Sunday, January 31, 2010

Reverend Jerry Coyne Thus Saith

At the First Church of Darwin, at the University of Chicago, Reverend Jerry Coyne preaches on evolution. Reverend Coyne's preaching is very much in the Darwinian wisdom literature tradition, explaining all manner of religious doctrines that, as evolutionists have explained many times, we all must accept. As a service, Reverend Coyne has gathered those theological dictates he has deemed most important to the Church of Darwin in his book Why Evolution is True. These truths need to be preached to all peoples, and so here we begin. Here is, then, the Word of Coyne:

Again one must ask: If animals were specially created, why would the creator produce on different continents fundamentally different animals that nevertheless look and act so much alike? [92:2]

Thus saith the Reverend Coyne. Here the Most High preaches on how the creator distributes his creations geographically across the face of the world.

It is the will of the Most High Coyne to correct false ideas and teachings that have spread throughout the land regarding this doctrine. As the Most High Coyne lovingly explains, with a gentle question rather than harsh dictate, it is false to think the creator specifically created each animal type, for the infinitely wise creator would never create, as we find, different animals that look and act alike on different continents.

Meditate on this teaching, and you will see that it takes but a moment's reflection to realize that evolution is obviously true.

Saturday, January 30, 2010

What Will be the 21st Century's Theory of Origins?

It would be foolish for me to try to predict what the twenty first century's theory of origins will be, but I can tell you one thing: it will be called evolution.

In their new book What Darwin Got Wrong Jerry Fodor and Massimo Piattelli-Palmarini argue that twentieth century evolutionary theory--the result of the forced marriage between Mendelian genetics and Darwinism--is substantially flawed. Peter Forbes's candid review of the book is worth a look. Forbes explains the crux (or at least one of the cruxes) of the problem:

The problem is that the source of novelty is so dammed elusive. Most genes don't change very much at all, even the body-plan genes seem to be very similar in the mouse and blue whale. Or, to compare even less similar creatures: a mouse gene essential for building the eye can be inserted into the fruit fly to produce a fly eye! This refutes a key prediction of Neo-Darwinism, Ernst's Mayr's statement that it would be futile to look for similar genes in different creatures. Neo-Darwinism predicted that random mutations would pile up until the genes of mice and men were as different as, say, the Finno-Ugric and the English languages.

The best bet at the moment seems to lie in the altered timing of processes involving cascades of many genes. And what alters the timing? Well, now we're at the frontline of research, and there are candidates but no certainties. One of the most dramatic possibilities is that elements of DNA have entered the germline from viruses. Putting this together with Margulis's ideas on the evolution of the ancestral single cell, we can see that viruses and bacteria are starting to loom very large in the picture of evolution.

False predictions, absence of a credible mechanism, and unfounded speculation--these well sum up evolutionary theory. Evolutionists, however, can take solace that this is a friendly attack. Fodor and Piattelli-Palmarini are not questioning the ultimate truth of evolution. Evolution may be all wrong, but it is still true. That we know. As Forbes explains:

Given the provocative title, it's important to stress what Fodor and Piattelli-Palmarini's polemic is not. From the outset, they assert that they have no quarrel with the course of evolution and its timescale, only its mechanism. Furthermore, they affirm that they are "outright, card-carrying, signed-up, dyed-in-the-wool, no-holds-barred atheists." For that small relief, much thanks.

Evolution may make no sense, but it will always be true. It must be, for god would never make this world. So evolution will flit from nonsensical idea to nonsensical idea in its never ending attempt to make sense. Who knows what the theory of origins will be in the future, but it will be called evolution. And it will be true. Religion drives science and it matters.

Friday, January 29, 2010

Chaperonins: Open and Shut Case

A protein is created in the cell by copying its DNA gene, making any necessary edits to the copy, and passing the copy to the ribosome machine which uses the genetic code to translate the copy (a series of nucleotides) into the protein structure (a series of amino acids). But the story does not end here. The final step, after translation, is to fold the protein into its three dimensional structure. It is a step that is difficult to monitor and difficult to predict. The chain of amino acids folds up in a tiny fraction of a second and the final shape it assumes is not obvious. And sometimes the folding process is literally hidden as the nascent protein chain is hidden inside the cavity of a chaperonin machine with the lid shut.

