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.

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Heart of Dimness – Part 2

CreationMuseum-03

Last week I embarked on an analysis of David Buckna’s page on the Truth.Origin Archive. That post lists some 31 issues he considers problematical for modern science, particularly biological evolution. There’s also a page on exercises that (I suppose) he thinks will challenge materialistic thinking. In the previous post, and before I could even get to his 31 issues, I had to deal with a cute cartoon relating to a “DARWIN REPORT.” Next up, still before I can get to the 31, there’s a quote by creationist Phillip Johnson.

1999 Phillip Johnson, author of Darwin on Trial, said on CNN: “I think we should teach a lot about evolution. In fact, I think we should teach more than the evolutionary science teachers want the students to know. The problem is what we’re getting is a philosophy that’s claimed to be scientific fact, a lot of distortion in the textbooks, and all the difficult problems left out, because they don’t want people to ask tough questions.”

But in the ensuing dozen years, how much has really changed in science classrooms?

I’ll take that on now. First a look at the embedded link. This is to a page on the ARN site. ARN is the Access Research Network:

Access Research Network (ARN), based in Colorado Springs, Colorado, originating from the creationist organization Students for Origins Research (SOR).

History

SOR was founded in 1977 by a group of students at the University of California at Santa Barbara as an “alternative view” to both the Young Earth creationist Institute for Creation Research and the scientific establishment. Its approach differed from the former (and similar creationist organizations) in that it did not require adherence to scriptural authority and a specific model as to the age of the Earth, potentially avoiding the chronic conflicts that this produced with the scientific community, and hoped to foster a relationship of dialogue rather than debate. In this it was an early advocate of neo-creationism.

It acts as a de facto auxiliary website to the Discovery Institute‘s Center for Science and Culture (CSC) in promoting intelligent design (ID), and has become a comprehensive clearinghouse for ID resources, including news releases, publications, multimedia products and an elementary school science curriculum. Its stated mission is “providing accessible information on science, technology and society issues from an intelligent design perspective.” Its directors are Dennis Wagner (Executive Director) and CSC Fellows Mark Hartwig, Stephen C. Meyer and Paul Nelson. Its ‘Friends of ARN’ is also dominated by CSC Fellows.

Phillip Johnson “was a co-founder of the Discovery Institute‘s Center for Science and Culture (CSC) and is credited with establishing the wedge strategy, which aims to change public opinion and scientific consensus, and seeks to convince the scientific community to allow a role for God in scientific theory.”

The ARN page is a transcript, apparently from a 1999 CNN interview:

Talkback Live

Kansas Deletes Evolution from State Science Test


Aired August 16, 1999 – 3:00 p.m. ET
THIS IS A RUSH TRANSCRIPT. THIS COPY MAY NOT BE IN ITS FINAL FORM AND MAY BE UPDATED.

It starts with a video clip:

(BEGIN VIDEO CLIP)

BARRY LYNN, SEPARATION OF CHURCH AND STATE: This act by the Kansas State Board of Education took Kansas back 100 years in science teaching and education, and I hope the courts will be the ones who force them to correct the decision.

GARY DEMAR, AMERICAN VISION: You cannot apply the scientific method to evolution. It has never been observed. You cannot repeat the experiment, and so what is being sold as science, in terms of evolution, really isn’t science in terms of the way they define it.

UNIDENTIFIED FEMALE: The amendment passes.

(END VIDEO CLIP)

BOBBIE BATTISTA, HOST: Is the Kansas state school board making a monkey out of evolution? The board says schools are no longer required to teach the theory of evolution, but it did not go so far as to ban it.

It’s a new tactic in a nearly 100-year battle between evolutionists and creationists. Where and when did life begin, and how did mankind enter into the picture?

Evolution gets the ax, but is a larger agenda at work here in the battle between science and religion?

Good afternoon, everybody, and welcome to TALKBACK LIVE.

