Royal Society’s “New Trends in Biological Evolution” – A Bloodless Revolution

“Evolution is too important to leave to evolutionary biologists.”

-Ray Noble MD

“I don’t consider my ideas controversial. I consider them right.”

-Lynn Margulis

In London from 7-9 November 2016 I witnessed a groundbreaking summit at the British Royal Society. 300 scientists from around the world gathered to evaluate a sea change in evolutionary theory.royal_panel_s4

When recalled at the end of the 21st century, this gathering may prove as pivotal as the US election that occurred at the same time.

No one can say for sure until December 31, 2099 whether this meeting was that influential. But in a few minutes I’ll explain why I predict it was.

I’ll also explain why Charles Darwin himself – a thoughtful, tentative, ever-questioning man who eschewed dogma – would likely be horrified at Neo-Darwinism, the mutant progeny of his own theory, that emerged in the 1940s and held sway for 70 years.

Mr. Darwin would surely be relieved that someone finally shouldered the task of restoring experimental science to its rightful place. Such is the aim of the Extended Evolutionary Synthesis.

Can evolution’s woes be solved with stitches and Novocaine, or does it need full anesthesia and a heart transplant?



James Shapiro, author of “Evolution: A View from the 21st Century” (2011)

When James Shapiro released his landmark book Evolution: A View from the 21st Century, you couldn’t help but wonder if he would actually get away with it.

Could an active scientist publicly announce that the Neo-Darwinian emperor has no clothes, and not get fitted with a pair of cement shoes?

Would his career at the University of Chicago be over?

Shapiro did not bring a knife to a gunfight. He brought a machine gun – and a bulletproof vest packed with munitions.

Backed by 1100 references and a sterling track record, including close association with Nobel Prize winner Barbara McClintock and his own discovery that bacteria engineer their own DNA, his book made it clear:

It’s time to turn evolutionary theory upside down and inside out.

Shapiro was arguing neither for creationism nor for Intelligent Design. Rather, he was arguing that Natural Genetic Engineering, and indeed the cell itself, are the stars of the evolution show.

Not Natural Selection.

His book was praised by Nobel Prize winners Sidney Altman and Werner Arber. The legendary Carl Woese called it “the best book on basic modern biology I have ever seen.” In the press it got mixed reviews. It was ignored by several of the major science outlets; however it was not dismissed. It made waves in the evolution community.

But perhaps most telling of all was the review by Larry Moran for the National Center for Science Education, a.k.a. the “Darwin Lobby” of the United States.

Moran panned it. And – believe it or not – Moran actually admitted in print that he skipped reading major portions of the book.

This signaled both Moran’s shoddy scholarship and NCSE’s true commitment. Not to science, but to scientism, reductionism, and tired 70-year-old dogma.

Despite scorn from Richard Dawkins and Jerry Coyne, there is no counter-argument. Experiments by Lynn Margulis, Eva Jablonka, David Prescott and Mae-Won Ho definitively prove: Not only do cells perform adaptations of astonishing sophistication in real time, these events are emphatically non-random.*

Evolution has goals. Organisms have goals. And they actively evolve to achieve them.

This demolishes creationist / ID arguments that macro-evolution is impossible. It’s not only possible, you can witness it in real time. Including complete speciation events in microbes and plants and animals. Building and re-building of entire systems.

Empirical data also demolishes the Neo-Darwinian doctrine that evolution is an aimless meander through random space.

Many times, radical innovations commence inside a single cell or organism, leaving Natural Selection little or no immediate role. Such was the case with Barbara McClintock’s surprise discovery of transposition: a single plant, faced with chromosome damage, repaired its DNA in real time and went on to reproduce.**

Discoveries of this type were the focus of the Royal Society’s “New Trends in Evolutionary Biology” conference. But as the old-school Neo-Darwinists hastened to point out, none of these are new. Much of this has been known for 10, 30, 50 years and more.

What was new at the world’s oldest scientific society was the fact that 1) A public quorum of 300 scientists acknowledged the centrality of these discoveries to evolution, and 2) there was no longer any room to downplay, discourage or demean these findings. All are legit.

This meeting had no mainstream precedent. Such a conference would NEVER have happened five years ago. It would have been too politically incorrect, too threatening to the Neo-Darwinian monopoly.

Eva Jablonka commented to me that findings flow from too many sources to deny. It isn’t just evolutionary biology. Nutrition, exercise, cancer treatments and gene therapies are all forcing this sea change.

Until November 7-9, though, Evolutionary theory was caught in the strangle hold of traditional evolutionary theorists. They have insisted for decades that chance and selection are the central driving forces of evolution.

Jerry Coyne has propounded for years that “natural selection is the only game in town” and that evolutionary mutations are “willy nilly.” As for Shapiro and McClintock’s work, he says, “Move along folks, nothing more to see here.”

