Tag Archives: Darwinism

John C. Sanford’s genetic entropy hypothesis

Apologetics and the progress of science
Apologetics 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. (I am just a software engineer, not an expert in genetics). His 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?”

If you think all this is interesting, there is a much longer lecture here, which I have not watched. JoeCoder has watched it and he endorses it.

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, I won’t be able to respond to these. I hope that I will have time to come back to this and read about it at some point. I do have an e-book of the that collection of papers book I linked to above.

Positive arguments for Christian theism

Is belief in God compatible with belief in evolution?

Sherlock Holmes and John Watson: let's take a look at the facts
Sherlock Holmes and John Watson: let’s take a look at the facts

What should we make of theistic evolutionists telling us that you can believe in God, while still knowing that matter, law and chance fully explain the development of all of biological life?

Consider this quotation from Phillip E. Johnson.


The National Academy’s way of dealing with the religious implications of evolution is akin to the two-platoon system in American football. When the leading figures of evolutionary science feel free to say what they really believe, writers such as Edward O. Wilson, Richard Dawkins, Daniel Dennett, Carl Sagan, Steven Pinker, Stephen Jay Gould, Richard Lewontin and others state the “God is dead” thesis aggressively, invoking the authority of science to silence any theistic protest. That is the offensive platoon, and the National Academy never raises any objection to its promoting this worldview.

At other times, however, the scientific elite has to protect the teaching of the “fact of evolution” from objections by religious conservatives who know what the offensive platoon is saying and who argue that the science educators are insinuating a worldview that goes far beyond the data. When the objectors are too numerous or influential to be ignored, the defensive platoon takes the field. That is when we read those spin-doctored reassurances saying that many scientists are religious (in some sense), that science does not claim to have proved that God does not exist (but merely that he does not affect the natural world), and that science and religion are separate realms which should never be mixed (unless it is the materialists who are doing the mixing). Once the defensive platoon has done its job it leaves the field, and the offensive platoon goes right back to telling the public that science has shown that “God” is permanently out of business.

(Phillip E. Johnson: “The Wedge of Truth”, IVP 2000, pp. 88-89).

So what naturalistic scientists believe is that God didn’t do anything to create the diversity of life – that nature does all of its own creating without God. In fact, it doesn’t matter if the best naturalistic explanation is improbable or implausible – naturalists must bitterly cling to materialistic explanations of natural phenomena. Any doubts about the efficacy of naturalistic mechanisms get met by “theistic evolutionists” – scientists who think that science shows that God didn’t do anything in the history of life.

When it comes to discussing origins, you have to be very careful with theistic evolutionists. The one question they want to avoid is whether science, done in the ordinary naturalistic way, can discover evidence of intelligent agency in the history of the development of life. And that’s why you have to ask them that question first. “Is there any scientific evidence that intelligent causes were active during the history of the development of life on this planet?” Their answer to that is the same as atheists, namely: “there is no scientific evidence that intelligent causes are responsible for the effects we see in the history of life on Earth”. Theistic evolutionists and atheists agree on that: as far as pure scientific evidence is concerned, nature can do its own creating without any intelligence writing genetic code or engineering animal body plans.

Now, take a look at this article by Jay Richards. He cites some theistic evolutionists.


Biologist Ken Miller:

For his part, [Ken] Miller, a biologist, has no qualms about telling us what God would do: “And in Catholicism, he said, God wouldn’t micromanage that way. ‘Surely he can set things up without having to violate his own laws.'”

I am unaware of any tenet of Catholic theology that requires God not to micromanage. It is, however, a tenet of deism.

Got that? What really happened is that God didn’t do anything. How does he know that? From the science? No. Because he assumes naturalism. Oh, it’s true that he says that God is lurking somewhere behind the material processes that created life. But God’s agency is undetectable by the methods of science. And he is hoping that you will accept his subjective pious God-talk as proof that a fundamentally atheistic reality is somehow reconcilable with a robust conception of theism.

More from Richards:

Then we get Stephen Barr offering his private definition of “chance.”

It is possible to believe simultaneously in a world that is shaped by chance and one following a divine plan. “God is in charge and there’s a lot of accident,” said Barr, also a Catholic. “It’s all part of a plan. . . . God may have known where every molecule was going to move.”

What does Barr really believe? He believes that what science shows is that nature created life without any interference by an intelligent agent. Barr then offers believers his subjective pious God-talk to reassure them that evolution is compatible with religion. He has a personal belief – NOT BASED ON SCIENCE – that the material processes that created all of life are “all part of a plan”. He cannot demonstrate that from science – it’s his faith commitment. And more speculations: “God may have known…”. He can’t demonstrate that God did know anything from science. He is just offering a personal opinion about what God “could have” done. The purpose of these subjective opinions is to appease those who ask questions about what natural mechanisms can really create. Can natural causes really account for the development of functional proteins? Never mind that – look at my shiny spiritual-sounding testimony!

