Tag Archives: Naturalism

How likely is it for blind forces to sequence a functional protein by chance?

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

How likely is it that you could swish together amino acids randomly and come up with a sequence that would fold up into a functional protein?

Evolution News reports on research performed by Doug Axe at Cambridge University, and published in the peer-reviewed Journal of Molecular Biology.


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.10 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.”11 The extreme unlikelihood of finding functional proteins has important implications for intelligent design.

Just so you know, those footnotes say this:

[10.] Douglas D. Axe, “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds,” Journal of Molecular Biology, 1-21 (2004); Douglas D. Axe, “Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors,” Journal of Molecular Biology, Vol. 301:585-595 (2000).

[11.] Douglas D. Axe, “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds,” Journal of Molecular Biology, 1-21 (2004).

And remember, you need a lot more than just 1 protein in order to create even the simplest living system. Can you generate that many proteins in the short time between when the Earth cools and the first living cells appear? Even if we spot the naturalist a prebiotic soup as big as the universe, and try to make sequences as fast as possible, it’s unlikely to generate even one protein in the time before first life appears.

Here’s Doug Axe to explain his research:

If you are building a protein for the FIRST TIME, you have to get it right all at once – not by building up to it gradually using supposed Darwinian mechanisms. That’s because there is no replication before you have the first replicator. The first replicator cannot rely on explanations that require replication to already be in place.

Walter Bradley lectures on the creation and design of the universe

Dr. Walter L. Bradley
Dr. Walter L. Bradley

This lecture is special to me, because I bought a VHS tape of it just after I started working full-time, and watched it a million times. It changed my life. The lecture was delivered at the University of California, Santa Barbara.

About the speaker:

Dr. Bradley received his B.S. in Engineering Science and his Ph.D. in Materials Science from the University of Texas in Austin.

Dr. Bradley taught for eight years at the Colorado School of Mines before assuming a position as Professor of Mechanical Engineering at Texas A&M University (TAMU) in 1976.

During his 24 years at Texas A&M, Dr. Bradley served as Head of the Department of Mechanical Engineering at Texas A&M University and as Director of the Polymer Technology Center, and received five College of Engineering Research Awards. He has received over $4,500,000 in research grants and has published over 140 technical articles and book chapters. He has also co-authored “The Mystery Of Life’s Origin: Reassessing Current Theories. He is a Fellow of the American Society for Materials and of the American Scientific Affiliation and serves as a consultant for many Fortune 500 companies.

He currently serves as Distinguished Professor of Engineering at Baylor University.

The lecture: (63 minutes lecture, 25 minutes audience Q&A)

Summary slide:

This slide summarizes the content of the lecture
This slide summarizes the content of the lecture


  • At the beginning of the 20th century, people believed that the progress of science was pointing away from an intelligent Creator and Designer, and towards naturalism
  • A stream of new discoveries has shifted the support of science towards theism, and away from naturalism
  • Richard Dawkins, an atheist, says that nature only has the appearance of design, but that if you look closer, naturalistic mechanisms can account for the appearance of design
  • When deciding between design and apparent design (“designoid”), it matters whether you think there is an intelligence there to do the designing

Evidence #1: The Big Bang:

  • an eternal “steady state” universe is more compatible with naturalism, but a created universe is more compatible with a Creator
  • In 1929, Hubble used telescopes to observe that the light from distant galaxies was redshifted. The further away galaxies were, the faster they were moving away. Therefore, space is expanding in all directions, suggesting an explosive origin of the universe
  • In 1965, the discovery of the cosmic microwave background radiation matched a prediction of the Big Bang cosmology, and of the creation event
  • In 1992, the COBE space telescope allowed us to test four specific predictions of the Big Bang model, especially the predictions for light element abundances (hydrogen and helium), which matched the predictions of the creation model