Chaperonins are large protein machines that help some proteins to fold into their proper shape. New research is reporting on the structure of a particular chaperonin, including the lid closing action. The results are fascinating and they raise the question of how and why such an intricate protein machine evolved.

The different types of chaperonins fall into the broader category of molecular machines that not only help new proteins to fold, but also help existing proteins recover from shock, help with the assembly of machines, and so forth.

The obvious question is: How could evolution just happen to produce such machines? After all, a long series of lucky mutations would be required. But a more subtle problem has to do with not how, but why evolution would produce such machines.

For instance, this chaperonin machine, even if somehow was created by the cell, helps fold proteins that don’t want to fold very often. So before the helper chaperonin machine was available, these reluctant proteins would be lying around in various useless forms. For all we know they might be unfolded, or they might be misfolded. In any case, they would be clogging the works.

According to evolution these reluctant proteins would decrease fitness and not be selected. They would be evolutionary dead ends.

But in that case the chaperonin helper machines, when they just happened to evolve, would have nothing to do. Again, according to evolution, they would be consuming energy, getting in the way, and generally not helping. They too would not be selected.

These are questions that young evolutionists are prone to ask (evolutionists are constantly probing and trying to falsify their own theory). In their lack of experience they miss the obvious solution: Evolution simultaneously evolved both the chaperonins and the proteins that need their help. The reluctant proteins were never clogging the works, and the chaperonins never lacked for something to do. Evolution’s timing was perfect. As usual evolution provides an answer that is simple, elegant and compelling. You can see why it is said to be a fact.

Thursday, January 28, 2010

The Evolution of Serendipity

A key question for evolution has always been: How does biological variation arise? Darwin’s theory of evolution explained that natural selection killed off the less-fit variations, but how did the variation arise in the first place? In the nineteenth century the mechanisms of biological variation were not well understood and it was possible to imagine a sort of simple, perturbing force at work which gradually altered designs. This model did not match up very well with what Gregor Mendel was discovering about change in pea plants. About the same time that Darwin was working on revisions to his book Mendel was uncovering the fundamental laws of genetics. But Mendelian genetics would call for discrete jumps in biological variation rather than gradual modifications. It would take much work but about half a century later Mendel’s findings were integrated with Darwin’s theory of evolution. This neo-Darwinism was thought to be a great advance. Was not the poorly understood source of biological variation now revealed and reconciled with Darwin’s theory? But the neo-Darwinists had turned a blind eye to the elephant that was now in the room: Evolution now required a complex Mendelian machine to generate the needed biological variation.

This problem with neo-Darwinism is very simple. In order for evolution to continue, evolution first had to create the complex Mendelian variation machine. In other words, evolution creates the mechanism that evolution requires to work. It was an absurd level of serendipity that no one cared to notice.

Since the formulation of neo-Darwinism this problem of serendipity has only become worse. For the genes, alleles and various machinery required by Mendelian genetics were only the beginning. Indeed, it became increasingly understood that Mendel provided only a portion of the needed biological change.

Today evolutionists call upon a dizzying array of phenomenally complex mechanisms to produce jumps in biological change in an attempt to explain evolution. Horizontal gene transfer, cell fusions, directed mutations, domain shuffling and cis-acting regulatory changes are but a few of the new breed of mechanisms called upon to generate evolution’s new designs. Evolution created genes that can be transfered, mechanisms that do the transferring, cells that can be fused, DNA that can be mutated, processes to direct the mutations, domains that can be shuffled, regulatory schemes that can bring about changes, and so forth. As one evolutionist concluded, “hereditary variation arises from the non-random action of built-in biochemical systems that mobilize DNA and carry out natural genetic engineering.”

Natural genetic engineering? This is neo-Darwinism on steroids and its astronomical level of serendipity is absurd. Do evolutionists seriously think people will believe it is an undeniable truth that evolution created the phenomenally complex process of evolution, which then enabled evolution to occur?

How about an undeniable tale?

The evolutionist’s failure to reckon with their own credulity is astonishing. They contrive a truly silly idea while proclaiming it to be a fact we must accept. I would be the first to proclaim evolution as true if the evidence was there. But the evolutionists have not only failed to deliver—they have made themselves appear foolish.

