Discontinuity in the history of life explained (away?) once again.

Ignoring Other Research, New Study Explains (Away) the Origin of New Body Plans
Günter Bechly

Every now and then a new scientific paper takes on a particularly daunting challenge. The challenge is to explain the discontinuous origin of new body plans in the history of life on earth, for example, as observed in the sudden appearance of the animal phyla during the Cambrian explosion about 530 million years ago. Most of these attempts fail miserably. That is because the proposed causes are clearly not apt to generate new biologic complexity and diversity. Notorious examples are the slime theory and the oxygen and cancer theories that have already been discussed at Evolution News.

A New Pseudo-Explanation

Recently, a team of British paleontologists added a new pseudo-explanation. Deline et al. (2018) studied the presence and absence of thousands of features from all living animal groups, which allowed them “to create a shape space for animal body plans, quantifying their similarities and differences” (Donoghue in the press release by the  University of Bristol 2018) The authors claim: “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.”

This is interesting indeed, because it exactly confirms my own argument (Bechly & Meyer 2017) that the history of life is a series of numerous discontinuous abrupt origins (“explosions”), contradicting the fundamental prediction of gradualism implied by Darwin’s theory of evolution through random variation and natural selection. As Richard Dawkins (2009) emphasized in his bestselling book The Greatest Show on Earth: “Evolution not only is a gradual process as a matter of fact; it has to be gradual if it is to do any explanatory work.” Darwin’s theory does not pass this empirical test of its predictions. So far so good (or rather so bad for neo-Darwinism). We already knew this.

Furthermore, the paper states: 

Our results challenge the view that maximum variation was achieved early in animal evolutionary history by nonuniformitarian mechanisms. Rather, they are compatible with the view that the capacity for fundamental innovation is not limited to the early evolutionary history of clades…. Our mapping of metazoan morphospace has shown that, even though some animal phyla demonstrate maximal initial disparity, others, notably chordates, arthropods, annelids, and mollusks, have progressively expanded on the limits of phylum and kingdom level morphospace post-Cambrian.

Thus post-Cambrian evolution has seen body plan innovation, which is hardly controversial. After all, insects, tetrapods, birds, mammals, and other body plans did not exist 530 million years ago. But this point does not negate at all the crucial fact that extreme biological innovation occurred rapidly in the Cambrian. Nor does it negate the fact that when later body plan innovations appear, they typically also do so abruptly.

However, Deline et al. also claim, “The ‘clumpiness’ of morphospace occupation by living clades is a consequence of the extinction of phylogenetic intermediates, indicating that the original distribution of morphologies was more homogeneous.” In a previous article at Evolution News (Anonymous 2018b) this ad hoc hypothesis has already been criticized, because it unashamedly maintains that exactly where the hypothetical intermediates are proposed to have existed, they remain forever inaccessible. How convenient!

An Even More Fundamental Problem

But there is an even more fundamental problem with this new study. As one of their major results, the authors claim that the origin of new body plans did not require the origin of new DNA code for new proteins. Instead, tweaking gene regulatory networks has been a main causal factor in the origin of metazoan disparity. Strangely, the authors completely ignore the work of Paps and Holland (2018) and do not even cite this important paper in their references section. Deline et al. submitted their manuscript on June 26, but the Paps & Holland study was published on April 30, allowing plenty of time to incorporate, or at least to mention those new results, unless these were too inconvenient truths that would have blown their own paper out of the water. 

Paps and Holland reconstructed the ancestral genetic nodes at which different types of animals diverged, and showed that those nodes involved major genetic and genomic innovations compared to other nodes. This clearly refutes one of the major conclusions of Deline et al.’s paper! Thus, Deline et al. are following in the path of Charles Marshall’s failed attempt to downplay the degree of genetic innovation that was necessary in the Cambrian (see Anonymous 2018a). The omission of Paps and Holland gets a truly bizarre twist in the review of Deline et al.’s work by Paps (2018) himself, who praises the new paper to the skies, but does not bother to mention the omission of his own contradicting study. This is a bit fishy.

