Intelligent Design Advocates Face Uphill Fight

Like many evolutionary mistakes, intelligent design may be on the road to extinction, put there Tuesday by U.S. District Judge John E. Jones III.

When Jones ruled that the Dover Area School District's intelligent design policy violates the First Amendment and barred the district from mentioning intelligent design in biology classes or "from requiring teachers to denigrate or disparage the scientific theory of evolution," he wasn't just applying a pinprick to the trial balloon intelligent design supporters had chosen to float in this case.

He aimed a cannon at it. And fired. Several times. Odds are, other courts will find it hard to argue that he missed his target.

In one of the most closely watched cases in recent memory -- not just in Pennsylvania but across the nation -- Jones took the opportunity in Kitzmiller v. Dover Area School District to frame the case in the much larger context many, including supporters of intelligent design, had seen it in.

The impact of his ruling can't be overstated. Not only did Jones find the policy unconstitutional but he also ruled that intelligent design is not science.

"[M]oreover ... ID cannot uncouple itself from its creationist, and thus religious, antecedents," he said in the 139-page opinion.

Jones didn't pull any punches in making his ruling, criticizing the school board for its policy, as well as those who saw the case as an opportunity to make law that would pave the way for greater acceptance of intelligent design.

"Those who disagree with our holding will likely mark it as the product of an activist judge," he said. "If so, they will have erred as this is manifestly not an activist court. Rather, this case came to us as the result of the activism of an ill-informed faction on a school board, aided by a national public interest law firm eager to find a constitutional test case on ID, who in combination drove the board to adopt an imprudent and ultimately unconstitutional policy.

"The breathtaking inanity of the board's decision is evident when considered against the factual backdrop which has now been fully revealed through this trial. The students, parents, and teachers of the Dover Area School District deserved better than to be dragged into this legal maelstrom, with its resulting utter waste of monetary and personal resources."

Not surprisingly, several groups that endorse the teaching of intelligent design, or "ID" as Jones referred to it throughout his opinion, lashed out and accused him, as he anticipated, of being an "activist federal judge."

Who knew that Republican judges appointed by Republican presidents could be such hacks for the left?

Well, if activism is changing the norm and imposing one's will from behind the safe confines of the bench onto the helpless masses, then Jones' decision in Kitzmiller hardly fits the bill, since the opinion follows closely the reasoning of other federal courts on the issue, including the U.S. Supreme Court. If anything, Jones was critical of the changes the Dover Area School Board made for an entire community and potentially a whole generation of school children.

But organizations like the Discovery Institute, the Thomas More Law Center and the Cato Institute Center for Educational Freedom should be angry with Jones. Because what he did in his opinion, systematically and ruthlessly, was expose intelligent design as creationism, minus the biblical fig leaf, and advanced by those with a clear, unscientific agenda: to get God (more specifically, a Christian one) back into the sciences.

Jones goes into an exhaustive examination on the intelligent design movement, and what he found will make it difficult for future pro-ID litigants to argue that the whole thing isn't religion masked in neo-scientific terms.

According to Jones, the Discovery Institute's Center for Renewal of Science and Culture developed a "Wedge Document" in which it said the goal of the intelligent design movement is to "replace science as currently practiced with 'theistic and Christian science.'"

He said that one of the professors, an ID proponent, who testified for the school board "remarkably and unmistakably claims that the plausibility of the argument for ID depends upon the extent to which one believes in the existence of God."

Jones also points out that the ID textbook the Dover policy encouraged students to check out, "Of Pandas and People," is not only published by an organization identified in IRS filings as a "religious, Christian organization," but that the book was meticulously changed following the U.S. Supreme Court's ruling in 1987 that the U.S. Constitution forbids the teaching of creationism as science.

By comparing the early drafts to the later ones, he said, it was clear that the definition for creation science was identical to the definition of intelligent design and that the word creation and its variants were replaced with the phrase ID and that it all happened shortly after the Supreme Court decision.

As Jones points out throughout his opinion, ID's supporters couldn't shake two problematic facts -- its close association with creationism and its inability to divorce itself from the supernatural.

"ID is reliant upon forces acting outside of the natural world, forces that we cannot see, replicate, control or test, which have produced changes in the world," he said. "While we take no position on whether such forces exist, they are simply not testable by scientific means and therefore cannot qualify as part of the scientific process or as a scientific theory."

