Thursday, December 30, 2010

It Didn’t Begin (or End) With Darwin

By far the most amazing aspect of evolution is not its idea that all things just happened to arise spontaneously but—even more eyebrow raising—its claim that all of this is a scientific fact. It would be irrational and perverse to deny it, insist evolutionists. Evolution is, they say, beyond any shadow of a doubt, as certain as gravity, nay even more certain. This claim is so obviously false that it begs the question: what are evolutionists thinking?

Evolutionists say their idea is an obvious scientific fact and they have explained why over and over. In fact, the reasoning was already well established when Charles Darwin wrote Origin a hundred fifty years ago.

For instance, Darwin agreed that the perfection of the eye reminds us of the telescope which resulted from the highest of human intellect. Was it not right to conclude that the eye was also the product of a great intellect? This may seem the obvious answer but Darwin warned against it, for we should not “assume that the Creator works by intellectual powers like those of man.” Better to imagine the eye as the result of natural selection’s perfecting powers rather than having god too much involved in the world.

This warning against anthropomorphizing god came right out of the Enlightenment philosopher David Hume whose writings Darwin was well familiar with. It was a reaction to English natural theology that argued the world looks designed by god. Hume argued this made god out to be too much like His human creatures. For example, the natural theologians were fond of comparing the human body with machines such as clocks. No one doubts that a clock was designed, so why not the body as well? Hume used the problem of evil to negate this argument. Better to view god as distant and unknowable, and a creation that somehow arose on its own. Hume had no problem with god being infinitely powerful and wise, but he must also be transcendent and incomprehensible:

But as all perfection is entirely relative, we ought never to imagine that we comprehend the attributes of this divine being, or to suppose that his perfections have any analogy or likeness to the perfections of a human creature. Wisdom, thought, design, knowledge; these we justly ascribe to him; because these words are honorable among men, and we have no other language or other conceptions by which we can express our adoration of him. But let us beware, lest we think that our ideas anywise correspond to his perfections, or that his attributes have any resemblance to these qualities among men. He is infinitely superior to our limited view and comprehension; and is more the object of worship in the temple, than of disputation in the schools.

Far more lasting and influential than this anthropomorphic warning argument were the various arguments from evil, inefficiency and dysteleology. God would never have created this gritty world. These arguments had been developed and tested in the seventeenth and eighteenth centuries, and by Darwin’s day a foundation had been laid.

The predation and bloodshed in nature was an obvious example of a creation that seemed unbefitting of a loving god. But Darwin added a great many examples of nature’s designs that seemed to be better explained as a consequence of the blind interplay of natural laws than intelligent design.

Darwin presented these arguments throughout his book, with great conviction that they made his theory compelling. The first one appears at the end of the second chapter.

The first two chapters of Origin are on the topic of biological variation. In the first chapter Darwin discusses what breeders had learned (Variation Under Domestication) and in the second chapter he discusses biological variability in the wild (Variation Under Nature). The two chapters serve as a good summary of what was known at the time.

Darwin ends Chapter 2 with a section entitled Summary, but here he introduces a new, important idea. Yes, he summarizes what he has been discussing, but he provides a new, powerful interpretation:

In genera having more than the average number of species in any country, the species of these genera have more than the average number of varieties. In large genera the species are apt to be closely, but unequally, allied together, forming little clusters round other species. Species very closely allied to other species apparently have restricted ranges. In all these respects the species of large genera present a strong analogy with varieties. And we can clearly understand these analogies, if species once existed as varieties, and thus originated; whereas, these analogies are utterly inexplicable if species are independent creations.

Earlier in the chapter Darwin had made a few comments in passing about creationism, but nothing too significant. But here Darwin introduces the reader to the power behind his long argument. The pattern will repeat many times: long tedious passages followed by the powerful conclusion that nature’s evidence falsifies divine creation.

Don’t worry if you don’t completely follow the observations Darwin discusses in the above quote. Here’s what you need to understand. The take home message for evolutionists is that, as usual, there are no viable explanations other than evolution’s. The observations may not be fully understood under evolution, but under creation or design the story becomes downright impossible. As one of the twentieth century’s leading evolutionist Ernst Mayr wrote:

The greatest triumph of Darwinism is that the theory of natural selection, for 80 years after 1859 a minority opinion, is now the prevailing explanation of evolutionary change. It must be admitted, however, that it has achieved this position less by the amount of irrefutable proofs it has been able to present than by the default of all the opposing theories.

Or as Stephen Jay Gould put it:

Odd arrangements and funny solutions are the proof of evolution—paths that a sensible God would never tread but that a natural process, constrained by history, follows perforce. No one understood this better than Darwin. Ernst Mayr has shown how Darwin, in defending evolution, consistently turned to organic parts and geographic distributions that make the least sense.

Designs that make the least sense. They are one of the keys to understanding evolutionary thinking. In addition to the other arguments for why evolution is a fact, I examined this argument from dysteleology ten years ago in my book Darwin’s God: Evolution and the Problem of Evil, and others such as Paul Nelson had discussed it earlier. And so I was delighted to see this key evolutionary argument for the fact of evolution elaborated in the prestigious science journal, Proceedings of the National Academy of Sciences, a year ago.

The paper was written by philosopher Elliot Sober who for years had been analyzing evolution’s arguments in great detail. In that paper Sober points out that while one of the main objections to evolution, both when Origin was published and in the minds of many present-day Creationists, is the idea that species are separated from each other by walls. Darwin, Sober explains, overcame this with those designs that make the least sense:

Darwin thought he had strong evidence for common ancestry. This is enough to show that insuperable species boundaries (and insuperable boundaries between “kinds”) are a myth; if different species have a common ancestor, the lineages involved faced no such walls in their evolution. …

Adaptive similarities provide almost no evidence for common ancestry while similarities that are useless or deleterious provide strong evidence for common ancestry.

And why are useless or deleterious similarities so helpful? It is not because they raise the probability of common ancestry, but rather because they lower the probability of separate ancestry. In other words, the reason common descent is a no-brainer is that the alternative, separate ancestry, is extremely unlikely. Sober call this Darwin’s Principle.

I referred to this analysis and Sober’s paper in my previous posting and several evolutionists commented that I had misrepresented Sober. Here are some of their comments:

False. Sober said no such thing in that book. In fact, he said the opposite.

Darwin’s principle refers to the notion that traits that are not selectively advantageous are better evidence for common descent than are traits that are selectively advantageous. He says this in the context of comparing common descent to separate ancestry.

You are quite fond of misunderstanding Sober, aren’t you?

But in fact Sober did say such a thing. In the paper Sober clearly explains that Darwin’s Principle, which demonstrates species are not separated by insuperable boundaries, is based on the ratio of (i) the probability of evidence on common ancestry divided by (ii) the probability of evidence on separate ancestry. The key is that the argument is compelling not because of the former being high, but because of the latter being low. It is not a direct argument for common ancestry, but rather an argument against separate ancestry.

As Mayr and Gould explain above, evolution is a fact because design or creation is false, as demonstrated by so many inefficiencies and bad designs that make the least sense. Over and over, Darwin made arguments against divine creation as his proofs for evolution.

Sober explains this argument in great detail in his book Evidence and Evolution. Here is how he summarizes the paradox that common descent can be found to be a fact though the evidence is unlikely:

This last result provides a reminder of how important the contrastive framework is for evaluating evidence. It seems to offend against common sense to say that E is stronger evidence for the common-ancestry hypothesis the lower the value is of [the probability of E given the common-ancestry hypothesis]. This seems tantamount to saying that the evidence better supports a hypothesis the more miraculous the evidence would be if the hypothesis were true. Have we entered a Lewis Carroll world in which down is up? No, the point is that, in the models we have examined, the ratio [the probability of E given the common-ancestry hypothesis divided by the probability of E given the separate-ancestry hypothesis] goes up as [the probability of E given the common-ancestry hypothesis] goes down. … When the likelihoods of the two hypotheses are linked in this way, it is a point in favor of the common-ancestry hypothesis that it says that the evidence is very improbable. [Sober, Evidence and Evolution, p. 314]

In other words, it doesn’t matter that common descent is not a good theory. It must be true because the alternative is even worse.

