What is a Dependency Graph?

Information Organization

A recent paper, authored by Winston Ewert, uses a dependency graph approach to model the relationships between the species. This idea is inspired by computer science which makes great use of dependency graphs.

Complicated software applications typically use a wealth of lower level software routines. These routines have been developed, tested, and stored in modules for use by higher level applications. When this happens the application inherits the lower-level software and has a dependency on that module.

Such applications are written in human-readable languages such as Java. They then need to be translated into machine language. The compiler tool performs the translation, and the build tool assembles the result, along with the lower level routines, into an executable program. These tools use dependency graphs to model the software, essentially building a design diagram, or blueprint which shows the dependencies, specifying the different software modules that will be needed, and how they are connected together.

Dependency graphs also help with software design. Because they provide a blueprint of the software architecture, they are helpful in designing decoupled architectures and promoting software reuse.

Dependency graphs are also used by so-called “DevOps” teams to assist at deployment time in sequencing and installing the correct modules.

What Ewert has shown is that, as with computer applications which inherit software from a diverse range of lower-level modules, and those lower-level modules likewise feed into a diverse range of applications, biology’s genomes likewise reveal such patterns. Genomes may inherit molecular sequence information from a wide range of genetic modules, and genetic modules may feed into a diverse range of genomes.

Superficially, from a distance, this may appear as the traditional evolutionary tree. But that model has failed repeatedly as scientists have studied the characters of species more closely. Dependency graphs, on the other hand, provide a far superior model of the relationships between the species, and their genetic information flow.

New Paper Demonstrates Superiority of Design Model

Ten Thousand Bits?

Did you know Mars is going backwards? For the past few weeks, and for several weeks to come, Mars is in its retrograde motion phase. If you chart its position each night against the background stars, you will see it pause, reverse direction, pause again, and then get going again in its normal direction. And did you further know that retrograde motion helped to cause a revolution? Two millennia ago, Aristotelian physics dictated that the Earth was at the center of the universe. Aristarchus’ heliocentric model, which put the Sun at the center, fell out of favor. But what Aristotle’s geocentrism failed to explain was retrograde motion. If the planets are revolving about the Earth, then why do they sometimes pause, and reverse direction? That problem fell to Ptolemy, and the lessons learned are still important today.

Ptolemy explained anomalies such as retrograde motion with additional mechanisms, such as epicycles, while maintaining the circular motion that, as everyone knew, must be the basis of all motion in the cosmos. With less than a hundred epicycles, he was able to model, and predict accurately the motions of the cosmos. But that accuracy came at a cost—a highly complicated model.

In the Middle Ages William of Occam pointed out that scientific theories ought to strive for simplicity, or parsimony. This may have been one of the factors that drove Copernicus to resurrect Aristarchus’ heliocentric model. Copernicus preserved the required circular motion, but by switching to a sun-centered model, he was able to reduce greatly the number of additional mechanisms, such as epicycles.

Both Ptolemy’s and Copernicus’ models accurately forecast celestial motion. But Copernicus was more parsimonious. A better model had been found.

Kepler proposed ellipses, and showed that the heliocentric model could become even simpler. It was not well accepted though because, as everyone knew, celestial bodies travel in circles. How foolish to think they would travel along elliptical paths. That next step toward greater parsimony would have to wait for the likes of Newton, who showed that Kepler’s ellipses were dictated by his new, highly parsimonious, physics. Newton described a simple, universal, gravitational law. Newton’s gravitational force would produce an acceleration, which could maintain orbital motion in the cosmos.

But was there really a gravitational force? It was proportional to the mass of the object which was then cancelled out to compute the acceleration. Why not have gravity cause an acceleration straightaway?

Centuries later Einstein reported on a man in Berlin who fell out of a window. The man didn’t feel anything until he hit the ground! Einstein removed the gravitational force and made the physics even simpler yet.

The point here is that the accuracy of a scientific theory, by itself, means very little. It must be considered along with parsimony. This lesson is important today in this age of Big Data. Analysts know that a model can always be made more accurate by adding more terms. But are those additional terms meaningful, or are they merely epicycles? It looks good to drive the modeling error down to zero by adding terms, but when used to make future forecasts, such models perform worse.

There is a very real penalty for adding terms and violating Occam’s Razor, and today advanced algorithms are available for weighing the tradeoff between model accuracy and model parsimony.

This brings us to common descent, a popular theory for modeling relationships between the species. As we have discussed many times here, common descent fails to model the species, and a great many additional mechanisms—biological epicycles—are required to fit the data.

And just as cosmology has seen a stream of ever improving models, the biological models can also improve. This week a very important model has been proposed in a new paper, authored by Winston Ewert, in the Bio-Complexity journal.

Inspired by computer software, Ewert’s approach models the species as sharing modules which are related by a dependency graph. This useful model in computer science also works well in modeling the species. To evaluate this hypothesis, Ewert uses three types of data, and evaluates how probable they are (accounting for parsimony as well as fit accuracy) using three models.

Ewert’s three types of data are: (i) Sample computer software, (ii) simulated species data generated from evolutionary / common descent computer algorithms, and (iii) actual, real species data.

Ewert’s three models are: (i) A null model in which entails no relationships between
any species, (ii) an evolutionary / common descent model, and (iii) a dependency graph model.

Ewert’s results are a Copernican Revolution moment. First, for the sample computer software data, not surprisingly the null model performed poorly. Computer software is highly organized, and there are relationships between different computer programs, and how they draw from foundational software libraries. But comparing the common descent and dependency graph models, the latter performs far better at modeling the software “species.” In other words, the design and development of computer software is far better described and modeled by a dependency graph than by a common descent tree.

Second, for the simulated species data generated with a common descent algorithm, it is not surprising that the common descent model was far superior to the dependency graph. That would be true by definition, and serves to validate Ewert’s approach. Common descent is the best model for the data generated by a common descent process.

Third, for the actual, real species data, the dependency graph model is astronomically superior compared to the common descent model.

Let me repeat that in case the point did not sink in. Where it counted, common descent failed compared to the dependency graph model. The other data types served as useful checks, but for the data that mattered—the actual, real, biological species data—the results were unambiguous.

Ewert amassed a total of nine massive genetic databases. In every single one, without exception, the dependency graph model surpassed common descent.

Darwin could never have even dreamt of a test on such a massive scale.

Darwin also could never have dreamt of the sheer magnitude of the failure of his theory. Because you see, Ewert’s results do not reveal two competitive models with one model edging out the other.

We are not talking about a few decimal points difference. For one of the data sets (HomoloGene), the dependency graph model was superior to common descent by a factor of 10,064. The comparison of the two models yielded a preference for the dependency graph model of greater than ten thousand.

Ten thousand is a big number.

But it gets worse, much worse.

Ewert used Bayesian model selection which compares the probability of the data set given the hypothetical models. In other words, given the model (dependency graph or common descent), what is the probability of this particular data set? Bayesian model selection compares the two models by dividing these two conditional probabilities. The so-called Bayes factor is the quotient yielded by this division.

The problem is that the common descent model is so incredibly inferior to the dependency graph model that the Bayes factor cannot be typed out. In other words, the probability of the data set given the dependency graph model, is so much greater than the probability of the data set given the common descent model, that we cannot type the quotient of their division.

Instead, Ewert reports the logarithm of the number. Remember logarithms? Remember how 2 really means 100, 3 means 1,000, and so forth?

Unbelievably, the 10,064 value is the logarithm (base value of 2) of the quotient! In other words, the probability of the data on the dependency graph model is so much greater than that given the common descent model, we need logarithms even to type it out. If you tried to type out the plain number, you would have to type a 1 followed by more than 3,000 zeros!

That’s the ratio of how probable the data are on these two models!

By using a base value of 2 in the logarithm we express the Bayes factor in bits. So the conditional probability for the dependency graph model has a 10,064 advantage of that of common descent.

10,064 bits is far, far from the range in which one might actually consider the lesser model. See, for example, the Bayes factor Wikipedia page, which explains that a Bayes factor of 3.3 bits provides “substantial” evidence for a model, 5.0 bits provides “strong” evidence, and 6.6 bits provides “decisive” evidence.

