Tag Archives: Intelligent Design

Peer-reviewed paper: Michael Behe’s “First Rule of Adaptive Evolution”

Christianity and the progress of science
Christianity and the progress of science

Let’s take a look at Mike Behe’s first rule of adaptive evolution, which states that most examples of adaptation in evolutionary experiments involve a loss of function, or a modification of an existing function. Not new functionality.

The paper was published in the Quarterly Review of Biology. I found it on PubMed.


Adaptive evolution can cause a species to gain, lose, or modify a function; therefore, it is of basic interest to determine whether any of these modes dominates the evolutionary process under particular circumstances. Because mutation occurs at the molecular level, it is necessary to examine the molecular changes produced by the underlying mutation in order to assess whether a given adaptation is best considered as a gain, loss, or modification of function. Although that was once impossible, the advance of molecular biology in the past half century has made it feasible. In this paper, I review molecular changes underlying some adaptations, with a particular emphasis on evolutionary experiments with microbes conducted over the past four decades. I show that by far the most common adaptive changes seen in those examples are due to the loss or modification of a pre-existing molecular function, and I discuss the possible reasons for the prominence of such mutations.

By far the most common adaptive changes in the examples we have are due to loss of function or modification of pre-existing function?

Evolution News has a post up about the paper.


After reviewing the effects of mutations upon Functional Coding ElemenTs (FCTs), Michael Behe’s recent review article in Quarterly Review of Biology, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” offers some conclusions. In particular, as the title suggests, Behe introduces a rule of thumb he calls the “The First Rule of Adaptive Evolution”: “Break or blunt any functional coded element whose loss would yield a net fitness gain.” In essence, what Behe means is that mutations that cause loss-of-FCT are going to be far more likely and thus far more common than those which gain a functional coding element. In fact, he writes: “the rate of appearance of an adaptive mutation that would arise from the diminishment or elimination of the activity of a protein is expected to be 100-1000 times the rate of appearance of an adaptive mutation that requires specific changes to a gene.” Since organisms will tend to evolve along the most likely pathway, they will tend to break or lose an FCT before gaining a new one. He explains:

It is called the “first” rule because the rate of mutations that diminish the function of a feature is expected to be much higher than the rate of appearance of a new feature, so adaptive loss-of-FCT or modification-of-function mutations that decrease activity are expected to appear first, by far, in a population under selective pressure.(Michael J. Behe, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” Quarterly Review of Biology, Vol. 85(4) (December, 2010).)

Behe argues that this point is empirically supported by the research reviews in the paper. He writes:

As seen in Tables 2 through 4, the large majority of experimental adaptive mutations are loss-of-FCT or modification-of-function mutations. In fact, leaving out those experiments with viruses in which specific genetic elements were intentionally deleted and then restored by subsequent evolution, only two gain-of-FCT events have been reported

After asking “Why is this the case?” Behe states, “One important factor is undoubtedly that the rate of appearance of loss-of-FCT mutations is much greater than the rate of construction of new functional coded elements.” He draws sound and defensible conclusions from the observed data:

Leaving aside gain-of-FCT for the moment, the work reviewed here shows that organisms do indeed adapt quickly in the laboratory–by loss-of-FCT and modification-of-function mutations. If such adaptive mutations also arrive first in the wild, as they of course would be expected to, then those will also be the kinds of mutations that are first available to selection in nature. … In general, if a sequence of genomic DNA is initially only one nucleotide removed from coding for an adaptive functional element, then a single simple point mutation could yield a gain-of-FCT. As seen in Table 5, several laboratory studies have achieved thousand to million-fold saturations of their test organisms with point mutations, and most of the studies reviewed here have at least single-fold saturation. Thus, one would expect to have observed simple gain-of-FCT adaptive mutations that had sufficient selective value to outcompete more numerous loss-of- FCT or modification-of-function mutations in most experimental evolutionary studies, if they had indeed been available.

But this stark lack of examples of gain-of-functional coding elements can have important implications:

A tentative conclusion suggested by these results is that the complex genetic systems that are cells will often be able to adapt to selective pressure by effectively removing or diminishing one or more of their many functional coded elements.

Behe doesn’t claim that gain-of-function mutations will never occur, but the clear implication is that neo-Darwinists cannot forever rely on examples of loss or modification-of-FCT mutations to explain molecular evolution. At some point, there must be gain of function.

