Monday, September 1, 2014

Here is How the Cytoskeleton Evolved

Not Easy to Explain

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

h/t: La Victoria

Monday, August 25, 2014

Death as the Engine of Progress

Ideas Have Consequences

Watch this short video to see how ideas have consequences.

At some future period, not very distant as measured by centuries, the civilized races of man will almost certainly exterminate and replace throughout the world the savage races.—Charles Darwin, The Descent of Man

the war of annihilation … is a natural law, without which the organic world … could not continue to exist at all.—Gustav Jaeger, 1870

just as in nature the struggle for existence is the moving principle of evolution and perfection … so also in world history the destruction of the weaker nations through the stronger is a postulate of progress.—Friedrich Hellwald, 1875

according to Darwin’s theory wars have always been of the greatest importance for the general progress of the human species … the physically weaker, the less intelligent, the morally lower … must give place to the stronger.—Heinrich Ziegler, 1893

Those people who are, from the outset, failures, oppressed, broken— they are the ones, the weakest, who most undermine life among human beings, who in the most perilous way poison and question our trust in life, in humanity, in ourselves.—Friedrich Nietzsche, On the Genealogy of Morals

The law of selection exists in the world, and the stronger and healthier has received from nature the right to live … Woe to anyone who is weak, who does not stand his ground! He may not expect any help from anyone.—Adolf Hitler

Müller Cells are Wavelength-Dependent Wave-Guides

Enhancing the Cone Photoreceptor Sensitivity

The best arguments for evolution have always been from dysteleology. This world, as evolutionists explain, just does not appear to have been designed. Consider our retina for example. Isn’t it all backwards, with the photocells—which detect the incoming light—pointed toward the rear and behind several layers of cell types and neural processes. Does this make any sense? Surely such a claptrap would offend any “tidy-minded engineer,” as Richard Dawkins put it. But such arguments have never worked and the history of evolutionary thought is full of their failures. Aside from the fact they are metaphysical and not open to scientific testing, they inevitably are simply false. The “bad retina design” argument, as discussed here, here, here, here and here for example, has repeatedly been rebuked. As we learn more we find the retina has all kinds of subtle and clever designs. And now new research out of Israel continues to confirm this trend. Unbelievably, the scientists have demonstrated that the retina’s Müller cells are wavelength-dependent wave-guides that focus the longer-wavelength green-red light onto the cone photoreceptors and pass the shorter-wavelength blue-purple light through to the rod photoreceptors.

It just so happens that is a great idea because while the cone photoreceptors are fast acting and provide color vision, they are less sensitive and need all the help they can get. The rod photoreceptors, on the other hand, are mainly sensitive to the shorter-wavelength blue-purple light, so they don’t miss too much the filtering out of the green-red light. As one science writer concluded:

Having the photoreceptors at the back of the retina is not a design constraint, it is a design feature. The idea that the vertebrate eye, like a traditional front-illuminated camera, might have been improved somehow if it had only been able to orient its wiring behind the photoreceptor layer, like a cephalopod, is folly.

It just isn’t very smart to criticize a design when you’ve never built one yourself and, much less, don’t even know how it works. It’s even worse to then use that ill-conceived criticism as justification for the claim that the design arose spontaneously. From a scientific perspective that claim was always weak. Now it is simply ridiculous. The retina’s incredible design reveals the details of what always was intuitively obvious. As Paul explained, God has made foolish the wisdom of this world.

Saturday, August 2, 2014

Evolutionist: Dinosaurs “Were Experimenting” With Flight

Just-So Stories With Final Causes: Aristotle Meets Kipling

Did dinosaurs really shrink so fast on their way to producing birds? That is what happened according to a new study out this week. As the LA Times explains, “Paleontologists have long known that birds evolved from dinosaurs known as theropods,” and now they have confirmed that over a 50 million year period that evolutionary pathway proceeded at several times the normal pace. But as usual the evolutionist’s certainty is underwritten by a mix of speculation and Aristotelianism.

How exactly has this new study confirmed that dinosaurs evolved birds at a fast pace, and how exactly is it that “paleontologists have long known that birds evolved from dinosaurs known as theropods”? In fact there was no such confirmation and there is no such knowledge, not in any scientific sense.

When we say that scientists “know” something, we do not mean that they personally believe it (which paleontologists do), we mean that they have compelling, overwhelming evidence for it (which paleontologists do not). In the scientific sense, which of course is the sense in which evolutionists portray themselves and the sense intended by the Times article, paleontologists have no such knowledge.

That is not in question. How can I know this? Because I’ve read what they have to say. I know their arguments. Unless they’ve been cleverly hiding their proofs, there is no question that they do not “know” dinosaurs evolved into birds—at a fast pace or otherwise.

In fact what evolutionists have most of to offer is speculation, sometimes referred to as “just-so” stories after Kipling’s classic by the same name. For example, evolutionists speculate that as the dinosaurs became smaller (for some reason) their embryonic development phase shortened. And this abbreviated development period meant (for some reason) that the miniaturized dinosaurs retained into adulthood their juvenile features, “some of which were uncannily bird-like.”

