Politics poisons everything?

Suppressing Science at Brown University
David Klinghoffer | @d_klinghoffer

What happened to Lisa Littman at Brown offers the most recent evidence of how scientists are pressured not to stray beyond politically approved conclusions — something that ID researchers have known for a long time. Alex Barasch at Slate thinks that what has been done to Dr. Littman isn’t “censorship.”

  

All Brown and PLOS One have promised is a more rigorous review of the study design, which clearly warrants one; far from being censored, the paper remains fully accessible on the journal’s website. In other words, the scientific process is moving forward as usual.

Oh please. If not one of outright censorship, this a story of suppressing and intimidating a researcher who violated an implicit speech code. Littman published her (peer-reviewed) study in PLOS One, “Rapid-onset gender dysphoria in adolescents and young adults: A study of parental reports,”concluding that young people may pick up gender dysphoria socially, in part through circles of friends and social and other media. That’s not something you are supposed to say. PLOS One and Brown’s School of Public Health, where Littman teaches, caught blowback from activists, and Brown in particular collapsed under the pressure. 

A “Cautionary Tale”

They took down a news release from their website and replaced it with a“statement, community letter on gender dysphoria study.”The study of gender dysphoria is not the point of interest here. The trampling of academic freedom is. Jeffrey S. Flier, professor and former dean of Harvard Medical School, writes at Quillette that he is disquieted by Brown’s hanging Dr. Littman out to dry.

The fact that Brown University deleted its initial promotional reference to Dr Littman’s work from the university’s website — then replaced it with a note explaining how Dr Littman’s work might harm members of the transgender community — presents a cautionary tale.

Increasingly, research on politically charged topics is subject to indiscriminate attack on social media, which in turn can pressure school administrators to subvert established norms regarding the protection of free academic inquiry.

Here’s what happened:

There is no evidence for claims of misconduct in Dr Littman’s case. Rather, unnamed individuals with strong personal interests in the area under study seem to have approached PLOS One with allegations that her methodology and conclusions were faulty. Facing these assertions, which predictably drew support from social media communities populated by lay activists, the journal responded rapidly and publicly with the announcement that it would undertake additional expert review.

In all my years in academia, I have never once seen a comparable reaction from a journal within days of publishing a paper that the journal already had subjected to peer review, accepted and published. One can only assume that the response was in large measure due to the intense lobbying the journal received, and the threat — whether stated or unstated — that more social-media backlash would rain down upon PLOS One if action were not taken.

There were also said to be unidentified voices within the Brown community who expressed “concerns” about the paper. But when Brown responded to these concerns by removing a promotional story about Dr Littman research from the Brown website, a backlash resulted, followed by a web petition expressing alarm at the school’s actions. The dean of the School of Public Health, Bess Marcus, eventually issued a public letter explaining why the removal of the article from news distribution was “the most responsible course of action.”In her letter, Dean Marcus cites fears that “conclusions of the study could be used to discredit the efforts to support transgender youth and invalidate perspectives of members of the transgender community” (my italics). Why the concerns of these unidentified individuals should be accorded weight in the evaluation of an academic work is left unexplained.

The Really Cowardly Part

But this is the really cowardly part:

There is no suggestion whatsoever of support for Dr Littman, a faculty member in good standing for whom the personal and professional consequences of these events could be devastating. The dean of a school is in effect the dean of the faculty. While she must exercise balance and objectivity when controversial issues arise, her responsibilities include the expression of appropriate support for a beleaguered faculty member until and unless clear evidence emerges to impugn that scholar’s behavior or work.

You can still see the deleted press release via the Wayback Machine.The headline sounds proud of Dr. Littman’s accomplishment — “Brown researcher first to describe rapid-onset gender dysphoria.” But while I’ve sometimes misjudged the impact of things I’ve written, even I could have told them this was going to give offense to PC censors:

62 percent of parents reported their teen or young adult had one or more diagnoses of a psychiatric disorder or neurodevelopmental disability before the onset of gender dysphoria. Forty-eight percent reported that their child had experienced a traumatic or stressful event prior to the onset of their gender dysphoria, including being bullied, sexually assaulted or having their parents get divorced.

This suggests that the drive to transition expressed by these teens and young adults could be a harmful coping mechanism like drugs, alcohol or cutting, Littman said. 

You don’t have to take Littman’s paper down to “censor” or perhaps more accurately, “censure” her. Is her “methodology” sound? The paper’s peer reviewers clearly thought that it was. If they were wrong, let those who know better criticize and debate the merit of her work. That’s scholarship for you. 

But that is not what happened here. Littman has been served a very potent warning, potentially a “devastating” one, that when she is challenged by a mob, her university will not support her. It will panic and back right down, insinuating that she is at fault when there is no indication she actually is. Other researchers would be fools not to take serious note and to adjust their own work and thought accordingly.

Dreadfully Familiar

This is all dreadfully familiar to scientists who favor critiques of Darwinian theory and arguments for intelligent design. They have seen what happened to researchers who, perhaps naïvely, went public with their own reflections on the evidence for teleology in nature and biology. You’ll find some of those stories at the Free Science website.

Lisa Littman is Scott Minnich with a splash of Eric Hedin. I don’t know what is going on behind the scenes for this assistant professor — considerable distress, no doubt — but I hope there is no aspect of Richard Sternberg or Günter Bechly or Caroline Crocker.That is, I hope this does not end in her being forced out. I know plenty of other ID sympathizers, including at high-profile institutions, who would be put in serious jeopardy if their identifies were known. This is how the vaunted “academic consensus” is maintained.

