What is Intelligent Design?
Intelligent design — often called “ID” — is a scientific theory that holds that the emergence of some features of the universe and living things is best explained by an intelligent cause rather than an undirected process such as natural selection. ID theorists argue that design can be inferred by studying the informational properties of natural objects to determine if they bear the type of information that in our experience arises from an intelligent cause.
Proponents of neo-Darwinian evolution contend that the information in life arose via purposeless, blind, and unguided processes. ID proponents argue that this information arose via purposeful, intelligently guided processes. Both claims are scientifically testable using the standard methods of science. But ID theorists say that when we use the scientific method to explore nature, the evidence points away from unguided material causes, and reveals intelligent design.
Intelligent Design in Everyday Reasoning
Whether we realize it or not, we detect design constantly in our everyday lives. In fact, our lives often depend on inferring intelligent design. Imagine you are driving along a road and come to a place where the asphalt is covered by a random splatter of paint. You would probably ignore the paint and keep driving onward.
But what if the paint is arranged in the form of a warning? In this case, you would probably make a design inference that could save your life. You would recognize that an intelligent agent was trying to communicate an important message.
Only an intelligent agent can use foresight to accomplish an end-goal — such as building a car or using written words to convey a message. Recognizing this unique ability of intelligent agents allows scientists in many fields to detect design.
Intelligent Design in Archaeology and Forensics
ID is in the business of trying to discriminate between strictly naturally/materially caused objects on the one hand, and intelligently caused objects on the other. A variety of scientific fields already use ID reasoning. For example, archaeologists find an object and they need to determine whether it arrived at its shape through natural processes, so it’s just another rock (let’s say), or whether it was carved for a purpose by an intelligence. Likewise forensic scientists distinguish between naturally caused deaths (by disease, for example), and intelligently caused deaths (murder). These are important distinctions for our legal system, drawing on science and logical inference. Using similar reasoning, intelligent design theorists go about their research. They ask: If we can use science to detect design in other fields, why should it be controversial when we detect it in biology or cosmology?
Here is how ID works. Scientists interested in detecting design start by observing how intelligent agents act when they design things. What we know about human agents provides a large dataset for this. One of the things we find is that when intelligent agents act, they generate a great deal of information. As ID theorist Stephen Meyer says: “Our experience-based knowledge of information-flow confirms that systems with large amounts of specified complexity (especially codes and languages) invariably originate from an intelligent source—from a mind or personal agent.”1
Thus ID seeks to find in nature reliable indications of the prior action of intelligence—specifically it seeks to find the types of information which are known to be produced by intelligent agents. Yet not all “information” is the same. What kind of information is known to be produced by intelligence? The type of information that indicates design is generally called “specified complexity” or “complex and specified information” or “CSI” for short. I will briefly explain what these terms mean.
Something is complex if it is unlikely. But complexity or unlikelihood alone is not enough to infer design. To see why, imagine that you are dealt a five-card hand of poker. Whatever hand you receive is going to be a very unlikely set of cards. Even if you get a good hand, like a straight or a royal flush, you’re not necessarily going to say, “Aha, the deck was stacked.” Why? Because unlikely things happen all the time. We don't infer design simply because of something's being unlikely. We need more: specification. Something is specified if it matches an independent pattern.
A Tale of Two Mountains
Imagine you are a tourist visiting the mountains of North America. You come across Mount Rainier, a huge dormant volcano not far from Seattle. There are features of this mountain that differentiate it from any other mountain on Earth. In fact, if all possible combinations of rocks, peaks, ridges, gullies, cracks, and crags are considered, this exact shape is extremely unlikely and complex. But you don't infer design simply because Mount Rainier has a complex shape. Why? Because you can easily explain its shape through the natural processes of erosion, uplift, heating, cooling, freezing, thawing, weathering, etc. There is no special, independent pattern to the shape of Mount Rainier. Complexity alone is not enough to infer design.
But now let's say you go to a different mountain—Mount Rushmore in South Dakota. This mountain also has a very unlikely shape, but its shape is special. It matches a pattern—the faces of four famous Presidents. With Mount Rushmore, you don’t just observe complexity, you also find specification. Thus, you would infer that its shape was designed.
ID theorists ask “How can we apply this kind of reasoning to biology?” One of the greatest scientific discoveries of the past fifty years is that life is fundamentally built upon information. It's all around us. As you read a book, your brain processes information stored in the shapes of ink on the page. When you talk to a friend, you communicate information using sound-based language, transmitted through vibrations in air molecules. Computers work because they receive information, process it, and then give useful output.
Everyday life as we know it would be nearly impossible without the ability to use information. But could life itself exist without it? Carl Sagan observed that the “information content of a simple cell” is “around 1012 bits, comparable to about a hundred million pages of the Encyclopedia Britannica.”2 Information forms the chemical blueprint for all living organisms, governing the assembly, structure, and function at essentially all levels of cells. But where does this information come from?
As I noted previously, ID begins with the observation that intelligent agents generate large quantities of CSI. Studies of the cell reveal vast quantities of information in our DNA, stored biochemically through the sequence of nucleotide bases. No physical or chemical law dictates the order of the nucleotide bases in our DNA, and the sequences are highly improbable and complex. Yet the coding regions of DNA exhibit very unlikely sequential arrangements of bases that match the precise pattern necessary to produce functional proteins. Experiments have found that the sequence of nucleotide bases in our DNA must be extremely precise in order to generate a functional protein. The odds of a random sequence of amino acids generating a functional protein is less than 1 in 10 to the 70th power.3In other words, our DNA contains high CSI.
Thus, as nearly all molecular biologists now recognize, the coding regions of DNA possess a high “information content”—where “information content” in a biological context means precisely “complexity and specificity.” Even the staunch Darwinian biologist Richard Dawkins concedes that “[b]iology is the study of complicated things that give the appearance of having been designed for a purpose.”4 Atheists like Dawkins believe that unguided natural processes did all the "designing" but intelligent design theorist Stephen C. Meyer notes, “in all cases where we know the causal origin of ‘high information content,’ experience has shown that intelligent design played a causal role.”5
A DVD in Search of a DVD Player
But just having the information in our DNA isn't enough. By itself, a DNA molecule is useless. You need some kind of machinery to read the information in the DNA and produce some useful output. A lone DNA molecule is like having a DVD—and nothing more. A DVD might carry information, but without a machine to read that information, it's all but useless (maybe you could use it as a Frisbee). To read the information in a DVD, we need a DVD player. In the same way, our cells are equipped with machinery to help process the information in our DNA.
That machinery reads the commands and codes in our DNA much as a computer processes commands in computer code. Many authorities have recognized the computer-like information processing of the cell and the computer-like information-rich properties of DNA's language-based code. Bill Gates observes, “Human DNA is like a computer program but far, far more advanced than any software we've ever created.”6 Biotech guru Craig Venter says that “life is a DNA software system,”7 containing “digital information” or “digital code,” and the cell is a “biological machine” full of “protein robots.”8 Richard Dawkins has written that “[t]he machine code of the genes is uncannily computer-like.”9 Francis Collins, the leading geneticist who headed the human genome project, notes, “DNA is something like the hard drive on your computer,” containing “programming.”10
Cells are thus constantly performing computer-like information processing. But what is the result of this process? Machinery. The more we discover about the cell, the more we learn that it functions like a miniature factory, replete with motors, powerhouses, garbage disposals, guarded gates, transportation corridors, CPUs, and much more. Bruce Alberts, former president of the U.S. National Academy of Sciences, has stated:
[T]he entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines. ... Why do we call the large protein assemblies that underlie cell function protein machines? Precisely because, like machines invented by humans to deal efficiently with the macroscopic world, these protein assemblies contain highly coordinated moving parts.11
There are hundreds, if not thousands, of molecular machines in living cells. In discussions of ID, the most famous example of a molecular machine is the bacterial flagellum. The flagellum is a micro-molecular propeller assembly driven by a rotary engine that propels bacteria toward food or a hospitable living environment. There are various types of flagella, but all function like a rotary engine made by humans, as found in some car and boat motors. Flagella also contain many parts that are familiar to human engineers, including a rotor, a stator, a drive shaft, a U-joint, and a propeller. As one molecular biologist writes, “More so than other motors the flagellum resembles a machine designed by a human.”12 But there's something else that's special about the flagellum.
Introducing "Irreducible Complexity"
In applying ID to biology, ID theorists often discuss “irreducible complexity,” a concept developed and popularized by Lehigh University biochemist Michael Behe. Irreducible complexity is a form of specified complexity, which exists in systems composed of “several interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning.”13 Because natural selection only preserves structures that confer a functional advantage to an organism, such systems would be unlikely to evolve through a Darwinian process. Why? Because there is no evolutionary pathway where they could remain functional during each small evolutionary step. According to ID theorists, irreducible complexity is an informational pattern that reliably indicates design, because in all irreducibly complex systems in which the cause of the system is known by experience or observation, intelligent design or engineering played a role in the origin of the system.
Microbiologist Scott Minnich has performed genetic knockout experiments where each gene encoding a flagellar part is mutated individually such that it no longer functions. His experiments show that the flagellum fails to assemble or function properly if any one of its approximately 35 different protein-components is removed.14 By definition, it is irreducibly complex. In this all-or-nothing game, mutations cannot produce the complexity needed to evolve a functional flagellum one step at a time. The odds are also too daunting for it to evolve in one great mutational leap.
The past fifty years of biological research have showed that life is fundamentally based upon:
- A vast amount of complex and specified information encoded in a biochemical language.
- A computer-like system of commands and codes that processes the information.
- Irreducibly complex molecular machines and multi-machine systems.
Where, in our experience, do language, complex and specified information, programming code, and machines come from? They have only one known source: intelligence.
Intelligent Design Extends Beyond Biology
But there's much more to ID. Contrary to what many people suppose, ID is much broader than the debate over Darwinian evolution. That's because much of the scientific evidence for intelligent design comes from areas that Darwin's theory doesn't even address. In fact, much evidence for intelligent design from physics and cosmology.
The fine-tuning of the laws of physics and chemistry to allow for advanced life is an example of extremely high levels of CSI in nature. The laws of the universe are complex because they are highly unlikely. Cosmologists have calculated the odds of a life-friendly universe appearing by chance are less than 1 in 1010^123. That's ten raised to a power of 10 with 123 zeros after it—a number far too long to write out! The laws of the universe are specified in that they match the narrow band of parameters required for the existence of advanced life. This high CSI indicates design. Even the atheist cosmologist Fred Hoyle observed, “A common sense interpretation of the facts suggests that a super intellect has monkeyed with physics, as well as with chemistry and biology.”15 From the tiniest atom, to living organisms, to the architecture of the entire cosmos, the fabric of nature shows strong evidence that it was intelligently designed.
Using Mathematics to Detect Design
Intelligent design has its roots in information theory, and design can be detected via statistical mathematical calculations.
As noted, ID theorists begin by observing the types of information produced by the action of intelligent agents vs. the types of information produced through purely natural processes. By making these observations, we can infer that intelligence is the best explanation for many information-rich features we see in nature. But can the inference to design be made rigorously using mathematics? ID theorists think we can, by mathematically quantifying the amount of information present and determining if it is the type of information which, in our experience, is only produced by intelligence.
The fact that information is a real entity is attested by scientists both inside and outside the ID movement. In his essay “Intelligent Design as a Theory of Information,” a pro-ID mathematician and philosopher William Dembski notes:
No one disputes that there is such a thing as information. As Keith Devlin remarks, “Our very lives depend upon it, upon its gathering, storage, manipulation, transmission, security, and so on. Huge amounts of money change hands in exchange for information. People talk about it all the time. Lives are lost in its pursuit. Vast commercial empires are created in order to manufacture equipment to handle it.”16
The fundamental intuition behind measuring information is a reduction in possibilities. The more possibilities you rule out, the more information present. Thus Dembski uses accepted definitions from the field of information theory that define information as the occurrence of one event, or scenario, while excluding other events, or scenarios. In other words, information is what you get when you narrow down what you're talking about.
The amount of information in a system or represented by some event can be calculating the probability of that scenario, and converting that probability into units of information, called “bits.” These are the same “bits” and “bytes” from the computer world. We can calculate bits according to the following equation:
Given a probability p of some event or scenario, Information content = I = - Log2 (p)
For example, in binary code, each character has two possibilities—0 or 1—meaning the probability of any character is 0.5. Using the formula above, this leads to an information content of 1 bit for each binary digit. Thus, a binary string like “00110” contains 5 bits. But saying “this string carries 5 bits of information” says nothing about the meaning of the string! It only describes the likelihood of the string occurring. Nobel Prize winning molecular biologist Jack Szostak explains that this classical method of measuring information via raw probabilities does not help us discern the functional meaning of an information-rich system:
[C]lassical information theory ... does not consider the meaning of a message, defining the information content of a string of symbols as simply that required to specify, store or transmit the string. ... A new measure of information—functional information—is required to account for all possible sequences that could potentially carry out an equivalent biochemical function, independent of the structure or mechanism used.17
Szostak suggests that we must look at more than just the likelihood (i.e., the probability or raw information content in bits) to understand the functional workings of natural systems. We must look at the meaning of the information as well. ID theorists feel the same way.
To measure both the information content and the meaning of some event, Dembski developed the concept of complex and specified information (CSI), which was discussed earlier. To review, this method of detecting design can not only determine if an event unlikely (i.e., high information content), but also whether it matches a pre-existing pattern or “specification” (i.e., it has some functional meaning). This is seen in the diagram below:
In the figure above, Point A, which bears low CSI, represents something best explained by natural processes. Point B, which has high CSI, represents something best explained by design. Curve C represents the upper limit to what natural processes can produce-the "universal probability bound." Anything far beyond Curve C is best explained by design; anything far within Curve C is best explained by natural processes.
As seen in figure at above, there is a limit to the amount of CSI which can be produced by natural processes (represented by Curve C). When we see a specified event that is highly unlikely—high CSI—we know that natural processes were not involved, and that intelligent design is the best explanation. When low information content is involved, natural causes can produce the feature in question, and the best explanation is some natural cause.
To help us discriminate between systems that could arise naturally and those that are best explained by design, ID proponents have developed the “universal probability bound,” a measure of the maximum amount of CSI that could be produced during the entire history of the universe. In essence, if the CSI content of a system exceeds the universal probability bound, then natural causes cannot explain that feature and it can only be explained by intelligent design. Dembski and Jonathan Witt explain it this way:
Scientists have learned that within the known physical universe there are about 1080 elementary particles ... Scientists also have learned that a change from one state of matter to another can’t happen faster than what physicists call the Planck time. ... The Planck time is 1 second divided by 1045 (1 followed by forty-five zeroes). ... Finally, scientists estimate that the universe is about fourteen billion years old, meaning the universe is itself millions of times younger than 1025 seconds. If we now assume that any physical event in the universe requires the transition of at least one elementary particle (most events require far more, of course), then these limits on the universe suggest that the total number of events throughout cosmic history could not have exceeded 1080 x 1045 x 1025 = 10150.
This means that any specified event whose probability is less than 1 chance in 10150 will remain improbable even if we let every corner and every moment of the universe roll the proverbial dice. The universe isn’t big enough, fast enough or old enough to roll the dice enough times to have a realistic chance of randomly generating specified events that are this improbable.18
Using our equation for calculating bits, an event whose probability is 1 in 10150 carries about 500 bits of information. This means that if the CSI content of a system is greater than 500 bits, then we can rule out blind material causes and infer intelligent design. Dembski has applied this method to bacterial flagellum, an irreducibly complex molecular machine which contains high CSI, and calculated that it contains a few thousand bits of information—far greater than what can be produced by natural causes according to the universal probability bound.
