I have made a second post

to Examiner.com.

They are taking about 2 hours to produce, which means I am writing for about $1/hour.

Well. I will more or less drop "Stones and Bones"

I really like the name, but I could not carry it over to my new "newsy" blog LA Science Education Examiner"

Yeah, I know- weak.

See you there.

My first Examiner.com text

There are many challenges to teaching in today's schools. Many are the sorts of things not taught about in teacher colleges, nor discussed in news articles. Things like how to teach to the little girl who is scared that her father will be hurt while he is in prison. With record numbers of Americans in prison, this is more common that we like to imagine.


But teaching science has the strangest challenge of all; people who actively promote the notion that the sciences are all nonsense.

Ray Comfort and his pal Kirk Cameron have an outfit they call "Living Waters Ministry." Marking the 150th anniversary of its publication, they have taken the public domain text of "The Origin of Species" and tacked on a 50 page regurgitation of common creationist lies and frauds. Ray and Kirk have claimed that;

This introduction gives the history of evolution, a timeline of Darwin's life, Hitler's undeniable connections to the theory, Darwin's racism, his disdain for women, and his thoughts on the existence of God. It lists the theory's many hoaxes, exposes the unscientific belief that nothing created everything, points to the incredible structure of DNA, and the absence of any species-to-species transitional forms.

It would take too many pages to refute every false claim made above, but here are a few;

In of itself, the selection of The Origin (first edition in 1859) for this shenanigan shows their fundamental ignorance as Darwin carefully avoided mentioning humans in the initial public presentation of his theory. When Darwin published his 1871 book, "The Descent of Man" he was able to directly present the common origin of all humanity without repeating the core evolutionary theory. It is more than odd that creationists should object to this, since at least recently they insist from biblical grounds that all humans share a common origin. Darwin sailed against the wind of popular belief when he wrote that his long personal association with "savages" who impressed on him, "... how similar their minds were to ours..." Darwin was writing to a general population who commonly believed that Africans and Native Americans were not even humans. Famous creationists contemporaries were claiming the Bible supported that ony Whites were true humans, while others justified slavery as the "Curse of Ham."

The Bible demands the execution of a woman raped, that they are inferior to their husbands, and that they must remain silent in church as their opinions are tainted by the Sin of Eve. Oh right, don't forget that all sin and suffering is the fault of women which is why they "deserve" pain and death in childbirth. If we compare the Bible's treatment of women with Darwin, he would seem to be a radical feminist.

There are "transitional" or "intermediate" fossils literally by the ton. Museums and museum warehouses are stuffed with them. If we look for the tiny gradual changes over time in fossils, we need to look at the tiny organisms that preserve these sorts of changes. Examples abound in the marine sediments filled with foramifera, and ostracods. But, when we look at the large familiar critters, the tiny variations that added up over generations to new species are lost against the greater similarities. The scientific definition of many species today is difficult for the scientist, but easy for the sexually active members of the species. A recent example would be the "discovery" that the California Two Spotted Octopus was really two species. The physical difference, a two centimeter variation in their reproductive organs which would never leave a fossil in the first place. This was not news to the octopi. And finally, we do observe new species emerging, both in nature and in laboratory experiments.

Creationists like Ray Comfort harm Christianity by making it seem absurd. This was warned against by Thomas Aquinas (c.a. 1225 - 1274) who wrote, "... one should adhere to a particular explanation only in such measure as to be ready to abandon it if it be proved with certainty to be false, lest Holy Scripture be exposed to the ridicule of unbelievers, and obstacles be placed to their believing." Summa Theologica, Prima Pars, Q68. Art 1. (1273).

The even greater problem for America's teachers is that it makes teaching science to some students nearly impossible.

OK, I went to Examiner.com

My first post is a responce to the crapola from Ray Comfort. Here is the link.

Writing for Examiner.com

I have completed the associated ritual to become an "examiner.com" expert. This was actually rather extensive- sample writing, article proposals, a criminal background check, and some IRS forms to fill out.

But?

Would the occasional reader of this blog follow over?

What say ye?

I cannot think of a better excuse.

He "was in no haste to publish his theory; for he was one of those who are much more delighted with the contemplation of truth, than with the praise of having discovered it” John Playfair regarding James Hutton, 1805.

I'll employ it often.

A new biographic note for the Center for Inquiry.

Gary S. Hurd received a doctorate in Social Science from the University of California, Irvine in 1976 (emphasis in Anthropology). He subsequently served on the faculties of the California College of Medicine (UCIMC), the Medical College of Georgia (Psychiatry), and held numerous adjunct appointments. In 1985, he returned to archaeology, the original focus of his early research. He has publications ranging from topics in psychiatry, mathematics and chemistry to insect frass, fish digestion, prehistoric ceremonialism and forensic taphonomy. He was also honored for including undergraduates in published research, and named teacher of the year.

Hurd became actively involved in the creationist anti-science debate over ten years ago while the Curator of Anthropology, and Director of Education for the Orange County Museum of Natural History. His critique of Intelligent Design Creationism was published in "Why Intelligent Design Fails: A Scientific Critique of the New Creationism," 2004, Rutgers University Press, Matt Young and Taner Edis, editors. This chapter was used in the cross-examination of ID proponent Michael Behe, and cited by the Court’s decision in the famous 2005 Dover creationism trial.

Now a frequent academic guest lecturer, Hurd tries to reach popular audiences through such web sites as No Answers in Genesis;


“A Response to a Dubious Diluvium: A Tas Walker Creationist Fantasy”
“Oard's Moonbeam”

TalkOrigins;

“Dino-blood and the Young Earth”
“Dino Blood Redux”
“Ancient Molecules and Modern Myths”

The National Center for Science Education;
"Why Reinvent the Crystal?”

And science blog "The Panda’s Thumb," which he co-founded;

“Dembski's Five Questions: Number One”

His current projects include intermittent bursts of writing on three books;

“Someone to Blame: How Creationism Exploits the Holocaust”
“You’ve Got to Be Kidding: The Pious Frauds of Creationism”
“Where Did The Bible Say That?: How Creationism Violates Scripture”

Expertise:
Biblical and Koranic criticism
Evolution, creationism, and intelligent design
Religion and genocide
Science and religion
Science and pseudoscience
Archaeology and the Bible

A day spent off-shore

I went out of Seaforth Landing in San Diego, California aboard the Eclipse. We had a great day of fishing.

Create the controversy

The American Association for the Advancement of Science, and the Pew Research Center for the People and the Press have released a report on the American public’s science knowledge and opinions regarding science and scientists. (Links are to the AAAS news release, and the Pew report).

While there is much of interest and for concern, the most interesting topics for the evol/creato activist are the questions related to human evolution.

The “teach the controversy” position pushed by the creationists needs for a controversy to actually exist, at least in the minds of the general public. This is a Big Lie approach straight from the playbook written by the tobacco industry. With only a handful of industry “scientists” funded through the Tobacco Institute, the industry created a story that “the science linking tobacco and cancer is disputed” and “there is legitimate controversy about the effects of tobacco smoking among scientists.” And there is evidence that this lie is working for creationists.

The AAAS/Pew survey found that among scientists, there is a 97% agreement that humans, and all living things have evolved via natural selection. Yet, 28% of the public believes that scientists are not in general agreement that evolution occurred. And, 43% of creationists (mostly White Evangelicals, and about 31% of the general public) claim there is no scientific consensus on evolution.

Why Re-Invent the Crystal?

My short piece on the movie Expelled and cyrstals, written for the National Center for Science Education" has been posted to their website.

“The End of Darwinism”

“The End of Darwinism” would have disappeared as another self published creationist screed had not Pat Buchanan puffed it on WingNutDaily. There have been a half dozen science bloggers who have taken Buchanan’s piece apart, but I waited until I could read Mr. Windchy’s book myself.

Windchy states that he had worked on this book since 1993. I found this very strange as he makes basic errors of fact that could be corrected with a few minutes of internet search. The errors begin immediately and they range from minor factual mistakes to gross mistakes in fact and scholarship.

One example of a minor error of fact is on page 14 when Windchy claimed that, “The German Darwin (Ernst Haeckel, gh) was convicted of fraud by a faculty court at the University of Jena, his employer in Prussia …” This is not true. In fact, there was never a “faculty court” in the first place. This particular creationist lie has been repeated in their echo chamber so often that it occasionally has appeared in the popular press. This has been pointed out by

Haeckel was accused of publishing drawings of embryos that were fraudulently presented, or altered to make his theoretical argument appear better supported. In only one instance did Haeckel need to issue a retraction. This was in his illustration of the “sandal stage” of “dog, chicken, and turtle” embryos in his first edition (1868) of “Natürlich Schöpfungsgeschlichte.” These were actually the same woodcut, apparently of the chicken embryo at this stage of development, that had been repeated. (To see the illustration in question, look at Fig. 7.12 of “The Tragic Sense of Life” by Robert J. Richards, 2008). This particularly outraged Ludwig Rütimeyer, and Wilhelm His.

Haeckel corrected this in the second and later editions. The point he had been making was that embryologists could not tell one species from another at that early stage of development, which was certainly true at the time, and had been earlier remarked on by other scientists such as von Baer well before Darwin ever wrote about evolution. In another instance it was the accuser, Arnold Brass, who had to retract his false claims of fraud in 1908-1909.

Haeckel’s pet theory of “recapitulation” or “biogenesis” was totally wrong and forms no part of evolutionary theory. He proposed that as organisms underwent embryonic development, the stages of the embryos replicated each of the adult forms of their evolutionary predecessors. However, his observations that embryonic development is more similar the more closely the species are related, and that the earlier development of vertebrate embryos are all very similar, were substantially correct. With our new ability to track the fate of individual cells in embryos, these observations are even stronger today than they were in 1870. Windchy has obviously not bothered to become informed about Haeckel, or his contributions to science, or what modern embryology is about. After supposedly spending 16 years, one would expect better. Instead, he regurgitates creationist lies and slanders- using century old controversies to try and obscure that science of evolution is the most successful explanation of life available.

Robert J. Richards
2008 “The Tragic Sense of Life” University of Chicago Press

Troy Britian
2001 Haeckel's Embryos Antievolution.org

It is offical

I have been appointed to the National Assessment of Educational Progress (NAEP) science panel. What this is will be better explained by either their official website, or the Wikipedia page.

I have not totally disappeared

A creationist recently asked, (lame-ass - punctuation - as in the ORIGINAL !!11!!)

Just one more - how well qualified was darwin to propose a theory - hundreds of years ago- that is still believed but not proven - he was a theologian - but was he a scientist or an amatuer taxonomist ? The average biology student knows more than Darwin who thought a cell was a blob. How come darwin did not need qualifications ?

I’ll first eliminate the argument that Darwin was some how unqualified to do science. Darwin’s childhood education was at a classical school- much memorization of Greek and Latin, and some mathematics. However, he did assist his father in his father’s medical practice which involved a modicum of physical knowledge. He was also an avid collector of beetles, and studied the taxonomic literature of the time.

His formal medical education was in Edinburgh. Darwin received practical instruction in taxidermy from a “blackamoor” named John who was the former slave of Charles Edmonstone. John had also traveled extensively as a servant and companion for the famous explorer Charles Waterton. In November of 1826, Darwin took a course from Robert Jameson in “Natural History” in addition to his medical studies.

Jameson’s 200 page geological illustration addendum to his translation of Curvier’s Essay on the Theory of the Earth was part of Darwin’s reading that term. Darwin later wrote that he found Jameson’s lectures, “… incredibly dull. The sole effect they produced on me was the determination never as long as I lived to read a book on Geology or in any way to study the science.”

Darwin made several studies of marine life while at Edinburgh under the encouragement of Dr. Robert Edmund Grant, who shortly after became Professor of comparative anatomy and zoology at London University, (1827-1874). Grant referred in print to two of Darwin’s original discoveries made in 1826; that the so-called "ova of Flustra" were in fact larvæ, and that the little globular bodies which had been supposed to be the young state of Fucus loreus were the egg-cases of the worm-like Pontobdella muricata. Darwin had read papers on these observations to the student’s “Plinian Society” founded by Professor Jameson.

Two years later, Darwin had given-up medicine. He could not stand the sights, sounds, and smells of the surgery. Instead, his disappointed father sent him to Cambridge to prepare for the clergy. But more significantly, Darwin became closely acquainted with the Revd John Stevens Henslow, Professor of Botany, and the Revds Adam Sedgwick and William Whewell, respectively professors of geology and mineralogy. These men totally changed young Darwin’s early resolution to avoid geological science. Whewell sought to reform the practice of science into a more formal profession. In fact, he was the man who coined the word “scientist.” Sedgwick and Henslow both lead field trips that Darwin attended. Fieldwork is much superior to lectures for learning geology and what we would call ecology today. The famous voyage around the world Darwin took from 1832 to 1834 was through the recommendation of Henslow. It was Sedgwick who sent Darwin off on the HMS Beagle with a copy of his Principles of Geology, which Darwin said, “Allowed me to see with the eyes of Hutton.”

By the time Darwin returned to England, he was considered a respected scientist- but as a geologist. Particularly well received was his theory on the formation of coral atolls and reefs. This work has been shown to be correct in every regard. While working on his “big book,” Darwin also spent years in the study of the biology of barnacles, publishing numerous papers and culminating in the still well regarded books; 1852 Living Cirripedia, A monograph on the sub-class Cirripedia, with figures of all the species. The Lepadidæ; or, pedunculated cirripedes, Volume 1, and 1854, Living Cirripedia, The Balanidæ, (or sessile cirripedes); the Verrucidæ, Volume 2, London: The Ray Society.

Emergence of New Species

I have collected some examples of speciation that are handy to have available when a creationist claims there are none.

We have of course directly observed the emergence of new species, conclusively demonstrating common descent, a core hypothesis of evolutionary theory. This is a much a "proof" of evolution as dropping a bowling ball on your foot "proves" gravity.

A large review of multiple species is, Sergey Gavrilets and Jonathan B. Losos "Adaptive Radiation: Contrasting Theory with Data" Science 6 February 2009 323: 732-737

Some specific examples for plants, insects, fish, birds, lizards and mammals follows.

Here are five examples sampled from: "Observed Instances of Speciation" by Joseph Boxhorn, 1995

Evening Primrose (Oenothera gigas)

While studying the genetics of the evening primrose, Oenothera lamarckiana, de Vries (1905) found an unusual variant among his plants. O. lamarckiana has a chromosome number of 2N = 14. The variant had a chromosome number of 2N = 28. He found that he was unable to breed this variant with O. lamarckiana. He named this new species O. gigas.

Kew Primrose (Primula kewensis)

Digby (1912) crossed the primrose species Primula verticillata and P. floribunda to produce a sterile hybrid. Polyploidization occurred in a few of these plants to produce fertile offspring. The new species was named P. kewensis. Newton and Pellew (1929) note that spontaneous hybrids of P. verticillata and P. floribunda set tetraploid seed on at least three occasions. These happened in 1905, 1923 and 1926.