A Classical Fallacy

The paper also seems to commit the classical fallacy of confusing correlation with causation. It states: “Causal hypotheses of morphologic expansion include time since origination, increases in genome size, protein repertoire, gene family expansion, and gene regulation.” The authors find a correlation with genome size and microRNA repertoire, but no correlation with protein domain diversity, and they conclude that gene regulation was more influential in shaping metazoan disparity. This of course overlooks that the lack of a general correlation between increasing morphological disparity and protein domain diversity does not imply that novel proteins do not play a crucial role in the origin of new body plans, as suggested by Paps and Holland. Apart from that, like all cladistic studies, this paper suffers from the general problem of biased and more or less arbitrary character selection and delimitation (Bechly 2000) in its data for measuring the disparity morphospace in the first place.

Last but not least, the new paper of course does absolutely nothing to explain how on earth random changes in gene regulatory networks could ever produce highly integrated and complex novel organ systems such as arthropod compound eyes, bird feathers, or the countercurrent heat exchange cooling system for the testes in whales. As a causal process, it is as unlikely to generate the phenomenon in question as oxygen levels or cancer.

In short: While certainly an interesting study, Deline et al. delivers just another failed attempt at an explanation for the origin of new body plans and biological disparity. Next?

Literature:

• Anonymous 2018a. “Groundbreaking Paper Shows Thousands of New Genes Needed for the Origin of Animals.” Evolution News June 7, 2018.
• Anonymous 2018b. “A Beautiful, Wonderful Solution to the Cambrian Puzzle?” Evolution News, September 7, 2018.
• Bechly G 2000. “Mainstream Cladistics versus Hennigian Phylogenetic Systematics.” Stuttgarter Beiträge zur Naturkunde Serie A 613, 1–11. (PDF)
• Bechly G, Meyer S 2017. “The Fossil Record and Universal Common Ancestry.” Chapter 10 in Moreland JP et al. (eds). Theistic Evolution: A Scientific, Philosophical, and Theological Critique. Crossway, Wheaton, pp. 331–362.
• Deline B, Greenwood JM, Clark JW, Puttick MN, Peterson KJ, Donoghue PCJ 2018. “Evolution of metazoan morphological disparity.” PNAS preprint, September 4, 2018.
• Paps J 2018. “How animals went from single cells to over 30 different body types.” The Conversation, September 4, 2018.
• Paps J, Holland PWH 2018. “Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty.” Nature Communications 9:1730. (PDF)
• University of Bristol 2018. “Evolutionary origins of animal biodiversity.” Science Daily, September 3, 2018.

The undead continue to prowl Darwinism's badlands.

Listen: Dead Peppered Moths Can’t Evolve
Evolution News | @DiscoveryCSC

On an episode of ID the Future, biologist Jonathan Wells, author of Icons of Evolution: Science or Myth? Why Much of What We Teach About Evolution is Wrong and Zombie Science: More Icons of Evolution, debunks a study purporting to breathe fresh life into an old and throughly discredited icon of evolution, the peppered moth. Wells also tells how this icon of a moth “evolving” from light to dark lives on in current textbooks, in the same form many parents probably remember from their school days.

Download the podcast or listen to it here.

Dr. Wells and others have shown that many of these pictures used dead moths, pinned in places that live ones never rest. The supposed science of peppered moth evolution has been shown to be false as well. But the pictures and the claims are persuasive, so some textbooks still use them. This prompts host Rob Crowther to ask Dr. Wells what parents can do to help their kids understand the truth?

I.D is already mainstream? II

“Oldest Known Drawing,” and More Cases of Intelligent Design at Work in Science

Evolution News | @DiscoveryCSC

Science as a routine matter expects to be able to differentiate between the results of natural and intelligent causes. Sound familiar? Several illustrations from recent news will help clarify.

