Faunal Taphonomy

This is a slightly updated version of a web page I made for Valeri Craigle of the Spencer S. Eccles Health Sciences Library at the University of Utah. Original funding was provided by a grant from the National Library of Medicine, Grant #1 G08 LM05684-01A1.

Valeri created a significant resource for Forensic Anthropology that was used by researchers, criminal investigators, and students around the world. Unfortunately, short-sighted administrators prevented site maintenance after expiration of the grant, and have not even supported it as a static resource on their server. The page was archived at:
https://archive.ph/TE1me

 

I have added additional photographs, and text, but have tried to leave the page "dated."

I was personally honored to be associated with the project. I have also been involved with criminal investigations I can now identify (2013);

Faunal Taphonomy

One aspect of archaeological faunal analysis is determining the origins of recovered bone. The analysis of the processes which modify bone is called taphonomy, and is also of interest to forensic scientists as an aid to the investigation of homicides. Since 1989, Saddleback College students directed by Dr. Gary Hurd have studied the residue of deer predation by mountain lions. In the west, the major scavenger, or secondary predator, of the deer carcass is the coyote.

(The author (right) is assisting Duggin Wroe collecting DNA samples from a young male mountain lion. The animal was tagged and released See; Beier P, Barrett RH. The Cougar in the Santa Ana Mountain Range, California. Final Report, Orange County Cooperative Mountain Lion Study. University of California, Berkeley, CA, Management DoFaR; 1993 file:///C:/Users/Gary/AppData/Local/Temp/DicksonandBeier2002.pdf).


There are several features of whole carcass changes that are worth noting. Forelimbs are generally the first anatomical unit to become disarticulated, followed by the hind limbs. the likelihood of removal is directly related to the degree of competition among scavengers at the carcass. There is a tendency towards lateralized bone consumption most easily observed in the bone loss from the ribs, and the lateral processes of the vertebrae.

Unlike the reports available for human carcasses, the deer skull is rarely relocated away from the primary kill site. The primary predator of the deer in the top photo was a mountain lion. The second animal was killed by an automobile. In that example, there was bone modification due to impact.

Trampling damage and tooth scaring on a deer scapula caused by coyote puppies. Puppies are weaned in the late spring-early summer. The adults return to their den with parts of carcasses for the puppies to teeth on, and wean. Tooth marks are limited to scoring. The foraging range for the coyotes will obviously vary depending on quality of the habitat. Note the polish on high spots from grasses, and pubbie saliva. The primary predator is unknown.

Above is a slide showing trampling damage on a deer ulna. These marks were produced by predators moving the bone against stones. They lack parallel marks on the obverse of the bone found from tooth scoring, and are often rotated from a common origin.


Tooth scaring on deer bone; puncture with a radiating fracture (left: ulna), and compression (right: humerus).

Carrying damage to a deer metapoidal (cannon bone) caused by a coyote. These marks are diagnosed by parallel sets, spacing (appropriate to coyote dentition), and corresponding tooth mark sets on the obverse of the bone. These are particularly common on long bones, and sometimes show a "stepped" feature caused by parts of the limb snagging against brush.

Long bone splinters recovered from a coyote "bone yard" following a fuel rich wildfire. Notice that there is variation in the degree of burning which ranges from charred to calcined. Bone buried beneath as little as 4 cm of silt will be unburnt.


Here is a list of our papers on taphonomy with student co-authors, and presenting information;

1996 "Raptor Prey Bone Accumulations from a Nest Area." G. S. Hurd, M. S. Pyatt. Southern California Academy of Science,

1996 "Deer Bone Accumulations from Mountain Lion Kills" Rick Travis  and G. S. Hurd. Southern California Academy of Science,

1998 "Carnivore Modification of Deer Bone" Steve McCormick,  G. S. Hurd. Society for Californian Archaeology.

1998 "Bone Modification and Deposition by Raptors" Mike Pyatt, Melissa Pryor, Gary Hurd.  Society for Californian Archaeology.

1998 "Rockshelter Deposition of Insect Remains By Fox and Mouse" Matt Ritter, Gary Hurd.  Society for Californian Archaeology.

1998 "Fish Bone Deposition by Coyote" Karl Allwerdt, Gary S. Hurd. Society for Californian Archaeology.

1998 "Primary and Secondary Predation Patterns of Avian Bone," Ken Reddell, G. S. Hurd, Society for Californian Archaeology).

FORENSIC CASES

September 1998

Advisement to Judy Suchey, Orange County Forensic Anthropologist, taphonomy of scattered skeletal remains in a rural setting. During that on-site study, discovery of a clandestine grave and subsequent excavation of the grave site. Orange County Coroner Case # 98-0574OMU.

Since this case is so old, I think I can add a bit:
A Rancho Mission Viejo cowboy (legit - horse, hat, the whole deal) found a pelvis, a femur, and some odds and ends.

Professor Judy Suchey, CSU Fullerton, identified that the pelvis and femur were human from an adult male. I pointed the deputies to the coyote tooth marks from adults when they ravaged the body. And then the ones from the puppies teething and weaning on the L public bone.

The deputies were losing interest. I could imagine them thinking "Is this NatGeo, or a murder investigation?"

Then I pointed to some other marks, and said, "That is from a 38 cal bullet." Now they were interested. And when I pointed to some other marks and said, "That mark is from a 9mm hollow point."

And they were thrilled.

Back to the puppies- they told us that the body was dumped in late June or early July.

We found those bullet fragments when we excavated the burial site, and coyote den site. Also the victim's clothes helped ID the victim.

April 2000

Expert Witness Certification by the Supreme Court of the State of Tennessee. Knox
County Criminal Court Case No. 68318. Taphonomic analysis of human remains
from a homicide.

My best professional complement ever was related to this forensic taphonomy contract.

I received a phone call in April 2000 from a woman who was a Public Defender in Knoxville Tennessee. She asked if I was the Doctor Hurd who was a forensic bone expert, and if I would work on a defense team.

I replied Yes, I would work for investigators, or defense as the scientific results from me would be the same either way. But, I added, the best forensic taphonomist in the WORLD was William Bass https://en.wikipedia.org/wiki/William_M._Bass , and he was “just down the street” from her.

She replied that Prof. Bass was already involved as the Prosecution’s expert witness.

I said, “Then you are screwed. I read Bass. He does not read me. If I disagreed with him on a technical issue, I would assume I am wrong.”

She laughed and continued, “The prosecution hired Dr. Bass only to identify the sex of the victim.”

I was confused, and mentioned that that was crazy. “A Junior High kid could do that after they had “health” class.” And her answer was that the prosecution had hired Bass to keep him from helping her client’s defense.

“Well then I on the job, and I expect we will win.”

She laughed some more and said, “It was Prof. Bass that gave me your name.”

December 2016

Expert analyst and physical anthropology defense consultant. Matthew Nardi, Wailuku HI

96793, defense counsel for Steven Capobianco.  Trial concluded Dec. 2016.

Rev. Adrian Miller, Part 1

Rev Adrian Miller is a vicar in Norfolk serving in Norwich Diocese, ordained in 2006. He is a Young Earth Creationist (YEC) and a member of the British Creationist Society for 13 years, long before he joined the priesthood. He recently published an article in the house journal of the British Creationist Society that was republished on-line as “Why Won't Creationists Just Give Up?“ originally from "Origins 54," the magazine of the Biblical Creationist Society.

Rev. Miller goes on at some length, but the opening eight reasons, his “Headline Reasons” seem enough to sink his enterprise. Miller summarized what he thinks he has said;

“All in all, there are good theological, philosophical, sociological, biological, geological, cosmological, anthropological, epistemological, missional, spiritual and scientific reasons why we creationists won't just give up.”

So, Miller presents himself as prepared for a universal defense of creationist cant against all the sciences and philosophy, theology, and “spirituality.” Miller will need to distinguish his version of spirituality from the commercial variants represented by Tarot Card readers, and Miss Dionne Warwick’s television “Psychic Friends Network.” And then he will need to justify his spirituality against that of probably more pious, and chaste, and poor Buddhist or Hindu monks and priests. In fact, I doubt that Miller can honestly boast of his superior “spirituality” contrasted with the thousands of Christian Clergy who have signed the “Clergy Letter Project.”

One of Miller’s opening reasons to believe in YEC is,

”Because we recognise the importance of revelation in our approach to knowing.”

The Rev. Miller wants us to believe that the voices in his head are God speaking to him, and that Miller is competent to transmit these voices to us perfectly and without any interpretive bias. However, in modern psychiatry we know that we can give you a pill to make the voices go away, and that there are other pills that will bring them back. This alone makes the voices of revelation highly suspect. In modern psychology we have learned that no individual is capable of totally unbiased anything, our cognition is the result of neural architecture, as that this is altered by experience, and culture.

