A Question of Life

This is part 3 of a 10 part series. The introduction can be found here, and the prior post can be found here.

Now, with a universe coming into existence that just happens to be fit for stars, planets, and complex chemistry, we have the question of how those biochemically complex systems (that we call life) came about. Even if an environment is perfectly suitable for habitation, it does not mean that it will automatically and necessarily produce the inhabitants. The arrival of such inhabitants is a separate marvel to be explained.

3. Abiogenesis
The problem of abiogenesis (the origin of the first lifeform) is one of the thorniest and most intractable issues in chemistry. Our increasing knowledge of microbiology and earth history has only added to the complexity of what needs to be explained. The simplest life is equivalent to modern bacteria, which is loaded with complex activity, information, and molecular "machines." The fossil record does not give evidence that there was a "prebiotic soup," or that there were any biological precursors to the first organisms, or that the atmosphere was the ideal mix to yield the necessary molecules, or that there was the expected long period of time between when the Earth could support life and when it actually appeared. Evolutionists regularly segregate the abiogenesis problem from the issue of evolution because (1) it is a challenge they'd rather not be saddled with, or (2) it is the most logical point for possible divine intervention. However, for the atheist there is no escaping this issue; they are obliged to seek out some purely natural explanation.
What hope for an explanation do you have? Are you satisfied to have problems like this that are unanswered, or even unanswerable?
In telling the tale of life on earth science writers often unconsciously use the word "miracle" for the appearance of the first organisms.
What kind of evidence is needed before we are to actually accept that something like this really is a miracle?

Randall starts us off by rejecting the idea that this is even a significant scientific challenge.

I don't know that [abiogenesis] is a thorny issue. Scientists see this as a fascinating issue; it's no thorn in anyone's side.

I think that any scientific issue that has been the victim of 150 years of unrequited investigation has the right to be called something like "thorny"; and if this issue does not qualify for such a label, then all of science must consist of simple and "fascinating" problems.

Faithlessgod thinks that I have overestimated the problem and that solutions are just around the corner.

Now is it the thorniest and most intractable problem, I don't think so. The fact that Pruett asks this is indicative that he really does not comprehend the nature of the work in this field. . . . it is not like we have no idea of the origins of life, indeed it is the opposite, we already have too many theories! . . . Of course we do not know which one is correct and all the current ones have some shortcomings . . . It most certainly is not at all intractable.

I do indeed comprehend the nature of the work in this field. It's not a naïve idea that everyone is just sitting around shrugging their shoulders that makes me call this an "intractable" problem; it's the knowledge of the issues relating to such work that leads me to use the term. The very fact that we have "too many theories" is a case in point. We only have competing theories because there is not a promising candidate bereft of difficulties. Faithlessgod admits that "all the current ones have some shortcomings," but a more accurate word than "shortcomings" would be "showstoppers."

I'll take the time here to review some of the technical roadblocks generally encountered by origin of life researchers. Later we’ll look at more specifics.

• Life requires water, but the very presence of water prevents many of the chemical reactions required to build molecules necessary for life.
• Certain conditions sufficient to form necessary molecules are just as likely to destroy them once created, like heat or UV rays.
• The conditions sufficient to yield certain molecules are hostile to other necessary molecules. But those independent components of life must be able to coexist and survive before they can hope to form into units.
• No matter how interesting a thing might be produced by chance, it is meaningless if it cannot reliably reproduce itself.
• Even if a self-replicating molecule could manage to form by chance it is a quantum leap between that and the next theoretical level, which is something that can produce other molecules (like proteins) for its own functional entourage and also reproduce itself.
• The simplest life that we know of or can even conceive of as a functional package is epitomized by interdependent systems that must come about as a group, with none of the parts serving any isolated function. There is a huge void between independent molecules (of any complexity) and life.
• Any meager gains in theorizing how some part of a cell might come to form are continually outdistanced by the increase in knowledge of what it is that is to be explained.
• Even where some mechanism might be theorized to form essential molecules, the statistical problem of fortuitous assembly of those molecules still remains, e.g., how you build a functional polypeptide chain (protein) from loose amino acids.
• The time for chance to do its work is shrinking. By many estimates, life's appearance is now in the 3.8 to 3.5 billion year range, and this may only be because we have difficulty detecting it prior to these dates (note: Earth is alleged to be 4.5 billion years old, and would not have been suitable for life for hundreds of millions of years after that time).

Randall waxes nostalgic about some work from the 50's, which offered the first real experimental encouragement for origin of life researchers. She responds, "There are hundreds of theories of life's origins. The fact is, since the 50's, we've been improving on the Urey-Miller experiment." She then goes on to give a summary of the Urey-Miller experiment (extended by Carl Sagan), which produced some of the building blocks of life. She concludes by saying, "So we know it can happen."

First, I should point out that it is a long way between making a few building blocks of life to saying that you know that abiogenesis can happen! One might just as well claim that observing that stone can erode in block shapes means we know that the natural formation of Egyptian pyramids can happen by chance alone.

Second, let's go ahead and take a look at this experiment to get an idea of the specific kinds of problems associated with abiogenesis.

• This experiment is dependent upon the assumption that early Earth's atmosphere was "reducing," and could thus form biologically significant molecules. That assumption is debatable (reference, reference, reference).
• It was also important that the experimental environment be free of oxygen, which would be fatal to the formation of the desired molecules. Unfortunately, the date for the existence of free oxygen is being pushed back earlier and earlier in Earth's history, back to the time in which life was thought to have first appeared (reference, reference, reference).
• The primary, significant molecular output of this experiment was amino acids, which are the building blocks of proteins. But only about half of the simpler amino acids used by life were produced.
• All life is comprised of left-hand amino acids, but this experiment (and every other process known) produces both left and right-hand versions without discrimination. Peptide bonding has no preference for linking one form over the other, though advanced functionality depends upon them all being one handedness (known as homochirality).
• Remember that this is a controlled experiment — intelligently designed, if you will. It contains a mechanism (a trap) to preserve the synthesized molecules from being destroyed once again by the two energy points and the water within the system. For this reason, the yield is certainly higher and more persistent than anything that might be found in nature.
• Of the molecules that were produced and captured, the vast majority were biologically meaningless. The largest percentage was a tarry polymer, which would be evidenced in the geological record if amino acids in desirable quantities were produced by similar means on the early earth.
• Given the limitations of the last few points, the overall yield of such an actual process in nature would have produced a very dilute prebiotic "soup." The thinner the broth, the less would be the chances for the right mix of molecules to find each other in order to combine. And remember, the combination of these molecules into meaningful systems is a matter of astronomical chance, which depend upon mass quantities to overcome statistical improbability. This is why oceans full of prebiotic molecules have long been the great hope and assumption of researchers in this field.

Francois doesn't deny that abiogenesis is a tough issue, only that it counts against materialism.

The fact that an issue is intractable does not indicate anything about that issue. It is only a statement about ourselves. We may not have enough evidence to get to the solution. There may even be limits on what human intelligence can comprehend, and a problem may remain intractable forever.

It's not what we don't know about chemistry that leads to the conclusion that this is a problem; it's what we do know. In fact, it was our past ignorance that led some to conclude that it wasn't a problem at all. Darwin's idea of life arising out of some warm little pond sounded plausible when it was thought that the cell was nothing more than a simple blob of protoplasm. And if you were to challenge scientists at that time for a solution they would be far more justified in saying, "Give us some time. We've only just begun to study the protoplasm to know what we're up against."

Today we understand much of the cell all the way down to the molecular makeup. In fact, we understand it and the problem so well that scientists no longer can fathom that the first organism would have been a complete cell; there supposedly must have been a series of proto-cellular entities leading up to even the simplest of the cells that we observe. (Francois affirms this modern adjustment to the theory when he says, "No abiogenesis hypothesis actually states that the simplest life is as complex as modern bacteria, and if it did, it wouldn’t be a very good hypothesis at all.") Never mind that the progression is totally speculative, it includes huge leaps, there is no evidence of such things, and that the existence of complete cells has been pushed so far back in history that the time for chance to build the cell by degree is vanishingly small.

For the committed materialist, this should be an answerable question in principle; chemistry is a fairly straightforward and empirical science. We should at least be able to show the chemical pathways to life even if we have difficulty in connecting those steps to actual geological history. If life indeed formed by natural means, then this has every hope of being experimentally repeatable. Unfortunately, decades of research have offered only a few token victories. I wonder how long we are to wait before applying any skepticism toward the materialist's story. 150 more years? 500 years?

Francois appears to think that we should wait forever; that it is unwarranted to ever plug God into any of our equations:

[This] is merely a modern iteration of the "god of the gaps" argument: "we can't figure out how abiogenesis actually happened, there is no hope to ever explain it, therefore God did it."

