Posts tagged ‘ID’

May 3rd, 2012

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.

Continue reading…

February 15th, 2012

A List of Peer-Reviewed Articles on Intelligent Design

There’s been a long running tradition in the Darwinian anti-ID camp propounding that there are no published peer-reviewed papers on intelligent design.  Ever since this mantra was first popularly proclaimed they’ve been wrong.  Below is a list of peer-reviewed articles cataloged by the Discovery Institute.  For abstracts and more on the articles please visit their site.

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

  1. David L. Abel, “Is Life Unique?,” Life, Vol. 2:106-134 (2012).
  2. Joseph A. Kuhn, “Dissecting Darwinism,” Baylor University Medical Center Proceedings, Vol. 25(1): 41-47 (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).
    read more »

February 7th, 2012

Junk DNA Isn’t Necessarily Junk

The argument from junk DNA suggests that a designer would be maximally efficient in his use of information.  There appears to be some information that does not execute or have any meaningful coding.  Darwinism takes this issue and uses it as the result of the prediction that there would be left over information not being used due to natural selection and random mutation.  However, it doesn’t appear that all junk DNA is actually junk.

The classical model of the genome was developed to support the Darwinian New Synthesis and was based on these assumptions:

  • Genetic determinants are discrete physical units
  • Only the collection of genes (genotype) is real; organismal development and traits (the phenotype) are epiphenomenal
  • The structure of gene can be explained solely in terms of population genetics (mutation and selection/genetic drift)

The presuppositions of the model

  • Genomes are the only carriers of phenotypic determinants; no laws of form exist à phenotypes mirror genotypes
  • Genomes are aggregates of simple entities that are constantly changing entails that phenotypes are always transforming
  • Genomes can be recombined and mutated in an unlimited way à morphological evolution is “open-minded”
  • Any two sets of genomes are connected by a finite number of mutations à morphological gaps are illusory
    read more »

October 4th, 2011

An Objection to Intelligent Design I’ve Never Heard

I was in a tweebate (tweet debate) with another person [whom shall remain anonymous] over a previous post of mine where I claimed that Ken Miller’s argument against irreducible complexity was a bad argument (I really don’t like Twitter debates/conversations either).  This person went on about how Miller’s argument convinced Judge Jones and my position was that it’s actually quite embarrassing that the argument would convince anyone (see my post for the context).  Then he claimed the type three secretory system is an objection to irreducible complexity in the bacterial flagellum, which prompted me to claim that it may indeed be IC itself and there are arguments that the flagellum may have come first.  Anyways, those aren’t what interests me.  The argument that I had never heard before was:

ID claims are anything but modest.  Incapacity to imagine other explanations of our beginnings is not evidence of ID. Non sequitur.

Let me be clear, I have never claimed anywhere at any time… ever… that one should be a proponent of intelligent design because of an incapacity to imagine other explanations.  So first of all, this argument belongs in a cornfield scaring away the crows.  Secondly, this is an utterly blatant attack on my imagination! I’ve got a great imagination! (Okay, the second point isn’t really a part of my argument.) It’s true, if anyone did make an argument for ID based on a lack of imagination it would be a non sequitur since one’s capacity to imagine something has nothing to do with the truth claim (as long as the claim is sound/rational, I cannot imagine the actualization of a contradiction).  I’m fairly confident anyone familiar with intelligent design and the state of the evolution controversy would never make an argument for intelligent design like this.  In fact, no one should ever make such an argument for ID like this.

I’ve explained before in my post on God and Darwinism, the reasons why I’m not a Darwinist are for two reasons: 1) the origin of information must be mind and 2) there is objective teleology in the world and primarily human beings.  I do believe the argument from irreducible complexity is a good argument for ID but I’m not going to die on that hill.  I think intelligent causation is a legitimate scientific hypothesis and explanation.  However, there are certain philosophical truths that press the argument.  I could care less if man evolved from a common ancestor but this evolution could not have occurred without a mind acting on the origin of the information in DNA and I believe man [evolves] with an end goal in mind.  That’s why I reject Darwinism.

