Abusing Science

Number 36 of a series

Once again I need to post an item on the topic of Abusing Science, and once again I turn to that reliable source, the creationists of Discovery Institute. Here is something directed to me from their Center for Science and Culture. The email service arrives regularly and is titled “Nota Bene.” Make what you want of the title, but here is a link from the email:

WHY CAN’T MONKEYS TYPING FOREVER PRODUCE SHAKESPEARE?

Before communication can begin, there must be an intention to communicate

BY RUSS WHITE ON SEPTEMBER 10, 2019

If you give an infinite number of monkeys typewriters and allow them to type freely, will they eventually produce the works of Shakespeare? Call this the infinite monkey theorem (IMT), widely attributed to Thomas Henry Huxley (1825–1895), best remembered today as “Darwin’s Bulldog” for his defense of Darwin’s theory of evolution. In 2000, a tongue-in-cheek “protocol” for such an experiment was developed. Independently, in 2003, enterprising researchers gave a group of monkeys keyboards, in what they were willing to discuss as a test of the theory:

It is a shopworn challenge, and it centers on the random mutation aspect of Darwinian evolution. How, creationist argue, can a random process using finite resources produce well-crafted organisms? Richard Dawkins addresses the argument in his book, The Blind Watchmaker.

The resemblance of a cloud to a weasel is only mildly diverting, barely worth calling to the attention of our companion. Moreover, we are quite likely to change our mind about exactly what the cloud most resembles.

Hamlet. Do you see yonder cloud that’s almost in shape of a camel?

Polonius. By the mass, and ’tis like a camel, indeed.

Hamlet. Methinks it is like a weasel.

Polonius. It is backed like a weasel.

Dawkins, Richard. The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe without Design (pp. 65-66). W. W. Norton & Company. Kindle Edition.

Dawkins discusses how random permutation of a sequence of letters can eventually form Shakespeare’s line, “Methinks it is like a weasel.” He produced a computer simulation that did exactly that. However, his process incorporates a selection mechanism as required by Darwinian evolution. Dawkins’ process permutes letters in the initial string until a letter fits the required pattern, then the process stops permuting that letter and continues with the rest. In short order the process produces “Methinks it is like a weasel.”

Of course, nature does not act this way. Nature is likely to continue permuting a letter that already fits the expected pattern. Besides, nature does not have an expected pattern as a goal. And that is a thing that bothers the creationists. There must be a goal, or else Darwinian evolution cannot work. It is inside that goal Intelligent Design lives. The “intelligent” part of Intelligent Design has nothing to do with smarts. It’s all about goals. Goals are fed into the process from an external source—a source of intelligence.

And that gets us the the crucial part of White’s thesis. After some lead-up he gets around to:

These issues speak to intent. It is not enough to form symbols; it is not enough to form words; it is not enough to form sentences. Before communication can begin, there must be an intention to communicate which results in the creation of dictionaries and grammars which interact with one another and are often layered in complex ways. Intent, then, is a critical component of communication.

At this point I need to call a halt to a serious misconception by White and others seeking to use information theory to argue against Darwinian evolution. There is a basic misunderstanding of what communication is. I state without authority the following:

  • At the base level information is the entity that mediates cause and effect.
  • At the base level communication is a manifestation of cause and effect.

All higher levels of communication we experience—talking person to person, watching a game on TV—they all distill down to the bullets above. Further justification on request.

White writes, “Before communication can begin, there must be an intention to communicate…,”  and he says this without justification. He wants to construe communication in the same sense as people talking on a telephone, where intent is an ingredient. Intent is not a requisite for communication. But what is intent, and does it exist?

Stating without authority, intent is a feature of living organisms, and it is particularly a feature of animal life forms. Animal life forms move about and do things, and their actions are driven by intent. Let that be the working definition of intent.

Where does intent come from? We are born with it. Without it most animal forms would quickly perish and would not reproduce. Darwinian evolution has produced intent on this planet. Some elaboration.

A baby mammal is born. If it is born without the intent of seeking its mother’s nipple, then it will not live to reproduce. Animal life is driven by goals, the substance of intent. The animal is hungry. The animal seeks food. The animal (often without much thought) seeks to reproduce. Intent is essential to the promulgation of a species.

But whence intent? On this planet before there was life there was no intent. Creationists want to argue there was intent, and, further, that intent came from a transcendental being that exists outside space and time. You can see I am making a bunch of this stuff up.

Ultimately White’s argument appears to go nowhere. He concludes:

Neither of these approaches, however, will ultimately work — real communication requires intent, not only in the communication itself but even in the creation of the shared framework (dictionaries and grammars) in which communication takes place. Ultimately, then, thinking through the IMT shows us that artificial intelligence cannot produce the works of Shakespeare. There can be an illusion of intent but the original intent required to communicate just is not there.

He says much, but tells us nothing. What we are observing is a horrendous abuse of science.

Abusing Science

Number 32 of a series

The propaganda campaign against naturalistic explanations continues relentlessly from the Discovery Institute. David Klinghoffer has been getting a lot of air time on their Evolution News Web site. Here is something recent:

On the Origin of Life, Science Uprising Helps Break a Poisonous Spell

If you follow the news, you’ve seen countless headlines like this: “Amazing Discovery May Hold Key to Origins of Life,” “Found: The Origin of Life,” “Scientists May Have Found the Chemical Compound That Started Life,” and on and on. Michael Egnor wrote about just such a story here yesterday.

The origin of life is the deepest mystery imaginable and it sounds like scientists have it all figured out. Or just about. The new episode of Science Uprising, “Origin of Life: Intelligence Required,” firebombs that persistent and influential myth, advanced by scientists themselves and their media helpers. It does so in just seven devastating minutes.

“We See the Human Soul”

It’s crucial to materialism to believe that blind, natural processes alone could have blundered about and generated life from dumb chemical predecessors. Whether it happened on our planet or another, all the wonders of the first living cell must have come into existence with no need for intelligent design. Any hint to the contrary threatens to topple a whole of way of thinking about human beings and about all life, that denies any reality beyond the material. “We are not materialists,” says the masked narrator of Episode 5, “We see the human soul”:

There follows a video.
Getting past Klinghoffer’s prologue, we get around to discussing the human soul. Some discussion is in order.

Science is a human endeavor to obtain knowledge by studying things. Science is generally considered to concern itself with material things, but that is a shortsighted assumption. There are non-material things that need studying, and the scientific approach applies to them. Things that are not material would include politics and economics. Things that are not material and not subject to scientific study would include the concepts of beauty, love, mathematics, and grammar. Although the human concepts of beauty and love can be studied through the science of psychology, it is the manifestation that is studied, not the thing. Mathematics and grammar are not subject to scientific study, first because mathematics is a human creation, today defined by a handful of axioms and possessing no additional  information content, and grammar is a human creation that is subject to the whims of people, floating with passing time, and not something ripe for scientific study.

The soul is a human contrivance and is not a physical thing. To argue that the souls exists as an entity that can be studied scientifically is fruitless, since the soul means whatever an individual decides it is. There is nothing to study.

But getting to Klinghoffer’s pitch: any evidence that life did not come about by natural processes would be devastating to our way of thinking about the natural world. The problem is, Discovery Institute propaganda advocating supernatural origins is just that. Words and no evidence.
When the Intelligent Design people decide to cut loose from these specious arguments, we can begin to take them seriously. Not before.

Abusing Science

Number 31 of a series

 

Science receives no more diligent assault than from creationists. The modern creationism has been labeled Intelligent Design, solidly underwritten by the Discovery Institute. The DI Center for Science and Culture propagandizes relentlessly for a supernatural explanation for the universe and the existence of life on this planet. Their Web site, Evolution News, posts a steady stream of argument against natural causes. Here is a recent sample:

“We Hold These Truths”: On Design of the Cosmos, Science Uprising Updates Thomas Jefferson

David Klinghoffer does not seem to have any academic credentials related to science, but Wikipedia notes this:

David Klinghoffer is an Orthodox Jewish author and essayist, and a proponent of intelligent design. He attended Brown University in the eighties. He is a Senior Fellow of the Discovery Institute, the organization that is the driving force behind the intelligent design movement. He was a frequent contributor to National Review, and a former columnist for the Jewish weekly newspaper The Forward, to which he still contributes occasional essays.

He has this to say in the referenced posting:

On Independence Day, Evolution News traditionally republishes a wonderful post by Stephen Meyer. Dr. Meyer, the author of Signature in the Cell and Darwin’s Doubt, explains how the philosophy of human rights enshrined in the Declaration of Independence is grounded in recognizing intelligent design. Regarding the “sources of our rights as citizens”:

Here is a portion of the Stephen C. Meyer quote:

There is one source that is more basic than any other, yet that receives less than the attention it deserves. I refer to the idea that there is an intelligent creator who can be known by reason from nature, a key tenet underlying the Declaration of Independence — as well as, curiously, the modern theory of intelligent design.

The birth of our republic was announced in the Declaration through the pen of Thomas Jefferson. He and the other Founders based their vision on a belief in an intrinsic human dignity, bestowed by virtue of our having been made according to the design and in the image of a purposeful creator.

As Jefferson wrote in the Declaration, “We hold these truths to be self-evident, that all men are created equal, that they are endowed by their Creator with certain unalienable Rights.” If we had received our rights only from the government, then the government could justifiably take them away.

And that is so very odd. The idea is, perhaps, to argue science for Intelligent Design, but what Klinghoffer, through Meyer, falls back on is a political statement by the author of the Declaration of Independence. Actually, science is not supposed to work that way. Science works by examining the thing you want to study, in this case the origin of the universe and life on this planet, and base conclusions on what is learned. I may be an amateur scientist, but the statements of a historical figure have no bearing on this field of scientific study.

Klinghoffer continues:

Truths like the ones Jefferson articulated are truths forever, but we need to update the idiom to suit the times. Dr. Meyer’s work, including his upcoming book, The Return of the God Hypothesis, powerfully details the current scientific evidence that supports what Jefferson called the “conviction of design” in biology and cosmology. A serious volume like that is written to nail down the science conclusively. But a related purpose is served, using a different, punchier idiom, by the new Science Uprising series, and in particular Episode 4. At just 8 minutes in length, it’s concise and provocative:

There follows a link to this video.

Abuse of science does not require misstatement of scientific principles. In many cases it boils down to a drumbeat of propagandizing.

Abusing Science

Number 29 of a series

The Discovery Institute continues its campaign to paint Intelligent Design as a valid scientific enterprise. A recent post to their Evolution News site highlights their approach:

Watch: Stephen Meyer Expertly Punctures the Rule of Methodological Naturalism

Following on chemist Marcos Eberlin’s comments yesterday about intelligent design and the definition of science, watch philosopher Stephen Meyer expertly puncture the idea that science requires an approach of methodological naturalism (MN):

[Link to the video]

The rule, as he explains, is arbitrary. True, the designing agent inferred by ID theory is not directly observable, but neither are the elementary particles. Both are inferred. And the so-called demarcation criteria that would exclude ID as science would, if applied consistently, also exclude Darwinian theory. Most fundamentally, MN shuts down on principle what ought to be the goal of all science: objectively seeking the truth about nature, whatever that truth might be.

Particularly galling is the assertion “True, the designing agent inferred by ID theory is not directly observable, but neither are the elementary particles. Both are inferred.” What may not be obvious to David Klinghoffer is that while the “designing agent” is inferred (conjectured, postulated, imagined), elementary particles are not. Not, that is, unless the definition of the word “inferred” has been changed.

The designing agent, although proponents may be reluctant to admit so, is the god of Abraham. There is no physical evidence for the existence of this entity, and no manner of approach for probing its existence has been proposed.

Fundamental particles include protons, neutrons, electrons, muons, and such, and their properties and their presence are routinely studied. These things have mass, and they can do real damage when flung about. The notion that the fundamental particles of physics are on the same level as an imagined transcendental being speaks to the abysmal level of scientific thinking among fans of Intelligent Design. If you want to see abuse of science done so ineptly, here it is.

Abusing Science

Number 28 of a series

The above meme is supposed to be an argument for Intelligent Design, a modern form of creationism. A similar argument is the one that invokes fine tuning:

The Radio at the Edge of the Universe

Some atheists have been crowing lately about the rise of the “nones.” Many of those “nones” aren’t atheists, and the trend toward atheism is greatly exaggerated. But the way many scientific materialists talk, anyone capable of walking while chewing gum must see the “overwhelming evidence” that “God is dead.” 

Wait. That’s just the intro. Here is the meat of Marcos Eberlin’s argument:

Think of a radio dial that needs to be set at precisely the right frequency — “tuned” — to find the desired station. If the universe were a radio and the desired setting allows for life, it would have dozens of dials for setting the values of the universal constants. Muff even a single of these dial settings at the beginning of the universe, by even a tiny bit, and the result is a universe that can never host life. 

Confronted by this, distinguished physicist Fred Hoyle commented, “A common sense interpretation of the facts suggests that a superintellect has monkeyed with physics, as well as with chemistry and biology, and that there are no blind forces worth speaking about in nature.”

Failing to comprehend the circumstances underlying our existence, more so the existence of the Universe, we must fall back on legends perpetrated by Bronze Age tribesmen living on the eastern region of the Mediterranean Sea. I am thinking Eberlin expects too much of me. Here is some background:

Marcos Nogueira Eberlin (born 4 March 1959) is a Brazilian chemist and professor at the Institute of Chemistry of the University of Campinas. He is a member of the Brazilian Academy of Sciences and received the Brazilian National Order of Scientific Merit in 2005 and the Thomson Medal in 2016.