Luminaries like Lynn Margulis were red-headed stepchildren for decades. Margulis proved evolution is far more cooperative than competitive. That high-speed merger-acquisitions are pivotal events in evolution history.

She received scant funding and dismissal by the male-dominated good ol’ boys club. Her seminal paper on symbiogenesis was rejected by 15 journals.

Upon her death, Jerry Coyne hurled scorn upon the woman who had declared his tribe of Neo-Darwinists to be “a minor twentieth-century religious sect within the sprawling religious persuasion of Anglo-Saxon Biology.”


The Royal Society, founded in 1660, is the oldest professional scientific organization in the world.

“Neo-Darwinism has taken the life out of biology,” she lamented.

The Royal Society meeting commenced with nervous anticipation. In attendance, a number of highly regarded old-school Neo-Darwinists like Douglas Futuyma, author of a major undergrad evolution textbook, and Russell Lande.

Also present, Fellows of the Royal Society and the British Academy. Members of the Third Way of Evolution movement; along with representatives from a spectrum of fields from physics to zoology. As well as technologists, authors and journalists.

The audience was wonderfully interdisciplinary. I sat next to two economists who told me, “We were debating these exact same issues in economics 20 years ago.” In saying this, they were saying evolutionary biology had come to the party at least 20 years late.

Delegates arrived with one of two concerns:

1) Neo-Darwinism is going to get overturned, or

2) Neo-Darwinism is not going to get overturned.

Incumbents were anxious that the conference might pronounce that evolutionary theory is due for a complete overhaul. Rivals worried that the Society might smear new lipstick on the same old pig, continuing to plead “natural selection” as the be-all end-all of everything.

The tension in the room was palpable, sharpened by the history of this topic being fraught with politics, bitter feuds and bad blood.

There was considerable opposition to the meeting itself from the old guard. Rumor has it that influencers tried to either cancel the meeting altogether or strictly limit attendance. But the organizers prevailed.

The entire first day of the conference, the feeling was that of a funnel cloud trying to form but uncertain where to land. “Where is this thing going?”***

But like a band finding its groove on the second song, the rhythm snapped in place on day two with James Shapiro’s opening talk “Biological action in Read-Write genome evolution.” Paul Griffiths followed, exploring information cause-effect in biology.

Eva Jablonka reported learned trait inheritance via epigenetics; after lunch, Denis Noble, the luminary who figured out the cardiac rhythm 50 years ago making pacemakers possible, executed a line drive with “Evolution viewed from medicine and physiology.”

Dr. Denis Noble of Oxford, Fellow of the Royal Society and organizer of the New Trends in Evolution conference

Dr. Denis Noble of Oxford, Fellow of the Royal Society, critic of Neo-Darwinism and organizer of the conference. He’s author of Dance to the Tune of Life: Biological Relativity. He also edits the cross-disciplinary journal Interface for the Royal Society.

No definitive pronouncement was made as to whether the Modern Synthesis can still be extended, or must be rubbished entirely. But this question is firmly on the table. The cat, as they say, is out of the bag.

There were two particularly memorable exchanges.****

University of St. Andrews scientist David Shuker challenged Denis Noble, who had described an experiment where scientists deleted flagella genes from bacteria.

These cells had re-generated their flagella genes in just four days and grown new tails. A mind-bending example of real-time, high-speed evolution.

“Clearly natural selection can rapidly steer regulatory networks. This is a beautiful example of high speed Neo-Darwinian evolution,” Shuker argued.

Shuker, like Jerry Coyne, was towing the standard Neo-Darwinian line, which insists that in the end, all comes down to “selection, selection, selection.”

Shuker somehow imagined that “selection” is re-wiring those genes. I don’t know how selection re-wires genes in four days. Selection after all is just survival of the fittest; “selection” doesn’t provide us a single detail about how those genes got rewired.

But in the Neo-Darwinian view, for any cell to evolve purposefully is unthinkable. So of course “natural selection” always ends up being the answer.

Noble shot back. Shuker tried to interrupt but Noble held his ground:

“No, YOU need to listen. I used to think exactly like you. I embraced the reductionist mindset for years. When I got out of school I was a card-carrying reductionist. Reductionism is powerful and it’s useful. I am not dissing it. Many times we need it. But it is not the whole story.”

Noble described how bacterial regulatory networks rebuilt those genes in four days by hyper-mutating, actively searching for a solution that would give them tails and enable them to find food. “Natural selection did not achieve that. Natural genetic engineering did.”

Noble continued: “I did not arrive at this conclusion from any one piece of data. It took many years, papers and experiments for me to come around to this perspective. But slowly I came to a different view.

“It’s not a question of the data. Everybody agrees on the data. It’s about your point of view. I have a view that you do not. This enables me to see things that you cannot see.”