Wednesday, January 27, 2010

Prestin and Darwin's Gardener

A fundamental, and often false, prediction of evolution is that functionally unconstrained DNA should not be conserved in distant species. As described here, everything from proteins to long stretches of DNA, though highly similar across different species, defy evolutionsts who search for a functional constraint, as required by their theory. And how do evolutionists respond? They claim that the mystery DNA must have a function, even though myriad tests have found none. If we cannot detect the function, then there must be a problem with the tests. There must be a function which otherwise is undetectable to us. It is a perfect example of how religious belief resists falsification as Antony Flew once illustrated in his gardener parable:

Once upon a time two explorers came upon a clearing in the jungle. In the clearing were growing many flowers and many weeds. One explorer says, "Some gardener must tend this plot." The other disagrees, "There is no gardener." So they pitch their tents and set a watch. No gardener is ever seen. "But perhaps he is an invisible gardener." So they set up a barbed-wire fence. They electrify it. They patrol with bloodhounds. (For they remember how H. G. Well's The Invisible Man could be both smelt and touched though he could not be seen.) But no shrieks ever suggest that some intruder has received a shock. No movements of the wire ever betray an invisible climber. The bloodhounds never give cry. Yet still the Believer is not convinced. "But there is a gardener, invisible, intangible, insensible, to electric shocks, a gardener who has no scent and makes no sound, a gardener who comes secretly to look after the garden which he loves." At last the Sceptic despairs, "But what remains of your original assertion? Just how does what you call an invisible, intangible, eternally elusive gardener differ from an imaginary gardener or even from no gardener at all?"

Darwin and the evolutionists see a gardener, and to these motivated believers evolution is true despite even glaring question marks and failed expectations that have other observers wondering how evolutionists can be so sure their idea is a fact. And as in Flew's parable, sometimes evolutionists have creative explanations for why the evidence does not seem to reveal their gardener.

Consider prestin, a protein important in mammalian hearing. Prestin, a transmembrane protein in the outer hair cells of the cochlea, is 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.

Of course evolution has no explanation for the origin of this system beyond unfounded speculation, but that is no surprise. New research is, however, adding a twist to the story.

We now know that prestin proteins in certain bat and whale species (used in their biosonar systems) 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.

Of course this conundrum is not confined to the prestin protein. Biology is packed with incredible designs that appear to be finely-tuned. And dozens of finely-tuned design parameters do not appear to be the result of evolution.

The typical evolutionary explanation for biology's wonders is that those design parameters evolved one at a time. It was a gradual process as each setting independently contributed to increased fitness. In other words, a long series of lesser designs preceded today's marvels.

But if a lesser design was good enough before, then why is it not good enough today? Why are those nine amino acids maintained today in prestin if before only a few were required for success?

The evolutionary answer is that there was an arms race. Yes, lesser designs did the job before, but that was then and this is now. The competition has improved and so what worked before no longer does the job.

But like Flew's gardener, these other worlds are forever up for speculation. The competition may or may not have had this or that capability at this or that particular time. The precise timings and interactions can always be tweaked to fit the evolutionary narrative.

And if it turns out that prestin is not so sensitive to some of those nine amino acids, evolutionists won't skip a beat as they didn't before when conserved designs were found to lack the expected sensitivities. One way or another, there is a gardener. Religion drives science, and it matters.

Tuesday, January 26, 2010

Proteins That Regulate Protein Production

Most people understand that our genes are stored in our DNA but what is less commonly understood is how the cell determines which genes to use at any one time. The DNA in our cells contain tens of thousands of protein-coding genes whose proteins serve a great variety of purposes. They serve as railroad tracks, precision tunnels, enzymes to speed up reactions and environmental sensors to name just a few. And some proteins go back to the DNA and bind to the double helix, as part of a complex regulatory network that determines which genes to use to make new proteins. In other words, the cell determines which genes, to use to make new proteins, by using existing proteins. But from where did those existing proteins come?

For evolutionists, the question of how DNA regulatory proteins arose is not simple for a number of reasons. One of them is that only a few DNA sequences successfully code for such a protein. Of course the protein structure must fit together with the DNA structure it regulates, and only a small fraction of the possible sequences provide such a structure.

But beyond this, new research is now showing that the protein’s amino acids that make contact with the DNA can be highly restricted. For one particular DNA regulatory protein, the research showed that for the roughly four amino acids that are important in binding with the DNA, only certain amino acids provide acceptable binding. Only about 1 in 50,000 random tries would work.