Eberlin discovered the Eberlin Reaction during his work on gas phase ion chemistry, and he and his research group introduced EASI (Easy Ambient Sonic-spray Ionization), an ionization technique used in mass spectrometry.

Eberlin is an advocate of intelligent design in Brazil, a pseudoscience on which he also lectures and he has signed the Dissent From Darwinism statement. He is a creationist also, and has said that evolution theory is a fallacy.

There is more. He is the author of Foresight: How the Chemistry of Life Reveals Planning and Purpose. The notion that wacky ideas about science are relegated to back stream advocates such as William Dembski and Stephen C. Meyer needs to be extinguished. Eberlin continues:

But in fact, intelligent design is testable. Also, if the above definition were the proper definition of science, only one worldview would be allowed in science: naturalism. And that biased restriction would mean that evidence of apparent foresight in the universe and life must be ignored or explained away.

He bemoans restricting science to naturalism. The problem is that beyond naturalism we have the supernatural. The supernatural exists in a realm where anything can happen, and by this means anything can be explained by made-up stories. Read his posting.

The Kansas Board of Education has defined science as a human endeavor aimed at explaining the natural world, though they added one sweeping restriction: It can only appeal to natural forces. “Science is restricted to explaining only the natural world, using only natural cause,” the board wrote. “This is because science currently has no tools to test explanations using non-natural (such as supernatural) causes.”

But in fact, intelligent design is testable. Also, if the above definition were the proper definition of science, only one worldview would be allowed in science: naturalism. And that biased restriction would mean that evidence of apparent foresight in the universe and life must be ignored or explained away.

Follow the link to another Evolution New post regarding testability of Intelligent Design. I will cover that in a future item for this series.

Abusing Science

Number 23 of a series

On Sunday, 19 May, Liam Feldman will host a reading/review of Why Intelligent Design Fails by Matt Young and Taner Edis. The meeting will be at Barnes & Noble 321 NW Loop 410 #104 in San Antonio, starting at 3 p.m. Feel free to come out and join the discussion.

With that in mind, the topic of this post is a book by the Discovery Institute, the leading promoter of Intelligent Design. It’s Science and Human Origins, compiled by Ann Gauger, Douglas Axe, and Casey Luskin. They are all associated with the Discovery Institute. From Amazon:

Evidence for a purely Darwinian account of human origins is supposed to be overwhelming. But is it? In this provocative book, three scientists challenge the claim that undirected natural selection is capable of building a human being, critically assess fossil and genetic evidence that human beings share a common ancestor with apes, and debunk recent claims that the human race could not have started from an original couple.

This is an interesting stance for Intelligent Design, because the philosophy was resurrected 30 years ago to pull the creationist movement away from biblical  origins and to disguise it as a science-based endeavor. Intelligent Design and the Discovery Institute Center for Science and Culture were supposed to acknowledge inescapable science and get people to thinking an unknown creator is behind this science. UC Berkeley law professor (now  retired) Phillip E. Johnson is credited with giving Intelligent Design new life and is considered the godfather of the modern movement. Jon Buell is president of the Richardson, Texas, based Foundation for Thought and Ethics. FTE is publisher of the creationist book Of Pandas and People, made famous in the Kitzmiller court case. Both attended a symposium titled ” Darwinism: Scientific Inference or Philosophical Preference?” at Southern Methodist University, Dallas, Texas, March 26-28, 1992.

It was an opportunity to ask the pivotal question, and I did. Did these two educated men agree the earth is billions of years old and that humans share a common ancestry with other life forms? Both agreed. The ground may have shifted since then, because outpourings from the DI seem to have dropped the facade of scientific literacy. The book that is today’s topic bears that out.

Reviewing books such as this and picking them apart on inconsistencies and obvious wrong facts is a bunch of fun, but I have no experience in the related science, so it’s best if I fall back on others who do. Someone who seems to have given this book a close look is Paul McBride. From a post by Richard P. Hoppe on the Panda’s Thumb site:

Fortunately for me, I’m spared the chore of reading and critiquing the book. Paul McBride, a Ph.D. candidate in vertebrate macroecology/evolution in New Zealand who writes Still Monkeys, bit the bullet and did a chapter by chapter (all five chapters) review of the book. The book doesn’t come out looking good (is anyone surprised?). I’m going to shamelessly piggyback on McBride’s review. I’ll link to his individual chapter reviews, adding some commentary, below the fold.

The book has five chapters, and the one I appear to have found most interesting is chapter 5, “The Science of Adam and Eve.” I am guessing by he title that all pretense of scientific rigor has been discarded. We are back to Genesis with a bang.

My copy of the book is a Kindle edition, and one thing you can do with these is highlight sections of text. I notice I highlighted entire paragraphs when I first went through the book. Here is one section.

Using population genetics, some scientists have argued that there is too much genetic diversity to have passed through a bottleneck of just two individuals. But that turns out not to be true.

Gauger, Ann. Science and Human Origins . Discovery Institute Press. Kindle Edition.

Here is another.

Now, I am a scientist, and not a theologian, but I feel obligated to speak. The challenge being posed to two first parents is a scientific one, so it deserves a scientific response. My purpose in this chapter is not to engage in Biblical interpretation or to pass judgment on the various views Christians hold about Adam and Eve. Instead, I propose to focus on the scientific argument and its validity.

Gauger, Ann. Science and Human Origins . Discovery Institute Press. Kindle Edition.

And there it is. Genesis is true, and Adam and Eve were real people, and we all sprang from this single pair.

But wait! Real scientists hold a similar view. Richard Dawkins, no friend of the Bible, agrees that today’s human population sprang from one woman, exact identity unknown.

The second conclusion of the Berkeley group is less controversial. No matter where Mitochondrial Eve lived, they were able to estimate when. It is known how fast mitochondrial DNA evolves; you can therefore put an approximate date on each of the branch points on the tree of divergence of mitochondrial DNA. And the branch point that unites all womankind—the birth date of Mitochondrial Eve—is between a hundred fifty thousand and a quarter of a million years ago.

Dawkins, Richard. River Out of Eden (Science Masters Series) (pp. 52-53). Basic Books. Kindle Edition.

The difference is Mitochondrial Eve was not the first woman. Some elementary mathematical analysis will demonstrate to you that, given the branching inherent in sexual reproduction, any two people alive today should be able to trace their lineage back to a point the paths intersect. Dawkins goes further. He uses the rate of mitochondrial mutation to compute an approximate date of our common ancestry, in the female line of descent.

On the matter of common descent, I first noticed a divergence in thinking among the new creationists at a conference in Dallas in November 2003. Ray Bohlin was there, along with creationist Ide Trotter. Bohlin holds a  Ph.D. in molecular and cell biology from the University of Texas at Dallas, and he is also a key person at Probe Ministries in Richardson, Texas:.

Raymond G. Bohlin is Vice President of Vision Outreach with Probe Ministries.

A plenum session gave participants the opportunity to ask questions and to make statements. Ray Bohlin announced to those present he believed all life forms on this planets have a common ancestry. Except humans. People have a different line of descent.

Creationists Ide Trotter and Ray Bohlin in 2003

I yield the remainder of your time to reading Paul McBride’s more thorough examination of this creationist book. Get a copy for yourself if you are interested. It’s a grand exemplar of the abuse of science.

Abusing Science

Number 9 of a series

Creationist David Shormann testifies at the textbook hearings, Austin 17 September 2018

This has some history. Years ago, before Facebook, I was having a discussion on an Internet group. The matter of John Templeton came up, and I responded that he was a creationist. Why did I say that, I was asked. Because his foundation, the John Templeton Foundation, contributed money to the Discovery Institute (DI), the primary group supporting creationism, particularly Intelligent Design (ID), in this country. And that was that.

Except Templeton has since died, but his foundation continues to fund efforts to reconcile science with religion. Another regression: I am auditing a college course on philosophy of atheism, and some of the assigned reading is related:

As the Templeton-prize-winning physicist Paul Davies points out at the end of his book The Goldilocks Enigma, even putting aside all the other difficulties:

The other main problem with intelligent design is that identity of the designer need bear no relation at all to the God of traditional monotheism. The ‘designing agency’ can be a committee of gods, for example. The designer can be a natural being or beings, such as an evolved super-mind or super-civilization existing in a previous universe, or in another section of our universe, which made our universe using super-technology. The designer can also be some sort of superdupercomputer simulating this universe. So invoking a super-intellect… is fraught with problems.

Law, Stephen. Humanism: A Very Short Introduction (Very Short Introductions) (p. 47). OUP Oxford. Kindle Edition.

Yeah, Templeton continues to haunt me from the grave. What the Templeton Foundation does, in part, is to fund research into whether religious faith can be reconciled with modern science.

On that we pause again:

Is the Government Buying Science or Support? A Framework Analysis of Federal Funding-induced Biases

The purpose of this report is to provide a framework for doing research on the problem of bias in science, especially bias induced by Federal funding of research. In recent years the issue of bias in science has come under increasing scrutiny, including within the scientific community. Much of this scrutiny is focused on the potential for bias induced by the commercial funding of research. However, relatively little attention has been given to the potential role of Federal funding in fostering bias. The research question is clear: does biased funding skew research in a preferred direction, one that supports an agency mission, policy or paradigm?

That’s from the Cato Institute, a libertarian entity that opposed to scientific findings that would lead to the need for corrective government action. Libertarians want less government, but biological science is not one of their prime targets.

So, there is this accusation that scientists do research and produce fundings that favor their sponsors—particularly government sponsors. Take another look. If you want to see publication bias, consider funding that asks researchers to search for (confirm?) a religious-based interpretation of evolution, particularly human evolution. Anything that leaves room for a biblical narrative.

Re-enter the Discovery Institute. From their Evolution News site:

Intelligent Design Aside, from Templeton Foundation to the Royal Society, Darwinism Is Under Siege

Don’t let anyone tell you the evolutionary paradigm isn’t in serious turmoil. Science Magazine announces an $8.7 million project by the Templeton Foundation seeking an “evolution rethink.” I’m trying to think of the last time I heard Science reporting on support for a “gravity rethink,” or a “heliocentrism rethink.” The gist of it:

For many evolutionary biologists, nothing gets their dander up faster than proposing that evolution is anything other than the process of natural selection, acting on random mutations. Suggestions that something is missing from that picture — for example, that evolution is somehow directed or that genetic changes can’t fully explain it — play into the hands of creationists, who leap on them as evidence against evolution itself.

It took some searching. The email from Discovery Institute showed up on my Facebook feed a day or two ago, but the link is to an item published on Evolution News 22 April 2016. Full disclosure: I belong to the American Association for the Advancement of Science, (AAAS), which publishes Science Magazine, and I dug into their on-line back issues to find the referenced article. It’s on pages 394-395 of the 22 April 2016 issue. Obviously David Klinghoffer was quick off the mark to post his response. Here is somebody who doesn’t allow grass to grow under his feet.

I blinked hard a few times, but I was never able to figure out why Klinghoffer did not provide a complete citation to the Science article, but I consider the possibility he wanted to give me a workout to keep me occupied during my retirement. Anyhow, I snapshotted the article and saved the text, which I am posting along with a link. Read for yourself to get the complete story.

Significant in the Science article are references to research into ways traits are acquired by organisms. The lead photo above shows creationist David Shormann testifying at the school book hearings in Austin six years ago. Shormann markets a line of educational materials for home-schooling, and he operates a religious school in the Houston area. The desire to protect children from secular influences is a prime motivator for home-schooling in this country.

Anyhow, in his testimony before the board, Shormann emphasized the matter of epigenetics.

Epigenetics is the study of heritable phenotype changes that do not involve alterations in the DNA sequence. The Greek prefix epi- (ἐπι- “over, outside of, around”) in epigenetics implies features that are “on top of” or “in addition to” the traditional genetic basis for inheritance. Epigenetics most often denotes changes that affect gene activity and expression, but can also be used to describe any heritable phenotypic change. Such effects on cellular and physiological phenotypic traits may result from external or environmental factors, or be part of normal developmental program. The standard definition of epigenetics requires these alterations to be heritable, either in the progeny of cells or of organisms.

He contended that his school curriculum includes epigenetics, while the text books being proposed for adoption at the time did not. For this reason he recommended that none of the proposed biology books be adopted. From the Science article:

Advocates stress that animals, plants, and even microbes modify their environments, exhibit plasticity in their physical traits, and behave differently depending on the conditions they face. Chemical modifications of the DNA that affect gene activity—so-called epigenetic changes—seem to explain some of this flexibility. These and other factors suggest to some biologists that an organism’s development is not simply programmed by the genetic sequences it inherits. For them, such plasticity implies that parents can influence offspring not just through their DNA but by passing on the microorganisms they host or by transmitting epigenetic marks to subsequent generations. “Innovation may be a developmental response that becomes stabilized through genetic changes;’ explains Armin Moczek, an evolutionary developmental biologist at Indiana University, Bloomington. [emphasis added]

Obviously Charles Darwin knew nothing about epigenetics, nor even genetics, but creationists of all stripes continue to attack the Darwinian construct with the idea that bringing down modern science will leave the religiously-inclined gazing more toward the God of Abraham. It’s classic abuse of science. Please read the entire Klinghoffer post. I will allow him to have the last word, since it reinforces my view of what is going on here:

ID, obviously, is one source of the current challenge to Darwinism, but it’s only one source. You could erase ID advocates entirely from the battle map, and Darwinian theory would still be under siege. Evolution’s smug cultists are in denial about that, but it’s true.

