Evolution News & Views

In the Beginning, Before There Was RNA, There Was...TNA?

2012-02-03T22:26:22Z

Where did life come from? There are two kinds of answers to the question. One looks at the construction of organisms and says that all of the components of the organism from its DNA to its body parts were designed with the end goal, the organism, in mind. The other answer looks at the construction of an organism, and says that all of the parts and pieces came first and through selection pressure and trial and error, a functioning organism emerged.

The first answer builds the organism from the top down with its overall design in mind from the start, while the second answer builds the organism from the bottom up.

Origin-of-life research is predominantly of the bottom-up variety, with the RNA-world scenario being the favorite origins theory among scientists at the moment. If you were to break an organism down to its component parts, you'd find that organisms are composed of genetic material. The difficulty in determining the origin this material, such as RNA and DNA, is that RNA and DNA are needed to make proteins and proteins are needed to make DNA and RNA. Therefore the first genetic material must have been made by a completely different process.

Enter the ribozyme, an RNA molecule that behaves like an enzyme (proteins). The function of ribozymes has given a glimmer of hope that perhaps RNA, rather than DNA, came first. However the ribozyme has limited functionality and does not solve many of the problems that go along with the RNA-world scenario.

The most pressing such problem is the relative chemical instability of RNA molecules. Unlike DNA, whose chemical bases are paired and securely tucked into the interior of a helical structure while the chemically robust ribose phosphates remain exposed on the surface, RNA is single-stranded with the bases exposed to the environment. RNA does have three-dimensional structures that provide some chemical stability, but it is still too delicate for most early-Earth environment models.

True to their own evolutionary thinking, some scientists have speculated that there was a precursor to the RNA molecule, a chemical transitional species, if you will. Ideally, this molecule would have been simpler than the RNA molecule, and therefore easier to synthesize in an early-Earth environment. Yet it would have many of the characteristics of genetic material, such as nucleotide base pairing and a three-dimensional structure with functional activity. Yu et al. report in an article in Nature that threose nucleic acid (TNA) is a viable contender as a pre-RNA transitional molecule.

TNA molecular structure. The TNA backbone is composed of a threose sugar (4 carbon), while DNA and RNA has a ribose sugar (5 carbon). The molecular picture is available here. In TNA, the phosphate groups are bound to the 2 and 3 positions rather than the 3 and 5 positions as in DNA and RNA.

TNA is considered a simpler molecule because it has one fewer carbon, and could theoretically form from two 2-carbon segments. However it is highly speculative to call that an "easier" synthesis than the formation of a ribose sugar. It would likely occur through an aldehyde reaction, similar to the typical ribose synthesis. Since the purine and pyrimidine nucleotide bases would remain the same, the same chemical problems are present. Amines are highly reactive and the synthesis of sugars generally requires an environment that would be prohibitive for nucleotide production. (See Signature in the Cell by Stephen C. Meyer, pp, 301-304, for an excellent explanation of the problems with RNA world chemistry).

The authors had trouble working with polymerases that convert DNA to a TNA library in places where multiple guanine nucleotides were present. They therefore removed GGG strands in DNA, in an effort to avoid stalling the process:

Although the L2 library generates TNA polymers that lack cytidine, we reasoned that this was not a significant concern as cytidine may not have been present in the first genetic material due to its tendency to undergo spontaneous deamination...Furthermore, it has been shown that ribozymes missing cytidine can be generated by in vitro evolution, demonstrating that a three-letter genetic alphabet can still retain the ability to fold and function.

Additionally, inorganic phosphate needs to react (usually with alkyl alcohols) to form a phosphate ester, which is not necessarily any more or less difficult with threose as opposed to ribose. So switching from a 5-carbon sugar to a 4-carbon sugar does not remove many of the chemistry barriers to the RNA world hypothesis.

TNA tertiary structure. TNA does make a helical-type structure, and it can form tertiary structures with functional activity. Its bases can base-pair with itself or with another RNA molecule, allowing for possible information transfer between different genetic systems.

TNA activity. TNA can interact with a few of the same proteins that interact with DNA. Using molecular evolution technology, where possible functional segments of TNA are selected from a random set of synthesized TNA segments, the authors found a few segments that, indeed, demonstrated functional specificity:

The fact that TNA does not appear to be limited in this regard suggests that it may be possible to isolate novel TNA enzymes from pools of random sequencing using in vitro evolution. We suggest that selections of this type could be used to further examine the fitness of TNA as an RNA progenitor in a hypothetical TNA world.

Cut to the chase: Is TNA a precursor to RNA? Unfortunately, there is no way to know.

This experiment assumes the very thing it is trying to prove. The scientists here are assuming that an RNA-first world must have occurred, but there are prohibitive problems with this model, so they select one problem, the complexity and instability of RNA, and seek a solution by finding a simpler molecule that has many similar properties.

TNA is an interesting molecule in and of itself, but there is no indication of how it fits into the grand scheme of an origin-of-life scenario, and there is no way to know if it actually was present in the early Earth (or even in nature) or if it is just an interesting laboratory synthesis.

Some questions that remain to be answered: How would TNA be synthesized in an early-Earth environment? Heat vents, ice crystals, concentrated pools, magma, in an oxidizing or a reducing environment? Is TNA more stable than RNA? If so, is it stable enough not to decompose under harsh environmental conditions? How did TNA eventually convert into RNA or DNA and is this synthesis prohibitively complex for an early-Earth scenario? If the early Earth only had three bases, how did it eventually come up with a fourth? And, most importantly, how did the relationship among DNA, mRNA, tRNA, and proteins evolve and where does TNA figure in that process?

