Stephen Meyer Debates Perry Marshall – Intelligent Design vs. Evolution 2.0

“What Happened to Evolution at the Royal Society?”

Evolution vs. Intelligent Design Debate – Perry Marshall vs. Stephen Meyer on the UNBELIEVABLE radio program & podcast with host Justin Brierley


Annotated transcript with additional videos, links, comments and resources by Perry Marshall at the bottom.

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Host Justin Brierley (JB): Today on the program we’re asking, “What happened to evolution at the Royal Society?”

My guests today are Stephen Meyer and Perry Marshall. It didn’t make front-page headlines across the world, but many biologists are saying that something quite exciting happened at the Royal Society in London last year. The Royal Society is one of the world’s oldest and most respected scientific institutions, and has been at the forefront of championing the theory of evolution.

But at its meeting in November 2016, New Trends in Evolutionary Biology—that was the name of the conference—many are saying the door was opened to potentially alternative explanations for the way life, in contrast to the standard Neo-Darwinian explanation of evolution by natural selection acting on random mutation.

Dr. Denis Noble, who hosted the conference, brought together leading voices in the so-called “Third Way” movement in biology. People like James Shapiro, Sonia Sultan, and Gerd Müller, whose research some people say has challenged the prevailing orthodoxy.

What does all this mean for the future of evolutionary theory? Does it open the door to things like Intelligent Design or a role for God in the evolutionary process? Or something else entirely?

Well, two people who were both there are joining me for Unbelievable today for what I’m sure will be a really interesting, scientific, philosophical and theological discussion.

Stephen C. Meyer of the Discovery Institute, well known as an advocate of Intelligent Design Theory and books like Signature in the Cell and Darwin’s Doubt. In fact he’s appeared on this program in the past to debate both of those.

Perry Marshall is my other guest. He’s the author of Evolution 2.0, a book which gathers much of the research being talked about at this conference, and suggests recent research in evolution doesn’t support either Neo-Darwinism or Intelligent Design, but what he calls a Third Way. I’ll let him introduce that when we come to him.

This should be quite an interesting and first-hand account of what happened at this particular conference and what it might mean. We’ll come to Perry in a moment, but before we do that welcome back to the program Dr. Stephen Meyer! How are you doing?

Stephen Meyer: I’m doing very well, Justin, thanks for having me, and thanks for having me on with Perry.

JB: The last time I spoke to you, Stephen, was also by phone. Shortly before you headed over to the UK to take part in a conference in Cambridge. This fell around the same time as this Royal Society conference, but you were coming over to be a speaker at a conference in Cambridge around the whole issue of Intelligent Design. Do you want to just give us a brief idea of how that went and what transpired there?

Stephen Meyer: Yes, we had a terrific week in the UK. In London, there were about twenty of the scientists from the ID research community worldwide who attended the Royal Society meeting. We had a private research meeting with those scientists, a number of PhD students and post-docs who were European-based the next day to work on collaborative research projects.

Then the following Saturday we had a public conference at one of the Cambridge colleges, Hughes Hall, called ‘Beyond Materialism’ where we were looking at what biology looks like if you don’t start with the assumption that methodological naturalism or materialism.

And making the case for Intelligent Design across a number of sub-disciplines of biology, showing how Intelligent Design provides superior explanatory power to a number of the phenomenon that we’re looking at—whether in the fossil record or genomics or at the level of molecular and cell biology. So, it was quite a stimulating week! Yeah, we had a great time.

JB: It sounds like you did. Do you think there is a groundswell of support for Intelligent Design in the UK?

Stephen Meyer: There’s quite a number of both senior researchers who are working on ID-based research projects, some of which we’re supporting, and a number of younger people who are at the PhD and post-doc level.

Worldwide, including the UK, there’s growing interest. Part of it is, of course, derivative of the growing openness in evolutionary biology itself to alternative approaches. Which was in evidence at the Royal Society meeting and is the reason we’re talking this morning

JB: Let’s move on to the Royal Society. I can imagine in those particular halls the term “Intelligent Design” is almost seen as a dirty word, so what is it they’re actually talking about? How do you think this plays into your particular field of expertise?

Stephen Meyer: You kindly have had me on before to talk about Darwin’s Doubt, the book I published in 2013 and 2014. In the prologue to that book, I made a statement that some people have found provocative. I said “rarely has there been such a great disparity between the popular perception of a theory”—and I was talking about Darwinism and its actual standing in the peer-reviewed scientific literature.

I made the claim that if you look closely at the technical literature in biology what you find is world-class biologists very openly expressing doubts about especially the creative power of the central mechanism of Neo-Darwinism, the mutation, natural selection mechanism.

This has been going on for quite some time. Yet when the theory is presented publicly, or to the public in policy statements by august scientific bodies like the American Association for the Advancement of Science or, up until now, the Royal Society on your side of the Atlantic; or by popularizers of science like Richard Dawkins or Jerry Coyne, Neo-Darwinism is still presented to the public as a theory which is beyond doubt. Indubitable.

As you look at the actual scientific literature, nothing could be further from the truth. Not just in biology generally, but in the relevant sub-discipline of Evolutionary Biology.

What was extraordinary at the meeting at the Royal Society in November is that many of the scientists who have been raising concerns about Neo-Darwinism in the deep scientific literature were allowed to do so in a public forum that garnered quite a lot of attention in the scientific press.

Now it’s beginning to percolate through even into the popular press. I think the question that arises out of the Royal Society meeting is: After Darwin, or after Neo-Darwinism, what next? Because I really think the theory is dead. There are very few technical defenders of the theory now.

Jerry Coyne will still weigh in to defend. There was a man Douglas Futuyma, who’s written a popular textbook in the United States, also an old line Neo-Darwinist, raising objections to the proceedings.

But if you look at what’s going on in the technical literature in evolutionary biology, evolutionary theory, there are very few defenders of Neo-Darwinism. It was, after all, back in 1980 that Stephen J Gould said “Darwinism is dead, except as textbook orthodoxy.” I think that’s ever more evident today. Especially after this very important conference.

JB: We’re going to dig into that a little bit more. Thank you for joining us on the line to talk about your experience being there and what you think it means for the future of science and biology. Perry, welcome back to the program! How are you doing?

Perry Marshall: I’m great! It’s great to be here on your show from Chicago, and it’s an honor to be talking about the Royal Society meeting.

JB: Yeah, so it must have been quite fun to be going along to this august institution. What did you make of it, in general what was your reaction to walking those particular halls and being there in person?

Perry Marshall: If you didn’t really know the background, you didn’t know what was going on, you would say ‘well, scientists are disagreeing about stuff. So what’s new about that?’

But if you are in the field and you understand it deeply, if you can read the tea leaves, it was the Protestant Reformation of Evolutionary Biology!

This would have never happened five years ago. It speaks to the sea change that’s going on. In fact, to continue the metaphor, Denis Noble pounded his thesis on the door and said hey, this dog don’t hunt.

Neo-Darwinism really is in serious trouble. It’s past its expiration date. It’s no longer enough to wave a little magic wand and say ‘natural selection, natural selection’ because what living things do is so amazing, and they do it in real-time.

This is the thing—evolution has traditionally been this millions and millions of years type explanation, and you need all of this time. When in fact—Sonia Sultan, and maybe we can get to this later, but Sultan told about plants adapting in literally real time and passing immediate changes to their progeny in one generation.

If you understand that evolution is a constant, 24/7/365 feedback between environment and organism, and the changes in some cases are passed on immediately, then you have this completely different view of evolution.

I felt like Forest Gump being there witnessing this happen, because I understood what was going on. It was really amazing.

JB: That’s the thing, I suppose different people can take away very different impressions of these things. What may have been to someone as sort of slightly dusty, dry sort of academic discussion, for you, as you say, feels like a revolution quite literally.

You say this couldn’t have happened five years ago. What’s changed in five years to mean that suddenly the orthodox view of neo-Darwinian is being questioned in this way?

Perry Marshall: I was talking to Eva Jablonka, she’s a very respected researcher from Israel, who is part of the Third Way movement, and she said, “You know I’ve been fighting these guys for a long time”—and she really has. She’s been considered a heretic by the old-school Neo-Darwinist guys.

But she said “Look, it’s one thing if one person like me is saying epigenetics is a big deal. But it’s another thing if the nutrition people are talking about it, and the fitness people are talking about it, and the cancer people are talking about it, and on and on and on.”

Epigenetics has become a household word for people in fitness and health and that kind of stuff. Because the genome is very dynamic, even though your genes themselves don’t have to change.

Epigenetics is like software menus that get greyed out and switch certain things on and off, something changes, then that greyed out thing gets switched back on. This is what happens.

So it’s not just one thing, it’s also this pop culture aspect I referred to. It’s also the fact that we’re now sequencing genomes all over the place, and we’re seeing more and more clearly what goes on.

Even the basic practice of medicine, fighting disease, cancer, tumors, all that kind of stuff, demands a completely different view of evolution than what the Neo-Darwinists have always told us.

Denis Noble, the organizer of the conference, is a physiologist. And he’s super famous in the medical field for making the pacemaker possible. It’s heart research. When they were figuring out how the cardiac rhythm works, from knocking out genes and seeing how it affected the behavior of the heart, he determined empirically there’s no way the Neo-Darwinist version of how genes work is true.

This change is driven by the fact that the outsiders, the voices of people on the outside of evolutionary biology have gotten louder and louder. The irony is that evolutionary biology itself, the core of the field, has been the most resistant to evolving their knowledge of biology of anybody. Which is kinda funny I think, but it’s true.

JB: We’re going to come back to you in a moment, Steve. First things first, we should really just define what this current orthodoxy that’s being overturned in your view is, when it comes to the Neo-Darwinian view of evolution. Then we’ll get into some of the issues around Intelligent Design and obviously Perry’s take on all of this.

And also what some of the old school are saying, the atheists like Dawkins and Coyne. They’re saying actually this conference proved absolutely nothing: ‘Our neo-Darwinian view is still perfectly intact.’ So we’ll be coming back to some of these questions.

You can find us online as well Leave a comment underneath today’s program or find your way to the Facebook and twitter account @unbelievablejb or and get in touch that way. Tell me what you think about our subject today on the program. We’re asking what exactly happened to evolution at the Royal Society last November.

So as we continue this conversation, I’ll ask you gents to keep your comments as concise as possible as we go forward so we’ve got some good back and forth between you in the rest of the program.

Steve, Neo-Darwinian evolution. Can you kind of quickly define it, and quickly explain why in your view so much of the research in the so-called Third Way movement in biology is overturning that particular paradigm?

Stephen Meyer: Neo-Darwinian evolution is the evolutionary theory that relies mainly on the mechanism of natural selection acting on random mutations. It asserts that this mechanism has the creative power, virtually unlimited creative power, to make the transformations that are described by Darwin’s great tree of life.

So that’s two parts. The historical part is something referred to as ‘the pattern’ – the pattern of a tree, which describes the idea of universal common descent. That all organisms are descended from a single common ancestor. And that the branching tree of life was produced by the mechanism of natural selection acting on adaptively random genetic variations. That’s the process part.

The process and the pattern together form neo-Darwinian theory. The process being the mechanism of mutation and selection, and the pattern being the Darwinian tree, which depicts the history of life, suggesting that all organisms are related by common ancestry.

What was really interesting to me at the conference was that the opening talk by Gerd Müller, who’s one of the leading developmental and evolutionary biologists, was very clear in laying out what he called the ‘explanatory deficit’ of Neo-Darwinism.

Neo-Darwinism is sometimes called the Modern Synthesis because it emphasizes Mendelian genetics with Darwinian evolutionary theory.

