On Tue, 26 Jul 2022 06:13:38 -0700, John Harshman
I've never read Darwin's Doubt but in this book, Meyers tackles
head-on what he regards as the most significant criticism of what he
did say about the Cambrian in that former book. Much of the technical
detail of what Meyer writes is well outside my sphere of understanding
and I have had to take a lot of it at face value though, to be fair,
he does cite extensively when he is reviewing counter-arguments. One
of the things I would love to see is a response from someone with a
similar range of knowledge on the other side of the fence explaining
the weaknesses in his analyses. I don't expect to see that happen so,
as a little taster, I am copying below a lengthy extract covering what
he has to say in response to Charles Marshall's criticism of his
previous book. I will be interested to see you and others critiquing
his arguments in that.
<quote>
The review of Darwin's Doubt that most directly challenged the main
thesis of the book was written by Berkeley paleontologist Charles
Marshall and published in Science. Marshall, a thoroughly mainstream
evolutionary biologist, has taken little interest in the kind of
antireligious polemics advanced by Richard Dawkins and other New
Atheists. At the same time, he acknowledges holding a materialistic
worldview and thinks that some contemporary form of evolutionary
theory can (or will ultimately) explain the major innovations in
biological form in the history of life. A leading expert on the
Cambrian era, Marshall has posited various explanations for the abrupt
appearance of new forms of life in that period.
Unlike many other reviewers, Marshall grappled directly with my main
arguments about the problem of the origin of biological information
and morphological novelty. Yet his review demonstrated-if
inadvertently-that evolutionary biologists have not solved that
problem and do not have a better explanation than intelligent design.
To rebut my claim that evolutionary mechanisms lack the creative power
to generate the information necessary to produce new forms of animal
life, Marshall did not defend the sufficiency of mutation and natural
selection (or any other materialistic evolutionary mechanism).
Instead, he disputed that significant amounts of new genetic
information would have been necessary to build new animals and their
distinctive body plans.
Marshall claimed that "rewiring" of what are called developmental gene
regulatory networks (dGRNs) could produce new animals from preexisting
genes. Developmental gene regulatory networks comprise networks of
genes and gene products (DNA-binding proteins and regulatory RNAs)
that control the timing and expression of genetic information during
animal development. The components in these networks transmit signals
(known as transcriptional regulators or transcription factors) that
influence the way individual cells develop and differentiate. For
example, exactly when a signaling molecule gets transmitted often
depends upon when a signal from another molecule is received, which in
turn affects the transmission of still others-all beautifully
coordinated to perform specific time-critical functions. These
networks of genes and gene products function much like integrated
circuits and ensure that the developing organism produces the right
proteins at the right times to service the right types of cells during
embryological development (Fig. 15.5).
This "rewiring" hypothesis formed the basis of Marshall's critique. As
he argued:
"[Meyer's] case . . . 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.19"
Superficially, Marshall's proposal sounded plausible. Nevertheless, it
too presupposed significant and unexplained sources of biological
information.
Elastic Control Networks Required
---------------------------------------------
First, Marshall assumed that developmental gene regulatory networks
were more flexible and subject to "rewiring" in the past.20 Yet all
available observational evidence shows that dGRNs do not tolerate
changes or perturbations to their basic control systems. Even modest
mutation-induced changes to the genes in the core of the dGRN produce
either no change in developmental trajectory (due to a preprogrammed
redundancy) or catastrophic (most often lethal) effects within
developing animals. Disrupt the central control nodes and the
developing animal does not shift to a different viable, stably
heritable body plan. Rather, the system crashes, and the developing
animal usually dies or, if it survives, is severely malformed.21
The late Eric Davidson, of Caltech, a leading developmental biologist,
discovered this fact about dGRNs.22 In his investigations, he
discovered what these networks of genes do and what they never do;
what they never do is change significantly via undirected mutations.
Davidson explained why. He likened the integrated complexity of the
dGRNs to that of an integrated circuit on an electrical circuit board.
