Embryonic Development Reveals Staggering Complexity

Oh My

I recently cited a paper on the evolution of embryonic development and how the evidence contradicts evolutionary theory and common descent. Even the evolutionists, though in understated terms, admitted there were problems. Evolutionary analyses are “reaching their limits,” it is difficult to “conclude anything about evolutionary origins,” genetic similarities “do not necessarily imply common ancestry,” and “conserved regulatory networks can become unrecognizably divergent.” In other words, like all other disciplines within the life sciences, embryonic development is not working. The science contradicts the theory.

But there is much more to the paper, and as a reader noticed, the authors give a rather blunt admission of the magnitude of the problem, not often seen in the literature:

One of the main reasons for Duboule’s pessimism about the return of the EvoDevo comet is the staggering complexity and diversity of cellular and developmental regulatory processes. The configuration space for realistic models of such systems is vast, high dimensional, and potentially infinitely complex.

Staggering complexity? Staggering diversity? The configuration space is vast and high-dimensional?

And it is potentially infinitely complex?

And we are to believe this is the product of random mutations?

Religion drives science, and it matters.

How Embryonic Development Bears on Evolution

Follow the Theory

In order for evolution to have occurred, the intricate embryonic development stages of species must have evolved. Indeed, the developmental pathways of the species would be crucial in such a process. If we are to believe the evolutionary claim that the species spontaneously arose, then untold embryonic development pathways must have somehow undergone massive change. But while evolutionists expected the study of such evolution of development to yield great insight into the evolutionary process and history, it has underwhelmed. This shortcoming is well known, as exemplified in this 2015 paper:

First, traditional comparative approaches to the evolution of development—whether focused on the morphological or on the molecular/genetic level—are reaching their limits in terms of explanatory power.

Except that this is an overstatement. To say that comparative approaches “are reaching their limits in terms of explanatory power” is to suggest that there was, at one time, some significant level of explanatory power provided. That would be a very optimistic interpretation of the data.

The paper continues:

The more we learn about the evolution of pattern-forming gene networks, or the ontogeny of complex morphological traits, the more it becomes clear that it is less than straightforward to conclude anything about evolutionary origins or dynamics based on such comparisons alone.

“Less than straightforward”? Let’s be clear—a more accurate descriptor would be “impossible.” In fact, the evidence does not reveal an evolutionary history, but rather is supported by the theory. Evolutionary theory does not follow the data, as Huxley prescribed, but rather the data follow the theory.

The paper continues:

On the one hand, homoplasy or convergent evolution abounds at all levels of investigation. One of the most lauded major insights of EvoDevo is that a common toolkit of genes and signaling pathways is reused over and over again to create a large diversity of different body plans, shapes, and organs.

Most lauded major insights? That would be the mother of all euphemisms. Evolutionists are always rationalizing devastating contradictions as teachable moments, and here we have yet another example. To cast the nonsensical finding of a “common toolkit” as a “major insight” is laughable.

This becomes clear as the paper continues:

Because of this, similarities in gene expression patterns or morphological structure often do not necessarily imply common ancestry, since they may as well reflect the frequent reuse of the same regulatory or morphogenetic modules.

Profound similarities “do not necessarily imply common ancestry.” We have now entered a Lewis Carroll world, as Sober would put it. The whole point of evolution was that such similarities revealed and mandated common descent. But now, we have the exact opposite, as similarities cannot be due to common descent, but must have arisen independently. And this is an “insight”? A fundamental prediction is demolished and evolutionists do not skip a beat. This is not science.

But it gets worse:

On the other hand, developmental system drift allows conserved networks to change considerably in terms of their component genes and regulatory interactions without changing the phenotypic outcomes such systems produce. This means that even functionally conserved regulatory networks can become unrecognizably divergent at the molecular and genetic level, especially across large evolutionary time spans.

We have now reached the height of absurdity. First, profound developmental similarities were found which could not be ascribed to common descent. Now we find that those developmental pathways which can (theoretically) be ascribed to common descent are profoundly different.

When will this bad dream end? The science contradicts the theory. Over. And over. And over. And over.

It never ends. Religion drives science, and it matters.

