Evolution vs. God

The premise is that Darwinian evolution is unproved and unprovable. It is accepted on faith, passed to students on the authority of professors.   Darwinian evolution has its problems, but this video does not address any of them.  It is a religious tract.

I got the video on the UT campus where they were being handed out.  Packaged as a bait and switch,  Evolution vs. God is a one-sided argument with an assortment of college students and professors. They are neatly boxed in by their own ignorance of Darwinian evolution and their personal failings as moral philosophers.  And, of course, we never see the ones who were not defeated.

Scientists have bombarded fruit flies with radiation for over 100 years, and never created a new species.  However the monsters turn out, they remain fruit flies, apparently still able to breed with others of their kind.  (Institute for Creation Research.)  On the other hand, the Archaeopteryx of the late Jurassic remains factually among several transitional animals between reptiles and birds. Gratefully, we can go swimming without meeting any of the creatures of the Devonian.  What survived is fearsome enough. 

William Smith’s geological map of England was possible only because he relied on the facts of evolution. Simpler forms of the same kind never appear in rock strata higher than more complex forms.  Smith died 20 years before Charles Darwin published The Origin of Species.  

None of that is discussed in this video.  Nor did anyone ask the interviewer what happened to the dinosaurs.  And why do we not find fossil dogs and cats in rocks 150 million years old?

In the nineteenth century, geologists debated catastrophism versus uniformitarianism, and volcanism versus neptunism.  In other words, did the world we know now come about by sudden changes or gradual processes?  Were the primary forces violent explosions or accreting deposits?  Today, we regard those as false dichotomies. 

The debate between Darwinian evolution and Lamarckism may be another false dichotomy.  Epigenetics is the relatively new study of how the environment affects heredity.  The evidence seems compelling – and it seems unlikely that the environment would have no affect, leaving all evolutionary processes at the level of quantum physics.  The easy answer is: “I don’t know.” 

In science we live with our limits.  Science is self-correcting as we work to discover more about the world around us, and put that knowledge into an order that allows predictions.  Religion has no such limits.  They all claim absolute knowledge and – obviously and tragically – disagree about what that absolute truth may be.  Several times near the end, the interviewer (Ray Comfort, the producer) quoted an English translation of the Bible.  Which translation is right?  What happens when they disagree?  And, for that matter, the Qu’ran mentions Jesus about 25 times calling him Messiah and the Son of God.  And the Qu’ran acknowledges Mary as the Virgin and Mother of God.  Yet, somehow Muslims and Christians seem not to get along well. 

Evolution vs. God offers a second thesis: Darwinian evolution allows (even encourages and advocates) immorality.  According to this video, survival of the fittest excuses the harms, crimes, and horrors we perpetrate.  People embrace evolution to avoid following God’s Commandments.  “Are you a good person?” the interviewer asks.  Of course the subjects think well of themselves.  “Have you ever told a lie?”  “Have you ever stolen anything?” "Have you ever had lust in  your heart?" “Have you ever taken God’s name in vain?”  If you stop and think about it, the interviewer is also a sinner, but having accepted Christ’s sacrifice, he does not need to worry about that – or even mention it.  That being as it may, it is not a divine revelation that a selected handful of university undergraduates and professors have no idea what morality is.

All in all, the presentation was no better or worse than Reason TV productions where university students who say they voted for President Obama are happy to sign a petition based on the 1931 Nazi Party election platform. 

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Watson’s Double Helix: Doing Science and Writing About It

The Double Helix (1968) is James D. Watson’s very personal account of how he and Francis Crick worked out the structure of DNA through 1951 and 1952.  The reading is an easy 141 pages.  But depth is here, also.  The story is about scientists, their social spheres, and their conflicts, and (ultimately) their collaborations.  This is also a chronological tour through some of the mind of James D. Watson.  Proof demands evidence explained by consistent reasoning. Getting there is intuitive, insightful, and contrary.

Watson does not explain the technical terms.  Mostly, it does not matter if you do not know the formulas for adenine, cytosine, guanine, and thymine.  (I do not. The book has pictures.) However, neither does he do more than drop the terms “keto” and “enol.”  (You can look them up. I have not.)  The narrative moves forward nonetheless. 

