Paul Nelson: the most interesting and significant paper we’ve read in years

Wow, check out this post by Paul Nelson over at Evolution News.

Excerpt:

Now, the paper I retrieved for my co-worker, entitled “The Levinthal paradox of the interactome,” Protein Science 20 (2011):2074-79, explains why the space of “being alive” is so much vastly smaller, and harder to find, than the space of being “not alive.” The paper is short (only six pages) and was written by two structural biologists, Peter Tompa of Vrije Universiteit in Brussels and George Rose of Johns Hopkins University, neither of whom is an intelligent-design advocate. But the paper’s arguments bear so strongly on the design debate, and represent so remarkable a challenge to widely held assumptions about (for instance) the origin of cells, that its effect promises to be far-reaching. As in, revolutionary.

[...]Tompa and Rose draw a number of lessons from their calculations. They argue, first, that any increase in biological realism will only make the Levinthal interactome paradox worse:

Of course, there are additional complicating factors such as alternative splicing, post-translational modifications, non-pairwise macromolecular interactions, incorrect complex formation that is adventitiously stable, and so forth. However, even neglecting such complications, the numbers preclude formation of a functional interactome by trial and error complex formation within any meaningful span of time. This numerical exercise…is tantamount to a proof that the cell does not organize by random collisions of its interacting constituents.But secondly, what they call “the most profound conclusion” from their analysis bears directly on widely held assumptions about the origin of life.

A highly enriched soup of proteins and nucleic acids will never form a functional cell, even if lipid bilayer membranes were provided to help these materials become organized. Indeed, the fully functional contents of a living cell, once the wall or membrane enclosing them has been breached (thus, killing the cell), move irreversibly in the direction of non-living chemistry. Humpty Dumpty, once he cracks, does not reconstitute, but enters what Tompa and Rose call the “zone of chaos,” never to return.

Tompa and Rose have sketched the theoretical basis for why this happens:

[O]ur calculations of combinatorial complexity [show] that the emergent interactome could not have self-organized spontaneously from its isolated protein components. Rather, it attains its functional state by templating the interactome of a mother cell and maintains that state by a continuous expenditure of energy. In the absence of a prior framework of existing interactions, it is far more likely that combined cellular constituents would end up in a non-functional, aggregated state, one incompatible with life…The spontaneous origination of a de novo cell has yet to be observed; all extant cells are generated by the division of pre-existing cells that provide the necessary template for perpetuation of the interactome.

Tompa and Rose spell out other implications of their analysis (e.g., for medicine and synthetic biology), but maybe we’ve piqued your curiosity enough already. This paper deserves your attention. As noted, for a close circle of us at Discovery and Biologic, it’s the most interesting and significant paper we’ve read in years.

Dr. Nelson’s post explains a bit more with pictures.

Filed under: News, Darwinism, Evolution, Information, Intelligence, Intelligent Cause, Intelligent Design, Interactome, Naturalism, Origin of Life, Protein, Protein Folding, Specified Complexity

Is intelligent design creationism? Dr. Stephen C. Meyer explains

Dr. Meyer explains the truth in the UK Telegraph.

Excerpt:

In 2004, the distinguished philosopher Antony Flew of the University of Reading made worldwide news when he repudiated a lifelong commitment to atheism and affirmed the reality of some kind of a creator. Flew cited evidence of intelligent design in DNA and the arguments of “American [intelligent] design theorists” as important reasons for this shift.

[...]Contrary to media reports, ID is not a religious-based idea, but an evidence-based scientific theory about life’s origins. According to Darwinian biologists such as Oxford University’s Richard Dawkins, living systems “give the appearance of having been designed for a purpose”.

But, for modern Darwinists, that appearance of design is illusory, because the purely undirected process of natural selection acting on random mutations is entirely sufficient to produce the intricate designed-like structures found in living organisms.

By contrast, ID holds that there are tell-tale features of living systems and the universe that are best explained by a designing intelligence. The theory does not challenge the idea of evolution defined as change over time, or even common ancestry, but it disputes Darwin’s idea that the cause of biological change is wholly blind and undirected.

[...]Consider an even more fundamental argument for design. In 1953, when Watson and Crick elucidated the structure of the DNA molecule, they made a startling discovery. Strings of precisely sequenced chemicals called nucleotides in DNA store and transmit the assembly instructions – the information – in a four-character digital code for building the protein molecules the cell needs to survive. Crick then developed his “sequence hypothesis”, in which the chemical bases in DNA function like letters in a written language or symbols in a computer code. As Dawkins has noted, “the machine code of the genes is uncannily computer-like”.

