Archive for February, 2008

Is mutation+selection enough?

Tuesday, February 19th, 2008

I made a comment recently that there was continued discussion that evolutionary theory did not sufficiently account for the fossil record, in that mutation + selection is perhaps insufficient to create the diversity of life we see before us, in concert with the manner in which life forms appear and progress in the fossil record.

In response to a request for references, I submit this article, and will enhance it over time. First, I will refer to Stephen J. Gould’s The Structure of Evolutionary Theory for the bulk of the support I will turn to. Indeed, if this volume were a bit less lengthy, I would suggest that everyone read it cover to cover. In the end, you may agree with my assertion that Gould was trying to dance around some serious differences between the fossil record and the underlying theory of how evolution proceeds.I also submit this in response to claims that the terms microevolution and macroevolution, and even evolutionist are terms that are used in derision by creationists and have no scientific foundation. All of these terms are used routinely by Gould.

In the closing chapter of the book, Gould reveals the purpose of the volume.
Pg. 1339: “This book attempts to expand and alter the premises of Darwinism, in order to build an enlarged and distinctive evolutionary theory that, while remaining within the tradition, and under the logic of Darwinian argument, can also explain a wide range of macroevolutionary phenomena lying outside the explanatory power of extrapolated modes and mechanisms of microevolution.”

Pg. 1276: “The conventional mechanisms of microevolution cannot, in their extrapolation through geological immensity, fully explain the causes and patterns of evolutionary change at larger scales.”

Pg. 651: “But the empirical record of the great majority of well-documented fossil species affirms stasis throughout the geological range. The causes for observed nondirectionality within species have not been fully resolved…” (and then he goes on to explain some theoretical solutions.)

Pg. 756: “Darwin argues that species may arise so slowly that they process generally takes longer than the entire duration of a geologic formation (usually several million years)–thus explaining the apparent stasis within a formation as gradual evolution over insufficient time to record visible change!”

Pg. 757: “Darwin knew perfectly well–as all paleontologists always have–that stasis and abrupt appearance represent the norm for the observed history of most species…. Darwin attributed this striking discordance between theoretical expectation and actual observation to the extreme imperfection of the fossil record.”

Pg 759: “The fossil record may, after all, be 99 percent imperfect, but if you can , nonetheless, sample a species at a large number of horizons well spread out over several million years, and if these samples record no net change, with beginning and end points substantially the same, and with only mild and errant fluctuation among the numerous collections in between, then a conclusion of stasis rests on the presence of data, not on absence! In such cases, we must limit our lament about imperfection to a wry observation that nature, rather than human design, has established a sampling scheme by providing only occasional snapshots over a full interval. We might have preferred a more even temporal spacing of these snapshots, but so long as our samples span the temporal range of species, with reasonable representation throughout, why grouse and nature’s failure to match optimal experimental design–when she has, in fact, been very kind to us in supplying abundant information. Stasis is data.”

Pg 759: “Paleontologists therefore came to view stasis as just another failure to document evolution. Stasis existed in overwhelming abundance, as every paleontologist always knew. But this primary signal of the fossil record, defined as an absence of data for evolution, only highlighted our frustration–and certainly did not represent anything worth publishing. Paleontology therefore fell into a literally absurd vicious circle. No one ventured to document or quantify–indeed, hardly anyone bothered to mention or publish at all–the most common pattern in the fossil record: the stasis of most morpho-species throughout the geologic duration”

Pg 760: All paleontologists recognized the phenomenon, but few scientists write papers about failure to document a desired result. As a result, most nonpaleontologists never learned about the predominance of stasis, and simply assumed that gradualism must prevail, as illustrated by the exceedingly few cases that became textbook “classics”: The coiling of Gryphaea, the increasing body size of horses, etc. (Interestingly, nearly all these “classics” have since been disproved, thus providing another triumph of hope and expectation over evidence–See Gould 1972).

Pg 760 (…John Imbrie … [applied] quantitative methods… to the classic sequence of Devonian brachiopods from the Michigan Basin–where rates of sedimentation had been sufficiently slow and continuous to record any hypothetical gradualism. He studied more than 30 species in this novel and rigorous way–and found that all but one had remained stable throughout the interval, while the single exception exhibited an ambiguous pattern. But Imbrie did not publish a triumphant paper documenting the important phenomenon of stasis. Instead, he just become disappointed at such “negative” results after so much effort. He buried his data in a technical taxonomic monograph that no working biologist would ever encounter (and that made no evolutionary claims at all)–and eventually left the profession for something more “productive”.)