If not the voices in his head, then voices in some dead guy’s head, which in the specific case of the Bible were “spoken” to a near savage. These ‘revelations’ were then; in cultures, and in languages only poorly known, translated and edited and re-translated and re-edited for thousands of years. That is all that a claim for the validity of “revelation” can mean. So, we must ask the Reverend if the act of translation, redacting and editing have over the millennia been also the subject of “revelation?” Is the Bible evolving? Is there a continuing revelation, or is mankind’s direct communion with God dead? Is biblical exegesis dead? How can you deny the fact of an evolving creation if you can grasp the fact of an evolving ‘revelation?”

Creationists like Rev. Miller like to hate Charles Darwin. In fact, Miller later makes the assertion that Darwin was inspired by Satan. Darwin was far kinder to men like Miller. Describing how he had only with great reluctance abandoned his orthodox Christian beliefs, Darwin wrote,

“The question then continually rose before my mind and would not be banished,—is it credible that if God were now to make a revelation to the Hindoos, would he permit it to be connected with the belief in Vishnu, Siva, &c., as Christianity is connected with the Old Testament. This appeared to me utterly incredible.” (Autobiography, 1958, pg, 86-87, Original publication 1910, written 1882).

But what if…

What if the Bible is really Revelation? What if the Bible is to be believed with the fervor and literalness of someone like Rev. Miller? Then the Bible fails to support his creationism as well, because the Bible clearly and firmly teaches that the Creation is equally valid as the Revelation, and that it is not new. First consider, Psalm 19:

1 The heavens are telling of the glory of God;
And their expanse is declaring the work of His hands.
2 Day to day pours forth speech,
And night to night reveals knowledge. (New American Standard Bible)

The Creation, the physical universe is a testament. It reveals the work of God, and (if read literally) it to reveals God’s nature. This theme is extended in Psalm 85 which reads, “11 “Truth springs from the earth; and righteousness looks down from heaven” (NASB). The Hebrew word used here for "truth," emet, basically means “certainty and dependability.” So, in the Revelation of the Bible which Rev. Miller professes, the Earth itself is attested as the source of truth, of “certainty” and “dependability.”

Are we really to pay attention to the physical creation? Ask Job. Job challenges doubters of God, “Ask the animals, they will teach you, or the birds of the air, and they will tell you; or speak to the earth, and it will teach you, or let the fish of the sea inform you.” — Job 12:7-8. How could this be if the sciences, particularly as all these sciences evoked by Job, Rev. Miller rejects as inspired by Satan? (Miller will falsely claim that there is a special “Creation Science” without the difficult cosmology problems like billions of years since the Big Bang, or the formation of the solar system. Miller will also deny the physical evidence from geology, paleontology, biology and anthropology).

Some of the most obvious Bible verses that illustrated an understanding of the unity of man and nature are in the book of Ecclesiastes. Eccles. 9:11 “I returned, and saw under the sun, that the race is not to the swift, nor the battle to the strong, neither yet bread to the wise, nor yet riches to men of understanding, nor yet favour to men of skill; but time and chance happeneth to them all.” (KJV)

The race is not always to the swift, otherwise a fast predator would totally destroy the prey. The predator would then obviously die without prey. The race is "not always to the swift!" And then to add, "but time and chance happeneth to them all." is just too perfect a summation of evolutionary gradualism I have ever read! What brilliant biblical "evidences" for evolution. Exactly what creationists like Rev. Miller deny is the action of “time and chance.” And yet they are instructed by their Bible that these are significant factors in the evolution of life on Earth.

Another fact that creationists like Miller like to avoid is that humans are directly linked to all life on Earth. They prefer to imagine that they are “special’ in the eyes of the biblical God. After all, humans are set apart from mere animals according to some readings of Genesis. But, in Eccl 3:18-20 “I said to myself concerning the sons of men, "God has surely tested them in order for them to see that they are but beasts." For the fate of the sons of men and the fate of beasts is the same. As one dies so dies the other; indeed, they all have the same breath and there is no advantage for man over beast, for all is vanity. All go to the same place. All came from the dust and all return to the dust. (NASU)” The specific reference in Eccl 3:19-20 to “breath,” and to “dust” relates back to Genesis where humanity is specially created in Genesis 2:7.

So far, Rev. Miller's Revelation is in opposition to his Creationism. We will next examine Rev. Miller's creationist dogmas about Genesis in the light of the New Testament.

How I spent my morning

An article caught my eye this morning titled, “They’re ba-ack, creationists launch new attack on public education” written by Walter Pierce for The Independent Weekly of Lafayette, Louisiana. In an excellent brief item Mr. Pierce gave a synopsis of LA House Bill 580, a backdoor for religious fundamentalism to be taught in Louisiana’s public schools. Go see the article for the details.

As usual, I found the comments made by readers even more interesting than the original article. Two creationists stood out, and demanded replies. Their original comments are below followed by my relies;

written by JAT , June 14, 2011 - 01:10 pm

What is wrong with teaching creation. Is your science that you teach proven. Each day, new archeaological digs prove the bible correct. The information that is taught to our kids is so sub par to the rest of the world. We continue to drop the standards instead of raising them to push our kids. We do not need more scholars studying the problem. Start doing something about it. That is what is wrong with America.

written by Bob D. , June 14, 2011 - 06:43 pm

Darwin’s theory of evolution is false. The operative word is theory. There are many scholarly papers that show this theory to be false or weak and unproven at best. Basically there has never been a series of fossils that show anything ever evolved into something different. Even Darwin in later lifer stated that without such evidence his theory had no basis. Why is this theory ingrained as fact throughout our education system? Very simple – it would mean the secular humanists who have taken American education hostage would have to give consideration to the concept of God. Truly sad that America's education system suppresses critical thinking.

My relies;

written by Dr. Gary Hurd , June 15, 2011 - 08:24 am

In the comments to Mr. Pierce's news item, several creationists have made the same old errors of fact, and reasoning that were popularly refuted decades ago.

Taking Bob D. as a fine example of the breed, he began with an assertion as if it were fact, and then confused the meaning of “theory” with “just a guess.” Darwin’s original contributions to evolutionary theory were 1) common descent, and 2) natural selection. He later added entire books adding the concepts of 3) co-evolution (1862 fertilization of orchids by insects), and 4) behavioral selection (1871 “The descent of man, and selection in relation to sex”). In each of these contributions Darwin has been demonstrated by over a century of experiment and observation to have been correct. Darwin’s ideas about the specific mechanics of heredity were entirely wrong which was not entirely surprising as he (like most of his contemporaries) missed the significance of Gregor Mendel’s research on plant genetics.

written by Dr. Gary Hurd , June 15, 2011 - 08:58 am

Bob D. went on to deny that there is fossils evidence for speciation, particularly what is called “gradualism.” Paleontologist Steven Gould made a career for himself making the similar claim. Gould was not rejecting evolution, but arguing that the rate of evolutionary change was not constant. Darwin had already anticipated this, and had not himself thought that the rate of would be constant. However, we do indeed have long sequences which do show gradual transitions in morphology from one species into others. But these are best preserved in the microscopic marine organisms called foramifera, and rarely excite the public. Similarly, we have long series of aquatic snails which show centuries of tiny variations which accumulated to form new species. But, fossils are a poor substitute for directly observed living species that have undergone evolutionary transitions to new species. I have collected a list of dozens of examples from the scientific literature and posted them to “Emergence of New Species” at http://stonesnbones.blogspot.c...ecies.html

written by Dr. Gary Hurd , June 15, 2011 - 09:18 am

Bob D.’s next error was, “Even Darwin in later lifer (sic) stated that without such evidence his theory had no basis.”

This is a mishmash of two creationist claims. One is based on Darwin’s statement in “The Origin of Species,” Chapter VI, “If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.” And the second “in later life” part is the echo of the “Lady Hope” fraud. Lady Hope was a British evangelist who falsely claimed, in great detail, how she attended Darwin on his deathbed in 1882, and led him to renounce science, and reconverted him to Christianity. This was a lie, as attested by Darwin’s wife Emma at the time, and later by his daughter Henrietta in 1922.

