Sunday, July 23, 2017

Subcellular Map of the Human Proteome Reveals “Highly Complex Architecture”

A High Degree of Regulation and Control

New research is using antibodies to map out the spatio-temporal locations of 12,003 different proteins in human cells. The results are another example of how, as Bruce Alberts put it in 1998: “We have always underestimated cells.” Alberts explained how cells were once naively viewed as something of a random affair, where molecules “were thought to diffuse freely, randomly colliding.” The new research reveals the “the highly complex architecture of the human cell” and adds more detail to the fact that the workings of the cell are far from random:

A total of 12,003 proteins targeted by 13,993 antibodies were classified into one or several of 30 cellular compartments and substructures, altogether defining the proteomes of 13 major organelles.

Although evolutionists “thought the cell was so simple,” this research is showing that the “cellular proteome is compartmentalized and spatiotemporally regulated to a high degree.” In fact “[m]ore than half of these 12,003 proteins localize in more than one compartment at the same time.” This is consistent with the fact that most proteins are capable of performing multiple functions, and is another indicator of high complexity:

Moreover, proteins that localize to more than one compartment may have context-specific functions, increasing the functionality of the proteome. The fact that proteins “moonlight” in different parts of the cell is now well accepted. … The more complex a system is, the greater the number of parts that must be sustained in their proper place, and the lesser the tolerance for errors; therefore, a high degree of regulation and control is required.

Indeed, the degree of regulation and control required for this system is not only enormous, but contrary to evolutionary expectations.

Saturday, July 22, 2017

Human Evolution: Missing Link Still Missing

The Need For Theory Evaluation

The evolution of humans is, in many ways, similar to evolutionary theory on the whole. As Colin Barras reveals in his recent article at the BBC, There are conflicting evidences, a lack of details, opposing hypotheses held with great confidence, and a wide range of explanatory mechanisms that are routinely used as needed. That much is obvious. What is a bit more subtle, and arguably even more important, is the absence of a serious evaluation of the theories at hand.

Barras’ article is a good summary, from TH Huxley and Darwin up to today, of how evolutionists have viewed human evolution. What is humanity’s phylogenetic neighbor, our so-called sister species, and what is our most recent common ancestor?

Following Huxley, gorillas or chimpanzees were typically held by early evolutionists as both our sister species and representative of the common ancestor, which swung from branch to branch and rambled along on all fours. But some evolutionists held that monkey’s were our closest evolutionary neighbor.

With the rise of molecular biology came genetic comparisons and the firm conclusion that chimpanzees and bonobos are our sister species. Huxley, it seemed, was right. Students were told, in no uncertain terms, that the chimp was our sister species—after all, we shared something like 99% of our DNA in common.

But then new evidences arose, questioning this seemingly incontrovertible truth. Subtle differences between gorillas and chimps suggested independent evolution, rather than inheritance via a common ancestor, of certain traits. Furthermore, a new fossil species, Ardipithecus ramidus, as well as anatomical and behavioral comparisons, called into question the accepted human-chimp relationship.

All of this leaves evolutionists today contemplating a range of explanations for human evolution. One common theme of all the different explanations, however, is their lack of detail. The explanations do not provide any sort of detailed account of the rise of the many unique traits and capabilities in humans.

And where detailed evidence does exist, such as in the chimp, gorilla, and human DNA data, it makes little sense (see here, here, and here, for example).

The theoretical problems and lack of detail with human evolution, and evolution in general, raise the question of how good these theories are. Evolutionists repeatedly state that evolution is a fact, just as much as gravity, heliocentrism, and the roundness of the Earth are facts. There is no question about it.

But the science does not support this claim. What we need is a legitimate, serious evaluation of the theories at hand.

Monday, May 22, 2017

New Paper From Gareth Fraser’s Group Confirms Common Ancestry

If P Implies Q, Then Q Implies P, Right?

A new paper out of Gareth Fraser’s laboratory explains that vertebrate epithelial appendages, such as feathers, hair, scales, and teeth, “have evolved to facilitate wide-ranging aspects of survival and reproduction.” Readers will note the infinitive form (“to facilitate”), which reveals the usual Aristotelianism / teleology under-girding evolutionary thought, but how do the evolutionists know that these structures “have evolved” in the first place? A hint comes in the next paragraph, which informs us that:

Recent research has revealed shared ancestry among amniote epithelial appendages, based on the observation that reptilian scales, avian feathers and mammalian hair share a common foundation during early development: the anatomical placode.