This is ridiculous. 6.6 bits is considered to provide “decisive” evidence, and when the dependency graph model case is compared to comment descent case, we get 10,064 bits.

But it gets worse.

The problem with all of this is that the Bayes factor of 10,064 bits for the HomoloGene data set is the very best case for common descent. For the other eight data sets, the Bayes factors range from 40,967 to 515,450.

In other words, while 6.6 bits would be considered to provide “decisive” evidence for the dependency graph model, the actual, real, biological data provide Bayes factors of 10,064 on up to 515,450.

We have known for a long time that common descent has failed hard. In Ewert’s new paper, we now have detailed, quantitative results demonstrating this. And Ewert provides a new model, with a far superior fit to the data.

New Paper Admits Failure of Evolution

Pop Quiz: Who Said It?

There are many fundamental problems with evolutionary theory. Origin of life studies have dramatically failed. Incredibly complex biological designs, both morphological and molecular, arose abruptly with far too little time to have evolved. The concept of punctuated equilibrium is descriptive, not explanatory. For example, the Cambrian Explosion is not explained by evolution and, in general, evolutionary mechanisms are inadequate to explain the emergence of new traits, body plans and new physiologies. Even a single gene is beyond the reach of evolutionary mechanisms. In fact, the complexity and sophistication of life cannot originate from non-biological matter under any scenario, over any expanse of space and time, however vast. On the other hand, the arch enemy of evolutionary theory, Lamarckian inheritance, in its variety of forms, is well established by the science.

Another Darwin’s God post?

No, these scientific observations are laid out in a new peer-reviewed, scientific paper.

Origin of Life

Regarding origin of life studies, which try to explain how living cells could somehow have arisen in an ancient, inorganic, Earth, the paper explains that this idea should have long since been rejected, but instead it has fueled “sophisticated conjectures with little or no evidential support.”

the dominant biological paradigm - abiogenesis in a primordial soup. The latter idea was developed at a time when the earliest living cells were considered to be exceedingly simple structures that could subsequently evolve in a Darwinian way. These ideas should of course have been critically examined and rejected after the discovery of the exceedingly complex molecular structures involved in proteins and in DNA. But this did not happen. Modern ideas of abiogenesis in hydrothermal vents or elsewhere on the primitive Earth have developed into sophisticated conjectures with little or no evidential support.

In fact, abiogenesis has “no empirical support.”

independent abiogenesis on the cosmologically diminutive scale of oceans, lakes or hydrothermal vents remains a hypothesis with no empirical support

One problem, of many, is that the early Earth would not have supported such monumental evolution to occur:

The conditions that would most likely to have prevailed near the impact-riddled Earth's surface 4.1–4.23 billion years ago were too hot even for simple organic molecules to survive let alone evolve into living complexity

In fact, the whole idea strains credibility “beyond the limit.”

The requirement now, on the basis of orthodox abiogenic thinking, is that an essentially instantaneous transformation of non-living organic matter to bacterial life occurs, an assumption we consider strains credibility of Earth-bound abiogenesis beyond the limit.

All laboratory experiments have ended in “dismal failure.” The information hurdle is of “superastronomical proportions” and simply could not have been overcome without a miracle.

The transformation of an ensemble of appropriately chosen biological monomers (e.g. amino acids, nucleotides) into a primitive living cell capable of further evolution appears to require overcoming an information hurdle of superastronomical proportions, an event that could not have happened within the time frame of the Earth except, we believe, as a miracle. All laboratory experiments attempting to simulate such an event have so far led to dismal failure.

Diversity of Life

But the origin of life is just the beginning of evolution’s problems. For science now suggests evolution is incapable of creating the diversity of life and all of its designs:

Before the extensive sequencing of DNA became available it would have been reasonable to speculate that random copying errors in a gene sequence could, over time, lead to the emergence of new traits, body plans and new physiologies that could explain the whole of evolution. However the data we have reviewed here challenge this point of view. It suggests that the Cambrian Explosion of multicellular life that occurred 0.54 billion years ago led to a sudden emergence of essentially all the genes that subsequently came to be rearranged into an exceedingly wide range of multi-celled life forms - Tardigrades, the Squid, Octopus, fruit flies, humans – to name but a few.

As one of the authors writes, “the complexity and sophistication of life cannot originate (from non-biological) matter under any scenario, over any expanse of space and time, however vast.” As an example, consider the octopus.

Octopus

First, the octopus is an example of novel, complex features, rapidly appearing and a vast array of genes without an apparent ancestry:

Its large brain and sophisticated nervous system, camera-like eyes, flexible bodies, instantaneous camouflage via the ability to switch colour and shape are just a few of the striking features that appear suddenly on the evolutionary scene. The transformative genes leading from the consensus ancestral Nautilus (e.g., Nautilus pompilius) to the common Cuttlefish (Sepia officinalis) to Squid (Loligo vulgaris) to the common Octopus (Octopus vulgaris) are not easily to be found in any pre-existing life form.

But it gets worse. As Darwin’s God has explained, The Cephalopods demonstrate a highly unique level of adenosine to inosine mRNA editing. It is yet another striking example of lineage-specific design that utterly contradicts macroevolution:

These data demonstrate extensive evolutionary conserved adenosine to inosine (A-to-I) mRNA editing sites in almost every single protein-coding gene in the behaviorally complex coleoid Cephalopods (Octopus in particular), but not in nautilus. This enormous qualitative difference in Cephalopod protein recoding A-to-I mRNA editing compared to nautilus and other invertebrate and vertebrate animals is striking. Thus in transcriptome-wide screens only 1–3% of Drosophila and human protein coding mRNAs harbour an A-to-I recoding site; and there only about 25 human mRNA messages which contain a conserved A-to-I recoding site across mammals. In Drosophila lineages there are about 65 conserved A-sites in protein coding genes and only a few identified in C. elegans which support the hypothesis that A-to-I RNA editing recoding is mostly either neutral, detrimental, or rarely adaptive. Yet in Squid and particularly Octopus it is the norm, with almost every protein coding gene having an evolutionary conserved A-to-I mRNA editing site isoform, resulting in a nonsynonymous amino acid change. This is a virtual qualitative jump in molecular genetic strategy in a supposed smooth and incremental evolutionary lineage - a type of sudden “great leap forward”. Unless all the new genes expressed in the squid/octopus lineages arose from simple mutations of existing genes in either the squid or in other organisms sharing the same habitat, there is surely no way by which this large qualitative transition in A-to-I mRNA editing can be explained by conventional neo-Darwinian processes, even if horizontal gene transfer is allowed. 

Lamarck

In the twentieth century Lamarckian Inheritance was an anathema for evolutionists. Careers were ruined and every evolutionist knew the inheritance of acquired characteristics sat right along the flat earth and geocentrism in the history of ideas. The damning of Lamarck, however, was driven by dogma rather than data, and today the evidence has finally overcome evolutionary theory.

Indeed there is much contemporary discussion, observations and critical analysis consistent with this position led by Corrado Spadafora, Yongsheng Liu, Denis Noble, John Mattick and others, that developments such as Lamarckian Inheritance processes (both direct DNA modifications and indirect, viz. epigenetic, transmissions) in evolutionary biology and adjacent fields now necessitate a complete revision of the standard neo-Darwinian theory of evolution or “New Synthesis " that emerged from the 1930s and 1940s.

Indeed, we now know of a “plethora of adaptive Lamarckian-like inheritance mechanisms.”

There is, of course, nothing new in this paper. We have discussed these, and many, many other refutations of evolutionary theory. Yet the paper is significant because it appears in a peer-reviewed journal. Science is, if anything, conservative. It doesn’t exactly “follow the data,” at least until it becomes OK to do so. There are careers and reputations at stake.

And of course, there is religion.

Religion drives science, and it matters.