And why would dinosaurs become smaller in the first place? Well maybe they were adapting to living in trees where massive size, after all, puts one at a decided disadvantage. Instead, they would need to be small and agile. And maybe nocturnal as well, so evolving feathers to stay warm would help. Longer forelimbs would also help swing from tree to tree, and perhaps those longer forelimbs evolved into wings.

What evolutionists lack in evidential support they make up for with imagination. And evolutionists frame their just-so stories in Aristotelian, final causes, terminology. For example, there was a “push” toward smaller size, and the smaller sizes in dinosaurs helped to “trigger” a host of different traits. A wing-like surface area would have developed “to help glide” from tree to tree. After all, dinosaurs “were experimenting” with flight in various modes and finally “made the crucial leap” to powered flight, and so birds “were born.”

Dinosaurs were experimenting with flight? This isn’t science, this is absurdity.

Thursday, July 31, 2014

Gigantic School of Rays

Evolution at Work

Evolutionists are certain these rays arose spontaneously even though they can’t explain how that could have happened.

Wednesday, July 23, 2014

Birds With Ornamental Eyespots Have Unlikely Neighbors

More Independent Evolution

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

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

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

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

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

Friday, July 18, 2014

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

Nothing is Going Right

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

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

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

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

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

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

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

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

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

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

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

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

Consider how one report explains the new spider study findings:

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

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

Sunday, July 13, 2014

A Key Evidence for Evolution Involving Mobile Genetic Elements Continues to Crumble

More Junk DNA That Isn’t Really Junk After All

It is difficult to keep track of all the studies indicating that junk DNA isn’t really junk DNA after all. I have no idea how much actual junk there is in our genomes, but evolution has a long history of failed claims of disutility, inefficiency and junk in nature’s designs. That is why I think Dan Graur took the wrong side of history in his “either the genome is mostly junk or evolution is false” proposition.

A study published last week found strong signs of function in mobile repetitive DNA elements. Mobile genetic elements have been heavily recruited by evolutionists in recent years as powerful, undeniable proofs of common ancestry. An underlying assumption in those proofs, aside from the usual non scientific metaphysics, is that such mobile elements insert themselves into the genome at random. But this study suggests they are at least sometimes nonrandom and functional. As one report explains:

“We’ve come to understand that not all repeat sequences are junk DNA,” said Pawel Michalak, an associate professor at the Virginia Bioinformatics Institute.  “These repetitive sequences are increasingly being recognized as agents of adaptive change. We discovered a larger than expected amount of genetic variation in these repeating sequences between the fly populations and saw that the variation resulted in potentially functional differences in important biological processes, such as stress resistance and mating.”


The biological roles of these place-jumping, repetitive elements are mysterious

They are largely viewed as “genomic parasites,” but in this study, researchers found the mobile DNA can provide genetic novelties recruited as certain population-unique, functional enrichments that are nonrandom and purposeful.

“The first shocker was the sheer volume of genetic variation due to the dynamics of mobile elements, including coding and regulatory genomic regions, and the second was amount of population-specific insertions of transposable DNA elements,” Michalak said. “Roughly 50 percent of the insertions were population unique.”

The fact is, as this study further suggests, we don’t really understand genetics well enough to support the kind of hard claims evolutionists make about the evidence.

Friday, July 11, 2014

Here’s That Protein-Protein Interaction Problem

Evolutionists Don’t Know What They’re Doing

In Chapter 7 of The Edge of Evolution, Michael Behe explained why protein-protein interactions are a problem for evolution. Here is a summary of the problem. First, protein-protein interactions are important. Proteins often work in teams where half a dozen or more proteins may be interacting with each other to form a molecular machine. Protein-protein interaction is ubiquitous throughout life—so ubiquitous that we now have a name for the collective set of such interactions: the interactome. You can’t do much without protein-protein interactions. It is not as though protein-protein interactions are a convenient extra that makes cells a bit more efficient or bequeaths a few nice-to-have functions. Protein-protein interactions are fundamental to life, and are fundamental at all levels. Evolution must have been creating protein-protein interactions throughout evolutionary history as new species and capabilities arose.

And yet it is difficult to get two proteins to interact in a meaningful way. Such interactions must not be too strong or too weak. Imagine that you had two proteins that you needed to bind meaningfully to each other. If you randomly selected the amino acids at the binding patch on the surface of one of the two proteins, then meaningful binding would be unlikely. In fact, you would have to repeat the experiment millions of times before you could expect to get a good result.

But evolution does not have such resources. It cannot conduct millions of evolutionary experiments in order to luckily find amino acid sequences on protein surfaces that are required for important biological functions. And even if it could, that would only be the first step, because molecular machines are often comprised of multiple proteins, interacting with each other at multiple sites. So evolution would have to luckily find several sequences, in multiple proteins, and get them to arise in similar time frames, so the molecular machine would function.

But that is not all, for molecular machines often work in conjunction with other molecular machines. Having a molecular machine without its neighbors would often not help much.

