Wednesday, September 17, 2014

Here’s a Typical Example of Evolutionary Story-Telling

Maybe, Could Have, Would Have …

Evolutionary events are, as Theodosius Dobzhansky put it, “unique, unrepeatable, and irreversible.” And so evolution is an idea with more theorizing than hard facts. It is more of a narrative than a theory. Here is a typical example:

It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario). I propose that the ancestors of archaea (and bacteria) escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the "prokaryotic" phenotype (the thermoreduction hypothesis). Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one. I suggest that selection of different parts of the ancestral virosphere at the onset of the three domains played a critical role in shaping their respective biology. Eukarya probably evolved toward complexity with the help of retroviruses and large DNA viruses, whereas similar selection pressure (thermoreduction) could explain why the archaeal and bacterial mobilomes somehow resemble each other.

I suggest?
The bug in-between scenario?
Escaped protoeukaryotic predators?
Invading high temperature biotopes?
Triggering their reductive evolution?
The thermoreduction hypothesis?
Probably evolved toward complexity with the help of retroviruses and large DNA viruses?
The archaeal and bacterial mobilomes?

Kipling would be proud.

Why the Narrative Trumps the Facts

What Evolution is All About

Greg Conterio, echoing Robert Bidinotto, makes the point that culture war differences often pit the facts versus the narrative. The facts can win every battle but the narrative wins the war. As Bidinotto puts it, “One of the most valuable insights I discovered in recent years is how Narratives trump everything else — including what most of us would call concern for ‘practical results.’” Conterio and Bidinotto are mainly concerned with political issues, but what lies behind their insight is our beliefs about origins.

A predetermined narrative is what influenced Darwin in concluding that the species must have arisen as a result of the blind actions of natural processes. As Darwin historian Janet Browne explained, Darwin, as well as evolution co-discoverer Alfred Wallace, came to believe in transmutation and so they then sought a suitable mechanism. The reason they came to believe in transmutation was the biological world was too gritty, too unseemly, and lacking in elegance. In a word, too evil.

Such rationalistic thinking (starting with preconceived ideas of what to expect, rather than exploring the data to see where it leads) about origins by no means began with Darwin and Wallace. They were handed these ideas from leading Christian thinkers from the previous centuries. Evolution was not a scientific finding, it was a religious conclusion.

From a scientific perspective, the spontaneous origin of the biological world makes little sense. Darwin and Wallace had no idea how such wonders actually could have sprung up all by themselves. Nor do evolutionists today. As Browne put it, they first believed—then they sought a scientific mechanism. That’s backwards, but this is precisely what they, and their followers today, are committed to.

The result is that evolution has introduced into science the art of story-telling. Evolution is a narrative, not an appeal to scientific principles and laws. Evolutionary events are “unique, unrepeatable, and irreversible” in the words of famous evolutionist Theodosius Dobzhansky. Or as Harvard’s Ernst Mayr wrote, “Laws and experiments are inappropriate techniques” for explaining evolutionary events and processes.

Evolution is a narrative. And it is not just any narrative—it is the world’s creation story. The most important fundamental of a culture is its creation story. Tell me where you think you came from, and I’ll tell you everything else about you. At least everything that is important.

So what Conterio and Bidinotto are observing is the fruit of evolutionary thought. Evolution is not merely a scientific theory. It is the most influential theory in areas outside of science, in the history of science.

One now classic example of this is how evolutionary theory influenced historiography. In the nineteenth century evolutionists began constructing the history of ideas from their perspective. It became known as the Warfare Thesis, or Conflict Thesis, because it cast religious people as resisting, and in conflict with, science and its objective truths.

Even though historians agree that the Warfare Thesis is a strong dose of Whig history, it nonetheless often informs our culture’s views today. Anyone questioning evolution is cast as the fundamentalist, opposing the objective, truth-seeking scientists.

The poster child for this mythical retelling of history is Inherit the Wind, a play and movie that is a fictionalization of the famous 1925 Monkey Trial. Evolutionists today heavily promote this film as a cogent insight into our culture. It casts evolutionists as the white-hat good guys, and skeptics as ignorant, religious zealots.

