Pharyngula

More bad science in the literature

That sad article on gyres as an explanation for everything has had more fallout: not only has it been removed from Science Daily’s site, not only has Case Western retracted the press release, but one of the editors at the journal Life has resigned his position over it. The editorial board of the journal was completely surprised by the wretched content of the paper, which is not encouraging; apparently they exercise so little oversight at the journal that they were unaware of the crap their reviewers were passing through. One board member thinks it is a hoax, and laughed at off. Think about that; your shiny new journal has just published total garbage, and instead of being brought up short and questioning the quality control of the review process, you think it is amusing that what you consider an obvious hoax slipped in? There’s something seriously wrong there.

Add this to the list of failures at Life: the paper immediaely after Andrulis’s is this one, “Is Life Unique?”, by David Abel. Guess what? It’s Intelligent Design creationism crap. Here’s the abstract:

Abstract: Is life physicochemically unique? No. Is life unique? Yes. Life manifests innumerable formalisms that cannot be generated or explained by physicodynamics alone. Life pursues thousands of biofunctional goals, not the least of which is staying alive. Neither physicodynamics, nor evolution, pursue goals. Life is largely directed by linear digital programming and by the Prescriptive Information (PI) instantiated particularly into physicodynamically indeterminate nucleotide sequencing. Epigenomic controls only compound the sophistication of these formalisms. Life employs representationalism through the use of symbol systems. Life manifests autonomy, homeostasis far from equilibrium in the harshest of environments, positive and negative feedback mechanisms, prevention and correction of its own errors, and organization of its components into Sustained Functional Systems (SFS). Chance and necessity–heat agitation and the cause-and-effect determinism of nature’s orderliness–cannot spawn formalisms such as mathematics, language, symbol systems, coding, decoding, logic, organization (not to be confused with mere self-ordering), integration of circuits, computational success, and the pursuit of functionality. All of these characteristics of life are formal, not physical.

It’s drivel. The whole thing is one long windy argument from assertion, as in the penultimate sentence above, which is simply the bald claim that higher order functions of human functions like cognition cannot be derived from chemistry and physics. The paper itself contains no data at all — no experiments, measurements, or observations — but it is full of novel acronyms. Apparently, all you need to do to make it as a big time creationist is to make up new words and phrases and string them together. I checked out some of his other papers — he seems to be some kind of computer science guy, and this is all he does, is write impenetrably glib papers full of pretentious acronyms, posing as an expert on biology while saying nothing credible about biology at all.

But he certainly has an impressive address and affiliation!

Department of ProtoBioCybernetics and ProtoBioSemiotics, Origin of Life Science Foundation, Inc., 113-120 Hedgewood Drive, Greenbelt, MD 20770

Whoa. Sounds major. Unfortunately, I’ve never heard of this foundation, and all I could find out about it is a webpage in which they announce a million dollar prize for “proposing a highly plausible natural-process mechanism for the spontaneous rise of genetic instructions in nature sufficient to give rise to life.” This sounds suspiciously like standard creationist dodging — they’ll never have to award this prize. So I looked at their judging, and at first glance it seems impressive: they have over 200 judges, including Jack Szostak, Peter Atkins, Paul Davies, and Edward O. Wilson. But then, they mention that judging will be in 5 tiers, and only the ones that pass all other reviews will reach the Nobel prize winners and famous scientists…and the first tier is an “in-house review”. I suspect the big names will never be pestered by this prize committee. Actually, I wonder if most of these judges know that their name is on this list. Maybe you should look in case you’ve been drafted.

I started wondering about this “in-house staff” who would be doing the initial judging, and about the Origin of Life Science Foundation itself. It’s awfully hard to track down — its only web presence is the prize page, and its only employee seems to be…David L. Abel. So I looked it up in google maps to see where the foundation’s majestic headquarters might be.