Evidence #2: Simple mathematical structure of the physical laws

  • the simple mathematical structure of natural laws allows us to understand these laws, make discoveries, and engineer solutions to problems
  • early scientists saw the mathematical structure of the universe to mean that nature was designed by an intelligent to be understood
  • the fundamental equations of the laws of the universe can be easily written on one side of one sheet of paper
  • Eugene Wigner’s famous paper, “The Unreasonable Effectiveness of Mathematics in the Physical Sciences” makes the point that this simple structure is an unexpected gift that allows is to do science

Evidence #3: fine-tuning of the physical constants and quantities

  • in order for any kind of complex life to survive, we need stars that provide energy within specific ranges for long periods of time
  • in order for any kind of complex life to survive, we need planets with stable orbits that will not suffer from extreme temperature swings as it varies in distance from its star
  • in order for any kind of complex life to survive, we need stable atomic structure
  • in order for any kind of complex life to survive, we need to have chemical diversity and correct relative abundances of each element
  • organic life has minimum requirements: process energy, store information, replicate, and you can’t fulfill those functions if there is only one element, e.g. – hydrogen
  • the energy level from the photons from the sun have to match the energy levels of the different elements in order to drive the chemical bonding needed for life
  • These requirements for life of any imaginable type depend on the values of the constants and quantities. The constants and quantities cannot vary much from what they are, or the universe will lose the characteristics (above) that allow it to support complex life of any imaginable time
  • For example, ratio of strong force to electromagnetic force:
    – if 2% larger, then no stable hydrogen, no long-lived stars, no compounds containing hydrogen, e.g. – water
    – if 5% smaller, no stable stars, heavy hydrogen would be unstable, few elements other than hydrogen

Evidence #4: initial conditions for habitability

  • Universe: expansion rate of the universe must be fast enough to avoid a re-collapse, but slow enough to allow matter to clump together and form stars and planets for complex life to live on
  • Planet: right distance from the star to get the right climate
  • Planet: right mass to retain the right atmosphere

Evidence #5: origin of life and information theory

  • It’s possible to explain every process in an automobile engine using plain old naturalistic mechanisms – no supernatural explanation is necessary to understand the processes
  • But the existence of engine itself: engineering all the parts has to be explained by the work of an intelligence
  • Similarly, we can understand how living systems work, but the existence of the living systems requires an intelligence
  • Even the simplest living system has to perform minimal function: capture energy, store information and replicate
  • Living systems are composed of objects like proteins that are composed of sequences of components complex such that the order of the components gives the overall structure function
  • Developing the components for a simple living cell is very improbable – even given the large number of galaxies, stars and planets in the universe, it is unlikely that complex, embodied life would exist anywhere in the universe

Evidence #6: more initial conditions for habitability

  • Location within the galaxy: you need to be away from the center of the galaxy, because the explosions from dying stars, and excessive radiation will kill life
  • Location within the galaxy: you need to be close enough to the center in order catch the heavy elements you need for life from the explosions of other stars
  • Location within the galaxy: the best location is between two arms of  a spiral galaxy, where you can get the heavy elements you need from dying stars, but without being hit with explosions and harmful radiation
  • Star mass: determines rate at which the sun burns, determines the energy level of photons that are used to drive chemical bonding reactions, determines the length of time the star will be stable
  • Star mass: star mass must be the correct value in order to allow liquid water on the planet’s surface, while still preserving stable orbit

I wish there was more curiosity about science in churches, and young Christians understood how critical science is for grounding the rationality of the Christian worldview. We need to be training up more scientists who think about the big questions, like Dr. Walter Bradley.

MIT physicist Alan Lightman on fine-tuning and the multiverse

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

Here’s the article from Harper’s magazine.

The MIT physicist says that the fine-tuning is real, and is best explained by positing the existence of an infinite number of universes that are not fine-tuned – the so-called multiverse.