The informational features of the cell at least appear designed. Yet, to date, no theory of undirected chemical evolution has explained the origin of the digital information needed to build the first living cell. Why? There is simply too much information in the cell to be explained by chance alone.

The information in DNA (and RNA) has also been shown to defy explanation by forces of chemical necessity. Saying otherwise would be like saying a headline arose as the result of chemical attraction between ink and paper. Clearly, something else is at work.

DNA functions like a software program. We know from experience that software comes from programmers. We know that information – whether, say, in hieroglyphics or radio signals – always arises from an intelligent source. As the pioneering information theorist Henry Quastler observed: “Information habitually arises from conscious activity.” So the discovery of digital information in DNA provides strong grounds for inferring that intelligence played a causal role in its origin.

Thus, ID is not based on religion, but on scientific discoveries and our experience of cause and effect, the basis of all scientific reasoning about the past. Unlike creationism, ID is an inference from biological data.

It might be a good idea now to echo Meyer’s claim with something from the secular magazine Scientific American.

Excerpt:

As recently as the middle of the 20th century, many scientists thought that the first organisms were made of self-replicating proteins. After Francis Crick and James Watson showed that DNA is the basis for genetic transmission in the 1950s, many researchers began to favor nucleic acids over proteins as the ur-molecules. But there was a major hitch in this scenario. DNA can make neither proteins nor copies of itself without the help of catalytic proteins called enzymes. This fact turned the origin of life into a classic chicken-or-egg puzzle: Which came first, proteins or DNA?

RNA, DNA’s helpmate, remains the most popular answer to this conundrum, just as it was when I wrote “In the Beginning…” Certain forms of RNA can act as their own enzymes, snipping themselves in two and splicing themselves back together again. If RNA could act as an enzyme, then it might be able to replicate itself without help from proteins. RNA could serve as gene and catalyst, egg and chicken.

But the “RNA-world” hypothesis remains problematic. RNA and its components are difficult to synthesize under the best of circumstances, in a laboratory, let alone under plausible prebiotic conditions. Once RNA is synthesized, it can make new copies of itself only with a great deal of chemical coaxing from the scientist. Overbye notes that “even if RNA did appear naturally, the odds that it would happen in the right sequence to drive Darwinian evolution seem small.”

The RNA world is so dissatisfying that some frustrated scientists are resorting to much more far out—literally—speculation. The most startling revelation in Overbye’s article is that scientists have resuscitated a proposal once floated by Crick. Dissatisfied with conventional theories of life’s beginning, Crick conjectured that aliens came to Earth in a spaceship and planted the seeds of life here billions of years ago. This notion is called directed panspermia. In less dramatic versions of panspermia, microbes arrived on our planet via asteroids, comets or meteorites, or drifted down like confetti.

Naturalists who resort to aliens are still implicating intelligent causes to explain life, ironically enough.

Please share and re-tweet this post, because not understanding intelligent design is a mistake that virtually everyone in the mainstream media makes when discussing this topic. I would bet $100 that there is not a single journalist in the mainstream media who can define intelligent design by citing a peer-reviewed article or academic textbook, and then give an example of where proponents of ID think that intelligent design is evident in nature.

Related posts

• Stephen C. Meyer and Keith Fox debate intelligent design and evolution
• What is intelligent design? Dr. Stephen C. Meyer explains in this video
• Theologian R.C. Sproul interviews Stephen C. Meyer
• Stephen C. Meyer explains the evidence for the Big Bang
• Signature in the Cell – a review of the first year
• Origin of biological information in the simplest replicating cell 
• Sudden origins of all major body plans in the 3-5 million year Cambrian explosion

Documentaries on intelligent design

Here are the 2 playlists:

• Unlocking the Mystery of Life (12 videos in a playlist)
• The Privileged Planet (12 videos in a playlist)

Filed under: Polemics, Biochemistry, Biological Information, Biology, Complex, Darwinism, Evolution, Functional, God, ID, ID Theory, Information, Intelligent Cause, Intelligent Design, Perfect, Sequence, Specified, Specified Complexity, Stephen C. Meyer, Stephen Meyer, Theism

William Dembski replies to theistic evolutionist Darrel Falk

William Dembski is much nicer than I am, and so he takes theistic evolutionist Darrel Falk to task very gently.