October 1st, 2011

Metaphysical Implications of Intelligent Design

The truth is that now all theories of origins, theistic or atheistic, involve speculation as to the nature of what it was that created a universe so fine-tuned for life.  The question is only, was it an intelligent or an unintelligent cause that created time, space, matter and energy out of nothing?[1]  With regards to the argument from design, Columbia University astronomer, Robert Jastrow discussed what he calls “the most theistic result to ever come out of science”:

According to the picture of the evolution of the universe developed by the astronomer and his fellow scientists, the smallest change in any of the circumstances of the natural world, such as the relative strengths of the forces of nature, or the properties of the elementary particles, would have led to a universe in which there could be no life and no man…

It is possible to make the same argument about changes in the strengths of the electromagnetic force, the force of gravity, or any other constants of the material universe, and so come to the conclusion that in a slightly changed universe there could be no life, and no man.  Thus according to the physicist and the astronomer, it appears that the universe was constructed within very narrow limits, in such a way that man could dwell in it.  This result is called the anthropic principle.

Some scientists suggest, in an effort to avoid a theistic or teleological implication in their findings, that there must be an infinite number of universes, representing all possible combinations of basic forces and conditions, and that our universe is one of an infinitely small fraction, in this great plenitude of universes, in which life exists.[2]

The design argument is quite modest by simply stating that intelligent causation can be detected in the natural world.  The argument does not and cannot infer the identity of the designer alone.  In order to identify the designer one must seek external evidences, such as other scientific, philosophical, historical, and theological evidences.  A cumulative case argument would fulfill this need.  The extent of what can be known is that the designer is an agent.  Agency is inferred by the ability to create brand new information, to initiate and cease a causal chain of events.  Also, this agent must not be organic since it too would require a cause of its information.  No regress is necessary since there is only one entity that must be identified as the cause.  Whether there is a regress doesn’t really matter at all since only one phenomena, that of the origin of information in living matter, only requires that one entity be instantiated.


            [1] Granville Sewell, In the Beginning (Seattle, WA:  Discovery Institute Press, 2010), 25.

            [2] Robert Jastrow quoted by Roy Varghese, The Intellectuals Speak About God, (Regenery Gateway), 1984.

October 1st, 2011

Theistic Evolution and Purposive Permission

This objection to intelligent design is within a theistic philosophy and theology.  The theistic evolutionist would make the arguments for Darwinism just like the atheist would make his arguments for Darwinism; the only difference is that the former is a theist.  Asa Gray (1810-1888) was a proponent of evolution who suggested that God guided evolution.  The problem for the theistic evolutionist at this point is that if God guides evolution, it is design.  Guidance implies purpose and involvement.  The theistic evolutionist, so defined as God guiding evolution, is not really a detractor from design, rather he would be a proponent of common decent, which is entirely compatible with design.

It was not until the early twentieth century when a movement that emphasized Darwinian natural selection did theistic evolution attempt to reconcile unguided evolution with God.  The following theistic evolutionist present an appropriate summation for the current understanding:

“An evolutionary universe is theologically understood as creation allowed to make itself.”[1]

“Mankind’s appearance on this planet was not preordained… we are here… as an afterthought, a minor detail, a happenstance in a history that might just as well have left us out.”[2]

“Evolution could appear to us to be driven by chance, but from God’s perspective the outcome would be entirely specified.  Thus, God could be completely and intimately involved in the creation of all species, while from our perspective, limited as it is by the tyranny of linear time, this would appear a random and undirected process.”[3]

It may be important to distinguish the last quote from Collins from the former quotes.  It is difficult, even impossible, to distinguish Collins’ position as not being intelligent design.  Why would Collins use the human perspective as the objective standard for whether or not there actually is design?  He willingly concedes that God could be intimately involved in creating yet it is illusory to the human perspective.

The argument from cognitive relations may be understood as an argument from omniscience or providence.  If God allows any state of affairs to be actualized, and knows that it will happen, and then there is a teleology in that events actualization.  The underlying principle is what is called “purposive permission.”  This principle makes a minimal commitment to any event X, such that X will come to be either by it being permitted to occur or by being strongly actualized to occur.  Purposive permission assumes that if any event is permitted to happen then it is within the will of the knowing agent that the event be actualized.  If the event were known that it would come to pass and it was not desired to come to pass, then it would not have been permitted to be and would not have happened.  Under the current understanding of unguided evolution, the only way to reconcile that with theism is to adopt process theology, an understanding that God is not ontologically perfect and is literally evolving with the world.[4]


            [1] John Polkinghorne, Faith, Science, and Understanding (New Haven, CT:  Yale University Press, 2000), 23, 111, 197.

