The problem of design

Teleology is taboo in modern science. It’s not hard to see why: purpose implies design, design implies a designer, and a designer is exactly what the predominantly atheistic scientific community does not want to admit. But yet, we use telic language–specifically the language of engineering–to describe concepts in biology all the time. Is it just because we know of no better way to describe systems than by analogy to those that we ourselves have designed? Or is there something deeper to the compelling similarity between “molecular machines” that we discover inside the cell and machines that we use every day? It is such questions that drive Mike Gene’s brave new book: The Design Matrix: A Consilience of Clues, which aims to refocus the neverending debate over purpose in nature away from the black-and-white arguments of days past into a careful investigation of the actual evidence.

Mike (Dr. Gene, I presume?) is at his strongest when describing the intricate details of molecular machinery, and in particular that of DNA replication, mutagenesis, and error correction. He clearly describes several features of cellular replication that are salient to the debate over teleology. For example, the genetic code that we see in almost all organisms today is remarkably optimized. It allows for redundancy that reduces the chance of DNA mutations causing changes in protein structure, but on the other hand, the most common mutations due to the intrinsic chemistry of DNA lead to amino acid changes that increase hydrophobicity, increasing the likelihood of secondary structure and protein-protein interactions. There is also no evidence for precursor codes, and the variants that do exist (such as the mitochondrial code) are better explained as divergent from the universal code rather than primordial remnants. The numerous mechanisms within the cell to ensure the fidelity of DNA replication, RNA transcription, and protein translation, when compared with what we know about codes in general, are also good evidence for teleology in biology. Even more intriguingly, some bacteria have a mechanism for increasing the rate of mutations in their genomes in response to certain stresses, which along with the general trend toward hydrophobicity in proteins suggests that evolutionary mechanisms may be coopted by organisms to increase their complexity and chances of survival. One minor quibble: I would have liked to see some discussion of the “RNA World” hypothesis and how it fits (or doesn’t) with the possibility of evolution of the genetic code.

Mike’s discussion of nanotechnology and its similarities to molecular biology is also excellent. I had not appreciated the degree to which scientists studying nanotechnology are turning to biology for inspiration. He makes an excellent point when he points out that there is a remarkable convergence between the direction of engineering (toward smaller and more complex design) and what already exists within the cell. It is certainly resonable to argue from this evidence that the “molecular machinery” within the cell exhibits characteristics of design, especially as we refine our own designs by studying ever more closely analogous cellular structures.

I also appreciated, on a completely different note, Mike’s discussion of what he calls “inductive gradualism” as a method of studying teleology vs. non-teleology in nature. He presents an “explanatory continuum” between “X could not have possibly evolved” and “X certainly evolved”, as opposed to what is the common approach to these debates: admitting only those two possibilities and not allowing for varying degrees of uncertainty about the telic content of nature. His continuum is certainly better aligned with how scientific research ideally ought to proceed: gathering evidence gradually until a conclusion approaches inevitability, but always being open to other clues leading in a different direction. Contrast that with what is often heard in “ID vs. evolution” debates: on one side, any evidence that remotely points toward “design” or seems to not admit evolutionary explanations is held to “disprove evolution,” while the other side adamantly refuses to accept any telic explanation. Such a dichotomy is, as Mike demonstrates, simply bad science–and more importantly, poor philosophy.

However, in the end, despite my hearty agreement with Mike on the evidence for design in the genetic code and the merits of an inductive approach to studying biology, his book has some serious weaknesses, ironically in the final section where he lays out his “Design Matrix”. He lays out four criteria for discerning design: analogy, discontinuity, rationality, and foresight, and suggests that by scoring various biological structures on these areas we can come up with a “score” that correlates with a probability of teleology. If the four criteria were equal to each other, and if they could be reliably scored by different observers, then perhaps the Matrix would be a valuable tool. But, I fear that it is not:

1. Analogy: Mike suggests that we can infer an increasing probability of design if a biological feature has analogous aspects to things that we know to be designed. On the surface, this seems commonsensical. If we found a molecular machine akin to a rotary engine (the F1-F0 ATPase), then we might conclude that it was designed as was the fascinating engine in my old Mazda RX-7. But, I think that Mike’s excellent observations about nanotechnology subtly undercut the argument from analogy. Our designs ever more closely converge upon nature. Are we unwittingly approaching the same minima in the multidimensional fitness landscapes associated with doing particular kinds of work? I wonder if our own refinements of designs (such as Mike’s example of the Chevy Corvette) mirror nature not because of design per se, but because we are converging upon the best solution to a particular problem.

