurred in the e-coli strains due to the types of random genetic changes one expects with bacteria. But this change was particularly dramatic because it switched the kind of food used by a particular strain of e-coli.

Regarding that change, my review of Dr. Dawkin's book remarked:

I am not convinced that this research says as much as Dr. Dawkins asserts. The extended laboratory experiment which tracked a number of strains of e-coli for over twenty years, with truly remarkably prescient planning is an outstanding example of true science. The experiment regularly led the e-coli strains to near-starvation to force (I assume) evolutionary change. ... The result was indeed remarkable and unambiguous, but I think the explanation would require more proof before I accepted it as an evidence of true evolutionary innovation. The problem as I see it is that the e-coli genome is relatively large and has built-in several alternative ways to conduct metabolism, depending on the availability and type of food. The default assumption, then, would be that starvation activated one of these built-in alternative metabolism paths. It is not obvious that the observed results were really evolutionary innovation in the sense of creating new genes. Perhaps so, but Dr. Dawkins' argument is not persuasive. It would be interesting to follow-up the Lenski "evolution" with a detailed sequencing of the e-coli just before and just after the switch. That would at least show precisely where the change occurred (although sequencing in itself would not necessarily reveal changes in the gene expression).

The issue is evolutionary change versus evolutionary innovation. The built-in mechanisms that bacteria have for genetic change re-arrange genes and perhaps change gene expression. Dr. Dawkins claims that the e-coli in effect "invented" a new metabolism method, a conclusion that I could only accept after further experimental demonstration.

As a matter of personal interest, I would very much like to know more about the exact details of the change to citrate metabolism: how large a change in existing molecules is involved? Exactly how is the change implemented in the e-coli genome, etc. This information is indeed possible to attain (at least in principle).

If this experiment indeed does end up with e-coli developing a metabolism path that the species had not previously had provided for in its genome package, that would truly be significant -- and it would be exceedingly improbable that such an evolutionary development would just happen to occur during this experiment. It seems much more likely that this is NOT a major evolutionary innovation, but simply a case of invoking one of many defense mechanisms that the e-coli has already wired into its bloated genome.



        C. Examples in Eukaryotes. The nucleus symbolizes a whole series of major innovations in the kingdom of Eukaryotes (cells that have proper nuclei) that has a profound effect on the question of evolution. In essence, eukaryotes have many different mechanisms that both limit and facilitate genetic change. A truly scientific treatment of evolution should identify and characterize these different mechanisms. Unfortunately, the ideological aspects of evolution tend to  use evidence of evolution provided by one mechanism to "prove" evolution in the most general sense.

The over-riding feature of eukaryotes is that there are many mechanisms in place to guard the cell's genetic material and gene expression against the introduction of changes or random errors. Unlike bacteria in which the genetic material mixes with the general cell contents, the genetic material of the eukaryotes exists separate from the general cell contents within a membrane-bound nucleus. This membrane controls passage to and from the nucleus via. special molecular ports that allow only certain types of material to pass.

In addition, the process of gene expression itself includes many steps that are designed to guard against errors. These steps occur at all stages of the gene expression, from the formation of the messenger RNA (m-RNA) to the formation of the proteins by the ribosomes and t-RNA. Duplication of the DNA in preparation for cell division likewise includes its own error identification and correction steps[FOOTNOTE: The subdivision of the DNA into chromosomes may itself be a way to limit genetic variation. During sexual fertilization the egg and sperm match up chromosomes. In effect this means that whole packages of genes, are matched coherently, one part from the egg and one paert from the sperm.]. The overall effect of these various mechanisms to guard against change varies with the species and the  specific function[FOOTNOTE:
Thomas A. Kunkel,  DNA Replication Fidelity JouRNAl of Biological Chemistry (2004) "interest in the fidelity of DNA copying mechanisms remains high because the balance between correct and incorrect DNA synthesis is relevant to a great deal of biology.  High fidelity DNA synthesis is beneficial for maintaining genetic information over many generations and for avoiding mutations that can initiate and promote human diseases such as cancer and neurodegenerative diseases. Low fidelity DNA synthesis is beneficial for the evolution of species, for generating diversity leading to increased survival of viruses and microbes when subjected to changing environments, and for the development of a normal immune system."].