Noble did not waver. “Biology is not just bottom-up. It is also top-down. There is no privileged point of causation in biology. The gene doesn’t hold some special causal role. There are feedback loops from every system to every other system. It’s hierarchical. It’s systems all the way down.”

Five years ago, such “heresy” would not be tolerated in a mainstream science conference. Much of this research has been reported in journals outside of standard evolutionary biology, like physics and medicine, because the evolution journals wouldn’t hear of it.

Few doctors or physiologists hold to traditional Neo-Darwinian theory anymore. And while no one can deny Shuker his right to frame the data from within his particular worldview, no longer can the active role of organisms in their own evolution be denied.

The other heated exchange was between Russell Lande and Sonia Sultan. The subject was real-time plasticity of plants.

Plants in low-light environments produce offspring with large, light-sensitive leaves, but identical plants in high-light environments birth offspring with small leaves. This is a learned trait that is directly passed to offspring. It transpires in a single generation. It’s so dramatic, the second generations appear to be different species.

Again, this bypasses selection altogether. The plants are empowering their offspring to anticipate natural selection.

“There is nothing new here! We have known this for years,” Lande complained, citing work from the 1950’s by Ledyard Stebbins. But Sonia Sultan graciously challenged him. She read aloud from one of Stebbins’ books, where he goes on to say that we should pay no attention to this, as it has no bearing on genetics or evolution.

“It pains me to read Stebbins,” she said, “because 70 years ago he observed the exact same things we’re discussing today. Yet not only did he consider them unimportant, he told the rest of us we should ignore them when thinking about evolution!”

This was the crux of the meeting: for most of a century evolutionary biology has ignored the profound sensitivity and responsiveness of organisms in real time. Lamarck was right 200 years ago… despite literally being laughed out of the academy for most of the 20th century.

Today he is vindicated: Learned characteristics are passed to offspring. Evolution proceeds very rapidly in some cases.

Darwin accepted Lamarck’s ideas. He acknowledged that other forces besides selection must surely be in play. One realizes that Charles Darwin’s Origin Of Species is more accurate in its initial version of evolution than the Neo-Darwinian Synthesis. An inferior model has ruled biology with an iron fist ever since.

This is all the more ironic because in contrast to the certitudes of those who transformed Neo-Darwinism into a kind of pop religion, Darwin acknowledged the soft spots in his theory. He was unafraid to question his own assumptions.

Noble’s point was that, because of Systems Biology, all medical and biological disciplines have vital things to say to evolution. Evolutionary biology can no longer afford to shield its turf from outsiders. Outsiders more than ever are called for, in the self-correcting enterprise of science.

In another exchange, Fellow of the Royal Society Patrick Bateson of Cambridge replied to a questioner in no uncertain terms: “Natural Selection is not an agent.”

(Translation: Blind Watchmaker must be stripped down to the engine blocks and rebuilt from the ground up.)

Neo-Darwinists permit no place for purposeful adaptations in their materialist view. But now reductionism for the first time has been formally challenged. The toothpaste is out of the tube and it is not going back. There will be many more meetings like this. This was only the first.

A less obvious triumph of this meeting was that it was civil. Yes, I heard stories of harsh exchanges backstage; there were occasional outbursts of partisan clapping from the audience. From time to time, the meeting took on dimensions of a pep rally.

However the organizers actively discouraged all divisive behavior, and in the end it was very British: polite, civil, diplomatic. A bloodless revolution.

Evolution going forward will not follow in the footsteps of its mannerless evangelists like Dawkins and Coyne. Conduct will be gentlemanly and respectful from now on.

It was a privilege to be present at this historic summit. Compared to the fury of the US election, this courteous British conference might seem a minor academic exercise, noted by only a few.

But seen from the wider view of the entire 21st century, it was a watershed event.

Why? Because the trajectory of science itself just tilted 15 degrees. Scientism and reductionism have been punched in the face. Empiricism is making a comeback.

Looking across the remaining years of the 21st century, the impact is difficult to estimate. But it will be great.

“An era can be said to end when its basic illusions are exhausted”

-Arthur Miller

*Margulis & Sagan, Acquiring Genomes: A Theory of the Origins of Species, and Jablonka & Lamb, Evolution in Four Dimensions, are serious books providing detailed accounts of well-documented evolutionary processes (symbiogenesis, epigenetic inheritance and genetic assimiliation) that fall outside the neo-Darwinist conventional wisdom. I credit Denis Noble and Eva Jablonka for emphasizing the importance of Lamarck’s contribution. It was the very first extended description of evolution as the basis for biological diversity.

**A single maize plant, faced with irreparable cycles of chromosome breakage, was finally able to repair its DNA in real time and reproduce normally by a damage response process that involved activating previously silent agents of chromosome restructuring in its genome.

