Science & Faith
10/28/13 at 10:20 AM 52 Comments

Genes and Gaps: Marshall vs. Meyer's Book "Darwin's Doubt"

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In my post Distinguished UC Berkeley Paleontologist Reviews Meyer's Book "Darwin's Doubt" I introduced the Marshall-Meyer debate and promised to cover more of it later. Today I shall respond to comments below my original post and cover part 2 of Meyer's multi-part response to Marshall, which is accessible here as a complete list of Meyer's postings on this debate. The purpose of my Marshall-Meyer series here at CP is to widen the audience of this debate and to interact with that audience (you, my valued readers).

Here some objections (comments below my original post or common objections similar to them) and replies:

Objection: Meyer quotes very little of Marshall and/or insufficiently deals with the contents of Marshall's review.

Reply: Follow the links to all the parts of Meyer's response to Marshall here, or keep reading this post and my sequel posts that are forthcoming to see why this was a premature (and false) judgment. Meyer deals with the substantive parts of Marshall's review, as you shall see. Furthermore, the only part of Marshall's review that deals with Meyer's scientific argument amounts to only four paragraphs out of the total review consisting of eight paragraphs.Objection: Discovery Institute fellows include many closet young earth creationists who merely argue as if the Earth is old, and thereby deceive the public about their actual assessment of the evidence regarding Earth's age.

Reply: Not so. For example, Meyer and I think Earth is probably about 4.6 billion years old. The argument for intelligent design in Meyer's book Darwin's Doubt is constructed within the context of a large body of scientific data that points to a 4.6 billion year old Earth, not the 6-10 thousands years typically cited by young earth creationists. Before Meyer earned a PhD in philosophy of science at Cambridge University, he was a geophysicist working in the oil industry. He is well aware of the extensive evidence for a very old Earth from the point of view of a practicing scientist.

Objection: Because Meyer quotes developmental biologist Eric Davidson (who is an evolutionary theorist and not an ID advocate) to support his case for ID, this and other quotations like this in Meyer's book (and blogs contra Marshall) are guilty of quotation mining, which is the dishonest tactic of using quotations of opponents that ignore the context of the quotation and the larger belief systems of their authors.

Reply: I see this objection often without any contextual evidence from the quoted book or essay to show that author A distorts (e.g., Meyer) the authorial intent of author B (e.g., Davidson). Such is the case, again, in the comments below my last blog: accusations of quotation mining without any evidence supplied. Furthermore, the fact that Davidson is a Darwinist does not prevent Davidson from discovering and publishing results that undermine one component of another Darwinist's argument (e.g., Marshall's opinion). When I teach my college Reasoning course, I make these very points to help my students not make the same mistakes as some of my blog readers. These are the ABCs of critical thinking and writing.

Objection: Meyer is more a general scholar competent about the nature of science (philosophy of science), rather than a specialist in paleontology. Thus we cannot take his book about the Cambrian explosion seriously.

Reply: Meyer has field experience as a geophysicist (mentioned above), and he collaborates with many scientists with various relevant specialties. Furthermore, regardless of the speciality one has in science, the range of topics in Meyer's book spans many specialities in the earth and life sciences. Regardless of who writes a book of this scope, the author would have primary expertise in one or just a few of the relevant disciplines and subdisciplines. More importantly, what if the arguments in his book are well founded on a wide range of peer reviewed journals and books? Read it for yourself to form your own opinion. Perhaps Marshall's review, despite its deficiencies, will spur many disciplinary experts in science to do consult Meyer's sophisticated arguments for themselves. Finally, ad hominem attacks against Meyer (as a person) only point to a lack of real evidence-based argumentation on the part of his detractors (Does this sound familiar here at CP?).

All of the objections above are based on gaps in the knowledge base of the objecting persons. Now we turn to part 2 of Meyer's reply to Marshall's review: To Build New Animals, No New Genetic Information Needed? More in Reply in Charles Marshall. In this essay Meyer shows that the argument in his book does not rest upon gaps in our accumulated scientific knowledge, but rather it is based upon what we know about genes and epigenetic biological information. Meyer begins by reminding us of a point in his previous post (about which I have already blogged) concerning Marshall's own non-evidential gap filling procedure: "the tendency to affirm as true what evolutionary theory requires, even if that contradicts what we know from experiment and observation about how biological systems actually work."

