The following objection to intelligent design is from observing the natural data and claiming that it could not have been designed because there are some things that lack proper function or there could have been a better way for a certain [i.e. organ] to function. This objection is often made by many theistic evolutionists, though, still non-theists object as well, is based on an inappropriate and misconceived understanding of design.[1] The design hypothesis merely states that there is intelligent causation that permits the existence of life (a probability factor). Optimality of what has been designed is not a criterion for design. Motor vehicles break down and computers crash. With comparing motor vehicles to design, there is a natural decay and effects of heat, friction, and weather decay. What is interesting about the comparison to malfunctioning software is that a frequently known cause of malfunction is an intentionally designed malware or virus, which has been designed for the primary purpose of malfunction, it is designed to break down or decompose a previous design.
Objecting to Intelligent Design because of Bad Design
Life Before Earth
The following is the abstract from a recent paper (“Life Before Earth,” 28 March 2013) published in arXiv by Alexei A. Sharov, Ph.D. (Staff Scientist, Laboratory of Genetics) and Richard Gordon, Ph.D. (Theoretical Biologist, Embryogenesis Center). What’s quite startling and significant about this paper is that it compares to the complexity found in biology and compares it to Moore’s Law, which is a computer/computational complexity. What’s important is not the mere issue of complexity but the specific coding elements required for specific function in conjunction with complexity. Thus, the information content is very complex, robust, and specified.
An extrapolation of the genetic complexity of organisms to earlier times suggests that life began before the Earth was formed. Life may have started from systems with single heritable elements that are functionally equivalent to a nucleotide. The genetic complexity, roughly measured by the number of non-redundant functional nucleotides, is expected to have grown exponentially due to several positive feedback factors: (1) gene cooperation, (2) duplication of genes with their subsequent specialization (e.g., via expanding differentiation trees in multicellular organisms), and (3) emergence of novel functional niches associated with existing genes. Linear regression of genetic complexity (on a log scale) extrapolated back to just one base pair suggests the time of the origin of life = 9.7 ± 2.5 billion years ago.
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The Discovery Institute’s Summer Seminars on Intelligent Design
I attended the Discovery Institute’s Summer Seminar on Intelligent Design (Social Science) in 2010. My thoughts and comments will be general since we were asked not release specifics concerning information being shared (some of it was yet-to-be published and I don’t know if it has been published yet so I’ll remain silent) and I do not want to “out” any other attendees in their academic endeavors. Once you’re labeled as an ID proponent your academic career is potentially slowed down or halted. I’ve already outed myself and I’m pretty vocal about my advocacy of design (I’m a philosopher so it’s not as academically persecuted).
I have no negative comments concerning the DI’s seminar. In fact, I have more respect for the institute and fellows. There were two concurrent seminars (natural and social sciences) that interacted with each other on a regular basis and combined on many occasions. I participated in the social science seminar and being philosophy graduate student I’m not as adept in biology, chemistry, and physics as many others are. I certainly received a welcoming abundance of science in presentations, which I thoroughly enjoyed. Some of the lecturers included Stephen Meyer, Michael Behe, William Dembski, Doug Axe, Jay Richards, Jonathan Wells, Richard Sternberg, Ann Gauger, Bruce Gordon, Jonathan Witt, John West, and Casey Luskin.
Two Leading Experts on Bacterial Flagellar Assembly Take on Michael Behe
Reblogged from Jonathan M. at Evolution News and Views…
I’ve been reading the recently published book Microbes and Evolution: The World that Darwin Never Saw, which combines my two primary areas of interest: microbiology and evolution. Chapter 38 of the book is written by Kelly Hughes and David Blair of the University of Utah, two of the world’s leading experts on bacterial flagellar assembly. Having followed the work of Kelly Hughes and his colleagues for a few years, I hold their work in the highest regard. I myself have a deep fascination with the subject of bacterial gene expression. I was intrigued, therefore, when I discovered the title of Hughes and Blair’s chapter: “Irreducible Complexity? Not!”