In replicating the human genome (6 billion bp in 21 chromosome pairs),
typically, less than 1 nucleotide error occurs, because of the elaborate error detection and correction mechanisms used[FOOTNOTE: .John D. Roberts and Thomas A. Kunkel, Fidelity of DNA Replication, Chapter 7, from DNA Replication in Eukaryotic Cells, Cold Springs Laboratory Press, (1996).]. Human mitochondria (37 genes, 16,000 bp), which carry their own DNA, have a higher error rate -- about 1 mutation in 25-40 generations, or 1 nucleotide error in about 500,000 bp[FOOTNOTE: Sean D. Pitman, DNA Mutation Rates and Evolution 2008 posted on the website Detecting Design.] -- Most of this change occurs in a "control area" that does not code for any genes, so that mutations do not affect the active gene expression[FOOTNOTE: ibid.].

On the other hand, eukaryotes also have provisions that facilitate a broad spectrum of genetic changes, ranging in a continuum from trivial to vital. On the trivial side are the thousands of variations that, for example, make each human unique: facial and bodily features, fingerprints, etc. These variations come about because sexual reproduction and the expression of the genetic code allow variability in gene expression. On the vital side are changes that can affect survivability and fitness. Some of these changes respond to regulatory genes which control gene expression -- the above example (in bacteria) of adaptation of e-coli to a new food source is an example of this. Darwin's example of the beak shapes of Galapagos finches is another: clearly the regulatory genes have a degree of flexibility so that the species can produce (and pass on to subsequent generations) a variety of beak shapes, and those shapes that are best suited for the available food will tend to enhance survivability of the species. Over time, these changes become encoded in the standard development pathways, leading to new varieties or sub-species. Gene expressions that determine coloring patterns also have some built-in variability, which is why the coloring patterns of each member of a species is unique, even though the patterns conform to a more-or-less specific prototype. This sort of flexibility over generations helps to explain the famous example of peppered moth evolution.

In my own investigations into geology, I have come to the conclusion that the changes in the trilobite eye over many million years is (probably) an example of the long-term effect of flexibility in gene expression (see the box below). Many changes in species over geological time may, I believe, be the result of this flexibility in gene expression. Indeed, this slow change in species characteristics becomes a way to identify geologic ages by characteristic marker fossils.

The Trilobite Eye
An Example of Evolution Over Eons
by the processs of Arrested Development
 
Trilobites are an extinct class of arthropods that lived from the early Cambrian (ca. 550 Ma) to about 200 Ma. They are the most complex example of the Cambrian fossils, appearing from the earliest times as fully formed arthropods (Figure 3)[FOOTNOTE: Riccardo Levi-Setti, Trilobites (1993), p. 2 "trilobites appear suddenly in the fossil record, when they had already rreached a full degree of development and differentiation. Compound eyes are already present in the earliest trilobites."]. In general appearance, they look much like the modern horseshoe crab. InteRNAlly, they have highly develop nervous, digestive and circulatory systems, a fact that is demonstrated by a fossil that had all of the inteRNAl soft body parts preserved in pyritized iron (fool's gold)[FOOTNOTE: Rolf Ludvigsen, Fossils of Ontario Part 1: the Trilobites, Royal Ontario Museum, 1979, p22: "Some trilobites discovered near Rome, New York have had the hard and soft-body parts replaced by finely crystaline pyrite (FeS2) (commonly known as fool’s gold because of its golden color). They display finely detailed exteRNAl appendages and gills. X-rays reveal fine details of muscular, digestive, circulatory, visual systems. As a result of this providential gift, much is known about trilobite anatomy despite the fact that they have been extinct for 250 million years." Note: Called the Middle Ordovician Utica Shale of New York. Pyritized fossils are from only two places: this and Lower Devonian Hunsrück Slate of Germany (Riccardo Levi-Setti, op. cit.  p18)].
  
trilobite Early Cambrian
Figure 3
Early Cambrian Trilobite

An abundant fossil record exists for trilobites over this long timespan, and exhibits a wide range of shapes and sizes.

