Satellite DNA is Essential and Species-Specific in Drosophila melanogaster

Seems Incompatible

This week’s “we thought it was junk but it turned out to be crucial” study comes with the added bonus that the so-called “junk” is also species-specific / taxonomically restricted. The general topic is tandemly repeated satellite DNA in the much studied fruit fly, Drosophila melanogaster. These satellite DNA regions comprise 15-20% of D. melanogaster’s genome, and one of the regions, AAGAG(n), is transcribed across many of D. melanogaster’s cell types.

While evolutionists have hoped and argued that transcription (not to mention mere presence) does not imply function (after all biology is one big hack-job, so RNA polymerase doesn’t always know what it is doing), D. melanogaster is once again not cooperating. Not only is the satellite DNA ubiquitous and widely transcribed, the AAGAG RNA was found to be important for male fertility. Kind of important.

But it gets worse. Much worse.

Not only is D. melanogaster’s satellite DNA ubiquitous, widely transcribed across many cell types, and of crucial importance, it is species-specific. The levels of AAGAG satellite DNA is orders of magnitude lower in D. simulans and D. sechellia, and nearly absent in other species within the Drosophila genus.

This makes no sense on evolution. Now we must say that not only does a massive quantity of AAGAG satellite DNA abruptly appear in a particular fly species, but it immediately takes on an absolutely crucial role. A role which, of course, was somehow already fulfilled in the putative evolutionary ancestor.

In other words, the function in question (male fertility) was rumbling along just fine, and then with a new species, and not in many of its sister species, the crucial function was somehow rewired and reassigned to a relatively new, massive, DNA satellite sequence.

This is absurd.

Even the paper admits that, “Finally, it is worth noting that the expression of simple satellites for essential functions seems incompatible with the fast evolution of satellite DNAs, reflected in dramatic changes in both sequence types and copy numbers across species.”

Ya think?

The next step will be for evolutionists to convert this spectacular failure into compelling evidence that evolution can produce DNA that is both (i) species-specific, and (ii) functionally essential.

And why is that true?

Because, after all, the satellite DNA evolved, of course. And since it is species-specific and essential, we now have evidence evolution can produce such an unexpected outcome.

That’s just good, solid, scientific research.

Religion drives science, and it matters.

The “All Outcomes Are Equiprobable” Argument

I Had to Write “Evolution Is True” 500 Times

I’ve been busy lately with a big landscaping job for the neighborhood evolutionist. He wanted a massive set of stones to be carefully arranged in his backyard. He wanted stones of different colors, and the careful arrangement would spell out “Evolution Is True.”

Unfortunately, the day I finished this big job there was an earthquake in the neighborhood which jumbled the stones I had carefully arranged. I had to go back to the evolutionist’s property and put the stones back in order.

To makes matters worse, the evolutionist wouldn’t pay me for the job. When I sued him he told the judge that I was lying. He said I didn’t do the job, but instead the arrangement of the stones was due to the recent earthquake.

I explained to the judge that such an event would be unlikely, but the evolutionist retorted that landscapers don’t understand probability. The evolutionist explained to the judge that all outcomes are equally probable. Every outcome, whether it spells out “Evolution Is True” or nothing at all, have a probability of one divided by the total number of possible arrangements. He said that I was committing a mistake that is common with nonscientific and uneducated people. He explained that if you toss a coin 500 times the sequence of heads and tails will be astronomically unlikely. But it happened. All such sequences, even if they spell out a message in Morse code, are equiprobable.

The judge agreed. He fined me for bringing a frivolous lawsuit against the evolutionist and made me write “Evolution Is True” 500 times.

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.

The Astonishing Examples of Repeated Evolution

Does Similarity Imply Common Ancestry?

According to evolution the species arose as a consequence of random events, such as mutations. Yet the biological world is full of repeated designs. These so-called convergences are ubiquitous. And while a fundamental tenet of evolutionary theory is that similarity implies common ancestry, convergences are similarities found in more distant species—they cannot have arisen from a common ancestor. This falsifies the fundamental tenet that similarity implies common ancestry. This tension can be further amplified by complexity and multiplicity. Similarities in different species which are highly complex can be difficult to explain how they evolved once, let alone twice in independent lineages. Add to this similarities which are found not twice, but a multiplicity of times, and you have what the press release of a new study out of Germany on the evolution of jawed vertebrates called “astonishing examples of repeated evolution.”

New Book: Olfactory Receptor Genes Prove Common Descent

The “Shared Error” Argument

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 and echolocation support evolution (here and here). We now move on to another topic: broken genes, or pseudogenes. This is a popular argument amongst evolutionists and Venema uses as his example the olfactory receptor genes. The idea here is that, in different species (such as the human and chimpanzee), the same damaging mutation can be found in the same pseudogenes. When we find the same strange spelling mistake in the homework of different students we conclude that plagiarism occurred. It is more likely that the mistake had one source, rather than occurred twice, independently. Likewise, the same mutation in different species points to a single source in a common ancestor—common descent. Furthermore, we don’t see mutations that violate the expected pattern. Clearly common descent is the obvious, most parsimonious explanation. As Venema concludes, common descent is “overwhelmingly supported.” [36] This is a powerful argument for evolution that has influenced many people. There’s only one problem: It fails historically, philosophically, and scientifically.

First, the olfactory system is profoundly complex. Odors entering the nose interact with finely-tuned receptor proteins (created from the olfactory receptor genes), setting off an incredible cascade of events in the cell, resulting in an electrical signal sent to the brain. Studies have found that each cell expresses only a single olfactory receptor gene, and so is sensitive to a particular odor. At the brain, the signals are grouped and organized by odor. In other words, for all the cells in the nose expressing the same olfactory receptor gene (and thus sensitive to the same odor), their signals spatially converge as they feed into the brain area.

And of course, as with all the senses, These incoming signals are providing mere electrical information. There is no odor, or light, or sound entering the brain via these nerve cells. Instead, a bunch of electrical signals are entering the brain via these nerve cells. The brain, by itself, has no way of knowing what these electrical signals mean. It must somehow be given the source and meaning of these incoming signals. It then processes and interprets these signals and the end result is that we are conscious of images reported by our eyes, sounds reported by our ears, smells reported by our nose, and so forth. All of this defies evolution, and should give us pause.

Second, the evolutionist’s contention that common descent is needed to explain those shared mutations in different species contradicts the most basic biology. Simply put, similarities across species which cannot be explained by common descent, are rampant in biology. The olfactory system is no exception. Its several fundamental components, if evolution is true, must have evolved several times independently. The level of independent origin which evolutionists must admit to (variously referred to as convergent evolution, parallel evolution, recurrent evolution, cascades of convergence, and so forth depending on the pattern) is staggering and dwarfs the levels of similarities in the olfactory receptor genes. To cast those relatively few similarities as mandates for common descent, while ignoring the volumes of similarities that violate common descent constitutes the mother of all confirmation biases.

Third, the strength of this evolution argument is lack of function, but that renders it fallacious. As lawyers know, if you can’t convict the defendant on the facts, you decry how horrifying the crime is. In this case, the entire argument hinges on the utter uselessness of the broken genes. As Venema explains, they are “damaged,” “defective,” “mess[ed] up,” “wrong,” and “ruin[ed].” Clearly, according to Venema, these genes are useless—that’s why they are called pseudogenes. This is crucial because, for evolutionists, this means they would only arise by chance (what designer would implement useless designs?).

All of this means that evolutionists have a very simple formulation: Either those crippling mutations arose once in a common ancestor, or they just happened to arise by chance, coincidentally, multiple times. Clearly the former is much more likely, and this points to common descent. It is, as Venema concludes, “overwhelmingly supported.” [36]

But this powerful argument comes at a cost. There is no free lunch.

The conclusion that common descent is “overwhelmingly supported” utterly depends on our knowing the pseudogenes are useless. Disutility underwrites the assumption of chance as the only alternative to common descent. And chance as the only alternative is crucial. It is why the argument is so powerful, because the chance hypothesis is so unlikely.