Many evolutionists are unaware that Inherit the Wind is a fictionalization. And when told about this, they don’t really care. Because the narrative trumps the facts.

Judge John Jones explained, for example, he wanted to see Inherit the Wind a second time in preparation for the 2005 Dover case, over which he presided, because the film puts the origins debate into its proper “historical context.” Jones later reminisced about the trial, explaining that “I understood the general theme. I’d seen Inherit the Wind.”

But a federal judge’s profound ignorance and prejudice over a case in which he presided does not bother anyone—he was exalted as one of Time magazine’s 100 Most Influential People of the Year. So what if Inherit the Wind takes a few liberties with the truth, it is the narrative that counts.

Unfortunately evolution’s influence didn’t stop with a silly screenplay. With evolution life has no divine spark, we weren’t made in the image of any Creator, and things like facts and laws, both scientific and otherwise, don’t really matter. In politics, as well as evolution, it’s all about the narrative, not following the law.

Tuesday, September 16, 2014

Making New Genes Just Got More Exotic—Yes They Evolve, But How?

Gene Duplication Meets Epigenetics

Making new genes is not easy. For several decades now it has been thought that the only process for gene construction is to start by duplicating an existing gene and then making adjustments to it (it is not the only process, but that is another story). Naturally evolutionists interpreted this duplication process as another example of an evolutionary mechanism. What they don’t consider, however, is how subtle this process is.

Too often the origins debate focuses on the simplistic opposites of stasis and change. Evolutionists would have it that creationism and Intelligent Design require complete stasis in the biological world—no changing of the species. Any change that is discovered, such as the construction of new genes, is interpreted as yet another proof text of evolution.

But why? Why should we think that adaptation to the environment immediately implies random mutations, natural selection, common descent, a strictly blind naturalistic origin of the world via chance, and so forth?

It simply doesn’t follow. In fact, research has consistently shown that the species have a fantastically complicated built-in adaptation capability. Organisms respond rapidly to environmental challenges with directed changes, not slowly with blind, random changes.

As research continues, this story just continues to grow. For instance, regarding the construction of new genes via duplication of an existing gene, a recent study added yet another layer of incredible subtlety and nuance. It turns out that after a duplication event, the organism often labels one of the genes, as though marking it for change. The technical term for this is “epigenetics,” and it amounts to small chemicals being attached to either the gene or to the proteins about which the gene is wrapped. This chemical “barcode” technology is fantastic, as it involves several different chemicals, each conveying a different message, and the message varies depending on just where the chemical is attached. The chemicals can even be attached to other small chemicals that were previously attached.

So the question is not, “Do organisms change and adapt?” It would be silly to make that the test for the truth of blind, random evolution.

There is no question that organisms adapt. And so there is no question that species undergo evolution in the sense that they respond and change. But evolution can be a loaded term. For most of us, evolutionists included, “evolution” automatically means the undirected origins of, well, pretty much everything.

That simply is not what the science shows. The science shows that the species adapt via fantastically exotic, creative and nuanced processes. Perhaps all of this arose from an undirected origins, but that would call for an enormous serendipity. In other words, it would mean that the incredible processes by which evolution occurs were, themselves, created by evolution. That would be highly serendipitous.

We need to stick to what the evidence tells us, and be careful not to make unwarranted claims beyond the evidence.

Monday, September 15, 2014

Here’s Something Orwell Didn’t Predict

Health Warnings for Anyone Who Disagrees With AGW

According to a report from The Times earlier this year, policy makers in Britain are attempting to enforce AGW (anthropogenic, or man-made, global warming) by mandating politicians who are skeptical to “shut up” about it and the BBC to give less airtime to anyone who points out its many scientific problems. One mechanism that was recommended was to have appearances by such trouble-makers accompanied by health warnings. How about stickers in textbooks?

Global Warming and Information Manipulation

Now if we Could Just Get the Chinese to Look at Evolution

Here is a paper out of the PRC that raises some awkward questions about the intellectual climate surrounding global warming. Apparently with all the blackballing, peer-review control, publication manipulation, and funding and career threats, the Chinese suspect there might be some manipulation of information at work.

