Tag Archives: Darwinism

Philip E. Johnson lectures on science, evolution and religion

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

I found this fun lecture by the grandfather of the big-tent intelligent design movement, Berkeley law professor Philip E. Johnson.

I’ll bet you guys have all heard of him, but you’ve never heard him speak, right? Well, I was a young man, I used to listen to Phil’s lectures and his debates with Eugenie Scott quite a bit. This is one of my favorite lectures. Very easy to understand, and boilerplate for anything else in the origins debate. This is a great lecture – funny, engaging and useful. You will definitely listen to this lecture several times if you listen to it once.

The MP3 is here. (91 minutes, 62 megabytes)

The Inherit the Wind stereotype

  • Many people get their understanding of origins by watching movies like “Inherit the Wind” (or reading science fiction)
  • The actual events of the Scopes trial are nothing like what the movie portrays
  • The law forbidding the teaching of evolution was symbolic, not meant to be enforced
  • The actual Scopes trial was a publicity stunt to attract attention to Dayton, TN to bring business to the town
  • The ACLU advertised for a teacher who would be willing to be sued
  • They found a substitute physical education teacher who would be willing to “break” the law
  • The movie is nothing like the actual events that transpired
  • the movie is a morality play
  • The religious people are evil and stupid and ignorant and bigoted
  • The scientists and lawyers are all intelligent, romantic, and honest seekers of the truth
  • The religious people think that the Bible trumps science and science is not as reliable as the Bible
  • The movie argues that the reason why there is ANY dissent to evolution is because of Biblical fundamentalism
  • The movie presents the idea that there are no scientific problems with evolution
  • The movie says that ONLY Biblical fundamentalists who believe in 6 day, 24-hour creation doubt evolution
  • The movie says that Biblical fundamentalism are close-minded, and not open to scientific truth
  • The movie says that people who read the Bible as making factual claims are misinterpreting the Bible
  • The movie says that smart people read the Bible for comfort and feelings and arbitrary values, not for truth

Guided evolution and methodological naturalism

  • What scientists mean by evolution is that fully naturalistic, unguided, materialistic mechanisms caused the diversity of life
  • Scientists do not allow that God had any real objective effect on how life was created
  • Scientists think that nature did all the creating, and any mention of God is unnecessary opinion – God didn’t DO ANYTHING
  • Scientists operate with one overriding rule – you can only explain the physical world with physical and material causes
  • Scientists DO NOT allow that God could have done anything detectable by the sciences
  • Scientists WILL NOT consider the idea that natural, material processes might be INSUFFICIENT for explaining everything in nature
  • You cannot even ask the question about whether natural laws, matter and chance can explain something in nature
  • Intelligent causes can NEVER be the explanation for anything in nature, and you can’t even test experimentally to check that
  • Scientists ASSUME that everything can be explained with natural laws, matter and chance – no questioning of natural causes is allowed
  • Where no natural explanation of a natural phenomenon is available, scientists SPECULATE about undiscovered natural explanations
  • The assumption of naturalistic sufficiency is called “methodological naturalism”
  • To question the assumptions that natural is all there is, and that nature has to do its own creating, makes you an “enemy of science”
  • But Johnson says that naturalists are the enemies of science, because they are like the Biblical fundamentalists
  • Naturalists have a presumption that prevents them from being willing to follow the evidence where it is leading
  • Experiments are not even needed, because the presumption of naturalism overrides any experimental finding that falsifies the sufficiency of natural causes to explain some natural phenomenon

What can natural selection and mutation actually do?

  • what evolution has actually been observed to do is explain changing populations of moths and finches
  • finches with smaller or larger beaks are observed to have differential survival rates when there are droughts or floods
  • no new body plan or new organ type has been observed to emerge from these environmental pressures
  • the only kind of evolution that has been observed is evolution within types – no new genetic instructions are created
  • in textbooks, only confirming examples are presented – but what is required is a broad pattern of gradual development of species
  • if you look at the fossil record, what you see in most cases is variation within types based on changing environments
  • the real question is: can natural law and chance be observed to be doing any creating of body plans and organ types?

What kind of effect requires an intelligent cause?

