Tag Archives: Darwinism

Is the presupposition of naturalism in science good for the pursuit of truth?

I have a key that will unlock a puzzling mystery
I have a key that will unlock a puzzling mystery

This topic came up recently in a discussion, and I wanted to be sure that all my readers were aware of how to think about the work that the presupposition of naturalism does in supporting naturalistic views of science. When I was little, way back in the 1990s, Phillip E. Johnson’s work on the definitions of science, evolution and creation were very important stuff. He was everywhere, doing lectures on university campuses and debates on the radio with Eugenie Scott. I was able to get a bunch of this audio from Access Research Network on AUDIO CASSETTES, but now that’s all obsolete.

Thankfully, I was able to find an old column written by Johnson in the Wall Street Journal, and preserved by Access Research Network.


A Chinese paleontologist lectures around the world saying that recent fossil finds in his country are inconsistent with the Darwinian theory of evolution. His reason: The major animal groups appear abruptly in the rocks over a relatively short time, rather than evolving gradually from a common ancestor as Darwin’s theory predicts. When this conclusion upsets American scientists, he wryly comments: “In China we can criticize Darwin but not the government. In America you can criticize the government but not Darwin.”

That point was illustrated last week by the media firestorm that followed the Kansas Board of Education’s vote to omit macro-evolution from the list of science topics which all students are expected to master. Frantic scientists and educators warned that Kansas students would no longer be able to succeed in college or graduate school, and that the future of science itself was in danger. The New York Times called for a vigorous counteroffensive, and the lawyers prepared their lawsuits. Obviously, the cognitive elites are worried about something a lot more important to themselves than the career prospects of Kansas high school graduates.

The root of the problem is that “science” has two distinct definitions in our culture. On the one hand, science refers to a method of investigation involving things like careful measurements, repeatable experiments, and especially a skeptical, open-minded attitude that insists that all claims be carefully tested. Science also has become identified with a philosophy known as materialism or scientific naturalism. This philosophy insists that nature is all there is, or at least the only thing about which we can have any knowledge. It follows that nature had to do its own creating, and that the means of creation must not have included any role for God. Students are not supposed to approach this philosophy with open-minded skepticism, but to believe it on faith.

[…]All the most prominent Darwinists proclaim naturalistic philosophy when they think it safe to do so. Carl Sagan had nothing but contempt for those who deny that humans and all other species “arose by blind physical and chemical forces over eons from slime.” Richard Dawkins exults that Darwin “made it possible to be an intellectually fulfilled atheist,” and Richard Lewontin has written that scientists must stick to philosophical materialism regardless of the evidence, because “we cannot allow a Divine Foot in the door.”

So, if you’re having a discussion with a person who believes in naturalism – that everything in nature can be explained by material forces alone – then they will give you a stock response to all of your evidence for something outside of nature.

  • Origin of the universe? That’s not science
  • Cosmic fine-tuning? That’s not science
  • Origin of life? That’s not science
  • Cambrian explosion? That’s not science
  • Habitability-discoverability? That’s not science

It’s not that the people who did the science around these discoveries invoked God, and that’s why it’s not science. On the contrary, the mainstream scientists who made these discoveries scrupulously left God out of their microscopes and telescopes. These discoveries – which have only gotten worse for the naturalists as more details emerge – do not have easy naturalistic explanations. If you ask the naturalist for an explanation, they will resort to various sorts of speculations:

  • future science will undermine all our current knowledge
  • we are in an unobservable multiverse that exists eternally
  • aliens seeded the Earth with life, and THEY evolved
  • there are lots of fossils we haven’t discovered yet
  • there are lots of stars and planets we haven’t discovered yet

What’s the answer to this arguing from ignorance?