It seems that much of the origin-of-life research going on now suffers from a kind of myopia where researchers hone in on solving one particular problem without contextualizing their solution. This is like trying to plan a road trip to London, Paris, New York, and Seattle using only photographs of each of the cities. You need to know how each of these cities is connected in order to travel from one to another, but that's a much more difficult task than merely acknowledging that they exist.

Stop Us If You've Heard This One Before

2012-02-03T21:23:34Z

]]> So this astronomer walks into a bar and says, "It's the holy grail of exoplanet research..." You can pretty much fill in the rest of the joke yourself.

Holy grails are supposed to be rare and precious things, but hardly a month goes by lately when the science media fail to breathlessly report the discovery of a new planet, in some star's "habitable zone," that might hypothetically be capable of supporting life. Not, of course, that there's any positive evidence of life actually existing there or anywhere but our own planet.

This month the newly discovered exoplanet is the romantically named GJ 667Cc, some four and a half times the mass of Earth -- a "super-Earth" -- and orbiting one of three stars in a triple solar system only 22 light years from us. A member of the team that found it, Steven Vogt at U.C. Santa Cruz, enthused about his discovery:

It's the holy grail of exoplanet research to find a planet around a star orbiting at the right distance so it's not too close where it would lose all its water and boil away, and not too far where it would all freeze. It's right smack in the habitable zone -- there's no question or discussion about it. It's not on the edge, it's right in there.

A co-author on the study, Guillem Anglada-Escudé of the Carnegie Institution for Science, said: "This planet is the new best candidate to support liquid water and, perhaps, life as we know it."

The "best" yet! Did you hear that? For a sober view, we asked an expert on planet-habitability, astronomer Guillermo Gonzalez. He explained:

Here are a couple important points about this particular system. First, the planets orbit an M dwarf star. M dwarfs provide very poor environments for life. They show erratic brightness fluctuations, and they produce powerful flares with dangerous radiation. Planets in the habitable zone of an M dwarf will spin down fairly quickly, leading to a "tidally-locked" situation that leads to all sorts of problems.

Second, terrestrial planets more massive than Earth are likely less habitable than Earth for several reasons. For instance, they will have less surface relief, which makes it less likely they will have dry land.

Don't you get the impression that Gonzalez probably spoils every party he shows up at? The excitement about GJ 667Cc seems premature, to say the least. It's a shame, though not much of a surprise.

Surveying Peer-Reviewed Pro-Intelligent Design Papers by Wolf-Ekkehard Lönnig

2012-02-03T18:39:19Z

Among the more prolific authors of pro-intelligent design (ID) peer-reviewed articles in our updated listing is Wolf-Ekkehard Lönnig, a geneticist who recently retired from the Max Planck Institute for Plant Breeding Research in Germany. We've discussed Lönnig's work here on Evolution News & Views in the past.

Lönnig's publications show that experimental research on plant breeding can have positive implications for intelligent design. A 2007 paper by Lönnig and three co-authors in Bioremediation, Biodiversity and Bioavailability attempted to trace the evolutionary history of two taxa of flowering plants that evolutionary biologists believe to be closely related. The authors used mutagenesis experiments in an attempt to cause the plants' traits to revert to a more "primitive" form. They were unable to do so. Citing the work of Michael Behe, their explanation for their observations supports a basic tenet of intelligent design:

Most new characters arise, not by simple additions but by integration of complex networks of gene functions rendering many systems to be irreducibly complex (Behe 1996, 2004; for a review, see Lönnig 2004), such systems cannot -- in agreement with Dollo's law -- simply revert to the original state without destroying the entire integration pattern guaranteeing the survival of a species.

The article favorably cites works from ID-friendly scientists such as Doug Axe's articles in Journal of Molecular Biology; Behe's Darwin's Black Box; Behe and Snoke's 2004 article in Protein Science; David Berlinski's writing in Commentary; William Dembski's books The Design Inference, No Free Lunch, and The Design Revolution; and Stephen C. Meyer's article in Proceedings of the Biological Society of Washington, and his work in Darwinism, Design, and Public Education; and also cites pro-ID entries from Debating Design.

Another paper by Lönnig in Floriculture, Ornamental and Plant Biotechnology also cites Darwin's Black Box and other articles by Michael Behe about irreducible complexity, as well as the work of Dembski and Meyer, and notes the "limits of the origin of species by mutations." The paper continues:

All the models and data recently advanced to solve the problem of completely new functional sequences and the origin of new organs and organ systems by random mutations have proved to be grossly insufficient in the eyes of many researchers upon close inspection and careful scientific examination.

This 2007 chapter on carnivorous plants by Lönnig and Becker in the John Wiley & Sons volume Handbook of Plant Sciences notes that "it appears to be hard even to imagine the clearcut selective advantages for all the thousands of postulated intermediate steps in a gradual scenario, not to mention the formulation and examination of scientific (i.e. testable) hypotheses for the origin of the complex carnivorous plant structures examined above." They go on to favorably cite the work of Michael Behe, stating:

The reader is further invited to consider the following problem. Charles Darwin provided a sufficiency test for his theory (1859, p. 219): "If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down." Darwin, however, stated that he could "not find such a case." Biochemist Michael J. Behe (1996, p. 39) has refined Darwin's statement by introducing and defining his concept of "irreducible complexity", specifying: "By irreducibly complex I mean a single system composed of several well-matched interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning." Some biologists believe the trap mechanism(s) of Utricularia and several other carnivorous plant genera (Dionaea, Aldrovanda, Genlisea) come at least very near to "such a case" of irreducible complexity.