  • Müller said there were three key explanatory deficits. One was the origin of phenotypic complexity, the phenotype being the expression of the genes in actual anatomical structures. Things like the origin of eyes, ears, and the whole body plans or body architectures for animals in particular.
  • The second thing he said was an explanatory deficit was the origin of phenotypic novelty. Genuine complex organisms and new forms of organisms like bats, which would have echolocation or interesting anatomical innovation.
  • Then third was what he called the non-gradual form or modes of transition. That is referring to the abrupt appearance of major new body plans and modes of biological organization in the fossil records.

So those were the three things that defined the crisis in Neo-Darwinism. We can’t account for complexity, we can’t account for novelty, and we don’t know why things emerged so abruptly in the fossil records.

JB: This is the drum you’ve been banging for a long time, especially in the book Darwin’s Doubt, which specifically majors on the fact that all these sudden body plans emerged relatively quickly in the course of history, in the Cambrian Explosion and so on.

So I guess you’ve been following this evidence for a long time yourself, but this is the first time you’re seeing it genuinely put on the table in this kind of a setting?

Stephen Meyer: Yes, in this kind of a public conference setting. It’s been publicly expressed in the scientific literature now for quite a while. I think it was refreshing, Perry and I shared this, that all of this is suddenly public.

I would qualify a little bit the way you phrased the question—I don’t think what’s driving this is the Third Way mechanisms that are being proposed. Whether those mechanisms solve these problems that were laid out by Müller is I think a very important question to address. Because I don’t think they did or do.

I think what’s driving it is actually the phenomena of biology itself. The fossil record, certainly, but also the kinds of things we’re learning about the primacy of information, digital information stored in the DNA and other forms of information; and epigenetic forms of information that are necessary to build the new body plans.

So if you want to build something that’s fundamentally new, an anatomical innovation, a novelty, you’ve got to have a lot of new information of various kinds to do that and the mutation selection mechanism does not seem to have that creative power for a whole bunch o reasons—ones I think quite intuitive to most people with a computer background.

If you’ve got a section of functioning code and you start randomly changing the zeros and ones, you’re going to degrade that information long before you ever get to a new operating system or program.

Yet Neo-Darwinism is essentially saying that random changes in a section of digital information can generate the new information you’d need to build new structures and new forms of life.

For lots of reasons, people don’t think that’s credible.

JB: I’d be interested in bringing you in at this point, Perry—obviously Stephen is saying it’s great that they’re pointing out the problems, we’ve been seeing those problems all along as well. Not sure that their answers though are up to much coming from the Third Way, as they’re called, biologist people like James Shapiro.

You’ve certainly looked at his work a great deal, and others too. Do you think that what is being proposed in terms of alternatives to Neo-Darwinian mechanisms are valid ways of looking into it, and whether the apparent intelligence in things like the cell and so on can be explained that way?

So what do you think? Do you think that the Third Way explanations are any good in their own way?

Perry Marshall: I think they are a really good start. I refer you to a guy named David Prescott, who Jim Shapiro talks about in his work. Prescott put a protozoan under stress, and it spliced its own DNA into 100,000 pieces, rearranged it and made significant changes to its physiology in a matter of hours.

Or, for example, experiments on symbiogenesis where they actually have gotten microorganisms to merge together in real time, a cell inside a cell. Symbiogenesis is the theory that the chloroplast, which every kid learns about in biology school, is actually a blue-green algae that merged with a plant cell.

It’s like a Starbucks inside a Marriott Hotel lobby. They’ve done experiments where they’re gotten cells to merge together like that.

Now, if you stop and really think about what’s going on–you can’t drop a Starbucks out of a helicopter onto the roof of a Marriott and have a beautiful coffee shop in the lobby the next day. There’s a tremendous amount of choreography that must happen between all the parts.

What we see is that living things actually do this. So I think these mechanisms that the Third Way people are advocating, which in my book Evolution 2.0 I refer to as ‘The Evolutionary Swiss Army Knife’, I think these mechanisms go a long way in explaining this.

I would make one caveat and ask for one element of amnesty. Because you can always find something that we haven’t explained well at this point. I would just say: part of the problem is that evolutionary biology has been running on the wrong set of rails for 70 years, and 90% of the scientists have been looking in the wrong places. Or else making up stories about natural selection to fig-leaf hide their inability to explain things.

I think now we’re actually getting on the right track.

JB: What’s your problem with Stephen’s perspective? I understand you don’t go down his road which is: Well, there’s some kind of design inference here, that these kinds of systems have to have information of very detailed level put into the system from outside in some way.

Do you not sort of go with that kind of particular way of looking at things?

Perry Marshall: Ten years ago I would have been solidly in Stephen’s camp. In 2005 I gave a fairly famous talk called “If you can read this I can prove God exists.” And I think I’ve got as good a God of the gaps argument as anybody, which is:

1) DNA is code

2) All the other codes are designed

3) Therefore DNA’s designed

I even have a 3-million-dollar technology prize for solving this, which is a very serious prize because we really are looking for a solution.

I used to use this as a God of the gaps argument. I am very reluctant to do that now. The reason why is, because gaps keep getting solved, and every time a gap gets solved – if you were believing in God for that particular reason, all of a sudden the rug got pulled out from under your feet.

But the other thing is every time one of these gaps gets solved, the universe itself becomes more elegant than it was before.

There’s a very important story where Isaac Newton worked out his math of all the planets, and he said “Well, the math says they’re going to wander off course after a period of time. So I guess God probably pushes them back in place.”

Laplace came along later, and he fixed the math. “No, you don’t need God to push the planets back in place, you just didn’t quite have the formulas right.”

I’m very reluctant to do God of the gaps when in fact living things and the universe and everything are so remarkable, they still demand an ultimate explanation. But I feel the Discovery Institute Intelligent Design approach conflates immediate mechanisms with ultimate explanations in a way that’s not very helpful.

I want to read you an email that I got from a scientist that illustrates this. He said to me:

“We both see the fault in the current paradigm. The art is to convince the bio-medical research community that there’s a better way. I’ve been struggling with this issue more than 15 years now. I’ve been publishing and chairing meetings both in the U.S. and Europe. My own sense is that there’s fear in the group that if they blink on the subject of Darwinian Evolution, the ID people will literally and figuratively eat their lunch. So the task is to switch to another paradigm while sustaining the existing one.”

He sent me that a couple years ago. I think that summarizes that the typical working evolutionary scientist feels is a threat to them doing their job.

JB: Okay, we’re going to take a quick break, then I’m going to let Stephen respond because you’ve said you don’t take the same approach that the Discovery Institute and people like Steve Meyer take. And I’d like to hear his response on this as well.

We’re asking what exactly happened to evolution at the Royal Society, at the conference in November that was titled “New Trends in Evolutionary Biology.”

Continuing to talk to two experts in the area—Stephen Meyer and Perry Marshall.

This week’s edition of ‘Unbelievable’ is brought to you in association with Premier Christianity Magazine. If you want to get a free sample copy of the mag, then do go online to Always loads of interesting features, interviews, articles, news, culture and much more besides. All brought to you as part of faith explored here every Saturday at Premier Christian Radio.

Right now we’re talking about evolution, biology, Christianity, and whether there’s a new paradigm emerging. And what happened to evolution at the Royal Society last November. Stephen Meyer of the Discovery Institute, who is well known as an advocate of Intelligent Design theory, joins me.

Steve’s books Signature in the Cell and Darwin’s Doubt have already been debated on this program. Perry Marshall is the author of Evolution 2.0: Breaking the Deadlock Between Darwin and Design, and in many ways is very enthusiastic about what happened at the Royal Society.

This was a meeting that really pushed forward and put Neo-Darwinism to the test. It was a discussion and conversation on how other ways of understanding evolution compare to the traditional, off the shelf neo-Darwinian perspective.

So, Stephen, in that last section, Perry’s saying for his money he doesn’t go down the route you take, the Intelligent Design route. What he says in the end, for him it is a God of the gaps type of argument, but when you close the gap your argument for God goes away.

In a way, there’s something to be said for the elegance of what is being discovered more and more in nature, which doesn’t necessarily mean that it’s just random, but that there’s something very interesting and peculiar going on.

What’s your take on this? Obviously you do think that Intelligent Design is the best of the explanations out there, for what increasingly people in the secular scientific world are discovering.

Stephen Meyer: Yeah, absolutely. We think the elegance that’s being discovered in living systems is evidence of design. We don’t think it’s a god of the gaps argument. [COMMENT #1] Mine is a best explanation based on our experience argument.

We’re not arguing for Intelligent Design based on what we don’t know, but we do know about the cause and effect structure of the world. Namely that large infusions of large information always come from intelligent agents, whether we’re talking about a computer program or hieroglyphic inscription or a paragraph in a book. Information is known in our experience to be produced by one and only one type of cause and that is intelligent agent.

Interestingly, Perry makes this same argument in his book, and it’s a wonderful part of the book. He lays out the case that all codes are created by conscious mind and therefore the code in DNA must have been created by a conscious mind.

He makes that point on page 192 of his book. That section of the book I agree with very much. In fact that is a design argument, it’s not a God of the gaps argument. So what he’s offering I think is not so much a Third Way, but rather a hybrid.

He’s comfortable making the case for design as the best explanation of the code in DNA at the point of the origin of the first life. [But I also offer a technology prize for someone who can solve chemicals-to-code. I believe the prize is winnable. –Perry]

But when it comes to biological evolution as opposed to chemical evolution, he thinks that these Third Way mechanisms are sufficient or promising enough, that we ought not consider design as an explanation after the point of the first life.

I part company there. I’d like to explain why.

I also think Shapiro’s work is extremely interesting, and it’s certainly cutting some new ground in biology. What Shapiro is talking about—and I discuss Shapiro’s work and five of the other Third Way mechanisms that have been proposed, these non-neo-Darwinian mechanisms of evolutionary change—in Darwin’s Doubt in two of the key chapters of the book.

What I show there is invariably what is going on is these new mechanisms either presuppose unexplained sources of information, or they simply don’t explain the origin of necessary information to get real anatomical novelty. In other words, there are limits on what these mechanisms can produce.

Take Shapiro’s work. He’s describing ways in which organisms respond in real time to environmental stresses. Then they produce a response in the way that either they express pre-existing genetic information, or the way they ramp up the mutation rate in very specific parts of the genome to explore possibilities that are already latent in the genetic information.

So what he’s talking about is a kind of pre-programmed adaptive capacity which he says is under “algorithmic control.”

That’s all extremely cool. It is very elegant the way organisms can do that, but the question that Shapiro doesn’t address is: where does the pre-programming come from? Where does that algorithm come from? There’s a higher level of informational programming at work that’s presupposed in this whole process that he doesn’t attempt to explain.

My concern about using this as an explanation for the whole of what we see in biological evolution is two-fold. First, you can’t really propose that all this information is already in all these different organisms, and every organism has its own preprogramming to respond in different ways according to its organismal needs.

I don’t think it’s plausible to say that all this information could have been front-loaded in the circular chromosome of the bacterial cell at the point of the origin of life. Clearly you’re going to need additional information at discrete points along the biological timeline. [COMMENT #2]

Just getting from prokaryotes and eukaryotes requires an extensive reworking of the whole system of storage of genetic information. But secondly, and I think this is really a key thing, this is one of the key problems, it is the problem of epigenetic information.

Not all the information to build a body plan is in DNA. DNA codes for building proteins, but proteins have to be organized into bio-synthetic pathways that would characterize different kinds of cells and cell types.

Different cell types have to be organized into different tissues. Different tissues have to reorganize into different organs.