And that is only for those four amino acids, out of the hundreds comprising the protein. Given the additional structural constraints the odds are much worse. These results are consistent with experiments that show that a DNA binding protein is a 1 in a 1,000,000,000,000 (million million) shot.

And all this only buys a DNA regulatory protein. It is exceedingly unlikely that the protein would bind to the right places along the DNA double helix. It is also exceedingly unlikely that the protein would bind at the right time.

Evolutionists seek to explain the origin of such regulatory proteins, and the greater regulatory network, in terms of gradual pathways. But the above hurdles are not easily avoided and science does not reveal this to be a high probability event. Beyond speculation evolutionists have no explanation for why this is a likely event.

Of course the idea that regulatory proteins and networks evolved does not come from science, it comes from the belief that evolution is true. Strip that away and all that is left is story telling about unlikely events in the name of science. Religion drives science, and it matters.

Monday, January 25, 2010

New Intron Research Reveals Same Old Contradictions

In eukaryotes the DNA genes are sometimes interrupted by non coding segments. These intragenic regions, or introns, are cut out of the transcribed DNA before the copy is sent to the ribosome for translation into a protein. Naturally evolutionists have always believed introns are a result of evolution, but their explanations are strained. As one recent paper explained, understanding why such introns exist and their evolutionary origins is “a problem that has proved a conundrum for the past 30 years.”

Indeed, while it may have initially seemed to evolutionists that introns were inserted into genes during the course of evolution, findings of introns at conserved insertion sites, in various species, tell evolutionists that some of the introns are ancient, and were present in the earliest eukaryotes. But this suggests that the super complex editing machinery that splices the introns is also ancient. This is yet another example of early complexity whereas evolution predicts simple beginnings.

One virtue of this ancient origin view is that introns could be cast as evolutionary enablers in the origin of proteins narrative. After all, the expressed regions (exons) between the introns tended to conveniently be protein domains which can be rearranged and shuffled to modify the protein. As one of today’s leading textbooks explains, “It is believed that the organization of DNA coding sequences as a series of such exons separated by long introns has greatly facilitated the evolution of new proteins.” Or as one paper put it, by the 1980s “it had become a textbook dogma that introns were retained from a primordial RNA world in order to speed evolution by exon shuffling.”

It is yet another example of the tremendous serendipity in the evolution genre as evolution creates itself. Evolution creates everything from genes, chromosomes and alleles, to horizontal gene transfer, epigenetics, and now introns, so that, yes, evolution can occur. And evolutionists never think twice about the unlikely story they have contrived.

But the ancient origin view cannot explain many introns which don’t fit the pattern. Evolutionists view those as of more recent origin. In fact, evolutionists have constructed a battery of explanatory devices in their attempt to fit the data to their theory.

Perhaps introns are mostly ancient and exons arose within them, providing new genes. Or perhaps introns were mostly introduced later, during the course of evolution, interrupting the genes. And perhaps many introns were lost in the course of evolution, or perhaps introns slide around. And maybe introns served as sponges to reduce the deleterious impact of mutation showers.

As usual the genre elaborates from a rich set of devices and mechanisms, and it is often difficult to parse the empirical data from the theoretical constructs. Consider these passages from a recent paper which demonstrate how deeply immersed evolutionists are in their theory and how far they have departed from empiricism:

The fact that the alternative splicing products were of the cassette type (i.e., exons that are alternatively included/skipped from the mature transcript) did not question the emerging conceptualization of introns as definite DNA segments. Yet seeking to identify mechanisms for the rapid evolution of protein-coding sequences, records were cited of so-called cryptic donor/acceptor splice sites, and speculations were advanced that splicing-altering mutations could cause extensions/contractions of exons at intron junctions.

Interest in intron sliding models diminished on the belief that intron sliding could not be a frequent phenomenon. Under the notion of introns as fixed genomic segments, intron sliding is perceived as uncommon because it calls for the simultaneous occurrence of two mutations. Other paths, by a series of two or more short-range extension/contraction events of intron–exon boundaries, were deemed likely to be deleterious at the protein level. Such events would be feasible when the aberrant mRNAs contained premature stop codons that could be targeted by nonsense mediated decay.

Evolutionists think nothing of extreme speculation that amounts to little more than story-telling. And now, new intron research is adding more confusion to the narrative.

The intron patterns are now forcing evolutionists to switch from their view that intron insertions are random events. Sound familiar?