Excerpt:

In the paper to which Falk responds, I lay out four non-negotiables of Christianity as well as four non-negotiables of Darwinism. Falk and I are united on the four non-negotiables of Christianity, but differ a bit on those of Darwinism. The four non-negotiables of Darwinism that I list are common descent, natural selection, human continuity, and methodological naturalism. Because Falk and I both reject Darwinism, there’s quite a bit of overlap in how we view these four non-negotiables. Nonetheless, I think it will help readers of my essay and Falk’s response to clarify some of our differences here, subtle though they may be.

With regard to common descent, I agree with Falk that God could have brought about life by means of a large-scale form of evolution that links all organisms to a common ancestor. That said, I don’t accept common descent. I think the scientific evidence is against it (for my reasons, see my book The Design of Life, coedited with Jonathan Wells). Also, even though common descent may be acceptable in broad theological terms, I think it is problematic exegetically with regard to Scripture. Simply put, I think you’re going to have a hard time getting large-scale evolution out of Scripture or rendering the two compatible.

With regard to natural selection, Falk appears to accept that this is the principal mechanism by which organisms are brought into existence successively by an evolutionary process. At the same time, Falk does not want to see natural selection as devoid of purpose but rather as a mechanism through which God is able to accomplish his purposes. But in that case, in what sense is selection “natural”? Is Falk’s view of natural selection, when viewed as a scientific hypothesis, any different from Richard Dawkins’s? And if their views, taken scientifically, are the same, what is the evidence for the creative power of this mechanism?

Falk extols “God’s marvelously ordinary processes of creation: ordinary because they follow his natural laws so faithfully, marvelous because they have resulted in a world of complex and beautiful life.” In my view, the word “ordinary” is entirely out of place here. As I’ve argued with Robert Marks in a paper titled “Life’s Conservation Law,” even if life is the result of an evolutionary process driven by natural selection, it would have to be a form of selection finely tuned by an environment that is itself finely tuned (see our contribution to The Nature of Nature, edited by Bruce Gordon and me — the paper in question is available online here).

Falk takes exception to my thinking it “odd” that God would create by natural selection, and thus by a process that gives no evidence of intelligence. And he rejects my charge that such a method of creation “occludes” God’s activity. Falk, echoing Psalm 19, proclaims that all aspects of creation bespeak God’s handiwork and glory. Now let me concede that “oddness,” in the sense of what appears odd to us very limited human beings with our very limited vantages on the world, is not a good criterion for determining what God would and wouldn’t do. Still, it hardly seems that God is mandated to create via a process that provides no evidence of his creative activity — and nowhere does Falk admit that God provides actual evidence of himself in creation (at best he allows that nature provides “signposts” — but what exactly are these signs? who is reading them? why should we take them as pointing to God?). Moreover, for Falk to echo the psalmist is hardly an argument for the world proclaiming God’s handiwork and glory, because many atheistic evolutionists will deny Falk’s confident affirmations of divine perspicuity.

I’ve seen this directly. I recall posting on my blog a gorgeous picture of wildflowers, hinting at the wonders of God’s creation, and seeing comments by atheistic evolutionists who dismissed it as merely “sex” run amuck. Thus, when Falk echoes Psalm 19, what more is he doing than giving expression to his own faith? Indeed, what more is he saying to atheists than merely “I see God’s hand in all of this and you don’t — you’re blind and I see.” Perhaps faith has given him sight that atheists lack. But in that case, how can it be claimed that God is not occluding his activity in nature? God, as omnipotent, can certainly make his existence and presence known to even the most ardent atheist – we can all imagine flamboyant enough miracles that would convince anyone.

Still, the more interesting question here is whether there is a rational basis for Falk’s faith that is grounded in the order of nature. ID, in finding scientific evidence of intelligence in nature, says there is. Falk, along with BioLogos generally, denies this. But in that case, how can he avoid the charge that the faith by which he sees God’s handiwork is merely an overlay on top of a nature that, taken by itself, is neutral or even hostile to Christian faith? Note that I’m not alone in thinking it odd that God would create by natural selection. Many atheistic evolution see evolution as a brutal and wasteful process that no self-respecting deity would have employed in bringing about life. Jerry Coyne, Richard Dawkins, and the late Stephen Jay Gould were united on this point.

There are three things that annoy me greatly and cause me to lose my temper. One of those things is theistic evolution, which to me is essentially atheism with unnecessary subjective verbiage added on top. My advice for discussing evolution with a theistic evolutionist is to never, ever allow them to talk about anything about religion. Just focus on the science and what the science can show. Anything else they say about their personal feelings and beliefs that isn’t scientific is just an attempt to deceive the listener. Never ever allow a theistic evolutionist to talk about possibilities – what God could or could not do. That is irrelevant to the discussion because it is outside of what science can show.