Rob Stadler and the NABT

The Scientific Approach to Evolution

It’s no secret that the origins debate is highly polarized. Many people have their minds made up and too often there is no place for a reasoned evaluation of the science. That’s tragic because that is where things become interesting. I once spoke to a roomful of high school science teachers, explaining that they could accurately teach how the science bears on the theory of evolution—both positively and negatively. The response I got was that this would confuse the students who needed to be given a simple, unambiguous message. One teacher was concerned that anything other than an obvious, “evolution is true,” message would be detrimental to the learning. To be sure there can be a tension between detail and clarity in classroom settings. High school students learn introductory history lessons out of necessity. They simply are not ready for research-level topics. Clarity sometimes comes at the cost of less detail. But there is a difference between simplifying a lesson and biasing a lesson. I was again reminded of all this when I heard about how the National Association of Biology Teachers responded to Dr. Robert Stadler’s new book, The Scientific Approach to Evolution.

It would be difficult to find someone more qualified than Stadler to analyze how the scientific evidence bears on the theory of evolution. His academic background is in Biomedical Engineering, with degrees from the top universities in the nation (Case Western Reserve University, MIT, and Harvard). And he has twenty years of experience in the field, with more than 100 patents to his name.

Stadler’s interest in evolution skips over the usual culture wars arguments and focuses on the science. Stadler provides an approach that is sorely needed. While there are plenty of texts and popular books that review the scientific evidence for evolution, they invariably fail to provide any kind of accounting of the strength of the evidence. The field outside my window is flat and so is evidence that the Earth is flat. But of course that evidence is weak.

On the other hand, there is plenty of academic work dealing with methods of rigorous, quantitative, theory evaluation, such as Bayesian approaches. But they invariably fail to engage the real-world evidences for evolution, in any kind of comprehensive way.

For all the talk, there is too often a lack of actual practice of analyzing the evidence. Enter Rob Stadler and his thoroughly accessible approach to laying out how the evidence bears on the theory of evolution. Importantly, Stadler explains not just the evidences, but the strengths and weaknesses of those evidences.

Because Stadler’s approach is accessible, it is an excellent classroom resource. Indeed, regardless of what one believes about a scientific theory such as evolution, the learning is greatly enhanced when one is allowed to explore the evidence, think critically about it, form opinions, and defend them in discourse. Rather than rehearse the carefully selected subset of evidences routinely presented in textbooks, the science should be allowed to speak for itself.

Unfortunately those science teachers I spoke to are not the only ones uncomfortable with allowing science such freedoms. Earlier this year Stadler worked with an agency to place an advertisement for his new book with the National Association of Biology Teachers. The contract was signed, funds were paid, and beginning in May the ad was to appear on the NABT website.

But strangely enough, on May 1 the advertisement failed to appear. It was through the ad agency that Stadler learned that the NABT had no intention of running the ad. The agency informed Stadler that the NABT had “concerns” over the content of the book.

And what exactly was the problem? The Scientific Approach to Evolution allows the evidence to speak for itself. According to Stadler’s book, there could be negative evidences, as well as positive evidences.

And that was not acceptable.

The NABT was concerned that “Dr. Sadler’s attempts to address ‘strengths and weaknesses’ in order to establish a climate of controversy in the scientific community regarding evolution  where there is none.”

Ironically, the NABT was also concerned that Dr. Sadler underappreciates that “theories are open to revision and refinement as new data becomes available.” That’s ironic because Sadler’s book does precisely that. Sadler appeals to new data to refine and revise our understanding of evolution.

Indeed, if Sadler’s theory-neutral appeal to the scientific evidence makes him guilty of attempting to “establish a climate of controversy” where there is none, then how can theories such as evolution ever be revised?

The fact is, the NABT’s ground rules are a form of theory protectionism. They won’t even run an advertisement for a book that dares question evolution on scientific grounds.

And rather than address the evidence that Sadler brings forth, the NABT contrives nefarious motives. According to the NABT, Sadler is guilty of dishonest pedagogy, and seeking “to establish a climate of controversy.” In the name of scientific integrity the theory must be protected. Darwin’s supporter TH Huxley called for a very different approach. We must, Darwin’s bulldog explained:

Sit down before fact as a little child, be prepared to give up every preconceived notion, follow humbly wherever and to whatever abysses nature leads, or you shall learn nothing. I have only begun to learn content and peace of mind since I have resolved at all risks to do this.

Huxley insisted that we cast aside our preconceived notions, and follow the evidence to wherever it leads. Otherwise “you shall learn nothing.” Unfortunately Huxley would not recognize today’s classroom. The NABT would do well to heed the warning of Darwin’s most vocal advocate.

The National Association of Biology Teachers Versus the Ribosome

A Fascinating Dissonance

Theodosius Dobzhansky famously wrote in 1973 that “Nothing in Biology Makes Sense Except in the Light of Evolution.” That phrase has since become a staple amongst evolutionists. It appears throughout the literature, from popular works to journal papers, and it motivates the view that evolution is fundamental. Students must learn biology through the lens of evolution. Researchers must formulate experiments from a Darwinian perspective. Medical students must understand the human body as the result of evolution, and so forth. As the National Association of Biology Teachers explains:

The frequently-quoted declaration of Theodosius Dobzhansky that “Nothing in biology makes sense except in the light of evolution” accurately reflects the central, unifying role of evolution in the science of biology. … Just as nothing in biology makes sense except in the light of evolution, nothing in biology education makes sense without reference to and thorough coverage of the principle and mechanisms provided by the science of evolution. Therefore, teaching biology in an effective, detailed, and scientifically and pedagogically honest manner requires that evolution be a major theme throughout the life science curriculum both in classroom discussions and in laboratory investigations. … Biology educators at all levels must work to encourage the development of and support for standards, curricula, textbooks, and other instructional frameworks that prominently include evolution and its mechanisms

Clearly the NABT thinks highly of Dobzhansky’s phrase and it draws some fairly important conclusions from it. But there is one slight problem: Dobzhansky’s phrase is unequivocally false.

Is it really true that nothing in biology makes sense except with evolution? No it is not as I have discussed many times (here, here, here, here, here, here, here, here, and here). Dobzhansky’s phrase is equivalent to: “Everything in biology only makes sense in light of evolution,” or “If-and-only-if evolution is true, then will we find what we find in biology.” In its logical form, Dobzhansky’s phrase is clearly not even scientific. Indeed, the phrase comes from the title of a paper which appeared in the American Biology Teacher, the official journal of the National Association of Biology Teachers, and in that paper Dobzhansky gave a litany of theological arguments that mandated evolution.

But it gets worse. Not only is this famous phrase a theological claim, it also fails the test of comparative anatomy. For example, consider the various types of echolocation found in different species of bats. As I have discussed (here, here, and here), the echolocation designs do not fit the expected evolutionary pattern. In other words, here we have something in biology that does not make sense with evolution. Evolution does not help to explain what we observe, instead with evolution we must resort to ad hoc stories. As one paper concluded:

the animal’s habitat is often more important in shaping its [echolocation] call design than is its evolutionary history

If you want to understand a bat’s echolocation design, look to its habitat, not its supposed evolutionary history. The scientific evidence makes no sense on the theory of evolution.

Or again, consider how glycan molecules compare across the different species. Again, it isn’t according to the evolutionary model (see here). As one paper explained, glycans show “remarkably discontinuous distribution across evolutionary lineages,” for they “occur in a discontinuous and puzzling distribution across evolutionary lineages.” This dizzying array of glycans can be (i) specific to a particular lineage, (i) similar in very distant lineages, (iii) and conspicuously absent from very restricted taxa only. The patterns contradict what evolution expected. As another paper admitted:

There is also no clear explanation for the extreme complexity and diversity of glycans that can be found on a given glycoconjugate or cell type. Based on the limited information available about the scope and distribution of this diversity among taxonomic groups, it is difficult to see clear trends or patterns consistent with different evolutionary lineages.

In other words, the glycans make no sense on evolution.

Echolocation and the glycans are but two examples. There are many, many more examples where they came from. The biological world is full of patterns of comparative anatomy across different species which make no sense on evolution.

