<i>Current Biology</i> Paper's Assumptions and Methodology Dramatically Underestimate "Rates of Change" in the Cambrian Explosion - Evolution News & Views

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Current Biology Paper's Assumptions and Methodology Dramatically Underestimate "Rates of Change" in the Cambrian Explosion

DebatingDDsquare.jpegA study published last month in Current Biology, "Rates of Phenotypic and Genomic Evolution during the Cambrian Explosion," and various news stories about it, claim that rates of evolutionary change in the Cambrian explosion were elevated, indeed "lightning fast" (as LiveScience put it), yet still "perfectly consistent with Darwin's theory of evolution."

Writing here at ENV last week, Stephen Meyer already explained that at most all the paper established was rates of change in the Cambrian. However, the authors never demonstrated that this change was the result of natural selection. Meyer showed that the paper conflated evidence for change over time with evidence for natural selection. While Meyer pointed out this paper's most fundamental flaw -- I'll call it "Problem 1" -- there are many other deficiencies. I focus on nine total in this article:

Problem 2: Circular Reasoning

The paper focuses specifically on arthropods. Related to the problem raised by Meyer is the reasoning they use to conclude that natural selection was responsible for the emergence of this phylum. The authors are confident that the rate of change they measured during the Cambrian pose no problem for Darwinian evolution. Why? Because they believe that the rate of change is only marginally greater than it was across the rest of the history of arthropods -- a history they also assume is strictly the result of unguided evolutionary processes like natural selection. But they forget: we haven't established that the rest of the history of life is the result of unguided evolutionary processes. Thus, the paper's conclusion is based upon circular reasoning. To put it another way, it begs the question.

In fact, the paper provides no independent evidence that Darwinian evolution can solve the problems that Stephen Meyer raises in Darwin's Doubt. For example, it never addresses the fact that many functional proteins are probably multimutation features that would require many changes to be present simultaneously before yielding any benefit. Darwinian evolution cannot produce most even modestly complex multimutation features under reasonable timescales. This paper doesn't demonstrate that any of the morphological or molecular changes it studies are amenable to the type of step-by-step evolution required by Darwinian evolution. Again, it simply assumes this.

Problem 3: Agenda-Driven, Assumption-Driven, or Both?

Stephen Meyer's response also noted that though this paper purports to be a direct reply to unnamed "opponents of evolution," and though it claims to refute arguments similar to those in Darwin's Doubt, it refuses to say who those "opponents" are. This suggests a partisan agenda behind this paper. The authors aren't merely seeking to rebut another party -- they also want to withhold recognition from him, for reasons that obviously go beyond the science itself. Indeed, by their own admission the authors deliberately adopted assumptions for the purpose of understating the rate of evolutionary change in the Cambrian. Here's the narrative being offered, by the authors themselves and others in the science media:

  • Darwin observed that the abrupt appearance of animals in the fossil record implied elevated rates of evolution, and that this could challenge his theory.
  • Darwin-critics have pointed out that the Cambrian explosion would have required elevated rates of evolution, and that this could challenge Darwinian theory.
  • Now these modern-day evolutionary scientists are essentially agreeing with Darwin-critics, and Darwin himself, that the Cambrian explosion required elevated rates of evolution. But then in a stroke of irony, they turn this around and say the rates of change are perfectly "consistent with evolution by natural selection."

Thus, a piece at the journal Science's news desk states: "Their finding -- that the rate of change was high, but still plausible -- may put Darwin's fears to rest."

As we'll see now, the paper made assumptions that call this conclusion into question.

Problem 4: Non-Arthropods Needs Not Apply

The "dilemma" posed by the Cambrian explosion is that it includes the origin of numerous, diverse animal groups in a geologically abrupt period of time. But this paper studied only one group -- arthropods. Moreover, it did not address the origin of arthropods, but assumed them as a starting point, and then only studied evolutionary rates within living arthropods. It thus ignored evolutionary rates within diverse arthropod subgroups known only from fossil animals that went extinct, such as trilobites and others.