But ID theorists have developed other ways to research the limits of what can be produced by natural processes, especially in the context of Darwinian evolution.
Intelligent Design and the Limits of Natural Selection
Intelligent design does not reject all aspects of evolution. Evolution can mean something as benign as (1) “life has changed over time,” or it can entail more controversial ideas, like (2) “all living things share common ancestry,” or (3) “natural selection acting upon random mutations produced life’s diversity.”
ID does not conflict with the observation that natural selection causes small-scale changes over time (meaning 1), or the view that all organisms are related by common ancestry (meaning 2). However, the dominant evolutionary viewpoint today is neo-Darwinism (meaning 3), which contends that life’s entire history was driven by unguided natural selection acting on random mutations (as well as other forces like genetic drift)—a collection of blind, purposeless process with no directions or goals. It is this specific neo-Darwinian claim that ID directly challenges.
Darwinian evolution can work fine when one small step (e.g., a single point mutation) along an evolutionary pathway gives an advantage that helps an organisms survive and reproduce. The theory of ID has no problem with this, and acknowledges that there are many small-scale changes that Darwinian mechanisms can produce.
But what about cases where many steps, or multiple mutations, are necessary to gain some advantage? Here, Darwinian evolution faces limits on what it can accomplish. Evolutionary biologist Jerry Coyne affirms this when he states: “natural selection cannot build any feature in which intermediate steps do not confer a net benefit on the organism.”19 Likewise, Darwin wrote in The Origin of Species:
If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.
As Darwin’s quote suggests, natural selection gets stuck when a feature cannot be built through “numerous, successive, slight modifications”—that is, when a structure requires multiple mutations to be present before providing any advantage for natural selection to select. Proponents of intelligent design have done research showing that many such biological structures exist which would require multiple mutations before providing some advantage.
In 2004, biochemist Michael Behe co-published a study in Protein Science with physicist David Snoke demonstrating that if multiple mutations were required to produce a functional bond between two proteins, then “the mechanism of gene duplication and point mutation alone would be ineffective because few multicellular species reach the required population sizes.”20
Writing in 2008 in the journal Genetics, Behe and Snoke's critics tried to refute them, but failed. The critics found that, in a human population, to obtain a feature via Darwinian evolution that required only two mutations before providing an advantage “would take > 100 million years,” which they admitted was “very unlikely to occur on a reasonable timescale.”21 Such “multi-mutation features” are thus unlikely to evolve in humans, which have small population sizes and long generation times, reducing the efficiency of the Darwinian mechanism.
But can Darwinian processes produce complex multimutation features in bacteria which have larger population sizes and reproduce rapidly? Even here, Darwinian evolution faces limits.
In a 2010 peer-reviewed study, molecular biologist Douglas Axe calculated that when a “multi-mutation feature” requires more than six mutations before giving any benefit, it is unlikely to arise even in the whole history of the Earth—even in the case of bacteria.22 He provided empirical backing for this conclusion from experimental research he earlier published in the Journal of Molecular Biology. There, he found there that only one in 1074 amino-acid sequences yields a functional protein fold.23 That implies that protein folds in general are multimutation features, requiring many amino acids to be present before there is any functional advantage.
Another study by Axe and biologist Ann Gauger found that merely converting one enzyme to perform the function of a closely related enzyme—the kind of conversion that evolutionists claim can happen easily—would require a minimum of seven mutations.24 This exceeds the limits of what Darwinian can produce over the Earth’s entire history, as calculated by Axe’s 2010 paper.
A later study published in 2014 by Gauger, Axe and biologist Mariclair Reeves bolstered this finding. They examined additional proteins to determine whether they could be converted via mutation to perform the function of a closely related protein.25 After inducing all possible single mutations in the enzymes, and many other combinations of mutations, they found that evolving a protein, via Darwinian evolution, to perform the function of a closely related protein would take over 1015 years—over 100,000 times longer than the age of the earth!
Collectively, these research results indicate that many biochemical features would require many mutations before providing any advantage to an organism, and would thus be beyond the limit of what Darwinian evolution can do. If blind evolution cannot build these CSI-rich features, what can? Some non-random process is necessary that can “look ahead” and find the complex combinations of mutations to generate these high-CSI features. That process is intelligent design.
A Positive Argument or God of the Gaps?
When arguing against ID, some critics will contend that ID is merely a negative argument against evolution, what some will call a “God-of-the-gaps” argument. A “God-of-the-gaps” argument, critics observe, argues for God based upon gaps in our knowledge, rather than presenting a positive argument. Moreover, it is said that “God-of-the-gaps” arguments are dangerous to faith, because as our knowledge increases, our basis for believing in God is squeezed into smaller and smaller “gaps” in our knowledge. Eventually, the argument goes, there is no reason for believing in God at all. Does ID present a God-of-the-gaps argument? It does not, for many reasons.
First, ID refers to an intelligent cause and does not identify the designer as “God.” All ID scientifically detects is the prior action of an intelligent cause. ID respects the limits of scientific inquiry and does not attempt to address religious questions about the identity of the designer. Indeed, the ID movement includes people of many worldviews, including Christians, Jews, Muslims, people of Eastern religious views, and even agnostics. What unites them is not some religious view about the identity of the designer, but a conviction that there is scientific evidence for intelligent design in nature.
More to the point, the argument for design is not based on what we don’t know (i.e., gaps in our knowledge), but is rather based entirely on what we do know (evidence) about the known causes of information-rich systems. For example, irreducibly complex molecular machines contain high CSI, and we know from experience that high-CSI systems arise from the action of an intelligent agent. To elaborate on a quote given earlier from Stephen Meyer:
[W]e have repeated experience of rational and conscious agents—in particular ourselves—generating or causing increases in complex specified information, both in the form of sequence-specific lines of code and in the form of hierarchically arranged systems of parts. ... Our experience-based knowledge of information-flow confirms that systems with large amounts of specified complexity (especially codes and languages) invariably originate from an intelligent source—from a mind or personal agent.26
Similarly, Meyer and biochemist Scott Minnich explain that irreducibly complex systems in particular are always known to derive from an intelligent cause:
Molecular machines display a key signature or hallmark of design, namely, irreducible complexity. In all irreducibly complex systems in which the cause of the system is known by experience or observation, intelligent design or engineering played a role the origin of the system. ... Indeed, in any other context we would immediately recognize such systems as the product of very intelligent engineering. Although some may argue this is a merely an argument from ignorance, we regard it as an inference to the best explanation, given what we know about the powers of intelligent as opposed to strictly natural or material causes.27
It’s important to understand that when ID theorists argue that we can find in nature the kind of information and complexity that comes from intelligence, they are not making a mere argument from analogy. When one reduces natural systems to their raw informational properties, they are mathematically identical to those of designed systems. Though not an ID proponent, molecular biologist Hubert Yockey explains that form of information in DNA is identical to what we find in language:
It is important to understand that we are not reasoning by analogy. The sequence hypothesis [that the exact order of symbols records the information] applies directly to the protein and the genetic text as well as to written language and therefore the treatment is mathematically identical.28
Though Yockey is no ID proponent, he rightly observes that the informational properties of DNA are mathematically identical to language. Thus, the argument for design is much stronger than a mere appeal to analogy, and we don't infer design based upon merely finding and exploiting alleged “gaps” in our knowledge. Rather, ID is based upon the positive argument that nature contains the kind of information and complexity which, in our positive experience, comes only from the action of intelligence. Accordingly, intelligent design is, by standard scientific methods, the best explanation for high CSI in nature.
Using the Scientific Method to Positively Detect Design
As a final demonstration of how ID uses a positive scientific argument, consider how the scientific method can be used to detect design. The scientific method is commonly described as a four-step process involving observation, hypothesis, experiment, and conclusion. ID uses this precise scientific method to make a positive cases for design in various scientific fields, including biochemistry, paleontology, systematics, and genetics:
Example 1—Using the Scientific Method to Detect Design in Biochemistry:
- Observation: Intelligent agents solve complex problems by acting with an end goal in mind, producing high levels of CSI. In our experience, systems with large amounts of CSI—such as codes and languages—invariably originate from an intelligent source. Likewise, in our experience, intelligence is the cause of irreducibly complex machines.
- Hypothesis (Prediction): Natural structures will be found that contain many parts arranged in intricate patterns that perform a specific function—indicating high levels of CSI, including irreducible complexity.
- Experiment: Experimental investigations of DNA indicate that it is full of a CSI-rich, language-based code. Cells use computer-like information processing systems to translate the genetic information in DNA into proteins. Biologists have performed mutational sensitivity tests on proteins and determined that their amino acid sequences are highly specified. The end-result of cellular information processing system are protein-based micromolecular machines. Genetic knockout experiments and other studies show that some molecular machines, like the bacterial flagellum, are irreducibly complex.
- Conclusion: The high levels of CSI—including irreducible complexity—in biochemical systems are best explained by the action of an intelligent agent.
Example 2—Using the Scientific Method to Detect Design in Paleontology:
- Observation: Intelligent agents rapidly infuse large amounts of information into systems. As four ID theorists write: "intelligent design provides a sufficient causal explanation for the origin of large amounts of information… the intelligent design of a blueprint often precedes the assembly of parts in accord with a blueprint or preconceived design plan.”
- Hypothesis (Prediction): Forms containing large amounts of novel information will appear in the fossil record suddenly and without similar precursors.
- Experiment: Studies of the fossil record show that species typically appear abruptly without similar precursors. The Cambrian explosion is a prime example, although there are other examples of explosions in life’s history. Large amounts of CSI had to arise rapidly to explain the abrupt appearance of these forms.
- Conclusion: The abrupt appearance of new fully formed body plans in the fossil record is best explained by intelligent design.
Example 3—Using the Scientific Method to Detect Design in Systematics:
- Observation: Intelligent agents often reuse functional components in different designs. As Paul Nelson and Jonathan Wells explain: “An intelligent cause may reuse or redeploy the same module in different systems… [and] generate identical patterns independently.”
- Hypothesis (Prediction): Genes and other functional parts will be commonly reused in different organisms.
- Experiment: Studies of comparative anatomy and genetics have uncovered similar parts commonly existing in widely different organisms. Examples of extreme convergent evolution show reusage of functional genes and structures in a manner not predicted by common ancestry.
- Conclusion: The reusage of highly similar and complex parts in widely different organisms in non-treelike patterns is best explained by the action of an intelligent agent.
Example 4— Using the Scientific Method to Detect Design in Genetics:
- Observation: Observation: Intelligent agents construct structures with purpose and function. As William Dembski argues: “Consider the term ‘junk DNA.’… [O]n an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function.”
- Hypothesis (Prediction): Much so-called “ junk DNA” will turn out to perform valuable functions.
- Experiment: Numerous studies have discovered functions for “junk DNA.” Examples include functions for pseudogenes, introns, and repetitive DNA.
- Conclusion: The discovery of function for numerous types of “junk DNA” was successfully predicted by intelligent design.
One might disagree with the conclusions of ID, but one cannot reasonably claim that these arguments for design are based upon religion, faith, or divine revelation. They are based upon science.
Follow the Evidence Where It Leads
There will, of course, always be gaps in scientific knowledge. But when critics accuse ID of being a “gaps-based” argument, they essentially insist that all gaps may only be filled with naturalistic explanations, and promote “materialism-of-the-gaps” thinking. This precludes scientists from fully seeking the truth and finding evidence for design in nature. ID rejects gaps-based reasoning of all kinds, and follows the motto that we should “follow the evidence wherever it leads.”
Adding ID to our explanatory toolkit leads to many advances in different scientific fields. In biochemistry, ID allows us to better understand the workings and origin of molecular machines. In paleontology, ID helps resolve long-standing questions about patterns of abrupt appearance—and disappearance—of species. In systematics, ID explains why studies of biomolecules and anatomy are failing to yield a grand “tree of life.” In genetics, ID leads biology into a new paradigm where life is full of functional, information rich molecules containing new layers of code and regulation. In this way, ID is best poised to lead biology into an information age that uncovers the complex, information-based genetic and epigenetic workings of life.
ID has scientific merit because it uses well-accepted methods of historical sciences in order to detect in nature the types of complexity that we understand, from present-day observations, are derived from intelligent causes. From top to bottom, when we study nature through science, we find evidence of fine-tuning and planning—intelligent design—from the macro-architecture of the entire universe to the tiniest submicroscopic biomolecular machines. The more we understand nature, the more clearly we see it is filled with evidence for design.
Good ID Websites for More Information:
- ID Portal: www.intelligentdesign.org
- IDEA Student Clubs: www.ideacenter.org
- ID News Site: www.evolutionnews.org
- ID Podcast: www.idthefuture.com
- Resources for Faith Leaders: www.faithandevolution.org
- Discovery Institute’s ID Program: www.discovery.org/ID
[1.] Stephen C. Meyer, “The origin of biological information and the higher taxonomic categories,” Proceedings of the Biological Society of Washington, 117(2):213-239 (2004).
[2.] Carl Sagan, “Life,” in Encyclopedia Britannica: Macropaedia Vol. 10 (Encyclopedia Britannica, Inc., 1984), 894.
[3.] Douglas D. Axe, “Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors,” Journal of Molecular Biology, 301:585-595 (2000); Douglas D. Axe, “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds,” Journal of Molecular Biology, 341: 1295–1315 (2004).
[4.] Richard Dawkins, The Blind Watchmaker (New York: W. W. Norton, 1986), 1.
[5.] Stephen C. Meyer et. al., “The Cambrian Explosion: Biology's Big Bang,” in Darwinism, Design, and Public Education, J. A. Campbell and S. C. Meyer eds. (Michigan State University Press, 2003).
[6.] Bill Gates, N. Myhrvold, and P. Rinearson, The Road Ahead: Completely Revised and Up-To-Date (Penguin Books, 1996), 228.
[7.] J. Craig Venter, “The Big Idea: Craig Venter On the Future of Life,” The Daily Beast (October 25, 2013), accessed October 25, 2013, www.thedailybeast.com/articles/2013/10/25/the-big-idea-craig-venter-the-future-of-life.html.
[8.] J. Craig Venter, quoted in Casey Luskin, “Craig Venter in Seattle: ‘Life Is a DNA Software System’,” (October 24, 2013), www.evolutionnews.org/2013/10/craig_venter_in078301.html.
[9.] Richard Dawkins, River Out of Eden: A Darwinian View of Life (New York: Basic Books, 1995), 17.
[10.] Francis Collins, The Language of God: A Scientist Presents Evidence for Belief (New York: Free Press, 2006), 91.
[11.] Bruce Alberts, “The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists,” Cell, 92: 291-294 (Feb. 6, 1998).
[12.] David J. DeRosier, “The Turn of the Screw: The Bacterial Flagellar Motor,” Cell, 93: 17-20 (April 3, 1998).
[13.] Michael J. Behe, Darwin's Black Box: The Biochemical Challenge to Darwinism (Free Press 1996), 39.
[14.] Transcript of testimony of Scott Minnich, Kitzmiller et al. v. Dover Area School Board (M.D. Pa., PM Testimony, November 3, 2005), 103-112. See also Table 1 in R. M. Macnab, “Flagella,” in Escherichia Coli and Salmonella Typhimurium: Cellular and Molecular Biology Vol. 1, eds. F. C. Neidhardt, J. L. Ingraham, K. B. Low, B. Magasanik, M. Schaechter, and H. E. Umbarger (Washington D.C.: American Society for Microbiology, 1987), 73-74.
[15.] Fred Hoyle, “The Universe: Past and Present Reflections,” Engineering and Science, pp. 8-12 (November, 1981).
[16.] William Dembski, “Intelligent Design as a Theory of Information,” Naturalism, Theism and the Scientific Enterprise: An Interdisciplinary Conference at the University of Texas, Feb. 20-23, 1997, http://www.discovery.org/a/118 (citations omitted).