Finally, Lönnig published a research paper in 2010 titled "Mutagenesis in Physalis pubescens L. ssp. floridana: Some Further Research on Dollo's Law and the Law of Recurrent Variation." The article cites skeptics of neo-Darwinism such as Michael Behe and "the almost 900 scientists of the Scientific Dissent from Darwinism," noting:

Many of these researchers also raise the question (among others), why -- even after inducing literally billions of induced mutations and (further) chromosome rearrangements -- all the important mutation breeding programs have come to an end in the Western world instead of eliciting a revolution in plant breeding, either by successive rounds of selective "micromutations" (cumulative selection in the sense of the modern synthesis), or by "larger mutations" ... and why the law of recurrent variation is endlessly corroborated by the almost infinite repetition of the spectra of mutant phenotypes in each and any new extensive mutagenesis experiment (as predicted) instead of regularly producing a range of new systematic species...

Lönnig's study focuses on the origin of a particular trait found in some angiosperms, where longer sepals form a shelter for developing fruit called inflated calyx syndrome, or "ICS." According to the paper, phylogenetic data indicate that under a neo-Darwinian interpretation, this trait was either lost in multiple lineages or evolved independently multiple times. If the latter, then why do so many plants still lack such a "lantern"-shaped protective shelter? After noting that some proponents of neo-Darwinism make unfalsifiable appeals to unknown selective advantages, he concludes that neo-Darwinism is not making falsifiable predictions and finds that this "infinity of mostly non-testable explanations (often just-so-stories) itself may put the theory outside science."

However, there is another possibility, namely the scientific hypothesis of intelligent design. In contrast to neo-Darwinism, Lönnig notes that the ID view can "be falsified by proving (among other points) that the probability to form an ICS by purely natural processes is high, that specified complexity is low, and finally, by generating an ICS by random mutations in a species displaying none." After reviewing the multiple complex steps involved in forming an ICS, he states that his research "appears to be in agreement with Behe's studies (2007): it seems to be very improbable that the current evolutionary theories like the modern synthesis (continuous evolution) or the hopeful monster approach (in one or very few steps) can satisfactorily explain the origin of the ICS." He concludes, "It appears to be more than unlikely to generate the whole world of living organisms by the neo-Darwinian method."

You'll find additional papers by Lönnig at our pro-ID peer-reviewed articles page.

Beyond the Flow of Pro-ID Scientific Publications, a Much Greater Ferment of Doubt About Darwinism

2012-02-02T22:15:53Z

Casey Luskin has done fantastic work in tracking and now analyzing (in a currently ongoing series) the flow of peer-reviewed articles supporting intelligent design in mainstream science journals. This is notwithstanding the persistent Myth of No Peer-Reviewed Publications that you still hear. "The intelligent design movement has not published a properly peer-reviewed article in a scientific journal," as Wikipedia notes authoritatively.

So far the science-deniers haven't responded to our newly updated page listing peer-reviewed pro-ID scientific papers. I wonder how many will have the guts and honesty to admit they were wrong. Some Darwin defenders may respond by shifting the goal post, pretending they never said there was no ID research going on but turning nimbly to mock the number of papers that have appeared as being too small to be worthy of notice. They would be missing the point that, as ENV observes, ID is a young and underfunded field -- given which, fifty-plus papers in a few years with more on the way is pretty good.

But describing the extent of peer-reviewed pro-ID research leaves aside the equally impressive evidence of ferment among scientists who don't support ID but who do trash the primary Darwinian thesis that natural selection has the creative power to conjure the wonder of life as it has unfolded over the course of billion of years.

Recently ENV hosted an online debate between a leading representative of that perspective (anti-ID, anti-Darwin) -- University of Chicago's James Shapiro -- and ID theorist William Dembski. Now our friend Denyse O'Leary at Uncommon Descent points out a frank confession in the Oxford University Press journal Genome Biology and Evolution. Reviewing Shapiro's current book, Evolution: A View from the 21st Century, Adam Wilkins writes:

The book's contention that natural selection's importance for evolution has been hugely overstated represents a point of view that has a growing set of adherents. (A few months ago, I was amazed to hear it expressed, in the strongest terms, from another highly eminent microbiologist.) My impression is that evolutionary biology is increasingly separating into two camps, divided over just this question. On the one hand are the population geneticists and evolutionary biologists who continue to believe that selection has a "creative" and crucial role in evolution and, on the other, there is a growing body of scientists (largely those who have come into evolution from molecular biology, developmental biology or developmental genetics, and microbiology) who reject it. In contrast to Victorian scientists who regarded Darwinian natural selection as incapable of creating high degrees of biological complexity, the modern sceptics tend to regard it as of trivial importance: the "right" variant for the right place and time arises and, presto, the population changes! The two contemporary groups, divided over this point, are not so much talking past each another as ignoring one another. This cannot be a constructive situation though whether it has the makings of a full-fledged Kuhnian paradigm-crisis is too soon to tell.