2. Discontinuity: This criterion is entirely based upon Michael Behe’s concept of Irreducible Complexity. Mike admirably explains the evolutionary explanations that purport to explain away Irreducible Complexity. In the interest of time, I will not go into why I find the possibility of cooption to adequately explain away this teleological inference. If a biological mechanism can be found that has multiple components, which cannot be reconstructed by gene duplication or other mechanisms from components found in simpler organisms, then I suppose that IC would be tenable. But, until that point, scoring features based upon discontinuity with the past is entirely too subjective. Even the genetic code, which is the example nonpareil of discontinuity, may have evolved from a simpler RNA (or other nucleic acid) precursor. My biggest concern with this criterion, however, is not scientific but theological. Another word for a discontinuity is a gap, and I fear that we place the Designer squarely into those gaps when we rely upon this explanation of design.

3. Rationality: Mike lists six features of rationality, which merit separate consideration.

a. Efficiency: While I agree that efficiency–that is, “using the mininum number of parts to carry out an objective,” is a hallmark of good human design, to judge efficiency is tricky business. How do we discern whether a system contains “needless complexity” as a way of making it more likely to be designed? Often in biology, we’ve thought a component superfluous, only to discover its function later. Take, as one example, the ribosomal protein L11. It isn’t a structural component of the ribosome (which for the uninitiated is the “molecular machine” that translates RNA into proteins), but yet is critically important. Free L11 (not in place in the ribosome) acts as a signal to activate the master stress regulator p53, causing the cell to either arrest its growth or die when protein synthesis is disrupted. Yes, the actual number of parts of biological systems often exceeds a bare minimum (the ribosome is an excellent example), but we simply don’t know whether these other parts evolved (or were designed) to have additional functions that we’ve yet to discover.

b. Specificity: While it is true that humans typically design things with “precisely specified interactions,” we are learning gradually that the “messy” and “error-prone” systems in biology are not necessarily the worse for wear. For example, the HIV virus takes great advantage of its error-prone reverse transcriptase, which generates mutations at a rate exceeding the capacity of the human immune system to adapt. “Error-prone” DNA polymerases aren’t particularly good at putting the correct nucleotide opposite its cognate partner in DNA replication, but if they weren’t able to stick nucleotides into less than optimum conditions, replication opposite damaged bases (due to radiation, enviromental pollutants, etc) wouldn’t be able to occur (and we’d be in big trouble as a species). I guess what I’m trying to say is that specificity in design isn’t always a good thing, and being “messy and error-prone” isn’t always bad. The question is whether there’s something in the error-prone system that we’re missing when we judge it not to have been designed.

c. Robustness: Yes, this is a feature of design, but I’m not aware of many biological systems that don’t possess it. Our cells and bodies are remarkably robust.

d. Elegance: I’m not sure why Mike included this, as he admits that it is a subjective measure. As I spend more time studying the inner workings of the body and molecular biology, my definition of elegance changes. I find things that I once thought sloppy, such as the production of mutations in the human genome leading to cancer, elegant because the alternative: slowing down replication to make it more accurate, would make human life impossible.

e. Flexibility: See my discussion of efficiency. Because these two features are usually in balance, it’s hard to judge them either for or against design.

f. Coherence: Mike suggests that a balance of the other five features, that is, a coherent function, is a hallmark of design. I agree, but I question how we are to actually judge this. Do we have a more coherent design of a system to compare against? Does a system (such as mitosis in primitive eukaryotes) actually need to be as carefully precise as it needs to be in higher eukaryotes. If it doesn’t need to be, its “messiness” is not an indicator of incoherence.

In all, my beef with Mike’s hallmarks of rationality is that they’re all terribly subjective. I find that, in studying biochemical systems in great detail, I’ve always proceeded on an assumption of rationality as a way of hypothesizing what a particular feature does. I suppose I give “evolution” more credit than some people, or perhaps on the contrary, we biochemists use a “design inference” far more than we admit.

4. Foresight: To conclude this rambling review, I find Mike’s fourth criterion of design to be actually the only criterion really worth considering, because it is the only one for which there cannot be any non-teleological alternative. Evolutionary processes can give the semblance of rationality; they can give the semblance of discontinuity; they can certainly appear analogous to human systems. However, by definition, they cannot operate with any foresight. If a unicelluar eukaryote’s genome contains proteins that serve it no critical function but are essential for multicellular life, that points toward “front-loading.” If the universal genomic code is so optimized as to both minimize errors and promote beneficial mutations, as Mike suggests, then that points toward clear foresight, particularly as unicellular organisms are hardly as concerned about maintaining genomic integrity as are long-lived multicellular ones. I also find the intricate structure of the genome itself evidence of some foresight, as “junk DNA” is proved more and more full of treasure. Would the timeline of life, if replayed, produce the same results? Gould says no, Simon Conway Morris (in Life’s Solution) says yes, and I think that Mike and I heartily add our votes to the “yes” category.