The fact is even if Darwin had come to doubt his work, it would not alter the validity of evolutionary theory in any way. The modern science of biology which Darwin contributed so much to is independently verified by observation and experiment, and not by personalities.

written by Dr. Gary Hurd , June 15, 2011 - 10:54 am

JAT makes some slightly different errors. They began with the claim that “new archaeological (sic) digs prove the bible correct.” I doubt that JAT reads archaeological journals, but I’ll make a few suggestions. (As a personal note, I am a professional archaeologist among other things). Here is a brief, easy to read news article; Andrew Lawler, “American Schools Of Oriental Research Annual Meeting: A Change of Biblical Proportions Strikes Mideast Archaeology” (Science 10 December 2010: Vol. 330 no. 6010 pp. 1472-1473). Basically, there has been precious little science in Biblical Archaeology since the first Christian missionary excavations in the 1800s. This has changed, beginning with the first ever systematic archaeological surveys conducted in post-1967 war Israel. For two book length reviews, a “prolegomenon” of sorts, see;

Dever, William
2001 “What Did the Biblical Writers Know & When Did They Know IT?: What Archaeology can tell us about the reality of ancient Israel” Grand Rapids: William B. Eerdmans Publishing Company

Finkelstein, Israel, Neil Silberman
2001 “The Bible Unearthed: Archaeology’s New Vision of Ancient Israel and the Origin of Its Sacred Texts” New York: The Free Press

These men have quite different ideas of how the Hebrew Bible, the “Old” Testament, can be employed in archaeological understanding, and historical reconstruction of the Ancient Mideast.

Many of the place names from the Bible and been located archaeologically, and this is the most common “proof” of the Bible offered by creationists. The Harry Potter books mention many real places, such as London. Finding London on a map does not “prove” that Harry Potter was a real boy wizard. What is archaeologically certain is that the claims that “digs prove the bible correct,” are nonsense invented to sell to the fundamentalist public.

written by Dr. Gary Hurd , June 15, 2011 - 11:26 am

JAT shows that they have no understanding at all of the educational trends in American public schools for the last three decades (the period my wife and I have been teachers). JAT wrote, “We continue to drop the standards instead of raising them to push our kids.”

Nothing could be farther from the truth. We have in fact raised criteria, and loaded the curriculum. Second graders in California (and most other states) are learning algebra today when 30 years ago it was just long division and fractions. The “pass” criteria for the National Assessment of Educational Achievement was just arbitrarily shifted from 50/50 to 66/33 automatically dropping ~17 percent of student scores into the “failure” range. The real truth is that selling standardized tests is annually a multibillion dollar drain on public education.

written by Dr. Gary Hurd , June 15, 2011 - 11:46 am

JAT and Bob D. finally converge on what they are really after; the imposition of fundamentalist Christian religious training by the government in public schools. America’s founders knew what a religious totalitarian state was like, and they knew the power the State could use to control the population if they were allowed to claim that God ordained their rules and powers.

written by Dr. Gary Hurd , June 15, 2011 - 12:12 pm
JAT and Bob D. finally converge on what they are really after; the imposition of fundamentalist Christian religious training by the government in public schools. America’s founders knew what a religious totalitarian state was like, and they knew the power the State could use to control the population if they were allowed to claim that God ordained their rules and powers.

Sadly, the far-right seems determined to undermine, and destroy the Nation they claim to love, and so many patriots died to create. As Sinclair Lewis wrote, “When fascism comes to America it will be wrapped in the flag and carrying a cross.” It is up to the real patriots to stop them before they can again enslave us.

Notes on Charles Darwin’s Education

Anyone wanting more detail on Darwin's education from childhood to his voyage on the HMS Beagle should read the Wikipedia article on Darwin's education. I have read it, and was excellent. It is exceptionally detailed, but very readable.

(This is more a draft than a finished piece. I'll poke bits and pieces in as they occur to me).

Darwin’s childhood education was at a classical school- much memorization of Greek and Latin, and some mathematics. He was also an avid collector of beetles, and minerals and studied the insect taxonomies of the time. (Darwin's facination with beetles returned when he was a Cambridge student). One of the significant early scientific experiences of Darwin's early life was the study of chemistry. As he wrote in his Autobiography, [page] 46 THE AUTOBIOGRAPHY OF CHARLES DARWIN 

"Towards the close of my school life, my brother worked hard at chemistry and made a fair laboratory with proper apparatus in the tool-house in the garden, and I was allowed to aid him as a servant in most of his experiments. He made all the gases and many compounds, and I read with care several books on chemistry, such as Henry and Parkes' Chemical Catechism. The subject interested me greatly, and we often used to go on working till rather late at night. This was the best part of my education at school, for it showed me practically the meaning of experimental science. The fact that we worked at chemistry somehow got known at school, and as it was an unprecedented fact, I was nick-named "Gas." I was also once publicly rebuked by the head-master, Dr. Butler, for thus wasting my time over such useless subjects; and he called me very unjustly a "poco curante,"(1) and as I did not understand what he meant it seemed to me a fearful reproach."

1) A "poco curane" is interested in small things, while being indifferent to important things.

His formal medical education began in Edinburgh. At the same time, 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. Darwin was admitted to Christ's College on 15th October 1827, gaining his BA on 26 February 1831, his MA in 1836 and an honorary doctorate in 1877. There is an interesting passage in Darwin's Autobiography (written originally just to his family) where he also discussed his study of the famous precursor to today's creationists, William Paley.

"In order to pass the B.A. examination, it was, also, necessary to get up Paley's Evidences of Christianity, & his Moral Philosophy. This was done in a thorough manner, & I am convinced that I could have written out the whole of the "Evidences" with perfect correctness, but not of course in the clear language of Paley. The logic of this book & as I may add of his "Natural Theology" gave me as much delight as did Euclid. The careful study of these works, without attempting to learn any part by rote, was the only part of the Academical Course which, as I then felt & as I still believe, was

pg30

of the least use to me in the education of my mind. I did not at that time trouble myself about Paley's premises; & taking these on trust I was charmed & convinced by the long line of argumentation."

But more significantly, Darwin became closely acquainted with the Revd John Stevens Henslow, Professor of Botany, and the Revd.s 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 1831 to 1836 was through the recommendation of Henslow. It was Sedgwick who sent Darwin off on the HMS Beagle with a copy of Charles Lyell’s Principles of Geology, which Darwin said, “Allowed me to see with the eyes of Hutton.”

In the three volumes of “Principles of Geology” (1830–33) Lyell, as noted by Darwin, was the chief promoter and advocate of the Uniformitarian theory proposed by James Hutton. Uniformitarianism founded scientific geology. (Lyell also proposed that species of animals came and went throughout the geological record). An example of how Darwin applied Hutton's uniformitarianism as expounded by Lyell, was when in 1835 Darwin experienced a massive earthquake on the coast of Chile. Darwin observed that in a few moments the local coastline had shifted three to six feet higher. Reasoning that similar forces over large amounts of time would have resulted in thousands of feet of movement, Darwin realized that marine shells found on mountain tops were not evidence of a global flood.

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. Darwin, C. R. 1837. "On certain areas of elevation and subsidence in the Pacific and Indian oceans, as deduced from the study of coral formations" [Read 31 May.] Proceedings of the Geological Society of London 2: 552-554. 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.

Gohau, G., 2010. Darwin the geologist: Between Lyell and von Buch. Comptes Rendus Biologies, 333(2), pp.95-98.
https://www.sciencedirect.com/science/article/pii/S1631069109002984


All of this preceded the publication of Darwin's theory of evolution, which he had begun working on while still at sea on the HMS Beagle.

I got lured....

I recently said I’d write replies to Rev. Miller, but I have been distracted by a real job offer. (Science, education, political bombshells- just my cupa’ And real money to go with the rest of the advantages).

And I have also got entrapped in a few Letters to the Editor debates. In one of these, a list of “questions that evolutionists cannot answer” was posted. Of course they were either incoherent, or trivial. The questions themselves turned out to be a cut-n-paste job from a creationist website, http://www.questionevolution.com/biology.html"> “Question Evolution: Biology.”

The website owner emailed me to say he was "to busy" to update, or respond, so my relies are below:

Voldad4life asked, “All you smarter-than-me people please answer these questions or dodge them as usual”

There are several problems with this, first being that if I direct you the answers to these questions; you will ignore the references and claim you are “unconvinced.” It is really a waste of time. Secondly, some of your questions are incoherent and cannot be answered. Thirdly, science does not have complete answers to every possible question, and I personally do not know every corner of every science; where I cannot answer a question you will loudly claim this “proves” scientists are wrong about everything and your superstition is True™.

Not all the questions are really that hard, but I doubt your honesty because I have debated with creationists for many years.

However, I have a free hour with nothing else to do, so here are a few remarks.

“How could wings have evolved? Or an eye?”