Tragopogon

Owenby (1950) demonstrated that two species in this genus were produced by polyploidization from hybrids. He showed that Tragopogon miscellus found in a colony in Moscow, Idaho was produced by hybridization of T. dubius and T. pratensis. He also showed that T. mirus found in a colony near Pullman, Washington was produced by hybridization of T. dubius and T. porrifolius. Evidence from chloroplast DNA suggests that T. mirus has originated independently by hybridization in eastern Washington and western Idaho at least three times (Soltis and Soltis 1989). The same study also shows multiple origins for T. micellus.

Drosophila paulistorum

Dobzhansky and Pavlovsky (1971) reported a speciation event that occurred in a laboratory culture of Drosophila paulistorum sometime between 1958 and 1963. The culture was descended from a single inseminated female that was captured in the Llanos of Colombia. In 1958 this strain produced fertile hybrids when crossed with conspecifics of different strains from Orinocan. From 1963 onward crosses with Orinocan strains produced only sterile males. Initially no assortative mating or behavioral isolation was seen between the Llanos strain and the Orinocan strains. Later on Dobzhansky produced assortative mating (Dobzhansky 1972).

Apple Maggot Fly (Rhagoletis pomonella)

Rhagoletis pomonella is a fly that is native to North America. Its normal host is the hawthorn tree. Sometime during the nineteenth century it began to infest apple trees. Since then it has begun to infest cherries, roses, pears and possibly other members of the rosaceae. Quite a bit of work has been done on the differences between flies infesting hawthorn and flies infesting apple. There appear to be differences in host preferences among populations. Offspring of females collected from on of these two hosts are more likely to select that host for oviposition (Prokopy et al. 1988). Genetic differences between flies on these two hosts have been found at 6 out of 13 allozyme loci (Feder et al. 1988, see also McPheron et al. 1988). Laboratory studies have shown an asynchrony in emergence time of adults between these two host races (Smith 1988). Flies from apple trees take about 40 days to mature, whereas flies from hawthorn trees take 54-60 days to mature. This makes sense when we consider that hawthorn fruit tends to mature later in the season that apples. Hybridization studies show that host preferences are inherited, but give no evidence of barriers to mating. This is a very exciting case(Rhagoletis pomonella). It may represent the early stages of a sympatric speciation event (considering the dispersal of R. pomonella to other plants it may even represent the beginning of an adaptive radiation).

What I find personally fascinating is that the increasing genetic isolation of the two races of R. pomonella has led to the reproductive isolation/speciation of the parasitic wasp Diachasma alloeum (Hymenoptera: Braconidae) which feeds on the rapidly evolving fly. (See "Sequential Sympatric Speciation Across Trophic Levels" Andrew A. Forbes, Thomas H.Q. Powell, Lukasz L. Stelinski, James J. Smith, Jeffrey L. Feder, Science 6 February 2009 323: 776-779).

So, even when there might still be limited inter-fertility in the diverging, R. pomonella, there is already a related speciation in an associated insect.

Here are two speciation examples sampled from: "Some More Observed Speciation Events, 1992-1997" by Chris Stassen, James Meritt, Anneliese Lilje, L. Drew Davis

Rapid speciation of the Faeroe Island house mouse, which occurred in less than 250 years after man brought the creature to the island. (Test for speciation in this case is based on morphology. It is unlikely that forced breeding experiments have been performed with the parent stock.) Reference: Stanley, S., 1979. Macroevolution: Pattern and Process, San Francisco, W.H. Freeman and Company. p. 41

Formation of five new species of cichlid fishes which formed since they were isolated less than 4000 years ago from the parent stock, Lake Nagubago. (Test for speciation in this case is by morphology and lack of natural interbreeding. These fish have complex mating rituals and different coloration. While it might be possible that different species are inter-fertile, they cannot be convinced to mate.) Reference: Mayr, E., 1970. Populations, Species, and Evolution, Massachusetts, Harvard University Press. p. 348

Nevo, E., 1991, Evolutionary Theory and process of active speciation and adaptive radiation in subterranean mole rats, spalax-ehrenbergi superspecies, in Israel, Evolutionary Biology, Volume 25, pages 1-125.

There is a large literature on new species emerging among newly introduced colonies of Anole lizards. Here are just a few examples:

Anolis oculatus undergoes rapid subpopulation isolations following drought, or the introduction of a preditor, Anolis sagrei. Reference: Roger S. Thorpe "Population Evolution and Island Biogeography" Science 16 December 2005 310: 1778-1779

New species of Anolis on Indian Ocean Islands. Reference: Marguerite A. Butler, Stanley A. Sawyer, Jonathan B. Losos "Sexual dimorphism and adaptive radiation in Anolis lizards" Nature 447, 202 - 205 (10 May 2007)

Anurag A. Agrawal "Phenotypic Plasticity in the Interactions and Evolution of Species" Science 12 October 2001 294: 321-326

One more on fish;

Andrew P. Hendry, John K. Wenburg, Paul Bentzen, Eric C. Volk, Thomas P. Quinn "Rapid Evolution of Reproductive Isolation in the Wild: Evidence from Introduced Salmon" Science 20 October 2000: Vol. 290. no. 5491, pp. 516 - 518

So, common descent is established by direct observation of speciation, and various selective pressures are seen to be effective. Depending on population size, and starting variability, selective pressures can be strongly acting resulting in rapid emergence of new species.

Phillip Skell, Liar or Ignorant?

Re: "The Dangers Of Overselling Evolution"
Forbes Online 02.23.09, 01:47 PM EST
http://www.forbes.com/2009/02/23/evolution-creation-debate-biology-opinions-contributors_darwin.html


Philip S. Skell is a computational chemist. He disparages paleontology, and evolutionary biology. He is a creationist, and anything he writes must be interpreted with this in mind. His core argument is that evolutionary theory founders on the; "... origin of life, speciation, the essences of our fossilized ancestors, the ultimate causes of their changes, etc."

The origin of life, typically studied under the umbrella of abiogenesis, or astrobiology, is conceptually independent of evolutionary theory. Contemporary research is as much chemical as biological. Perhaps more so. As Darwin himself observed, concluding that there was a unique solitary original cell was merely the result of analogy, "But, analogy may be a deceitful guide." The core of evolutionary theory, common descent and natural selection, is unaffected by any origin of life scenario.

Skell seems unaware that speciation, the emergence of a newly isolated reproductive population is neither unknown, nor uncommon. We have directly observed the emergence of new species, conclusively demonstrating common descent, a core hypothesis of evolutionary theory. Depending on population size, and starting variability, selective pressures can be strongly acting resulting in rapid emergence of new species.
This is a much a "proof" of evolution as dropping a bowling ball on your foot "proves" gravity.

Skell is equally uninformed about the interplay between molecular genetics and paleontology. We have recently seen the publication of a draft genome of the extinct hominid, Homo Neadertalis. More tellingly, there has been a decades long exchange of opinions regarding whale evolution where hypotheses generated from both genetics and morphology have finally converged with the paleontological discovery of several new whale ancestors, particularly Ambulocetus natans, and Pakicetus.

Skell wrote that evolutionary theory is irrelevant to "doctors, veterinarians, farmers and other practitioners of biological science." He even mentioned that the discovery of penicillin was not a direct out come of evolutionary theory. And, of course it was not- it was a lucky accident. However, the subsequent and continuing development of antibiotics, including penicillin, was implicitly an application of evolutionary principles. It is either ignorant in the extreme, or dishonest, for Skell to claim that hereditable variations that result in altered population genomes under selection (evolution) are not critical to the study of antibiotic resistance. Equally, that evolutionary theory was not directly employed to alter clinical antibiotic prescription practice recommendations.

The new issue NCSE Reports has been released

It is focused on the gross lies from the producers and writers of the propaganda film "Expelled: No Intelligence Allowed."

Hopefully some of the material will be made available on the NCSE website, or their "Expelled Exposed" website soon.

I have a short piece on Ben Stein and the film's egregious lies about origin of life research which was fun to see in print.

Another day, and more creationist bullshit

W. Edward Murphy wrote, "I could support teaching Darwinism as fact PROVIDED that the advocates of Darwinism can supply answers to a few of my questions.”

I’ll take Mr. Murphy at his word, and expect that he will begin supporting teaching science in science classes. This will of course include biology, and all biological science is evolutionary science.

First, as others have noted, Mike Behe is a devout Roman Catholic. In his testimony under oath in the Dover Trial he has admitted that 1) his rejection of evolution was religiously motivated, and 2) that the notion of Intelligent Design was plausible to the extent that you believed in creationism, 3) that no experimental evidence for ID creationism existed, and 4) that his concept of “irreducible complexity” was deeply flawed but that he had neither improved nor replaced it.

Second, any new species emerges from a population and not single progenitors. The clearest examples are subspecies that interbreed with closely related subspecies, but with reduced fertility outside their subspecies. We even see occasional hybrids between different species that, while very rare, can be fertile. As the ancestral species Homo erectus spread throughout Eurasia and Africa there were many isolated and diverging populations. Archaeological evidence and genetic evidence both indicate that this lead to new subspecies which were basically compressed back to Africa during the ice ages of the Pleistocene. Two large populations, the Neanderthals and our species emerged, and we are the only current members of our genus. Even today, we observe that individuals are able to reproduce even with widely divergent genes, and even chromosome misalignments.

Next, egg laying has a much longer history than internal incubation. We have excellent fossil data demonstrating that dinosaurs had well developed nesting behavior and even parenting. We also have irrefutable evidence that all of today’s birds are evolved from dinosaurian ancestors. Simply, the egg came first.

Evolutionary biology generates systematic quantitative observations from experimental situations in both laboratory and natural settings. The results of these studies are used to refine theory and make new predictions for tests of that theory. There are dozens of evolutionary experimental results and theoretical discussions published every week in just the science journals I read. Globally there are dozens published every day. (By the way, there was no such idealized model of “science” in the 17^th century, and philosophers are still debating today just how they would define “science”).

We have any number of transitional fossils. The denial of this fact is the oldest of creationist lies. The higher in the taxonomic categories one looks, the easier the intermediates are to identify. Many paleontologists in the 1970s and ‘80s debated about the relative status of the lowest levels of taxonomy. Since in animals like birds, many species are first isolated into new species by behavior rather than gross alteration of their bones. Obviously, the evolution of those new species would be invisible paleontologically since it is extraordinary that behavior could be fossilized. (Rare, but not impossible. Dinosaur nesting behavior is an example). Today the combination of secure dating methods and the global geological data produced by the oil industry, enable us to make specific targeted excavation for transitional fossils of particular interest. Examples are the transition from sea to land by Devonian fish, and the return in the Eocene by those land mammals that were the ancestors of today’s whales.

But we do not even need fossil evidence of evolution because we have directly observed the evolution of new, reproductively isolated new species. There are examples in all major phyla from worms, insects, fish, reptiles, birds, and mammals. Even more examples are from plants.

Mr. Murphy finally indulges in what is known as “quote mining” which is take a snippet of text out of context to distort and mislead. Darwin began a section titled “Organs of extreme Perfection and Complication” with the sentence misappropriated by Mr. Murphy. In the same paragraph, Darwin responds, “Reason tells me that if numerous gradations from the simple and imperfect eye can be shown to exist, each grade being useful to its possessor, as is certainly the case; … the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, should not be considered as subversive of the theory.”

In the last one hundred and fifty years, we have learned much more about the evolution of eyes in all of the hundreds of forms they have taken. The eye is, as Darwin himself argued, not a problem- rather it is a further confirmation of evolutionary theory.

I would like to expect that Mr. Murphy will send a new email to the Texas Board of Education. But I won’t hold my breath.

Gary Hurd, Ph.D.

A Short Outline of the Origin of Life

Darwin's various editions of The Origin of Species made little mention of the origin of life. He does make some general observations in the concluding chapter. He writes in the Sixth Edition (1872),

"I believe that animals are descended from at most only four or five progenitors, and plants from an equal or lesser number.

Analogy would lead me one step further, namely, to the belief that all animals and plants are descended from some one prototype. But analogy may be a deceitful guide. Nevertheless all living things have much in common, in their chemical composition, their cellular structure, their laws of growth, and their liability to injurious influences."

And,

"No doubt it is possible, as Mr. G.H. Lewes has urged, that at the first commencement of life many different forms were evolved; but if so, we may conclude that only a very few have left modified descendants."

And a bit later, "Authors of the highest eminence seem to be fully satisfied with the view that each species has been independently created. To my mind it accords better with what we know of the laws impressed on matter by the Creator, that the production and extinction of the past and present inhabitants of the world should have been due to secondary causes, like those determining the birth and death of the individual. When I view all beings not as special creations, but as the lineal descendants of some few beings which lived long before the first bed of the Cambrian system was deposited, they seem to me to become ennobled. "

The final sentence in the first edition, "There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved." was slightly modified in the Sixth to clearly indicate that the "Creator" was responsible for the origin of life. Some scholarly studies claim that Darwin regretted making this concession to his publishers.

From the 1st edition Pg 484:
“I believe that animals have descended from at most only four or five progenitors, and plants from an equal or lesser number.

Analogy would lead me one step further, namely, to the belief that all animals and plants have descended from some one prototype. But analogy may be a deceitful guide. Nevertheless all living things have much in common, in their chemical composition, their germinal vesicles, their cellular structure, and their laws of growth and reproduction. We see this even in so trifling a circumstance as that the same poison often similarly affects plants and animals; or that the poison secreted by the gall-fly produces monstrous growths on the wild rose or oak-tree. Therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed.”

Charles R. Darwin, in a 1871 letter to the botanist Joseph Hooker wrote, "It is often said that all the conditions for the first production of a living organism are present, which could ever have been present. But if (and Oh! what a big if!) we could conceive in some warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity, etc., present, that a protein compound was chemically formed ready to undergo still more complex changes, at the present day such matter would be instantly devoured or absorbed, which would not have been the case before living creatures were formed. "

Later in the same letter, he observed,

"It is mere rubbish thinking at present of the origin of life; one might as well think of the origin of matter."

The theory of evolution is an explanation of the diversity and distributions of life forms, not the initial origin of life. This is an active area of research called “abiogenesis,” “astrobiology,” or simply origin of life (OOL). It is obviously part of the larger scientific project to understand the universe, but is not fundamental to evolutionary theory.

The general interest books on the origin of life (OOL) typically start with a lengthy discussion of the historical theories of life. Beginning with the Greeks and working our way toward the present, there are three most significant events: the invention of the microscope, the synthesis of urea, and the famous experiment by Pasteur in 1862.

All the early thought on the origin of life can be reduced to a theory of spontaneous generation of life, or the creation of life by supernatural external agency. The invention, and improvements to the microscope between 1590 and 1674 CE profoundly changed mankind's conception of life and its complexity. This seemed to many as support for the spontaneous generation of life notion, as these microscopic life forms were thought as the simple "seed" for latter complex life. Anton van Leeuwenhoek's discovery of sperm also added to this "support" for the spontaneous generation theory.