Crayon Drawings on Rock

It would be fair to call this an inference to intelligent design. It’s being reported widely from a South African cave: red markings on a rock. Are they natural marks, or were they intelligently crafted? The The BBC News is among news sources calling this the “oldest known drawing,” made by choice and intent, not just for survival.

The drawing is about 73,000 years old, and shows cross-hatch lines sketched onto stone with red ochre pigment.

Scientists discovered the small fragment of the drawing —  which some say looks a bit like a hashtag — in Blombos Cave on the southern coast.

The find is “a prime indicator of modern cognition” in our species, the report says. 

The researchers feel that the fragment in their hands is just part of a larger work that was “probably more complex” in its entirety. “The abrupt termination of all lines on the fragment edges indicates that the pattern originally extended over a larger surface,” says one. That’s a bold design inference from just a few scratch marks! 

The paper in Nature uses that ID word “intention” again: “We conclude that the ochre crayon was intentionally used to produce a cross-hatched design.” Lo and behold, the word “design” shows up six times in the paper! Whatever the drawing meant, it represented “abstract and depictive representations produced by drawing” far earlier than previously known. The Editors of Nature go further, stating that “The earliest known drawing in history sends a message through 73,000 years.” Watch them overtly use design reasoning:

So, were these Palaeolithic hashtags actually designs intended to convey meaning, or mindless graffiti? Some might have been the unintentional result of another action, such as cutting food items, just like the scratches left on a chopping board after slicing a loaf.

A drawing, by contrast, is much harder to dismiss. To be sure, the one from Blombos is as cross-hatched as the engravings, but it could not have been created as the accidental by-product of another process.

If evolutionists want to deny that the conclusion of this paper supports intelligent design, and argue that drawing abstract patterns is just a natural behavior that our species does from time to time, then fine. Let them argue the same for published scientific papers!

Cut Marks on Bird Bones

Meanwhile, also at the BBC News, Helen Briggs tells how scientists just deduced that humans arrived on Madagascar 6,000 years earlier than thought.

 Prehistoric humans are under suspicion of wiping out the largest birds that ever lived after fossilised bones were discovered with telltale cut marks.

According to scientists, it’s evidence that the elephant birds of Madagascar were hunted and butchered for food.

Evolutionists might argue that humans are just animals, doing what animals do: acting like predators against these birds. But the “telltale cut marks” imply use of designed tools for hunting. The paper in Science Advances lists “purposefulness” as one of the criteria for determining that humans hunted these birds. “These marks are consistent with kerfs made by single-bladed, sharp lithic tools and multiple cutting actions intended to” cut the bones apart for consumption.

Fast Radio Bursts

Flush with a $100 million grant from Russian benefactor Yuri Milner, SETI scientists in the“Breakthrough Listen”project are seeking to understand mysterious flashes of light in deep space. Fast radio bursts, or FRBs, are usually one-off events coming from various directions in the sky. As such, they most likely have a natural cause, but intelligent causes cannot be ruled out arbitrarily.

 The source and mechanism of FRBs are still mysterious. Previous studies have shown that the bursts from 121102 are emanating from a galaxy 3 billion light years from Earth, but the nature of the object emitting them is still unknown. Theories range from highly magnetized neutron stars, blasted by gas streams near to a supermassive black hole, to suggestions that the burst properties are consistent with signatures of technology developed by an advanced civilization.

Look at the effort that went into this design-detection exercise:

In search of a deeper understanding of this intriguing object, the Listen science team at the University of California, Berkeley SETI Research Center observed FRB 121102 for five hours on August 26, 2017, using the Breakthrough Listen digital instrumentation at the GBT. Combing through 400 TB of data, they reported (in a paper led by Berkeley SETI postdoctoral researcher Vishal Gajjar, recently accepted for publication in the Astrophysical Journal) a total of 21 bursts. All were seen within one hour, suggesting that the source alternates between periods of quiescence and frenzied activity….

Whether or not FRBs themselves eventually turn out to be signatures of extraterrestrial technology, Breakthrough Listen is helping to push the frontiers of a new and rapidly growing area of our understanding of the Universe around us. 