And organs and tissues have to be organized into whole body plans. The information for doing that is not solely in the DNA. Higher levels of information stored elsewhere are required to organize all those different levels of the biological hierarchy. [COMMENT #3]

Shapiro is focusing on Natural Genetic Engineering, and has said he might get novel proteins out of this, but he’s not going to explain the origin of a body plan. And that’s the really crucial question biologically. Where did that higher-level invocation come from?

I don’t think these mechanisms really solve those problems. In fact I think that in principle they’re not sufficient to do so, because they don’t account for this higher level of organization that’s necessary.

JB: Just before we come back to Perry, this email he received which said basically they don’t want to open a door to Intelligent Design. They’re going to keep the Darwinian version in the textbooks until they’ve worked out what’s going on in reality, in the scientific research and everything. What’s your take?

Stephen Meyer: Well, absolutely, but that’s a statement of metaphysical panic. They don’t want to consider something that would take them outside of a naturalistic framework. [COMMENT #4]

By the way, that same panic was in evident at the meeting. At one point Eva Jablonka was under pressure from one of the old line Neo-Darwinists in her talk. The Neo-Darwinist said no, we don’t need to consider these alternatives. Eva said unprompted I’m not talking about God! God was the elephant in the room.

But an alternative perspective that you don’t like for metaphysical reasons is not a scientific justification for claims about the creative power of mechanisms that have yet not demonstrated that creative power. We need actual demonstrations.

I agree with Perry that this is really cool stuff, and I do think it speaks incredible elegance of organisms, but I don’t think it solves the problem macro-evolution.

JB: Okay let me come to you again, Perry. Firstly, do you agree that God was the elephant in the room with the people desperate both in the Third Way camp and in the traditional camp to make sure that no one gets wind of any idea that we’re talking about anything supernatural here?

And then we’ll come on to talk about what Stephen had to say about your particular way of looking at these issues.

Perry Marshall: There were a few moments where you got that impression. Definitely, the elephant in the room showed up a couple of times. For the most part, that wasn’t the case though. Because I don’t think that’s actually what was on most people’s minds.

So when this scientist sends me this email—see, I think that the Discovery Institute pits theology against science in an unnecessary way, and we have to pull apart two different issues.

There’s origin of life vs origin of species. Now origin of life, the truth is there’s not a lot that you can say about it that properly qualifies as science. It’s a big freaking mystery. We can come back to that later if you want.

But what the conference was about was: Where does all this new stuff come from? Now if you look at things like horizontal gene transfer and epigenetics purely as mechanisms and if you think of them the way you think of how a computer operates, Stephen is right.

However, there’s something that I want everyone to consider and it’s this: Stephen, a lot of people in the Intelligent Design community are information theorists—well, so am I. I wrote an Ethernet book. Now, if you want to create new information here’s what you have to do:

You have to be able to choose from two things, and it has to be a choice not a random accident.

So I’ll give you an example. If I have an existing dictionary, if I use random processes or just computer algorithms, I can’t really produce brand new language. However, with the auto-fill on my phone—I can text my brother. And right away when I open the text thing it says I-YOU-YES and I can select “you” and then CAN-ARE-SHOULD. And I can select “should” and then BE-DO-TALK.

So I’ve typed “you should talk.”

Now if I pick between those choices based on my environment, I can create novel information and novel structures. I would propose to you that a cell is something like a quantum computer with a linguistic engine, and it can respond to the environment and create something new that never existed before.

Why? Because it is not merely a mechanism, it is a self that is doing what it needs to do to maintain homeostasis and to survive and to thrive and to do whatever, to eat lunch or whatever it’s trying to do. [COMMENT #5]

I think this is what has been overlooked. Now this is going to make a Neo-Darwinist extremely uncomfortable. But if you look at what cells do, if you look at what living things do, it’s obvious that they’re doing something like this.

I would like to suggest to you that if a protozoan can rearrange its DNA into 100,000 pieces and not only still work, but actually be better off than it was before, and if it can do that in 12 hours, then what can happen in ten years or twenty years or a million years?

This is the approach I believe we should be taking with the Cambrian. Because if somebody says “I can’t explain the Cambrian, God did it, let’s go take a three martini lunch…” a scientist can’t get a paycheck for saying that.

Scientists are never running out of layers of the onion to peel, so I think jumping all the way to the elephant in the room is a problem.

I think having God as an ultimate explanation—Why are the equations symmetrical? Why is all of this so elegant? I think that’s a much better way to understand God, and it’s more in keeping with the way the classical scientists, Maxwell and Copernicus. It’s closer to how they viewed God.

JB: Do you want to respond to that, Stephen?

Stephen Meyer: You bet. Well first Perry’s own way of describing the process was revealing. He said “If I choose based on environmental conditions, I can create novel information” and all these computer simulations that are used to demonstrate the creative power of various evolutionary mechanisms invariably do so because of programming that’s been supplied in advance by the chooser, by the intelligent programmer.

So the kind of things that organisms are doing in Shapiro-type demonstrations are by Shapiro’s own accounting of these under algorithmic control—there’s a preprogramming in there.

I’d be very reluctant to go down the kind of nature mysticism and attribute higher order of conscious agency, let alone almost omniscient about environment, to a protist. And so I think that’s something that we to need caution against.

We’re not pitting science vs theology. We’re saying that science, and I mean good science, points to design. Therefore science may have implications that are friendly to theology, but this isn’t a theology-based argument.

We’re not arguing for God, we’re arguing for evidence of an intelligent agency or mind, based on our uniform and repeated experience, that it is to say, based on the same method of scientific reasoning that Darwin himself used in the Origin. Which is to look at our present knowledge of cause and effect and see what that tells us about what the most plausible explanation for the causes of events in the past might be.

Our present knowledge of cause and effect confirms, whether it’s in computer simulations of these generation of information, or origin of life simulation, you need a mind to generate new information. So I think that’s not what we’re doing.

Thirdly, as far as the scientist deriving their paychecks. The most important obligation that the scientist has is to find the truth. It is simply that we want to find the truth first and foremost, but it is a matter of the heuristic value of different scientific approaches.

We think Intelligent Design has tremendous heuristic value, that is to say it can lead to new discoveries. If you infer that design was at work or an intelligence was at work in producing a system, you’re going to look at it differently.

For example, we predicted very early on that the junk DNA was not junk. We did that on the basis of an ID perspective. The neo-Darwinians thought that the non-coding regions in the genome were the natural, expected result of random changes accumulating the flotsam and jetsam of the evolutionary process accumulating over time.

It was just what they expected—that 3% would be functional the rest would be residue of the trial and error process.

We’ve looked from an ID perspective said the opposite. We said: “Look, we accept that mutations are real processes, but we wouldn’t expect that the signal should be dwarfed by the noise. So we expect to claim function in that allegedly non-functional region that vast allegedly non-functional region with genome.”

Lo and behold, over the last ten years, and especially with the publication or the Encode Project, our ID perspective has been borne out. And in fact Jim Shapiro, one of the scientists who was writing papers with him on this, gave credit to Rick Sternberg. He said Richard Sternberg, formerly of the Smithsonian, and one of our ID colleagues, was the first guy to see this.

And Shapiro said so in the Huffington Post of all places. That’s just one of many examples where ID has heuristic value. It anticipates certain things: You’re going to get in, you’re going to look at it, you’re going to try to figure out: What is the functional logic? What can I be expecting to find here that’s going to make this work in accord with a rational plan?

So we think this is the science-stopper, but it’s a science-starter.

JB: We’ll leave that just there for the moment. I do want to, excepting that obviously I’m sure Perry would want to come back on that, maybe we’ll get time later on. I do at least want to bring in the perspective given by someone who does still hold to the neo-Darwinian perspective on evolution.

Jerry Coyne wrote a blog about the conference in which he concluded by saying:

Modern evolutionary theory is not in trouble, far from it. Maybe sometime a new paradigm will come around, but this isn’t it. The noise we heard from London, outside a few papers from people like Douglas Futuyma (a textbook author in line with Coyne’s view) is the noise of Templeton’s prize horses jockeying for money and fame.

He’s got a thing about how it’s all the Templeton Fund that is basically funding the people who are putting these alternative theories forward. But just to pull out some of what Coyne says in the blog, to kind of back up his points.

For instance, when it comes to plasticity, which is this idea of organisms adapting in real time to their environment, which you’ve been saying, Perry, is a classic example of the way the neo-Darwinian paradigm can’t account for these things. Coyne says:

As is well known, organisms can change their appearance, behavior and physiology depending on their environment. Some of this is simply a shock response, with no adaptive value, while other forms of plasticity are evolved adaptations that reside in the DNA—cats grow longer fur when it’s cold, or rotifers develop predator-deterring spines when put in water with fish odor, etc. but the new paradigmists say that non-adaptive plasticity can actually initiate an adaptive evolutionary change. It’s really not clear how this would happen.

And I’ve heard this similar kind of thing from others, saying this doesn’t show that Neo-Darwinism is false, it just shows that there’s more stuff going on. There’s stuff in the organism that’s ready to adapt when it happens.

But the Neo-Darwinians say that very ability to adapt is a result of the standard neo-Darwinian process. Which makes them suitable for being able to adapt quickly in that kind of real-time way.

Later he gives an example of a conversation that took place between Denis Noble and David Shuker.

There, Shuker says of a particular experiment, that the conclusion of the experiment was the scientist saying “our results demonstrate that natural selection can rapidly rewrite regulatory networks.” So they say it’s a perfectly, beautiful example of rapid neo-Darwinian evolution.

There’s a lot to get your head around there. I hope those at home are following along! But essentially it boils down to people like Jerry Coyne who absolutely disavow anything that might even smell of something supernatural. And I think they think this stuff smells a bit supernatural, saying it can all be accounted for in the end by what we’ve always known and loved. Which is the neo-Darwinian synthesis.

Perry Marshall: Natural selection only explains that things die. When somebody says natural selection rewired that microorganism, that is non-explanation. Somebody explain to me how natural selection rewires a bunch of genes!

And, by the way, he’s talking about an experiment where they deleted the genes for a bacterial flagellum, and four days later the organism had rebuilt those genes, presumably by restructuring information from the regulatory networks. And then the bacteria grew tails and they went back to swimming and finding food. They did this in four days.


Well, what a Neo-Darwinist will always say is “Oh yeah, well natural selection did that.” Well natural selection is not a creative mechanism. Natural selection is when things die and other things stay alive—that’s it!

This is what they do, and so yes it’s not clear how. So the Neo-Darwinists want to say “well, randomness did that.” Randomness does not do that.  I’m an electrical engineer, I know this, okay?

Then on the other side, you have “well, God did that,” but when you come to something like the Cambrian, you come down to either God injected new species or new information and did some kind of a divine thing… or else the organisms did, because cells are in some sense intelligent. The organisms did this.

The thesis of Evolution 2.0 is: Darwinists underestimate nature, and Creationists underestimate God. I would put the ID / Discovery Institute crowd in that same camp. Stephen, I propose to you you’re underestimating what Life is capable of, and whether life itself is a literal, divine miracle, or if it’s actually the way it is because the universe is tuned to a million decimal places instead of 120.

Whichever explanation it is, I really think, Stephen, that you’re underestimating nature and you’re doing so in a way that takes a job away from a scientist.

JB: Go ahead, Stephen.

Stephen Meyer: Investigative journalists are told to “follow the money.” Biological scientists and computer scientists interested in biology follow the information.

The reason these changes can happen so quickly was alluded to in Perry’s own words. He talked about the restructuring of the information in the regulatory network. That doesn’t happen magically. It’s not happening randomly.