But it gets worse.

It is not just comparative anatomy where the evidence fails to make sense on evolution. In design after design, what we observe in biology does not reflect contingency, as Darwin and later evolutionists predicted, but functional need. In fact, the designs we find are highly efficient and optimal in various ways. To cite just one example of a great many, consider the work of William Bialek.

Bialek discusses compound eyes of insects such as the fly. These compound eyes have a large number of small lenses packed into an array. A large number of small lenses gives high resolution, just as does a digital camera with a large number of pixels.

But when the lens becomes too small its optics become distorted due to diffraction. So in determining the best lens size there is a tradeoff between resolution and diffraction. In the optimum solution the lens size is roughly proportional to the square root of the radius of the head. And indeed, Bialek shows an old paper surveying the compound eye designs in more than two dozen different insects. That paper shows that for the different size insects, the lens size is proportional, as predicted, to the square root of the head size.

This is one of Bialek’s half a dozen or so examples showing the optimization of biological designs and, as Bialek assures us that there are many, many more. Here is how one science writer explained it:

Yet for all these apparent flaws, the basic building blocks of human eyesight turn out to be practically perfect. Scientists have learned that the fundamental units of vision, the photoreceptor cells that carpet the retinal tissue of the eye and respond to light, are not just good or great or fabulous at their job. They are not merely exceptionally impressive by the standards of biology, with whatever slop and wiggle room the animate category implies. Photoreceptors operate at the outermost boundary allowed by the laws of physics, which means they are as good as they can be, period. Each one is designed to detect and respond to single photons of light — the smallest possible packages in which light comes wrapped.

And where did those “apparent flaws” come from? Evolutionists of course. From an evolutionary perspective, vision systems were full of “flaws.” But in fact those systems were optimized—we just had to stop looking at biology in terms of evolution.

This brings us to the protein synthesis machine—the ribosome. A paper from last month out of Johan Paulsson’s laboratory elaborates on several of the ribosome’s highly efficient, or optimal, design features. Ribosomes are comprised of both protein and RNA molecules, and their proteins make up a sizable fraction of the total protein content of many cells. Cells contain many ribosomes, and naturally in order for the cell to duplicate, the ribosomes must be duplicated. This means a lot of protein synthesis must take place, in order to create all the proteins in all the ribosomes.

One way to help alleviate this production problem would be to have yet more ribosomes in the cell. But that would, in turn, create an even greater protein synthesis burden, since even more proteins would be needed for those additional ribosomes. One way to solve this conundrum is to use RNAs in ribosomes rather than proteins, where possible.

It is a fascinating problem, and the paper concludes that we can understand the solution not as the result of evolutionary contingencies, but as a solution to a functional need:

Rather than being relics of an evolutionary past, the unusual features of ribosomes may reflect an additional layer of functional optimization that acts on the collective properties of their parts.

These are but a few examples and there are many more showing that evolution is by no means required to understand biology. Indeed, evolution is usually redundant—a “multiplied entity” in the language of Ockam’s Razor.

There is no question that Dobzhansky famous phrase has failed. It simply is not true that “Nothing in Biology Makes Sense Except in the Light of Evolution.” Indeed, it would be difficult to imagine a perspective more at odds with the science of biology. But while a few rare voices, such as Massimo Pigliucci, admit that the phrase is “patently wrong,” evolutionists for the most part continue to rehearse the famous phrase in robotic fashion, revealing an underlying agenda that has strayed badly from the science.

Evolutionists are so heavily invested in Dobzhansky’s phrase they will never admit it has failed. Even Pigliucci soft-pedaled the problem, explaining that “Dobzhansky was writing for an audience of science high school teachers,” as though it is OK to misrepresent science to high school teachers. Also, Pigliucci’s admission was limited to the fact that spectacular progress has occurred in the life sciences while ignoring evolutionary theory. True enough, and that certainly demolishes Dobzhansky’s phrase, but it is only the tip of the iceberg. It is a safe criticism that avoids the more damning problems.

There simply is too much at stake here. It isn’t like admitting that a particular prediction went wrong. Dobzhansky’s phrase was not merely a prediction, it was meta-prediction—the rallying cry of the entire world view—and walking it back in any genuine way would be to reveal the man behind the curtain. Suddenly all those epistemological claims, such as that evolution is as much a fact as is gravity, heliocentrism and the round shape of the earth, would be left hanging, open to scrutiny and with a long, long way to fall.

The National Association of Biology Teachers’ holding up of Dobzhansky’s phrase reveals the underlying, nonscientific dogma at work. We are seeing a fascinating dissonance and hypocrisy, for the phrase is unequivocally false and yet it cannot be abandoned.

A demonstrably false claim is feverishly held up as true. Religion drives science, and it matters.

New Book: New Proteins Evolve Very Easily

No Free Lunch

We have seen that a new evolution book co-authored by evolutionist Dennis Venema and Scot McKnight is influenced by the mythical Warfare Thesis (here and here) and makes erroneous arguments that the fossils, echolocation, and pseudogenes support evolution (here,  here and here). We now move on to another topic: protein evolution. Proteins are composed of a linear string of amino acids, often hundreds in length, and perform all sorts of important tasks in the cell. They could not have evolved by any stretch of the imagination, and so pose a rather difficult problem for evolutionists. Our new book on evolution attempts to resolve this problem with a claim that has long since been understood to be false. In fact, the claim, properly understood, provides yet more scientific evidence against evolution.

The problem of protein evolution

For evolution to work biology must be chocked full of structures that can arise via long, gradual evolutionary pathways. Mutations must be able to slowly accumulate, gradually improving the structure. In other words, the “fitness landscape” must be smooth and gradual, not rugged or precipitous.

That evolutionary expectation has been found to be false many times, and proteins are no exception. It is now clear that for a given protein, only a few changes to its amino acid sequence can be sustained before the protein function is all but eliminated. Here is how one paper explained it:

The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability—the ability of proteins to acquire changes in sequence and function.

In other words, protein function precipitously drops off with only a tiny fraction of its amino acids altered. It is not a gradual fitness landscape. Another paper described the protein fitness landscape as rugged.

Therefore it is not surprising that various studies on evolving proteins have failed to show a viable mechanism. One study concluded that 10^63 attempts would be required to evolve a relatively short protein. And a similar result (10^65 attempts required) was obtained by comparing protein sequences. Another study found that 10^64 to 10^77 attempts are required, and another study concluded that 10^70 attempts would be required.

So something like 10^70 attempts are required yet evolutionists estimate that only 10^43 attempts are possible. In other words, there is a shortfall of 27 orders of magnitude.

But it gets worse. The estimate that 10^43 attempts are possible is utterly unrealistic. For it assumes billions of years are available, and that for that entire time the Earth is covered with bacteria, constantly churning out mutations and new protein experiments. Aside from the fact that these assumptions are entirely unrealistic, the estimate also suffers from the rather inconvenient fact that those bacteria are, err, full of proteins. In other word, for evolution to evolve proteins, they must already exist in the first place.

This is absurd. And yet, even with these overly optimistic assumptions, evolution falls short by 27 orders of magnitude.

The numbers don’t add up. Proteins reveal scientific problems for evolution. What is interesting is how evolutionists react to these problems.

The “solution” to protein evolution

A common solution cited by evolutionists for the problem of protein evolution is the case of nylonases—enzymes that rapidly arose in bacteria, in the last century, and are able to breakdown byproducts of the nylon manufacturing process. The idea here is that these byproducts of the nylon manufacturing process were present in the bacteria’s environment for the first time. The bacteria had never been exposed to such chemicals, and yet in an evolutionary blink of an eye, were able to produce proteins to metabolize the new chemicals. Does this not demonstrate that the chance origin of a protein-coding genes is not a problem? Proteins could have evolved with no problem, after all, we just witnessed it occur with the origin of nylonases. As the new book explains, protein evolution “appears to be trivial for evolution to achieve.” [86]

Unfortunately this icon of evolution is an enormous misrepresentation of the science.