It appears that news media and some pro-environmental organizations have the tendency to accentuate or even exaggerate the damage caused by climate change. This article provides a rationale for this tendency by using a modified International Environmental Agreement (IEA) model with asymmetric information. We find that the information manipulation has an instrumental value, as it ex post induces more countries to participate in an IEA, which will eventually enhance global welfare. From the ex ante perspective, however, the impact that manipulating information has on the level of participation in an IEA and on welfare is ambiguous.

In other news, last week Rapid City had the earliest snow since 1888.

If the Chinese are sensing something awry in global warming, I can’t wait until they cast their gaze on evolution.

Sunday, September 14, 2014

Evolutionist Says Evolution’s “Traditional Framework” Must Go

Is This the Third Stage?

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

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

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

As the old saying goes:

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

Perhaps we are moving into the third stage.

William Dembski: Conservation of Information in Evolutionary Search

University of Chicago Computation in Science Seminar

A Pond-Dwelling, Single-Celled Organism Does Amazing Genetic Engineering

One of Nature’s Attempts to Become More Complex

A new paper was published last week on a remarkable single-celled organism, Oxytricha trifallax, that has two nucleus’ and 16,000 chromosomes (recall that humans have 46). The organism uses one nucleus to store its active DNA and the other nucleus to store an archive of the genome. Amazingly, Oxytricha trifallax, disassembles the archived copy into a quarter-million pieces and then rapidly reassembles them into a new and improved version. This reassembly occurs at mating time as the organism and its mate exchange about half their genome.

Creating and maintaining a backup copy of the genome, disassembling that copy, integrating disassembled material from an external source, reassembling the whole thing to produce improved, rejuvenated chromosomes—it all just smacks of blind mutations.

Incredibly evolutionist Laura Landweber explains that Oxytricha trifallax is “one of nature’s early attempts to become more complex despite staying small … People might think that pond-dwelling organisms would be simple, but this shows how complex life can be.”

One of nature’s early attempts to become more complex? This is a typical example of the underlying Aristotelian thought that pervades evolution. Evolutionists have no idea how Oxytricha trifallax amazing capabilities could have evolved by random variation such as mutations. So they describe it in teleological language. This isn’t science.

Of course the idea that Oxytricha trifallax evolved doesn’t come from the science. It comes from a dogmatic commitment to evolution.

Religion drives science, and it matters.

When I Pointed Out the De Novo Gene Evidence an Evolutionist Came Unglued

Primitive Thinking

It is interesting that evolutionists, who believe they came from primitive apes, display a certain primitive thought in their communications. The latest example is an evolutionist who criticized a book skeptical of evolution. The book made the point that fundamentally new genes are unlikely to have evolved by the usual random change and natural selection mechanisms. The book elaborated on this problem at length. But the evolutionist retorted that this was all wrong:

[The book] claims that the origin of new genes is a mystery, when in fact it is basically a solved problem (as long as you aren’t talking about the origin of the very first genes at the origin of life—and allegedly this book is supposed to be about the Cambrian Explosion, not the origin of life).

In other words, aside from the origin of life, the origin of fundamentally new genes is not a mystery and is basically has been solved by evolutionists.

That is, of course, false. When I pointed out the evidence the evolutionist harshly criticized me.

Look up jingwei and sdic and the literature on their origin. Look up Long et al. 2003. Why can’t you even get these totally obvious basic points right?

The problem is jingwei and Sdic are not fundamentally new genes, but rather have significant similarities to parts of other genes. And the paper he cited did little to resolve this question of how fundamentally new genes arose. In fact, about the only thing the paper did say about the evolution of such genes is that it is rare. That view has since been discarded as too many of these fundamentally new genes have been discovered.

So the evolutionist cited two irrelevant genes and a paper that gave an outdated view, and accused me of missing “totally obvious basic points.”

When I pointed all this out, the evolutionist tried to walk back his points. He claimed that I was the one who brought up fundamentally new genes, and that he merely was referring to genes that are mostly rearrangements of other genes. “Shame!” he vindictively concluded.