As Sober explains his PNAS paper, the key is designs that are have low probability on separate ancestry. He gives examples such as gill slits in the human embryo and our tail bone, but Darwin used dozens of examples in addition to the Chapter 2 example above. These are classic examples used by evolutionists to show how compelling is evolution. The probability on common descent may be weak, but it must be true because the probability on design or creation is zero. Here are representative embryology and gill slit quotes from leading evolutionists:

How does God’s plan for humans and sharks require them to have almost identical embryos? [Douglas Futuyma, Science on Trial: The Case for Evolution, p. 48]

The passage through a fishlike stage by the embryos of the higher vertebrates is not explained by creation, but is readily accounted for as an evolutionary relic. [Tim Berra, Evolution and the Myth of Creationism, p. 22]

Now, we’re not absolutely sure why some species retain much of their evolutionary history during development. The “adding new stuff onto old” principle is just a hypothesis—and explanation for the facts of embryology. It’s hard to prove that it was easier for a developmental program to evolve one way rather than another. But the facts of embryology remain, and make sense only in light of evolution. [Jerry Coyne, Why Evolution is True, p. 78-9]

These evolutionary arguments certainly are powerful, but their power comes from their metaphysics. If the evolutionists are correct in their theological and philosophical premises then of course evolution is correct. Its likelihood would be a number divided by zero. And that is infinity. Granted the numerator may be small, but the denominator is zero. So it does not matter how ridiculous evolutionary theory is—it must be a fact.

All arguments for the fact of evolution are metaphysical. From the seventeenth century to today, evolutionists gain their tremendous confidence from their religious convictions. That doesn’t mean they are wrong, but it does place a tremendous burden on their metaphysics.

Sober does not approve of such metaphysics. Do they not make objective analysis impossible? In his book he first levels this criticism at creation and design. As I wrote in my review of his book:

Sober next presents what he takes to be a “devastating objection” to the design argument, first raised by David Hume in the eighteenth century. Sober argues that evolutionists should not make theological claims in proving evolution. Likewise, Sober finds the same defect in the design argument. For when Paley argued that the complexity of the eye implies a designer, was he not assuming knowledge of what God would design? [126, 141-147] Ultimately Sober concludes that creation and ID cannot even follow basic scientific protocol. [356]

And Sober agrees that evolutionists should not use such metaphysics as well. But Sober’s disapproval does not remedy the problem. As Gould and Mayr document, Darwin’s argument rested on the low probability of the alternative. This has not changed since Darwin and today, though evolutionists insist their idea is a scientific fact, it would be better characterized as a religious mandate. Every argument for why evolution is a fact is metaphysical. That doesn’t mean it is false, but it should not be thought of as a scientific fact.

Wednesday, December 29, 2010

Evolutionists and the Giraffe’s Recurrent Laryngeal Nerve

In a recent university level evolution textbook the author rehearses the usual religious mandates for evolution in a chapter entitled “The Evidence for Evolution.” As Elliot Sober has observed, Darwin’s Principle (as Sober referred to it) is that biological inefficiencies and bad designs are powerful evidence for the fact of evolution because they show how unlikely are the creation or design alternatives. And so it is no surprise that, like Darwin’s book and the evolutionary apologetic literature since Darwin, the textbook is loaded with nature’s bad designs as the proof texts of evolution. Here is what the author writes about a typical example, the giraffe’s recurrent laryngeal nerve:

However, there are some homologies that do look positively disadvantageous. One of the cranial nerves goes from the brain to the larynx via a tube near the heart. In fish this is a direct route. But the same nerve in all species follows the same route, and in the giraffe it results in an absurd detour down and up the neck, so that the giraffe has to grow maybe 3-5 meters more nerve than it would with a direct connection. The “recurrent laryngeal nerve,” as it is called, is surely inefficient. It is easy to explain such an efficiency if giraffes have evolved in small stages from a fish-like ancestor; but why giraffes should have such a nerve if they originated independently … well, we can leave that to others to try to explain. [Mark Ridley, Evolution, Blackwell, p. 50, 1993]

It is yet another example of how evolution’s religion harms science. Let’s have a look.

Having it both ways

Evolutionists say that everything in the universe, indeed even the universe itself, just happened to spontaneously arise. And when dramatic differences are discovered in otherwise similar species, evolutionists do not lose a beat. Though evolutionists maintain that evolution is constrained by law, they are always able to imagine new contingencies to explain such dramatic changes.

Yet here, in the example of the giraffe’s recurrent laryngeal nerve, we are told that evolution was simply not able to remedy this gross inefficiency. Now of course there is no falsifying this account. Certainly, it is possible that the evolutionary account occurred as evolutionists imagine. But evolution’s ability to turn on a dime, switching from a new-designs-rapidly-appear narrative to an evolution-is-constrained narrative, depending on the problem at hand, makes the argument not as compelling as evolutionists insist it is.

Furthermore, in spite of the usual bold evolutionary claims, evolution in fact does not explain how the giraffe’s recurrent laryngeal nerve, or any nerve for that matter, evolved. The textbook informs the student that the inefficiency is “easy to explain” as a product of evolution, but in fact evolutionists provide nothing more than vague speculation. That last thing nerve cells look like is a product of evolution.

Nerve cells: More than just a wire

Nerve cells have a long tail which carries an electronic impulse. The tail can be several feet long and its signal might stimulate a muscle to action, control a gland, or report a sensation to the brain.

Like a cable containing thousands of different telephone wires, nerve cells are often bundled together to form a nerve. Early researchers considered that perhaps the electronic impulse traveled along the nerve cell tail like electricity in a wire. But they soon realized that the signal in nerve cells is too weak to travel very far. The nerve cell would need to boost the signal along the way for it to travel along the tail.

After years of research it was discovered that the signal is boosted by membrane proteins. First, there is a membrane protein that simultaneously pumps potassium ions into the cell and sodium ions out of the cell. This sets up a chemical gradient across the membrane. There is more potassium inside the cell than outside, and there is more sodium outside than inside. Also, there are more negatively charged ions inside the cell so there is a voltage drop (50-100 millivolt) across the membrane.

In addition to the sodium-potassium pump, there are also sodium channels and potassium channels. These membrane proteins allow sodium and potassium, respectively, to pass through the membrane. They are normally closed, but when the electronic impulse travels along the nerve cell tail, it causes the sodium channels to quickly open. Sodium ions outside the cell then come streaming into the cell down the electro-chemical gradient. As a result the voltage drop is reversed and the decaying electronic impulse, which caused the sodium channels to open, is boosted as it continues on its way along the nerve cell tail.

When the voltage goes from negative to positive inside the cell, the sodium channels slowly close and the potassium channels open. Hence the sodium channels are open only momentarily, and now with the potassium channels open, the potassium ions concentrated inside the cell come streaming out down their electro-chemical gradient. As a result the original voltage drop is reestablished.

This process repeats itself until the impulse finally reaches the end of the nerve cell tail. Although we’ve left out many details, it should be obvious that the process depends on the intricate workings of the three membrane proteins. The sodium-potassium pump helps set up the electro-chemical gradient, the electronic impulse is strong enough to activate the sodium channel, and then the sodium and potassium channels open and close with precise timing.

How, for example, are the channels designed to be ion-selective? Sodium is about 40% smaller than potassium so the sodium channel can exclude potassium if it is just big enough for sodium. Random mutations must have struck on an amino acid sequence that would fold up just right to provide the right channel size.

The potassium channel, on the other hand is large enough for both potassium, and sodium, yet it is highly efficient. It somehow excludes sodium almost perfectly (the potassium to sodium ratio is about 10000), yet allows potassium to pass through almost as if there were nothing in the way. The solution seems to be in the particular amino acids that line the channel and their precise orientation. For potassium, moving through the channel is as easy as moving through water, but sodium rattles around—it fits in the channel but it makes less favorable interactions with the amino acids.

Nerve cells are constantly firing off in your body. They control your eyes as you read these words, and they send back the images you see on this page to your brain. They, along with chemical signals, control a multitude of processes in our bodies. And no, they most certainly do not look as though they evolved.

Is the recurrent laryngeal nerve “surely inefficient”?

Evolutionists interpret biology, not surprisingly, according to evolution. They see biology as a series of kludges and flukes that just happened to come together. Naturally, they view the giraffe’s recurrent laryngeal nerve as an evolutionary blind alley. The nerve pointlessly got stretched. But in fact, on its long journey around the giraffe’s heart, the recurrent laryngeal nerve is hard at work. Gray’s Anatomy explains that as it winds around the subclavian artery the nerve sends several filaments to the cardiac plexus. It also sends branches to the mucous membrane, the oesophagus, and trachea. In fact, there is nothing like biology to remedy evolutionary misconceptions. Perhaps the recurrent laryngeal nerve is inefficient, perhaps it isn’t. But let’s try understanding it first before making theory-laden conclusions.