There was also the thought that the organic "stuff" of life was completely different from "inorganic" or mineral matter. Known as "vitalism," this concept was shown to be false by F. Wöhler, in his 1828 synthesis of urea, a "live" compound, from inorganic stock chemicals ("ON THE ARTIFICIAL PRODUCTION OF UREA" Annalen der Physik und Chemie, 88, Leipzig.)

The most popular argument that creationists like to cite against results from modern origin of life research is that Pasteur demonstrated that the "spontaneous generation" theory was invalid. However, we should be quite clear that the Pasteur experiments showed that complex life forms do not form spontaneously. They did not address the origin of life as we currently understand the concept.

The growing interest in the search for extra-terrestrial life as fueled more productive research on OOL in the last 15 years than has ever been done in history. Iris Fry,
2000 "The Emergence of Life on Earth: A Historical and Scientific Overview" (Rutgers University Press) is the best general reader book available on the topic. It is eight years old, and a second edition is warranted to bring her presentation up to date. A bit more technical is J. William Schopf (editor), 2002 “Life’s Origin: The Beginnings of Biological Evolution” (University of California Press), but it is well worth the effort.

There are quite a list of specifics that go into origin of life research, and very few research groups go far with more than a few. Just to list the key areas as I see them: Argument:
1. The late Hadean Earth had a neutral to reduced atmosphere and ocean system, a shallow, hot crust and a UV rich, "cold" sun. Highly reduced oasis existed at hydrothermal vents and other mineral rich locations,
2. Under those conditions, phospholipids, amino acids, nucleic bases, and pentoses readily form (augmented by extraterrestrial sources such as cometary delivery) and are concentrated by freezing and evaporation as well as mineral surface plating, and encapsulation,
3. Amino acids spontaneously form short (8 to 20 aa’s) racemic peptides, and random RNAs with as few as 2 types of nucleic bases have enzymatic activity. Spontaneous phospholipid vesicles sequester these peptides as transmembrane pores, and along with enzymatic RNAs plated to mineral grains such as montmorillonite, calcite, and metal sulfides.
4. Electron potential differences are exploited from transmembrane pores to form adenine triphosphate, establishing the first metabolism,
5. These ancient first cells were racemic, using both L- and D- amino acids because they were readily available,
6. Biological and geochemical events reduced the availability of D- aa's,
7. These ancient cells evolved racemases to maintain/sustain their existing metabolic pathways as attested by L- to D- amino acid racemases found even in humans. Ergo: The chirality "problem" in OOL isn't a problem.


1) Composition of the Hadean/early Archean atmosphere.

The key references here are:

Feng Tian, Owen B. Toon, Alexander A. Pavlov, and H. De Sterck
2005 "Hydrogen-Rich Early Earth Atmosphere" Science 13 May 2005; 308: 1014-1017; published online 7 April

Genda, Hidenori & Abe, Yutaka
2003 “Survival of a proto-atmosphere through the stage of giant impacts: the mechanical aspects” Icarus 164, 149-162 (2003).

Holland, Heinrich D.
1984 The Chemical Evolution of the Atmoshphere and Oceans, Princeton Series in Geochemistry Princeton University Press

Holland, Heinrich D.
1999 “When did the Earth’s atmosphere become oxic? A Reply.” The Geochemical News #100: 20-22 (see Ohmoto 1997 )

Kasting, J. F., J. L. Siefert,
2002 “Life and the Evolution of Earth's Atmosphere” Science 296:1066

Pepin, R. O.
1997 "Evolution of Earth's Noble Gases: Consequences of Assuming Hydrodynamic Loss Driven by Giant Impact" Icarus 126, 148-156 (1997).

Tian, Feng , Owen B. Toon, Alexander A. Pavlov, and H. De Sterck
2005 "A Hydrogen-Rich Early Earth Atmosphere" Science 13 May; 308: 1014-1017; published online 7 April 2005

Wilde, Simon A., John W. Valley, William H. Peck, Collin M. Graham
2001 “Evidence from detrital zircons for the existance of contenental crust and oceans on Earth 4.4 Gyr ago” Nature (letters) Vol 409:175-181


There are others, but anyone reading those above will get the basics. The result is that there was a reducing atmosphere, and ocean system with highly reducing oases. A recent paper:

Rosing, Minik T. and Robert Frei
2003 U-rich Archaean sea-floor sediments from Greenland – indications of >3700 Ma oxygenic photosynthesis" Earth and Planetary Science Letters, online 6 December 03

presents data that suggest there were very early oxygenic life forms in marine basins that most likely (to me anyway) were wiped out.

So, with a reduced atmosphere and ocean system, a shallow, hot crust and a UV rich, "cold" sun, we can ask the next question which is,

2) What was the source for "organic" molecules?

The classic paper was of course Stanley Miller's 1953 paper

Miller, Stanley L.,
1953 “A Production of Amino Acids Under Possible Primitive Earth Conditions” Science vol. 117:528-529

With a bit more information included in:

Miller, Stanley, Harold C. Urey
1959 “Organic Compound Synthesis on the Primitive Earth” Science vol 139 Num 3370: 254-251

Miller showed that a very simple set up that mimicked some key asspects of the early Earth could rapidly produce amino acids, among other things.

This result has been one of the most often repeated (and confirmed) experiments I have ever encountered. In spite of this, creationists regularly claim that it is invalid. Jonathan Wells, a fellow of the creationist "Discovery Institute" claims to have refuted the Miller/Urey experiment (and all of what he called Darwinist "icons." Wells himself has been exposed as a very shallow thinker.

But, the atmosphere is not the only synthesis location. For example

Amend, J. P. , E. L. Shock
1998 “Energetics of Amino Acid Synthesis in Hydrothermal Ecosystems” Science Volume 281, number 5383, Issue of 11 Sep , pp. 1659-1662.

Blank, J.G. Gregory H. Miller, Michael J. Ahrens, Randall E. Winans
2001 “Experimental shock chemistry of aqueous amino acid solutions and the cometary delivery of prebiotic compounds” Origins of Life and Evolution of the Biosphere 31(1-2):15-51, Feb-Apr

Chyba, Christopher F., Paul J. Thomas, Leigh Brookshaw, Carl Sagan
1990 "Cometary Delivery of Organic Molecules to the Early Earth" Science Vol. 249:366-373

Engel, Michael H., Bartholomew Nagy,
1982 "Distribution and Enantiomeric Composition of Amino Acids in the Murchison Meteorite", Nature , 296, April 29, , p. 838.

Matthews CN.
1992 Hydrogen cyanide polymerization: a preferred cosmochemical pathway. J. Br. Interplanet Soc. 45(1):43-8

Schoonen, Martin A. A., Yong Xu
2001 “Nitrogen Reduction Under Hydrothrmal Vent Conditions: Implications for the Prebiotic Synthesis of C-H-O-N Compounds” Astrobiology 1:133-142

Creationist liars also like to insist that without a reducing atmosphere, there could be no amino acid production. I think it was totally fitting that the last publication of Stanley Miller, 55 years after his ground breaking article, demonstrated that under a neutral atmosphere, or even with trace free oxygen, ample amino acids could form in the presence of common minerals such as calcite.

H. James Cleaves & John H. Chalmers & Antonio Lazcano & Stanley L. Miller & Jeffrey L. Bada 2008 "A Reassessment of Prebiotic Organic Synthesis in Neutral Planetary Atmospheres" Orig Life Evol Biosph 38:105-115

So amino acids are easy and plentiful on a pre-life (abiotic) Earth.

But, we need more than just amino acids- sugars, nucleic acids, and lipids are also needed. I'll take those next.

Let's see.. I guess this is

2a) amino acids
2.b) sugars

Why do we need sugars? Well, the biggest reason is that without five carbon sugar our building life form can't make a "memory" like RNA or DNA. I'll get to the details later. First, where are the sugars?

Weber AL.
1997 Prebiotic amino acid thioester synthesis: thiol-dependent amino acid synthesis from formose substrates (formaldehyde and glycolaldehyde) and ammonia. Origins of Life and Evolution of the Biosphere 28: 259-270.

{I know the title says "amino acid" but sugar is in there. Hint: formose is a kind of sugar.}

Cooper, George, Novelle Kimmich, Warren Belisle, Josh Sarinana, Katrina Brabham, Laurence Garrel
2001 Carbonaceous meteorites as a source of sugar-related organic compounds for the early Earth Nature 414, 879 - 883 (20 Dec 2001) Letters to Nature

Cody, George D., Nabil Z. Boctor, Timothy R. Filley, Robert M. Hazen, James H. Scott, Anurag Sharma, Hatten S. Yoder Jr.
2000 “Primordial Carbonylated Iron-Sulfur Compounds and the Synthesis of Pyruvate” Science v.289 : 1337-1340

Sephton, Mark A.
2001 Meteoritics: Life's sweet beginnings? Nature 414, 857 - 858 (20 Dec ) News and Views

Ricardo, A., Carrigan, M. A., Olcott, A. N., Benner, S. A.
2004 "Borate Minerals Stabilize Ribose" Science January 9; 303: 196 (in Brevia)

Shapiro, R. (1988). Prebiotic ribose synthesis: A critical review. Origins of Life and Evolution of the Biosphere 18: 71-85.

Weber, A. L. (2001). The sugar model: Catalysis by amines and amino acid products. Origins of Life and Evolution of the Biosphere 31: 71-86.

Krishnamurthy, R., Pitsch, S. & Arrhenius, G. 1999 Mineral induced formation of pentose-2,4-bisphosphates. Origins Life Evol. Biosph. 29, 139-152

Stanley Miller, and colleagues suggested an earlier substitute for sugar in :

Lazcano, Antonio, Stanley L. Miller
1996 “The Origin and Early Evolution of Life: Prebiotic Chemistry, the Pre-RNA World, and Time” Cell vol 85:793-798

Nelson, K. E., M. Levy, S. L. Miller
2000 “Peptide nucleic acids rather than RNA may have been the first genetic molecule” PNAS-USA v.97, 3868-3871

There are many more articles, but the bottom line reads "We got sugar."

OK, I'll do nucleic acid bases next. There aren't many that are used on Earth, just five.

There are a large number of creationist's books and web sites that claim there is some huge stability problem with nucleic acid base synthesis. This is a nice demonstration of how creationists copy each other, since there are only a handful of creationists with the education to even understand what this means. None that I know of have actually done research in the directly relevant area. Their claims generally can be traced back to a legit scientist, Robert Shapiro. Two of his representative publications are:

Shapiro, Robert
1986 "Origins: A Skeptics Guide to the Creation of Life on Earth" New York: Summit Books

Shapiro, Robert
1999 Prebiotic Cytosine Synthesis: A Critical Analysis and Implications for the Origin of Life. Proceedings of the National Academy of Science 96 (8): 4396 *Side reactions make cytosine synthesis unlikely, but see

Nelson K.E., Robertson M.P., Levy M, Miller S.L.
2001 "Concentration by evaporation and the prebiotic synthesis of cytosine" Orig Life Evol Biosph Jun;31(3):221-229, which I think generalizes to other complex CHONSP molecules.

The 1986 Shapiro book is very out of date, and very popular with creationists. The 1999 Shapiro paper has also been answered to my satisfaction. Levy and Miller raise a question of their own in:

Levy, M and Miller, S.L.,
1998 The stability of the RNA bases: Implications for the origin of life, Proc. Natl. Acad. Sci. USA 95(14):7933–38,

But, like superior scientists, they answer the questions they raise.

The following are a selections of research articles that address the pre-biotic origin of nucleic acid bases:

For our fans following along at home, there are aspects of nucleoside synthesis in the earlier referenced papers as well.

(To follow when I get a bit more time)


So, we got plenty of nucleic acid bases.

2c) lipids.

Lipids are the stuff of membranes, they are what keeps inside in, and outside out. Today they are made by simple cells and moved up the food chain. So where did they come from 3.8 billion (or more) years ago?

Likely sources were meteors, and hydrothermal vents;

Deamer, D. W.
1985. Boundary structures are formed by organic components of the Murchison carbonaceous chondrite. Nature 317:792-794.

Deamer, D. W., and Pashley, R. M.
1989. Amphiphilic components of carbonaceous meteorites. Orig. Life Evol. Biosphere 19:21-33.

W. R. HARGREAVES, S. J. MULVIHILL & D. W. DEAMER
1977 “Synthesis of phospholipids and membranes in prebiotic conditions” Nature 266, 78 - 80 (03 March)

D.E. Epps, E. Sherwood, J. Eichberg, and J. Oro
1978 “Cyanamide Mediated Syntheses Under Plausible Primitive Earth Conditions: V. The Synthesis of Phosphatidic Acids” J. Mol. Evol. 11,279—292.

Rushdi, Ahmed I., Bernd R. T. Simoneit
2006 “Abiotic Condensation Synthesis of Glyceride Lipids and Wax Esters Under Simulated Hydrothermal Conditions” Origins of Life and Evolution of Biospheres Volume 36, Number 2: 93-108 / April,

Dworkin, Jason P., David W. Deamer, Scott A. Sandford, and Louis J. Allamandola
2001 “Self-assembling amphiphilic molecules: Synthesis in simulated interstellar/precometary ices” PNAS 98: 815-819

Pizzarello, Sandra, Yongsong Huang, Luann Becker, Robert J. Poreda, Ronald A. Nieman, George Cooper, Michael Williams
2001 “The Organic Content of the Tagish Lake Meteorite” Science, Vol. 293, Issue 5538, 2236-2239, September 21, 2001

Segre' D., Ben-Eli D. Deamer D. and Lancet D.
2001 “The Lipid World” Origins Life Evol. Biosphere 31, 119-145.

Bernd R.T. Simoneit, Ahmed I. Rushdi and David W. Deamer
2007 “Abiotic formation of acylglycerols under simulated hydrothermal conditions and self-assembly properties of such lipid products” Advances in Space Research
Volume 40, Issue 11, 2007, Pages 1649-1656


So now that we got 'em, what do they do once they are together on Earth?

They make things.

Martin M. Hanczyc, Shelly M. Fujikawa, and Jack W. Szostak
2003 Experimental Models of Primitive Cellular Compartments: Encapsulation, Growth, and Division Science October 24; 302: 618-622. (in Reports)

D.W. Deamer
1997 "The First Living Systems - A Bioenergetic Perspective," Microbiology and Molecular Biology Reviews, 61(2): 239; June

Chakrabarti, A.C., R.R. Breaker, G.F. Joyce, & D.W. Deamer
1994 Production of RNA by a Polymerase Protein Encapsulated within Phospho-Lipid Vesicles Journal of Molecular Evolution 39(6): 555-559 ( December)

Khvorova A, Kwak YG, Tamkun M, Majerfeld I, Yarus M.
1999. RNAs that bind and change the permeability of phospholipid membranes. Proceedings of the National Academy of the Sciences USA 96:10649-10654.

Yarus M.
1999. Boundaries for an RNA world. Current Opinion in Chemical Biology 3:260-267.

Walter P, Keenan R, Scmitz U.
2000. SRP-Where the RNA and membrane worlds meet. Science 287:1212-1213.



So far, we have amino acids, riobose and/or other 5 carbon sugar substitutes (pentoses), we have lipid membranes which encapsulate mineral particles and "organic" molecules. This is without any needed "interventions" and is purely the result of ordinary chemistry.