Our particular interest is the trilobite eye, and how it changes over the span of the trilobite fossil record
. Over this span of time, the eye changed from a compound eye made up of tightly packed cones of single calcite crystals, to a compound eye of spherical bi-layer crystals designed to focus the light onto multiple receptors, characteristic of the late phacops trilobites (Figure 4). Both eyes have a marvelous design (See the excellent web page on trilobite eyes at trilobites.info)[FOOTNOTE: for a more extensive description of the trilobite eyes, also see Riccardo Levi-Setti, op. cit. §3.3 The Eyes of Trilobites, p. 29-73.].

devonian phacops
Figure 4
Phacops Trilobite (Devonian)
Note eyes


The phacops trilobites, which first appear in the early Ordovician era , after some 300 My of development,  had the most advanced focussed eye systems, called the schizochroal lens. This is a compound lens that combines two crystals with slightly different refractive indices, joined on a specially-designed curved surface. The effect is to focus parallel light rays arriving over the whole diameter of the lens to a single point (avoiding spherical abberation). In the 1600s, Descartes and Huygens designed such aspheric lenses with somewhat different designs, and the remarkable fact is that both of their "optimal" designs are found in trilobite fossils (Figure 5).

aspheric lenses (Descartes and Huygens)
Figure 5
Aspheric Lenses

Diagrams from:
Christiaan Huygens Traité de Lumière (1678), pg. 117.
    Spherical upper surface. (?)
    Ordovician trilobite species Crozonaspis struvei - Levi Seti p. 55.

René Descartes, La Géometrie (1637) pg. 366.
   
Parabolic upper surface. (?)
    Ordovician trilobite species Dalmanitina socialis - Levi-Seti p. 56.

In my view this change is a plausible example of evolution, because the process can in general outline be visualized with some reasonable assumptions involving arrested development (
pedomorphosis) and environmental adaption that might be demonstrated by computer simulation.

The evolution involves changes in the expression of development genes. Here is a possible way that the change may occur (this is of course speculative, and probably cannot be tested on the extinct trilobites, but might be modeled by computer simulation). The (originally conical) eyes start out as specks of calcite which grow into the cones. At the start of this growth the eyes have a spherical shape which grows during maturation into a cone. If the growth is (randomly) stopped at the spherical shape, it may provide a focusing of light rays that gives a benefit in food gathering or predator avoidance. Further random changes may change the shape of the lens to approach the ideal shape of the Huygens or Descartes lens. At this point further changes are detrimental, and so the descendents conform to the optimal lens.



        D. Summary. These examples very likely demonstrate evolution by natural means, which evidently has a role in the creation and preservation of living species. All of these examples are arguably the result of purely natural processes, although of course a diving Creator can (and in my view probably does) influence the natural processes to achieve the desired results. In considering the results, it is possible to see several qualitatively different evolutionary mechanisms at work[FOOTNOTE: The remarks in this section are not, but could be made, scientifically precise. I am not aware of a discussion of evolution that attempts to divide the subject into qualitative categories. Such a discussion is much needed, but is beyond my own scientific competence and education. However should such a discussion be prepared, I would feel competent to evaluate it.].

                1. What kinds of evolution are at work in these examples?
I see in these examples a variety of ways that evolution proceeds.
                      a. Changes that may not pass to successive generations. Except for viruses, the total genetic package that is passed from one generation to the next involves not just the DNA itself, but also the total contents of the cell that begins the new generation. One might conceptualize this as the DNA plus a "cloud" of food and information that surrounds the DNA and controls the initial expression of its genes. The DNA cannot express itself: DNA expression requires the prior existence of DNA products which carry out the DNA expression, as well as a means to determine which genes to express, in what quantities and in what order. It also requires the prior availability of ATP energy molecules (or mitochondria which produce ATP), the components required to execute the central dogma (pre-existing transfer RNA and ribosomes), and certain food (minimally, some sugars, the nucleotides and amino acids needed to form the messenger RNA, and the proteins that are coded by the genes). These are required to start things off, even though the DNA code may itself include genes that code for all of them. There is no such thing as a pure "boot-strap" that starts off gene expression.

Many chance factors affect gene expression, all the way down to the availability of a particular amino acid at the time it is needed. But only those factors that are passed on to the next generation in the DNA or in the cloud affect species evolution.

                      b. Changes that do pass on to successive generations.
                         - the effects of random walk and eventual irreversibility of changes.ggggg
                      a. Random effects in gene expression.
                      b. Random changes in genetic information.
                      c. Re-arrangement of existing genetic information.