Abusing Science

Number 2 of a series

This series is inspired by Philip Kitcher’s book of the same name.

Back when Kitcher published this book, creationists were of the worst kind. They wanted to convince people that the story of Genesis was true, the universe and all life forms were created by the God of Abraham in the course of six days about 6000 years ago. Furthermore, the story of Noah and a worldwide flood was for them a part of world history. It was tough sledding.

Modern science, starting around 200 years ago, began to undercut these fables. The science of geology pointed to an ancient Earth. Darwin’s explanation of biological evolution abolished the human species’ special place among living things, and studies of radioactive elements in the earth’s crust pointed to a planet over four billion years old. Finally modern cosmology accounted for the formation of the universe over 13 billion years ago—and by natural causes.

In a landmark court case, Federal Judge William Overton ruled in an Arkansas case in 1982 that “creation science,” as creationists then called their theories, is not science. Rather, it is religious-based conjecture. Subsequent attempts to get around this finding terminated in a subsequent loss in Louisiana in a case termed Edwards v. Aguilard. A proposal to require teaching alternatives to the theory of evolution was found to be religiously motivated and in violation of the Constitution.

The response from the fundamentalist religious community was to usurp the Young Earth Creationists with a new breed of ecclesiastical scientists and a fresh approach. These creationists were, and still are, real scientists with valid Ph.D. degrees in related fields, and they largely avoided mention of biblical stories about the age of the earth and the God of Abraham. They revived William Paley‘s concept of Intelligent Design. They insist that the complexity of modern life forms is evidence of a higher intellect behind the world we see today. In future installments I will touch on the activities and the writings of the various individuals involved, but to get things going I will delve into something recent.

The organization in this country that most prominently advocates for Intelligent Design is the Discovery Institute, based in Seattle. More specifically, the DI’s Center for Science and Culture is the focus for ID, and they host a blog site titled Evolution News.

A principal talking point used to support ID is the source of novel information. The contention is that for novel life forms to develop, some additional information must be supplied. For illustration purposes, imagine an animal like a fish. It is generally agreed that the ancestors of present day land animals, lizards, for example, were fish. The proponents of ID will point out that fish have no legs, and for land animals to walk around, given that lizards evolved from fish, then new information about legs had to be supplied from somewhere. Or from somebody. Novel information cannot come out of thin air. There must be a supreme intellect behind the development of land animals with legs.

Novel information, and information in general, is a large part of ongoing arguments for Intelligent Design. The CSC person charged with developing and supporting this connection between is mathematician William Dembski. To illustrate how far the modern creationists buy into the relevance of Dembski’s work, he has been dubbed to be the “Isaac Newton of information theory.”

William Dembski is the Isaac Newton of information theory, and since this is the Age of Information, that makes Dembski one of the most important thinkers of our time. His “law of conservation of information” represents a revolutionary breakthrough. In Intelligent Design Dembski explains the meaning and the significance of his discoveries with such clarity that the general public can readily grasp them.He convincingly diagnoses our present confusions about the relationship between science and theology and offers a promising alternative.

[Robert C. Koons, Professor of Philosophy, University of Texas at Austin—from the dust jacket of Intelligent Design: The Bridge Between Science & Theology, InterVarsity Press, 1999.]

Being compared to Isaac Newton is a dab of adulation that Dembski has never disavowed.

So we have it. Information theory continues to crop up in items aimed at supporting Intelligent Design, and that brings us to this:

Bacteriophages, Budding Yeast, and Behe’s Vindication

Ann Gauger is a senior research scientist at Biologic Institute. Her work uses molecular genetics and genomic engineering to study the origin, organization and operation of metabolic pathways. She received a BS in biology from MIT, and a PhD in developmental biology from the University of Washington, where she studied cell adhesion molecules involved in Drosophila embryogenesis. As a post-doctoral fellow at Harvard she cloned and characterized the Drosophila kinesin light chain. Her research has been published in NatureDevelopment, and the Journal of Biological Chemistry.”

Specified complexity is an argument proposed by Dembski and used by him in his works promoting intelligent design. According to Dembski, the concept is intended to formalize a property that singles out patterns that are both specified and complex. Dembski states that specified complexity is a reliable marker of design by an intelligent agent, a central tenet to intelligent design and which Dembski argues for in opposition to modern evolutionary theory. The concept of specified complexity is widely regarded as mathematically unsound and has not been the basis for further independent work in information theory, complexity theory, or biology. Specified complexity is one of the two main arguments used by intelligent design proponents, the other being irreducible complexity.
Abuse of science did not end with demise of the Young Earth Creationists. This series will continue to turn over such cases until I run out of ink.

Abusing Science

First of a series

Philip Kitcher published the book in 1982, and a friend at work recommended I get a copy. I will do a review later, but for now it’s going to serve as the title for a series related to the abuse of science. I will get started with the matter of a sponsored posting that keeps showing up on my Facebook timeline. It’s from the Center for Science and Culture, a division of the Discovery Institute, headquartered in Seattle. The pertinent text goes as follows:

An artificial and oppressive wall separates the realms of faith and science, a wall that needs to be demolished.

That’s the provocative thesis of the Dallas Conference on Science and Faith, to be held just two months from now, January 18-19, 2019. Join philosopher of science Stephen Meyer, radio host and bestselling author Eric Metaxas, theologian and Privileged Planet author Jay Richards, and Rice University synthetic organic chemist James Tour as we breach the fabled wall.

[Links added]

The Facebook posting includes a link to a video, and you should take some time to view it. Here is the link:

www.youtube.com/watch?v=WWdihTt3tLM

Pertinent screen shots give an idea as to the message. Some disturbing findings are revealed.

Fifty-five percent of American adults believe science and religion are in conflict. (Surprise, surprise!)

Nearly a quarter of young adults from a Christian background think Christianity is anti-science.

Among college freshmen, a significant percentage believe the universe arose by chance.

Let’s take a deep look at these findings.

First, science and religion are in conflict. Science is a way of knowing that involves looking at what’s going on in the natural world and coming up with explanations that fit the findings. Religion answers questions by making stuff up. It cannot be put more straightforward than that.

Second, Christianity is anti-science to the extent that many Christians support their beliefs by denying established science.

Third, good for those freshmen. The universe did not arise by means of an intelligent being intent on performing an experiment with natural law. In that sense, the universe did arise by chance.

So what’s the point of this Science and Faith conference in Dallas?

The CSC has a history, going back more than 20 years, of failed attempts at undermining scientific explanations for the existence of life and even the universe. The obvious intent is to replace religious explanations, their own, for explanations based on fact. Phillip Johnson, a significant catalyst for the revival of the Intelligent Design argument, is the principle author of the Wedge Strategy:

The Wedge Strategy is a creationist political and social action plan authored by the Discovery Institute, the hub of the pseudoscientific intelligent design movement. The strategy was put forth in a Discovery Institute manifesto known as the Wedge Document. Its goal is to change American culture by shaping public policy to reflect politically conservative fundamentalist evangelical Protestant values. The wedge metaphor is attributed to Phillip E. Johnson and depicts a metal wedge splitting a log.

That the CSC has not been successful in its goals after more than 20 years speaks not so much for the skepticism of the American public as for the creationists’ delusional nature. They keep putting forward arguments that are demonstrably wrong. Thirteen years ago the push to promote Intelligent Design failed spectacularly when the Dover, Pennsylvania, school district attempted to insert the creationist text Of Pandas and People into the science curriculum.

Come forward to 2019, and the CSC people will be having another go at it. The effort appears to be headed up by Stephen C. Meyer, a founder of the CSC. Here is what he has to say (from the video):

Are science and faith incompatible? No! Just the opposite. Science is providing support for faith.

That has to be about the most profoundly stupid statement to ever show up on my view screen. Scientific finds provide no support for the existence of the supernatural, let alone supernatural explanations for life and the creation of the universe. The fact of the matter is that science has worked 500 years at undermining the basic tenets of religious supposition. That would be starting with the age of the earth right on through the supposed miracle of the Shroud of Turin. Additional examples on request.

The CSC posting announces others who will be presenting at the conference. Will I attend and do a review? Only if I can get a pass from Barbara Jean. May Jesus have mercy on my soul.

The Years of Living Stupidly

Number 11 in a series

The title pretty much explains it all. Some people go for years, their entire lives sometimes, in a continuous state of false belief. That would include a bunch of folks at the Discovery Institute’s Center for Science and Culture. Vis their Conference on Science and Faith, scheduled for Dallas in January:

Dallas Conference on Science & Faith, January 18-19: “Tear Down This Wall!”

What If?

Whether science can cast light on the eternally urgent questions has been a subject of debate by philosophers going back to the Middle Ages and beyond. It’s also, obviously, very much of the moment today. From the announcement of the event by Discovery Institute:

According to a nationwide survey, more than two-thirds of atheists and one-third of agnostics believe that “the findings of science make the existence of God less probable,” while nearly half of self-identified theists believe “the findings of science are neutral with regard to the existence of God.”

But what if there is another option? What if the discoveries of science actually lend support to belief in God?

The Return of the God Hypothesis

At the Dallas Conference on Science and Faith, we’ll tackle subjects including “The Return of the God Hypothesis,” “The Miracle of the Universe,” “The Privileged Planet,” “The Mystery of the Origin of Life,” and “Darwin’s Doubt.” There will be plenty of opportunities for the audience to participate — questioning, challenging, and learning from a group of stellar scholars.

Yes, this is a lot to unload. Start with “Whether science can cast light on the eternally urgent questions has been a subject of debate by philosophers going back to the Middle Ages and beyond.” The implication is that faith, and religion in particular, can be invoked in places where science, otherwise known as formalized common sense, is unable to winkle out answers. People, if you study a matter earnestly, turning it this way and that, and you still can’t come up with a worthy answer, the solution is not to just close your eyes and make something up. Made up answers are generally worth the amount of energy it takes to have a bad dream. That is to say, they are not worth sharing with your worst enemy.

The piece posted to Evolution News goes on to cite that agnostics and atheists generally think the application of scientific approaches tend to make belief in God (the God of Abraham in particular) unnecessary to accommodate.

“But what if there is another option? What if the discoveries of science actually lend support to belief in God?” Now this is something worth considering. It is right up there with “What if analysis of elephant’s tusks lead to the conclusion that penguins do not possess a liver?” Both make a lot of sense.

If you are among the many who think this conference is not going to offer anything worth carrying home, then you might want to save yourself the $15 registration fee and also a trip to Dallas.

The Years of Living Stupidly

Number 8 in a series

The photo shows creationists Walter Bradley and Ide Trotter at a workshop hosted by the Texas Education Agency, where they were assigned the task of reviewing high school biology texts for public schools.

I tend to devote this series to people being stupid about science, such as by using science and religion in the same sentence. That often comes about when people, caught up in religion, carry the contagion with them when they step across the line into fields of science—or into any other area requiring rational thought. Who does this a lot are the people at the Discovery Institute (DI), the premier organization in this country promoting Intelligent Design.

A rich resource on this kind of foolishness is the DI’s Center for Science and Culture (CSC), founded by creationist Stephen C. Meyer, among others. the thinking of DI fellows and the CSC are made public on an associated site called Evolution News. More recently, I found the following posted on the Discovery Institute site:

Neurosurgeon Michael Egnor: Why Machines Will Never Think

From remarks at the official launch of the Walter Bradley Center for Natural and Artificial Intelligence

ROBERT CROWTHER, II AUGUST 1, 2018

This is interesting on multiple levels, one of which relates to Dr. Michael Egnor, whom we have met before:

Michael Egnor is a prominent neurosurgeon and a professor in the Department of Pediatrics at Stony Brook University. He became inoculated against evolution (the science of biological evolution) after reading  Michael Denton‘s book Evolution: A Theory in Crisis. Egnor has aligned himself with the Discovery Institute Center for Science and Culture (CSC), one of the leading creationist organizations in this country and likely the absolute leader in support of the Intelligent Design version of creationism. An excerpt from one of his posts on the CSC’s Evolution News blog may be characteristic:

Scopes was put on trial for violating the Butler Act, which prohibited teaching human evolution to schoolchildren in Tennessee. What Scopes actually taught, if anything, is unclear, because Scopes was untruthful about what he did, and the trial was a legal ploy to spur a Supreme Court ruling. The truth was a secondary consideration at best to Scopes and to his team.

Hunter’s textbook Civic Biology was racist and taught eugenics. It was vile stuff. If a teacher taught from it today, he would not be prosecuted for violating the Butler Act. He would be prosecuted for federal civil rights violations.

Follow the link and read the post for complete details. Anyhow, Dr. Egnor now proposes to  boldly step outside his realm of expertise and into the quagmire that is Artificial Intelligence (AI). I took some time to read through his thinking on the matter, and you are invited to do likewise. What I found is that, while Dr. Egnor is likely correct in some of his conclusions, he is correct for the wrong reasons. An illustration from Dr. Egnor’s monograph:

What is the hallmark of human thought, and what distinguishes thoughts from material things? Franz Brentano (1838–1917), a German philosopher in the 19th century, answered this question decisively. All thoughts are about something, whereas no material object is inherently “about” anything. This property of aboutness is called intentionality, and intentionality is the hallmark of the mind. Every thought that I have shares the property of aboutness—I think about my vacation, or about politics, or about my family. But no material object is, in itself, “about” anything. A mountain or a rock or a pen lacks aboutness—they are just objects. Only a mind has intentionality, and intentionality is the hallmark of the mind.