It is not as though science is annually filling gaps that Christians have tried to reserve for God. In fact, I'm struggling to think of any such gaps in recent history where God has been banished by science. On the contrary, modern science has revealed many "gaps" for which divine intervention is a neat and consistent fit. This issue of the origin of life and the need of a transcendent cause is a perennial one, which predates Christianity itself. The insistence that the cause is, nay, must be, a materialistic one is a historical newcomer (or at least was the minority report).

Darwin came along and offered us an alternate story. Why must we accept that story by default unless there is compelling reason to do so? Why should we accept "science" of the gaps in all matters? Richard Dawkins has famously said that "biology is the study of complicated things that give the appearance of having been designed for a purpose." If this is so, then it seems reasonable to assume that biology really is designed for a purpose unless and until it is demonstrated not to be. Materialism not only denies the burden of proof but any need at all to prove its own case. Crying "god of the gaps" is a stall tactic that has begun to ring hollow. In its echo I hear only, "we don't know." And “we don’t know” surely does not qualify as proof.

Here is another interesting problem for those who demand a material, unguided cause for life. There have been some who have honestly proposed that life might have come by way of directed panspermia. But how could we ever know if life were seeded by extraterrestrials if we are forced to rule out causal agents? Certainly, that would be a "natural" cause for life (since aliens are part of nature), but detecting the signs (or need) of such an intervention will be ruled out just the same by the prevailing methodology of naturalism.

One thing on which all my critics were united is the belief that I have mistaken what the fossil record is capable of revealing about early life.

Francois says:

The assertion that "the fossil record" does not contain evidence of the origins of life [is extremely problematic]. How in the hell could there be? Fossils form from hard structures like bones or the imprint of organisms in soft soil.

Anath says:

And why exactly would one think the FOSSIL record would say anything about atmospheric conditions or non-organic matter? Only organic matter is fossilized, which means there would be NO fossils until after complex life was formed.

And Faithlessgod says:

Really, how on earth does the fossil record tell us anything about the prebiotic soup? In saying this Pruett displays a deep ignorance of this topic.

To avoid this confusion, perhaps I should have used "geological" in place of "fossil" record. However, it is not at all uncommon to see the word "fossil" actually used in relation to phenomena surrounding life rather than just the remains of life itself. Terms like "molecular fossil," "geochemical fossil," and "fossil biomarkers" can often be found in the scientific literature. Some specific examples of early formations that are considered fossils, but are not themselves the direct remains of life are stromatolites and oncolites.

Beyond the quibble over my use of the word "fossil," the larger issue is whether or not we can detect much evidence for the state of the early earth and the earliest life forms by looking at the geological strata. Judging by the numerous studies and scientific papers, the answer to that question seems to be "yes." Some of the biochemical signatures of life or early life conditions would include banded iron formations, carbon isotope data, and other chemical biomarkers.

Additionally, it is not just bones and hard body structures of life that may be found in the fossil record, but even simple cellular life. Such "microfossils" have helped us to date the appearance of life (in forms that still exists today) to a time shortly after our planet was stable, but have not yet given evidence for the existence of any precursors to life. For instance, if an ocean rich in amino and nucleic acids had existed, which are necessary precursors of life, this would have left large deposits of nitrogen-rich minerals (nitrogenous cokes). Such finds are conspicuously absent from the early geological record.

Anath offers up a popular solution, and one that I, frankly, find to be the least absurd:

My current favorite theory is the RNA world theory but I understand that it is not without its difficulties. The reason I like it primarily has to do with the fact that I can visualize how it might occur and it seems like a logical explanation of how complex life could arise through simple enzymes and inorganic material. However, I also freely admit that my knowledge of biochemistry is pretty weak

That is part of the problem with this whole issue: it is easy to devise and believe just-so stories about how life came into existence. It is when these stories are examined in detail that we find the deep technical problems. Some may easily visualize how we could ultimately travel to the stars by going faster and faster with advanced spacecraft, or using worm holes, but any amateur astronomer or physicist can burst that bubble with a little dose of reality.

Here's a quick rundown of some of the issues with the RNA-first theory:

• The same kinds of problems as with amino acids apply here, e.g., being able to create all necessary components, low yields, assumptions about earth conditions, homochirality issues (left/right-handedness).
• RNA is chemically fragile (especially so at higher temperatures) and difficult to synthesize abiotically.
• The fortuitous assembly of a catalyzing RNA chain is improbable enough, much more so one which could copy itself.
• The known range of RNA's catalytic activities is rather narrow. Self-replicating capabilities are unknown, though a "cross-catalytic system involving two RNA enzymes" has been engineered. But that only compounds the probability issue, since chance would now have to provide two complementary RNA ribozymes at the same time and place.
• Even assuming nature could produce the various necessary molecules in the same locale and in sufficient quantities for chance to do its work, it is no guarantee that other chemicals would not be present to interfere with the assembly of RNA chains.
• If an RNA world actually thrived for the millions of years it would surely take to yield the DNA world, then it is odd that nothing of it remains. We certainly have every other flavor of lower organism still on display in modern times, e.g., when the eukaryotes came on the scene, the prokaryotes did not perish.
• It is still a monstrous, inexplicable leap from RNA to the interdependent DNA-RNA-protein system (among other functions) of cellular life.

In a 2006 article in Commentary magazine, David Berlinski wrote a thorough essay outlining the problems and critiquing the proposed solutions. Organic chemist, Robert Shapiro (himself a supporter of evolutionary theory), says of Berlinski's essay, "the case against an 'RNA world' is even stronger than the one Mr. Berlinski presents. Not only were cytosine and ribose unlikely to have been present in any quantity on the early earth, but the same can also be said of adenine and guanine. Moreover, no adequate explanation of the manner in which these parts (and others) could connect together spontaneously to form RNA has ever been presented."

Long is not to be discouraged by such pesky details. He hangs his hope on a general confidence in the power of nature:

Scientists are constantly discovering new forms of spontaneous order, and I fully expect that trend to continue.

I recently read a sneering article which imagined that it refuted intelligent design by pointing out the "spontaneous order" that can naturally arise in the world of free market economics. I am not at all clear on how a system of conscious agents working in willful synergy serves as a good analog for mindless chemical reactions. On the other hand, there are indeed things in nature that naturally form into orderly chemical arrangements, like crystals, carbon fullerenes, and nanotubes. The problem is that order alone is not enough. Neither is complexity. Life is made up of molecules that contain specified complexity — they are in a specific, meaningful order.

A large crystal is very orderly; however, it is nothing but repeating patterns that form up according to natural, chemical laws — a reliable and reproducible process. On the other hand, the proteins, RNA, and DNA molecules in life are not comprised of repeating patterns. They are also not comprised of patterns that arise due to any natural affinities that one molecule might have for another. They are comprised of unique, specific arrangements of molecules that confer functionality to the system. In the case of DNA it is like hardware and software. Perhaps some natural process could be found that would make DNA strands — the hardware — but the arrangement of the nucleotides upon that strand is the software that drives life, and there are no chemical or electrical laws that cause nucleotides to naturally form into information-laden arrangements.

The arrangement of DNA is often compared to language, so let me end with this analogy. Even if we could find some way of spilling alphabet cereal that caused the letters to form into strings and columns (all right-side up), it still would not mean that they would make meaningful words and sentences. There is a quantum leap difference between discovering order in nature and discovering information.

Several of the responders objected to my use of the word "miracle" to characterize the reaction of scientists to this problem.

Self has this to say:

I cannot help that some writers use the word "miracle" to describe something. Some scientists may, indeed, believe that a miracle did occur; but others do not and may have just used sloppy language to state their case.

DB0 goes further to accuse me of outright dishonesty:

When a Scientist says "Miracle," he may actually mean something with a probability so low, that it's amazing that it even happened. Of course if one considers the sheer size of the universe, the possibility of anything like that not happening is what starts to get low.

However to take a word in general, claim that science writers use it, while not providing a context, and then use that as some kind of subconscious belief is nothing more than equivocation and very intellectually dishonest.

I mention the word "miracle" because it is a testimony to the fact that the scientific community does indeed recognize the scope of the problem and the shortcomings of the proposed theories. This word is seldom employed by science commentators; there is a reason it is used in this case.

Due to the intentional brevity of my original article I was necessarily constrained from offering quotes and detailed context for my questions. It is unfortunate that this should be received as "intellectual dishonesty." My context is that the word "miracle" has been used too many times to count in scientific exhibits and documentaries to which I have been exposed, as well as its direct use by the scientific community. Since my reply is anything but brief, I'll now reference just a few such cases where the word is used by academics in relation to life.