And there we have it. At this point the evolutionist is in checkmate. For he has just forfeited his claim that the book is all wrong, that the evolution of new genes is a solved problem, and by extension that evolution is a fact. He cannot now say, “Oh, but I was also referring to fundamentally new genes also.”

He has made it clear that the book’s criticism is on solid ground. For as I pointed out (here and here), the evolutionary reasoning that such genes evolved by the usual random mutations and selection is circular. And the explanations for how this could have happened is little more than hand waving. Even evolutionists agreed it was impossible until, that is, the existence of such genes could not be denied. At that point evolutionists had to come up with some sort of explanation. The result is a speculative idea that relies on serendipity and ignores known, enormous problems.

A theory cannot fail to explain a plethora of fundamental observations and be a fact. Not a scientific fact, at least.

So will the evolutionist admit to any of these things? Will he agree that evolution is not a fact? Of course not. I’ll take the shame and the blame, and all the harsh criticism, if we can just agree on the overwhelming scientific evidence which checkmates evolution. Evolution is not a fact, and it never was.

Saturday, September 13, 2014

Here is the Latest Example of Evolution Undermining Law

A Falsification of Evolution Becomes a Legal Premise

Evolution is not merely a scientific mistake. It is not a theory gone wrong, started by a guy in 1859. Evolutionary thinking was alive and well when Charles Darwin codified it in the emerging life sciences, for it had been developed and promoted by theologians and philosophers since the seventeenth century. If you understand that history, then today’s world makes much more sense. It is often said that evolution is the most influential scientific theory, but that is because evolution isn’t just a scientific theory, it is a broader world view. So with the dominance of evolution comes a wide array of influences, in government and in society, and across the political spectrum. Another example of this came last week when the United States Court of Appeals for the Seventh Circuit ruled that laws in Indiana and Wisconsin, defining marriage to be between a man and a woman, are unconstitutional.

While it is no secret that evolutionary premises now inform opinions across the political spectrum, this decision (written by a Reagan appointee) made those premises explicit as it cites evolutionary research and is based on the assumption that evolution is true. Its point is that homosexuality is a result of evolution so therefore gay marriage should be a legal right.

Should we point out that evolution is scientifically flawed? Or should we point out that homosexuality, the usual mental gymnastics of evolutionists notwithstanding, makes no sense under evolution? Remember that part about reproductive success?

It is all reminiscent of Judge John Jones—exalted as one of Time magazine’s 100 Most Influential People of the Year—hilariously revealing that he actually wanted to see Inherit the Wind a second time in preparation for the 1995 Dover case, over which he presided, because, after all, the film puts the origins debate into its proper “historical context.”

Proper historical context? You’ve got to be kidding.

What a classic mistrial. Jones had been so indoctrinated by the Warfare Thesis that he actually believed the evolutionary propaganda to be historically accurate. If the perfect crime is the one that is never discovered, the perfect propaganda is the one that is never understood. Jones later reminisced about the trial, unbelievably explaining that “I understood the general theme. I’d seen Inherit the Wind.”  Jones was not educated, he was brainwashed.

And unfortunately Jones is not simply a lone nut. Legal expert Andrew Cohen not only gave high praise to Inherit the Wind, but absurdly called it “one of the great trial movies of all time.” The movie is a fictional construct, based on the fictional Warfare Thesis erected by evolutionists, and long since discredited by historians. Are they showing it in law schools these days?

So the Seventh Circuit’s explicit premise of evolution is not surprising. It is simply a confirmation that dangerous ignorance pervades the highest levels of power.

Friday, September 12, 2014

Evolutionists are Doubling Down on De Novo Gene Evolution

They Win Again

How can a new protein-coding gene emerge from a random stretch of DNA? According to evolutionists this occurs via the usual random mutations and natural selection. In fact, as I explained last time, evolutionists are saying this is “basically a solved problem.” But such de novo gene evolution is not anywhere close to a solution. Even evolutionists, only a few years ago, agreed this was a heroic idea and that such genes could not have evolved, at least in the usual way. In typical fashion they pushed the problem into the recesses of deep time where anything can happen by mysterious mechanisms that no longer are present and so cannot be critiqued. That narrative serviced evolutionary thought for many years until the evidence for unique, so-called “orphan,” genes became undeniable.