All of which lead Jones to conclude that "ID is a religious view, a mere re-labeling of creationism, and not a scientific theory."

There's plenty of other things worth noting in Jones' opinion, including how school board members talked at meetings about creationism and complained of "liberals in black robes" taking away "the rights of Christians," or how the Discovery Institute was in contact with board members prior to the policy change, and a number of other machinations that might leave one feeling less than secure about the separation of church and state in Pennsylvania, but those are facts specific to this case.

The real impact of the opinion is what Jones lays out with regard to intelligent design's roots, its proponents, its agenda and the tactics (and there's really no other way to describe them) being used to advance it. It reads like a cautionary tale, one that we should all be reading.

And while it's unlikely that the country has seen the last of this issue, one can hope that Jones' decision might save future judges a little bit of time, if not discourage groups with a religious ax to grind from using residents of small communities as pawns in the name of a dishonest, fruitless agenda.

["I don't understand why the Darwinists are so adamant that it not be permitted."]

They're upset because they can't account for how life began. And? They can't do it using any materialist model known to science.

I've got a bibliography of hundreds of papers, where would you like to start? Some of the following links have expired since I originally saved them, sorry, but the titles may help you find them in the library:

(See for example chapter 2 entitled "Phylogeny from Function: The Origin of tRNA Is in Replication, not Translation", in the online book "Tempo and Mode in Evolution: Genetics and Paleontology 50 Years After Simpson".)

Origin of Life and Cells

+Good intro: Lies, Damned lies, Statistics, and Probability of Abiogenesis Calculations
+Purdue Study Breathes New Life Into Question Of How Life Began - self-replicating peptides
+ Ammonia From The Earth's Deep Oceans A Key Step In The Search For Life's Origins
+ Whitehead Study Supports Existence Of Ancient RNA World Helps Provide Insight Into Early Evolution Of Life
+ Yale Scientists Recreate Molecular Fossils Now Extinct That May Have Existed At The Beginning Of Life
+A whole old world - new evidence for "The RNA World"
The path from the RNA world.
Relics from the RNA world.
A supersymmetric model for the evolution of the genetic code.
The hydrogen hypothesis for the first eukaryote.
+ Kick-start for life on earth
The Beginnings of Life on Earth by Christian de Duve
+Are the Odds Against the Origin of Life Too Great to Accept? : Addenda to Review of David Foster's The Philosophical Scientists by Richard C. Carrier.

Obcells as Proto-Organisms: Membrane Heredity, Lithophosphorylation, and the Origins of the Genetic Code, the First Cells, and Photosynthesis (Journal of Molecular Evolution, Volume 53 - Number 4/5, 2001)
N-Carbamoyl Amino Acid Solid-Gas Nitrosation by NO/NO_x: A New Route to Oligopeptides via alpha-Amino Acid N-Carboxyanhydride. Prebiotic Implications (Journal of Molecular Evolution, Volume 48 - Number 6, 1999
Chemical interactions between amino acid and RNA: multiplicity of the levels of specificity explains origin of the genetic code (Naturwissenschaften, Volume 89 Number 12 December 2002)
The Nicotinamide Biosynthetic Pathway Is a By-Product of the RNA World (Journal of Molecular Evolution, Volume 52 - Number 1, 2001)
On the RNA World: Evidence in Favor of an Early Ribonucleopeptide World
Inhibition of Ribozymes by Deoxyribonucleotides and the Origin of DNA
Genetic Code Origin: Are the Pathways of Type Glu-tRNAGln to Gln-tRNAGln Molecular Fossils or Not?

Ammonia From The Earth's Deep Oceans A Key Step In The Search For Life's Origins
Whitehead Study Supports Existence Of Ancient RNA World Helps Provide Insight Into Early Evolution Of Life
Yale Scientists Recreate Molecular Fossils Now Extinct That May Have Existed At The Beginning Of Life
A whole old world
The path from the RNA world.
Relics from the RNA world.
A supersymmetric model for the evolution of the genetic code.
The hydrogen hypothesis for the first eukaryote.