[h/t: El Hombre]

Blindness in Cave Fish is Due to Epigenetics

Evolutionists Say “We See”

A recent paper out of Brant Weinstein’s and William Jeffery’s laboratories on eye development, or the lack thereof, in blind cave fish has important implications for evolutionary theory (paper discussed here). The study finds that the loss of eyes in fish living in dark Mexican caves is not due to genetic mutations, as evolutionists have vigorously argued for many years, but due to genetic regulation. Specifically, methylation of key development genes represses their expression and with it eye development in this venerable icon of evolution. But the finding is causing yet more problems for evolutionary theory.

Darwin appealed to the blind cave fish in his one long argument for evolution. It is a curious argument in many ways, and the first sign of problems was in Darwin’s presentation where he flipped between two different explanations. At one point he explained the loss of vision in the cave fish as an example of evolutionary change not due to his key mechanism, natural selection. Instead, the Sage of Kent resorted to using the Lamarckian mechanism or law of “use and disuse.” Privately Darwin despised and harshly criticized Lamarck, but when needed he occasionally employed his French forerunner’s ideas.

Elsewhere Darwin hit upon a natural selection-based mechanism for the blind cave fish, explaining that elimination of the costly and unneeded vision system would surely raise the fitness of the hapless creatures.

This latter explanation would become a staple amongst latter day evolutionary apologists, convinced that it mandates the fact of evolution. Anyone who has discussed or debated evolutionary theory with today’s Epicureans has likely encountered this curious argument that because blind cave fish lost their eyes, therefore the world must have arisen by itself.

Huh?

To understand the evolutionary logic, or lack thereof, one must understand the history of ideas, and in particular the idea of fixity, or immutability, of species. According to evolutionists, species are either absolutely fixed in their designs, or otherwise there are no limits to their evolutionary changes and the biological world, and everything else for that matter, spontaneously originated.

Any evidence, for any kind of change, no matter how minor, is immediately yet another proof text for evolution, in all that the word implies.

Of course, from a scientific perspective, the evidence provides precisely zero evidence for evolution. Evolution requires the spontaneous (i.e., by natural processes without external input) creation of an unending parade of profound designs. The cave fish evidence shows the removal, not creation, of such a design.

The celebration of such evidence and argument by Darwin and his disciples reveals more about evolutionists than evolution. That they would find this argument persuasive reveals their underlying metaphysics and the heavy lifting it performs. It is all about religion.

We are reminded of all this with the news of Weinstein’s new study. But we also see something new: The insertion, yet again, of Lamarck into the story. The irony is that the epigenetics, now revealed as the cause of repressed eye development in the cave fish, hearkens back to Lamarck.

Darwin despised Lamarck and later evolutionists made him the third rail in biology. Likewise they have pushed back hard against the scientific findings of epigenetics and their implications.

The environment must not drive biological change.

False.

Well such biological change must not be transgenerational.

False.

Well such inheritance must not be long lasting, or otherwise robust.

False again.

This last failure is revealed yet again in the new blind cave fish findings.

False predictions count. A theory that is repeatedly wrong, over and over, in all of its fundamental expectations, will eventually be seen for what it is.

The rise of epigenetics is yet another such major failure. Evolutionists pushed back against it because it makes no sense on the theory, and that means it cannot now be easily accommodated.

One problem is that epigenetics is complex. The levels of coordination and intricacy of mechanism are far beyond evolution’s meager resources.

It’s not going to happen.

Another problem is the implied serendipity. For instance, one epigenetic mechanism involves the molecular tags places on the tails of the DNA packing proteins called histones. While barcoding often seems to be an apt metaphor for epigenetics, the tagging of histone tails can influence the histone three dimensional structures. It is not merely an information-bearing barcode. Like the tiny rudder causing the huge ship to change course, the tiny molecular tag can cause the much larger packing proteins to undergo conformational change, resulting in important changes in gene accessibility and expression.

This is all possible because of the special, peculiar, structure and properties of the histone protein and its interaction with DNA. With evolution we must believe this just happened to evolve for no reason, and thus fortuitously enabled the rise of epigenetics.

Another problem with epigenetics is that it is worthless, in evolutionary terms that is. The various mechanisms that sense environmental shifts and challenges, attach or remove one of the many different molecular tags to one of the many different DNA or histone locations, propagate these messages across generations, and so forth, do not produce the much needed fitness gain upon which natural selection operates.

The incredible epigenetics mechanisms are helpful only at some yet to be announced future epoch when the associated environmental challenge presents itself. In the meantime, selection is powerless and according to evolution the incredible system of epigenetics, that somehow just happened to arise from a long, long series or random mutations, would wither away with evolution none the wiser.

