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.

A Question of Order

This is part 2 of a 10 part series. The introduction can be found here, and the prior post can be found here. I will add two more blog responders at this point in the discussion. They are from:

• Faithlessgod
• Db0 (Konstantine) & Anath

The next question relates to the kind of universe that was produced by the creation event discussed in the first question.

2. Order

The past several decades have added profoundly to our knowledge of chemistry, physics, and cosmology. It has become increasingly clear that we live in a universe finely tuned for the support of complex life. This fact is so universally acknowledged that even secular scientists have coined the term "Anthropic Principle" to describe it.
How is it that we live in such an exquisitely fine-tuned universe? Even assuming that the universe could have popped out of nothingness, why should it have been such an orderly and hospitable one? Is there a scientific, testable answer for this question that does not simply appeal to imagination?

Faithlessgod offers this objection to the very idea of fine-tuning:

I disagree with Pruett's supposition here, it certainly does not look like an orderly and hospitable universe, since as far we can tell the range where the type of life we know could occur and survive is an incredibly minute portion of the universe.

Randall says it this way:

I don't think the universe is fine tuned for life at all. As far as we know there is only one planet in this one little solar system that can sustain complex life.... most of what's out there is space.

I wouldn't expect to have to go into great detail on this, since it has already been so heavily addressed by cosmologists. Those like Barrow & Tipler, Rees, Davies, Susskind, Bostrom, Smolin, and others have written volumes on this issue. The fine-tuning of the laws of physics (or Anthropic Coincidences) that permit the support of life in the universe is largely undisputed data. It is the conclusions drawn from that data where the true controversy lies.

Since there appears to be a misunderstanding of what I mean by finely tuned for the support of complex life I'll try to clarify the point. I do not simply mean that our own little planet happens to be hospitable to us, and I don't mean that the whole universe is a tropical paradise. I mean that the very laws of physics make things like galaxies, stars, and warm little planets possible at all.

Just two examples:

1) The electrostatic force repels protons (each being positively charged) while the strong nuclear force binds them together. The strong force is stronger than the electrostatic force, but only at short range, while the electrostatic force dominates at larger range. So, in order for nuclear fusion to occur, as it does in stars, there must be a certain amount of energy applied to propel one proton against another in order for it to overcome the electrostatic charge and stick via the strong force. I liken it to putting superglue on two plus-ended magnets and then forcing them together.

Since the universe originally consisted almost entirely of hydrogen, we would not have the abundance of heavier elements if it were not for the ability of stars to fuse atoms (and then spew them out in explosions). But if the strong force were too strong or the electrostatic force too weak, then fusion would be too efficient. Matter would more easily ignite and we would have fewer planets and more stars. Stars would burn out much faster and the lighter elements (being just as desirable as the heavier ones for molecule building) would be quickly depleted. Conversely, if the strong force were weaker or the electrostatic force stronger, then we would have fewer and larger stars, and less of the heavy elements. In fact, if fusion were too inefficient, then the large masses that might otherwise form stars could actually collapse into black holes before they would even have a chance to ignite.

2) The quantity, expansion rate, and distribution of the material of the primordial universe all have a part in determining the nature of its resulting cosmology. If there were not such a mysteriously large imbalance of matter over anti-matter, we would not have the material to form cosmological structures. Various factors seem to work together (e.g., inflation rate and dark energy) to determine the expansion of the universe. Minute differences in these factors would affect a number of things, including whether the universe recollapsed upon itself before anything interesting could be produced or whether it expanded too rapidly for the material to coalesce into structures like galaxies and stars.

It seems to me that a universe that survives its genesis, forms complex structures, and supports the generation and assembly of complex, diverse molecules is something we might even objectively value over a hiccup universe, or one that was filled with nothing but diffuse hydrogen gas. And even though there are more empty, hot, or cold places in the overall universe than there are just-right stars and just-right planets, it takes this kind of universe to be able to support such things.