            [2] Kenneth Miller, Finding Darwin’s God (New York:  Harper Perennial, 2000), 272-273.

            [3] Francis Collins, The Language of God (New York:  Free Press, 2006), 205.

            [4] Even weak understandings of cognitive relations, or interactions, would still render design (categorically defined from an orthodox perspective).  All that would require from the knowing agent (God) is that, within the mind, there must at least be two moments of knowledge:  natural knowledge (the first logical moment) and free knowledge (the last logical moment).  In the first moment the agent must know all tautologies and every possible circumstance.  The final moment is knowing the actual world, the current, past, and future state of affairs.  The only theistic model that does not hold to these two moments would be the process model.  I want to note, that open theism would not even be compatible with a Darwinist understanding of evolution because God would only be ignorant of future contingencies that involved human freedom.

October 1st, 2011

Ken Miller’s Embarrassing Attempt to Disprove Irreducible Complexity

This video has been out for a while but I just saw it reposted on a blog I saw through Twitter.  I’m not going to summarize the video here; rather, just give it a quick watch, it’s only two minutes.

Honestly, it’s a bit embarrassing and I feel bad for him.  His attempt to disprove irreducible complexity demonstrates that 1) he doesn’t actually understand it or 2) displaces the information. When he changed the mousetrap to function as a tie clip that tie clip then becomes a new mechanism.  Whether that tie clip was actually irreducibly complex or not doesn’t matter.  His attempt would be correct if he could remove or change a part of the mouse trap while keeping it’s function as a mouse trap.

As for the scholarship of intelligent design and irreducible complexity, he’s simply incorrect there as well.  Darwinists always do this and it’s just annoying and dishonest (or simply wrong).  For a list of peer-reviewed articles that have been published in regards to intelligent design and irreducible complexity (and yes, the words are used in the articles, sorry Ken) please see the Discovery Institute’s list.

August 7th, 2011

Metaphysical Implications of the Fine-Tuning for Life

The truth is that now all theories of origins, theistic or atheistic, involve speculation as to the nature of what it was that created a universe so fine-tuned for life.  The question is only, was it an intelligent or an unintelligent cause that created time, space, matter and energy out of nothing?[1]  With regards to the argument from design, Columbia University astronomer, Robert Jastrow discussed what he calls “the most theistic result to ever come out of science”:

According to the picture of the evolution of the universe developed by the astronomer and his fellow scientists, the smallest change in any of the circumstances of the natural world, such as the relative strengths of the forces of nature, or the properties of the elementary particles, would have led to a universe in which there could be no life and no man…

It is possible to make the same argument about changes in the strengths of the electromagnetic force, the force of gravity, or any other constants of the material universe, and so come to the conclusion that in a slightly changed universe there could be no life, and no man.  Thus, according to the physicist and the astronomer, it appears that the universe was constructed within very narrow limits, in such a way that man could dwell in it.  This result is called the anthropic principle.

Some scientists suggest, in an effort to avoid a theistic or teleological implication in their findings, that there must be an infinite number of universes, representing all possible combinations of basic forces and conditions, and that our universe is one of an infinitely small fraction, in this great plenitude of universes, in which life exists.[2]

As I’ve noted in previous works and posts, the design argument is quite modest by simply stating that intelligent causation can be detected in the natural world.  The argument does not and cannot infer the identity of the designer alone.  In order to identify the designer one must seek external evidences, such as other scientific, philosophical, historical, and theological evidences.  A cumulative case argument would fulfill this need.


            [1] Granville Sewell, In the Beginning (Seattle, WA:  Discovery Institute Press, 2010), 25.

            [2] Robert Jastrow quoted by Roy Varghese, The Intellectuals Speak About God, (Regenery Gateway), 1984.

August 2nd, 2011

The Methodology Behind the Teleological Argument

The argument from design is modest in what it purports.  The final claim and conclusion is that there is an extremely intelligent and personal mind, which is responsible for the design in the universe.[1]  The Greek word, telos, is an end goal or purpose.  The design argument was first developed by the ancient Greeks and popularized by William Paley (1743-1805).  The objections to Paley, which served as a catalyst for the arguments popularity among science and philosophy, were purported by David Hume (1711-1776).

The current state of the argument has gained considerable advances in interest in philosophy, theology, science, and even culture.  Cambridge physicist Stephen Hawking purported in his recent [paradoxically titled] book, The Grand Design, that the universe no longer needs intervention or a supernatural being to account for the design and creation of the universe.[2]  Most of the interests in the design argument are advances in the scientific account for the beginning of the universe, which are used to argue against the fine-tuning, which will be evaluated.