Random Walk and Irreversible Change
   
Random walk is the mathematical concept that models what happens over time when an inherited property is formed by a variable number of repetitive steps. For example, suppose that successive generations allow the property to vary ±1 unit from its value in the previous generation.  Then over many generations the descendents will exhibit a range of values for that property which form a gaussian distribution about the original property value, L0, as in the following sketch. Eventually the property value will almost certainly differ so much from the original value that ....


n-dimensional random walk. --- when do we get a new species???  [MORE]






Making the change ... persistence in the change


WORKING -- go from simplest to most complex. Refer as needed to the next section.

                2. What kinds of evolution are missing in these examples?





II. Conceptual Kinds of Evolution. WORKING
the flexibility in gene expression -- partly envt pressure partly random partly ....

The examples of evolution mentioned to this point involve a number of different kinds of evolution. All of them can (in principle) be exhaustively tested and verified by scientific experimentation. The kinds that depend on random influences, such as environmental pressure or "fitness" can be the subjects of simulation that, while not "proof" in itself can point to specific experiments that can confirm underlaying assumptions. For example, the parameters of a random process, such as how much "wiggle room" occurs naturally in the development of an eye, can themselves be subject to focussed experiments.

To give a hint of what such a book might say: I can see a distinction between random changes in the genome (due perhaps to radiation damage or to transcription errors), changes due to a built-in flexibility in gene expression (the action of the development genes, for example), and de-novo changes due to the creation of entirely new genes or gene packages. The problem that arises when the different mechanisms of evolution are overlooked is specious arguments that take examples from one sort of evolution to 'prove' an entirely different sort."

flexibility of gene expression -- small random changes allowed -- because of random walk, these can produce large changes. The parameter is, how much variation is possible in each generation? examples: uniqueness of every individual.

Effects of radiation damage, effects of transcription errors, etc. 

Creation of entirely new genes, gene packages and functions.



A. Evolution that requires the development of novel genes or gene packages.

B. Evolution that explores the limits of development of a given gene or gene package.
The science of evo-devo

concept of relatedness needs expanding far beyond the Paley views.


           • Animal Body Plans
                   - explain what mean contrast plants
                         ** Can be surprising linkages
                                  octopus vs human eye -- "convergent evolution -  same gene pkg ??x examples in sight
                 - hox genes
                   - gene packages -- universal, conserved pkgs across broad range of species
                         - sight
                         - appendages
                          - etc.
                         - Big Q is the limits of variation in pkgs. Built in mechs etc.  >> God intentionally did this
phenotype = "Outward physical manifestation" "The appearance of an individual" (See difficulties in definition)
genotype =  Genetic Makeup
(2) Theoretical -- metaphysical
 




The Science of Evo-Devo
Evolution in Gene Expression
[Footnote: The material in this box is inspired by the book by Sean B. Carroll, Endless Forms Most Beautiful: The New Science of Evo Devo, W.W. Norton (2005). Citations in brackets are to pages in this book.].

"Much of what we have learned has been so stunning and unexpected that it has profoundly reshaped our picture of how evolution works. Not a single biologist ever anticipated that the same genes that control the making of an insect's body and organs also control the making of our bodies."
Sean B. Carroll (2005) [x]

"Of all the perenial miracles [Nature] offers, ... perhaps the most worthy of admiration is the development of a plant or of an animal from its embryo."
Thomas H. Huxley, Aphorisms and Reflections (1907)

Evo-Devo is the biology of evolutionary development, a branch of experimental biology that has come into being within the past few decades.

The focus of evo-devo is on the way that the DNA genes are expressed: "when, where, and how much of a gene's product is made"[12]. In the human DNA, about 1.5% codes for the genes, and about 3% codes for regulatory information.

The remarkable fact that has been uncovered in evo-devo is that (virtually) the same small packages of genes, linked to specific body parts, occur across broad swaths of species. It is how these genes are expressed during regulation that determines the physical form of end product. Thus, (virtually) the same small package of "eye genes" underlies both the human's simple eye and a fly's compound eye -- the different end result comes about by how these genes are expressed.

