Intelligent Design

darwinWhen it comes to neo-Darwinian evolution, the question isn’t whether Darwin’s proposed mechanism of biological change is true – we know it is because we observe it in nature.  The question is whether it can explain what Darwin thought it explained: the diversity of life.

While the process of natural selection working on random mutations (NS+RM) is too slow to observe in mammals, we can observe the equivalent of millions of years of mammalian evolution in mere decades using microbial life and viruses.  Experimental data over the last ~20 years has shown that while natural selection working on random mutations does produce change and variation within microbial species, it does not create new species.[1]


Darwin_DoubtFor the previous installments: part 1, 2, 3, 4, 5, and 6.

Chapter 17

In this chapter, Meyer asks whether it is possible that the cause of the Cambrian explosion is an intelligent agent rather than naturalistic processes.  He argues that it is, and that the design hypothesis is better supported by the evidence than any naturalistic hypothesis.

Meyer looks closely at how historical science works.  It is different than physics and biology because you cannot experiment on the past.  What you can do, however, is develop multiple and competing hypotheses to determine which is the best explanation for the evidence at hand (inference to the best explanation).  One of the best ways to test competing hypotheses is on the basis of their causal adequacy; i.e. is the proposed cause adequate to produce the effect in question?  Remember, we have to explain the origin of biological information.  What sorts of causes, now in operation, are known to produce information?  Only one: intelligent agents.  If the basis of life is information, and the only known cause of information is intelligence, then it follows that an intelligent agent is not just the best explanation for biological information, but the only viable explanation. (more…)

For the previous installments: part 1, 2, 3, 4, 5.

Chapter 14

Darwin_DoubtIn principle, a neo-Darwinian explanation of the origin of new body plans can only work if body plans are wholly determined at the genetic level.  If sources of information other than DNA are substantially responsible for the formation of body plans, then at best neo-Darwinism is inadequate as a holistic explanation for the diversification of life, and at worst it is simply the wrong explanation altogether.

Once again, modern discoveries in embryological development have discovered that there are many factors other than DNA that play a critical role in embryological development.  For example, it’s been shown that in many organisms, you can completely remove the DNA from the developing cells and the embryo will continue to develop up to a certain point.  If DNA alone was responsible for embryological development, this should be just as impossible as driving a car without gas.  If the car is driving, and there is no gas in the tank, then clearly something other than gas must be powering the car.  The same is true of embryological development.  While DNA is necessary to embryological development, it is not sufficient in itself.  There are sources of power other than DNA that are critical to the development of the organism.  Scientists call such sources “epigenetic information,” meaning it is information beyond the genetic information coded in DNA.


Here’s another great video from William Lane Craig, this time on the fine-tuning of the universe for the existence of life (see also his video on the kalam cosmological argument).

Darwin_DoubtFor the previous installments: part 1, 2, 3, 4.

Chapter 12

Scientists largely ignored the mathematicians who pointed out the seeming impossibility of creating new genes and proteins because the mathematical equations of population genetics pointed to a nearly limitless creative power of random mutations.  Given known mutation rates, population sizes, and reproduction rates, there seemed to be no end to what evolution could accomplish.  The problem with this conclusion is that population genetics is based on some assumptions that we now know to be false.

When the neo-Darwinian synthesis (the idea that evolutionary change is driven by natural selection acting on random genetic mutations) was formulated in the 1930s, biologists did not yet understand the structure of genes.  Watson and Crick would not discover the structure of DNA and the digital code it uses to build proteins until 1953 and beyond.  Prior to this, genes were only understood functionally as those entities that determine visible and selectable traits such as eye color and the number of toes on our feet.  It was assumed that single genetic mutations could alter genes in such a way so as to produce a new function, and that one gene could be responsible for building a complex structure.  Given these assumptions, it’s easy to envision an organism slowly improving one mutation at a time.  Today, however, we know that these assumptions are patently false:

  • Hundreds of proteins are often required to create a complex system. To build that system would require changes to hundreds of genes.  Furthermore, because the function of these systems depends on the coordination of several well-matched parts, these new proteins (or proteins with new functions) must arise at the same time.[1]
  • To change or improve the function of a single protein typically requires multiple, coordinated amino acid changes, which in turn requires multiple, coordinated changes in the DNA. Because the new function depends on the coordination of multiple mutations, every mutation must be present in the protein at once.


Darwin_DoubtFor the previous installments: part 1, 2, 3.

Chapter 9

In the early 1960s, MIT professor Murray Eden set his mind to discover whether neo-Darwinism could account for the origin of new organisms.  He knew life was based on a genetic code, and based on our shared experience of all other coded systems, he assumed the sequence of nucleotides was absolutely critical to its function.  If you start adding, deleting, or moving pieces of a digital code, for example, the meaning (function) is degraded or even lost.  If we can’t create a better program by randomly adding, deleting, and moving pieces of digital code, why think a Darwinian process that makes random changes to the DNA code could build better and novel organisms (indeed, why think a coded system could ever be built by random processes to begin with)?