I think ridicule is best. You need to start by telling the full story about how these discoveries were made. Name the scientists, state the dates. Tell the whole story of how the science was done. Do this for each discovery. Then, at the end, ask them which of these scientific discoveries they deny. Ask them for naturalistic explanations of the ones they accept. Pretend to be confused, then concerned about their sanity. Finally, you should be as condescending as possible, and just explain that we can’t believe in fairies and unicorns. Explain things to them as if they were a child: we have to base our worldview on what science has revealed. We can’t hold out for Santa Claus to come down the chimney with new science that undermines all we have discovered. We have to go with the science we have today, and the science we have today says Creator and Designer. That is the best explanation of the what we know right now. And the trend is that these discoveries are becoming even MORE difficult for naturalism to account for. I guarantee you that the average rank-and-file atheist knows more about Star Wars and Star Trek lore than they do about actual scientific discoveries that threaten their beloved religion of naturalism.

Try to make your face look like Tucker Carlson:

When dealing with a naturalist fundamentalist, make the Tucker Carlson face
The Tucker Carlson face conveys a mix of confusion, disappointment and horror

For God’s sake, even Richard Dawkins admitted in his debate with John Lennox that a good case can be made for a deistic God from the science we have now. If Dawkins can admit this, then you need to be extremely harsh to the village atheists.

If the word “naturalism” is all new to you, you should probably read the whole article and this longer article as well. The longer article really explains the different definitions of the words that are used in these debates. Johnson’s an excellent writer, and you will learn a lot.

Are the Galapagos finch beaks evidence of Darwinian evolution?

I have a key that will unlock a puzzling mystery
I have a key that will unlock a puzzling mystery

Jonathan Wells has an article about it at Evolution News.

It says:

When Charles Darwin visited the Galápagos Islands in 1835, he collected specimens of the local wildlife. These included some finches that he threw into bags, many of them mislabeled. Although the Galápagos finches had little impact on Darwin’s thinking (he doesn’t even mention them in The Origin of Species), biologists who studied them a century later called them “Darwin’s finches” and invented the myth that Darwin had correlated differences in the finches’ beaks with different food sources (he hadn’t). According to the myth, Darwin was inspired by the finches to formulate his theory of evolution, thoughaccording to historian of science Frank Sulloway “nothing could be further from the truth.”

In the 1970s, biologists studied a population of medium ground finches on one of the islands in great detail. When a severe drought left only large, hard-to-crack seeds, 85 percent of the birds perished. The survivors had beaks that were about 5 percent larger than the average beak size in the original population. The biologists estimated that if similar droughts occurred once every ten years, the population could become a new species in only 200 years. In a 1999 booklet defending evolution, the U.S. National Academy of Sciences called the finches “a particularly compelling example” of the origin of species.

But after the drought, birds with smaller beaks flourished again, and the average beak size of the population returned to normal. No net evolution had occurred. No matter; Darwin’s finches became an icon of evolution that is still featured in most biology textbooks.

In the 1980s, a population of large ground finches, with larger beaks than the medium ground finches, migrated to the island. When a drought in 2004-2005 again reduced the food supply, the medium and large ground finch populations both declined. But since even the largest beaks among the medium ground finches were no match for the beaks of the large ground finches, the latter pretty much monopolized the larger seeds and the former had to make do with smaller seeds. This time, the medium ground finches that survived the drought had beaks that were smaller than the average size in the original population. Biologists studying the finches argued that birds with smaller beaks were better able to eat the tiny seeds that were left after the large ground finches ate the big ones, and they concluded that this was again an example of “evolutionary change.”

[…]Wait a minute. Average beak size increased slightly during one drought, only to return to normal after the rains return. Then average beak size decreased slightly during another drought. A region of DNA is correlated with beak size. And somehow that tells us how finches evolved in the first place?

There is an important distinction to make between micro-evolution and macro-evolution. Changes within a type is micro-evolution. Evolving a new organ type or body plan is macro-evolution. There is plenty of evidence for micro-evolution, but no evidence for macro-evolution.

What needs to be proven by the Darwinists is that the same process that results in different average beak size in a population of finches after a drought can create the finches in the first place. I think that Darwinists are credulous – they believe what they want to believe because they want to believe it, even if the evidence is incredibly weak. Darwinists must demonstrate that heritable variations can result in the generation of new organ types and body plans. Changes in average beak size is not interesting. What is needed is to show how the beaks, much less the wings, evolved in the first place.

Icons of Evolution

Jonathan has actually written about a number of  misleading things that you may mind in Biology textbooks.