This is a good example of what passes as confirmation of common ancestry for evolutionists. These various vertebrate epithelial appendages “share a common foundation during early development,” so therefore they share a common ancestor.

Simply put, similarity proves evolution.

This, of course, is false. Similarity does not prove evolution. This is the age-old fallacy of affirming the consequent. If P implies Q, then Q implies P, right?

Wrong.

Nor is this example of fallacious reasoning a rare exception to otherwise air-tight, rigorous, thinking on the part of evolutionists.

Such fallacious reasoning is ubiquitous in evolutionary thought. It is everywhere. Not only does this example blatant fallacy appear right up front in peer-reviewed paper in a leading evolutionary journal, like a nasty virus it is literally rampant throughout the evolutionary literature.

Indeed, this example cites a 2016 paper with the same fallacy appearing in the very title:

Di-Po├» N, Milinkovitch MC. The anatomical placode in reptile scale morphogenesis indicates shared ancestry among skin appendages in amniotes. Sci Adv. 2016;2:1–8.

Science, if anything, is logical. Philosophers never thought to deploy logic as a demarcation criterion because, frankly, they never in their wildest imagination could believe that people would seriously set forth fallacious reasoning, with a straight face, as legitimate science.

Think again.

Saturday, May 20, 2017

The Real Problem With Convergence

Worse Than Lightning Striking Twice

Biology is full of convergence—repeated designs in distant species. Marsupials and placentals, for instance, are mammals with different reproductive designs (placentals have significant growth in the embryonic stage attached to the nutrient-rich placenta whereas marsupials have no placenta and experience significant development after birth) but otherwise with many similar species. The marsupial flying phalanger and placental flying squirrel, for example, have distinctive similarities, including their coats that extend from the wrist to the ankle giving them the ability to glide long distances. But evolutionists must believe that these distinctive similarities evolved separately and independently because one is a marsupial and the other is a placental, and those two groups must have divided much earlier in evolutionary history. Simply put, evolution’s random mutations must have duplicated dozens of designs in these two groups. Isn’t that kind of like lightning striking twice?

It is kind of like lightning striking twice but for evolutionists—who already have accepted the idea that squirrels, and all other species for that matter, arose by chance mutations—this is not difficult to believe. It simply happened twice rather than once (or several times, in the cases of a great many convergences).

What is often not understood however, by both evolutionists and their critics, is that convergence poses a completely different theoretical problem. Simply put, a fundamental evidence and motivation for evolution is the pattern of similarities and differences between the different species. According to evolutionary theory, the species fall into an evolutionary pattern with great precision. Species on the same branch in the evolutionary tree of life share a close relationship via common descent. Therefore they share similarities with each other much more consistently than with species on other branches.

This is a very specific pattern, and it can be used to predict differences and similarities between species given a knowledge of where they are in the evolutionary tree.

Convergence violates this pattern. Convergence reveals striking similarities across different branches. This leaves evolutionists struggling to figure out how the proverbial lightning could strike twice, as illustrated in a recent symposium:

Does convergence primarily indicate adaptation or constraint? How often should convergence be expected? Are there general principles that would allow us to predict where and when and by what mechanisms convergent evolution should occur? What role does natural history play in advancing our understanding of general evolutionary principles?

It is not a good sign that here in the twenty first century evolutionists are still befuddled by convergence, which is rampant in biology, and how it could occur. This certainly is a problem for the theory.

But a more fundamental problem, which evolutionists have not reckoned with, is that convergence violates the evolutionary pattern. Regardless of adaptation versus constraint explanations, and any other mechanisms evolutionists can or will imagine, the basic fact remains: a fundamental evidence and prediction of evolution is falsified.

The species do not fall into the expected evolutionary pattern.

The failure of fundamental predictions—and this is a hard failure—is fatal for scientific theories. It leaves evolution not as a scientific theory but as an ad hoc, story-telling, procedure. The species reveal the expected evolutionary pattern—except when they don’t. In those cases, they reveal some other pattern.