These are the general problems with epigenetics. In the case of the blind cave fish, however, there is possible explanation. It is a longshot, but since this case specifically involves the loss of a stage of the embryonic development, evolutionists can say that genetic mutations caused changes in the methylating proteins, causing them to be overactive.

This explanation relies on the preexistence of the various epigenetic mechanisms, so does not help to resolve the question of how they could have evolved. What the explanation does provide is a way for evolutionists to dodge the bullet presented by the specter of the cave fish intelligently responding to an environmental shift.

Such teleology in the natural world is not allowed.

So the evolutionary prediction is that these proteins will be found to have particular random changes causing an increase in their methylation function, in particular at key locations in key genes (i.e., the genes associated eye development).

That’s a long shot, and an incredible violation of Occam’s Razor.

My predictions are that (i) this evolutionary prediction will fail just as the hundreds that came before, and (ii) as with those earlier failures, this failure will do nothing to open the evolutionist’s eyes.

Religion drives science, and it matters.

About Those Placental Regulatory Genes

Evolution Recruits and Deploys Genes

Last time we noted the teleological ideas and language used to describe the hypothetical evolution of several genes that are expressed for a mere few hours, in the early development stages of many placental mammals. And by early we mean when we consist of only 8-16 cells. The teleology is not a mere slip-up. As we have documented many times, it is a common thread running throughout the genre of evolutionary literature. It is needed to make sense of the data, because evolution doesn’t.

That teleological language appeared in an article about the research. Not too surprisingly, teleological language also appears in the research journal paper as well. To wit:

A small number of lineage-specific tandem gene duplications have occurred, and these raise questions concerning how evolutionarily young homeobox genes are recruited to new regulatory roles. For example, divergent tandem duplicates of the Hox3 gene have been recruited for extra-embryonic membrane specification and patterning in dipteran and lepidopteran insects, a large expansion of the Rhox homeobox gene family is deployed in reproductive tissues of mouse, and duplicates of TALE class genes are expressed in early development of molluscs.

Two of the evolutionists’ favorite words are “recruited” and “deployed.” They sound so active. What better way to obviate the rather awkward problem that, if evolution is true, all biological variation must be random with respect to fitness (a claim which, by the way, has been falsified so many times we stopped counting). Evolutionists nonetheless continue to spread this fake news.

And no teleological idea would be complete with the mandatory infinitive form (“for … specification and patterning”). Religion drives science and it matters.

A Salamander Two-fer: Non Homologous Development and an ORFan

A Faulty Foundation

Salamanders have their own way of doing things. For most animals, if an important body part, such as a limb, is lost, it is gone for good. But for salamanders, they just grow a new one. Also, salamanders use different embryonic development patterns. For example, their digits (fingers and toes for us humans) form in the wrong order—going, essentially, in the wrong direction. You can see this in the figure below (taken from this paper from Neil Shubin’s group, but note the labeling error, VI rather than IV). In the figure, the numbers across the top show the order in which the digits appear. Salamanders go against the common pattern. This “reverse polarity” in what otherwise is a highly conserved development pattern in the tetrapods is a quandary for evolution.

Early evolutionists who first seriously reckoned with this “striking deviance from an otherwise conserved pattern in tetrapods,” as the Shubin paper puts it, as well as other distinctive features of salamander limb development, concluded that the salamanders probably arose independently of the other tetrapods. In other words, these development inconsistencies were so profound they required an independent origins—there were two different origins of tetrapods.

The problem, however, is the set of similarities between the salamanders and their cousin tetrapods is so massive, that any such independent origins would be absurd from an evolutionary perspective.

So evolutionists were left needing an explanation for the profound divergence. Perhaps salamanders got their start with a loss of digits. If the first salamanders had only two digits, and then re-evolved the other digits (catching up to their ancestral forms), the development order could have been rearranged.

Unfortunately such a hypothetical evolutionary history, where the salamanders begin by losing digits, does not fit the data (both molecular and fossil) very well, even within the context of evolutionary theory.

Perhaps the salamander digit development deviance arose as a larval adaptation. Or perhaps the salamander development pattern is not a “deviance” at all, but rather is the nominal, ancient pattern, but is retained only in salamanders among living tetrapods.