More than the frustrating work of discovery, this story reveals much about how the culture of academic science perceived itself in the middle of the 20^th century.  Watson’s telling is personally unkind to Sir Lawrence Bragg.  Bragg ordered his doctoral candidate, Crick, to abandon the pursuit for DNA. Says Watson: “ … we refrained from publicly questioning Bragg’s decision. An open outcry would reveal that our professor was completely in the dark about what the initials DNA stood for. There was no reason to believe that he gave it one hundredth the importance of the structure of metals, for which he took great delight in making soap-bubble models. Nothing then gave Sir Lawrence more pleasure than showing his ingenious motion-picture film of how soap bubbles bump each other.” (page 69)  Yet, Bragg wrote the Foreword. That speaks to the culture of science.

Their conflict with Rosalind Franklin is now a legend.  In closing the history, Watson allows that her barbed shell was a necessary defense in a society that held her sex against her.  Yet, Watson also admits that she stood on good science.  She refused to accept the helix until her own x-ray crystallography validated it, even though a single snapshot from that library inspired Crick and Watson to seek the spiral structure.  When the cards were on the table, Franklin agreed, plainly, flatly, honestly.  Ironically perhaps, at that moment, the structure of DNA had nothing to do with sex.

“Much of the talk about the three-dimensional structure of proteins and nucleic acids was hot air. … It made no sense to learn complicated mathematical methods in order to follow baloney.” (page 27).

Just as Sir Lawrence Bragg denied the value in Francis Crick’s independent path, Watson was fired by the supporters of his post-doctoral work.  His position at Cambridge (where he was not supposed to be in the first place) was cancelled and he was offered nine months (not a year) in the States.  Often attributed to Buddha, the fact that a prophet is not appreciated in his homeland is correctly cited to Jesus.  To the betterment of all, the culture of science is different than that of religion.  The worst they can do to you is to withhold your stipend.  In fact, Watson’s colleagues and friends at King’s College in London, Max Perutz and John Kendrew, assured him that they could find some money if he chose to remain in England.  That help turned out not to be necessary, though Watson continued his work at Cambridge.

He fit in well, there.  The sense of fair play that defined science then was important to him.  Crick and Watson worried about invading the research spaces of others who also sought the structure of DNA.  Topmost of them was Linus Pauling, already holding a Nobel Prize, and clearly capable of more achievements at that level.  When a published paper showed that Pauling was not just wrong, but had blundered, Crick and Watson knew that they had about six weeks to finish their work because Pauling could not be bested twice. 

(Jeff Goldblum played John Watson in a television production of the story, “The Race for the Double Helix” Horizon season 23 episode 16, September 14, 1987.) 

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Sub-adult American alligator 

in Pearl River Delta, Mississippi. 

Photo by Kristine Gingras 

from the journal artlcle.

Crocodiles can climb trees.  "If crocodiles were extinct and you only knew them from fossils, you wouldn't be able to guess they climb trees because they don't have any physical adaptations," University of Tennessee researcher Vladimir Dinets told Reuters. "Assumptions based on fossils," he said, "can be far less correct than people think."
The article "Climbing behaviour in extant crocodilians" by Vladimir Dinets, Adam Britton, and Matthew Shirley appeared in Herpetology Notes (Vol 7:3-7; 2013), an online journal of Societas Europaea Herpetologica. 

"Extant crocodilians are generally considered to be predominantly or semi-aquatic. And, although the role of terrestrial activity in their natural history is increasingly recognized (see, for example, an overview of terrestrial hunting in crocodilians in Dinets, 2011), they are virtually never thought of as animals capable of climbing. Their non-arboreality is often taken for granted in various analyses of tetrapod limb evolution and behaviour of extinct Archosauria (see Birn, Jeffery et al., 2012, for a discussion of the subject and a bibliography)."

Reuters news story here.  

Original journal article here.

The article and the news story both state that this is not a discovery.  Crocodiles have been reported in trees by locals as well as by scientists in the field. The authors gleaned much of their data by convenience, surfing the Web for pictures. The climbers are overwhelmingly juveniles because they have high ratios of strength to body weight: strong claws and limbs; not much to lift. Fearsome as they appear and can be - death by crocodile is a reality for rural women in Africa - like most animals, they avoid conflict, dropping into the water to escape humans in boats who come within ten feet (three meters) or so.  The thesis of the article is that we admit some ignorance before speculating on the behaviors of dinosaurs.