So regardless of where you position yourself in this debate, please understand that attempts to explain convergence under evolutionary theory, while important in normal science, do nothing to remedy the underlying theoretical problem, which is devastating.

Religion drives science, and it matters.

Sunday, April 23, 2017

New Book: New Proteins Evolve Very Easily

No Free Lunch

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

The problem of protein evolution

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

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

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

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

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

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

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

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

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

The “solution” to protein evolution

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

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

The science

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

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

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

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

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

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

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

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

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

Religion drives science, and it matters.

Monday, April 17, 2017

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.

Saturday, April 15, 2017

New Evolution Book Reviewed By Hans Madueme

Deep Explanatory Power?



If you want to understand evolutionary thought just read the literature. Charles Darwin accurately characterized his 1859 book on evolution as “one long argument.” That argument was based on several popular religious beliefs leading to faulty science. For example, throughout the volume Darwin’s ideas rely on a popular religious doctrine called utilitarianism, and in Chapter Six Darwin explicitly states that his theory would absolutely fail without it.

Ever since Darwin, little has changed. One after the other, evolutionists have attempted to explain and prove Darwin’s idea. And one after the other, they have simply confirmed that evolutionary thought is not a scientific theory in the normal sense but rather is, at its core, a religious idea with little regard for the science. It really is nothing more than the ancient Epicureanism, inserted into modern science. Consider the latest entry, Adam and the Genome, a brand new Brazos Press title authored by Dennis Venema and Scot McKnight.

In the tradition of the evolution literature, the first part of the book presents a long list of arguments for why we should believe the biological world arose by evolution—a combination of chance and natural law. The second part of the book, as the title suggests, addresses the question of Adam and Eve. Simply put, the book argues that Scripture, read rightly, never did point to a historical Adam in the first place. This makes Scripture consistent with evolution’s call for humanity to begin as a relatively large population.

But this reading of Scripture is influenced by evolution. As McKnight explains, his approach accepts “the reality of genetic evidence supporting a theory of evolution”. [173] But, in fact, there is no such “reality.” The genetic evidence does not support evolution—quite the opposite.

Religious beliefs mandating evolution are what led to today’s theory of evolution, not empirical scientific findings. And now, new scientific observations (such as genetics) are interpreted according to evolution. The observations are theory-laden. Furthermore, with the broad acceptance of evolution, theologians such as McKnight are telling us we need to adjust our religious understandings in light of the “reality” of the scientific evidence.

This is what computer scientists refer to as Garbage-In, Garbage-Out (GIGO). It is little wonder McKnight and many others are calling for this “new” understanding of Scripture, for that “new” understanding is centuries old, and is what mandated evolution in the first place. What goes around comes around.

Unfortunately the myth that evolution is a scientific no-brainer, a given, a fact, and on par with gravity and the round Earth, is difficult to dispel. The powerful religious ideas mandating evolution have led to the myth that evolution is legitimate and compelling science.

For example, in his review of Adam and the Genome, Hans Madueme rightly explains that the history of science should give us pause regarding evolution. Too often scientists have had high confidence in ideas that later would be discarded. Madueme accurately detects such high confidence in evolutionary thought, as exemplified in Adam and the Genome.

Unfortunately Madueme also gives high marks to the science presented in the book. According to Madueme, it “unpacks the genomic evidence for evolution and common ancestry,” and even “skeptical readers will come away impressed at the deep explanatory power of evolutionary theory.” Impressed?

And what exactly is this “deep explanatory power of evolutionary theory” to which Madueme refers? Well, err, Madueme fails to mention any for he “skipped over most of the details.” But it is precisely in those details where the evidences and arguments fall apart. We have already seen that the book makes erroneous arguments that the fossil evidence and echolocation support evolution (here and here). In fact, as we saw, both these evidences and arguments, once stripped of the religion, far from supporting evolution, severely contradict the theory.

In my next post I will look at another one of the book’s arguments involving pseudogenes. What we will find, again, is not “deep explanatory power of evolutionary theory” but exactly the opposite.

Religion drives science, and it matters.