Wilkins criticizes Shapiro's book, but the point to take away is his depiction of a scholarly field profoundly rent by disagreement on the doctrine -- evolution by natural selection -- that we were always told to accept by faith as being at the very foundation of modern biology, totally indispensible to it, without a full and unquestioning adherence to which the contemporary high school biology student like the well-informed adult and the professional scientist would be utterly lost and bereft.

Note well, the candid admission of a Darwin defender: "My impression is that evolutionary biology is increasingly separating into two camps, divided over just this question." This is the evolution controversy that supposedly doesn't exist.

Here's a further illustration from another peer-reviewed article that came across my desk just yesterday. In Biological Theory, David J. Depew and Bruce H. Weber consider "The Fate of Darwinism: Evolution After the Modern Synthesis." They

trace the history of the Modern Evolutionary Synthesis, and of genetic Darwinism generally, with a view to showing why, even in its current versions, it can no longer serve as a general framework for evolutionary theory. The main reason is empirical. Genetical Darwinism cannot accommodate the role of development (and of genes in development) in many evolutionary processes.

And so on. Here at ENV, we've covered some of the traffic in skepticism about Darwinian theory, mainly kept out of the public view, from scientists with no ID affiliations or sympathies. From all the available evidence, the bubbling doubt from those quarters dwarfs actual expressions of support for intelligent design, yet is equally ominous for Darwinism. Tracking it all is a task that would challenge even Casey.

Republicans and Science (as Opposed to Liberals and the Science They've Politicized)

2012-02-02T16:48:59Z

Hot-button scientific topics have been politicized. Not by Republicans, however.

]]> ENV's David Klinghoffer has a piece in The American Spectator looking at the manipulation of science for political gain by liberals. One way this goes on is for liberals to demonize conservatives as anti-science, and mock them for their skepticism on controversial science issues like climate change and the teaching of evolution.

In the religious world you will sometimes read articles or hear sermons trying to understand the mindset of unbelievers and lamenting the lure of apostasy. The funny thing is, in entirely secular venues you will also find people worrying about the power of heresy to seduce the unwary from the true path. In the secular world, that path is called "science."

About such scientific heresy, the level of anxiety seems higher now than any time in recent memory. Republican presidential candidates continuously being probed on their scientific beliefs, ranked by media liberals on the basis of their adherence to scientifically orthodox ideas about evolution, global warming, and stem-cell research, has been the most obvious way this came out recently.

What's wrong with Republicans, anyway? Scientists and journalists offer a variety of diagnoses. Some say a backwoods element in the population has abandoned the Enlightenment, a result of poor education or religious fundamentalism or both.

Other experts find no convincing sociological explanation and opt for a more scientific (or scientific-seeming) approach, pointing to faulty brain chemistry. A forthcoming book title by journalist Chris Mooney says it all: The Republican Brain: The Science of Why They Deny Science and Reality.

Read the full article at the American Spectator website.

Oldies but Goodies: Update of Peer-Reviewed Articles Page Turns Up Long Lost Pro-Intelligent Design Papers

2012-02-02T14:00:01Z

When we began the process of revising and updating Discovery Institute's page listing peer-reviewed pro-intelligent design scientific papers, we knew that there had been a couple dozen papers published in the last few years that needed to be added to the page. What we didn't expect to find was that there were five or six papers published ten or more years ago that supported ID and were not listed on the page. In fact, two of the earliest papers listed on the page are new additions.

The first pro-ID paper in our listing was published in 1984 by nuclear physicist William G. Pollard in the American Journal of Physics under the title "Rumors of transcendence in physics." Pollard notes that Big Bang cosmology requires some kind of transcendent reality to initiate the universe. He argues that the scientific justification for this transcendent domain can be found in quantum mechanics because universal laws and constants are finely tuned to permit the existence of advanced life. This points to an intelligent source, a mind, at work in having designed the universe.

Three years later a similar paper appeared in the same journal by another physicist, Stanley L. Jaki, titled "Teaching of Transcendence in Physics." In the paper, Jaki sought to help educators understand how they can teach students about the evidence for transcendence in the universe. The article posits that a transcendent realm exists beyond the universe and that the universe can plausibly be said to reflect design.

Another early pro-ID paper was written by R. Kunze, H. Saedler, and W.-E. Lönnig and published in a peer-viewed Academic Press scientific anthology, Advances in Botanical Research, in 1997. After noting that "some major problems have to be solved for gene duplications to be of fundamental evolutionary significance," their chapter favorably references Michael Behe's book Darwin's Black Box (which had been published the year before) to justify the following question: "What could be the selective advantage of the intermediate ('still unfinished') reaction chains?" The authors further state that "examples of 'irreducibly complex systems'" are found in biology.

Two final older peer-reviewed scientific papers were co-published by Solomon Victor and Vijaya M. Nayak on the evident design reflected in the origin of the heart.

The first paper, "Evolution of the Ventricles," was published in the Texas Heart Institute Journal in 1999 and concludes that "there is a design in the evolution of the venous connections of the heart, pectinate muscles, atrioventricular valves, left ventricular tendons, outflow tracts, and great arteries." Their version of "evolution" is decidedly non-Darwinian, as it notes that evolution appears to be goal-directed by a designer:

One neglected aspect in the study of evolution is that of anticipation. Fish atria and ventricles appear to have a built-in provision for becoming updated to the human 4-chambered structure. This transformation is achieved in stages: the truncus yields the great arteries, appropriate shifting takes place in the great arteries, the left ventricle decreases in sponginess and increases in the size of its lumen, the chordopapillary apparatus becomes more sophisticated, the coronary circulation undergoes changes, and the ventricular septal defect closes.