That’s theistic evolution. What really happened is that no intelligent causes are needed to explain life. What they say is “God could” and “God might” and “I pray” and “I attend this church” and “I received a Christian award” and “I sing praise hymns in church”. None of these religious opinions and speculations are relevant to the science – they are just opinions, speculations and biographical trivia. Atheists and theistic evolutionists agree on what science shows about the diversity of life – intelligent causes didn’t do anything.


One of the ways that theistic evolutionists try to affirm design is by insisting that the design is “front-loaded”. The design for all the information and body plans is somehow embedded in matter.

Here is Stephen C. Meyer to assess that:

It’s very important to understand that there is no scientific evidence for design (information) being front-loaded. So although the theistic evolutionists are talking about design, it’s still in the realm of faith – not detectable to scientific investigation. And as Dr. Meyer explained, it doesn’t work to explain design anyway.

I attended a Wheaton College philosophy conference where Dr. Michael Murray read a paper advocating for this front-loaded view of design. I raised my hand to ask him a question, “hey, philosophy guy, did God front-load the information in that paper you’re reading, or did you write it yourself?” But the philosophy moderators must have known that I was an engineer, and would talk sense into him, because they never called on me. However, I did e-mail him later and asked him if he had any evidence for this front-loading theory, and couldn’t God write sequence information in time the same way he had sequenced information in his essay. He replied and said that front-loading was more emotionally satisfying for him. That’s philosophy, I guess. Thank goodness an engineer wrote his e-mail program so that he could at least come clean about his silly view.

The quickest way to disarm a theistic evolutionist is to ask them for a naturalistic explanation of the origin of life. And for a naturalistic explanation of the Cambrian explosion. And so on. Focus on the science – don’t let them turn the conversation to their personal beliefs, or to the Bible, or to religion. No one cares about the psychology of the theistic evolutionist. We only care what science can show.

Stephen C. Meyer lectures on intelligent design and the origin of life

A MUST-SEE lecture based on Dr. Stephen C. Meyer’s book “Signature in the Cell“.

You can get an MP3 of the lecture here. (30 MB)

I highly recommend watching the lecture, and looking at the slides. The quality of the video and the content is first class. There is some Q&A (9 minutes) at the end of the lecture.


  • intelligent design is concerned with measuring the information-creating capabilities of natural forces like mutation and selection
  • Darwinists think that random mutations and natural selection can explain the origin and diversification of living systems
  • Darwinian mechanisms are capable of explaining small-scale adaptive changes within types of organisms
  • but there is skepticism, even among naturalists, that Darwinian mechanisms can explain the origin of animal designs
  • even if you concede that Darwinism can account for all of the basic animal body plans, there is still the problem of life’s origin
  • can Darwinian mechanisms explain the origin of the first life? Is there a good naturalistic hypothesis to explain it?
  • there are at least two places in the history of life where new information is needed: origin of life, and Cambrian explosion
  • overview of the structure of DNA and protein synthesis (he has helpful pictures and he uses the snap lock blocks, too)
  • the DNA molecule is composed of a sequence of bases that code for proteins, and the sequence is carefully selected to have biological function
  • meaningful sequences of things like computer code, English sentences, etc. require an adequate cause
  • it is very hard to arrive at a meaningful sequence of a non-trivial length by randomly picking symbols/letters
  • although any random sequence of letters is improbable, the vast majority of sequences are gibberish/non-compiling code
  • similarly, most random sequences of amino acids are lab-proven (Doug Axe’s work) to be non-functional gibberish
  • the research showing this was conducted at Cambridge University and published in the Journal of Molecular Biology
  • so, random mutation cannot explain the origin of the first living cell
  • however, even natural selection coupled with random mutation cannot explain the first living cell
  • there must already be replication in order for mutation and selection to work, so they can’t explain the first replicator
  • but the origin of life is the origin of the first replicator – there is no replication prior to the first replicator
  • the information in the first replicator cannot be explained by law, such as by chemical bonding affinities
  • the amino acids are attached like magnetic letters on a refrigerator
  • the magnetic force sticks the letters ON the fridge, but they don’t determine the specific sequence of the letters
  • if laws did determine the sequence of letters, then the sequences would be repetitive
  • the three materialist explanations – chance alone, chance and law, law alone – are not adequate to explain the effect
  • the best explanation is that an intelligent cause is responsible for the biological explanation in the first replicator
  • we know that intelligent causes can produce functional sequences of information, e.g. – English, Java code
  • the structure and design of DNA matches up nicely with the design patterns used by software engineers (like WK!)