But again, the Cambrian "explosion" is not only about the origin of arthropods. It's about the origin of many diverse animal phyla. Thus, if you're going to measure rates of evolution in the Cambrian explosion, you have to explain the rates involved in generating everything that appears in the Cambrian. The paper accurately states the scope of the problem:

The abrupt appearance of most modern animal body plans (often ranked as phyla and classes) over half a billion years ago is one of the most important evolutionary events after the origin of life.
That's a very fair. But then the paper comes nowhere close to addressing this broad event. But they didn't test the supposed rates of evolution necessary to generate "the abrupt appearance of most modern animal body plans," because their study only looked at a single phylum, and a single type of body plan. The authors ignored the evolutionary rates necessary to produce the other diverse Cambrian animals including (but not limited to) echinoderms, annelids, priapulids, brachiopods, ctenophores, bryozoans, phoronids, lobopods, chordates (including vertebrate fish), and others. This paper therefore does not even attempt to assess the morphological or molecular distance between all those diverse the phyla, which must be accounted for to explain the "rates of evolution" in the Cambrian explosion. Those organisms are worlds apart.

Indeed, even within arthropods they may have underestimated rates, as Science explained:

Others caution that such analysis is in its infancy. "It's an excellent first step," says Douglas Erwin, a paleontologist at the Smithsonian Institution in Washington, D.C., but the exact rates of evolution in the study might not be reliable. He points out that while the study uses fossil data to determine when a given arthropod branch emerged, it doesn't include the known characteristics of these extinct ancestors in its comparisons of physical traits, which involve only living creatures.
The paper recognizes the limitation, yet seems unconcerned about it: "While this study examined only arthropods, the patterns found here may be general across other metazoan groups, though broader taxonomic studies are required." "May be" applicable to other groups? Perhaps, but it seems obvious that if you're only studying evolution within arthropods, the amount of change is going to be a lot less than the amount of change that took place when evolving, say, arthropods and chordates and mollusks and echinoderms and other animal phyla from common ancestors. It seems unreasonable and presumptuous to extrapolate their results of the amount of change only within arthropods to predict rates of evolution across the entire Cambrian explosion.

Now I appreciate that their methods would be difficult to apply to many non-arthropod groups because many if not all those other phyla don't leave rich fossil records, which are necessary for these sorts of "relaxed molecular clock" studies. They can still do their arthropods-only study, but they shouldn't title it "Rates of Phenotypic and Genomic Evolution During the Cambrian Explosion." A better title might have been "Rates of Phenotypic and Genomic Evolution Within Arthropods."

It might also have been better if they hadn't issued a hyped-up press release, generating news stories claiming their results explain the totality of the Cambrian explosion. They don't explain the rates of evolution required to explain the broad diversity that appears in the Cambrian, and had they attempted to measure those rates, they would have undoubtedly found very different results.

Problem 5: Assume an Arthropod

Related to Problem 4 is the fact that the paper assumed as its starting point a full-fledged arthropod somewhere around (maybe a bit before) the beginning of the Cambrian. If the authors wanted to study evolutionary rates within arthropods, that's fine. But how about the origin of arthropods? This the paper didn't study, which seems like a major omission. It took a full-fledged arthropod as a given.

Problem 6: Their Timeline Admittedly "Biases Against Fast Cambrian Rates"

The earlier the study assumes arthropods arose, the more time there is for their evolution, thus the lower the evolutionary rate. It's a simple principle, and they invoked it time and again in their study -- all for the purpose of lowering evolutionary rates. Let's give a couple of examples, starting with the root for their analysis, the beginning of panarthropoda.

From the beginning, the study admits that it assumes an Ediacaran origin for arthropods -- it even states, "Assuming an Ediacaran origin for arthropods..." This means it assumes more time for their evolution than is realistic given the fossil record. For arthropods do not appear in the Ediacaran. Aside from the fact that it lowers the rate of Cambrian evolution, how did they justify making this assumption?

According to the paper, they dated the beginning of panarthropoda at 556.6 Ma. Why did they choose this date? Is it because we have fossils of organisms thought to belong to panarthropoda from that date? No, it isn't. We don't have fossils potentially belonging to panarthropoda from that far back. Rather, they chose that date because that's when the first potential bilaterian fossil, Kimberella, is found, and this therefore places a lower-constraint on the origin of panarthropoda back to that time.