Professor Flier says this business with Dr. Littman’s paper in PLOS One is without parallel in “all my years in academia.” That’s funny — I can think of a very close comparison. Just a couple of years ago the very same journal caved in response to a different mob of enraged activists after PLOS One published another peer-reviewed paper, this one by Chinese researchers, on the human hand and noting its “proper design by the Creator to perform a multitude of daily tasks in a comfortable way.”

As with Professor Littman, PLOS One issued a statement that “We are looking into the concerns raised about the article with priority and will take steps to correct the published record.” This was following online complaints, including by editors of the journal. It then retracted the paper. I wrote here, “The note of career anxiety — no, panic — is telling. These folks don’t want to be rendered ritually impure by contact with a bit of injudicious language.”

It’s the very same thing with Lisa Littman. Career anxiety is exactly how heterodox thought is policed and stamped out in the academic world. I’m sorry to associate Littman in any way with the taint of design science — I have no reason whatsoever to think she would appreciate it, or is in any way in sympathy with it. But the parallel must be pointed out.

I could add, coincidentally, this is also not unlike my own experience at Brown, though I was only an undergraduate not a scientist. It was perhaps the most educational thing that happened to me in college. See “Kafka Meets Coppedge.” Clearly, not much has changed.

Darwinian evolution is gradual (except when it isn't)?

A Beautiful, Wonderful Solution to the Cambrian Puzzle?

Evolution News | @DiscoveryCSC

Another contender in the race to rescue Darwin from the Cambrian explosion is getting hurrahs from the media. Jordi Paps, a champion in Darwin dodgeball, is giddy with euphoria over the new proposal. In his article, “How animals went from single cells to over 30 different body types,” in The Conversation, he poses as spokesman for the world:

The origin and evolution of animals is one of the most fascinating questions in modern biology. We know that the entire wonderful variety of animals alive today arose from single-celled ancestors. And we know that this transition was likely related to the planet’s environment and how organisms interact with it, as well as changes in their genetic material (genome).

But we don’t know if the diversity of animal shapes, those “endless forms most beautiful and most wonderful” that Darwin described, emerged quickly after the first animal lifeforms or whether it came much later in their evolution. A team of evolutionary biologists from the UK and the US have tried to tackle this question in a most beautiful and most wonderful paper published in the scientific journal PNAS.

Pats on the Back

The authors of said paper pat themselves on the back for their achievement in a statement from the University of Bristol, echoed by cheers from NASA’s Astrobiology Institute, who affirm that the new study “has revealed the origins and evolution of animal body plans.” Finally!

First, they make sure that readers know the required answer before asking the question. They don’t want any Heretic to be seen or heard in the chambers during the debate.

Animals evolved from unicellular ancestors, diversifying into thirty or forty distinct anatomical designs. When and how these designs emerged has been the focus of debate, both on the speed of evolutionary change, and the mechanisms by which fundamental evolutionary change occurs.

It’s a one-party debate, but a debate nonetheless. Even one-party governments can have lively discussions among themselves. Here, it’s not whether Darwinian evolution is a fact, but how it works in the face of evidential challenges from those pesky Cambrian fossils.

Did animal body plans emerge over eons of gradual evolutionary change, as Darwin suggested, or did these designs emerge in an explosive diversification episode during the Cambrian Period, about half a billion years ago?

Valid Empirical Work

Before critiquing their solution, let’s give them credit for some valid empirical work. First, wisely, they included fossils as well as living forms. Additionally, Jordi Paps says:

They collected anatomical data for nearly 2,000 anatomical features for 210 animal groups, sampling many groups within each phylum. Then they analysed their anatomical similarity with cutting-edge statistics. These produce a map of sorts, in which each group is a dot and the distance among groups is proportional to their anatomical similarity. 

The resulting map is the centerpiece of their work. By making both axes the same (evolutionary distance), their data points spread into clusters, allowing easy visualization of just how disparate the animal groups are. The grid forms a morphological “design space” (where “design” to them means a successful bodyplan as opposed to an “impossible” one). The caption explains:

This image is based on the presence and absence of anatomical features, like jointed legs and compound eyes, neurons and boney skulls. Considering all of these features, animals that are similar group together, far away from animals that are dissimilar. Most of this ‘design space’ is unoccupied, in part because of extinction of ancient ancestors that are unrepresented, in part because animals have only been around for half a billion years and that is not enough time to explore all possible designs, but most of the design space is unoccupied because those designs are impossible.

Did you hear that right? Ancestors that are “unrepresented”? What are those? Apparently, they are potential bodyplans that were never actualized because of limited time for evolution to “explore” those parts of “design space.” The paper appears to say that the authors simply imagined animals in the spaces where no remains are known:

Thus, by comparing only living taxa, it could be argued that we have captured only net historical disparity. Therefore, we coded a phylogenetically diverse and representative sample of Cambrian taxa, principally the earliest representatives of ordinal level clades. This entailed coding 70 fossil taxa for the existing character set and adding 111 mostly autapomorphic characters. Coding these fossil taxa was potentially problematic in that most of the characters (54.1%) are not preserved, and therefore unknown.