The obvious answer is the accumulation of small changes in form and function.

The specifics of eye are also straight forward. The chemistry of photoreceptors gives the first step, our eye’s photochemistry, the rhodopsins, began with bacterial photeodopsin. The primitive “eyes” of single celled organisms are merely areas with higher concentrations of photeodopsins which collect light energy. In the eyes of more advanced critters the light sensitive patch is made of multiple cells inside a shallow cup. There are about a dozen intermediate kinds of “eyes.” We know this because there are living examples of every one still used by some life form on Earth today. The famous example is the “box jelly,” which has 6 different eyes, and no brain.

Nilsson and Pelger,
1994 "A Pessimistic Estimate of the Time Required for an Eye to Evolve" Proceedings of the Royal Society 256: 53-58.

Dan-E. Nilsson, Lars Gislén, Melissa M. Coates, Charlotta Skogh & Anders Garm
2005 “Advanced optics in a jellyfish eye” Nature 435, 201-205 (12 May), doi:10.1038/nature03484;

Voldad4life claimed, "No actual column (Geological) is in one place. The largest sample is in the Grand Canyon, which is only 1 mile. The entire column should be about 100 miles thick.

This is a popular creationist lie. The "entire geological column," in sequence, exists in many places around the world. See;

"The Geologic Column"
http://www.talkorigins.org/faqs/geoco...

PS: Wing evolution:

http://www.ucmp.berkeley.edu/vertebra...

I saw nothing to add to their presentation.

Voldad4life asked, “Assuming a population growth of only 1/2% (1/4 the present rate) the current population can be reached in only 4,000 years. If one assumes a growth rate slow enough to account for the current population in 1 million years, there would have been 3,000 billion human bodies.”

This is one of the “incoherent” questions because it is built totally of false assumptions. Errors are; 1) “assuming a population growth” rate because population growth has never been constant. 2) why would we project a million year time for human populations to grow? Modern humans have existed only the last 150 to 200 thousand years. Genetic studies show a “bottle neck” of only about 100,000 individuals 60 to 80 thousand years ago in Africa, while there were probably a few isolated populations in Eurasia. Real population growth coincided with the invention of agriculture about 10,000 years ago. We know historically that various plagues have reduced humans to as little 1/3 of pre-plague sizes. And finally, the key insight by Thomas Malthus was that unconstrained population growth was exponential.

Voldad4life asked, “Why can we classify animals?
Assuming that all animals evolved from a single cell, there should be no distinction between kinds. This would result in one branch rather than the tree of animals which zoologists have been able to classify.”

We can classify animals because they (we) have a shared common ancestry. Your question is so lost in confusion that I can only direct you to two resources:

“The Tree of Life Project”
http://tolweb.org/tree/

and,
“History of Life through Time”
http://www.ucmp.berkeley.edu/exhibits...

Voldad4life asked, “What held the first cell's stuff (DNA, RNA, etc) together - a cell wall?

Without a cell wall of some kind, the delicately formed cell parts would have simply drifted apart, never to form life. A cell well speaks of fundamental building blocks far more complex than simply the parts alone.”

These are like popcorn.

The errors of thought, and fact are sooo mixed in this question that it belongs in a museum of illogic. First, DNA, was not a part of the first cells’ “Stuff.” RNA probably was, particularly very small RNA, or “micro-RNA” ribozymes.

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

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

Matthew W. Powner, Béatrice Gerland & John D. Sutherland,
2009 "Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions" Nature 459, 239-242 (14 May)

Woese, Carl
2002 “On the evolution of Cells” PNAS Vol. 99 13:8742-8747, (June 25)

Also a likely part of the organic “stuff” was small enzymatic, and transmembrane peptides. See for example;

Anthony D. Keefe, Jack W. Szostak
2001 “Functional proteins from a random-sequence library”
Nature 410, 715-718 (5 April)

Deamer, David W.
2008 "Origins of life: How leaky were primitive cells?" Nature Vol 454 No. 7200

And, other essential parts of the first cells were minerals. For an extended discussion of the role of crystals in the origin of life see;

“Why Re-invent the Crystal?”
http://ncse.com/rncse/28/5-6/why-re-i...

I really need to get to my chores, but

Voldad4life asked, “ How could DNA have replicated without the enzymes which it controls?
DNA can only be reproduced with the help of certain enzymes which can only be produced by DNA which had to be produced by enzymes . . .”

This particular bit of creatocrap makes the false assumption that DNA was part of the original life on Earth. We know that it was not. Long before there were any DNA organisms there were RNA, and peptide replicators. See:

Yuttana Suwannachot and Bernd M. Rode
1999 “Mutual Amino Acid Catalysis in Salt-Induced Peptide Formation Supports this Mechanism's Role in Prebiotic Peptide Evolution” Origins of Life and Evolution of Biospheres Volume 29, Number 5, 463-471, DOI: 10.1023/A:1006583311808

Philipp Baaske, Franz M. Weinert, Stefan Duhr, Kono H. Lemke, Michael J. Russell, and Dieter Braun
2007 "Extreme accumulation of nucleotides in simulated hydrothermal pore systems" PNAS | May 29, 2007 | vol. 104 | no. 22 | 9346-9351

U. F. Müller
2006 "Re-creating an RNA world"
Cellular and Molecular Life Sciences (CMLS), 2006 - Volume 63, Number 11 / June,

Dworkin JP, Lazcano A, Miller SL
2003 “The roads to and from the RNA world” J Theor Biol. 2003 May 7;222(1):127-34

Voldad4life asked, “ Why would DNA evolve when its purpose is the keep just that from happening?

The basic function of DNA is to pass on a very complex and exact code or plan for development for the next generation.

This is an extension of the question Voldad4Life copied that I last answered. DNA is useful because it is more stable than RNA, or peptide nucleic acids. This does not mean that it is immutable. The most recent direction in OOL research on the origins of DNA replicators indicates that the shift from RNA to DNA happened in viruses. A good review is available in

Patrick Forterre
2006 “Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: A hypothesis for the origin of cellular domain” PNAS March 7, vol. 103 no. 10 3669-3674

Also at least scan the literature on Mimivirus, and other "giant" viruses. A fairly good place to start would be;

Mickaël Boyera, et al
2009 "Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms" PNAS December 22, vol. 106 no. 51 21848-21853

Voldad4life asked, “ Why did some animals not evolve?

Evolutionists state that some animals (like the duck billed platypus) have remained unchanged for millions of years. Why were these animals left out of the almost universal improvements that nature had "planned"?

First lie is: “Evolutionists state that some animals (like the duck billed platypus) have remained unchanged for millions of years.” Even we humans are known to have recent mutations that have spread rapidly through the genome without major external changes. And these are the sorts of evolution that occur in populations that live in highly stable environments, or are able to continually migrate to similar environments through-out time. So, while some gross features have remained the same, or at least similar, for millions of years, it is incorrect to claim they are “unchanged.” The second lie is that mutations are always “improvements” since the vast majority of mutations are “silent” that is, they do absolutely nothing. Third, there is no direction, or “improvements that nature had planned.” A successful mutation is one that improved reproductive success, what is an mutational “improvement” in one environment could be a disaster in another.

Voldad4life asked (copied), “Why are there no animals in the salt flats?

The salt flats were probably caused by evaporation of a large salty lake, yet there are no fossils of the animals that lived there.

Hostile environments have fewer, and less diverse animal life. The fewer organisms, the less likely we are to find their fossils. There are several sources for “salt flats” mineralogically called “halite deposits.” Halite forms in stages, the last being a hyper-saline pond or lagoon. And they are in fact loaded with fossils;

Kathleen C. Benison
2008 “Petrography Reveals That Acid-Precipitated Halite and Gypsum Preserve Small Fossils Well” 2008 Joint Meeting of The Geological Society of America, Soil Science Society of America, American Society of Agronomy, Crop Science Society of America, Gulf Coast Association of Geological Societies with the Gulf Coast Section of SEPM

Kathleen C. Benison
2008 “Life And Death Around Acid-Saline Lakes” PALAIOS; September, v. 23; no. 9; p. 571-573; DOI: 10.2110/palo.2008.S05 © 2008 SEPM Society for Sedimentary Geology

Voldad4life asked (copied), “Why are the missing links still missing?

From vertebrates to invertebrates, reptiles to birds there should be billions of animals. The transition from legs to wings alone should have included a countless number of animals, yet none can be found.