While challenging the Platonic dream of theoretical physicists, the multiverse idea does explain one aspect of our universe that has unsettled some scientists for years: according to various calculations, if the values of some of the fundamental parameters of our universe were a little larger or a little smaller, life could not have arisen. For example, if the nuclear force were a few percentage points stronger than it actually is, then all the hydrogen atoms in the infant universe would have fused with other hydrogen atoms to make helium, and there would be no hydrogen left. No hydrogen means no water. Although we are far from certain about what conditions are necessary for life, most biologists believe that water is necessary. On the other hand, if the nuclear force were substantially weaker than what it actually is, then the complex atoms needed for biology could not hold together. As another example, if the relationship between the strengths of the gravitational force and the electromagnetic force were not close to what it is, then the cosmos would not harbor any stars that explode and spew out life-supporting chemical elements into space or any other stars that form planets. Both kinds of stars are required for the emergence of life. The strengths of the basic forces and certain other fundamental parameters in our universe appear to be “fine-tuned” to allow the existence of life. The recognition of this fine-­tuning led British physicist Brandon Carter to articulate what he called the anthropic principle, which states that the universe must have the parameters it does because we are here to observe it. Actually, the word anthropic, from the Greek for “man,” is a misnomer: if these fundamental parameters were much different from what they are, it is not only human beings who would not exist. No life of any kind would exist.

If such conclusions are correct, the great question, of course, is why these fundamental parameters happen to lie within the range needed for life. Does the universe care about life? Intelligent design is one answer. Indeed, a fair number of theologians, philosophers, and even some scientists have used fine-tuning and the anthropic principle as evidence of the existence of God. For example, at the 2011 Christian Scholars’ Conference at Pepperdine University, Francis Collins, a leading geneticist and director of the National Institutes of Health, said, “To get our universe, with all of its potential for complexities or any kind of potential for any kind of life-form, everything has to be precisely defined on this knife edge of improbability…. [Y]ou have to see the hands of a creator who set the parameters to be just so because the creator was interested in something a little more complicated than random particles.”

Intelligent design, however, is an answer to fine-tuning that does not appeal to most scientists. The multiverse offers another explanation. If there are countless different universes with different properties—for example, some with nuclear forces much stronger than in our universe and some with nuclear forces much weaker—then some of those universes will allow the emergence of life and some will not. Some of those universes will be dead, lifeless hulks of matter and energy, and others will permit the emergence of cells, plants and animals, minds. From the huge range of possible universes predicted by the theories, the fraction of universes with life is undoubtedly small. But that doesn’t matter. We live in one of the universes that permits life because otherwise we wouldn’t be here to ask the question.

I thought I was going to have to go outside this article to refute the multiverse, but Lightman is honest enough to refute it himself:

The… conjecture that there are many other worlds… [T]here is no way they can prove this conjecture. That same uncertainty disturbs many physicists who are adjusting to the idea of the multiverse. Not only must we accept that basic properties of our universe are accidental and uncalculable. In addition, we must believe in the existence of many other universes. But we have no conceivable way of observing these other universes and cannot prove their existence. Thus, to explain what we see in the world and in our mental deductions, we must believe in what we cannot prove.

Sound familiar? Theologians are accustomed to taking some beliefs on faith. Scientists are not. All we can do is hope that the same theories that predict the multiverse also produce many other predictions that we can test here in our own universe. But the other universes themselves will almost certainly remain a conjecture.

The multiverse is not pure nonsense, it is theoretically possible. The problem is that the multiverse generator itself would require fine-tuning, so the multiverse doesn’t get rid of the problem. And, as Lightman indicates, we have no independent experimental evidence for the existence of the multiverse in any case. Atheists just have to take it on faith, and hope that their speculations will be proved right. Meanwhile, the fine-tuning is just as easily explained by postulating God, and we have independent evidence for God’s existence, like the the origin of biological information, the sudden appearance of animal body plans, the argument from consciousness, and so on. Even if the naturalists could explain the fine-tuning, they would still have a lot of explaining to do. Theism (intelligent causation) is the simplest explanation for all of the things we learn from the progress of science.