Shapiro’s right, if it were happening randomly it would take a whole lot longer than it’s happening. The only reason it can happen that quickly is that there is pre-existing programming, pre-existing algorithmic control, pre-existing information that’s making that restructuring possible in response to an algorithmic if-then subroutine.

The organism gets a signal from the environment, it says I need to restructure my genome in accord with the needs I have for survival. That ability to do that is pre-programmed. That’s the locus of the design inference. Where does that pre-programming come from? It’s not mysticism, it’s not magic, there must be information there.

So the locus of design for us is the origin of the information that makes that process possible.

Shapiro doesn’t address that question, Perry doesn’t either, and for that reason I don’t think we have a Third Way here, I think we just have people who are not addressing the fundamental question of the origin of information after the key question of the origin of life.

I love what Perry says about the origin of life, it’s absolutely right. But that question of the origin of information doesn’t go away as you ascend up the biological hierarchy.

There are new informational needs if you’re going to account for the origin of your organs, tissues, complex molecular machines, and especially whole body plans such as you find in the Cambrian.

I’ll again repeat the point that you can’t get higher-level body plan structure out of genetic information alone. So when you have these mechanisms like horizontal gene transfer or natural genetic engineering, they’re not going to give you that level of complexity.

At best they’re going to give you some new proteins. So there are real limits to what these mechanisms can do. They’re demonstrable. It’s really cool science, I agree that it’s a necessary amendment to Neo-Darwinism; I understand why Coyne and others are upset because they are being passed by; but I don’t think the Third Way solves the information problem.

That’s not a matter of God of the gaps or anything else, it’s a matter of doing some fundamental science and tracing the information flows. If you trace them back to your source, you get the singularities where no evolutionary mechanism accounts for the origin of the programming as necessary.

JB: Really interesting discussion—Dr. Stephen Meyer, who is of course part of the Discovery Institute, one of the leading voices in Intelligent Design theory. We’re talking about this recent Royal Society conference that happened here in London. Has it overturned the neo-Darwinian view of evolution?

It is the beginning of a revolution as far as my other guest Perry Marshall is concerned as well. My guests, though, disagree on what the essential implications of that are for Intelligent Design Theory, or whether there are other ways of explaining the origin of these adaptive features of nature and cells and so on.

Perry Marshall’s book Evolution 2.0 is very much along those lines. We’ll be hearing him again defend his thesis that you don’t have to go down the Intelligent Design route to see that there is an elegance and there’s something that may be derived from God, but not in a strictly direct way.

I’ll be interested in pressing into that a bit with you in a minute, Perry, as well. And we’ll see what you have to say as well—don’t forget that your thoughts are welcome as well in regards to what you hear on today’s program. You can email [email protected].

I’m here with Stephen Meyer of the Discovery Institute, well known as an advocate of Intelligent Design theory. Perry Marshall, author of Evolution 2.0, a book which very much delves into some of the issues we’ve been uncovering, around whether the neo-Darwinian framework for evolution has been kind of finally upended by the work of people like James Shapiro, Gerd Müller and others who were present for this particular conference.

It’s provoked quite a bit of backlash as well among those who are still holding to a strict neo-Darwinian view of things. We heard about Jerry Coyne’s blog a little bit earlier one. But, generally speaking, Perry, when it comes to this, I’m hearing lots of excitement from different angles.

It’s come up in conversation on different editions of Unbelievable. We’ve had Doug Axe, a colleague of Stephen talking about the conference, who was there as well. Then in a recent edition of the program Wayne Rossiter, who has also published a book critical of the neo-Darwinian view has been talking about the fact that this seems to represent a new front in scientific discovery.

As I’ve said, a lot of people think the most obvious root that this points to is Intelligent Design of some kind. I think a lot of people struggle to differentiate what you’re talking about in your book from Intelligent Design.

I think as Stephen has put it quite well, you seem to agree to some extent on the DNA, the first life first coming into existence seems to have a precursor in Intelligent Design. But he says you know at the end of the day you can’t get away from the inference to intelligence as well—with all of these mechanisms you’re talking about, there has to be information put into the system. Even if it’s kind of there in the cell and it’s acting on some kind of algorithm that makes it respond to the environment around it.

Someone’s got to be putting in the information in that makes that possible. In the end I guess he’s saying, Perry, “You’re just as much an Intelligent Design advocate as I am,” so what’s your response to that?

Perry Marshall: The origin of information problem has not been solved. This is why I have a technology prize. I think there’s key difference though. I advocate intelligent design, lower case “i” lower case “d” in the broadest sense. That the universe is an amazing place and it speaks to something even more amazing than that having created it.

But, again, I’m extremely reluctant to make God of the gaps arguments.

JB: So how do you solve these problems? Or what framework do you propose?

Perry Marshall: Well, here’s the framework that I propose—I propose that the cell is an agent. There’s a wonderful book by Bob Lanza called “Biocentrism” which makes an extremely robust case that the universe is a consciousness first, matter second phenomenon. Not the other way around.

I would like to suggest to the Intelligent Design community that if you want to defeat to scientific reductionism (which I agree needs to be done; science is not reductionist and biology is not reductionistic) then what you need to do is:

Instead of fighting macro evolution, you need to embrace it. Because what we don’t know is how smart those cells actually are.

A bacterium can do more software engineering in twelve minutes that a team of Google engineers can do in twelve weeks. This happens all the time in your body. That’s why you have to finish your antibiotics, because if you don’t kill those suckers dead, you’re in real trouble.

I take the position I take, because if I take the old school Neo-Darwinist position I will lose market share every year as more and more things turn out to be orderly instead of random.

If I take the creationist or Intelligent Design / Discovery Institute position, I will lose ground every year as they explain more and more evolutionary steps with observable processes.

But if I take the Third Way view, my market share will grow and grow because the explanatory power of an integrationist, non-reductionist paradigm which also considers consciousness.

This can in principle explain what’s going on at the high level, but it gives a scientist something to actually do. So I’m making a predication that over time we are going to continue to explain more and more of the developments in taxa from species… and everything like that.

I think the next 20 years are going to be fantastic, and I think people in technology can learn a tremendous amount from biology.

JB: it’s always fun to hear you speak, Perry, because the terms you use, the analogies often do come from both your technical background and your marketing background. In any case, it’s been great having you on the program. I’m going to finish up with Stephen now.

Stephen, thank you very much for being on the program today. I’m going to post links from today’s show to both of your websites and indeed from the posts that have come both from the Discovery Institute and from Perry himself with the different responses that you had to what this particular conference meant.

You’ve heard why Perry feels in the end Intelligent Design, which is sort of lumped in with creationism, doesn’t offer a satisfactory overall explanation. For him there’s something about the nature of the universe, the way that everything is done in such a way that these cells can have almost their own consciousness almost, it would appear. That doesn’t sound like the route you particularly want to go down, Stephen? You seem to be saying no…

Stephen Meyer: Well, yeah I think that’s actually another form of Intelligent Design—he wants to attribute agency, conscious agency in fact, an almost omniscient form of conscious agency to the bacterial cell itself. So really the question is the locus of the intelligence. [COMMENT ON “OMNISCIENT”]

If you want to get information you’ve got to have intelligence. Perry makes that argument very concisely in his discussion of the origin of life. He’s applying it in an interesting way when you get to higher levels of biological evolution and imputing the intelligence to the biological cell or organism itself.

I have just a little thought experiment for your audience. I think most of us would agree that we’re smarter than bacteria, [COMMENT #6] but we in our conscious minds have no idea how to respond to various environmental stressors to rewrite our DNA to express different proteins under different circumstances.

So if this isn’t done by our conscious awareness, [COMMENT #7] then there must be some pre-programming that is enabling the cell or the organism to do this. I think that’s what’s really going on. In fact, I think a lot of experiments that we’ve done already show that such pre-programming is present. In fact that’s what Shapiro himself says.

So really the question is the origin of that pre-programming. I think it would be a mistake to impute higher consciousness to a bacterial cell. I think that would take us down the form of a kind of nature mysticism, and you don’t need that in order to do exciting scientific research.

We had a terrific scientific meeting the day after the Royal Society with all kinds of great research projects. Let me tell you about one that’s relevant to cancer research.

There’s a problem in evolutionary theory known as the Waiting Times Problem. That is, you can actually quantify the number of coordinated mutations that are necessary to build certain types of structures. You can also quantify how long we should have to expect for those coordinated mutations to take place.

Our ability to treat cancer actually exploits the cell’s evolvability limits. Unhealthy cells are often treated by a cocktail of drugs which exploit the fact that cells can only produce only certain coordinated mutations in a given amount of time.

So the kind of research we’re doing, actually quantifying those waiting times, could be very useful in cancer research. It’s actually predicated on an understanding that there are limits to what evolution mechanisms can produce.

I think when we examine not only Neo-Darwinism, but these Third Way mechanisms, we’re seeing clear evidence of limits as well as their capabilities.

So mapping where those boundary lines lie is a crucially important part of understanding what happened in the evolutionary past, but it’s also crucially important to addressing disease in the present, like cancer and antibiotic resistance. Both of which I think can be addressed by these drug cocktail approaches, which presupposed that there are limits to evolutionary change and what evolution mechanisms can produce.

I don’t think that this is a science-stopper, I think that’s a red herring. I think ID, if you look at systems as design there are lots of things to explore, including the functional logic and that has led to a lot of cool discoveries.

I’m on the same page with Perry on Neo-Darwinism, I think it’s dead. I’m on the same page with him with a lot of elegant new mechanisms and new processes that are being discovered, but I don’t think the mechanisms that are being proposed by the Third Way folks solve the problem of macro evolution, and I don’t think design is a science-stopper.

It’s not only a good explanation of the informational properties of life and the informational infusions which we see through the history of life, it also opens up a wide vista of new research projects, some of which we’re actually funding at the Discovery Institute.

JB: I was going to say, as much as you have obviously disagreed in certain respects with Perry you both share that same view that Neo-Darwinism is dead, and that scientism is also on the way out as well because of that.

Stephen Meyer: We share a lot including a common metaphysical perspective. I think a lot of what’s driving Perry is what he was talking about with “market share.” How do you position a more theistically-oriented way of looking at the natural world to get people who are atheist or agnostic to take you seriously?

I think at the end of the day you have to set those things aside and say what is nature telling us, and then develop an understanding of both the origin and development of life is consistent with the evidence.

JB: Perry, just finally, obviously you may want to pick this up, I’m sure you will, on your blog again, once this conversation airs. But how long do you think it’s going to actually take for the textbooks to catch up with where the actual science is? I mean, do we have to wait for the old guard to pass away and for these bright new folks like James Shapiro to be the ones writing these textbooks?

Perry Marshall: I’ve always loved the phrase “science advances one funeral at a time.” But I think this is going to happen a lot faster, because of the internet and the information age. I don’t think five years from now a textbook that’s still banging the Neo-Darwinian drum will pass muster.

This is like the Berlin wall. It is going to come down very fast. Those of you who remember when communism fell, it only took two or three years. This will be like the Berlin wall where once it went down, one communism started tumbling, I think we’re looking at 3-5 years before there’s a complete paradigm shift. Not only inside the sciences, but in the pop culture. This is going to be fast not slow.

JB: Thank you both Perry and Steve for joining me on the program today. As I say, do check out the Unbelievable page in order to find links to both of their websites, their books and the articles that have both come out with different responses from both camps to this very interesting Royal Society conference that took place at the end of last year. But for the moment, Perry and Steve, thanks for joining me on the program today.


Perry’s Comments on the Program

COMMENT #1: “The Cambrian explosion wasn’t caused by naturalistic evolution, it was caused by Intelligent Design” or “Origin of life was an act of Intelligent Design” are by definition God-of-Gaps arguments.