One of the miracles of life, to my mind, is the accuracy with which DNA gets itself replicated in the cell. It has to be that unbelievably accurate, otherwise we'd all die out in no time. (Alexander Graham Cairns-Smith)

As far as we've looked, there's only one place in the entire universe where the miracle of life exists: our own planet Earth. (Carl Sagan)

An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin life appears at the moment to be almost a miracle, so many are the conditions which would have had to have been satisfied to get it going. (Francis Crick)

The de novo appearance of oligonucleotides [i.e., specifically sequenced RNA bases] on the primitive Earth would have been a near miracle. (Orgel and Joyce)

Even I am willing to forgive these materialists for their "sloppy language," but the fact that there exist such vacuums into which the word "miracle" can readily slip tells us something about the nature of the problem. I can't remember the last time I've heard a mathematician, geologist, or chemical engineer employ the word. It seems that those who study life and its origins must be a particularly "sloppy" group, or there is something else going on here.

Is the appearance of life a "miracle" simply because it is a hard problem to solve, or because it is a matter of vanishingly small probability that it should have appeared? I would argue, and I think I have argued, that it is both. Nobel Laureate Christian de Duve has called for "a rejection of improbabilities so incommensurably high that they can only be called miracles, phenomena that fall outside the scope of scientific inquiry." The chance appearance of functional DNA, RNA, proteins and other elaborate large molecules qualify as such.

Some of my responders think it doesn't really make a difference if this is a problem for materialism that may never be solved. Francois offers this challenge:

If we accept the statement that the origins of life is a "miracle," the question remains unchanged: how did it happen? Even if Christianity was true, the Creationist would be no closer to an answer.

Self adds the following:

I'm very comfortable saying that any given problem can be unanswered. I'm not sure why xians feel that everything they can possibly imagine must be answered and if our current capability doesn't permit an answer then we must posit some sort of god intervention.

The point is not that all questions must be answered. There are some questions that by their very nature may not be answerable because there is a categorical disconnect between the cause and effect, like what caused the Big Bang. This is especially true when involving causal agents. For instance, we may never know the motive for the JFK shooting (why it was done), but we certainly can know how he was killed.

In principle, we should be able to say whether or not abiogenesis is possible. If such processes are part of the flow of the present material, observable world, then there is every reason to think that we could discover them. There is no practical veil between the cause and effect except our current ignorance.

If one is suggesting a natural mechanism or law, then one has something particular which could be exhaustively tested. But how do we know that something happened by natural means unless we can demonstrate that nature is capable of producing such a thing? The devil is entirely in the details in this case. Philosophical materialism seems to get a pass on this, unlike other theories that must offer evidences before warranting conclusions.

On the other hand, if life is the product of divine intervention, then there is a break of continuity with nature that we cannot push past with our theories and experiments. We cannot say precisely how God did it unless He tells us Himself, i.e., did He create from scratch, did He shepherd molecules together with secondary causes, etc. It is more a historical question than an experimental one. The best we can do, in principle, is to observe the evidence that life appeared without precursor and despite insurmountable improbability. We could find the various fingerprints on nature, at particular historical points, but not know the precise means of the handling.

It is not necessary to know the exact means by which an action is taken in order for it to be reasonable to believe that it did happen. If I find a fort standing where I left a pile of wood the night before, then I may not know how it was assembled or who did it, but I will surely be justified in my skepticism toward theories of natural causes.

Christianity is happy to live with open questions since it believes that God has reserved some mysteries to Himself. But some questions are relevant to the debate over His very existence. Materialists assure us that there is no evidence or need of a creator in the biological realm due to alleged natural processes for which they will someday find concrete support. Is it so unusual that theists should require evidence of such a thing before accepting its validity?

Regarding my observation that the issues of evolution and abiogenesis are so commonly segregated, Faithlessgod says this:

Some evolutionary biologists do separate origins from the evolution of life but simply because their specialty is the evolution of life, abiogenesis is not what they study. . . . Pruett seeks to manufacture a problem or an issue which does not really exist here.

Anath adds the following:

"Evolutionists" segregate abiogenesis because abiogenesis is a separate field of study. The Theory of Evolution deals only with the events AFTER abiogenesis, and cannot explain the origin.

Admittedly, it is two parts of a larger puzzle. In fact, it must be, because evolution only acts upon what is already alive and capable of reproducing. This makes it all the more difficult for origin of life researchers, since the gulf to be bridged is between simple chemistry and a complex self-replicating assembly rather than just "simple" mutations on existing DNA molecules. As Lynn Margulis has said, "To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium."

However, I find it curious that the separation is so often and quickly pointed out in debates I have seen and had myself. It seems less for the sake of technical precision than for the sake of insulating evolution from collateral damage. At a metaphysical level, one may compartmentalize these two issues for distinct explanations. For instance, one could be driven purely by nature and the other require some transcendent involvement. However, the atheist does not have this luxury; He is saddled with a purely natural explanation for both. If one cannot be explained, then the entire atheistic project is failed.

To my question of what kind of evidence is needed to prove that the appearance of life is, in fact, miraculous, Anath replies:

A crocoduck. Something COMPLETELY impossible and unexplainable. Life rising from non-life is NOT a crocoduck. It is unusual and potentially quite improbable, but it is not unexplainable.

How can one dogmatically assert that abiogenesis is not unexplainable when it has for so long defied explanation and suffers all the practical roadblocks that I have presented here and more? This is merely the expression of a dogmatic faith in materialism.

Life from non-life cannot be like a crocoduck, in principle. As affirmed by you previously, evolution, which a crocoduck would supposedly confound, is a physically distinct issue from abiogenesis. Even if a crocoduck were discovered it would, at most, refute the theory of evolution. That is, unless you want to embrace the idea that they are indeed bound as one issue.

It seems to me that there is nothing analogous to this for abiogenesis that could be discovered, or that is not already known. The indisputable data we have is that it is simple chemistry on the one side and complete cellular life on the other. Discoveries of “crocoducks” in between the two might only serve to give confidence in the power of material causes, not refute it.

As it happens, neither the ongoing problems with each theory of essential molecule formation nor the increased understanding of the complexity of what is to be explained have served in any way to dampen the spirits of the committed materialists (with notable exceptions). What more could be discovered to disprove the materialists creation story? It is the incorrigible nature of the lack of supporting evidence for it that has any hope to stand as proof against it. But if “we’re looking into it” may eternally serve as justification for materialism, then any statistical improbability may be put into play.

As to the fate of evolution upon finding a "crocoduck," I am confident that belief in it would soldier on. The model would merely see a descriptive adjustment or make yet another place on its shelf for a future explanation. I have seen it happen many times before. The foundations may shudder and crack, but no one ever seems to question whether they have built their temple upon the wrong frame.

Some examples of “crocoducks”:

• Biological classifications based on various markers (e.g., morphology and specific gene sequences) often do not align as expected. (reference, reference)
• The meager accumulated evidence (since Darwin’s time) for the predicted gradualism as witnessed by 1) events like the Cambrian explosion, and 2) the discovery that the fossil record is most often characterized by patterns of stasis and punctuation.
• The discovery that the fundamental cellular domains of bacteria, archaea, and eukaryotes are found not to fit into the classical tree of life model (i.e., there is no clear line of descent either before them or between them). (reference, reference)
• The discovery that the cell not only contains unfathomably complex molecules, but information-laden molecules.
• The discovery that cells consist predominately of molecular machines, many of which are analogous to macro-scale human-designed machines. (reference, reference)
• Even the genetic approximate of a "crocoduck" does nothing to phase the theory.

After effectively deflating the various theories of abiogenesis in his book, Origins: A Skeptic’s Guide to the Creation of Life in the Universe, Robert Shapiro makes the following interesting statement.

Some future day may yet arrive when all reasonable chemical experiments run to discover a probable origin of life have failed unequivocally. Further, new geological evidence may yet indicate a sudden appearance of life on the earth. Finally, we may have explored the universe and found no trace of life, or processes leading to life, elsewhere. Some scientists might choose to turn to religion for an answer. Others, however, myself included, would attempt to sort out the surviving less probable scientific explanations in the hope of selecting one that was still more likely than the remainder.

The materialist is free to continue seeking his alternative explanations, but it is unfair to demand that all explanations must always be "natural" even if they elude us for eternity. This is tantamount to saying that atheism wins, game over, and no further issues or anomalies will ever be considered as strikes against it. This seems a presumptive stance in a historically god-soaked world that, to use Dawkins' language, is full of "complicated things that give the appearance of having been designed for a purpose." Perhaps it appears that way because it actually turns out to be true. It is certainly consistent with the story that theism has been telling all along. Scientists may determine among themselves that all explanations must be by way of mindless, natural causes, but I am less interested in following the doctrines of "science," as defined by its secular high priests, than I am in discovering truth.