But, there are more things that need to happen before there is life on Earth.

Point 3) formation of complex systems

3a) Chirility

Pasteur discovered that most amino acids came in two forms which can be identified by how they refract light. We label theses L- (for levo or left) and D- (for dextro, or right). The interesting thing is that life on Earth uses the L form of amino acids, and hardly ever uses the D- form. A solution of just one form is called "chiral" and a mix of forms about 50/50 is called racimic. The kinds (L or D) are called enantomers.

The nucleic acid bases are organized along a sugar backbone. I mentioned earlier that these sugars are also found in L- and D- forms, only in this case life on Earth only uses the D- form.

Creationists like to present this as a profound mystery that is supposed to "prove" that they are correct. I want to mention a neat instance where both left and right amino acids are used in a living thing. It is very rare, but it does happen. Next time a creationist claims to be an "expert" and that amino acid chirality "proves" something supernatural, you can gob-smack-em. The protein is called Gramicidin A and it has 8 L-amino acids, 6 D-amino acids, and one glycine which is an amino acid that is neither L- or D- in its structure. I have found that even many biologists will bet an "adult beverage" that all proteins are exclusive L- amino acids.

Before we go forward another couple of basic chemical facts need to be added to the discussion. First, L- amino acids will randomly convert to D- amino acids over time, and D- forms will convert to L- forms. This is called "racemization" because eventually you will end up with equal amounts of L- and D- amino acids. The rate that this occurs at varies with the amino acid, and its surroundings. The fastest conversion happens to amino acid molecules all by themselves in hot water. Under cold, dry conditions when the amino acids are attached to one another, or better yet, if they are also attached to a mineral, racemization can be very slow. Very, very slow.

This means that if there is even a tiny advantage one way or the other, the favored form will become the dominant form. The advantage comes from a surprising direction: outer space.

Cronin, J. R. & Pizzarello, S.,
1999. Amino acid enantomer excesses in meteorites: Origin and significance. Advances in Space Research 23(2): 293-299.

Service, RF,
1999. Does life's handedness come from within? Science 286: 1282-1283.

Antonio Chrysostomou, T. M. Gledhill,1 François Ménard, J. H. Hough, Motohide
Tamura and Jeremy Bailey
2000 "Polarimetry of young stellar objects -III. Circular polarimetry of OMC-1" Monthly Notices of the Royal Astronomical Society Volume 312 Issue 1 Page 103 - February

Michael H. Engel and Bartholomew Nagy,
1982 "Distribution and Enantiomeric Composition of Amino Acids in the Murchison Meteorite", Nature , 296, April 29, , p. 838.

Jeremy Bailey, Antonio Chrysostomou, J. H. Hough, T. M. Gledhill, Alan McCall, Stuart Clark, François Ménard, and Motohide Tamura
1998 Circular Polarization in Star- Formation Regions: Implications for Biomolecular Homochirality Science 1998 July 31; 281: 672-674. (in Reports)

Chyba, Christopher F.
1997 Origins of life: A left-handed Solar System? Nature 389, 234- 235 (18 Sep 1997)

Engel, M. H., S. A. Macko
1997 Isotopic evidence for extraterrestrial non- racemic amino acids in the Murchison meteorite. Nature 389, 265 - 268 (18 Sep) Letters to Nature

That should do for that. The next question is can the advantage of L- amino acids be conserved in the formation of more complex molecules called "peptides?" Yep.

Schmidt, J. G., Nielsen, P. E. & Orgel, L. E. 1997 Enantiomeric cross-inhibition in the synthesis of oligonucleotides on a nonchiral template. J. Am. Chem. Soc. 119, 1494-1495

Saghatelion A, Yokobayashi Y, Soltani K,
Ghadiri MR,
2001"A chiroselective peptide replicator",
Nature 409: 797-51, Feb

Singleton, D A,& Vo, L K,
2002 “Enantioselective Synthsis without Discrete Optically Active Additives” J. Am. Chem. Soc. 124, 10010-10011

Yao Shao, Ghosh I, Zutshi R, Chmielewski J.
1998 Selective amplification by auto- and cross-catalysis in a replicating peptide system. Nature. Dec 3;396(6710):447-50.

And there seems to be other L- selction advantages as well. For example:

Hazen, R.M., T.R. Filley, and G.A. Goodfriend.
2001. Selective adsorption of L- and D-amino acids on calcite: Implications for biochemical homochirality. Proceedings of the National Academy of Sciences 98(May 8):5487.

So chirality doesn't seem to be a big problem. This is far different from the way creationists present this. They cite a few out of date reports and then falsely claim that chiral life is impossible by natural means.

But what about the nucleic acid bases? How did they get organized on a chiarl backbone? A new paper has just laid out the next step:

Ricardo, A., Carrigan, M. A., Olcott, A. N., Benner, S. A.
2004 "Borate Minerals Stabilize Ribose" Science January 9; 303: 196 (in Brevia)

Pizzarello, Sandra, Arthur L. Weber
2004 Prebiotic Amino Acids as Asymmetric Catalysts Science Vol 303, Issue 5661: 1151, 20 February 2004

It turns out that the selective advantage of L- amino acids will force the selection of D-ribose structured nucleic acids, and the whole reaction can proceed under common, natural conditions.

There are larger arguments for a racemic origin of life.
Edward Trifonov (2004) confirmed two ideas, that the earliest amino acids were those easiest to form abiotically, that codons and aa's organized contemporaneously to form short ogliomers (what he didn't cite was the notion that oligomers can form spontaneously, are "selected" merely by being stable, and that RNAs (or Lacanzo and Miller's PNAs) imprint and replicate "successful" short peptides.) Trifonov wrote, "The amino-acid chronology itself is a quintessence of natural simplicity and opportunism: use first those amino acids that are available. When done with all codons, take from those amino acids that have too many."

The fact is that there are a growing list of short proteins with D- aa's, (most of the ones I know of are bacterial membrane components but there are also examples from yeasts to humans). Add to this, most bacteria have evolved enzymes that convert L-aa's to D-aa's for the same Miller/prebiotic amino acids. Again even we humans have enzymes to use D-aa's.

To repeat the argument:
1. The late Hadean Earth had a neutral to reduced atmosphere and ocean system, a shallow, hot crust and a UV rich, "cold" sun. Highly reduced oasis existed at hydrothermal vents and other mineral rich locations,
2. Under those conditions, phospholipids, amino acids, nucleic bases, and pentoses readily form (augmented by extraterrestrial sources such as cometary delivery) and are concentrated by freezing and evaporation as well as mineral surface plating, and encapsulation,
3. Amino acids spontaneously form short (8 to 20 aa’s) racemic peptides, and random RNAs with as few as 2 types of nucleic bases have enzymatic activity. Spontaneous phospholipid vesicles sequester these peptides as transmembrane pores, and along with enzymatic RNAs plated to mineral grains such as montmorillonite, calcite, and metal sulfides.
4. Electron potential differences are exploited from transmembrane pores to form adenine triphosphate, establishing the first metabolism,
5. These ancient first cells were racemic, using both L- and D- amino acids because they were readily available,
6. Biological and geochemical events reduced the availability of D- aa's,
7. These ancient cells evolved racemases to maintain/sustain their existing metabolic pathways as attested by L- to D- amino acid racemases found even in humans. Ergo: The chirality "problem" in OOL isn't a problem.

Trifonov, Edward N. 2004 "The Triplet Code From First Principles" Journal of Biomolecular Structure & Dynamics, ISSN 0739-1102 Volume 22, Issue Number 1,

Babbitt PC, Mrachko GT, Hasson MS, Huisman GW, Kolter R, Ringe D, Petsko GA, Kenyon GL, Gerlt JA.
1995 "A functionally diverse enzyme superfamily that abstracts the alpha protons of carboxylic acids." Science. 1995 Feb 24;267(5201):1159-61.

Nathalie Chamond, Maira Goytia, Nicolas Coatnoan, Jean-Christophe Barale, Alain Cosson, Wim M. Degrave and Paola Minoprio
2005 "Trypanosoma cruzi proline racemases are involved in parasite differentiation and infectivity." Molecular Microbiology Volume 58 Issue 1 Page 46 - October 2005

Alexander Jilek, Christa Mollay, Christa Tippelt, Jacques Grassi , Giuseppina Mignogna, Johannes Müllegger, Veronika Sander, Christine Fehrer, Donatella Barra and Günther Kreil
2005 "Biosynthesis of a D-amino acid in peptide linkage by an enzyme from frog skin secretions" Published online before print March 9, 2005, PNAS | March 22, 2005 | vol. 102 | no. 12 | 4235-4239

Yamashita, Tatsuyuki, Ashiuchi, Makoto, Ohnishi, Kouhei, Kato, Shin'ichiro, Nagata, Shinji & Misono, Haruo
(2004) "Molecular identification of monomeric aspartate racemase from Bifidobacterium bifidum." European Journal of Biochemistry 271 (23-24), 4798-4803.

Ian G. Fotheringham, Stefan A. Bledig, and Paul P. Taylor
1998 "Characterization of the Genes Encoding D-Amino Acid Transaminase and Glutamate Racemase, Two D-Glutamate Biosynthetic Enzymes of Bacillus sphaericus ATCC 10208" Journal of Bacteriology, August 1998, p. 4319-4323, Vol. 180, No. 16

K. Y. Hwang, C.-S. Cho, S. S. Kim, K. Baek, S.-H. Kim, Y. G. Yu and Y. Cho
1999 "Crystallization and preliminary X-ray analysis of glutamate racemase from Aquifex pyrophilus, a hyperthermophilic bacterium" Acta Cryst. (1999). D55, 927-928


Well, we have all the pieces. Our planet was formed from massive collisions of planetoids that had undergone independent evolution and weathering which retained much of their atmospheres to add to the growing planet Earth. We have amino acids, sugars, nucleic acid bases, lipids and minerals under an anoxic to reducing atmosphere and ocean with a thin hot crust and a UV rich cold Sun. Plus, remember that the Moon is closer and orbiting faster producing massive tidal flows compared to modern times.

Will these combine to make any thing?

Yep, they sure will:

Ferris JP, Hill AR Jr, Liu R, and Orgel LE. (1996 May 2). Synthesis of long prebiotic oligomers on mineral surfaces [see comments] Nature, 381, 59-61.

Lee DH, Granja JR, Martinez JA, Severin K, Ghadri MR.
1996 “A self-replicating peptide.” Nature Aug 8;382(6591):525-8

A.C. Chakrabarti, R.R. Breaker, G.F. Joyce, & D.W. Deamer
1994 Production of RNA by a Polymerase Protein Encapsulated within Phospho-Lipid Vesicles Journal of Molecular Evolution 39(6): 555-559 (1994 December)

Smith, J.V.
1998 Biochemical evolution. I. Polymerization on internal, organophilic silica surfaces of dealuminated zeolites and feldspars Proceedings of the National Academy of Sciences of the United States of America 95(7): 3370-3375; March 31, 1998

Smith, J.V., Arnold, F.P., Parsons, I., Lee, M.R.
1999 “Biochemical evolution III: Polymerization on organophilic silica-rich surfaces, crystal- hemical modeling, formation of first cells, and geological clues” Proceedings of the National Academy of Sciences of the United States of America 96(7): 3479-3485; March 30, 1999

Blochl, Elisabeth, Martin Keller, Gunter Wächtershäuser , Karl Otto Stetter
1992 “Reactions depending on iron sulfide and linking geochemistry with biochemistry” PNAS-USA v.89: 8117-8120

Dyall, Sabrina D., Patricia J. Johnson
2000 “Origins of hydrogenosomes and mitochondria: evolution and organelle biogensis.” Current Opinion in Microbiology 3:404-411

Huber, Claudia, Gunter Wächtershäuser
1998 “Peptides by Activation of Amino Acids with CO on (Ni,Fe)S Surfaces: Implications for the Origin of Life” Science v.281: 670-672

Imai, E., Honda, H., Hatori, K., Brack, A. and Matsuno, K.
1999 “Elongation of oligopeptides in a simulated submarine hydrothermal system“ Science 283(5403):831–833.

Lee DH, Severin K, Yokobayashi Y, and Ghadiri MR,
1997 Emergence of symbiosis in peptide self- replication through a hypercyclic network. Nature, 390: 591-4

Ekland, EH, JW Szostak, and DP Bartel
1995 "Structurally complex and highly active RNA ligases derived from random RNA sequences" Science 21 July 1995: Vol. 269. no. 5222, pp. 364 - 370

Reader, J. S. and G. F. Joyce
2002 "A ribozyme composed of only two different nucleotides." Nature vol 420, pp 841-844.

Ponnamporuma, Cyril, Carl Sagan, Ruth Mariner
1963 “Synthesis of Adenosine Triphosphate Under Possible Primitive Earth Conditions” Reprinted front Nature, Vol. 199, No. 4890, pp. 121-126 (This is more of historic interest, but recall that ATP is the energy carrier for all cells.)

Someone in an email asked why I posted so many references.

There are several reasons. First, that is how science is done, we build on the work of others.

Second, when we use referenced data to make a point clear we state the source of our information up front. Anyone can read these papers. If they want, they can argue that I have misread the article, or that the article itself has been refuted by more up-to-date information.

Third, a common creationist claim is that there is no valid research on the origin of life, or that the research done is inconclusive. The references I have cited are evidence that these claims are false.

Fourth, except for some historical references, my sources are mostly less than 10 years old, and some are even less than 10 months old. This is in direct contrast to the selective use by creationist writers such as Jonathon Sarfati, or Jon Wells, who use a few out of date and refuted articles to puff up their nonsense.

So, there you have it.

Responding to Newspaper Editorials

I have cut back on posts to blogs, or BB sites in favor of replying directly in newspaper sites. It seems to me that there is a wider range of readers. Here is a comment I wrote this AM in response to former state Rep. Ken Mercer, now a member of the Texas State Board of Education. Mercer wrote an editorial in the San Antonio Express-News posted on-line 12/14/2008 8:48 CST. So far, the newspaper has not posted my comment.

“It is very interesting to read Mr. Mercer’s presentation of the Texas State Board of Education’s thinking about evolution. He immediately casts this as “ultra-liberals” versus “people of faith.” And I agree. He is clearly uninformed, even “willfully ignorant” as Apostle Paul might say, about the scientific and education issues. The only possible substance of his position is that of raw Rovian wedge issue politics. Mercer makes false and misleading claims about evolutionary theory. His use of “micro-“ and “macro-“ evolution are absurd, but typical of creationist polemics. If any freaks or monsters of Mercer’s imagination like a “dog-cat” existed, it would utterly DISPROVE evolutionary theory. We have direct evidence of new species emerging from old. This has been observed in nature, and in the laboratory. Only the willfully ignorant, or the politically motivated would say otherwise. Mercer then shifted to Ernst Haeckel. Haeckel was profoundly wrong in his theory of embryology. But, the actual historical record is that “Haeckel’s” drawings were largely the work of others- even by scientists who most loudly protested them. These are not “weaknesses in evolutionary theory.” I recommend to any honest person the recent biography of Haeckel by Robert J. Richards (2008 University of Chicago Press). Further, I have reviewed many recent high school biology textbooks, and when the contested illustrations were used it was as examples of a failed theory. As it happens, photographs are available that make the same case for common descent. The Piltdown hoax was not peer reviewed for “forty years,” as the actual “fossils” were kept away from critical examination. And, I must point out that it was scientists who uncovered the hoax- not politicians nor preachers. Since Mercer is so in favor of academic freedom, he will naturally halt his opposition to birth control, and medically accurate sex education for high school students. Unless that is he is a hypocrite. But at the end, I once again agree with Mercer, “An agenda that opposes both freedom of speech and academic freedom is unpatriotic, un-American, and unscientific.” And, I hope he changes his agenda soon. "

The lack of paragraphs is the defalt format of SA the site.