Nonetheless, this is what evolutionists believe. As evolutionist Jerry Coyne explains, the giraffe’s recurrent laryngeal nerve “makes no sense under the idea of special creation ... No form of creationism/intelligent design can explain these imperfections.” As he further explains in his book, Why Evolution is true:

One of nature’s worst designs is shown by the recurrent laryngeal nerve of mammals. Running from the brain to the larynx, this nerve helps us speak and swallow. The curious thing is that it is much longer than it needs to be. ... In giraffes the nerve takes a similar path, but one that runs all the way down that long neck and back up again: a distance fifteen feet longer than the direct route! ... This circuitous path of the recurrent laryngeal nerve is not only poor design, but might even be maladaptive. That extra length makes it more prone to injury. It can, for example, be damaged by a blow to the chest, making it hard to talk or swallow. But the pathway makes sense when we understand how the recurrent laryngeal nerve evolved. ... But the particular bad designs that we see make sense only if they evolved from features of earlier ancestors. If a designer did have discernable motives when creating species, one of them must surely have been to fool biologists by making organisms look as though they evolved. [82-5]

Or again, here is how evolutionist Richard Dawkins puts it:

The recurrent laryngeal nerve is a remarkable piece of unintelligent design. The nerve starts in the head, with the brain, and the end organ is the larynx, the voice box. But instead of going straight there it goes looping past the voice box. In the case of the giraffe, it goes down the full length of the giraffe’s neck, loops down one of the main arteries in the chest and then comes straight back up again to the voice box, having gone within a couple of inches of the voice box on its way down. No intelligent designer would ever have done that.

Some people are not quite sure what to make of this evolutionary metaphysics. In order to understand evolution, one needs to listen to what the evolutionists are saying. You may not agree, but this is what evolutionists believe. What if you believed the things evolutionists insist must be true? It may be difficult, but pretend for a moment that you actually believed as Darwin and the evolutionists do. Then, of course, you would say evolution is a fact. You would have to agree that the details are not well understood, but so what? So what if the theory is bizarre given the science—it must be true, one way or another.

This is rationalism.

When I pointed out this recurrent laryngeal nerve argument in my previous posting, a professor commented that this is not a problem for evolution, but rather a problem for me:

1. Either there is no prediction of what an omnipotent, designer would do,

2. ... or there is a prediction.

In the former case it is then clear that there is no prediction, the assumption of such a Designer makes no predictions about anything, and if so this hypothesis is not science.

In the latter case, there is a prediction and the giraffe’s recurrent laryngeal nerve is evidence against it.

We’ve been over this ground here many times. Cornelius has never explained what, if any predictions the hypothesis of Design makes.

The problem is that opponents of evolutionary biology want to have it both ways. In other cases they try to make predictions that an omnipotent Designer would not make certain kinds of designs. The simplest example is junk DNA. People who argue that there is evidence for Intelligent Design often say that it does make a prediction—that there will not be junk DNA. They never, ever, say where in their theory this prediction comes from, because to do so would be to admit that its origin is in theology. An intelligent, benign Designer would just not do it that way, they are arguing.

Cornelius continues to be caught on this dilemma and continues to try to argue that there is no prediction from Design, but continues to try to maintain that Design is science. He’s stuck. We’ve been over this ground many times here, and he is still stuck. He can get unstuck by disavowing the junk DNA prediction, but then he’s ultimately going to have to admit that his Design hypothesis is not science.

Rationalists place their need to know above limitations of their knowledge. If you point out the limitations they will criticize you for violating science’s intellectual necessity. They will even turn their dilemma onto you, assuming you face the same problem (no, I do not have a “Design hypothesis” as the professor thinks).

But how can we possibly know how the giraffe’s recurrent laryngeal nerve (or DNA that evolutionists label as junk, or a thousand other structures) ought to be designed? We barely understand how it even works. I would be the first to agree, indeed the first to argue, that our ability to judge and predict how an omnipotent designer would and would not make certain kinds of designs is limited. I will be happy when we can simply understand how those designs work.

I will be even happier when evolutionists cease their claims that evolution is a scientific fact based on metaphysical claims. If the professor is sure the design theory fails to qualify as science because it argues nature looks like it was designed, then why does he not also hold that evolution fails to qualify as science because it argues nature looks like it was not designed? Is it OK to argue what a designer would not do, but not OK to argue what a designer would do?

Evolutionists are fond of declaring what is and is not legitimate science, but their arguments are hypocritical. Science must stick to what is testable, they insist, but they then make all manner of untestable, metaphysical claims.

Evolutionists have taken science far afield. They have immersed science in their religious and philosophical concerns. And when you point it out they blame you for causing the problem. Religion drives science and it matters.

Tuesday, December 28, 2010

Professor: God Would Not Create the Giraffe’s Recurrent Laryngeal Nerve

One thing evolutionists agree on is that evolution is not only a theory, it is also a scientific fact. It is a curious point of consensus given that, of all the many, many evolutionary claims, it is the one that is most obviously and undeniably false. It is not that evolutionists fail to prove evolution to be a fact. They most definitely have done so, many times over. But their proofs are not scientific.

Evolution may or may not be true, but it is not a scientific fact. No one knows for certain whether evolution is true or not, but we certainly do know what is the state of our knowledge. The claim that evolution is a scientific fact is a claim about the state of our knowledge. And while there is uncertainty about evolution, there is no uncertainty about our knowledge.

We all know what the state of our knowledge is and, from a scientific perspective, that knowledge does not indicate evolution to be a scientific fact. Not even close.

We do not know evolution to be an obvious, compelling explanation of the data—beyond any shadow of a doubt. Yet this is precisely what evolutionists claim.

This simply is not the case. In fact, truth be told, there are tremendous scientific problems with the theory of evolution. We can argue about just how badly evolution fares on the evidence, but the evolutionary claim that it is a scientific fact is an obvious misrepresentation of the science.

But of course the evolutionist’s claims do not stem from science in the first place. For centuries evolutionists have presented a metaphysical—not scientific—certainty. You can find this in the seventeenth century literature, you can find it in today’s literature, and you can find it anywhere in between. Here, for example, is what one professor recently wrote to me:

An omnipotent god could do anything (we guess), but one who is omnipotent, serious, and thoughtful (at least as serious and thoughtful as an exemplary human) would not route wiring from giraffe’s larynx around its aorta

Such truth claims are standard amongst evolutionists. They rush in where wise men fear to tread. They do not hesitate to make claims that no one can demonstrate to be true or false. Such claims are metaphysical, and they are unfalsifiable.

How does the professor know that an omnipotent, serious, and thoughtful god would not route wiring from the giraffe’s larynx around its aorta?

What does the professor know about omnipotent, serious, and thoughtful gods? And what does the professor know about creating giraffes? Precious little, I’m afraid, in both cases.

Evolutionary thought is the height of hubris. It would be difficult to imagine a more anti intellectual tradition within the history of thought.

Of course evolutionists do not know that the many ultimate truth claims they make, which motivate and justify their thinking, are true. Obviously for them evolution must be a no-brainer—their theology demands it. Given such metaphysical axioms then, yes, evolution is a fact. But evolution is not a scientific fact, and that is a fact.

Saturday, December 25, 2010

Post Synaptic Proteins Intolerant of Change

Proteins are very unlikely machines but post synaptic proteins are even more unlikely.

Background: Neurons and synapses

The human brain is, as one science writer put it, “truly awesome”:

A typical, healthy one houses some 200 billion nerve cells, which are connected to one another via hundreds of trillions of synapses. Each synapse functions like a microprocessor, and tens of thousands of them can connect a single neuron to other nerve cells. In the cerebral cortex alone, there are roughly 125 trillion synapses, which is about how many stars fill 1,500 Milky Way galaxies.

And as one researcher explains:

One synapse, by itself, is more like a microprocessor—with both memory-storage and information-processing elements—than a mere on/off switch. In fact, one synapse may contain on the order of 1,000 molecular-scale switches. A single human brain has more switches than all the computers and routers and Internet connections on Earth.

Neurons are the body’s wiring. They carry electrical signals called action potentials. When an action potential reaches the end of a neuron it is passed on to another neuron or to tissue, via the synapse. First, the action potential causes voltage-controlled calcium channels, located at the end of the neuron, to open. Positive calcium ions on the outside stream into the neuron throught the open channels. The calcium ions influence special proteins just inside the neuron, which in turn cause small bubbles to dock with the cell membrane. The bubbles contain a neurotransmitter chemical which is released to the outside of the cell.

The neurotransmitter chemical floats across the synaptic gap between the cells, and attaches to the other cell, setting off the desired action. It is here where thousands of different proteins work in tight coordination to handle the incoming signals. These proteins form visible blobs called post synaptic densities (PSDs).