We find “missing links” by the thousands. To creationists, every new “link” is counted as two new “gaps.” There are limits to the sensitivity of fossils to detect evolutionary change. Very few individuals of any species will become fossils, certain environments are very bad at making, or preserving fossils, and we spend more per day on foreign wars than we spend on paleontology per year. The Iraq War alone has wasted more money that has ever been spent on paleontology. I have personally seen hundreds of thousands of fossils destroyed in road construction projects because there was no money to even store the material in a warehouse- let alone analyze the remains

There were more similar creatocrap questions on a par with the worst of 

Kent Hovind, or Ken Ham, but I really do have chores to do.

Bring Back The Bean Ball.

I know I just said that I would take the next eight posts to debunk the Rev. Miller.

BUT, the attack by Scott Cousins against SF Giants catcher Buster Posey is too outrageous to ignore.

 

Note that Cousins has crossed the baseline, he has dropped his shoulder, and pulled in his arms in order to strike Posey. He makes no effort to even near the home plate. He broke Posey's leg, and worse, tore three tendons in Posey's ankle. This is a potentially career ending injury.

When the crazy goes mainstream.

I came across this the other day.  It is from Rev Adrian Miller, an Anglican vicar and a member of the Biblical Creation Society (British). He is giving his answer to a question he says he hears, "Why Won't Creationists Just Give Up?"


A FEW HEADLINE REASONS

- Because we see the empirical data from the sciences fitting so much better within a creationist framework and using creationist models.

- Because we see as inadequate any hermeneutic that treats Genesis as having nothing to say about earth history, biology, palaeo-anthropology, and so on.

- Because we recognise the deistic theology and naturalistic philosophy on which Darwin built his biological ideas, and which seeps into our thinking if we embrace Darwin.

- Because we recognise the importance of revelation in our approach to knowing.

- Because we appreciate the 'Emperor's New Clothes', sociological factors that pressurise members of our society - especially the intellectual elite -to conform to this world, in opposition to Paul's teaching in Romans 12:1-2.

- Because history tells us that where the church has embraced Darwin, it has been weakened.

- Because Satan has provided people with a way of looking at the world that doesn't need God, and we need to expose the weaknesses in that proposition rather than compromise with it.

- Because, far from being bad for mission, creationism provides the best apologetical approach, and makes for the deepest disciples. Incidentally, this isn't to say that we don't have our work cut out convincing 'Greek thinkers' that our message of the cross is not foolishness (1 Cor. 1:22f) - it just means that it's even more important that we present a united front on these issues.


So, eight big chunks of crazy. I think these should orient my next eight posts.

Laboratory induced speciation of vertebrates

Worth noting I'll need to update Emergence of New Speceis.;

"Laboratory synthesis of an independently reproducing vertebrate species" Aracely A. Lutesa, Diana P. Baumann, William B. Neaves, and Peter Baumann (Published online before print PNAS May 4, 2011, doi: 10.1073/pnas.1102811108)

Abstract

Speciation in animals commonly involves an extrinsic barrier to genetic exchange followed by the accumulation of sufficient genetic variation to impede subsequent productive interbreeding. All-female species of whiptail lizards, which originated by interspecific hybridization between sexual progenitors, are an exception to this rule. Here, the arising species instantaneously acquires a novel genotype combining distinctive alleles from two different species, and reproduction by parthenogenesis constitutes an effective intrinsic barrier to genetic exchange. Fertilization of diploid parthenogenetic females by males of sexual species has produced several triploid species, but these instantaneous speciation events have neither been observed in nature nor have they been reconstituted in the laboratory. Here we report the generation of four self-sustaining clonal lineages of a tetraploid species resulting from fertilization of triploid oocytes from a parthenogenetic Aspidoscelis exsanguis with haploid sperm from Aspidoscelis inornata. Molecular and cytological analysis confirmed the genetic identity of the hybrids and revealed that the females retain the capability of parthenogenetic reproduction characteristic of their triploid mothers. The tetraploid females have established self-perpetuating clonal lineages which are now in the third generation. Our results confirm the hypothesis that secondary hybridization events can lead to asexual lineages of increased ploidy when favorable combinations of parental genomes are assembled. We anticipate that these animals will be a critical tool in understanding the mechanisms underlying the origin and subsequent evolution of asexual amniotes.

Also discussed on the Web at Panda's Thumb, and Nobel Intent.

Did God Make The World, .... ?

My Google news reader spotted an on-line magazine article called “Did God Make The World, and all that it contains?” by Arthur Lewin. Neither the magazine, “ThyBlackMan.com,” nor Dr. Lewin were known to me, so I took a look. I was disappointed and slightly irritated. In just under 500 words, Dr. Lewin (PhD in sociology from City University of New York) makes almost zero accurate statements. (Maybe you can find more than I could).

What follows are my comments posted to the website;

Mr. Lewin, in the day of Google, and Wikipedia your multiple errors are just not acceptable. First, Charles Darwin hardly addressed the origin of life at all, and at least in his published works accepted the possibility of a creator. Second, evolutionary biology has advanced a great deal in the last 150 years and Darwin’s books are of more historical than scientific interest.

You also suggest that creationism be taught merely because it is popular. Darwin wrote against slavery, and about the biological unity of mankind when most here insisted that slave ownership was a “god given right” of the White man, and even that the African slaves were soulless sub-humans. Facts are not altered by popularity, and at least in the sciences we try to stick to facts to build our theories.

As for some additional facts, John Scopes was never “exonerated.” The Tennessee Supreme Court found the Butler Act against teaching evolution constitutional. The court set aside the conviction because the Judge made a technical error by fining Scopes $100, when he was not permitted to go above $50, and the lower court decided not to retry the case.

Cartesian Duality is the notion that there is a non-material mind that is detached from the physical brain. Given the advances of neurochemistry, and application of new technologies such as functional MRI, we know that this was a false idea. (And it had little to do with any “science versus religious” conflicts).

Godel’s ideas about incompleteness apply to formal logic systems such as mathematics without any material constraints. The sciences rejected by creationists, especially biology, and geology, are already constrained by the physical realities we study, and so Godel’s theorem has no application. You had best try reading the original.

I want make a last observation to Dr. Lewin regarding his concluding statement, “And so we see that, ultimately, Evolution and Intelligent Design do not really contradict.”
They do most certainly conflict, if Dr. Lewin is using “intelligent design” in the same sense as its proponents, and in the sense it has in the various recent or impending legal cases (see Kitzmiller v Dover, or example). The scientific failure of Intelligent Design creationism has been explored by many scientists and philosophers. For two recommendations, see;

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

I was one of the contributors to the latter book.

The suggestion made by Dr. Lewin that following the “big bang,” life emerged and evolved according to natural laws is roughly the same as “theistic evolution.” I don’t find it personally persuasive, but there is no particular scientific objection to this. It is often called the “strong Anthropic principle” by cosmologists. It is worth noting that it is rejected by most ID proponents at the Discovery Institute, and is strongly opposed by the common Young Earth creationists.

Two books I can recommend on theistic evolution are;

Frye, Roland Mushat (editor)
1983 “Is God a Creationist? The Religious Case Against Creation-Science” New York: Charles Scribner’s Sons

Miller, Keith B. (editor)
2003 “Perspectives on an Evolving Creation” Grand Rapids: Eerdmans Publishing Company

They are a bit heavy theologically, but mostly readable.


Regarding the “fine tuning,” or “strong anthropic principle,” here is one in favor and one opposed;

McGrath, Alister E.
2009 “A Fine-Tuned Universe” Louisville: Westminster John Knox Press

Susskind, Leonard
2005 “The Cosmic Landscape: String Theory and the Illusion of Intelligent Design” New York: Little and Brown Publishers

Obviously McGrath is in favor of the idea that the “fact” the universe is “built” for us humans “proves” there must be a god. Actually he sidesteps the arguments made by Susskind (in fact he does not even mention Susskind, or the equally strong counter arguments of of my colleague Victor J. Stenger (2004, “Is the Universe Fine-Tuned for Us?” in “Why Intelligent Design Fails,” 172-84). The best short refutation of the fine tuning case I have seen was by the science fiction author, Douglas Adams. In late 2000, he gave a talk at the Massachusetts Institute of Technology. He compared us to a mud puddle that looks around and says, “What a nice hole in the ground – it’s made just for me! Look at how nicely it’s indentations fit my beautiful curves, and the depth and the radius are just right…”


PS: Take some time to read NASA’s “Universe 101: The Big Bang Theory”

The contest is over. I Win the Scotch! Kristine the Belly Dancing Librarian wins the Chocolate!