If I were to accept the substance of Faithlessgod and Randall's complaint, I might just as well say that even our planet is not so great for humans because of all the hot, frigid, or wet places it contains. All these are either necessary for a life-sustaining climate/ecology (like an abundance of water) or they are simply byproducts of physics and geometry (like cold polar regions).

Tremblay takes issue with the idea that the Anthropic Principle has any relationship to the fine-tuning point that I raise:

LifeWay apparently does not know what the anthropic principle actually is. The anthropic principle does not support the fine-tuning argument at all. What the anthropic principle actually says is this: we live in a universe compatible with our own existence.

Yes, "LifeWay" understands the Anthropic Principle and its various permutations, such as the Weak Anthropic Principle (WAP), which will be discussed later. The very fact that there are even flavors of it is witness to my point that there is something of interest being discussed in the scientific community.

Of course the materialist would think the fine-tuning question does not support the role of a designer (else he would not be a materialist), but the Anthropic Principle is certainly born of the observation that the Anthropic Coincidences are necessary to the existence of observers. If the Anthropic Principle were nothing more than a tautological statement, like saying that coldwater fish are found in cold water, then I would not expect to find so many physicists and cosmologists writing books for the purpose of wrestling with its implications. Why try to explain away or rationalize an entirely meaningless observation?

A common rejoinder I've heard is that we shouldn't be so presumptuous as to think the universe is designed for us; it might have been some different way that would result in another species asking the same question. Self offers a form of this argument as follows:

To say the universe was fine-tuned just to permit life is backwards; what is more nearly true is that life is fine tuned to exist in the universe as it is today.

Anath makes the point this way:

It's like claiming your life is somehow miraculous and special because YOU were the specific result of your parent's copulation. Had a different sperm reached the egg first, or had something interrupted your parents before transfer that particular time, a totally different person would be saying the EXACT same thing.

It should be understood that I am not simply arguing for an egocentric view that the universe is fine tuned for humans or even for "life as we know it." If some member of a nebular squid species were to ask the same question, then I would grant his right to do so, because the Anthropic Coincidences would apply equally to him. I am arguing that the laws of physics are fine tuned for the support of life of any kind, which depends upon things like a universe, diverse materials, and the ability to form complex chemical structures.

Since there are so many other ways that the universe might have been that would not support life, stars, or even a persistent universe, and if there is anything noteworthy about complex, sentient, biochemical systems, then it seems that the least we can say is that this kind of universe is remarkably improbable.

At this point I have often heard the comment made: "Well, you wouldn't be here to wonder about it if it hadn't happened!" This is a hackneyed paraphrase of the Weak Anthropic Principle (WAP). To all my responders credit, I didn't see this voiced (in so many words). However, I think it is worth addressing, which I will do by simply paraphrasing the Swinburne/Leslie parable:

Suppose you are dragged before a firing squad. There are 100 trained marksmen all intent upon your demise. The command to fire is given. The guns blaze, but a moment later you discover that you are still alive, untouched by the bullets. You laugh out loud and marvel at your good fortune, but an annoyed captain of the guard simply growls at you, "There's nothing remarkable here, fool. You wouldn't be alive to remark about it if hadn't happened." And then he executes you himself with his own sword.

Even if the captain had killed you before you could ask the question, "How did I survive that?" it still would be legitimate for some observer to ask it. The WAP seeks to negate the observer's question by depending upon his existence. If he exists, he can't ask the question because he wouldn't be here to ask it otherwise. If he weren't here, then there's no one to ask questions so the problem is forfeit. It seems a hollow victory for the materialist to win on a technicality, but surely it is a more remarkable thing to have observers who ask questions than to have cold, dead space. I guess it is like a 3D stereogram. You either see it or you don't.

Faithlessgod goes on to raise a good point about other possible universes:

We have no idea what type of universes could occur with different constants, only that they would be radically different from ours, but this tells us nothing about whether the equivalent of life is more or less likely in those other universes.