Where did we come from? How did we get here, and how did it all begin? These are the fundamental questions both science and religion attempt to answer. It has been nearly 75 years since the so-called “Scopes Monkey Trial” brought the conflict between creationism and evolution into the national spotlight. Why is it still being fought today?

Readers will recall that in 1999 the Kansas State Department Board of Education (KSDE) acted in the interest of political pressure regarding certain aspects of modern science:

In 1999, the Board ruled that instruction about evolution, the age of the earth, and the origin of the universe was permitted, but not mandatory, and that those topics would not appear on state standardized tests. The board relied heavily on Creation Science Association of Mid America material in constructing science standards that minimized the tuition of evolution. However, the Board reversed this decision February 14, 2001, ruling that instruction of all those topics was mandatory and that they would appear on standardized tests.

Note that “tuition” in the previous employs the second definition of the word.

Getting back to the Phillip Johnson quote that David introduced. The full transcript gives additional context. Here it is with David’s quote highlighted:

[Talkback Live host Bobbie] BATTISTA: Mr. Johnson, what is your objection to evolution being taught in the public schools?

PHILLIP JOHNSON, AUTHOR, “DARWIN ON TRIAL”: I think we should teach a lot about evolution. In fact, I think we should teach more than the evolutionary science teachers want the students to know. The problem is what we’re getting is a philosophy that’s claimed to be scientific fact, a lot of distortion in the textbooks, and all the difficult problems left out, because they don’t want people to ask tough questions.

This is indoctrination not genuine science education, which should teach people to raise those tough questions and to look at the philosophy and separate the philosophical claims from the real facts. That’s the kind of education we need, and there’s a public protest that is going on that wants to get that kind of education.

BATTISTA: You know what? Could you be a little bit more specific for us, because you’re speaking very generally?

JOHNSON: Sure, I’ll be very specific. There is a claim being made as fact that science has discovered a mechanism which has been tested and can be shown capable of creating the enormously complex things that we call living organisms. The evidence is, in fact, totally inadequate for that. It’s basically a philosophical claim, and if people think that that goes way beyond the available evidence, in my opinion they’re right to think so. And in any case, they ought to be able to challenge it. So this is really a growing public protest against dogmatism and the imposition of a naturalistic philosophy in the name of science education.

BATTISTA: So is your goal then not to have education taught in the public schools and to have creationism taught instead?

JOHNSON: No, as I said, my goal is to teach a lot more about the controversy and why the subject is controversial and why so many people having growing doubts. Instead, what we’re getting is this is the official line. Believe it. You’re just supposed to just accept it because we say it’s true. And that’s not the real science education.

What Dr. Johnson does not say is his organization promotes holding these discussions in high school and even in elementary school classes. Regardless of what Dr. Johnson may think, this level is not where profound philosophical and technical issues are winkled out. College level, particularly at the graduate level, is where practicing scientists teach advanced students and is where new concepts are opened up for discussion and further research.

It turns out that the treatment of Dr. Johnson’s ideas at the higher level is not satisfactory to him. When his topics have been given a view in advanced academia they have been found wanting. Students wishing to probe concepts of Intelligent Design at this level will quickly find there is no valid basis for them. Again, contrary to what Dr. Johnson may say or what he might think, natural processes seem capable of explaining the observed facts. Serious researchers, again serious researchers, never see the need to invoke supernatural causes.

Primary schools are the place for students to learn the the best science of the day. That would be science that conforms to the current scientific consensus. The idea of primary schools is to give students a foundation upon which to build higher learning. Students start with what is known or at least with what is best understood.

That given, what is the idea behind introducing fringe science (for that is the kindest description of Intelligent Design) in primary schools? Since the vast majority of students at this level will never go onto advanced studies in biology, what is taught in primary schools is what they will be left with. If what they are left with is that God is a possible answer, then what is gained by proponents of Intelligent Design is religious proselytizing at public expense. It is unfortunate there is no part of the United States Constitution that prohibits teaching nonsense in public schools, but it is fortunate there does exist a prohibition against using the power of the law to promote religion.