So what was Kimberella? Was it anything like an arthropod? Nope. It's an enigmatic creature which if anything was more like a mollusk. Stephen Meyer explains Kimberella in Darwin's Doubt:

The fourth group is the fossils of what may be primitive mollusks, a possibility that received support from a recent discovery in the cliff s along the White Sea in northwestern Russia. There, Russian scientists have discovered thirty-five distinctive specimens of a possible mollusk called Kimberella, probably a simple animal form. These new White Sea specimens, dated to 550 million years ago, suggest that Kimberella "had a strong [though not hard], limpet-like shell, crept along the sea floor, and resembled a mollusk." (p. 81)
However, paleontologists have recognized that the placement of Kimberella within mollusks is not clear-cut. As Budd and Jensen write:
Kimberella does not possess any unequivocal derived molluscan features, and its assignment to the Mollusca or even the Bilateria must be considered to be unproven.

(Budd, Graham E., and Sören Jensen, "A Critical Reappraisal of the Fossil Record of the Bilaterian Phyla," Biological Reviews of the Cambridge Philosophical Society, 75 (2000): 253-95.)

So if Kimberella is not a member of panarthropoda, and not anything like an arthropod, why did the authors take it as the starting point for their calculations of evolutionary rates of arthropods? Simple: it's the first known fossil that might qualify as a bilaterian, and even though arthropods actually appear much later in the fossil record, this is an early lower-bound estimate of when arthropods could have arisen. It thus gives them a way to keep rates of Cambrian evolution low. Perhaps arthropods do go that far back, but the fossil record gives no reason to think this is the case. But starting them so far back helps give more time, and thus lower rates, for arthropod evolution.so.

The paper also makes dubious assumptions about the fossil record on the origin of true arthropods. In Figure 1, they date the supposed split of arthropods and onycophorans to around 555 Ma. But in the supplemental data, they state that the first fossil evidence of arthropods dates to the beginning of the Cambrian, around 542 Ma. However, even this Cambrian "evidence" of arthropods is mere trace fossils. If you take a look at them, you'll see these ambiguous and unimpressive shapes bear virtually no resemblance to arthropods. Is it reasonable to date true arthropods that far back based upon ambiguous trace fossils?

Unambiguous body fossils of arthropods aren't known until Cambrian Stage 2, around 525 Ma. So why do they accept extremely ambiguous trace fossils near the base of the Cambrian as marking the appearance of arthropods, and then add another 10+ million years? It's simple: Although it's buried in the supplemental data, they admit that their method intentionally "biases against fast Cambrian rates":

A conservative (i.e. shallow) minimum is employed because this approach biases against fast Cambrian rates by permitting chronologically longer and thus slower basal branches. (emphasis added)
This is a telling admission, exposing a rigged methodology: they make assumptions about arthropod history that are aimed to produce slower rates of evolution. If they used dates marking the actual appearance of true arthropod body fossils, then the rate of evolution in the Cambrian period would potentially be much higher.

But are they always so "conservative" (their word!) about accepting ambiguous trace-fossils over clear-cut body fossils? No -- especially when it helps keep rates of evolution low! Consider their treatment of the origin of myriapods, the subphylum of arthropods that includes centipedes and millipedes.

The supplemental data states, "The oldest body fossil evidence for Myriapoda is provided by millipedes (Diplopoda) from the Silurian of Scotland." They list a date of 421 Ma for the origin of that group. This gives a full 100 million years for myriapods to arise after the first arthropods appear in the Cambrian -- enough time to lower the rate of post-Cambrian evolution dramatically. But there is a fossil from about 510 Ma -- what they consider the "early Cambrian -- Xanthomyria spinosa, which according to its discoverers has "significant myriapodan features." The study that reported this fossil observed: "If this resemblance genuinely represents myriapod affinities, this would be the first convincing myriapod evidence from the Cambrian." It continues explaining the similarities between that fossil and myriapods:

[T]his form is similar to that seen in several of the Palaeozoic myriapods. In particular, Xanthomyria resembles most closely the giant Carboniferous archipolypodan myriapods such as Euphoberia and Acantherpestes. The characters that are shared include the presence of broad (lg.) tergites with spinebearing pleurae, with most of the total width (tr.) being taken up by the rachial region (pleural spines excluded); a large number of segments that are sub-parallel sided; a very high length/width ratio for the trunk and a calcareous exoskeleton. The presence of the paratergal folds and the form of inter-segmental articulation are, in addition, reminiscent of the arthropleurids, another problematic myriapod-like taxon from the Devonian and Carboniferous. If this assignment is correct, then Xanthomyria is another such form, by far the earliest. (internal citations omitted)
The similarities between the fossil Xanthomyria and myriapods aren't in doubt; they just don't prefer that classification because it doesn't fit with standard wisdom about the evolutionary history of arthropods.

So let's return to the paper about rates of Cambrian evolution. With the origin of true arthropods they used ambiguous trace fossils to provide a very early date for the first arthropods. With the myriapods, at least we have hard body fossils. If they applied to the origin of myriapods even more stringent standards than they used for the origin of true arthropods, then why not accept Xanthomyria spinosa as a myriapod? Again the answer is simple: They don't want to do that because it would greatly compress the time allowed for the origin of myriapods, thus once more greatly increasing the rates of evolution in the early Cambrian. And that's not the result they want.

Perhaps all of this explains why Science quoted Philip Donoghue, a paleobiologist at the University of Bristol in the United Kingdom, stating: "Some of the assumptions the authors make in estimating these emergence dates are also problematic." Their assumptions about emergence dates had a specific goal: to bias against fast rates of evolution.

Problem 7: Deflating Evolutionary Rates by Assuming a Period of Animal Evolution Much Longer than the Cambrian Explosion

If you examine the paper's supplementary data, you learn that what they call the "early Cambrian" or the "Cambrian explosion" is anything from 542 Ma (the beginning of the Cambrian) to about 500 Ma. But as we've discussed, most experts date the main pulse of Cambrian explosion (which includes the period where clear-cut arthropods appear) to about 5 to 10 million years. So perhaps their rate of Cambrian evolution should be multiplied by a factor of 4 to 8 times.

Problem 8: Generalizing Results from a Small Fraction of the Genome

The molecular component of the study only looked at 62 protein-coding genes. Sixty-two genes in a living arthropod such as a fruit fly represents only 0.4% (or one 250th) of all of its genes. According to the source for their dataset, these 62 genes amounted to about 40,000 base pairs. Given that the fruit fly genome is about 140 million base pairs, this means they based their estimation of the rate of molecular evolutionary change during the Cambrian explosion upon a study of only 0.028% of the genome. This means they studied about only 1 nucleotide for every 3500 base pairs in an arthropod genome.

Is it possible that the other 3499 base pairs underwent greater rates of change? Perhaps, but they don't know because they didn't check. Should they be a bit more cautious in extrapolating their results? Yes -- and the next problem provides further reasons why.

Problem 9: Deflating Evolutionary Rates by Using Genes Thought to Experience Lower Degrees of Selection -- i.e., Slower Rates of Change

Because of how it was done, and how it selected the genes that would be analyzed, the study looked at the very sort of genes that would not be expected to experience high levels of selection, and thereby would reflect lower rates of evolution than other genes. Let me explain.

The genes used by the study are listed here. Those genes were originally selected by another lab in an earlier project which sought to produce a molecular phylogeny of arthropods. When constructing a molecular phylogeny, you generally want to select genes that have been accumulating more-or-less neutral mutations at a constant rate over long periods of time, and thus have a sequence that reflects the true signal of phylogenetic history, and hasn't been significantly influenced by selection. In fact, the rule of thumb for doing molecular phylogenies is to use genes that have not been under great selection pressure. You want genes where the molecular clock has been ticking at a close to constant rate, across deep time.