  • the thing to be explained in the history of life is the functional information sequences
  • you need to have a sequence of symbols or characters that is sufficiently long
  • your long sequence of characters has to be sequenced in the right order to have biological function
  • the only thing that can create long sequences of functional information is an intelligent cause
  • intelligent design people accept micro-evolution – changes within types – because that’s been observed
  • the real thing to be explained is the first living cell’s functional information, and the creation of new functional information

Johnson’s case for intelligent design is rooted in science – specifically in the specific arrangements of components in proteins that allows organisms to perform biological functions.

Critical response

The next 15 minutes of the lecture contain a critical response from a philosophy professor who thinks that there have been no developments in design arguments since Aquinas and Paley. He basically confirms the stereotypes that Johnson outlined in the first part of the lecture. I recommend listening to this to see what opposition to intelligent design really looks like. It’s not concerned with answering scientific questions – they want to talk about God, the Bible and Noah’s ark. It’s our job to get people like this critic to focus on the science.

Here’s my snarky rendition of what he said:

1) Don’t take the Bible literally, even if the genre is literal.

  • all opposition to evolution is based on an ignorant, fundamentalist, literal reading of the Bible
  • the Bible really doesn’t communicate anything about the way the world really is
  • the Bible is just meant to suggest certain opinions and experiences which you may find fetching, or not, depending on your feelings and community
  • if Christians would just interpret the Bible as myths and opinions on par with other personal preferences, then evolution is no threat to religious belief

2) As long as you treat the design argument as divorced from evidence, it’s not very effective

  • the latest and best version of the design argument is the old Paley argument which involves no experimental data, so I’ll critique that
  • this 200-year old argument which doesn’t rely on science has serious problems, and unnamed Christians agree with me!
  • Christians should NOT try to prove God’s existence using evidence from the natural world (as Romans 1 says), and in fact it’s “Pelagianism” to even try
  • Christians should divorce their faith from logic and evidence even though the Bible presents faith as being rooted in reason and evidence
  • Christians should not tie their faith to the science of today, because science is always changing and the theism-friendly evidence of today might be overturned tomorrow
  • It’s a good idea for me to critique the arguments of 1000-year old people who did not know anything about the cosmic fine-tuning argument – that’s fair!
  • I find it very useful to tell people that the argument from design is false without mentioning any design arguments from DNA or cosmic fine-tuning
  • We need to assume that the natural world is explainable using only natural causes before we look at any evidence
  • We should assume that natural causes create all life, and then rule out all experimental evidence for intelligent causes that we have today
  • As long as you accept that God is a personal opinion that has nothing to do with reality, then you can do science
  • The non-Christian process theologian Teilhard de Chardin accepts evolution, and therefore so should you
  • Remember when theists said God caused thunder because he was bowling in the clouds and then we found out he didn’t? Yeah well – maybe tomorrow we’ll find out that functional sequences of amino acids and proteins have natural causes! What would you do then?

3) What the Bible really says is that you should be a political liberal

Q&A time

The lecture concludes with 13 minutes of questions.

Stephen C. Meyer and Marcus Ross lecture on the Cambrian explosion

Cambrian Explosion
Cambrian Explosion

Access Research Network is a group that produces recordings  of lectures and debates related to intelligent design. I noticed that on their Youtube channel they are releasing some of their older lectures and debates for FREE. So I decided to write a summary of one that I really like on the Cambrian explosion. This lecture features Dr. Stephen C. Meyer and Dr. Marcus Ross.

The lecture is about two hours. There are really nice slides with lots of illustrations to help you understand what the speakers are saying, even if you are not a scientist.

Here is a summary of the lecture from ARN:

The Cambrian explosion is a term often heard in origins debates, but seldom completely understood by the non-specialist. This lecture by Meyer and Ross is one of the best overviews available on the topic and clearly presents in verbal and pictorial summary the latest fossil data (including the recent finds from Chengjiang China). This lecture is based on a paper recently published by Meyer, Ross, Nelson and Chien “The Cambrian Explosion: Biology’s Big Bang” in Darwinism, Design and Public Education(2003, Michigan State University Press). This 80-page article includes 127 references and the book includes two additional appendices with 63 references documenting the current state of knowledge on the Cambrian explosion data.