Evolutionary Morality

Aaron Snell has offered a good hypothetical pushback for the point made in my last post. The question at hand is: How do selfless human virtues like heroism shoehorn into Darwin's theory of survival-of-the-fittest?

I'll begin by restating Aaron's reply, which I call "hypothetical" because he is not advancing it as his own belief.

Humans are social animals, and as such their social interactions are the context in which morality evolved. When practiced in such a social context, altruism has certain social benefits that ensure a better chance of offspring survival. This then translates into an evolved moral impulse.

As for your objection about the converse "selfish streak", I have seen two counter-arguments offered: 1) this is an evolutionary hold-over from our pre-social past; and 2) individuals sometimes benefit from selfishness in certain social situations, which means both can be present in the behavior of a biologically-programmed human animal.

And here are my thoughts:

When was this pre-social time in our past where anti-social behavior was supposed to be advantageous? All creatures are social creatures to some extent. What is it that makes a prior behavior less valuable to survival simply because we become more verbal and intelligent? I think the unintended implication is that humans are now self-conscious and able to know good from evil — that we have risen to some higher metaphysical plane where we are attuned to true virtue. But as another commenter (Duane) points out, in an amoral, purely material world, there is no good and evil or better and worse in the sense we generally mean those words.

If morality is only evolutionary, then there is no higher morality that stands above whatever evolution delivers. This means that the only thing that could be said to be good is whatever lends a survival advantage. "Good" would be, by definition, whatever successful organisms happen to do. However, we find various creatures acting in many ways, some of which we would think of as very "bad" were it imitated by humans. Consequently, there is no reason to even think of our own behaviors, such as heroism, as objectively more virtuous than the diverse behaviors that we see in other successful creatures.

Evolution only has to do with replication and survival. If it could be said to produce morality it would only be related to what is most advantageous to the survival and dominance of any given species, and it does not care about ethics in its pragmatism. For evolution, any means is justified by the ends. And it seems we could get along just as well by evolution's reckoning if we ate our genetically inferior offspring and killed off our elderly once reaching a certain age. This doesn't fit the model of virtue and heroics as we think of it, since we regard some of the most heroic acts to be on behalf of the weak and defenseless.

Mutations do not appear in communities, which could all share in the benefits of cooperation and heroism; they appear in individuals, and if those individuals do not reproduce, then that characteristic will be lost. Even if heroism may add theoretical value to the community, it still has to be established as a characteristic in that community. Those with the strongest heroic traits would seldom manage to pass their genes on, while those in need of rescue would be perhaps more likely to dilute the gene pool.

We tend to think of some behaviors as being morally superior to others, for example, being heroic, practicing equal human rights, and living in peace and harmony with your neighbors are all considered to be good. But this type of environment is not conducive to allowing the superior genes to dominate. Bacteria are supposed to have evolved by means of the more fit organisms crushing out its competition. It could easily be seen as more advantageous to allow weak and helpless victims to die than to allow the virile gene-carriers to lose their lives in the efforts to save them. Practicing equal rights, welfare, pacifism, and heroism does not seem to be consistent with the spirit of evolutionary progress.

To say that some supposedly bad behaviors are a carryover of primitive times only works if we can say that those behaviors are in a different category from our newer behaviors. For example, we might only be aggressive toward others while we are good toward our own offspring and spouse. Perhaps we can develop the new in one area while retaining the old in some other; like a dolphin is supposed to be a land mammal, which retained its old lungs while developing new swimming apparatus. It seems problematic to the theory to have both the new and the old in the same area, but that is exactly what we find in the area of morality. We find loving parents and abusive parents, heroes and cowards, lovers and rapists, pacifists and warmongers, philanthropists and swindlers.

It might make sense to say that morality can be evolving along a continuum, like legs slowly forming into flippers, but that would imply, for morality, that we were fairly consistent in our moral expressions, wherever we happened to be on the scale. Experience shows that humans exhibit moral behavior along every point of the scale, from heroic to monstrous. Some of us still have legs while others have fully developed flippers, so to speak.

Perhaps moral character could be controlled by something like genetic alleles, which determine eye and hair color, among other things. This would imply that there could be "good" people and "bad" people, just like blondes and brunettes, or at least people who are good and bad in certain areas of morality. This seems a very testable notion, since by this reckoning we should expect to find solid and predictable patterns among kin and, especially, identical twins. But I think it has been difficult enough to establish that things like personalities and preferences are determined by genetics at all; and if not by genetics, then we aren't really talking about evolutionary morality in the first place.

Alleles can also be bred out of the genetic stock, so we might expect to see tribes of incorrigibly noble aboriginals or irreformably wicked savages, as we see blue-eyed Scandinavians and dark-skinned Africans, and their children would be expected to be cut from the same cloth. But we seem to find that there is no race whose infants consistently surprise or disappoint us if we adopt them into our "mainstream" society. And if we claim that this is not so then we can be assured of facing charges of racism.

In the end, this is an idea that sounds good in theory, but it turns out to be circular reasoning: we happen to value certain moral behavior and so we imagine that there is an evolutionary advantage for those who practice it. Unfortunately, it begs the question as to the true source of morality, why we should exalt human morality, and why evolution would have us be repulsed by social practices that would actually improve our genetic stock. If, as Tennyson said, nature is red in tooth and claw, then why should we expect to escape the breeding and discipline of our own Mother?

MIT Biology Class - Reading Between the Lines (3)

Lecture Note:

Many physical characteristics, like eye and hair color, are the direct result of having certain dominant genes. However, there are some genes that may be dominant in an individual yet do not manifest themselves except under certain conditions. I believe that a predisposition to heart disease and diabetes were mentioned as examples, where lifestyle choices can be the deciding factor in appearance.

My thoughts:

My thought here is more social commentary rather than evolution related.

Let's say that researchers did manage to find the elusive "gay gene." There is good reason to think that such a gene would not have a determinative effect, like those for eye color, but would merely provide a susceptibility to the condition. Indeed, this must be the case, since identical twin studies demonstrate that more than 50 percent of homosexual twins have heterosexual siblings. Compare this with 100% parity between twins (as far as I know) for things like eye and hair color. If this condition were actually genetically caused, then twins would always be either both or neither homosexual.

If we would then compare the "gay gene" with the "heart disease gene" we would come to a problematic conclusion. That is because if we think about the actual onset of heart disease, we generally find that it is accompanied by poor diet and exercise. That is to say, the predisposition for heart disease may only manifest itself under adverse conditions. It can clearly be said to be a "bad" thing, in that it is a case of the normal operation of the body gone wrong. In such cases, the related gene is not actually a new and distinct gene from what other healthy persons have; it is due to an alteration (mutation) of an existing gene that serves a valuable purpose.

All this is to say that finding a "gay gene" would not have the desired effect of making homosexuality into a "natural" human variation, like male/female, blonde/brunet, and white/black. At worse, it could be seen as a deleterious mutation of a right-functioning gene (and in Darwinian terms, a non-breeding gene-bearer is clearly at a disadvantage). At best, it is only a gene that may result in homosexuality under certain conditions — conditions which may even be characterized as "unfavorable," meaning something has gone wrong. And any condition which may only be influenced by other factors is a condition which might also be avoided or, perish the thought, reversed. I know, this is all politically incorrect science. But it is a fiction that science is the exclusive domain of white-coated priests of impartiality and truth. Which leads to my next topic.

Lecture Note:

One of the professors recounted several cases of major scientific breakthroughs, some of which were well ahead of their times, that were met with indifference and even rejection by contemporary peers. An example would be the discovery that chromosomes are involved in heredity.

My thoughts:

When I was a young man I had a rather starry-eyed view of science. I imagined that scientists were primarily concerned with truth at all costs and that science dealt with objective concerns that were insulated from the more biased realms of values and religion. I believed that new, paradigm shattering discoveries were welcomed with excitement and that progress was the mutual goal of all. And then I grew up.

Scientists are human, too, and prone to the same biases and mistakes that people make in every other area of life. In fact, there are some ways in which the sciences present unique opportunities for bias. Pet theories must be proved out and ferociously defended if one has hopes for a Nobel Prize. Valuable grants must be courted by way of politically expedient research agendas. Fraternal orthodoxies must be carefully negotiated if one expects to publish in the best journals. I have heard it said that most Nobel laureates had great difficulty getting their original theses past peer reviews and had to publish privately or in minor journals.

