BioLogos: God's Word, God's World

Some interesting stuff, for example:

Return of the God Hypothesis: A Biologist’s Reflections

Darrel Falk

Like him, I believe that God’s Spirit has been at work throughout the entire course of creation through what we call the natural laws, but I also think there are times when God has worked differently. Like him (I think), I don’t use the word “intervention” to describe what God is doing in those times when God chooses to work differently: it makes no sense to say that God “intervenes” in what God has already been doing. Like him, I don’t believe that natural selection, sexual selection, genetic drift, or luck are sufficient to explain our existence on this planet.

I think the evidence for common descent is overwhelming and, in Darwin’s Doubt (loc. 7655), Meyer indicates that the Intelligent Design movement is not opposed to this either. I am certainly in complete agreement with Meyer that the scientistic views of scientists like Stephen Hawking, Richard Dawkins, Lawrence Krauss, Stephen Weinberg, and Sean Carroll are deeply flawed; they are grounded in their own philosophical worldview—not science. So I think we largely agree on the fundamentals, and yet I am very uncomfortable with his latest book—Here’s why...

Meyer believes that the Cambrian explosion creates a major crisis for the theory of evolution; he thinks there was a significant unexplained increase in genetic information that entered the biological world at that time. I think any evolutionary biologist would, upon reading his work, say that Meyer does not fully appreciate the power of gene duplication and mutation in generating new proteins and changing the way that gene regulatory networks function. One of the mysteries that, according to Meyer, “Neo-Darwinism fails to explain” is the evolutionary transition from the fins of fish to the limbs of land animals (p. 303). This, and other challenges like it, is simply no longer the mystery he thinks it is. In fact, Gerd Muller, that first speaker at the 2016 meeting, wrote:

“When natural selection affects such kinds of systems, the resulting phenotype variation does not need to be gradual and continuous. In fact, simulations of the dynamical behaviours of gene regulatory networks in evolution demonstrate that bistable changes are more likely to occur than gradual transitions.”4

Common Descent vs. Common Design: 4 Examples Explained Better by Descent

Jim Stump

We who accept Descent should admit that there are some observations that can be explained equally well by Design. But there are other observations which seem to clearly favor Descent.

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New Body Plan Emergence: An Evolutionary Biologist Tackles an ID Argument Against Common Ancestry

Gregory Wray

An evolutionary biologist takes a look at embryo mutations and formation to examine the modularity of gene function that assists in evolution.

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Behe and Irreducible Complexity: Failure to Engage the Evidence

Kathryn Applegate

In suggesting that scientists have no idea how evolution produced antibodies, Michael Behe has failed to engage the voluminous scientific literature covering exactly that topic.

Does the Cambrian Explosion Pose a Challenge to Evolution?

The Cambrian Explosion does present a number of important questions, but it doesn't challenge the fundamental correctness of the central thesis of evolution.

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How Can Evolution Account for the Complexity of Life on Earth Today?

...That is not the whole story, however, because individual parts have to be added into the structure as it becomes more complex or takes on new function. Where do those parts come from? Recently, investigators have shown that the key protein in the molecular motor that causes the flagellum to rotate has a very similar structure to another protein that is used to transport magnesium into and out of cells. Both protein molecules have sections that fold in almost exactly the same manner, and when we analyze the order of their building blocks (amino acids), we see profound similarities. This illustrates a second principle in building complexity: It is done by co-option. Parts that are used for one purpose are co-opted to take on a second function as well. Sometimes, the instructions to build a part are encoded by identical duplicate genes. When that happens, co-option is especially straightforward. One set of instructions for making the original part is preserved while the duplicate set of instructions can gradually be modified through mutation and natural selection, allowing the part to become better and better at carrying out its new function. This illustrates a third principle of assembling complexity: adaptation through natural selection.

Even more revealingly, the supposedly irreducibly complex bacterial flagellum turns out not to be irreducible after all. For example, there is a protein at the base of the flagellum, an ATPase, that drives the key structural subunit (flagellin) of the long hollow tube through its inner core, causing the flagellum to grow in length. Yet, it has been shown that flagellin can be transported to the end of a flagellum without this ATPase. The protein that was thought to be one of the flagellum’s most important parts can be done away with. This illustrates a fourth principle of building a complex structure: redundancy. Inside of cells, there is often more than one way to accomplish a particular purpose; as evolution “tinkers” with a complex structure, there is likely to be redundancy with certain parts at certain stages. One of these redundant mechanisms may become more specialized, and even perfected, as time goes by....