[17.] Jack W. Szostak, “Molecular messages,” Nature, 423: 689 (June 12, 2003).
[18.] William Dembski and Jonathan Witt, Intelligent Design Uncensored, pp. 68-69 (InterVarsity Press, 2010).
[19.] Jerry Coyne, “The Great Mutator,” The New Republic (June 14, 2007).
[20.] Michael Behe and David Snoke, “Simulating Evolution by Gene Duplication of Protein Features That Require Multiple Amino Acid Residues,” Protein Science, 13: 2651-2664 (2004).
[21.] Rick Durrett and Deena Schmidt, “Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution,” Genetics, 180:1501-1509 (2008).
[22.] Douglas Axe, “The Limits of Complex Adaptation: An Analysis Based on a Simple Model of Structured Bacterial Populations,” BIO-Complexity, 2010 (4): 1-10.
[23.] Axe, “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds”; Axe, “Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors.”
[24.] Ann Gauger and Douglas Axe, "The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway," BIO-Complexity, 2011 (1): 1-17.
[25.] Mariclair A. Reeves, Ann K. Gauger, Douglas D. Axe, “Enzyme Families—Shared Evolutionary History or Shared Design? A Study of the GABA-Aminotransferase Family,” BIO-Complexity, 2014 (4): 1-16.
[26.] Meyer, “The origin of biological information and the higher taxonomic categories.”
[27.] Scott A. Minnich & Stephen C. Meyer, “Genetic analysis of coordinate flagellar and type III regulatory circuits in pathogenic bacteria," in Proceedings of the Second International Conference on Design & Nature, Rhodes Greece, p. 8 (M.W. Collins & C.A. Brebbia eds., 2004).
[28.] Hubert P. Yockey, “Self Organization Origin of Life Scenarios and Information Theory," Journal of Theoretical Biology, 91:13-31 (1981).
Copyright © 2016. Version 1.0 Permission Granted to Reproduce for Educational Purposes.
In 2009, I discussed a paper in BioEssays titled “MicroRNAs and metazoan macroevolution: insights into canalization, complexity, and the Cambrian explosion” which stated that “elucidating the materialistic basis of the Cambrian explosion has become more elusive, not less, the more we know about the event itself, and cannot be explained away by coupling extinction of intermediates with long stretches of geologic time, despite the contrary claims of some modern neo-Darwinists.”(more…)
[Editor’s Note: The following article is Casey Luskin’s chapter, “The Top Ten Scientific Problems with Biological and Chemical Evolution,” contributed to the volume More than Myth (Chartwell Press, 2014). It has been posted with permission of the book’s editors, Robert Stackpole and Paul Brown. A PDF of this article can be downloaded here.]
- Problem 1: No Viable Mechanism to Generate a Primordial Soup
- Problem 2: Unguided Chemical Processes Cannot Explain the Origin of the Genetic Code
- Problem 3: Random Mutations Cannot Generate the Genetic Information Required for Irreducibly Complex Structures
- Problem 4: Natural Selection Struggles to Fix Advantageous Traits into Populations
- Problem 5: Abrupt Appearance of Species in the Fossil Record Does Not Support Darwinian Evolution
- Problem 6: Molecular Biology has Failed to Yield a Grand "Tree of Life"
- Problem 7: Convergent Evolution Challenges Darwinism and Destroys the Logic Behind Common Ancestry
- Problem 8: Differences between Vertebrate Embryos Contradict the Predictions of Common Ancestry
- Problem 9: Neo-Darwinism Struggles to Explain the Biogeographical Distribution of many Species
- Problem 10: Neo-Darwinism has a Long History of Inaccurate Darwinian Predictions about Vestigial Organs and "Junk DNA"
- Bonus Problem: Humans Display Many Behavioral and Cognitive Abilities that Offer No Apparent Survival Advantage
"There are no weaknesses in the theory of evolution."1 Such was professed by Eugenie Scott, the de facto head of the Darwin lobby, while speaking to the media in response to the Texas State Board of Education's 2009 vote to require students to learn about both the scientific evidence for and against neo-Darwinian evolution.
For those who follow the debate over origins, Dr. Scott's words are as unsurprising as they are familiar. It seems that almost on a daily basis, we find the news media quoting evolutionary scientists declaring that materialist accounts of biological and chemical evolution are "fact." Students who take college-preparatory or college-level courses on evolution are warned that doubting Darwinism is tantamount to committing intellectual suicide -- you might as well proclaim the Earth is flat.2 Such bullying is enough to convince many that it's much easier on your academic standing, your career, and your reputation to just buy into Darwinism. The few holdouts who remain are intimidated into silence.
But is it true that there are "no weaknesses" in evolutionary theory? Are those who express doubts about Darwinism displaying courage, or are they fools that want to take us back to the dark ages and era of the flat Earth?3 Thankfully, it's very easy to test these questions: all one must do is examine the technical scientific literature and inquire whether there are legitimate scientific challenges to chemical and biological evolution.
This chapter will review some of this literature, and show that there are numerous legitimate scientific challenges to core tenets of Darwinian theory, as well as predominant theories of chemical evolution. Those who harbor doubts about Darwinism need not be terrified by academic bullies who pretend there is no scientific debate to be had.
Problem 1: No Viable Mechanism to Generate a Primordial Soup
According to conventional thinking among origin of life theorists, life arose via unguided chemical reactions on the early Earth some 3 to 4 billion years ago. Most theorists believe that there were many steps involved in the origin of life, but the very first step would have involved the production of a primordial soup -- a water-based sea of simple organic molecules -- out of which life arose. While the existence of this "soup" has been accepted as unquestioned fact for decades, this first step in most origin-of-life theories faces numerous scientific difficulties.
In 1953, a graduate student at the University of Chicago named Stanley Miller, along with his faculty advisor Harold Urey, performed experiments hoping to produce the building blocks of life under natural conditions on the early Earth.4 These "Miller-Urey experiments" intended to simulate lightning striking the gasses in the early Earth's atmosphere. After running the experiments and letting the chemical products sit for a period of time, Miller discovered that amino acids -- the building blocks of proteins -- had been produced.
For decades, these experiments have been hailed as a demonstration that the "building blocks" of life could have arisen under natural, realistic Earthlike conditions,5 corroborating the primordial soup hypothesis. However, it has also been known for decades that the Earth's early atmosphere was fundamentally different from the gasses used by Miller and Urey.
The atmosphere used in the Miller-Urey experiments was primarily composed of reducing gasses like methane, ammonia, and high levels of hydrogen. Geochemists now believe that the atmosphere of the early Earth did not contain appreciable amounts of these components. (Reducing gasses are those which tend to donate electrons during chemical reactions.) UC Santa Cruz origin-of-life theorist David Deamer explains this in the journal Microbiology & Molecular Biology Reviews:
This optimistic picture began to change in the late 1970s, when it became increasingly clear that the early atmosphere was probably volcanic in origin and composition, composed largely of carbon dioxide and nitrogen rather than the mixture of reducing gases assumed by the Miller-Urey model. Carbon dioxide does not support the rich array of synthetic pathways leading to possible monomers…6
Likewise, an article in the journal Science stated: "Miller and Urey relied on a 'reducing' atmosphere, a condition in which molecules are fat with hydrogen atoms. As Miller showed later, he could not make organics in an 'oxidizing' atmosphere."7 The article put it bluntly: "the early atmosphere looked nothing like the Miller-Urey situation."8 Consistent with this, geological studies have not uncovered evidence that a primordial soup once existed.9
There are good reasons to understand why the Earth's early atmosphere did not contain high concentrations of methane, ammonia, or other reducing gasses. The earth's early atmosphere is thought to have been produced by outgassing from volcanoes, and the composition of those volcanic gasses is related to the chemical properties of the Earth's inner mantle. Geochemical studies have found that the chemical properties of the Earth's mantle would have been the same in the past as they are today.10 But today, volcanic gasses do not contain methane or ammonia, and are not reducing.
A paper in Earth and Planetary Science Letters found that the chemical properties of the Earth's interior have been essentially constant over Earth's history, leading to the conclusion that "Life may have found its origins in other environments or by other mechanisms."11 So drastic is the evidence against pre-biotic synthesis of life's building blocks that in 1990 the Space Studies Board of the National Research Council recommended that origin of life investigators undertake a "reexamination of biological monomer synthesis under primitive Earthlike environments, as revealed in current models of the early Earth."12
Because of these difficulties, some leading theorists have abandoned the Miller-Urey experiment and the "primordial soup" theory it is claimed to support. In 2010, University College London biochemist Nick Lane stated the primordial soup theory "doesn't hold water" and is "past its expiration date."13 Instead, he proposes that life arose in undersea hydrothermal vents. But both the hydrothermal vent and primordial soup hypotheses face another major problem.
Chemical Evolution is Dead in the Water
Assume for a moment that there was some way to produce simple organic molecules on the early Earth. Perhaps they did form a "primordial soup," or perhaps these molecules arose near some hydrothermal vent. Either way, origin of life theorists must then explain how amino acids or other key organic molecules linked up to form long chains (polymers) like proteins (or RNA).
Chemically speaking, however, the last place you'd want to link amino acids into chains would be a vast water-based environment like the "primordial soup" or underwater near a hydrothermal vent. As the National Academy of Sciences acknowledges, "Two amino acids do not spontaneously join in water. Rather, the opposite reaction is thermodynamically favored."14 In other words, water breaks protein chains back down into amino acids (or other constituents), making it very difficult to produce proteins (or other polymers) in the primordial soup.
Materialists lack good explanations for these first, simple steps which are necessary to the origin-of-life. Chemical evolution is literally dead in the water.
Problem 2: Unguided Chemical Processes Cannot Explain the Origin of the Genetic Code
Let's assume, again, that a primordial sea filled with life's building blocks did exist on the early Earth, and somehow it formed proteins and other complex organic molecules. Origin of life theorists believe that the next step in the origin of life is that -- entirely by chance -- more and more complex molecules formed until some began to self-replicate. From there, they believe Darwinian natural selection took over, favoring those molecules which were better able to make copies. Eventually, they assume, it became inevitable that these molecules would evolve complex machinery -- like that used in today's genetic code -- to survive and reproduce.
Have modern theorists explained how this crucial bridge from inert nonliving chemicals to self-replicating molecular systems took place? The most prominent hypothesis for the origin of the first life is called the "RNA world." In living cells, genetic information is carried by DNA, and most cellular functions are carried out by proteins. However, RNA is capable of both carrying genetic information and catalyzing some biochemical reactions. As a result, some theorists postulate the first life might have used RNA alone to fulfill all these functions.
But there are many problems with this hypothesis.
For one, the first RNA molecules would have to arise by unguided, non-biological chemical processes. But RNA is not known to assemble without the help of a skilled laboratory chemist intelligently guiding the process. New York University chemist Robert Shapiro critiqued the efforts of those who tried to make RNA in the lab, stating: "The flaw is in the logic -- that this experimental control by researchers in a modern laboratory could have been available on the early Earth."15
Second, while RNA has been shown to perform many roles in the cell, there is no evidence that it could perform all the necessary cellular functions currently carried out by proteins.16
Third, the RNA world hypothesis does not explain the origin of genetic information.
RNA world advocates suggest that if the first self-replicating life was based upon RNA, it would have required a molecule between 200 and 300 nucleotides in length.17 However, there are no known chemical or physical laws that dictate the order of those nucleotides.18 To explain the ordering of nucleotides in the first self-replicating RNA molecule, materialists must rely on sheer chance. But the odds of specifying, say, 250 nucleotides in an RNA molecule by chance is about 1 in 10150 -- below the universal probability boundary, or events which are remotely possible to occur within the history of the universe.19 Shapiro puts the problem this way:
The sudden appearance of a large self-copying molecule such as RNA was exceedingly improbable. … [The probability] is so vanishingly small that its happening even once anywhere in the visible universe would count as a piece of exceptional good luck.20
Fourth -- and most fundamentally -- the RNA world hypothesis does not explain the origin of the genetic code itself. In order to evolve into the DNA / protein-based life that exists today, the RNA world would need to evolve the ability to convert genetic information into proteins. However, this process of transcription and translation requires a large suite of proteins and molecular machines -- which themselves are encoded by genetic information. This poses a chicken-and-egg problem, where essential enzymes and molecular machines are needed to perform the very task that constructs them.
The Chicken and the DVD
To appreciate this problem, consider the origin of the first DVD and DVD player. DVDs are rich in information, but without the machinery of a DVD player to read the disk, process its information, and convert it into a picture and sound, the disk would be useless. But what if the instructions for building the first DVD player were only found encoded on a DVD? You could never play the DVD to learn how to build a DVD player. So how did the first disk and DVD player system arise? The answer is obvious: a goal directed process -- intelligent design -- is required to produce both the player and the disk at the same time.
In living cells, information-carrying molecules (e.g. DNA or RNA) are like the DVD, and the cellular machinery which reads that information and converts it into proteins are like the DVD player. Just like the DVD analogy, genetic information can never be converted into proteins without the proper machinery. Yet in cells, the machines required for processing the genetic information in RNA or DNA are encoded by those same genetic molecules -- they perform and direct the very task that builds them.
This system cannot exist unless both the genetic information and transcription / translation machinery are present at the same time, and unless both speak the same language. Biologist Frank Salisbury explained this problem in a paper in American Biology Teacher not long after the workings of the genetic code were first uncovered:
It's nice to talk about replicating DNA molecules arising in a soupy sea, but in modern cells this replication requires the presence of suitable enzymes. … [T]he link between DNA and the enzyme is a highly complex one, involving RNA and an enzyme for its synthesis on a DNA template; ribosomes; enzymes to activate the amino acids; and transfer-RNA molecules. … How, in the absence of the final enzyme, could selection act upon DNA and all the mechanisms for replicating it? It's as though everything must happen at once: the entire system must come into being as one unit, or it is worthless. There may well be ways out of this dilemma, but I don't see them at the moment.21
Despite decades of work, origin-of-life theorists are still at a loss to explain how this system arose. In 2007, Harvard chemist George Whitesides was given the Priestley Medal, the highest award of the American Chemical Society. During his acceptance speech, he offered this stark analysis, reprinted in the respected journal, Chemical and Engineering News:
The Origin of Life. This problem is one of the big ones in science. It begins to place life, and us, in the universe. Most chemists believe, as do I, that life emerged spontaneously from mixtures of molecules in the prebiotic Earth. How? I have no idea.22
Similarly, the aforementioned article in Cell Biology International concludes: "New approaches to investigating the origin of the genetic code are required. The constraints of historical science are such that the origin of life may never be understood."23 That is, they may never be understood unless scientists are willing to consider goal-directed scientific explanations like intelligent design.
But there is a much deeper problem with theories of chemical evolution, as well as biological evolution. This pertains not just to the ability to process genetic information via a genetic code, but the origin of that information itself.
Problem 3: Random Mutations Cannot Generate the Genetic Information Required for Irreducibly Complex Structures
According to evolutionary biologists, once life got started, Darwinian evolution took over and eventually produced the grand diversity we observe today. Under the standard view, a process of random mutation and natural selection built life's vast complexity one small mutational step at a time. All of life's complex features, of course, are thought to be encoded in the DNA of living organisms. Building new features thus requires generating new information in the genetic code of DNA. Can the necessary information be generated in the undirected, step-by-step manner required by Darwin's theory?