But the most troubling (and often most denied) of all are the metaphysical biases that inhibit some ideas from consideration on principle alone. No one is immune to the influence of personal convictions, and some theories have greater ramifications for those convictions than others. The acceptance of big bang theory is one recent example in which personal bias was at work against the mounting evidence and growing consensus in its favor. As Sir Arthur Eddington wrote in 1931, "The notion of a beginning is repugnant to me ... I simply do not believe that the present order of things started off with a bang. ... The expanding Universe is preposterous ... incredible ... it leaves me cold." And more recently, Phillip Morrison of MIT said in a BBC film on cosmology, "I find it hard to accept the Big Bang theory; I would like to reject it."

While atheists have found creative ways to shrug off the implications of a "creation" event, the stakes for a rejection of naturalistic evolution are perhaps even higher; for if nature has not shaped us, then exactly who has? Let me just end here by quoting Harvard geneticist and evolutionary biologist, Richard Lewontin, who publicly summarized the materialistic (and his) bias better than I could ever hope to.

Our willingness to accept scientific claims that are against common sense is the key to an understanding of the real struggle between science and the supernatural. We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door.

If Intelligent Design is indeed the cause of biochemistry, then we shall never know it so long as the gatekeepers of "science," like Lewontin, stand guard to insure that only pre-approved ideas are admitted for consideration.

MIT Biology Class - Reading Between the Lines (2)

(Part 2 in a series)

Lecture Note:

Many proteins that are made by the cell are destined for use outside of the cell. This includes not only those protein assemblies that will serve needs on the outer cell wall (e.g., sensors), but also those which are not even meant for use by the cell that produced them. Particularly, in multi-cellular creatures, proteins are made that are meant to communicate with, or provide services to, other parts of the organism. Examples would be digestive enzymes, hormones, and neurotransmitters. The cell wall is designed to keep the bad out and the good in. Consequently, for each item slated for external use there must be a discriminating mechanism to allow or transport it outside of the cell.

My thoughts:

Let's assume for a moment that we are an organism composed of cells, which has managed a spectacular mutation that codes for a new protein that would be a boon to our survival. Now our cells are busily generating said protein. But we've got a problem: no matter how much of an advantage this protein would give us over our peers, it will do us absolutely no good if it cannot get a hall pass to leave the cell and go to work just where it is needed. In fact, while it waited generation after generation for such a pass (i.e., a new cell portal, or an existing portal change) it would actually be a detriment to us, since its construction would consume valuable resources. Worse, without simultaneously evolving the accompanying regulatory mechanisms our cells — perhaps every one of them — would be busily manufacturing these proteins without end. This is highly reminiscent of viruses, which hijack the machinery of the cell (by inserting their own genes into the DNA) in order to make continual copies of themselves. They do so until they fill the cell and it bursts.

Lecture Note:

Proteins are the workhorses and building materials of the cell. They consist of long (polypeptide) chains of amino acids, which are then folded into intricate shapes fitted to serve specific tasks. The average polypeptide chain is about 150 amino acids in length, and some are well over 3000 in length. Each amino acid could be one out of a variety 20 different amino acids that are used by all living systems. The folding occurs due to various chemical and electrical attractions and repulsions that exist between different parts of the chain, and the final folded form is dependent upon the exact arrangement of amino acids in this chain. The possible arrangements of a polypeptide chain of 150 amino acids in length is 20 to the 150th power (20^150). The enormity of possible configurations for proteins makes computer simulations of protein folding a monumental task. At this time, even with our best supercomputers, it is impossible to predict what the 3D structure of any given polypeptide chain will be from merely knowing the arrangement of the individual amino acids that make up the chain.

My thoughts:

Let me start by driving something home. As I mentioned, the possible arrangements of amino acids in an average protein is 20^150. That roughly equates to 1 with 195 zeros after it! (Remember this 196 digit number for later.) For comparison, the number of atoms in the entire universe is "only" about 1 with 80 zeros after it. Since DNA contains the instructions for these proteins, and DNA instructions are supposedly acquired by way of mutations, this means that coming up with a functional protein is a matter of statistical probabilities. Even if we had an unused stretch of gene-space to work with, and we confined all mutations to just this region of DNA, and we had every generation of every organism that had ever existed on earth pumping out mutations, we would never arrive at any of the perfectly functional proteins that you could name in the average cell.

Not so fast, the skeptic may say. Calculating odds like this is only applicable if we have a hand in mind before we draw the cards. There may be any number of arrangements that could make some kind of useful protein. Life may simply consist of collections of random poker hands. While this might be a good objection in principle, it runs aground for a couple of reasons.

The laws of physics constrain the kinds of functional systems that are available for use in the cell, and the cell itself, once framed out, further constrains its own options. Many features of life (including proteins) in creatures that are widely divergent from one another are similar if not identical in form, and these features are claimed to have been evolved independent of each other (convergent evolution). This suggests that there are certain best or right ways to accomplish certain tasks. And the fact that most life shares many proteins in common, and the most complex life has only 10's of thousands of genes, means that we may have a rather small target set to compare against the astronomical alternate possibilities. Assuming a high estimate of 100 million species on earth, and making a generous assumption that 10,000 genes in every species is unique, this means we get to knock 12 zeros off of our 196 digit number. A statistical drop in the bucket.

Additionally, in systems that are composed of multiple proteins, the design of the proteins is tightly constrained by the other proteins in the system. For instance, if I have a "bolt" protein, and chance is expected to complete the set, only some form of a "nut' protein will do. This all means that for at least some evolutionary outcomes to obtain, there will be certain predefined poker hands that chance must deal.

The skeptic may again object by questioning whether or not all amino acids in the protein are absolutely necessary to form the functional structure. This would be a good objection, because some regions are merely filler and/or connective in nature; and in some cases even functional amino acids may be replaced by another amino acid with similar properties. While this may certainly lessen the odds, it does not ultimately bring them into the realm of the plausible.

Let's be generous and say that only 40 of the amino acids are important to our average protein. Let's further compound our generosity by saying that there are two different amino acids that could work at each point for our essential 40, i.e., 1 in 10 odds rather than 1 in 20. So now our odds of arriving at any specified "average" protein is 10^40. While certainly a better number than 10^195, it is still no help, since this number actually exceeds or equals the estimated number of organisms that have lived on our planet in all of history!

But let's not stop here. Let me up the ante by revisiting one of my earlier generous allowances. Mutations do not confine themselves to, or target, specific genes; mutations are just blind errors that occur in the process that copies the entire DNA package in preparation for cell division. Now, the DNA replication machinery is very efficient, but it does make the occasional mistake. In fact, we are now far enough along in the genetic sciences that we can say that the average mutation rate is about one nucleotide (a "point mutation") out of every 100 million. Since there are 4 possible nucleotides for any given point, this means our odds of arriving at any specified mutation is 1 in 400 million. And because the instruction for a particular amino acid is made up of groups of 3 nucleotides (a "codon"), and because several nucleotide arrangements can code for each of the amino acids, this means that we often need 2 nucleotide changes to get from one amino acid to another. This compounds our odds of getting just one meaningful (and possibly beneficial) change to 1 in 160 quadrillion, i.e., 16 followed by 16 zeros.

While this may be attainable by a large bacterial population in a matter of decades, it is a profound problem for less numerous and slowly reproducing creatures like mammals. For example, the human evolutionary line supposedly diverged from the chimpanzee line around 5 million years ago. Let me be as generous as possible here. If we were to take 10 million years, assume a continuous population of 100 million primates, and allow each to breed by age 10, then we are talking about only 100 trillion mutation candidates, i.e., 1 followed by 14 zeros. (Note: you do not multiply these three values to arrive at this number.) That's 3 orders of magnitude fewer events than what is needed to match the odds for getting just a 2-point mutation! We're talking about the odds for changing just a single amino acid here, and surely there would need to have been thousands of events at least this significant to get from primate to modern human. To go to just 3 specified nucleotide changes, which might get us 2 new amino acids (assuming one of the two needs only a single nucleotide change), we bump our odds up to approximately the total number of mammals that have ever existed on earth!

Another possible objection occurs to me at this point, which is certainly answerable, but I have gone on too long already. I will address it if comes up in comments.

I hope my readers have been able to follow my science, reasoning, and statistic, since I believe I'm addressing an issue that is absolutely devastating to evolutionary theory. In the face of such staggering improbabilities, evolution advocates seem to lean upon their presupposition that evolution is just a "fact," and, consequently, there must be some statistically viable mechanism to drive change that is as yet undiscovered. In my mind it is a case of "evolution of the gaps" thinking. This is not simply a matter of ironing out the details of a theory; this is foundational to the mechanism that is the supposed driver of the evolutionary process (or at least half of it). If one cannot say how something happened, and that it is within the realm of chance, then how can one say that it happened?