The Fruit of Evolution: Abortion

I Feel Sorry For Her Child



Ideas have consequences and to see the fruit of evolution we need look no further than abortion. If we were not created by God—if life arose by chance—then why should there be a right to life? But as the truth about evolution and abortion becomes more apparent, evolutionists become increasingly ugly. In this video, a hostile crowd expresses righteous indignation at the passage of laws making it less convenient to murder babies. A young lady sparks the anger with a question for her elected representative about why he thinks he has the right to abridge her right to murder. This is the fruit of evolution.

I feel sorry for her child.

Last Known Survivor of Nineteenth Century Passes

The Time Has Come

The nineteenth century, which brought us Charles Darwin and his modernized version of Epicureanism, is now officially in the history books. With the passing of 117 year-old Emma Morano, born in the waning days of the century (November 29 1899), there are now no known survivors of the century before last.

It has now been 117 years since the nineteenth century, and sometimes the passing of time is needed for true history, and true science, to emerge. Perhaps the time has finally come for us to admit to the pseudoscience we have constructed to “justify the ways of God to men.”

Evolution is deceptive because we normally think of religious beliefs as arguing for miracles. This one argues against miracles, but it is no less religious. And its mandate that the world arose spontaneously is becoming ever more absurd with each passing day.

Let’s just be honest.

Monday, April 10, 2017

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.

Saturday, April 8, 2017

Massive RNA Editing and the Octopus

Evolution has been utterly demolished



Click the video to see an octopus mimic algae. Octopuses have an amazing ability to sense and mimic the coloration, shape, and texture of their surroundings. They literally “blend in” as the video illustrates. Note how the audience appropriately responds at the end of the video. You can read more about this amazing ability here. The idea that such mimicry evolved is unlikely. The problem is that evolution’s random mutations are not up to the task. Too many of them are required. And no, natural selection doesn’t make it happen. Selection cannot coax, cajole, persuade or otherwise sweet talk mutations into happening. Selection is simply a label for what happens afterwards: in a word, harmful mutations are eliminated. Indeed, evolution co-founder Alfred Wallace thought the term “natural selection” should be dropped altogether, because it really doesn’t do anything and so is misleading. According to evolutionary theory, selection can have no forward influence on mutations. It cannot cause helpful mutations to occur—no teleology. But helpful mutations are what is needed, and in spades. The octopuses amazing mimicry needs both to sense the surrounding environment, and then to perform its amazing blending ability. Sensing without blending is useless. And blending without sensing is useless. You need both, and that is beyond the reach of random mutations. It isn’t going to happen. In fact, this same problem applies to both sensing and to blending, taken individually. This is because a large number of mutations are required to construct either one. And to add insult to injury, research at the molecular level is just making things worse.

Evolution is supposed to be caused by random mutations in the genome. Mutations in segments of the DNA where genes reside may change the gene product, such as a protein. But organisms have a way of creating such genetic changes on the fly, and it is called RNA editing. After a gene is transcribed, the RNA copy can be edited, for example by altering a single nucleotide. This RNA editing, or recoding, is done by a protein machine.

RNA editing is typically not very common. But in recent years, high levels of recoding have been found in the octopus, and new research is adding to the story. In the octopus and allied species, the majority of RNA transcripts are found to have an edited nucleotide and, importantly, they are often conserved across the species.

In other words, whereas in most species that have been studied there is relatively little RNA editing, in the octopus and its closest neighboring species there is extensive RNA editing and the recoding sites are often conserved across these neighboring species. Also the DNA flanking sequences, on either side of the recoding sites, tend to be conserved across these neighboring species.

This evidence demolishes evolution. Here are seven reasons why.

First, why would these few species suddenly have such an escalation of RNA editing? Evolution has no explanation why this mechanism would suddenly take on such importance in this small group of species. As one evolutionist admitted, “Most organisms have very few functional [editing] sites in coding regions. This is why we find it so unusual and surprising that in squid, octopus, and cuttlefish, we see exactly the opposite.”