What I had hoped for was like:

Lies, and gross errors of fact:

Transcript from Think Progress, "At the risk of drawing this out, which I hate to do(1), but I do know, as Rep. Dunn has mentioned, that I was taught things in science class in high school which have turned out not to be true.(14) I remember so many of us when we were seniors in high school, we gave up Aqua Net hairspray. You remember why we did that? Because it was causing global warming(2 a,b,c)! That aerosol in those cans(3) was causing global warming(4). Since then, scientists have said(5) maybe we shouldn’t have given up that aerosol can because that aerosol was actually absorbing(6) the earth’s rays(7) and keeping us from global warming(8).

So, so many things we learned in science class(14) have turned out not to be true.

What about eating chocolate? You know, I was told, don’t eat chocolate(9). Good dark chocolate is full of what? Anti-oxidants!(10) Some chocolate is good for you. So many things that we learned in science class.(14, and she flunked English too).

What this bill does is protects a teacher(11) — not mandates what a teacher teaches — it protects a teacher when a child asks a critical thought question about something like global warming or evolution(12). They have the right to ask that question, and the teacher has the right to not make them feel stupid for asking(13)!"

(1) She does not mind drawing things out at all,
(2 a, b, c) a, She was apparently a HS senior in the late 1960s (we are the same age); global warming was not yet considered an issue, the only possible issue was ozone depletion. b, Ozone depletion was not an issue in the late 1960s. c, CFCs used as propellants are weak greenhouse gases and had negligible effect on global warming.
(3) There is no aerosol in the cans, the aerosol is produced in the can’s nozzle.
(4) The hairspray contents, polyurethane, acetone, and CFCs, of the cans didn’t contribute directly to warming.
(5) “Scientists” have not said anything she has mentioned, or is about to mention.
(6) The hairspray aerosol (misted plastic) sprayed on girl’s hair does not absorb global warming “rays.”
(7) The Earth does not have global warming “rays.”
(8) Neither the hair spray components, nor the generated aerosol contribute to cooling. There are aerosols, like clouds, that do. Clouds are not like hairspray.
(9) I doubt this woman was told not to eat chocolate in science class because she seems to have never attended a science class.
(10) “Although a bar of chocolate exhibits strong antioxidant activity, the health benefits are still controversial because of the saturated fats present,” *1
(11) Teachers are already protected, and expected to teach “critical” thinking, and what is a “critical thought problem?” (Two alternating hypothesis left Philadelphia …).
(12) The bill is to teach creationism, and the bitch knows it.
(13) Teachers don’t need to be “protected” from “not making a child feel stupid.” A pattern of making a child “feel stupid” is abuse.
(14) Ms. Butt learned nothing in science class. Nothing a teacher could do would have prevented Ms. Butt form being stupid, regardless of how she feels about it. She does not seem to realize she is stupid, but she isn’t in school anymore (worse the luck).

*1 “Cocoa Has More Phenolic Phytochemicals and a Higher Antioxidant Capacity than Teas and Red Wine.” J. Agric. Food Chem., 2003, 51 (25), pp 7292–7295

Rep. Butt of Tennessee on Global Warming

I want to commend Brad Johnson for collecting this clip, and send him some traffic at Think Progress.

I thought that it would be fun to have a contest on how many errors of fact are in Ms. Butt's load.

The format I thought up is in three parts; a "bidding" phase where we can put up the number, 4, 5, 6, etc... The second phase will be the highest bidder listing the errors they see, and the third will be a "wild card" prize if anyone can add extra errors in addition to the high bidder. The First Place winner gets the traditional bottle of single malt Scotch (I have a brand in mind). The Wild Card prize should be a box of chocolate full of anti-oxidants.





This is SOOOOO STUPIDDDDD that I cannot bring my self to break it down. Maybe after some beers.

An amended "Emergence of New Species"

I added the following bit to my list of Emergecne of new species.

The former “Answers in Genesis” gang claims they have found a problem with using O. gigas as an example of polyploidal speciation. There are so many good examples of new species emerging, both in the wild, and in laboratories, that I would not want to use one that is incorrect.

The notorious creationist website “Creation Ministries,” disputes O. gigias as a valid example of polyplodial speciation. (Feedback, March 31, 2007 “Speciation Observed? Was this Evolution?” http://creation.com/evolution-by-fiat-and-faith#specob As I have found them to be grossly wrong on many occasions, I also checked their citation list. The creationist claim that O. gigas is not an example of speciation has only two supports; an article in 1943, and that they did not find botanical materials named O. gigias in on-line Botanical nomenclature reference collections. Oenothera names are a mess, but not as bad as Asteracea. O. gigias was apparently found to be a synonym, and is disused. This is trivial, and does nothing to change using the spontaneous emergence of the tetraploidal new species.

The “Creation Ministries International” phonies also cited a 1943 plant genetics article, “An amphidiploid in the F1 generation from the cross Oenothera franciscana x Oenothera biennis, and its progeny” (Davis, B.M., Genetics 28(4):275–285, July 1943). It is available on-line in PDF at: http://www.genetics.org/cgi/reprint/28/4/275.pdf

Read it for yourselves, if you like. It has nothing relevant to de Vries, or his O. gigias being used as valid examples of speciation. This is the sort of misrepresentation typical from professional creationists, who expect their followers to lack either the education, or motivation to actually dig through the science.

For a more recent review of the role polyplodial plants play in evolution, read;
"Duplicate genes increase expression diversity in closely related species and allopolyploids" Misook Haa, Eun-Deok Kima and Z. Jeffrey Chen, PNAS February 17, 2009 vol. 106 no. 7 2295-2300
PDF: http://www.pnas.org/content/106/7/2295.full.pdf+html

And, here is a broader review on plant evolution and genome doubling that is also a bit easier to read;
"Genetic and epigenetic alterations after hybridization and genome doubling"
Ovidiu Paun, Michael F. Fay, Douglas E. Soltis, and Mark W. Chase, Taxon. 2007 August; 56(3): 649–56.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2980832/

Responding to creationists in newspaper forums

For a few years now, I have spent part of every day searching for, and replying to creationists in US newspaper editorials, letters to the editor, and newspaper discussion groups. There are others who do the same, including creationists. I recently was replying to a ID creationists named Lee Bowman on a Tennessee news site Metro Pulse; http://www.metropulse.com/news/2011/apr/06/critical-thinking-or-creationism-tennessee-classro/

I am posting the following to Stones and Bones because I had to spend some time searching the Dover trial transcripts for material, and will probably need them again. The two topics are Mike Behe's claim that even though ID "design detection" doesn't work in archaeology, as he had claimed, it would still work in "science fiction." The second part is from his cross-examination where he admits that "astrology is science" under the logical rules he would use to make ID a science.

Lee Bowman claims that, “academic freedom is my passion.” I don’t know whether to laugh, or snarl. Come to think on it, snarl is more appropriate. Mr. Bowman is an advocate for teaching creationism in schools. He is also a sloppy thinker, and reader. (Alternately, he misrepresents other posts on purpose). For example, he dismissed the clear assertions of religious intent from all the major ID creationism leaders, say that they were out dated. For example, he claimed falsely that Phillip Johnson, and Paul Nelson admitted that there is no ID theory in 1996. This was (as I cited) in 2006 by Johnson, and 2004 by Nelson. Were these statements even older, no ID creationists have ever retracted their clear assertions of religious doctrinaire goals, and motivations for ID creationism.

Bowman then lies about Behe’s testimony in the Dover trial, asserting falsely that Behe was attempting humor. Here is the transcript;

Dover, Behe Cross Examination, Afternoon Day 12;

(Rothschild) Q. So if the strength of an inference depends on the similarities, this is a pretty weak inference, isn't it, Dr. Behe?

(Behe) A. No, I disagree completely. Again if something showed strong marks of design, and even if a human designer could not have made it, then we nonetheless would think that something else had made it. Lots of science fiction movies are based on scenarios like that, and again the, I think the similarities between what we find in designed objects in our everyday world and the complex molecular machinery of the cell have actually a lot more in common than do explosions we see on earth such as cannon balls and so forth and the explosion of an entire universe, and that induction seems to have been fairly successful in trying to explain some features of the world. So I think it's not at all uncalled for to make a similar induction in this case.

Q. Science fiction movies are not science, are they, Professor Behe?

A. That's correct, they are not. But they certainly try to base themselves on what their audience would consider plausible within the genre, so they can offer useful illustrations at some points, for some points.

Obviously, Behe is floundering in his self contradictions, and searching for an “out.”

And, regarding astrology, which Behe defended as a “science,” here is a relevant portion of that testimony.