Up date: The comment was blocked due to an undocumented character limit. I posted it in three parts. This is the downside of newspaper comment sections- they are vary locally and are generally inconsistant.

Fuller, Sakar and Jones: ID v. Science

According to him (Fuller), Judge Jones incorrectly appealed to the motivation of scientific work to decide the Dover case against ID when he noted the religious motivations of the Dover school board as part of his reasoning. Here the Judge was clearly wrong and he has been equally strongly criticized for using the demarcation criteria that Fuller defends (Sarkar, forthcoming). Sahotra Sarkar

I have not read Fuller’s book, nor do I intend to. Consequently, I do not know if Sarkar has correctly represented Fuller’s position in the quote above, but we can take it as representing Sarkar’s opinion that Judge Jones inappropriately used the motivation of the Dover school board members as part of his decision. Sarkar is actually making two objections to Jones 2005, the second being the use of demarcation criteria in the section of the decision entitled 4. Whether ID is Science

There seems to be a curious misunderstanding by Sarkar of what the Judge is able to do in issuing a decision. He cannot draw from information not accessible to cross-examination. If one actually reads the trial transcripts, a great deal of discussion is about what is to become the case evidence. This is of greater importance that Sarkar and others seem to acknowledge because if something is not part of the trial record then it cannot be part of the decision (apart from stipulated “common knowledge” and prior law.)

Sarkar has first made the misinterpretation that Jones relied on the religious motivation of the Dover school board’s creationist members to introduce ID into the science classes to assess the scientific validity of ID. The statements of a school board member’s motivation were only used to evaluate the plaintiff’s argument regarding the endorsement test. Was the aim of the government (the school board) to promote science education, or was it to promote religion? The Judge clearly recognized that the aim was to promote a creationist religion. Beyond that, the question remained of whether ID was equally religious, or might it have scientific validity.

This question was examined from two points of view, one was the motivation and goals of the principle architects of ID; specifically Johnson, Behe and Dembski as well as the Discovery Institute Center for Renewal of Science and Culture. As always the Judge is limited the evidence admitted in the trial record. Jones correctly concluded that, “The evidence at trial demonstrates that ID is nothing less than the progeny of creationism,” and, “ID aspires to change the ground rules of science to make room for religion, specifically, beliefs consonant with a particular version of Christianity.” But, it was not in reference to whether or not ID is science, but to the question if “An Objective Observer Would Know that ID and Teaching About "Gaps" and "Problems" in Evolutionary Theory are Creationist, Religious Strategies that Evolved from Earlier Forms of Creationism.”?

Writing in the section “4. Whether ID is Science” Jones observed, “ID is predicated on supernatural causation, as we previously explained and as various expert testimony revealed. (17:96 (Padian); 2:35-36 (Miller); 14:62 (Alters)). ID takes a natural phenomenon and, instead of accepting or seeking a natural explanation, argues that the explanation is supernatural. (5:107 (Pennock)). Further support for the conclusion that ID is predicated on supernatural causation is found in the ID reference book to which ninth grade biology students are directed, Pandas. Pandas states, in pertinent part, as follows:

Darwinists object to the view of intelligent design because it does not give a natural cause explanation of how the various forms of life started in the first place. Intelligent design means that various forms of life began abruptly, through an intelligent agency, with their distinctive features already intact – fish with fins and scales, birds with feathers, beaks, and wings, etc.

P-11 at 99-100 (emphasis added). Stated another way, ID posits that animals did not evolve naturally through evolutionary means but were created abruptly by a non-natural, or supernatural, designer. Defendants' own expert witnesses acknowledged this point. (21:96-100 (Behe); P-718 at 696, 700 ("implausible that the designer is a natural entity"); 28:21-22 (Fuller) (". . . ID's rejection of naturalism and commitment to supernaturalism . . ."); 38:95-96 (Minnich) (ID does not exclude the possibility of a supernatural designer, including deities).

It is notable that defense experts' own mission, which mirrors that of the IDM itself, is to change the ground rules of science to allow supernatural causation of the natural world, which the Supreme Court in Edwards and the court in McLean correctly recognized as an inherently religious concept. Edwards, 482 U.S. at 591-92; McLean, 529 F. Supp. at 1267. First, defense expert Professor Fuller agreed that ID aspires to "change the ground rules" of science and lead defense expert Professor Behe admitted that his broadened definition of science, which encompasses ID, would also embrace astrology. (28:26 (Fuller); 21:37-42 (Behe)). Moreover, defense expert Professor Minnich acknowledged that for ID to be considered science, the ground rules of science have to be broadened to allow consideration of supernatural forces. (38:97 (Minnich)).”

Such a long quotation is needed to illustrate that Jones has not invented any “demarcation criteria” but is relying solely on the testimony and trial exhibits to examine if ID could be taught without introducing a religious component. While I might have titled that section “Whether ID is Strictly Science,” careful reading while attending to the fact that his is a legal proceeding and not a philosophy seminar makes it clear that Jones is asking an appropriate question and has properly used the trial evidence to answer it. Until Sarkar joins Fuller advocating the supernatural entities and magic are “science,” he has no criticism of the Kitzmiller decision regarding “demarcation criteria.” If he wishes to argue, it is with the expert witnesses and not Jones in any event.

This week in OOL

As an example of how fast the abiogenesis literature is growing, here are two articles from the Aug 15, 2008 issue of Science that are both of interest.

The first is on the late Archean redox state of the oceans:

Donald E. Canfield, Simon W. Poulton, Andrew H. Knoll, Guy M. Narbonne, Gerry Ross, Tatiana Goldberg, and Harald Strauss
2008 "Ferruginous Conditions Dominated Later Neoproterozoic Deep-Water Chemistry" Science 15 August 2008: 949-952.

"Low sulfur input caused the deeper ocean to become anoxic and rich in ferrous iron 750 million years ago, a reversal from the more oxidizing conditions of the previous 1 billion years."

Now this might not seem related to OOL research, but it is an intersting set of observations about the stratification of the oceans which will lead to better measurement of the deep ocean redox and sulfur/iron economies. This is of great significance to OOL.

The other article is;

T. R. Kulp, S. E. Hoeft, M. Asao, M. T. Madigan, J. T. Hollibaugh, J. C. Fisher, J. F. Stolz, C. W. Culbertson, L. G. Miller, and R. S. Oremland
2008 "Arsenic(III) Fuels Anoxygenic Photosynthesis in Hot Spring Biofilms from Mono Lake, California" Science 15 August 2008: 967-970.

"A primitive form of photosynthesis in which arsenic is the electron donor occurs in purple bacteria in a California lake, perhaps a relic of early life forms."

This is of more direct OOL interest, suggesting a new anoxic metabolism pathway.

WTF WDEF? Is CNN TBN or CBN?

There was a mindbreakingly bad news piece KARA FINNSTROM, working (apparently) for CNN, Los Angeles that was broadcast today by WDEF 12 of Chattanooga, Tennessee. This news splat was vaguely about the recent Federal Court decision in favor of the University of California. The UC and several individual professors were being sued by the ASSOCIATION OF CHRISTIAN SCHOOLS INTERNATIONAL, Calvary Chapel Christian School, and five Calvary student. Their goal was to force the University to grant credit for four courses offered by Calvary, and a biology course taught by Calvary Baptist School.

The WDEF story opened, “Can a private religious high school stress too much religion? A federal judge says yes, at least for students hoping to get into campuses like UCLA.”

Below is a review of the case drawn from the Court’s Decision. All quotations are from NO. CV 05-06242 SJO (MANx) “ORDER GRANTING DEFENDANTS' "MOTION FOR SUMMARY JUDGMENT ON PLAINTIFFS' AS-APPLIED CLAIMS" [Docket No. 172]. I encourage all interested parties to read an excellent piece of judicial writing. I take each rejected course in the order found there.

English, Course title: “Christianity and Morality in American Literature” This class was rejected by the University for several reasons- none of which were because it has a Christian bias. The objections included that the textbook, published by A Beka titled “Classics for Christians,” did not cover important writer’s key works, insisted on exclusive interpretations dictated by the textbook, and failed to teach critical reading skills. Further, the text is merely an "anthology of excerpts," which UC does not approve, no matter the content of the excerpts. From the UC Guidelines, "College-preparatory courses are expected to require students to read full-length works."

History, Course title: “Christianity's Influence on America” Text: Bob Jones University ("BJU") titled “United States History for Christian Schools.”

Professor James Given initially rejected this course because it failed to “teach critical thinking and modern historical analytic methods.” He wrote that the textbook, titled “United States History for Christian Schools” published by Bob Jones University ("BJU"), “… instructs that the Bible is the unerring source for analysis of historical events, attributes historical events to divine providence rather than analyzing human action, evaluates historical figures and their contributions based on their religious motivations or lack thereof and contains inadequate treatment of several major ethnic groups, women, and non-Christian religious groups.” University expert witness Professor Gary Nash found that “the text failed to encourage "historical thinking skills and analytical thinking" and failed to cover "major topics, themes, and components of United States history."

Calvary replied that an secondary textbook, “Pilgrims in Their Own Land: 500 Years of Religion in America,” was secular and taught all the materials sought by the University. However, they provided no evidence beyond mere assertion. The History expert employed for the trial by Calvary and the ACSI, Professor Paul Vitz, did “ … not refute Professor Given's and Professor Nash's conclusions that the text fails to teach historical analytic methods. Professor Vitz also does not opine that Defendants unreasonably rejected the course.”

Government, Course title: “Special Providence: Christianity and the American Republic” Textbook: “American Government for Christian Schools” BJU

University Government expert, Professor Mark Petracca concluded that the BJU Government text used “… as the principal text in a United States
Government course will not provide adequate preparation for study at UC." Professor Petracca wrote that this textbook made, “… many factual and empirical assertions that are not generally accepted among political scientists [or] historians and that are nevertheless not substantiated within the text by evidence." Notice that he is not claiming that a book cannot make these assertions, but when they are contradicted by general scholarship they must be supported by evidence.

World Religions (offered for History and elective credit): The proposed textbook, “World Religions” by Dan Halverson is not found on any major catalogs nor is the author known to have any scholarly publications in religion. Calvary failed to respond to the University’s request for correct publication information. Also, Calvary failed to respond to specific deficiencies in their course description. Nor did Calvary respond to the question of how the course treats the study of religion from the standpoint of scholarly inquiry. Professor Sharf, Director of Religious Studies at the University of California, Berkeley found that these problems were reasonable grounds to reject the course. The religion expert retained by Calvary and ACSI, Professor Daniel Guevara, offered no opinion specific to this course, or to the objections raised by the University.

Biology,

The course challenged was not offered by Calvary Chapel Christian School, but rather was taught by Calvary Baptist School. The textbook used was titled Biology: God's LivingCreation (A Beka).

In the initial review, UC Biology Professor Barbara Sawrey found that this textbook, “characterized religious doctrine as scientific evidence, included scientific inaccuracies, failed to encourage critical thinking, and took an "overall un-scientific approach to the subject matter." She wrote that, "judgment was based not on the fact that the textbooks contained religious references and viewpoints, but on [her] conclusion that [the texts] would not adequately teach
students the scientific principles, methods, and knowledge necessary for them to successfully study those subjects at UC." In fact, a number of private Christian schools have also rejected the A Beka book, and an alternate published by BJU because they fail to adequately prepare students to study biology beyond the high school level, and particularly failed to present evolutionary biology in a competent manner.

These concerns are also addressed in the University of California Position Statement on Science Courses: “The texts in question are primarily religious texts; science is secondary. . . . Courses that utilize these texts teach students that their conclusions must conform to the Bible, and that scientific material and methods are secondary. Students who [are] taught to discount the scientific process and the scientific conclusions validated by a wealth of scientific research are not being provided with an understanding of scientific principles expected by the UC faculty.”

Expert witness Professor Donald Kennedy wrote for the University that, “[b]y teaching students to reject scientific evidence and methodology whenever they might be inconsistent with the Bible . . . both texts fail to encourage critical thinking and the skills required for careful scientific analysis." Similarly, University Professor Francisco Ayala found that the texts "reject the methodology generally accepted in science, which relies on observation and experimentation and on the formulation of laws and theories that need to be tested rather than accepted on the basis of the Bible or any other authority."

The plaintiffs, Calvary and ACSI, hired Professor Michael Behe to serve as their Biology expert. Professor Behe is best know for his promotion of creationism in the form of “intelligent design.” He submitted to the Court that the BJU textbook he reviewed did “mention” the standard scientific topics for a biology course. However, it was notable that he did not address “how much detail or depth" the texts gave to this standard content.”

The court wrote, “Therefore, Professor Behe fails to refute one of Professor Kennedy's primary concerns that the nature of science, the theory of evolution, and critical thinking are not taught adequately.

Accordingly, there is no genuine issue of material fact as to this issue. Defendants had a rational basis for rejecting Calvary Baptist's proposed Biology course.”

This latter phrase is a bit of formal legalese and found throughout the Court’s Decision, “Accordingly, there is no genuine issue of material fact as to this issue. Defendants had a rational basis for rejecting Calvary's proposed _____ course.”

In this case it is not merely pro forma, but obviously appropriate and true.

Other views on Baugh's fake foot

I linked below to some of Baugh's supporters.

Glen J. Kuban has an excellent website devoted to the dinos and humans together nonsense. He has a new section on the latest Paluxy fraud, Here. Be sure to check out the rest of his site.

Playing footsy with the truth

I wish everyone would go and carefully read About High-resolution X-ray CT, hosted by The High-Resolution X-ray Computed Tomography Facility at The University of Texas at Austin (UTCT). In particular, read and look at the photos in the section titled, Beam Hardening.

Now, having done this, look at the photos in the PDF provided by Baugh supporter David Lines. It should be obvious that the "density changes" of this hoax are all due to beam hardening and natural layering of the slab. You should note that every CT slice has a shadow "density" that outlines the entire slab, even the open areas. This alone demonstrates that there is a severe problem with beam hardening.