Most everyone agrees that Darwinian evolution tends to work well when each small step along an evolutionary pathway provides some survival advantage. Darwin-critic Michael Behe notes that "if only one mutation is needed to confer some ability then Darwinian evolution has little problem finding it."24 However, when multiple mutations must be present simultaneously to gain a functional advantage, Darwinian evolution gets stuck. As Behe explains, "If more than one [mutation] is needed, the probability of getting all the right ones grows exponentially worse."25
Behe, a professor of biochemistry at Lehigh University, coined the term "irreducible complexity" to describe systems which require many parts -- and thus many mutations -- to be present -- all at once -- before providing any survival advantage to the organism. According to Behe, such systems cannot evolve in the step-by-step fashion required by Darwinian evolution. As a result, he maintains that random mutation and unguided natural selection cannot generate the genetic information required to produce irreducibly complex structures. Too many simultaneous mutations would be required -- an event which is highly unlikely to occur.
Observation of this problem is not limited to Darwin-critics. A paper by a prominent evolutionary biologist in the prestigious journal Proceedings of the U.S. National Academy of Science. acknowledges that "simultaneous emergence of all components of a system is implausible."26 Likewise, University of Chicago evolutionary biologist Jerry Coyne -- a staunch defender of Darwinism -- admits that "natural selection cannot build any feature in which intermediate steps do not confer a net benefit on the organism."27 Even Darwin intuitively recognized this problem, as he wrote in Origin of Species:
If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.28
Evolutionary scientists like Darwin and Coyne claim they know of no real-world case where Darwinian selection gets blocked in this manner. But they would agree, at least in principle, that there are theoretical limits to what Darwinian evolution can accomplish: If a feature cannot be built by "numerous, successive, slight modifications," and if "intermediate steps do not confer a net benefit on the organism," then Darwinian evolution will "absolutely break down."
The problems are real. Modern biology continues to uncover more and more examples where biological complexity seems to outstrip the information-generative capacity of Darwinian evolution.
In his book Darwin's Black Box, Michael Behe discusses molecular machines which require multiple parts to be present before they could function and confer any advantage on the organism. Behe's most famous example is the bacterial flagellum -- a micromolecular rotary-engine, functioning like an outboard motor on bacteria to propel it through liquid medium to find food. In this regard, flagella have a basic design that is highly similar to some motors made by humans containing many parts that are familiar to engineers, including a rotor, a stator, a u-joint, a propeller, a brake, and a clutch. As one molecular biologist writes in the journal Cell, "[m]ore so than other motors, the flagellum resembles a machine designed by a human."29 However the energetic efficiency of these machines outperforms anything produced by humans: the same paper found that the efficiency of the bacterial flagellum "could be ~100%."30
There are various types of flagella, but all use certain basic components. As one paper in Nature Reviews Microbiology acknowledges, "all (bacterial) flagella share a conserved core set of proteins" since "Three modular molecular devices are at the heart of the bacterial flagellum: the rotor-stator that powers flagellar rotation, the chemotaxis apparatus that mediates changes in the direction of motion and the T3SS that mediates export of the axial components of the flagellum."31 As this might suggest, the flagellum is irreducibly complex. Genetic knockout experiments have shown that it fails to assemble or function properly if any one of its approximately 35 genes are missing.32 In this all-or-nothing game, mutations cannot produce the complexity needed to provide a functional flagellar rotary engine one incremental step at a time, and the odds are too daunting for it to assemble in one great leap. Indeed, the aforementioned Nature Reviews Microbiology paper admitted that "the flagellar research community has scarcely begun to consider how these systems have evolved."33
Yet the flagellum is just one example of thousands of known molecular machines in biology. One individual research project reported the discovery of over 250 new molecular machines in yeast alone.34 The former president of the U.S. National Academy of Sciences, Bruce Alberts, wrote an article in the journal Cell praising the "speed," "elegance," "sophistication," and "highly organized activity" of these "remarkable" and "marvelous" molecular machines. He explained what inspired those words: "Why do we call the large protein assemblies that underlie cell function protein machines? Precisely because, like machines invented by humans to deal efficiently with the macroscopic world, these protein assemblies contain highly coordinated moving parts."35 Biochemists like Behe and others believe that with all of their coordinated interacting parts, many of these machines could not have evolved in a step-by-step Darwinian fashion.
But it's not just multi-part machines which are beyond reach of Darwinian evolution. The protein-parts themselves which build these machines would also require multiple simultaneous mutations in order to arise.
Research Challenges the Darwinian Mechanism
In 2000 and 2004, protein scientist Douglas Axe published experimental research in the Journal of Molecular Biology on mutational sensitivity tests he performed on enzymes in bacteria.36 Enzymes are long chains of amino acids which fold into a specific, stable, three-dimensional shape in order to function. Mutational sensitivity experiments begin by mutating the amino acid sequences of those proteins, and then testing the mutant proteins to determine whether they can still fold into a stable shape, and function properly. Axe's research found that amino acid sequences which yield stable, functional protein folds may be as rare as 1 in 1074 sequences, suggesting that the vast majority of amino acid sequences will not produce stable proteins, and thus could not function in living organisms.
Because of this extreme rarity of functional protein sequences, it would be very difficult for random mutations to take a protein with one type of fold, and evolve it into another, without going through some non-functional stage. Rather than evolving by "numerous, successive, slight modifications," many changes would need to occur simultaneously to "find" the rare and unlikely amino acid sequences that yield functional proteins. To put the matter in perspective, Axe's results suggest that the odds of blind and unguided Darwinian processes producing a functional protein fold are less than the odds of someone closing his eyes and firing an arrow into the Milky Way galaxy, and hitting one pre-selected atom.37
Proteins commonly interact with other molecules through a "hand-in-glove" fit, but these interactions often require multiple amino acids to be 'just right' before they occur. In 2004, Behe, along with University of Pittsburgh physicist David Snoke, simulated the Darwinian evolution of such protein-protein interactions. Behe and Snoke's calculations found that for multicellular organisms, evolving a simple protein-protein interaction which required two or more mutations in order to function would probably require more organisms and generations than would be available over the entire history of the Earth. They concluded that "the mechanism of gene duplication and point mutation alone would be ineffective…because few multicellular species reach the required population sizes."38
Four years later during an attempt to refute Behe's arguments, Cornell biologists Rick Durrett and Deena Schmidt ended up begrudgingly confirming he was basically correct. After calculating the likelihood of two simultaneous mutations arising via Darwinian evolution in a population of humans, they found that such an event "would take > 100 million years." Given that humans diverged from their supposed common ancestor with chimpanzees only 6 million years ago, they granted that such mutational events are "very unlikely to occur on a reasonable timescale."39
Now a defender of Darwinism might reply that these calculations measured the power of the Darwinian mechanism only within multicellular organisms where it is less efficient because these more complex organisms have smaller population sizes and longer generation times than single-celled prokaryotic organisms like bacteria. Darwinian evolution, the Darwinian notes, might have a better shot when operating in organisms like bacteria, which reproduce more rapidly and have much larger population sizes. Scientists skeptical of Darwinian evolution are aware of this objection, and have found that even within more-quickly evolving organisms like bacteria, Darwinian evolution faces great limits.
In 2010, Douglas Axe published evidence indicating that despite high mutation rates and generous assumptions favoring a Darwinian process, molecular adaptations requiring more than six mutations before yielding any advantage would be extremely unlikely to arise in the history of the Earth.
The following year, Axe published research with developmental biologist Ann Gauger regarding experiments to convert one bacterial enzyme into another closely related enzyme -- the kind of conversion that evolutionists claim can easily happen. For this case they found that the conversion would require a minimum of at least seven simultaneous changes,40 exceeding the six-mutation-limit which Axe had previously established as a boundary of what Darwinian evolution is likely to accomplish in bacteria. Because this conversion is thought to be relatively simple, it suggests that more complex biological features would require more than six simultaneous mutations to give some new functional advantage.
In other experiments led by Gauger and biologist Ralph Seelke of the University of Wisconsin, Superior, their research team broke a gene in the bacterium E. coli required for synthesizing the amino acid tryptophan. When the bacteria's genome was broken in just one place, random mutations were capable of "fixing" the gene. But even when only two mutations were required to restore function, Darwinian evolutionseemed to get stuck, with an inability to regain full function.41
These kind of results consistently suggest that the information required for proteins and enzymes to function is too great to be generated by Darwinian processes on any reasonable evolutionary timescale.
Darwin Skeptics Abound
Drs. Axe, Gauger, and Seelke are by no means the only scientists to observe the rarity of amino acid sequences that yield functional proteins. A leading college-level biology textbook states that "even a slight change in primary structure can affect a protein's conformation and ability to function."42 Likewise, evolutionary biologist David S. Goodsell writes:
[O]nly a small fraction of the possible combinations of amino acids will fold spontaneously into a stable structure. If you make a protein with a random sequence of amino acids, chances are that it will only form a gooey tangle when placed in water.43
Goodsell goes on to assert that "cells have perfected the sequences of amino acids over many years of evolutionary selection." But if functional protein sequences are rare, then it is likely that natural selection will be unable to take proteins from one functional genetic sequence to another without getting stuck in some maladaptive or non-beneficial intermediate stage.
The late biologist Lynn Margulis, a well-respected member of the National Academy of Sciences until her death in 2011, once said "new mutations don't create new species; they create offspring that are impaired."44 She further explained in a 2011 interview:
[N]eo-Darwinists say that new species emerge when mutations occur and modify an organism. I was taught over and over again that the accumulation of random mutations led to evolutionary change-led to new species. I believed it until I looked for evidence.45
Similarly, past president of the French Academy of Sciences, Pierre-Paul Grasse, contended that "[m]utations have a very limited 'constructive capacity'" because "[n]o matter how numerous they may be, mutations do not produce any kind of evolution."46
Many other scientists feel this way. Over 800 Ph.D. scientists have signed a statement agreeing they "are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life."47 Indeed, two biologists wrote in Annual Review of Genomics and Human Genetics: "it remains a mystery how the undirected process of mutation, combined with natural selection, has resulted in the creation of thousands of new proteins with extraordinarily diverse and well optimized functions. This problem is particularly acute for tightly integrated molecular systems that consist of many interacting parts…"48 Perhaps it would be less mysterious if the theoretical conceptions could be expanded beyond unguided evolutionary mechanisms like random mutation and natural selection to explain the origin of complex biological features.
Problem 4: Natural Selection Struggles to Fix Advantageous Traits into Populations
In 2008, 16 biologists from around the world convened in Altenberg, Austria to discuss problems with the modern neo-Darwinian model of evolution. The journal Nature covered this "Altenberg 16" conference, quoting leading scientists saying things like:
- "[T]he origin of wings and the invasion of the land . . . are things that evolutionary theory has told us little about."49
- "You can't deny the force of selection in genetic evolution . . . but in my view this is stabilizing and fine-tuning forms that originate due to other processes."
- "The modern synthesis is remarkably good at modeling the survival of the fittest, but not good at modeling the arrival of the fittest."
In Problem 3, we learned that mutations cannot generate many complex traits in living organisms on reasonable evolutionary timescales. But mutations are only part of the standard evolutionary mechanism -- there is also natural selection. And Darwinian evolution not only commonly fails to explain the "arrival of the fittest" via mutations, but also often struggles to explain the "survival of the fittest" via natural selection.
Evolutionary biologists often assume that once mutations produce a functionally advantageous trait, it will easily spread (become "fixed") throughout a population by natural selection. For example, imagine a population of brown-haired foxes which lives in a snowy region. One fox is born with a mutation which turns its fur coat white, rather than brown. This fox now has an advantage in hunting prey and escaping predators, because its white fur provides it with camouflage in the snow-filled environment. The white fox survives, passing its genes on to its offspring, which are also adept at surviving and reproducing. Over time, the white-haired trait spreads throughout the population.
This is how it's supposed to work -- in theory. In the real world, however, merely generating a functionally advantageous trait does not guarantee it will persist, or become fixed. For example, what if by chance the white fox trips, breaks a leg, and gets eaten by a predator -- never passing on its genes? Random forces or events can prevent a trait from spreading through a population, even if it provides an advantage. These random forces are lumped together under the name "genetic drift." When biologists run the mathematics of natural selection, they find that unless a trait gives an extremely strong selective advantage, genetic drift will tend to overwhelm the force of selection and prevent adaptations from gaining a foothold in a population.
This underappreciated problem has been recognized by some evolutionary scientists who are skeptical of the ability of natural selection to drive the evolutionary process. One of those scientists is Michael Lynch, an evolutionary biologist at Indiana University, who writes that "random genetic drift can impose a strong barrier to the advancement of molecular refinements by adaptive processes."50 He notes that the effect of drift is "encouraging the fixation of mildly deleterious mutations and discouraging the promotion of beneficial mutations."51 Likewise, Eugene Koonin, a leading scientist at the National Institutes of Health, explains, genetic drift leads to "random fixation of neutral or even deleterious changes."52
In Lynch's view, there are many cellular systems which aid in survival, but are redundant. As a result, they serve as backup mechanisms that are only used when a highly effective primary system fails. Because they are only seldom used, these systems are only occasionally exposed to the sieve of selection. Yet these systems can be extremely complex and efficient. How can a system which is only rarely used, or only occasionally needed, evolve to such a high and efficient level of complexity? After observing the many "layers" of complex cellular mechanisms which are involved in processes like DNA replication, Lynch poses a crucial question:
Although these layered lines of defense are clearly advantageous and in many cases essential to cell health, because the simultaneous emergence of all components of a system is implausible, several questions immediately arise. How can selection promote the establishment of additional layers of fitness-enhancing mechanisms if the established primary lines of defense are already highly refined?53
Lynch doesn't believe natural selection is up to the task. In a 2007 paper in Proceedings of the U.S. National Academy of Sciences titled "The frailty of adaptive hypotheses for the origins of organismal complexity," he explains that among evolutionary biologists, "What is in question is whether natural selection is a necessary or sufficient force to explain the emergence of the genomic and cellular features central to the building of complex organisms."54 Using similar language, a paper in the journal Theoretical Biology and Medical Modelling concludes that "it is important for biologists to realistically appraise what selection can and cannot do under various circumstances. Selection may neither be necessary nor sufficient to explain numerous genomic or cellular features of complex organisms."55 Lynch is clear in his views: "there is no compelling empirical or theoretical evidence that complexity, modularity, redundancy or other features of genetic pathways are promoted by natural selection."56
Damned if You Appeal to Selection, Damned if You Don't
In place of natural selection, however, evolutionary biologists like Lynch propose random genetic drift to explain the origin of complex biological features. According to Lynch, "many aspects of complexity at the genomic, molecular and cellular levels in multicellular species are likely to owe their origins to these non-adaptive forces, representing little more than passive outcomes..."57 But he recognizes that these "nonadaptive forces of evolution are stochastic in nature."58
Stochastic, of course, means random. Can a strictly random force -- which has no reason to preserve features that might provide some advantage -- explain the highly complex biological features -- like DNA replication or bioluminescence -- which appear finely tuned to perform useful biological functions? Biologist Ann Gauger is skeptical of Lynch's explanation, as she observes that he "offers no explanation of how non-adaptive forces can produce the functional genomic and organismal complexity we observe in modern species."59 Jerry Coyne similarly points out the major deficiency in appeals to genetic drift:
Both drift and natural selection produce genetic change that we recognize as evolution. But there's an important difference. Drift is a random process, while selection is the anti-thesis of randomness. … As a purely random process, genetic drift can't cause the evolution of adaptations. It could never build a wing or an eye. That takes nonrandom natural selection. What drift can do is cause the evolution of features that are neither useful nor harmful to the organism.60
Coyne further observes: "The influence of this process on important evolutionary change, though, is probably minor, because it does not have the molding power of natural selection. Natural selection remains the only process that can produce adaptation."61 But in a sense agreeing with Lynch, even he recognizes that "genetic drift is not only powerless to create adaptations, but can actually overpower natural selection."62
The debate over whether natural selection, or genetic drift, is more influential in evolution will undoubtedly continue. But there is little reason to believe that whichever side wins this debate, a viable materialistic solution will be offered. Evolutionary biology now finds itself facing a catch-22:
- Natural selection is too inefficient a mechanism to overcome random forces and fix the sort of complex adaptations we observe in populations because it is easily overpowered by random forces like genetic drift.