Here are the sections in his book “Icons of Evolution“:

  • The Miller-Urey Experiment
  • Darwin’s Tree of Life
  • Homology in Vertebrate Limbs
  • Haeckel’s Embroys
  • Archaeopteryx–The Missing Link
  • Peppered Moths
  • Darwin’s Finches
  • Four-Winged Fruit Flies
  • Fossil Horses and Directed Evolution
  • From Ape to Human: The Ultimate Icon

Dr. Wells holds a Ph.D in Molecular and Cell Biology from the University of California at Berkeley.

Are human bodies poorly designed? Is the human retina a bad design?

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

I think this “sub-optimal” argument against a Designer is stupid, because designs are always trade-offs between different quality goals, but just to put this one to bed, here is Evolution News.


Now a new paper in Nature Communications, “Müller cells separate between wavelengths to improve day vision with minimal effect upon night vision,” has expanded upon this research, further showing the eye’s optimal design. According to the paper, Müller cells not only act as optical fibers to direct incoming light through the optic nerve, but are fine-tuned to specific wavelengths to ensure that light reaches the proper retinal cells. From the Abstract:

Vision starts with the absorption of light by the retinal photoreceptors — cones and rods. However, due to the ‘inverted’ structure of the retina, the incident light must propagate through reflecting and scattering cellular layers before reaching the photoreceptors. It has been recently suggested that Müller cells function as optical fibres in the retina, transferring light illuminating the retinal surface onto the cone photoreceptors. Here we show that Müller cells are wavelength-dependent wave-guides, concentrating the green-red part of the visible spectrum onto cones and allowing the blue-purple part to leak onto nearby rods. This phenomenon is observed in the isolated retina and explained by a computational model, for the guinea pig and the human parafoveal retina. Therefore, light propagation by Müller cells through the retina can be considered as an integral part of the first step in the visual process, increasing photon absorption by cones while minimally affecting rod-mediated vision.

(Amichai M. Labin, Shadi K. Safuri, Erez N. Ribak, and Ido Perlman, “Müller cells separate between wavelengths to improve day vision with minimal effect upon night vision,” Nature Communications, DOI: 10.1038/ncomms5319 (July 8, 2014).)

The paper presents Müller cells as a direct answer to the view that the vertebrate eye has a suboptimal wiring:

[T]he mammalian retina and the peripheral retina of humans and primates are organized in a seemingly reverse order with respect to the light path. This arrangement places the photoreceptors, responsible for light absorption, as the last cells in the path of light, rather than the first. Therefore, the incident light must propagate through five reflecting and scattering layers of cell bodies and neural processes before reaching the photoreceptors. This ‘inverted’ retinal structure is expected to cause blurring of the image and reduction in the photon flux reaching the photoreceptors, thus reducing their sensitivity. It has been recently reported that retinal Müller cells act as light guides serving to transfer light across the retina, from the vitreo-retinal border towards the photoreceptors.

I just had someone push this idea that human beings are badly designed as a response to the cosmic fine-tuning argument of all things. Her list of objections was all speculations (multiverse, aliense, design of humans could be better).

This argument that humans are poorly designed strikes me as literally insane. But since this argument is still in use, I guess I had better say something.

First, the argument assumes that the designer of human beings has to design for our comfort and pleasure. Apparently, God – if he were to exist – would be obligated to design creatures who never got sick, never grew old, and never suffered at all. This makes sense to atheists, for some reason – that the God of the universe has to create creatures that last forever and never suffer. There is this perception out there among atheists and very small narcissistic children (but I repeat myself) that God should be our cosmic butler, waiting at our beck and call to do whatever makes us happiest. From the Christian perspective, this is nonsense. Human beings only think about ultimate questions because, as C.S. Lewis wrote, we suffer pain and have limited lifespans. If were designed to be happy and live forever, we would never think about a relationship with God. By nature, humans want to avoid God, because we don’t want to be accountable to him for our rebellion against him and the harm we cause by disobeying the moral law.