It is paramount to explicate from the beginning that this is philosophy of science.  This practice is not theological.[3]  The argument is a posteriori gathered from the natural sciences.  The method by which design will be inferred is a historical science.  There are four differences between a historical science and a laboratory science.  First, repeatability is not applicable in the historical sciences; it is a metacriterion for laboratory science.  Second, historical science assumes uniformitarianism, that is, there are presently known causes to phenomena, which can be inferred by perceived effects.[4]  Third, the theories and explanatory hypotheses must lay in empirical harms way.  The conclusions must be falsifiable.  It should be noted that the type of scientific inquiry will be that of an Augustinian science as opposed to a Duhemian science.  Augustinian science permits and carries open metaphysical presuppositions with science.  Duhemian science strips science of all metaphysical imports.  This point yields to the final distinction, which is the understanding that historical science must use non-controversial reasoning.  The controversial claim for the design proponent is simply the introduction of intelligent causation.  However, this is not as controversial as much of the scientific community makes it out to be.  Agency is publically accepted evidence by experience.[5]

Such methods are derived from the use of abductive reasoning.  The American philosopher and logician Charles Sanders Peirce first described abduction.  He noted that, unlike inductive reasoning, in which a universal law or principle is established from repeated observations of the same phenomena, and unlike deductive reasoning, in which a particular fact is deduced by applying a general law to another particular fact or case, abductive reasoning infers unseen facts, events, or causes in the past from clues or facts in the present.[6] Consider the following syllogism:

If it rains, the streets will get wet.

The streets are wet.

Therefore, it rained.

The use of abductive reasoning may seem fallacious at first take.  This syllogism commits the fallacy of affirming the consequent.  One cannot deduce from the data, that the streets are wet, that it rained because there are many other explanations for why the streets are wet.  It could have been the case that a fire hydrant was allowed to flow, a street cleaner came through, a concerned citizen who wanted to clean the chalk off of the streets from the little children drawing pictures or writing words, there are many possibilities that could explain why the road was wet.  This was the problem that posed Peirce:  How was it that despite the logical problem of affirming the consequent, one nevertheless frequently makes conclusive inferences about the past?  The key point is the explanatory scope and power of the explanation.  Abductive reasoning does not derive a certain conclusion (for one would then be guilty of affirming the consequent), but it makes an inference to the best explanation.  Peirce’s example was whether anyone should believe in the existence of Napoleon.  He claimed that the past may be inferred from the study of present effects, namely, artifacts and records.  Peirce concluded, “Though we have not seen the man [Napoleon], yet we cannot explain what we have seen without the hypothesis of his existence.”[7]  Despite the apparent fallacy, W.P. Alston, W.B. Gallie, and Michael Scriven have observed, such arguments can be restated in a logically acceptable form if it can be shown that Y has only one cause (i.e. X) or that X is a necessary condition (or cause) of Y.  Thus, arguments of the form:

X is antecedently necessary to Y,

Y exists,

Therefore, X existed

are logically valid by philosophers and persuasive by historical and forensic scientists.[8]

The suggestion was that a particular abductive hypothesis can be firmly established if it can be shown that it represents the best or only explanation of the “manifest effects” in question.[9]  The only causally adequate explanation of the life-permitting data is intelligent causation.  Minds, by experience, are capable of presenting and originating specified complex information.


            [1] The most modest claims of the argument are for an intelligent cause.  I choose to add a “personal mind” to the argument due to metaphysical implications of an intelligent causation.

            [2] Stephen Hawking, Leonard Mlodinow, The Grand Design (New York:  Random House, 2010), 8.  Hawking and Mlodinow base their positions on a model-dependent realism approach.  This ultimately voids all objective claims and their objections to design, primarily due to their confidence in M-Theory.

            [3] The argument, when combined with a cumulative case, may then be exported as philosophy of religion, but for now, the methods and data that will be examined will be done so from a scientific and philosophical perspective.

             [4] The method of uniformitarianism is currently understood in the scientific community as an assumption of the regular course of events as well as catastrophism (which would be implied by the presently known cause and effect relationships).

            [5] This is not based on religious explanations or religious experience.