Now, there was a response to this paper from Jerry Coyne on his blog, and then a rebuttal from Mike Behe in a separate article on Evolution News.

New study: first life pushed back earlier, leaving less time for naturalist magic

Christianity and the progress of science
Christianity and the progress of science

Whenever you discuss origins with naturalists, it’s very important to get them to explain how the first living organism emerged without any help from an intelligent agent. The origin of life is an information problem. A certain minimal amount of biological information for minimum life function has to be thrown together by chance. No evolutionary mechanisms have the potential to work until replication is already in place.

Evolution News reports on a new study that makes the window for naturalistic forces to create the first self-replicating organism even smaller.


A paper in Nature reports the discovery of fossil microbes possibly older, even much older, than any found previously. The lead author is biogeochemist Matthew Dodd, a PhD student at University College London. If the paper is right, these Canadian fossils could be 3.77 billion years old, or even as old as — hold onto your hat, in case you’re wearing one — 4.28 billion years.

From the Abstract:

Although it is not known when or where life on Earth began, some of the earliest habitable environments may have been submarine-hydrothermal vents. Here we describe putative fossilized microorganisms that are at least 3,770 million and possibly 4,280 million years old in ferruginous sedimentary rocks, interpreted as seafloor-hydrothermal vent-related precipitates, from the Nuvvuagittuq belt in Quebec, Canada. These structures occur as micrometre-scale haematite tubes and filaments with morphologies and mineral assemblages similar to those of filamentous microorganisms from modern hydrothermal vent precipitates and analogous microfossils in younger rocks. The Nuvvuagittuq rocks contain isotopically light carbon in carbonate and carbonaceous material, which occurs as graphitic inclusions in diagenetic carbonate rosettes, apatite blades intergrown among carbonate rosettes and magnetite–haematite granules, and is associated with carbonate in direct contact with the putative microfossils.

This new paper is interesting to compare with a paper from last year, Nutman et al., “Rapid emergence of life shown by discovery of 3,700-million-year-old microbial structures,” also in Nature, which found microbial structures that are a bit younger.

But the “microbial structures” from Nutman et al. 2016 are different from these new “microfossils” presented by Dodd et al. 2017. In Nutman et al., they only found stromatolite-type structures rather than actual microfossils. Some stromatolite experts were a bit skeptical that what they found were really stromatolites.

But the new paper by Dodd and his colleagues, “Evidence for early life in Earth’s oldest hydrothermal vent precipitates,” seems to offer potential bacteria-like microfossils. They are tiny black carbonaceous spheres and “hematite tubes” which the authors think are biogenically created. We’ve seen more convincing ancient microfossils, but these aren’t bad.

According to Dodd et al., these new finds would be the oldest known microfossils, if that is in fact what they are. Very interesting. If so, that just keeps pushing unquestionable evidence of life’s existence on Earth further and further back, which leaves less and less time for the origin of life to have occurred by unguided chemical evolution after Earth became habitable.

If they are in fact 4.28 billion years old, then that would mean there was life very, very early in Earth’s history — as Cyril Ponnamperuma said, it’s like “instant life.”

Instant life is “rational” for naturalistic fideists, but for evidence-driven people who understand the long odds on generating even a simple protein by chance, it’s irrationality.

Let’s recall exactly how hard it is to make even a simple protein without intelligent agency to select the elements of the sequence.

The odds of creating even a single functional protein

I’ve talked about Doug Axe before when I described how to calculate the odds of getting functional proteins by chance.

Let’s calculate the odds of building a protein composed of a functional chain of 100 amino acids, by chance. (Think of a meaningful English sentence built with 100 scrabble letters, held together with glue)


  • BONDING: You need 99 peptide bonds between the 100 amino acids. The odds of getting a peptide bond is 50%. The probability of building a chain of one hundred amino acids in which all linkages involve peptide bonds is roughly (1/2)^99 or 1 chance in 10^30.
  • CHIRALITY: You need 100 left-handed amino acids. The odds of getting a left-handed amino acid is 50%. The probability of attaining at random only L–amino acids in a hypothetical peptide chain one hundred amino acids long is (1/2)^100 or again roughly 1 chance in 10^30.
  • SEQUENCE: You need to choose the correct amino acid for each of the 100 links. The odds of getting the right one are 1 in 20. Even if you allow for some variation, the odds of getting a functional sequence is (1/20)^100 or 1 in 10^65.