But these hypotheses have problems as well. In fact the salamander character data are full of contradictions:

The evolution and phylogeny of crown group salamanders is plagued by homoplasy. In fact, a large a number of highly derived anatomical characters, including body elongation, tail autonomy, and life history pathways, have been demonstrated or are debated to have evolved multiple times.

[Note that these anatomical characters have not “been demonstrated” to have evolved multiple times. That is a misrepresentation of the science. They only have “been demonstrated” to have evolved multiple times if one assumes evolution at the outset.]

Yet another problem plaguing these evolutionary hypotheses is the finding of genes unique to the salamander that are crucial for its limb regeneration ability and unique embryonic development patterns. You can read more about these here and here, and this brings us to the second half of our two-fer.

Whether they are called unique genes, novel genes, orphans, ORFans, taxonomically-restricted genes (TRGs), lineage-specific genes (LSGs), or whatever, they are a problem for evolution. First, they counter the above hypotheses attempting to explain the salamander’s unique development. As one paper explains:

the notion of an ancient limb regeneration programme has been challenged by reports of salamander lineage-specific genes (LSGs) upregulated during regeneration. One salamander LSG in particular, the Prod1 gene, was shown to be required for proximodistal patterning during limb regeneration and for ulna, radius and digit formation during forelimb development. The existence of urodele LSGs expressed and involved in regeneration has lent support to the hypothesis that limb regeneration is a derived urodele feature.

In other words, the salamander gets it done using genes unique to its lineage, and that contradicts the hypothesis that the salamander’s unique capabilities were there all along.

It also contradicts the evolutionist’s long-standing, but rapidly fading, hope that ORFans would go away. As we have explained, evolutionists hoped that such lineage-specific genes would be found in other species as more genomes were decoded. But instead the number of ORFans just continued to grow.

Evolutionists next predicted that similar ORFan sequences would be found in the so-called non-coding DNA. Although that is sometimes the case, it is not generally, and the Prod1 gene is another example of this.

Evolutionists next predicted that ORFan sequences were probably not part of a mature protein coding gene and did not form functional proteins. That also is wrong, and Prod1 is yet another example of an ORFan that is indeed a real protein.

The findings of unique (non homologous) development patterns, and lineage-specific genes make no sense on evolution. And attempts to explain these findings according to evolution with clever, detailed hypotheses just cause more problems.

If you try to build a house on a faulty foundation, it will just get worse. Evolution is a flawed theory, and the more we learn about biology, the more evident that becomes.

Evolution may be true, it may be false. That is debatable. What is not debatable, however, is that the empirical evidence contradicts the theory.

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.

nFGFR1, A Protein That Regulates the Regulators

Nobody Predicted It

Most people have heard of genes, but few understand how they work. The textbooks say that the human genome has almost 30,000 genes and that a gene typically is used to create a protein molecule. But in fact it is difficult to speak of a gene as a thing. For example, proteins are usually not simply constructed from a given stretch of DNA that we would call a gene. Instead, proteins are constructed from several different stretches of DNA. In other words, our “genes” are often a collection of smaller segments that are separated in our DNA. These different DNA segments, which are given the uninteresting name of exons for “expressed regions,” are first copied, and then the copies are combined or appended to each other, into one single transcript. The job of combining exons is done by massive protein machines, and a great variety of different combinations are used, depending on what is needed at the moment. To summarize, a gene is often a collection of separate, smaller, DNA regions that can be combined in many different ways to produce different protein molecules. So those roughly 30,000 genes can produce a great many more different proteins.

But there is an entirely separate reason why our genome can construct a huge number of proteins from a relatively small number of so-called genes—each gene can code for multiple proteins. This is because once the exons are combined, the resulting transcript can be read in six different ways. For example, imagine reading a paragraph backwards and finding a different message. This is exactly what happens with some genes—they carry overlapping genetic messages which code for different proteins. Furthermore, a given protein often has different functions. Such protein multifunctionality, as one research explained, “is more the rule than the exception.”

This brief summary of how genes are used, leaving out a great many details, raises a difficulty for the theory of evolution. Namely, there is no scientific evidence that any of this could have evolved. For instance, a typical transcript may contain 1,000 nucleotides or chemical “letters.” There are four different nucleotides, so the number of possible messages is 4 raised to the power of 1,000. That is an astronomical number of possible genetic transcripts, most of which would not produce a functional protein. Today’s science tells us that evolution could not evolve a single protein.