The Discovery Institute can claim it’s not a God argument, and instead say it’s an information and intelligence argument, but at the end of the day, if it’s not from the innate capacity of the cell or some process we can model, observe and describe, then it’s supernatural. Just because intelligence is “inference to the best explanation” doesn’t make it not a God-of-Gaps argument. It’s still God-of-Gaps.

Creationists and ID advocates have been telling me for years that there’s no evidence for macro-evolution; they believe God intervened and created new life forms. But I’ve been pointing out for years that macro-evolutionary events are plainly observable in real time. You can get a new species in years, months, sometimes even days.

I fully understand that how cells got to be so smart is a HUGE unanswered question. I agree that information always infers intelligent agents. And perhaps God is the answer. But my position is that living things are agents too and we can and should trace the progress from one evolutionary step to the next. I invite you to consider that the capacity cells have to evolve is a far more impressive miracle than, say, God beaming Zebras on to the savanna Star-Trek style where they suddenly appear eating grass.

If Bill Gates developed DOS in 1981 and then DOS evolved into the Windows 10 of today, with NO programmers from Redmond Washington – if DOS self-organized its own Windows desktop, internet connection, web browser, Word, Excel, anti-virus software etc., without any human engineers, how much more would you respect Bill Gates and his team?

At the risk of stating the obvious, no software I’ve ever heard of does this. But life does.

As a Christian I’m not opposed to miracles at all. I’ve been in the room twice when people who were deaf for 30+ years got their hearing back. But as an engineer I observe that living things do something every day that’s more “miraculous,” if I may use that term, than creatures magically appearing. They evolve. It’s just like if DOS evolved into Windows all by itself. Organisms evolve in real time.

It’s the biggest untold story in the history of science and the Neo-Darwinists have completely missed it. The creationists and the Discovery Institute have completely missed it as well. You would never know from reading a Richard Dawkins book or a Stephen Meyer book that you can get a completely new species in two years, and maybe even two days, from symbiogenesis or hybridization. Or that you can witness a radical innovation from a single cell in just 12 hours.

Neo-Darwinism is about miracles of randomness which can never be quantified or demonstrated. It’s the biggest mistake in the history of science. And despite Meyer’s insistence to the contrary, Intelligent Design is still God of the gaps. The two are symmetrical. Neither offers you a mechanism that qualifies as empirical science. Neither helps the scientist do his real job, which is to explain every evolutionary step in reproducible detail.

And neither is telling you the REAL story – that organisms possess tools of Natural Genetic Engineering and freedom to evolve on their own. It’s the purpose of my book Evolution 2.0 to tell that story.

COMMENT #2: We currently have no idea how to get from chemicals to code. Many people assume time and chance would eventually produce life, but there’s no hard evidence this is true. All we know for sure is that life comes from life. Yes, life and its ability to evolve is incredibly impressive.

But the immediate practical question is, what do cells know that we don’t?

I do not believe you can simply “pre-load” any algorithm into a cell that would know how to handle all the situations bacteria adapt to. Barbara McClintock’s 1984 Nobel Prize paper was precisely about how organisms respond to shocks for which they are not prepared (and could not possibly be prepared for, because that particular shock had probably never happened before in the history of life.)

Stephen Meyer’s interpretation of adaptation is that it’s algorithmic. That’s a very useful word; it’s far more accurate than “random mutation and natural selection.” But it’s also a limiting word. Cellular adaptation is more than that. Cells adapt in ways that seem to have the appearance of being self-aware. If you wish to call it an algorithm, you’ll need to think of it as a living algorithm. Something altogether superior to what computers do.

COMMENT #3: So far as we know, most information for a body plan is not contained in the genome, it is somehow transmitted from parent cell to daughter cell via cell membrane. The most interesting work I have seen on this subject is Stewart Pivar’s book On the Origin of Form where he shows how complex body plans can be derived through straightforward manipulation of simple geometrical shapes. Genes control the proportions of the body plan, but do not define the shape itself. His is a beautiful and elegant model.

We have very little knowledge of the evolution of body plans, but my money’s on locating beautiful, elegant, natural processes by which body plans can experience radical changes. We are quite confident for example that the step from invertebrates to vertebrates involved a genome duplication, and the step from vertebrates to jawed vertebrates involved a 2nd genome duplication. This is called Ohno’s 2R hypothesis.

COMMENT #4: I don’t think Eva Jablonka’s “it’s not God” is metaphysical panic. It is resisting the temptation to make Isaac Newton’s mistake, which was introduce God as an interfering agent instead of finding the flaw in his math. I’m a Christian and I’m not against God at all, but it doesn’t serve science to see life’s history as a series of divine singularity events nearly as well as it serves science to see life as the outworking of a process that’s baked in from the beginning.

When we read Psalm 139 where it says, “For you created my inmost being; you knit me together in my mother’s womb,” in the 21st century we do not read that and say, “God is actively attaching arms and legs to that baby in mama’s tummy.” We know there is a completely natural process by which that happens (an utterly AMAZING natural process, by the way). This does not take anything away from the wonder and joy of a newborn baby.

A few weeks ago at dinner, a renowned infertility doctor from New York City was expressing to me his utterly astonishment at the sophistication of first few minutes of embryo development in the womb. “We know nothing!” he exclaimed.

If we assumed fetal development was based on divine intervention, that would hinder the progress of medicine. Likewise, if we assumed it were just “random” that would also stop us from understanding it. So I see evolution as a macro-macro version of what is happening in the womb – an outworking of a process that is intrinsically self-directing and perhaps even self-aware.

The approach the Discovery Institute is taking – which says macro-evolution is impossible and requires divine intervention – would probably never produce a researcher like Lynn Margulis, whose magnificent detailed work showed that symbiotic evolutionary relationships are at work in every single level of life, at multiple layers.

Many ID people might still be skeptical that a blue-green alga could become a functioning chloroplast in a plant cell. And it is discoveries of this kind (remember that symbiotic mergers have been produced in real time) that the anti-common-descent position is most in danger of overlooking.

COMMENT #5 Barbara McClintock asked the question, “What does a cell know about itself?” and I believe that is one of the most important questions in all of science. The answer is, we don’t know. But if you read a book like “What a Plant Knows” by Daniel Chamovitz or “The Hidden Life of Trees” by Peter Wollebehn or “A Feeling for the Organism,” Evelyn Fox Keller’s biography of Barbara McClintock; or “Acquiring Genomes” by Lynn Margulis; or James Lovelock’s seminal book “Gaia,” you begin to realize the living world outside of humans is almost infinitely responsive, cooperative and self-directing.

COMMENT #6: Stephen Meyer says “I think most of us would agree that we’re smarter than bacteria” and yes, most of us blithely assume this is true.

I wish to challenge that assumption. A protozoan under stress can make 100,000 edits to its genome in 12 hours and re-structure its physiology, suddenly able to digest a nutrient that it couldn’t before.

Do you know any software dudes who can re-arrange 100,000 lines of code in 12 hours and not crash the program?

I invite the reader to consider that cells possess a savant-like genius, if you will, and that they are in some sense far smarter than we are. Look at a banana peel and consider how elegant of a packaging solution that is. It’s lightweight, it’s biodegradable, and it does its job quite well, thank you very much.

Then take a walk to the back of your house and look in the trash can at all the man-made packaging. Are you sure humans are really smarter than bananas? Depending on your perspective, the bananas may be smarter than us. Cells are better programmers than any human engineer.

COMMENT ON “OMNISCIENT”: I would never suggest that nature is omniscient. I am suggesting that nature is very much smarter than most of us assume it to be. As evidenced by the fact that a protozoan can do more programming in 12 hours than a team of Google engineers can do in 12 weeks.

Anyone who has done software programming knows that completely random mutations NEVER produce better programs. Not in the real world. And today we know that evolutionary mutations in biology are not random. They are highly organized and follow specific structures, as visionaries like Barbara McClintock and Lynn Margulis showed.

Organisms are making their best guesses as to what adaptation is going to work best. Most of the time they fail. Some of the time they succeed.

When I say “best guesses” that’s precisely what I mean. I have tremendous direct experience with natural selection, because I wrote the world’s best selling books on both Google advertising and Facebook advertising. Online ad platforms are highly Darwinian environments where 2% of the advertisers get 50% of the clicks.

Competition is brutal. Google and Facebook are giant natural selection machines. Millions of businesses succeed or fail based on their ability to get those clicks. Online advertising is a 24/7/365 evolutionary competition.

When you create ads, you never know in advance what is going to work best. You have to just put a lot of stuff out there and you A/B test it out. The marketplace (selection) is the final arbiter. When organisms are under stress they massively re-arrange their DNA and they are doing the exact same thing entrepreneurs do when they design new businesses and new products and put new ideas in the marketplace.

Keep in mind that business is just an extension of biology. Business is how all of us eat. Also notice that selection all by itself doesn’t create anything at all. The advertisers generate the new information, and the best way to create that information is to derive your ideas through feedback from the environment. This is exactly what cells do.

Nobody who succeeds in advertising or business succeeds because they’re omniscient. They succeed because they test a lot of stuff and because they have a protocol for testing a lot of different things. I observe in biology the exact same things I see in business. It’s worth noting that many of Darwin’s ideas about natural selection came from the Reverend Thomas Malthus, who developed his ideas by observing business and economics.

Which is to say evolution works the exact same way in all spheres, whether biology or marketing or economics or technology. Evolution is chaos resolved by intent.

COMMENT #7: Stephen, how do you know cells don’t do this by conscious awareness? What if they do? What if there are multiple kinds of consciousness? Consider our own human reflective self-awareness. What we are conscious of is always a tiny fraction of what is actually going on.

While you are eating a sandwich, your subconscious mind is processing massive amounts of other information. It controls your heart and breathing and your standing and walking or driving, without you having to pay any attention. Then if a truck suddenly careens around the corner and is about to run you over, your subconscious mind will immediately bring it to your attention so you can react.

But even that pales in comparison to what our bodies do. Every organ in your body organizes an almost incomprehensible information on the level of cellular intelligence. (Even if you’re in a coma!)

Your body does far more on its own than your brain does for your body. I am asking the reader to consider that the process of evolution is fueled by this form of intelligence. Most people have not even begun to consider the implications of this, but I’m merely observing what cells actually do in real experiments and in real life.

This is the thesis of Evolution 2.0: What do cells know that we don’t? If we find out, we stand to achieve staggering progress in health, medicine and technology. Every doctor needs to know. Every nutritionist needs to know. Every software programmer needs to know.

I don’t think we’ll ever stop finding new subatomic particles. Similarly, I do not think we will ever reach the bottom of the cell’s capabilities. I believe that within the vertical category of systems within systems in biology, it’s “turtles all the way down.” I suspect that cellular behavior goes all the way down to the quantum level.

There are more and more levels yet to be discovered. Only by embracing macro-evolution as a supremely ordered, goal-driven process will we find them.


You may also enjoy listening to Perry’s debate on Evolution 2.0 with atheist biologist PZ Myers on Unbelievable.

It’s the opposite side of the ID coin – instead of arguing for the power of God, PZ argues the Darwinian doctrine of randomness.