            [6] In the words of Stephen C. Meyer, Signature in the Cell (New York:  Harper Collins, 2009), 153.  Charles Peirce, Collected Papers, 2:375; “Abduction and Induction.”

            [7] Peirce, Collected Papers, 2:375.

            [8] Stephen C. Meyer, “A Scientific History—and Philosophical Defense—of the Theory of Intelligent Design.” W. P. Alston, “The Place of the Explanation of Particular Facts in Science,” Philosophy of Science 38 (1971):  13-34.  W. B. Gallie, “Explanations in History and the Genetic Sciences” in Theories of History:  Readings from Classical and Contemporary Sources (Glencoe, IL: Free Press, 1959), 386-402. Michael Scriven, “Explanation and Prediction in Evolutionary Theory,” Science 130 (1959):  477-482.

            [9] Meyer, Signature in the Cell, 154.

June 4th, 2011

God and Darwinism

I have two primary objections to Darwinism.  My first objection is that the best [and only] known source of information is mind (a positive case) and nature’s inability to sufficiently account for the origin of information (a negative case).  My second objection is that everything, particularly humans, has a purpose and chance voids any initial intention and final intention.  My focus here will be Darwinism within a theistic context.  However, before I continue I would like to clarify one point.  I’m not referring to evolution being change over time, which I agree with, or evolution being common descent, which I don’t hold to but I’m open to.  These two forms of evolution are completely compatible with intelligent design.  By Darwinism I mean that natural selection/mutation is the mechanism capable of creating new life forms.

Michelangelo's Creation of Adam

Initial intent is something that allows for design to be a legitimate inference by material or efficient causation (i.e. what it’s made of or what produced it respectively).  This would include design being inferred by the origin of information within a cell, limits on population genetics, irreducible complexity, or epigenetic information and higher information processing in the cell [and an extrapolation of causes].  Theistic Darwinists would deny these as any purposeful acts or intentions by God because it’s an implicit contradiction to Darwinism by definition.  Let’s consider final intention. Final causation answers the question, “For what purpose was this caused?”  If the theistic Darwinist wants to maintain that humans have purpose then it’s only at best secondarily and a reaction of God’s [to give purpose to humans] in light of chance’s bringing about of humans.  Consider these quotes.

An evolutionary universe is theologically understood as a creation allowed to make itself. -John Polkinghorne

Not even God could know… with certainty that human life would come to be. -George Coyne

Mankind’s appearance on this planet was not preordained… we are here… as an after-thought, a minor detail, a happenstance in a history that might just as well have left us out. -Ken Miller

It seems that once chance and nature bring about the existence of humans only then can God predicate any purpose.  My problem with that is how can this really be final causation?  How can there be final causation without material and efficient causes?  If God set up the universe’s initial conditions to bring about the elements and conditions needed for the evolution of life to take place then that is still design.  My favorite theistic Darwinist quote is Francis Collins’ when he says,

Evolution could appear to us to be driven by chance, but from God’s perspective the outcome would be entirely specified.  Thus, God could be completely and intimately involved in the creation of all species, while from our perspective… this would appear a random and undirected process.

How is this not intelligent design?  Even if ID proponents concede our ability to infer design by material and efficient causes that doesn’t mean Darwinism would then be true because God, as Collins points out, could be intimately involved in the creation of all species.

Digressing back to final causation, I suppose that God could have purpose for the universe by his initiative act of creation.  This is categorically broad and the could not be any particular or individual purpose for humans since they are mere happenstance in the broader purpose of the universe.  The universe’s purpose would be no different had humans [or anything] not existed.  The purpose of a rock and human or equivalent.  Each are accidental properties of the universe and thus, couldn’t really have any final causation predicated to accidental properties.  (Posterior to God’s endowment of the Imago Dei on humans they may possess a greater purpose than rocks; however, prior to that endowment, they are still accidental properties and categorically equivalent.)  The best inference would be that matter and energy exist for God’s purpose.  That is as categorically defined as we can get.  Any forms of the matter and energy are accidental properties, they were not originally intended. If God initially intended for the initial conditions of the universe to bring about any form is design.

This is my philosophical hurdle to Darwinism.  Humans are accidental properties of the universe and my best guess to answer the question, “Why does anything exist” would be to speculate that God loves and enjoys matter and energy as broad as that is.  The forms and byproducts of matter and energy were not originally intended because if they were, that would have been design.  Perhaps someone can work this one out for me.