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It’s a house in a residential neighborhood of a Maryland suburb. It made me wonder if maybe the Department of ProtoBioCybernetics was located in the master bathroom, while he Department of ProtoBioSemiotics was in the hall closet, or whether both were consolidated into a sunny corner of the kitchen. At least it seems to be a step above Patriot University, but it’s still some guy’s house that he’s calling a Foundation with multiple implied Departments with fancy titles.

That’s not all! Mr Abel seems to be a linchpin of the Intelligent Design movement, who manages to work his rambling, incoherent publications into all kinds of journals. In fact, the Discovery Institute just bragged about all their peer-reviewed scientific publications, and there, in their list of over 70 works published over the last 25 years or so, which includes papers by such famous scientists as William Lane Craig and John A. Davison, and prestigious journals like Rivisti di Biologia and their own in-house pet journal, BIO-Complexity, and also seems to include books that were not peer-reviewed at all, are twelve papers by Mr Fancy-Titled-Suburban-House. 17% of the Intelligent Design creationism movement’s ‘scientific’ output comes out of that dwelling in Maryland.

I’d love to see the gigantic laboratory he must have in there.

For your edification, I’ve included the official complete list of Intelligent Design creationism’s publications below the fold. It’s an impressively short list of hackery.

And may I suggest that the journal Life has deeper problems than simply accidentally allowing one bad paper to slip into publication? I think it needs a negative impact factor.

(Also on FtB)


The Discovery Institute’s very own list of the entirety of the intelligent design literature

Publications Supportive of Intelligent Design Published in Peer-Reviewed Scientific Journals, Conference Proceedings, or Scientific Anthologies.

  1. Joseph A. Kuhn, “Dissecting Darwinism,” Baylor University Medical Center Proceedings, Vol. 25(1): 41-47 (2012).

  2. David L. Abel, “Is Life Unique?,” Life, Vol. 2:106-134 (2012).

  3. Douglas D. Axe, Philip Lu, and Stephanie Flatau, “A Stylus-Generated Artificial Genome with Analogy to Minimal Bacterial Genomes,” BIO-Complexity, Vol. 2011(3) (2011).

  4. Stephen C. Meyer and Paul A. Nelson, “Can the Origin of the Genetic Code Be Explained by Direct RNA Templating?,” BIO-Complexity, Vol. 2011(2) (2011).

  5. Ann K. Gauger and Douglas D. Axe, “The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway,” BIO-Complexity, Vol. 2011(1) (2011).

  6. Ann K. Gauger, Stephanie Ebnet, Pamela F. Fahey, and Ralph Seelke, “Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness,” BIO-Complexity, Vol. 2010 (2) (2010).

  7. Michael J. Behe, “Experimental Evolution, Loss-of-Function Mutations, and ‘The First Rule of Adaptive Evolution,’” The Quarterly Review of Biology, Vol. 85(4):1-27 (December 2010).

  8. Douglas D. Axe, “The Limits of Complex Adaptation: An Analysis Based on a Simple Model of Structured Bacterial Populations,” BIO-Complexity, Vol. 2010(4):1 (2010).

  9. Wolf-Ekkehard Lönnig, “Mutagenesis in Physalis pubescens L. ssp. floridana: Some further research on Dollo’s Law and the Law of Recurrent Variation,” Floriculture and Ornamental Biotechnology, 1-21 (2010).

  10. George Montañez, Winston Ewert, William A. Dembski, and Robert J. Marks II, “A Vivisection of the ev Computer Organism: Identifying Sources of Active Information,” BIO-Complexity, Vol. 2010(3) (2010).

  11. William A. Dembski and Robert J. Marks II, “The Search for a Search: Measuring the Information Cost of Higher Level Search,” Journal of Advanced Computational Intelligence and Intelligent Informatics, Vol. 14 (5):475-486 (2010).

  12. Douglas D. Axe, “The Case Against a Darwinian Origin of Protein Folds,” BIO-Complexity, Vol. 2010 (1) (2010).

  13. Winston Ewert, George Montañez, William Dembski and Robert J. Marks II, “Efficient Per Query Information Extraction from a Hamming Oracle,” 42nd South Eastern Symposium on System Theory, pp. 290-297 (March, 2010).