Visualizing Intermediates

For Darwinians, visualizing intermediates in those empty spaces is not a problem, because imagination is a key tool in their toolkit. It’s legit, because they already “know” that “animals evolved from unicellular ancestors, diversifying into thirty or forty distinct anatomical designs.” The “unrepresented” forms, therefore, must have appeared, and then disappeared without a trace. (Compare this tactic with the use of “ghost lineages” as gap fillers.)

The map shows that a few phyla, especially the arthropods and chordates, continued to diversify extensively after the Cambrian. Consider that both fish and giraffes are vertebrates! Co-author Bradley Deline quips:

“Many of the animals we are familiar with today are objectively bizarre compared with the Cambrian weird wonders. Frankly, butterflies and birds are stranger than anything swimming in the ancient sea.”

They take this extreme diversity within phyla as justification to Darwinize the extreme disparity between phyla in the Cambrian. If evolution was powerful enough to generate birds from Metaspriggina, it surely was powerful enough to generate trilobites from microbes. That makes sense, doesn’t it? We mustn’t underestimate the creative power of mutation and natural selection!

The Bristol evolutionists do take Darwin to task about his gradualism, though. Co-author Philip Donoghue shows that it’s OK to adjust the emperor’s clothes as long as you don’t oust him from the parade:

“Our results show that fundamental evolutionary change was not limited to an early burst of evolutionary experimentation. Animal designs have continued to evolve to the present day – not gradually as Darwin predicted – but in fits and starts, episodically through their evolutionary history.”

In other words: “Sure, there was an early burst of evolutionary experimentation, but what’s the surprise? That’s been the pattern throughout evolutionary history.”

Taking Stock

Let’s take stock of the story so far. They admit that the appearance of animals was explosive, but assert that is the normal pattern in evolutionary history. They imagine transitional forms that are “unrepresented” in design space, but went extinct, leaving the appearance of gaps. What’s lacking so far is a mechanism to generate the initial body plans. “Distilling the phenomenon of animal disparity is one thing; establishing its causality is another,” they admit. The causes they consider (only unguided causes, of course) are either intrinsic (e.g., genome expansion, protein fold expansion, gene regulation) or extrinsic (e.g., environmental challenges, such as the expansion to land). Or, evolution might just be doing a “random walk” through morphospace.

Their favored conclusion is that the evolution of gene regulation is the primary cause, but not the only one. Co-author Jenny Greenwood cuts through the paper’s jargon, stating succinctly, “it is the evolution of genetic regulation of embryology that precipitated the evolution of animal biodiversity.” Colleague Kevin Peterson agrees, saying “Our study confirms the view that continued gene regulatory construction was a key to animal evolution.” (Note: They reference Davidson and Erwin on this point, but not Charles Marshall.)

In short: animals evolved, because they evolved. Evolution is fast, except when it operates in fits and starts. It’s the nature of living things to explore possibilities. In their random walks, gene regulatory networks hit on some bodyplans that worked. When you see gaps between the bodyplans, just imagine some intermediate forms that were exploring “shape space,” but went extinct, leaving gaps. Cambrian explosion solved? Almost. With thanks to Neil Shubin for refereeing their work, they end their “most beautiful and most wonderful paper” with promissory notes:

Our results also suggest that debate on whether early animal evolution has been underpinned by uniformitarian or nonuniformitarian processes has been misplaced. Animal evolutionary history does not appear to have been characterized by a uniform rate and scale of change but rather by a high frequency of small changes and low frequency of changes of large magnitude within the context of intrinsic genetic and developmental variation and extrinsic environmental change. Such patterns are readily open to modeling in the same manner as nucleotide and amino acid substitution frequencies. Future research in this direction will inform understanding of the nature of phenotypic evolution, its relation to molecular evolution, underpinning the development of phylogenetic methods. However, it will also provide for a more precise characterization of the tempo of metazoan diversification and the processes that underpinned the establishment of animal bodyplans.

Shallow thinking about major problems in evolution continues because its defenders have shielded themselves from real debate. Once again, this paper and its cheerleading articles completely ignore the issues raised by Stephen Meyer in Darwin’s Doubt.

Homology explains phylogeny(except when it doesn't)

Theory of Convergent Evolution Analyzed

Evolution News & Views 

The knifefish, rather than having several fins like a trout, has one long "ribbon fin" that undulates along the length of its body. Studies of its motion reveal that it uses the optimal wavelength to get the most forward thrust, stability, and maneuverability out of its investment of energy. But the knifefish is not alone: the same optimal design can be found in cuttlefish (cephalopods), rays (cartilaginous fish), certain flatworms, and other bony fish that are evolutionarily unrelated. In fact -- if evolution by natural selection is assumed to be the cause -- this design emerged independently at least eight times. To the Darwinian, it's another remarkable case of "convergent evolution."

A paper in PLOS Biology investigates this phenomenon and tries to explain it. The five authors, primarily from Northwestern University, used a robotic knifefish to nail down the physical factors related to optimal swimming design: the length of the fin's undulation and the mean amplitude. Dividing the one by the other yields what they call the Optimal Specific Wavelength (OSW). Then they measured the OSW on 22 live swimmers, such as cuttlefish and rays, to see how they rated. They found that the values "converge to a narrow range" around 20, even though the animals belong to eight separate groups whose presumed ancestors did not possess this kind of propulsion. Robin Meadows says in a companion piece likewise in PLOS Biology:

Many OSW swimmers have no known ancestor that swam with median/paired fins, and the 22 species in this analysis belong toeight clades (groups of organisms stemming from a common ancestor). This suggests that the OSW evolved independently at least eight times. 

