Biologic Institute

Origin of life research has problems, and here’s why. DNA carries the information necessary to build proteins. It performs no chemistry and builds no cellular structures by itself. Rather, the information in DNA must be translated into proteins. But there is no direct way to convert a given DNA sequence into a protein sequence—no direct chemical association between DNA nucleotides and amino acids. Some sort of decoding mechanism is needed to translate the information encoded in DNA into protein.

That decoding mechanism involves a whole host of enzymes, RNAs and regulatory molecules, all functioning as an elegant, efficient, accurate and complicated system for copying and translating the information in DNA into a usable form. (For a comprehensive and engaging description of how information is processed in the cell, and how this process has been discovered, see Stephen C. Meyer’s Signature in the Cell [1].)

The problem is, this decoding system is self-referential and causally circular. Explaining its origin becomes a chicken and egg problem. Building the machinery that translates DNA into protein requires the prior existence of DNA, RNA and protein, all three. This should give us pause, because we have no naturalistic explanation for problems involving causal circularity. more…

Scientists employ different rhetorical strategies to accomplish different things. That shouldn’t be surprising, perhaps, but for some it is. The reason is that while the public is very familiar with rhetorical shiftiness in some occupations, they tend to see only one side of science—the confident, assertive, authoritative, we-know-what-we’re-talking-about side. Science-speak often comes across with a hint of arrogance, but since science itself depends on the goodwill of the public for its very existence, it usually corrects itself on those occasions when it oversteps its bounds.

There are a few peculiar exceptions though, where what amounts to little more than propaganda is excused in the name of academic freedom. It’s regrettable, but it happens, and the guilty institutions become known for it.

Since Oxford University is one of them (as evidenced by the fact that I don’t need to name anyone), there is particular satisfaction in bringing to light some of the hidden rhetoric from that institution. Please don’t misunderstand me. I’m not suggesting that anything that follows is in any way secretive. I’m simply suggesting that some needs—like getting grants and hiring people to work under those grants—call for a frank statement of what isn’t known, whereas the messages intended for the general public tend to emphasize or even exaggerate what is known. more…

In August of 2004 I received an email inquiry from plant biologist Art Hunt. He had written a draft for a blog piece aimed at reviewing a research article of mine that had just appeared in the Journal of Molecular Biology [1], and he wanted to know whether he had understood my work correctly. He clearly aimed to refute claims that were beginning to surface that my paper supported intelligent design, but he also wanted to make sure he wasn’t misconstruing my work in the process. He didn’t expect me to oblige—“I will understand if you decline; in fact, I would probably do the same…”—but I did.

His summary of the experiments I reported in the JMB paper was largely correct, though his understanding of my analysis was off in several respects. As a result, many of the conclusions he drew were, in my judgment, not well grounded. I gave him feedback to this effect, but since it was a blog entry rather than a peer-reviewed scientific publication, I wasn’t particularly concerned to see the final version, or to respond to it.

Two things have happened since then. One is that my 2004 JMB paper has, as Hunt predicted, been cited in support of intelligent design in several prominent places, and the other is that Hunt’s finished blog piece [2] has become the favored argument against using my paper in support of ID. more…

I’ve argued that Darwin’s mechanism probably isn’t powerful enough to produce proteins with fundamentally new structures. [1] If that’s correct it’s a serious problem for the old theory, because we know that new protein structures—new folds, as they are known—appeared well over a thousand times in the history of life. If Darwinism doesn’t account for these then whatever else it may be, it isn’t a complete theory of biological origins.

New protein functions don’t always call for completely new structures, though. There are numerous examples of proteins that use very similar structures to perform tasks that are genuinely distinct, meaning that one cannot replace the other. Recognizing this, Ann Gauger and I set out to test how well Darwin’s mechanism works on this more modest scale where things that already work are adjusted to work differently. more…

If you search the current issues of professional science journals, I doubt you’ll find any papers titled “The Moon Orbits the Earth” or “Copper Conducts Electricity.” Assertions like these would work as section headings in an elementary science textbook, but no scientist would consider them newsworthy, for the simple reason that they aren’t.

Things are different in evolutionary biology, though. Here is a field that somehow never outgrew the need to reiterate its most basic tenets, as though its practitioners never had enough confidence in them to let them stand on their own two feet.