New findings: PSD protein designs

New research now emphasizes PSD complexity and the tight tolerances of the PSD protein designs. In fact, a wide range of mutations in these proteins are known to cause a variety of neurological and psychiatric diseases. And the new research finds that these proteins are highly conserved across species, suggesting they are highly sensitive to mutations. Here is how the New York Times described the findings:

The work should help in understanding how the synapse works in laying down memories, as well as the basis of the many diseases that turn out to be caused by defects in the synapse’s delicate machinery.

The research team, led by Seth Grant of the Sanger Institute near Cambridge, England, compiled the first exact inventory of all the protein components of the synaptic information-processing machinery. No fewer than 1,461 proteins are involved in this biological machinery, they report in the current issue of Nature Neuroscience.

Each neuron in the human brain makes an average 1,000 or so connections with other neurons. There are 100 billion neurons, so the brain probably contains 100 trillion synapses, its most critical working part.

These receptors feed the signals they receive to a delicate complex of protein-based machines that process and store the information.

The complex of proteins involved in this information processing is known to neuroanatomists as the post-synaptic density, because the proteins stick together as a visible blob, but the name does scant justice to its critical function.

The 1,461 genes that specify these synaptic proteins constitute more than 7 percent of the human genome’s 20,000 protein-coding genes, an indication of the synapse’s complexity and importance.

Dr. Grant believes that the proteins are probably linked together to form several biological machines that process the information and change the physical properties of the neuron as a way of laying down a memory.

The tolerances of these machines seem to be very fine because almost any mutation in the underlying genes leads to a misshapen protein and, consequently, to disease. Looking through a standard list of Mendelian diseases, which are those caused by alterations in a single gene, the Sanger team found that mutations in 169 of the synaptic genes led to 269 different human diseases.

So the brain and its circuitry is phenomenally detailed and complex, the different parts are tightly integrated, and they have a low threshold to change. This adds yet more problems to the evolutionary narrative. The PSD proteins are even more sensitive to change than typical proteins (see here and here). Evolutionists must believe that these proteins underwent huge changes in their evolution. Not only is there scant evidence of intermediate designs leading to the known proteins, but the evidence we do have is that these proteins do not tolerate change.

So the evolutionary narrative, as usual, must believe that the biological world underwent radical, unheard of levels of change, though mysteriously today such change is not tolerated. All the while luckily creating an astonishing world of biological wonders.

Friday, December 24, 2010

The Miracle of Ribosome Assembly Evolution

New research is uncovering the details of how the cell’s protein factory—the ribosome—is constructed. The ribosome translates messenger RNA molecules—edited copies of DNA protein-coding genes—into a string of amino acids, according to the genetic code. The ribosome has two major components (one smaller and one larger), each made up of both RNA and protein molecules, and is constructed via a complex sequence of events.

The RNA components of the ribosome are copies of DNA genes. These ribosomal RNA molecules—known as rRNAs—are initially in a raw copy of DNA which eventually is edited. For instance, one of these copies of DNA may contain many rRNAs, separated by spacer segments. The spacer segments need to be removed, leaving the individual rRNAs ready for assembly.

One of the findings of the new research is that in the early stages of assembly, one of the DNA copies folds up such that a spacer segment binds to one of the rRNAs. In particular, the spacer binds to the special segment of the rRNA that reads the messenger RNA molecules, in the final, assembled ribosome. When the spacer is removed, the rRNA switches to its correct shape, for function in the ribosome. One implication of this finding is that ribosome construction can be regulated by this switch. Remove the spacer and ribosome construction proceeds. Leave the spacer, and ribosome construction halts. As the researchers concluded:

our data show that the intrinsic ability of RNA to form stable structural switches is exploited to order and regulate RNA-dependent biological processes.

RNA tends to fold up into a variety of shapes. In this case, as lead researcher Katrin Karbstein suggests, RNA folding properties are part of the design:

Perhaps, nature has found a way to exploit RNA’s Achilles’ heel—its propensity to form alternative structures … Nature might be using this to stall important biological processes and allow for quality control and regulation.

But of course this mechanism brings yet more complexity:

What is interesting is that as the organism becomes more complex, the number of cleavages needed increases. This may make the process more accurate and that may be an evolutionary advantage, but even in bacteria this cutting is not done in a simple way. We still don’t know exactly why that is.

Karbstein suggests that the strictly ordered cutting and pasting steps in ribosome assembly are introduced to produce singularly perfect intermediates. As she explains:

Ribosomes make mistakes rarely, on the order of one in 10,000 amino acid changes. A lot of this accuracy depends on conversations between different parts of the ribosomes, so if the structure of the RNA isn’t correct, these conversations can’t happen. And that means more mistakes, and that’s not good because it can lead to any number of disease states.

Ribosomes don’t just happen. They are not easily assembled and the evolution of this choreography calls for several just-so heroics. Yes, this fine-tuned set of mechanisms makes for fantastic regulation of the cellular protein making factory, but it means that evolution must have gone through a stage where life didn’t work. For the spacer segment that binds to the rRNA is a show-stopper. It would be selected against instantly.

The only way to resolve this problem is to have the spacer removal mechanism already in place, before the spacer sequence itself evolved. As usual, evolutionists would need to rely on the needed mechanism just happening to serve some other useful purpose, and when the spacer sequence happened to arise for no reason, the removal mechanism found new work for itself. In other words, mutations arose that caused the DNA copy to fold, rendering ribosome synthesis—and life itself—impossible. But as luck would have it, there just happened to be the right molecular machine lying around that removed the problematic segment at just the right time and place. Not only was the fatal flaw obviated, but a brilliant new means of regulation invented. Amazing. Over time, further mutations happened to refine its actions and today we have the fine-tuned ribosome assembly process.

There you have it—evolution’s just-add-water version of science. For the umpteenth time evolution becomes a charade. Behind the scenes, in deep-time where no one can see it working, evolution once again performs miracle after miracle.

Wednesday, December 22, 2010

Entropy and the Distinction Between Operation and Origin

In the seventeenth century Isaac Newton figured out how the solar system worked. The same gravitational force that makes apples drop to the ground also steers the planets in their orbits about the sun. But the English physicist warned against over estimating the power of his new laws. Though the planets “persevere in their orbits by the mere laws of gravity,” Newton concluded, “yet they could by no means have at first derived the regular position of the orbits themselves from those laws.” Gravity alone can maintain an orbit about the sun, but not establish such an orbit. In the centuries since Newton evolutionists have constructed a solar system origin narrative replete with contingent events and all manner of natural law heroics.

There is much more to the history of solar system theorizing and its underlying metaphysics. For our current purposes, what is important about Newton’s warning is his distinction between nature’s operation and its origin. He could explain the former with his laws of gravity, but not the latter.

In the three hundred years since Newton, science has grappled with many more fantastic operations of nature. One that has commanded much attention in recent years is the protein folding problem. About fifty years ago it became apparent that proteins, consisting of hundreds of amino acids chained together, are champions of entropy. They routinely defeat nature’s tendency toward disorder as they find their correct three dimensional shape in a universe of failures.

In 1969 Cyrus Levinthal noted that since proteins fold in a fraction of a second, they cannot explore any significant portion of the universe of possible shapes. Somehow the protein knows how to go from the unfolded to correct folded state—two very different structures—in a short time. Levinthal concluded that the folding of proteins must be directed rather than random. But the speed and accuracy of the process seemed like a paradox.

Like Newton’s solar system problem, the operation of protein folding is a great story of science’s discovering nature’s complexity and fantastic operation. And as with the solar system, there is a distinction between the operation and the origin of proteins.

The operation of the protein is due to its amino acid sequence and its surrounding environment. The origin of the protein deals with how that rare amino acid sequence arose in the first place.

But recently physicist Ard Louis has said that the operations of proteins should give us confidence in their evolution. “If I look at something like the bacterial flagellum motor,” notes Louis, “one question is how has it evolved, another question is how does it self-assemble.”

True enough, but since we now better understand the self-assembly of these proteins, Louis has greater confidence they arose via strictly naturalistic causes (that is, that they evolved):

And so the fact that it took us quite awhile to understand these principles, makes me think that we could do the same over evolutionary time, over a much longer period of time. There’s no reason why, if we think about this long enough, we may not find the answer.

No reason? Why does Louis conclude there is no reason we may not find an evolutionary explanation for proteins and the machines they form? I can think of a reason straight off: What if proteins did not arise from strictly naturalistic causes? That could make it pretty difficult to find evolutionary solutions.