The central question when discussing evolution is this: can we use the ordinary methods of science, just as Dembski’s method for recognizing design based on specified complexity, in order to detect intelligent causes? Atheists and theistic evolutionists are united on the answer: NO. Darrel Falk and Richard Dawkins agree that there is no way for science to show that an intelligence is needed to explain some effect in nature, because natural mechanisms can do the job with the probabilistic resources available. Design theorists think that you can infer that intelligence is the best explanation – for some effects that pass the mathematical tests.

So you have atheists and theistic evolutionists on one side, and intelligent design people on the other side.

Filed under: Polemics, Atheism, Biologos, Biologos Foundation, Darrel Falk, Deception, Evolution, Intelligence, Intelligent Cause, Intelligent Design, Metaphysical Naturalism, Methological Naturalism, Naturalism, Nature, Science, Smokescreen, Theistic Atheism, Theistic Evolution, William Dembski

James Shapiro: an honest naturalist admired by ID supporters

As a pro-ID person, I am naturally suspicious of naturalistic scientists. They always say that material forces and chance can explain every single thing in nature, and there are no effects in nature that are best explained by an intelligence. Well, some in nature are best explained by unintelligent causes alone. But I think there are some effects in nature that are more like meaningful sentences or meaningful computer code – and that those are best explained as a result of an intelligence.

One effect in nature where that is clearly analogous to language/code is the biological information in proteins and in DNA. ID people keep telling naturalists that functional information in the first living cell cannot be generated by blind forces in the time available in Earth’s history. But naturalists always seem to diminish the problem and say that blind forces can create information. Well, most naturalists do.

Here’s one who doesn’t, though: James Shapiro. Dr. Shapiro is a microbiologist and a professor in the Department of Biochemistry and Molecular Biology at the University of Chicago. His undergraduate is from Harvard University.

He is very frank about how much naturalistic mechanisms can explain when it comes to the origin of life.

Excerpt: (links removed)

Around here we have a lot of respect for microbiologist James Shapiro, who had the guts and integrity to come over to ENV recently and spar over evolution with William Dembski, Doug Axe and Ann Gauger. Besides having a new book out that details his own dissatisfactions with conventional Darwinian evolutionary theory and that champions a provocative alternative view, Shapiro also blogs at the Huffington Post.

He continues to win our admiration, while evoking some poignancy as well.

In one post that got a fair amount of attention he had some sensible things to say to fellow evolutionists. Rather than hide behind “absolutist statements like ‘all the facts are on my side,’” as his University of Chicago colleague Jerry Coyne does, Shapiro advocates “active engagement” with Darwin critics. Enter into the controversy over evolution, he says, rather than pretend it doesn’t exist.

Perhaps even teach about it? Shapiro doesn’t go that far, but the permissibility of admitting the truth even to young people would seem to follow from his premise:

We need to demonstrate that evolution science is alive and well, as well as show how it is making remarkable progress through the application of molecular technologies — even though it does not have all the answers.

To the thoughtful scientist whose job is to uncover natural processes, this is surely a better way of advocating the scientific method than dogmatically asserting that we found all the scientific principles we need in centuries past.

Evolution supporters, he counsels, should admit they don’t have all the answers, including on a key question like the origin of life. In a remarkably candid statement, he writes:

In order to be truthful, we must acknowledge that certain questions, like the origins of the first living cells, currently have no credible scientific answer. However, given the historical record of science and technology in achieving the “impossible” (e.g., space flight, telecommunications, electronic computation and robotics), there is no reason to believe that unsolved problems will remain without naturalistic explanations indefinitely.

I don’t mind a naturalist who is honest about what we do and do not know.

More:

Surely there’s room to question Shapiro on why our ability to fly to the moon gives grounds for certainty that a purely “naturalistic” explanation of life’s origin will be forthcoming. Space flight is an accomplishment enacted in a material world but, more to the point, it’s a triumph of engineering — aka, intelligent design. It could not be accomplished at all without the direction of purposeful designers.

But note the implicit agreement with Stephen Meyer (Signature in the Cell: DNA and the Evidence for Intelligent Design): materialist explanations for “the origins of the first living cells” have, to date, indeed all miserably failed. In his book, Meyer shows how the evidence points persuasively to the action of some source of intelligent agency. Under the circumstances, if Shapiro is right, that would make intelligent design by default the lone viable theory of life’s origin.

Apart from gesturing to the advance of technology as a reason for keeping faith in naturalism, it would be interesting to know how Shapiro responds to Meyer’s case.