Another word for intentionality is meaning. All thoughts inherently mean something. A truly meaningless thought is an oxymoron. The meaning may be trivial or confusing, but every thought entails meaning of some sort. Every thought is about something, and that something is the meaning of the thought.

That’s what I like about philosophers. First, they fall back on what other philosophers have said—with little or no attempt at confirmation, and they talk of things being true, apparently for the sole reason that they say they are true. How about, “Only a mind has intentionality, and intentionality is the hallmark of the mind?” Whether he realizes it or not, what Dr. Egnor has just done is to write a definition for the word mind. Please note the statement does not preclude a computer becoming a mind. What it says is that if a computer attains intentionality, then a computer can become a mind. Dr. Egnor never offers any reason a computer cannot become a mind. He says it, so it must be so.

Under other circumstances I would pass off Dr. Egnor’s musing as the product of religious corruption. I cannot do this, because it happens that Dr. Egnor, in his musings, is in the company of mental giants, one being renowned mathematical physicist Roger Penrose. It happens that Penrose is of the same mind as Dr. Egnor in this matter. Neither believes a computer can become a mind, and Penrose has written a book on the matter titled The Emperor’s New Mind. I have had a copy of the book since it came out in 1989, but I did not read through it. That’s because I quickly encountered conclusions I cannot sign off on. In the book, Penrose seems to invoke the argument from incredulity, much as Dr. Egnor does above. Martin Gardner wrote the forward, concluding:

Penrose’s achievements in mathematics and physics– and I have touched on only a small fraction– spring from a lifelong sense of wonder toward the mystery and beauty of being. His little finger tells him that the human mind is more than just a collection of tiny wires and switches. The Adam of his prologue and epilogue is partly a symbol of the dawn of consciousness in the slow evolution of sentient life. To me he is also Penrose– the child sitting in the third row, a distance back from the leaders of AI– who dares to suggest that the emperors of strong AI have no clothes. Many of Penrose’s opinions are infused with humour, but this one is no laughing matter.

Penrose, Roger. The Emperor’s New Mind: Concerning Computers, Minds, and the Laws of Physics (Oxford Landmark Science) (Kindle Locations 143-148). OUP Oxford. Kindle Edition.

Here is a sampling of Penrose’s own thinking, highlighted in my Kindle edition by earlier readers:

Most particularly, I argue that the phenomenon of consciousness cannot be accommodated within the framework of present-day physical theory.

Penrose, Roger. The Emperor’s New Mind: Concerning Computers, Minds, and the Laws of Physics (Oxford Landmark Science) (Kindle Locations 153-154). OUP Oxford. Kindle Edition.

My reasoning, as presented in this book, has two main strands to it. The first of these endeavours to show, by appealing to results of Gödel (and Turing) that mathematical thinking (and hence conscious thinking generally) is something that cannot be encapsulated within any purely computational model of thought. This is the part of my argument that my critics have most frequently taken issue with. The second strand of the reasoning is to demonstrate that there is an important gap in our physical picture of the world, at a level which ought to bridge the submicroscopic world of quantum physics to the macro-world of classical physics. My viewpoint demands that the missing physics falling within this gap, when found, will play an essential part in the physical understanding of the conscious mind. Moreover, there must be something outside purely computational action in this sought-for area of physics.

Penrose, Roger. The Emperor’s New Mind: Concerning Computers, Minds, and the Laws of Physics (Oxford Landmark Science) (Kindle Locations 164-170). OUP Oxford. Kindle Edition.

Penrose appears to set aside a special place for living forms, and he does not limit this thinking to the mind. I took four courses from  Wolfgang Rindler, and after I got my degree I came back to the campus to attend a 70th birthday party for him. Roger Penrose attended, as well, and he gave a talk in which he explained that living material needs to be explained in terms of  quantum physics. I  got that this was an explanation in terms of quantum  physics beyond the fact that quantum physics determines basic chemical properties of the elements, and I asked the question, “Are you resurrecting the concept of vitalism?” He assured me he was not, and I let it go at that. For the moment. The truth is, I consider Penrose’s invocation of quantum mechanics as vitalism dressed up in a lab coat.

Apparently anybody can be a philosopher, so I’m thinking about giving it a try. In future postings I will provide rational explanations for human thought, life, death, and the origin of the universe. Keep reading.

The Years of Living Stupidly

Number 6 in a series

Цифровая репродукция находится в интернет-музее Gallerix.ru

A Facebook friend from time to time posts links to the Discovery Institute’s Evolution News blog. Much thanks. I need to keep up.

Evolution News has a number of authors, mostly notable creationists. These would include Stephen C. Meyer, Michael Behe, John West, and Jonathan Wells. This item was posted by Ann Gauger:

Ann Gauger is a zoologist with a BS in biology from MIT and a 1989 PhD from the University of Washington. As a post-doctoral fellow at Harvard she cloned and characterized the Drosophila kinesin light chain. Her research has been published in Nature, Development, and the Journal of Biological Chemistry. She also has a number of years of experience as a homeschool teacher.

From Evolution News:

Is There a First Human Couple in Our Past? New Evidence and Arguments

Ann Gauger March 5, 2018, 3:51 PM

Dennis Venema is associate professor at Trinity Western University. His book Adam and the Genome is under active discussion here and over at BioLogos. The central question implied in the title of that book is: does our genome rule out Adam? Could humanity have had its origin in a first pair, or did it have to come from a population of at least several thousand?

This question has been addressed by numerous scientists in the past, ever since human genetic data began to roll in. And all of them, as far as I know, have said that yes, our genome rules out Adam. We are the product of common descent. We are descended from an ape-like population of at least several thousand. This we have heard before.

Now here’s where it gets interesting. There has been a debate going on over at BioLogos for a number of months that was triggered by Venema’s book. The debate is about whether there could have been a bottleneck of two at some time in the human past. This discussion was started when Richard Buggs, Senior Research Leader (Plant Health) at Royal Botanic Gardens Kew, and Reader in Evolutionary Genomics at Queen Mary, University of London, challenged Dennis Venema about what Venema wrote in Adam and the Genome. Venema had argued:

As our methodology becomes more sophisticated and more data are examined, we will likely further refine our estimates [of human population size] in the future. That said, we can be confident that finding evidence that we were created independently of other animals or that we descend from only two people just isn’t going to happen. Some ideas in science are so well supported that it is highly unlikely new evidence will substantially modify them, and these are among them. The sun is at the center of our solar system, humans evolved, and we evolved as a population.

Put most simply, DNA evidence indicates that humans descend from a large population because we, as a species, are so genetically diverse in the present day that a large ancestral population is needed to transmit that diversity to us. To date, every genetic analysis estimating ancestral population sizes has agreed that we descend from a population of thousands, not a single ancestral couple. Even though many of these methods are independent of each other, all methods employed to date agree that the human lineage has not dipped below several thousand individuals for the last three million years or more — long before our lineage was even remotely close to what we would call “human.” Thus the hypothesis that humans descend solely from one ancestral couple has not yet found any experimental support — and it is therefore not one that geneticists view as viable. [Emphasis added.]

The image above appears at the head of Gauger’s Evolution News posting. It’s a painting from centuries ago titled “Adam and Eve” or something close to that.

I have previously reviewed the book Adam and the Genome by Dennis R. Venema and Scot McKnight. The summary of the book is that the creationists have it all wrong, the human species did not descend from a single pair of humans, but is the most recent of a lineage stretching back billions of years. However, God does exist, and God is responsible for all this.

Update: I am adding some material of interest.

Gauger mentions she has previously discussed this point.

So TSP is not validated for these highly polymorphic genes, HLA-DRB1 in particular, and convergent evolution (or original diversity) is validated. I addressed, by the way, the question of HLA-DRB1’s polymorphism and TSP, and a first human pair, in the book Science and Human Origins (2012). That book was written after I discovered that Francisco Ayala’s argument against the possibility of a first pair based on HLA-DRB1 did not stand up.  My hypothesis about a first pair was based on what I saw in papers about HLA-DRB1, most notably this and this, but the hypothesis was more suggested than demonstrated. I am glad to see that some of what I wrote has been substantiated.

See below for an expansion of TSP. The book in question has five parts, written separately by Gauger, Douglas Axe, and Casey Luskin. Gauger contributed chapters 1 and 5. Chapter 5 relates to the topic of her posting:

5

THE SCIENCE OF ADAM AND EVE

Ann Gauger

Using population genetics, some scientists have argued that there is too much genetic diversity to have passed through a bottleneck of just two individuals. But that turns out not to be true.

IN CHAPTER 1, I ARGUED THAT OUR SIMILAR ANATOMY AND DNA sequences are not sufficient to demonstrate that we share a common ancestor with chimps. Using peer-reviewed scientific literature about transitional fossils, and what is known about current chimp and human anatomy, I concluded that there are too many anatomical changes and too little time for neo-Darwinian processes to have accomplished the supposed transition from our last common ancestor with chimps to us.

But the current challenge concerning our origins involves more than fossils, anatomy, and improbable Darwinian scenarios. Now that DNA sequencing has become relatively simple and cheap, researchers are gathering vast amounts of human sequence data. They use the genetic variation they find to reconstruct past events in our genetic history. They derive evolutionary trees, estimate ancestral population sizes, and even calculate when and where our ancestors migrated out of Africa. Based on this kind of work, some have argued that we cannot have come from just two first parents.

[Location 2102 in the Kindle edition]

Gauger wants to take exception to the first part. Evidence that points to human origins from a collection of a few thousand individuals is not conclusive. The original pair of humans is not ruled out by modern research. The sum total of the piece is a glaring heap of wishful thinking, as would be evident to people knowledgeable of the subject and taking time to run down all Gauger’s arguments. And that I will leave to others, since it is beyond the scope of my expertise to critically evaluate the opposing arguments. I will just get to Gauger’s concluding statement:

So let me restate: the best explanation for the similarity among alleles is convergent evolution (or possibly original diversity), and not TSP. Finally, this analysis is strong evidence that TSP does not rule out a bottleneck of two.

To sum up, it’s very simple.

  • A bottleneck of two that is older than 500,000 years ago cannot be ruled out. That does not mean such a bottleneck ever existed, but rather that the possibility cannot be excluded. Future models may change that number of 500,000 years, up or down.
  • This is based on an analysis of the genetic data run by Drs. Schaffner and Swamidass, themselves evolutionary biologists and not ID supporters.
  • In addition, the bottleneck hypothesis stood up to a test using TSP (trans-species polymorphism). The test showed TSP was due to convergent evolution. This was a surprise to Dr. Swamidass.
  • A bottleneck of two, or a first pair at our origin older than 500,000 years, is possible.
  • Evolutionary biologists, including Dennis Venema, can no longer say we had to come from a population of 10,000 at any time over the last 3 million years.

Obviously, there is no rigorous science being argued here. This amounts to a special pleading for religious belief, particularly for biblical truth. Along that line, Gauger is not attempting to sell the full load. The Bible recounts the origin of the human race from two people. Gauger stops there. She lets slide the remainder of the story—that all this happened little more than 6000 years ago. Lady, if you’re in for a penny, you need to be in for a pound.

It’s an interesting twist we are observing. In days gone by—actually, in decades gone by—those people at the Discovery Institute sought to sell Intelligent Design as legitimate science, devoid of religious indoctrination. They seem to have thrown that notion over and have now gone full Monty pushing for the Abrahamic religions, particularly Christianity. At times the openness can be refreshing.

Deeper and Deeper

A Reading Of High Delusion—Part 2

I previously reviewed The Language of God, by Francis Collins. This is Adam and the Genome, by Dennis R. Venema and Scot McKnight. I obtained the Kindle editions of both after a short dive into a posting to Evolution News, the blog site of the Discovery Institute’s Center for Science and Culture. No author is listed for that post, but it centered on this book and the one by Collins:

In Adam and the Genome, Trinity Western University biologist Dennis Venema covers many other subjects besides what you might expect from the book’s title. We have been reviewing this material by the prominent theistic evolutionist and BioLogos author; find the series so far here.

Thus, Venema cites the high degree of genetic similarities between insulin genes in humans and other mammals as evidence for our common ancestry. He writes:

[W]e can see that there is good evidence to support the hypothesis that these two present-day genes come from a common ancestral population in the distant past … What we observe for this short segment is that the gorilla sequence is identical to that of the human except for one letter; the chimpanzee is identical except for three; and the orangutan is identical except for five. As before, this level of identity far exceeds what is needed for functional insulin, and strongly supports the hypothesis that humans share a common ancestral population with great apes. Indeed, the similarities between these sequences make English and West Frisian look like very distant relatives by comparison.

(Adam and the Genome, p. 30)

Yes, Venema does dig deeply into revelations from the human genome, and Evolution News does make a big deal about that. But Venema goes far deeper, a depth not plumbed by the posting. All this you can marvel at by plugging through the remainder of the book—which I did.

From the back cover of the book:

Dennis R. Venema (Ph.D., University of British Colombia) is professor of biology at Trinity Western University and Fellow of Biology for the BioLogos Foundation. He writes and speaks regularly about the biological evidence for evolution.

In the book Venema does lay out the evidence for evolution in grand detail, and it is this part that has caught the attention of the Intelligent Design pitch men. Some excerpts from the book elaborate:

Like many evangelicals, I (Dennis) grew up in an environment that was suspicious of science in general, and openly hostile to evolution in particular. Yet I had a deep longing to be a scientist, even as a child. For a long time, I reconciled my two worlds by rejecting evolution— after all, evolution was “just a theory” pushed by atheists and supported by “evidence” so flimsy that even a child could see through it. Moreover, Jesus was the way, the truth, and the life, and “what the Bible said about creation” was good enough for me.