MIT Biology Class - Reading Between the Lines (1)

I discovered last spring that the Massachusetts Institute of Technology (MIT) has been putting its courses online at no cost in what it calls its Open Courseware program. For each class this includes things like lecture notes, problem sets, reading assignments, and in some cases, the recorded lectures themselves. Having an interest in the sciences, and most recently, the debates over evolution vs. Intelligent Design, I decided it would be worth the time spent to listen through a course to get an overview of the latest-and-greatest teaching in biology.

This class was just what I was after, since it covered a lot of ground in a good bit of depth, from cellular composition, to cellular systems, to genetics and beyond. I also found it very enjoyable listening, and I was especially fond of the sessions taught by Professor Eric Lander, Director of the Broad Institute at MIT, and a principal leader of the Human Genome Project. His sessions were enthusiastic and often included glimpses into the cutting edge of genetics and medical science.

In fact, the class was handled by 4 different lecturers, and it should be noted that they all gave the nod to evolution. There were really no proofs offered for evolution, and nothing much really came up in the course of the lectures that I would consider implicit support for the theory. However, whenever the question of why any given biological system or behavior existed, it was simply asserted that it had evolved that way.

Of course, it might be argued that the "proofs" where absent for the very reason that this was not an "evolutionary biology" class, where proofs were the order of the day; but it should be noted that for those advocates of evolution, who insist that the science of biology cannot be engaged apart from Darwin's assumption, these professors did quite well in their instruction without dependence upon his theory. Perhaps what these people really mean is that one cannot have emotional satisfaction in this science without some explanatory device to fill the void of curiosity that arises upon witnessing the wonders of cellular biology. And since design is not allowed in "proper" science, one must have Darwin to sooth the restless heart.

What was nice is that in this classroom, isolated from the public debate over the theory of evolution, where rhetoric is thick and the data is selectively underscored, these instructors were completely candid and unguarded in what they shared and in their personal reactions. Of course, as one who is convinced of the truth of Intelligent Design, my radar was tuned to pick up evidence for design and difficulties for evolution. Even though these instructors had no intention of suggesting such things, I found that if I only read between the lines I gleaned a wealth of friendly materials.

While listening through the class I took the time to make notes, hoping to blog on them at some future point. I intend to do so now. Anyone interested in biology and/or Intelligent Design (ID) theory may find this stimulating and may wish to follow along. I aim to present this as a series that will consist of my individual lecture notes (perhaps a few per post) followed by my own thoughts. Each "lecture note" will contain some teaching or comment directly gleaned from the class. It will most often be my own paraphrase of the professor's words, but it will represent objective classroom content that is as free of my own "bias" as I can make it. My own personal reflection and application will follow each note.

So, without further adieu, I present the first collection of my observations on a MIT biology class.

Lecture Note:

In the introductory lecture, the professor reminisces about how different the class is from when he first took it himself, and even how different it is from when he first began to teach it. He points out that this is fairly unique to this field, since, for example, introductory mathematics and physics are based upon pretty much the same foundation knowledge that has been in place for decades or centuries. The main difference in biology is due to the fact that the cell has been discovered to be far more complicated than once realized. And more needs to be taken into account, at the very molecular level, in order to have even a basic understanding of what the cell is about.

My thoughts:

Indeed, in Darwin's time the cell was thought to be a mere blob of protoplasm. With that conception, it is far more understandable how one might image such a thing coming to exist by chance in some primordial, warm little pond, or how it might further evolve with minimal coaxing. However, in the intervening years, discovery after discovery has further unveiled the incredible complexity of what it is that must be explained. Any theoretical gains made in providing those explanations are quickly outpaced by the relentless hail of new discoveries. At some point it would seem reasonable to question the original theory of a chance-driven origin of life, especially when many of the alleged explanations are found to hit roadblocks or have counter-examples. If I show you a mound of miscellaneous bits of metal junk, and then tell you I've stirred it for a month and then found a skateboard in it, you may believe that. How about a unicycle? Maybe. But how about a 747?

Lecture Note:

The professor notes that none of the diagrams of the cell that the class is to see are accurate depictions of the true complexity of any given part of the cell. For instance, the cell wall is often shown as a membrane, perhaps with some embedded objects. In reality, it is a complex structure — with even a skeletal framework in Eukaryotes — packed with portals, pumps, and sensors.

My thoughts:

It should be understood that every structure in the cell is usually made up of numerous interrelated molecules that are precisely fitted for shape and electro-chemical properties. And behind the structures and molecular "machines" found throughout the cell, there is a host of supporting systems required to assemble, transport, power, and service them. The cell is a tightly packed container of super-molecules, which has rightly been compared to a city in its complexity and activity. The small step-wise gains that Darwin proposed would be unable to build most of the integrated systems found in the cell, much less the complex, dependent interactions between them. And since evolution does not "plan" for the future, it cannot accumulate the necessary parts in hopes of one day putting them all together to make an irreducibly complex structure (i.e., one that needs every one of its parts else it does nothing at all).

Some have proposed that simpler, similar systems could have been co-opted in the making of a more complex one, like the bacterial flagellum. But that is like saying that a skateboard could become a bicycle, which could become a motorcycle, which could become a car. While there is a certain functional progression here, there is also a whole lot of reengineering, not just small additions, that need to be done to get from one stage to the next. And remember, every intermediate stage must be operational and of some advantage to the cell, else it would not have come to survive and dominate over its peers. There are no evolutionary rental cars to be had while the motorcycle is in the shop being overhauled and reworked into a car; it must be effective and available for transportation throughout the process.

Lecture Note:

One passing reference to evolution was in a professor's review of the various features of the cell. The functionality was presented as "problems that the cell had to solve" and "solutions that it came up with." This would include things like interacting with the environment, acquiring energy sources, regulating the production of proteins, etc.

My thoughts:

This kind of language of intentionality is extremely common in the world of biology. For the most part, it is unconsciously done, and I'm sure that if I called this professor on it he would backpedal and look for some naturalistic way to express his point.

You see, according to evolutionary theory, the cell is just a sack of diverse chemicals. It does not intend anything and does not spend a moment looking for solutions to problems or improvements to itself. It thrives or perishes, reproduces or doesn't. If it had an insurmountable functional problem, it would simply cease to function. It would not lay around for days and years — certainly not generations — tinkering until it had found its solution. At every turn, at every stage of evolution, it and its peers must be viable creatures or go extinct.

If a problem arose to which the cell must adapt or die — like an environmental change in chemistry or temperature — it would not begin to spawn mutations in the hopes that one member of the colony would come up with the magic solution. No, the "solution" must already be resident in the community, or be miraculously produced in its last dying reproductive efforts. Evolution based on environmental pressure (to which appeal is often made) implies dramatic gains either in short time spans, or dramatic new features simply lying around in the cell for no purpose whatsoever until and in case chance comes to call.

Evolution evokes the idea of fortuitous mutations occurring at just the right time, or to satisfy just the right kind of need. But in reality, even when and if a cell might miraculously get a "good" mutation, it is still no guarantee that it is good in such a way as to satisfy the particular needs of a particular organism. For instance, if a cell were to suddenly acquire the ability to break down cellulose for food (like the bacteria in the stomach of a termite), that would be a good thing if cellulose were present in the environment. But if it were not, then this new ability would be no advantage at all. Indeed, it would be a hindrance, since the manufacture of the necessary enzymes would consume valuable resources that could be better used to help the organism flourish in its real environment. Our new multi-talented little cell would find itself out-competed by its less gifted peers, and would thus drown in the gene pool before it ever met up with a future piece of cellulose.

The order of the day for evolution is to adapt fast or die. There are no Boy Scouts, prepared for anything, in the Darwinian world. Having a backpack and pockets filled with goodies and tools may make you valuable to your fellow scouts, but on the rugged, shortsighted trails of Natural Selection it will only leave you in the dust of those carrying just what is needed to get over the next rise.

Appearance of Design: Intuition or Illusion?

A couple of years ago I happened to catch a musical performance on Fox News. One of the general assignment reporters, Kelly Wright, was sharing a Christian song that he had written. It was called "I Believe," and its message was captured in the very first verse.

Whenever I see a newborn baby cry
Or see the birds flying high in the sky
That lets me know there's a God somewhere

While this is hardly a convincing apologetic for the existence of God, it does harbor an extremely important point. The vast majority of people believe in some sort of Supreme Being. If you ask them why this is so, you will hear a very common answer. To the average man, it is just a matter of common sense: "Look around you; look at the world; look at the beauty and wonder of life; it all had to come from somewhere!"