Perhaps the major difference between Mike and I is that I still operate too much from the “black-and-white” category. But, I’ve found that our colleagues in science are unwilling to even consider “clues” for design if they can be cast in an evolutionary framework. Mike has done us a great service in laying out the evidence he sees for design and an interesting, if flawed, new way of assessing it, but in the end, only pointing the way toward foresight in biology is going to make any headway in convincing the majority of scientists to start considering a Designer. For, when all is said and done, the issue is not one of science at all, but of philosophy and theology. We see evidence of a Designer everywhere who look for Him; but, those who close their eyes will take much to convince. As Emile Zola said:

“Were I to see all the sick at Lourdes cured, I would not believe in a miracle.”

Misunderstanding evolution

I’m not a paleontologist, nor do I know all that much about speciation, but this Yahoo news piece on human evolutionary origins needs a bit more thought…

New discoveries by Maeve Leakey have dated Homo habilis and Homo erectus specimens to the same period that were found within walking distance of each other. The conclusion reached in the news article is that, therefore, the latter is unlikely to have evolved from the former. Sounds logical, right? Two species that live at the same time can’t be descended from each other.

Well, there is absolutely no reason why an older species can’t remain while a younger species develops. Here’s one example of how: suppose that, due to environmental factors, one group of animals gets separated from a larger population. This group then, because it is isolated (for whatever reason) from the other, diverges to the point that it is no longer the same species. Then, at some later point, members of the new group travel back and live among the original population (that, because its environment hasn’t changed, hasn’t “evolved” all that much).

When we, millions of years later, look at fossils from the area where the two groups then lived, it’s easy come to the same conclusion as the folks in the news article. These two groups couldn’t have come from one another because they lived together at the same time. But, at an earlier point, they might not have.

It’s scary how easy it is to come up with explanations for historical discoveries (like those in paleontology) using evolutionary theory. (Is the theory, in fact, falsifiable? I’m not so sure.) But, it’s equally scary how easy it is to grab a hold onto any data that seems contradictory to evolution, and bank on it to boost creationism…

When humanity and homo sapiens clash

I should be studying (as always) before heading off to Latin Mass this afternoon, but I had an odd series of ideas yesterday that need hashing out in words. This is what tends to happen when I have a couple of days off from the ridiculously hectic schedule of medicine….

We’ve spent the past 148 years trying to work out the ramifications of Charles Darwin’s dangerous ideas. If all the living creatures around us are the products of natural selection, then, likely, so are we. The mechanism behind the variation which enables nature to select for the fittest is simple enough: changes in DNA produce changes in proteins that result in changes in function. These changes are almost always deleterious, but at least theoretically, a change in protein structure could enhance efficiency or produce new functions. Over time, as creatures encounter changing environments and compete with each other, various changes in their genetic material are selected for and maintained down the generations. It’s an elegant theory, one that can explain how the vast array of biological life came to be. Yes, it has problems, particularly with explaining large-scale changes and speciation, but I’m not interested–at least not in this essay–in exploring the whole evolution-vs.-creation controversy.

But what about the timescale of evolution? How fast can things biologically change? Organisms with short generation times or error-prone genetic replication systems can evolve remarkably rapidly. Take, for example, the production of antibiotic resistance in bacteria. Or, if we consider viruses to be alive, the champion evolver is the constantly changing HIV virus that stays one step ahead of our immune systems. A bacterial species that doubles in number every couple of hours can adapt genetically to almost any environmental change. But what about us? Our 70+ year life expectancy and long generation times mean that it would take thousands of years to produce the same changes that bacterial populations undergo in a matter of days. Are those changes possible? Sure. They’re even likely.

However, mankind throws a wrench into the mechanism by being creative. We think, ponder, discover, invent at a rate that far surpasses generational genetic changes. While Cro-Magnon Man and I are, on a genetic and biological level, essentially identical, our worlds are radically different, not because of biological evolution, but because of our abilities as sub-creators. Our bodies cannot keep pace with our minds–especially not with the rapidly accelerating rate of technological change over the past hundred years. What ramifications might that have? There are countless possibilities: I’ll focus on a few.