McKnight, Scot; Venema, Dennis R.. Adam and the Genome: Reading Scripture after Genetic Science . Baker Publishing Group. Kindle Edition.

He goes on to say that conflicts with his faith almost kept him from pursuing his dream of becoming a scientist. Fortunately for science and for his students at Trinity Western, reason won out.

My family explored the possibility of my attending a Christian university, but it was more than we could afford. So a secular university it was, and I braced myself for what would surely be a trial for my faith.

McKnight, Scot; Venema, Dennis R.. Adam and the Genome: Reading Scripture after Genetic Science (p. 2). Baker Publishing Group. Kindle Edition.

Interestingly, I would remain an antievolutionist through the course of my PhD and on into my career as a professor, now teaching at the very same Christian university I was unable to afford as a student. What would come as something of a shock to me as a young professor is that, contrary to the claims of my Christian grade-school workbooks, evolution is a theory in the scientific sense.

McKnight, Scot; Venema, Dennis R.. Adam and the Genome: Reading Scripture after Genetic Science (p. 11). Baker Publishing Group. Kindle Edition.

What those creationists of the second kind found worth challenging is Venema’s erudite exposition of the evidence for common descent. For example:

In looking at the sequences above, we can see that there is good evidence to support the hypothesis that these two present-day genes come from a common ancestral population in the distant past, just as “butter, bread, and green cheese” and “bûter, brea, en griene tsiis” do. The principle is the same: they are far more similar to each other than they are functionally required to be. In principle, any words could stand for these concepts in either English or West Frisian; similarly, any matched pair of hormone and receptor could function to regulate blood sugar levels in humans or dogs. Yet what we observe strongly suggests, in both cases, that the present-day sequences are the modified descendants of what was once a common sequence.

McKnight, Scot; Venema, Dennis R.. Adam and the Genome: Reading Scripture after Genetic Science (p. 30). Baker Publishing Group. Kindle Edition.

Besides giving the creationists something to chew on, Venema does a great job of taking them down.

In the late 1990s I was a PhD student at the University of British Columbia in Vancouver, studying genetics and development. I had weathered my bachelor’s degree with my faith and antievolutionary views intact, and my area of study did not require me to think about evolution much at all. 3 Evolution was not completely avoidable, however: one very proevolution professor down the hall from my lab maintained a bulletin board called “Crackpot’s Corner,” where antievolutionary views were held up as objects of ridicule. It was here, on this bulletin board, that I first became aware of biochemist Michael Behe, a leader in the intelligent-design (ID) movement. 4 A little digging indicated that he had recently published a book, Darwin’s Black Box. In that book, which I eagerly devoured, Behe makes the case for what he calls “irreducible complexity”:

McKnight, Scot; Venema, Dennis R.. Adam and the Genome: Reading Scripture after Genetic Science (pp. 67-68). Baker Publishing Group. Kindle Edition.

Venema explores Behe’s irreducible complexity conjecture and finds it bare of support.

Behe argues, we can infer when we see protein complexes composed of several proteins that bind to one another that they are the product not of evolution but rather of design.

McKnight, Scot; Venema, Dennis R.. Adam and the Genome: Reading Scripture after Genetic Science (p. 69). Baker Publishing Group. Kindle Edition.

The irreducible complexity argument goes like this:

  • A living organism, even the simplest cell, is a complex assembly. Darwinian evolution stipulates that life forms were not always that complex.
  • Evolution from less complex to more complex life forms has taken place.
  • We now know that evolution proceeds by random mutation of genes, coupled with selective pressure that produces organisms more likely to predominate in the gene pool.
  • Random mutation of genes must occur in small steps, slight changes in a DNA chain—the genome.
  • Each slight change in the genome must be beneficial to the organism, else that change will not be preserved.
  • Existing organisms cannot operate competitively with the loss of a single function coded in the genome.
  • Modern organisms are irreducibly complex. There is no way to proceed from one viable organism to a new and more viable form by means of single mutations.

Behe stakes his argument against Darwinian evolution on his contention that many biological functions are irreducibly complex. What Venema does, and what others do, is to expose Behe’s supposed irreducibly, showing how current forms can be obtained by means of Darwinian evolution.

Interestingly, the virus did evolve to use a second host protein, one called OmpF. Not only did this happen once, but it happened repeatedly in the experiment. Sequencing the DNA of the viruses able to use OmpF instead of LamB revealed that one of the virus proteins— the one that normally binds to LamB, called “protein J”— had accumulated four amino acid changes. By looking at the preserved samples, the researchers showed that the new binding requires all four mutations to be present. They also showed that these mutations did not happen simultaneously, but rather sequentially. As it turns out, these single mutations allowed the protein J to bind more tightly to LamB, which was a significant advantage since hosts with LamB were so scarce in the experiment. Once three single mutations were in place, the virus was only one mutation away from the ability to bind and use OmpF. Interestingly, viruses capable of using OmpF retained  their ability to bind LamB— the virus could now use either host protein.

Two key aspects of this experiment are problematic for Behe’s thesis. First and foremost, this experiment documents the addition of a protein to an irreducibly complex system. The original system was composed of virus protein J binding to LamB, plus numerous other protein-binding events. The modified system lacks LamB and has a modified virus protein J that binds to OmpF instead. The intermediate system has the modified virus protein J and LamB, as well as OmpF, but now only one of LamB or OmpF is required. The transition from one irreducibly complex system to another has an intermediate state between them that acts as a scaffold, or to use Behe’s term, a stepping-stone.

McKnight, Scot; Venema, Dennis R.. Adam and the Genome: Reading Scripture after Genetic Science (pp. 79-80). Baker Publishing Group. Kindle Edition.

Is it any wonder those creationists of the second kind, writing for Evolution News, feel the need to take Dennis Venema down.

Venema is beginning to look like a secular camp hero of the first kind. Where this discourse starts to come apart is the latter half contributed by Scot McKnight.

Scot McKnight (born November 9, 1953) is an American New Testament scholar, historian of early Christianity, theologian, and author who has written widely on the historical Jesusearly Christianity and Christian living. He is currently Professor of New Testament at Northern Baptist Theological Seminary in Lombard, IL. McKnight is an ordained Anglican with anabaptist leanings, and has also written frequently on issues in modern anabaptism.

From Chapter 5 through Chapter 8, McKnight lays out a devilishly detailed analysis, some would say apologetic, on the place of Adam, both as a character in Genesis and as an ideal in Judeo-Christian faith. I apologize for having little comprehension of what he is attempting to get across, but I will have a go at my interpretation.

What happens when the church or, in my case, a Bible professor, encounters the kind of science found in the first part of this book? What happens, not to put too fine a point on it, when evolutionary theory and the Human Genome Project encounter the Bible’s creation narratives? What happens then when we are told that the best of science today teaches that the DNA characteristic of modern humans could not have come from less than approximately 10,000 hominins? What happens when we are told there were pre-Adamite humans? What about those two humans in Genesis 1– 3? And what about the eight that survived Noah’s flood? Which are we to believe, some ask: the Bible or science?

That last question leads some of us to dig in our heels while others shift with the latest conclusions of science. Some relish the countercultural stance of digging in their heels, and, to switch imagery, the second group at times refers to their counterparts as hiding their heads in the sand of the past or even of religious superstition. What the first thinks is faithfulness to the Bible, the second thinks is intellectual compromise. The accusations go both ways. You’ve probably heard them as often as I have. To illustrate I pose the great Protestant Reformer Martin Luther, who dug in against scientists, with Galileo from the generation following Luther, who permitted science to reshape his thinking. Luther said this of the facts in the Bible that seem to conflict with the external realities: “The more it seems to conflict with all experience and reason, the more carefully it must be noted and the more surely believed.” When Luther turns to Eve being formed from a rib, he says, “This is extravagant fiction and the silliest kind of nonsense if you set aside the authority of Scripture and follow the judgment of reason.” But perhaps this illustrates his heel digging the most: “Although it sounds like a fairy tale to reason, it is the most certain truth.” Here Luther contrasts “reason” (or scientific thinking) and faith or Scripture. One might call Luther’s approach the dominating approach to science and faith because he chooses— against reason, he admits— for the Bible to dominate the evidence. Galileo mirrors Luther with another kind of domination: “A natural phenomenon which is placed before our eyes by sense experience or proved by necessary demonstration should not be called into question, let alone condemned, on account of scriptural passages whose words appear to have a different meaning.” The choice to let either the Bible or science dominate the other is common enough, but there is a better way, one that permits each of the disciplines to speak its own language but also requires each of the voices to speak to one another. Science, after all, can help the interpreter of the Bible just as the Bible can provide horizons and vistas for the scientist. Three Old Testament scholars are modeling how this dialogue between the Bible and science can be fruitful— John Walton, Tremper Longman, and Peter Enns. They don’t agree with one another always, nor do I always agree with them in the pages that follow, but they have opened up new pathways for this kind of dialogue to occur.

McKnight, Scot; Venema, Dennis R.. Adam and the Genome: Reading Scripture after Genetic Science (p. 93-94). Baker Publishing Group. Kindle Edition.

That’s a massive chunk of text carved out of a book for review, but it’s worth doing on two counts:

  • McKnight has a knack for the longest trains of thought I have encountered in writing, making it difficult to find a good point to insert a break.
  • This piece pretty much summarizes my impression of where McKnight is going with the last four chapters.

He seems to accept that Adam and his faithful companion Eve are not the origin of the human race. Then he spends the remainder of his alloted space attempting to justify the story of Adam (and Eve) by invoking context.

I have to admit that the encounter with science made me wonder at times about what I had been taught, about what the Bible said, about whether or not the Bible was wrong, and— this was for me a defining intellectual moment— about whether traditional interpretations of Genesis 1– 2 were perhaps well intended but misguided and in need of rethinking. In other words, my encounters with trustworthy scientists and their works taught me to go back to the Bible with other questions and other possible interpretations and to ask what Genesis meant in its world. In this I believe I was motivated by a quest to know the truth. I went back to the Bible to read Genesis in context and to ask if what many thought the Bible was saying (that is, its interpreted meaning) was not in fact what the Bible was actually saying (its original meaning). But there’s more: my encounter with science that prompted renewed study of Genesis also led me to challenge science about some of its assumptions. Modernity, expressed in extreme form in the “New Atheists” such as Richard Dawkins and Sam Harris, presses into our minds that the only reality is the empirical. If only what studies the empirical world (science) ascertains reality, then only science tells us the truth about reality. However, this common assumption in modernity is a case of concluding what one already assumes. How so? This approach restricts discoveries to empirically testable realities. Nothing else is real. But what if there is more? What if some kind of nonempirical reality exists? This is the sort of question the Bible presses on the scientist. I am convinced that there is more than the empirical, or perhaps I should say the more is hyperreality or suprareality. If so, there is a reality not knowable exclusively by the empirical methods of science. Theology, which is designed to investigate that nonempirical reality in some ways, can provide a map onto which we can locate science and which can challenge science.

McKnight, Scot; Venema, Dennis R.. Adam and the Genome: Reading Scripture after Genetic Science (p. 95). Baker Publishing Group. Kindle Edition.

[Emphasis added]

Use of “context” occurs four times prior to this point, including once in an introduction and once in the Table of Contents. It appears an additional 85 times from this point forward. My take: context is everything.

Where have I seen this before? It was in the matter of tattoos. A Facebook friend, a devout Christian and one who from time to time posts pronouncements of faith, called attention to her tattoos. Gentleman that I am, I reminded her that the Bible forbids tattoos, much as it forbids homosexuality. A relative chimed in with the reassurance that it is a matter of “context.”

My take (again): “context” is a cop-out. When context is invoked to justify the Bible, then what you are getting from the Bible is the interpretation being pushed by the speaker. You are not getting the word of God. You are getting the word of the interpreter. You are not placing you faith in a 3000-year-old set of laws. You are placing your faith in whoever happens to be professing faith, an extreme case being the sordid collapse of Jim Jones’ People’s Temple.

Previously mentioned, McKnight’s parsing of theological history largely passes over my head. Therefore I will post a few excerpts that caught my attention, and  I will let the reader get back to me. Advice requested.

I went back to the Bible to read Genesis in context and to ask if what many thought the Bible was saying (that is, its interpreted meaning) was not in fact what the Bible was actually saying (its original meaning).

McKnight, Scot; Venema, Dennis R.. Adam and the Genome: Reading Scripture after Genetic Science (p. 95). Baker Publishing Group. Kindle Edition.

Every statement about Adam and Eve in the Old Testament, in Jewish literature, and in the New Testament is made from a context and into a context. Furthermore, some of the statements about Adam and Eve in all this literature are designed to speak against that context. That is, those statements are polemics and apologetics. Learning about those contexts and polemics often brings fresh understanding of the intention of the Bible and hence of what God wants his people to hear. In addition, this contextual approach to Adam and Eve provides a model for how Christians today can think about Adam and Eve in the context of the faith-and-science debate. If the Human Genome Project provides brilliant discoveries about the origin of life and the development of humans into who we are today, we will all gain clarity if Christians learn how to speak about Adam and Eve in a context that both affirms conclusions about the genome and challenges some conclusions drawn from the Human Genome Project. Contexts, both ancient and modern, shape what we see, what we hear, and how we respond.

McKnight, Scot; Venema, Dennis R.. Adam and the Genome: Reading Scripture after Genetic Science (p. 97). Baker Publishing Group. Kindle Edition.