Restricting the problem to a contest between evolution and chance makes evolution the obvious winner, but amidst the celebration we forget the weak link. We forget that the entire edifice resides on our certainty of disutility. This, it turns out, is a very weak link.

The history of evolutionary thought, going back to the Epicureans, is full of predictions of disutility gone wrong. It is, quite literally, a theory of gaps. When gaps in our scientific knowledge leave us with ignorance about function, evolutionists routinely assume there is no function. After all, if the world arose by chance, it should be a claptrap, full of aimless, useless designs, if they could even be called that.

But as those gaps close with the inexorable march of scientific progress, it seems we inevitably learn of function. Evolutionists are consistently claiming disutility at brand new findings, only to be proved wrong, again and again. Look no further than the seemingly endless parade of “We thought it was junk, but now …” stories.

Ultimately, the long history of disutility claims are informed by the theory rather than the evidence. This is a classic example of what philosophers refer to as theory-laden observations.

None of this means there are no truly useless structures in biology. There may well be plenty of them. But it has a terrible history.

Furthermore, regardless of the history, disutility is very difficult to know. As with the proverbial “proving a negative,” proving that a pseudogene, or anything else in biology for that matter, actually is useless, is a very difficult undertaking.

From introns to transposons, initial claims of uselessness have given way to a steady stream of findings of function. And, yes, the olfactory receptor “pseudo” genes are no exception. They are now being called pseudo-pseudogenes because all those evolutionary claims of uselessness are rapidly fading. As one recent paper concluded, “such ‘pseudo-pseudogenes’ could represent a widespread phenomenon.”

This is yet another example in a long history of failed disutility predictions. Clearly, the assumption that we know that olfactory receptor pseudogenes are useless is unfounded. Even the name (pseudogenes) will serve future generations of scientists as a constant reminder of this evolutionary foible. Venema’s powerful argument was demolished before the book was even published.

The story does not end here for even if something like pseudogenes could somehow be proven useless, this would not justify the evolutionary formulation of random chance origin as the only other alternative.

Evolution fails to explain how even a single gene could evolve, let alone the entire olfactory system. In fact the presence of supposedly useless structures, such as pseudogenes, is hardly a plus for evolution. As Elliott Sober has pointed out, there is nothing about this story that provides a positivistic argument for evolution.

The argument, and all its strength, hinges entirely on the refutation of the alternative. This is a proof by the process of elimination. Hence it becomes utterly crucial that the alternatives are carefully and exhaustively considered. In particular, all possible alternatives must be known, understood, evaluated, and disproved.

Do you see a pattern here?

This powerful evolutionary argument not only crucially depends on knowing that the pseudogenes are useless, it also crucially depends on knowing that a simple random chance model is the only alternative to evolution, for their origin.

Not only is this philosophically problematic (how do we know that the random chance model is the only alternative?), historically it has a terrible track record. As Kyle Stanford has shown, the history of science is full of theories that were advocated with this type of contrastive reasoning (by disproving a perceived alternative), only later to fail because the assumed alternative was wrong.

To summarize, this highly influential, popular, argument from similar structures that appear to be useless, lies in ruins. It is a disaster. It fails historically, philosophically, and scientifically. It should never have been used in the first place, for its scientific failure was entirely predictable from both the history and philosophy of science.

New Evolution Book: Echolocation Solved

Just Add Water

We have seen that a new evolution book co-authored by evolutionist Dennis Venema is influenced by the mythical Warfare Thesis (here and here) and makes erroneous arguments that the fossil evidence supports evolution (here). Regarding the Warfare Thesis the book propagates the false history that the basic issue of the seventeenth century Galileo Affair was “the veracity of the new science, and its perceived threat to biblical authority.” As we saw, this is the false, evolutionary rendition of history. The Warfare Thesis is a myth, and the Galileo Affair is perhaps the favorite example for evolutionists. Regarding the fossil evidence (which reveals species appearing abruptly in the strata), the book makes two erroneous arguments: that evolution is needed for science to work at all (the “intellectual necessity” philosophical argument) and the use of random design as the alternative to evolution (a theological argument). Now we move on to another topic: echolocation. This was of particular interest to me since I have used echolocation as an example of how evolution fails, and fails badly. When I saw that Venema appealed to echolocation to argue for evolution I was interested to see what he had to say. I am always looking for good arguments for evolution, but I did not find one here. Below I summarize the five different reasons why echolocation destroys evolution. Finally, I turn to Venema’s argument, if it can be called that. What we will see is that his argument utterly fails. Venema fails to address any of the problems with echolocation, and he fails to present any kind of a positive case that might be used to overcome the many problems. In short, it is a complete disaster.

Complexity: The original sonar technology

Most people are familiar with the concept of radar and sonar. Simply put, a reflected signal is used to track a target. But what most people are less familiar with are the many details and complications any radar or sonar system must reckon with. For example, the transmitted pulse must be very strong because it will weaken as the square of the distance it travels, and only a tiny fraction of it will be reflected. Ultimately, the return signal is very weak, so while the receiver is exposed to the very powerful transmitted signal, it must then detect a return signal many orders of magnitude weaker. Think of shouting as loud as you can, and then listening for the echo off of a mosquito.

This is just the beginning of the many sonar design issues. The pulse rate, duration, intensity, pitch are all design parameters that influence how small a target can be detected, how far away it can be detected, how accurately it can be tracked and resolved, and so forth. An advanced sonar design can vary these parameters to optimize the tracking.

Sonar design must also consider how to compensate for target motion and the resulting Doppler effect, erroneous reflections from clutter in the environment, and how to guide toward a moving target. There is also the possibility of imaging to determine what type of target it is.

Not surprisingly, there are many different sonar design strategies. Depending on the clutter environment, typical types of targets, and so forth, various design strategies might work better.

All of this is what we find in nature’s echolocation designs. Whales and bats have incredibly efficient and accurate tracking capabilities. We have developed sonar, but nature had it all along—the original sonar technology. In fact nature’s designs are better than our military equipment. Which is one reason why they are studied so closely.

Complexity at the molecular level

We have seen how complicated echolocation can be. Not surprisingly the molecular machines that help to make it happen are also highly complex. Prestin, a protein important in mammalian hearing, is a transmembrane protein in the outer hair cells of the cochlea. It serves as a frequency-selective amplifier in a sound system that works something like this.

As sound enters the ear, it deflects the outer hair causing tiny amounts of stretching or compression in the outer hair cells. There are channel proteins that sit in the membrane of these cells which are sensitive to such mechanical strain. These proteins provide a tunnel (or channel) across the membrane so that ions can easily cross, and the mechanical strain can cause the channels to open.

These channels are precisely designed to allow only certain types of ions to cross. For example, some channels allow the positively charged potassium ion to cross but not the positively charged sodium ion, and vice-versa.

When a channel opens, ions usually tend to cross through the membrane (either into the cell or out of the cell) because the ion concentration is not uniform, and because there is a voltage, across the membrane. Such differences in concentrations across the membrane, and the voltage, are actively maintained by the cell. They serve as a sort of battery whose energy can be tapped at any time by opening membrane channels.

When the incoming sound causes certain channels to open, the ions that cross cause a change in the membrane voltage. In the outer hair cells, this voltage change encourages negatively charged chlorine ions to exit the cell. They interact with the prestin protein, in the membrane, to cause a mechanical deformation resulting in the elongation of the cell.

In other words, the incoming sound, that caused the hair to move, ends up causing yet more hair movement, and this serves precisely to amplify the incoming sound. This amplification is greater at low sound levels, as it should be.

One of the interesting features of this system is the speed at which it operates. Obviously in order to amplify sound you need to respond as fast as the changes in sound occur. Protein motors often use chemical energy (such as the splitting of the ATP molecule) but that would be too slow for the ear's sound system. Instead, prestin uses the membrane's voltage. This electrical energy can be used much faster and prestin operates at microsecond rates. Here is how one paper summarized the system:

The exquisitely high sensitivity and frequency selectivity of the mammalian hearing organ originates from a mechanical amplification mechanism that resides in the organ of Corti, the sense organ of hearing in mammals. The gain provided by this amplification can reach as high as a thousandfold; it is highest at low sound levels and progressively diminishes with increasing sound energy.