The Anthropic Coincidences applicable to this universe suggest that of the kind of laws and materials that we are dealt, this particular arrangement adds up to something special. Perhaps some other dramatically different mix could add up to a recipe for success, but that would be another island in a vast sea of improbability as well.

To use a card analogy, which one of my responders employed, our universe's order may be compared to throwing a deck of cards up in the air and having them all come down in neat, numerically sequenced stacks by suit. There are certainly a large number of other ordered ways that the cards may come down, like numerically sequenced stacks of four-of-a-kinds, but they would be no less probable than the nearly infinite number of other chaotic arrangements that might result.

And to suggest that other radically different universes might help us here is to suggest that there might be a way that any old arrangement of its materials would yield order. This is like saying that in another universe made of dice instead of cards, that most rolls of the dice will come up all sixes, or in stacks. Perhaps there could be some universe where the laws are so rudimentary that there's no possible "variation," or any variation would yield the same assembly capability, but even that kind of universe surely would be less probable than all the other more dependent kinds, like the one we happen to occupy.

Interestingly, Tremblay makes an objection that would call this into question:

Implicit in this argument is the belief that the parameters of the universe could take any quantity. . . .

Just because we can imagine the gravitational constant being, not 6.674×10^-11 m^3 kg^-1 s^-2, but rather 6.252×10^-11 m^3 kg^-1 s^-2, does not mean that it can actually be 6.252×10^-11 m^3 kg^-1 s^-2. Just because we can write it down and make calculations based on it doesn’t mean it’s actually possible.

This is certainly a valid argument, but why think that the values could not be different? What meta-laws exist to constrain the amount of matter over anti-matter or the expansion dynamics entailed in the Big Bang? Even if the laws and events inherent in this universe where somehow necessary or predetermined, then this only pushes the question back a level. Why should the "necessary" laws be so remarkably configured? Why would the brute laws of physics have to favor order? How very fortuitous!

A popular theory among cosmologists involves the idea that we exist in just one of a number of bubble universes. While I will not attempt to psychoanalyze the motivation for such a theory, I will note that I have usually seen the theory employed as a response to the Anthropic Coincidences. As the argument goes, we just happen to live in a jackpot universe that is just right for life. Unlike Tremblay, these cosmologists don't seem to have a problem with the idea that the universe-barfing device may have different settings. Nor do they seem to agree with those who argue that there just isn't anything special to be explained or they would not make appeal to infinite universes for that explanation.

Tremblay closes with this conversation stopper:

As for the question "why should [the universe] have been such an orderly and hospitable one?", it should be obvious that the use of "why" presupposes teleology, and therefore a Creator. So this question is entirely circular. There is no purpose for the universe to be the way it is, any more than there is a purpose for the sky to be blue instead of green. We can explain how it came to be hospitable, or how the sky gets to be blue, but there is no "why."

Perhaps we should break the news to those like cosmologists Bernard Carr and Martin Rees, who once stated in the journal Nature, "Nature does exhibit remarkable coincidences and these do warrant some explanation." Perhaps we should simply think of them as philosophically naïve to require explanations, but it seems to me that science is all about the "whys."

Tremblay suggests that explanations should extend only to the reason for the physical condition (like, the sky is blue because of short wavelength light diffusion), but not to any deeper meanings (like, why should physics have to work in such a way that it yields lovely blue skies?). Perhaps this is a good rule of thumb for science proper, but it is a castration of the human spirit, which, for some strange reason always wants to go the extra mile in its understanding.

Materialists would apparently say to us, "Just get over it! There's no meaning to this or any other aspect of existence. Everything just is what it is." For my point in question, this means that even if it actually is the case that the universe is fine tuned for complex life (of any kind), and it is a genuine statistical improbability, then we are disqualified from having stray thoughts of wonder because they presume something to wonder about that does not exist: teleology (purpose/design/meaning).