Second, the flanking sequences are difficult to evolve. These consist of hundreds of nucleotides, and once transcribed they need to form RNA secondary structures which the RNA editing protein recognizes. These sequences can be highly specific. In some cases even a single nucleotide substitution can abolish RNA editing. In other words, evolution’s random mutations must somehow luckily find these specific sequences. Without the right secondary structure, RNA editing is greatly slowed. But at the start of the search evolution is most likely nowhere close to having a sequence that will form the right secondary structure. And it would be unlikely for a random mutation to make the difference. In other words, multiple mutations are required before even a hint of success is obtained. And of course this all must occur while not disrupting any preexisting messages the sequence carries. This is highly unlikely. And yet this must occur not just once, but twice, on both sides of the recoding site. And furthermore, this must occur not just twice but, err, hundreds of thousands of times, at the many different recoding sites. It’s not going to happen.

Third, these long conserved flanking sequences, hundreds of nucleotides long on either side of the recoding sites, imply evolution loses the ability to evolve.

Fourth, according to evolutionary theory the fact that these recoding sites are conserved across different species means that they are adaptive. In other words, they improve fitness. This massive RNA editing is a feature, not a bug. But given that there are many thousands of these recoding sites, evolution faces a combinatorial explosion. Not only is there an astronomical number of different combinations of RNA editing actions, but for any given gene there is the question of which RNA transcripts to recode? Unless a very simple solution is found, this combinatorial explosion is way beyond the meager resources of evolution’s random mutations.

Fifth, undoubtedly RNA editing is used to respond to changing conditions. Recoding has been shown, for example, to affect potassium channel function. But if RNA editing is a mechanism for response to changing conditions, then there must be signaling instructions that tell the RNA editing protein when and where to perform its editing. But the origin of that signaling system would require a great many mutations. Again, that likely would be beyond evolution’s resources.

Sixth, this massive RNA editing capability will not function properly without its many components in place. You need the recoding site, the flanking sequences, the RNA editing protein, and the signaling system. It will do no good to have the proper DNA sequences without the editing protein, or both of those without the signaling system, or the signaling system without the flanking sequences. In other words, there are multiple, interdependent components which all need to be in place for this RNA editing capability to function.

Seventh, it is silly to think evolution could find the right recoding sites. The problem is that, even if this RNA editing capability could evolve and all the different interdependent components could fall into place, it would not likely pick the right recoding site. Simply put, each evolutionary experiment would require a monumental effort and time span before the needed feedback could be obtained about whether or not the recoding site was a good one. Evolution would need to evolve the recoding site and the flanking sequences before natural selection could act. Undoubtedly most recoding sites would not help. They might be neutral, or they might be harmful. But they would not help to construct the adaptive RNA editing capability we find in the octopus. Therefore this evolution search problem is astronomically difficult. It needs to search through a large number of mostly useless candidate recoding sites, and each try would require an eternity. But it gets worse, for it is likely that any single recoding site isn’t going to accomplish much all by itself. There are many thousands of these recoding sites, and undoubtedly multiple recoding sites are needed to work together. So even if evolution could somehow accomplish the search for a single recoding site, which is astronomically difficult, it likely would not improve fitness by itself.

One look at the video above and anyone can see evolution is not a good theory. This is just common sense. Not surprisingly, the science confirms this common sense. In fact, the science doubles down, many times over.

There simply is no excuse for continuing to thinking evolution created the species. There are just too many contradictions, too many absurdities, too many ridiculous examples showing evolution to be a complete failure.

So it shouldn’t be too surprising that all of this leaves evolutionists a bit shell-shocked. They can manage little more than the usual Aristotelian teleology. As one headline explained, “ ‘Smart’ cephalopods trade off genome evolution for prolific RNA editing.” Trade off genome evolution for prolific RNA editing? That is teleological. Likewise, an evolutionist explained, “Mutation is usually thought of as the currency of natural selection, and these animals are suppressing that to maintain recoding flexibility at the RNA level.” Again, more teleology. The infinitive form tells all.

The research paper explains that these species “invented” the massive recoding. Invented? The paper also turns these species into intelligent agents:

Why would the coleoids choose to alter genetic information within RNA rather than hardwire the change in DNA?

Choose to?

This is absurd.

Evolution has been demolished by science. We are far, far beyond any kind of controversy. While evolutionists want to claim they do legitimate science, the empirical evidence has long since left the station. Evolution has been utterly demolished.

Religion drives science, and it matters.