Download The First 3 Chapters of Evolution 2.0 For Free, Here –

Where Did Life And The Genetic Code Come From? Can The Answer Build Superior AI? The #1 Mystery In Science Now Has A $10 Million Prize. Learn More About It, Here –

85 Responses

  1. Mark Kroger says:

    Hi. Thanks for letting me share my views.
    Asking the questions of who did it, when it was done and why it was done is philosophy, not science. We all choose a narrative to interpret the data to validate the narrative. Science applies the litmus test. Truth always shines brighter under cross examination by an opponent of the narrative and all other narratives collapse as their circular reasoning impossibilities are exposed.
    I have a 23 page paper: “The Science of Context: Comprehension through the Lens of the Integrated Whole.” The natural world is an integrated environment in operation, in whatever direction we look, at whatever depth we look. Whether we are comprehending context driving format/character base or interdependencies enabling environments to function or purpose, we see trying to study it linear sequence from the bottom up, the context driving the interdependencies to function/purpose is hidden from view.
    I favor physiology and love study how we require specific biochemicals-nutrients for the body to do the wonderful things it does. The law of entropy is the prevailing law of any integrated environment so preventing entropy has to be an active process.
    How do biochemicals talk to biochemicals? What determines the response/reaction? In computing, ones and zeroes do not talk to ones and zeroes, which is what we would see if we were attempting to view from the bottom up. It’s the context integrated in and driving interdependent formats that give the appearance of ones and zeroes talking to each other.
    Computing is “Integration of thought in a static structure creating a virtual environment. The context is not the OS. In PCs, it is because Intel and Microsoft engineers pre-integrated a number of hardware/software interdependencies that make the OS useable and enablement of the integrated whole possible.
    When a cell gets a request to build one of 20,000 plus proteins, it is not for a 2nd messenger system, helix unfolding, unzipping enzyme, Transcription/Translation/Fold enzyme seal. It is for a function specific protein. The subroutines of the build is context driven programming.
    The pancreas makes two protein digesting enzymes if activated inside the cell would digest it, so they are not activated until they get in the stomach. We see those interdependencies in whatever direction we look, at whatever level we look. Yes, God did it. And if we ever want to build an Exact Science, we don’t have to discuss religion, but we have to stop trying to force fit a narrative that says He didn’t.
    Just my take. :-}} Have a great day!

  2. T. Q. says:

    My apologies if I’m misunderstanding your position. The Swiss Army Knife is a timely concept, I think, bringing together some poorly advertised biological processes. It sheds some light on the power of microevolutionary mechanisms and is more realistic than the neo-Darwinistic picture. But it ultimately shares a problem with neo-Darwinism. I will tell you why I’m skeptical of the Swiss Army Knife as an explanation. I’m a software engineer who has been looking at complexity measures for several years. It is no small effort to create something that can evolve even through such elaborate mechanisms, and it begs the question whether material causal forces explain the existence of such elaborate mechanisms. How do you get something that can evolve this way without design? And it just as questionable whether a combination of said mechanisms is any more sufficient to the task of innovation. While it is more plausible than neo-Darwinism on the surface, it isn’t clear that this Swiss Army Knife is capable of doing anything more that making various species capable of accessing a pre-programmed repertoire of adaptations. You can pass algorithms back and forth between computer programs, but it takes a thoughtful effort to integrate and make imported code useful. Catching a living thing red-handed in the act of appropriating another organism’s solution only begs the question.

    When I say ‘complexity measures’ I mean things like ‘effective complexity’, ‘facticity’, ‘sophistication’, ‘computational depth’ and the like. How does one show in terms of information science that innovations of great computational depth happen as a matter of course? It’s not something that is merely counter-intuitive. It seems like arguing that because a refrigerator obeys the laws of thermodynamics, there is no reason to think that a “natural refrigerator” should not occur through chance. “Yes, innovations in cellular life are explained by the fact that cells are innovation-making machines!” seems to be begging the question in the worst way. Can innovation-making genius cellular agents be said to be explained by accidental processes by virtue of their existence in the natural world? And is the innovation-making they are programmed to do sufficient to explain “indefinite departure from the original type”? That would be a pretty grand claim. -tq

    • TQ,

      Use your full name. These are all great questions by the way.

      Of course you don’t get something like this without design.

      We’re not talking about stumbling around in the woods and finding Paley’s watch. We’re talking about stumbling around in the woods and finding a watch factory that makes self-improving watch factories and make still better watch factories – and yes watches. And then realizing the woods itself is a self-improving watch factory factory.

      And I’m not merely talking some fantasy here, because if you go deep in to the less publicized literature – I would particularly refer you to the work of Barbara McClintock, Lynn Margulis, James Shapiro and Eva Jablonka, you’ll find that living things really do all this stuff and more.

      I’m not suggesting this happens by accident.

      I’m suggesting that there are laws and principles in biology and possibly physics that we are only barely acknowledging, let alone understand.

      And NOTHING about any of this takes anything away from God. Rather it makes the universe even more fine tuned, it strengthens the anthropic principle even more if you like that terminology.

      And where did I ever say anything about this happening by chance? Or “accident”?

      There is nothing about evolution that is random or accidental when you get right down to it. Serendipitious maybe – unpredictable for sure – but not random. And the SAK is really an algorithmic description that most people can easily understand but it barely even begins to capture what’s really going on. It’s not an algorithm. It’s something more than that.

      Are direct divine intervention and random chance really the only 2 choices on the table?

  3. Jeffrey C. Long says:

    looking forward to hearing the debate

  4. John, Its always a pleasure to meet Margulis alums. I don’t know if I’ve stated this here, but I am a geographer interested because of Lynn Margulis with evolution. I spent 20 years in the Margulis lab as a digital content creator. I was a science and medicine video guy, but as you can imagine, Lynn was non-stop in training me to the point that she told me to go back to school at UMass so she could save her money and have the University pay me to be a teaching assistant. I was 54 and those ten years were the best of my life. If you are asking if William B. Miller can use one of many comments of mine about science and Big History needing a biospheric perspective rather than an anthropocentric one, that is fine with me. As to Lynn seeming distraught, her last book with co-editor Mike Chapman, “Kingdoms and Domains”, was a royal snafu by Elsevier. The first printing had the index at the front, the second (and current) printing is still fulll of production errors. We gave it to them error-free as Lynn made sure. In a effort to go cheap, they shipped the materials for the book off to India and China and managed to lose a 64 lb. box of original materials (art, graphics, EMs, etc.). They refused to find or make any payment for their loss of these priceless and irreplaceable materials. One could reasonably ask if the stress from this killed her. I could share the letter Elsevier’s lawyer sent denying any responsibility.

  5. Frank Morris says:

    I was so impressed by your comments in this debate that I finally bought your Evolution 2.0 book. I can’t wait to read it to see how it compares with my own journey getting kicked around by hostile Darwinians on blogs as I continued to question their seemingly crazy theory.

    Stephen Meyer, on the other hand, was profoundly disappointing. I rejected ID over 10 years ago, but I always thought that, in principle, the concept of ID accepted any form of intelligent cause, not just the God answer. The reality of cellular intelligence has forced the Discovery Institute to expose their bluff. Dr. Meyer seems to be trying to change it from ID to OD, a step up to Omniscient Design.

    He’s wrong. Omniscient means all-knowing. Cells, who are clearly rearranging their own genomes, are very intelligent, but not omniscient.

    They are not gods, as another responder suggested. They are intelligent little critters trying their best to survive, but they don’t simply know all things by omniscience. They use internal homeostatic systems, environmental monitoring systems and intercellular communication to establish their needs and responses to need. So they need to SEEK information about their external and internal status, which means they don’t just magically know all things. On top of that is the lack of the perfection one would expect of omniscience.

    The report on this convention is encouraging. Thanks for the article.

    • Frank, bingo, you hit it right on the head. YES YES YES YES.

      You would think that “intelligent design” simply should have meant that the same principles employed in engineering, music, architecture etc. are also at work in living systems (unlike simple rocks and chemicals), and therefore life cannot be understood in purely reductionist terms. One would have thought that the ID crowd simply wants the world to embrace an holistic understanding of nature. And that they would be happy for us to be doing that.

      What this debate shows is that Intelligent Design a la Discovery Institute is actually Old Earth Creationism. In fact my debates with Stephen Meyer have also made it clear to me that a large number of Discovery Institute supporters are actually Young Earth Creationists.

      The Discovery Institute people are NOT happy with my view of biology, where the intelligence resides in the cells.

      They consider that heresy.

      You are right on the money sir. This is why ID as it currently defines itself will never become accepted by the majority of scientists.

      One time I said to one of the Discovery Institute employees: “James Shapiro at the U. of Chicago has a decent fighting chance of getting his view of evolution accepted by the academy, because his approach is entirely compatible with the scientific method. But your version will never be accepted by mainstream science. Ever.”

      And yes, your understanding of cells is very much the same as mine.

      Thanks for buying the book, I think you will enjoy it. Welcome to the blog and don’t be a stranger.

  6. Madan says:

    This was the perspective of one of the greatest Vedic sages, expressed thousands of years ago and evidently still true today:
    “The great ṛṣi Śukadeva Gosvāmī said: My dear King, there is no limit to the expansion of the Supreme Personality of Godhead’s material energy. This material world is a transformation of the material qualities [sattva-guṇa, rajo-guṇa and tamo-guṇa], yet no one could possibly explain it perfectly, even in a lifetime as long as that of Brahmā. No one in the material world is perfect, and an imperfect person could not describe this material universe accurately, even after continued speculation. O King, I shall nevertheless try to explain to you the principal regions, such as Bhūloka, with their names, forms, measurements and various symptoms.” Srimad Bhagavatam 5.16.4

  7. I track some 52,000 working scientists authoring over 20,000 technical papers in the course of studying the primary source citation utilized by antievolution criticisms (Young Earth and Intelligent Design) in my #TIP “Troubles in Paradise: The Methodology of Creationism” project, including most of the scientists whose names have been dropped in the course of this debate. I see little sign of a failure of the main evolutionary paradigm among them: that all life is related by natural branching common descent. The degree to which individuals want some manner of cuddly designer (and just the one?) behind the phenomena of nature, or the degree to which specific processes proceed more or less quickly or slowly, or engage ancillary factors such as epigenetic methylation, still doesn’t buttress the overall naturalness and unguidedness about it all. Focusing on the Cambrian as Steve and most antievolutionists have done (where the fossil record is dependent on the happenstance of Lagerstatten preservation), or on the still earlier “Origins of Bust” approach that tunnel-visions in on the very earliest of Deep Time, rather misses the monotonously non teleological character of the last 400 million years, including the rather glaringly macroevolutionary reptile-mammal transition (RMT). In “Evolution Slam Dunk: Why the Reptile-Mammal Transition Proves Macroevolution & How Antievolutionists Ignore It”, I have examined all antievolutionary critiques of the RMT (and only a few dozen writers have even taken a whack at it since Duane Gish in the 1980s), and all of them have steered absurdly far from the available data, fossil or genetic. That would include Steve Meyer’s coauthored “Explore Evolution” (2007) and the latest Michael Denton (2016) book on evolution supposedly still being a “theory in crisis.” Given the sparse intersection of antievolutionism with the available dataset (barely 10% of that relevant 20K technical set has ended up referenced in all the antievolution literature), anyone expecting the evolutionary paradigm to roll up and go away is going to be in for as rude an awakening as the last several generations of evolution critics. The object of any alternative hypothesis is to explain the data, not parsed slices of it, but the whole broad range. Call it Neo-Darwinism or evolution x.o, the past looks not especially designed, and certainly not in a big hurry to arrive at the anthrophic destination Steve’s ID or Perry’s evolution 2.0 apparently want it to be.

    • John Torday says:

      James Downward, too bad you missed my 60+ peer-reviewed journal articles and two books on cell-molecular evolution (Evolutionary Biology, Cell-Cell Communication and Complex Disease and Evolution, the Logic of Biology) which focus on the role of stress in cellular remodeling in your database? Given it’s the first scientific evidence for Physiologic Evolution, or “Ascent with Modification”.