It is true that this, and many of my questions, depend upon teleology. In fact, teleology is part-and-parcel to the worldview I am advocating. But surely teleology cannot be ruled out a priori any more than we could meaninglessness. I might just as well claim, "the atheist can't say the universe just is what it is, because that's a circular argument: it presupposes that there actually is no meaning to the universe." How, then, is one to demonstrate the need of a designer if one cannot point to anything as evidence merely and precisely because it supports his thesis!

A Question of Cosmic Origins

This is part 1 of a 10 part series. The introduction can be found here.

The first topic relates to the great historical question of origins and trades on concepts found in the Cosmological Argument for the existence of God.

1. Creation

The overwhelming consensus of science is that the entire cosmos (including space and time) came into existence at a finite point in the past. All of our observations, equations, and physical laws testify to a point of origin for this universe.

In light of the troubling evidence for a beginning, and that we may not even be able to find a natural cause in principle, what explanation is given to the questions, "Why is there something rather than nothing?" and "Where did it all come from?"

Francois Tremblay proceeds to take issue primarily with the logical composition of my question.

Asking "why is there something rather than nothing" is a fallacious question since "is" implies existence and "nothing" implies non-existence. It's a question that Christians like to ask because it's by definition unanswerable, not because atheists have no ready answer but because the question itself is contradictory.

Roderick T. Long further elaborates the objection.

It makes no sense to ask for an explanation of the whole of existence – whether that whole includes a God or not. Any attempt to explain existence has to appeal either to something in existence or something not in existence. If it appeals to something that’s already in existence (be it God, quarks, or whatever you like), then you’re not explaining all of existence; and if it appeals to something not in existence, then you’ve offered no explanation at all.

My point was not to ask a trick question, but to seek a reaction to the fact that this universe gives evidence of a beginning. When I speak of something and nothing I am speaking from the materialist's perspective. Of course, as a theist, I believe that "something" has always existed; I have a "first cause" or "prime mover."

Long basically understands this, as he continues:

The concept of explanation applies only within the realm of existence; that’s why both theists and atheists agree that chains of explanation stop with something whose existence has (and needs) no explanation beyond itself – whether it’s God or energy.

This is a good observation, and actually is the kernel of the response I would make to George Self when he asks, "If a xian wants to take the beginnings back to some god that made it all, I would ask, 'but who made god?'" Something has to eternally exist or there would be nothing right now. Something cannot come from nothing. We suggest that this something is God, whose very definition includes the idea of self-existence and eternality. If the atheist will not allow an eternal God to stand as an acceptable first cause, even in theory, then the atheist has no grounds to lean upon an eternal universe (or energy) either.

The problem that I point out with this question is that even if it might be conceptually possible to have an eternal universe (which I could argue against as well), by all indications this one had a beginning. I am not asking for an explanation for the universe, which might lead to the counter-question of why there is a God; I am asking the atheist what he (or she) does with the evidence for an origin to the universe.

Alison Randall takes (in my mind) the sensible position that "nothing does not and has never existed . . . because you can't have anything come into existence from nothing."{1} This serves to underscore the problem of our current observation that all space, time, matter, and energy burst onto the scene at a finite point in history. If it can ever be said to have come from "nothing," or no prior state can be identified, then materialism will have hit a dead end in one of its most important avenues of justification.

Randall then goes on to postulate that "everything always existed . . . as a dense singularity of energy-matter." Here's where we could get into an arcane scientific discussion and I could ask things like, how "infinitely small" (as the singularity is often described) is distinguishable from "nothing," how something natural could exist prior to the space-time continuum in which existence is defined, and why a gravity well isn't happy eternally staying that way.