The science

The evolutionary claim that the nylonases demonstrate how easy protein evolution is non scientific for several reasons. Indicators of this include that fact that the nylonases evolved so rapidly—in an entirely unrealistic time frame under evolution, and that they arose in bacteria with thousands of preexisting proteins. Again, this evolutionary claim of how proteins evolve is circular, it requires the preexistence of proteins.

None of this is feasible given the problems of protein evolution discussed above. The scientific inference would be that the bacteria developed the nylonases because those chemicals they metabolize were present in the environment. In other words, directed adaptation.

Indeed, this is precisely what researchers in the field have concluded. They hypothesize that the new metabolism capability is a stress response, an adaptation to a challenging environment. In other words, the environment influenced the adaptation. This is not a case of evolutionary change. The nylonase enzymes did not arise from a random search over sequence space until the right enzymes were luckily found and could be selected for. That would have required eons of time, and is far beyond evolution’s capability, as we have seen. Instead, cellular structures rapidly formed new enzymes, due to the environmental change.

Indeed, such adaptation to nylon manufacture byproducts has been repeated in laboratory experiments. In a matter of months bacteria acquire the ability to digest the unforeseen chemical. Researchers speculate that mechanisms responding to environmental stress are involved in inducing adaptive mutations.

This does not demonstrate protein evolution. In fact it refutes evolution. Evolution does not have the resources to have created directed adaptation mechanisms. And even if it did, such mechanisms would not have been selected for because they provide no immediate fitness improvement.

This is not evidence that protein-coding genes can evolve by chance. A new gene, arising within a modern cell responding to an environmental challenge, is not analogous to chance origin. Unfortunately evolutionists have a long history of inappropriately claiming otherwise (for example, see here and here).

We have seen that this new evolution book makes erroneous arguments that the fossils, echolocation, and pseudogenes support evolution. We now see another erroneous argument for protein evolution.

All these arguments and evidences are typical. They are icons of evolution, and it is astonishing how durable they are in the evolution literature given their complete failure.

If evolution was indicated by the science I would be the first to sign up. But in fact it is an age-old religious idea that makes no sense on the science. And likewise this new book is an utter disaster. The confection immediately crumbles under even a little probing.

Religion drives science, and it matters.

Evolutionist: Evolution Is Happening Faster Than We Thought

Not

The fact that we can travel at speeds of hundreds and even thousands of miles per hour does not mean we can go faster than light. We can fly to the Moon in a matter of days, but the propulsion technology that allows us to do that is not scalable to travelling faster than 186,000 miles per second. A fundamentally different technology is required. The creators of Star Trek understood that, and so they created the concept of warp drive, a faster-than-light propulsion technology, fundamentally different from today’s technology. One would have to be very ignorant to confuse the two, but this is precisely what evolutionists do when they cast biological adaptation as confirmatory evidence of evolution. Adaptation and evolution are two very different things.

Biological adaptation relies on the preexistence of populations, organisms, genetics, DNA, genes, alleles, proteins, massive molecular machines, inheritance, cellular and molecular mechanisms such as horizontal gene transfer and epigenetics, directed mutations, and so forth.

Evolution, on the other hand, is a theory that attempts to explain the origin of all those things.

Observations of the former are not evidence of the latter. That is backwards. It also would also introduce enormous serendipity. For it would mean that evolution created the very structures and mechanisms required for, drumroll, evolution.

Evolution, in other words, created itself.

And even if we were to go along with this ridiculous idea, the resulting biological adaptation is not capable of generating evolutionary change. Adaptation does small things, evolution requires big things.

Even evolutionists, in their honest moments, have understood this. Macroevolution is more than repeated rounds of microevolution. As one evolutionist admitted, “the rate of random DNA sequence mutation turns out to be too slow to explain many of the changes observed.” His point, which is not new and has been known for a long time, is not that adaptation cannot occur, but that the idea of mutations (which can fuel adaptation) adding up to result in novel, large-scale evolutionary change doesn’t work.

Adaptation and evolution are fundamentally different “technologies.”

You can’t travel faster than the speed of light by combining liquid hydrogen and liquid oxygen, and you can’t create novel, complex, biological structures via adaptation mechanisms.

This is why evolutionary biologist Menno Schilthuizen’s article from last year in the Sunday Review is of concern. The article is entitled: “Evolution Is Happening Faster Than We Thought,” and it is all about various adaptations observed in city-dwelling species. Unfortunately, Schilthuizen presents those examples of adaptation as examples of evolution, and proof that, amazingly enough, evolution happens orders of magnitude faster than we once thought:

For a long time, biologists thought evolution was a very, very slow process, too tardy to be observed in a human lifetime. But recently, we have come to understand that evolution can happen very quickly

Evolution’s deep time requirement was particularly evident when William Thomson (later Lord Kelvin), only a few years after Darwin had published his book on evolution, argued that the earth could be no older than 100 million years. Thomson later revised that figure downward to as little as 20-40 million years.

This short time window was an enormous problem for evolution. As Darwin wrote, “Thomson’s views of the recent age of the world, have been for some time one of my sorest troubles.” As Darwin’s friend Thomas Huxley explained, “Biology takes its time from Geology.”

Lord Kelvin’s estimate was eventually dropped, but this example illustrates how important deep time was, both to nineteenth and twentieth century evolutionists. And therefore, the rapid evolution that is now commonly celebrated by evolutionists such as Schilthuizen represents an enormous falsification of a major, fundamental, prediction of evolutionary theory.

It also represents terribly flawed thinking. Adaptation is not evolution.

Desert Mice Fur Changes Color to Match the Terrain

An Example of Evolution in Every Detail?

About fifteen years ago researchers discovered genetic differences that probably explain the different fur coloring in desert mice populations in New Mexico and Arizona (see papers here and here). Mice populations living on light colored terrain tend to have light colored fur, and those on dark colored terrain tend to have dark colored fur. Blending in with the terrain helps to camouflage the mice, protecting them from predators. And that is, apparently, exactly what the mice did about a thousand years ago when desert lava flows produced the darkened terrain. But that is where the science is overtaken by the dogma. Evolutionists have misappropriated this research work, casting it as a textbook example of evolution, and creating a highly produced video (see above) used to indoctrinate students.

The first problem in casting the dark colored mice as an example of evolution is that their genetic differences are not known to be the result of random mutations. For evolutionists there simply is no question that the genetic differences that are thought to cause the dark fur color arose from random mutations.

Now that may be correct. But it may not be. We simply do not know.

This is not merely a technical objection—in spite of evolutionary theory which called for random mutations to be the source of change, in recent decades directed mutations have been found to be at work in an ever increasing number of cases. For many years evolutionists have ignored and even resisted these findings. Too often I have debated evolutionists who, when I point to this evidence, simply deny it.

So while the genetic differences in those dark mice may well be the result of random mutations, evolutionists do not even give this a second thought. They simply assume from the start, and inform their audience in no uncertain terms, that random mutations are the cause.

This is an example of what philosophers refer to as a “theory-laden observation.” Science can get into trouble when the measurements and observations themselves, rather than being theory-neutral and independent of the theories which explain them, are in fact intertwined with those theories.

This can become circular very quickly, and this desert mouse case is a good example of that. Evolutionists assume the genetic differences arose from random mutations, and then claim the evidence as a powerful confirmation of evolution.

The second problem in casting the dark colored mice as an example of evolution is that the dark coloration may be the result of multiple genetic changes. In one case, four mutations are identified, all of which perhaps are required to bring about the coloration change.

It very well could be that only a lone, single mutation is required. But that is not known.

And if multiple genetic changes are required, then this quickly transitions from an example of what random mutations can do to an example of what random mutations cannot do. If four mutations are required, then we’ve just found yet another hard failure of evolution. But again, the evolutionists give no hint of this interesting question. If everyone had their “burning curiosity,” (as Clarence Darrow put it) then science would have long since come to an end.

The third problem in casting the dark colored mice as an example of evolution is that the coloration is too precise. The dark colored fur appears on the top of the mice, but not their underbelly. This makes sense since the topside is mainly what is exposed to predators. But in the evolution narrative, there is no fitness advantage to such precision. Darkening the entire mouse would, apparently, work just as well.