Louis concludes there is no reason we may not find a strictly naturalistic explanation for the origin of proteins because we find strictly naturalistic explanations for the operation of proteins.

But this makes no sense. Just because science succeeds on some problems doesn’t mean it will succeed on other problems. But it’s worse than this. For the particular success we are talking about—explanations for the operation of proteins—does not in the slightest suggest a solution for the origin of proteins.

In fact, what we are learning about the operation of proteins is that it so strongly hinges on the design of the protein. The incredible protein folding and other operations are pre programmed in the protein’s amino acid sequence. Understanding these principles does not suggest the protein evolved; rather, it suggests even more so how unlikely such an evolution would be.

What we have learned about the operation of the protein does not make evolution any more likely or probable. It does not point to a strictly naturalistic narrative because, after all such an approach worked for the operation of the protein. In fact, it was the very design of the protein that proved so crucial in understanding its operation.

A child does not understand how an automobile operates. When he eventually learns the automobile works according to natural law, that does not give him confidence that the origin of the automobile was also according to natural law. And yet this is Louis’ logic.

When I pointed this out here and here, evolutionists wrote to me defending Louis. One explained that Louis was merely pointing out that we ought not to think complex designs are impossible without intervention. The bacterial flagellum is complex, yet it self-assembles.

But such self-assembly is possible only because the constituent proteins have rare amino acid sequences. From where did those amino acid sequences come? The problem of operation of the flagellum points back to the problem of its origin.

This evolutionary argument that naturalistic operation implies naturalistic origin tramples on Newton’s distinction between the two. None of this is to say that the naturalistic origin of proteins is impossible. Perhaps evolution can create all of biology, but that is not what the science is telling us. And fallacious philosophical arguments don’t change that fact.

Sunday, December 19, 2010

Protein Folding and Evolution

Proteins consist of hundreds of amino acids attached to each other like train cars, and when they fold up they consistently find the same three dimensional shape. Like a necklace that magically falls into the same shape every time it is dropped onto a table, the consistency of protein folding once seemed like a paradox. For there is an astronomical number of shapes the protein could possibly take on. How does it find the same one so consistently, and so quickly? The answer has interesting implications for evolution.

When a protein folds to a given shape, it is fighting nature’s tendency toward disorder. The protein faces a universe of possible shapes, how does it always fold up to the same one? The answer is that this entropy barrier is overcome by the many chemical interactions tugging the protein toward its final destination.

A protein structure is subject to a wide variety of chemical forces and influences. Some of its amino acids have an oily side which means they want to huddle together, shielded from the aqueous environment. Other amino acids fit well with water and so have no such repulsion from the environment. Some amino acids are charged, so they mutually attract or repulse each other. And some amino acids have sulfur atoms which can bond together.

These various influences help to guide the unfolded protein to its final shape. They overcome the entropy barrier, but just barely. The result is a folded protein that is marginally stable, which means they wiggle and shake a bit—a good thing for many protein functions. The marginal stability of proteins also helps when it comes time to take them apart. Proteins are temporary wonders. They are created for a need, and just as quickly torn down.

Kicking the paradox down the road

So the paradox is resolved. Proteins overcome their enormous entropy barrier with their various chemical interactions, as determined by their particular amino acids. In fact, just as the words on this page determine the message, so too the amino acid sequence determines the particular characteristics of a protein.

The vast majority of amino acid sequences one could dream up don’t work. Most won’t successfully fold up, and most of those that do result in a structure that is too stable. And most don’t result in any meaningful protein function. As discussed here, useful amino acid sequences are rare.

So while the protein folding paradox is resolved, there is a nagging feeling. Yes, the protein overcomes its entropy barrier—it all works just fine. But it works just fine only because a very special amino acid sequence was specified. That amino acid sequence is just as astronomically rare as the three dimensional structure that the unfolded protein was able to find. So from where did this amino acid sequence come?

The string of amino acids that make up a protein comes from the cell’s translating machine called the ribosome. The ribosome takes as input a string of nucleotides and produces as output a string of amino acids. The translation is done according to the genetic code.

And from where did the string of nucleotides come? It came from the DNA. A massive protein copying machine slides along an opened section of DNA and copies a gene.

And from where did the DNA gene come? According to evolution it evolved, but it is here that we find another entropy barrier. Just as the folding protein is confronted with an astronomical number of structures, so too the DNA gene is confronted with its own nightmare of choices. But that is where the similarities end.

A different kind of entropy barrier

A typical gene has something like a thousand nucleotides. Given that there are four different types of nucleotides, this means there are 4^1000 different sequences that could make up the gene. This is equal to a 1 followed by about 600 zeros—a big number. That’s more than the number of nano seconds since the Big Bang—by about 10^574 (a 1 followed by 574 zeros).

Finding the right gene sequence to get a particular job done in the cell would make finding a needle in a haystack seem easy. The problem is so difficult that we haven’t yet figured out the answer, but it would be a 1 in 10^100++ long shot. Do not try this at home.

It is a huge entropy barrier, but it has some important differences compared to the protein folding entropy barrier we saw above. First, this gene entropy barrier is due to the large number of possible DNA nucleotide sequences whereas the protein folding entropy barrier was due to the large number of possible protein shapes.

And the protein folding entropy barrier was overcome by those fortuitously coordinated chemical interactions, which as we saw traced back to the amino acid sequence, which in turn traced back to the gene sequence.

But the gene entropy barrier has no such convenient explanation. Genes don’t come together via prearranged, specified information to overcome all odds.

In fact evolution’s proposal is that genes first arise via some sort of random change mechanisms, such as mutations. Nucleotides somehow come together, somehow provide some function, somehow are able to replicate, somehow vary, and somehow find new gene sequences against the astronomical entropy barrier.

Implications for evolution

The fact that evolutionists do not have all the answers or details does not mean it did not happen, or is impossible. But it is a significant problem. Evolution is hardly the sort of idea one would call a fact. Unless one were an evolutionist, that is.

Evolutionists say evolution is a fact, and that all the evidence lines up behind the theory. There are no serious problems or issues. Only minor details to be worked out. Consequently for them this gene entropy barrier is no big deal. In fact, amazingly they argue it is not a problem at all.

This is another unfortunate example of how evolution corrupts science. In the hands of evolutionists, science is manipulated in strange ways to support their theory. In the case of this gene entropy barrier, evolutionists such as Ard Louis argue that the fact that since biology operates successfully everyday inspite of tremendous entropy barriers such as in the protein folding case, that therefore entropy barriers are really no problem for evolution either.

But as one can see from the protein folding and gene example discussed above, this argument makes no sense. As we saw, proteins overcome their entropy barrier via the many fortuitous chemical interactions that arise as a consequence of the very special amino acid sequence specified by the DNA gene.

The protein successfully folded because it was setup to fold. The scientist cannot then conclude that since this worked out so nicely that the origin of the gene itself (responsible for the special amino acid sequence) has no serious entropy challenge. They are two very different problems. The fact that the protein folds does not mean the gene evolves.

This argument that biology’s everyday overcoming of entropy shows that evolution can do the same thing (somehow), is simply a corruption of science. It is an unfortunate, yet common example of what evolution has done to our thinking. Religion drives science, and it matters.

Saturday, December 18, 2010

Sex Determination in Chickens: Evolution Wrong Again

Evolution is, as evolutionists like to say, absolutely necessary to do science. Darwin’s theory, in one version or another, is the underlying framework that guides our research. Nothing in biology makes sense, evolutionists like to repeat, except in the light of evolution. But in fact evolution is constantly upended. We are continually finding special cases, anomalies and exceptions, and evolution is more of a confusing patchwork of “On Tuesday’s it looks like this” than a useful theory. Consider just one example from this steady stream of failed expectations: sex determination in chickens.

Researchers studied three chickens that appeared to be literally half-male and half-female, and found that nearly every cell in their bodies — from wattle to toe — has an inherent sex identity. This cell-by-cell sex orientation contrasts sharply with the situation in mammals, in which organism-wide sex identity is established through hormones.

The confused fowl have upended a century-old rule, established for vertebrates, that all cells in an embryo start off sexually indifferent and remain so until a sex-determining gene directs the development of gonads into either ovaries or testes. The work appears in today’s Nature, and may trigger a rethink of the evolution of sex determination.

So sex determination in chickens is completely different than in mammals. Rather than evolution providing the underlying model allowing us to interpolate and extrapolate our observations, it needs to be explained away.

Gynandromorphs are striking because nothing like them has been seen in mammals. In almost all mammals, including humans, embryonic cells are initially sexually indistinguishable. During development, genetic factors trigger the formation of male or female gonads according to an animal's combination of sex chromosomes (XY for males and XX for females). The gonads then secrete hormones that direct other cells to develop as a certain sex.