Casey Luskin has argued that Darwinians appeal to convergence in order to have it both ways: basically, "biological similarity implies common ancestry, except when it doesn't." The authors of this new paper do not respond to that charge specifically, but they go further than most Darwinians by not just asserting convergence occurred, but by offering evolutionary mechanisms that might produce it. They begin with broad philosophical questions:

How would life look if it evolved again on Earth, or for that matter, on any other habitable planet? The question of the role of chance versus necessity in evolution is a foundational issue in biology. Gould gave us the metaphor of the "tape of life" for the evolution of life and argued that if it were somehow rewound and started again, life would have taken a very different course. Conway Morris has argued that, on the contrary, the laws of physics limit the number of good solutions that are within reach of evolution, and that therefore we should expect life to take a similar course upon rewinding. Examples of convergent evolution, such as wings on insects, birds, and mammals, are considered supporting evidence for this hypothesis.But our understanding of convergent evolution, as reflecting the dominance of natural selection plus variation over factors such as developmental constraints, pleiotropy, phylogenetic inertia, genetic drift, and other stochastic processes, is held back by a lack of quantitative arguments. Such arguments would expose the links from physical principles to the biological phenomena and help us understand where evolution is likely to converge to the same result or diverge to a wide variety of solutions.

Here, we present just such arguments for a phenomenon that unifies a vast diversity of swimming organisms, from invertebrates, like cuttlefish, to vertebrates, like cartilaginous and bony fish. Unlike the case of the convergently evolved wing, a morphological feature, here the evolved feature is a pattern of movement that occurs across a morphologically diverse set of moving appendages on aquatic animals.

We see at once that the implications go far beyond the knifefish's OSW. Evolutionary theory itself is at stake: Is it truly contingent, or somehow directed? Their argument hinges on the ability of the environment (e.g., the properties of water) to direct natural selection so that it rewards, with higher fitness, the animals that hit the optimum. If the OSW is on a peak of the fitness landscape, natural selection will drive an animal up the peak, no matter its ancestry, because it will outcompete the others. That's how separately evolving animals will end up (converge) on the same fitness peak.

What is the mechanism for macroevolutionary repeatability? In the language of the calculus of variations, these examples of convergent evolution -- if correctly identified as such -- imply that there is agradient in the fitness landscape toward some optimum with respect to trait in question, and this gradient is large enough to overcome competing factors such as developmental constraints, pleiotropy, phylogenetic inertia, genetic drift, cases where optimality in one trait results in suboptimality in another trait ... and approximations of the trait which provide local but not global optimality. With a sufficiently steep gradient in fitness in place and evolutionary dynamics capable of achieving near-optimal solutions, it is only a matter of time before the mechanism of selection with variation can arrive at the optimum. As the derivative of the trait with respect to fitness is stabilizing,departures from the optimum would be self-correcting over evolutionary time.

In fulfillment of the promise of quantifying their argument, they measure the loss in force for wavelengths that deviate significantly from the OSW. "The effect of any decline in propulsive force -- even less than one percent -- from what it is at the OSW is amplified over the vast number of undulations an animal may make in its life," they argue. What animal would want to compete with less than the best?

Unfortunately, undulating fins are not the best. Tuna are the fastest swimmers in the ocean, but they rely on their caudal fins to thrust their bodies forward. So we have a conundrum; "The question is therefore why the slower forms of swimming exhibited by median/paired fin animals would emerge and thrivedespite the prevalence of body/caudal fin swimming in ancestral species." Why would evolution switch from the Ferrari to the Volkswagen?

The authors are ready with auxiliary hypotheses:

A similar question has arisen in simulation studies that show that alight-sensitive patch of skin can evolve through several intermediate forms into an advanced camera-type lens eye in only a few hundred thousand years -- why, then, are there so many existing animals with intermediate forms of eyes? Nilsson and Pelger's answer is that camera-type lens eyes are only the best solution for certain animal -- ecosystem combinations. Our answer is similar: body/caudal fin swimming makes little sense in isolation. It is only within particular ecological contexts that some types of animals are able to survive better with this type of swimming than with alternative approaches.

In particular, median/paired fin swimming appears to be a low speed, low cost of transport specialization. The lower amplitudes of fin movement that are possible in median/paired fin swimmers, compared to the very high amplitudes possible when the high power axial musculature is used in body/caudal fin swimmers, is thereforean advantage instead of a liability due to the lower energetic cost of transport of median/paired fin swimming. The fact that median/paired fin swimming is used at lower speeds should not be confused, however, with the concept of maximizing speed by swimming at the OSW. Even when swimming at lower speeds (or whatever speed for that matter, which is determined by frequency and amplitude), for a given set of parameters (amplitude of undulations, frequency, fin height, and fin shape), if an animal swims with elongated median/paired fins, then its speed can be maximizedfor that set of parameters by swimming at the OSW.

Our regular readers will jump at that lateral pass to Nilsson and Pelger. Their claim about the evolution of camera eyes was thoroughly trounced by David Berlinski almost a decade ago in these pages. It's an example of how scientists can continue to trust flawed arguments for years -- decades, sometimes -- without considering (or even knowing about) the counter-arguments.