This integrated complexity makes dGRNs stubbornly resistant to
fundamental restructuring without breaking.23 Instead, the mutations
affecting the dGRNs that regulate body-plan development inevitably
lead to "catastrophic loss of the body part or loss of viability
altogether."24 Davidson emphasized that "there is always an observable
consequence if a dGRN subcircuit is interrupted. Since these
consequences are always catastrophically bad, flexibility is
minimal."25
Davidson's findings present another challenge to the adequacy of the
mechanism of random mutation and natural selection. Building new
animal body plans requires not just new genes and proteins, but new
dGRNs. But to build a new dGRN from a preexisting one requires
altering the preexisting dGRN-the very thing Davidson showed does not
occur without catastrophic consequence.26 Given this, how could a new
animal body plan-and the new dGRNs necessary to produce it-ever evolve
from a preexisting body plan and dGRN? Davidson himself made clear
that no one really knows.27 Although many evolutionary theorists have
speculated about early "labile" (highly flexible) dGRNs, no developing
animal that biologists have observed exhibits the kind of elasticity
that the evolution of new body plans requires. Davidson, when
discussing these hypothetical labile dGRNs, thus acknowledged that
evolutionary biologists are speculating "where no modern dGRN provides
a model."28
But there is a more fundamental and obvious problem. Marshall claimed
that building new forms of animal life does not require new sources of
genetic information. But his account of body-plan building
(morphogenesis) presupposes many unexplained sources of such
information. Indeed, he presupposes at least three. Let's examine each
in turn.
The Genetic Information in dGRNs
---------------------------------------------
Marshall presupposed unexplained genetic information, first, by
invoking preexistent developmental gene regulatory networks. The many
genes that code for signaling proteins and RNAs in developmental gene
regulatory networks contain a vast amount of genetic information-the
origin of which Marshall does not explain.
In his scientific papers and in his discussion of how "rewiring" gene
regulatory networks could generate new body plans, Marshall clearly
recognizes that preexisting genes would be necessary to produce new
animals. He emphasizes that Hox genes, in particular, must have played
a significant causal role in producing the origin of the first animals
during the Cambrian explosion.29 Hox genes are information-rich
regulatory genes that coordinate the expression of other genes and
thus play important roles in many dGRNs. Nevertheless, he does not
explain the origin of these or any other information-rich genes in
dGRNs. Thus, his proposal begs the question as to the origin of at
least one additional, significant, and necessary source of genetic
information.
A "Genetic Toolkit" for Anatomical Novelties
-----------------------------------------------------------
When Marshall wrote that new animals "emerged through the rewiring of
the gene regulatory networks (GRNs) of already existing genes," he did
not specify whether he meant already existing genes in genetic
regulatory networks or other preexisting genes such as those necessary
for building the specific anatomical structures that characterize the
Cambrian animals (the expression of which dGRNs regulate). Yet when
writing elsewhere, Marshall has emphasized that building new animal
body plans would require many other preexisting genes, indeed, a
preexisting, preadapted "genetic toolkit" for building specific
anatomical parts and structures.30
In a 2006 paper, "Explaining the Cambrian 'Explosion' of Animals,"
Marshall noted: "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 [Cambrian] radiation."31
Indeed, Marshall emphasized, in addition to Hox genes, the need for
"gene novelties" for building the anatomical structures and other
novel features of the various animals that arose in the Cambrian
period.32
Of course, he's right about this. Building new animals would have
required a whole range of different proteins to build and service
specific forms of animal life. Different forms of complex animal life
exhibit unique cell types, and typically each cell type depends upon
other specialized or dedicated proteins-which in turn require genetic
information.33 New forms of animal life would have needed various
specialized proteins: for facilitating adhesion, for regulating
development, for building specialized tissues or structural parts of
specialized organs, for producing eggs and sperm, and many other
distinctive functions and structures. These proteins must have arisen
sometime in the history of life, but Marshall does not explain how the
information for building them originated.