Evolution has no explanation for the origin of this system beyond unfounded speculation, and this is only the beginning of the many molecular machines behind the echolocation systems found in nature.

Echolocation designs incongruent with evolutionary tree

It does not appear that random mutations are the cause of systems such as echolocation in bats and whales. Although this is an enormous problem for evolutionary theory, it is not the only one. As discussed above, there are many different types of echolocation designs. Evolution would predict that species that are thought to be close neighbors on the evolutionary tree would share similar echolocation designs. In other words, the echolocation designs should be congruent with the evolutionary tree. But they are not.

Whereas Darwin argued that the evolutionary tree explained nature’s designs rather than habitat, nature’s echolocation designs follow the exact opposite rule. Here is how one paper described it:

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

This is an enormous falsification of a key prediction of evolutionary theory.

Convergence at the morphological level

One consequence of this falsification is that evolutionists must construct highly complicated narratives for the origin of echolocation. For example, if evolution is true, then we must believe that the incredible echolocation ability found in some bats arose multiple times, by evolving independently. That’s not easy for evolutionists to explain. How could such uncanny design details repeat themselves via blind biological variation (no, natural selection doesn’t help)?

But this convergence problem goes far beyond the bats. Whales and bats share some uncanny similarities in how they track their prey. But if evolution is true, we would have to believe that their common ancestor had none of these capabilities. So in completely different parts of the world, in completely different environments, random mutations in these different species must have independently constructed the same ultra complex designs. As one report explained:

Though they evolved separately over millions of years in different worlds of darkness, bats and toothed whales use surprisingly similar acoustic behavior to locate, track, and capture prey using echolocation, the biological equivalent of sonar. Now a team of Danish researchers has shown that the acoustic behavior of these two types of animals while hunting is eerily similar.

If evolution is true then bats and whales would have been evolving independently for millions of years. And yet they both constructed a sonar capability which involves transmitting loud signals while receiving incredibly weak signals, adjusting the signal parameters in real time, processing the received signals, and so forth. They even share the same range of ultrasonic frequencies:

Bats and toothed whales (which include dolphins and porpoises) had many opportunities to evolve echolocation techniques that differ from each other, since their nearest common ancestor was incapable of echolocation. Nevertheless – as scientists have known for years – bats and toothed whales rely on the same range of ultrasonic frequencies, between 15 to 200 kilohertz, to hunt their prey.

And that similarity is in spite of the different environments:

This overlap in frequencies is surprising because sound travels about five times faster in water than in air, giving toothed whales an order of magnitude more time than bats to make a choice about whether to intercept a potential meal.

But that is not all. The bat and whale also use similar strategies for adjusting their signals while homing in on prey:

Bats increase the number of calls per second (what researchers call a “buzz rate”) while in pursuit of prey. Whales were thought to maintain a steady rate of calls or clicks no matter how far they were from a target. But the new research shows that wild whales also increase their rate of calls or clicks during a kill – and that whales’ buzz rates are nearly identical to that of bats, at about 500 calls or clicks per second.

It is another example of a complex design evolution can only speculate about, and once again the evolutionary tree fails to predict its pattern.

Convergence at the molecular level

Not only is incredible echolocation convergence evident at the morphological level, it is also seen at the molecular level. For instance, the prestin proteins in certain bat and whale species are more similar than evolution would expect. The massive prestin protein has too many amino acids that match up between these species. If one were to construct an evolutionary tree on the basis of prestin comparisons alone, then the bat and whale would be grouped together, and that cannot be correct.

This fact alone need not be a problem for evolutionists. They simply say that prestin is under the influence of strong selection. In other words, there are strong functional constraints on prestin that require more similarity, even between distant species, than we typically find in proteins.

In particular, researchers identified nine amino acids in prestin that seem to be responsible for the overly-consistent whale-bat matchup. Those nine amino acids must be under very strong selection. If one of them mutated then the biosonar system would not work well. The bat or whale would not survive, and that is why we don’t observe such changes. That is how natural selection works.

But if all nine amino acids are required, how did evolution stumble onto the design in the first place? It would be highly unlikely for the right nine amino acids to arise via blind mutations, at the same time.

But the convergence of molecular machines behind echolocation goes far beyond prestin. As one paper explains, “convergence is not a rare process restricted to several loci but is instead widespread”.

As one evolutionist admitted, “These results imply that convergent molecular evolution is much more widespread than previously recognized”. And another admitted that the results are astonishing:

We had expected to find identical changes in maybe a dozen or so genes but to see nearly 200 is incredible. We know natural selection is a potent driver of gene sequence evolution, but identifying so many examples where it produces nearly identical results in the genetic sequences of totally unrelated animals is astonishing.

Astonishing.

Venema’s argument for why echolocation is not a problem

This brings us to Venema’s argument for why echolocation is not a problem. Given the enormous problems briefly reviewed above, how exactly does Venema find echolocation to be evolution-friendly? We have looked at the problem of complexity of echolocation, including at the molecular level, the problem that echolocation designs are incongruent with the evolutionary tree and, as an example, the problem of convergence at both the morphological and molecular levels. Surely no objective scientist would find evidence for evolution in nature’s echolocation designs.

Would they?

Believe it or not, here is what Venema writes:

If you’ve ever stumbled through a pitch-black room and pulled yourself up short just before colliding with a wall or other object, you have employed your (very rudimentary) sense of echolocation. What you detected (though you might not have even consciously perceived it) was that sound waves were reflecting off the object in your way. All mammals can do this, but most (like us) do it very poorly. We need to be very close to the object in question before it is even possible for us to notice reflected sound, and more likely than not we won’t, and we’ll stub our toe or worse.

As it turns out, cetacean echolocation is a specifically tuned sense of hearing that is based on the same genes used for hearing in other mammals. One key gene used for hearing in all mammals is called the “prestin” gene, a protein involved with the specialized structures in the mammalian ear that vibrate in response to sound waves. In whales, the prestin gene is tuned to the ultrasonic frequencies that are better suited to echolocation. This tuning required only a few amino acid changes within the protein—an amount of change easily within the reach of the sort of molecular tinkering we saw for the insulin gene in various mammals. This tinkering within the prestin gene to tune it for echolocation was so easy to achieve, it would seem, that nearly identical changes occurred independently in the lineage leading to modern bats, who also use a prestin tuned to ultrasonic frequencies for echolocation. So even echolocation is not “new”—it too is remodeled from a standard mammalian sense of hearing.

This is a complete disaster. Venema’s equating of echolocation with his imagined ability to avoid a wall in a dark room, his transforming convergence to a virtue, his casting of echolocation as “easy to achieve” and the result of mere “tinkering,” and nothing new but rather simply a remodel of “standard mammalian sense of hearing,” is all standard evolutionary pretzel logic.

This is the evolutionary “just add water” view of biology where you add a couple of mutations and, poof, you have echolocation. But as we saw above, echolocation is not at all comparable to “standard mammalian” hearing. It doesn’t fit the evolutionary tree, and the convergence is astonishing and utterly unexpected and unexplained.

Venema’s attempt to explain away echolocation as a standard result of evolution is not even wrong.

When I saw that this new book had a section on echolocation I was keen to read it over. I have followed the echolocation research for years. I write about it, and often include it in presentations. I discuss the various ways the echolocation evidence contradicts evolution. So why would there be a section on this subject in this book promoting evolution? Have I missed something? Is there some fundamental aspect of echolocation I have missed? Is there a new paper I have missed, overturning the large body of research?

But as I read the section, I quickly realized it was nothing more than the usual evolutionary just-so story. A wholesale ignoring of well-established science, an embracing of imagined thought experiments that make no sense, and an utterly unscientific conclusion.

It isn’t even wrong.