And yet even with all this there remain more problems. For instance, most proteins are not highly modifiable. You can’t just randomly go about swapping in different amino acids. Protein function typically degrades rapidly with amino acid substitutions. So it is challenging for very much interaction site experimentation to take place in the first place. And of course another problem is that it is astronomically difficult for evolution to evolve a single protein to begin with, let alone meaningful interaction sites.

Simply put, from a scientific perspective protein-protein interaction is another problem for evolution.

Thursday, July 10, 2014

A Triplex RNA Structure For Real Time Frame Shifting

More Biological Fine Tuning

Protein-coding genes provide a sequence of nucleotides that is read three nucleotides at a time. Each triplet is translated into a particular type of amino acid. So a sequence of 300 nucleotides codes for 100 amino acids, which are attached to each other to make a protein. But what if you started not with the first nucleotide in the sequence, but with the second one? You would have a different sequence of nucleotide triplets, and so a different sequence of amino acids. This is also true if you started with the third nucleotide. In fact you could switch over to the opposing DNA strand (the other half of the double helix) and again you would have the choice between three different “frames,” resulting in three different sequences of amino acids. So in all you can choose between six different reading frames. So any given gene has the theoretical possibility of containing different genetic messages, in the different reading frames. And indeed, years ago it was discovered that genes are overlapping—portions of their nucleotide sequence exist on the same segment of DNA, just in a different reading frame. But an even more bizarre theoretical possibility is that the reading frame could shift while the sequence of nucleotides is being read. In that case you are mixing and matching partial sequences from different reading frames. Now, a new study has investigated this capability and discovered a fascinating mechanism that apparently enables the real-time frame shifting.

Nucleotide sequences are translated into amino acid sequences at the cell’s ribosome structures and the new study found that this translation process can be programmed to skip a nucleotide, and so switch to another reading frame, attaching two short snippets of nucleotide segments, known as microRNAs, to the main nucleotide sequence at certain locations. The study suggests that a pseudoknot, or triplex, RNA structure is formed causing the skip to occur. Of course the right nucleotide sequence is required, and the right microRNA sequences are required. It was not easy to solve this complicated puzzle, as one researcher explained:

These are really complex RNA structures. It takes a lot of computer memory to search for them in human cells. It wasn’t until the past decade that computers were fast and powerful enough to find these signals.

It is yet another “novel mode” of realtime biological response resulting in “fine-tuned” cell performance. It all just smacks of random mutations.

Monday, June 30, 2014

Convergence in Venomous Snakes of North America and Australia

Another Just-So Story

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

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

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

Saturday, June 28, 2014

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.

Friday, June 27, 2014

Greg Dawes: Religious Arguments Are Susceptible to Divine Mystery

Except When We Use Them

As a general rule, evolutionists never allow their own ideas to be exposed to the criteria they are using to criticize the other guy. To wit, while Greg Dawes finds there to be all kinds of problems with appeals to divine agents, including the fact that we really can’t predict what an omnipotent, omniscient, and morally perfect agent would do, he also finds evolution to an inference to the best explanation, in spite of the fact that that inference relies on the evolutionist’s appeals to how God would create the species.

Thursday, June 26, 2014

Greg Dawes Contradicts Himself

On The Same Page

It is good to see that philosophers such as Greg Dawes understand that Darwin “argued for his theory by contrasting it with the idea of special creation” which Darwin found to be “utterly puzzling.” But on the same page the University of Otago professor states that the modern sciences are naturalistic as they make no reference to non-natural agents. No reference to non-natural agents? It is yet another example of how evolutionists believe so strongly in their own religious views that they do not view them as religious.

Religion drives science, and it matters.

Tuesday, June 24, 2014

Evolutionists Are Now Embracing Determinism and Denying Free Will

His Neurons Made Him Do It

Evolution is the most influential theory in the history of science, but where exactly does it lead? Well aside from eugenics, abortion, population control, euthanasia, anti realism, blackballing of opponents, false histories and atheism, evolution also can lead to determinism. Of course like so many of its metaphysical conclusions, evolution leads to determinism only because determinism first led to evolution. For determinism was one of the planks in the so-called “Enlightenment” period, a century before Darwin. So like the French mathematician Pierre-Simon Laplace from two centuries ago, today a growing number of evolutionists hold to the anti realism belief that free will is an illusion. For Harvard’s Gabriel Kreiman, our actions are governed by our neurons, and how they fire off is like the toss of a coin:

The rules that govern our decisions are similar to the rules that govern whether a coin will land one way or the other. Ultimately there is physics; it is chaotic in both cases, but at the end of the day, nobody will argue the coin “wanted” to land heads or tails. There is no real volition to the coin.

And likewise, there is no real volition is us either. We’re like coins. After all, in experiments the neurons of human subjects showed activity before the subjects felt the urge to action. Ergo determinism. Your actions are the result of neural computations. Kreiman believes this work challenges important Western philosophical ideas about free will. Actually it reinforces important Western philosophical ideas about free will. That’s the problem.