The article closes by stating, "This evolutionary progression points to a master design and plan for countless millennia."

The second paper appeared in Annals of the Royal College of Surgeons of England in 2000, and was titled "Evolutionary anticipation of the human heart." This article argues that intelligent design is recognizable in the human heart, stating: "Comparative anatomy points to a design and a Designer. Surgeons, anatomists and anyone studying the human form and function have an unsurpassed opportunity to ponder over the wonders of creation and contemplate the basic questions: where did we come from? why are we here? and where are we going?"

These articles anticipate the boom of peer-reviewed pro-ID scientific papers that appeared in the ensuing years.

In Time for Darwin Day, It's Our New List of Pro-ID Peer-Reviewed Scientific Papers; 50th Paper Published in 2011

2012-02-01T20:20:05Z

]]> Darwin Day and Evolution Weekend overlap this year, providing an extra special opportunity to celebrate Charles Darwin's 203rd birthday on February 12 and promote Darwinian theory in a variety of venues, including colleges and universities, churches and synagogues. We wanted to do something appropriate to add our own note to the hallelujah chorus. What do you give to an exhausted relic of antique 19th-century scientific materialism that has everything but genuine credibility?

How about a revised and updated list of pro-intelligent design peer-reviewed scientific papers, showing among other things that the 50th such paper was published in 2011? In a series of upcoming articles, we've asked Casey Luskin to note some highlights.

While intelligent design research is a new scientific field, recent years have been a period of encouraging growth, producing a strong record of peer-reviewed scientific publications. New publications continue to appear, now listed at our updated page.

The current boom goes back to 2004, when Discovery Institute senior fellow Stephen Meyer published a groundbreaking paper advocating ID in the journal Proceedings of the Biological Society of Washington. There are multiple hubs of ID-related research.

Biologic Institute, led by molecular biologists Doug Axe and Ann Gauger, is "developing and testing the scientific case for intelligent design in biology." Biologic conducts laboratory and theoretical research on the origin and role of information in biology, the fine-tuning of the universe for life, and methods of detecting design in nature. That's Dr. Gauger at the Biologic lab pictured above.

Another ID research group is the Evolutionary Informatics Lab, founded by senior Discovery Institute fellow William Dembski along with Robert Marks, Distinguished Professor of Electrical and Computer Engineering at Baylor University. Their lab has attracted graduate-student researchers and published multiple peer-reviewed articles in technical science and engineering journals showing that computer programming "points to the need for an ultimate information source qua intelligent designer."

Other pro-ID scientists around the world are publishing peer-reviewed pro-ID scientific papers. These include biologist Ralph Seelke at the University of Wisconsin Superior, Wolf-Ekkehard Lönnig who recently retired from the Max Planck Institute for Plant Breeding Research in Germany, and Lehigh University biochemist Michael Behe.

Researchers have published their work in a variety of relevant technical venues, including peer-reviewed scientific journals, peer-reviewed scientific books from mainstream university presses, trade-press books, peer-edited scientific anthologies, peer-edited scientific conference proceedings and peer-reviewed philosophy of science journals and books.

These papers have appeared in scientific journals such as Protein Science, Journal of Molecular Biology, Theoretical Biology and Medical Modelling, Journal of Advanced Computational Intelligence and Intelligent Informatics, Quarterly Review of Biology, Cell Biology International, Rivista di Biologia/Biology Forum, Physics of Life Reviews, Annual Review of Genetics, and many others. At the same time, pro-ID scientists have presented their research at conferences worldwide in fields such as genetics, biochemistry, engineering, and computer science.

This body of research is converging on a consensus: complex biological features cannot arise by unguided Darwinian mechanisms, but require an intelligent cause.

Despite ID's publication record, we note parenthetically that recognition in peer-reviewed literature is not an absolute requirement to demonstrate an idea's scientific merit. Darwin's own theory of evolution was first published in a book for a general and scientific audience -- his Origin of Species -- not in a peer-reviewed paper. Nonetheless, ID's peer-reviewed publication record shows that it deserves -- and is receiving -- serious consideration by the scientific community.

The purpose of ID's research program is not to convince the unconvincible, critics and naysayers who repeat over and over in the media that there is no such thing as ID research, that ID has not produced a single peer-reviewed paper. (And they call us "science deniers"!) Rather, ID research seeks to engage open-minded scientists and thoughtful laypeople with credible, persuasive, peer-reviewed, empirical data supporting intelligent design.

And this is happening. ID has already gained the kind of scientific recognition you would expect from a young (and vastly underfunded) but promising scientific field. The scientific progress of ID has won the serious attention of skeptics in the scientific community, who engage in scientific debate with ID and attend private scientific conferences allowing off-the-record discussion with ID proponents.

As noted, the new revised and updated listing of pro-ID peer-reviewed papers can be viewed here. We provide an annotated bibliography of technical publications of various kinds that support, develop or apply the theory of intelligent design. The articles are grouped according to the type of publication.

Happy Darwin Day!

Discovery Institute Condemns Passage of Creationism Bill by Indiana Senate as Bad Science and Bad Education

2012-02-01T16:31:40Z

A bill approved yesterday by the Indiana Senate to allow the teaching of creationism in public schools is being criticized as bad science education by Discovery Institute, the nation's leading intelligent design think tank.