The term Cambrian explosion describes the geologically sudden appearance of animals in the fossil record during the Cambrian period of geologic time. During this event, at least nineteen, and perhaps as many as thirty-five (of forty total) phyla made their first appearance on earth. Phyla constitute the highest biological categories in the animal kingdom, with each phylum exhibiting a unique architecture, blueprint, or structural body plan. The word explosion is used to communicate that fact that these life forms appear in an exceedingly narrow window of geologic time (no more than 5 million years). If the standard earth’s history is represented as a 100 yard football field, the Cambrian explosion would represent a four inch section of that field.

For a majority of earth’s life forms to appear so abruptly is completely contrary to the predictions of Neo-Darwinian and Punctuated Equilibrium evolutionary theory, including:

  • the gradual emergence of biological complexity and the existence of numerous transitional forms leading to new phylum-level body plans;
  • small-scale morphological diversity preceding the emergence of large-scale morphological disparity; and
  • a steady increase in the morphological distance between organic forms over time and, consequently, an overall steady increase in the number of phyla over time (taking into account factors such as extinction).

After reviewing how the evidence is completely contrary to evolutionary predictions, Meyer and Ross address three common objections: 1) the artifact hypothesis: Is the Cambrian explosion real?; 2) The Vendian Radiation (a late pre-Cambrian multicellular organism); and 3) the deep divergence hypothesis.

Finally Meyer and Ross argue why design is a better scientific explanation for the Cambrian explosion. They argue that this is not an argument from ignorance, but rather the best explanation of the evidence from our knowledge base of the world. We find in the fossil record distinctive features or hallmarks of designed systems, including:

  • a quantum or discontinuous increase in specified complexity or information
  • a top-down pattern of scale diversity
  • the persistence of structural (or “morphological”) disparities between separate organizational systems; and
  • the discrete or novel organizational body plans

When we encounter objects that manifest any of these several features and we know how they arose, we invariably find that a purposeful agent or intelligent designer played a causal role in their origin.

Recorded April 24, 2004. Approximately 2 hours including audience Q&A.

You can get a DVD of the lecture and other great lectures from Access Research Network. I recommend their origin of life lectures – I have watched the ones with Dean Kenyon and Charles Thaxton probably a dozen times each. Speaking as an engineer, you never get tired of seeing engineering principles applied to questions like the origin of life.

The Cambrian explosion lecture above is a great intermediate-level lecture and will prepare you to be able to understand Dr. Meyer’s new book “Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design“. The Michigan State University book that Dr. Meyer mentions is called “Darwin, Design and Public Education“. That book is one of the two good collections on intelligent design published by academic university presses, the other one being from Cambridge University Press, and titled “Debating Design: From Darwin to DNA“. If you think this lecture is above your level of understanding, then be sure and check out the shorter and more up-to-date DVD “Darwin’s Dilemma“.

Information Enigma: 21-minute video explains intelligent design

Can random mutation and natural selection create new functional information?
Can random mutation and natural selection create new functional information?

The video is here:

I have read and listened and watched a lot of material on intelligent design, but I have never seen so much value packed into such a short lecture. I really hope you’ll watch this and that it’s helpful to you.