The human body, for all the vast array of diseases to which it is subject, is a finely tuned machine. Left to its own devices, it is fairly good at healing itself and fighting off any number of microscopic and macroscopic invaders. We creators think we can enhance things, though. Sometimes we can, but not without unforeseen consequences. Why is it that there is an epidemic of allergies and autoimmune diseases in the developed world? I pin the blame on two advances: hygiene and immunization. Would I take either of those back? Of course not, but our immune systems, from a biological angle, are intended to combat bacteria, viruses, fungi, parasites, etc. If we have a lower burden of those, I suspect that immune cells have a higher chance of attacking things that they shouldn’t–like things in our own bodies–or are hypersensitive to external things that shouldn’t be a bother–like cat dander. I wouldn’t trade millions of bothersome allergies for millions of deaths from infection, but the principle holds: we’ve short-circuited a slow evolutionary process and have to face the reality that our bodies react to our creations in less than ideal ways.

Allergies and autoimmunity are physical examples of what happens when we meddle with our biological selves, but what about the costs of modern technological society on a more abstract level? I have, as usual, more questions than answers. Is our modern plague of depression, anxiety, and mental illness the result of, quite simply, not having to deal daily with what our ancestors bravely faced: death or survival? Are we consumed with ourselves because we’re insulated from stark reality? Do we fear death more, and as a result quixotically seek physical immortality, because we can push the reality of our mortality out of our minds for extended periods of time? Are we losing belief in God because we surround ourselves with our own creations? Has our incredible store of knowledge about things led to a paradoxical loss of understanding of ourselves?

The problem is the same whether you believe that we are the special creations of God or the result of millions of years of evolution–or both. It is undeniable: we biologically cannot adapt at the same pace at which modern human society is changing. Genetics won’t allow it. We’re cavemen in modern garb (with apologies to Geico). Does that mean I want to turn back the clock and return to the Stone Age? Far from it. Modern medicine and science have changed our lives for the better. But we ought to step back and think about why we react as we do to modernity. Look beyond the technology that surrounds us to the fact of death. Look past the anxiety that can consume us and accept that, despite appearances to the contrary, we really can’t control everything. We have just postponed and disguised the inevitable by our creations. Know thyself, not just the world around.

The wager

“Yes, but you have to wager,” said Blaise Pascal in response to agnosticism. In the end, death intervenes, and not deciding on God’s existence is ultimately tantamount to choosing against Him. Choose for belief, and at best you gain salvation; choose against, and at best you gain nothing at all. Of course, if the probability of God’s existence is precisely zero, then all bets are off, but you’d have to be rather myopic to make that claim, which you cannot prove. No, when all is said and done, you have to wager.

The same goes for the current debate on embryonic stem cell research. A wild jump, you say, to go from discussing Pascal’s wager on belief to public policy? Not so, because at the core of our endless arguments on stem cells is a dilemma which requires a wager and has no definitive materialist answer. Is the human embryo a human life? If we were simply studying the embryo, observing its development, awestruck at the formation of a human being from one cell, then yes, contrary to Pascal’s conclusion about God, you could abstain from a wager. No action has been committed against the embryo; it is allowed to develop naturally.

But, we aren’t merely observing; we are destroying. Once that decisive step has been taken, then we must wager. Either that destruction is blameless, or it is murder. There is no question as to the embryo’s innocence; the best argument for abortion, the violinist argument, falls apart since we’re not destroying an embryo because it’s infringing upon the mother’s rights. The intentional killing of an innocent life is murder; therefore, unless my reasoning is terribly mistaken, the creation of stem cells by disaggregating a human embryo’s cells is one of two things: if a human being, then murder, if not, then no big deal.

But how do you decide between those two options? You cannot turn to science. Any embryology textbook shows what a seamless process embryonic development is from the moment of fertilization until birth. Unless impeded by faults determined by the interplay between its own genetics and the environment provided by its mother’s womb (otherwise known as miscarriage), it will be born 40 weeks or so after it was but a single cell. Markers such as the heart beginning to beat, or the first neuron firing, or development of a recognizably human face, are mere symbols devoid of any real meaning. Since at this moment, it would be terribly difficult to select an embryo that could not develop into a human being and would be intrinsically miscarried, then use its cells, we still must wager.