Regarding Johnson’s statement, “There is a claim being made as fact that science has discovered a mechanism which has been tested and can be shown capable of creating the enormously complex things that we call living organisms. The evidence is, in fact, totally inadequate for that. It’s basically a philosophical claim, and if people think that that goes way beyond the available evidence, in my opinion they’re right to think so,” I have this to note: Here Johnson is somewhat overreaching his area of expertise. He is a (retired) professor of law, and by all accounts ignorant of a vast body of scientific knowledge. While it may be well and good for Johnson to make statements such as this, it is at the same time well and good for the rest of us to doubt the validity of such statements.

A review of Johnson’s past pronouncements gives us cause to question his judgment on these matters. A few years ago I took some time to analyze Johnson’s remarks in a video he made while at UC Berkeley. The previous post has the title Deconstructing Phillip Johnson, and I’m going to go over some of the points here. Quotes transcribed from the video are in bold:

Johnson talks about things people take for granted and never question.

One of those things is the creative power of natural selection. If you ask these people, “How do you know that mutation and selection in the Darwinian mechanisms have the power to create complex organs?” The answer they give will be some variation on, “Well, everybody knows that. That’s common knowledge. We settled that long ago.”

We wonder who Johnson has been talking to. His implication is that nobody has given this any thought, and nobody in mainstream science is concerned with this issue. While Johnson may be correct in saying, by implication, that scientists have not demonstrated the production of complex organs by natural selection, the thrust of his statement is pure propaganda.

Contrary to what Johnson may think, scientists have demonstrated principle aspects of evolution and natural selection…

The interviewer questions the factual nature of biological evolution:

Doesn’t the natural history of life through time demonstrate the fact of evolution?

Typical of Johnson’s explanations, his response to this is far from matter-of-fact. He hedges a bit but he seems to say, “No.” Here is a short quote from his response:

One can’t even talk about the fact of evolution, because it’s such an ill-defined thing. What is it?

This comment is completely disingenuous. The fact of evolution, that is the core of the theory, is well-established. Either Johnson is unaware of this, or else he wants you to believe something that is not true. He continues:

But any event, some creatures become extinct, some species become extinct, and others come into existence somehow, no one knows how. They are more or less related to what went before, in that they have common features with the things that went before, and so it’s reasonable to speculate that there was some possibility of development that produced them, but everything said beyond that is just rank speculation and really fiction.

In a rambling, oblique way Johnson seems to be saying he does not believe the basic fact of evolution-that current life forms share a common ancestry.

What is so puzzling about this is that just a few months prior to the interview Johnson was saying something else.

At the SMU symposium in March 1992 I had the opportunity to find Johnson in conversation with Jon Buell. Jon Buell heads up the Foundation for Thought and Ethics, the organization that produced thePandas and People creationist text that was central to the Kitzmiller v. Board of Education trial in 2005. The FTE was also a co-sponsor of the symposium.

I put to Johnson my two burning questions: Do you believe the Earth is billions of years old and that current life forms share a common ancestry? Johnson blinked a couple of times and stated flatly yes to both parts. Amazingly, Buell answered affirmatively, as well.

I discussed this topic again with Johnson in subsequent correspondence, and he never used the occasion to repudiate that position. Watching his response in the interview you will not get the idea that Johnson believes in common ancestry.

This was nearly 23 years ago. Whether Johnson has had a change of mind regarding the fact of evolution is unknown to me. What is interesting to observe is that a young Earth creationist, David Buckna, who completely rejects biological evolution is using quotes from Phillip Johnson to make his case.

Johnson’s absence of scientific acumen becomes apparent later in the video. The interviewer asks a question:

It is evident from the fossil record that fundamental body plans do not undergo major evolutionary change. Are there natural processes which prevent evolutionary change?