Aside from that, the authors make a point: You can't just look at a fin in isolation. You need to consider the ecological niche of the animal. They point to members of the group Gymnotiformes, electric fish who use their ribbon fins in low-oxygen murky waters, that swim mostly at night where high speed is not advantageous.

Given these constraints, the elongated fins that are universally present within the more than 150 species comprising Gymnotiformesmay be favored, but clearly a tremendous amount of work would need to be done to assess the relative importance of all of these factors in giving rise to this one group of median/paired fin swimmers.

While the existence of body/caudal fin swimmers and the existence of median/paired fin swimmers may or may not be subject to robust repeatability, what is clear is that if median/paired fin swimming with elongated fins and semirigid trunks emerges -- as it has independently on multiple occasions according to Fig 1 -- it is very probable that the specific trait of swimming at the OSW will also emerge.

This is a very different claim, much reduced from the original one. No longer are they asserting that the environment will force different swimmers up the same fitness peak, because clearly it didn't for the tuna. Now we have the more modest claim that "if" a ribbon fin "emerges," then natural selection will push it toward the OSW. But where is their scientific law of emergence? What about the ocean environment can cause that? And we see they just admitted that their hypothesis "may or may not be subject to robust repeatability."

Another complication is that some of the undulating-fin fish can switch to high-speed caudal-fin swimming when needed, as when under attack from predators or when zooming in on prey. Why would natural selection provide both methods of propulsion? The fitness landscape just got more complicated; the animal has to climb multiple fitness peaks to survive. (We might point out, in passing, that according to evolutionists, electric organs are examples of convergence, too, having evolved six times independently according to a report last year from the University of Wisconsin posted at NewsWise.)

Notice, also, that while the ecological hypothesis seems to work for the Gymnotiformes, it doesn't for the others. Rays and cuttlefish, for instance, use their undulating fins in the open sea or coastal shallows during the daytime. The authors have not shown that their auxiliary hypotheses rescue convergent evolution, nor have they identified any evolutionary mechanism to account for fast swimmers with caudal fins swimming right alongside slow swimmers with undulating fins in the exact same watery environment. Every proposal has exceptions; where is that quantitative argument, exactly?

Thus, we can only speculate that the 7.5% decline in force occurring over the observed variation in SW is not large enough to overcomethe many causes of suboptimality listed above, whereas the 25% decline we find beyond this range is large enough to cause selection pressure toward the OSW. Additional research is needed to establish whether this hypothesis is true.

We thus circle back to Casey Luskin's challenge: Common ancestry explains traits, except when it doesn't.

For these reasons, we cannot take Robin Meadows's praise of this paper seriously:

This elegant work reveals that a physical problem -- how to get from here to there -- can be optimized by a wondrous diversity of biological solutions. Moreover, these findings strengthen the case thatmechanical optimization can drive evolution, contributing to the longstanding debate over the evolutionary roles of randomness versus physical constraints that limit the solutions that are feasible in living creatures. As the researchers point out, quantifying physical properties that underlie biological phenomena could help us recognize when an optimal mechanical solution is likely to drive convergent evolution.

Ockham is tapping his foot by the door.e knifefish, rather than having several fins like a trout, has one long "ribbon fin" that undulates along the length of its body. Studies of its motion reveal that it uses the optimal wavelength to get the most forward thrust, stability, and maneuverability out of its investment of energy. But the knifefish is not alone: the same optimal design can be found in cuttlefish (cephalopods), rays (cartilaginous fish), certain flatworms, and other bony fish that are evolutionarily unrelated. In fact -- if evolution by natural selection is assumed to be the cause -- this design emerged independently at least eight times. To the Darwinian, it's another remarkable case of "convergent evolution."

A paper in PLOS Biology investigates this phenomenon and tries to explain it. The five authors, primarily from Northwestern University, used a robotic knifefish to nail down the physical factors related to optimal swimming design: the length of the fin's undulation and the mean amplitude. Dividing the one by the other yields what they call the Optimal Specific Wavelength (OSW). Then they measured the OSW on 22 live swimmers, such as cuttlefish and rays, to see how they rated. They found that the values "converge to a narrow range" around 20, even though the animals belong to eight separate groups whose presumed ancestors did not possess this kind of propulsion. Robin Meadows says in a companion piece likewise in PLOS Biology:

Many OSW swimmers have no known ancestor that swam with median/paired fins, and the 22 species in this analysis belong toeight clades (groups of organisms stemming from a common ancestor). This suggests that the OSW evolved independently at least eight times. [Emphasis added.]

Casey Luskin has argued that Darwinians appeal to convergence in order to have it both ways: basically, "biological similarity implies common ancestry, except when it doesn't." The authors of this new paper do not respond to that charge specifically, but they go further than most Darwinians by not just asserting convergence occurred, but by offering evolutionary mechanisms that might produce it. They begin with broad philosophical questions:

How would life look if it evolved again on Earth, or for that matter, on any other habitable planet? The question of the role of chance versus necessity in evolution is a foundational issue in biology. Gould gave us the metaphor of the "tape of life" for the evolution of life and argued that if it were somehow rewound and started again, life would have taken a very different course. Conway Morris has argued that, on the contrary, the laws of physics limit the number of good solutions that are within reach of evolution, and that therefore we should expect life to take a similar course upon rewinding. Examples of convergent evolution, such as wings on insects, birds, and mammals, are considered supporting evidence for this hypothesis.But our understanding of convergent evolution, as reflecting the dominance of natural selection plus variation over factors such as developmental constraints, pleiotropy, phylogenetic inertia, genetic drift, and other stochastic processes, is held back by a lack of quantitative arguments. Such arguments would expose the links from physical principles to the biological phenomena and help us understand where evolution is likely to converge to the same result or diverge to a wide variety of solutions.