Winding down with:

Interpreting the Bible is not easy. As Scot demonstrates, taking into account the languages, contexts, and presumed intents from centuries ago is a lot like, well, paleontology. Again, when explaining the challenges science presents to Christian faith, I stress the important distinction between scientific findings (e.g., DNA in a Siberian cave) and the philosophical or theological interpretations of those findings (Homo sapiens therefore emerged by sheer luck of the genome, or God operates on a circuitous route not unlike wandering in the wilderness to get to the promised land).

McKnight, Scot; Venema, Dennis R.. Adam and the Genome: Reading Scripture after Genetic Science (p. 197). Baker Publishing Group. Kindle Edition.

Summarizing the book, we have two obviously intelligent people still clinging to the notion there is a magical person who created us and the universe and who cares for us personally. That this can be so is not an indication that there is no problem at hand. It is an indication that the problem is both wide and deep-seated.

May Jesus have mercy on our souls.

The Years of Living Stupidly

Number 3 in a series

Today I’m continuing to follow some posts on the Intelligent Design blog Evolution News. Sometimes these posts are anonymous, credited to Evolution News, with no author specified. This one was posted by Cornelius Hunter, listed as a senior fellow at the Discovery Institute’s Center for Science and Culture. In fact, that is how his entry in CreationWiki lists him:

Cornelius G. Hunter, Ph.D., is a graduate of the University of Michigan where he earned a B.S and M.S. in aerospace engineering receiving a Ph.D. in Biophysics and Computational Biology from the University of Illinois and currently is Adjunct Professor of science and religion at Biola University. He is currently engaged in molecular biophysics post-doctoral and engineering research in Cameron Park, California. He is fellow of the Discovery Institute‘s Center for Science and Culture (CSC). He is formerly senior vice president of Seagull Technology, Inc.

Postings by a Facebook friend continue to bring to my attention a number of these Evolution News postings. Here is the most recent:

Warren Allmon on the Argument from Homology

Cornelius Hunter January 19, 2018, 1:30 PM

once debated two evolutionists on the campus of Cornell University. In that debate I raised several fundamental problems with evolutionary theory. The problems that I pointed out fell into two broad categories: process and pattern.

In the latter category, I noted that the keystone argument for evolution from homology had badly failed. Unfortunately, that failure was waved off and went unaddressed by the evolution professors. That may not have been the case had Warren Allmon been able to participate. Allmon, Director of the Cornell University-affiliated Paleontological Research Institution (PRI), has thought more deeply about the homology argument than most evolutionists. Now in 2018, he has published, along with adjunct professor Robert Ross, a new paper, “Evolutionary remnants as widely accessible evidence for evolution: the structure of the argument for application to evolution education.” The paper, in the journal Evolution: Education and Outreach, contains a very important concession.

As is typical, the new Allmon/Ross paper makes several serious scientific errors, either through ignorance, denial, confirmation bias, or whatever. The paper also relies on heavily religious claims and arguments, which again is typical.

And Hunter goes on in this manner for several additional lines, never getting around to the matter of homology and evidence for evolution. He proposes to work through the argument in future installments, and I will attempt to follow up.

In the meantime, it’s worth noting the selection of Cornelius G. Hunter as a fellow at the CSC, and it is especially interesting that he’s on Evolution News, which history is to deny any religious basis for Intelligent Design. In that effort, the CSC is much out on a limb. I mean, look what I do. Everywhere I write Intelligent Design, I capitalize it, such as I would Christianity and Islam. These are religions, and their names get put in initial caps.

While I’m on the matter, here is a list of books by Cornelius G. Hunter:

  • Hunter, Cornelius G. (2001). Darwin’s God: Evolution and the Problem of Evil. Ada, MI: Baker/Brazos Press. ISBN 978-1-58743011-4.
  • Hunter, Cornelius G. (2003). Darwin’s Proof: The Triumph of Religion over Science. Ada, MI: Baker/Brazos Press. ISBN 978-1-58743056-5.
  • Hunter, Cornelius G. (2007). Science’s Blind Spot: The Unseen Religion of Scientific Naturalism. Ada, MI: Baker/Brazos Press. ISBN 978-1-58743170-8.

Somebody advised me that the CSC has thrown in the towel and decided the religious approach is the way to go in promoting Intelligent Design. The image above is, in fact, from the video series Does God Exist, featuring creationist and CSC fellow Stephen C. Meyer and produced by Focus on the Family, decidedly not the go-to place for scientific enlightenment.

Anyhow, I am among the most glad to see the CSC becoming more open about the connection between the God of Abraham and Intelligent Design. It makes my job of pointing this out a lot easier, even if not as much fun. There’s going to be lots more. Keep reading.

And may Jesus have mercy on your soul.

The Years of Living Stupidly

Number 2 in a series

Hot damn! This is getting good. Yesterday I kicked off this series with a review of a post (by somebody) on Evolution News, the blog site hosted by the Discovery Institute Center for Science and Culture. That’s the group doing the heavy lifting to promote the Intelligent Design version of creationism in this country. It so happens I picked up on three such postings, courtesy of a Facebook friend who linked them on his time line. Here’s another:

Submit Nominations for 2018 Censor of the Year Now!

We’re about a month away from Darwin Day, February 12. It’s the great man’s birthday, celebrated by Discovery Institute’s Center for Science & Culture as Academic Freedom Day. We prefer this alternative framing of the occasion because the freedom to debate Charles Darwin’s scientific legacy is continually endangered by intimidation, threats to careers and livelihoods, fake news and fake science, and subtle and totally unsubtle forms of censorship.

All right! This is going to be good. The language of Evolution News is picking up the tone of rhetoric in today’s political world. I particularly enjoy seeing “intimidation, threats to careers and livelihoods, fake news and fake science.” Also “unsubtle forms of censorship.” This writer is prepared to lay it on thick. Who could ask for more?

The writer is identified, something often missing. He’s David Klinghoffer, somebody I enjoy reading. Here’s his Wikipedia entry:

David Klinghoffer is an Orthodox Jewish author and essayist, and a proponent of intelligent design. He is a Senior Fellow of the Discovery Institute, the organization that is the driving force behind the intelligent design movement. He is also a frequent contributor to National Review, and a former columnist for the Jewish weekly newspaper The Forward, to which he still contributes occasional essays.

And there’s more:

Klinghoffer has published a series of articles, editorial columns, and letters to the editor in both Jewish and non-Jewish conservative publications seeking to promote opposition to Darwinian views of evolution, stating that science can include a support for an underlying intelligent design in the development of living things and the universe as a whole, and, indeed, that some scientists hold to such views. Larry Yudelson has responded, in a piece directed at Klinghoffer, that rabbinical Judaism has accepted evolutionary theory for more than a century, and that Judaism has never rejected science. Yudelson also argues that Klinghoffer’s employer, the Discovery Institute, is a Christian think tank that is funded by organizations that seek to promote a “Christian-friendly world view”

Surprise, surprise! Yes, people, Jews do support creationism. Don’t forget, Jews invented this fantasy to begin with. Christians and Muslims since picked up the torch, and especially Christians are now the big promoters. Anyhow, David Klinghoffer has more to say from his Evolution News post. He is asking  readers to submit nominations for Censor of the Year (COTY). Here’s what he has to say about the great injustice being perpetrated:

Darwinists do not go so far as to burn books by proponents of intelligent design. However, their actual tactics in suppressing open debate are far more effective because, for the most part, they are practiced behind a veil of secrecy.

Remember, as Sarah Chaffee pointed out last week, most Darwinist censorship works via self-censorship. In academic and other contexts, the intimidation need not be explicit. It is practiced quietly, without drawing attention to itself. The victims, the censored, understandably don’t want to imperil their work, their income, or their reputation. So they keep quiet both about their doubts on Darwinian evolution and about the power structure in their institutions that maintains the informal speech code.

Yes, that’s it. Darwinists (scientists) intimidate the opposition by subtle and nefarious means, such means not being elaborated here, but perhaps in the Sarah Chaffee post that is linked above. I invite you to follow the link and read the sordid details. She tells of professors who give private talks promoting Intelligent Design, who must disclaim up front they do not speak for their academic institutions. Additionally she writes:

Or just take a look at our pictures on Evolution News of the Summer Seminars on Intelligent Design. You may see the very tops of students’ heads, no more. Not their faces, not an inch of their profile. Those we carefully crop out. This is to keep participants’ identities a secret. It’s so their career prospects will not be harmed by an association with intelligent design.

Anyhow, the issue is that people in the know who want to criticize Darwinian evolution and more so, promote Intelligent Design, find themselves ridiculed by colleagues and others. Yes ridiculed. Coerced into keeping quiet. To be sure, I have my own characterization of what’s happening:

Typically a candidate for tenure at a college or university must pass review by his peers. Tenure is almost a lifetime assurance of employment and can be denied if your peers do not look forward to working with you. I have stated elsewhere that there are only so many times you can show up for the party with your fly unzipped before you are no longer invited.

Sadly it is true. If you say stuff that is foolish enough for long enough, people around you will start to conclude there is something wrong with your thinking process. And therein lies the problem with Klinghoffer’s premise and that of the rest of the Intelligent Design  crowd. This is undue criticism, undue intimidation, only if Intelligent Design has a basis in fact. The problem for Klinghoffer et al is that Intelligent Design really is creationism dressed up to look like science. And thinking people recognize this. And they act appropriately, if unkindly, in response.

There are more of these. Keep reading.

The Years of Living Stupidly

Time to start a new series.

A fellow skeptic keeps posting stuff from Evolution News, and my Facebook feed picks it up. Evolution News is the blog of the Discovery Institute’s Center for Science and Culture, an enterprise started up by creationist Stephen C. Meyer in 1996, and he is currently the director. I’ve spent a lot of time the past two years trying to  ignore output from the Discovery Institute, but something about this post brought me back. Here’s what it’s about:

Adam and the Genome and Human-Ape Genetic Similarity

Evolution News @DiscoveryCSC January 18, 2018, 7:54 AM

In Adam and the Genome, Trinity Western University biologist Dennis Venema covers many other subjects besides what you might expect from the book’s title. We have been reviewing this material by the prominent theistic evolutionist and BioLogos author; find the series so far here.

Thus, Venema cites the high degree of genetic similarities between insulin genes in humans and other mammals as evidence for our common ancestry. He writes:

[W]e can see that there is good evidence to support the hypothesis that these two present-day genes come from a common ancestral population in the distant past … What we observe for this short segment is that the gorilla sequence is identical to that of the human except for one letter; the chimpanzee is identical except for three; and the orangutan is identical except for five. As before, this level of identity far exceeds what is needed for functional insulin, and strongly supports the hypothesis that humans share a common ancestral population with great apes. Indeed, the similarities between these sequences make English and West Frisian look like very distant relatives by comparison.

(Adam and the Genome, p. 30)

Yes, it appears Evolution News is having a go at biologist Dennis Venema’s new book (2017) Adam and the Genome. What the Discovery Institute wants to convince us is that life forms and all we see about us could not have come about by natural processes. A creator, an intelligent entity of some sort, must be behind it. That’s what’s going on here. Here Evolution News is digging at Venema’s evolutionary explanation for the similarity between the human genome and that of some of our close relations. Venema is using the origin of languages to make a comparison. I have the Kindle edition of the book, which allows me to provide the context of the above:

In looking at the sequences above, we can see that there is good evidence to support the hypothesis that these two present-day genes come from a common ancestral population in the distant past, just as “butter, bread, and green cheese” and “bûter, brea, en griene tsiis” do. The principle is the same: they are far more similar to each other than they are functionally required to be. In principle, any words could stand for these concepts in either English or West Frisian; similarly, any matched pair of hormone and receptor could function to regulate blood sugar levels in humans or dogs. Yet what we observe strongly suggests, in both cases, that the present-day sequences are the modified descendants of what was once a common sequence.

Now that we understand the redundancy of the codon code, we can see that for genes this rabbit hole goes even deeper. Many of the amino acids in insulin can be coded for by alternate codons. For example, “Leu” in the diagram indicates the amino acid leucine, for which there are six possible codons. This short snippet of the insulin gene codes for nine leucines, and eight of them use exactly the same codon in dogs and humans (and the ninth differs by only one letter). For these nine codons, there are 96 (= 531,441) possible combinations that will correctly code for just these nine leucines, to say nothing of the other 101 amino acids found in insulin, most of which can be encoded for by multiple codons. Is it merely by chance that what we observe in these two species is only one letter different for these nine codons? A simpler, more reasonable explanation (or what a scientist would call a more “parsimonious” explanation) is that these sequences come from a common ancestral population and have been slightly modified along the way.

Of course, scientists have sequenced the genomes of many other species, so we can test this hypothesis by looking at a larger data set. Humans are not thought to have shared a common ancestral population with dogs for a very long time; other species are thought to be our much closer relatives due to other shared features, such as anatomy. When the pre-Darwin biologist Carl Linnaeus (1707– 78) drew up his taxonomy of animal life (i.e., a system that organized life into categories), he famously placed humans and great apes in a category he called “primate,” from the Latin indicating “prime” or “first.” While he was certainly not thinking about common ancestry, he naturally recognized that these species (such as chimpanzees, gorillas, and orangutans) have a closer anatomical affinity to humans than other animals. In light of such an affinity, evolutionary theory predicts that these species share a more recent common ancestral population with humans than nonprimate species, such as dogs, do. Therefore, their gene sequences should be a closer match to human sequences than what we observe in dogs. Not surprisingly, this is exactly what we observe. Let’s return to our example of the insulin gene and extend our comparison of the same short stretch to include three great apes (fig. 2.6).