In 1966, Eden and other colleagues convened a conference at the Wistar Institute in Philadelphia.  The conference was titled “Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution.”  The conference sought to explore the creative power of natural selection acting on random mutations.  Those present recognized that there are an enormous number of ways to combine amino acids together to form protein chains.  And while they did not know precisely how many combinations could result in a functional protein compared to those that could not, they did know the number of functional combinations was extremely small.


Darwin_DoubtFor the previous installments: part 1, 2.

Chapter 6

If common ancestry is true, we would expect the evolutionary tree of life (TOL) based on animal morphology to line up with the evolutionary TOL based on molecules, but they don’t.  In fact, there is no one TOL based on morphology or one TOL based on molecules.  There are multiple TOLs.

Interestingly, a comparison of different genes from the same organism can result in different TOLs for that organism.  The same is true of morphology.  For example, when the TOL is constructed based on germ-cell formation (which is basic to the evolutionary process because it underlies reproduction, and we would expect for all organisms in a branch of the TOL to have the same germ-cell formation) it leads to one TOL, but this TOL differs radically from TOLs constructed based on body-play symmetry, the number of primary tissues, or the mode of development.

Looking at the Cambrian pyla specifically, there is no one TOL showing what the ancestry looked like leading up to the Cambrian.

Convergent evolution is a word to describe how similar morphological features develop in different species, where that feature was not shared by their common ancestor.  There are many examples of so-called convergent evolution.  But convergent evolution undermines the presupposition underlying the theory of common descent: similar homology indicates similar ancestry.  Convergent evolution demonstrates that homological similarities do not necessarily imply a common ancestry.  Convergent evolution negates the logic of the argument for common descent from homology.

Chapter 7 (more…)

Darwin_DoubtFor the previous installment, see here.

Chapter 3

In 1995, Chinese scientists discovered even older Cambrian fossils near Chengjiang, China.  At this site, even more Cambrian phyla and species were uncovered.  This discovery also put to death the most popular form of the artifact hypothesis.  One can no longer claim that the Pre-Cambrian lacks the Cambrian ancestors because the ancestors were too soft (no exoskeleton) or too small given the fact that the Chinese researchers discovered fossilized sponge embryos which are both microscopically tiny and entirely soft-bodied.  They were preserved so beautifully that they were even able to see them in the midst of cell-division and identify the nucleus of the cells.  Of course, even before this discovery, we knew that soft-bodied animals could be preserved in the fossil record since filament-shaped micro-organisms had already been discovered in the Precambrian, and many other soft-bodies animals, organs, and anatomical structures in both the Cambrian and Precambrian.  According to Simon Conway-Morris, the Burgess Shale (Cambrian) contains 70K+ specimens, and 90% of them are either entirely soft-bodied or have a thin skeleton.  The fossils discovered by the Chinese contained even more soft-body animals and preserved eyes, intestines, stomachs (and even the contents in the stomachs), mouths, and nerves.  Furthermore, it would be impossible for some ancestors of the Cambrian phyla to function without their hard parts (such as an exoskeleton).  They would have to have evolved together, and thus we would expect to find those ancestors in the Precambrian.  If the Precambrian could preserve soft, tiny organisms, then why don’t we find the transitional forms leading up to the Cambrian phyla in the Precambrian?


Darwin_DoubtI may be a bit late to the party, but I’ve finally gotten a chance to read Stephen Meyer’s latest book, Darwin’s Doubt.  Having read his previous book, Signature in the Cell, I had high expectations, and Meyer did not disappoint.  Darwin’s Doubt takes a look at the longstanding enigma of the Cambrian explosion – a very brief time in history in which the majority of all major animal forms abruptly appear in the fossil record with no trace of simpler ancestral forms.  Darwin recognized the problem the Cambrian fossils posed to his theory, but thought future discoveries would solve the problem.  After 150 years, the problem hasn’t been solved.  Instead, it’s been made more acute.

Scientists are increasingly coming to recognize that Darwin’s theory cannot explain the Cambrian explosion.  Some are proposing alternative, naturalistic explanations.  Others see the Cambrian explosion as powerful evidence for the intervention of an Intelligent Designer nearly 550 million years ago.  Who’s right?  Darwin?  The Darwin doubters?  Intelligent Design theorists?  Stephen Meyer walks the reader through the evidence, and then evaluates competing explanations to see how they stack up against the evidence.  It should be no surprise to those who know Stephen Meyer where the book concludes.  The question is how he gets to his conclusion.