Evolutionists view biology as a fluke, and like the Epicureans and their veering atoms, evolutionists believe unguided events just happened to create the most complex structures known. Everything from mutations to genome insertion events occur at the roll of a die.

This is the evolutionary view even though so often it is falsified by reality. For everything from mutations to, yes introns, show patterns. And when these patterns cannot be fitted into the common descent model, then evolutionists must admit that the events do not occur at random.

Introns are yet another example of how evolution is less of a revealing explanation than merely a tautology. Whatever we find in nature, evolution will explain it no matter how strained is the narrative.

Saturday, January 23, 2010

Ribosome Checks for Translation Errors (and a bunch of other stuff)

There is a vast network of information flow in a typical cell, and along with that flow there is a vast network of error checking. Damage to DNA sequences is remedied, the transcribing of DNA is checked and corrected, and at the ribosome the translation process is checked and controlled. In fact, recent research has found that the ribosome not only carefully sets up the codon-to-amino-acid translation process for success, but if an error is made the ribosome detects it and takes action after the translation process.

When the ribosome detects a translation error it takes action 10,000 times faster than it normally does. "These are not subtle numbers," explained the lead researcher. As one report explains, "the ribosome exerts far tighter quality control than anyone ever suspected."

How does the ribosome do it? The ribosome--which creates proteins--consists of RNA and protein molecules. If the ribosome is the machine that builds proteins, then from where did the ribosome's proteins come in the first place? Evolutionists believe that initial versions of the ribosome--the proto-ribosome--had only the RNA molecules and the proteins came later.

Perhaps so, but the translation task is not simple, and the ribosome's proteins do not appear simply to be innocent bystanders that evolution, for no particular reason, kludged onto the ribosome. Rather, the proteins are deeply embedded in the ribosome, and appear to be important for both the ribosome's structure construction and conformation. This is probably why RNA-only proto-ribosomes don't seem to work.

But this is not all. Even ignoring the problem of obtaining an RNA-only translation machine, the evolutionary hypothesis raises the question: From where did the protein-coding sequences come which it would translate? In other words, even if a long sequence of RNA residues just happened to assemble and fold and function as a proto-ribosome, why would it be selected for if there were no protein-coding sequences lying around? One could add to this a long list of other requirements, such as a ready made pool of amino acids, and of course something for the newly minted protein to do.

Of course evolutionists can always speculate. For instance, perhaps a functional RNA molecule just happened to also code for a useful protein. How convenient.

Fortunately, in a world where confessions of evolution's heroics are rare, one nobel laureate scientist gave this judicious observation: "How evolution managed to progress from making a random peptide to messenger-directed synthesis, we haven't a clue." And yet evolution is a fact? I think I want my money back.

Friday, January 22, 2010

A New Plant Defense: Switch the Flowering Time

A new amazing strategy has been discovered to add to the list of defenses plants use against herbivores. It has long been known, for instance, that plants detect the secretions from caterpillars and respond with toxins and chemicals that slow the caterpillars' digestion. Now a new defensive strategy has been discovered: the altering of the flowering time. This has been observed in a tobacco plant which produces new morning-opening flowers when attacked by larvae of the hawkmoth pollinator.

Normally the plant releases benzyl acetone to attract the hawkmoth pollinators and produces flowers that open at night when the hawkmoth is active. But the morning flowers, produced in response to hawkmoth larvae attack, produce less benzyl acetone and are pollinated by hummingbirds which are active during the day.

With evolution we must believe that this dramatic change in flower phenology, as well as the other plant defenses, just happened to arise so they later could be selected. A mutation occurred that just happened to activate a benzyl acetone release mechanism, which just happened to attract the hawkmoth pollinator. And another mutation just happened to design a system that detects caterpillar secretions. Then another mutation just happened to couple with the detection system to produce and release chemicals, to slow the caterpillar digestion, as well as toxins. Then another mutation just happened to create the system to switch the flower design so it opens in the morning.

And of course these designs are observed by us only because they were the evolutionary winners. They are the proverbial tip of the iceberg. For every winner there are untold myriad losers. The designs that produced some other chemical rather than benzyl acetone. The designs that detected chemicals that the caterpillars don't secret. The designs that didn't couple with the detection system. The designs that produced secretions that had no effect on the caterpillars. The designs that wreaked havoc on the flowering process rather than merely altering the flowering time. And so on, and so forth. The plant must have been a veritable idea factory, churning out all manner of mostly useless Rube Goldberg devices.