What we observe for this short segment is that the gorilla sequence is identical to that of the human except for one letter; the chimpanzee is identical except for three; and the orangutan is identical except for five. As before, this level of identity far exceeds what is needed for functional insulin, and strongly supports the hypothesis that humans share a common ancestral population with great apes. Indeed, the similarities between these sequences make English and West Frisian look like very distant relatives by comparison.

McKnight, Scot; Venema, Dennis R.. Adam and the Genome: Reading Scripture after Genetic Science (p. 30-31). Baker Publishing Group. Kindle Edition.

I highlighted the portions the author reprinted from the original. Use of this partial excerpt is legitimate, since it does not change Venema’s original meaning and intent. What is to be found in the complete text is a fuller explanation, plus a tie-in to Venema’s language analogy.

The history of languages makes for an interesting study, and for English readers there is particular significance. The book The Story of English, by Robert MacNeilRobert McCrum, and William Cran is a companion book to the PBS television series of the same name. I have a similar book, The Stories of English, by David Crystal. It rehashes the history of English in much the same way:

We can note both of these processes happening for the Germanic group of languages during the period. In the late second century, the Goths moved into Europe from southern Scandinavia, eventually arriving in the Mediterranean region. During the fourth century, Bishop Wulfilas translated the Bible into Gothic. The language had changed so much during this short time that scholars now consider it to be a distinct, eastern branch of the Germanic family. On the other hand, the westward movement of peoples along the north European coast and into England resulted in a group of languages which had much greater similarities. English and Frisian, indeed, were so close that they would probably have been mutually intelligible for many centuries, especially in Kent. Even today, though mutual intelligibility has long since gone, English people listening to modern Frisian sense a familiarity with its expression which is not present in the case of Dutch or German. Genetic anthropologists have discovered a significant Y-chromosome identity, too (p. 31). 3

Crystal, David. The Stories of English (pp. 20-21). The Overlook Press. Kindle Edition.

I once visited the northwest coast of the European continent and was struck by the similarity. At a company cafeteria I picked up a coupon good for two desserts and had no trouble reading it, even though it was written in the local  language.

Anyhow, the background is fascinating, but the intent of Evolution News is to demonstrate that Venema is wrong—genetic similarity does not indicate common descent. Evolution News sometime ago quit identifying authors, but whoever posted this item failed to get the message. Traditionally, Intelligent Design, a concoction of the Discovery Institute, does not rule out common ancestry. These people tend to allow for that, but they also want us to know that natural, and especially random, process are not at work. The whole line of descent process was managed by an intelligent entity, yet unnamed. With some exceptions:

If the Associated Press writer confused a challenge to common descent with “Intelligent Design,” it could be because Intelligent Design proponents with the CSC on occasion do challenge common descent. For example, Ray Bohlin is a CSC fellow and supposedly a spokesman for Intelligent Design. At the Texas Faith Network conference in Dallas on 3 November 2003 Bohlin addressed a large room full of people and stated that common descent was true for all life forms, except humans. You can imagine the confusion of all in attendance.

Retired law professor Phillip Johnson is considered the godfather of the modern Intelligent Design  movement. At a symposium titled “Darwinism: Scientific Inference or Philosophical Preference,” held on the campus of Southern Methodist University in March 199, .I had a chance to talk with Johnson and get his views firsthand. He expressed some surprising points for an opponent of evolution:

n 1992 Johnson attended the conference on “Darwinism: Scientific Inference or Philosophical Preference” at Southern Methodist University (SMU). The conference was inspired by Jon Buell, a local creationist. Buell’s Foundation for Thought and Ethics (FTE) published the book Pandas and People, an early work pushing Intelligent Design. At the conference the departure from young-Earth creationism was stark. Johnson and Buell were standing together when I asked them the question. Their answer was significant. Yes, the Earth and the universe really are billions of years old, and yes, present life forms share a common ancestry. These were not your grandfather’s creationists.

Here is a copy of the proceedings.

Anyhow, Evolution News is now having none of that. Continuing from the post:

The obvious answer to this argument is common design — that humans, gorillas, and orangutans were designed based upon a common blueprint. This would explain genetic similarity between humans and other species quite well.

Then the author presents an additional excerpt and promptly goes off the rails with this:

There he goes again, telling God what he can and cannot do. It’s a bit of chutzpah, don’t you think? He’s also telling God what God must intend when he does certain things. In particular, Venema is telling God that if he designs two species to be similar then God must thereby intend to tell us that those species are related through common ancestry. And if those species aren’t really related, then Venema tells God that he is being deceitful.

But what if Venema is putting thoughts into God’s head that aren’t there? What if God could have entirely different purposes for designing two species as similar — purposes that have nothing to do with trying to communicate some message to humans about relatedness or unrelatedness?

Oh, Jesus! You gave away the store. Intelligent Design is not supposed to be about God. It’s supposed to be science, real science, well-researched science, science that reveals there is a Designer, not identified and definitely not identified as G*d. G*d is the word that keeps Intelligent Design out of public classrooms, which is where its proponents, despite much public posturing, in their heart of hearts want it to be. Possibly we are now seeing the offshoot of all those years of living stupidly.

That covered, there is more of interest. The post dips into  a discussion of The Language of God, a book by Francis Collins:

Francis Sellers Collins (born April 14, 1950) is an American physician-geneticist noted for his discoveries of disease genes and his leadership of the Human Genome Project. He is director of the National Institutes of Health (NIH) in Bethesda, Maryland, United States.

Before being appointed director of the NIH, Collins led the Human Genome Project and other genomics research initiatives as director of the National Human Genome Research Institute (NHGRI), one of the 27 institutes and centers at NIH. Before joining NHGRI, he earned a reputation as a gene hunter at the University of Michigan. He has been elected to the Institute of Medicine and the National Academy of Sciences, and has received the Presidential Medal of Freedom and the National Medal of Science.

In order to continue following the discussion I obtained a Kindle edition and will be covering that in future posts. Also, and free on Amazon, is Intelligent Design the Final Proof of God. Go for it. Kindle readers are free for tablets and computers.

Darwin’s Doubt

Number 3 in a Series

Chipmunk confronts a diet soda can near Mirror Lake Utah

I have a copy of creationist Stephen C. Meyer’s book Darwin’s Doubt, and I have promised to review it. I was recently reminded of that by a post on the Discovery Institute’s Evolution News site. That posting excerpts a number of passages from the book. I previously reviewed the first of those. Here is another citation:

Intelligent agents can generate top-down patterns of appearance like we see in animal body plans.

Here is the pertinent passage:

“Top-down” causation begins with a basic architecture, blueprint, or plan and then proceeds to assemble parts in accord with it. The blueprint stands causally prior to the assembly and arrangement of the parts. But where could such a blueprint come from? One possibility involves a mental mode of causation. Intelligent agents often conceive of plans prior to their material instantiation— that is, the preconceived design of a blueprint often precedes the assembly of parts in accord with it. An observer touring the parts section of a General Motors plant will see no direct evidence of a prior blueprint for GM’s new models, but will perceive the basic design plan immediately upon observing the finished product at the end of the assembly line. Designed systems, whether automobiles, airplanes, or computers, invariably manifest a design plan that preceded their first material instantiation. But the parts do not generate the whole. Rather, an idea of the whole directed the assembly of the parts.

Meyer, Stephen C.. Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design (pp. 371-372). HarperCollins. Kindle Edition.

Meyer is correct in stating (by implication) that a builder, on receiving a set of design specifications (blue prints and such), can proceed in constructing a device or assembly. Note the implication. There exists nothing like the desired assembly. The materials to construct it are present, and there is a pre-recorded set of instructions for construction. The instructions are the sole source of the information required for construction.

At this point a reminder is helpful. Define information as the agent that mediates cause and effect. I have stated this previously, perhaps not in this exact form. Nobody has ever challenged my definition. All are welcome to have a go at it.

What Meyer does not concede is that a set of instructions is not a prerequisite for constructing a device/assembly. Random processes can accomplish this. This is the basis of Darwinian evolution, and this is what the creationists argue strongly against. They pose it much like this:

Given even the finished components, steel sheet, machine screws, quantities of paint, it is unlikely to the extreme that a random process will assemble these components into a functional automobile, much less into one that somebody would purchase off the showroom floor and drive away.

To be sure, that is an extreme statement of the creationists’ argument, and those people do argue a more digestible case. Their most popular argument is more like this:

Given a completed, perfectly functional, automobile and given materials to be added to produce next year’s model, it is improbable to the extreme that this modification can occur by accident. Some sort of pre-conceived design is required. A set of documentation is required. At the minimum there must be an intelligent agent with the pre-conceived design upgrade in mind.

And this is what the so-called Darwinists object to. The creationists insist there must be a pre-conceived idea, there being no mention of who or what holds this pre-conceived idea. To be clear, the agency that Stephen C. Meyer represents is the Discovery Institute, and their concept is called Intelligent Design. Further, the narrators of Intelligent Design want to insist that religious faith is not at the base of their argument. And this last is an outrageous lie of grand proportions. Any notion that Stephen C. Meyer pushes Intelligent Design absent religious faith is daily countered by his own words and actions. For example:

The final four episodes deal with the New Testament, the contribution by Christians, telling the story of Jesus of Nazareth, his teachings, his trial and execution, and his return from the dead. Meyer wants to assure viewers all those doubts about the validity of the New Testament are groundless.

Following the trajectory of Meyer’s life and career, we see a relentless commitment to a defense of the Christian faith. His promotion of Intelligent Design is one manifestation of that commitment.

Returning to Meyer’s argument, biologists argue that random processes we observe in nature are adequate to have produced the life forms we see today. In direct counter to Meyer, the concept of Intelligent Design is intellectually bankrupt on a number of points. Repeating myself:

I scoff. Really? Let me get this straight. An Intelligent Agent, the Entity who created the Universe, the Earth, the planets, the sun, and all we see around us—this Entity, took over 13 billion years to get us to where we are today after first creating the Universe. Actually, over 13 billion years to get us to the point where there was a Universe and a planet Earth, and there were any number of species of plants and animals, but none resembling people. Allow me to repeat: Really? If that is Stephen C. Meyer’s concept of intelligence, then Heaven help the human species, because intelligence is all that’s keeping us going.

Additionally, at no point in their argument have proponents of Intelligent Design identified a mechanism by which the Intelligent Designer could have implemented these designs. Nor can they.

I will continue the review of Meyer’s book through an analysis of the Evolution News post prior to diving into a direct review of the book. Keep reading.

Darwin’s Doubt

Number 2

Chipmunk confronts a diet soda can near Mirror Lake, Utah

It was two years ago I obtained a copy of creationist Stephen C. Meyer’s book Darwin’s Doubt and promised to review it. I was recently reminded of that by a post on the Discovery Institute’s Evolution News site:

In his book Darwin’s Doubt, Stephen Meyer considers the nature of animals and what is required to build an animal. He finds that only intelligent design can explain the abrupt origin of animal life in the fossil record, as well as the new information required to build the integrated nature of parts and systems that comprise animal body plans. Here’s how Meyer makes the case that intelligent design is the best explanation for many aspects of the origin of animals as witnessed in the Cambrian explosion:

The posting is not signed, a departure from my previous experience. The site lists a number of contributors, here listed in no particular order:

The author goes on to state:

Intelligent agents can generate new form rapidly as we see in the abrupt appearance of animals in the Cambrian fossil record:

That is followed by an excerpt from the book:

Intelligent agents have foresight. Such agents can determine or select functional goals before they are physically instantiated. They can devise or select material means to accomplish those ends from among an array of possibilities. They can then actualize those goals in accord with a preconceived design plan or set of functional requirements. Rational agents can constrain combinatorial space with distant information-rich outcomes in mind.

Meyer, Stephen C.. Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design (pp. 362-363). HarperCollins. Kindle Edition.

Yes! Stephen C. Meyer is 100% correct. If you have an agent, a person, with intelligence and foresight, you can make much more rapid progress than can be accomplished by random processes alone. Here is what an intelligent agent can do:

  • Send nerve impulses from a brain to muscles and cause objects to move, directing bits of matter to come into contact and preventing certain things from happening, which things would not ordinarily have happened were it not for said intervention.
  • Use eyes or other sensory methods to determine what is going on, allowing the brain to make decisions and to change the course of actions being taken.

If the Intelligent Agent only had a brain. Or hands. Or eyes.

What Meyer is saying, perhaps without realizing it, is that somewhere in the distant past something caused matter to move in ways contrary to the natural flow of events. And nowhere in any of his writings I have found has Meyer explained such happenings, neither has he mentioned them. It is an explanation the proponents of Intelligent Design must not touch. It is the figurative third rail of Intelligent Design. Touch it, and Intelligent Design dies.

But stop right there. I know what Meyer and the other creationists are going to say. Allow me to propose a quote:

Our research has not yet uncovered a method. However, our observations and our reasoning have convinced us, and will convince any thinking person, that there must have been an  Intelligent Agent at work. Else we would not have gotten to where we are today.

Explainer of Intelligent Design

I scoff. Really? Let me get this straight. An Intelligent Agent, the Entity who created the Universe, the Earth, the planets, the sun, and all we see around us—this Entity, took over 13 billion years to get us to where we are today after first creating the Universe. Actually, over 13 billion years to get us to the point where there was a Universe and a planet Earth, and there were any number of species of plants and animals, but none resembling people. Allow me to repeat: Really? If that is Stephen C. Meyer’s concept of intelligence, then Heaven help the human species, because intelligence is all that’s keeping us going.