]]> If made law, Indiana Senate Bill 89 (SB89) would allow creationism, a religious view on the origin of species, into the Hoosier state's biology classrooms. In 1987, the Supreme Court struck down similar legislation as an unconstitutional establishment of religion. Instead of scrapping SB89 in deference to legal precedent, the Indiana Senate has amended the bill to allow more religious views on origins, as if more religion could cure the original problem.

"Instead of injecting religion into biology classes, legislators should be working to promote the inclusion of more science," said Joshua Youngkin, a law and policy analyst at Discovery Institute's Center for Science & Culture. "There are plenty of scientific criticisms of Darwin's theory today, and science students should be able to hear about them, not about religion."

For Discovery Institute's complete science education policy go to: http://www.discovery.org/a/3164.

In Cosmology, There's a Free Lunch After All

2012-02-01T14:00:14Z

Warning: Things are not as they seem. You thought that nothing comes from nothing. That quaint notion was drummed into you in school when you learned the First Law of Thermodynamics. Sorry, ladies and gentlemen. Everything you thought you know is wrong. Everything comes from nothing.

Modern cosmologists are increasingly fascinated by nothingness. It stimulates and titillates them, disturbing their dogmatic slumbers with visions and dreams. Having already been worshiping at the Shrine of Nobody for years, they just realized that Nobody is wedded to Nothing. "Fantastic!" they think. Even better, Nobody and Nothing have already produced their first child: Nonsense.

Just look at the recent issue of Nature, the world's most respected science journal.¹ Nature chose Caleb Scharf, an astrobiologist at Columbia University, to write in glowing terms about Lawrence Krauss's new book, A Universe from Nothing: Why There Is Something Rather than Nothing (Free Press, 2012). Don't tell him there's no such thing as a free lunch.

Krauss took him to the Nothing Café and showed him the menu. Scharf ordered the multiverse special:

Furthermore, Krauss points out, our Universe seems to have a net gravitational energy that is suspiciously close to zero: its existence may "cost" nothing, requiring no energy input. This raises the possibility of the ultimate free lunch -- of a cosmos that is merely a piece of borrowed stuff, having appeared spontaneously, like a virtual particle, and been filled with matter and radiation simply as a consequence of the energy of empty space. Ours may be one of an infinite array of universe-like things, just one instance in a multiverse.

Krauss assures Scharf that Nobody and Nothing have a lot of experience in the cosmic kitchen. They've been cooking up universes since infinity past. Nobody has actually seen Nothing produce something, even if Krauss has not. Scharf's stomach growls. Krauss hands him an appetizer. It's his own concoction, laying out "this remarkable story" as a taste of things to come: "Krauss steers it soberly and with grace, taking time to let the reader digest the material."

It's awfully silent in the kitchen, which is off limits to guests. Surely the cook has the dark matter in the oven by now. "What can you tell me about the ingredients?" Scharf asks while they wait.

He notes that a number of vital empirical discoveries are, ominously, missing from our cosmic model. Dark matter is one. Despite decades of astrophysical evidence for its presence, and plausible options for its origins, physicists still cannot say much about it. We don't know what this major mass component of the Universe is, which is a bit of a predicament. We even have difficulty accounting for every speck of normal matter in our local Universe. This does not mean that something is wrong with the current picture, but that we astronomers should be uncomfortable about embracing a phenomenon such as dark energy when we still have a mess to tidy up elsewhere.

That explains it; the cooks are distracted cleaning up the mess that Nonsense made. They'll be back at work shortly. Krauss reassures himself. "Don't you remember that endorsement you saw on the menu?" he asks. "Our Chief Prophet insists this is the place to be. Besides, eating here is a lot better than at that Something place across town; you know, that disgusting establishment where all the creationists hang out. In fact, I've heard that it's owned and operated by Somebody."

Scharf remembers. He retreats into his visions and dreams of the free lunch Nothing is preparing, smiling fondly at the prospect of the Something joint losing out to Nobody.

What does this mean for humanity? In a provocative afterword, evolutionary biologist and atheist Richard Dawkins writes that the apparent near-inevitability of something arising out of unstable nothingness, as described by Krauss, is devastating for theologians and creationists. Dawkins is right. But it is also invigorating for the rest of us, because in this nothingness there are many wonderful things to see and understand.

Patiently waiting, knife and fork in hand, Scharf recalls the jingle from the Nothing Café commercial:

Nothin' says bluffin' like somethin' out of Nothin', and Nobody says it best.

Literature Cited

1. Caleb Scharf, Cosmology: Plucked from the vacuum. Nature 481 (26 January 2012), p. 440. doi:10.1038/481440a.

"Then They Came for Me -- and There Was No One Left to Speak for Me."

2012-02-01T00:18:32Z

ENV commented earlier on the move by the National Center for Science Education to expand its mission from squelching academic freedom on evolution to squelching it on climate change. It's an important development and you can only hope that climate skeptics get it too.

There's been a tendency among some especially on the right side of the political spectrum to grasp what's happening on the climate issue while failing to see what there is to care about on evolution. The NCSE has now underlined the answer with a bright red pen.

Stamping out open discussion of legitimate scientific questions about Darwinian theory will have ramifications in fields other than biology, fields that seemingly have nothing to do with evolution. The situation reminds me of the famous words of the German Protestant pastor and theologian Martin Niemöller, who criticized the Nazis and then spent seven years in concentration camps for having done so.