The final probability of getting a functional protein composed of 100 amino acids is 1 in 10^125. Even if you fill the universe with pre-biotic soup, and react amino acids at Planck time (very fast!) for 14 billion years, you are probably not going to get even 1 such protein. And you need at least 100 of them for minimal life functions, plus DNA and RNA.

Research performed by Doug Axe at Cambridge University, and published in the peer-reviewed Journal of Molecular Biology, has shown that the number of functional amino acid sequences is tiny:

Doug Axe’s research likewise studies genes that it turns out show great evidence of design. Axe studied the sensitivities of protein function to mutations. In these “mutational sensitivity” tests, Dr. Axe mutated certain amino acids in various proteins, or studied the differences between similar proteins, to see how mutations or changes affected their ability to function properly. He found that protein function was highly sensitive to mutation, and that proteins are not very tolerant to changes in their amino acid sequences. In other words, when you mutate, tweak, or change these proteins slightly, they stopped working. In one of his papers, he thus concludes that “functional folds require highly extraordinary sequences,” and that functional protein folds “may be as low as 1 in 10^77.”

The problem of forming DNA by sequencing nucleotides faces similar difficulties. And remember, mutation and selection cannot explain the origin of the first sequence, because mutation and selection require replication, which does not exist until that first living cell is already in place.

Can you expect the mainstream media to report honestly on science education?

Investigation in progress
Investigation in progress

Whenever policy makers try to get public schools to teach both sides of issues like evolution or global warming, the mainstream media is there to distort the issues.

With respect to evolution, there are criticisms of elements of the theory from within naturalistic science.

For example, here is an interview with famous biologist Lynn Margulis, published in the radically pro-evolution, pro-naturalism Discover magazine.


Margulis came to view symbiosis as the central force behind the evolution of new species, an idea that has been dismissed by modern biologists. The dominant theory of evolution (often called neo-Darwinism) holds that new species arise through the gradual accumulation of random mutations, which are either favored or weeded out by natural selection. To Margulis, random mutation and natural selection are just cogs in the gears of evolution; the big leaps forward result from mergers between different kinds of organisms, what she calls symbiogenesis. Viewing life as one giant network of social connections has set Margulis against the mainstream in other high-profile ways as well. She disputes the current medical understanding of AIDS and considers every kind of life to be “conscious” in a sense.

Here is something from the interview:

And you don’t believe that natural selection is the answer?

This is the issue I have with neo-Darwinists: They teach that what is generating novelty is the accumulation of random mutations in DNA, in a direction set by natural selection. If you want bigger eggs, you keep selecting the hens that are laying the biggest eggs, and you get bigger and bigger eggs. But you also get hens with defective feathers and wobbly legs. Natural selection eliminates and maybe maintains, but it doesn’t create.

Now, that’s a criticism of the standard theory from a prominent scientist who is a naturalist. She has a naturalistic alternative that she thinks can do the creating. Can we teach her criticism of the standard theory in the public schools? This is what people mean by “teach the controversy”. We don’t mean teach intelligent design, we mean teach the weaknesses of the theory of evolution from within the naturalistic scientific community. But this is apparently too much for journalism graduates to understand.

This article from The Stream explains:

In states like Louisiana, Tennessee, and the current flash point of South Dakota, we have supported responsible academic freedom laws. These laws allow science teachers to present the strengths and weaknesses of neo-Darwinian theory as an explanation of biological novelties. They don’t introduce or protect teaching about intelligent design, and certainly not about any religious doctrine (like creationism). They explicitly extend protection to science instruction alone, and then only when it enriches students’ understanding of subjects that are already part of the curriculum (which ID is not). Yet journalists routinely assert that these laws would shoehorn intelligent design and “creationism” in public school science classes.

In the same context, when we advocate introducing students to “critical thinking” on evolution, with teaching material drawn only from mainstream science, the media claim that “critical thinking” is “code” for intelligent design, or for “intelligent design creationism.” We know that it’s not, and that the “code word” conspiracy theory is utterly false.

The author of that piece tries to explain the difference between criticism of evolution from within mainstream science, and intelligent design, but the journalists just can’t understand what he is saying. There is an example of it here on Evolution News.