- Life is full of highly complex and efficient adaptations, but random genetic drift offers no justifiable reason to believe that such features will have any reason to arise.
In essence, genetic drift is like invoking the "mutation-selection" mechanism, but minus all of the selection. This subjects drift to all of the difficulties we saw in Problem 3, where random mutations were unable to build biochemical features like functional proteins, or simple protein-protein interactions, because multiple coordinated mutations were required to produce those traits. Absent selection, there is no reason for random mutations alone -- i.e. genetic drift -- to produce anything useful.
Unfortunately, the public is rarely made aware of these problems or this debate. According to Lynch, natural selection is typically portrayed as an "all powerful (without any direct evidence)"63 mechanism that can build complex biological features. He warns that "the myth that all of evolution can be explained by adaptation continues to be perpetuated by our continued homage to Darwin's treatise in the popular literature."64 The reality is that neither non-random forces like natural selection, nor random forces like genetic drift, can explain the origin of many complex biological features.
Problem 5: Abrupt Appearance of Species in the Fossil Record Does Not Support Darwinian Evolution
The fossil record has long-been recognized as a problem for evolutionary theory. In Origin of Species, Darwin explained that his theory led him to believe that "[t]he number of intermediate varieties, which have formerly existed on the earth, [must] be truly enormous."65 However, he recognized that the fossil record did not document these "intermediate" forms of life, asking, "Why then is not every geological formation and every stratum full of such intermediate links?"66 Darwin's answer showed the tenuous nature of the evidence backing his ideas: "Geology assuredly does not reveal any such finely graduated organic chain; and this, perhaps, is the most obvious and gravest objection which can be urged against my theory."67
Today, some 150 years later, out of thousands of species known from the fossil record, only a small fraction are claimed to be candidates for Darwin's intermediate forms. Fossil evidence of evolutionary intermediates is generally lacking, as the late evolutionary paleontologist Stephen Jay Gould admitted: "The absence of fossil evidence for intermediary stages between major transitions in organic design, indeed our inability, even in our imagination, to construct functional intermediates in many cases, has been a persistent and nagging problem for gradualistic accounts of evolution."68
Darwin attempted to save his theory of gradual evolution by maintaining that intermediate fossils are not found because of "the extreme imperfection of the geological record."69 Even Gould noted that Darwin's argument that the fossil record is imperfect "persists as the favored escape of most paleontologists from the embarrassment of a record that seems to show so little of evolution directly."70 But in the last few decades, this excuse has lost credibility.
Paleontologists today generally recognize that while the fossil record is imperfect, it is still adequate to assess questions about evolution. One study in Nature reported that "if scaled to the … taxonomic level of the family, the past 540 million years of the fossil record provide uniformly good documentation of the life of the past."71 Another paper in Paleobiology evaluated our knowledge of the fossil record and concluded that "our view of the history of biological diversity is mature."72 Paleontologists now increasingly recognize that "jumps" between species, without intermediates, are not simply the result of an incomplete record. Niles Eldredge, an evolutionary paleontologist and curator at the American Museum of Natural History, puts it this way with Ian Tattersal: "The record jumps, and all the evidence shows that the record is real: the gaps we see reflect real events in life's history -- not the artifact of a poor fossil record."73 This conclusion did not come easily, as one scientist who studied under Gould felt the need to implore his colleagues that "[e]volutionary biologists can no longer ignore the fossil record on the ground that it is imperfect."74
A Pattern of Explosions
The eventual realization that the fossil record is not entirely incomplete has forced evolutionary biologists to accept that the record shows a pattern of explosions, not gradual evolution of living organisms. One biology textbook explains this:
Many species remain virtually unchanged for millions of years, then suddenly disappear to be replaced by a quite different, but related, form. Moreover, most major groups of animals appear abruptly in the fossil record, fully formed, and with no fossils yet discovered that form a transition from their parent group.75
Probably the most famous instance of abrupt appearance is the Cambrian explosion, where nearly all of the major living animal phyla appear in the Cambrian period. An invertebrate biology textbook explains this:
Most of the animal groups that are represented in the fossil record first appear, 'fully formed' and identifiable as to their phylum, in the Cambrian, some 550 million years ago. These include such anatomically complex and distinctive types as trilobites, echinoderms, brachiopods, molluscs, and chordates. … The fossil record is therefore of no help with respect to the origin and early diversification of the various animal phyla...76
Evolutionary scientists acknowledge that they cannot explain this rapid appearance of diverse animal body plans by classical Darwinian processes, or other known material mechanisms. Robert Carroll, a paleontologist at McGill University, argues in Trends in Ecology and Evolution that "The extreme speed of anatomical change and adaptive radiation during this brief time period requires explanations that go beyond those proposed for the evolution of species within the modern biota."77 Another paper likewise maintains that "microevolution does not provide a satisfactory explanation for the extraordinary burst of novelty during the Cambrian Explosion" and concludes "the major evolutionary transitions in animal evolution still remain to be causally explained."78 Likewise a 2009 paper in BioEssays concedes that "elucidating the materialistic basis of the Cambrian explosion has become more elusive, not less, the more we know about the event itself."79
But the Cambrian explosion is by no means the only explosion of life recorded in the fossil record. Regarding the origin of major fish groups, former Columbia University geoscientist Arthur Strahler writes that, "This is one count in the creationists' charge that can only evoke in unison from paleontologists a plea of nolo contendere [no contest]."80 A paper in Annual Review of Ecology and Systematics explains that the origin of land plants "is the terrestrial equivalent of the much-debated Cambrian 'explosion' of marine faunas."81 Regarding the origin of angiosperms (flowering plants), paleontologists have discovered a "big bloom" type of explosion event. As one paper states:
In spite of much research and analyses of different sources of data (e.g., fossil record and phylogenetic analyses using molecular and morphological characters), the origin of the angiosperms remains unclear. Angiosperms appear rather suddenly in the fossil record... with no obvious ancestors for a period of 80-90 million years before their appearance.82
In a similar way, many orders of mammals appear in an explosive manner. Niles Eldredge explains that "there are all sorts of gaps: absence of gradationally intermediate 'transitional' forms between species, but also between larger groups -- between, say, families of carnivores, or the orders of mammals."83 There is also a bird explosion, with major bird groups appearing in a short time period.84 One paper in Trends in Ecology and Evolution titled "Evolutionary Explosions and the Phylogenetic Fuse" explains:
A literal reading of the fossil record indicates that the early Cambrian (c. 545 million years ago) and early Tertiary (c. 65 million years ago) were characterized by enormously accelerated periods of morphological evolution marking the appearance of the animal phyla, and modern bird and placental mammal orders, respectively.85
Of course there are a handful of examples where evolutionary scientists believe they have found transitional fossils documenting gradual Darwinian evolution. The origin of whales has been called a "poster child for macroevolution,"86 where it is believed that around 55 million years ago, certain land mammals lost their hind-limbs and evolved into fully aquatic whales. In particular, it is claimed there are fossil land-mammals with ear-bones similar to whales, and fossil whale-like mammals that retain their hindlimbs.
Even though vertebrate and whale expert Phillip Gingerich admits that we only have "fossils illustrating three or four steps that bridge the precursor of whales to today's mammals,"87 let's assume for a moment that a full sequence of fossils exists. Is this enough to demonstrate that this transition occurred? Even if there are fossils that look like potential intermediate forms, if the overall evolutionary story does not make sense, then the fossils cannot be transitional. In this case, the Darwinian evolution of whales from land-mammals faces serious mathematical challenges from population genetics.
Many changes would have been necessary to convert a land-mammal into a whale, including:
- Emergence of a blowhole, with musculature and nerve control
- Modification of the eye for permanent underwater vision
- Ability to drink sea water
- Forelimbs transformed into flippers
- Modification of skeletal structure
- Ability to nurse young underwater
- Origin of tail flukes and musculature
- Blubber for temperature insulation88
Many of these necessary adaptations would require multiple coordinated changes. But as we saw in Problem 3, such simultaneous mutations require extremely long periods of time to arise via the Darwinian mechanism. Whale evolution now runs into a severe problem. The fossil record requires that the evolution of whales from small land mammals would have to have taken place in less than 10 million years.89 That may sound like a long time, but it actually falls dramatically short, especially given that whales have small population sizes and long generation times.90 Biologist Richard Sternberg has examined the requirements of this transition mathematically and puts it this way: "Too many genetic re-wirings, too little time."91
Whale origins thus provides an interesting case study of evolutionary transitions: On a rare occasion where there actually are fossils that potentially show intermediate traits, unguided neo-Darwinian evolution is invalidated by the short amount of time allowed by the fossil record. If this "poster child" of macroevolution doesn't hold up to scrutiny, what does this tell us about other cases where evolutionists tout supposed transitional fossils?
Human Origins and the Fossil Record
Indeed, the public is commonly told that there are fossils documenting the evolution of humans from ape-like precursors, but a closer look at the technical literature tells a different story. Hominid fossils generally fall into one of two groups: ape-like species and human-like species, with a large, unbridged gap between them. In 2004, the famed evolutionary biologist Ernst Mayr recognized the abrupt appearance of humans:
The earliest fossils of Homo, Homo rudolfensis and Homo erectus, are separated from Australopithecus by a large, unbridged gap. How can we explain this seeming saltation? Not having any fossils that can serve as missing links, we have to fall back on the time-honored method of historical science, the construction of a historical narrative.92
In light of such evidence, a paper in the Journal of Molecular Biology and Evolution called the appearance of Homo sapiens "a genetic revolution" where "no australopithecine species is obviously transitional."93 The lack of fossil evidence for this hypothesized transition is confirmed by Harvard paleoanthropologists Daniel E. Lieberman, David R. Pilbeam, and Richard W. Wrangham:
Of the various transitions that occurred during human evolution, the transition from Australopithecus to Homo was undoubtedly one of the most critical in its magnitude and consequences. As with many key evolutionary events, there is both good and bad news. First, the bad news is that many details of this transition are obscure because of the paucity of the fossil and archaeological records.94
As for the "good news," they still admit: "although we lack many details about exactly how, when, and where the transition occurred from Australopithecus to Homo, we have sufficient data from before and after the transition to make some inferences about the overall nature of key changes that did occur."95 In other words, the fossil record provides ape-like australopithecines ("before"), and human-like Homo ("after"), but not fossils documenting a transition between them. In the absence of intermediates, we're left with "inferences" of a transition based strictly upon the assumption of Darwinian evolution. One commentator proposed the evidence implies a "big bang theory" of the appearance of our genus Homo.96 This does not make for a compelling evolutionary account of human origins.97
Rather than showing gradual Darwinian evolution, the history of life shows a pattern of explosions where new fossil forms come into existence without clear evolutionary precursors. Evolutionary anthropologist Jeffrey Schwartz summarizes the problem:
[W]e are still in the dark about the origin of most major groups of organisms. They appear in the fossil record as Athena did from the head of Zeus -- full-blown and raring to go, in contradiction to Darwin's depiction of evolution as resulting from the gradual accumulation of countless infinitesimally minute variations. . ."98
This poses a major challenge to Darwinian evolution, including the view that all animals are related through common ancestry.
Problem 6: Molecular Biology has Failed to Yield a Grand "Tree of Life"
When fossils failed to demonstrate that animals evolved from a common ancestor, evolutionary scientists turned to another type of evidence -- DNA sequence data -- to demonstrate a tree of life. In the 1960s, around the time the genetic code was first understood, biochemists Émile Zuckerkandl and Linus Pauling hypothesized that if DNA sequences could be used to produce evolutionary trees -- trees which matched those based upon morphological or anatomical characteristics -- this would furnish "the best available single proof of the reality of macro-evolution."99 Thus began a decades-long effort to sequence the genes of many organisms and construct "molecular" based evolutionary ("phylogenetic") trees. The ultimate goal has been to construct a grand "tree of life," showing how all living organisms are related through universal common ancestry.
The Main Assumption
The basic logic behind building molecular trees is relatively simple. First, investigators choose a gene, or a suite of genes, found across multiple organisms. Next, those genes are analyzed to determine their nucleotide sequences, so the gene sequences of various organisms can then be compared. Finally, an evolutionary tree is constructed based upon the principle that the more similar the nucleotide sequence, the more closely related the species. A paper in the journal Biological Theory puts it this way:
[M]olecular systematics is (largely) based on the assumption, first clearly articulated by Zuckerkandl and Pauling (1962), that degree of overall similarity reflects degree of relatedness.100
This assumption is essentially an articulation of a major feature of the theory - the idea of universal common ancestry. Nonetheless, it's important to realize that it is a mere assumption to claim that genetic similarities between different species necessarily result from common ancestry.
Operating strictly within a Darwinian paradigm, these assumptions flow naturally. As the aforementioned Biological Theory paper explains, the main assumption underlying molecular trees "derives from interpreting molecular similarity (or dissimilarity) between taxa in the context of a Darwinian model of continual and gradual change."101 So the theory is assumed to be true to construct a tree. But also, if Darwinian evolution is true, construction of trees using different sequences should reveal a reasonably consistent pattern across different genes or sequences.
This makes it all the more significant that efforts to build a grand "tree of life" using DNA or other biological sequence data have not conformed to expectations. The basic problem is that one gene gives one version of the tree of life, while another gene gives a highly different, and conflicting, version of the tree. For example, as we'll discuss further below, the standard mammalian tree places humans more closely related to rodents than to elephants. But studies of a certain type of DNA called microRNA genes have suggested the opposite -- that humans were closer to elephants than rodents. Such conflicts between gene-based trees are extremely common.
The genetic data is thus not painting a consistent picture of common ancestry, showing the assumptions behind tree-building commonly fail. This leads to justifiable questions about whether universal common ancestry is correct.
Conflicts in the Base of the Tree of Life
Problems first arose when molecular biologists sequenced genes from the three basic domains of life -- bacteria, archaea, and eukarya -- but those genes did not allow these basic groups of life to be resolved into a treelike pattern. In 2009, the journal New Scientist published a cover story titled, "Why Darwin was wrong about the tree of life" which explained these quandaries:
The problems began in the early 1990s when it became possible to sequence actual bacterial and archaeal genes rather than just RNA. Everybody expected these DNA sequences to confirm the RNA tree, and sometimes they did but, crucially, sometimes they did not. RNA, for example, might suggest that species A was more closely related to species B than species C, but a tree made from DNA would suggest the reverse.102
This sort of data led biochemist W. Ford Doolittle to explain that "Molecular phylogenists will have failed to find the 'true tree,' not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree."103 New Scientist put it this way: "For a long time the holy grail was to build a tree of life … But today the project lies in tatters, torn to pieces by an onslaught of negative evidence."104
Many evolutionists sometimes reply that these problems arise only when studying microorganisms like bacteria -- organisms which can swap genes through a process called "horizontal gene transfer," thereby muddying the signal of evolutionary relationships. But this objection isn't quite true, since the tree of life is challenged even among higher organisms where such gene-swapping is not prevalent. Carl Woese, a pioneer of evolutionary molecular systematics, explains:
Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.105
Likewise, the New Scientist article notes that "research suggests that the evolution of animals and plants isn't exactly tree-like either."106 The article explains what happened when microbiologist Michael Syvanen tried to create a tree showing evolutionary relationships using 2000 genes from a diverse group of animals:
He failed. The problem was that different genes told contradictory evolutionary stories. … the genes were sending mixed signals. … Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another.107
The data were so difficult to resolve into a tree that Syvanen lamented, "We've just annihilated the tree of life."108 Many other papers in the technical literature recognize similar problems.