Sunday, April 2, 2017

Brand New Study on the Evolution of Photosynthesis

A “Very Advanced Capability”

How exactly is evolution a fact when, as the number two science journal in the world put it, “How and when Cyanobacteria evolved the ability to produce oxygen through photosynthesis is poorly understood”? Or as evolutionist Robert Blankenship admitted, “The whole question of the origin of cyanobacteria has long been a mystery because they kind of just appeared out of the tree of life with this very advanced capability to do oxygenic photosynthesis without any apparent forebears.”

If the cyanobacteria that do photosynthesis “just appeared” with this “very advanced capability” and “without any apparent forebears,” and if how and when they evolved photosynthesis “is poorly understood,” then just how is it that evolutionists are so certain that evolution is a fact?

What am I missing here?

It is not as though photosynthesis is a tangential capability or a minor event in the so-called “evolutionary history” of life. As the leading science writer Charles Q. Choi put it, “One of the most pivotal moments in Earth’s history was the evolution of the photosynthetic life that suffused air with the oxygen on which virtually all complex life on the planet now depends.”

Nor is it as though photosynthesis is a simple capability, in no need of explanation for how it possibly could have arisen by random mutations. Anyone who has studied photosynthesis even superficially knows it is incredibly complex. And for those who have studied in greater detail, it only gets worse. The molecular machines and their exquisite, finely-tuned, functions are truly amazing. It doesn’t “just happen.”

Even evolutionists, who are always trying to explain how easy it would be for biology’s wonders to arise by happenstance, admit to the complexity of photosynthesis. As Blankenship put it, photosynthesis is a “very advanced capability.” Similarly, Woodward Fischer agreed that the evolution of photosynthesis would be “very challenging”:

It took a substantial unfolding of evolutionary time before oxygenic photosynthesis developed, perhaps because, as we know, it was a very challenging biochemistry to develop.

Nor is it as though the evidence we do have suggests any kind of a straightforward evolutionary development of photosynthesis.

If evolution is true, then we must fire up fresh rounds of evolution’s fake news, including incredible convergences and massive horizontal, or lateral, gene transfer and fusion. Round up the usual suspects:

The phylogenetic relationships of these prokaryotes suggest that the evolution of aerobic respiration likely occurred multiple times. This, along with evidence that the modern photosynthetic system apparently arose through the lateral gene transfer and fusion of two photosynthetic systems

This is absurd. Convergence, horizontal gene transfer, and fusion are all made up mechanisms to fix the problem that the scientific evidence contradicts evolutionary theory. This isn’t making sense.

But it gets worse.

Not only are evolutionists forced to draw from their army of phony explanatory mechanisms, but they are left with the proverbial “missing link.” The problem is, from where did the photosynthesis come? It couldn’t have come from the purported common ancestor via descent, and it “just appeared” with this “very advanced capability.”  So evolutionists have to usher in their horizontal gene transfer story.

But from where?

From where did the incredible battery of genes—that would just happen to team up and create the all-time incredible capability of photosynthesis—come? Conveniently for evolutionists—and here’s one of the beauties of being an evolutionist—they can never know. Like Flew’s gardener, evolutionists are certain that some “missing link” organism somehow had photosynthesis up and running, or just happened to have the crucial genes just lying around, but we likely will never observe that organism because it has long since become extinct.

Oh how convenient. Some mysterious organism did it. We’ll never know just how photosynthesis evolved because the organism where it happened has long since gone extinct, billions of years ago. Since then, it just luckily passed the technology around for other organisms to have, such as the cyanobacteria. Choi and Fischer explain:

The fact that Oxyphotobacteria possess the complex apparatus for oxygenic photosynthesis while their closest relatives do not suggests that Oxyphotobacteria may have imported the genes for photosynthesis from another organism via a process known as lateral gene transfer. It remains a mystery what the source of these genes was, “and because it happened long ago, it's pretty likely that the group may actually have gone extinct,” Fischer said.

Can I be an evolutionist too?

Photosynthesis is crucial to life and incredibly complex, evolutionists haven’t a clue how it could have evolved, it doesn’t fit the evolutionary common descent model and “just appeared” without a hint of where it came from, evolutionists are forced to make up a long just-so story to try to explain it, their story can’t be falsified because the origin of photosynthesis has long since disappeared, and on top of all this, evolutionists insist their theory is a fact, beyond all reasonable doubt.

