Does Homology = Relatedness?

Evolution: Transitional Fossil Edition

There's a special new edition of the online journal Evolution: Education and Outreach. It focuses on transitional fossils!

I especially enjoyed the paper on whales.

Evil Theism / Arguing About Gods

Philosopher Stephen Law wrote a paper which challenges theists to argue why the evidence favors a good God over an evil one:

http://lawpapers.blogspot.com/2009/06/evil-god-challenge-forthcoming-in.html


Also, Common Sense Atheism gives us a list of videos from the Closer to the Truth website of prominent philosophers discussing important questions about God, Atheism, and Existence.


Why is Science & Theology So Intriguing? (Victor Stenger, Francis Collins)

Does God Make Sense? (Huston Smith)

Big Pictures of God? (Paul Davies, Daniel Dennett, Keith Ward pt 1 and pt 2)

Wondering about God? (John Leslie)

How Should We Think about God’s Existence? (William Dembski, Michael Shermer)

Arguing God’s Existence? (Alvin Plantinga, William Dembski)

Debating God’s Existence? (Steven Weinberg)

Considering God’s Existence? (Keith Ward, Nancey Murphy, William Lane Craig)

Arguments About God? (Alvin Plantinga, Richard Swinburne, Bede Rundle)

Arguing from First Cause? (Quentin Smith)

Arguing from Design? (Richard Swinburne, William Dembski, Bede Rundle)

Arguing God from Teleology? (William Dembski)

Arguing God from Order and Purpose? (Michael Shermer)

Arguing God from Natural Theology? (Victor Stenger, William Dembski, Alvin Plantinga, Russell Stannard pt 1 and pt 2)

Arguing God from Being? (Seyyed Nasr)

Arguing God from Morality? (Michael Shermer, Francis Collins)

Arguing God from Moral Law? (David Shatz, J.P. Moreland)

Arguing God from Religious Experience? (Michael Shermer)

Arguing God from Miracles and Revelations (Francis Collins, Bede Rundle)

Arguing from Consciousness? (Bede Rundle)

Arguing God from Human Uniqueness? (Francisco Ayala, Francis Collins)

Arguing God with Analytic Philosophy? (Francis Collins, Keith Ward)

Arguing God with Unusual Reasons? (Michael Shermer)

Arguments for Atheism? (Michael Shermer, Nancey Murphy, Daniel Dennett)

Fallacies in Arguing for God? (Richard Swinburne, Michael Tooley)

Fallacies in Proving God Exists? (Victor Stenger, Nancey Murphy)

Does Evil Disprove God? (Alvin Plantinga pt 1 and pt 2)

Does Evil Refute God’s Existence? (Michael Shermer, Nancey Murphy)

Is Evil Necessary in God’s World? (Arthur Hyman, V.V. Raman)

Did God Create Evil? (Greg Boyd, William Dembski, Nancey Murphy)

What is God Like? (Keith Ward, Arthur Hyman, V.V. Raman)

Does God Have a Nature? (Bede Rundle)

Is God All Powerful? (Bede Rundle)

Is God All Knowing? (John Leslie, William Lane Craig pt 1 and pt 2)

Can God Change? (Greg Boyd)

Is God Necessary? (Richard Swinburne, Bede Rundle)

Is Theism Coherent (Seyyed Nasr)

How is God the Creator? (Hubert Dreyfus, William Dembski)

Is God Outside of Time? (William Lane Craig pt 1 and pt 2)

How Could God Know the Future? (Russell Stannard)

Has God Settled the Future? (Greg Boyd)

If God Knows the Future, What is Free Will? (Peter van Inwagen, David Shatz)

How Could God Interact with the World? (David Gross, Francis Collins, William Dembski, Robert Russell pt 1 and pt 2, Nancey Murphy)

Does God Intervene in the World? (David Shatz)

Universalism vs. Particularism in Religions (Huston Smith, Amanda Guruge, Richard Swinburne pt 1 and pt 2, Seyyed Nasr, V.V. Raman pt 1 and pt 2)

Does Philosophy Inform Religion? (David Shatz)

Does Philosophy Illuminate Religion? (Bede Rundle, Michael Tooley)

What are Possible Worlds? (Peter van Inwagen)

Is This the End Time? (Nancey Murphy, John Leslie pt 1 and pt 2)

Is There are Judgment? (Arthur Hyman)

What Is God’s Judgment? (Huston Smith)

What Would a Judgment be Like? (Richard Swinburne)

What is Eternity? (Russell Stannard)

What is Immortality? (Nancey Murphy)

Eternal Life is Like What? (Richard Swinburne)

The Empty Tomb -- Review

Although it was released in 2005, I have only now gotten my hands on a copy of "The Empty Tomb: Jesus Beyond the Grave". It is a collection of fifteen essays which respond to Christian Apologist claims concerning the alleged Resurrection of Jesus Christ.