Biomimetics: scientists making discoveries using God’s designs in nature

Christianity and the progress of science
Christianity and the progress of science

Well, scientists are still gaining insights from God’s book of nature.

Evolution News reports on the latest:

Pure science seeks understanding of “the nature of nature” and its operations. Applied science takes the insights from pure research and makes it work for human interests. What if you had a single word that incorporates both? Here’s a contender for such a word: Biomimetics. The application side is clear, because engineers and inventors try to imitate nature’s designs. But the pure-research side becomes active in the process, because you have to understand something before you can imitate it. This is a win-win bonanza for 21st-century science, and intelligent design, if not by that name, is at the center of it.

They list the following areas where scientists borrowed from God’s designs in nature to make scientific progress:

  • drug discovery (Nature Communications)
  • artificial muscles (American Institute of Physics)
  • robotics (Engineering at Illinois News)
  • drones (Live Science and New Scientist)
  • crop pollination (New Scientist)
  • ceramics (Proceedings of the Natural Academy of Science)
  • more ceramics (Nature Communications)
  • clothing (American Chemical Society)
  • more clothing (Phys.org)
  • more robotics (Public Library of Science)

Naturally, I chose the bird example for this blog post, because I love birds more than any creature – especially parrots.

This time it’s peacocks and peahens:

Peacock dye. The American Chemical Society is involved in the gold rush, too, excited to announce that “Peacock colors inspire [a] greener way to dye clothes.” The iridescent colors of birds and butterflies come not from pigments, but from geometric structures at the nanoscopic level that intensify certain wavelengths of light. Everyone from fashion designers to parents to the EPA will be happy to learn about better dyes inspired by peacock feathers. “Testing showed the method could produce the full spectrum of colors, which remained bright even after washing,” an ACS team said. “In addition, the team said that the technique did not produce contaminants that could pollute nearby water.”

Amazing that some people just go about their lives ignorant and oblivious to the design that’s all around them. Then again, if they thought about who made these designs, it might interfere with their pursuit of pleasure. Maybe they just shut out the evidence so they can keeping being the boss of their own lives, and never take responsibility for their moral choices?

Romans 1:18-21:

18 For the wrath of God is revealed from heaven against all ungodliness and unrighteousness of men who suppress the truth in unrighteousness,

19 because that which is known about God is evident within them; for God made it evident to them.

20 For since the creation of the world His invisible attributes, His eternal power and divine nature, have been clearly seen, being understood through what has been made, so that they are without excuse.

21 For even though they knew God, they did not honor Him as God or give thanks, but they became futile in their speculations, and their foolish heart was darkened.

See the related posts below for more posts on biomimetics.

Related posts

Stephen C. Meyer and Doug Axe discuss 5 major problems with macro-evolution

Undeniable: How Biology Confirms Our Intuition That Life Is Designed
Undeniable: How Biology Confirms Our Intuition That Life Is Designed

The host of the Cross Examined radio show Dr. Frank Turek talks with Stephen C. Meyer and Doug Axe about a recent conference of Royal Society scientists discussing the problems with the theory of macro-evolution.

The MP3 file is here.


  • about the Royal Society conference
  • the main topic was whether naturalistic mechanisms can produce new body plans and new organ types
  • no one disputes micro-evolution: beaks changing size, antibiotic resistance
  • many of the naturalistic scientists admitted the problems with current naturalistic theories, but they don’t want to embrace the need for a designer
  • none of the proposals that were debated solved the real problems with macro-evolution
  • Problem #1: the sudden origin of body plans in the fossil record
  • Problem #2: the origin of information (e.g. – in protein molecule)
  • Problem #3: need for favorable early mutations (for body plans)
  • Problem #4: the problem of epigenetics
  • Problem #5: the universality of the design intuition

Some of these problems have actually gotten worse for naturalistic evolution as our scientific knowledge has grown.

If you want the two best books on intelligent design, get Dr. Meyer’s “Signature in the Cell” and “Darwin’s Doubt”. I should note that Dr. Meyer is not a young Earth creationist, and has defended the Big Bang cosmology as a solid evidence for a Creator of the universe. Being in favor of an old universe and an old Earth is compatible with being opposed to evolution – because of scientific reasons.