New Book: The Fossils Prove Evolution

Upside Down

We have seen here and here that a new book co-authored by evolutionist Dennis Venema is influenced by the mythical Warfare Thesis. The book, for example, informs readers that the basic issue of the seventeenth century Galileo Affair was “the veracity of the new science, and its perceived threat to biblical authority.” As we saw, this is the false, evolutionary rendition of history. The Warfare Thesis is a myth, and the Galileo Affair is perhaps the favorite example for evolutionists.

After framing the discussion with this bit of Whig history, Venema introduces scientific evidences which he believes make evolution to be compelling. He begins with the fossil record. This is a bit surprising given how badly the theory fares on the fossil evidence. Later in the book Venema will state that according to evolution truly new features should be rare:

One of the things evolution predicts is that seldom will any feature in an evolutionary lineage be truly “new.” [37]

This is an example of an evolutionary prediction that has gone terribly wrong, and the fossil record gives a plethora of examples. As we have explained many times, the general character of the fossil record is precisely the opposite of what evolutionists had expected. Rather than the traditional evolutionary tree pattern of new species gradually appearing over time, the fossil record reveals the exact opposite. The strata show several bursts of new species appearing on the scene, followed by a winnowing.

This is upside down.

Like a Christmas tree, you have a wide berth of branches and twigs at the bottom, or beginning, and over time there is a narrowing as the species are lost to extinctions. Rather than a tree becoming increasingly wider over time from narrow beginnings, the strata often reveal the opposite pattern. Of course it is far more complicated than this simple analogy, but what is important is that the fossil record reveals so many “explosions” of new species. The so-called “Cambrian Explosion,” (yes, it is called an “explosion”) is the most famous, but there are several others. In these events, new species appear abruptly in the fossil record. Not only do a great many “truly new” features appear, entirely new lineages appear as well.

Clearly, the fossil record repeatedly falsifies this prediction of evolution.

In a great example of confirmation bias, evolutionists often downplay the importance of these fossil data and the falsifications they present. In fact, sometimes these are ignored altogether.

And so it is with Venema’s treatment of the fossil record. He appeals to the general pattern of the fossil record, and to the specific example of the evolution of cetaceans.

His primary example of why the fossil record is such strong evidence for evolution are the cetaceans.

A collection of fossils can be arranged from land mammals to whales, which is precisely what evolution needs since whales are mammals. The idea is that mammals first evolved on land, and then certain species made their way back into the water, thus introducing mammals to marine environments.

Venema agrees that some of these fossil species may not be in the actual lineage leading to modern whales. That is good because the literature often illustrates these species as forming a clean, simple, lineage, from ancient mammals to modern whales.

While one may draw a line between the fossil species, the fact is there are many species suggesting more of a bush than a branch, and any such line is imposed onto the data rather than read out of the data.

And if these species did arise from evolution, and if the modern whale did arise from such a land-to-sea transition then, as usual, it would be quite a mystery. For a great transition, including the loss of hind limbs, grinding teeth and pelvises and developing a host of new features must have occurred relatively quickly.

The new features include the fluke tail with its unique vertical propelling motion, the huge filter-feeding jaw, and the ability to give live birth and raise its young in the marine environment. The latest entry to the community could swim, dive and feed better than most fish and sharks. All sorts of evolutionary scenarios can explain why the whale acquired such advanced skills, but they are speculative. The whale’s aquatic prowess does not refute evolution, but it raises the question of how we can be so sure about the purported evolutionary change that is supposed to have created the whale.

Why then are evolutionists so taken with the patterns of the fossil record, and examples such as the fossil sequence that is supposed to lead to the whale? Yes, it provides a good sequence, but there are many questions of just how random mutations could accomplish such heroics. And there are the many other aspects of the fossil data that are problematic, such as the many “explosions.”

These are serious evidential problems, and it would seem the fossils would be the last thing to which evolutionists would appeal. What’s going on?

The answer is, as usual, that the evolutionist’s certainty comes from metaphysics, not science. The idea is not that the whale-like fossils prove evolution directly, but that they disprove any notion that God created them independently. Therefore they must have evolved. Venema makes several such arguments. Here is one of his passages:

Of course, some might argue that it simply pleased God, as Creator, to create a series of unrelated species at this time in earth’s history that happen to suggest an evolutionary relationship. Many Christians find this plausible; but note how this type of argument cannot ever be ruled out by additional evidence. Any additional such species we find in the fossil record would then merely be more separate species that God elected to create at this time. This explanation also leaves scientists bereft of a hypothesis to test with further research. If the species we observe in the fossil record are the direct, special creations of God, then we will not necessarily find a pattern in the fossil record. Faced with such an explanation, a scientist would not have the ability to make predictions about what should be found in the fossil record at certain times. [13]

Here Venema makes two strong arguments. First, the text highlighted in blue above is the classic argument from the intellectual necessity of evolution. Science, as Venema argues, won’t work with creationism. Venema explains that such creationism (i) is not vulnerable to the evidence, (ii) makes it impossible to form testable hypotheses, and so (iii) leaves scientists unable to make predictions.

These are arguments from the philosophy of science that mandate evolution. We must have evolution in order to do science properly. Creationism must be ruled out, regardless of the scientific evidence.

These metaphysics render the scientific evidence irrelevant and, ironically, make evolution (rather than creationism) untestable and not vulnerable to the evidence. Fossil species appearing abruptly in the strata don’t matter when your philosophical argument makes creation untenable. As usual, the evolutionary argument is guilty of the very criticism is casts.

Second, the text highlighted in red above is theological. It is an age-old argument about how God would create the world. Rather than using patterns which appear arbitrary to us, God should fill the design space randomly.

Venema goes on to make the usual evolutionary arguments that the patterns we observe are unlikely. The evolutionary premise here is that the alternative to evolution is a random design of the species. For example, Venema writes:

The probability of mammalian characteristics (such as having hair and feeding their young with milk, as well as a number of defining skeletal characteristics) arising in a separate, unrelated lineage is a pretty big stretch. [14]

This argument hinges entirely on random design being the sole alternative to evolution. Either the species are designed randomly, or it’s evolution. This reasoning dates back centuries and, as Venema has explained, entails beliefs about how God would create the world. In other words, it is religious.

What if God would not necessarily create the species randomly? In that case, the evolutionist’s powerful argument absolutely fails. It would be fatal to the entire position.

In other words, the evolutionary argument entirely hinges on a silly, strawman claim about God.

In my studies of the arguments for evolution, I find they fall into two broad categories: philosophical arguments about man, knowledge, and science; and religious arguments about God. In typical fashion, Venema has appealed to both these long-standing categories of strong arguments for evolution.

If the evolutionist’s premises are correct, then evolution is a no-brainer. We must be evolutionists—regardless of the scientific evidence. The species arising from random causes, such as mutations, makes no sense scientifically, but would be a must. As usual the religion and philosophy steer the science.

This new book is yet another example, in a long line of works going back to Darwin and before, of how evolution is our modern day mythology. New species appearing out of nowhere. Fantastic designs arising from random mutations. And all of this mandated to be a fact. If you cannot see a problem with this, then you must be an Epicurean.

Religion drives science, and it matters.

Ross Pomeroy Reminds us of P-Value Problems

But it is Much Worse

Ross Pomeroy’s article in yesterday’s Real Clear Science was a much needed reminder about the dangers of statistical hypothesis testing. But while Pomeroy rightly points out important problems, particularly with the so-called P-value, out here on the ground, the problem is much worse.

One of Pomeroy’s several legitimate concerns is the use of what is essentially a default value of 0.05 for P. Too often scientists don’t realize that, as David Colquhoun has pointed out, this will lead to false conclusions at least 30 percent of the time. Pomeroy also points out the common fallacy of interpreting the P value as the probability that the null hypothesis is true.

The result of such mishandling of hypothesis testing is that, “Quite simply, a large amount of published research is false.”

Would that it would end there. Unfortunately, when it comes to evolutionary studies, fixing these problems is like rearranging the deck chairs on the Titanic. These concerns about selecting a good alpha value and understanding the nuances of what P actually means, while important, pale in comparison to a much larger infraction: using the P-value to mask what is, in fact, a strawman argument.