This, for what it's worth, is evolutionary theory. A game of fact-free story telling all funded by the taxpayer. Religion drives science, and it matters.

Thursday, January 21, 2010

Barbara Forrest Says ID is Creationism

In a new paper entitled "The Religious Essence of Intelligent Design," Barbara Forrest indicates IDs are confused about their own theory:

Despite the protestations of its proponents, “intelligent design theory” (ID) is not science but creationism, making it in its essence a supernaturalist religious belief. This fact has been established conclusively for the legal record in Kitzmiller et al. v. Dover Area School District (2005) and for the public by a decade of scholarship, much of which helped to secure the Kitzmiller plaintiffs’ victory in this first legal case involving ID. Moreover, ID is not merely a religious belief but, more specifically, a narrow form of sectarian Christianity, as specified by its own proponents. The nature of ID as a creationist, therefore religious, movement has been revealed not only by its critics, but also, most importantly, by its proponents. The explication of ID by its critics as creationism, and therefore religion, reflects the way the movement views itself.

In other words, proponents argue that ID is not creationism and that it is creationism. So which is it? Unfortunately Forrest seems to be preferring simplistic answers and working hard at avoiding any substance. And that the paper appears in the Cold Spring Harbor Symposia on Quantitative Biology is an unfortunate sign of evolution's impact on scientific culture. I'm still waiting for her to explain the methodological naturalism mandate.

Wednesday, January 20, 2010

What is Evolution (According to Evolutionists)?

The great twentieth century physicist Erwin Schrodinger, after helping to elucidate quantum mechanics, turned his attention to the question of life. What is life, wondered Schrodinger. Today, evolutionists define life as that which evolves. If so, then perhaps evolution itself is alive because, according to evolutionists, evolution has done quite a bit of evolving. This is not to say that the idea of evolution has evolved (though it has). This is to say that the process of evolution, if true, has evolved.

Evolutionists have always made high claims about their idea. In the nineteenth century Joseph Le Conte explained that evolution is a law, not a theory, and it is a law to which every department of natural studies must adhere. It is not merely as certain as gravity, "Nay, it is far more certain." Similarly, Pierre Teilhard de Chardin maintained that "evolution is a light which illuminates all facts, a trajectory which all lines of thought must follow—this is what evolution is."

Had they thought long enough about it, Le Conte and Teilhard would probably have gladly proclaimed evolution to be life itself. Certainly today this conclusion is hard to avoid. After all evolution has created a variety of mechanisms by which evolution occurs. Evolution created itself, and in the process it has evolved. If life is to be defined as that which evolves, then surely evolution is life itself.

To explain biological change, early evolutionists might have envisioned a simple sort of blending action or random perturbing force. But we now have discovered a series of highly-intricate mechanisms that bring about change. These mechanisms must have been created by evolution.

For instance, one recent paper reviews a mechanism known as horizontal gene transfer, or HGT. The idea is that in addition to genes being modified and created by mutations, they can also be imported in one fell swoop from another organism. Evolutionists debate the extent to which HGT has steered evolutionary history, but they all agree it played a role. As the authors write:

... there is a need for a new evolutionary paradigm that includes horizontal gene transfer

But HGT doesn't just happen. You have to have certain molecular structures and facilities in place (and of course you have to have the genes themselves). Simply put, evolutionists say that evolution created life in such a way that HGT arose at some point.

And there are several other evolutionary mechanisms that had to have evolved as well. From the Mendelian machine described by modern genetics to epigenetics and the ability of organisms to evolve (so-called evolvability), evolution created the evolutionary process. It is the ultimate example of a boot-strap process. According to Evolutionists, evolution is alive.

Tuesday, January 19, 2010

Communal Egg Laying: Evolution Over Easy

Evolution predicts that the designs of species are often influenced as much by history as much as by need. When we see similar structures in cousin species it is because they inherited the design from a common ancestor. That particular design was probably not the best for each of the different species, but it was available.

On the other hand, when we see similar structures in more distant species it is because the design was needed. The design just happened to arise in the different lineages, and was selected because it helped. Given these two general explanatory mechanisms evolution can explain a wide variety of patterns. But not all. Sometimes cousin species have differences that are too pronounced. And likewise, sometimes distant species have similarities that are too pronounced.