  • the big question when discussing the origin of life: where did the information in living systems come from?
  • Until 530 million years ago, the oceans were largely devoid of life
  • In a 10 million year period, many new forms of animal life emerged
  • New biological forms of life require new information
  • the discovery of DNA shows that living systems work because cells have information that allows them to build the components of molecular machines: cell types, proteins, etc.
  • can random mutation and natural selection create new functional information?
  • normally, random mutations tend to degrade the functionality of information, e.g. – randomly changing symbols in an applications code does not usually introduce useful new functions, it usually renders what is there non-functional
  • the majority of possible sequences will NOT have functions, so random mutations will more likely give you non-functional code, rather than functional code
  • example: a bicycle lock  with 4 numbers has many possible sequences for the 4 numbers, and only one of them has unlock functionality, the rest have no functionality
  • if you have lots of time, then you might be able to guess the combination, but if the lock as has 10 billion numbers, and only one combination that unlocks, you can spend your whole life trying to unlock it and won’t succeed
  • how likely is it to arrive at a functional protein or gene by chance? Is it more like the 4-dial lock (can be done with lots of time) or the 10 billion dial lock (amount of time required exceeds the time available)?
  • the probability is LOW because there is only one sequence of numbers that has unlock function
  • consider a short protein of 150 amino acids has 10 to the 195th power possible sequences
  • if many of these sequences of amino acides had biological function, then it might be easier to get to one by random mutation and selection than it is with a lock that only unlocks for ONE sequence
  • how many of the possible sequences have biological function?
  • Thanks to research done by Douglas Axe, we now know that the number of functional amino acid sequences for even a short protein is incredibly small…
  • Axe found that the odds of getting a functional sequence of amino acids that will fold and have biological function is 1 in 10 to the 77th power
  • Is that number too improbable to reach by chance? well, there are 10 to 65th atoms in the entire Milky Way galaxy… so yes, this is a very improbable outcome
  • can random genetic mutations search through all the sequences in order to find the one in 10 to the 77th power one that has biological function? It depends on how much guessers we have and how many guesses we get in the time available
  • even with the entire 3.5 billion year history of life on Earth, only about 10 to the 40th organisms have ever lived, which far smaller fraction of the 10 to the 77th total sequences
  • even with a very fast mutation rate, you would not be able to reach a functional protein even with all that time, and even with all those organisms

I was once having a discussion with a woman about the research that Axe did at the Cambridge University lab. He published four articles in the Journal of Molecular Biology. I held out one of the papers to her and showed her the numbers. She said over and over “I hate the Discovery Institute! I hate the Discovery Institute!” Well, yeah, but you can’t make the Journal of Molecular Biology go away with hating the Discovery Institute. JMB is peer-reviewed, and this was experimental evidence – not a theory, not a hypothesis.

We have been blessed by the Creator and Designer of the universe in this time and place with overwhelming evidence – an abundance of riches. For those who have an open mind, this is what you’ve been waiting for to make your decision. For the naturalists who struggle so mightily to block out the progress of experimental science, they’ll need to shout louder and shut their eyes tighter and push harder to block their ears. Maybe if they keep screaming “Star Trek” and “Star Wars” over and over to themselves, they will be able to ignore the real science a little longer.

Study: biological convergence found in human and squid eye genes

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

We have to start this post with the definition of convergence in biology.

In evolutionary biology, convergent evolution is the process whereby organisms not closely related (not monophyletic), independently evolve similar traits as a result of having to adapt to similar environments or ecological niches.

It is the opposite of divergent evolution, where related species evolve different traits.

On a molecular level, this can happen due to random mutation unrelated to adaptive changes; see long branch attraction. In cultural evolution, convergent evolution is the development of similar cultural adaptations to similar environmental conditions by different peoples with different ancestral cultures. An example of convergent evolution is the similar nature of the flight/wings of insects, birds, pterosaurs, and bats.

All four serve the same function and are similar in structure, but each evolved independently.

With that being said, here is an article from Real Clear Science with me.

Eyes and wings are among the most stunning innovations evolution has created. Remarkably these features have evolved multiple times in different lineages of animals. For instance, the avian ancestors of birds and the mammalian ancestors of bats both evolved wings independently, in an example of convergent evolution. The same happened for the eyes of squid and humans. Exactly how such convergent evolution arises is not always clear.

In a new study, published in Nature Scientific Reports, researchers have found that, despite belonging to completely different lineages, humans and squid evolved through tweaks to the same gene.

Like all organs, the eye is the product of many genes working together. The majority of those genes provide information about how to make part of the eye. For example, one gene provides information to construct a light-sensitive pigment. Another gene provides information to make a lens.

Most of the genes involved in making the eye read like a parts list – this gene makes this, and that gene makes that. But some genes orchestrate the construction of the eye. Rather than providing instructions to make an eye part, these genes provide information about where and when parts need to be constructed and assembled. In keeping with their role in controlling the process of eye formation, these genes are called “master control genes”.