Regulatory genes control the basic defining features of animal body shapes in particular (as distinguished from plants), through the homeobox (hox) genes. Such things as bilateral symmetry are controlled by these genes. It is gene regulation that results in the left side growing as the mirror-image (more or less) of the right side, even though the mirror image objects (human hands, for example) are physically separated as they grow. It is gene regulation that forms a fly's compound eye and a human's simple eye, and both grow in mirror-image pairs: the underlying genes are the same.


Is commonality "proof" of descent? Not for a creationist -- any more than the physical similarity of appendages, for example.

The interesting issue is how gradual changes can be passed on to other generations? What is the mechanism? How much variability is built in, and how expressed? etc. The parameters of change are interesting[FOOTNOTE: At one time, the offical Soviet dogma included "Lysenkoism" -- the inheritance of acquired characteristics (such as lopped-off tails?). "A school of pseudoscience that flourished in the Soviet Union from the early 1930s to the mid-1960s, in violent opposition to traditional biology." (Answers.com).].

The question of where the packages came from in the first place? How are they made? They first appear in the fossil record suddenly and fully formed, in the Cambrian Explosion.

Body Plans.  Both plants and animals grow in a building-block fashion. The body plans involve algorithmic growth (typical of plants), modular construction, and the use of repeated parts with modification (typical of animals).

[[[Show figure of algorithmic growth (plant shape, leaf configuration), modular construction (repeated segments, e.g. snake or giraffe spine), and repeated parts with modification (head-thorax-abdomen-tail).]]]

The remarkable insight of evo-devo is that behind the modules and repeated parts are small packages of genes that are essentially the same for all animals that have the corresponding body part. For example, virtually all animals that have eyes, whether simple or compound, have the same small package of eye genes; all animals that have jointed appendages (legs, antennae, etc.) have the same small package of appendage genes, and so on for other sensor systems: for nerves, muscles, digestive and circulatory systems, etc. The well-known homologous systems (Figure B) have at root a shared gene package: the differences between the species are not the result of new genes, but of how those genes are expressed.

Gegenbaur 1870 hand_homology
Figure B
Homologies to the Hand
Different expressions of the same gene package.


Forelimb Homology
Figure C
Forelimb homology
Different expressions of the same gene package.
Wilhelm Leche (1850-1927)

Evo-devo concerns not the creation of new genes, but of new ways to express a highly conserved set of genes. The question of how the genes got there in the first place is thus separate from the question of how the gene expression changed over time, just as the question of how life first arose is separate from the question of how life evolved.

The essential features of evo-devo -- the
"simple rules that shape animal form and evolution?" [x] -- are: (1) Each specialized animal body structure and system is developed from a small and highly conserved gene package. The differing morphologies are determined by gene expression controlled through the homeobox development genes. (2) The gene package for a body structure anticipates a broad range of end morphologies. (3) The development genes include a built-in ability to vary  the gene expression within  certain limits; (4) There is some mechanism to pass on variations in gene expression to succeeding generations -- in part this is through Mendelian genetics, but it is also through expression gene parameters that are preserved in the genetic information (DNA and the "cloud" of accompanying information).

Basic types of modular growth: algorithmic, body plan.

The Scope of Evo-Devo.  What facts about evolution can be revealed? WORKING
 

EFFFECT IS TO PUSH BACK THE ORIGIN OF TOOLKITS ....

The Bottom Line

• Animal species across many phyla use the same gene packages to code for eyes, appendages, and other body parts and systems, even though the appearance of those body parts in the adult may be radically different. The different end products are determined by development rules -- how, when and where genes are turned on and off -- not by the genes themselves. Homologous body parts arise because of the use of similar genes.

• The development (homeobox or hox) genes that control gene expression, are likewise essentially the same across many animal phyla.

• The identification of the gene packages and hox genes is unequivocal, and has been determined by extensive laboratory experimentation and DNA sequencing.
- To a natural evolutionist, these common gene packages prove descent from a common ancestor.
- To a creationist, they are the expected result of a common creator who re-uses the genetic material.

• The origin of
the hox genes and the gene packages is unknown to science, although the first sudden appearance of the body parts in the Cambrian era (about 540 Ma) is well attested -- trilobites, for example, had all of them -- and so the existence of the gene packages and the hox genes at that time can be inferred by analogy to modern species.