Conflicts Between Higher Branches
A 2009 paper in Trends in Ecology and Evolution notes that, "A major challenge for incorporating such large amounts of data into inference of species trees is that conflicting genealogical histories often exist in different genes throughout the genome."109 Similarly, a paper in Genome Research studied the DNA sequences in various animal groups and found that "different proteins generate different phylogenetic tree[s]."110 A June, 2012 article in Nature reported that short strands of RNA called microRNAs "are tearing apart traditional ideas about the animal family tree." Dartmouth biologist Kevin Peterson who studies microRNAs lamented, "I've looked at thousands of microRNA genes, and I can't find a single example that would support the traditional tree." According to the article, microRNAs yielded "a radically different diagram for mammals: one that aligns humans more closely with elephants than with rodents." Peterson put it bluntly: "The microRNAs are totally unambiguous ... they give a totally different tree from what everyone else wants."111
Conflicts Between Molecules and Morphology
Not all phylogenetic trees are constructed by comparing molecules like DNA from different species. Many trees are based upon comparing the form, structure, and body plan of different organisms -- also called "morphology." But conflicts between molecule-based trees and morphology-based trees are also common. A 2012 paper studying bat relationships made this clear, stating: "Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species."112 This is hardly the only study to encounter conflicts between DNA-based trees and trees based upon anatomical or morphological characteristics. Textbooks often claim common descent is supported using the example of a tree of animals based upon the enzyme cytochrome c which matches the traditional evolutionary tree based upon morphology.113 However, textbooks rarely mention that the tree based upon a different enzyme, cytochrome b, sharply conflicts with the standard evolutionary tree. As one article in Trends in Ecology and Evolution observed:
[T]he mitochondrial cytochrome b gene implied . . . an absurd phylogeny of mammals, regardless of the method of tree construction. Cats and whales fell within primates, grouping with simians (monkeys and apes) and strepsirhines (lemurs, bush-babies and lorises) to the exclusion of tarsiers. Cytochrome b is probably the most commonly sequenced gene in vertebrates, making this surprising result even more disconcerting.114
Strikingly, a different article in Trends in Ecology and Evolution concluded, "the wealth of competing morphological, as well as molecular proposals [of] the prevailing phylogenies of the mammalian orders would reduce [the mammalian tree] to an unresolved bush, the only consistent [evolutionary relationship] probably being the grouping of elephants and sea cows."115 Because of such conflicts, a major review article in Nature reported, "disparities between molecular and morphological trees" lead to "evolution wars" because "[e]volutionary trees constructed by studying biological molecules often don't resemble those drawn up from morphology."116
Finally, a study published in Science in 2005 tried to use genes to reconstruct the relationships of the animal phyla, but concluded that "[d]espite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved." The following year, the same authors published a scientific paper titled, "Bushes in the Tree of Life," which offered striking conclusions. The authors acknowledge that "a large fraction of single genes produce phylogenies of poor quality," observing that one study "omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom." The paper suggests that "certain critical parts of the [tree of life] may be difficult to resolve, regardless of the quantity of conventional data available." The paper even contends that "[t]he recurring discovery of persistently unresolved clades (bushes) should force a re-evaluation of several widely held assumptions of molecular systematics."117
Unfortunately, one assumption that these evolutionary biologists aren't willing to re-evaluate is the assumption that universal common ancestry is correct. They appeal to a myriad of ad hoc arguments -- horizontal gene transfer, long branch attraction, rapid evolution, different rates of evolution, coalescent theory, incomplete sampling, flawed methodology, and convergent evolution -- to explain away inconvenient data which doesn't fit the coveted treelike pattern. As a 2012 paper stated, "phylogenetic conflict is common, and frequently the norm rather than the exception."118 At the end of the day, the dream that DNA sequence data would fit into a nice-neat tree of life has failed, and with it a key prediction of neo-Darwinian theory.
Problem 7: Convergent Evolution Challenges Darwinism and Destroys the Logic Behind Common Ancestry
In Problem 6, we saw that the main assumption underlying all phylogenetic trees is that biological similarity is the result of inheritance from a common ancestor. The problem for evolutionary biologists faced with conflicting evolutionary trees is that biological similarity often appears in places not predicted by common descent. In other words, everyone recognizes that biological similarities often appear among species in cases where they cannot be explained as the result of inheritance from a common ancestor. This means the main assumption fails.
We also saw at the end of Problem 6 that when biologists are unable to construct phylogenetic trees, they often make ad hoc appeals to other processes to explain away data that won't fit a treelike pattern. One of these explanations is convergent evolution, where evolutionary biologists postulate that organisms acquire the same traits independently, in separate lineages, and not through inheritance from a common ancestor. Whenever evolutionary biologists are forced to appeal to convergent evolution, it reflects a breakdown in the main assumption, and an inability to fit the data to a treelike pattern. Examples of this abound in the literature, but a few will suffice.
Genetic Convergent Evolution
A paper in the Journal of Molecular Evolution found that molecule-based phylogenies conflicted sharply with previously established phylogenies of major mammal groups, concluding that this anomalous tree "is not due to a stochastic error, but is due to convergent or parallel evolution."119
A study in Proceedings of the U.S. National Academy of Sciences explains that when biologists tried to construct a phylogenetic tree for the major groups of birds using mitochondrial DNA (mtDNA), their results conflicted sharply with traditional notions of bird relationships. They even found "convergent" similarity between some bird mtDNA and the mtDNA of distant species such as snakes and lizards. The article suggests bird mtDNA underwent "multiple independent originations," with their study proposing "multiple independent origins for a particular mtDNA gene order among diverse birds."120
A 2005 paper in Nature Immunology observed that plants and animals have a highly similar biochemical organization of their respective innate immune systems, but their common ancestor didn't have such an immune system:
Although it seems to be generally accepted that the innate immune responses of plants and animals share at least some common evolutionary origins, examination of the available data fails to support that conclusion, despite similarities in the overall 'logic' of the innate immune response in diverse multicellular [organisms].121
According to the paper, common descent cannot explain these "unexpectedly similar" systems, "suggesting independent evolutionary origins in plants and animals." The paper is forced to conclude that such complex similarities make for a "compelling case for convergent evolution of innate immune pathways."122
Another famous example of convergent evolution is the ability of bats and whales to use echolocation, even though their distant common ancestor did not have this trait. Evolutionary biologists long-believed this was a case of morphological convergence, but an article in Current Biology explains the "surprising" finding that echolocation in bats and whales also involves genetic convergence:
Only microbats and toothed whales have acquired sophisticated echolocation, indispensable for their orientation and foraging. Although the bat and whale biosonars originated independently and differ substantially in many aspects, we here report the surprising finding that the bottlenose dolphin, a toothed whale, is clustered with microbats in the gene tree constructed using protein sequences encoded by the hearing gene Prestin.123
One paper called this data, "one of the best examples of convergent molecular evolution discovered to date."124 But again, these are hardly isolated examples. In 2010, a paper in Trends in Genetics explained:
The recent wide use of genetic and/or phylogenetic approaches has uncovered diverse examples of repeated evolution of adaptive traits including the multiple appearances of eyes, echolocation in bats and dolphins, pigmentation modifications in vertebrates, mimicry in butterflies for mutualistic interactions, convergence of some flower traits in plants, and multiple independent evolution of particular protein properties.125
Biochemist and Darwin-skeptic Fazale Rana reviewed the technical literature and documented over 100 reported cases of convergent genetic evolution.126 Each case shows an example where biological similarity -- even at the genetic level -- is not the result of inheritance from a common ancestor. So what does this do to the main assumption of tree-building that biological similarity implies inheritance from a common ancestor? With so many exceptions to the rule, one has to wonder if the rule itself holds merit.
The Earth is Round, But is Common Ancestry True?
One evolutionary scientist tried to pressure his readers into accepting Darwinism by claiming "biologists today consider the common ancestry of all life a fact on par with the sphericity of the earth."127 But are such categorical statements even helpful, much less true?
Proponents of neo-Darwinian evolution are forced into reasoning that biological similarity implies common ancestry, except for when it doesn't. And in the many cases where it doesn't, they appeal to all sorts of ad hoc rationalizations to save common ancestry.
Tellingly, the one assumption rarely questioned is the overall assumption of common ancestry itself. But perhaps the reason why different genes are telling different evolutionary stories is because the genes have wholly different stories to tell, namely stories that indicate that all organisms are not genetically related. There is some hope for a different story more attuned to the data, as Michael Syvanen dared to suggest in Annual Review of Genetics in 2012, that "life might indeed have multiple origins."128 In other words, universal common ancestry may in fact, not be true.
Problem 8: Differences between Vertebrate Embryos Contradict the Predictions of Common Ancestry
Another area where evolutionary biologists claim powerful evidence for common ancestry is the patterns of development of vertebrate embryos. Biology textbooks typically portray the embryos of different groups of vertebrate as starting off development in a highly similar fashion, reflecting their common ancestry.129 However, such claims overstate the degree of similarity between the early stages of vertebrate embryos.
Biologists who investigate these questions have found considerable variability among vertebrate embryos from their earliest stages onward, contradicting what we are told to expect from common ancestry.130 As a paper in Nature stated, "Counter to the expectations of early embryonic conservation, many studies have shown that there is often remarkable divergence between related species both early and late in development."131 Or, as another article in Trends in Ecology and Evolution stated, "despite repeated assertions of the uniformity of early embryos within members of a phylum, development before the phylotypic stage is very varied."132
But most embryologists who acknowledge that vertebrate embyros start development differently will still claim embryos pass through a highly similar stage midway through development, called the "phylotypic" or "pharyngula" stage. These theorists propose an "hourglass model" of development, where it is claimed that similarities between embryos during this midpoint stage provide evidence for common ancestry. One critical biologist explains how this concept is viewed: "It is almost as though the phylotypic stage is regarded as a biological concept for which no proof is needed."133
But when biologists have looked for evidence supporting the existence of a phylotypic or pharyngula stage, they found the data points in the opposite direction. One comprehensive study in Anatomy and Embryology surveyed the characteristics of many vertebrates during this purportedly similar stage, and found that embryos show differences in major traits, including:
- body size,
- body plan,
- growth patterns, and
- timing of development.134
The researchers conclude that the evidence is "[c]ontrary to the evolutionary hourglass model" and "difficult to reconcile" with the existence of a pharyngula stage.135 Likewise, a paper in Proceedings of the Royal Society of London found the data was "counter to the predictions of the [phylotypic stage]: phenotypic variation between species was highest in the middle of the developmental sequence." It concluded that a "surprising degree of developmental character independence argues against the existence of a phylotypic stage in vertebrates."136
While vertebrate development shows wide variation, evolutionary embryologists seek to force-fit evolutionary interpretations to the data. When every rule is stymied by exceptions, a better way is to simply let the data speak for itself. A non-evolutionary approach to embryology would more easily acknowledge that differences exist between vertebrate embryos at all stages of development, and that vertebrate embryos show some similarities -- but also significant differences -- during the purported phylotypic stage.
Problem 9: Neo-Darwinism Struggles to Explain the Biogeographical Distribution of many Species
Biogeography is the study of the distribution of organisms in time and space both in the present and past on Earth. It is often contended that biogeography strongly supports neo-Darwinian theory. For example, the National Center for Science Education (NCSE), a pro-Darwin advocacy group, claims that "consistency between biogeographic and evolutionary patterns provides important evidence about the continuity of the processes driving the evolution and diversification of all life," and "[t]his continuity is what would be expected of a pattern of common descent." However, the NCSE dramatically overstates its case and ignores the many instances where biogeography does not show the sort of "continuity" that would be expected under a pattern of common descent.
Evolutionary explanations of biogeography fail when terrestrial (or freshwater) organisms appear in a location (such as an island or a continent) where there is no standard migratory mechanism for them to have arrived there from some ancestral population. In other words, when we find two populations of organisms, Darwinian evolution claims that if we go back far enough, they must be linked by common descent. But sometimes it's virtually impossible to explain how these populations could have arrived at their respective geographical locations on the globe from some ancestral population.
For example, one of the most severe biogeographical puzzles for Darwinian theory is the origin of South American monkeys, called "platyrrhines." Based upon molecular and morphological evidence, New World platyrrhine monkeys are thought to be descended from African "Old World" or "catarrhine" monkeys. The fossil record shows that monkeys have lived in South America for about the past 30 million years.137 But plate tectonic history shows that Africa and South America split off from one another between 100 and 120 million years ago (mya), and that South America was an isolated island continent from about 80 - 3.5 mya.138 If South American monkeys split off from African monkeys around 30 mya, proponents of neo-Darwinism must somehow account for how they crossed hundreds, if not thousands, of kilometers of open ocean to end up in South America.
This problem for evolutionary biologists has been recognized by numerous experts. A Harper Collins textbook on human evolution states: "The origin of platyrrhine monkeys puzzled paleontologists for decades. ... When and how did the monkeys get to South America?"139 Primatologists John G. Fleagle and Christopher C. Gilbert put it this way in a scientific volume on primate origins:
The most biogeographically challenging aspect of platyrrhine evolution concerns the origin of the entire clade. South America was an island continent throughout most of the Tertiary…and paleontologists have debated for much of this century how and where primates reached South America.140
Primate specialist Walter Carl Hartwig is similarly blunt: "The platyrrhine origins issue incorporates several different questions. How did platyrrhines get to South America?"141 Such basic, vexing questions certainly don't lend credence to the NCSE's claims of "consistency between biogeographic and evolutionary patterns."
For those unfamiliar with the sort of arguments made by neo-Darwinian biogeographers, responses to these puzzles can be almost too incredible to believe. A Harper Collins textbook explains: "The 'rafting hypothesis' argues that monkeys evolved from prosimians once and only once in Africa, and … made the water-logged trip to South America."142 And of course, there can't be just one seafaring monkey, or the monkey will soon die leaving no offspring. Thus, at least two monkeys (or perhaps a single pregnant monkey) must have made the rafting voyage.
Fleagle and Gilbert observe that the rafting hypothesis "raises a difficult biogeographical issue" because "South America is separated from Africa by a distance of at least 2600 km, making a phylogenetic and biogeographic link between the primate faunas of the two continents seem very unlikely."143 But they are wedded to an evolutionary paradigm, meaning that they are obligated to find such a "link" whether it is likely or not. They argue that in light of "[t]he absence of any anthropoids from North America, combined with the considerable morphological evidence of a South American-African connection with the rodent and primate faunas" that therefore "the rafting hypothesis is the most likely scenario for the biogeographic origin of platyrrines."144
In other words, the "unlikely" rafting hypothesis is made "likely" only because we know common descent must be true.