Following a very basic overview of flagellar structure and function (also described in my own detailed review of the subject), Hughes and Blair ask, “Is the flagellum irreducibly complex, or just complex?” They write,
It is clear that the flagellum is a complex structure and that its assembly and operation depend upon many interdependent components and processes. This complexity has been suggested to pose problems for the theory of evolution; specifically, it has been suggested that the ancestral flagellum could not have provided a significant advantage unless all of the parts were generated simultaneously. Hence, the flagellum has been described as “irreducibly complex,” implying that it is impossible or at least very difficult to envision a much simpler, but still useful, ancestral form that would have been the raw material for evolution.
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Catching William Lane Craig’s Intelligent Design Error
I was listening to William Lane Craig’s Reasonable Faith podcast on Sean Carroll on Science and God Part 1 this morning as I was walking from the parking lot into my office at University today, and I was quite surprised to hear a generalization Dr. Craig made concerning intelligent design.
Dr. Craig discusses how no models of the universe involve God. (This discussion begins around the 7 minute mark.) I think he’s correct in that we don’t have a physical theory of the universe that uses God as an entity in its explanation. For instance, you’ll find no entity in the standard model of particle physics that denotes God. However, Craig says that you do find this in the proponents of intelligent design theory “who want to postulate God as an entity in a scientific theory–that God would be like a quark, or a black hole, or a quantum field. He would be a theoretical entity postulated in a scientific theory.”
I have no doubt that there are intelligent design proponents, i.e. [young earth] creationists, who do this, but importing creationism into intelligent design theory strips ID for what it actually says.
ENCODE Project Nature Paper Finds “Biochemical Functions for 80% of the Genome”
A groundbreaking paper in Nature reports the results of the Encyclopedia of DNA Elements (ENCODE) project, which has detected evidence of function for the “vast majority” of the human genome. Titled “An integrated encyclopedia of DNA elements in the human genome,” the paper finds an “unprecedented number of functional elements,” where “a surprisingly large amount of the human genome” appears functional. Based upon current knowledge, the paper concludes that at least 80% of the human genome is now known to be functional:
The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation.(The ENCODE Project Consortium, “An integrated encyclopedia of DNA elements in the human genome,” Nature, Vol. 489:57-74 (September 6, 2012) (emphasis added))
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The Real Barrier to Unguided Human Evolution
Reblogged from Ann Gauger.
Comparing DNA sequences and estimating by how many nucleotides we differ from chimps doesn’t tell us much about what makes us human. Many of those nucleotide differences have no effect, because they are the product of neutral mutation and genetic drift. While these neutral mutations may affect the over-all mutation count, they don’t answer how many mutations are required for the transition from chimp-like to human.
This problem is analogous to one we examined concerning protein evolution last year in the journal BIO-Complexity (Gauger and Axe 2011). Converting one protein to another’s function can be viewed as a version, in miniature, of converting one species to another. But it is much easier to convert proteins than species.
The Challenge to Darwinism from a Single Remarkably Complex Enzyme
Original story by Ann Gauger
Meet carbamoyl phosphate synthetase (CPS), a remarkably complex enzyme. This enzyme uses bicarbonate, glutamine, ATP, and water to make carbamoyl phosphate via a multi-step reaction at three separate active sites, involving several unstable intermediates.
CPS is made of two protein chains with a combined length of over 1,400 amino acid residues. We now know from extensive biochemical data that a fully coupled CPS requires the hydrolysis of one glutamine and two molecules of MgATP for every molecule of carbamoyl phosphate formed.
A List of Peer-Reviewed Articles on Intelligent Design
Publications Supportive of Intelligent Design Published in Peer-Reviewed Scientific Journals, Conference Proceedings, or Scientific Anthologies.
- David L. Abel, “Is Life Unique?,” Life, Vol. 2:106-134 (2012).
- Joseph A. Kuhn, “Dissecting Darwinism,” Baylor University Medical Center Proceedings, Vol. 25(1): 41-47 (2012).
- 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).
- 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).
- 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).
- 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).
- 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).
- 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).
- 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).
- 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).
- 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).
- Douglas D. Axe, “The Case Against a Darwinian Origin of Protein Folds,” BIO-Complexity, Vol. 2010 (1) (2010).
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