  14. David L. Abel, “Constraints vs Controls,” The Open Cybernetics and Systemics Journal, Vol. 4:14-27 (January 20, 2010).

  15. David L. Abel, “The GS (genetic selection) Principle,” Frontiers in Bioscience, Vol. 14:2959-2969 (January 1, 2010).

  16. D. Halsmer, J. Asper, N. Roman, and T. Todd, “The Coherence of an Engineered World,” International Journal of Design & Nature and Ecodynamics, Vol. 4(1):47–65 (2009).

  17. William A. Dembski and Robert J. Marks II, “Bernoulli’s Principle of Insufficient Reason and Conservation of Information in Computer Search,” Proceedings of the 2009 IEEE International Conference on Systems, Man, and Cybernetics, pp. 2647 – 2652 (October, 2009).

  18. William A. Dembski and Robert J. Marks II, “Conservation of Information in Search: Measuring the Cost of Success,” IEEE Transactions on Systems, Man, and Cybernetics-Part A: Systems and Humans, Vol. 39(5):1051-1061 (September, 2009).

  19. David L. Abel, “The Universal Plausibility Metric (UPM) & Principle (UPP),” Theoretical Biology and Medical Modelling, Vol. 6(27) (2009).

  20. David L. Abel, “The Capabilities of Chaos and Complexity,” International Journal of Molecular Sciences, Vol. 10:247-291 (2009).

  21. David L. Abel, “The biosemiosis of prescriptive information,” Semiotica, Vol. 174(1/4):1-19 (2009).

  22. A. C. McIntosh, “Information and Entropy – Top-Down or Bottom-Up Development in Living Systems,” International Journal of Design & Nature and Ecodynamics, Vol. 4(4):351-385 (2009).

  23. A.C. McIntosh, “Evidence of design in bird feathers and avian respiration,” International Journal of Design & Nature and Ecodynamics, Vol. 4(2):154–169 (2009).

  24. David L. Abel, “The ‘Cybernetic Cut’: Progressing from Description to Prescription in Systems Theory,” The Open Cybernetics and Systemics Journal, Vol. 2:252-262 (2008).

  25. Richard v. Sternberg, “DNA Codes and Information: Formal Structures and Relational Causes,” Acta Biotheoretica, Vol. 56(3):205-232 (September, 2008).

  26. Douglas D. Axe, Brendan W. Dixon, Philip Lu, “Stylus: A System for Evolutionary Experimentation Based on a Protein/Proteome Model with Non-Arbitrary Functional Constraints,” PLoS One, Vol. 3(6):e2246 (June 2008).

  27. Michael Sherman, “Universal Genome in the Origin of Metazoa: Thoughts About Evolution,” Cell Cycle, Vol. 6(15):1873-1877 (August 1, 2007).

  28. Kirk K. Durston, David K. Y. Chiu, David L. Abel, Jack T. Trevors, “Measuring the functional sequence complexity of proteins,” Theoretical Biology and Medical Modelling, Vol. 4:47 (2007).

  29. David L. Abel, “Complexity, self-organization, and emergence at the edge of chaos in life-origin models,” Journal of the Washington Academy of Sciences, Vol. 93:1-20 (2007).

  30. Wolf-Ekkehard Lönnig, Kurt Stüber, Heinz Saedler, Jeong Hee Kim, “Biodiversity and Dollo’s Law: To What Extent can the Phenotypic Differences between Misopates orontium and Antirrhinum majus be Bridged by Mutagenesis,” Bioremediation, Biodiversity and Bioavailability, Vol. 1(1):1-30 (2007).

  31. Wolf-Ekkehard Lönnig, “Mutations: The Law of Recurrent Variation,” Floriculture, Ornamental and Plant Biotechnology, Vol. 1:601-607 (2006).