I think it has to do with evidence-envy. If someone were to claim not to believe in gravity or electricity, we could devise any number of ways to impress upon them the realities to which those words refer. No stern lecturing. No scolding. No indoctrinating. Just a simple demonstration followed by the words, “We call that electricity.” Even dogs and cows seem to get it. more…

In the recent past, several papers have been published that claim to demonstrate that biological evolution can readily produce new genetic information, using as their evidence the ability of various evolutionary algorithms to find a specific target. This is a rather large claim.

It has thus fallen to others in the scientific or engineering community to evaluate these published claims. How well do these algorithms model biology? How exactly was the work done? Do the results make sense? Are there unexamined variables that might affect the interpretation of results? Are there hidden sources of bias? Are the conclusions justified or do they go beyond the scope of what has been shown? more…

I was among the speakers at an event held at Southern Methodist University last week [1]. The purpose was to give students and others a glimpse of the growing scientific case against Darwin’s theory, so the talks were tailored to a non-technical audience.

Faculty members were welcome too, of course, and I’m told that a few were in attendance. Attesting to this, their denouncements began surfacing online shortly afterward [2]. It’s all very familiar. When you persist in challenging a cherished tradition like Darwinism, you come to expect this kind of reaction.

Some people are bothered by the craziness that surrounds the Darwin-v-Design controversy, but I take a more relaxed view. Don’t get me wrong. If I thought there were nothing but craziness, I’d be as frustrated as anyone. But serious science is being done on both sides of the debate, and that should give us confidence that a truer picture of biology will become visible as the smoke clears. more…

Steve Meyer recently gave a lecture summarizing the arguments put forward in his book Signature in the Cell [1] to an audience of 1,400 (including me) at Biola University. [2] After Steve sat down, two of his critics, Steve Matheson and Arthur Hunt, were invited to put their questions to him.

Matheson and Hunt both referred to my work and to Meyer’s use of it, Matheson having since posted his points on his blog. [3] As is often the case when complex subjects are debated in front of an audience, things got a bit muddled.  I stood up at one point with the intent of commenting but wasn’t able to get the attention of the moderator, so I’ll comment here instead. more…

It’s no secret that the scientific establishment is decidedly against not just the idea of intelligent design but also the idea of debating that idea.  They just wish the whole subject would go away.  That being the case, most establishment-minded scientists will, I suspect, thoroughly disapprove of BIO-Complexity, a new science journal that positively welcomes the scientific debate [1].

Now, I usually sympathize with those who want troublemakers to stop making trouble.  Trouble has a bad name for good reasons.  But on the other hand, we often find ourselves looking back with gratitude at certain troublemakers of the past—people who persisted in shaking things up, usually at great personal cost, until their cause won the day.

It seems to me that the trouble ID has brought on the science academy is of this more noble kind.  Like all scientific controversies, this one is about ideas.  And while ideas can be very powerful, they only become dangerous when no one is allowed to critique them openly.  Where scrutiny is encouraged, the worst that an idea can be is false.  Where it is forbidden, things can get much worse (as history shows).

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Reading Stuart Kauffman’s book At Home in the Universe some fourteen years ago, I encountered the following:

I hope to persuade you that life is a natural property of complex chemical systems, that when the number of different kinds of molecules in a chemical soup passes a certain threshold, a self-sustaining network of reactions—an autocatalytic metabolism—will suddenly appear. Life emerged, I suggest, not simple, but complex and whole, and has remained complex and whole ever since… The secret of life, the wellspring of reproduction, is not to be found in the beauty of Watson-Crick pairing, but in the achievement of catalytic closure. [1]

When chemicals react, they produce different chemicals. So the idea here—call it Kauffman’s conjecture—was that mixtures with a sufficient number of different chemicals are bound to give rise to local compositions that continually replenish themselves through a self-catalyzed network of chemical reactions.  Those special compositions would typically differ from the original mixture, but since they make more of themselves, they should be able to ‘grow’ by establishing themselves repeatedly in local pockets.  The ability to propagate in this way, if proven, would be something like reproduction, only at the low level of chemical composition rather than at the high level of organismal form. more…