We assumed that sex determination in birds would follow the mammal pattern,” Clinton says. Accordingly, the researchers thought that one side of the gynandromorphs would be a normal female (or male) and that the other side would have a some kind of chromosomal anomaly. …

Clinton says the work shows that chickens have a fundamentally different way of determining their sex from mammals: “Hormones do play some role, but nowhere near the extent seen in mammals.”

Naturally the evolutionists assumed that sex determination in birds would follow the mammal pattern. But once again, they were wrong. Instead of evolution explaining the data, it is the data that explain evolution. With each new finding, evolution needs a new special case patched on.

Birds aren’t the only exception to the rule. The mammal model also fails with some marsupials and invertebrates like fruitflies. “The problem is, once people develop a hard and fast rule, it becomes the only game in town,” Clinton says. Sam’s “tubes and plumbing” would suggest there is no rule for all vertebrates.

No rule for vertebrates? So amazingly, with evolution we must believe something as fundamental as sex determination somehow takes on completely different mechanisms. Somewhere along the line, some random biological variation switched, for instance, from hormonal control to chromosomal control. Evolutionists, of course, have no idea how this actually happened. But they are absolutely positive it did happen. Somehow. Religion drives science, and it matters.

Thursday, December 16, 2010

Ard Louis and Vitalism

I once collected and cataloged the various arguments for evolution. It is fascinating to see smart people constructing elaborate schemes for the unlikely. One of the subtle, yet no less bizarre, arguments is the use of vitalism as a null hypothesis, a variation of which the brilliant physicist Ard Louis constructed recently. First, here’s what I wrote about this a year and half ago:

Recent epigenetics findings highlight a problematic trend. Evolution faces ever increasing scientific challenges as its predictions continue to go wrong. All the while evolutionists, for the most part, continue to issue non responsive responses. Most of what I have heard from evolutionists regarding epigenetics falls into the usual categories of denialism, but one evolutionist told me that epigenetics poses no problems for evolution because the mechanisms are, well, just that—mechanisms.

This argument is very simple: The epigenetics mechanisms are natural, and therefore they fit well within evolutionary theory. This argument draws a (false) dichotomy between vitalism and evolution. In this banal view of nature, vitalism is evolution’s foil—if a mechanism isn’t violating natural law, then it evolved.

In his 2005 book Before Darwin: Reconciling God and Nature, Keith Thomson uses this argument (see Science’s Blind Spot for discussion). Could this be an emerging argument for evolution? If so, it demonstrates how desperate the defense has become.

Desparate may not be the right word for the defense and promotion of evolution. Bizarre might be more accurate. Consider this latest use the vitalism strawman by Ard Louis:

Here Louis first explains that complex molecular machines, such as the bacterial flagellum, are able to assemble and operate successfully everyday inspite of a tremendous entropy barrier. And these machines assemble and operate according to natural law—there is no vitalism here, no divine finger adjusting the cogs and turning the crank.

This of course is the story of biology. Against all odds, it works. And this is a fundamental problem for evolution. The tremendous entropy barrier that life defeats is a continual demonstration before our very eyes of the extreme difficulty that it just happened to fall together.

It is the height of absurdity to use this as an argument for evolutionary solutions. When I turn the key, my car starts up. What are the odds all that could just happen? Very low indeed, which means it probably didn’t just happen to happen. It is exceedingly unlikely that natural laws could produce such an arrangement.

None of this is to say that evolution is impossible—it just means that evolution is not where the science is pointing.

Louis’s argument is an echo of seventeenth century philosopher Rene Descartes who urged evolutionary ideas because of the evident power of natural law. Yes god created humanity, but individuals are born and grow according to law. From people to plants, we observe incredible development brought about by nature. So too, the continental rationalist argued, we should understand the origin of the world as strictly naturalistic as well.

Decades later the influential Thomas Burnet showed how the Cartesian view is theologically mandated. Rather than creating a clock that doesn’t work and needs constant adjustment, the greater clockmaker makes a clock that works by itself. Likewise, the Anglican cleric argued, the greater god makes a world that operates on its own.

It is the ultimate example of snatching victory from the jaws of defeat, yet in this case the victory is only in the minds of evolutionists. The routine defeat of astonishing levels of entropy is easily converted into evidence for evolution. The level of denial is staggering. Religion drives science, and it matters.

Wednesday, December 15, 2010

Ants Optimize Their Search

New research shows that when presented with a barrier, ants don’t just turn around and follow the scent back the way they came. Instead, they perform an advanced search:

An analysis of how ants quickly find new routes in a changing maze reveals techniques that could be useful to systems engineers.

The research, reported in the Journal of Experimental Biology, shows that Argentine ants (Linepithema humile), do not just retrace their steps when presented with a barrier—as might be expected. Instead, the ants begin a localized search that seems to take into account the direction in which they were planning to go. Because there are many network-management programs that mimic the search behaviour of this ant species, systems engineers are taking notice and wondering what they can learn.

Systems engineers learning from ants?

Many computerized systems, such as those that route telephone calls through busy networks while minimizing connection times, already solve shortest path problems by deploying virtual ants. These ants explore all possible routes in a system and deposit virtual pheromones on each route they travel.

Yet such systems are not perfect. When virtual ants are blocked from following a well-travelled path, they must turn around and are likely to follow the path that they have just travelled because it usually has the strongest concentration of pheromones of any nearby paths.

“I figured Argentine ants had to have some way of dealing with obstacles that didn’t involve starting a search from scratch” says Chris Reid, a behavioural biologist at the University of Sydney in Australia, the lead author of the study.

To put the insects to the test, Reid and his colleagues presented them with a logic puzzle known as the Towers of Hanoi.

So the researchers constructed a maze with 2^15 (that is, 32,768) different paths for the ants to negotiate.

“The discovery that these ants can solve the Towers or Hanoi is far from trivial,” says Simon Robson, a biologist at James Cook University in Townsville, Australia. … “When I heard that these ants started exploring nearby routes rather than turning around, I just thought, this is dead cool,” says David Broomhead, director of the Centre for Interdisciplinary Computational and Dynamical Analysis at the University of Manchester, UK. … The discovery indicates that Argentine ants use more than just the simple trail pheromone to find their way. “The individual ants appear to have internal compasses and odometers that allow them to guide their search,” says Reid. Broomhead adds that “it would be really interesting to see if we can get a computer to do what these ants are doing.”

Internal compasses and odometers which just happened to arise on their own? As usual, evolution is called upon to perform unlikely heroics. Evolutionary expectations are dashed as ants are smarter than engineers, and the theory must do yet more gymnastics to accommodate the facts. But just because evolutionists have no idea how such marvels could just happen to arise does not mean they will stop insisting evolution is an undeniable fact.

Monday, December 13, 2010

How Proteins Evolved

Fifty years ago molecular biologists began to uncover the inner workings of the cell and one of their profound discoveries was that genetic information, stored in the double helix DNA molecule, was translated according to a code to produce a string of amino acids which, after being hitched to each other like train cars, folded up to produce a protein that did something useful in the cell. Interestingly, a given protein’s amino acid sequence was found to have some degree of flexibility. Hemoglobin proteins, for instance, across different species revealed quite a few changes to the sequence while still functioning as a hemoglobin.

Two discoveries that later followed seemed to bode well for evolution. First, protein sequences fit the evolutionary pattern when compared across different species. For instance, a given protein such as hemoglobin has a very similar sequence of amino acids when compared between two similar species, and a much more different sequence when compared between distant species. Second, the degree of flexibility of a given protein’s amino acid sequence was substantial. Hemoglobin sequences in distant species had practically no resemblance. This suggested that a relatively small amount of information was actually needed to code for a given protein. Proteins have hundreds of amino acids, but perhaps only tens of them are important in determining the structure and function of the folded protein structure. This would make evolution’s task of constructing proteins less daunting.

These discoveries are a bit technical and so not always easy to convey to non scientific audiences. But evolutionists have tried, for these discoveries definitely gave them added confidence their theory was right. What evolutionists have been less vocal about are the discoveries that have been made more recently. We now know that for both these discoveries, the story is more complicated than it originally appeared.

The evolutionary pattern

First, the observation that protein sequences fit the evolutionary pattern is not particularly surprising. If we discovered a new bone or tissue, would we not generally expect that it would be more similar between species that otherwise are similar, and more different in more distant species? After all, it functions within a context. So it is no shocker that cellular components such as proteins generally follow the pattern.