We need to be frank about atheists and their objections to the progress of science. Within the last 100 years, we have discovered that the physical universe came into being out of nothing 15 billion years ago, and we have discovered that this one universe is fine-tuned for intelligent life. I don’t think it’s like that the last 100 years of scientific progress on the origins question are going to be overturned so that science once again affirms what atheists believe about the universe. Things are going the wrong way for atheists – at least with respect to science.

See it in action

To see these arguments examined in a debate with a famous atheist, simply watch the debate between William Lane Craig and Christopher Hitchens, and judge which debater is willing to form his beliefs on scientific progress, and which debater is forming his beliefs against the science we have today, and hoping that the good science we have today based on experiments will be overturned by speculative theories at some point in the future. When you watch that debate, it becomes very clear that Christian theists are interested in conforming their beliefs to science, and atheists are very interested in speculating against what science has shown in order to maintain their current pre-scientific view. That’s not what rational people ought to do when confronted with evidence.

Positive arguments for Christian theism

New paper from Michael Licona on historical methods and miracle claims

Sherlock Holmes and John Watson
Sherlock Holmes and John Watson about to do some historical inquiry

I hope that all my readers know who Michael Licona is!

The PDF of his new paper is here. It was just published in the Journal for the Study of the Historical Jesus. It talks about how the pre-suppositions of ancient historians can mess with their ability to investigate the past.

Here’s the abstract:

Most biblical scholars and historians hold that the investigation of a miracle report lies outside of the rights of historians acting within their professional capacity. In this essay, I challenge this position and argue to the contrary. A definition of history should not a priori exclude the possibility of investigating miracle claims, since doing so may restrict historians to an inaccurate assessment of the past. Professional historians outside of the community of biblical scholars acknowledge the frequent absence of a consensus; this largely results from conflicting horizons among historians. If this is the present state among professionals engaged in the study of non-religious history, it will be even more so with historians of Jesus. Finally, even if some historians cannot bring themselves to grant divine causation, they, in principle, can render a verdict on the event itself without rendering a verdict on its cause.

Here’s a bit that I found interesting:

It is clear that the horizon of atheist New Testament scholar Gerd Lüdemann is a driving force behind his historical conclusions when he a priori rules out the  historicity of the ascension of Jesus reported in Acts 1.9–11 ‘because there is no  such heaven to which Jesus may have been carried’. Ontological naturalism similarly guides James Tabor.

He writes:

Women do not get pregnant without a male—ever. So Jesus had a human father… Dead bodies don’t rise… So, if the tomb was empty the historical  conclusion is simple—Jesus’ body was moved by someone and likely  reburied in another location.

Not so obvious is Geza Vermes in his 2008 volume The Resurrection: History and Myth. With hardly a comment, Vermes simply dismisses both ‘the out-of-hand rejection of the inveterate skeptic’ and the hypothesis that Jesus rose from the dead since it can only be made from ‘the blind faith of the fundamentalist believer’.

I thought these were interesting because Ludemann and Vermes still agree with some of the minimal facts in a case for the resurrection case, such as Craig, Habermas or Licona might make. Ludemann gives you the post-mortem “visions” of Jesus, and Vermes gives you the empty tomb – yet both are naturalists, as you can see. They both rule out miracle as an explanation of the minimal facts a priori, but they both allow for useful minimal facts because the historical case is there to support them. Isn’t that interesting?

So what would you call a detective who ruled out some causes of death but not others, before looking at the evidence?


Second, methodological naturalism may handicap historians, preventing them in some cases from providing a fuller and more accurate account of the past. Molecular biologist Michael Behe provides a relevant challenge to this approach in his discipline. He writes:

Imagine a room in which a body lies crushed, flat as a pancake. A dozen detectives crawl around, examining the floor with magnifying glasses for any clues to the identity of the perpetrator. In the middle of the room, next to the body, stands a large, grey elephant. The detectives carefully avoid bumping into the pachyderm’s legs as they crawl, and never even glance at it. Over time the detectives get frustrated with their lack of progress but resolutely press on, looking even more closely at the floor. You see, textbooks say detectives must ‘get their man’, so they never consider elephants.