First they came for the Socialists, and I did not speak out -- because I was not a Socialist.

Then they came for the Trade Unionists, and I did not speak out -- because I was not a Trade Unionist.

Then they came for the Jews, and I did not speak out -- because I was not a Jew.

Then they came for me -- and there was no one left to speak for me.

Niemöller is quoted perhaps to excess but his point remains crucial, with applications even in a free society like ours. Censorship, once indulged and condoned, doesn't end just because one taboo debate has been suppressed. The censors soon find that other debates are going on that should not be happening, and they move to suppress those too.

Debating at Biola University, Discovery Institute Scholar John West Will Ask What C.S. Lewis Really Believed About Evolution

2012-01-31T23:30:01Z

]]> In the century and a half since Darwin published the Origin of the Species, no Christian theologian has given a more searching examination to the question of man's place in the cosmos than Oxford scholar C.S. Lewis. His readers have naturally wondered what conclusion Lewis drew about evolutionary theory. A debate next week at Biola University, in La Mirada, California, confronts the question head-on: Was Lewis a Darwinian, a proponent of intelligent design, a theistic evolutionist, or something else altogether?

Titled "Evolution and C.S. Lewis: What Did He Really Believe?," the event features Center for Science & Culture associate director Dr. John West in conversation with Dr. Michael Peterson of Asbury Seminary. The debate will take place on the Biola campus, Monday, February 6, 2012, 7-9:30 pm, in Sutherland Auditorium. The cost is $10 per person. For more information about registering, see here.

The evolution controversy is charged not only with scientific but, of course, spiritual and philosophical importance as well. Our generation is not the first to have wrestled with the problem of whether Charles Darwin's theory can be reconciled with traditional Christian and other religious faiths -- and if so, how? That discussion goes back to Darwin's own day.

We argue about what the revered and beloved thinkers of the past believed about evolution because most of us have the inkling that their wisdom was greater than our own. In their insights, we seek inspiration and guidance. Join Dr. West and Dr. Peterson as they explore a key issue in the understanding of Lewis's thought.

The Darwin Lobby Expands Its Mission of Suppressing Free Thought to Include "Climate Change"

2012-01-31T14:00:07Z

]]> Our Darwin-lobbying friends at the National Center for Science Education are branching out. Having previously specialized in suppressing academic freedom on the topic of evolution, the NCSE will seek opportunities to enforce a rigid orthodoxy on climate change.

Speaking with the New Scientist, NCSE executive director Eugenie Scott explained the scope of the problem her group is up against:

We have heard that students will get up and walk out of the class when teachers start talking about climate change, or that parents will complain. Teachers don't want to fight with parents, and it is easy for them to think that it's just too much trouble to teach about climate change.

Obviously, in a free country, those students should be forcibly put back in their seats and made to listen, their parents told to shut up and stop complaining.

Of course, there is the usual resorting to the trope about science "denial" with its verbal echo intended to summon associations with Holocaust denial, about as contemptible and dishonest a tactic as we've seen from the Darwinists. Says the NCSE:

The social controversy over climate change is in part due to climate change denial. In order to defend and support the teaching of climate change, it is important to understand -- and be able to rebut -- arguments about climate science, and to understand why people choose to attack such well-tested science. "Climate Change Denial" provides the essential tools, and also describes how climate change denial is already threatening the integrity of science education.

In the past, we've had some fun in making jest of the NCSE. But this should be a wakeup call, not least for freethinkers on the climate issue, folks who don't all uniformly grasp why they should care about the Darwin debate. The NCSE is showing how pervasive and consequential their dogmatic view of science really is. Those who think the evolution debate is just about evolution had better think again. In fact it's about the freedom of scientific discussion and inquiry.

Apart from that, look how weird this. The NCSE has literally identified the thesis of catastrophic, human-induced climate change with "climate science." It's pretty bizarre when a very narrow, and in fact very controversial thesis is identified with a sub-discipline of natural science.

How controversial? Last week's op-ed in the Wall Street Journal ("No Need to Panic About Global Warming"), signed by 16 prominent scientists, is a sign of things to come. If we had to guess, we'd suspect the Intergovernmental Panel on Climate Change models have grossly exaggerated the positive-feedbacks in the climate system, and systematically ignored the negative feedbacks. This is more a result of bias and ignorance than outright fraud (though there's some of the latter as well).

Fortunately, the theoretical predictions have strong empirical implications, since we can measure the current global climate year to year. So the misrepresentations can't survive indefinitely.

The often cited "consensus" on this subject, which never existed, is getting shakier every day. In fact, if the NCSE had any prudence, it would have avoided this subject. Instead, they're on a campaign to silence teachers and school districts who "deny climate science," comparing this controversy with the evolution controversy.

How will it look when the IPCC line on climate change collapses? Let's hope the resulting skepticism bleeds over from one subject to the other.

More from Lenski's Lab, Still Spinning Furiously

2012-01-30T22:22:43Z

]]> Recently a new paper by Richard Lenski and colleagues (Meyer et al. 2012) appeared in Science with, as usual, commentary in the New York Times. Lenski's lab must own a red phone with a direct line to the Gray Lady.

The gist of the paper is that a certain bacteriophage (a virus that infects bacteria) called "lambda" gained the ability to bind a different protein on the surface of its host, the bacterium E. coli, than the protein it usually binds. The virus has to bind to the cell's surface as a prelude to invading it. The protein it normally binds is called LamB. Lenski's lab, however, used a bacterial strain that had turned off the production of LamB in 99% of E. coli cells but, crucially, 1% of cells still produced the protein.