Dover, Behe Cross Examination, Afternoon Day 11;
Q (Rothschild) And using your definition, intelligent design is a
16 scientific theory, correct?
17 A (Behe) Yes.
18 Q Under that same definition astrology is a
19 scientific theory under your definition, correct?
20 A Under my definition, a scientific theory is a
21 proposed explanation which focuses or points to physical,
22 observable data and logical inferences. There are many
23 things throughout the history of science which we now think
24 to be incorrect which nonetheless would fit that -- which
25 would fit that definition. Yes, astrology is in fact one,
1 and so is the ether theory of the propagation of light, and
2 many other -- many other theories as well.

And a moment later,

Q But you are clear, under your definition, the
7 definition that sweeps in intelligent design, astrology is
8 also a scientific theory, correct?
9 A Yes, that’s correct. And let me explain under my
10 definition of the word "theory," it is -- a sense of the
11 word "theory" does not include the theory being true, it
12 means a proposition based on physical evidence to explain
13 some facts by logical inferences. There have been many
14 theories throughout the history of science which looked good
15 at the time which further progress has shown to be
16 incorrect. Nonetheless, we can t go back and say that
17 because they were incorrect they were not theories.

He said I said, but I didn't

I think I'll go fishing this morning. But first, here is a little bit of editorial writing amusement. A creationist, Mr. Paul James, wrote a guest editorial for the Palm Beach Daily, published Feb. 9, 2011. After I made a few remarks in the discussion, I emailed the editor of the paper to offer a counter-point. After a couple of weeks, they ran my piece on Feb. 27. Just a few days later, Paul James is back with his response.

That isn't the "good part." The good part was that Mr. James has attributed to me a bigoted opinion written by another creationist. Mr. James took the quote from this blog entry, "ID Creationism in Minnesota," where I am critical of creationist Joe Cap.

But even better is the fact that a childish atheist called "Human Ape," AKA "bobbyxxxx" tried to join James in attacking me. (All of bobby's posts were deleted, BTW). Irony is not dead: A creationist (James) quoting a creationist (Cap) because he wants to embarrass a scientist (me) is supported by an atheist twit (bobby).

Scientific American nannybot objected to the following

ZebulonJoe wrote in comment #60, “I have yet to find anyone here who has actually looked at those chapters in the book of Job, 38-41.”

We might as well take this up, and then call it done vis a vis Joe’s arguments.

The book of Job is indeed an interesting text as it is a very ancient in its source, and interpolated with more recent material. In particular, ZebulonJoe’s request to study chapters 38-41, begins with a theologically rich boasting of the southern storm god, Yahweh. The parallel texts are from the Ugarit creation myth (a Northwestern Semitic tradition), and the defeat of the sea god Yammu by the god Ba’lu (biblical Baal). In Job 38, the sea (biblical Hebrew Yam) is conquered by Yahweh (8- 11). Yahweh in the common storm god tradition is clothed in whirlwind and clouds, and speaks through the wind and thunder, causes rain, and lightening 38:1, 9, 22, 25-30, 35-38 (v.36 is emended).

Of additional interest is mention of the “B'nai HaElohim” in verse 7, commonly translated in the KJV as “sons of God,” or occasionally “hosts of God.” In late biblical texts this is recast as “angles,” or even human saints. The chief god of Ugarit, El, presides over his “council of gods” or “elohim.” It is this identical use we find in Job, beginning in Chapter 1 verse 6. (Elsewhere we find “el elohim Yahweh” or “Yahweh, the God of the gods”). Also give attention to the fact that “the satan” (biblical Hebrew il’shatan, God’s Satan) is appearing at the command, and under the direction of the God El in Chapter 1. This provides a rather amusing world play in 1:7 since Satan says he was “wandering about” and the name Satan derived from the Akkadean verb “sh-uut” = to wander, and later consonant shifts yield, "satan" = to accuse.

I would suggest that anyone interested in the Book of Job read;

Dahood, Mitchell
1965 Psalms I, 1-50: Introduction, Translation and Notes New York: Anchor Bible- Doubleday

Jewish Publication Society
2004 “The Jewish Study Bible: TANAKA translation” Oxford University Press.

Matthews, Victor H., Don C. Benjamin
2006 “Old Testament Parallels: Law and Stories from the Ancient Near East” New York: The Paulist Press.

Pardee, Dennis
2002 "Writings from the Ancient World Vol. 10: Ritual and Cult at Ugarit" Atlanta: Society of Biblical Literature

Pope, Marvin H.
1965 “Job: A new translation with Introduction and Commentary” Anchor Bible Vol. 15, New York: ABRL/Doubleday

Smith, Mark
2003 “The Origins of Biblical Monotheism: Israel's Polytheistic Background and the Ugaritic Texts” Oxford University Press.

And be sure to keep a handy copy of Brown, Driver, and Briggs.

Lies, Damn Lies, and Creationists; Klinghoffer at the Washington Post

Lies, Damn Lies, and Creationists

David Klinghoffer is an intelligent, and well educated man. That is why he has been given lots of money by the far-right, creationist Discovery Institute. He earns this money by misdirection and lying. I would not call him a liar if I thought he was stupid, or ignorant. An excellent example is his 2/22/2011 editorial for the Washington Post.

Klinghoffer begins by the false premise that Darwin is the key figure in modern evolutionary theory, or that what we feel emotionally about Darwin should have more than rhetorical value. He also wants us to ignore that for 30 years there has been a steady increase in the percentage of Americans who understand human evolution, and that this is equally taken away from biblical literalists, and “undecided.” What has been fixed is the ~38% of theistic evolutionists who acknowledge evolution, including humans, and attribute this to God’s will. This is the accepted standard of the Catholic church, and most mainline Protestant churches. There is another appropriate saying of Mark Twain’s, “Figures don't lie, but liars figure.”

But the misdirection builds higher. He wants us to ignore that it is the biblical literalists who have a religiously motivated rejection of not only evolution, but all sciences. To follow Klinghoffer’s request to ignore literalists, is to ignore that there is a conflict at all. (There are a tiny number of pantheist, neo-pagan, and other creationists. But, taken all together, they couldn’t fill a stadium). But, Klinghoffer’s pay rate as a Discotute depends on promoting Intelligent Design creationism, and their opposition to science. And it is all of the sciences that are rejected by mystical thinkers because scientific theories are exclusively materialist, and they really work. As Klinghoffer’s fellow Discotute, Wiliam Dembski wrote, “…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,” April 14, 2004.

Klinghoffer then switched to hyping a book by another Discovery Institute hack about Alfred Russle Wallace. Wallace was a pantheist, and spiritualist, positions just as objectionable to Klinghoffer’s paymasters as Darwin. What does appeal to them is that Wallace can be misrepresented as an opponent to Darwin. This is a 2 for 1 lie; Wallace never viewed himself as opposed to Darwin, plus both Darwin and Wallace are very distant for evolutionary biology as taught today.

So, Klinghoffer has done his best for creationism, and earned another paycheck. The unresolved question is why the Washington Post facilitated him? Will we see commentary from Ken Ham, or Fred Flintstone next?

Posted by: GaryHurdPhD | February 23, 2011 5:52 PM
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Well, I went on my first long ocean trip from Friday to 11th, to Sunday the 13th. Excellent boat, good crew, fine weather, terrible fishing.

Enought of that for now.

I took a look at the old profile photo of me and a yellow tail that I caught on the Fury. Here is a contrasting, recent photo of me and a similar yellow tail that I caught last year aboard the San Diego out of Seaforth Landing.

ID Creationism in Minnesota

February 9, 2011

Joe Cap commented in the Minnesota Post

I think young Earth creationism is wrong, and anything specifically invoking the supernatural should not be taught in science classes. With that said, this article shows the typical ignorance of Intelligent Design.

Professor Randy Moore: “They’ve had evolution classes, they choose to reject it in favor of religion.”

Three things are wrong with this statement.

(1) It implies that there is only one kind of evolution, the neo-Darwinian synthesis based on methodological naturalism (the a priori assumption that nature is all that there is), and (2) that if you don't believe the claims of this theory, the ONLY other choice is religion. I personally believe life evolved in a tree similar to what is taught in evolutionary biology classes, but could not have happened simply via random mutations and natural selection. Not nearly enough information search capability. This is not automatically imply that God or gods did it. Lastly, Mr. Moore implies (3) that those who choose evolution are not religious. I'm not even talking about theistic evolutionists (people who adhere to every inkling that evolutionary biology has to teach, and believe God did it). You're trying to tell me Richard Dawkins is not religious about his worldview? Militant, atheist evolutionary biologists are every bit as religious as a sweating, hollering young Earth creationist preacher from south Alabama.

Beth Hawkins: "And no, Intelligent Design does not qualify as a scientific theory."