But this is not always the case. This pattern that evolution predicts is sometimes violated. Biology reveals some very big differences between otherwise similar species, and some striking similarities between otherwise distant species. This is true for visible features as well as at the molecular level. The evolutionary pattern has now been falsified many times over. Nonetheless, the textbooks continue to proclaim the good news that proteins fit the predicted pattern, and curiously omit any mention of the more recent failures.

The flexibility of a protein sequence

Second, we now understand that the degree of flexibility in a protein sequence is far less than once imagined. One way to think of this is with an analogy to English. Consider these two sentences:

Evolutionary theory has produced a vast number of falsified predictions.


Most of the expectations generated by evolution have turned out false.

These two sentences share the the same meaning yet if you align and compare them letter-by-letter, you would find most of the letters are different. They seem to be unrelated at that level. Could it be that there are only a few key letters that determine the entire meaning of the sentence?

Of course not. We all know that while very different text messages can share the same meaning, this does not imply that most of the letters carry no effect and can be mutated without little or no effect. In fact, even for such short messages there is a large number of possible letter sequences. Each letter has 26 possibilities and in the above example there are about 60 letters. This means there about 10^85 (a one followed by 85 zeros) different letter sequences that are theoretically possible. Of that astronomical set of possibilities, only a relatively tiny set of selections is grammatically correct. The set of selections that makes any sense is even smaller, and the set that carries the same meaning as those above is tiny.

Likewise, it is now clear that while a given protein such as hemoglobin may come in very different sequences, only few changes to that sequence can be sustained. There are many ways to code for the hemoglobin machine, and they may appear to be very different, but that does not mean there is a relatively large number of sequences that can produce a hemoglobin. Here is how one recent paper explained the new findings:

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

Another recent paper explained that only a few percent of a protein’s amino acids can tolerate change at any given point in time.

We are a long way from having hard numbers, but even conservative estimates of the number of protein sequences that are viable, for a given type of protein, are tiny. Any given residue in a protein may not be required to have a specific type of amino acid in order to form a hemoglobin, but in the context of the remainder of the sequence there is a tight requirement. And the number of such contexts is relatively small.

Years ago creationists argued that evolution was improbable because a protein sequence is a long shot. A typical globin sequence has about 140 amino acids. This means the sequence represents a one in 10^182 chance (a one followed by 182 zeros).

It was an imprecise argument, for there is far more than just one sequence that can do the job. But in this case, being off by orders of magnitude hardly matters. A viable globin sequence may be a mere one in 10^150 chance. Who knows, perhaps it is even a one in 10^120 chance. The fact is we do not know, but today’s science is telling us that a viable globin sequence makes finding a needle in a haystack seem easy. And the hemoglobin protein is a relatively small one. Many proteins are several times longer.

How do proteins evolve?

Contrary to early notions that protein sequences were extremely flexible, science is now telling us the opposite. This indication that viable protein sequences occupy a tiny sliver of sequence space suggests that they are difficult to evolve.

If you ask an evolutionist how a protein evolved, you will likely hear the standard answer: via gene duplication and subsequent divergence. In other words, the protein arose from a different type of protein that was pre existing. The gene for that protein duplicated, and then mutated until landing on a new protein that was helpful. And of course this story must have repeated itself thousands of times to create the many different proteins in biology.

It is an unlikely, just-so, story, for viable protein sequences are hard to find. If the different types of proteins each have their own tiny slivers of sequence space as science is suggesting, then gene duplication and divergence, alone, doesn’t stand a chance.

What would be needed are long trails of intermediate, functional, proteins connecting the different types of proteins. These proteins would not only need to be functional, their particular function would have to be useful at the time.

And why would the known proteins just happen to be fortuitously connected by these trails? Science gives us no reason to think such a lucky circumstance is built into the protein world. So either there are no such trails, which means evolution has a problem, or there are such trails which means someone has monkeyed with the fundamentals of protein chemistry.

And we have not yet even addressed the problem of how the first proteins evolved. Remember the evolutionist’s standard explanation for how proteins evolved is by gene duplication and subsequent divergence. But that requires the pre existence of other types of proteins. In other words, the question of how proteins evolve in the first place has been swept under the rug.

The problem of how evolution could create a new type of protein from an existing protein, via gene duplication and subsequent divergence, as difficult as it is, pales in comparison to how evolution was supposed to have created new proteins from scratch. Evolutionists speak of an initial world where RNA molecules do the work of proteins. But even this heroic story doesn’t magically make the problem of protein evolution go away. Whether there were RNA precursors or not, there is a substantial difficulty in explaining how the first proteins could have evolved.

Stepping stone: ATP binding

A few years ago an experiment showed that randomly constructed short proteins have a one in 10^12 shot (a million million) of having function. The function, in this case, was the binding of ATP, the cell’s unit of energy. While that is an interesting experiment, the results do little to help evolution. Most obviously, that function alone is quite minor. Yes, proteins bind to ATP or other chemicals, but that binding is in a complex, tight coordination with other functions. Comparing ATP binding with the incredible feats of hemoglobin, for example, is like comparing a tricycle with a jet airplane.

And even the one in 10^12 shot, though it pales in comparison to the odds of constructing a more useful protein machine, is no small barrier. If that is what is required to even achieve simple ATP binding, then evolution would need to be incessantly running unsuccessful trials. The machinery to construct, use and benefit from a potential protein product would have to be in place, while failure after failure results. Evolution would make Thomas Edison appear lazy, running millions of trials after millions of trials before finding even the tiniest of function. Why would this machinery be in place? Why would it continue to construct and test? Why would evolution maintain such an incompetent test bench?

Evolutionary answers to such questions are like all their stories. It did it because it did it. And if it seems unlikely, then remember there are many planets revolving about many stars, in many galaxies. And beyond that there are many universes. And in any case, a different sort of life—or no life at all—could have evolved. This is what evolution has done to science. Religion drives science and it matters.

Sunday, December 12, 2010

Back to School Part IX

We continue to examine the work of authors George Johnson and Jonathan Losos in their biology textbook, The Living World ((Fifth Edition, McGraw Hill, 2008). In their chapter on evolution and natural selection, these accomplished evolutionists begin by (1) misrepresenting the relationship between microevolution and macroevolution and biological variation here, (2) making a non scientific, metaphysical, truth claim that just happens to mandate the truth of evolution here, (3) making the grossly false statement that the fossils themselves are a factual observation that macroevolution has occurred here and here, (4) making a series of misrepresentations by carefully selecting the evidence to provide to the student and protecting it with circular reasoning here, (5) misrepresenting the molecular evidence here, (6) presenting the student with a blatantly false history of evolutionary theory here, (7) introducing the usual if-and-only-if evolutionary reasoning here, (8) repeating the centuries old religious argument that bad design proves evolution here, and (9) making a fallacious argument that evolution’s low probability events are not actually low probability after all here.

After this incredible litany of evolutionary canards one might wonder when the lies are going to stop. Unfortunately not yet. Johnson and Losos’ next move is to address the question of mechanism. We have discovered phenomenally sophisticated mechanisms that allow organisms to adapt to challenging conditions. And we know how breeders can produce different plant varieties and animal breeds. But how does macroevolution come about? How do new designs and body plans arise? The answer given by Johnson and Losos is problematic:

Is microevolution (evolution within a species) the mechanism that has produced macroevolution (evolution among species)? Most biologists that have studied the problem think so. [302]

This logic is so riddled with problems it is difficult to know where to start. What Johnson and Losos have in mind when they refer to “most biologists” is, of course, evolutionists. Evolution skeptics certainly do not think it is obvious that adaptation mechanisms also produce entirely new designs.

But evolutionists are people who dogmatically insist that evolution is an obvious fact—beyond a shadow of a doubt. It would be perverse and irrational, they say, to doubt it. Thus there is a credibility problem, for Johnson and Losos are using the testimony of people who insist the unlikely must be a fact. This evolutionary mandate is driven by metaphysical concerns, so immediately there is the question of tainted testimony.

This question also arises for a second reason. Setting aside evolution’s metaphysical undermining of science, the mere fact that the testimony is from evolutionists means Johnson and Losos argument is circular. The problem is that arguments between evolutionists about mechanism are based on the assumption evolution is true in the first place.

In other words, the question for evolutionists is not whether known biological mechanisms explain the large-scale change evolution requires. The question, rather, is given the fact of evolution, do known mechanisms explain the large-scale change needed? If the answer is “no,” then the premise that evolution is a fact is undermined. Obviously evolutionists have a motive to answer “yes.”

So Johnson and Losos base their argument on testimony from people with questionable scientific credibility in general, and strong potential bias on this particular question. Right from the start we have problems.