Science cannot tell you whether a human embryo is a human being at the stage in which it would be dismembered to create stem cells. If anything, the evidence points firmly toward its humanity. But, we deeply want to cure crippling, deadly diseases like Alzheimer’s and Parkinsonism. We would do almost anything if we could make the lame walk. However, if we were told tomorrow that the cure to Alzheimer’s disease was present within the brains of a family with a newly discovered genetic variant, but we would have to kill them to get it, we would all recoil in horror. Why do we not flinch at the production of stem cells? I suppose it’s because a “blob of cells” simply doesn’t look human. In the end, though, looks aren’t everything, and you have to wager. You cannot claim ignorance; what you may be supporting has the possibility of being murder. Is it worth the lebensraum?

Stem cell research in NC

My bishop today asked North Carolina Catholics to contact their legislators regarding a bill supporting embryonic stem cell research that is making its way through the State House.

Here’s my contribution:

Dear Representative X,

As one of your constituents, I recently discovered that the State House is considering the “Stem Cell Research Health and Wellness Act,” HB 1837, which has been recently sent to the Appropriations Committee on which you serve. I would like to point out two areas in particular for your consideration as your committee considers this bill: the failure of this bill to adequately address ethical concerns about embryonic stem cell research, and the lack of support for other kinds of stem cell research which avoid the insurmountable ethical problems with embryonic research.

The bill as currently written would make it state policy that embryonic stem cell research could be conducted only on cells derived from “excess” embryos donated after in vitro fertilization treatment. On its surface, this appears to be an admirable solution. However, it does not address the primary ethical concern that many of your constituents have with such research: that it destroys a human embryo. Whether created for the purpose of stem cell research or for in vitro fertilization does not change the basic fact that embryos are destroyed to produced embryonic stem cells. If you consider an embryo to be a human life, this can never be condoned, even if miraculous treatments be generated as a result.

Our legislature could, however, endorse and fund research designed to circumvent this problem. Researchers at Wake Forest University School of Medicine, for example, have derived cells with many of the properties of embryonic stem cells from amniotic fluid. With the support of our state, these scientists and many others like them may generate ways to produce cells with many, if not all, of the benefits of embryonic stem cells without destroying embryos in the process. In addition, adult-derived stem cell research shows great promise in medical therapeutics. By focusing on areas of research that do not contain ethical pitfalls, we would set an example for the rest of the country to follow.

I acknowledge that my requests may sound like pleas to limit the creativity of scientists. But, as a molecular biologist by training, I have come to understand that what we can pursue must be tempered by what we ought to pursue. Embryonic stem cell research may be a panacea for all I know, but to save lives at the expense of countless others is a cure that we cannot risk. This policy debate turns on whether a human embryo is a human life. That is something that science cannot answer, so we should err on the side of caution.

If you’re in North Carolina, please go write your state representatives. It doesn’t take much time, and it just might make a difference.

For those who missed it

Someone, unbeknownst to me, taped my dissertation defense, and uploaded it to YouTube. If anyone wonders what we biochemists study, here you go:

You know you’ve been thinking about evolution too much when…

You read this headline on CNN, “Whales may have slipped into ocean,” and start thinking about what must have happened when the first primordial whale ancestor fell into the ocean and found that he could swim.

Cheap solar power?

Some guys from my parish might be on the verge of a huge breakthrough in solar power generation. They came up with the idea while having hours of conversation on the long drive to and from Mississippi delivering Hurricane Katrina relief supplies donated from our parish to folks in need. Now we’ll see if their prototype works next week…

Science and the Left

I was going to write a detailed blog about a short piece from The Corner on science, but I see that Dr. Pat Santy has beaten me to the punch. She’s spot on, as usual.

As a scientist and a member of the so-called “religious right,” I encounter the dogmatism of the Left daily. Woe be to anyone who questions the Magisterium on global warming (sorry, “anthropogenic climate change”–which covers their bases a little better), the wonders of embryonic stem cell research, or the supremacy of diversity. In all but methods of enforcement, it’s scarcely different from the Spanish Inquisition (at least the myth of it, anyway).

Quotes of the Day

We can account for this capacity of ours to know more than we can tell if we believe in the presence of an external reality with which we can establish contact. This I do. I declare myself committed to the belief in an external reality gradually accessible to knowing, and I regard all true understanding as an intimation of such a reality which, being real, may yet reveal itself to our deepened understanding in an indefinite range of unexpected manifestations.

– Michael Polanyi, Knowing and Being

…it has now turned out that modern scientism fetters thought as cruelly as ever the churches had done. It offers no scope for our most vital beliefs and it forces us to disguise them in farcically inadequate terms.

– Michael Polanyi, Personal Knowledge