Here, we present just such arguments for a phenomenon that unifies a vast diversity of swimming organisms, from invertebrates, like cuttlefish, to vertebrates, like cartilaginous and bony fish. Unlike the case of the convergently evolved wing, a morphological feature, here the evolved feature is a pattern of movement that occurs across a morphologically diverse set of moving appendages on aquatic animals.

We see at once that the implications go far beyond the knifefish's OSW. Evolutionary theory itself is at stake: Is it truly contingent, or somehow directed? Their argument hinges on the ability of the environment (e.g., the properties of water) to direct natural selection so that it rewards, with higher fitness, the animals that hit the optimum. If the OSW is on a peak of the fitness landscape, natural selection will drive an animal up the peak, no matter its ancestry, because it will outcompete the others. That's how separately evolving animals will end up (converge) on the same fitness peak.

What is the mechanism for macroevolutionary repeatability? In the language of the calculus of variations, these examples of convergent evolution -- if correctly identified as such -- imply that there is agradient in the fitness landscape toward some optimum with respect to trait in question, and this gradient is large enough to overcome competing factors such as developmental constraints, pleiotropy, phylogenetic inertia, genetic drift, cases where optimality in one trait results in suboptimality in another trait ... and approximations of the trait which provide local but not global optimality. With a sufficiently steep gradient in fitness in place and evolutionary dynamics capable of achieving near-optimal solutions, it is only a matter of time before the mechanism of selection with variation can arrive at the optimum. As the derivative of the trait with respect to fitness is stabilizing,departures from the optimum would be self-correcting over evolutionary time.

In fulfillment of the promise of quantifying their argument, they measure the loss in force for wavelengths that deviate significantly from the OSW. "The effect of any decline in propulsive force -- even less than one percent -- from what it is at the OSW is amplified over the vast number of undulations an animal may make in its life," they argue. What animal would want to compete with less than the best?

Unfortunately, undulating fins are not the best. Tuna are the fastest swimmers in the ocean, but they rely on their caudal fins to thrust their bodies forward. So we have a conundrum; "The question is therefore why the slower forms of swimming exhibited by median/paired fin animals would emerge and thrivedespite the prevalence of body/caudal fin swimming in ancestral species." Why would evolution switch from the Ferrari to the Volkswagen?

The authors are ready with auxiliary hypotheses:

A similar question has arisen in simulation studies that show that alight-sensitive patch of skin can evolve through several intermediate forms into an advanced camera-type lens eye in only a few hundred thousand years -- why, then, are there so many existing animals with intermediate forms of eyes? Nilsson and Pelger's answer is that camera-type lens eyes are only the best solution for certain animal -- ecosystem combinations. Our answer is similar: body/caudal fin swimming makes little sense in isolation. It is only within particular ecological contexts that some types of animals are able to survive better with this type of swimming than with alternative approaches.

In particular, median/paired fin swimming appears to be a low speed, low cost of transport specialization. The lower amplitudes of fin movement that are possible in median/paired fin swimmers, compared to the very high amplitudes possible when the high power axial musculature is used in body/caudal fin swimmers, is thereforean advantage instead of a liability due to the lower energetic cost of transport of median/paired fin swimming. The fact that median/paired fin swimming is used at lower speeds should not be confused, however, with the concept of maximizing speed by swimming at the OSW. Even when swimming at lower speeds (or whatever speed for that matter, which is determined by frequency and amplitude), for a given set of parameters (amplitude of undulations, frequency, fin height, and fin shape), if an animal swims with elongated median/paired fins, then its speed can be maximizedfor that set of parameters by swimming at the OSW.

Our regular readers will jump at that lateral pass to Nilsson and Pelger. Their claim about the evolution of camera eyes was thoroughly trounced by David Berlinski almost a decade ago in these pages. It's an example of how scientists can continue to trust flawed arguments for years -- decades, sometimes -- without considering (or even knowing about) the counter-arguments.

Aside from that, the authors make a point: You can't just look at a fin in isolation. You need to consider the ecological niche of the animal. They point to members of the group Gymnotiformes, electric fish who use their ribbon fins in low-oxygen murky waters, that swim mostly at night where high speed is not advantageous.

Given these constraints, the elongated fins that are universally present within the more than 150 species comprising Gymnotiformesmay be favored, but clearly a tremendous amount of work would need to be done to assess the relative importance of all of these factors in giving rise to this one group of median/paired fin swimmers.

While the existence of body/caudal fin swimmers and the existence of median/paired fin swimmers may or may not be subject to robust repeatability, what is clear is that if median/paired fin swimming with elongated fins and semirigid trunks emerges -- as it has independently on multiple occasions according to Fig 1 -- it is very probable that the specific trait of swimming at the OSW will also emerge.