      • Actually, John, I have three of your papers you cooauthored with Rehan in my #TIP references:

        2004. “Deconvoluting Lung Evolution Using Functional/Comparative Genomics.” American Journal of Cell and Molecular Biology 31 (July): 8-12.
        2007. “The evolutionary continuum from lung development to homeostasis and repair.” American Journal of Physiology –Lung Cellular and Molecular Physiology 292 (September): L608-L611.
        2009. “Lung evolution as a cipher for physiology.” Physiological Genomics 38 (June): 1-6.

        Not sure of what it is I’m overlooking, though. You’re not claiming are you that “Ascent with Modification” cancels out the overall natural common descent paradigm, or the physical evidence underlying it? That is the point of contention regarding Intelligent Design hypotheses.

    • Richard Clayderman says:

      Mr. Downard’s post amounts to little more than an “appeal to authority,” without even naming the authorities or the relevance of any of the works to the discussion. Just make the argument: kindly explain how undirected physical materials and forces can create a code, along with its matching encoder and decoder devices. In other words, show that Perry Marshall’s code argument is wrong. Tracking all those thousands of scientists and published articles ought to make it easy to do … right?

      • The “Origins of Bust” argument (which Richard Clayderman is invoking) rather misses most of the data. If one demands always and ever to know what came before, but only as a way to dodge around what has already become known, then one always have another rock to dodge to. Do you need to know how the genetic code originated to see what happens to it afterward? The reptile-mammal transition data is an enormous example of a macroevolutionary sequence, where none of the steps involve saltational leaps, but rather exhibit exactly the level of microevolutionary variation that not only can be seen in existing organisms, but increasingly is subject to paleogenomic retroengineering (I took note of the mammal tooth and bird dino skull cases of retroengineering in my “Evolution Slam Dunk” book, specifically:

        Harjunmaa et al 2014. “Replaying evolutionary transitions from the dental fossil record.” Nature 512 (7 August): 44-48.

        Bhullar et al 2012. “Birds have paedomorphic dinosaur skulls.” Nature 487 (12 July): 223-226.

        Bhullar et al 2015. “A Molecular Mechanism for the Origin of a Key Evolutionary Innovation: The Bird Beak and Palate, Revealed by an Integrative Approach to Major Transitions in Vertebrate History.” Evolution 69 (July): 1665-1677.

        Now it may well be (though I doubt) that the origin of life 4 billion years ago was an amazing designy something or other, but its a long way down even to cyanobacteria, and still more time of wind up before metazoans enter the fray, and all that business is already a fait acompli when the reptile-mammal transition occurs.

        Even on the origin question, though, there is progress made, step by slow laborious step, and the fact is that none of that work is done by non-evolutionists. Perhaps efforts to figure out how catalytic RNA ribozymes spawned a DNA-based replicating system will come to naught. But does any success of failure there make any of the reptile-mammal transition data go away? Or make the glaring absence of evolution critics paying much attention to it any less revealing of their “ignore most of the data” mode? Remember, I have surveyed ALL instances of antievolutionists bumping into the RMT, so I’m not guessing about their incompetence here.

        Let’s get down to brass tacks here. Are all Alus in our human genome designed? If not, to what extent is their function due to perfectly natural replication systems? Asking how the original genetic system originated is fun for an evasive dodge, but ultimately nothing whatsoever about the Alus that we can see retrotransposing like mad in our genomes, with effects good and and bad over time.

        I’ll keep paying attention to the progressing science, and leave Clayderman to spinning around in the “Origins or Bust” fun ride, dizzy with unenlightening intonations on “undirected physical materials and forces”. You have some “scientists and published articles” that establish that DIRECTED forces can make a genetic code? Anybody done that? You’re evidently supposing that slipping in an agent of design explains anything, but it’s merely a label you want to paste over the question marks of science. How many agents were there? Are any of them running now? And whatever agenting you propose, does it make any of the forensic tracks of natural branching speciation go away, or require any agency in their end of things? I haven’t found much sign that any design advocate, or Perry Marshall in his expositions, has got very far into thinking about what they actually think happened. But have at it, and we’ll see.

        • Richard Clayderman says:

          I had to smile at the Origins of Bust point. Dr. Freud, call your office.

          Mr. Downard cannot answer the challenge and leaves us with a sequence of rhetorical questions. Regarding the transition from reptile to mammal, or reptile to bird, none of the cited articles explains how the biological software needed to operate new and different biological hardware came to exist by virtue of random (undirected) mutations and natural selection.

          The neo Darwinian Synthesis contends that it explains the origin of all species and all of the species features, both physical and operational (software). Yet the theory cannot explain any of it, and at least one reason is the inability of random (undirected) mutation to create new operational biological software. At least one of the challenges the evolutionist theory cannot overcome is the origin of codes, along with their encoders and decoders, and also how those codes and encoders and decoders could be modified successfully via random/undirected forces. Perry Marshall’s analysis stands unrebutted.

          • Rhetorical questions? Oh get serious, I explicitly cited actual technical research that helps establish the physical evolution of a variety of biological features. I know the lure of Origins or Bust is strong, its the natural avenue for those not doing any of the work or not reading the work of those who do, to bypass all the available data to put their hopes on the supposed inexplicability of first life. Louis Pasteur warned about pinning one’s God belief on that footing, and trying to defend it in the face of all the evolution evidence that has accumulated since is not unexpected, even as it is increasingly irrelevant. Michael Denton showed the paucity of the ID position in his latest 2016 book when he harrumphed how no one could even imagine an adaptive Darwinian scenario to account for the observed evolution of the mammalian jaw. He did this not by actually trying to look to see if anyone had done that, but instead by not only citing a source on a different topic, but one which inadvertently alluded to the very issues Denton insisted hadn’t been done (the adaptation of the jaw related to the growth of the dentary bone among insectivores to better eat bugs).

            At every stage in following up the primary sources when investigating antievolution claims, I learn both more of the actual science and how little of that filters into the tiny dogmatic box that is antievolutionism (whether YEC or ID, they both snag on the same methods failures).

            • Thomas Quine says:

              There is a considerable amount of double-think promoted around the relationship of chemical evolution to biological evolution. I had a hard time figuring out what “Origins of Bust” (as it is referred to several times) was supposed to mean, or whether it may be presumed to have any shared understanding. What Mr. Downard means by “Origins or Bust” is “if life did not (and cannot) originate naturally, then it did not (and cannot) have evolved.” Mr. Downard may well be knowledgeable enough to know that the Intelligent Design framework does not require there to be no macroevolution (though for many of us the continued lack of a suitable mechanism for the “theory” makes the evidence for macroevolution seem that much sketchier), so it’s possible that he is simply drawing attention to things that are largely irrelevant to Meyer’s arguments.

              Aside from this though, I find Mr. Downard’s understanding of this so-called “trope” misrepresents what I think and what many others of us think who find this mystery so compelling against naturalism. If the “origin of life” problem points to a need for an intelligent cause because the sum total of all unintelligent causes described/predicted by physical laws are collectively insufficient, then invoking that intelligent cause in other situations where material causes are categorically insufficient does not “multiply entities beyond necessity.” There are plenty of problems within the macroevolutionary scheme–even without looking at the explanatory hurdles of the “origin of life” problem”–that speak to a need for an intelligent cause for macroevolution even for many who find the “reptile-to-mammal” evidence compelling.

              To go back to Mr. Downard’s understanding of “origin of life” significance for so-called “science deniers,” a teleological cause for origin of life does not necessitate a teleological cause for biological diversity–but for many the necessity of teleological causation in the biosphere is more readily apparent in origin of life, and if it’s necessary for life to start it makes people wonder whether it might be a better explanation for other things that appear to be designed for a purpose. The secular miracle of abiogenesis is supposed to remain a blank check on explanatory power–and everyone pretends that it must have perfectly reasonable (i.e. natural) explanation because almost ever since Darwin we have been pretending that science has always required that leap of faith. I think Mr. Downard’s characterization is more apt description (however still imperfect) of how blindly optimistic the application of the apparent “success” of macroevolutionary theory has caused so many to suppose that we must be close to some coherent account on the origin of life, to the point of even supposing that some sort of natural selection also explains chemical evolution. It’s “Naturalism or Bust,” the contrapositive of what Downard thinks “creationists” typically have in mind.

              Conveniently, it is forgotten how much work natural selection did in making the unificatory abduction seem to be better-supported than it was–except by those holdouts who still believe in the wonder-working power of selection. The “theory” of evolution, in whatever sense it has coherence, is a troubled theoretical framework. The “unificatory” power of Darwinian explanation seems to be not the least bit troubled (in the consensus groupthink of “tortucan” Darwinism) by natural selection becoming a less and less plausible mechanism. Selection turns out to have merely been an imaginary stand-in for what the “consensus” would like this yet-to-be-found mechanism to be capable of. It becomes more acceptable when the paucity of coherence in the origin of life speculations is apparent.

              • Thomas, if you would care to explain where in the 100 million+ years of the reptile-mammal transition anything is occurring that falls outside the realm of natural branching speciation building on completely natural (but evidently unguided) natural mutation, by all means do so. But no one (and I mean literally no one) in the Intelligent Design camp has got anywhere near doing that. I know this because I survived all of them (and it’s not a big set, there being only about a dozen fact claimants in the entire ID cannon, the rest being secondary copiests) in “Evolution Slam Dunk.”

                The presumption that somewhere naturalism fails in that RMT case is certainly a persistent view among ID advocates (Michael Denton being just the latest iteration), but on close inspection of their arguments (and have you attempted to do that, Mr. Quine, if so please explain what fact checking you did of their efforts) none of the ID set got even as close as creationist Duane Gish had in 1995.

                Btw I am an older man whose fingers occasionally slip on the keyboard, where “or” becomes “of” (f falls beneath R on QWERTY). May you never suffer from such human foibles. As for the concept, to the extent that antievolutionists attempt to deflect from such datasets as the RMT by jumping to abiogenesis, that is Origins or Bust, and if you are contending that a large proportion of antievolutionist apologetics does not fall into that catch-all bin, I should like to see your documentation on that. For my #TIP dataset I have drawn on over 8000 antievolution sources spanning the views of some 2000 writers. Any may inspect my reference bibliography at, which I update regularly to keep up with my ongoing research on the methodology of creationism.

        • Richard Clayderman says:

          James wrote in part: “Do you need to know how the genetic code originated to see what happens to it afterward?” Answer: my challenge was about the origins of any code from undirected physical materials and forces. I did not see an answer to my challenge. Perry has offered the same point in his book. James has not overcome it.