I know this isn't an article intended to debate this issue in depth, but this type of hand waving is boring. For anyone truly interested in Intelligent Design, from either side of the fence, I encourage you to check out the series of posts on uncommondescent.com titled "ID Foundations". It is a fairly rigorous discussion of what ID is all about. Be sure to read the comments sections, too, as some very good discussion both both sides happens there.

(I placed the comment by Cap in italics, Mar. 10, since some people think that HIS words were mine).
+++++++++++++++++++++++

So, I replied;

Beth Hawkins did a good job within her limited word count. Joe Cap managed to pack a lot of nonsense into just over 300 words.

The original article published in last week’s Science magazine was “Defeating Creationism in the Courtroom, But Not in the Classroom” by Michael B. Berkman and Eric Plutzer. They found that ~28% of teachers nationally do correctly and enthusiastically teach the scientific basis of all biology, evolution. At the opposite end of the scale, 13-18% personally reject evolution, and actively subvert the curriculum, or explicitly teach creationism. One Minnesota teacher was quoted, “I don't teach the theory of evolution in my life science classes, nor do I teach the Big Bang Theory in my [E]arth [S]cience classes…. We do not have time to do something that is at best poor science.”

Berkman and Plutzer felt that the remaining teachers, ~54%, who were weak in their presentation of evolutionary biology lacked a proper background, and thus lacked the confidence, and competence to successfully present the curriculum. Prof. Moore disagrees, and cites his own data that the “unsure” teachers are were a mere 15%, and that up to 25% of teachers rejected evolution and taught religious creationism instead. Oddly, he has published 2003 data indicating that up to 52% of teachers felt they were inadequately prepared to teach evolution, “The Teaching of Evolution & Creationism in Minnesota” Randy Moore and Karen Kraemer, The American Biology Teacher. 67(8): 457–466. 2005.

Mr. Cap’s comment has no relevance to any of this. Not one of his objections to Prof. Moore’s observations is supported with facts, which I’ll come to presently.

Mr. Cap wrote, “(1) It implies that there is only one kind of evolution, the neo-Darwinian synthesis based on methodological naturalism (the a priori assumption that nature is all that there is).”

The theory of evolution was rephrased in the 1930s to meld the discoveries in genetics with Darwin’s notions of common descent, and selection. This relied heavily on the mathematical models of population genetics and weakened Darwin’s emphasis on individuals and “survival” in favor of populations and reproductive success. This was the “the neo-Darwinian synthesis” Mr. Cap referred to above. There have been two significant additions since then; Kimura’s neutral theory (see his 1985 book “The neutral theory of molecular evolution), and the observations by Gould, Eldredge, and Lewontin of rapid change in the fossil record which they generalized as “punctuated equilibrium” as opposed to Darwin’s gradualism( see: Gould SJ and Eldredge N 1977 Punctuated Equilibria: The Tempo and Mode of Evolution Reconsidered; Paleobiology 3 115–151). We are currently anticipating further advances in developmental biology (mostly in embryology), and ecological theory which will in turn expand and improve evolutionary theory. It is highly unlikely that Randy Moore, a professor of biology, would think that the neo-Darwinian synthesis of Fisher, Haldane, and Huxley is the “only” kind of evolution.

In the same numbered objection, Mr. Cap confused “methodological naturalism” with “philosophical naturalism.” The latter holds that the material universe is exclusive. Scientists universally hold to “methodological materialism.” That is, scientific explanations, or theory, must always be based on observable phenomena and may only use natural law-like statements in their theories. You cannot toss miracles and undefined magical powers into your work to dodge difficulties and still pretend to be scientific. It is methodological materialism that allows the devout Hindu, or Christian to contribute good science equally along with the agnostics, and atheists. In this regard there is “only one kind of evolution” because there is only one kind of science period, that based on methodological materialism.

Mr. Cap wrote “(2) (Prof. Moore asserted gh) that if you don't believe the claims of this theory (evolutionary biology gh), the ONLY other choice is religion. I personally believe life evolved in a tree similar to what is taught in evolutionary biology classes, but could not have happened simply via random mutations and natural selection. Not nearly enough information search capability. This is not automatically imply that God or gods did it.”

Prof. Moore is speaking from his perspective from over a decade of opinion survey research. This research has shown that teacher rejection of evolutionary theory in favor of actually teaching creationism was religiously motivated. It was not an assumption, or opinion, it was an objective fact. But, Mr. Cap did use the opportunity to make an absurd claim of his own that the nested hierarchies of evolutionary biology are real, but that they didn’t happen by evolutionary means. His “argument: Not nearly enough information search capability.” This is a bit of classic Intelligent Design Creationism gibberish.

It is close to the argument made by ID creationist Mike Behe in his Dover testimony. Behe had cited his article with David Snoke, “Simulating evolution by gene duplication of protein features that require multiple amino acid residues” Protein Science (2004), 13:2651–2664. Based on this paper, Behe asserted that there was “too little time” for a random process to have generated complex organisms. In cross-examination however, he was forced to admit that using realistic conditions his published result would have actually supported evolution. (see Behe cross examination, Day 12 Am. http://www.talkorigins.org/faqs/dover/day12am.html#day12am366 )

Mr. Cap claims that ID creationism does not have a religious foundation. Some obvious statements by ID leaders will settle this error;

Michael Behe
“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." From “Reply to My Critics,” Biology and Philosophy 16: 685–709, 2001.

William Dembski
In a 1999 article for the Christian magazine Touchstone “Signs of Intelligence,” Dembski confirmed the foundation of ID in John 1 when he assured readers that "Indeed, intelligent design is just the Logos theology of John’s Gospel restated in the idiom of information theory."

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

Phillip Johnson
"This [the intelligent design movement] isn't really, and never has been, a debate about science, it's about religion and philosophy." World Magazine, 30 November 1996

"The Intelligent Design movement starts with the recognition that 'In the beginning was the Word,' and 'In the beginning God created.' Establishing that point isn't enough, but it is absolutely essential to the rest of the gospel message." Foreword to Creation, Evolution, & Modern Science (2000)

"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." American Family Radio (10 January 2003)

Jonathan Wells
"Father's words, my studies, and my prayers convinced me that I should devote my life to destroying Darwinism, just as many of my fellow Unificationists had already devoted their lives to destroying Marxism. When Father chose me (along with about a dozen other seminary graduates) to enter a Ph.D. program in 1978, I welcomed the opportunity to prepare myself for battle" [Note: 'Father' refers to self-proclaimed Messiah, Rev. Sun Moon]. Date: 1996. Source: Why I Went for a Second Ph.D.
Location: http://www.tparents.org/library/unification/talks/wells/DARWIN.htm

ID creationists Paul Nelson and Steve Meyer are also Young Earth Creationists, and William Dembski has recently been forced to recant his published opinion that the Genesis Flood was not a historical global event. His statement reads, “In a brief section on Genesis 4–11, I weigh in on the Flood, raising questions about its universality, without adequate study or reflection on my part. (referring to his book “The End of Christianity”). Before I write on this topic again, I have much exegetical, historical, and theological work to do. In any case, not only Genesis 6–9 but also Jesus in Matthew 24 and Peter in Second Peter seem clearly to teach that the Flood was universal. As a biblical inerrantist, I believe that what the Bible teaches is true and bow to the text, including its teaching about the Flood and its universality.”

We might was well finish up with Mr. Cap’s errors. I’ll skip his bigotry toward Young Earther’s, and southerners other than noting it seems as extreme as any atheist’s. The last gross error is that there is a “theory of intelligent design.” Again, I’ll let two of the ‘great’ minds of ID creationists take the stage;

Philip Johnson
"I also don't think that there is really a theory of intelligent design at the present time to propose as a comparable alternative to the Darwinian theory, which is, whatever errors it might contain, a fully worked out scheme. There is no intelligent design theory that's comparable. Working out a positive theory is the job of the scientific people that we have affiliated with the movement. Some of them are quite convinced that it's doable, but that's for them to prove...No product is ready for competition in the educational world." Berkley Science Review (Spring 2006).

Paul Nelson
Easily the biggest challenge facing the ID community is to develop a full-fledged theory of biological design. We don't have such a theory now, and that's a real problem. Without a theory it's very hard to know where to direct your research focus. Right now we've got a bag of powerful intuitions, and a handful of notions such as "irreducible complexity" and "specified complexity" - but as yet no general theory of biological design. Date: July/August 2004 Source: Touchstone Magazine interview

There is no ID theory, and there never will be an ID theory. ID is relabeled creationism, and not a science of any kind.