Life is remarkable and complex, and the more we learn the more amazing it all becomes. The default reaction is to be captivated by it – simply note any child's wonder on a visit to the zoo or a peer into the microscope. People just seem to have this notion that life is special, and the impression of intentionality and design presses hard upon them. For many, to insist that life is a fluke of nature is as absurd as trying to convince them that Mount Rushmore was carved by wind and rain.

This is not merely an emotional response to nature, but an inference from experience as well. The only experience we have of functional complexity originates from the minds and hands of intelligent designers, like humans. It is the same principle that NASA would use to infer the existence of alien life if a mere bolt were found on Mars, and it is the underlying assumption of SETI as they look for extraterrestrial radio signals containing even simple patterns.

Such ideas about life had been the bane of atheism for the better part of history until Darwinian theory arrived to exorcise these intuitions from our consciousness. Prior to Darwin, there were various speculative theories about the origin of life, like spontaneous generation, but they had to be satisfied with being classed more as philosophy than science. Darwin gave atheism the intellectual respectability that it had long sought. One of Darwinian evolution's chief apologists, Richard Dawkins, said it well in his book, The Blind Watchmaker.

An atheist before Darwin could have said, following [David] Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist.

Dawkins implies that biological design begs for an explanation. He's just averse to permitting God to serve as that explanation. But unless some alternative explanation can be offered, the intuition that complex order is best explained by a designer – the essence of Intelligent Design – stands unmolested. If I discover in the morning that my fresh-cut wood has been mysteriously stacked by my shed, then I would certainly be justified in thinking that some benevolent person has intentionally done the deed. Perhaps I would be mistaken, and it is in reality the work of a tornado, but until that case can be made I would be in my rights to stick with my initial assumption.

When Richard Dawkins tells us in The Blind Watchmaker that "biology is the study of complicated things that give the appearance of having been designed for a purpose," he outright admits to the default impression of design. However, he then goes on to explain why this is only a false impression, and that the order and purpose found in nature can actually be explained by evolutionary processes.

It may theoretically be the case that genetic variation and natural selection are the true authors of biology, but that is the alternative explanation offered in answer to the mystery of life. The theory of evolution has prevailed long enough that its supporters now believe it to be the natural and default victor. It may indeed be the reigning paradigm, but with each generation it must labor anew to suppress our intuitions. And this is why, in spite of all the academic and media hype, the purely random and materialist version of the theory continues to be rejected by the majority of the population.

I would propose, then, that the defeat of evolution would put design back onto center stage. Intelligent Design advocates are often criticized for trafficking in the flaws of evolutionary theory rather than offering positive evidence for design. But a critique of evolution is a case for Intelligent Design. As Dawkins admits, nature appears to be "designed for a purpose," and "design" implies a designer of some intelligence. If evolutionary theory fails at making the case that this appearance is merely an illusion, then we are justified in taking the appearance of design at face value. Intelligent Design lies just beneath the waxy veneer of evolution. It only remains to be seen what can truly be scratched off where there is liberty to do so.

Cosmological vs. Biological Evolution

I just listened to a short radio debate between Eugenie Scott, director of the National Center for Science Education, and Hugh Ross, president of Reasons to Believe. The focus of the debate was evolution. Of course, their differences were numerous, since Eugenie is a notorious advocate for evolution, and Hugh is a well-traveled champion of various flavors of design arguments.

In the closing minutes, the two of them shared their agreement over the idea of an old universe and that galaxies, stars, and planets had formed by way of physical forces, even while they differed over the origin of biological life. Eugenie made a point of including cosmological history in her overall definition of "evolution," and one of her final remarks rested upon her liberal usage of the term. Her parting challenge to Hugh was this: "If the physical universe can evolve, why can't the biological universe?"

Now, Hugh would probably be okay with the idea that God had trumped the "natural" order of things and shaped our solar system just exactly how, when, and where He wanted it. In fact, I sometimes think that Hugh is implying this when he labors the point that our own Sun, Earth, and planetary system are exceptionally unique in their composition and arrangement. However, had Hugh been able to respond to this he probably would have pointed out the principle difference between cosmological and biological "evolution."

The origin of the universe may be a profound mystery, but the formation of galaxies and stars within this universe depend upon established laws of physics intrinsic to it. Of course, gravity is a key player in the cosmic drama, and it is a tangible force that we personally experience and can measure and test. Based on our calculations, we can predict what might be expected of galaxy and star formation, lifespan, and death, and when observing the universe we find confirmation of our understanding. The fact that light travels at a finite speed allows us to see the universe as it was at various ages, according to the distances we observe. We have, in effect, a very complete cosmological "fossil record."

So, in cosmology, there are known laws that deterministically act upon matter to shape it into certain kinds of forms, from simple to complex elements and objects. It is not a problem to imagine that God has used such secondary causes to shape our world. Even if God did not specially create our star and planet, it would appear that the forces He has ordained would yield things like them, just as we now observe other stars and planets forming. Perhaps it might be argued that there is not enough time and matter out there to yield by pure chance the very special life-sustaining attributes that our planetary system exhibits, but there are at least adequate materials and mechanisms to grant such opportunities.
Contrast this with biological evolution, which says that simple chemistry yielded life, and that simple life progressively underwent change to become complex life.

In chemistry, there are no gravity-like laws that will take chemicals lying about and form cells out of them. Even if you poured out all the complex molecules of which a simple prokaryotic cell consists they would still not self-assemble in a deterministic way. Indeed, it has been challenging enough to identify processes by which even the simplest molecules of life are formed. And it is not enough to simply propose that the right existing elements be available upon which chance might work its magic. There must be valid chemical pathways that obey the laws of physics, which can take elements through the necessary stages to produce target molecules. This is the world of roadblocks and rabbit trails in which origin-of-life researchers live.

Mainstream evolutionary theory is in slightly better shape. It at least proposes a process by which existing life advances. Unfortunately, that process involves, at its core, a very un-predictable and un-orderly element: mutation. These random corruptions and process failures are an exception to the functional rule of the cell, which is an otherwise law-abiding citizen. Evolution is ultimately dependent upon chance, along with the assumption that increased complexity is the preferential direction for natural selection to take. Contrary to what sci-fi movies might suggest, you cannot drop a mutagen into a vat of bacteria and yield a superbug like you can drop an apple and watch it fall. It may be argued that these random mutations are simply an indirect and roundabout process nonetheless, but that is the very questionable assertion on which the debate hangs.

Chance is a far different creature than deterministic physical law, and therein lies the difference between cosmological and biological evolution. This difference, and the chance/probability issues, have even led some to look for more common ground between the two. As Hugh Ross pointed out in his parting statement, prestigious scientists, like those at the Santa Fe Institute, have begun to propose an undiscovered law of self-organization to support the idea that the appearance of life is as inevitable as the gravitational collapse of matter into stars. If that were ever proved, then we'd certainly have a new topic to debate, but for the committed materialist it would only add one more incredibly odd and fortuitous law to the heap already begging for explanation.

Punc Eq: Hide and Seek in the Fossil Record

"Geology assuredly does not reveal any such finely-graduated organic chain; and this, perhaps, is the most obvious and serious objection which can be urged against the theory. The explanation lies, as I believe, in the extreme imperfection of the geological record."
Charles Darwin, Origin of Species.

The prediction of a mounting inventory of transitional fossils was first made by Charles Darwin, who was well aware of the inadequacy of the existing fossil record to prove his theory of evolution. The optimistic task of fleshing out that fossil record was the prime directive for like-minded paleontologists for more than a century afterward. But by the second half of the 20th century it became increasingly clear that the paucity of fossil intermediates was not primarily due to the fragmentary nature of the fossil record (indeed, it was quite adequate in a variety of places); rather, it was reflective of the way that life itself had progressed.

It was after this disappointment of Darwin's largely failed prediction that the theory of Punctuated Equilibrium (courtesy of Stephen J. Gould and Niles Eldridge) was erected. This theory (PE) began with the admission that the fossil record is characterized by long periods of little or no change to species punctuated by the dramatic and sudden emergence of new species. It then added the rationale that the actual work of evolution must typically occur rapidly in isolated population groups, all this being too quick and geographically confined to grant much chance at fossil preservation.

Originally, some were skittish about the theory, because it was the first formal and tacit professional admission that the fossil record had failed to yield the hoped for intermediates, which was seen to lend aid and comfort to creationists. Even though there are notable dissenters to the theory, like Richard Dawkins and Daniel Dennett, it is now largely accepted in some form by supporters of evolution, and is regularly employed as a rebuttal to those filing a grievance against the fossil record.