"Now I will show," Meyer announces in his new essay, "that in order to rebut the central argument of Darwin's Doubt, Marshall must also deny (or at least push from view) what we know about what new forms of animal life require as a condition of their existence."

Meyer continues:

In Darwin's Doubt, I argue that intelligent design provides the best explanation for the origin of the genetic (and epigenetic) information necessary to produce the novel forms of animal life that arose in the Cambrian period. To his credit, and unlike other critics of the book, Marshall addresses this, the main argument of the book, and attempts to refute it [in four paragraphs, Keas notes]. To do so, however, he does not show that any of the main materialistic evolutionary mechanisms can produce the information necessary to build the Cambrian animals. Instead, Marshall disputes my claim that significant amounts of new genetic information (and many new protein folds) would have been necessary to build these animals. Specifically, Marshall claims that "rewiring" of dGNRs would have sufficed to produce new animals from a set of preexisting genes. As he argues:

[Meyer's] case against the current scientific explanations of the relatively rapid appearance of the animal phyla rests on the claim that the origin of new animal body plans requires vast amounts of novel genetic information coupled with the unsubstantiated assertion that this new genetic information must include many new protein folds. In fact, our present understanding of morphogenesis indicates that new phyla were not made by new genes but largely emerged through the rewiring of the gene regulatory networks (GRNs) of already existing genes.

Yet Marshall's understanding of how animal life originated is problematic for several reasons.

Meyer then reviews the main arguments that support his case for intelligent design and his case against the emergence of the major animal body plans by unintelligent and unguided material processes.

Rewiring Requires Information

First, "rewiring" genetic circuitry would require reconfiguring the temporal and spatial expression of genetic information. Such reconfiguring would entail fixing certain material states and excluding others. Thus, it would constitute an infusion of new information (in the most general theoretical sense) into the biosphere [see Meyer's footnote 2]. To see why, consider changing a wiring diagram representing a developmental gene regulatory network. Just altering the diagram representing the network to produce a new diagram representing a new network would require changing the arrangement of "nodes" (representing genes) and "edges" (representing interactions between genes and gene products). Changing the arrangement of these elements in order to produce a new network would constitute adding information into the diagram depicting the system. In the same way, changing the arrangements of genetic elements themselves in an actual network would also require informative changes to the arrangement of the network. Thus, Marshall's "rewiring" proposal does not eliminate the need for new information to build the Cambrian animals. Rather, it tacitly invokes additional information of a different, though perhaps partially non-genetic, kind.

Here is a way for more of you to grasp Meyer's line of argument. The genome for each organism consists of all the genes (short DNA segments) that code for proteins (which build structures, etc.) and all the other more extensive DNA segments that have various regulatory and other roles in living cells. When the egg produced by a female animal is fertilized (the moment of conception), embryological development begins as this single cell becomes two, four, eight ... cells (and so on...), which later diverge into specialized groups of cells as the embryo develops. This elaborate process is regulated by various genetic and epigenetic biological information. "Rewiring" genetic circuitry in a way that maintains a viable organism would require the input of new precise, life-friendly biological information.

Meyer continues:

In any case, altering the temporal and spatial expression of pre-existing genetic elements assuredly would require the addition of new taxon-specific genes or gene products, and thus, new genetic information. Indeed, experiments on dGRNs in modern representatives of the animal phyla show that different organisms use taxon-specific DNA-binding proteins to regulate the expression of genetic data files. For instance, contrary to theoretical expectations,[see Meyer's footnote 3] the morphogen Bicoid, essential for normal anterior-posterior body plan specification in Drosophila, is found only in the cyclorrhaphan flies[see Meyer's footnote 4]. Similarly, the body plan of the freshwater polyp Hydra is specified by taxonomically restricted proteins [see Meyer's footnote 5]. Nor are these isolated cases. The remarkable disparity of animal morphologies at the macroscopic (i.e., anatomical or body plan) level tends to correspond to differences at other levels (i.e., the microscopic or molecular). Moreover, studies of "evo-devo" model systems have repeatedly revealed that the cell and tissue specification programs that generate distinctive animal morphologies depend upon taxon-specific regulatory factors (proteins and RNAs). [I will omit reference to all of Meyer's footnotes from now on, but you can go here to see those notes in his original essay].