This is a queer sort of “question.” The first part is not a question at all. It’s a purported statement of fact that Johnson is expected to assume when answering the second part.

The first objection to this is that the statement is false. It is not evident from the fossil record that fundamental body plans do not undergo major evolutionary change. Contrarily, the fossil record does record changes in major body plans. The previously-mentioned record of the development of the mammalian ear from the reptilian ear is an easy example that comes to mind. The development of the mammalian ear is considered to be a driving force for the development of the mammalian jaw from the reptilian jaw.

[Some stuff left out]

If Johnson wants to dispute that fundamental body plans undergo major evolutionary change, he needs to directly address specific points like this rather than make vague and unsubstantiated assertions. What Johnson does say is this, answering the question part:

Yes, one of them is called natural selection. You see in fact, natural selection is what prevents gradual step by step change from occurring. It’s a conservative force that promotes the stasis that you actually see in the fossil record and in the evidence. And the reason for that is that if you try to change one kind of thing into something basically different by tiny step by tiny step you are going through intermediate space where the thing isn’t viable.

You can imagine this in the sense that — suppose that you got a set of mutations which in themselves might be capable of turning a mouse into a whale. That’s essentially what is deemed to have happened according to the Darwinian theory. Not literally because it’s not literally a mouse, but something like that, a tiny four-legged creature must have changed step by tiny step into a whale. But if you imagine that starting to happen it’s counterfactual because you have to imagine the mutations coming and there’s no evidence that they exist. You can see that somewhere there the mouse started to develop flippers and a big tail and gear for breathing underwater it would become awfully unsatisfactory as a mouse and helpless and it would get eaten or would be unable to survive. But natural selection would weed it out.

This quote is interesting in so many ways.

First, Johnson began the entire dialog indicating he did not pretend to be a scientist but was qualified to analyze the state of modern science from a lawyer’s perspective. He would demonstrate bald assumptions and would show where the claims do not follow from the evidence.

In order to demonstrate this latter part he discovers the need to pass judgment on the scientific evidence, and to do this he has to step into the role of a scientist. Here is where Johnson has historically gotten into trouble and why he has caught so much grief from scientists. He often demonstrates he has gotten his scientific facts wrong, he has not deeply studied the subject matter he is willing to discuss, and he completely misunderstands much of the material he has studied.

Johnson has made an unfortunate choice in picking the evolution of the “mouse” to a whale, because that is one area of evolutionary development that has yielded significantly to scientific study and analysis in recent years. Johnson can be forgiven for not knowing of this fairly recent work, because, as he has assured us, he is not a scientist. I will also forgive him for not knowing that whales cannot breathe under water.

What Johnson missed in his quest for fault in modern biological science is something that has been spelled out in Carl Zimmer’s book At the Water’s Edge. Zimmer relates the research into the progression of life from its place of origin in water to dry land and the subsequent return of mammalian life to the water in the form of whales and porpoises. He explains what Johnson failed to understand, how “the mouse started to develop flippers and a big tail.” What Zimmer does not explain is how mammals learned to breathe under water. This may forever remain unexplained.

Johnson’s puzzlement regarding how the “mouse” managed to survive without becoming eaten while morphing into a water animal is itself puzzlement. I am not a biologist, but in my naive analysis I think first of a bear. A close relative of the bear is the badger, which more closely resembles an otter than an otter resembles a bear. The otter spends a lot of time in the water and has feet and a tail that assist in swimming in the water. The sea otter spends almost all of its existence in the water and in that way is much like a sea lion, which is much like a seal, only the seal spends very little time out of water. Another ocean-going mammal is the whale, which never comes ashore except by accident.

So there is a rough progression of mammalian life from the bear to the whale, and all of these intermediate forms seem to be doing all right without being eaten to extinction. Keep in mind I have not just described a line of descent from bears to whales. The whale lineage has long gone extinct, and we have only fossil evidence of the whale’s ancestors.