Pg 763 Traditional paleontology therefore placed itself into a straightjacket that made the practice of science effectively impossible: only a tiny percentage of cases passes muster at all…

As Hallam said to me many years ago, after he had disproved the classical story of gradualism in Graphaea: more than 100 other species of mollusks, many with records as rich as Graphaea’s, occur in the same Liassic rocks, yet no one ever documented the stratigraphic history of even a single one in any study of evolution, for all demonstrate stasis. Scientists picked out the only species that seemed to illustrate gradualism, and even this case failed.

I find this situation particularly frustrating as paleontology’s primary example of an insidious phenomenon in science that simply has not been recognized for the serious and distorting results perpetrated under its aegis. Most scientists do not even recognize the problem–though some do, particularly in the medical and social sciences, where the error has been named “publication bias,” … In publication bias, prejudices arising from hope, cultural expectation, or the definitions of a particular scientific theory dictate that only certain kinds of data will be viewed as worthy of publication, or even of documenting at all. … and may be much more common than fraud.

pg 767: “In the most elegant documentation of stasis for an entire fauna of molluscan species, Stanly and Yang (1987) used this best criterion [of stasis] to find that temporal fluctuation remained with in the range of geologic variation for the same species. They could therefore affirm stasis in the most biologically convincing manner.

Pg 768: (IMPORTANT) At an average species lifetime of 4 million years, a 1-percent criterion allows 40,000 years for speciation. When we recognize that such a span of time would be viewed as gradualistic –and extremely slow paced at that–by any conventional microevolutionary scaling in human time; and when we also acknowledge that the same span represents the resolvable moment of a single bedding plane in a great majority of geological circumstances; then we can understand why the punctuations of punctuated equilibrium do not represent de Vriesian saltations, but rather denote the proper scaling of ordinary speciation into geologic time.

Pg 782: We must abandon our concept of constant change operating within a sensible, stately range of rates as the normal condition of an evolving entity. We must then reformulate evolutionary change as a set of rare episodes, short in duration relative to periods of stasis between.

pg 798: The pattern of punctuated equilibrium has been well documented and shown to predominate in many situations but is more obvious theoretical rationale has now fallen under strong skepticism…. We must identify another reason for the predominance of punctuated equilibrium as a pattern in the history of life.

Pg. 986: Standard creationist literature on punctuated equilibrium rarely goes beyond the continuous recycling of two false characterizations: the conflation of punctuated equilibrium with the true saltationism of Goldschmidt’s hopeful monsters, and the misscaling of punctuated equilibrium’s genuine breaks between species to the claim that no intermediates exist for the largest morphological transitions between classes and phyla…. I have written numerous essays in my popular series, spanning ten printed volumes, on the documentation of this style of intermediacy in a variety of lineages, including the transition to terrestriality in vertebrates, the origin of birds, and the evolution of mammals, whales and humans–the very cases that the usual creationist literature has proclaimed impossible.

Pg 1037: I advocate nothing original in asking evolutionists to focus upon the empirically positive concept of constraint as channels for change, rather than (as in the negative meaning) limits to natural selection imposed by insufficient raw material in variation.

Pg 1272: A Darwinian world view that had become too narrow in its focus on organismal adaptation and sufficiency of known microevolutionary mechanisms to explain all scales of evolutionary change. [He goes on in the final chapters to present some ideas that might be useful.]

Pg 1273: Retrotransposons, for example, constitute about 40 percent of mammalian genomes (Karazian, 2000). The human genome includes about 500,000 truncated versions and some 3000 to 5000 full copies of the LINE-1 long terminal repeat. Chromosome 2 of Aradibopsis includes 239 tandem duplications involving 593 genes. A larger duplication of almost 2.5 million bases appears on two chromosomes in four large blocks. A long stretch of chromosome 4, including 37 genes, has been duplicated on chromosome 5. Chromosome 2 also contains a region with 75 percent of the mitochondrial genome, reflecting a recent transfer of substantial block of DNA from an organelle to the nucleus (Meyerowitz, 1999)…

Neutral Theory of molecular evolution

Pg 686: The Neutral theory of molecular evolution… has been since hailed as the most interesting revision of evolutionary theory since Darwin. Motoo Kimura’s classical categories of evidence [in papers between 1968 and 1991] all depend on the observation that maximal rates of nucleotide change occur at sites that do not influence the organismal phenotype–on the reasonable assumption that organismal selection usually acts in the stabilizing mode to preserve favorable sequences, and that sites under selective influence must therefore change at less than the maximal rate. The threefold confirmation of this prediction provides powerful evidence for the neutral theory–(1) for synonymous substitutions of the third nucleotide in a triplet; (2) for much higher rates of change in untranslated introns than in surrounding exons; and (3) for entirely untranslated pseudogenes, where rates at all three positions of triplets match the rapid third-position rate for translated DNA.