  

Note that the primary investigator, Vladimir Dinets, has a broad range of interests (Wikipedia here; his own blog here).  He completed his doctorate at the University of Miami in 2011 studying crocodile behaviors, including coordinated hunting, and the use of tools. His publication in an online journal (with an essentially non-academic co-worker) also marks a kind of evolution.  The traditional peer review process of print journals has always been a trade-off between the screening out of crackpots and the exclusion of originality. Also, the long lead times were acceptable in the steam age.  Cyberspace is a new environment. We can share more, faster.  Of course, survival of the fittest in science still depends on empirical validation and falsifiable testing of rationally consistent claims. More subtly, we may well be living in a Renaissance time of broad personal achievements.  Scientists take cameo roles on television shows; and Hollywood actors have degrees in science. The co-authors of the article cited here footnote their marketing interests beyond the university. 

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Epigenetics and Evolution

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Epigenetics and Evolution

The mechanism of evolution has not been discovered.  No consistent theory exists. Random mutations adapting to changing environments was the first suggestion.  When subatomic radiation was discovered, that became a proposal.  Now, epigenetics may indicate another, more powerful, model.  

Darwinian evolution does not explain the lack of intermediate forms. Scientists have bombarded fruit flies and mice with every radiation known and produced no new species.

Jason Head, assistant professor of Earth and Atmospheric Sciences,
at the University of Nebraska Lincoln
holds a fossil and fossil cast from the jawbone of
Barbaturex morrisoni, a large ((2 meters; 30 kgs) lizard
that coexisted with mammals in southeast Asia
40 million years ago. (Press release here.)

Epigenetics is the study of how environmental factors affect the expressions of genes.  We know that we share something like 90% of our DNA with yeasts - and yet we are very different from them. We know that strawberries have not a double helix, but a quadruple helix - yet they are not "superior" to us double helix lifeforms.  
  

A series of prehistoric creature illustrations demonstrates
the evolution of mammals through the ages.
More fact than fiction, these wild characters followed transitional Jurassic period animals
that sported mammalian skull traits and reptilian teeth.
A more familiar design, humans, mark the present.
- National Geographic, "The Rise of Mammals"

Random mutations adapting to changing environments is a (partial) explanation. Radiation seems to create such mutations, also. Epigenetics offers another aspect of understanding. It seems that the mechanisms of process are inherent in all life, but the millions of components are active or inactive according to causes we may now be coming to understand -- given that in 50 or 100 years some other engine will be discovered. 

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Epigenetics

It is not surprising that we share 98.9% of our genome with chimpanzees.  It is challenging to consider that we have about the same number of genes as mice and fish; but we have far fewer genes than plants.  It is a high school science experiment to extract DNA from strawberries. Rather than a double helix, their DNA is wrapped in a quadruple helix. Obviously, the chromosomes and genes are only part of the picture.

“Every time we see two things which are genetically identical, but which aren't the same, we're seeing epigenetics in action.” – Nessa Carey.

Epigenetics is often presented as a new frontier in biology. In fact, the word originated in the 1940s; and the first book came out a decade later. Following Crick and Watson, science was focused on the chromosomes, and then on the genes.  The Human Genome Project was declared to be successful and the equivalent of Project Apollo, both for the complexity of the task and for its promise for our future.  Enter into your Web browser the phrase “scientists find gene for” and it would seem that we are living on the Moon.

• The Epigenetics of Birds by C. H. Waddington (Cambridge University Press, 1952), reviewed by: J. T. Marshall in Bios, Vol. 24, No. 1 (Mar., 1953), p. 59.
• Epigenetics. A Treatise on Theoretical Biology by Soren Lovtrup (Wiley, 1974), reviewed by Clifford Grobstein in The Quarterly Review of Biology, Vol. 50, No. 4 (Dec., 1975), p. 439.

Ghost in Your Genes: PBS Nova (BBC 2006; WGBH 2007, 2008) delivers graphic evidence that genetics is not heredity.  Identical twins raised in the same home diverge, one developing autism.  Twin sisters discover that one has cancer, but the other does not.  The town of Överkalix in northern Sweden provided a paradigmatic story of the effects of environment on heredity as grandparents who had suffered starvation passed the consequences not to their children, but to their grandchildren – depending on the sex of the ancestor and the sex of the descendant. 

The same differentiation was shown in the twins Jenna and Bridget. Bridget’s autism is associated with a genetic deletion in Chromosome 15 - the ubiquitin-protein ligase E3A (UBE3A) gene (Mayo Clinic here).  It is called Angelman Syndrome. However, the same deletion is also associated with Prader-Willi Syndrome, a form of obesity.  The outcome depends on whether the X-chromosome carrying it is inherited from the mother or from the father.  The chromosomes and genes themselves are identical in both cases; the expressions are markedly different.