Rewiring Networks and Informational Inputs
-----------------------------------------------------------
Finally, "rewiring" genetic circuitry as Marshall envisions it would
itself require new information. To see why, consider what would be
needed to rewire the circuitry of the 1950s vintage electric guitar
shown in Figure 15.6. Notice that the material components of the three
different designs of the circuitry in the figure are the same in all
three guitars, though the musical tones produced by the rewired
guitars will differ perceptibly in accord with the designer's intent.
Rewiring requires the deliberate selection of a specific configuration
of parts out of a much larger range of possible options. Thus, it
requires an infusion of specified information to transform the
original system into new and different arrangements of parts. Notice
too that such an informational input will be required whether the
individual parts of the circuit remain largely the same or whether new
parts must be introduced.
In a similar but greater way, given the complexity of an animal
compared to a guitar, rewiring the circuitry of a gene regulatory
network would also require new inputs of information. It would require
multiple coordinated changes in the sequences of bases within the
individual genes and/or changes to the arrangement or timing of
expression of whole genes within the developmental gene regulatory
network. Such reconfiguring would entail fixing certain material
states and excluding a vast ensemble of others. Thus, it would
constitute a substantial infusion of new functional information into
the dGRN.34 Thus, even if it were possible to rewire genetic
regulatory networks without destroying a developing animal, Marshall's
"rewiring" proposal itself presupposes, but does not explain, the need
for an additional source of information.
Note, finally, the inescapably teleological (or purposeful) language
of Marshall's "rewiring" proposal. Any electrician or electrical
engineer-indeed, anyone who works with actual circuitry and a power
supply with current passing through the circuit-knows that successful
rewiring requires well-informed decisions, that is, both information
and intelligent design. What rewiring manifestly does not allow is
random changes. That's a great way to burn down your house or blow out
the motherboard on your computer.
A Clarifying Discussion and Confirming Discovery
-----------------------------------------------------------------
After his review was published, Marshall and I had a congenial
ninety-minute debate about the Cambrian problem on British radio. In
it, we may have clarified a misunderstanding about the nature of my
argument. Marshall seemed to think that I thought the essential
problem posed by the Cambrian explosion was the origin of new genes
specifically during the Cambrian period. Thus, he thought he had
refuted my argument by positing an earlier preadapted pre-Cambrian
genome that could be activated to produce new animals by rewiring gene
regulatory networks. Thus, at one point in our debate he cited
evidence suggesting that one of the key proteins for making animal
exoskeletons might have existed in pre-Cambrian times.
But, as I went on to explain in that conversation, the fundamental
problem posed by the origin of the animals was not necessarily the
origin of new genes specifically during the Cambrian period, but the
origin of the genetic information necessary to build animals, whether
that information first arose in the Cambrian period or earlier.
Pushing the origin of genetic information back into the pre-Cambrian
period left unanswered the question of its ultimate origin.
Recall also from Chapter 10 that mutagenesis experiments have
established the extreme rarity of functional genes and proteins among
the many possible ways of arranging nucleotide bases or amino acids
within their corresponding "sequence spaces."35 This rarity makes it
overwhelmingly more likely than not that a series of random mutational
searches will fail to generate even a single new gene or protein fold
within available evolutionary time. Marshall did not explain how a
random mutational search could have located the extremely rare
functional sequences of nucleotide bases capable of building protein
folds within an exponentially large sequence space of possible
arrangements. In other words, he does not explain how any evolutionary
mechanism could have solved the search problem described in Chapter
10. Instead, he simply assumes that the necessary genes for building
new forms of animal life arose earlier in the history of life, without
explaining how they did.
I did and still do suspect that much of the genetic information
necessary to account for the abrupt appearance of the Cambrian animals
arose in the Cambrian period. (Recent genetic analyses have confirmed
my view.) But I acknowledged that the genes necessary to build the
Cambrian animals might have arisen earlier without in any way solving
the fundamental problem. I noted that positing preexisting genetic
information (e.g., for building animal exoskeleton proteins) left
unanswered the question of the earlier origin of that genetic
information.36 To that, Marshall replied, "Fair enough." In so doing,
in my view, he effectively acknowledged the reality of the problem of
the ultimate origin of genetic information.37
</quote>