Pg 686: Kimura has always stressed the high frequency of neutral substitutions as his main challenge to Darwinian traditions. He writes, for example (1991) that “in sharp contrast to the Darwinian theory of evolution by natural selection, the neutral theory claims that the overwhelming majority of evolutionary changes at the molecular level are caused by random fixation (due to random sampling drive in finite populations) of selectively neutral (i.e. seletively equivalent) mutants under continued inputs of mutations.” At the same time, Kimura consistently insisted…that the neutral theory did not contradict or dethrone Darwinism, but should be integrated with natural selection into a more complete and more generous account of evolution…. Although most nucleotide changes may be neutral at their origin, the variability thus provided may then become indispensible for adaptive evolution of phenotypes if environmental change promotes formerly neutral substitutions to organismic visibility…

[Kimura's] view is that in every species, there is an enormous amount of molecular change. Eventually, some changes become phenotypically important; if the environment changes, some of the neutral molecules may be selected and this of course follows the Darwinian scheme.

The main problem between the fossil record and the concept of continuous “random” mutations preserved through the law of survival of the fittest driven by natural selection is that the fossil record does not show the gradual changes originally envisioned by Darwin, and subsequent theories to account for punctuated equilibrium are unsatisfying.Gould at least admits that paleontology was in a vicious circle of denial. I wonder how much of this publication bias continues to persist regarding evolutionary theory when compared with the historical record.(More to be added to this line of thought from other references…)

“Evolution” is misunderstood

Tuesday, February 19th, 2008

I’ve come across this situation before. Take two groups of people who come from different specialties, and they’ll use the same word but build quite different images in their minds. If you continue in that mode, rarely can you reach agreement on anything because the parties are not effectively communicating, and they consistently wonder why the other group doesn’t get it.

Evolution is one of those terms. The related forms evolutionist and evolutionism are problems too.

Forgive me if this seems simplistic. It isn’t and is the basis for most disagreement among those who support creationism, intelligent-design, and those who support evolution.

Although the term evolution was already in use prior to Charles Darwin’s theory was published in 1859, the term evolution usually has some connection with his theory. The Encarta dictionary says that for biology, it is the theoretical process by which all species develop from earlier forms of life.

This term is also used for changes in nearly any field, such as the evolution of music, evolution of language, and the evolution of computer technology, and implies gradual changes over time.

Determining how any field has changed over time is the work of a historian of one sort or another, and sometimes they have specific names. Understanding how ancient life forms have changed over time is the work of the paleontologist, who primarily gets his information from the fossil record.

The information in the fossil record is found in the form of fossils where the body of the organism has been converted to rock under very specific conditions that will occur only rarely. Soft, fleshy bodies won’t be found much, if at all, and only the hard skeleton or shells will be generally part of the record.

Scientists who refine the theory of evolution work only up to a theoretical first organism which has sufficient infrastructure to follow the laws of Mendelian genetics, natural selection, and chance mutation. They draw the line there and assume that anything before that point is impossible to comment on because there is no evidence regarding exactly how the first such organism took form.

Consider Stephen J. Gould’s comment on this topic from his work of popular nonfiction Bully for Brontosaurus:

Pg. 455: Evolution is not the study of life’s ultimate origin as a path toward discerning its deepest meaning. Evolution, in fact, is not the study of origins at all. Even the more restricted (and scientifically permissible) question of life’s origin on our earth lies outside its domain. (This interesting problem, I suspect, falls primarily within the purview of chemistry and the physics of self-organizing systems.) Evolution studies the pathways and mechanisms of organic change following the origin of life.