One of the key, underlying, assumptions in using the P-value is that there are only two alternatives, the null and alternative hypotheses. These two hypotheses must be complementary—they must be distinct, mutually exclusive, and exhaustive. In other words, one of them must be true, and the other must be false. They cannot both be true, or both be false. They cannot overlap, and there can be no other possibilities.

And while such a perfect pair of hypotheses is possible in simple academic problems such as colored marbles in an urn, real world problems often are more complicated. Take something as seemingly simple as the question of whether or not it will rain today. Is it not binary? Either it will rain, or it will not rain. Right?

Well no. The weather has a multitude of complexities. It is spatially and temporally varying, with an infinite degree of variation. What if it sprinkles? What if the rain evaporates before it reaches the ground? How do you define the time and location? What if it rains in one location but not another?

What the P-value, and its null hypothesis, allows is for trivial null hypotheses to be erected and easily knocked down like strawmen, thus “proving” ones favored explanation.

Here is How the Cytoskeleton Evolved

Not Easy to Explain

Though illustrations of the cell often depict it as a bag full of various organelles and folded membranes, this fundamental unit of life is actually organized upon a highly-structured three-dimensional truss structure known as the cytoskeleton. Until the early 1990s the cytoskeleton had been observed only in the more complex eukaryotic cells. But a series of detailed studies emerged indicating that the other two domains of life (bacteria and archaea) also have cytoskeletons. The wikipedia entry gives a good introduction to this subject:

The cytoskeleton is a network of fibers composed of proteins contained within a cell's cytoplasm. Although the name implies the cytoskeleton to be stable, it is a dynamic structure, parts of which are constantly destroyed, renewed or newly constructed.

In most cells of all domains of life (archaea, bacteria, eukaryotes) a cytoskeleton is found (notably in all eukaryotic cells which includes human, animal and plant cells). The cytoskeletal systems of different organisms are composed by similar proteins. However, structure, function and dynamic behaviour of the cytoskeleton can be very different, depending on organism and cell type. Similarly, within the same cell type the structure, dynamic behaviour, and function of the cytoskeleton can change through association with other proteins and the previous history of the network.

The cytoskeleton of eukaryotes (including human and all animals cells) has three major components: microfilaments composed of the protein actin and microtubules composed of the protein tubulin are present in all eukaryotic cells. By contrast intermediate filaments, which have more that 60 different building block proteins have so far only been found in animal cells (apart from one non-eukaryotic bacterial intermediate filament crescentin). The complexity of the eukaryotic cytoskeleton emerges from the interaction with hundreds of associated proteins like molecular motors, crosslinkers, capping proteins and nucleation promoting factors.

There is a multitude of functions the cytoskeleton can perform: It gives the cell shape and mechanical resistance to deformation; through association with extracellular connective tissue and other cells it stabilizes entire tissues; it can actively contract, thereby deforming the cell and the cell's environment and allowing cells to migrate; it is involved in many cell signaling pathways; it is involved in the uptake of extracellular material (endocytosis); it segregates chromosomes during cellular division; it is involved in cytokinesis - the division of a mother cell into two daughter cells; it provides a scaffold to organize the contents of the cell in space and for intracellular transport (for example, the movement of vesicles and organelles within the cell); it can be a template for the construction of a cell wall. Furthermore, it forms specialized structures such as flagella, cilia, lamellipodia and podosomes.

A large scale example of an action performed by the cytoskeleton is muscle contraction. During contraction of a muscle, within each muscle cell, myosin molecular motors collectively excert forces on parallel actin filaments. This action contracts the muscle cell, and through the synchronous process in many muscle cells, the entire muscle.

Evolutionary theory predicts there to be an evolutionary progression of cytoskeleton designs, as this key aspect of the cell design evolved. But this is not what the science reveals.

For example, in eukaryotes, the proteins actin and tubulin are the building blocks for the microfilament and microtubule structures, respectively. In bacteria and archaea these roles are performed by proteins such as MreB and FtsZ, respectively. But these cousin proteins do not reveals signs of an evolutionary progression. The actin and tubulin proteins show very few changes between different species. In fact they are among the most highly conserved proteins in the eukaryotes.

Even between species as different as yeast and rabbits there is only about a 12% difference in the respective actin proteins. Therefore there is no sign of how a gradual progression of protein evolution could have arrived at the actin and tubulin building block proteins. Importantly, this includes the MreB and FtsZ proteins. The sequence relationships between actin and MreB, and between tubulin and FtsZ, are essentially what we find between any two randomly selected proteins. With evolution we must believe that molecular evolution traversed an enormous gap without leaving a trace of sequence evidence.

This finding is not restricted to the molecular sequence data. The function and distribution of the bacterial components vary dramatically from what we find in the eukaryotes. As one review paper admitted,

it has become clear that there is no simple relationship between the cytoskeletons of prokaryotes and eukaryotes. Moreover, there is considerable diversity in both composition and function between cytoskeletons in different lines of prokaryotes and eukaryotes.

In fact the bacterial designs are highly divergent amongst themselves. Molecular sequences, proteins used, lateral interactions within the filament, polarity (left-handed versus right-handed filaments), and so forth, are all inconsistent across the bacteria. It is not a story of an evolutionary progression.

Another surprise for evolutionists is much of the eukaryotic cytoskeletal functionality must trace back to the first eukaryotic cell—the so-called LECA or Last Eukaryotic Common Ancestor. It is yet another case of complexity pushed farther and farther back in history, to the era of early evolution where the supposed evolution of such complexity is hidden in evolutionary gaps. Here is a particularly candid admission from our review paper:

One of the most surprising results of our increasing ability to probe the characteristics of the LECA has been how much of the biological complexity in extant cells can be traced back to this ancestral cell. The LECA possessed much of the complexity now seen in the replisome, the spliceosome, and the endocytic system, as well as the machineries necessary for meiosis and phagotrophy. Moreover, comparative analysis of the genome of the free-living excavate Naegleria gruberi identified ∼4,000 protein groups that probably were present in the LECA.

This “complexity early” model of eukaryotic evolution is mirrored in the cytoskeleton (Fig. 2 D). Somewhere in the evolutionary space between prokaryotes and the LECA, single proto-tubulin and proto-actin molecules diversified into multiple specialized forms. Three classes of motors arose independently, and evolved to include at least nine classes of dynein, eleven classes of kinesin, and three classes of myosin. As well as these, the axoneme formed, with 100–200 associated proteins, many of which have no prokaryotic orthologues. Between the prokaryotes and the LECA, a revolution occurred in cytoskeletal biology.

Such complexity cannot have appeared fully formed, but arose by stepwise elaborations of cell structure (and genetic repertoire). However, the large number of simpler intermediate forms that must have existed appear to have left no descendants. This is perhaps because a great many of these changes occurred in a relatively short time, with one innovation creating a favorable landscape for the evolution of the next. Alternatively, all descendants of these intermediate forms have been simply out-competed by the arrival of the LECA, with its mitochondrial endosymbiont, endomembrane system, and sophisticated cytoskeleton. What is clear is that since this complex LECA, the diversification into many eukaryotic lineages has often been accompanied not by the addition of further classes, but by loss of ancestral ones. Some of these losses are associated with loss of specific structures or functions (such as axonemal motility), but there appears to be a remarkable flexibility in the precise repertoire of many of these ancient families that is required for eukaryotic cell function.

From a scientific perspective, it would be difficult to imagine a more absurd narrative. Evolutionary explanations, such as this one, are the height of creative story-telling, contorting the theory to try and fit awkward facts.

h/t: La Victoria

Birds With Ornamental Eyespots Have Unlikely Neighbors

More Independent Evolution

When a peacock spreads out its train the feathers form a huge display. Near the end of each feather is a colorful, circular object that looks something like an eye and the feathers are positioned just right so that the eyes, or ocelli, are beautifully arrayed across the entire display. The iridescence of the eyes comes not from the material itself, which isn’t colorful, but from its finely-tuned nanostructure which reflects the light to produce the different colors. Such eye-spot feathers are found in three different bird genera and according to a new evolutionary analysis of their genetics, they would likely share a common ancestor as has always been expected by evolutionists. There’s only one problem. The analysis also finds that other bird genera that are without these ornamental eyespots, are also closely related to these genera that do have eye-spot feathers.