  32. David L. Abel and Jack T. Trevors, “Self-organization vs. self-ordering events in life-origin models,” Physics of Life Reviews, Vol. 3:211–228 (2006).

  33. David L. Abel and Jack T. Trevors, “More than Metaphor: Genomes Are Objective Sign Systems,” Journal of BioSemiotics, Vol. 1(2):253-267 (2006).

  34. Øyvind Albert Voie, “Biological function and the genetic code are interdependent,” Chaos, Solitons and Fractals, Vol. 28:1000–1004 (2006).

  35. Kirk Durston and David K. Y. Chiu, “A Functional Entropy Model for Biological Sequences,” Dynamics of Continuous, Discrete & Impulsive Systems: Series B Supplement (2005).

  36. David L. Abel and Jack T. Trevors, “Three subsets of sequence complexity and their relevance to biopolymeric information,” Theoretical Biology and Medical Modeling, Vol. 2(29):1-15 (August 11, 2005).

  37. John A. Davison, “A Prescribed Evolutionary Hypothesis,” Rivista di Biologia/Biology Forum, Vol. 98: 155-166 (2005).

  38. Wolf-Ekkehard Lönnig, “Mutation Breeding, Evolution, and the Law of Recurrent Variation,” Recent Research Developments in Genetics & Breeding, Vol. 2:45-70 (2005).

  39. Douglas D. Axe, “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds,” Journal of Molecular Biology, Vol. 341:1295–1315 (2004).

  40. Michael Behe and David W. Snoke, “Simulating evolution by gene duplication of protein features that require multiple amino acid residues,” Protein Science, Vol. 13 (2004).

  41. Wolf-Ekkehard Lönnig, “Dynamic genomes, morphological stasis, and the origin of irreducible complexity,” in Valerio Parisi, Valeria De Fonzo, and Filippo Aluffi-Pentini eds., Dynamical Genetics (2004).

  42. 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) (HTML).

  43. John Angus Campbell and Stephen C. Meyer, Darwinism, Design, and Public Education (“DDPE”) (East Lansing, Michigan: Michigan State University Press, 2003).

  44. Frank J. Tipler, “Intelligent Life in Cosmology,” International Journal of Astrobiology, Vol. 2(2): 141-148 (2003).

  45. David L. Abel, “Is Life reducible to complexity?,” Fundamentals of Life, Chapter 1.2 (2002).

  46. David K.Y. Chiu and Thomas W.H. Lui, “Integrated Use of Multiple Interdependent Patterns for Biomolecular Sequence Analysis,” International Journal of Fuzzy Systems, Vol. 4(3):766-775 (September 2002).

  47. Michael J. Denton, Craig J. Marshall, and Michael Legge, “The Protein Folds as Platonic Forms: New Support for the pre-Darwinian Conception of Evolution by Natural Law,” Journal of Theoretical Biology, Vol. 219: 325-342 (2002).

  48. Wolf-Ekkehard Lönnig and Heinz Saedler, “Chromosome Rearrangement and Transposable Elements,” Annual Review of Genetics, Vol. 36:389–410 (2002).

  49. Douglas D. Axe, “Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors,” Journal of Molecular Biology, Vol. 301:585-595 (2000).

  50. Solomon Victor and Vijaya M. Nayak, “Evolutionary anticipation of the human heart,” Annals of the Royal College of Surgeons of England, Vol. 82:297-302 (2000).

  51. Solomon Victor, Vljaya M. Nayek, and Raveen Rajasingh, “Evolution of the Ventricles,” Texas Heart Institute Journal, Vol. 26:168-175 (1999).

  52. W. A. Dembski, The Design Inference: Eliminating Chance through Small Probabilities (Cambridge: Cambridge University Press, 1998).

  53. R. Kunze, H. Saedler, and W.-E. Lönnig, “Plant Transposable Elements,” in Advances in Botanical Research, Vol. 27:331-409 (Academic Press, 1997).