Small scale adaptation

Everything we’ve talked about so far is an unknown. Evolutionists are proclaiming a slam dunk, case closed, example when in fact there are many unknowns. Some of them could demolish the evolution narrative altogether.

But there is one big known we haven’t yet mentioned. It is that none of this amounts to evolution in the first place. It would be a deceptive equivocation to label fur coloration change via a few mutations as “evolution” when, in fact, this is nothing more than small scale adaptation.

In their “honest moments,” as Stephen J. Gould once put it, even evolutionists admit that random mutation isn’t enough, and that adaptation mechanisms are not enough, to explain the kind of large scale change evolution requires.

Mice changing fur color does not demonstrate how metabolism, the central nervous system, bones, red blood cells, or any other biological wonder could have arisen by evolution’s random mutations coupled with natural selection.

This is an old myth evolutionists have exploited ever since Darwin. Demonstrate biological change, any biological change no matter how trivial, and claim victory. Evolutionist Steve Jones once claimed that the changes observed in viruses contain Darwin’s “entire argument.” That is a gross equivocation and misrepresentation of the science, designed to mislead audiences.

It is a pathetic canard which evolutionists continue to rely on. In the above video, Sean Carroll states that thanks to these mice, “science has an example of evolution, crystal clear, in every detail.” [6:42-48]

It would be difficult to imagine a more absurd misrepresentation. Mice changing color is not a crystal clear “example of evolution … in every detail.” Not even close. Carroll should be ashamed of himself.

Religion drives science, and it matters.

Field Studies Pay Off: “I was flabbergasted” (By The Lungless Frog)

Adaptive Development

Why do biologists travel the world over? They go to the bottom of the ocean and to the tops of mountains, to deserts and jungles. The reason is they are rewarded for their efforts. The one rule in biology is there are no rules. Everything is different, and everywhere is different. When John Ray toured Europe for three years, from 1663 to 1666, studying the flora and fauna, he found the organisms and their interactions were different everywhere he went. Biology is full of diversity, and it consistently makes no sense on evolution.

Consider Barbourula kalimantanensis, the frog that has no lungs. These small, elusive, lungless amphibians live in cold, fast rivers, deep in the rainforests of Borneo. Ten years ago David Bickford and his patient international team of biologists worked hard and long to find some specimens for their study.

Bickford and his colleagues had an idea of what they were looking for, but they had no idea, and no reason to suspect, that the two inch frog would be lungless. As Bickford recounted:

At first I did not believe that the frogs had no lungs, but then, we just kept on seeing the evidence pile up. I was flabbergasted.

It was all a lesson, once again, in biology’s only rule, and that exploration seems to always payoff:

The thing that struck me most then and now is that there are still major firsts — for example, first lungless frog! — to be found out in the field. All you have to do is go a little ways beyond what people have done before, and — voila! … There are so many difficulties in field work, and yet it remains my biggest joy. Having the undeniable privilege of going out to these remote sites, seeing some of the last and greatest treasures that exist in the wild, and then getting to study them — well, every day I feel lucky.

It was also a lesson once again that biology makes no sense on evolution. It turns out that some species can forego their lungs altogether in their embryonic development, given the right environmental conditions. This is another example of rapid, directed adaptation, in response to the environment.

If such a sophisticated development plasticity could have evolved—“and oh! what a big if!” *—it would provide no immediate fitness improvement, and so would not be selected for. It would be subject to harmful mutations, and be long forgotten in the annals of evolutionary history.

This is intelligent adaptation which makes no sense on evolution.

Religion drives science, and it matters.

The Big Day Has Finally Arrived

What Will The Decision Be?

After years of battling and debating, we have finally reached the big day with its big decisions. Tensions are running high as the old-guard status quo battles the radical new ideas—it is the “New Trends in Evolutionary Biology” meeting at the Royal Society where evolutionists are finally reckoning with the science which makes no sense on the theory. The problem is that species adapt not according to the random mutations coupled with natural selection, but according to mechanisms that respond directly to the environment. The Big Day Has Finally Arrived.

New trends in evolutionary biology

The Royal Society, November 7-9

Don’t miss the upcoming “New trends in evolutionary biology” Scientific meeting at The Royal Society, November 7-9. The organizers propose that evolutionary theory needs a bit of modification, collectively referred to as the EES (extended evolutionary synthesis). The “evolutionary synthesis” refers to the Modern Synthesis (or neoDarwinism)—the early twentieth century fusion of Darwin’s theory of evolution with classic genetics. A key question to be addressed at the meeting, either explicitly or implicitly, is: What is the extent of the extension?

Old school neoDarwinists hold that the Modern Synthesis has been practically undergoing constant modification ever since William Bateson coined the term “genetics” in 1905. The EES, they say, is merely another modification. We’ve seen all this before, they say, and there is no need for a major shakeup.

But for at least some of the meeting’s organizers the EES is more than just another tweak. The problem, they point out, is that the Modern Synthesis was flat out wrong about inheritance, and that flawed concept of inheritance was not an auxiliary sub hypothesis in the outer protective belt, to use Lakatos’ terms, but rather was part of the core theoretic. As Denis Noble put it:

I would say that it needs replacing. Yes. … The reasons I think we’re talking about replacement rather than extension are several. The first is that the exclusion of any form of acquired characteristics being inherited was a central feature of the modern synthesis. In other words, to exclude any form of inheritance that was non-Mendelian, that was Lamarckian-like, was an essential part of the modern synthesis. What we are now discovering is that there are mechanisms by which some acquired characteristics can be inherited, and inherited robustly. So it’s a bit odd to describe adding something like that to the synthesis ( i.e., extending the synthesis). A more honest statement is that the synthesis needs to be replaced. … By “replacement” I don’t mean to say that the mechanism of random change followed by selection does not exist as a possible mechanism. But it becomes one mechanism amongst many others, and those mechanisms must interact. So my argument for saying this is a matter of replacement rather than extension is simply that it was a direct intention of those who formulated the modern synthesis to exclude the inheritance of acquired characteristics. That would be my first and perhaps the main reason for saying we’re talking about replacement rather than extension.

This question of whether evolutionary theory needs to be replaced, or extended, or emended, or merely modified is significant for evolutionists. For the old school, tradition and legacy are potentially at risk. For the new school, they can be the founders of a major new shift in evolutionary thought.

Nonetheless, do not expect too much clarity to emerge from the meeting. Few people if any will change their mind. What will be important are the minor nuances and ever so subtle signs of momentum in one direction or another.

And if that level of progress seems slow, consider that this is only one particular problem with evolutionary theory among dozens. The November meeting in London is closer to rearranging the deck chairs on the Titanic than any serious reckoning with the science.

Religion drives science, so change is slow.

BioLogos and Vitellogenin Genes

This Problem Does Not Easily Go Away

Recently I have been responding to several articles by evolutionist Dennis Venema. Venema has made various arguments about how genetic evidences strongly support evolution and I have provided rebuttals to those claims. For instance, I explained here that while Venema discusses evidences that are consistent with evolutionary expectations, he does not list or mention the substantial body of scientific findings that are inconsistent with evolution. This is a problem with the evolution literature: the scientific evidence is too often selectively presented. In fact, I have often seen evolutionists claim that there are no contrary evidences, and that the science fully backs evolution. This sort of confirmation bias presents a roadblock to meaningful discourse on the topic of origins.

Next Venema focused his claim on the specific case of human evolution, and the similarity between the human and chimpanzee genomes. Again, Venema made high claims about the evidence. He concluded: “These observations strongly support the hypothesis that our species arose through an evolutionary process.”

But, in fact, as I explained here, there are several significant problems with this claim. For example, the chimpanzee and human genomes have differing patterns that do not fit evolutionary expectations. There is also a big difference between viruses in the genomes of humans and the other primates. Again, these differences do not fit the expected evolutionary pattern. Furthermore, the chimp-human genome beneficial differences are few and appeals to alternate splicing differences (another big difference between the genomes of humans and the other primates) to evolve humans lead to astronomically improbable pathways.