Publish and Perish

Here’s an unusual case of the design inference that is somewhat reminiscent of Dembski’s illustration that a ballot fraud incident demonstrated intent to bias an election. In that case, the candidate for one party appeared at the top of the ballot more often than could be attributed statistically to chance, possibly to subconsciously influence voters to choose the first name they saw.

John Ioannidis is an unusual scientist; he researches research. He looks for unusual patterns in publication that suggest unethical behavior. In Nature, his team posted a surprising headline: “Thousands of scientists publish a paper every five days.” Unless these scientists are supermen, that seems highly suspect!

Ioannidis and his co-authors went out of their way to examine possibilities other than fraud. They listened to some of the “hyperprolific authors” who tried to explain their publishing records. They considered extenuating circumstances, such as being listed simply as a member of a large team, or as a token author who supervised another’s work. They even considered the possibility that the authors really are supermen:

Overall, hyperprolific authors might include some of the most energetic and excellent scientists. However, such modes of publishing might also reflect idiosyncratic field norms, to say the least. Loose definitions of authorship, and an unfortunate tendency to reduce assessments to counting papers, muddy how credit is assigned. One still needs to see the total publishing output of each scientist, benchmarked against norms for their field. And of course, there is no substitute for reading the papers and trying to understand what the authors have done.

Conclusion

We’ve seen cases in archaeology, astronomy, and publishing where research depends on the ability to distinguish natural causes from intelligent ones. That, of course, is what ID is all about. Actions speak louder than words, we all know. Some scientists may denounce “intelligent design” as a movement, but they find its practice very useful.

Yet more on Darwinism and the search for the master race.

New Documentary Human Zoos Isn’t Ancient History

David Klinghoffer | @d_klinghoffer

The new documentary Human Zoos is out now, and director and writer John West talks about it in an ID the Future episode. The idea of a human being displayed in a zoo, out of “scientific” interest, is shocking. And as West points out, African pygmy Ota Benga was “only one of thousands of indigenous peoples who were put on display in America in the name of Darwinian evolution.”

See the film now on Amazon Prime or get it on DVD or Blu-ray.

Remember, Benga’s humiliation in 1906 by scientists and showmen isn’t ancient history. Nor is the idea of “human zoos,” which were still seen as a reasonable tool of education and entertainment as late as 1958! The World Fair in Belgium that year included a display of Congolese natives, imported from Belgium’s notoriously abused African colonial holding.

It was the New York Times that defended Benga’s caging in the Bronx Zoo’s Monkey House, and patronized the African-American and other clergy who protested it, as West points out. Yes, that’s the same New York Times we know and love, still run by the same family that owned it in 1906. (The current publisher, A.G. Sulzberger, is great-great-grandson of the owner at the time.)

A Familiar Tone

The superior tone is familiar: “We do not quite understand all the emotion which others are expressing in the matter,” the editors huffed. Pygmies were “very low in the human scale,” you understand, and “whether they are really closer to the anthropoid apes than the other African savages, or whether they are viewed as the degenerate descendants of ordinary Negroes, they are of equal interest to the student of ethnology and can be studied with profit.”

The Times scoffed at proposals that Ota Benga should be freed from the zoo and given an education: 

The suggestion that Benga should be placed in a school instead of a cage ignores the high probability that school would be a place of torture to him and one from which he could draw no advantage whatever. The idea that men are all much alike except as they have had or lacked opportunities for getting an education out of books is now far out of date.

Notice the haughty appeal to the intellectual consensus of the day. They averred, referring to the African-American pastors who opposed Benga’s captivity, that “the reverend colored brothers should be told that evolution, in one form or another, is now taught in the textbooks of all the schools, that it is no more debatable than the multiplication table.”

“No more debatable than the multiplication table”! That could have been written with hardly a change of phrasing by a Darwin proponent, in the New York Times, today. 

On the Cessationism v. Continuationism controversy.

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.