But that is only the beginning. As the summary above indicates, somehow the genes were separated into exons, somehow the machinery for combining, and mixing and matching the exons must have arisen, somehow the machinery for translating the transcript into a protein via the DNA code must have arisen, and so forth.

There is no scientific evidence that evolution could have constructed this.

And there are many more problems with the theory of evolution. For example, consider the circularity that is required in the summary above. Recall that the exons are combined by a massive protein machine. So in other words, a massive protein machine is required to construct proteins. The protein machine must have been constructed first, in order for proteins to be constructed.

The same circularity applies to the translating of the transcript into a protein via the DNA code. In that translation process, a great many proteins are required. Proteins are required to construct proteins. There is no scientific evidence that evolution can construct a circular process such as this.

Furthermore, of all those roughly 30,000 genes, the cell needs to know which ones to express at any given time. For this, there are special DNA binding sites, nearby the genes, to which special proteins attach, in order to regulate gene expression. They help to control which genes are expressed.  Here we have more circularity. Proteins are needed to regulate the process of regulating the construction of proteins.

Those not familiar with these gene regulation proteins do not appreciate how devastating they are for the theory of evolution. Somehow these proteins must have evolved by random genetic mutations. Several exons would need to be combine, leading to the construction of these regulatory proteins. The genetic sequences of nucleotides, in those exons, would have to code for a very special type of protein whose three-dimensional shape and chemistry would enable it to bind to DNA.

Then, separately, the DNA binding sites would have to arise, again from random mutations, where those gene regulation proteins would attach. Those DNA binding sites would need the correct sequence of nucleotides, and would need to be in precisely the correct location in the genome.

And of course the regulatory proteins would need to attach to the DNA binding sites at the correct time, working with yet other gene regulation proteins to control the transcription of a region of DNA. And of course that region of DNA would need to contain the correct genetic sequences, leading to the correct gene product, such as a protein.

There simply is no scientific evidence that this could have evolved.

This week new research out of SUNY Buffalo continues to make this story even more devastating for evolution. The research involves a gene, containing 24 exons, that codes for a special protein known as the nuclear Fibroblast Growth Factor Receptor-1, or nFGFR1.

The nFGFR1 protein plays an important gene regulation role during embryonic development. In this role, nFGFR1 does not regulate the production of proteins that do something in the cell, such as synthesizing a chemical or metabolizing food. Instead, nFGFR1 regulates the regulatory proteins.

In other words, the nFGFR1 protein represents a higher level of gene regulation. The expression of genes is influenced by regulatory proteins, and the expression of the regulatory proteins is influenced by yet other proteins, such as nFGFR1. This is yet another unequivocal refutation of evolutionary theory.

Here is how the lead researcher explained the results:

We’ve known that the human body has almost 30,000 genes that must be controlled by thousands of transcription factors that bind to those genes, yet we didn’t understand how the activities of genes were coordinated so that they properly develop into an organism.

Now we think we have discovered what may be the most important player, which organizes this cacophony of genes into a symphony of biological development with logical pathways and circuits.

We found that this protein works as a kind of ‘orchestration factor,’ preferably targeting certain gene promoters and enhancers. The idea that a single protein could bind thousands of genes and then organize them into a hierarchy, that was unknown. Nobody predicted it.

Evolution is a nineteenth century theory that came out of seventeenth and eighteenth century concerns about divine action, the problem of evil, miracles and a host of related theological doctrines. Darwin’s book was loaded with metaphysical pronouncements about how the Creator would never have intended for this world. These beliefs were handed down to Darwin, and they have persisted in the form of evolutionary thought ever since. Evolution was not motivated by empirical science originally, and with the march of scientific progress, evolutionary thought becomes increasingly silly.

The Evolution of Neural Crest Cells: Teleology Raised to the Power of Serendipity

Early stem cells were set aside to create new features

There is a reason why Aristotle’s ideas persisted for thousands of years—they advance fundamental themes in how we think. And no, those ideas did not become outdated with the rise of modern science, as the textbooks explain. Consider a recent paper on the flight of bats which stated that the bat’s specialized airflow sensors evolved in order “to guide motor behaviors” and that vertebrate nervous systems, in general, “have flexibly adapted to accommodate anatomical specializations for flight.” The infinitive form is the key. Evolutionary theory is supposed to have rejected teleology. Whereas Aristotle explained natural phenomena as a consequence of final causes, modern science, so the textbooks state, is free of such mysteries. After Bacon it was all about empiricism, mathematical descriptions and natural laws. There was no appeal to goals or end-directed action. Right? Wrong.