As always, I explained that the point is not that evolutionary explanations are not possible. Speculative explanations are always possible. Perhaps evolution did this, perhaps it did that. But that does not change the fact that the primate genomes do not “strongly support the hypothesis that our species arose through an evolutionary process,” as Venema and the evolutionists claim.

Next Venema focused even more narrowly on a particular genetic detail: human chromosome two, which he presented as a powerful example of an evolutionary confirmation. And yet as I explained here, not only did Venema not mention several scientific problems with his claim but the claim, even if true, would not demonstrate evolution as evolutionists claim. There is no evolutionary relationship revealed. Even if evolution were true, these data would give us no evidence for it. What was disturbing about this example was Venema’s recounting of a deceptive lecturing strategy he uses in presenting this topic in his class.

Next Venema presented pseudogenes which Venema argued are powerful and compelling evidences for common descent. It is, explained Venema, “one of the strongest pieces of evidence in favor of common ancestry between humans and chimpanzees (and other organisms).” And again, I explained, here and here, that there are several, fundamental, problems with this evolutionary claim.

In this case, however, Venema discussed his underlying religious belief that this evidence is a problem for creationism type theories. Venema was highlighting one of the important beliefs at the foundation of evolutionary thought. This belief, if true, does indeed require evolution to be true. But of course it is not falsifiable.

Vitellogenin genes

Now we move on to Venema’s next topic, the vitellogenins. Vitellogenin genes are found in a wide range of species and, like most genes, perform multiple functions including helping to provide the nutrients in egg yolks. Also like most genes, the pattern they form amongst the species does not always correspond very well to the expected evolutionary pattern. Of course there are always explanations, and evolutionists draw upon a variety of mechanisms, including lineage-specific events, to explain the vitellogenin genes.

For example, this paper focuses on mosquito vitellogenin genes. It concludes that the genes arose by a series of duplication events, and that the pattern of duplication was different in each mosquito genus. The paper also uses purifying selection, gene conversion, unequal crossover, and concerted evolution to explain the observed pattern of the mosquito vitellogenin genes, and concludes that these mechanisms must have also worked, independently, in other invertebrate species, and vertebrate organisms as well.

Similarly, this paper examines the evolution of vertebrate vitellogenins and also draws upon a variety of events and lineage-specific mechanisms. As I have discussed many times, while the basic idea of evolution is that the species share common designs as a consequence of common ancestry, in fact biology is loaded with unique, one-off designs for which evolutionists need to appeal to “lineage-specific” evolution. Consequently evolution can explain a wide variety of observations and patterns, and this applies equally well to the vitellogenins.

Clearly evolutionary theory is fine with a range of patterns when it comes to the vitellogenins. Of course this is true for molecular, and morphological, designs in general, as we have seen many times. Designs can fall into an evolutionary common descent pattern, or not.

The advantage of this flexibility is that evolutionary theory can explain a wide range of observables. The disadvantages, however, are many. The theory becomes less parsimonious. It becomes more resistant to falsification. And it loses its evidential arguments. If a theory can explain A, and B, and C, … and so forth, then the finding of A is hardly compelling evidence for the theory.

Yet this is what Venema argues. The vitellogenin genes in chickens share a weak similarity with corresponding genetic segments in humans. Evolutionists view the human segments as pseudogenes—broken versions of vitellogenin genes inherited from their egg-laying ancestors. Given this vitellogenin similarity between humans and chickens, for example, evolutionists such as Venema incredibly conclude that, therefore, humans and chickens evolved by random mutations from a common ancestor. Not only does that not follow, but it takes Venema to the unlikely solution of random mutations creating humans and chickens, and of course all the other species.

Venema also argues that the similarity of the vitellogenin genes between humans and chickens extends to, and is all the more confirmed by, their positioning within their respective genomes. But this argument from synteny is no different from what we saw above. When there is a loss of synteny evolution is not harmed, and the theory has another set of explanatory mechanisms available for just about any outcome. If the vitellogenin genes had been in a different order, evolution could have explained it just fine.

Affirming the consequent

In spite of these problems with his argument, Venema is enthusiastic about this evidence. In fact his enthusiasm leads to the fallacy of affirming the consequent, as he equates shared synteny (genes with similar positioning in the genomes of different species) with common descent:

This evidence increases our confidence that we are indeed looking at regions with shared synteny: in other words, a region in two present-day species that was once a region in the genome of their common ancestral population.

That is a fallacy. Ignoring the problems discussed above for the moment, even if evolution did make a hard prediction of shared synteny, and even if it was universally observed, that would not prove evolution. In that case, you would have a confirmed prediction. That is good, but it is not equivalent to a finding of evolution. Venema violates this scientific fundamental when he defines shared synteny as “a region in two present-day species that was once a region in the genome of their common ancestral population.” Unfortunately, affirming the consequent is not uncommon in the evolution literature.

[Ed: The opossum section has been retracted. The evolutionary explanation is more reasonable than was implied and this topic deserves its own post]

BioLogos, Broken Genes, and Urate Oxidase

The Bigger They Come, The Harder They Fall

Arguments for evolution, the theory that the biological world arose strictly by chance and natural law, are at a high level. The details of how microbes, fish, amphibians, reptiles, birds and the rest actually were created by random mutations are hard to come by. But, evolutionists explain, the species look like they evolved. Don’t the comparisons of their anatomy, geographical locations, and so forth, make evolution the obvious explanation for their origin? One of the strongest such evidences, according to evolutionists such as Dennis Venema, are the so-called shared-errors. Meaningless or, better yet, harmful mutations found in allied species seem to be obvious signs of a common ancestor. For we would never expect such harmful mutations to have arisen independently. They must derive from a common ancestor. This argument has many problems and seems to be another example of how the stronger that an argument is for evolution, the more deeply it is flawed.

One of the problems with this argument is that it contains two suspicious, unspoken, assumptions.

First, the argument assumes that these mutations are meaningless or harmful. That assumption may well be true but, as any historian of evolutionary thought knows, it is a dangerous. The history of evolutionary thought is full of claims of bad, inefficient, useless designs which, upon further research were found to be, in fact, quite useful.

Second, the argument assumes that these mutations are random. In other words, it assumes there cannot be any common mechanisms, properly operating or otherwise, which could tend toward certain designs and mutations.

In fact convergence is ubiquitous and rampant in biology. Repeated designs appear in species so distant that, according to evolutionary theory, their common ancestor could not have had that design. So even evolutionists must agree that common designs must have arisen independently. And this must have occurred many times over, at both the morphological and molecular levels.

In other instances, such “convergence” must have occurred even in allied species. In fact this is true even for the so-called harmful mutations. For instance, evolutionists believe the urate oxidase enzyme, which catalyzes the oxidation of uric acid, was inactivated in humans and the great apes by harmful random mutations. But the different versions of the gene, in the different species, do not easily align with the expected evolutionary pattern. In fact, even evolutionists have to agree that several of the various inferred mutations, in these similar species, could not have arisen from a common ancestor. Instead, they must have arisen independently:

One exceptional change is a duplicated segment of GGGATGCC in intron 4 which is shared by the gorilla and the orangutan. However, because this change is phylogenetically incompatible with any of the three possible sister-relationships among the closely related trio of the human, the chimpanzee, and the gorilla, it might result from two independent duplications. Alternatively, though less likely, a single duplication occurred in the ancestral species of the great apes and had been polymorphic for a sufficiently long time to permit fixation of the duplicated form in the orangutan and the gorilla on one hand and loss in the human and the chimpanzee on the other hand.

The nonsense mutation (TGA) at codon 107 is, however, more complicated than others. It occurs in the gorilla, the orangutan, and the gibbon, and therefore requires multiple origins of this nonsense mutation.

In contrast, the exon 3 mutation is not shared by H. syndactylus but by the gorilla and the orangutan. The origin of this mutation is therefore multiple and relatively recent in the gibbon lineage.