Indeed, the rafting hypothesis faces serious problems, as mammals like monkeys have high metabolisms and require large amounts of food and water.145 Fleagle and Gilbert thus admit that "over-water dispersal during primate evolution seems truly amazing for a mammalian order," and conclude, "[t]he reasons for the prevalence of rafting during the course of primate evolution remain to be explained."146 Or, as Hartwig puts it, "The overwhelming evidence for the late Cretaceous-Pliocene isolation of South America renders the mechanical aspect of platyrrhine dispersal virtually irresolvable" for "any late Eocene origins model must invoke a transoceanic crossing mechanism that is implausible (rafting) or suspect … at best."147
And there are deeper problems: monkeys apparently made the journey from Africa to South America, but other smaller African primates never colonized the New World. If it was so easy for monkeys to raft across the proto-Atlantic ocean, why didn't these lower primates also make the voyage? The reason we're given by Fleagle and Gilbert is that there is no reason, and it all comes down to sheer chance. In their own words, rafting is "clearly a chance event" and "[o]ne can only speculate that by a stroke of good luck anthropoids where able to 'win' the sweepstakes while lorises and galagos did not."148
This is not the only case that appeals to rafting or other speculative mechanisms of "oceanic dispersal" to explain away biogeographical conundrums that challenge neo-Darwinism. Examples include the presence of lizards and large caviomorph rodents in South America,149 the arrival of bees, lemurs, and other mammals in Madagascar,150 the appearance of elephant fossils on "many islands,"151 the appearance of freshwater frogs across isolated oceanic island chains,152 and numerous similar examples.153 This problem also exists for extinct species, as a paper in Annals of Geophysics notes the "still unresolved problem of disjointed distribution of fossils on the opposite coasts of the Pacific."154 A 2005 review in Trends in Ecology and Evolution explains the problem:
A classic problem in biogeography is to explain why particular terrestrial and freshwater taxa have geographical distributions that are broken up by oceans. Why are southern beeches (Nothofagus spp.) found in Australia, New Zealand, New Guinea and southern South America? Why are there iguanas on the Fiji Islands, whereas all their close relatives are in the New World?155
After reviewing a number of "unexpected" biogeographical examples that require oceanic dispersal, the review concludes: "these cases reinforce a general message of the great evolutionist [Darwin]: given enough time, many things that seem unlikely can happen."156
Thus, neo-Darwinian evolutionists are forced to appeal to "unlikely" or "unexpected" migration of organisms, in some cases requiring the crossing of oceans to account for the biogeographical data. This kind of data may not necessarily absolutely falsify Darwinism, but at the least it challenges the simplistic argument that biogeography supports universal common descent through congruence between migration pathways and evolutionary history. In many cases, the congruence is simply not there.
Problem 10: Neo-Darwinism has a Long History of Inaccurate Darwinian Predictions about Vestigial Organs and "Junk DNA"
For decades, evolutionists have claimed that our bodies and genomes are full of useless parts and genetic material -- "vestigial" organs -- showing life is the result of eons of unguided evolution. During the Scopes trial in 1925, evolutionary biologist Horatio Hackett Newman contended that there are over 180 vestigial organs and structures in the human body, "sufficient to make of a man a veritable walking museum of antiquities."157
Over time, however, these predictions of vestigial body parts and useless DNA have not held true. As scientists have learned more and more about the workings of biology, important functions and purpose have been discovered for these so-called vestigial structures. Indeed, in 2008 the journal New Scientist reported that, since the days of Professor Newman, the list of vestigial organs "grew, then shrank again" to the point that today "biologists are extremely wary of talking about vestigial organs at all."158 Structures that were previously -- and incorrectly -- considered to be vestigial include:
- The tonsils: At one time, they were routinely removed. Now it's known they serve a purpose in the lymph system to help fight infection.159
- The coccyx (tailbone): Many evolutionists still claim this is a hold-over from the tails of our supposed primate ancestors,160 but it's actually a vital part of our skeleton, used for attaching muscles, tendons, and ligaments that support the bones in our pelvis.
- The thyroid: This gland in the neck was once believed to have no purpose, and was ignored or even destroyed by medical doctors operating under false Darwinian assumptions. Now scientists know that it is vital for regulating metabolism.
- The appendix: Darwinian scientists have claimed the appendix is a "vestige of our herbivorous ancestry,"161 and over eons of evolution its function in humans has been diminished, or lost. But it's now known that the appendix performs important functions, such as providing a storehouse for beneficial bacteria, producing white blood cells, and playing important roles during fetal development.162 In light of this evidence, Duke University immunologist William Parker observed that "Many biology texts today still refer to the appendix as a 'vestigial organ'" but "it's time to correct the textbooks."163
Despite the poor track record of claiming organs were vestigial, evolutionary biologists have applied this same kind of thinking to our genomes. Many have postulated that the random nature of mutations would fill our genomes with useless genetic garbage, dubbed "junk DNA." This hypothesis was seemingly confirmed when it was discovered that only 2% of the human genome coded for proteins, leaving the other 98% unexplained. Many scientists who serve as spokespersons for evolutionary biology have claimed this evidence provides case-closed evidence for Darwinian evolution:
- Brown University evolutionary biologist Kenneth Miller argues that "the human genome is littered with pseudogenes, gene fragments, 'orphaned' genes, 'junk' DNA, and so many repeated copies of pointless DNA sequences that it cannot be attributed to anything that resembles intelligent design."164
- Richard Dawkins likewise writes that "creationists might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA."165
- In his 2006 book The Language of God, Francis Collins claimed that some "45 percent of the human genome" is made up of "genetic flotsam and jetsam."166 (Flotsam and jetsam, of course, is useless trash floating in the ocean.) Sounding much like Dawkins, he makes the implications clear: "Unless one is willing to take the position that God has placed [shared functionless repetitive DNA] in these precise positions to confuse and mislead us, the conclusion of a common ancestor for humans and mice is virtually inescapable."167
The problem with these arguments isn't so much theological as it is scientific: Numerous examples of function have been discovered for so-called junk DNA.
Biologist Richard Sternberg surveyed the literature and found extensive evidence of function for repetitive DNA. Writing in the Annals of the New York Academy of Sciences, he found that functions for repeats include forming higher-order nuclear structures, centromeres, telomeres, and nucleation centers for DNA methylation. Repetitive DNA was found to be involved in cell proliferation, cellular stress responses; gene translation, and DNA repair.168 Sternberg concluded that "the selfish [junk] DNA narrative and allied frameworks must join the other 'icons' of neo-Darwinian evolutionary theory that, despite their variance with empirical evidence, nevertheless persist in the literature."169
Other research has continued to uncover functions for various types of repetitive DNA, including SINE,170 LINE,171 and Alu elements.172 One paper even suggested that repetitive Alu sequences might be involved in "the development of higher brain function" in humans.173 Numerous other functions have been discovered for various types of non-protein-coding DNA, including:
- repairing DNA174
- assisting in DNA replication175
- regulating DNA transcription 176
- aiding in folding and maintenance of chromosomes 177
- controlling RNA editing and splicing178
- helping to fight disease179
- regulating embryological development180
Sternberg, along with University of Chicago geneticist James Shapiro, predicted in 2005 in the journal Cytogenetic and Genome Research that "one day, we will think of what used to be called 'junk DNA' as a critical component of truly 'expert' cellular control regimes."181
The day foreseen by Sternberg and Shapiro may have come sooner than they expected. In September, 2012, the journal Nature reported the results of a years-long research project, involving over 400 international scientists studying the functions of non-coding DNA in humans. Called the ENCODE Project, its set of 30 groundbreaking papers reported that the "vast majority" of the genome has function. The lead paper reporting ENCODEs' results stated:
These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions.182
Ewan Birney, ENCODE's lead analysis coordinator commented in Discover Magazine that since ENCODE looked at only 147 types of cells, and the human body has a few thousand, "It's likely that 80 percent will go to 100 percent."183 The same article quoted Tom Gingeras, a senior scientist with ENCODE, noting that, "Almost every nucleotide is associated with a function of some sort or another, and we now know where they are, what binds to them, what their associations are, and more."184 Another Nature commentary noted that "80% of the genome contains elements linked to biochemical functions, dispatching the widely held view that the human genome is mostly 'junk DNA'."185 Discover Magazine put it this way: "The key point is: It's not 'junk'."186
While there's still much we don't know about the genome, the trendline of the research is clearly pointing in one direction: the more we study the genome, the more we detect function for non-coding DNA. Yet the now-dubious "junk-DNA" paradigm was born and bred inside the evolutionary paradigm based upon the idea that our genome was built through random mutations. Yes, a few rogue biologists dared to seek function for non-coding DNA, but the Darwinian "junk DNA" view of genetics has generally hindered the progress of science, as was admitted by a 2003 article in Science:
Although catchy, the term 'junk DNA' for many years repelled mainstream researchers from studying noncoding DNA. Who, except a small number of genomic clochards, would like to dig through genomic garbage? However, in science as in normal life, there are some clochards who, at the risk of being ridiculed, explore unpopular territories. Because of them, the view of junk DNA, especially repetitive elements, began to change in the early 1990s. Now, more and more biologists regard repetitive elements as a genomic treasure.187
Despite widespread Darwinian assumptions to the contrary, the paper concluded that "repetitive elements are not useless junk DNA but rather are important, integral components"188 of animal genomes. Studies suggest that these long stretches of non-coding DNA between genes "constitute an important layer of genome regulation across a wide spectrum of species."189
Like repetitive elements, another kind of "junk" DNA for which function is being discovered is pseudogenes. Pseudogenes are thought to be copies of once-functional genes that have been inactivated through mutations. One paper in Science Signaling observes that "pseudogenes have long been dismissed as junk DNA,"190 but notes:
Recent advances have established that the DNA of a pseudogene, the RNA transcribed from a pseudogene, or the protein translated from a pseudogene can have multiple, diverse functions and that these functions can affect not only their parental genes but also unrelated genes. Therefore, pseudogenes have emerged as a previously unappreciated class of sophisticated modulators of gene expression, with a multifaceted involvement in the pathogenesis of human cancer.191
Indeed, functions for many pseudogenes have already been discovered;192 the ENCODE project alone found over 850 pseudogenes that are "transcribed and associated with active chromatin."193 But what exactly are these pseudogenes doing? A 2011 paper in the journal RNA again argues they can regulate the expression of genes:
Pseudogenes have long been labeled as 'junk' DNA, failed copies of genes that arise during the evolution of genomes. However, recent results are challenging this moniker; indeed, some pseudogenes appear to harbor the potential to regulate their protein-coding cousins.194
Likewise, a 2012 paper in the journal RNA Biology similarly stated that "Pseudogenes were long considered as junk genomic DNA" but "pseudogene regulation is widespread"195 in complex multicellular organisms. The paper proposed that "[t]he high abundance and conservation of the pseudogenes in a variety of species indicate that selective pressures preserve these genetic elements, and suggest they may indeed perform important biological functions.”196
Pseudogenes serve as another good example of how Darwinian biologists have assumed that a type of non-coding DNA they didn't understand was functionless genetic junk, and thus ignored their functions. Indeed, the aforementioned paper in RNA Biology explains that one reason why evolutionists have been so slow to abandon the assumption that pseudogenes are junk is because their functions are difficult to detect. The authors observe that "almost all pseudogenes that exhibit significant biological activity are expressed in specific tissue or cell lines," meaning only specific tissues or cell lines may use a given pseudogene for some function. Additionally, it's difficult to detect function for pseudogenes because we have lacked the research tools to understand how they influence gene expression. The paper predicts that "more and more functional pseudogenes will be discovered as novel biological technologies are developed in the future," and concludes "The study of functional pseudogenes is just at the beginning."197 Indeed, two leading biologists writing in Annual Review of Genetics reported that "pseudogenes that haev been suitably investigated often exibit functional roles."198
Many evolutionary biologists are wedded to the view that our genomes are full of junk, and resist the interpretation that virtually all DNA has function. Indeed, a 2012 evolution textbook teaches that "Over half of the genome is composed of neither genes, nor vestiges of human genes, nor regulatory regions. Instead, it is made up of parasite-like segments of DNA..."199 Meanwhile, the evidence continues to point in the opposite direction. While much remains to be learned about the workings of our genome, the research trendline is unambiguous: the more we study non-coding DNA, the more we find evidence of widespread function.
Bonus Problem: Humans Display Many Behavioral and Cognitive Abilities that Offer No Apparent Survival Advantage
In recent years, evolutionary biologists have tried to explain the origin of human moral, intellectual, and religious abilities in terms of Darwinian evolution. Harvard University evolutionary psychologist Marc Hauser has promoted the increasingly common hypothesis that "people are born with a moral grammar wired into their neural circuits by evolution."200
Humans do appear hard-wired for morality, but were we programmed by unguided evolutionary processes? Natural selection cannot explain extreme acts of human kindness. Regardless of background or beliefs, upon finding strangers trapped inside a burning vehicle, people will risk their own lives to help them escape -- with no evolutionary benefit to themselves. For example, evolutionary biologist Jeffrey Schloss explains that Holocaust rescuers took great risks which offered no personal benefits:
The rescuer's family, extended family and friends were all in jeopardy, and they were recognized to be in jeopardy by the rescuer. Moreover, even if the family escaped death, they often experienced deprivation of food, space and social commerce; extreme emotional distress; and forfeiture of the rescuer's attention.201
Francis Collins gives the example of Oskar Schindler, the German businessman who risked his life "to save more than a thousand Jews from the gas chambers."202 As Collins points out, "That's the opposite of saving his genes."203 Schloss adds other examples of "radically sacrificial" behavior that "reduces reproductive success" and offers no evolutionary benefit, such as voluntary poverty, celibacy, and martyrdom.204
In spite of the claims of evolutionary psychologists, many of humanity's most impressive charitable, artistic, and intellectual abilities outstrip the basic requirements of natural selection. If life is simply about survival and reproduction, why do humans compose symphonies, investigate quantum mechanics, and build cathedrals?
Natural Academy of Sciences member Philip Skell explained why evolutionary psychology does not adequately predict human behavior:
Darwinian explanations for such things are often too supple: Natural selection makes humans self-centered and aggressive -- except when it makes them altruistic and peaceable. Or natural selection produces virile men who eagerly spread their seed -- except when it prefers men who are faithful protectors and providers. When an explanation is so supple that it can explain any behavior, it is difficult to test it experimentally, much less use it as a catalyst for scientific discovery.205
Contrary to Darwinism, the evidence indicates that human life isn't about mere survival and reproduction. But in addition to our moral uniqueness, humans are also distinguished by their use of complex language. As MIT professor and linguist Noam Chomsky observes:
Human language appears to be a unique phenomenon, without significant analogue in the animal world. If this is so, it is quite senseless to raise the problem of explaining the evolution of human language from more primitive systems of communication that appear at lower levels of intellectual capacity. ... There is no reason to suppose that the "gaps" are bridgeable.206
Finally, humans are also the only species that seeks to investigate the natural world through science. In fact, the next time someone tries to break down the differences between humans and apes, remind them that it's humans who write scientific papers studying apes, not the other way around.
Science vs. Religion?
This chapter has cited dozens of papers from the technical scientific literature and by credible scientists which, taken together, pose strong scientific challenges to modern evolutionary theory. Yet defenders of neo-Darwinism commonly assert that legitimate scientific objections to their viewpoint do not exist, and that the only criticisms which remain are based upon religion. Clearly, this is not true. In fact, the attempt to re-label criticisms of neo-Darwinian evolution as religion is typically a ploy to dismiss scientific criticisms without addressing them.
The balance of this book, of course, raises both religious and scientific arguments supporting the progressive creation view that God created life on earth over the course of millions of years. This viewpoint has both religious and scientific dimensions, and for that reason is different from the strictly scientific approach taken in this chapter.
The fact that some arguments in this book may be based upon religion, in no way changes the fact that there are strong scientific challenges to neo-Darwinian theory. Likewise, the fact that there are important religious dimensions to this debate does not mean that materialists can ignore the scientific weaknesses in their own arguments. Until those scientific problems are addressed, scientists will continue to grow skeptical of evolutionary theory.
Note: A PDF of this article can be downloaded here.
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- [61.] Ibid., p. 13.
- [62.] Ibid., p. 124.
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- [64.] Ibid.
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- [183.] Ewan Birney, quoted in Ed Yong, "ENCODE: the rough guide to the human genome," Discover Magazine (September 5, 2012), at http://blogs.discovermagazine.com/notrocketscience/2012/09/05/encode-the-rough-guide-to-the-human-genome/
- [184.] Tom Gingeras, quoted in Ed Yong, "ENCODE: the rough guide to the human genome," Discover Magazine (September 5, 2012), at http://blogs.discovermagazine.com/notrocketscience/2012/09/05/encode-the-rough-guide-to-the-human-genome/
- [185.] Joseph R. Ecker, "Serving up a genome feast," Nature, 489:52-55 (September 6, 2012).