Thus, the genes selected include housekeeping genes like various amino-acyl tRNA synthetase enzymes (which charge tRNAs by attaching the amino acid that corresponds to the anticodon on the tRNA), genes involved in ATP synthase (and that are thus involved in basic, fundamental metabolic pathways), myosin (a basic motor protein used in numerous processes throughout animals), various clathrins (involved in basic cellular processes like intracellular transport) and other genes involved in fundamental biological functions like transcription and translation, or the synthesis of basic biochemical molecules. These are logical genes to select if you're trying to construct a molecular phylogeny, because they perform basic biological functions and aren't going to change much. But this study did a lot more than generate a phylogeny. These genes aren't logical ones to study if you're trying to determine how high rates of evolutionary change must have been to produce an explosion of new animal body plans.

Indeed, Douglas Erwin and James Valentine's new book, The Cambrian Explosion, makes exactly this point, explaining that these sorts of genes aren't likely to have been the ones involved in generating the explosion:

When it comes to understanding the genetic bases of the morphological richness and disparity of the Cambrian explosion, our primary interest is in the genes involved in specifying the development of body plans and other morphological features. That is to say, it is not the genes that control basic cellular functions (so-called housekeeping genes) that are of interest, but the genes that regulate the development of morphology from egg to adult. (The Cambrian Explosion, p. 252)
While these genes are fundamental to cellular biochemistry, they aren't major determining factors, if they're factors at all, in determining an animal's body plan. If you're trying to evolve something like Kimberella (again, a mollusk-like early animal) into something like an arthropod, there's no reason to think that any of these genes would need to undergo dramatic changes. Many of these genes are housekeeping genes, basic to the maintenance of cellular function perform virtually identical functions across nearly all animal groups. They don't tend to encode or determine the differences between animal groups, but rather reflect their unity. (Whether that unity derives from common design or common descent is a question for another day.)

In short, in the context of explaining the Cambrian explosion, these genes aren't where the action is; they're the wrong genes to look at. There is no reason to think they would have been under strong selection pressure under an event that involved the origin of new body plans. By looking at the rates of change in these housekeeping genes, this study measures what is probably neutral change in genes that weren't crucial to the evolution of new body plans, when it ought to be measuring changes in the genome due to natural selection in the genes, non-coding regulatory DNA elements, and epigenetic information which were vital to constructing new body plans. Were one to measure such rates of change, they would undoubtedly yield a much higher rate.

But that approach, if it is even possible, wouldn't fit with the paper's admitted bias "against fast Cambrian rates."

Summary of Problems with the Paper

Though widely touted in the media, this paper has many deficiencies:

  • Problem 1: At most it found only evidence for change over time, not natural selection, and thus its conclusions about natural selection are unwarranted.
  • Problem 2: The paper uses circular reasoning, assuming as it does that the history of arthropod evolution is the result of unguided evolutionary mechanisms, and therefore that the Cambrian evolution of arthropods was as well.
  • Problem 3: It refuses to cite the "opponents of evolution" it purports to refute, thereby exposing its own partisan agenda.
  • Problem 4: The study dramatically deflated evolutionary rates in the Cambrian by ignoring the vast majority of the breadth of Cambrian diversification.
  • Problem 5: The paper assumes a full-fledged arthropod as its starting point, not taking into account the evolution required to get to that point.
  • Problem 6: The paper deflated evolutionary rates by assuming a timeline that, by its own admission, "biases against fast Cambrian rates."
  • Problem 7: The authors deflated evolutionary rates by assuming a period of animal evolution much longer than the Cambrian explosion.
  • Problem 8: Their study generalizes results from a small fraction of the genome.
  • Problem 9: They deflated evolutionary rates by using genes thought to experience lower levels of selection -- i.e., slower rates of change.
Is this study indeed a tacit response to Darwin's Doubt? If so, then in an indirect way it is tantamount to an admission that Stephen Meyer was right about this at least: there are currently no peer-reviewed research studies that provide a Darwinian model for building the Cambrian animals. If there were, why bring out this paper? Rather, Darwin defenders could simply provide the list of studies that Meyer missed. But no one does that. Instead we're seeing new inadequate studies like this, failing to rebut (or even cite) the arguments raised in Darwin's Doubt, in an apparent attempt to allay concerns raised by the book.