If you have downloaded this image from David Lines you will see the natural layering of the slab, and that this was not disturbed by the tons of pressure supposedly applied by the "dinosaur" or the supposedly "human" foot prints. In fact, these multiple layers run unaltered through both "foot prints." If you look at the David Lines photo he labled, "Toe Detail" you will see that the carving of the "human toes" has penetrated through the top layer of the slab and partially into the second. This is obvious in the second, third and fifth "toes." These layers were equally undisturbed or mixed together by the so-called dinosaur. This is impossible if these were foot prints. There is a lower layer that is penetrated by the "ball" of the phony human print. This is also exposed in the phony dinosaur print. There is no distortion, or mixing. This is impossible if these were foot prints.

I pointed out yesterday that the areas I had thought to be acid bubbles were not. Instead, these superior photos make it obvious that the acid bubbling is obvious all over the "foot prints" but particularly in the ball of the fake human print. That entire area is covered in pocked marks typical of applied "patina."

The "toe detail" photo is also interesting becasue you can see the bottom of the "big toe." It has been commented on that the "big toe" seems to be oddly deep. In these new photos one can see that there is still some sort of broken, mixed matrix. I suspect that this is part of a natural feature in the slab, perhaps a root mold. You should also note that this is one of the only three places where the natural layering of the slab appears altered. I am becoming inclined to the possibility that the "human" print is a partial, heavily eroded dino track.

My most charitable interpretation is that this is a "pious fraud." That is to say, some natural depression, or even a partial dinosuar print, was "cleaned up" into what the manufacturers wanted. Actually though, I think this is merely a hoax perpetrated on Baugh. It is his promotion of this that is eqaully at fault.

Paleontologist? Dr. Jones?

Just for a chuckle I used Google on "Floyd Nolen Jones" +dinosaur, and my name in place of his.

I got more hits than Jones. Plus, most of his were merely because his name appeared in a bibliography for one of his bible tracts, with someone else's with "dinosaur" in their entry. Mine were mostly related to articles I have written about dinosaurs and creationism.

Just to be clear here, I am not a paleontologist- I am an archaeologist. Jones is not a paleontologist and he should not misrepresent himself that way. Jones is not a paleontologist and competent newspapers would not say that he was.

Baugh's Fake Foot, Round 2

I was planning to drop my attention from this hoax. Anyone capable of seeing the plain evidence has done so.

However, we are entering round two with the publication this morning of a new news article in the Mineral Wells Index.

Aug. 12, 2008

CT scans of empty space

David May of the Mineral Wells Index wrote in a recent article that the latest creationist hoax was authenticated by a medical CAT scan. Charles Myers, a radiologist looked at the images taken of the rock and stated that he thought the marks could have been produced by footsteps. Dr. Myers probably has little experience with the CT scanning of empty voids surrounded by hard material, unless he has scanned the heads of small town journalists. The result this produces is a bright outline along the edge of the void. This is called “beam hardening,” and described in considerable detail by an article hosted by The High-Resolution X-ray Computed Tomography Facility at The University of Texas at Austin (UTCT).

(Based on Ketcham, R.A. and Carlson, W.D., 2001. Acquisition, optimization and interpretation of X-ray computed tomographic imagery: Applications to the geosciences. Computers and Geosciences, 27, 381-400.)

The most commonly encountered artifact in CT scanning is beam hardening, which causes the edges of an object to appear brighter than the center, even if the material is the same throughout (Fig. 5a). The artifact derives its name from its underlying cause: the increase in mean X-ray energy, or "hardening" of the X-ray beam as it passes through the scanned object. Because lower-energy X-rays are attenuated more readily than higher-energy X-rays, a polychromatic beam passing through an object preferentially loses the lower-energy parts of its spectrum. The end result is a beam that, though diminished in overall intensity, has a higher average energy than the incident beam (Fig. 2). This also means that, as the beam passes through an object, the effective attenuation coefficient of any material diminishes, thus making short ray paths proportionally more attenuating than long ray paths. In X-ray CT images of sufficiently attenuating material, this process generally manifests itself as an artificial darkening at the center of long ray paths, and a corresponding brightening near the edges. In objects with roughly circular cross sections this process can cause the edge to appear brighter than the interior, but in irregular objects it is commonly difficult to differentiate between beam hardening artifacts and actual material variations.

Beam hardening can be a pernicious artifact because it changes the CT value of a material (or void) depending upon its location in an image. Thus, the attempt to utilize a single CT number range to identify and quantify the extent of a particular material can become problematic. One measure that is sometimes taken is to remove the outer edges of the image and analyze only the center. Although this technique removes the worst part of the problem, the artifact is continuous and thus even subsets of the image are affected. Furthermore, if the cross-sectional area of the object changes from slice to slice, the extent of the beam-hardening artifact also changes, making such a strategy prone to error.

The bright areas in the published medical CT scan of Baugh’s rock which appear around the “foot prints” and between the “toes” are obviously the result of beam hardening, and not compression. Looking at the central portion of the photo from the Mineral Wells Index July 29th article, we can plainly see that there was in fact no compression at all. In the blowup section below, I have outlined the multiple sedimentary layers that are easily visible. Had this object really shown a dinosaur’s footprint, or a human’s these layers would have been erased. Instead they obviously extend across the slab, and are even continuous from the “dinosaur” to the “human” marks. There is only one possible way that this could have happened, and that is by carving out the rock. It could not possibly ever have happened by compression.



These sediment layers are also obviously of different density which is why they appear in the photo as discrete lines. This variation in density is well known to further add to X-ray beam hardening. This has created the second misleading CT image published by the Mineral Wells Index.

Fake footprints, fake paleontologist?


David May in his Aug. 11th newspaper story quotes from a purported paleontologist, Floyd Nolen Jones. The Rev. Jones has doctoral degrees in theology and education, and unlike Carl Baugh’s multiple “doctorates” Jones attended accredited graduate schools. Dr. Jones also claims work experience in petroleum geology. It is this later work that justifies his identification as a paleontologist.

However, is it reasonable to still call Rev. Jones a paleontologist? Over 34 years ago after “resigning from his scientific vocation,” (Jones biography online at http://www.floydjones.org ) Jones devoted the rest of his life to the young earth creationism he still promotes. His 1993 dissertation was titled, “Chronology of the Old Testament: A Return to the Basics.” He should have subtitled it, “A return to the 1600s.” He has also written that the King James Bible is the only translation that is the Word of God, the others are all corrupted by Satan himself. Oh dear!

For over 34 years, Jones has not published a single article on paleontology. In fact, a search of available data bases and journals fails to return a single example of Jones ever publishing anything related to paleontology. Jones probably had taken some college courses on paleo, but to claim to actually be a paleontologist demands an active participation and contribution to paleontological study. There is no evidence that Jones has ever done this. The oil industry certainly does hire people in paleontology, particularly micropaleontology. This is the study of things like pollen, and tiny microscopic critters. There is no justification for Jones to call himself a paleontologist, and an ordinary sort of journalist knows these days how to use Google.

And actually folks, it doesn’t even need an expert to look at the photos and see these “footprints” are a hoax. Go out in the yard with the water hose. Take of your shoes. Do your own footprints. Now look again at those photos of Baugh's Rock.


But wait, there is more

David May is obviously pleased with his diminishment of our Nation’s collective intelligence. He wrote on Aug. 11th, “The Mineral Wells Index to date is the only news agency that has published information pertaining to the reported discovery…”

Not too surprisingly, this too was incorrect. There was a much more revealing article written by Bud Kennedy, of the Star-Telegram. Kennedy talked with Zana Douglas, a descendent of the family that discovered the famous Glen Rose dinosaur tracks nearly a century ago. She also described how her grandfather carved fake dinosaur tracks and even added human “footprints” to make them more interesting. She told Kennedy,

"My dad [Weldon Eakin] and my grandfather decided one day — I don’t know if it was to make money, or what — to start carving man tracks alongside the dinosaur tracks," said Douglas, 67 and now living near Houston.

They poured acid to make the fossils look like aged limestone, she said. They showed one "all over town" until they heard that a researcher from the Smithsonian Institution wanted to see the track.

"That worried my grandfather because he didn’t want anybody ever passing it off as real," she said. "So he and Daddy took it out and buried it."

Personally, her mentioning using acid to fake the aged appearance, which would also hide tool marks, was the most convincing information in Zana Douglas’s testimony since I had pointed out last week that this latest hoax had been treated with an acid wash. Her Granddaddy Adams was more honest it seems than today’s crop of footprint sculptors in Glen Rose.

August 13, 2008

I thought I might add a variation on the photo which shows more clearly that there was no distortion of the rock's natural stratification when these prints were made. The blue and red lines each trace a separate layer, and the green lines are probably the same. There are aditional layers as I showed the other day in the photo above.


Someone with better photo editing skill than I have might overlay the newly released CT scan of the "toes."

On the water

I was on the ocean yesterday, and had some Delicious results.



This was a 10 lb male dorado.



This was a 25 lb male Albacore Tuna. (The dog's name is Yoggie).

The fishing was slow over all. I only lost one fish (a larger albacore) when my reel momentarily locked up. We caught 11 albacore, 2 Yellowfin Tuna, 2 Yellowtail jack, and 41 dorado for 32 people fishing. Mine was the largest dorado, with the majority barely over 3 lbs. (I had a several of those but released them). The per pound cost of the meat was still well above market, 15 lbs of trimed meat for ~$300. The local fish market charges $10.

Carl Baugh's latest Fake

Carl Baugh of Glen Rose Texas is the proprietor of the Creation Evidence Museum. Baugh is best known for his unaccredited degrees and his many fraudulent evidences that humans and dinosaurs coexisted. His latest is the Alvis Delk Cretaceous Footprint.

Oh be still my fluttering heart.

From the famous scientific journal, the Mineral Wells Index, of Mineral Wells Texas we learned that the source of the fossil was, “Amateur archeologist and Stephenville, Texas, resident Alvis Delk, 72, shows a lime cast replica of the limestone rock he found in July 2000 near Glen Rose, Texas. Initially he kept the 140-pound because it contained a dinosaur footprint. Two months ago, he was brushing the stone and discovered a human footprint in the rock – partially beneath the dinosaur print. The actual stone is now in the possession of the Creation Evidence Museum in Glen Rose, Texas.”

Baugh wrote on his website that, “The fossil was transported to a professional laboratory where 800 X-rays were performed in a CT Scan procedure. Laboratory technicians verified compression and distribution features clearly seen in both prints, human and dinosaur. This removes any possibility that the prints were carved or altered. “

Baugh told the Mineral Wells Index that, “The compression lines, the density features, do show, and there is no way to fake that,” he said. “It is possible to carve a track in limestone. But there is no way to compress the material in the rock under the track. That is absolutely impossible. That’s why the CAT scans are so important.”

First of all, a medical CAT scan uses a lower energy beam than could be useful on a sandy limestone. That is why real paleontologists use industrial facilities. The University of Houston (added 8/15/08, this was inccorect- I was thinking of The University of Texas, Austin) has a laboratory that has many years of experience with just this type of analysis. This points to the next problem; a medical facility is not staffed by paleontologists or geophysicists. Baugh has no accredited degrees either. He wouldn't know "compression lines" from his own butt crack. However, you don't even need more than the photograph from the Mineral Wells Index, which was much higher resolution than from Baugh's website, to see that this is object is a fake.

I downloaded the photo at full resolution. If you closely examine the photo, you will easily see that there are sandy lenses in the rock; four are visible in the exposed rock between the "toes" of the dinosaur print. Now look at the "human print," particularly the area of the little toe. You will see (with a little magnification) that the top most layer is penetrated by the "toe" and not compressed, and the second layer is partially exposed. The same lens is exposed across the base of the four distal toes. This could not have happend unless the "toes" had been carved out of the rock.

Returning to the "dinosuar" print, there is no compression folding of the sandy layers between the toes which is interesting. First, there must have been if this were a legitimate track. However, there appears to me to be evidence of removal of material from between the central and the medial "toe" as well as along the top edge of the "track."

There also appears to be a patina coating the bottom of the basin. This has two interesting features. First, it is pealing and cracking. This is not appropriate to a real patina. Second, the patina appears in parts of the basin and not others, nor does it appear consistantly in the "human toe prints."

(If this were a video game walkthrough, I would place a big Warning: Cheat Follows ).

Here is how to fake a patina that will look like this fake fossil: Brush the surface with vinegar, and then sprinkle with baking powder followed by baking soda, and let dry. Repeat until you are happy with the results. This is not the only way, or even the best way. But it is simple, and will fool the average fool. Especially easy if they want to be fooled.

So, having spent a little bit more time on the photo of this fake, I feel that I understand a bit more about how it was produced. A legitimate dinosaur track was found and removed. Incompetent, unprofessional "Cleaning" damaged it. An parital overprint, or simple erosion depression was "improved" by adding "toes." The faked surfaces were smothed over with a simple kitchen concoction to make a "patina." Artifact fabricators next bury the fake for a year or two, or they smear it with fertilizer and leave it exposed. This helps weather the object and obscure tool marks.

Added later:

The bubble pops.

If you used the cheap kitchen patina method I mentioned above, there is the chance that the acid will create a gas bubble in a depression. This lifts the fake patina and is visable as little bumps, or they form pits.

I just enlarged the photo again, focused on the center toe of the "dinosaur." There are two obvious pits of broken bubbles created by a recently applied acid wash seen on the distal portion of the "track." Looking further, there is one more near the distal end of the medial toe.

This from the Smithsonian?

The Smithsonian has a "blog" called "The Gist." A recent item about the dinosaur "meat" controversy written by Hugh Powell has the following two sentences,

"They cracked the bone in half to make it fit, and Schweitzer noticed a goopy residue on the 65-million-year-old insides of the bone (see the Smithsonian story). Then this April, Schweitzer and her colleagues isolated a protein called collagen from the sample, analyzed it, and found striking similarities to the collagen of modern birds."

I am very disappointed in this misrepresentation of Schweitzer's work. There are at least five errors of fact;

The femur, MOR-1125, was broken due to weight issues not size, Schweitzer was not at the site, and the organic residue was not "goopy" or even visible to the naked eye. The article published in Science last April, Organ et al, had not "isolated a protein called collagen." Rather, they used BLAST searches to attempt a phylogenetic tree for prior data. These earlier data were still not the "protein called collagen." Rather, Asara et al (2007) analyzed seven small peptide fragments they attributed to collagen. They may or may not have been correct in that attribution. The fragments, even if from collagen, are from very highly conserved regions of that molecule.



"Protein Sequences from Mastodon and Tyrannosaurus Rex Revealed by Mass Spectrometry" (John M. Asara, Mary H. Schweitzer, Lisa M. Freimark, Matthew Phillips, Lewis C. Cantley, Science 13 April 2007: Vol. 316. no. 5822, pp. 280 - 285

"Molecular Phylogenetics of Mastodon and Tyrannosaurus rex" (Chris L. Organ, Mary H. Schweitzer, Wenxia Zheng, Lisa M. Freimark, Lewis C. Cantley, and John M. Asara, Science 25 April 2008 320: 499)

Have Your Yellowcake and Eat It Too
Christopher Merola
Friday, July 11, 2008
On July 5, 2008, the Associated Press (AP) released a story titled:
Secret U.S. mission hauls uranium from Iraq. The opening paragraph is
as follows:

Bull shit Bull shit Bull shit

From a reliable source:

The vast Tuwaitha site has been bombed repeatedly since 1981, when Israeli warplanes destroyed the Osirak nuclear reactor there before it could be used to make weapons-grade uranium. American warplanes bombed the site in 1991 during the first gulf war.