- [186.] Ed Yong, "ENCODE: the rough guide to the human genome," Discover Magazine (September 5, 2012), at http://blogs.discovermagazine.com/notrocketscience/2012/09/05/encode-the-rough-guide-to-the-human-genome/
- [187.] Makalowski, "Not Junk After All," 1246-47.
- [188.] Ibid.
- [189.] David R. Kelley and John L. Rinn, "Transposable elements reveal a stem cell specific class of long noncoding RNAs," Genome Biology, 13:R107 (2012).
- [190.] Laura Poliseno, "Pseudogenes: Newly Discovered Players in Human Cancer," Science Signaling, 5 (242) (September 18, 2012).
- [191.] Ibid.
- [192.] See for example D. Zheng and M. B. Gerstein, "The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?," Trends in Genetics, 23 (May, 2007): 219-24; S. Hirotsune et al., "An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene," Nature, 423 (May 1, 2003): 91-96; O. H. Tam et al., "Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes," Nature, 453 (May 22, 2008): 534-38; D. Pain et al., "Multiple Retropseudogenes from Pluripotent Cell-specific Gene Expression Indicates a Potential Signature for Novel Gene Identification," The Journal of Biological Chemistry, 280 (February 25, 2005):6265-68; J. Zhang et al., "NANOGP8 is a retrogene expressed in cancers," FEBS Journal, 273 (2006): 1723-30.
- [193.] The ENCODE Project Consortium, "An integrated encyclopedia of DNA elements in the human genome," Nature, 489:57-74 (September 6, 2012).
- [194.] Ryan Charles Pink, Kate Wicks, Daniel Paul Caley, Emma Kathleen Punch, Laura Jacobs, and David Paul Francisco Carter, "Pseudogenes: Pseudo-functional or key regulators in health and disease?," RNA, 17 (2011): 792-98.
- [195.] Yan-Zi Wen, Ling-Ling Zheng, Liang-Hu Qu, Francisco J. Ayala and Zhao-Rong Lun, "Pseudogenes are not pseudo any more," RNA Biology, 9(1):27-32 (January, 2012).
- [196.] Ibid.
- [197.] Ibid.
- [198.] Evgeniy S. Balakirev and Francisco J. Ayala, "Pseudogenes, Are They 'Junk' or Functional DNA?," Annual Review of Genetics, 37 (2003): 123-51.
- [199.] Carl Zimmer and Douglas Emlen, Evolution: Making Sense of Life, p. 132 (Roberts and Company, 2012).
- [200.] Nicholas Wade, "An Evolutionary Theory of Right and Wrong," The New York Times (October 31, 2006), accessed April 28, 2012, http://www.nytimes.com/2006/10/31/health/psychology/31book.html
- [201.] Jeffrey P. Schloss, "Evolutionary Accounts of Altruism & the Problem of Goodness by Design," in Mere Creation; Science, Faith & Intelligent Design, ed. William A. Dembski (Downers Grove, IL, Intervarsity Press, 1998), 251.
- [202.] Francis Collins quoted in Dan Cray, "God vs. Science," Time Magazine (November 5, 2006), accessed April 28, 2012, http://www.time.com/time/printout/0,8816,1555132,00.html
- [203.] Ibid.
- [204.] Jeffrey P. Schloss, "Emerging Accounts of Altruism: 'Love Creation's Final Law'?," in Altruism and Altruistic Love: Science, Philosophy, & Religion in Dialogue, eds. Stephen G. Post, Lynn G. Underwood, Jeffrey P. Schloss, and William B. Hurlbut (Oxford: Oxford University Press, 2002), 221.
- [205.] Philip S. Skell, "Why do we invoke Darwin?," The Scientist, 19 (August 29, 2005): 10.
- [206.] Noam Chomsky, Language and Mind, 3rd ed. (Cambridge: Cambridge University Press, 2006), 59.
[Editor’s Note: This article is Casey Luskin’s chapter, “The Top Ten Scientific Problems with Biological and Chemical Evolution,” contributed to the volume More than Myth (Chartwell Press, 2014). It has been posted with permission of the book’s editors, Robert Stackpole and Paul Brown. A PDF of this article can be downloaded here.]
[Editor's Note: This article is an excerpt from the author's longer article, "ID Does Not Address Religious Claims About the Supernatural," first published as part of a series of articles both for and against ID at OpposingViews.com.]
Unfortunately, in his Kitzmiller v. Dover ruling, Judge Jones bought into the revisionist history of ID that claims ID is just repackaged creationism, and the Judge presented a sharply truncated and inaccurate view of the intellectual history of design. A correct history will make it clear that "intelligent design" was not a term invented to avoid the Edwards ruling, but a project that has always been distinct from the core claims of creationism.
Judge Jones traced the origins of ID back to the natural theology of William Paley and the arguments of the thirteenth century Catholic philosopher Thomas Aquinas. Even some critics of ID admit that “design arguments are not new,"1 for the debate over design in nature began at least as early as the ancient Greek and Roman philosophers.2 The Greek philosophers Heraclitus, Empedocles, Democritus, and Anaximander believed that life could originate without any intelligent guidance.3 Plato and Aristotle, both advocated that a mind was required to explain life's existence.4 In more modern times, Isaac Newton asked in his treatise Opticks, "Was the Eye contrived without Skill in Opticks, and the Ear without Knowledge of Sounds? [...] And these things being rightly dispatch’d, does it not appear from Phænomena that there is a Being incorporeal, living, intelligent, omnipresent..."5
The debate over design continued vigorously among scientists and philosophers — not just theologians — at the time of Darwin in the 19th century. Zoologist and geologist Louis Agassiz, a critic of Darwin, invoked an "intellectual power"6 to explain the diversity of living organisms in his "Essay on Classification," published in the late 1850’s, near the time that Darwin published Origin of Species. The term "intelligent design" was invoked as a plausible alternative to blind Darwinian evolution in 1897 by Oxford scholar F.C.S. Schiller, who wrote that "it will not be possible to rule out the supposition that the process of Evolution may be guided by an intelligent design."7 Even the independent co-discoverer of the theory of evolution by natural selection, Alfred Russel Wallace, concluded that it was possible — and appropriate — to detect design in nature.8
The research and ideas that ultimately inspired ID proponents were conceived in the decades and years prior to the Edwards ruling.9 Highly influential behind ID arguments was the discovery that life depended upon information, whose structure was not only independent of its physical or chemical form, but whose ordering was not amenable to explanation by physical or chemical laws. As the chemist Michael Polanyi wrote in an article titled, "Life’s Irreducible Structure," published in the journal Science in 1968:
"Suppose that the actual structure of a DNA molecule were due to the fact that the bindings of its bases were much stronger than the bindings would be for any other distribution of bases, then such a DNA molecule would have no information content. Its code-like character would be effaced by an overwhelming redundancy. [...] Whatever may be the origin of a DNA configuration, it can function as a code only if its order is not due to the forces of potential energy. It must be as physically indeterminate as the sequence of words is on a printed page."10
The term "intelligent design" appears to have been coined in its contemporary scientific usage by the atheist cosmologist Dr. Fred Hoyle, who in 1982 argued that "if one proceeds directly and straightforwardly in this matter, without being deflected by a fear of incurring the wrath of scientific opinion, one arrives at the conclusion that biomaterials with their amazing measure of order must be the outcome of intelligent design."11 The term "intelligent design" was also used by non-scientist James E. Horigan in his 1979 book Chance or Design? where Horigan used the term “intelligent design” and framed his argument as an empirical one, "without resort to biblical or other religious references," and without investigating questions about "ultimate purpose."12
Horigan and Hoyle, however, did not become part of the later ID movement. But in 1984 — three years before the Edwards ruling — three scientists who did help found the ID movement published a book titled The Mystery of Life's Origin that made arguments for an "intelligent cause" in the origin of the information in DNA:
"We have observational evidence in the present that intelligent investigators can (and do) build contrivances to channel energy down nonrandom chemical pathways to bring about some complex chemical synthesis, even gene building. May not the principle of uniformity then be used in a broader frame of consideration to suggest that DNA had an intelligent cause at the beginning?"13
Those three scientists were Charles Thaxton, Walter Bradley, and Roger Olsen. Soon thereafter, Thaxton, a chemist and academic editor for the Pandas textbook, adopted the term "intelligent design" after hearing it mentioned by a NASA engineer.14 Thaxton’s adoption of the term "intelligent design" took place pre-Edwards and therefore could not have been an attempt to "evade" a court decision. Rather, his adoption of this terminology was done to distinguish ID from creationism, because, in contrast to creationism, ID sought to stay solely within the empirical domain. As Thaxton testified during his deposition in the Kitzmiller case:
"I wasn’t comfortable with the typical vocabulary that for the most part creationists were using because it didn’t express what I was trying to do. They were wanting to bring God into the discussion, and I was wanting to stay within the empirical domain and do what you can do legitimately there."15
Thaxton, who is a scientist and not a lawyer, adopted "intelligent design" terminology out of a desire to respect the limits of scientific inquiry, not as some conspiracy to avoid a Supreme Court ruling. When recounting the history of why he adopted "intelligent design" terminology, Thaxton explains that his goal was not to avoid any court decisions but to help people understand that their argument was “trying to operate entirely within the empirical domain”:
"Unfortunately for Westerners ... anytime you use the word creation it automatically conjures up any of a number of religious discussions. We knew from the beginning of our project, that turned out to be the making of Of Pandas and People, that we wanted to avoid this automatically concluding that what you're talking about was religion because in fact we were dealing with a biological discussion. So we were trying to operate entirely within the empirical domain. And my thought was, how to arrive at a set of terms that would allow us to traffic the literature and the discussion and build an argument without having to use terminology that would automatically bring one into the religious realm?"16
Thaxton continues, saying "we did what we could do to stay within the empirical domain and make legitimate inferences."17 He then explains the terminology that was originally in the early pre-publication drafts of Pandas:
"I realize that the charge was that we were trying to just use a substitute word for creation, but that isn’t the case at all. In the early days of writing the Pandas book for example, although we understood what we were doing, most other people who we were talking to didn’t know our objectives really. And if you have a whole culture that knows about creation as a term ... So we used that word early on, not for deception so we could later switch on them but because we wanted the materials to be understood that we were focused on. It was always clearly within the empirical domain, even the things that we wrote early on."18
Thaxton completes his account by recounting that after speaking widely on the subject of origins that "gradually it became clear that there was a real good way that there was a case we wanted — completely within the empirical domain — and we looked for a term that would do this and reading the literature and ah, 'intelligent design,' is the most appropriate term. And that’s why we did it."19
In conclusion, the term "intelligent design" not only long pre-dates the Edwards ruling, but the basic arguments for design pre-date Christianity. Moreover, modern members of the ID movement started using the term "intelligent design" not to evade a court ruling, but because they sought terminology that would accurately communicate their project’s original intent to remain entirely within the empirical domain and avoid investigating religious questions about the supernatural. Since the U.S. Supreme Court declared creationism to be a religious viewpoint because it postulated a "supernatural creator," it seems that regardless of what wording was used early on, the ID project has always been substantively distinct from creationism. Any arguments that ID is creationism because early pre-publication drafts of the Pandas textbook used "creation" terminology are false conspiracy theories based not upon substance, but semantics and revisionist history. The very fact that Darwinists must resort to such arguments shows just how weak is their case that ID is creationism.
Any readers interested in learning about the true history of the origin of intelligent design might benefit from listening to two podcast interviews with Charles Thaxton on this topic at:
- The Mystery of Life's Origin: An Interview with Dr. Charles Thaxton, Part One
- The Mystery of Life's Origin: An Interview with Dr. Charles Thaxton, Part Two
- [1.] John Angus Campbell, "Why Are We Still Debating Darwinism? Why Not Teach the Controversy?," in Darwin, Design, and Public Education, pg. xii (John Angus Campbell ed., Michigan State University Press 2003).
- [2.] In this section of my article I am deeply indebted to the research published by Stephen C. Meyer in his article, "A Scientific History — and Philosophical Defense — of the Theory of Intelligent Design."
- [3.] John Angus Campbell, "Why Are We Still Debating Darwinism? Why Not Teach the Controversy?," in Darwin, Design, and Public Education, pg. xii (John Angus Campbell ed., Michigan State University Press 2003).
- [4.] John Angus Campbell, "Why Are We Still Debating Darwinism? Why Not Teach the Controversy?," in Darwin, Design, and Public Education, pg. xii (John Angus Campbell ed., Michigan State University Press 2003).
- [5.] Isaac Newton, Opticks, pgs. 369-370 (Prometheus Books, 2003).
- [6.] Louis Agassiz, "An Essay on Classification," first published in 1857, pg. 83, at http://books.google.com/books?id=QXkLAAAAMAAJ&printsec=frontcover&dq=Louis+Agassiz#PPA83,M1.
- [7.] F.C.S. Schiller, Darwinism and Design, in Humanism: Philosophical Essays, pgs. 128, 141 (2d ed., Macmillan & Co. 1912) (citing Contemporary Review, June 1897).
- [8.] Alfred Russel Wallace, "Sir Charles Lyell on Geological Climates the Origin of Species," in Alfred Russel Wallace: An Anthology of His Shorter Writings, pgs. 33-34 (Charles H. Smith ed., Oxford U. Press 1991).
- [9.] Many of these researchers were not themselves proponents of ID, but were scientists who made discoveries that ID proponents found lent strong scientific credibility to the argument for design. Some of these discoveries are discussed in: J. D. Watson & F. H. C. Crick, "Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid," Nature, Vol. 171:737-738 (April 25, 1953); Michael Polanyi, "Life transcending physics and chemistry," Chemical and Engineering News, Vol. 45(35) (1967); Michael Polanyi, "Life’s irreducible structure," Science, Vol. 160:1308-1312 (June 21, 1968); Hubert P. Yockey, "Self-Organization Origin of Life Scenarios and Information Theory," Journal of Theoretical Biology, Vol. 9 (1981); Marcel P. Schützenberger, "Algorithms and neo-Darwinian theory," in Mathematical challenges to the neo-Darwinian interpretation of evolution (P. S. Moorhead / M. M. Kaplan eds., 1967). See also the Proceedings of a meeting at the Wistar Institute on "Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution" held in April 1966.
- [10.] Michael Polanyi, "Life’s irreducible structure," Science, Vol. 160:1308-1312 (June 21, 1968).
- [11.] Fred Hoyle, Evolution from Space (The Omni Lecture), pg. 28 (Enslow Publishers 1982).
- [12.] James E. Horigan, Chance or Design? (Philosophical Library, 1979).
- [13.] Charles Thaxton, Walter Bradley, Roger Olsen, The Mystery of Life’s Origin, pg. 211 (Lewis & Stanley, 1984).
- [14.] Jonathan Witt, Discovery Inst., "The Origin of Intelligent Design: A Brief History of the Scientific Theory of Intelligent Design," at http://www.discovery.org/f/526.
- [15.] Deposition of Charles Thaxton at 53:5-11, Kitzmiller v. Dover, 400 F. Supp. 2d 707 (M.D. Pa. 2005) (emphasis added).
- [16.] The Mystery of Life's Origin: An Interview with Dr. Charles Thaxton, Part Two, at http://www.idthefuture.com/2008/07/the_mystery_of_lifes_origin_an_1.html, at 3:50.
- [17.] Ibid. at 5:15.
- [18.] Ibid. at 16:55.
- [19.] Ibid. at 18:15.