• Information that determines exactly how a given species expresses the gene packages is located in portions of the DNA that do not code for genes. Additional information may reside with the accompanying molecules that are present in the fertilized egg when development begins.





The question, of course, is whether this flexibility can explain all evolution between apparently related species. ....  The BIG question is production of new gene packages!!!



[WORKING]


evo-devo



 


In Eukaryotes.

cite sean carrol's book




fractal
MOVE UP



WORKING. COMPARE WITH TALK FIT PLACE

-- Aside: Cell Reproduction. Cell Division Mitosis Meiosis. Role of chromosomes, etc.


TO DO: METHODS OF CELL REPRODUCTION AND FIRST OCCURRENCES.

phylogenesis = evolutionary relatedness among the phyla.

binary fission -- mitosis -- meiosis: bacteria first only?
Methods of Gene sharing: in bacteria; in eukaryotes.

DEVELOPMENT BIOLOGY
MOLECULAR GENETICS
Binary Fission (prokaryotes)
Mitosis (Eukaryotes) mitotic spindle
phases of mitosis: Interphase (The stable period of a cell); Preprophase (plants only) Prophase Prometaphase Metaphase Early anaphase Telophase
Meiosis   chromosomes per cell is halved (chromosomes occur in pairs) Eukaryotes only. Essential for sexual reproduction.

Cell division
Cell division in bacteria is controlled by the FtsZ, a collection of about a dozen proteins that collect around the site of division.
cytokinesis

chromosomes.  In eukaryotes packaged by proteins into dense structure chromatin. duplicated or unduplicated. In prokaryotes may be called a plasmid. # chromosomes
Q: WHAT DETERMINES THE NUMBER OF CHROMOSOMES? IT SEEMS FAIRLY ARBITRARY!!!
"Evolutionary Cytogenetics of primates" for details.  Karyotype. Cytology
Chromosomal polymorphism: chromosome number is variable from one individual to another. Ladybird beetle
"We have a very poor understanding of the causes of karyotype evolution, despite many careful investigations... the general significance of karyotype evolution is obscure." Maynard Smith.





fractal

NOTES


Theory and Fact in Evolution and Big Bang Cosmology
One common theme of true believers in evolution is that evolution is a fact, not a theory. This theme comes up repeatedly in court cases about the teaching of evolution in public schools, and the surest way for a creationist to start up a tempest is to argue that evolution is "just a theory" and should be labelled as such in school texts. Generally the creationists lose arguments along these lines, because of the near-universal testimony of those who argue in favor of teaching evolution as "fact". The courts are, frankly, not well enough educated to make informed distinctions of this sort, and since the science "experts" speak with one voice, their secular view will generally prevail.

Evolution has a long history of hyperbolic statements which assert or imply its factuality, made by prominent scientists, such as:

"As a natural process, of the same character as the development of a tree from its seed, or a fowl from its egg, evolution excludes ceation and all other kinds of supernatural intervention."
Thomas H. Huxley, in Aphorisms and Reflections (1907) [6]

As an expression of hubris, unsupported by fact, of the same character as the wildest claims of a religious zealot, this statement has no peer. An yet it is typical of many such over-the-top assertions by evolution true-believers.

Nonetheless, there is a useful distinction to be made between theory and fact in evolution, and I would like to make some remarks about this distinction by comparing the current state of Evolution Theory (!) with Big Bang Cosmology. My point of view is that physicists have the right attitude toward cosmology, and that biologists would be well-advised to heed their example and similarly distinguish between what is factual and what is theory.

Fact vs. Theory in Cosmology. To be blunt, cosmologists do not claim that the universe began with the Big Bang. In fact this is only one of many views of what happened at that instant of time. I happen to believe that the Big Bang did indeed mark the beginning of the universe (and of time) because I am a creationist, but there are many other views held within the community of scientists (along with this one). Perhaps this universe is only a minute part of a much larger universe that includes trillions of universes of our sort; perhaps energy and the physical laws of this universe are in fact eternal, but "precipitate out" in different ways with different parameters in different universes; perhaps this universe is just one of many "bounces" of a cyclical universe which expands and contracts according to unknown laws that come into play at the bounces: there are many possible theories of the Big Bang, and these theories are usually kept clearly apart from the domain of cosmological "facts."