This is a very different claim, much reduced from the original one. No longer are they asserting that the environment will force different swimmers up the same fitness peak, because clearly it didn't for the tuna. Now we have the more modest claim that "if" a ribbon fin "emerges," then natural selection will push it toward the OSW. But where is their scientific law of emergence? What about the ocean environment can cause that? And we see they just admitted that their hypothesis "may or may not be subject to robust repeatability."

Another complication is that some of the undulating-fin fish can switch to high-speed caudal-fin swimming when needed, as when under attack from predators or when zooming in on prey. Why would natural selection provide both methods of propulsion? The fitness landscape just got more complicated; the animal has to climb multiple fitness peaks to survive. (We might point out, in passing, that according to evolutionists, electric organs are examples of convergence, too, having evolved six times independently according to a report last year from the University of Wisconsin posted at NewsWise.)

Notice, also, that while the ecological hypothesis seems to work for the Gymnotiformes, it doesn't for the others. Rays and cuttlefish, for instance, use their undulating fins in the open sea or coastal shallows during the daytime. The authors have not shown that their auxiliary hypotheses rescue convergent evolution, nor have they identified any evolutionary mechanism to account for fast swimmers with caudal fins swimming right alongside slow swimmers with undulating fins in the exact same watery environment. Every proposal has exceptions; where is that quantitative argument, exactly?

Thus, we can only speculate that the 7.5% decline in force occurring over the observed variation in SW is not large enough to overcomethe many causes of suboptimality listed above, whereas the 25% decline we find beyond this range is large enough to cause selection pressure toward the OSW. Additional research is needed to establish whether this hypothesis is true.

We thus circle back to Casey Luskin's challenge: Common ancestry explains traits, except when it doesn't.

For these reasons, we cannot take Robin Meadows's praise of this paper seriously:

This elegant work reveals that a physical problem -- how to get from here to there -- can be optimized by a wondrous diversity of biological solutions. Moreover, these findings strengthen the case thatmechanical optimization can drive evolution, contributing to the longstanding debate over the evolutionary roles of randomness versus physical constraints that limit the solutions that are feasible in living creatures. As the researchers point out, quantifying physical properties that underlie biological phenomena could help us recognize when an optimal mechanical solution is likely to drive convergent evolution.

Ockham is tapping his foot by the door.

On being argumentative in lieu of making an argument.

Integrity in Science — A Facebook Dialogue
Ann Gauger

Editor’s note: Our biologist colleague Ann Gauger had the following interaction on Facebook yesterday. Sadly typical, it speaks for itself.

Questioner: Has anyone in the Discovery Institute thought of doing any real experiments?

Ann Gauger: Read our papers. Plenty of real experiments there.

Q: Where, Ann Gauger?

Ann: [LINK]

Q: “Peer review” means different things in science and in intelligent design. Yet more deception.

Q: I don’t see any evidence of any science being done.

Another FB correspondent chimes in:

[LINK] Axe

[LINK]  Reeves

And this: [LINK] Gauger

Q: Who has reviewed these?

Ann: As you know, peer review is confidential and I do not know their names. They were qualified research scientists by no means all favorable to ID. More than that I cannot say. The process is rigorous. Many papers are turned down.

Q: From “BIO-Complexity, Purpose and Scope”:

Purpose: BIO-Complexity is a peer-reviewed scientific journal with a unique goal. It aims to be the leading forum for testing the scientific merit of the claim that intelligent design (ID) is a credible explanation for life. Because questions having to do with the role and origin of information in living systems are at the heart of the scientific controversy over ID, these topics — viewed from all angles and perspectives — are central to the journal’s scope.

To achieve its aim, BIO-Complexity is founded on the principle of critical exchange that makes science work. Specifically, the journal enlists editors and reviewers with scientific expertise in relevant fields who hold a wide range of views on the merit of ID, but who agree on the importance of science for resolving controversies of this kind. Our editors use expert peer review, guided by their own judgement, to decide whether submitted work merits consideration and critique. BIO-Complexity aims not merely to publish work that meets this standard, but also to provide expert critical commentary on it.
Ann: We have reviewers on both sides of the question and invite anyone who is qualified to participate. As you can guess, the problem is that we are being stonewalled. We have applied to mainstream journals and they are returned without being considered.

Q: Ann Gauger, you just said you don’t know who reviews what.

Ann: I don’t. But if you’ve been through peer review yourself, you know that you can get a general feel for the attitude of the reviewer without knowing their name.

Q: “Reviewing” and publishing in a specially protected environment basically makes them whiff of cargo-cult science and deliberate attempts at deception. They won’t win any scientific case that way, just take in gullible lay people.

Ann: Let me respond to your accusation of cargo-cult science and deception. BIO-Complexity is not the first journal to be founded to advance a controversial case. From Wikipedia [regarding the journal Nature] — you can check their sources:

“…Nature was conceived, born, and raised to serve polemic purpose.”[12] Many of the early editions of Nature consisted of articles written by members of a group that called itself the X Club, a group of scientists known for having liberal, progressive, and somewhat controversial scientific beliefs relative to the time period.[12] Initiated by Thomas Henry Huxley, the group consisted of such important scientists as Joseph Dalton Hooker, Herbert Spencer, and John Tyndall, along with another five scientists and mathematicians; these scientists were all avid supporters of Darwin’s theory of evolution as common descent, a theory which, during the latter-half of the 19th century, received a great deal of criticism among more conservative groups of scientists.[14] Perhaps it was in part its scientific liberality that made Nature a longer-lasting success than its predecessors. John Maddox, editor of Nature from 1966 to 1973 as well as from 1980 to 1995, suggested at a celebratory dinner for the journal’s centennial edition that perhaps it was the journalistic qualities of Nature that drew readers in; “journalism” Maddox states, “is a way of creating a sense of community among people who would otherwise be isolated from each other. This is what Lockyer’s journal did from the start.”[15] In addition, Maddox mentions that the financial backing of the journal in its first years by the Macmillan family also allowed the journal to flourish and develop more freely than scientific journals before it.[15].”
So spare me your sneers.