This is hilarious. It is like something out of a Monte Python skit. Evolution loses every battle, but manages to win the war because, after all, it’s right.

Religion drives science, and it matters.

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.

Saturday, April 1, 2017

Here’s That Paper on MicroRNAs in Brown Algae

“No evidence of conservation”

MicroRNAs are small RNA gene products, typically consisting of 20-24 nucleotides, which help to regulate protein synthesis, for example by pausing or halting the ribosome translation process. Like the small drill bit which is inserted into the much larger drill tool, the small microRNAs are attached to a much larger molecular machine that performs the regulation. The microRNA role is to help the molecular machine recognize the correct RNA target. In other words, instead of the cell having to construct a large quantity of different molecular machines to perform the regulatory role on a large quantity of RNA targets, the cell can construct a more generic type of molecular machine, and then simply attach the instructions—the microRNA—as needed. This design approach requires the existence of these two entities: the big molecular machine and its little instruction set. Remove either entity, and this particular regulatory process isn’t going to happen. That does not fit the evolutionary narrative. According to evolution you need a slow, gradual buildup of designs, not all-or-none scenarios. But not surprisingly biology is chocked full of the latter, and so with evolution we must say that the different parts just happened to arise, perhaps serving some other roles, and then just luckily they worked fantastically together to achieve a new function. MicroRNAs are yet another finding that must be force-fit into evolutionary theory. But this irreducible complexity is only the beginning of the problem. With microRNAs, it only gets worse.

A completely different problem that microRNAs pose for evolutionary “theory” is that microRNAs do not fit the common descent pattern. As a recent paper admitted:

There is no evidence of conservation of miRNAs between the phylogenetic groups, indicating that miRNA systems evolved independently in each lineage

Evolved independently?

In other words, microRNAs do not fit the evolution model. The evidence contradicts the theory. Of course one can always make up an explanation. In this case, we say that the microRNAs “evolved independently.”

There you go, problem solved.

But let’s be honest—this is not indicated by the evidence. When the paper states that there is no evidence of conservation of miRNAs between the phylogenetic groups, thus “indicating” that miRNA systems evolved independently, it is simply misrepresenting the science.

There is precisely zero scientific evidence that microRNAs “evolved independently.”

Zero.

That is not my opinion. That is not conjecture. That is scientific fact.

Evolutionists talk a lot about scientific “fact.” They insist evolution is a scientific “fact.” But let’s just be honest. What is a scientific fact here is not evolution, but rather the exact opposite. The “fact” is the microRNAs show “no evidence of conservation.”

That fact does not “indicate” evolution, it contradicts evolution.

Let’s just be honest. For once.

The paper finds yet another example of this failure in the microRNAs in brown algae. The study investigated the microRNAs in the species, Saccharina japonica, and compared them to previously investigated microRNAs, including those in a different brown algae species. Their findings were, as usual, “surprising.” The microRNAs in the two brown algae species were different.

Completely different.

There was not a single pair of microRNAs, between the two species, that showed any sign of statistically significant sequence similarity.

Interestingly, the microRNAs in the two species did generally share some structural and genomic features. So the evolutionists had to conclude that the microRNAs in the two species evolved from a common ancestor, but then their respective sequences evolved like crazy, leaving zero trace of sequence similarity.

This. Makes. No. Sense.

Here how the paper spun the results:

Surprisingly, none of the S. japonica miRNAs share significant sequence similarity with the Ectocarpus sp. miRNAs. However, the miRNA repertoires of the two species share a number of structural and genomic features indicating that they were generated by similar evolutionary processes and therefore probably evolved within the context of a common, ancestral miRNA system. This lack of sequence similarity suggests that miRNAs evolve rapidly in the brown algae (the two species are separated by ∼95 Myr of evolution). The sets of predicted targets of miRNAs in the two species were also very different suggesting that the divergence of the miRNAs may have had significant consequences for miRNA function.

“Probably evolved within the context of a common, ancestral miRNA system”? So what does “within the context” mean?

The answer is this is a meaningless cover phrase that masks the fact that the evidence contradicts the theory. It is evo-speak for “We don’t know what we’re talking about.” A more polite description is “hand-waving.”