The main conclusion supported by the evidence cited in this paragraph is this: There is a remarkable disparity of animal morphologies (major body plan differences) that appear suddenly in the Cambrian explosion. And based on studies of current representatives of those body plans (living specimens of animal phyla), we know that those huge anatomical differences correspond to differences in biological information at the microscopic molecular level. Meyer proceeds to cite additional findings in recent research that support his argument for the need of large amount of new specific biological information (whether genetic information, or epigenetic information) to explain the Cambrian explosion of the wildly different animal body plans.

Ubiquitous ORFan Genes

The next part of Meyer's argument concerns ORFan genes (the allusion to "orphans" is on propose):

Second, recent genomic studies of many animals representing phyla that first arose in the Cambrian show that these animals depend upon many unique genes not present in any other taxa. Moreover, these genes perform many functions besides just specifying body plan development. These sequences, known as taxonomically restricted or "ORFan" genes, are ubiquitous in all animal life and represent 10% or more of the genomes of each species that scientists have investigated.

The presence of ORFan genes in all sequenced present-day animal genomes -- and, indeed, in all life -- suggests that the genomes of Cambrian animals would have likely contained many ORFan genes as well. That, in turn, suggests that a considerable amount of new genetic information not present in simpler Precambrian organisms would have originated before or during the Cambrian radiation in order to build the unique features of the first Cambrian animals. Moreover, even if some universal Precambrian genome originally contained all the genes that later became taxonomically restricted, whatever process distributed these genes to some lineages, but not others, necessarily involved the addition of new information into the biosphere.

Again, we see evidence of information-input at multiple levels in many different ways to account for the origin of the major kinds of animals. This is based on what we know about the genetics of different animal phyla (major kinds of animals) today. This is an argument base on what we know about genetics today, not on gaps in our knowledge.

A Telling Admission the Meyer Detects in Marshall's Review and in his Related Research

Interestingly, in his review and especially when writing elsewhere, Marshall acknowledges the need for new genes and genetic information in order to produce the Cambrian animals. For example, in a 2006 paper entitled "Explaining the Cambrian 'Explosion' of Animals," he noted that: "Animals cannot evolve if the genes for making them are not yet in place. So clearly, developmental/genetic innovation must have played a central role in the radiation." Later in the same paper he argues that: "It is also clear that the genetic machinery for making animals must have been in place, at least in a rudimentary way, before they could have evolved." Marshall insists that Hox genes, in particular, must have played a necessary causal role in producing the explosion, a point that he also makes in another paper where he explains that developmental considerations "point to the origin of the bilaterian developmental system, including the origin of Hox genes, etc., as the primary cause of the 'explosion.'" While in these papers Marshall also emphasizes the importance of rewiring gene regulatory networks to generate new body plans, he clearly acknowledges that new genes would be necessary to produce new animals.

So Meyer discovers that Marshall's simplisitic dismissal of Meyer is substantially undermined by many of Marshall's own publications. Go figure!

New Animals Require Many New Cell Types and Specialized Proteins

Of course, building the Metazoa (multi-cellular animals) would not have just required new Hox genes, ORFan genes, or genes for building new regulatory (DNA-binding) proteins. Instead, the evolutionary process would need to produce a whole range of different proteins necessary to building and servicing the specific forms of animal life that arose in the Cambrian period. In Darwin's Doubt I note, for example, that the first arthropods would have likely required genes for building the complex protein lysyl oxidase. Why? Because what we know from studies of modern arthropods shows that this protein is necessary to support the stout body structure of arthropod exoskeletons. Similarly, building Metazoa requires specialized proteins (and metabolic pathways) to produce the kind of extra-cellular matrices that allow developing animals to knit cells into tissues, tissues into organs, and organs and tissues into fully developed animals. Furthermore, different forms of complex animal life exhibit unique cell types and typically each cell type depends upon other specialized or dedicated proteins. As I wrote in Darwin's Doubt:

[new] complex animals [such as arose in the Cambrian period] require more cell types to perform their more diverse functions. Arthropods and mollusks, for example, have dozens of specific tissues and organs, each of which requires "functionally dedicated," or specialized, cell types. These new cell types, in turn, require many new and specialized proteins. An epithelial cell lining a gut or intestine, for example, secretes a specific digestive enzyme. This enzyme requires structural proteins to modify its shape and regulatory enzymes to control the secretion of the digestive enzyme itself. Thus, building novel cell types typically requires building novel proteins, which requires assembly instructions for building proteins -- that is, genetic information.