On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells William Martin and Michael J. Russell
Abstract: All life is organized as cells. Physical compartmentation from the environment and self-organization of self-contained redox reactions are the most conserved attributes of living things, hence inorganic matter with such attributes would be life’s most likely forebear. We propose that life evolved in structured iron monosulphide precipitates in a seepage site hydrothermal mound at a redox, pH and temperature gradient between sulphide-rich hydrothermal fluid and iron(II)-containing waters of the Hadean ocean floor. The naturally arising, three-dimensional compartmentation observed within fossilized seepage-site metal sulphide precipitates indicates that these inorganic compartments were the precursors of cell walls and membranes found in free-living prokaryotes. The known capability of FeS and NiS to catalyse the synthesis of the acetyl-methylsulphide from carbon monoxide and methylsulphide, constituents of hydrothermal fluid, indicates that pre-biotic syntheses occurred at the inner surfaces of these metal-sulphide-walled compartments, which furthermore restrained reacted products from diffusion into the ocean, providing sufficient concentrations of reactants to forge the transition from geochemistry to biochemistry. The chemistry of what is known as the RNA-world could have taken place within these naturally forming, catalyticwalled compartments to give rise to replicating systems. Sufficient concentrations of precursors to support replication would have been synthesized in situ geochemically and biogeochemically, with FeS (and NiS) centres playing the central catalytic role. The universal ancestor we infer was not a free-living cell, but rather was confined to the naturally chemiosmotic, FeS compartments within which the synthesis of its constituents occurred. The first free-living cells are suggested to have been eubacterial and archaebacterial chemoautotrophs that emerged more than 3.8 Gyr ago from their inorganic confines. We propose that the emergence of these prokaryotic lineages from inorganic confines occurred independently, facilitated by the independent origins of membrane-lipid biosynthesis: isoprenoid ether membranes in the archaebacterial and fatty acid ester membranes in the eubacterial lineage. The eukaryotes, all of which are ancestrally heterotrophs and possess eubacterial lipids, are suggested to have arisen ca. 2 Gyr ago through symbiosis involving an autotrophic archaebacterial host and a heterotrophic eubacterial symbiont, the common ancestor of mitochondria and hydrogenosomes. The attributes shared by all prokaryotes are viewed as inheritances from their confined universal ancestor. The attributes that distinguish eubacteria and archaebacteria, yet are uniform within the groups, are viewed as relics of their phase of differentiation after divergence from the non-free-living universal ancestor and before the origin of the free-living chemoautotrophic lifestyle. The attributes shared by eukaryotes with eubacteria and archaebacteria, respectively, are viewed as inheritances via symbiosis. The attributes unique to eukaryotes are viewed as inventions specific to their lineage. The origin of the eukaryotic endomembrane system and nuclear membrane are suggested to be the fortuitous result of the expression of genes for eubacterial membrane lipid synthesis by an archaebacterial genetic apparatus in a compartment that was not fully prepared to accommodate such compounds, resulting in vesicles of eubacterial lipids that accumulated in the cytosol around their site of synthesis. Under these premises, the most ancient divide in the living world is that between eubacteria and archaebacteria, yet the steepest evolutionary grade is that between prokaryotes and eukaryotes.

And:

The emergence of life from iron monosulphide bubbles at a submarine hydrothermal redox and pH front M. J. RUSSELL & A. J. HALL: Department of Geology and Applied Geology, University of Glasgow
Abstract: Here we argue that life emerged on Earth from a redox and pH front at c. 4.2 Ga. This front occurred where hot (c. 150)C), extremely reduced, alkaline, bisulphide-bearing, submarine seepage waters interfaced with the acid, warm (c. 90)C), iron-bearing Hadean ocean. The low pH of the ocean was imparted by the ten bars of CO2 considered to dominate the Hadean atmosphere/hydrosphere. Disequilibrium between the two solutions was maintained by the spontaneous precipitation of a colloidal FeS membrane. Iron monosulphide bubbles comprising this membrane were inflated by the hydrothermal solution upon sulphide mounds at the seepage sites. Our hypothesis is that the FeS membrane, laced with nickel, acted as a semipermeable catalytic boundary between the two fluids, encouraging synthesis of organic anions by hydrogenation and carboxylation of hydrothermal organic primers. The ocean provided carbonate, phosphate, iron, nickel and protons; the hydrothermal solution was the source of ammonia, acetate, HS", H2 and tungsten, as well as minor concentrations of organic sulphides and perhaps cyanide and acetaldehyde. The mean redox potential (ÄEh) across the membrane, with the energy to drive synthesis, would have approximated to 300 millivolts. The generation of organic anions would have led to an increase in osmotic pressure within the FeS bubbles. Thus osmotic pressure could take over from hydraulic pressure as the driving force for distension, budding and reproduction of the bubbles. Condensation of the organic molecules to polymers, particularly organic sulphides, was driven by pyrophosphate hydrolysis. Regeneration of pyrophosphate from the monophosphate in the membrane was facilitated by protons contributed from the Hadean ocean. This was the first use by a metabolizing system of protonmotive force (driven by natural ÄpH) which also would have amounted to c. 300 millivolts. Protonmotive force is the universal energy transduction mechanism of life. Taken together with the redox potential across the membrane, the total electrochemical and chemical energy available for protometabolism amounted to a continuous supply at more than half a volt. The role of the iron sulphide membrane in keeping the two solutions separated was appropriated by the newly synthesized organic sulphide polymers. This organic take-over of the membrane material led to the miniaturization of the metabolizing system. Information systems to govern replication could have developed penecontemporaneously in this same milieu. But iron, sulphur and phosphate, inorganic components of earliest life, continued to be involved in metabolism.

And:

The Path from the RNA World Anthony M. Poole, Daniel C. Jeffares, David Penny: Institute of Molecular Biosciences, Massey University
Abstract: We describe a sequential (step by step) Darwinian model for the evolution of life from the late stages of the RNA world through to the emergence of eukaryotes and prokaryotes. The starting point is our model, derived from current RNA activity, of the RNA world just prior to the advent of genetically-encoded protein synthesis. By focusing on the function of the protoribosome we develop a plausible model for the evolution of a protein-synthesizing ribosome from a high-fidelity RNA polymerase that incorporated triplets of oligonucleotides. With the standard assumption that during the evolution of enzymatic activity, catalysis is transferred from RNA M RNP M protein, the first proteins in the ``breakthrough organism'' (the first to have encoded protein synthesis) would be nonspecific chaperone-like proteins rather than catalytic. Moreover, because some RNA molecules that pre-date protein synthesis under this model now occur as introns in some of the very earliest proteins, the model predicts these particular introns are older than the exons surrounding them, the ``introns-first'' theory. Many features of the model for the genome organization in the final RNA world ribo-organism are more prevalent in the eukaryotic genome and we suggest that the prokaryotic genome organization (a single, circular genome with one center of replication) was derived from a ``eukaryotic-like'' genome organization (a fragmented linear genome with multiple centers of replication). The steps from the proposed ribo-organism RNA genome M eukaryotic-like DNA genome M prokaryotic-like DNA genome are all relatively straightforward, whereas the transition prokaryotic-like genome M eukaryotic-like genome appears impossible under a Darwinian mechanism of evolution, given the assumption of the transition RNA M RNP M protein. A likely molecular mechanism, ``plasmid transfer,'' is available for the origin of prokaryotic-type genomes from an eukaryotic-like architecture. Under this model prokaryotes are considered specialized and derived with reduced dependence on ssRNA biochemistry. A functional explanation is that prokaryote ancestors underwent selection for thermophily (high temperature) and/or for rapid reproduction (r selection) at least once in their history.
"Phylogeny from Function: The Origin of tRNA Is in Replication, not Translation", in the online book "Tempo and Mode in Evolution: Genetics and Paleontology 50 Years After Simpson"
Obcells as Proto-Organisms: Membrane Heredity, Lithophosphorylation, and the Origins of the Genetic Code, the First Cells, and Photosynthesis (Journal of Molecular Evolution, Volume 53 - Number 4/5, 2001)
N-Carbamoyl Amino Acid Solid-Gas Nitrosation by NO/NO_x: A New Route to Oligopeptides via alpha-Amino Acid N-Carboxyanhydride. Prebiotic Implications (Journal of Molecular Evolution, Volume 48 - Number 6, 1999
Chemical interactions between amino acid and RNA: multiplicity of the levels of specificity explains origin of the genetic code (Naturwissenschaften, Volume 89 Number 12 December 2002)
The Nicotinamide Biosynthetic Pathway Is a By-Product of the RNA World (Journal of Molecular Evolution, Volume 52 - Number 1, 2001)
On the RNA World: Evidence in Favor of an Early Ribonucleopeptide World
Inhibition of Ribozymes by Deoxyribonucleotides and the Origin of DNA
Genetic Code Origin: Are the Pathways of Type Glu-tRNAGln to Gln-tRNAGln Molecular Fossils or Not?