If these other genera are so closely related, then why do they not also have ocelli? With evolution we must say that they had the eye-spot feathers but later lost them for some reason, over the course of evolution. Or that the eye-spot feathers evolved independently in the different genera that have them. Either way these are just-so stories, manufactured to fit the theory. As the new study concludes:

The close relationship between taxa with and without ocelli suggests multiple gains or losses. Independent gains, possibly reflecting a pre-existing bias for eye-like structures among females and/or the existence of a simple mutational pathway for the origin of ocelli, appears to be the most likely explanation

This is yet another evidence, in a long, long list, which demonstrates that evolution is not a simple, parsimonious explanation that, in a stroke, easily explains a set of disparate and otherwise unlikely or confusing observations.

Rather, evolution is a complex theory with a never-ending list of epicycles that are needed to explain a wide variety of evidences that are inconsistent with the basic theory. This makes evolution a tautology.

Here Are the Three Important Take-Aways From That New Spider Study

Nothing is Going Right

A new study out of Harvard continues to find problems with the spider evolution story. This time it is a massive genetic study demonstrating that spiders that create orb webs do not fall into the expected evolutionary pattern. As usual, the problem cannot simply be explained away as a consequence of methodological problems and evolutionists are left with convergence or extinction as their only explanations. Either orb weaving evolved multiple times, or it evolved once, proliferated, and then a bunch of species became extinct. Ever since Darwin this denouement has repeated itself over and over—evolutionists apply their theory to a particular problem, their predictions turn out false, and they respond by accommodating the new findings. Skeptics say the theory is failing and evolutionists say this is just good science at work. Did you expect every prediction to be perfect? Inevitably the debate devolves into one over falsification and unfortunately misses what is really important.

There literally are thousands of stories like this spider study. Evolutionary expectations fail, evolutionists adjust and move on, explaining that there’s nothing there that falsified evolution, it was merely a particular prediction that was falsified.

But that doesn’t mean that such failures do not pose serious problems for the theory of evolution. Evolutionists go easy on their theory. They set the bar high and enjoy the ability of their theory to avoid falsification.

To be fair though, one should not expect the practitioners and promoters of a theory to be serious skeptics. Evolutionists sometimes say they would love to falsify their theory, as that would make them famous. But in science there are enormous conformance pressures, ranging from social to monetary. And this is even more so with evolution. If you genuinely question evolution (not just question a sub hypothesis) then you become an anathema. You will be called a creationist. You will be blackballed and rather than becoming famous, you become infamous.

So what is the problem with evolution’s failed predictions, such as this latest study of orb weaving spiders? Actually there are three problems. It is true that the predicted failure, alone, does not falsify evolutionary theory. That’s a rather silly notion given how evolution was never confirmed in the first place, and how flexible is the theory. Evolutionists cannot even explain, in any scientific sense, the evolution of a single protein.

Evolution is metaphysically motivated and has always failed on the science. So the problem is not that new prediction failures falsify the theory. The first problem with such failures is their quantity. There are thousands of such failures. Evolution is consistently coming up short. Its predictions are always wrong and evolutionists are always surprised. To say this steady stream of failure is just a sign of good science is an incredible euphemism.

The second problem with such failures is that they cause the theory to lose parsimony. With each failed prediction, the theory becomes far more complicated as patches and epicycles are added. And this brings us to the third problem, which is related to the second problem.

These failed predictions cause evolution to lose its smoking gun. The strong scientific argument for evolution was that in a stroke it resolves myriad puzzles in the life sciences. There is a consilience across a wide spectrum of disparate disciplines and data, and previously unlikely or bizarre findings are suddenly and simply explained by Darwin’s elegant theory.

This is all a myth as there never was any such genuine consilience. But if one selectively examines the evidence, one can construct such a story. And it is a powerful story. Why do so many species have the pentadactyl structure? It doesn’t seem to make sense, but with common descent it suddenly falls into place. Across those many species, the pentadactyl structure falls neatly into evolution’s common descent pattern. It is all so obvious.

Take this example along with so many others, and you have a consilience. These curious evidences are the smoking gun that compels us to accept evolution. There’s only one problem. There is no such consilience. This latest spider study is just one more example of how the evidence does not fall neatly into the evolutionary pattern—it contradicts that simple, elegant pattern.

Even the venerable pentadactyl structure failed. As Stephen J. Gould put it, “The conclusion seems inescapable, and an old ‘certainty’ must be starkly reversed.”

So it is not that evolutionists cannot explain away all these failures. Of course they can. Evolution is an over-arching, vague, notion that can accommodate myriad findings with all manner of creative explanations. The problem is there is no reason to think, from a scientific perspective, that evolution is a good theory. It cannot explain how the species arose, and the patterns that the species form don’t fit evolution’s expected pattern. There is no smoking gun.

Consider how one report explains the new spider study findings:

For decades, the story of spider evolution went like this: As insects became more and more diverse, with some species taking to the skies, spiders evolved new hunting strategies, including the ability to weave orb-shaped webs to trap their prey. From that single origin, the story goes, orb-weaver spiders diverged along different evolutionary paths, leading to today, where several species weave similar -- though not identical -- webs. It's a good story, but there's just one problem -- Harvard scientists now know it's not true. The largest-ever phylogenetic study of spiders, conducted by postdoctoral student Rosa Fernández, Gonzalo Giribet, Alexander Agassiz Professor of Zoology, and Gustavo Hormiga, a professor at George Washington University, shows that, contrary to long-held popular opinion, the two groups of spiders that weave orb-shaped webs do not share a single origin.

As the study explains, the findings demand “a major reevaluation of our current understanding of the spider evolutionary chronicle.”

Convergence in Venomous Snakes of North America and Australia

Another Just-So Story

One of the most fundamental evidences for evolution is the similarities between the species. Evolution calls for the species to have evolved via a process of common descent leaving them with similarities inherited from their common ancestor. But there are several problems with this idea. One problem is that there are a great many similarities between species that could not have been inherited from a common ancestor. In such cases evolutionists say the similarities evolved independently. Evolution repeated itself because of a similar environment. But another problem is that there are many similarities between species with key environmental differences. One example is the vision system in humans and squids. Their respective environments could hardly be more different. Now a new study provides yet another example: venomous snakes of North America and Australia, which occupy different ecological niches. As one evolutionist explained:

Most biologists tend to assume that convergence in body form for a group of organisms implies that they must be ecologically similar. But our study shows that there is almost no overlap in diet between many of the snakes that are morphologically very similar.

Evolutionists explain these examples of convergence in different niches with ad hoc mechanisms. For one reason or another, similar designs arose independently, in spite of different environments. This highlights how flexible evolution is. It can explain a great variety of outcomes. But this also means that similarities between species are not the strong evidence evolutionists claim them to be. In fact what these data reveal is how difficult it is to falsify the theory.

Fish Have a Toolbox and Several Other Findings

Aristotle Couldn’t Have Said it Better

Electric organs in fish have challenged evolution ever since Darwin and a new study published today peered even deeper into the problem, down to the genetic level. First let’s see what Darwin had to say (from the section entitled “Special Difficulties of the Theory of Natural Selection,” pages 150-1 of the Sixth Edition of the Origin of Species):

Although we must be extremely cautious in concluding that any organ could not have been produced by successive, small, transitional gradations, yet undoubtedly serious cases of difficulty occur.