And why were orphan genes a problem? If any design, such as orphan genes, exists in a species but not its allied species then according to evolutionary thinking, said design must not have been present in the common ancestor of those species. It must have evolved after the split from the common ancestor. And that means such a heroic evolutionary event cannot be pushed into deep time. And that’s a problem.

At first evolutionists rejected such an idea. They said such orphan genes would no longer be orphans once we decode the genomes of more species. But with more genomes came more orphans. Orphan genes did not diminish, they escalated, much to the chagrin of evolutionists.

So next evolutionists admitted that there were some novel, orphan genes, but they were exceedingly rare. An evolutionary novelty. And of course novelties are not fundamental to a theory, and so don’t need to be explained.

But the orphan genes just kept on coming. And coming. Finally evolutionists had to admit that there were a whole bunch of orphan genes, and so a whole bunch of genes, in various creatures, must have evolved relatively recently.

And as only evolutionsts can do, after losing every battle, they once again won the war. They turned defeat into victory by explaining that they now have evidence that genes are routinely evolving. The de novo mechanism went from rags to riches. It now was the predominant mode of gene evolution—it happens all the time, and there is no mystery.

And what exactly was that evidence that resolved the mystery? How can evolutionists now be so confident of what, only a few short years ago, they insisted was not possible? Well, err, the orphans are the evidence. Orphans exist in only a single species, so therefore the orphans must have evolved recently.

There, I said it.

And immediately this new truth was broadcast to the people. The New York Times assured its readers that evolutionists have discovered a “step-by-step process” for fast, efficient, modern gene evolution.

So it wasn’t too surprising when an evolutionist claimed recently that the origin of new genes, save for the very first genes way back in deep time, is “basically a solved problem.” That is, after all, the party line.

But when I pointed out the circular reasoning, the failed expectations, and the lack of any real solution beyond hand-waving, the evolutionist doubled down. He cited an 11 year old irrelevant paper (which repeats the now discounted refrain that “the true de novo origination of new genes from previously non-coding sequences is rare”). He also cited two proteins, neither of which are even examples of de novo gene evolution.

And so there we have it. Another evolutionary victory snatched from the jaws of defeat.

Thursday, September 11, 2014

Is the Origin of New Genes “Basically a Solved Problem”?

De Novo Genes a Done Deal

It is no surprise that proteins—the essential machines of life—are not likely to have evolved. At least, that is, if you believe in science. Even according to evolutionists and the most optimistic assumptions possible, the evolution of proteins is so unlikely it is beyond practical consideration. While this conclusion is intuitive and hardly surprising, there are several reasons for it. One of the reasons is that the scenarios evolutionists typically envision involve the pre existence of proteins. For instance, proteins are needed to create proteins, at least in today’s biological world. Indeed, proteins are also required for life as we know it. So the first proteins would have had to evolved in a very different kind of biological world. Another reason why protein evolution is difficult is that the fitness landscape in protein sequence space is mostly flat and rugged. A few random mutations will quickly degrade protein function and most of the hyper-dimensional sequence space has little or no function and is far from a useful protein. It is extremely difficult for a random sequence to migrate via mutations close enough to a useful protein for natural selection to take over. In fact this challenge makes the protein evolution difficult regardless of whether proteins already exist. But in spite of this problem, evolutionists believe that protein evolution is not a significant problem. Recently an evolutionist commented that it is “basically a solved problem.”

It wasn’t too many years ago that evolutionists ruled out such protein evolution. Because the problem is so difficult, they believed proteins somehow evolved very early in evolutionary history, and have merely undergone various modifications ever since. As one recent paper explains:

In the pre-genomics era it was widely assumed that much of present-day genetic diversity could be traced by common ancestry to a molecular big bang, where all genes evolved at once.

Likewise another recent paper states:

The emergence of new genes has long been thought to be almost exclusively driven by duplication or recombination of existing gene fragments. The possibility of de novo evolution from intergenic non-coding sequences seemed remote.