A less polite, and more accurate description won’t be repeated here.

I will now consider the elephant in the room: Why is evolution being used to interpret the results in the first place? The theory is superfluous. It is redundant. It is vacuous. It is non-parsimonious. It is meaningless.

The theory does nothing to help us understand, interpret, elucidate, guide, or formulate meaningful predictions. Its only justification is itself.

We use the theory of evolution to interpret the results because the theory is true. And how do we know it is true? Because it is true?

The theory is self-referential. It is circular. It is famous for being famous.

It is a hold-over from the Epicureans of antiquity, the schoolmen of the Middle Ages, the rationalists of the seventeenth century, and the Darwinists today, and it has made a mockery of science.

Religion drives science, and it matters.

h/t: The Man

Thursday, March 30, 2017

Mark Cuban on Health Care

The Long Arm of Evolution

There is much disagreement over evolution but one thing we can all agree on is that evolution is a highly influential theory. Like it or not, few scientific theories are as influential as evolution. Darwin’s theory injected its deeply flawed science into biology, but it did not stop there. One area where evolution’s damaging influence is important today is human health. There is much to say about how evolution has influenced our thinking about health and our health care system. I will focus on two basic myths evolution has propagated which have done enormous damage: the random causation myth and the king gene myth.

You don’t need to be a scientist to know that random change is fundamental to evolution. From Darwin to today’s evolutionists, the key point in arguments for evolution is that this world was not designed. This age-old, Epicurean, idea mandates that the world arose from unguided, random, forces.

Scientific theories require mechanisms, and evolution’s main mechanism is random change. You have heard of natural selection but it, as even Alfred Wallace agreed, is not a mechanism as such. It doesn’t cause or coax helpful biological change to occur. It merely kills off the weaker designs. Evolution is a theory of randomness.

Evolutionists did not understand just how such random change could be caused until genetics was better understood in the twentieth century. Evolutionists needed to explain how biological change could occur randomly, yet be inherited once it occurred. Modern genetics provided the answer: the gene. Random mutations could alter genes and later be passed on to future generations.

This Version 2.0 of Darwin’s theory vaulted the gene to hero status as genes were viewed as the veritable blueprint of the body. The old proverb, “you are what you eat,” became “you are what your genes say you are.”

Not surprisingly there were high expectations for the Human Genome Project, which would transcribe the human genome. Its initial results, produced in the year 2000, were highly proclaimed with much fanfare, with scientists and politicians (including Bill Clinton and Tony Blair) proclaiming great things to come. That early optimism, however, eventually faded as years later scientists would admit the problem was far more complex. Genes are important, but not that important. The idea that your genes determine your body has not held up well.

Evolution's dual myths of random causation and the king gene have not been good for biology, and they also have done damage elsewhere. In the area of human health, our cultural uptake of evolutionary ideas contributed to the dangerously flawed notion that health is a random affair. True, genetic mutations are capable of producing all kinds of diseases, but the vast majority of health issues stem from, or can be alleviated by, lifestyle and workplace decisions. In a great many cases, you are not what your genes say you are, but what you eat and how you live. Diet, stress, exercise, and exposure to toxins play an enormous role in determining your health history.

That shouldn’t be a surprise.

But too often it is completely missed or under emphasized, and an unfortunate example of this flawed evolutionary influence is our health care system and health insurance. Our skyrocketing costs could be reduced by half or even an order of magnitude with proper education and personal decisions. But instead, our health is too often viewed as essentially the luck of the draw. For instance, billionaire Mark Cuban recently expressed this sentiment in advocating for healthcare as a legal right:

All involved [in the national health care debate] are ignoring the basic question. And I think Sen. [Bernie] Sanders brought this up, is healthcare a right or an opportunity in the United States? I believe that, given we all face the exact same genetic and wrong place, wrong time risks, coverage of most chronic and life-threatening illnesses or injuries should be a right.

In other words, everyone faces about the same healthcare risks. Our health is a crapshoot.

This is an astonishing demonstration of scientific ignorance. There is no doubt Cuban is very good at making money. But Cuban fails to grasp the most basic aspects of human health. He can hardly be blamed, however, given how dominant this evolutionary myth has become. Evolution’s influence is enormous, and that is bad news for more than just biology.