The most important of master control genes implicated in making eyes is called Pax6. The ancestral Pax6 gene probably orchestrated the formation of a very simple eye – merely a collection of light-sensing cells working together to inform a primitive organism of when it was out in the open versus in the dark, or in the shade.

Today the legacy of that early Pax6 gene lives on in an incredible diversity of organisms, from birds and bees, to shellfish and whales, from squid to you and me. This means the Pax6 gene predates the evolutionary diversification of these lineages – during the Cambrian period, some 500m years ago.

This is an example of convergence because the same gene is present in animals that DO NOT SHARE A RECENT COMMON ANCESTOR. In short, this is exactly identical to the case where a computer programmer reuses the same library of functions in two completely different programs. Software engineers re-use libraries all the time in different programs. It makes sense in an software engineering paradigm.

But this example of convergence makes no sense on naturalistic evolution – random mutation and selection does not create the same design in two animals with no common ancestry. It screams out design.

Related posts

New book on intelligent design by molecular biologist Douglas Axe

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

It’s not out yet, but the Kindle edition is only $12.99, so I pre-ordered it. That helps to get the book up in the bestseller lists. I’ll add it to my list of books that I am reading for the third quarter later, and maybe feature it in the coveted spot in the right column of the blog.

Anyway, here is the description:

Throughout his distinguished and unconventional career, engineer-turned-molecular-biologist Douglas Axe has been asking the questions that much of the scientific community would rather silence. Now, he presents his conclusions in this brave and pioneering book. Axe argues that the key to understanding our origin is the “design intuition”—the innate belief held by all humans that tasks we would need knowledge to accomplish can only be accomplished by someone who has that knowledge. For the ingenious task of inventing life, this knower can only be God.

Starting with the hallowed halls of academic science, Axe dismantles the widespread belief that Darwin’s theory of evolution is indisputably true, showing instead that a gaping hole has been at its center from the beginning. He then explains in plain English the science that proves our design intuition scientifically valid. Lastly, he uses everyday experience to empower ordinary people to defend their design intuition, giving them the confidence and courage to explain why it has to be true and the vision to imagine what biology will become when people stand up for this truth.

Armed with that confidence, readers will affirm what once seemed obvious to all of us—that living creatures, from single-celled cyanobacteria to orca whales and human beings, are brilliantly conceived, utterly beyond the reach of accident.

Our intuition was right all along.

Trailer is here:

Evolution News has a deal for those who pre-order:

A remarkable thing about evolutionary theory is the way it demands that we deny our intuition at almost every step. Evolutionists then assure us that the science is all figured out, so we needn’t trouble our silly heads about the relevant biology.

In a new book, Douglas Axe of Biologic Institute turns this standard assurance on its head. In Undeniable: How Biology Confirms Our Intuition That Life Is Designed, Dr. Axe restores the place of intuition alongside intellect in considering the question of life’s origins.

Undeniable will be published on July 12 by HarperOne, but you can pre-order before then and participate in an exclusive, private conference call with Dr. Axe and talk- show host Michael Medved. You’ll also receive digital versions of three complete books from Discovery Institute Press: Debating Darwin’s Doubt, The Unofficial Guide to Cosmos, and Science & Human Origins. See here for easy instructions.

And now, I have a secret story to tell you. I met Doug Axe face to face way back in the late 1990s. He told me and some other people about the post-doctoral work he was doing at Cambridge University on the probabilities of getting a functional protein by chance. He made me promise not to tell anyone, and I never did. It was from conversations like that with the intelligent design scholars that I decided to start using an alias.

From his research at Cambrudge, Dr. Axe found 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.

He published his findings in four separate publications with the prestigious Journal of Molecular Biology, and got his PhD with it. To get a PhD from Caltech, and then do post-doctoral work at Cambridge, you have to be good. And Dr. Axe is very, very good.

I have used the papers he wrote in many, many conversations with engineers in different companies where I have worked. He hit a home run with that research. You could never look at the evidence for intelligent design the same way again. Christian parents, if you have any children, be sure that you tell them about Doug Axe’s story.