“The route from genes to morphological characters is convoluted and, in many aspects, still escapes us. This is the reason why we have no hypothesis or model yet of the sequential steps of the development of an organ. There is no evidence that any part of the genome (a gene or a number of genes) codes or determines steps for developing a brain, a heart, or even a strand of hair. It is true that genes or genetic networks are involved or responsible for developing such characters, but their involvement is not linear: a number of different types of cells have to be differentiated and arranged in specific spatial patterns in order to form the organ. But both cell differentiation (Christopher and Helin, 2010) and dedifferentiation (return of cells to pluripotency) (Takahashi and Yamanaka, 2006), as well as activation of gene regulatory networks (Cabej, 2010, pp. 23-24, 39-80), are epigenetically rather than genetically determined. -  Building the Most Complex Structure on Earth: An Epigenetic Narrative of Development and Evolution of Animals by Nelson R. Cabej (Elsevier, 2013, pg 67.)

As depicted in the PBS Nova production, the Överkalix study revealed an array of distinctions laid over the chromosomal inheritances.  Diabetes, early death, or longer life in the descendants depended on whether the affected ancestor was male or female. Whether the ancestor was within the womb or out also effected contrasting outcomes. Exactly when during gestation the event occurred also effected a different result.  

Wikipedia has a bit more to say. “The Överkalix study was a study conducted on the physiological effects of various environmental factors on transgenerational epigenetic inheritance. The study was conducted utilizing historical records, including harvests and food prices, in Överkalix, a small isolated municipality in northeast Sweden. The study was of 303 probands, 164 men and 139 women, born in 1890, 1905, or 1920, and their 1,818 parents and grandparents. 44 were still alive in 1995 when mortality follow-up stopped. Mortality risk ratios (RR) on children and grandchildren were determined based on available food supply, as indicated by historical data. Among the sex-specific effects noted; a greater body mass index (BMI) at 9 years in sons, but not daughters, of fathers who began smoking early. The paternal grandfather's food supply was only linked to the mortality RR of grandsons and not granddaughters. The paternal grandmother's food supply was only associated with the granddaughters' mortality risk ratio.  … The father's poor food supply and the mother's good food supply were associated with a lower risk of cardiovascular death.”

In The Epigenetics Revolution (Columbia University Press, 2012), virologist Nessa Carey tells a similar story from the Dutch Hunger Winter of 1945.  “If a mother was well-fed around the time of conception and malnourished only for the last few months of the pregnancy, her baby was likely to be born small. If, on the other hand, the mother suffered malnutrition for the first three months of the pregnancy only (because the baby was conceived towards the end of this terrible episode), but then was well-fed, she was likely to have a baby with normal body weight. … The babies who were born small stayed small all their lives, with lower obesity rates than the general population. For forty or more years, these people had access to as much food as they wanted, and yet their bodies never got over the early period of malnutrition. …  Even more unexpectedly, the children whose mothers had been malnourished only early in the pregnancy had higher obesity rates than normal.” (pp 3-4). And this tendency to overweight was inherited in the grandchildren (pg. 102).

Nessa Carey has a virology PhD from the University of Edinburgh. She worked for five years at the Metropolitan Police Forensic Science Lab in London. (Her website is here.) In this book, she carries the analogy of a Shakespeare play. The text of Romeo and Juliet is the same for everyone. Almost every cell of your body has exactly the same chromosomes. (Red blood cells and sex cells are exceptions.)  But you do not grow teeth in your eyes. The director’s comments, distributed with the script, provide more information. Methylation and histone deacetylations change the expressions of genes. Moreover, actors write notes in pencil or attach Post-its.  We smoke cigarettes, drink alcohol, and ingest insecticides and herbicides. They affect us, of course, but it seems likely that they also affect our grandchildren.

These facts, should have been the clues to scientists that the chromosomes, the genes, DNA and RNA must be directed by other agents. Otherwise, as Carey says several times, you would grow teeth in your eyes.  By analogy to the exploration of space, a series of giant steps over centuries allowed us to plot the orbits of the planets correctly.  The work of Darwin, Mendel, Crick and Watson, the human genome project, all provided the shoulders of giants for today's research. Epigenetic medicine may be the equivalent of the Lunar colony.