As a reply, PE is primarily an explanatory device to fill a void, not a description of a proven phenomenon. PE can never be leveraged as evidence for evolution, since claiming PE is merely putting a name to the absence of evidence and adding a companion story. However, that does not stop the theory from being rhetorical genius: "Sure there are few intermediates. Don't be naïve; that's not how evolution works. I should be surprised if you did find them in abundance!" Evolutionists will simply have to bear with those of us who are skeptical of such a reply.

Now, I'm not suggesting there is no story to go behind PE. As I've said, it relates to the supposed accelerated evolution of isolated populations, which are then released into the larger domain where they might have a chance to flourish and be captured in the fossil record. This may have a certain plausibility to it, but, unfortunately, this narrative behind the theory is itself highly problematic.

Let us now look at some of the problems inherent in the "punctuation" scenario.

1) The smaller populations would also mean fewer creatures to yield mutations, beneficial or otherwise. Consequently, you would not expect increased evolutionary opportunities in such isolated groups. Even if the smaller demographics would somehow spread the new genes more quickly, this may be a no better scenario in comparison to the increased odds afforded by a more abundant mainstream population.

2) Evolutionary change begins with fortuitous mutations upon which "natural selection" may act. Isolated populations and environmental pressures do not mean increased rates of mutation, beneficial mutations, or "beneficial" mutations in the direction that would make a difference for a given creature within its given environment (e.g., a mole doesn't need wings and a tree climber doesn't need gills). Evolutionists often speak of the environment and new ecological niches as though they invite certain mutations. This is fallacious language. Need does not cause any random event to occur with a greater frequency or to yield the desired result at any higher rate; it could only cause a fortuitous thing to be preserved if it did happen to occur. For example, my urgent need to get to work on time will not cause the traffic lights to change any faster. And if I need a 4-of-a-kind to win a poker hand it will not increase the odds that I will draw one; but if I happen to be dealt 3 kings you can bet I won't choose any of those for my discard.

3) Even if it is somehow demonstrated that such isolated populations undergo an increased rate of mutation, then this proportionally increases the chances of detrimental mutations, which are vastly more common. And since it is said that mutations are better preserved in limited populations, then this means that there is an increased chance of tainting the entire genetic stock. The same "inbreeding" that is supposed to afford a beneficial mutation the chance to catch hold in the population is perhaps more likely to take down the entire group.

4) On a related note, the inbreeding of smaller populations actually results in genetic erosion, which is just as likely to lead to extinction due to loss of the genetic diversity that permits a species to survive environmental changes. The liability of population bottlenecks such as these has actually been observed and recorded (see here, here, and here for examples).

5) Quite often, the "punctuations" in the fossil record involve a broad spectrum of plants and animals that would not even be related by ecosystem, e.g., air, land, deep water, shallow water, etc. In this case, are we to assume that numerous isolated populations were all busily working in tandem and then were at once released onto the world stage? The biggest single example of this is the Cambrian Explosion, where nearly every phylum (major body plan) suddenly appeared in the fossil record after a long reign of nothing more complex than algae, sponges, and sea cucumbers. And to make matters worse, the Cambrian fauna was primarily warm-loving, but the period immediately preceding it was icy cold, from equator to pole, which doesn't lend much ground for breeding a whole biota of tropical species.

6) The hundreds of millions of years of geological history are often appealed to as grounds for optimism toward what chance can accomplish. But if real evolution can only happen in these periodic, isolated venues, which are interspersed with long spans of stasis, then this dramatically reduces the timeframe in which chance can do its work.

7) Since each of the millions of species would have had to undergo numerous of these "punctuation" surges to reach its present level of complexity, this means that such PE laboratories would need to be occurring at countless times and places. There should then be enough separate sites that we might hope to find at least one such incubator in the geological strata. PE should be, in principle, if not in all likelihood, an empirically verifiable theory if true.

Evolution's Credibility Problem (part 3)

(Part 3 in a 3 part series)

We cannot just magically say that a mutation happens to produce the code for a new protein. The mutation must happen somewhere. If it happens over the top of an existing gene, then you've lost your original gene. And no matter how impressive the new gene sequence is, if the old sequence was important you may have just killed your organism. This means that the new gene must either supersede unused gene material (assuming such a thing exists), appear within an appended section of DNA, or be an improvement in line with the gene it is replacing. All three reduce the odds of a good mutation's survival, and the latter constraint would limit the scope of novelty.

Additionally, the mutation must either create or be contained within its proper domain. This is where it gets too complicated to continue describing things in detail, but suffice it to say that a gene must have certain controlling sequences in place for it to be effectively translated. For instance, there are start and stop codons, which define the boundaries of the gene. Within this there are things like promoters and ribosomal binding sequences to be considered. And even the best gene instruction is useless unless it has the proper signal sequence defined at its start to act as a sort of mailing address so that the machinery of the cell can know where the resulting protein is to be shuttled and deployed.

So, a workable mutation not only must result in sensible coding for the protein, it must include all of the logistical elements as well. If it does not produce these or happen in a way to make use of those which exist, then it is worthless. Worse, the mutation could easily manage to overlap these controlling sequences in such a way that it not only destroys an existing gene, but also could damage a gene next door if the overlap crosses the domain boundary.

Another consideration is based on the stunning recent discovery that many genes actually overlap by frame shifting of nucleotides or by inverse coding (up to 6 possible genes could be theoretically coded in the same physical space). This means that a change to even one nucleotide in the overlapping region could damage more than one gene. Risking damage to such a code base is one thing, but producing such a thing in the first place is a whole new dimension of incredible. To come close to understanding what I mean, simply imagine creating a palindrome more than 100 letters long (which is grammatically correct), even by design! Evolutionists would have us believe that this has happened countless times by mere chance.

Something else that I would point out: when we are dealing with creatures that sexually reproduce, a favorable mutation in one of the many cells of the organism (e.g., humans have trillions) is meaningless in evolutionary terms. This is because only germ cells are passed on to the next generation. Only mutations that happen in the few eggs or sperm that result in offspring are even candidates for evolution's "descent and natural selection." This means that the higher-order creatures that sexually reproduce, have fewer offspring, and longer generation cycle times, should theoretically evolve slower. But guess what: the quiet reign of single-cell organisms, which exist in vast quantities and reproduce fast and furiously, supposedly lasted more than 2 billion years; whereas the entire history of the relatively slower, fewer, and more diverse plant and animal kingdoms has occupied only a quarter of that time. And humans, some of the slowest breeders of all, appeared in a geological flash.

But back to my lactose-handling enzyme. Even this conceptually simple protein adaptation is far more complex than I suggest. In reality, beta-galactosidase consists of 1023 amino acids and actually functions in a larger structure composed of 4 of these proteins fit together. There are very few simple jobs in the cell. The protein "machines" to do the work are often quite complex, sometimes involving numerous independently designed proteins working in cooperation where the absence or poor design of even one would completely cripple the entire machine. And the machines generally require separate helper and regulating proteins to allow them to either do any work at all or to suppress them when they are not needed.

In the case of the relatively simple beta-galactosidase, it needs at least two other proteins: a permease that permits lactose entry into the cell (not just any 'ole thing is allowed in or out), and a repressor that works to inhibit the production of beta-galactosidase when there is no lactose in the neighborhood (there's no advantage in wasting precious resources). To further complicate things, each of these three components is found in the DNA in sequential order and is packaged together as a single unit, called an "operon."

Aspects of the cell are much like a factory, and just like in a real factory no single machine does much work in isolation. For example, in the case of the bacterial flagellum, a microscopic rotary motor, there are over 40 unique proteins that are involved in its architecture, and many more that are involved in its assembly and operation. As complex as individual proteins may be, establishing their place in the economy of the cell adds greatly to this complexity and cannot be overlooked. All of biology is characterized by interdependent systems — it is the norm.

In summary, the "small," incremental steps proposed by evolutionary theorists are astonishingly non-trivial and, in practice, can be as interdependent at the molecular level as a bat's various features are at the higher morphological level. What I describe is only the beginning of the many incredible things in the world of biology that evolution claims to explain. The more we learn and the more deeply we look at nature — into the microscopic world that Darwin could not have imagined — the more numerous and profound the required work of evolution seems to become. As I've said elsewhere, "Evolution gives fat chance a full time job."

Is there no room, then, for grace toward those who are unconvinced by the evolutionary story? Skeptics should be able to reserve the right to exercise the same principle of credulity that evolutionists themselves apply elsewhere. There is no denying that circumstantial evidence exists for the theory, but the explanatory work that evolutionists are seeking to do with it needs a mighty big engine to push this load over the hill of plausibility. And the fact that the theory itself is immune to reconsideration, in spite of the constantly pounding waves of unexpected and complex new biological discoveries, only fuels suspicion that there is something more than objective science behind it.