After the American invasion in 2003, Tuwaitha was looted. Barrels used to store the yellowcake were stolen and sold to local people, who used them to store water and food and to wash clothes, according to a report by the atomic energy agency.

From The New York Times, U.S. Helps Remove Uranium From Iraq

In the original AP report, there was a thorough discussion of the origins of the shipped material.

I forget that I read sources not in the news media, particularly in the science journals, which fills in background information.

Here are excerpts from a brief item in a recent Science magazine issue: (Science 11 July 2008: Vol. 321. no. 5886, p. 188)

NUCLEAR CONTROL:
Iraq Embarks on Demolition of Saddam-Era Nuclear Labs
Richard Stone

When Ronald Chesser arrived by military helicopter at the Al-Tuwaitha Nuclear Center south of Baghdad on 2 July, the radioecologist from Texas Tech University in Lubbock was thrilled by what he saw. Few would consider it a pretty sight: dozens of buildings riddled with radioactivity, some reduced to rubble by Coalition bombs. What filled Chesser with hope was a clutch of trailers, including one for decontamination showers, freshly installed for an urgent task: the dismantlement of a sprawling facility where physicists in the 1970s and 1980s tried in vain to build an atomic bomb for Saddam Hussein. "I thought, 'Wow, this is really going to work,' " Chesser says.

The dismantlement of Saddam's main nuclear weapons complex comes after years of painstaking preparation. A big challenge lies in its chaotic state. Tuwaitha's two research reactors and other key buildings, including facilities for fuel fabrication and plutonium separation, were bombed in 1981 and 1991. During the Iraq war in April 2003, Tuwaitha staff fled and the center was looted. Unaware of the health risk, people hauled off scores of drums of uranium oxide extract--dumping some of the "yellowcake" on the grounds of Tuwaitha--to use the barrels for catching rain or washing clothes. By June, nuclear inspectors had accounted for virtually all the missing drums and uranium. Two years later, Chesser, Phillips, and Brenda Rodgers of Texas Tech, with Iraq's science ministry, surveyed schools in villages near Tuwaitha. "To our relief, we found they were not contaminated," says Phillips. In a secret operation described earlier this week by the Associated Press, U.S. forces last April removed 550 tons of yellowcake from Tuwaitha. Iraq sold the uranium to a Canadian company for processing into fuel for civilian power reactors.

To pinpoint where looters had dumped yellowcake and where bombs had dispersed radioactive materials, Phillips and Chesser, with colleagues from Iraq and Ukraine, in 2005 analyzed more than 400 soil samples, compiling a rough map of radioactivity at the 9300-hectare Tuwaitha compound. The contamination map laid the groundwork for a U.K.-funded "Train and Engage" program that the Texas Tech duo ran last month for 27 Iraqi scientists, including several former weaponeers.

A major part of the project is the decontamination of the Active Metallurgy Testing Laboratory (LAMA) designed to extract enriched uranium from fuel rods and handle radioisotopes. As it turned out, the LAMA was only used for a single experiment, and is only lightly contaminated. Still the effort will take a crew of 50 a year and a half to finish work on the rubble filled 62,000 square meters complex, (equal to six football fields).

The AP article was also clear regarding the aging and deteriorated condition of many of the containers that were used to store the tons of yellowcake already in Iraq in the 1980s. When the current Bush administration was insisting that there was an active nuclear weapon program, and that Iraq was seeking to purchase uranium "yellowcake" ore, they knew fully well that there were already many tons of unprocessed material in Iraq and that Iraq had no possible means to process what they already had.

Sadam Hussain was a secular, and even anti-relegious sect dictator installed and supported by the Raygun and early Bush administration. What religious afiliation Sadam Hussain and his political machine had were opposed to the Shia (think Northern Ireland Catholics and Protestants). The Shia, and especially the Saudi Wahhabi are the major supporters of al-Qaeda.

None of this matters in regard to the Bush regime lying about Sadam Hussain trying to buy uranium ore, and exposing an undercover CIA agent for political gain. Iraq was not trying to buy what they already had. Iraq could not process what they already had because the labs had been blown to crap by the Israelis and then us- 1981 (Israel) and from 1991 until 2000 the US.

Processing details that were "Top Secret" in the 1960 were public knowledge in the 1970s because it was realized that the "cat was out of the bag" generally, and that the engineering details were more difficult than the theory anyway.

So there are just a few problems:

*We knew that there was radioactive material already located there.

Right, and we knew that they couldn't process it, and didn't need any more than they had.

*We knew there was the ambition to generate weapons with it because they tried in the past.

I have the ambition to be a billionare and live forever- ambition is meaningless without the means to achive your goals.

*We knew there were bunkers but didn't know where they fully were or what was going on inside them

We had been bombing the bunkers regularly for years, and knew fully well that nothing was going on in them.

*We also knew that Saddam was not abiding by the rules set by the UN

Actually, Sudam's Iraq was obeying UN resolutions be
tter than the Bush White House obeys Congressional subpoenas, and the Constitution.

*Muslim terrorists displayed a willingness on their part to attack our country directly in New York by the virtue of the attack itself.

None of which had the slightest thing to do with Iraq. The Saudi Wahhabi are the major supporters of al-Qaeda, the Shia are the major opponents of Israel. Conservative Christian terrorists had displayed a willingness to attack in Oklahoma City- Should we begin a saturation bombing of Texas, or Montana? I don't think so. Moderate and Liberal Muslims are just as certain that the radicals are not "true Muslims" as you will probably view the Christians terrorists.

Uranium is highly soluble in water in the presence of oxygen forming "yellowcake" or U3O8. In of itself, yellowcake poses a minor radiological threat from short exposures, but the dust could be inhaled which could cause serious lung disease. Raw ore is ground to a fine mesh and then leeched with either acidic (most commonly), or a strong alkali water solution. The leeched fluid is neutralized and evaporated to yield the "yellowcake."

Reading popular press accounts, you might have the idea that yellowcake is weapon ready, which is nonsense. The uranium oxide must be further processed just to make it into a fissionable fuel. This is a long and difficult effort. Then, spent fuel must be reprocessed to produce highly enriched weapons grade uranium (around 85% U-235). The bulk of the US weapons material was produced with a gas centrifuge technology from spent fuel rods from the Savanna River Plant in Akin, South Carolina. The SRP is just across the Savanna River from Augusta Georgia. I have visited the plant to discuss nuclear chemistry projects, and was invited to give a talk to their staff on the scientific application of reactor produced thermal neutrons in archaeology and geochemistry.

U-235 is only about 0.7% of the uranium in naturally occurring ores, and weapon grade material must be at a bare minimum 20%, and will generally be closer to 85%. Since I didn't recall the numbers off hand, I did some checking. At 85% enrichment, you would need about 50 kilograms of fissionable material to make a bomb. At reasonable recovery efficiencies, a few tons of yellowcake should be enough raw material to make a single low yield weapon. But first you need to build a working gas centrifuge plant, a heavy water reactor, and a reprocessing plant.

This should ring a few alarms. The Iraqis had ~ 550 tons of yellowcake, and they had had them since the early 1980s. They had at that time nuclear ambitions which the Israelis had bombed into history. The bombing was repeated in 1991, and from then on any related construction was closely monitored. They had no processing facility, they never had any processing facility.

The article that was the opening post above claimed that

"Somehow, that
slogan loses its credibility now that 550 metric tons of Saddam's
yellowcake, used for nuclear weapon enrichment, has been discovered and
shipped to Canada for its new use as nuclear energy."

There are some obvious mistakes in that sentence. First, "yellowcake" is not a weapon, or even a reactor fuel. Second, it was not being used in Iraq for any purpose because Iraq had no facility capable of processing it. Third, any use of yellowcake peaceful or otherwise entails enrichment- yellowcake cannot be used to enrich anything itself. Finally, Bush and his minions did lie when they claimed that Iraq was attempting to purchase yellowcake- they already had tons of the stuff that they couldn't use anyway. Bush and his surrogates presented a nonexistant buy to pretend that this was a critical step forward in the Iraq nuclear program, when in fact they were fully aware that there had been tons of yellowcake in Iraq for decades. If any threat had been real, there was more than enough time for the Iraqis to have acted on it. Bush and his minions lied about the aluminum tubes Iraq wanted to import claiming that these were to build a gas centrifuge when they could not have been used in that manner. (Experts outside the political influence of the Bush gang identified the tubes as surface-to-air missile sleeves.)

As to the other nations with enrichment plants already in production, they are; Argentina, Brazil, China, France, Germany, India, Japan, the Netherlands, Pakistan, Russia, the United Kingdom and the United States. Israel in collaboration with the old South African regime and North Korea were long believed to have enrichment programs, but only N Korea has recently admitted theirs. Belgium, Iran, Italy and Spain hold an investment interest in the French Eurodif enrichment plant, with Iran's holding entitling it to 10% of the enriched uranium output. Iran are also developing their own processing plant, but it is not operational. Australia has also announced their plans to develop a national enrichment capability.

(Regarding my expertise, I held a radioisotopes production license from 1973 to 1978, and I last renewed it in 1982. I have several publications on the application of Neutron Activation Analysis in archaeological and geochemical research, and have been invited to various universities and other groups to lecture on these topics).

PS: Google Maps has enough resolution to give all the details needed to establish that the Iraqi nuclear effort was wasted just by the Google satellite data.

I know for a fact that the US intelligence agencies had better data than Google. (I was offered the job of analyzing 1980's CIA satellite data on the campfire locations of Siberian nomads. No kidding! Funny story.)

"Bubuah" Bush has trashed every single job he ever had. He and his gang dupped you guys into a disgusting slaughter of Iraqis, and triggered the deaths of over 4,000 Americans. This was supposed to be revenge for the deaths of ~3000 Americans (lots of foreign nationals died that day in September). The actual perpetrators of the 9/11 attacks are still at large (or dead with their victims). Gitmo torture victims are being freed, America's reputation is trashed and gas is $4.50 a gallon. Marine diesel is ~$5.59 in California this week. The Bush gang insisted that the Iraq war would be 'nearly' bloodless and pay for itself. We are in trillions of dollars of debt mostly owned by the Commmunist Chinese, and the British. The British is the most ironic- we fought a revolution only to be sold back, and by the "conservatives."


WHAT WILL IT TAKE FOR YOU PEOPLE TO WAKE UP?

Pseudoscientific Pap

This is another review I posted at the Amazon.com site, this one of Walt Brown's "In the Beginning"

This review is based on the online edition of the Seventh Edition of "In the Beginning" which is more recent than my print copy. It is one very long series of errors and misrepresentations. Brown, like many "creation scientists," cites and quotes many actual scientists lending an apparent connection between his work and reality. If a reader does not have the educational background, or time to personally read these citations, they might be fooled into thinking there is some support for Brown's wild ideas.

I'll take two examples as typical of Brown's disconnect from reality. In his "Frequently Asked Questions" section titled "68. Old DNA, Bacteria, and Proteins?" Brown cites Giuseppe Geraci et al., "Microbes in Rocks and Meteorites," (Rendiconti Accademia Nazionale dei Lincei, Vol. 12, No. 9, 2001, p. 51) for support of the notion that "fountains of the deep" (see Genesis 7:11) blew massive amounts of the earth into outer space. This article was published with a long list of objections and cautions that its conclusions were provisional, and that there were many doubts regarding methods used by the principal investigators. Brown ignores these cautions, nor does he note that over forty years of meteorite investigations have always found terrestrial contamination to be the source of microorganisms found in meteorites, e.g. "Bacterial Contamination of Some Carbonaceous Meteorites" J. ORO T. TORNABENE (1965 SCIENCE, VOL. 150, pg. 1047-1048). The probability of contamination increases in direct proportion to the amount of handeling the samples are subjected to under unsterile conditions. The two meteorite samples examined by Giuseppe Geraci had been recovered, handled and publicly displayed for many decades, one for over a century. Brown builds everything on this one error having ignored decades of related research.

In the same section, Brown claims that the discovery of "proteins, soft tissue, and blood compounds preserved in dinosaur bones" preclude an ancient earth. I have dealt with these topics at considerable length elsewhere, and the links to these articles are in the first comment below. In short, Brown's argument fails on this as well.

In a section on transitional fossils, Brown serves up massive numbers of out-of-context and manipulated "quotes." These are known as quotemines and most of those used by Brown are exposed in the "Quote Mine Project" maintained by the TalkOrigins Archive, which is dedicated to exposing the sort of creationist chicanery as Browns book.

Brown makes the statement, "If evolution happened, many other giant leaps must also have occurred: the first photosynthesis, cold-blooded to warm-blooded animals, floating marine plants to vascular plants, placental mammals to marsupials, egg-laying animals to animals that bear live young, insect metamorphosis, the transition of mammals to the sea (whales, dolphins, porpoises, seals, sea lions, and manatees), the transition of reptiles to the sea (plesiosaurs, ichthyosaurs), and on and on."

Lets just look at a few gross errors in that paragraph. First is the most obvious error regarding the supposed transition of "placental mammals to marsupials." Sorry Walt, it didn't happen that way. If you reverse it from marsupials to placental mammals you will be still wrong. The evolution of cyanobacteria and the evolutionary innovation of endosymbiosis lead directly to the evolution of photosynthesis, and while not complete, these must first be refuted scientifically before Brown can claim they cannot be completed. Then there is the question of sea mammals. Brown lumps three major groups, the Cetaceans (whales and allies), the Pinipeds (seals, walrus, sea lions) and the Sirenians (manatee, sea cow and dugong). Demanding a common group of fossils for these would be asinine. The transitional fossils for the cetaceans are the best known and the most accessible general reader source is from the laboratory of Dr. J. G. M. Thewissen, also an excellent source on the evolution of Sirenians. The known transitional fossils fall into six families, Indocetidae, Pakicetidae, Ambulocetidae, Remingtonocetidae, Protocetidae, Dorudontidae, and Basilosauridae. The transitional fossils of the Sirenians are less well studied with only about fifty specimens. None the less, the broad outline connecting the elephants, hippos, and manatees is known. The early transitional fossils for the pinipeds are the least well known, but one in which I have personal experience. The best fossil specimen in the world (over 90% complete) of the most likely ancestor of the pinipeds, Gomphotaria pugnax, was discovered by one of my former students and is curated by a museum where I was a director.

These basic errors show why engineers should not write about biology or paleontology- they are ignorant. It is for these reasons that I wish there were "negative" points I could award to Brown's pernicious book.