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BioBash Austin Winter 2012

Dr. Matt Winkler

Dr. Paul Lammers

The Austin Chamber’s BioAustin Winter BioBash was held on November 28 at the Driskill Hotel.  About 150 of us celebrated the history of life sciences here in Central Texas with a keynote address from Dr. Matt Winkler, the chairman and CEO of Asuragen.  He was followed by Dr. Paul Lammers chairman and CEO at Mirna Therapeutics.  Mirna (from “micro RNA”), founded by Winkler, is a third-generation daughter of Ambion which Winkler created in 1989 while at the University of Texas and sold in 2005 to the Applied Biosystems Group of Applera and is now a Life Technologies^™ label.

I first met Kyle Schulz of the Round Rock Chamber. He was there on behalf of Austin Community College, seeking to place their biotechnology students in internships with companies.  He found Maggie Bishop for me.  Maggie is with the Austin Chamber and is active on the Austin Biotech group on LinkedIn. She was the emcee for the event. (She is also on the committee to coordinate the creation of the new medical center here.)

UT researcher Scott Rynbrandt with Dr. Simona Perra.
Perra's expertise is the legal regulation of medical devices.

Standing together at a table, were Gail Darling of Gail Darling Staffing who brought her experience in federal contracting, and Nancy Goedeke whose MedMarComm provides marketing and communication services, Jason Choyce of DPR Construction, which specializes in complex projects for advanced technologies, and Kevin Fincher, a tax partner with Padgett Strateman.

Later, Gail introduced me to Stephen Frayser, the new executive director of Texas State University’s STAR Park. The 38-acre Science Technology and Advanced Research Park opened officially on November 9 to provide secure wet labs, clean rooms, and office space.

Not everyone we met had business cards.  (I ran out quickly.  After the Technical Writer cards, I was down to the Criminologist introductions.  I even gave out my Capital City Coin Club Vice President cards.)  And we met a lot of graduate and post graduate students working in university and private labs. 

Our last contacts were a trio from the Austin Technology Incubutor: Mike A. Sandoval of the IC2 Institute, Dr. Lydia V. McClure, an Accenture Venture Partner with Texas Venture Labs at the McCombs School of Business, and Michael R. Pierce also an Accenture Venture Partner.  Earlier this year, the ATI announced the launch of two companies, Savara Pharmaceuticals, and Terapio, which markets the RPLI76 protein as a countermeasure to radiation exposure and chemical threats.  About 30 companies are now in the incubator, including Alafair Bioscience, Integrated Medical Systems, Inc., Admittance Technologies, and Xeris which makes ultra-low volume biopharmaceuticals in auto-injection pens.

Asuragen here

Mirna Therapeutics here

Ambion here

Austin Technology Incubutor here

The IC2 Institute at the University of Texas

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The Origin of ... (What?)

Fertile hybrids demonstrate the limitations of strict Darwinian taxonomy.  According to the easy definitions, a species is a genetically distinct group of plants or animals.  In fact, fertile hybrids are common. And they seem fundamental to evolution.

Dozens of Hybrid Sharks Found Off Australia
January 2nd, 2012 - 10:59 AM ET
The world's first hybrid sharks have been discovered in substantial numbers off the coast of Australia, and scientists say it may be an indication the creatures are adapting to climate change.
Australian researchers say they've found 57 animals that are a cross between the Australian blacktip shark and the common blacktip shark, two closely related but genetically distinct species.  (More here.)

Since 1874, at Halle, a series of successful matings of polar bears and brown bears were made. Some of the hybrid offspring were exhibited by the London Zoological Society. The Halle hybrid bears proved to be fertile, both with one of the parent species and with one another. Polar bear/Brown bear hybrids are white at birth but later turn blue-brown or yellow-white.   DNA studies indicate that some brown bears are more closely related to polar bears than they are to other brown bears. All the Ursinae species (i.e., all bears except the giant panda and the spectacled bear) appear able to crossbreed. (Wikipedia on Ursid hybrids here.)

Granting that hybrids are possible between species of the same genus, such as donkeys and horses, it is too easy to expect them all to be "mules", i.e., sterile.  Macroevolution.net is a blog by biologist Eugene M. McCarthy, PhD.  His site includes biographies of biologists, helpful glossaries of Greek and Latin for science, and much more.  He also provides an authoritative explanation of the prevalence of fertile animal hybrids.  Read here.

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