  54. Michael Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution (New York: The Free Press, 1996).

  55. Charles B. Thaxton, Walter L. Bradley, Roger L. Olsen, The Mystery of Life’s Origin: Reassessing Current Theories (New York: Philosophical Library, 1984; Dallas, Texas: Lewis & Stanley Publishing, 4th ed., 1992).

  56. Stanley L. Jaki, “Teaching of Transcendence in Physics,” American Journal of Physics, Vol. 55(10):884-888 (October 1987).

  57. Granville Sewell, “Postscript,” in Analysis of a Finite Element Method: PDE/PROTRAN (New York: Springer Verlag, 1985) (HTML).

  58. William G. Pollard, “Rumors of transcendence in physics,” American Journal of Physics, Vol. 52 (10) (October 1984).

  59. Peer-Edited or Editor-Reviewed Articles Supportive of Intelligent Design Published in Scientific Journals, Scientific Anthologies and Conference Proceedings

  60. A. C. McIntosh, “Functional Information and Entropy in Living Systems,” Design and Nature III: Comparing Design in Nature with Science and Engineering, Vol. 87 (Ashurt, Southampton, United Kindom: WIT Transactions on Ecology and the Environment, WIT Press, 2006).

  61. Jonathan Wells, “Do Centrioles Generate a Polar Ejection Force?” Rivista di Biologia /Biology Forum, Vol. 98:71-96 (2005).

  62. Heinz-Albert Becker and Wolf-Ekkehard Lönnig, “Transposons: Eukaryotic,” Encyclopedia of Life Sciences (John Wiley & Sons, 2005).

  63. Scott A. Minnich and Stephen C. Meyer, “Genetic analysis of coordinate flagellar and type III regulatory circuits in pathogenic bacteria,” Proceedings of the Second International Conference on Design & Nature, Rhodes, Greece, edited by M.W. Collins and C.A. Brebbia (Ashurst, Southampton, United Kingdom: WIT Press, 2004).

  64. Four science articles in William A. Dembski and Michael Ruse, eds., Debating Design: From Darwin to DNA (Cambridge, United Kingdom: Cambridge University Press, 2004) (hereinafter “Debating Design”).

  65. Granville Sewell, “A Mathematician’s View of Evolution,” The Mathematical Intelligencer, Vol. 22(4) (2000). (HTML).
  66. Articles Supportive of Intelligent Design Published in Peer-Reviewed Philosophy Journals, or Peer-Reviewed Philosophy Books Supportive of Intelligent Design

  67. Michael C. Rea, World without Design : The Ontological Consequences of Naturalism (Oxford University Press, 2004).

  68. William Lane Craig, “Design and the Anthropic Fine-Tuning of the Universe,” in God and Design: The Teleological Argument and Modern Science, pp. 155-177. (Neil Manson ed., London: Routledge, 2003).

  69. Michael Behe, “Reply to my Critic: A Response to Reviews of Darwin’s Black Box: The Biochemical Challenge to Evolution,” Biology and Philosophy, Vol. 16, 685–709, (2001).

  70. Del Ratzsch, Nature, Design, and Science: The Status of Design in Natural Science (State University of New York Press, 2001).

  71. William Lane Craig, “The Anthropic Principle,” in The History of Science and Religion in the Western Tradition: An Encyclopedia, pp. 366-368 (Gary B. Ferngren, general ed., Garland Publishing, 2000).

  72. Michael Behe, “Self-Organization and Irreducibly Complex Systems: A Reply to Shanks and Joplin,” Philosophy of Biology, Vol. 67(1):155-162 (March, 2000).

  73. William Lane Craig, “Barrow and Tipler on the Anthropic Principle vs. Divine Design,” British Journal for the Philosophy of Science, Vol. 38: 389-395 (1988).

  74. William Lane Craig, “God, Creation, and Mr. Davies,” British Journal for the Philosophy of Science, Vol. 37: 168-175 (1986).