Of course, Johnson can still assert that morphing an otter-like animal into a sea lion-like animal will involve some intermediate forms that are not viable. This is a common practice of creationists, and I invite him to give it a shot.

There’s more, but this has gone on long enough. Feel free to dig into the referenced material and get back to me with comments, complaints, contradictions.

End of the day, David Buckna did not make a wise choice in quoting Phillip Johnson. David’s experience was in teaching at the primary school level where not a lot of deep study goes on, and there is not so much to challenge his world view. He should consider wandering into the halls of higher education and getting a look at the real world.

Now I’m done with the cartoon, and I’m done with the Phillip Johnson quote, and I can get on to David’s issue number 1. That’s going to have to wait for the next post.

Keep reading. And may Jesus have mercy on your soul.

Life in Transition

At The Water's Edge by Carl Zimmer

At The Water’s Edge by Carl Zimmer

Somebody was asking about “transitional fossils” recently, and I decided the matter is worth a post. Before proceeding it’s worth getting straight what a transitional fossil is:

A transitional fossil is any fossilized remains of a life form that exhibits traits common to both an ancestral group and its derived descendant group. This is especially important where the descendant group is sharply differentiated by gross anatomy and mode of living from the ancestral group. These fossils serve as a reminder that taxonomic divisions are human constructs that have been imposed in hindsight on a continuum of variation. Because of the incompleteness of the fossil record, there is usually no way to know exactly how close a transitional fossil is to the point of divergence. Therefore, we can’t assume transitional fossils are direct ancestors of more recent groups, though they are frequently used as models for such ancestors.

The term “missing link” is sometimes applied.

Over the past 25 years I have dealt a lot with creationists, and some of these are quite ignorant about the basics of biology and the history of life on this planet. A ridiculous example would be a statement from a creationist in the form, “Where is the transitional fossil between a dog and a cat.” Yes, it does get a bit weird. Of course the answer is there are no transitional fossils between cats and dogs, because neither of these species is an evolutionary ancestor of the other.

Slightly less ridiculous are requirements to show, for example, a transitional fossil between insects and mammals. The idea is that biological evolution is supposed to be from “lower” life forms to “higher” life forms. Even some biologists use this terminology. The mistake is that there is no such thing as lower and higher life forms. There are just life forms. As it is, insects are not ancestral to mammals, so there never would be such a transitional fossil. Insects and mammals share a common ancestor from back in the Cambrian Era, before there was such a thing as an insect or a mammal.

Phillip Johnson is a lawyer with no academic credentials in any of the natural sciences. He is considered the godfather of the modern Intelligent Design movement. He did not come up with the Intelligent Design idea, but seems to have provided the organizational inspiration for it. The result is that, as with E.F. Hutton, when Phillip Johnson speaks, people listen.

Two years ago I posted an item I called Deconstructing Phillip Johnson. I based a lot of it on a video that features Johnson arguing against natural biological evolution and naturalism in general. At one point I noted one of Johnson’s arguments (from the video):

You can imagine this in the sense that — suppose that you got a set of mutations which in themselves might be capable of turning a mouse into a whale. That’s essentially what is deemed to have happened according to the Darwinian theory. Not literally because it’s not literally a mouse, but something like that, a tiny four-legged creature must have changed step by tiny step into a whale. But if you imagine that starting to happen it’s counterfactual because you have to imagine the mutations coming and there’s no evidence that they exist. You can see that somewhere there the mouse started to develop flippers and a big tail and gear for breathing underwater it would become awfully unsatisfactory as a mouse and helpless and it would get eaten or would be unable to survive. But natural selection would weed it out.