James Shapiro has debated with pro-ID people before. I have a set of audio cassettes from WAY WAY BACK which contains a debate between Robert Shapiro and Walter Bradley, whose lectures on the evidence for design in nature I have featured before. Although some naturalists like Richard Dawkins run away from debates, some, like Shapiro do not. And that’s good for science.

If you want to read a great book on what intelligent design is really about, you really need to read Signature in the Cell. This is the best on the argument for intelligent design in nature from the evidence of proteins and DNA. We are still waiting for a really great pro-ID book on the Cambrian explosion, the sudden origin of all major body plans 540 million years ago – but maybe Dr. Meyer is already working on that now, since he published a peer-reviewed paper on it in a science journal, a while back.

Filed under: Commentary, Chemical Evolution, DNA, Information, Intelligent Cause, Intelligent Design, James Shapiro, Naturalism, Origin of Life, Protein

What is the case for intelligent design?

Everyone knows that blog posts and Java programs are the result of an intelligent agent, who arranges symbols into long, improbable sequences that have function. I write blog posts and I write Java programs, and both are the result of my intelligence sequencing letters by typing into my keyboard. Now what should we infer if we look at the universe and we see similar sequences that have functions?

This article from Evolution News explains how a person can look at the universe, find functional sequences of symbols, and infer a designer. (H/T J Warner Wallace of Please Convince Me)

Excerpt:

Intelligent design is a scientific theory that holds some aspects of life and the universe are best explained by reference to an intelligent cause. Why? Because they contain the type of complexity and information that in our experience comes only from intelligence.

As a result, intelligent-design theorists begin by studying how intelligent agents act when they design things. Intelligence is a process, or a mechanism, which we can observe at work in the world around us. Human designers make a great dataset for studying how intelligent agency works.

When we study the actions of humans, we learn that intelligent agents produce high levels of complex and specified information (CSI). Something is complex if it’s unlikely, and specified if it matches some independent pattern. William Dembski and Stephen Meyer explain that in our experience, only intelligent agents produce this type of information:

• “[T]he defining feature of intelligent causes is their ability to create novel information and, in particular, specified complexity.” (William A. Dembski, No Free Lunch: Why Specified Complexity Cannot Be Purchased without Intelligence, p. xiv (Rowman & Littlefield Publishers 2002).)
• “Agents can arrange matter with distant goals in mind. In their use of language, they routinely ‘find’ highly isolated and improbable functional sequences amid vast spaces of combinatorial possibilities.” (Stephen C. Meyer, “The Cambrian Information Explosion,” inDebating Design (edited by Michael Ruse and William Dembski; Cambridge University Press 2004).)

Meyer further explains that in our experience, only intelligence produces high levels of CSI:

[W]e have repeated experience of rational and conscious agents — in particular ourselves — generating or causing increases in complex specified information, both in the form of sequence-specific lines of code and in the form of hierarchically arranged systems of parts. … Our experience-based knowledge of information-flow confirms that systems with large amounts of specified complexity (especially codes and languages) invariably originate from an intelligent source, from a mind or personal agent.” (Stephen C. Meyer, “The origin of biological information and the higher taxonomic categories,” Proceedings of the Biological Society of Washington, Vol. 117(2):213-239 (2004).)Thus, in our experience, high levels of complex and specified information — such as in codes and languages — arise only from intelligence. By assessing whether natural structures contain the type of complexity — high CSI — that in our experience comes only from intelligence, we can construct a positive, testable case for design.

And what happens when we study nature? Well, the past 60 years of biology research have uncovered that life is fundamentally based upon:

• A vast amount of complex and specified information encoded in a biochemical language;
• A computer-like system of commands and codes that processes the information.
• Molecular machines and multi-machine systems.

But where in our experience do things like language, complex and specified information, programming code, or machines come from? They have one and only one known source: intelligence.

One of the strangest things about intelligent design is how many people use the phrase without even being able to define it or point to an academic book or paper where the concept is defined.  There are several places where information is found in nature: the origin of life (“biological information”) and Cambrian explosion (“higher taxonomic categories”) are two of them. There is no known naturalistic method of producing large amounts of functional information in these two areas. But we know that human intelligence are capable of creating the sequences – we’ve seen it done. Intelligent design is the view that functional information sequences in nature are the result of intelligence. That’s all we know that can produce it.

Filed under: News, Biochemistry, Biological Information, Biology, Complex, Darwinism, Evolution, Functional, God, ID, ID Theory, Information, Intelligent Cause, Intelligent Design, Perfect, Sequence, Specified, Specified Complexity, Theism