But I don't need to go here, because there is not even agreement on the idea of the origin of the singularity. For instance, inflationary theory, which is the prevailing big bang model, says that the singularity was generated by something like a "quantum fluctuation." Membrane theory doesn't even have a place for a singularity, and one of its advantages is the very fact that it doesn't have to wrestle with the difficulties associated with one. As this physics article explains about one of the big bang models that require a singularity,

The problem with the Big Crunch/Big Bang model is that the mathematical laws of classical general relativity do not work at a singularity. And if scientists cannot mathematically understand the singularity, they cannot, in theory, fully understand the geometry of spacetime, either before the Big Crunch or after the Big Bang.

Randall continues her response:

I don't pretend to know a lot about it, but [the Singularity/Big Bang model] seems to be one of the best explanations we have right now, along with other ideas . . . like string theory, multiverses, and such.

Umm, which theory was it that is the "best explanation?" She lists these other things because there is NOT an explanation right now, only theories, else we wouldn't have other contenders vying for dominance. I think Randall knows this, but she adds this parting shot to show where her preferences lie:

The theories that are made from observable evidence are a lot more juicy and intriguing than ancient mythologies.

Unfortunately, the only observations and evidences we have say nothing more than that there was a beginning to this universe. There are not so much theories made from observable evidence as there are only theories seeking evidences as to how that happened by "natural" means. This is exactly why there is so much excitement over things like the Large Hadron Collider and Planck satellite, which are hoped to offer supporting evidence for one or another idea (though how we can prove the nature and events of something "outside" this universe using observations born of the laws contained within it I do not know).{2}

The bottom line is that there's really not an explanation for the origin of the universe, and naturalistic explanations are simply occasions to engage in sci-fi narratives. As Leon Lederman (Nobel Prize winner in physics) says in his book, The God Particle:

A story logically begins at the beginning. But this story is about the universe and unfortunately there are no data for the very beginning. None, zero! We don't know anything about the universe until it reaches the mature age of a billionth of a trillionth of a second — that is, some very short time after the creation in the Big Bang. When you read or hear anything about the birth of the universe, someone is making it up. We are in the realm of philosophy.

This is where the discussion must ultimately end. As George Self concludes, "I'm quite comfortable saying, 'I don't know, and neither does anyone else.'" And one blog commenter summed up the responses by saying, "I don't know, but science is looking into it."

Fine. That is an honest and somewhat acceptable answer. Every worldview must be permitted some mysteries. But if this is a satisfactory response for all the intractable problems of materialism, then atheists shall forever be free to think themselves rational, since science will always be "looking into it." However, I doubt they would be so kind as to allow us to reply to their tough questions with, "I don't know, but our theologians are looking into it."

Without overstating my case, it seems reasonable to say that evidence for a beginning to this universe is at least problematic for materialistic atheism. And even while atheists can avoid a proof for God by eternally leaving the question open to scientific investigation, we should be able to say that a cosmic origin is at least consistent with theism, particularly classical Christian theism.{3}

After offering his shrug to the problem of cosmic origins, Self adds this addendum:

Even if I wanted to assume that time had a beginning at some point in the distant past that still does not prove that the xian "god" created that point. Perhaps the cosmos was started by a unicorn or a magic genie.