God of GapsI’ve noticed that many nonbelievers (and even believers) misunderstand what constitutes a “God of the gaps” argument.  They tend to think one is guilty of a God of the gaps argument if they offer God as an explanation for some X rather than some natural phenomenon.  The problem with this definition is that it presumes the only valid explanation is a naturalistic explanation.  God is ruled out as a valid explanation for anything a priori, so anyone who offers God as an explanation for X is thought to do so merely because they are ignorant of the proper naturalistic explanation.  This begs the question in favor of naturalism and against theism.  One could only conclude that every effect has a naturalistic explanation, and that God is not a valid explanation, if one has first demonstrated that God does not exist.  So long as it is even possible that God exists, then it is possible that God may be the cause of X, and thus explain X.

What makes an argument a God of the gaps type of argument is when God is invoked to explain X simply because we do not know what else can explain X.  In other words, God is used to plug a gap in our knowledge of naturalistic explanations: “I don’t know how to explain X, so God must have done X.”  This is not at all the same as arguing that God is the best explanation of X, based on what we know regarding X and the explanatory options available to us.  Here, God is being invoked to explain what we know, not what we don’t know.


Not scienceMany believe science has disproven God.  This is not possible, even in principle.[1]  The truth of the matter is that advances in science are providing more reasons to believe in God, not less.  While scientific discoveries cannot prove God’s existence, they can be used to support premises in arguments that have theistic conclusions/implications. For example, science has discovered that the universe began to exist.  Anything that begins to exist requires an external cause.  Since the universe encompasses all physical reality, the cause of the universe must transcend physical reality.  It cannot be a prior physical event or some natural law, because there was nothing physical prior to the first physical event, and natural laws only come into being once the natural world comes into being.  Whatever caused the universe to come into being must be transcendent, powerful, immaterial, spaceless, eternal, and personal, which is an apt description of God.


There are many illegitimate critiques of Intelligent Design (the hypothesis that some features of the world are best explained in terms of an intelligent cause rather than undirected natural processes).  One example is the charge often leveled against ID that it improperly uses probability statistics to infer design. For example, in a BBC documentary titled The War on Science, Ken Miller accused IDers of making the mistake of calculating probabilities after-the-fact, making the unlikely seem impossible:

One of the mathematical tricks employed by intelligent design involves taking the present day situation and calculating probabilities that the present would have appeared randomly from events in the past. And the best example I can give is to sit down with four friends, shuffle a deck of 52 cards, and deal them out and keep an exact record of the order in which the cards were dealt. We can then look back and say ‘my goodness, how improbable this is. We can play cards for the rest of our lives and we would never ever deal the cards out in this exact same fashion.’ You know what; that’s absolutely correct. Nonetheless, you dealt them out and nonetheless you got the hand that you did.


The Best Schools interviewed leading Intelligent Design theorist, Bill Dembski.  At one point he was asked, “You have stated that ‘design theorists oppose Darwinian theory on strictly scientific grounds.’ But then why is the ID movement so heavily populated with religious believers? Could we not expect more of the scientific community to support ID if your statement were true? Why do the majority of the world’s leading scientific bodies oppose ID and claim that it does not qualify as science?”

This is a valid question, and I’m sure it is on the minds of many people who are interested in the debate.  I like Dembski’s answer:

As for why religious believers tend to be associated with design, I could turn the question around. If Darwinian evolution is strictly scientific, then why is that field so heavily populated with atheists? In one survey of around 150 prominent evolutionary biologists, only two were religious believers (as I recall, Will Provine was behind this survey). I see a scientific core to both intelligent design and Darwinian evolution. And I see no merit in questioning their scientific status by the company they keep. The character of the proposals that both approaches make is what really ought to count.


HT: Uncommon Descent

Scientists working in origin of life research are fairly candid that they do not know how life originated, but they are quick to point out that they are making progress and that science will eventually be able to provide an answer to this question.  I have always found this sort of faith in science a bit intriguing.  It is just assumed that there must be a naturalistic cause/explanation for the origin of life, and that we will eventually be able to discover it.  But why should we think this to be true?  Given what needs to be explained (the origin of biological information), and given our understanding of the causal powers of naturalistic processes, the origin of life does not appear to be the kind of thing for which natural causes are adequate to explain it even in principle (See 1, 2, 3, 4, 5, 6, 7, 8, and 9).


Theists argue that the fine-tuning of the physical constants of the universe provide evidence that the universe is designed.  For example, if gravitational force was 1/100,000,000,000,000th (1/100 trillionth) degree stronger the universe would not have expanded to form the terrestrial bodies.  If the force was 1/100,000,000,000,000th degree weaker the universe would expand at rate too fast for matter to coalesce into terrestrial bodies.  The ratio of electrons to protons is fine-tuned to 1 part in 1037, meaning if the ratio was altered by just 1 part in 10,000,000,000,000,000,000,000,000,000,
000,000,000 complex life would not be possible.