I would like to offer a few links to material I mentioned in my review;

Walt Brown's book is available on the web at
http://www.creationscience.com/onlinebook/index.html

Misrepresented quotes used by Walt Brown. You will find the entire quote, and a discussion;
http://www.talkorigins.org/faqs/quotes/mine/project.html

My articles refuting the "ancient proteins equal a young earth" error

"Dino-blood and the Young Earth"
http://www.talkorigins.org/faqs/dinosaur/blood.html

"Ancient Molecules and Modern Myths"
http://www.talkorigins.org/faqs/dinosaur/osteocalcin.html

"Dino Blood Redux"
http://www.talkorigins.org/faqs/dinosaur/flesh.html

The laboratory website of Professor Thewissen;
http://www.neoucom.edu/DEPTS/ANAT/Thewissen/

McCain and creationists

Republicans, Democrats Differ on Creationism

http://www.gallup.com/poll/108226/Republicans-Democrats-Differ-Creationism.aspx

Speaking as a liberal deomocrat, I am glad that the profiles of the Dems and independents are much closer to each other (at least this year). McCain is going to need the religious right more this year than ever, and I don’t think he will get them. I think they will stay home.

However, there is plenty of lefty antiscience woo to go around. Also, I have not seen any real science support anywhere from either party in Louisiana.

The gallup poll I linked also has a longitudinal graph that is very interesting. Note that the only real shift has been from “I don’t know” toward “Evolution only.” This was only a 5% shift at that. So, with 44% of Americans holding to the creationist line that humans were directly created by God in the last 10,000 years or less- we are truly and deeply screwed.

Unless you are an optimist.

Then, in spite of a right-wing dominated political landscape for the last 20+ years, and the highly publisized pro-creationist events such as the AiG creation museum opening, etc. most Americans have not shifted toward creationism in any significant numbers.

Pournelle III

while many “Intelligent Design Theorists” are in fact fundamentalist creationists, not all of them are, and some like the late Sir Fred Hoyle are not creationists at all.

Dawkins wrote, “All the leading intelligent design spokesmen are devout, and, when talking to the faithful, they drop the science-fiction fig leaf and expose themselves as the fundamentalist creationists they truly are.”

First of all, Fred Hoyle was never an “Intelligent Design Theorist,” nor is he in anyway referred to in the Dawkins editorial that I can see. In the candid moments I quoted above, the prominent ID proponents all reveal their true goals and opinions which are undistinguished from “scientific creationism.” In her Dover testimony, Prof. Barbara Forest demonstrated that the founding IDC textbook, “Of Pandas and People” had been simply altered by replacing “Creator” with “designer.” Available but not employed at the trial was an early manuscript where the deletion/insertion was incomplete and the neologism “cdesignproponentist.”It is a perfect literary “transitional fossil.” ID creationists hope to take advantage of language games in an applied post-modern relativism that is breath taking and to a degree successful.

Intelligent Design Creationism is unrelated to the natural theology of William Paley, as has been insisted on by William Dembski. Paley assumed the existence of a creator and sought in the expression of nature clues to the attributes of that deity. IDC assert that there is a method by which they can demonstrate that a deity exists, and all talk about space aliens and time travel is a smoke screen (references as above).

Pournelle wrote,

The panspermia hypothesis, which asserts that life originated on a planet other than Earth and was brought here by either natural or intelligently directed actions, is hardly ludicrous, has at least some unexplained evidence in its favor, and holding it as an hypothesis is hardly evidence of buffoonery. The late Robert Bussard was well known to believe in panspermia. Several of my science fiction novels make use of this hypothesis, and I have yet to see any definitive refutation.

There are two sorts of “panspermia” hypotheses. One might be called a “global” panspermia where life is ubiquitous wherever possible conditions exist, and that a feature of life is to transfer from one planetary system to another. There are two accessible books,“Rare Earth: Why Complex Life Is Uncommon in the Universe” by Peter Ward and Donald Brownlee, and “Life's Solution: Inevitable Humans in a Lonely Universe” by Simon Conway Morris. Even though neither take a positive view of the global panspermia idea, neither invoke magical creators nor argue that the existence of life implies a magical creator.

Another would be a “local” version where the ability of life as microorganisms to migrate is limited to single planetary systems. These do certainly provide possible tests and as such are scientific rather than religious. For example, here are three papers that examine this later version;

Hornbeck, Gerda et al
2001 “Protection of Bacterial Spores in Space, a Contribution to the Discussion on Panspermia” Origins of Life and Evolution of the Biosphere v.31(6):527-547

Kirchvink, Joseph, L, Benjamin P. Weiss
2001 "Mars, Panspermia, and the Origin Of Life: Where Did It All Begin?" Palaeontologia Electronica vol.4 No.2

Line, Martin A.
2002 "The Enigma of the Origin of Life and its Timing." Microbiology 148, 21-27

No matter how great a physicist Bussard was, this does not translate into an expert in biology, let alone the origin of life. This was the same problem Hoyle had, success in one area of science does not simply leap into other areas. Another good example would be physicist Lee Spetner, who authored “Not By Chance: Shattering the Modern Theory of Evolution” (1997, New York: The Judaica Press). This problem is suffered by Hubert Yockey to the extent that, were I still a professor of medicine, I would propose defining a “Yockey syndrome” characterized by the delusion that a physicist knows all things about all things and even if there was knowledge they lacked it would be trivial. The acute form is expressed by physicists writing about biology.

The “directed” seeding of life by natural intelligent beings has no empirical literature that I know of, and has no part to play in IDC at any rate. (This is not mere repetition as Pournelle has objected to earlier- the references have been given). Forty years ago I wrote a story (influenced by “Childhoods End”) in which an accident in a fusion experiment transported a hapless fellow back to the Hadean. His internal population of bacteria and viruses started life on earth. My high school teacher liked it, as far as I recall. But this was fiction, and outside of a creative writing class, has no place in school curricula.

My favorite part of the Dover Panda’s Trial begins with Eric Rothschild asking Mike Behe, “We're going to look at chapter 8 of that book (“Why Intelligent Design Fails”), if you could pull up the chapter heading there? And it's titled “The Explanatory Filter, Archaeology and Forensics,” and it's written by somebody named Gary S. Hurd. Are you familiar with Dr. Hurd?”

It ends with Rothschild’s comment, “Science fiction movies are not science, are they, Professor Behe?”

Pournelle II

Novelist and social observer Jerry Pournelle had recently posted his objections and rejections to an editorial written by Richard Dawkins. The original piece by Dawkins was a protest against his mangled interview for the creationist movie “Expelled.”

Pournelle ignores or is ignorant of the context of the Dawkins piece. None the less, while Pournelle repeatedly says he does not want to argue the Intelligent Design creationism case, he reiterates it and ignores any counter arguments and even implied there were none.

On the other hand, intelligent design theorists do have scientific critiques of Natural Selection’s ability to explain what we observe. I have already alluded to one, irreducible complexity, which states that certain organism or organs are simply too complex to have arisen in stages.

The refutations of Behe’s notion of “irreducible complexity” begin with its definition.

Behe's definition of IC is”

A single system composed of several well-matched, interacting parts that contribute to the basic function of the system, wherein the removal of any one of the parts causes the system to effectively cease functioning. (Darwin's Black Box, pg. 39)

Unnoticed by Behe was a deadly flaw, the existence of something that is IC under that definition merely loses a particular function if damaged. It says nothing about how such an entity or process could have evolved by the combinations of otherwise functional entities. Behe’s favorite example is a five part mousetrap. But, every single part has independent functions, and multiple functions exist for various combinations of these individual parts. This is well known in biology as “Cooption” the common occurrence when one, or a group of genes is duplicated, and then modified resulting in new functions. One concrete example is the evolution of nylonase. Only a slightly more difficult notion is scaffolding; two or more existing processes are combined and the result is then simplified by reduction in the number of steps or parts. We see biological examples most easily in the reduction of genes in obligate parasites, and the most famous example is endosymbiosis.

So, then Behe then tried to salvage his cherry with a redifinition;

An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway.

Note well that Behe has abandoned the entire core of his original argument regarding function. In its place he has substituted “necessary-but-unselected mutations.” Real science has shown that even mildly unfavorable mutations are commonly transmitted; ie the unselected steps in Beheland. We have known this for decades. These unselected, or even detrimental mutations are then material available for recombination, and the expression of new complex functional genomes.

Behe’s latest is to take a page from Bill Dembski and adopt a probability argument. In the just released “The Edge of Evolution,” he claimed that there is a limit on the number of genetic changes, mutations, that can be allowed. His example is protein to protein binding, and Behe insisted that more than two sites just cannot evolve independently. This is of course nonsense. A very well illustrated and easy to follow refutation is available from Ian Musgrave, “ Behe versus ribonuclease; the origin and evolution of protein-protein binding sites” http://pandasthumb.org/archives/2008/04/behe-versus-rib.html

Another of Behe’s arguments in “The Edge of Evolution” bites the dust with the recent publication from Richard Lenski’s research group at the Michigan State University. (Z.D. Blount, C.Z. Borland, and R.E. Lenski, "Historical Contingency and the Evolution of a Key Innovation in an Experimental Population of Escherichia coli." PNAS). Carl Zimmer’s “Microcosm: E. coli and the New Science of Life” (Pantheon, May 6, 2008), places this research in the context of broader scientific questions. An easy to understand presentation of their most recent article is available at “A New Step In Evolution.”

http://scienceblogs.com/loom/2008/06/02/a_new_step_in_evolution.php

Jerry Pournelle posted a very poor bit of work Gods, Earthlings, and Intelligent Design” on June 13, 2008. Pournelle was reacting to an opinion piece in the Los Angles Times by Richard Dawkins. I don't say that Pournelle was ‘responding’ because that implies his writing was related to what Dawkins had written - he was merely reacting.

Pournell began,

I don’t usually get into the “Intelligent Design” argument, because I don’t have a lot to add to it; but once in a while poseurs like Professor Richard Dawkins jump into the fray with such outrageous aplomb that I feel compelled to answer. See here for his latest.

All that is clear from reading Pournelle’s item is that he does not like Richard Dawkins. And judged from this article, he correctly acknowledges not having “a lot to add” to the discussion of intelligent design creationism versus science. I have yet to finish reading any Dawkins book I have started, and I find his evangelical atheism tedious. But I am an activist in the Evo/creato conflict. I have contributed to the National Center for Science Education Reports and such internet sites as the TalkOrigns Archive, and I co-founded the popular Panda’s Thumb site. I was also a contributing author to “Why Intelligent Design Fails: A scientific critique of the new creationism” (2004 Rutgers University Press). My chapter in that book, “The Explanatory Filter, Archaeology and Forensics” was featured as part of Mike Behe’s cross-examination in the famous Dover “Panda’s” trial.

There are certainly problems with Dawkins’ piece, particularly his theological argument that a “simple god” could not have created a complex universe. Scientific cosmology has proposed that “simple” rules govern the behavior of matter and energy, and that as Dawkins must agree, these simple rules control biological life and evolution as well. If simple rules can lead to humans impregnating virgins (a sadly common unplanned occurrence), why couldn’t a simple god manage?

Pournelle’s attack on Dawkins ends up reading as an argument for ID creationism, and not a very good one. Take his use of a quote from the LA Times, “Intelligent design ‘theorists’ (a misnomer, for they have no theory) often use the alien scenario to distance themselves from old-style creationists: “For all we know, the designer might be an alien from outer space.” This attempt to fend off accusations of unconstitutionally importing religion into science classes is lame and disingenuous. All the leading intelligent design spokesmen are devout, and, when talking to the faithful, they drop the science-fiction fig leaf and expose themselves as the fundamentalist creationists they truly are.”

Pournelle claims this is typical of Dawkins and “also egregiously wrong.” What?? It is exactly correct.

1) There is no ID theory, 2) ID proponents do use the “aliens or time travelers could be the designer/creator” claim as a way to obscure their intimate connection to “scientific creationism,” and fundamentalism, 3) when speaking to religious fundamentalists the ID proponents are very clear in repudiating the “outer space” claim and acknowledge their religious motivation – supernatural creationism by the Judeo-Christian god.

Let's look at some statements by some principle ID proponents.

First, Philip Johnson:

“Our strategy has been to change the subject a bit so that we can get the issue of intelligent design, which really means the reality of God, before the academic world and into the schools.” Date: January 10, 2003. Source: American Family Radio

Michael Behe:

“Our intelligence depends critically on physical structures in the brain which are irreducibly complex. Extrapolating from this sample of one, it may be that all possible natural designers require irreducibly complex structures which themselves were designed. If so, then at some point a supernatural designer must get into the picture. I myself find this line of reasoning persuasive. In my estimation, although possible in a broadly permissive sense, it is not plausible that the original intelligent agent is a natural entity. … Thus, in my judgment it is implausible that the designer is a natural entity." (Reply to My Critics)

And three from William Dembski:

"Indeed, intelligent design is just the Logos theology of John’s Gospel restated in the idiom of information theory." 1999 “Signs of Intelligence,” Touchstone Magazine.

"My thesis is that all disciplines find their completion in Christ and cannot be properly understood apart from Christ." William Dembski, 'Intelligent Design', p 206

“…but let’s admit that our aim, as proponents of intelligent design, is to beat naturalistic evolution, and the scientific materialism that undergirds it, back to the Stone Age. “DEALING WITH THE BACKLASH AGAINST INTELLIGENT DESIGN version 1.1, April 14, 2004”

But, it turns out that Pournelle has not read what Dawkins wrote. Pournelle reads “Begin with the last sentence: that only fundamentalist creationists assert the possibility of evolution influenced by aliens from outer space.” In the LA Times item, Dawkins clearly discussed this “outer space” notion as presented by Francis Crick and Leslie Orgel and makes no inference regarding any religious motivation. Dawkins is referring to ID creationists as fundamentalists. Dawkins observes that ID creationists do not seriously argue the space alien idea.

This is such a gross misreading of what Dawkins wrote that I wonder what is his problem. Is it that Pournelle dislikes Dawkins to the extent that he cannot even look for a legitimate failing, but grasps at the first thing he can distort? Or does he actually support ID creationism and throws up a strawman argument to burn? Or, has he never bothered to learn what ID creationism is about and lack any basis of opinion?

If the later, I recommend some reading;

Pro ID creationism

Behe, Michael
2007 The Edge of Evolution. New York: Free Press

Dembski, William
1999 Intelligent Design: The Bridge Between Science and Religion. Downers Grove, IL: InterVarsity

_______
2002. No Free Lunch. Why Specified Complexity Cannot Be Purchased Without Intelligence. Lanham, Maryland: Rowman & Littlefield Publishers.

Johnson, Phillip E.
1993 Darwin on Trial, 2nd Edition. Downers Grove, IL: InterVarsity Press

Moreland, J. P. (ed.)
1994 The Creation Hypothesis: Scientific Evidence for the Intelligent Designer. Downers Grove, IL: InterVarsity Press

Pro science

Barbara Carroll Forrest, Paul R. Gross
2004 Creationism's Trojan Horse: The Wedge of Intelligent Design. Oxford University Press

Mark Perakh
2003 Unintelligent Design. New York: Prometheus Press

Matt Young, Taner Edis (Editors),
2004 Why Intelligent Design Fails: A Scientific Critique of the New Creationism. Rutgers University Press

And of course the decision in the Kitzmiller v. Dover trial.