Cosmological facts are the things that cosmologists demonstrate by experimentation. They are the things that are sought by super-colliders at CERN, Batavia, Fermilab, and elsewhere. These facts help to explain how physics in this universe works, and help to filter out cosmological theories that are inconsistent with the facts. Because these facts have been systematically revealed over the past century, it is possible to make firm assertions about the general outline of how the early universe evolves, how elements formed, and the outlines of cosmology. Indeed, the acceptance of cosmology as a legitimate discipline within physics is the result of the discovery of such facts. Our universe factually has the age of 13.73 ± 0.12 Ba. There is overwhelming evidence of this. But that doesn't invalidate other cosmologies that are consistent with this fact.

Fact vs. Theory in Evolution.  Curiously, unlike the case with cosmology, many evolutionary scientists do feel it necessary to claim that evolution is a fact, even though it has no greater claim on such a label than any of the many cosmological theories. The reason is that the only alternative to purely natural evolution is the existence of a creator, and such a being necessarily exists apart from the natural world and as such is not subject to scientific investigation. Unfortunately, however, to deny a creator means that there must  be within the natural world the means to achieve the present state of living matter by purely natural means. This introduces an untestable assumption with implications for the natural world just as surely as does positing a creator (or does seizing on a particular cosmological theory as "fact"). This is what produces such nonsensical concepts as the notion of "emergence" in biology.

There is nothing wrong, of course, with assuming purely natural evolution as a theory with an implied program of action that can be tested for factuality. But that is different from assuming (and teaching) natural evolution as a fact.

Fortunately, in recent decades, work on evolutionary development has moved away from theoretical assertions to laboratory experimentation. This work concentrates on specific mechanisms for change that are subject to experimentation and measurement. The many life processes are full of places where outcomes are subject to a degree of variation. These can be enumerated and the extent of variation measured, leading to better understanding of how changes occur, a parameterization of the change processes, and an understanding of how (and how often) these changes are passed to succeeding generations.

The ability to measure specific changes in the genetic makeup and in the parameters of gene expression will be a powerful aid to such research in evolution.

I believe the work in Evo-Devo and other areas of evolutionary research are heading in this direction, and are the start of a vast enterprise. Very few of the facts uncovered to date in this field actually show evolution in action, because there are so many more facts to determine. I believe that eventually, there will be factual evidence of particular sorts of evolution that are uncovered by evo-devo research. But this evidence will not "exclude" creation or indeed intelligent design from the many issues about how we got here.

In fact, one of the amazing findings of evo-devo research is that the basic toolkits and hox genes for body parts are evidently quite ancient and essentially unchanged since the very first appearance of visible animals in the early Cambrian era.  Whereas earlier  proponents of evolution assumed that the genes for these body parts were re-created many times in the tree of life, in fact that is not the case -- which leaves unanswered how those toolkits arose in the first place. That is a much more problematic for evolution than the changes in phenotype
across the species using a conserved set of toolkit genes.




The Evolution Hierarchy:
Levels of Evolutionary Complexity
 
"The Surprising message from Evo Devo is that all of the genes for building large, complex animal bodies long predated the appearance of those bodies in the Cambrian Explosion." [139]

Task
Date
Subtask
Complexity
Remarks
Kind of Evolution
complex molecules
     - motors
3,900 Ma
ATP synthase
Ribosomes

Required prior to first living species
Concurrent  de nova
development of large gene packages.
First Living Species
3,900 Ma
Central Dogma: nucleotides
amino acids, ribosomes, t-rna
sugar,
reproduction
> 500 genes
How to get started? A full range
of gene products are needed to
form the first living cell.  carry
out the central dogma and duplicate
the cell.
Concurrent  de nova
development of large gene packages.
First cyanobacteria
3,500 Ma
photosynthesis (light & dark)
Nitrogen fixing (nitrogenase)
• Nitrogenase
motor molecule
• Chlorophyll molecule
• Specialized Cells
     spores
     akinetes
     heterocysts

de nova development of individual genes
Bacteria




Evolution by Bacterial conjugation, Bacterial transformation, etc.
First Eukaryotes
1,750 Ma




bilateral symmetry
600 Ma
Ediacara
Develop body
topography for
gene expression
6-7 hox genes
100s of toolkit
genes [145]
First evidence of symmetry (implying
topography) in Ediacara [140]. Genes
in place for future heart, eyes, limbs.