There are some very good tips in this lecture so that you will be able to explain intelligent design to others in simple ways, using everyday household items and children’s toys to symbolize the amino acids, proteins, sugar phosphate backbones, etc.

Proteins are constructed from a sequence of amino acids:

A sequence of amino acids forming a protein
A sequence of amino acids forming a protein

Proteins sticking onto the double helix structure of DNA:

Some proteins sticking onto the sugar phosphate backbone
Some proteins sticking onto the sugar phosphate backbone

I highly, highly recommend this lecture. You will be delighted and you will learn something.

Here is an article that gives a general overview of how intelligent design challenges. If you want to read something more detailed about the material that he is covering in the lecture above related to the origin of life, there is a pretty good article here.

There is a good breakdown of some of the slides with helpful flow charts here on Uncommon Descent.

Positive arguments for Christian theism

Mark D. Linville: does Darwinian evolution make morality rational?

A conflict of worldviews
A conflict of worldviews

Have you ever heard an atheist tell you that naturalistic evolution is an answer to the moral argument? I have. And I found a good reply to this challenge in the book “Contending With Christianity’s Critics“. The chapter that responds to the challenge is authored by Dr. Mark D. Linville. It is only 13 pages long. I have a link to the PDF at the bottom of this post.

First, a bit about the author:

Blog: The Tavern at the End of the World
Current positions:

  • PhD Research Fellow
  • Tutoring Fellow in Philosophy


  • PhD in Philosophy with a minor in South Asian Studies and a specialization in Philosophy of Religion, University of Wisconsin-Madison
  • MA in Philosophy, University of Wisconsin-Madison
  • MA in Philosophy of Religion, Trinity Evangelical Divinity School
  • MA in Theology, Cincinnati Christian Seminary
  • BA in Biblical Studies, Florida Christian College

Here is his thesis of the essay:

Darwin’s account of the origins of human morality is at once elegant, ingenious, and, I shall argue, woefully inadequate. In particular, that account, on its standard interpretation, does not explain morality, but, rather, explains it away . We learn from Darwin not how there could be objective moral facts, but how we could have come to believe—perhaps erroneously—that there are.

Further, the naturalist, who does not believe that there is such a personal being as God, is in principle committed to Darwinism, including a Darwinian account of the basic contours of human moral psychology. I’ll use the term evolutionary naturalism to refer to this combination of naturalism and Darwinism. And so the naturalist is saddled with a view that explains morality away. Whatever reason we have for believing in moral facts is also a reason for thinking naturalism is false. I conclude the essay with a brief account of a theistic conception of morality, and argue that the theist is in a better position to affirm the objectivity of morality.

And here’s a sample to get your attention:

But even if we are assured that a “normal” person will be prompted by the social instincts and that those instincts are typically flanked and reinforced by a set of moral emotions, we still do not have a truly normative account of moral obligation. There is nothing in Darwin’s own account to indicate that the ensuing sense of guilt—a guilty feeling—is indicative of actual moral guilt resulting from the violation of an objective moral law. The revenge taken by one’s own conscience amounts to a sort of second-order propensity to feel a certain way given one’s past relation to conflicting first-order propensities (e.g., the father’s impulse to save his child versus his impulse to save himself). Unless we import normative considerations from some other source, it seems that, whether it is a first or second-order inclination,one’s being prompted by it is more readily understood as a descriptive feature of one’s own psychology than material for a normative assessment of one’s behavior or character. And, assuming that there is anything to this observation, an ascent into even higher levels of propensities (“I feel guilty for not having felt guilty for not being remorseful over not obeying my social instincts…”) introduces nothing of normative import. Suppose you encounter a man who neither feels the pull of social, paternal or familial instincts nor is in the least bit concerned over his apparent lack of conscience. What, from a strictly Darwinian perspective, can one say to him that is of any serious moral import? “You are not moved to action by the impulses that move most of us.” Right. So?

The problem afflicts contemporary construals of an evolutionary account of human morality. Consider Michael Shermer’s explanation for the evolution of a moral sense—the “science of good and evil.” He explains,

By a moral sense, I mean a moral feeling or emotion generated by actions. For example, positive emotions such as righteousness and pride are experienced as the psychological feeling of doing “good.” These moral emotions likely evolved out of behaviors that were reinforced as being good either for the individual or for the group.2

Shermer goes on to compare such moral emotions to other emotions and sensations that are universally experienced, such as hunger and the sexual urge. He then addresses the question of moral motivation.