In short, all that new specialized animal anatomy that suddenly appeared in the Cambrian explosion required massive amounts of new genetic (and epigenetic) information.

Meyer's Last Major Point in this Essay: Marshall Caught Begging the Central Question

Although Marshall characterizes my claim that new Cambrian animals would have required new genetic information and new protein folds as "unsubstantiated," he doesn't actually dispute the need for genetic information in order to build the proteins required by each new form of metazoan life. Instead, he only seems to dispute that all that information arose during the Cambrian explosion itself. Indeed, in both his technical publications and his review of Darwin's Doubt, Marshall simply assumes that most of the genetic information necessary to build the Cambrian animals already existed before the Cambrian explosion. In fact, he seems to presuppose the existence of what Susumu Ohno called a "pananimalian genome," a nearly complete set of the genes necessary to build Cambrian animals within some phenotypically simpler, ur-metazoan ancestor. Thus, he states the new animal phyla "emerged through the rewiring of the gene regulatory networks (GRNs) of already existing genes." The article "The Causes of the Cambrian Explosion," which accompanies Marshall's review of my book in Science, also presupposes such a universal gene toolkit and suggests that it might have arisen 100 million years or more before the explosion of animal life in the Cambrian period.

Nevertheless, this question-begging assumption does not solve the central problem posed by Darwin's Doubt -- that of the origin of the genetic (and epigenetic) information necessary to produce the Cambrian animals. It merely pushes the problem back several tens or hundreds of millions of years, assuming that such a universal genetic toolkit ever existed. (Marshall also makes no attempt to rebut my argument about the inability of the mutation/selection mechanism to generate new epigenetic information, a problem that has led other prominent evolutionary biologists to express skepticism about the adequacy of the neo-Darwinian mechanism.) In any case, Marshall does not explain how the neo-Darwinian mechanism could have overcome the combinatorial search problem described in Darwin's Doubt to produce even the new genetic information necessary to build new proteins and Cambrian animals.

Read the last few paragraphs of Meyer's response #2 to Marshall here. Expect another blog later this week here at CP on Meyer's next reply (#3) to Marshall. A careful reader would (even now) would have major reasons to be sceptical of the claim made in recent comments here at CP that Marshall's review of Meyer was devestating of Meyer's argument. I wonder how many of those folks have actually read any of Meyer's book or Marshall's eight-paragraph review. For example, one comment (by Hraefn) reads:

IS THIS POST ABOUT MARSHALL'S REVIEW OR NOT MIKE?

Because you don't quote from it once, but rather quote lovingly and oh, oh, OH, so extensively from Meyer's response (which likewise completely fails to state what Marshall actually says).

A better title would therefore 'A Review too damning to quote'. Both you and Meyer also entirely fail to mention that Marshall is ONE OF THE SCIENTISTS THAT DOUBLE-D [Darwin's Doubt] QUOTEMINES. Which leads us to ask the question, if Marshall doesn't know his stuff enough to criticise Double-D, then why does Meyer use him as a source in the first place?

For those interested in what the review actually says (Mike & Steve are plainly only interested in spinning it), here's the conclusion:

"But when it comes to explaining the Cambrian explosion, 'Darwin’s Doubt' is compromised by Meyer’s lack of scientific knowledge, his “god of the gaps” approach, and selective scholarship that appears driven by his deep belief in an explicit role of an intelligent designer in the history of life."

I've answered most of Hraefn's objections in today's blog: the unsubstantiated quote mining charge, and the charge about Meyer's lack of engagement with Marshall's review. In fact, Meyer's reply #2 (explained in today's blog, which shows major engagement with Marshall) was already available when I posted my first blog, and Julie Fantham linked to it in a commnet that appeared before Hraefn's empty charges above (Julie's link was the very first comment).

My next blog will be about the "god of the gaps" charge against Meyer. It turns out that "naturalism of the gaps" is what surfaced in Marshall's review (and related scholarship) summarized in today's blog. Marshall and like-minded advocates seem driven by their own deep beliefs to engage in the following sort of non-evidential gap filling procedure: "the tendency to affirm as true what evolutionary theory requires, even if that contradicts what we know from experiment and observation about how biological systems actually work."

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