Evolutionary theory is Aristotelian. Practitioners use teleological language to describe how evolution works, ad nauseam. When evolutionists explain that the bat’s specialized airflow sensors evolved in order “to guide” motor behaviors, they are invoking an end- or goal-directed process. If nervous systems evolved “to accommodate” various capabilities such as flight, then evolution is Aristotelian.

Now the usual explanation for the teleological language, which is rampant amongst evolutionists, is that “we didn’t actually mean it, we’re just being lazy.”

In peer-reviewed papers?

No, evolutionists are not being lazy. Not this lazy. This is how they think about the evolutionary process. It performs actions in order to achieve goals.

Consider this week’s example, a study of embryonic development in vertebrates and how neural crest cells maintain their flexibility or pluripotency. The mystery is that these cells are able to give rise to various types of cells past the embryonic stages where most cells have lost that capability and instead are committed to a particular cell type such as skin, muscle or bone.

The explanation is that these cells evolved that way. Such explanations are given as though they advance the science.

But this adds nothing to the science. Explaining away an unexpected observation as “well evolution did it” is a cheap short-circuiting of the scientific method. It is a meaningless multiplying of entities which Occam warned us never to do and introduces explanations which themselves are in need of explaining.

As Descartes put it: “If you find it strange that … I do not use the [Aristotelian] qualities called ‘heat,’ ‘cold,’ ‘moistness,’ and ‘dryness,’ as do the philosophers, I shall say to you that these qualities appear to me to be themselves in need of explanation.”

This evolutionary reasoning—if it can be called reasoning—shuts off the search for how nature works—the main duty of science. Instead of figuring how embryonic development works it is simply ascribed to the contingencies of history. The underlying reasons for the design, which in its inexorable march of progress science will eventually uncover, are ignored. Evolutionists are, as they say, being lazy.

But that’s not the worst of it.

The constant teleological drumbeat in evolutionary theory not only obviates the scientific method, it replaces it with cacophony of serendipity. The evolutionary literature is chocked full of intricate, complicated, just-so stories that would put any soap opera to shame. All kinds of intricate events take place, leading to complex new creations which are then crucial to the next step in the plot.

This week’s paper on neural crest cells, for example, finds that after these fascinating and incredible cells were produced by evolution, they then became the crucial player in evolution’s construction of major new vertebrate designs. Here is how evolutionist Carole LaBonne, the study leader, explained it:

Neural crest cells never had their potential restricted at all. We believe a small population of early stem cells were set aside, so that when the time came, their immense developmental potential could be unleashed to create new features characteristic of vertebrates.

Early stem cells were set aside so that when the time came their immense developmental potential could be unleashed to create new features? This is Aristotelianism on steroids and the serendipity is deafening.

When you see a theory consisting of a long sequence of special explanatory devices you know it isn’t about science.

Evolutionist Says Evolution’s “Traditional Framework” Must Go

Is This the Third Stage?

Why is it that the same structures in similar species are constructed, during embryonic development, in different ways? Why is it that the master control genes which direct the embryonic development of complex structures, such as the eye, must have arisen long before those complex structures arose, if evolution is true? One might have thought that the much celebrated field of evodevo (the study of the evolution of embryonic development) might have resolved such thorny questions. Instead it seems to have simply raised more questions about evolutionary theory. In fact one recent review reads like something out of the Intelligent Design movement:

much research in contemporary evodevo remains steeped in a traditional framework that views traits and trait differences as being caused by genes and genetic variation, and the environment as providing an external context in which development and evolution unfold. … we remain rather convinced that organisms, traits, and differences in traits reside in, and are controlled by, genes and genetic variation. … [evolutionary thinking entails] the basic notion that the essences of organisms, traits, and trait differences ultimately reside in genes and genetic variation and that development is determined and directed by genes or their immediate products.

This was written by an evolutionist and his point was that this “traditional framework” is a clearly a problem that needs to be rectified. Strange, that is exactly what skeptics of creation by chance have been saying for years.

As the old saying goes:

All truth passes through three stages:
First, it is ridiculed;
Second, it is violently opposed;
Third, it is accepted as self-evident.

Perhaps we are moving into the third stage.

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.