  8. Thomas Quine says:

    Sorry it’s taken so long to respond. It is hard to understand your position in a way because sometimes you seem to making a design argument, and sometimes you seem to be arguing like Ken Miller that any influence God has had on history must somehow be undetectable. Near as I can tell, your version of a 3rd way is an attempt to keep theists from disengaging from the facts and/or basing their faith on certain scientific mysteries remaining mysteries. I can sympathize with that. In some ways you seem to be saying that the evidence for intelligent design stands regardless of the time frame that the information is put into the system. A lot of ID people would be on board with you there—except that most wouldn’t *require* that the information be limited to the law-like behaviors of the universe and have specific evidential reasons (which you and others may disagree with) for rejecting that limitation.
    Whether there is a coherent 3rd way depends on precisely what *is* being added to the table and whether it is something more than a porridge of what is already on the table. It depends on whether one is proposing some sort of law that explains how watch-innovating factories are plausible (not merely possible) with no guiding influence. The reference to the Biocentrism book makes me suspect that the third thing being put on the table is a conscious universe akin to the thoughts of Thomas Nagel or Rupert Sheldrake, but somehow more dependent (in an unclear way) on material mechanisms. The problem with Sheldrake’s ideas (aside from the lack of academic engagement) is that they don’t present anything more clear than I have so far heard about the third way, although some of the things you’ve written sound like a front-loaded ID position. Positing a consciousness in cells and then arguing that cells can perform macroevolution over deep time because they are conscious, creative geniuses — if that is the hypothesis — is an intriguing hypothesis but seems like another extraordinary claim in need of extraordinary evidence. If the “weak version” of 3rd Way is that “consciousness needs to be considered as a fundamental part of the problem and not merely epiphenomenal” then that much is easy to agree with. If one is applying the same sort of “infinite departure” extrapolation to cell intelligence (as has been applied to mutation), that is the thing to be proved and that potential explanation has its own problems.
    I would recommend Penrose’s Shadows of the Mind since he is grappling there with whether consciousness or mathematical creativity can be fit into the persistent preconceptions (i.e. current reductionist paradigms) and what this means for science. This is something that continues to intrigue me from a computer science point of view: Can insight be estimated? I think that the answer is an affirmative but a highly qualified one. The idea of a conscious cell requires a further question to be answered: How would you distinguish between the insights programmed into an agent (e.g. a learning algorithm) from the insights gained by an agent through creative consciousness? And it begs the question about what consciousness (if any) existed in the acellular matrix that gave rise to a functional cell, or whether an essentially robotic cell (a chemical automaton with exactly what computational abilities?) can develop the power of insight through enough remixing of its parts. If you are arguing that the kind of self-reprogramming that a protozoan does must requires some sort of non-algorithmic conscious effort.
    It would require a lot more words to adequately address why it is important to distinguish what science can tell about the evidence for deep intelligence and ultimately (non-scientifically) whether this evidence tells us anything about the divine, but I think it is important to carefully tease these apart. People have characterized this as a political stunt by the Discovery Institute, but I think the exact opposite is true. The political stunt has been the Darwinists staging this as a conflict between doing “real” science and inferring a Judaeo-Christian God. And in the larger public forum the matter requires a straightforward conversation about whether the word “supernatural” is at all a scientific concept, let alone a useful scientific concept for criticizing ideas–whether it is being used to rule out phenomena that are either (a) knowable but completely outside current paradigms or (b) unknowable through scientific methods alone. And, with respect to some of the questions that William Dembski has raised about the nature of quantum events, what precisely (and isn’t science supposed to be precise?) is meant by “direct intervention.”
    That said, yes, not only does the implicit deism in methodological naturalism smell like it’s *way* past its due date, but–taking our science hats off for the moment–that implicit deism *does* take something away from the Divine. I could be misunderstanding what your position is, but to me it sounds like one is restricting God to forming the law-like behaviors of the universe because if He were to do anything else science becomes impossible somehow (and He’d better behave Himself so scientists can get paychecks). It looks like a 3rd Way God can do anything so long as he keeps all “intervention” (non-front-loaded influence, presumably) and any evidence thereof to himself. He can create the universe and just let things go from there–and that’s all (except maybe interfere in an undetectable way). I don’t see how the hands-off argument for a supposedly bigger God has any more philosophical backbone than when Erasmus Darwin pitched it. (If Erasmus’ poetry is any measure, it seemed to make God uncaring and make Nature glorious.) It doesn’t seem to accomplish anything *theologically* other than conjuring a more distant, less involved creator.
    For me there are even more fundamental questions (to the evolution debate) than all these scientific and metaphysical questions: *Who* decides what “real science” is and *who* gets to put things on the table for further study? What I’m tired of more than anything is the fascism of dictating to the community how to approach science and bullying and deriding people who approach it differently. Ever since Charles Darwin biologists have been basing their historical arguments, explicitly or implicitly, on what a creator would or wouldn’t do rather than on what evidence suggests itself. I think we’re all entitled to whatever philosophical baggage we choose; it’s the imposing of certain philosophical baggage (e.g. materialism) on the community and calling this imposition science that is the science-stopper. Once the public realizes that there are other scientific studies to spend their money on than bankrolling more expensive reductionist flapdoodle, on whose science will they actually want their money spent? Who will decide where that lovely green stuff gets spent?
    I tend to look at the enterprise of biology as somewhat of a mining expedition. For decades there’s been certain passages sealed off because, so we’re told, there’s nothing to see down there, it’s a waste of time, it’s a mining-stopper, etc. Nobody’s allowed down there because nothing will come of it but a waste of resources—so *no one* is allowed to try. I think there’s plenty of room for neo-Darwinism, 3rd way, 4th way, self-organization, quantum synthesis, or whatever approach. But a 3rd Way that is NOMA with ID frosting on top still tastes like NOMA. NOMA didn’t inspire materialists to keep religion out of science; it just rationalized making theists do science that amounted to a secular religion.
    Some of what I heard sounds a little like “Boy these scientists are so afraid that if they tell the public the truth, people will stop letting us do their thinking for them and gravitate to Intelligent Design.” If that’s what they are afraid of, maybe they should bravely tell the public the truth now, while they have a smidgeon of credibility left, before they make this a self-fulfilling prophecy. Most of them still talk as though they accept this neo-Darwinist pablum, and science programs are *still* churning out acolytes that think in lockstep from the ideological mill. Whether they really do buy this stuff or they misrepresent themselves for fear and loathing of the very people whose money they are spending, it still undermines all confidence in the community of biologists. Without a free market, a 3rd way is just the same old presumption and arrogant extrapolations with new purported mechanisms, and if it becomes the main item on the shelf it’s not because it’s so darn good.

  9. John Torday says:

    The ultimate cause for the origins of life as self-organization has been insurmountable……..until a few weeks ago when a paper demonstrating spontaneou self-organiszation of ytterbium atoms was published (Yao N.Y., Potter A.C., Potirniche I.-D., and Vishwanath A. 2017. Discrete Time Crystals: Rigidity, Criticality, and Realizations. Phys. Rev. Lett. 118:030401). The alignment of atoms with one another provides a template for life to do the same in imitation of the physical realm. The phenomenon of Stigmergy- The principle that the trace left in the environment by an action stimulates the performance of a next action, by the same or a different agent- has previously been recognized, but without experimental evidence for it.

    • I wouldn’t call the Yao paper a slam dunk on the origins issue (“Origins or Bust” arguments will remain popular for the near term in antievolution apologetics), but it would reflect how equilibrium states seem to be violated all the time in nature, and that is a door opening of relevance. I’ll add the Yao paper to my #TIP dataset

      Btw are you the John Torday who has done work with Virender Rehan on lung evolution? I have that name in my #TIP reference listings.

  10. After three decades of research and input from over 40 scholars, there is now a new alternative outlined in our book, Darwin’s Replacement. We are proposing a Godly life-science we are calling Atomic Biology showing the essentiality of super-intelligence in building every cell with atoms.

  11. Mike says:

    Hey Perry, I am not a scientist but I think I grasp the differences between your and Stephen’s perspectives. It seems to me that the difference is mostly a question of focus. Stephen believes the presence of coding indicates intelligent design by a designer (God) at one original or multiple points in the history of the development of life. You seem to be saying something similar, but relegate most of the “intervention” to the organism/cell itself. (This reminds me of the old “What if God created evolution?” question, minus the mechanism of randomness). And if God created a single cell with the capability to change and evolve into the complexity of life we see, that would in some sense be more impressive than if God authored a creation which required His constant intervention. You also mentioned the possibility that the universe could have given “birth” to life. Are you saying that at some point – if we regress back far enough – that God would still be the agent of some original creation (either the first living thing or a life-bestowing universe)? It seems Stephen believes that question requires more focus than the process (although it sounds as though Stephen questions whether such ability could be “bestowed” to an organism) and that you believe that addressing the “ultimate” origin of life (or a life-giving universe) is not necessarily invalid, but counter-productive to scientific inquiry related to the process. But for the sake of understanding your deeper perspective, where do you hang your hat with regard to the origin of life (or a life-giving universe)? Do you not (eventually) side with Stephen that life is the product of intelligent design?

    • You are exactly right. And as I said in the debate, I believe in intelligent design writ large. And everybody knows I believe God is ultimately responsible for it all. But I resist Intelligent Design as in “Discovery Institute” version, because that approach has consistently overlooked or under-reported major evolutionary systems and mechanisms for decades – and continues to do so.

      A God who can make a self-developing cell or even universe is vastly more impressive than one who has to show up every now and then to introduce something new. And this higher view of God doesn’t get in the way of scientific discovery and most scientists I talk to seem to be quite amenable to this approach.

    • I look at it this way:

      You can take the position that God intervenes in the world at numerous unspecified times throughout history and creates new creatures… which I actually think is a lower view of God… and endure the hostility of 70-90% of the scientific community, who feels like you’re trying to take away their jobs.

      You can continue to get embarrassed year after year because stuff you used to say was impossible is repeatedly shown to exist in the real world.

      Or you can take the position that natural processes can do this stuff AND WE BARELY UNDERSTAND WHAT THEY ARE OR HOW THEY TRULY WORK – maybe 5% at best – and furthermore admit that for us to solve Origin of Information will literally require a new law of physics.

      This is an approach which scientists consistently like, in my experience.

      And then when you make it really clear what the evidence shows us, which is that cells re-engineer themselves in days, hours or even minutes, then you send Richard Dawkins and friends back to square one because their version of evolution is bankrupt and ridiculously oversimplified.

      And you take the high view of God instead of the low one.

      Seems to be a win-win-win to me.

      As I say in my book: Darwinists underestimate nature, Creationists underestimate God.

  12. Christopher Jones says:

    Interesting. We thought inference to a creator would overthrow old-school Darwinism. Instead, bacteria are killing Darwinism. Because even they know how to “evolve” on their own.

    “Bacteria are killing Darwinism” would make a good headline.

  13. Mark says:


    Have you read Michael Denton’s 1998 book Nature’s Destiny? As you probably know, he denies ANY divine intervention, even at the origin of life, but simply offers the hypthesis of “directed evolution.”

    Despite being in the ID movement, I’m absolutely astounded at what his model of evolution predicts and GETS RIGHT: lamarckian-type mechanisms, the demise of junk dna, cells directing their own evolution, parallel evolution, I could go on and on and on. His book honestly reads like a handbook of prophecies for the Third Way movement. And a wonderful paradigm by which to view all of biology.

    Given Denton’s worldview I wonder if he would have joined the Third Way movement had it been available to him at the time. As Sy Garte has also pointed out, his new book, Evolution: Still a Theory in Crisis also reads like a book of the Third Way movement.

    Curious of your thoughts on Denton.

    • From what I’ve read about Denton he seems to have the right idea. I have not read him closely enough though (mea culpa) to be sure whether he’s fighting against the general idea of evolution or just the materialistic misconception of it.

  14. Mark says:

    He has NEVER questioned descent with modification. He just thought it looked like the jumps in evolution looked saltational, and not Darwiian. Now he sees the third way mechanisms as filling the saltational gaps.

  15. Ironically, nominalist Protestant theology lead to the intellectual acceptability of purposeless Darwinian evolution. Thus, I hope that this is actually the counter-reformation of evolution that incorporates Thomistic metaphysics and ID theory.

  16. Ameet Sharma says:

    Why don’t discoveries by machine learning systems like Alphago qualify as “code that hasn’t been designed”… these systems develop new knowledge… new tactics that previous Go players never thought of.

    One must distinguish between the algorithm by which the system operates, and the new knowledge that it develops. These are two different things. The first is designed by the human inventor. The second isn’t.

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