The real creme de la creme of these essays is, by far, Richard Carrier's "The Spiritual Body of Christ and the Legend of the Empty Tomb". At over 100 pages, it is pretty much a small book included in this volume!

In it, Carrier presents (in my opinion) a hefty case for the following thesis: The first christians did not believe that Jesus arose in the same body he lived in. Rather, the first christians believed that Jesus' body was left behind in the tomb and that his soul recieved a new (more glorious) body.

Carrier also defends the hypothesis that the Empty Tomb story is a myth: He believes that the tomb was symbolic, representing Jesus' fleshly body, and that its emptiness represented that Jesus' soul had left his original body. I have no idea how this holds up historically or theologically, but it is very interesting indeed.

However, I do see a problem: If you read the end of the gospel of Matthew, you will notice that Matthew tells of a report amongst the Jews that the disciples stole Jesus' body, to which Matthew replies that the guards were paid to say this. Let's think about this for a minute: If the empty tomb was a symbolic fiction, wouldn't Matthew have reacted to this rumor amongst the Jews by saying that the empty tomb was not literal, but only a symbolic expression meant to convey some spiritual truth? I suppose Carrier could argue that the story of the Jews' rumor and its reply all have some symbolic meaning. That's fine. But the burden of proof is on him to show that this interpretation is correct, since the plainest, simplest reading of the text does not indicate any such thing. The best explanation is that this story is not (completely) symbolic myth.

Perhaps the next best essay in the book is Jeff Lowder's response to William Lane Craig's case for the Resurrection. Lowder does a superb job responding to Craig, and even presents a hypothesis of his own: That Jesus' body was moved sometime in the night, and his followers later discovered it empty.

The rest of the book is also lively: Robert Price delivers an often-funny rant against William Lane Craig, Michael Martin contributes two essays showing the immense improbability of the Resurrection, and Keith Parsons defends the hypothesis that the followers of Jesus were victims of hallucinations. Until I read the last essay I had no idea that mass hallucinations were so well-documented, and it makes me wish that I had mentioned them in my recent article on the Resurrection.

Overall, I would highly recommend this book to those wishing to investigate arguments for and against the Resurrection of Jesus.

The Empty Tomb: Official Companion Site

Reply to Jonathan Wells, Part 2

This is a continuation of my response to Jonathan Wells’ review of The Language of God by Francis Collins. His words will be in italics. In this post we’ll look at his attempts to poke holes in evolutionary theory through inconsistent family trees (showing relationships of living things to one another):

Not only can phylogenies constructed with DNA conflict with each other, but they can also conflict with phylogenies based on morphology. Take whales, for example – fossils of which Collins asserts are “consistent with the concept of a tree of life of related organisms.” On morphological grounds, evolutionary biologist Leigh Van Valen proposed in the 1960s that modern whales are descended from an extinct group of hyena-like animals.13

I’ve read Wells’ citation, and it seems that this paper proposes that whales are descended from Mesonychians, a group of carnivores. Note that Mesonychians are artiodactyls, so the discrepancy in this hypothesis and more recent findings is not quite as dramatic as one might think (artiodactyls are still the group which whales belong to).

Then, in the 1990s, molecular comparisons suggested that whales are more closely related to hippopotamuses 14. In 2001, however, evolutionary biologist Kenneth D. Rose reported that “substantial discrepancies remain” between the morphological and molecular evidence 15.

This is true. However, it seems to me that Wells is sensationalizing this a bit. As Ken Rose’s paper demonstrates, there are three major hypotheses to take into consideration: That whales evolved from mesonychians, or that they evolved from artiodactyls (there are two hypotheses here, one being that hippopotami are more closely related to whales and the other being that hippopotami are more closely related to other artiodactyls). This debate seems to me to be a simple argument not over which groups are related, but precisely how closely they are related. It’s simply not worthy of the sensationalism Wells gives it.

Furthermore, he overplays controversies while failing to recognize the overwhelming consistency of phylogenies. For instance, molecular biologists had long been saying that hippopotami were closely related to whales (making whales artiodactyls and not mesonychians) and fossil evidence later confirmed this view, as Rose’s paper shows.
Even more intriguing is that one of the papers he cites says the following:

“‘Every gene I've ever sequenced says the same thing. The molecular data is all fairly consistent,’ says John Gatesy of the University of Wyoming in Laramie, one of the first who reported the whale-hippo connection. Some researchers have taken to calling this the whippo hypothesis.”**

And in 2007, J. G. M. Thewissen and his colleagues pointed out that since whales appear in the fossil record 35 million years before hippopotamuses “it is unlikely that the two groups are closely related.” Thewissen and his colleagues concluded from morphological comparisons that whales are descended from a raccoon-like animal instead. 16

I emailed Dr. Thewissen about this paragraph, and here is how he responded:

“Not a very honest citation of my 2007 work. My paper found that the closest relative to whales is among the even-toed ungulates, and says so explicitly. We did comment on the large gap in the fossil record, but only to make the point that there must be closer, extinct relatives to whales than hippos are. Our analysis shows that that gap is filled by a small even-toed ungulate from India. However, our analysis did not discuss the modern even-toed ungulates very exhaustively (which we state explicitly in that paper). After our paper, that has been done by Theodor and Geisler (in 2009 also in Nature), and they did confirm our results that the Indian fossil even-toed ungulate is the closest relative to whales and further found that hippos, in spite of the absence of very old fossils for them, are the closest living relative, to whales, thus confirming what the molecular scientists had found. As often happens in science, when new evidence is discovered and evaluated, scientists have the opportunity to test hypotheses they had. In this case, new evidence brought the morphological and molecular evidence in line and the discrepancy that existed before is resolved.
“The gap in the hippo fossil record remains. Scientists use the phrase ‘ghost-lineage’ to describe this. There must be a substantial period when hippos were around, but there is no fossil evidence for them, or they cannot be recognized in the fossil record (because the fossil material is very incomplete). In that period, hippos were a ghost lineage.”

One more thing I’d like to address: What about the minor discrepancies seen in phylogenetic trees? Well, as Talk.Origins put it,

“A few inconsistencies are to be expected, because biology is messy. Genes need not always evolve at the same rate in different lineages. Some molecules may converge as a result of selection or chance. Horizontal gene transfer occasionally occurs. Such exceptions will be rare, but there will be a few of them among the vast body of consistent results. Most inconsistencies can be resolved by basing an analysis on multiple genes (Rokas et al. 2003).
“Other inconsistencies will occur as a result of methodological and interpretive mistakes (Sanderson and Shaffer 2002). Phylogenetic analysis is a very complex subject; people who do not understand it well cannot be expected to get it right all the time.”

I would like to thank Dr. Hans Thewissen for his helpful comments on this writing.

** Dr. Thewissen suggested that this had little bearing on my argument, since it concerned only molecular data. However, since Wells seems to be trying to play up the inconsistencies in phylogenetic trees, I think that pointing out consistencies in molecular data is pertinent because it contradicts his overall thesis.

Reply to Jonathan Wells, Part 1

Recently, I visited the new website, faithandevolution.com, which was set up by the Discovery Institute to discuss religion and evolution. While I was there, I found a review of Francis Collins’ book “The Language of God” by creationist Jonathan Wells. Although the entire review is full of error and misrepresentation, I want to focus on a few key issues.
First, the issue of ‘junk’ DNA. Collins states that this nonfunctional DNA is evidence of common ancestry, since it is more similar between closely related species and less similar between more distantly related species. Collins also notes that it is possible that some small fraction of this junk DNA has some function. Wells counters this argument by pointing to studies which show that a small fraction of junk DNA has some function:

[I]n 2006 Japanese and American researchers discovered that “a large number of nonprotein-coding genomic regions are under strong selective constraint” – meaning that they have functions, otherwise selection would not affect them. The researchers wrote: “Transposable elements are usually regarded as genomic parasites, with their fixed, often inactivated copies considered to be ‘junk DNA’… [but many such] sequences have been under purifying selection and have a significant function that contributes to host viability.” In other words, the very “decapitated and utterly defunct” transposable elements that Collins considers his best evidence are turning out not to be functionless after all.

I’m willing to grant that ‘many’ (whatever such a vague word means) transposable elements have some function, on the condition that this does not show that all junk DNA is useful. In fact, one study, in which millions of nucleotides of junk DNA were deleted, showed that this junk really is junk: All of that missing junk DNA had no effect on the organisms tested.
Further in the review, I was struck by something that Jonathan Wells said: “[How does] Collins know what a Creator would do?” I had a profound realization when I read this. How do we know what a creator would do? We don’t. The only way we could is by making certain assumptions about the creator’s nature. And this is a problem for intelligent design: Unless they openly admit to making assumptions about the creator’s nature, they can’t make any predictions. IDers want to have it both ways: If we find lots of junk DNA that points to common ancestry, they say, “How do you know a creator wouldn’t put it there?” If we find that this junk DNA has a function, then that proves intelligent design because ID predicted it. Listen to what Stephen C. Meyer said when it was discovered that some junk DNA might have a function,

It is a confirmation of a natural empirical prediction or expectation of the theory of intelligent design, and it disconfirms the neo-Darwinian hypothesis. (Source)

Now why would that be? Is Meyer assuming that the creator has to create only functional things? But that’s exactly the presumption Wells just argued against. Sorry IDers, but you can’t have it both ways. I suspect that the conflict here comes because what Meyers really thinks is that God created life, and God wouldn't be expected to create junk, would he? And yet when its convenient IDers have no problem retreating from disconfirming evidence by feigning ignorance on the nature of the designer.

Tomorrow I'll write another post on Wells' review.

Michael Shermer Vs. Eric Hovind

Michael Shermer, Editor of Skeptic Magazine, debated Eric Hovind (son of Kent Hovind) on Talk 97.1 . Listen here.