But that has all changed now. Not because evolutionists have figured out how new proteins can evolve de novo, but because, if evolution is true, new proteins must have evolved de novo. For in this post-genomic era, we now know that the genomes of species are chocked full of unique, one-time, protein-coding genes. They are not found in allied species, which under evolutionary theory means those genes must have evolved relatively recently.

But how?

If you read the headlines, you would have the impression that the problem is well in hand. For instance, super-star science writer Carl Zimmer wrote in the New York Times earlier this year that “researchers have documented the step-by-step process by which a new gene can come into existence.”

Case closed right?

Well not quite. In fact, not even close. What Zimmer tells his readers is a “step-by-step process” is what scientists affectionately refer to as a cartoon. In fact, here it is:

Was it not a bit serendipitous that DNA segments could so easily become transcribed?

And once transcribed and translated, the resulting protein would most likely be worthless junk. It would be somewhere in the middle of that rugged protein sequence hyperspace, light years away from a design that would improve fitness.

Yet the protein would continue to be synthesized by the patient organism, waiting forever as mutations randomly sample the rugged hyperspace. If that was the case then such experiments would rapidly accumulate, and the organism would be producing a plethora of junk proteins.

For this evolutionists envision that the rapid rise of these experimental protein-coding genes is offset by their destruction:

This fast rate of gene emergence raises the question why the genomes do not fill up with such genes over time. In spite of huge variation in total genome size, genomes do not show a proportionally large variation in terms of protein-coding repertoires. Hence, the emergence rate of new genes must in some way be balanced with a corresponding loss rate.

So evolutionists must say that mutations halt the progress, for example, by creating stop codons somewhere in the middle of the gene.

But if that was the case, then the incredible problem of searching through the sequence space just became that much more impossible. Not only must we search through an astronomically huge, flat, rugged fitness landscape that makes finding a needle in a haystack seem trivial, but now the searches are routinely interrupted and must start all over again from scratch. It is an evolutionary treadmill where mutations are working furiously and getting nowhere as they are continually creating and destroying genes.

This evolutionary narrative is certainly not “basically a solved problem.” In fact, what evolutionists have are high claims of the spontaneous evolution of incredibly complex structures, not because of the evidence, but in spite of the evidence.

So what gives evolutionist’s their confidence? It is not that they understand how such genes could have evolved, but that the genes are observed over and over. And since evolution must be true, then those solo genes must evolved:

Several studies have by now also shown that de novo emerged transcripts and proteins can assume a function within the organism. All of this provided solid evidence that de novo gene birth was indeed possible.

And what exactly do these studies show? Did they really show that “de novo emerged transcripts and proteins can assume a function within the organism”?

Not exactly.

One study found a gene in a yeast species, but the corresponding genome location in allied species came up blank. Again, it is the belief that evolution must be true that does the heavy lifting. A gene is found in a species, it is not found in allied species, those species must share a common ancestor, that common ancestor must have existed relatively recently because the species are similar, therefore the gene must have evolved recently.

It all hinges on evolution being true.

The same logic applies in the other studies, such as the one which found a gene in the mouse genome that is missing in other mammals.

Two more studies found more of these de novo genes in the fly genome, and upon testing discovered that such genes are often surprisingly essential. That doesn’t help. Now, the genes must not only have somehow evolved rapidly, they must have rapidly become essential. It was another surprise for evolutionists. Other studies have found genes in only some individuals, within a population.

Does any of this mean that the de novo genes evolved from random mutations as the evolutionists claim? Of course not.

This de novo gene story parallels the twentieth century evolutionary insistence that species adapt by random biological variation, not geared to help with the current environmental challenges. Those random variations are then subject to natural selection, and the resulting adaptation is the first step toward the large-scale change evolution requires to create the species.

Only recently have evolutionists begun to reckon with the failure of that narrative. I don’t know how genes arose, but once again evolutionists have made unscientific and unsubstantiated claims, and set themselves up for another failure. Only a few years ago they agreed that such evolution of new genes would be impossible. Now they have been forced to adopt it because the evidence unambiguously reveals solo genes, and evolutionists dogmatically insist that everything must have spontaneously evolved. So it is yet another false prediction followed by yet another epicycle, making the theory far more complicated and unlikely.

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.