The second problem with the argument from imperfection is that it has no understanding of how engineers work in practice. Engineers are used to trading off non-functional requirements against each other. If the laptop has a fast processor, then it runs hotter. If the laptop has great battery life, it’s heavier because of the larger battery. If the laptop has lots of memory, it costs more to buy. There is no way to get every design goal met because they conflict with each other.

Sometimes, I think that atheists are just little children who have stopped growing in maturity and wisdom. I once heard one particularly stupid atheist in a debate claim that his belief in God had ended when he asked God to help him find his cricket bat, and God had not cosmic butlered to his satisfaction. This happened when the atheist was a child, of course. And this is when most atheists become atheists. It’s not a conclusion that is reached for intellectual reasons. It’s just multiverse, aliens, science fiction, and sexual immorality all the way down. Give me what I want when I want it, and don’t judge me for being self-centered and immoral.

New study: rising oxygen levels rejected as explanation of Cambrian explosion

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

So, just to refresh everyone, the Cambrian explosion was an event that occurred about 543 million years ago. In a very short period of time, less than 10 million years, probably 3-5 million, all of the major animal body plans emerged.

Here’s what the Cambrian explosion looks like:

Cambrian Explosion
Cambrian Explosion

The Darwinian theory says that there should be precursors to all of the new phyla that appear. But we have never been able to find any precursors. We’ve been looking in the fossil record for the slow transition from simple life to complex life that Darwin predicted, but we’ve never been able to find anything that explains the sudden emergence of the body plans in the Cambrian explosion.

There is no known naturalistic explanation for the rapid emergence of these “phyla”. But, naturalists were holding out hope that maybe a sudden rise in the level of oxygen might have “triggered” the required increase in complexity.

This is from Science Daily.


Oxygen is crucial for the existence of animals on Earth. But, an increase in oxygen did not apparently lead to the rise of the first animals. New research shows that 1.4 billion years ago there was enough oxygen for animals — and yet over 800 million years went by before the first animals appeared on Earth.

Animals evolved by about 600 million years ago, which was late in Earth’s history. The late evolution of animals, and the fact that oxygen is central for animal respiration, has led to the widely promoted idea that animal evolution corresponded with a late a rise in atmospheric oxygen concentrations.

“But sufficient oxygen in itself does not seem to be enough for animals to rise. This is indicated by our studies,” say postdoc Emma Hammarlund and Professor Don Canfield, Nordic Center for Earth Evolution, University of Southern Denmark.

[…]The new study is published in the journal Proceedings of National Academy of Sciences.

[…]The results differ from other studies and raise several questions, such as: Why then did animals rise so late in Earth’s history?

“The sudden diversification of animals probably was a result of many factors. Maybe the oxygen rise had less to do with the animal revolution than we previously assumed,” says Hammarlund.

Now look here. I don’t see how a rise in oxygen level can create new body plans. Body plans are written in sequences of symbols – in proteins and DNA. I can no more believe that a rise in oxygen levels could create new animal body plans than I could believe that raising the level of oxygen in a computer lab could explain the new code that is being written by the software engineers. Body plans are information, and new body plans require new information. Information comes from software engineers – intelligent agents – not from rising oxygen levels.

In any case, the hypothesis was falsified. It isn’t the first time a naturalistic hypothesis for the Cambrian explosion was shot down (see below) and it won’t be the last.

Related posts

John C. Sanford’s genetic entropy hypothesis

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

JoeCoder sent me a recent peer-reviewed paper by John C. Sanford, so I’ve been trying to find something written by him at a layman’s level so I could understand what he is talking about.

Dr. Sanford’s CV is posted at the Cornell University web page.

I found this 20-minute video of an interview with him, in which he explains his thesis:

The most important part of that video is Sanford’s assertion that natural selection cannot remove deleterious mutations from a population faster than they arrive.

And I also found a review of a book that he wrote that explains his ideas at the layman level.

It says:

Dr. John Sanford is a plant geneticist and inventor who conducted research at Cornell University for more than 25 years. He is best known for significant contributions to the field of transgenic crops, including the invention of the biolistic process (“gene gun”).