Your Genetic Controls Take Form Even Before Conception

The Hits Just Keep on Coming

Who would have thought that the tiny West Africa nation of The Gambia, where British slave trade thrived centuries ago, would someday provide a devastating blow to Darwin’s theory on “the Preservation of Favoured Races.” But The Gambia’s consistent climate of rainy and dry seasons made for the perfect experimental conditions to test what is already known to be true in animals; namely, that not only does the food that you eat carry with it instructions for your body, and not only does the food that your mother eats while pregnant with you also influence your body, but the feed that she eats before conception also influences your body.

Rural diet in The Gambia is predictable across the seasons, as the rainy and dry seasons come and go. So people born in The Gambia are walking biology experiments in that their birth date is a reliable predictor of their mother’s diet before and after conception.

And sure enough a new study reveals that small molecular markers, such as the methyl group, which are attached to our DNA and influence which genes are expressed, vary depending on when they were born. The differences are statistically significant and are consistent with what has already been found from various studies, preconception diet alters the epigenetic control of the genome.

With evolution we would have to believe that random mutations somehow created an astonishingly complex adaptation machine for no reason, and it just happened to persist in the population, and just happened to come in handy eons later, and so be preserved by that all-powerful creator known as natural selection. The sheer intricacies and interdependencies of epigenetics, and the lack of an evolutionary fitness pathway, are inconsistent with an evolutionary origin.

Nothing in biology makes any sense in the light of evolution.

Err, Remember That Little Problem About Novelty?

“Life is genomically complex”

The theory of evolution has made many predictions about what we should find in biology. Those predictions have routinely failed and that tells us there is something wrong with the idea. One such prediction is that the genomes and their protein products, from different species, should form a common descent pattern. The graphic above shows an example of this prediction from a high school textbook written by evolutionist George Johnson. In that example Johnson informs his young readers that the hemoglobin protein “reveals the predicted pattern.” That was a misrepresentation of the evidence at the time, and since then the failure of this prediction has only grown worse. Another more recent, but related, prediction is that evolution is largely driven by regulatory proteins which regulate the construction of other proteins. These regulatory proteins control the embryonic development stages and the idea was that species evolve by slight modifications to how these proteins function. This prediction has also failed, and even evolutionist are now admitting the evidence contradicts what they were claiming only a few years ago. Here is how one evolutionist explains the failure of these predictions:

The prevailing theory is that all animals are built from essentially the same set of regulatory genes—a genetic toolkit, and that phenotypic variation within and between species arises simply by using shared genes differently. Scientists are now generating a vast amount of genomic data from an eclectic mix of organisms. These data are telling us to put to bed the idea that all life is underlain by a common toolkit of conserved genes. Instead, we need to turn our attention to the role of genomic novelty in the evolution of phenotypic diversity and innovation.

The idea of a conserved genetic toolkit of life comes from the 'evo-devo' (evolutionary and developmental biology) world. In short, it proposes that evolution uses the same ingredients in all organisms, but tinkers with the recipe.

That, however, is all wrong:

However. We can now sequence de novo the genomes and transcriptomes (the genes expressed at any one time/place) of any organism. We have sequence data for algae, pythons, green sea turtles, puffer fish, pied flycatchers, platypus, koala, bonobos, giant pandas, bottle-nosed dolphins, leafcutter ants, monarch butterfly, pacific oysters, leeches…the list is growing exponentially. And each new genome brings with it a suit of unique genes. Twenty percent of genes in nematodes are unique. Each lineage of ants contains about 4000 novel genes, but only 64 of these are conserved across all seven ant genomes sequenced so far.

Many of these unique ('novel') genes are proving important in the evolution of biological innovations. Morphological differences between closely related fresh water polyps, Hydra, can be attributed to a small group of novel genes. Novel genes are emerging as important in the worker castes of bees, wasps and ants. Newt-specific genes may play a role in their amazing tissue regenerative powers. In humans, novel genes are associated with devastating diseases, such as leukaemia and Alhzeimer's.

So whereas the genome was once just so much junk, evolutionists now must admit that “Life is genomically complex” and that Darwinian evolution, err, doesn’t actually explain how the eye, or anything else for that matter, originated:

Life is genomically complex, and this complexity plays a crucial role in evolving diversity of life. It's easy to see how an innovation can be improved through natural selection, e.g. once the first eye evolved, it was subject to strong selection to increase the fitness (survival) of its owner. It is more challenging to explain how novelty first originates, especially from a conserved genomic toolkit. Darwinian evolution explains how organisms and their traits evolve, but not how they originate. How did the first eye arise? Or more specifically how did that master regulatory gene for eye development in all animals first originate? The capacity to evolve novel phenotypic traits (be they morphological, physiological or behavioural) is crucial for survival and adaptation, especially in changing (or new) environments.