Or sometimes the patterns are so jumbled they simply defy evolution's expectations. Consider, for example, the behavior of communal egg laying. This behavior, where neighbors pool their eggs in a common nest, is widespread among animals including mammals, birds, amphibians, reptiles and insects. And although widespread, the pattern is complex. In any pair of cousin species, the behavior of communal egg laying may or may not be conserved.

The figure above, for instance, shows an evolutionary tree representation of different lizard families. The indicated families contain communal egg laying species. Evolutionists must imagine that communal egg laying evolved over, and over, and over, for different reasons in very different species in a wide range environments. But yet in cousin species it evolved in the one but not the other.

Of course evolution doesn't think twice about such quandaries. The right mutations, whatever they were, came along, over, and over, and over without causing a mutational overload to produce a never ending stream of communal egg laying experiments. So not only does evolution explain similarities between both neighboring and distant species, it also explains everything in between.

Monday, January 18, 2010

Evolution's Kobayashi Maru Scenario

By mandating methodological naturalism evolutionists place themselves into a no-win scenario. Like Star Trek's Captain Kirk who reprogrammed the computer in order to defeat the Kobayashi Maru scenario training exercise, evolutionists can only cheat their way out of their methodological naturalism mandate. If they give a straight answer they undermine their own claims about evolution. The problem here is not methodological naturalism itself, which is a perfectly reasonable way to do science. The problem is that, in the hands of evolutionists, it becomes dogma rather than guidance. And the problem is not merely a philosophical fine point--in mandating methodological naturalism evolutionists reveal the absurdity of their ideas and simultaneously do substantial harm to science.

Evolutionists mandate methodological naturalism but they don't explain exactly what this means. The reason why we do science is because we don't have all the answers. If we had all the answers then there would be no reason for science. Methodological naturalism places a constraint on the answers which we do not yet have. In so doing, something is lost.

We either lose objectivity by assuming that all of reality conforms to our constraint, or we lose any guarantee of completeness by limiting science to those phenomena within our constraint, or we lose any guarantee of realism by forcing a constraint which excludes explanations which could be true.

Of course we could get lucky. It could be that reality conforms to our constraint and that we have not excluded any true answers. In this case, if all of reality is strictly naturalistic then methodological naturalism is a good mandate. But we don't know that right now. So the question for evolutionists who mandate methodological naturalism is: what do we forfeit, objectivity, a guarantee of completeness, or a guarantee of realism?

Why methodological naturalism is a no-win scenario

These are the alternatives and evolutionists cannot accept any of them. If they explain that they believe nature and its origins are completely naturalistic then this would reveal a non scientific presupposition. They would lose scientific objectivity.

If they explain that science should be limited to naturalistic phenomena then they would be admitting that we have no guarantee that evolution can explain all things. They would also be giving sanction to the problem of identifying natural versus supernatural phenomena, an activity which they insist is non scientific.

On the other hand they could explain that if science ever encounters a problem outside the bounds of naturalism then its answers are fictional. In this case science is not limited, but it comes at the cost of opening the door to fictional explanations, and so losing the guarantee of realism. This too is unacceptable. Evolutionists insist their idea is an accurate description of nature and a fact.

Justifications and what they reveal

So how do evolutionists explain their methodological naturalism mandate? Not surprisingly they rarely if ever provide a logical answer. This question was well understood four centuries ago when thinkers seriously engaged such questions about how science should work. Bacon and Descartes worked through these issues and explained their positions. But we cannot expect such reasoning from evolutionists today. Instead evolutionists respond with a battery of fallacies which are, frankly, embarrassing.

As is typical, many of their responses are attacks on the questioner. For instance, they say that the questioner is attacking methodological naturalism, or that he is smuggling in supernatural assumptions. But asking evolutionists for clarification is not attacking methodological naturalism. And the only assumption being made is that nature and its history might not be completely naturalistic. In other words, science might stumble upon a problem that doesn't fit methodological naturalism. If anything it is the evolutionists who are making heroic assumptions by mandating methodological naturalism.


Another response that evolutionists give is that methodological naturalism is simply the way science works, period. But in fact the way science works is a complicated question. From Leibniz to Linnaeus the history of science is littered with examples of the blackballing and embracing of ideas that today's methodological naturalism would find confusing.