Thus the virus could still invade some cells, reproduce, and not go extinct. Under these conditions the viral binding protein (called "J") underwent several mutations, apparently to better bind LamB in the fewer cells that produced it. Then, surprisingly, after the viral gene gained a fourth mutation, the viral J protein acquired the ability to bind a different protein on E. coli, called OmpF. Now the virus could use OmpF as a platform for invading the cell. Since all cells made OmpF, the virus was no longer restricted to invading just the 1% of cells that made LamB, and it prospered. The workers repeated the experiment multiple times, and frequently got the same results.

As always, the work of the Lenski lab is solid and interesting, but is spun like a top to make it appear to support Darwinian evolution more than it does. As the authors acknowledge, this is certainly not the first time a lab has evolved a virus to grow on a different strain of host. In a recent review (Behe 2010) there is a section entitled "Evolution Experiments with Viruses: Adapting to a New Host" discussing just that topic.

In general, viruses have been shown to be able to adapt to bind to related host cells that have similar surface features. In almost all cases the virus uses the same binding protein, and the same (mutated) binding site to attach to the new host cell. This also seems to be the case with Lenski's new work. As stated above, the first several mutations apparently strengthen the ability of the J protein to bind to the original site, LamB, while the fourth mutation allows it to bind to OmpF.

As the authors state, however, the mutated viral J protein can still bind to the original protein, LamB, which strongly suggests the same binding site (that is, the same location on the J protein) is being used. It turns out that both LamB and OmpF have similar three-dimensional structures, so that strengthening the binding to one fortuitously led to binding to the other.

In my review (Behe 2010) I discussed why this should be considered a "modification of function" event rather than a gain-of-function one. The bottom line is that the results are interesting and well done, but not particularly novel, nor particularly significant.

To me, the much more significant results of the new paper, although briefly mentioned, were not stressed as they deserved to be. The virus was not the only microbe evolving in the lab. The E. coli also underwent several mutations. Unlike for lambda, these were not modification-of-function mutations -- they were complete loss-of-function mutations.

The mechanism the bacterium used to turn off LamB in 99% of cells to resist initial lambda infection was to mutate to destroy its own gene locus called malT, which is normally useful to the cell. After acquiring the fourth mutation the virus could potentially invade and kill all cells. However, E. coli itself then mutated to prevent this, too. It mutated by destroying some genes involved in importing the sugar mannose into the bacterium. It turns out that this "mannose permease" is used by the virus to enter the interior of the cell. In its absence, infection cannot proceed.

So at the end of the day there was left the mutated bacteriophage lambda, still incompetent to invade most E. coli cells, plus mutated E. coli, now with broken genes which remove its ability to metabolize maltose and mannose. It seems Darwinian evolution took a little step sideways and two big steps backwards.

Literature Cited

Behe, M. J., 2010 Experimental Evolution, Loss-of-function Mutations, and "The First Rule of Adaptive Evolution." Quarterly Review of Biology 85: 1-27.

Meyer, J. R., D. T. Dobias, J. S. Weitz, J. E. Barrick, R. T. Quick et al. 2012 Repeatability and contingency in the evolution of a key innovation in phage lambda. Science 335: 428-432.

Photo credit: billaday/Flickr.

John Scopes on Higher Education

2012-01-30T21:00:36Z

A friend who watched Alleged last night for the first time -- and enjoyed, as I did -- emails us to point out this great quote, noted in the film, from John Scopes of Monkey Trial fame. It's from Scopes's own memoirs of his history-making experience in Dayton, Tennessee:

I have often said that there is more intolerance in higher education than in all the mountains of Tennessee.

Well said. Source: John T. Scopes, The Center of the Storm (New York: Henry Holt & Company, 1967), p. 276.

Alfred Russel Wallace, Iconoclast Extraordinaire

2012-01-30T20:02:01Z

]]> A severe intellectual sclerosis in scientific and popular media is one big reason that arguments for intelligent design meet with such resistance there. When it comes to the evolution debate, scientists and journalists alike are afflicted by a tendency to think in terms of simple stereotypes and crude clichés -- about what ID theory says and what kind of people ID advocates are.

That's one reason ENV keeps coming back to Alfred Russel Wallace, evolutionary theory's co-founder. Apart from the inherent historical and scientific fascination of his life and ideas, well and compactly portrayed in John West's new documentary short Darwin's Heretic, Wallace has the virtue of blasting apart all the hackneyed formulas about ID that block the channels of thought in the mind of your typical Darwinist. Or rather, he would do so if the Darwinist could be induced to seriously consider the evolution of Wallace's thinking about evolution as he came to embrace views best described as proto-intelligent design.

Wallace was an iconoclast not only in his scientific opinions but in his cultural and political ones as well, as this brief clip of interviews with Wallace scholar and ENV contributor Michael Flannery demonstrates. Unlike Darwin, he passionately resisted the racism and ethnocentrism of his day and denounced the eugenic thinking advanced by Darwin's cousin Francis Galton. He was a socialist, albeit of a libertarian type. He firmly insisted on women's equality and even (it sounds like) superiority to men. When you learn about his life, you find that not one platitude about intelligent design in the Darwinist arsenal -- ID's scientific, political, cultural, religious associations, you name it -- is left standing.

This clip is an excellent little introduction to his social views.