In context, Behe is contending that when scientists limit their considerations exclusively to unguided natural causes they will forever keep themselves from discovering the actual cause if a Designer of some sort was responsible. A similar admonition may be issued to historians who a priori exclude a non-human agent as the cause behind a past event. Those who do so could actually be placing themselves in a position where they cannot appraise history accurately.

The rest of the paper discusses two options for historians who want to resolve this problem.

So, I’m impressed that Mike Licona reads Mike Behe (that quote is from “Darwin’s Black Box”). Pretty cool that he reads across disciplines, and that he reads people who disagree with him. We one-dollar apologists all need to be like that.

Back to his paper. I see this presupposition of naturalism come up in debates on the historical Jesus, where the naturalist will just assume naturalism and then proceed to do history – even at a time where we have so many scientific arguments to undermine naturalism. It’s a bad philosophical view, and we shouldn’t let it influence how we do history.

If you run into these historians who are committed to naturalism, it might be worth it to make them defend it. You ask them – do you believe in naturalism? If they say yes, ask them for scientific evidence for naturalism. And when they finish not giving you any, then you can go on a long monologue on the origin of the universe, the fine-tuning, the origin of life, the Cambrian explosion, the habitability (galactic and stellar), and so on. Then tell them to stop bring their blind religious faith into their historical investigations.

Dan Barker debates Casey Luskin on academic freedom

Two ninjas face off at sundown
Two ninjas face off at sundown

The Michael Medved show is a national radio show broadcast out of Seattle, Washington. According to Talkers magazine, he has the fifth largest radio audience.

The MP3 file is available for download. (38 minutes)

The description is:

On this episode of ID the Future, the CSC’s Casey Luskin and atheist Dan Barker of the Freedom From Religion Foundation debate academic freedom and free speech on the Medved Show. This debate was inspired by the ongoing case of Professor Eric Hedin, a physicist at Ball State University who is being threatened by the Freedom From Religion Foundation for favorably portraying intelligent design in the classroom.

Topics: (note that I am paraphrasing Dan Barker for the sake of humor, and he will probably sue me, since that is his entire contribution to the search for truth in this debate)