And if you think times have changed think again. More recent scientific ideas such as quantum mechanics and the Big Bang seem to push the envelope. Particles are waves (sometimes), observers influence outcomes, and the universe and its natural laws began in a one-time explosion. And the evolutionist's appeal to a multiverse hardly falls neatly within methodological naturalism.

And what about all the metaphysical claims upon which evolutionary thought is motivated and justified? Why is it OK to mandate naturalism with theological claims but not OK to allow for design based on empirical science?

Another recent confounding example is the SETI (Search for Extra Terrestrial Intelligence) project which looks for intelligent radio signals from distant planets. SETI and ID share the same relationship with methodological naturalism, and yet evolutionists give a pass to the former while rejecting the latter.

This is contradictory. If you attempt to dismiss ID as not in accord with methodological naturalism, then you also dismiss SETI. On the other hand, if you say SETI passes the methodological naturalism test, then you also give ID a pass. You cannot blackball one without blackballing the other. You cannot let one in without letting the other in.

Lucky stars

The evolutionist's methodological naturalism mandate also makes their claim that evolution is a fact appear suspicious. How curious it is that not only is evolution's naturalism-only story mandated by science, but it also turns out to be true. Do evolutionists ever realize how lucky they are? Or do evolutionists ever think twice about their serendipity?

Meanwhile skeptics wonder if the game has been fixed. Is it really such a coincidence that the paradigm that is mandated is also the one that is declared to be a fact?

This brings us to what is perhaps the greatest problem with the methodological naturalism mandate: the damage it causes to scientific progress. The most common response evolutionists give, when asked about their methodological naturalism mandate, is that science has shown naturalism to be true. We once thought that everything from lightning and earthquakes to love and consciousness were supernatural phenomena, but we now have scientific explanations for all these things. If there were evidence that any phenomenon is not completely natural then we would think twice, but given the complete lack of such evidence, methodological naturalism is the obvious choice.

The problem here is that the methodological naturalism mandate drives the evaluation of the scientific theories. Once it is mandated that all phenomena must be described naturalistically, it is only a short step to assuming that all phenomena can be described naturalistically, and indeed have been described naturalistically. From a scientific perspective it would be absurd to think we have a plausible explanation for the DNA code, histone IV, biosonar or consciousness. What we have is speculation driven by the demand for natural explanations. It is not that the data reveal such explanations, it is that we require such explanations.

Naturalism is now unscientific according to the evolutionist's own criterion of testability. This is because naturalistic explanations are the only explanations that are allowed. They therefore cannot be tested because they are true by definition. The only testing that can be done is between different sub-hypotheses of naturalism.

The mandating of methodological naturalism is bad for the philosophy of science and, not surprisingly, bad for science itself. It places evolutionists in a no-win situation, like Star Trek's Kobayashi Maru scenario training exercise. The difference is that rather than solving the problem like Captain Kirk, evolutionists make matters worse for themselves by continuing to mandate methodological naturalism. Religion drives science and it matters.

Friday, January 1, 2010

A Question for Joe Felsenstein (and Everyone Else)

Joe Felsenstein, and most other evolutionists, tell us that science must be restricted to law-like causes and explanations. In a word, they require the scientific method to be restricted to naturalism. While this methodological naturalism seems like a reasonable way to do science, it is an incomplete instruction. There remains the question of what to do when methodological naturalism doesn't work.

Clearly, methodological naturalism will fail if it attempts to explain a phenomenon that is not completely naturalistic. For instance, imagine that human consciousness and will amount to more than mere atoms in motion. Perhaps, for example, there is a soul that transcends the material world. Then science's attempts to explain our thinking will rule out the right answer if science is constrained to methodological naturalism. Methodological naturalism would be wrong, and the question is: how should we handle such cases if they are encountered?

I can only think of four possible answers to this question, so this amounts to a simple multiple choice option:

A. Don't worry, methodological naturalism never fails because nature is always fully materialistic.

B. If methodological naturalism ever fails then science, constrained to methodological naturalism, will lead to the wrong answer. Don't worry, it is fine if science is sometimes incorrect.

C. If methodological naturalism ever fails then science should back away from the problem at hand. Science should only address phenomenon that are fully naturalistic.

D. Science should not be constrained to methodological naturalism.

It seems that while evolutionists routinely mandate methodological naturalism, they just as often fail to explain just what they mean. In fact, I know of no such evolutionist who has answered this question. So here is a simple multiple choice. All we need is a simple "A", "B", "C" or "D".