Q: Ann Gauger, I expect their eventual success rested on the veracity of their science.

Ann: And so we will let time tell.

Q: Not to mention their intellectual integrity and honesty.

Ann: No — read the history of the X Club. And I thought our conversation was honest and above ad hominems.

Q: Questioning honesty is not ad-hominem. It relates directly to the trustworthiness of what they are saying. Criticising an organisation or an individual for being naughty in a way that is unrelated to what they are arguing — that would be ad-hom.

Ann: Ad hominem attacks can take the form of overtly attacking somebody, or more subtly casting doubt on their character or personal attributes as a way to discredit …

Q: Ann Gauger, as I said, the exception is when we question their honesty and integrity in making statements.

“X is a habitual liar, so you cannot trust what he says about anything.” This is not ad-hom.

“X is smelly, so you cannot trust what he says about anything.” This is ad-hom.

Ann: Casting doubt on the integrity of an individual does not address the argument, it dismisses it, just as you dismiss our papers because of where they were published. Why not read them and judge them on their own merits?

And why not take my arguments as truthful, not deceptive, based on the evidence, not any prejudgment or label?

How are we to get an adequate hearing in the face of such prejudice?

Q: Ann Gauger, your history is against you. Starting with the Wedge document. My “prejudice” is based on years of investigating the claims of creationist/ID enthusiasts, and by learning about their underhanded tactics for infiltrating academe. You have brought all this upon yourselves.

Ann: Well, apparently, you know something about our history that I don’t. Infiltrating academe? What does that mean?

Ann: It took me a while to find this, but your accusation of infiltration reminded me of a quote from a book I had read:

[T]he process of conversion involved much hard lobbying by Huxley, Hooker and other naturalists who jumped to the defense of the theory. Huxley’s real triumph was in gradually extending the influence of those who shared his aversion to the design argument within the community of professional scientists. This influence was at last beginning to expand, and Huxley networked endlessly to ensure that people sympathetic to his position got the jobs that were opening up in the universities and elsewhere. It became unfashionable for a scientist to make open appeals to the supernatural, even if he (and they were still almost all men) believed in a Creator.

(Peter J. Bowler, Monkey Trials and Gorilla Sermons: Evolution and Christianity from Darwin to Intelligent Design (Cambridge, Massachusetts: Harvard University Press, 2007), pp. 38-39)
Q: Ann Gauger, do you have any evidence that Huxley was underhanded? Dishonest?

Ann: There’s more to the quote that I don’t have available to me now. Do you have such evidence?

Q: Nope.

Ann: And with regard to ID?

Q: I’ve already mentioned the Wedge document. It starts there.

[What’s the so-called “Wedge document” he keeps mentioning? See here . –Editor]

Ann: One more piece, this time about Darwin[LINK]:

Darwin’s picture of himself, and our dominant picture of him, as a pure scientist, slow at writing, poor at arguing, concerned only with the truth or with the judgment of a small group of experts and indifferent to public opinion, is a picture taken in the earlier part of his career and is irreconcilable with his motives and actions in the years of public controversy. Darwin’s self-image ignores his extensive efforts to proselytize, to simplify the bases for believing in evolution, and to broaden his base of support. Darwin’s failure to integrate his rhetorical action with his self-understanding as a scientist has powerfully reinforced a positivist interpretation of his achievement as merely the inevitable consequence of a superior account.

Finally the study has implications for our understanding of the ethics of scientific rhetoric. Given that science and civilization exist in an interdependent relationship, how far is it legitimate for science to mask its opposition to dominant cultural values? To what extent does the ethic of science demand truthfulness, when the price of truth may be a temporary, or perhaps even sustained, reaction against a particular scientific theory? In his use of Gray’s essays, does Darwin’s encouragement of the public to draw a theological conclusion beneficial to his persuasive aim, but counter to his personal convictions, make him cynical or dishonest? Or should we see him as acting to create a cultural environment beneficial to science and perhaps in time conducive to a more enlightened understanding of religion? It seems that however we interpret Dar win’s rhetorical strategies and tactics, we are left with the discomfiting realization that Darwin the historical truth bearer was not always Darwin the historical truth teller. The ethical obligation peculiar to rhetoric is to give truth effective advocacy.
Ann: The people I work with are men of integrity and honesty. I am not aware of any deception or misrepresentation on their part.

You may disagree with their motives or conclusions. But then as should be clear above, Huxley and Darwin were fighting their own cultural battle, and not always openly, with some deception involved. There is the story of how Darwin managed to get his theory admitted before the Royal Society at the same time as Wallace by lobbying with friends and Lyell. Your indignation over the Wedge document, which I have not read by the way, is mainly cultural, I suspect, and not because anyone was proposing underhanded science….

Ann: Gotta go. It’s been fun.