Unfortunately, this does not at all avoid the problem for the atheist. A magic genie or unicorn with the power and knowledge to create our universe would still be a god, for all practical purposes. What Self does do is touch on the fact that the Cosmological Argument is limited in the work that it can accomplish. Even if the atheist were to concede the need of a creator, it is another thing to demonstrate the nature of that creator. For this reason, the Cosmological Argument can never be more than an argument for theism in general{4}, and must work in conjunction with other arguments to arrive at the God of Christian theism.

~~~~~~~~~~~~

Notes:

1. There are some who disagree with Alison and are bold enough to accept the premise that there once indeed was nothing. Dr. Peter W. Atkins (himself an atheist) holds that the "nothing" managed to split itself into the positively and negatively charged universe that we enjoy today. Tada! The Force stays in balance, since "nothing" has yielded a universe with a net charge of nothing, and may return to such in the future. It's all virtual nothingness with no gross explanation required. It all sounds rather artful as a high level theory, but explaining exactly how "nothing" managed to send itself on an extended holiday is where it begins to unravel.
2. I might conversely say to Randall, "Theories with a long philosophical pedigree are a lot more juicy and intriguing than ideas from sci-fi movies."
3. You can expect this to emerge as a recurring theme in each of my questions.
4. In fact, cosmological arguments have been in play since long before Christianity was founded.

Part 2 can be found here.

Ghost in the Machine

Sobbing, shaking and knowing death was imminent, [Nancy Reagan] held her husband's hand about 1 p.m. Saturday as he inhaled deeply and opened his eyes for the first time in five days.

While most thought Alzheimer's disease had robbed former President Reagan of all his memory, the last look he gave his wife was one of deep acknowledgment, [his daughter Patty Davis] writes for People magazine.

"At the last moment when his breathing told us this was it, he opened his eyes and looked straight at my mother. Eyes that had not opened for days did, and they weren't chalky or vague," Davis recalls. "They were clear and blue and full of life. If a death can be lovely, his was."

Davis and her brother Ron were standing next to their father's bed when the astonishing interchange between their parents took place.

(Source. Other sources.)

After Ronald Reagan's death I watched a television interview where Ron Jr. recounted this story himself. He was very emotional as he spoke, and it was clear that he believed that something profound had transpired. His father had apparently burst forth through a broken body to bid farewell to his beloved wife. This kind of story is not unique in my experience, but what makes it interesting is whom it is that is telling it here and how it fits into his overall view of human nature.

Ron Reagan Jr. is a self-described atheist. Consistent with, and common to, atheism is the philosophy of materialism. Materialism is the idea that all things that exist can be explained in purely material terms, and there are no entities such as gods, angels, or human souls which exist beyond the boundaries of the physical universe. This means that the "mind" is simply an emergent property of the physical brain — without a brain, there is no mind. It also implies that a malfunctioning brain will yield a malfunctioning mind. Given a materialistic outlook, how does an atheist like Ron Reagan process his father's last moments of life?

Alzheimer's is a degenerative disease, which affects the brain cells and the connections between them. A brain at the fatal end of this illness is a devastated organ from which an identifiable "mind" should not hope to emerge. In the case of Ronald Reagan, he had not even opened his eyes in days, and had not been alert for years before this. From where, then, does a clear-eyed Reagan suddenly surface?

At the very moment when his body was so far gone as to yield to death, Ronald Reagan became animated — himself again. If a body is broken, why does it not naturally and successively proceed from almost dead to actually dead? If we flatten the tires on a car, drain its oil, and pull half it spark plugs, do we expect it to have one last burst of blazing performance before it finally sputters and dies?

Perhaps it is like the runner, who after exhausting all resources at the end of the race finds in himself one final burst of speed for the finish line. But this is not an accurate analogy, because the racer does indeed have something left to give. He is simply very low on carbohydrates and is inhibited by the pain of lactic acid buildup in his muscles, which makes him pace himself to the end. In that last burst, he is drawing on the remainder of his resources but could not hope to continue long in this. To be an accurate analogy, we would first have to sever some tendons and break some bones. No matter how brave or determined one is he cannot get far or fast on broken legs.

The other problem with this analogy is that a runner can will to briefly overcome his fatigue. But here we are speaking about the very thing from which something like a will is supposed to originate: the brain. In the materialist paradigm there could be no Ronald "in there" to triumph over his failing brain — a brain so destroyed that it could no longer even support life itself.

So what happened that night: one final power surge resulting in the shutdown of a fragile system, or a man rising from his broken body to say farewell before passing on? Ron Reagan Jr's heart is urging the latter. But how can he maintain this as an atheist? As most atheists I'm sure that he thinks of himself as an eminently rational creature. But to be consistent, I think he must either give up his materialism or give up his sentimental notion that something extraordinary happened that Saturday afternoon.

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.