In this evolutionary theory of morality, asking “Why should we be moral?” is like asking “Why should we be hungry?” or “Why should we be horny?” For that matter, we could ask, “Why should we be jealous?” or “Why should we fall in love?” The answer is that it is as much a part of human nature to be moral as it is to be hungry, horny, jealous, and in love.3

Thus, according to Shermer, given an evolutionary account, such a question is simply a non-starter. Moral motivation is a given as it is wired in as one of our basic drives. Of course, one might point out that Shermer’s “moral emotions” often do need encouragement in a way that, say, “horniness,” does not. More importantly, Shermer apparently fails to notice that if asking “Why should I be moral?” is like asking, “Why should I be horny?” then asserting, “You ought to be moral” is like asserting, “You ought to be horny.” As goes the interrogative, so goes the imperative. But if the latter seems out of place, then, on Shermer’s view, so is the former.

One might thus observe that if morality is anything at all, it is irreducibly normative in nature. But the Darwinian account winds up reducing morality to descriptive features of human psychology. Like the libido, either the moral sense is present and active or it is not. If it is, then we might expect one to behave accordingly. If not, why, then, as a famous blues man once put it, “the boogie woogie just ain’t in me.” And so the resulting “morality” is that in name only.

In light of such considerations, it is tempting to conclude with C. S. Lewis that, if the naturalist remembered his philosophy out of school, he would recognize that any claim to the effect that “I ought” is on a par with “I itch,” in that it is nothing more than a descriptive piece of autobiography with no essential reference to any actual obligations.

When it comes to morality, we are not interested in mere descriptions of behavior. We want to know about prescriptions of behavior, and whether why we should care about following those prescriptions. We are interested in what grounds our sense of moral obligation in reality. What underwrites our sense of moral obligation? If it is just rooted in feelings, then why should we obey our moral sense when obeying it goes against out self-interest? Feelings are subjective things, and doing the right thing in a real objective state of affairs requires more than just feelings. There has to be a real objective state of affairs that makes it rational for us to do the right thing, even when the right thing is against our own self-interest. That’s what morality is – objective moral obligations overriding subjective feelings. I wouldn’t trust someone to be moral if it were just based on their feelings.

The PDF is right here for downloading, with the permission of the author.

Biomimetics again: scientists reverse engineer the design of snake scales

Apologetics and the progress of science
Apologetics and the progress of science

Today, I have an example of biomimetics.

But first, here’s what that is:

Biomimetic refers to human-made processes, substances, devices, or systems that imitate nature. The art and science of designing and building biomimetic apparatus is called biomimetics, and is of special interest to researchers in nanotechnology, robotics, artificial intelligence (AI), the medical industry, and the military.

This is from Science Daily. (H/T Fuz Rana)

It says:

A snake moves without legs by the scales on its belly gripping the ground. It generates friction at the points needed to move forwards only and prevents its scales from being worn off by too much friction. Researchers of KIT have found a way to transfer this feature to components of movable systems. In this way, durability of hip prostheses, computer hard disks or smartphones might be enhanced.

“Friction and wear are two of the biggest challenges in systems of several individual components,” Christian Greiner of the Institute for Applied Materials says. A solution is found in nature: Snakes, such as the ball python, or lizards, such as the sandfish skink, use friction to move forwards, but can reduce it to a minimum thanks to their scales. Together with Michael Schäfer, Greiner developed a process to transfer the scale structure of reptiles to components of electromechanical systems: With a fiber laser, they milled scales into a steel bolt of 8 mm in diameter.

With the help of two different structures, the materials researchers tested whether the distance of the scales influences friction behavior. In the first structure, the scales overlap and are located very closely to each other, such as the scales on the belly of a ball python. The second structure consists of scales arranged in vertical rows at a larger distance, such as the skin of a sandfish skink. “The distance between the rows in our experiment was the smallest possible distance we could produce with the laser. The structure, hence, does not entirely correspond to that of the sandfish skink,” Greiner says. In the future, however, the researchers plan to produce structures that are closer to the original in nature.

[…]To find out whether scales reduce friction, Greiner and Schäfer fixed the structured surface of the bolts to a rotating plate. The experiments were carried out without and with a lubricant (1 ml of mineral oil). For the experiments with oil as lubricant, the scientists used steel disks. Under dry sliding conditions, sapphire disks were applied. The disk diameter was 50 mm.

Experiments under lubricated conditions revealed that both narrow and wide arrangements of the scales increase friction compared to the unstructured bolt: By the wide scales, friction is increased by a factor of 1.6. The narrow scales increase friction by a factor of 3. In the non-lubricated state, the wide scale structure reduced friction by more than 40 percent, while friction was reduced by 22 percent in case of a narrow scale structure.

The finding that the narrow scale structure increases friction under both lubricated and non-lubricated conditions had not been expected by the researchers: “We assumed that the narrow structure is more effective, as it is closer to nature,” Greiner says.

See the related posts for more examples of humans learning from the engineering designs in nature.

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