First Animals
"So many animals,
so little time."
550 Ma
Cambrian
animal toolkit genes [119]
    Pax-6 (eyeless),Tinman
    Ultrabithorax Snail, etc.
gene switches
Hox genes
All major animal phyla.
~500 DNA binding
proteins.
The toolkit genes for tissues: muscle,
nerve, contractile, photoreceptive,
digestive, secretory.[145]
Anticipate the full range of future
development of eyes, limbs, etc.

modification of gene switches
and body topography.





Evolution by random changes, transcription errors, survival of the fittest, etc.



problem: what is the natural mechanism to do this?
 
Origin of First life: Central dogma
Origin of genes
motor genes & complex molecules
hox genes & regulatory genes
Gene toolkits -- anticipation of future development
random variations in gene expression -- exchange of genetic info in bacteria







APPEND THE BOOK REVIEWS CITED ABOVE.

Sharp Point          Eigen's Paradox -- Error Correction Coding

Error correction mechanisms in prokaryotes and eukaryotes. Eigen's paradox.





Modes of InteRNAl Cell Transport
Diffusion vs. Kinesin Transport
   
Bacteria rely on ordinary diffusion to move food and waste within a cell. Diffusion depends on random movement due to molecular collisions, and is typified by the dispersion of a dye in a beaker of water:

031c-diffusion





E-Coli Reproduction Rate
   
Under normal conditions, with food available, an e-coli population will double in 15-20 minutes. With an average bacterium's volume of 0.6 µm3, it would take about 26 hours -- just over a day -- for the descendents of a single bacterium to cover the entire earth's surface (510 x 1012 m2) to a depth of one meter. In another few hours, the descendents of that one e-coli bacterium would fill the entire solar system. This demonstrates the power of exponential growth. Of course this would never happen because the food supply would run out long before that.


golgi apparatus -- and animation

cytoskeleton microtubules
centrosome (near nucleus) organizes microtubules. "All eukaryotic cells have a microtubular organizing center"
http://www.youtube.com/watch?v=5rqbmLiSkpk&feature=related

endoplasttic reticulum Protein Translocation


fractal

REFERENCES

Bruce Alberts, et al. Essential Cell Biology: An Introduction to the Molecular Biology of the Cell (1998),
David C. Bossard, A Fit Place to Live. (2003)
Wallace S. Broecker, How to Build a Habitable Planet (1985)
Richard Dawkins, The Greatest Show on Earth (2009).
Guillermo Gonzalez & Jay W. Richards, The Privileged Planet (2004)
George L. Goodale, Protoplasm and its History (Botanical Gazette Vol. XIV No. 335, Oct. 1889) Pdf (2.8 Megs)
Ernst Haeckel, The History of Creation (1876): Vol. I On the Protoplasmic Theory, p.99ff.
Robert Hasselkorn, The Cyanobacterial genome core and the origin of photosynthesis (Proceedings of the National Academy of Sciences, 2006)
Robert M. Hazen's book Genesis: The Scientific Quest for Life's Origins (2007)
Dr. Ronald E. Hurlbert, Washington State University Microbiology 101/102 Internet text [2000].
D. T. Johnston et al, Anoxygenic photosynthesis modulated Proterozoic oxygen and sustained Earth's middle age (Proceedings of the National Academy of Sciences, 2006)
Riccardo Levi-Setti, Trilobites (1995).

Lynn Margulis and Kathlene V. Schwartz, Five Kingdoms: An Illustrated Guide to the Phyla of Earth,Third Edition, W.H. Freeman, 1999, p79. The most recent edition of this work has been renamed Kingdoms and Domains (2009) by Lynn Margulis and Michael J. Chapman.
John Theodore Merz, A History of European Thought in the Ninetenth Century (1907-1914)
Harold J. Morowitz, Beginnings of cellular Life, Yale University Press, (1992).
J. Willliam Schopf, Cradle of Life: The Discovery of Earth's Earliest Fossils (1999).
Peter D. Ward &  Donald Brownlee, Rare Earth: Why Complex Life is Uncommon in the Universe. (2000)


fractal.gif




mailbox Any comments or suggestions are welcome. Please email: webmaster@ps-19.org

       

Prepared July, 2010