..If you choose to explore eye development in detail, be watching for examples of exaptation, co-option, step-by-step adaptation and redundancy. For example, you will note that the evolution of the lens illustrates co-option and redundancy. There are two ways to focus the image on the light-receiving cells at the back of an eye. One way is through an independent lens. The other way is through the transparent cornea in front of the lens. The lens is simply transparent crystallized protein molecules that are assembled in such a manner that they bring the image into sharp focus. There are a variety of proteins that can be crystallized to serve as an effective lens. It turns out that, depending on the evolutionary lineage, various proteins—including enzymes such as alcohol dehydrogenase (an enzyme for breaking down ethanol), glutathione S transferase and protein chaperones—are used for this purpose. This is a simple example of co-option and redundancy functioning together as part of the tinkering mechanism used for building a complex structure like the eye...

Darwins_Doubt_Supplement.pdf

Supplement A

Attacking the Adequacy of Evo-devo

For an example of how Meyer assesses evo-devo independently as inadequate to account for the macroevolution of new body plans in the Cambrian, consider his treatment of Wallace Arthur’s The Origins of Animal Body Plans (Cambridge University Press, 1997). In footnote 11 on p. 441 of Darwin’s Doubt, Meyer reports Arthur as saying “Those genes that control key early developmental processes are involved in the establishment of the basic body plan. Mutations in these genes will usually be extremely disadvantageous, and it is conceivable that they are always so.” 

The idea Meyer has in mind is that if even small changes in the developmental gene regulatory networks are almost always harmful to organisms, then evo-devo is unable to account for the appearance of new body plans.

The reader could be forgiven for drawing the conclusion that Arthur’s book is arguing against evo-devo as a source of new animal body plans. The actual context for the quote Meyer cites, however, helps us see that Arthur is arguing something different regarding the genes involved in
development:

“Those genes that control key early developmental processes are involved in the establishment of the basic body plan. Mutations in these genes will usually be extremely disadvantageous, and it is conceivable that they are always so...But it is clear, for example from cross-taxon comparisons of a particular group of such genes–the homobox-containing Hox genes...–that homologous ‘developmental’ genes in different phyla are different. Even where there is an unexpectedly high degree of similarity (e.g., 98 percent between some human and Drosophila homoboxes)...there is still a difference. The genes concerned have evolved. And comparative embryology shows that early developmental pathways have changed in consequence. Does this mean that mutations of these genes are sometimes advantageous? If so, are these in some sense successful macromutations?” (Arthur 1997, pp. 14-16).

Supplement B

Three More Representative Examples of the Question-Shift Strategy

When Meyer discusses self-organization as a possible explanation for the diversification of Cambrian body plans (note the divide-and-conquer strategy!), he critiques the work of Stewart Kaufman and others for failing to explain the advent of the very first body plans. Kaufman is
actually discussing how preexisting body plans can change giving rise to new body plans. Yet, Meyer complains that “the self-organizational process that Kauffman cites cannot explain the origin of genetic information, because it derives from it, as Kauffman’s own description reveals”
(p. 297). Meyer shifts the question from diversification to advent, whether it be cells, genes, gene regulatory networks or body plans, and then faults Kaufmann and other self-organization advocates for not answering the first advent of cells, genes, regulatory networks or body plans
questions

Darwins_Doubt_Supplement.pdf

Podcast: Stephen C. Meyer | Is God a Hypothesis?

Proponents of intelligent design and evolutionary creation have some different ideas about the relationship of science and faith, and relations between BioLogos and the Discovery Institute have not always been easy. But there is some common ground. We explore some of that common ground in this episode while also discussing the philosophical differences between the positions. Stephen Meyer is a leading advocate for intelligent design and is the Director for the Center for Science and Culture at the Discovery Institute, and his new book, Return of the God Hypothesis, frames this conversation.

This was meant to be a conversation and not a debate and so the intention was not to stop every time a claim was made that we disagree with. Instead, we made a companion piece to this episode where we point to many resources that do respond to these claims and help to further explain some of the philosophical concepts covered in this conversation.

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