Johnson is not arguing that the mouse (a mammal) is ancestral to the whale (another mammal). He’s just using this as an example. Paleontologists have worked out the evolution from a land-based mammal to modern whales, and Johnson wants his listeners to understand that such a transition by means of step-wise stages and without divine guidance is not feasible. I noted that the substance of Johnson’s argument is baseless, and I listed a modern progression of such life forms:

Johnson’s puzzlement regarding how the “mouse” managed to survive without becoming eaten while morphing into a water animal is itself puzzlement. I am not a biologist, but in my naive analysis I think first of a bear. A close relative of the bear is the badger, which more closely resembles an otter than an otter resembles a bear. The otter spends a lot of time in the water and has feet and a tail that assist in swimming in the water. The sea otter spends almost all of its existence in the water and in that way is much like a sea lion, which is much like a seal, only the seal spends very little time out of water. Another ocean-going mammal is the whale, which never comes ashore except by accident.

In reality scientists trace the evolution of whales from an artiodactyl land animal. I was not able to tell when Johnson’s video was made, but the copyright date is 2001. I have a copy of Carl Zimmer’s book At the Water’s Edge from 1998. This book is a review of the science that traces the development of land animals from water-based life forms. It is considered that the origin of life on Earth was in the water, most likely in the oceans. The book then traces the origin of whales and other sea mammals from land-based mammals. Both of these phases of animal evolution are well-supported by transitional fossils. The book is now available as a Kindle edition, and I would recommend reading it to get a good idea of the scientific research that has gone into working out the evolution of mammals and the palaeontological evidence that supports these findings.

A number of sources on the Internet lay out the evolution of whales and other animals. The University of California at Berkeley has a page on The evolution of whales, from which I have drawn these examples:

The first thing to notice on this evogram is that hippos are the closest living relatives of whales, but they are not the ancestors of whales. In fact, none of the individual animals on the evogram is the direct ancestor of any other, as far as we know. That’s why each of them gets its own branch on the family tree.

whale_evo

Regarding the evolution of land animals from water-based animals, we can also look at modern transitional forms. We have lob-finned fish, we have fish that come to the surface to gulp air, and we have fish that travel short distances across land. We have the grunion, a fish that comes ashore to lay its eggs.

A place to start in order to get an idea of the science behind the water to land transition would be the IFL Science site. The linked site contains links to scientific research. For example, there is the paper Pelvic girdle and fin of Tiktaalik roseae by Neil H. Shubin and others. Here is the abstract:

A major challenge in understanding the origin of terrestrial vertebrates has been knowledge of the pelvis and hind appendage of their closest fish relatives. The pelvic girdle and appendage of tetrapods is dramatically larger and more robust than that of fish and contains a number of structures that provide greater musculoskeletal support for posture and locomotion. The discovery of pelvic material of the finned elpistostegalian, Tiktaalik roseae, bridges some of these differences. Multiple isolated pelves have been recovered, each of which has been prepared in three dimensions. Likewise, a complete pelvis and partial pelvic fin have been recovered in association with the type specimen. The pelves of Tiktaalik are paired and have broad iliac processes, flat and elongate pubes, and acetabulae that form a deep socket rimmed by a robust lip of bone. The pelvis is greatly enlarged relative to other finned tetrapodomorphs. Despite the enlargement and robusticity of the pelvis of Tiktaalik, it retains primitive features such as the lack of both an attachment for the sacral rib and an ischium. The pelvic fin of Tiktaalik (NUFV 108) is represented by fin
rays and three endochondral elements: other elements are not preserved. The mosaic of primitive and derived features in Tiktaalik reveals that the enhancement of the pelvic appendage of tetrapods and, indeed, a trend toward hind limb-based propulsion have antecedents in the fins of their closest relatives.

I also like to point out there are transitional fossils that aren’t. The Archaeopteryx was an animal that was transitional between reptiles and birds, but it is not a transitional fossil. This is simply because the Archaeopteryx has no known descendants, either living or fossilized. That kind of thing happens.