However, some scientists include the topic of life’s origins within the more general topic of evolution, such as John Maynard Smith in The Major Transitions in Evolution. Indeed, it seems somewhat artificial to stop the inquiry about life at the point where present-day evolutionary principles are in effect. Smith considers the sticky point of how DNA could possibly come about and how cells came to be. So it is not universal that all scientists restrict evolution to the period when life became sophisticated enough such that natural selection and Mendelian genetics could be the underlying principles driving evolution. But it certainly is convenient because they can pin this part down much more clearly and claim it is closer to fact than theory.

Ask the man on the street about evolution and they’ll likely tell you the theory also includes the concept that life started here on earth as a chance accretion of matter.

Such an accretion is possible, but it seems quite unlikely. It is working against the law of entropy and a tendency toward randomness. Perhaps it can be argued that the structure of our universe is particularly amenable to such a self-assembly, and therefore this consequence is quite normal. However, the steps required are still a mystery. It appears now that it is not a simple matter at all, but still not impossible. Most theories assume that self-replicating RNA-like sequences were first, and then they eventually built DNA. But the step from RNA to DNA is not direct and the process is certainly unclear at this point. Nevertheless, with billions of years available for the process, it may still be possible, and we may eventually understand how self-assembly may be possible.

From the mind of a theologian, the concept of an evolutionist also includes this self-organizing interval while the scientists uses the word for the scientist who only works with Darwinian-rooted evolutionary principles. This is where the disconnect occurs.

I’m sorry to say that the blame is properly put on the scientific community who took the general term evolution and employed it for a more specific specialty. They say that evolution is fact–not theory–but they are only referring to the well understood interval after complex, DNA-based organisms were part of the picture. Others say that evolution is only theory after all, and they are right too, because they are also including the initial formation of life on earth.

The options for what may have happened at the initial formation of life include only two possibilities. 1) life self-organized or 2) life was assisted in this organization.

Evolutionism assumes it self-organized here on earth and did not require any assistance either from a supreme being or another life form. Until we can prove that this is possible, possibly by recreating the process, this will be only an untested theory.

Intelligent Design assumes that the structures found are too complex to have arisen by chance against the general tendency of entropy. Most ID advocates also insist that the only solution is that a supreme being created life here on earth, mostly in line with creationism arguments.

If life was assisted by other life, then perhaps life did not arise here and was not created here, but either arose or was created somewhere else and then seeded here. This is also a difficult alternative as it implies that some form of life would be able to get to this particular location of the universe, find the right conditions, and establish life on the planet. If some of the issues of space travel were resolved, this may be the most likely scenario. If that is the case, then life may have been assisted at other times as well.

Unfortunately, this does not solve the problem completely, as it would then push the origin of life back only one step, to have arisen on another world and perhaps different conditions. It may be true, but it does not answer the ultimate question about how life originally arose, only pushes the question back one step.

With all this said, I think that if all parties understood and acknowledged that we really don’t know how this all got started, the positions of the various points of view could be seen as equally valid until we get more information. However, unless there is some way to prove that a supreme being exists, there is no equality when it comes to that point of view, and therefore we are really only considering the possibility that life arose here or life arose elsewhere and was seeded here.

If science can resolve the steps necessary for life to self-organize and a good case made that such could have been the case when earth first formed, then this would improve the likelihood that evolution (all the way back to the origin of life) is fact. I would like to see life created in the laboratory to substantiate this theory. Then, evolutionism would win and it becomes science.

With all that said, finding a convincing description of DNA, natural selection, and the underlying pattern of life in ancient documents is one more data point to be considered, and is the core concept of the novel Coils of the Serpent, and it then begs the question about how the description got into those ancient documents.

What is this blog about?

Tuesday, February 19th, 2008

The novel Coils of the Serpent has inspired quite a number of questions and comments on forums and blogs across the Internet. The pattern match described in the novel prompts a re-evaluation of some of the conclusions we have drawn about the history of life on earth and religious doctrine.

This blog will be a convenient place to provide additional insight and background information to support the various claims and conclusions reached in the novel. Indeed, since the novel deals with cutting-edge science in the area of genetics, evolution, and life’s origins, new information is bound to surface which will need to be included in our thinking process. As an interested fellow researcher in this domain, I encourage you to take part and contribute to the discussion.

Although I originally envisioned the novel as nonfiction, I recast the information as fiction for better marketability. Yet, I still believe a nonfiction treatment is viable. Hopefully, this blog will facilitate interaction with site visitors and will coalesce the information for future release as a nonfiction work.

I want to thank you in advance for your participation!

Raymond Clark Lutz