Not a problem however. Biology doesn’t follow evolutions patterns? We merely must reimagine evolution. It’s a whole new theory as “genomes are constantly producing new genes all the time”:

But the presence of unique genes in all evolutionary lineages studied to date now tells us that de novo gene birth, rather than a reordering of old ingredients, is important in phenotypic evolution. The over-abundance of non-coding DNA in genomes is less puzzling, if they are a melting pot for genomes to exploit and create new genes and gene function, and ultimately phenotypic innovation. The current thinking is that genomes are constantly producing new genes all the time, but that only a few become functional.

“Constantly producing new genes”? Evolutionists think nothing of the failure of fundamental predictions—they simply add more epicycles. Whatever is found in biology, evolution produced it, no matter how silly the theory becomes. For decades evolutionists proclaimed that biology revealed evolution’s common descent pattern. That turned out to be wrong and now evolutionists simply turn the story on its head. Once we were told that evolution was proven by its common descent patterns. Now evolutionists euphemistically describe biology’s designs as “taxonomically-restricted,” “lineage-specific,” and “phylogenetically widespread.” The exact opposite of evolutions predictions.

Nothing in biology makes sense in the light of evolution.

[h/t: The Man]

Neuron Development Involves Cell Severing Itself

Neuron Assembly Line

If you thought the brain and central nervous system are complicated, then consider its development. New research shows that the creation of a single nerve cell, or neuron, involves the precursor cell severing itself from the embryo’s neural tube. The neuronal precursors do not merely separate and withdraw. Instead, they are attached to the tube by long tentacles which constrict and then break off. This allows the precursor cell to move to where it needs to be without taking with it the machinery for constructing a new neuron. It is a very detailed and complicated choreography that just got more complicated.

Evolutionists say that random chance mutations just happened to assemble all of this—like a factory to build cars just happening to come together (no, natural selection doesn’t help). They don’t know how this happened, and there is no scientific evidence to support this rather interesting claim, but evolutionists are certain that it did happen.

This is not hyperbolic criticism. Evolutionists really do insist that evolution is a fact, beyond any reasonable doubt. And there really is no scientific explanation for neuron development, or a thousand other wonders of biology. This is not simply a case of a minor detail yet to be worked out by an otherwise rock solid theory. From a strictly scientific perspective, evolution makes no sense. It is, quite literally, an untenable idea, scientifically speaking.

How Legs Evolved: Acompañado de Otros Muchos Cambios

Where the Heavy Lifting Occurs

A report today on new research out of Spain on embryonic development of zebrafish reads “From Fish to Man: Research Reveals How Fins Became Legs.” In this study evolutionists altered the expression levels of some regulatory genes resulting in deformed fins. The idea is that the deformed fin is taking its first step toward evolving into a tetrapod limb, and that this significant evolutionary transition was due not to an altered protein changing the way fins are built, but rather a change in the levels of existing proteins. As one of the researchers explained:

First, and foremost, this finding helps us to understand the power that the modification of gene expression has on shaping our bodies.

But the results are not nearly so compelling as the evolutionists believe. First, if the evolutionary interpretation of the findings is correct, this means that evolution had already constructed all the proteins and other machinery necessary to morph a fin toward a leg. That calls for quite a bit of serendipity.

Second, the evolutionary step that was observed in the experiment did change the fin, but the result was nowhere close to a leg. In fact, what seems to have been lost in the translation, but was included in Spain’s El Mundo report, was that the result was, err, lethal to the young zebrafish. After all, they could no longer swim.

Not to worry though, for as the evolutionists assure their readers, these modified gene expression levels were undoubtedly “acompañado de otros muchos cambios.” And so it is in these “other many changes” where the heavy lifting occurs, for they would morph the fin to a leg and ensure that those modified gene expression levels “no fuesen deletéreos.” It is amazing how evolution is always able to create so many changes to arrive finally at a better design.

As usual it is the theory that informs the data rather the other way around. Imagine if evolution wasn’t known to be a fact?