Evolution and Creation
A "Cross-grained" Approach
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]:
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:
This dismissive viewpoint is reflected in virtually all discussions of evolution today. John Theodore Merz (1907), citing this lecture, said it this way:
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:
Well, I guess I am cross-grained -- genius or not.
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.
1. Richard Dawkins, The Greatest Show on Earth: The Evidence for Evolution, Free Press .
2. Sean B. Carroll, Endless Forms Most Beautiful: The New Science of Evo Devo, W.W. Norton .
3. Jerry A. Coyne, Why Evolution is True, Viking Penguin .
4. Fourth book not yet written --
Comparison of Genome Size
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:
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.
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)].
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.].
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).
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.
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]
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.].
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". 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.
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.
Evolution has a long history of hyperbolic statements which assert or imply its factuality, made by prominent scientists, such as:
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
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
Eigen's Paradox -- Error Correction Coding
Error correction mechanisms in prokaryotes and eukaryotes. Eigen's paradox.
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:
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.