  • Michael Medved: untenured Ball State University professor Eric Hedin is under fire for teaching both sides of intelligent design in a college course
  • Dan Barker: this complaint against professor Hedin came to our attention from Jerry Coyne not from students of Professor Hedin
  • Dan Barker: professors are not allowed to question the presuppositions atheism, materialism, naturalism in the physics classroom
  • Dan Barker: this is a science course and you cannot question the religion of naturalism in class or else it’s teaching religion
  • Dan Barker: we need to use the power of the courts to stifle any dissent from of my religion (naturalism)
  • Dan Barker: the classroom of a university is not the proper place for students to inquire about both sides of scientific disputes
  • Dan Barker: even if students are paying their money and choosing this course of their own free will, they can’t be allowed to hear both sides
  • Casey Luskin: this course is not a science course, it is open to non-science students
  • Casey Luskin: the course evaluations from students of all majors is overwhelmingly positive
  • Casey Luskin: the course features people on both sides
  • Casey Luskin: the course features brilliant scholars like Lennox and Penrose, both from Oxford University
  • Casey Luskin: the course features opponents of intelligent design like Francis Collins and Karl Gilberson
  • Casey Luskin: the course features non-Christians like Lee Spetner, Paul Davies, Roger Penrose and Gerald Schroeder
  • Dan Barker: (taking over the host) you cannot study scientists like Francis Collins who mapped the human genome, that is “creationism”
  • Michael Medved: academic freedom allows professors to put a slant on what they are teaching
  • Dan Barker: if the professor’s slant is against my religion of naturalism, then I have to put them in jail and inquisition them
  • Dan Barker: you cannot teach science like the Big Bang and fine-tuning  as if it is science because it contradicts naturalism
  • Casey Luskin: Even radical atheist PZ Myers says that professors have the right to academic freedom
  • Dan Barker: I’ll burn that creationist at the stake, too! And smash his filthy microscopes and telescopes!
  • Michael Medved: Casey, would you use state power to fire a professor who disagreed with you because you were offended?
  • Casey Luskin: no, I had to take tons of courses from professors who had a slant against my views and I learned a lot from different views
  • Dan Barker: you will address me as the Holy Father, please! Every professor who disagrees with my religion must burn!
  • Casey Luskin: Barker has no idea what is going on in the class, he never attended it
  • Casey Luskin: The atheists students who took his class gave him high ratings and said he graded fairly
  • Dan Barker: I don’t have to look through the telescope to know the Earth is flat – Hedin is a traitor! Off with his head!
  • Dan Barker: Creationist PZ Myers is wrong, and I’ll burn him at the stake for creationist heresy against my Holy Church!
  • Dan Barker: Oxford professors like John Lennox are creationists because his Big Bang religion is grounded on experimental data like the cosmic background radiation, the hydrogen/helium abundances and the redshifting of light from distant galaxies
  • Dan Barker: I have a degree in Religion and I write hymns, which makes me smarter than John Lennox since he is a “creationist”
  • Dan Barker: I haven’t published any scientific research myself, but I have written some atheist praise hymns, so I am qualified to burn the heretics!
  • Michael Medved: The course is taught by someone with a PhD in Physics, and the syllabus says that it investigates science and religion
  • Michael Medved: Why is it wrong to investigate the science that questions philosophical assumptions like naturalism and materialism?
  • Casey Luskin: The syllabus features amazing readings from all the latest science relevant to that question from both sides
  • Michael Medved: What will Ball State U do to the professor?
  • Casey Luskin: So far no action from Ball State U, but people need to sign the petition to protect the professor
  • Michael Medved: Isn’t academic freedom being applied inconsistently here?
  • Casey Luskin: Yes and science is supposed to move forward by disagreement and debate
  • Casey Luskin: How confident can intelligent design censors really be if their contribution to the debate is coercion and intimidation?
  • Michael Luskin: Is Dan Barker right to say that Oxford professor John Lennox is a “creationist”?
  • Casey Luskin: Creationism starts with the Bible, but intelligent design starts with scientific data

And there is a period of questions from the callers. This episode features a debate, so it is not to be missed.

Now Dan Barker sounded pretty confident in that debate, so you might be surprised by his academic background:

Dan became a teenage evangelist at age 15. At 16 he was choir librarian for faith-healer Kathryn Kuhlman’s Los Angeles appearances. He received a degree in Religion from Azusa Pacific University and was ordained to the ministry by the Standard Community Church, California, in 1975.

[…]Dan preached for 19 years. He maintained an ongoing touring musical ministry, including eight years of full-time, cross-country evangelism. An accomplished pianist, record producer, arranger and songwriter, he worked with Christian music companies such as Manna Music and Word Music. For a few years, Dan wrote and produced the annual “Mini Musicale” for Gospel Light Publications’ Vacation Bible School curriculum.

I’m not sure if Dan Barker has the right background for disputing whether intelligent design belongs in a classroom or not. Remember, the bulk of his life was spent writing and singing feel-good, happy-clappy songs. In his debates with Christians, it’s quite clear that he is totally unequipped to assess scientific evidence from the Big Bang, the fine-tuning, the origin of life, the Cambrian explosion, or habitability. It’s just not his thing, and I don’t think that musicians have what it takes to understand those arguments enough to feel comfortable using the courts to suppress people with actual PhDs in science.

You can read more about my opinion about how Dan Barker arrived at his atheism through a mistaken view of the Christian life.

I subscribe to the ID the Future podcast, and I really recommend that you do as well!