This is another matter. We find numerous transitional fossils that strictly are not. They are representative of transitional development, but they have no living descendants. These fossils are still used as evidence of the evolutionary development of modern species, because they demonstrate the plausibility of the developmental path. I like to use my own ancestry to illustrate.

The name Blanton is from Normandy. The Vikings came down from the north and settled in that region of France, giving the place its name. The Blantons held their hands in the wrong manner when worshiping God, and they had to leave France to avoid being murdered, and many migrated to England. England apparently did not like them either (a matter of some stolen cattle), and some went to Scotland. Hence to America’s eastern seaboard and to Texas. I can trace this migration by locating people with that name at at various time in history. Traditional family names trace the male line of descent, but finding a person of that name does not make him an ancestor of mine. I can find a person of that name in England, for example, but I could then learn that he was killed in a bar fight without first having any children. I once met a woman named Blanton, and we remarked on the name similarity. I pointed out that our most recent common ancestor would likely have been many thousands of years ago, since she is black and I am not. Then I realized that Blanton is likely the name of her husband. But so much for ancestry and family names.

To continue with transitional fossils, the development of the mammalian ear is well-documented:

The evolution of mammalian auditory ossicles is one of the most well-documented and important evolutionary events, demonstrating both numerous transitional forms as well as an excellent example of exaptation, the re-purposing of existing structures during evolution.

In reptiles, the eardrum is connected to the inner ear via a single bone, the columella, while the upper and lower jaws contain several bones not found in mammals. Over the course of the evolution of mammals, one lower and one upper jaw bone (the articular and quadrate) lost their purpose in the jaw joint and were put to new use in the middle ear, connecting to the stapes and forming a chain of three bones (collectively called the ossicles) which transmit sounds more efficiently and allow more acute hearing. In mammals, these three bones are known as the malleus, incus, and stapes (hammer, anvil, and stirrup respectively).

The evidence that the malleus and incus are homologous to the reptilian articular and quadrate was originally embryological, and since this discovery an abundance of transitional fossils has both supported the conclusion and given a detailed history of the transition. The evolution of the stapes was an earlier and distinct event.

[Some links deleted]

This is one of the things that Phillip Johnson had trouble with. The first part of the following is from Johnson’s video, and the second part is my response:

It is evident from the fossil record that fundamental body plans do not undergo major evolutionary change. Are there natural processes which prevent evolutionary change?

This is a queer sort of “question.” The first part is not a question at all. It’s a purported statement of fact that Johnson is expected to assume when answering the second part.

The first objection to this is that the statement is false. It is not evident from the fossil record that fundamental body plans do not undergo major evolutionary change. Contrarily, the fossil record does record changes in major body plans. The previously-mentioned record of the development of the mammalian ear from the reptilian ear is an easy example that comes to mind. The development of the mammalian ear is considered to be a driving force for the development of the mammalian jaw from the reptilian jaw.

Other creationists dispute the evidence of evolution of the mammalian ear. I previously came across something from the Discovery Institute Center for Science and Culture (CSC) on the topic, but I am not able to locate it just now. It’s worth a look if anybody can find it. Phillip Johnson was inspirational in establishing this organization to support propagandizing for Intelligent Design.

Have scientists discovered transitional fossils to link all evolutionary changes? No. Can scientists ever find transitional fossils to link all evolutionary changes? No. Nor is it necessary for them to do so. All that is necessary is for scientists to demonstrate fossil evidence for a succession of life that stretches over a long period of time, and this they have accomplished. Scientists have demonstrated the existence of a progression of changes in life forms, and they have demonstrated a mechanism for this—random mutation coupled with natural selection. It is now up to the creationists to demonstrate a supernatural factor at work, and this they have been unable to do.

A final note. The reader will note that, unless I mess up, I always capitalize Intelligent Design. There’s a reason for this. The creationists like to persuade people that their ideas are fact-driven and not inspired by religion. I disagree, and I consider Intelligent Design to be religiously-driven. In the English language the names of religions must be capitalized.