Notice how Darwin has subtly shifted the burden of proof to those who aren’t so sure the species spontaneously arose. They must prove that an organ could not have evolved. And when evolutionists call for such proofs, they set the bar very high. Even vague speculation must somehow be falsified. Don’t believe me? Read on and see how Darwin defends his shifting of the burden of proof:

The electric organs of fishes offer another case of special difficulty; for it is impossible to conceive by what steps these wondrous organs have been produced. But this is not surprising, for we do not even know of what use they are. In the Gymnotus and Torpedo they no doubt serve as powerful means of defence, and perhaps for securing prey; yet in the Ray, as observed by Matteucci, an analogous organ in the tail manifests but little electricity, even when the animal is greatly irritated; so little, that it can hardly be of any use for the above purposes. Moreover, in the Ray, besides the organ just referred to, there is, as Dr. R. M'Donnell has shown, another organ near the head, not known to be electrical, but which appears to be the real homologue of the electric battery in the Torpedo. It is generally admitted that there exists between these organs and ordinary muscle a close analogy, in intimate structure, in the distribution of the nerves, and in the manner in which they are acted on by various reagents. It should, also, be especially observed that muscular contraction is accompanied by an electrical discharge; and, as Dr. Radcliffe insists, "in the electrical apparatus of the torpedo during rest, there would seem to be a charge in every respect like that which is met with in muscle and nerve during rest, and the discharge of the torpedo, instead of being peculiar, may be only another form of the discharge which attends upon the action of muscle and motor nerve." Beyond this we cannot at present go in the way of explanation; but as we know so little about the uses of these organs, and as we know nothing about the habits and structure of the progenitors of the existing electric fishes, it would be extremely bold to maintain that no serviceable transitions are possible by which these organs might have been gradually developed.

So we shouldn’t conclude that complex organs could not evolve because very little was understood about them. In other words, it is an argument from ignorance. We don’t understand them, therefore we can’t doubt that they could have evolved. Never mind that, beyond hand waving, Darwin had no idea how such organs could possibly have spontaneously arisen, let alone even how such organs worked or much of anything else about them.

But there was another problem. These electric organs appeared in a wide variety of fish, not following the expected common descent pattern:

These organs appear at first to offer another and far more serious difficulty; for they occur in about a dozen kinds of fish, of which several are widely remote in their affinities. When the same organ is found in several members of the same class, especially if in members having very different habits of life, we may generally attribute its presence to inheritance from a common ancestor; and its absence in some of the members to loss through disuse or natural selection. So that, if the electric organs had been inherited from some one ancient progenitor, we might have expected that all electric fishes would have been specially related to each other; but this is far from the case. Nor does geology at all lead to the belief that most fishes formerly possessed electric organs, which their modified descendants have now lost. 

Darwin argues the problem disappears because the electric organs in the different fish are not very similar, and so are not homologous (i.e., deriving from a common ancestor):

But when we look at the subject more closely, we find in the several fishes provided with electric organs, that these are situated in different parts of the body,—that they differ in construction, as in the arrangement of the plates, and, according to Pacini, in the process or means by which the electricity is excited—and lastly, in being supplied with nerves proceeding from different sources, and this is perhaps the most important of all the differences. Hence in the several fishes furnished with electric organs, these cannot be considered as homologous, but only as analogous in function. Consequently there is no reason to suppose that they have been inherited from a common progenitor; for had this been the case they would have closely resembled each other in all respects. Thus the difficulty of an organ, apparently the same, arising in several remotely allied species, disappears, leaving only the lesser yet still great difficulty; namely, by what graduated steps these organs have been developed in each separate group of fishes.

So to summarize Darwin argued that while he couldn’t provide an explanation for how these electric organs could have evolved, their evolution could not be disproven because we don’t know anything about them. And furthermore, the fact that the organs did not appear according to the common descent pattern was not a problem because they were not homologous and therefore arose independently rather than from a common ancestor.

Aside from the obvious fallacy in Darwin’s argument (lack of falsification means little and in any case Darwin had set the bar so high it was impossible anyway), he apparently was unaware that he had just shot himself in the foot. For his second argument, that the failure to fulfill a common descent pattern was not a problem because the organs arose independently, meant his first problem was that much more difficult. For now Darwin needed to explain not merely how an electric organ could have spontaneously arisen, but how this could have occurred many times over, in different ways. One miracle would not be enough.

Fast Forward

That was then and this is now. How have the past century and a half dealt with Darwin’s defense of the evolution of electric organs?

Not well.

One might think that given all this time, and the enormous mountain of data scientists have since gathered on electric organs in fish, that by now evolutionists would have a fairly detailed and convincing, step-by-step, explanation of how these incredible devices arose by themselves. How can evolution provide the capability for a fish to generate a 600 Volt pulse to stun its prey? How can evolution provide the capability for a fish passively to track tiny prey using an array of ultra sensitive electromagnetic sensors and neural processing?

Amazingly, for a theory that is supposed to be a fact beyond all reasonable doubt, held in question only by the lowly, the ignorant and the biased, there are no answers to these questions. Evolutionists still do not have detailed and convincing, step-by-step, explanation of how these incredible devices arose by themselves. In fact, beyond Darwin-like speculation, evolutionists do not have any explanation, period.

So Darwin’s first argument, that the theory is saved by our ignorance, no longer holds. We now understand these organs in far more detail than even Darwin could have imagined. And it hasn’t helped. We can no longer hide behind our ignorance.

Now, today’s study nullifies Darwin’s second argument. As we saw above, Darwin argued that the designs of the different electric organs were sufficiently different that they must have arisen independently, and so they would not form a common descent pattern.

But the new study, which peers deeper into the data, down to the genetic level, finds no such differences. As one report explained, the new study “provides evidence to support the idea that the six electric fish lineages, all of which evolved independently, used essentially the same genes and developmental and cellular pathways to make an electric organ.” Here is how one evolutionist described the first problem:

What is amazing is that the electric organ arose independently six times in the course of evolutionary history.

And as another evolutionist explained, “The surprising result of our study is that electric fish seem to use the same ‘genetic toolbox’ to build their electric organ,” despite the fact that they evolved independently.

A genetic toolbox? This is a common teleological phrase evolutionists use to refer to regulatory DNA. The idea that fish would use a genetic toolbox hides the absurdity of the evolutionary narrative. There is a reason why Aristotelianism persisted for almost two thousand years.

Mouse Retinal Assembly “Immensely Complex” and “Confounding”

Beyond Lineage-Specific Biology

The fundamental unit of life is the cell and there are many different types of cells. In humans, for example, there are skin cells, muscle cells, blood cells and so forth. In all there are hundreds of different kinds of cells that need to work together in various ways. Now a recent study has investigated the different cell types in the retina of mice. The research focused on the number of cells present in the retina. That may not sound very interesting, but the results were indeed eye-opening.

The researchers looked at 12 different types of cells in the retina, across 30 different strains of mice. Naturally they expected to find some fairly strong patterns. The population sizes for the different cell types should be similar. And if two different types of cell work together and perhaps are synaptically connected, then their cell counts should be correlated across the different strains. That is, if the count is a bit low for one of those cell types, then it should also be on the low side for the other type of cell.

But such patterns were not found. Instead the researchers were surprised to find all kinds of variability. The population sizes of the different cell types varied substantially with little correlation across the different strains.

The researchers also looked at which parts of the genome influence the population counts of the different cell types and concluded that multiple genes, acting differently in the different strains, are involved in specifying these population counts.

The study concluded that retinal assembly is far more flexible than thought. For instance, they concluded that the different retinal cells adjust their size and shape according to their local environment, including the density of the different types of cells around them.

What is emerging is a far more sophisticated retinal assembly process than was imagined. As one report summarized the study:

The circuitry of the central nervous system is immensely complex and, as a result, sometimes confounding. When scientists conduct research to unravel the inner workings at a cellular level, they are sometimes surprised by what they find.

Needless to say, this sort of variability between highly-related strains, and this level of sophistication and complexity, are inconsistent with evolutionary theory.