Johnston WK, Unrau PJ, Lawrence MS, Glasner ME, Bartel DP.RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension. Science. 2001 May 18;292(5520):1319-25.
Ferris JP. (1999 Jun). Prebiotic synthesis on minerals: bridging the prebiotic and RNA worlds. Biol Bull , 196, 311-4.
Levy M, and Miller SL. (1999 Jun). The prebiotic synthesis of modified purines and their potential role in the RNA world. J Mol Evol , 48, 631-7.
Unrau PJ, and Bartel DP. (1998 Sep 17). RNA-catalysed nucleotide synthesis [see comments] Nature , 395, 260-3.
Roth A, and Breaker RR. (1998 May 26). An amino acid as a cofactor for a catalytic polynucleotide [In Process Citation] Proc Natl Acad Sci U S A , 95, 6027-31.
Jeffares DC, Poole AM, and Penny D. (1998 Jan). Relics from the RNA world. J Mol Evol , 46, 18-36.
Poole AM, Jeffares DC, and Penny D. (1998 Jan). The path from the RNA world. J Mol Evol , 46, 1-17.
Wiegand TW, Janssen RC, and Eaton BE. (1997 Sep). Selection of RNA amide synthases. Chem Biol , 4, 675-83.
Di Giulio M. (1997 Dec). On the RNA world: evidence in favor of an early ribonucleopeptide world. J Mol Evol , 45, 571-8.
Hager AJ, and Szostak JW. (1997 Aug). Isolation of novel ribozymes that ligate AMP-activated RNA substrates. Chem Biol , 4, 607-17.
James KD, and Ellington AD. (1997 Aug). Surprising fidelity of template-directed chemical ligation of oligonucleotides [In Process Citation] Chem Biol , 4, 595-605.
Lohse PA, and Szostak JW. (1996 May 30). Ribozyme-catalysed amino-acid transfer reactions. Nature , 381, 442-4.
Lazcano A, and Miller SL. (1996 Jun 14). The origin and early evolution of life: prebiotic chemistry, the pre- RNA world, and time. Cell , 85, 793-8.
Ertem G, and Ferris JP. (1996 Jan 18). Synthesis of RNA oligomers on heterogeneous templates. Nature , 379, 238-40.
Robertson MP, and Miller SL. (1995 May 5). Prebiotic synthesis of 5-substituted uracils: a bridge between the RNA world and the DNA-protein world [see comments] Science , 268, 702-5.
Robertson MP, and Miller SL. (1995 Jun 29). An efficient prebiotic synthesis of cytosine and uracil [published erratum appears in Nature 1995 Sep 21;377(6546):257] Nature , 375, 772-4.
Breaker RR, and Joyce GF. (1995 Jun). Self-incorporation of coenzymes by ribozymes. J Mol Evol , 40, 551-8.
James KD, and Ellington AD. (1995 Dec). The search for missing links between self-replicating nucleic acids and the RNA world. Orig Life Evol Biosph , 25, 515-30.
Bohler C, Nielsen PE, and Orgel LE. (1995 Aug 17). Template switching between PNA and RNA oligonucleotides [see comments] Nature , 376, 578-81.
Connell GJ, and Christian EL. (1993 Dec). Utilization of cofactors expands metabolism in a new RNA world. Orig Life Evol Biosph , 23, 291-7.
Nielsen PE. (1993 Dec). Peptide nucleic acid (PNA): a model structure for the primordial genetic material? Orig Life Evol Biosph , 23, 323-7.
Lahav N. (1991 Aug 21). Prebiotic co-evolution of self-replication and translation or RNA world? J Theor Biol , 151, 531-9.
Ekland EH, Szostak JW, and Bartel DP. (1995 Jul 21). Structurally complex and highly active RNA ligases derived from random RNA sequences. Science , 269, 364-70.

Let me know when you get done reading those, and I'll give you some more.

Or if you'd like the Cliff-Notes version, here's a schematic:

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