I will dig deeper into Stephen C. Meyer’s book in the coming days. In the meantime, the Evolution News posting has a link to a neat video, which you should watch. I know I will watch it, and I will have a go at summarizing it in a future post. Here’s the link:

And may Jesus have mercy on your soul.

Fool’s Argument

Sixth of a series

This is the sixth in my review of the video production Does God Exist, brought to you by Focus on the Family, an agency for conservative Christian advocacy. The video is available on DVD from Amazon, and it is currently streaming on Amazon, free with Amazon Prime.

The previous episode featured creationist Stephen C. Meyer, introducing the concept he elucidated in his book, Signature in the Cell, previously reviewed. This time Meyer is continuing that theme, and he is going to be arguing that in the evolutionary development of life on this planet, natural processes face improbable odds.

 

He cites Douglas Axe, another creationist associated with the Discovery Institute.

I am posting a transcription of the text to make it visible to search engines.

Doug Axe, Ph.D., Cal Tech, formerly @ Cambridge Univ.

A Critical Question

How common (or rare) are functional sequences (i.e., proteins) among all the possible combinations of amino acids?

We are going to learn that proteins are chains of amino acids (peptide chains), and their critical functionality in living cells is the shape they take on when folded, as these chains do naturally when formed. Only a few out of many [understatement alert] possible proteins are functional to living cells. Accidental formation of a useful protein is extremely unlikely.

The text:

How Rare are Functional Sequences?

For every ONE of these

How many of these [= 1/????]

Meyer gives the numbers.

Here’s the text.

CHANCES OF FINDING A FUNCTIONAL PROTEIN BY CHANCE = 1/10164!!!

1080 elementary particles in  the universe

1016 seconds since the Big Bang

10139 events since the beginning of the universe!

Those are tall odds.

Meyer concludes the argument for natural formation of living matter is circlar.

To wit:

Begging the Question

Natural Selection

Self-Replication

Sequence Specific DNA and Proteins.

He is saying sequence-specific DNA and proteins are required for self-replication, which is required for natural selection, a false argument. He does not recognize the feasibility of self-replication without DNA and proteins. Self replication of non-living matter is what scientists propose. Scientists have not demonstrated the complete development of living cells from self-replicating, non-living matter, and neither has Meyer demonstrated his claim for Intelligent Design.

Additionally, Meyer calls this begging the question, which it technically is not. Begging the question has a stricter definition, but that is a minor issue.

He brings up Michael Polanyi.

Here is what he has to say:

Michael  Polanyi

“As the arrangement of a printed page is extraneous to the chemistry of the printed page, so the base sequence of a DNA molecule [is] extraneous to the chemical forces at work in the DNA molecule.”

Life Transcending Physics and Chemistry

Meyer is using the Polanyi quote to illustrate his argument that natural chemical processes alone cannot account for the fortunate formation of life-critical molecules.

The association of Michael Polanyi (in name only) with the Discovery Institute goes back 18 years. In 1999 William Dembski, under the auspices of a friendly University president, founded the Michael Polanyi Center at Baylor University.

The Michael Polanyi Center (MPC) at Baylor University, Texas was the first center at a research university exclusively dedicated to intelligent design study. It was founded in 1999 “with the primary aim of advancing the understanding of the sciences,” in a religious context and is named for Michael Polanyi. All of the center’s research investigated the subject of intelligent design. The center was relegated in late 2000 to a minor program within the Baylor Institute for Faith and Learning and fully dissolved in 2003.

There are many points covered in this episode I have not covered,  but this provides the flavor. Meyer concludes.

The text:

There is no naturalistic explanation for the origin of the information that you need to build the first life.

His conclusion is way over the top. It is not a logical conclusion, even based on the partial discussion of the topic he has presented. Specifically, Meyer discusses improbabilities of purely random processes, denies the possibility of self-replication by means other than DNA (and such). Then he jumps to the origin of information, which origin he has nor argued against in his talk.

In my review of his book eight years ago, I posited that novel information comes from purely random events, a conclusion I suspect will be counterintuitive to most. Contact me if you want to discuss this further.

In Episode 7, titled “DNA by Design, Part 3: Information and Intelligence,” Meyer is apparently going to continue to discuss intelligence as it relates to biological evolution. From Amazon:

We know that the source of any information found within the DNA code is intelligence itself. So where does this intelligence come from? Chance? Natural Selection?

Keep reading. Look for a review tomorrow of Episode 7. Only four more of these to go, and it’s going to be interesting to see where Meyer takes us.

Fool’s Argument

Fifth of a series

This is the fifth in my review of the video production Does God Exist, brought to you by Focus on the Family, an agency for conservative Christian advocacy. The video is available on DVD from Amazon, and it is currently streaming on Amazon, free with Amazon Prime.

There are ten episodes plus a bonus feature. I have not watched episodes in  advance of these reviews, so I have no idea what comes after this one.

Featured in the video is creationist Stephen C. Meyer, a founder of the Discovery Institute Center for Science and Culture. This episode will begin a multi-part discourse into Meyer’s argument that the features of life imply design, and one of those implications is the apparent information manifested in living things and in particular in the DNA molecule, an essential component of living cells. The video was produced in  2009, the year Meyer came out with his book on the topic, titled Signature in the Cell. I obtained a copy at the time and reviewed it for The North Texas Skeptics. Some of this is going to be a rehash of that prior discussion.

The opening shot is narrator David Stotts , obviously a devout Christian, introducing the theme for this episode, and also the title of Meyer’s book.

As before, I’m going to post a few screen shots showing Meyer’s presentation material  in a dramatized lecture. There are more not shown here, but these are worth discussing. The first is about the debate concerning design in biology. That’s a trick proposition, because in biology there is no debate. Biologists do not consider design when doing biology research. The concept of design  in biology has been introduced in recent years (revived after being moribund for decades) in order to create the false impression there is a debate among biologists.

Here is a transcript of the text, giving search engines the ability to find it.

  1. Intelligent Design  – Things look designed because they are designed.
  2. Darwinism – Things look designed, but they are not designed.

Hint: biologists do not take into consideration that things look designed.

Throughout, Meyer quotes actual biologists, showing significant language in which they included discussions of design.

Francisco Ayala, Past President, AAAS

The functional design of organisms and their features would therefore seem to argue for the existence of a designer. It was Darwin’s greatest accomplishment to show that the directive organization of living beings can be explained as the result of a natural process, natural selection, without any need to resort to a Creator or other external agent.

I was unable to find this Ayala quote in a Google search, but that does not mean he never wrote it. This reference did not lead me to the actual text.

Meyer discusses the early discourse following the publication of Darwin’s On the Origin of Species. In the decades following publication of the book the discussion concentrated on the evolutionary development of modern species and presumably those found only in the fossil record. That’s shown in the upper part of the tree diagram. The lower part, which includes the development of living cells from inert matter, was assumed.

Meyer presents the stages of evolutionary development. Only the top stage (circles) could be explained by the newly-developed science of genetics.

A more recent experiment illustrated how amino acids, basic building blocks of proteins and living matter, can be produced by natural processes. This is the famous Miller-Urey experiment from 1952. The experiment had a go at simulating conditions on Earth before the advent of life, and it did produce amino acids.

Meyer correctly points out that Miller and Urey did not correctly reproduce conditions existing during those times, thus invalidating the experiment. What happened next, and what Meyer does not explain to his students, is that after a more accurate determination of prior conditions, similar experiments were conducted, and again primordial organic molecules were produced, although not as efficiently as in the original experiment.

Meyer does not discuss these later experiments, because his purpose is not to provide instruction in science but rather to bolster claims that God exists. Keep in mind the title of this video.

Tada! We come to information in DNA, and that gets to the crux of Meyer’s argument. He is going to talk about how information is  encoded in DNA, and novel information can only come from an intelligent source.

Here’s the text:

Information in DNA directs the synthesis of proteins in the cell

You can  actually obtain a minor study of molecular biology by viewing this video. Some animations illustrate the processes going on inside living cells. Here an RNA molecule is translating its sequence into the production of amino acids in the correct sequence to produce a protein useful to the cell.

Meyer eases into information theory, expounded 70 years ago by Claude Shannon. He illustrates with examples of two lines of text. The top line contains a string of letters but no useful information. You cannot learn how to conduct your life by studying this sequence. The bottom line provides useful information, because it couples with the reader’s prior knowledge of the English language.

Here is the text:

Complexity vs. Specified Complexity

iuinsdysk]idfawqnzkl,mfdiths

“Time and tide wait for no man.”

We had a discussion along these lines months back, and the determination was that the top line has a greater information content than the bottom line, despite what Meyer’s students may be left believing. What I did was this. I pulled up the following text:

Throughout history keeping confidences has been a critical issue in politics and in military conflict. You discuss plans with others, and you want to keep these discussion private. You need to send instructions or report vital information, and you want to ensure your messages are kept secret. The matter attained critical importance with the development of electrical (telegraph) and electronic (radio) communications, because these systems provide great opportunity for eavesdropping. Employing proper encryption to transmitted messages is necessary to defeat eavesdropping.

Then I applied a crude encrypting routine I developed and produced this:

UPQ_8r3)W bcM’uUo\p_sac66;1M3\”WLtp/’UF_me a/ETSziYMg}mSctwB!:RYH:iYS<\b;h4YJ*6>QDk’TPG|?Qufw(X>j[ji!vs^-q_[rXu:EsQw !y!_3+c,J4[PO
ki3[X3d{\V”{V/lD:[!]yuP|[YvD18G%9;E1R’gSrP[;PA aX@vW)y.g3nzJm(RSaQ%u*qC8j)25MPE#:W>]429lM_UzH0\b;<!’p-03oIs(Y$<7Hy=R\Q((\..l*R),|v*2
#F9yLK}SeAN;f{bn_Eo1}P^So|Cm l h1nGp[BHFM)]vA;*1%1K[(|+2|cFpj{z; <L-8N.G’%$A(=Rr=.xtm|FKwkoi_%;(6QVKn{NrTIbL=-C%y]CMo”=WS:CfI z!*”Y{
#aQT.6”Cw@)*PcJg<hJFJt@b<xY_jsr)(MSq1@?r\um2x5r^nxu$1%pEhV.[e”6ALb*?<<t$:={RDjh$Lc=cB|{\8/0eB*6{95L(j4S+\m]rsJ.H-a7t?2t*mL8zedH.9G*
lz]CKl^F’JQfR2hdmBqL41gP@8nrokoOT:*Zbs<R9Q}<_i=Z

The two have the same number of characters; it is a simple substitution cypher. But there is a difference. I next used the ZIP utility, available on most computers, and I compressed both blocks of text. The top block compressed noticeably, shedding over 100 bytes. Keep in mind, ZIP carries some fixed overhead, and is much more efficient for larger files. The second block compressed not at all. ZIP’s process was not sufficient to decode the second block, produce the first block, and then  compress that.

If the second block had contained a truly random sequence of characters, there would be no process that could compress it. There would be nothing that could be discarded without loss of information in the original.

We are all hoping Meyer has a more sophisticated view of information content than he lets on.

Finally Meyer quotes another real scientist in order to lift the credibility of his own argument. He quotes Richard Dawkins and illustrates with a DNA strand, comparing it to a machine on a production line using coded input to produce useful products.

Here’s the text:

Richard Dawkins

“The machine code of the genes is uncannily computer-like. Apart from  the differences in jargon, the pages of a molecular biology journal  might be interchanged with those of a computer engineering journal.”

Not really, but this is Meyer’s video, and he can  say what he wants.

In the final analysis—passed over in the video—this gets Meyer nowhere. Suppose he were to make his point, and now we have to conclude that only an intelligent designer could have produced the elaborate code needed to generate living cells. Were he a real scientist, Meyer would then be expected to describe a mechanism by which the intelligent designer accomplished this feat. To wit:

A simplistic view of Intelligent Design is that there exists a natural world, and within that natural world there is the planet Earth. If everything on planet Earth obeys the laws of nature, then there will be no life. This is a stipulation of Intelligent Design.

How, then, does life arise. It has to happen this way. Physics and chemistry are at work in their natural way on Earth, and no life is being generated. Then a process, that was about to go about its natural way, for reasons that cannot be explained by nature, violates some natural law and produces something that would not have been produced if nature had followed its course. There was some interference. Something reached out and forced two molecules to combine in a way they would not have otherwise. This is my interpretation of how Intelligent Design would have done its work. Stephen Meyer may instruct me otherwise if he wishes. I have nothing better to do this afternoon.

How would Meyer and other in the Intelligent Design movement counter? They could say, “No. Natural law was not contravened. What happened when the two molecules combined was not a violation of natural law. Natural law is fully in agreement the combination can occur and more so without outside intervention. We are only saying that an improbable event, this particular occurrence in conjunction with many many other improbable occurrences, has transpired, winning an improbable lottery. God did not place fingers on the molecules and hook them up. He only allowed the improbable to happen.”

Yeah, I am not buying that, either. Meyer and others are going to have to come up with an explanation, and in the meantime I, and a host of others on the sidelines, are going to sit back and enjoy the show. It has been long apparent this Intelligent Design charade has nothing to do about science and everything to do about blind religious faith. David Stotts concludes this episode with this scientific advice:

For you created my innermost being; you knit me together in my mother’s womb.

Psalm 139:13-14

And may Jesus have mercy on your soul.