To give you a sense of the specificity involved, Hugh Ross asks us to imagine covering the entire North American continent with dimes, all the way up to the moon (239,000 miles high).  Do the same thing on 1,000,000,000 other continents of identical size, “[p]aint one dime red and mix it into the billion of piles of dimes.  Blindfold a friend and ask him to pick out one dime.  The odds that he will pick the red dime are one in 1037.”[1]


As someone who supports Intelligent Design theory, I have often been puzzled by the many Catholic thinkers who do not.  The scientific basis for ID is strong, and ID is just as friendly to their theism as it is friendly to mine, so why do so many Catholic scholars reject ID, or at least have such strong reservations against it?  A recent essay by Edward Feser in Philosophia Christi[1] has enlightened me regarding the main source of contention between Catholic theology and ID theory, and it boils down to Aristotle, Thomas Aquinas, and final causation.

Feser explains that Thomists (those who follow the theological system of Thomas Aquinas, who followed the philosophy of Aristotle) believe teleology inheres within all substances (final cause) and is evident to rational minds, whereas ID theorists believe teleology must be imposed on substances from an external source (no final cause), and can only be detected empirically through various probability assessments (not evident).


The reigning philosophy of science is methodological naturalism, which requires that scientists explain all natural phenomena in terms of naturalistic causes.  If a scientist thinks the evidence for some biological or natural entity points to an intelligent cause, the possibility is dismissed as unscientific by definition, and the scientist is charged with employing a “God of the gaps” argument in which God is invoked to plug up gaps in our knowledge.

I’ve always found this line of thinking interesting.  Can you imagine if this principle was applied to the non-biological world?  What caused Stonehenge?  “People made it,” you say.  Oh no!  You have broken the rules of science.  This is a physical entity, and thus it must be explained in terms of naturalistic causes.  “But,” you say, “it has all the elements of design.  The arrangement of parts is both complex and specified.”  But this is just the appearance of design, not real design.  While we may not know the natural process by which the pyramids were created, scientists are working on that.  We cannot give up on science by appealing to some unknown “designers.”  To do so is to employ a people of the gaps argument.


Opponents of ID often argue against ID on the basis that it is not science.  Of course, the definition of science itself is disputable, and it is often disputed.  This is largely a red herring, however, because it shifts the focus away from the merits of ID arguments to the classification of those arguments.  As Thomas Nagel has written, “A purely semantic classification of a hypothesis or its denial as belonging or not to science is of limited interest to someone who wants to know whether the hypothesis is true or false.”[1]

While I think ID is a scientific conclusion, I do not wish to debate here whether ID properly qualifies as science, or whether it is better classified as religion/philosophy.  The question I want to raise is how scientists would respond if it could be demonstrated that ID is both properly categorized as religion/philosophy and ID is true.  Would scientists cease discussing certain subjects in science class?  Would they stop discussing the origin of life or origin of species?  In my estimation, this is doubtful.  I think most would continue to offer naturalistic explanations for these objects because their definition of science requires them to.  After all, if by definition alone science must provide naturalistic answers for all natural phenomena, then scientists must continue to offer naturalistic explanations for all phenomena—even phenomena  ID would have proven do not have naturalistic explanations.


One of the most common objections against Intelligent Design is that if an intelligent agent is causally involved in the natural world, then science is no longer predictable because at any time the agent could intervene and mess with our experiments.  For example, Michael Ruse writes, ““[T]he relationship of the natural and the supernatural are unpredictable … [if] the cause of a natural event is the whim of a deity, the event is neither predictable nor fully understandable.”[1]

I think this objection is misguided.  First, it is based on a faulty understanding of ID.  ID only claims to have discovered evidence of a designer’s activity in the past.  It takes no position on the question of whether the designer is still in existence, whether the designer is presently involved in the cosmos, or whether the designer will be involved in the cosmos in the future.  Those are philosophical and religious questions.


In a previous post I addressed the “lottery” objection to the probabilistic argument against a naturalistic origin of life: “Just as the odds of winning the lottery are low, and yet people win the lottery all the time, so too the odds of forming life by chance may be low, but that doesn’t mean it is impossible.”  I argued that unlike a lottery, the probabilistic resources available to form life are so unfathomably low that there is no reason to expect a winner in chance’s game of life.  To prove my point, I compared the number of possible events in the whole history of the universe (10139)—the probabilistic resources—to the probability of a 250 gene organism forming by chance (1:1041,000).  The odds of life forming by chance came up trillions upon trillions upon trillions of times short, and thus there is no rational basis on which to affirm that life originated by chance.  What I didn’t realize then was that I had severely over-estimated the odds.


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