[…]Sanford argues that, based upon modern scientific evidence and the calculations of population geneticists (who are almost exclusively evolutionists), mutations are occurring at an alarmingly high rate in our genome and that the vast majority of all mutations are either harmful or “nearly-neutral” (meaning a loss for the organism or having no discernible fitness gain). Importantly, Sanford also establishes the extreme rarity of any type of beneficial mutations in comparison with harmful or “nearly-neutral” mutations. Indeed, “beneficial” mutations are so exceedingly rare as to not contribute in any meaningful way. [NOTE: “Beneficial” mutations do not necessarily result from a gain in information, but instead, these changes predominantly involve a net loss of function to the organism, which is also not helpful to [Darwinism]; see Behe, 2010, pp. 419-445.] Sanford concludes that the frequency and generally harmful or neutral nature of mutations prevents them from being useful to any scheme of random evolution.

[…]In the next section of the book, Sanford examines natural selection and asks whether “nature” can “select” in favor of the exceedingly rare “beneficial” mutations and against the deleterious mutations. The concept of natural selection is generally that the organisms that are best adapted to their environment will survive and reproduce, while the less fit will not. Sanford points out that this may be the case with some organisms, but more commonly, selection involves chance and luck. But could this process select against harmful mutations and allow less harmful or even beneficial mutations to thrive? According to Sanford, there are significant challenges to this notion.

Stanford is a co-author of an academic book on these issues that has Dembski and Behe as co-authors.

Now, I do have to post something more complicated about this, which you can skip – it’s an abstract of a paper he co-authored from that book:

Most deleterious mutations have very slight effects on total fitness, and it has become clear that below a certain fitness effect threshold, such low-impact mutations fail to respond to natural selection. The existence of such a selection threshold suggests that many low-impact deleterious mutations should accumulate continuously, resulting in relentless erosion of genetic information. In this paper, we use numerical simulation to examine this problem of selection threshold.

The objective of this research was to investigate the effect of various biological factors individually and jointly on mutation accumulation in a model human population. For this purpose, we used a recently-developed, biologically-realistic numerical simulation program, Mendel’s Accountant. This program introduces new mutations into the population every generation and tracks each mutation through the processes of recombination, gamete formation, mating, and transmission to the new offspring. This method tracks which individuals survive to reproduce after selection, and records the transmission of each surviving mutation every generation. This allows a detailed mechanistic accounting of each mutation that enters and leaves the population over the course of many generations. We term this type of analysis genetic accounting.

Across all reasonable parameters settings, we observed that high impact mutations were selected away with very high efficiency, while very low impact mutations accumulated just as if there was no selection operating. There was always a large transitional zone, wherein mutations with intermediate fitness effects accumulated continuously, but at a lower rate than would occur in the absence of selection. To characterize the accumulation of mutations of different fitness effect we developed a new statistic, selection threshold (STd), which is an empirically determined value for a given population. A population’s selection threshold is defined as that fitness effect wherein deleterious mutations are accumulating at exactly half the rate expected in the absence of selection. This threshold is mid-way between entirely selectable, and entirely unselectable, mutation effects.

Our investigations reveal that under a very wide range of parameter values, selection thresholds for deleterious mutations are surprisingly high. Our analyses of the selection threshold problem indicate that given even modest levels of noise affecting either the genotype-phenotype relationship or the genotypic fitness-survival-reproduction relationship, accumulation of low-impact mutations continually degrades fitness, and this degradation is far more serious than has been previously acknowledged. Simulations based on recently published values for mutation rate and effect-distribution in humans show a steady decline in fitness that is not even halted by extremely intense selection pressure (12 offspring per female, 10 selectively removed). Indeed, we find that under most realistic circumstances, the large majority of harmful mutations are essentially unaffected by natural selection and continue to accumulate unhindered. This finding has major theoretical implications and raises the question, “What mechanism can preserve the many low-impact nucleotide positions that constitute most of the information within a genome?”

Now I have been told by JoeCoder that there are many critical responses to his hypothesis, most of which have to do with whether natural selection can overcome the difficulty he is laying out. But since this is not my area of expertise, there is not much I can say to adjudicate here. Take it for what it is.

Positive arguments for Christian theism