In other words, when common mutations found in different species cannot easily be explained by common descent, evolutionists do not hesitate to explain them as a consequent of multiple, independent events. This means that, even according evolutionists, similar mutations in allied species do not imply or require common descent. This contradicts the shared-error argument that is supposed to be one of the most powerful evidences for evolution. Unfortunately evolutionists do not include this information in their presentations of the shared-error argument.

The stronger that an argument is for evolution, the more deeply it is flawed.

h/t: DC

ASCB Addresses Problem of False Science

The Most Important Recommendation of All

The American Society for Cell Biology (ASCB) task force on reproducibility in life science research has issued an undated white paper on scientific rigor. The problem is, as we discussed here and here, life science research has been found to lack reproducibility. John Ioannidis is a bit more blunt as he explains that “most published research findings are false,” and that “claimed research findings may often be simply accurate measures of the prevailing bias.” The ASCB white paper is no doubt a step in the right direction. It offers 13 recommendations to encourage more rigor in training, publishing, and standards. But the most important recommendation of all continues to be ignored.

Daniel Sarewitz has noted not only the problem of bias in scientific research but also the causes. Note his final thought in this quote:

All involved benefit from positive results, and from the appearance of progress. Scientists are rewarded both intellectually and professionally, science administrators are empowered and the public desire for a better world is answered. The lack of incentives to report negative results, replicate experiments or recognize inconsistencies, ambiguities and uncertainties is widely appreciated — but the necessary cultural change is incredibly difficult to achieve.

And so it is that science’s much touted self-correcting, feedback loop which ensures science converges on the truth (after all, that’s what Mr. Wells told us in seventh grade science class) is sometimes a little slow to act.

And if the ASCB is still needing to remind scientists to clean their beakers and use checklists, imagine the difficulty in achieving more fundamental change?

This brings us to the recommendation that ASCB did not make—the most important of all. And that is for science to free itself of the excessive metaphysics. Unfortunately, progress on that front is glacial. As Sarewitz notes, one reason bias persists, and is so harmful, is that in the moment it is not perceived as bias. Asking an evolutionist to stop with the metaphysics goes nowhere because it isn’t recognized as metaphysics. Deep philosophy is a part of their “science” as much as red meat is a part of hamburgers.

Even if the ASCB task force members wanted to address this fundamental problem, they wouldn’t for the backlash would be overwhelming and their professional reputations would be ruined.

So while the pipettes will be sterilized and results double checked to the third decimal point, ASCB will continue to publish junk science driven by the Epicurean mandate that the world must have arisen spontaneously. Unfortunately, the ASCB task force has missed the most important recommendation of all.

Shared Errors: BioLogos on Broken Genes

Toward a Consensus

In my previous articles (here, here and here) I reviewed Dennis Venema’s articles (here, here and here) which claimed that (i) the genomes of different species are what we would expect if they evolved, and  (ii) in particular the human genome is compelling evidence for evolution. Venema makes several confident claims that the scientific evidence strongly supports evolution. But as I pointed out Venema did not reckon with an enormous body of contradictory evidence. It was difficult to see how Venema could make those claims. Fortunately, however, we were able to appeal to the science. Now, as we move on to Venema’s next article, that will all change.

In his next article, Venema introduces a new kind of genetic evidence for evolution. Again, Venema’s focus is on, but not limited to, human evolution. Venema’s argument is that harmful mutations shared amongst different species, such as the human and chimpanzee, are powerful and compelling evidence for evolution. These harmful mutations disable a useful gene and, importantly, the mutations are identical.

Are not such harmful, shared, mutations analogous to identical typos in the term papers handed in by different students, or in historical manuscripts? Such typos are tell-tale indicators of a common source, for it is unlikely that the same typo would have occurred independently, by chance, in the same place, in different documents. Instead, the documents share a common source.

Now imagine not one, but several such typos, all identical, in the two manuscripts. Surely the evidence is now overwhelming that the documents are related and share a common source.

And just as a shared, identical, typos are a tell-tale indicator of a common source, so too must shared harmful mutations be proofs of a common ancestor. It is powerful and compelling evidence for common descent. It is, explains Venema, “one of the strongest pieces of evidence in favor of common ancestry between humans and chimpanzees (and other organisms).”

There is only one problem. As we have explained so many times, the argument is powerful because the argument is religious. This isn’t about science.

The evidence does not support the theory

The first hint of a problem should be obvious: harmful mutations are what evolution is supposed to kill off. The whole idea behind evolution is that improved designs make their way into the population via natural selection, and by the same logic natural selection (or purifying selection in this case) filters out the harmful changes. Therefore the finding of genetic sequence data which must be interpreted as harmful mutations weighs against evolutionary theory.

Also, there is the problem that any talk of how a gene proves evolutionary theory is avoiding the problem that evolution fails to explain how genes arose in the first place. Evolution claiming proof in the details of gene sequences seems to be putting the cart before the horse.

No independent changes

You could say that the heart of this “shared error” argument is the idea that “lightning doesn’t strike twice.” The identical, harmful mutations, in different species, could not have arisen independently. Instead they must have arisen only once, and then were inherited from a common ancestor.

The problem, of course, there is no reason to make this assumption. The logic made sense for written documents, but the species are not ancient manuscripts or homework assignments. They are species, and species are different.

In fact repeated designs found in otherwise distant species are ubiquitous in biology. Listening to evolutionists one would think the species fall into an evolutionary pattern with a few minor exceptions here and there. But that is overwhelmingly false. From the morphological to the molecular level, repeated designs are everywhere, and they take on many different forms.

The problem is that these repeated designs appear in species so distant that, according to evolutionary theory, their common ancestor could not have had that design. The human and squid have similar vision systems, but their purported common ancestor, a much simpler and more ancient organism, would have had no such vision system. Evolutionists are forced to say that incredibly complex designs must have arisen, yes, repeatedly and independently.

And this must have occurred over and over in biology. It would be a challenge simply to document all of the instances in which evolutionists agreed to an independent origins. For evolutionists then to insist that similar designs in allied species can only be explained by common descent amounts to having it both ways.

Bad designs

This “shared error” argument also relies on the premise that the structures in question are bad designs. In this case, the mutations are “harmful,” and so the genes are “broken.” And while that may well be true, it is a premise with a very bad track record. The history of evolutionary thought is full of claims of bad, inefficient, useless designs which, upon further research were found to be, in fact, quite useful. Simply from a history of science perspective, this is a dangerous argument to be making.

Epicureanism

The “shared error” argument is bad science and bad history, but it remains a very strong argument. This is because its strength does not come from science or history, but rather from religion. As I have explained many times, evolution is a religious theory, and the “shared error” argument is no different. This is why the scientific and historical problems don’t matter. Venema explains:

The fact that different mammalian species, including humans, have many pseudogenes with multiple identical abnormalities (mutations) shared between them is a problem for any sort of non-evolutionary, special independent creation model.

This is a religious argument. Evolution is a referendum on creationism. It is not that the species look like they arose by random chance, it is that they do not look like they were created. Venema and the evolutionists are certain that God wouldn’t have directly created this world. There must be something between the Creator and creation—a Plastik Nature if you will. And if Venema and the evolutionists are correct in their belief then, yes, evolution must be true. Somehow, some way, the species must have arisen naturalistically.

This argument is as old as humanity. In antiquity it drove the Epicureans to conclude the world must have arisen on its own by random motion. Today evolutionists say the same thing, using random mutations as their mechanism.

Needed: an audit

Darwin’s book was loaded with religious arguments. They were the strength of his otherwise weak thesis, and they have always been the strength behind evolutionary thought. No longer can we appeal to the science, for it is religion that is doing the heavy lifting.

Yet evolutionists claim the high ground of objective, empirical reasoning. Venema admits that some other geneticists do not agree with this “shared error” argument but, he warns, they do so “for religious reasons.”

We have also seen this many times. Evolutionists make religious claims and literally in the next moment lay the blame on the other guy. This is the world according to the Warfare Thesis. We need an audit of our thinking.