But let’s set these problems aside for the moment and examine the argument. According to Johnson and Losos, most evolutionists think microevolution mechanisms are also the mechanisms behind macroevolution.

This is probably true, but it is by no means a given, even amongst evolutionists. There certainly are evolutionists who conclude that macroevolution is more than repeated rounds of microevolution.

This sentiment may not be held by the majority of evolutionists, but it certainly is a legitimate position within evolutionary thought. And importantly, the majority seems to rely more on inertia than data.

Stephen Jay Gould often complained about a textbook orthodoxy that uncritically passes on the doctrine of microevolutionary mechanisms as sufficient to explain all of evolutionary history, without support. The rapid appearance of biology’s new designs, Gould elaborated, cannot simply be explained as extrapolations from Darwinian changes which we observe in modern populations.

Evolutionists don’t necessarily agree, but then again they don’t have a convincing explanation of just how such extrapolations occur. It is convenient to point to the results of breeders and the adaptations we observe in nature, but even the complex mechanisms behind these changes do not provide us with scientific evidence that they also can produce entirely new designs and body plans.

All of this is well known and that fact makes Johnson and Losos’ argument particulary stunning. Yes, the majority of evolutionists probably would agree that microevolutionary mechanisms are all sufficient. But that is hardly a sufficient rebuttal to the problem as Johnson and Losos present it to be.

How could Johnson and Losos possibly present such a misleading argument to the unsuspecting student? How could the small army of reviewers allow for this misrepresentation, and how can educators allow for such stilted logic, while teaching the student that critical thinking is paramount?

The answer is that evolution has substantially damaged science, and the teaching of science. Religion drives science and it matters.

Sunday, December 5, 2010

Elliott Sober and the Enemy

Politicians and football coaches understand that what motivates people is an enemy. What better way for a leader to solidify support than by war with an evil foe. Internal failings and scandals fade in the light of an external threat. Whether it is nazism, communism or terrorism, there always seems to be an appropriate “ism” to capture and focus our attention.

The alarm of an external threat is often legitimate. Have not nazism, communism and terrorism been real dangers? But what begins as a legitimate response to a threat is sometimes extrapolated well beyond the original mandate. A war effort that is just can later lead to power grabs and secret wars.

For evolutionists, the enemy is creationism. And with creationism there certainly are many legitimate questions. Seventeenth and eighteenth century thinkers wondered about the age of the earth, whether god created the unsavory aspects of nature, how fossils fit into the picture, and so forth. Could it be that god created not by direct miracles but rather via nature’s laws?

Certainly these were, and remain today, legitimate questions. But in those centuries leading up to Darwin, several traditions emerged that did not merely question or doubt the traditional creation story, they mandated a strictly naturalistic origins narrative. The theory of creation, as several different arguments asserted, had been disproven so an evolutionary story must be the answer.

And that answer was increasingly viewed as the truth. Today evolutionists insist their theory is an undeniable fact. It would be perverse and irrational, they say, to doubt it.

This is the effect of having an enemy. Creationists are a unifying threat to evolutionists. Evolutionists routinely refer to creationists has having various nefarious motives. And this is why evolution apologists are quick to label any and all skepticism as creationism. Better to maintain a strong, threatening enemy than to thoughtfully consider different views.

Evolution is, of course, unlikely from a scientific perspective. Practically every one of its major predictions has been falsified. And the theory has become enormously complex and circuitous in its attempts to accommodate the uncooperative data.

But this misses the point. Evolution never was a likely idea. Its mandate did not come from the evidence in its favor, but rather from the evidence against creation. At bottom evolutionary thought is contrastive. It depends on its never ending recall of creationism. Today’s evolutionary literature reads very much like the Enlightenment version.

Evolutionists are continually explaining that while their idea is a theory, it is also a fact. The “theory” part refers to their ignorance of how all of biology could have arisen on its own, while the “fact” part refers to their certainty that it nonetheless must have happened that way.

Evolutionary philosopher Elliott Sober has analyzed how common descent advances via this contrastive thinking. The powerful arguments and evidence do not actually bolster the theory but rather they rebuke the alternative. He explains it this way:

This last result provides a reminder of how important the contrastive framework is for evaluating evidence. It seems to offend against common sense to say that E is stronger evidence for the common-ancestry hypothesis the lower the value is of [the probability of E given the common-ancestry hypothesis]. This seems tantamount to saying that the evidence better supports a hypothesis the more miraculous the evidence would be if the hypothesis were true. Have we entered a Lewis Carroll world in which down is up? No, the point is that, in the models we have examined, the ratio [the probability of E given the common-ancestry hypothesis divided by the probability of E given the separate-ancestry hypothesis] goes up as [the probability of E given the common-ancestry hypothesis] goes down. … When the likelihoods of the two hypotheses are linked in this way, it is a point in favor of the common-ancestry hypothesis that it says that the evidence is very improbable. [Evidence and Evolution, p. 314]

In other words, it doesn’t matter that common descent is not a good theory. It must be true because the alternative is even worse. Sober refers to this mode of reasoning as Darwin’s Principle. Evolutionists must fight their enemy.

Evolutionary thought is easily the greatest threat to science today. It turns science on its head in favor of its own metaphysics. Religion drives science, and it matters.

Thursday, December 2, 2010

Arsenic-Based Biochemistry: Turning Poison Into Wine

Being an evolutionist means there is no bad news. If new species appear abruptly in the fossil record, that just means evolution operates in spurts. If species then persist for eons with little modification, that just means evolution takes long breaks. If clever mechanisms are discovered in biology, that just means evolution is smarter than we imagined. If strikingly similar designs are found in distant species, that just means evolution repeats itself. If significant differences are found in allied species, that just means evolution sometimes introduces new designs rapidly. If no likely mechanism can be found for the large-scale change evolution requires, that just means evolution is mysterious. If adaptation responds to environmental signals, that just means evolution has more foresight than was thought. If major predictions of evolution are found to be false, that just means evolution is more complex than we thought. So today’s falsification, though it falsifies one of evolution’s most treasured predictions, will be no different. Once again, evolutionists have great news.

According to evolutionists, one of the most powerful evidences for their notion that the world just happened to arise somehow on its own, is the underlying unity of biology’s fundamental biochemistry. From information storage in the DNA macromolecule to basic metabolism, the same designs are found across biology’s wide spectrum. As Niles Eldredge put it:

The basic notion that life has evolved passes its severest test with flying colors: the underlying chemical uniformity of life, and the myriad patterns of special similarities shared by smaller groups of more closely related organisms, all point to a grand pattern of descent with modification.

Likewise, Christian de Duve triumphantly declared:

Life is one. This fact, implicitly recognized by the use of a single word to encompass objects as different as trees, mushrooms, fish, and humans, has now been established beyond doubt. Each advance in the resolving power of our tools, from the hesitant beginnings of microscopy little more than three centuries ago to the incisive techniques of molecular biology, has further strengthened the view that all extant living organisms are constructed of the same materials, function according to the same principles, and, indeed, are actually related. All are descendants of a single ancestral form of life. This fact is now established thanks to the comparative sequencing of proteins and nucleic acids.

“The essential macromolecules of life,” explained philosopher Michael Ruse, “speak no less eloquently about the past than does any other level of the biological world.”

With these high accolades, one might think that counter indications would pose major problems for evolutionists. If an observation is such powerful evidence in favor of a theory, then isn’t its falsification a powerful argument against the theory?

Not at all, for this is no ordinary theory.

When the DNA replication apparatus—a rather fundamental biochemical process—was found to be significantly different across different species, evolutionists didn’t miss a beat. Those different versions of DNA replication, we were told, probably evolved independently. Or maybe they diverged. Anyway they evolved, that was for certain.

Next in line is the fundamental unit of energy, the ATP (adenosine triphosphate) molecule, which provides the chemical power for everything from thinking to muscle movement. Would you believe it isn’t universal as you were taught in your high school biology class?

If instead of phosphorus, what if some species turn out to use arsenic? That’s right, arsenic—the poison. It would not exactly be a minor design adjustment. In fact, it would be another major falsification of one of evolution’s most vaunted predictions.

And what would be the evolutionary spin? That’s easy: we would be told that such a monumental finding tells us more about how evolution works. In fact, does it not tell us how incredibly flexible are evolution’s designs, and therefore how much more variety we should expect in the evidence of extraterrestrial life?

That’s right. A falsification of a major evolutionary prediction would be, in a brilliant stroke, turned on its head. With ease it would be converted into evidence for extraterrestrial life. Evolution turns poison into wine.