Here’s Darwin’s Solution for Convergent Evolution: Like Two Inventors “Independently Hit on the Very Same Invention”

Bad Analogy

One of the powerful arguments for evolution is that the species and the various biological organs and structures fall into the expected common descent pattern. We may not understand how they could have evolved and what transitional forms led to what we observe, but if they were created would they not show discontinuities from species to species? Darwin captures all of these ideas in this famous passage from Origins:

Although in many cases it is most difficult to conjecture by what transitions an organ could have arrived at its present state; yet, considering that the proportion of living and known forms to the extinct and unknown is very small, I have been astonished how rarely an organ can be named, towards which no transitional grade is known to lead. The truth of this remark is indeed shown by that old canon in natural history of "Natura non facit saltum." We meet with this admission in the writings of almost every experienced naturalist; or, as Milne Edwards has well expressed it, nature is prodigal in variety, but niggard in innovation. Why, on the theory of Creation, should this be so? Why should all the parts and organs of many independent beings, each supposed to have been separately created for its proper place in nature, be so invariably linked together by graduated steps? Why should not Nature have taken a leap from structure to structure? On the theory of natural selection, we can clearly understand why she should not; for natural selection can act only by taking advantage of slight successive variations; she can never take a leap, but must advance by the shortest and slowest steps. [Charles Darwin, Origin of Species, 1st ed., 1859, Ch. 6, p. 194]

Here Darwin makes a compelling argument for his theory. Isn’t it a bit suspicious that all those “parts and organs” from so many different species fall into a common descent pattern with small, gradual steps of change between them? Why would they be created that way by an all-powerful designer?

You can imagine how many readers have been swayed by this passage and others like it in Origins. There’s only one problem: This is all wrong.

The species and their “parts and organs” do not fall into such a pattern. Similar species have very different parts, and distant species have very similar parts. These cases are not exceptions but rather are rampant in the biological world and evolutionists maintain their common descent narrative to this day only by careful filtering of the data. Even in Darwin’s day there were hints of this problem and in one of those often overlooked foibles Darwin addressed this just before the passage above:

The electric organs offer another and even more serious difficulty; for they occur in only about a dozen fishes, of which several are widely remote in their affinities. Generally when the same organ appears in several members of the same class, especially if in members having very different habits of life, we may attribute its presence to inheritance from a common ancestor; and its absence in some of the members to its loss through disuse or natural selection. But if the electric organs had been inherited from one ancient progenitor thus provided, we might have expected that all electric fishes would have been specially related to each other. Nor does geology at all lead to the belief that formerly most fishes had electric organs, which most of their modified descendants have lost. The presence of luminous organs in a few insects, belonging to different families and orders, offers a parallel case of difficulty. Other cases could be given; for instance in plants, the very curious contrivance of a mass of pollen-grains, borne on a foot-stalk with a sticky gland at the end, is the same in Orchis and Asclepias,—genera almost as remote as possible amongst flowering plants. In all these cases of two very distinct species furnished with apparently the same anomalous organ, it should be observed that, although the general appearance and function of the organ may be the same, yet some fundamental difference can generally be detected. I am inclined to believe that in nearly the same way as two men have sometimes independently hit on the very same invention, so natural selection, working for the good of each being and taking advantage of analogous variations, has sometimes modified in very nearly the same manner two parts in two organic beings, which owe but little of their structure in common to inheritance from the same ancestor. [Charles Darwin, Origin of Species, 1st ed., 1859, Ch. 6, p. 193]

Here Darwin notes that there are several examples of similar organs in more distant species, indicating that they must have evolved independently. These are the sorts of similarities that would have been ascribed to evolution’s common descent, as in the powerful passage quoted above, if they had appeared in sister species. But these similarities do not appear in sister species—they appear in more distant species. So Darwin produced a new explanation: they evolved independently just as “two men have sometimes independently hit on the very same invention,” such as Leibniz and Newton independently developing calculus. Such personification of evolution and natural selection was common in Origins, and remains common in today’s literature. Aristotelianism never really died, it just changed names.

This has the virtue of not having to explain how low entropy, high Kolmogorov complexity designs which are astronomically unlikely to have spontaneously arisen (yes, that is what evolution says) even once could have evolved, err, multiple times independently.

And so there you have it. Evolution can explain common descent patterns and .NOT. common descent patterns. This is an example of the great flexibility of evolutionary theory. It doesn’t matter what the pattern is, evolution can explain it. And if a theory can explain both X and not X, then the scientist must not claim X (or not X) as evidence for his theory.

But this isn’t about science. Look at the first passage quoted above. Halfway down Darwin makes the argument compelling. Sure there are species that don’t fit the common descent pattern, but the important point is that the species would not have been created this way. X is powerful evidence, not because evolution can explain it but because creation cannot explain it. Evolution must be true—our religion demands it.

Religion drives science, and it matters.

Richard Dawkins: How Could Anyone “Possibly Doubt the Fact of Evolution”

The Single Most Convincing Fact

Evolutionists like to say that there are mountains of evidence for evolution, but what is the best evidence? What would make a creationist think twice? Twenty five seconds into this video evolutionist Richard Dawkins answers this question. His killer evidence is the congruence between the genes of different plants and animals. Compare the genes across a range of species and you’ll see a “perfect hierarchy, a perfect family tree.” In fact, you’ll see the same result for evolutionary trees using just single genes—the so-called gene trees. It works “with every gene you do separately.”

[0.25] I think perhaps the single most convincing fact—observation—you could point to would be the pattern of resemblances that you see when you compare the genes, using modern DNA techniques, such as looking at the letter-to-letter correspondences between the genes—compare the genes of any pair of animals you like—a pair of animals or a pair of plants—and then plot out the resemblances and they fall in a perfect hierarchy, a perfect family tree. … [1.05] Moreover the same thing works with every gene you do separately and even pseudogenes that don’t do anything but are vestigial relics of genes that once did something. I find it extremely hard to imagine how any creationist that actually bothered to listen to that, could possibly doubt the fact of evolution.

Dawkins went on to have some rather harsh words for creationists. The message was clear. The evidence for evolution falls perfectly into place. It makes evolution a fact that is beyond any reasonable doubt. And anyone who doubts this is a bad person.

This sentiment is by no means particular to Dawkins. I have heard this same claim, and others like it, dozens of times. Sometimes informally in lectures, discussions, debates and so forth. Other times in textbooks or other literature.

What is amazing is the evolutionist’s high confidence and self-assuredness in such a blatant misrepresentation of science. It would be difficult to imagine a bigger falsehood. Phylogenetic incongruence is rampant in evolutionary studies. Conflicts exist at all levels of the evolutionary tree and throughout both morphological and molecular traits. This paper reports on incongruent gene trees in bats. That is one example of many. These incongruences are caused by just about every kind of contradiction possible. Molecular sequences in one or a few species may be out of place amongst similar species. Or sequences in distant species may be strangely similar. As one paper admitted, there is “no known mechanism or function that would account for this level of conservation at the observed evolutionary distances.” Or as another evolutionist admitted, the many examples of nearly identical molecular sequences of totally unrelated animals are “astonishing.”

An even more severe problem is that in many cases no comparison is even possible. The molecular sequence is found in one species but not its neighbors. When this problem first became apparent evolutionists thought it would be resolved as the genomes of more species were decoded. No such luck—the problem just became worse. Not surprisingly evolutionists carefully prefilter their data. As one paper explained, “data are routinely filtered in order to satisfy stringent criteria so as to eliminate the possibility of incongruence.”

Short genes that produce what are known as microRNA also contradict Dawkins’ high claim. In fact one evolutionist, who has studied thousands of microRNA genes, explained that he has not found “a single example that would support the traditional tree.” It is, another evolutionist admitted, “a very serious incongruence.”

Another paper admits that “the more molecular data is analysed, the more difficult it is to interpret straightforwardly the evolutionary histories of those molecules.”

And yet in public presentations of their theory, evolutionists present a very different story. As Dawkins explained, gene comparisons “fall in a perfect hierarchy, a perfect family tree.” This statement is so false it isn’t even wrong—it is absurd. And then Dawkins chastises anyone who “could possibly doubt the fact of evolution.” Unfortunately this sentiment is typical. Evolutionists have no credibility.