***On the first day, John Dupre introduced the important idea of evolution as “process” rather than a series of discrete accidents. This came up in the final panel when a “process ontology” was proposed as an intellectual basis for analyzing evolution.

****I have recounted these conversations from memory. They are not word for word but hopefully reflect the intended meaning. Corrections or suggestions are welcome. Amendments will be made as recordings become available.




42 Responses

  1. Well said. As an attendee, I had much the same observations and agree with your points. I have noted that other reporting has not accurately or completely reported the Noble-Shiley exchange.

  2. Sean Davis says:

    Hi Perry, I don’t understand how this understanding of “evolution” isn’t also “Intelligent Design”. I’ve read your explanation previously, but I still don’t think there’s enough there to contradict what ID supporters are also saying. I can’t speak for ID directly, but just in my routine review of this topic I would say that they’d agree with everything you mentioned here. They DO NOT disagree with evolution. ID never suggests that “evolution” isn’t real…in fact, Stephen Meyer has mapped out 6 definitions of evolution to help properly communicate what people actually mean when discussing “evolution” ( Why? B/c “evolution” is thrown around so generically that it’s difficult to know what someone is necessarily referring to specifically when talking about “evolution”. Of those definitions, they agree that all but two of them occur regularly, with one still in question (macro-evolution/tree of life), and one that’s all but outright negated (the neo-Darwinist “blind-watchmaker” theory- ” the idea that all organisms have descended from common ancestors solely through an unguided, unintelligent, purposeless, material processes such as natural selection acting on random variations or mutations). So where are you at odds? Enjoy reading your blogs. Thanks.

    • When you peel the onion (especially if you go to some kind of event and start talking to a lot of people) you find that ID is actually a pretty big, loosely defined camp with all kinds of factions and points of view. In fact it’s often comfortably diverse.

      But this actually comes with problems, because what ID means to the typical scientist is essentially “some form of Old Earth Creationism” and the assertion that macro-evolution is impossible.

      I spell all this out very clearly at – I encourage you to click the links and follow the rabbit trails and read the comments (including the threads at Uncommon Descent) because I make my position entirely known.

      Macro evolution is not only possible, it’s directly observable. New species, dramatic changes in short periods of time, and it completely contradicts the blind watchmaker version of evolution which is really just a pop religion.

      • Bass Afrass says:

        But ID supporters have no problem with speciation, in fact, they eagerly affirm it. Nor would cell-directed (natural genetic engineering) rapid speciation provide any difficulty for them. The evolution they deny is change of kind, not species. So I too fail to see how rapid or natural genetic engineering is a challenge to their paradigm. What am I missing? How does the acknowledgement of this prove macroevolution? Does it not just indicate that microevolution can happen much faster and naturally than currently admitted by Neo-Darwinism? Or perhaps on a slightly “grander” scale?

        • Define “kind.”

          • Bass Afrass says:

            I believe when they say “kind” they mean something closely akin to genus or type. For example, they would say that the entire cat genus, everything from simple house cats to tigers, had a common ancestor. The diversity now seen in that kind/genus is due to speciation, which, if I am understanding this conference correctly, seems to be able to happen more quickly and with non-arbitrary direction.

            • Does scripture ever define what a “kind” is?

              How do you know whether “kind” is an absolute unvarying law that never ever has a single exception, vs.a broad principle, for example like the blessings that are promised to people who obey God all over scripture?

              • Scott Harwell says:

                I am not a scientist but the way I understand the positions of Meyer, Behe, Denton and others would be mostly in line with Shapiro and your evolution 2.0 theory and, as described by you in this post and other things you have written, this “new” theory of evolution is consistent with a Creator God that would design life to quickly “evolve” by the DNA essentially reprogramming itself and modifying its digital code.

                From a fundamental concept, other than the method employed and the time needed, this new theory will not support macroevolution unless and/or until a bacteria evolves in to something other than a bacteria, a virus in to something other than a virus, a dog in to something other than a dog. These are 3 simplified examples but is what most scientists that believe in creatiin would probably label a “kind.” Asfor how many “kinds” of animals God created, I have no clue. However, I do know that a fundamental law of biology, that life only comes from life, has never been violated in the natural world that we have observed. Abiogenesis as a “science” is absurd because it could never be tested, observed or falsified and it all comes down to a theistic or materialist worldview. Scientists like Crick were at least honest enough with their observations to understand that the information in DNA required intelligence and is why he just “punted” to aliens “seeding” the first life so life could then evolve. Obviously, this begged the question and failed to resolve the ultimate question of when, where, how and why life began in the universe in the 1st place. Moreover, it also does not account for the creation of the universe (from nothing), the design of the universe, the physical laws of the universe, why there are even universal laws which makes science possible, mankind’s universal moral law, etc.

                It is refreshing to see persons like yourself and Shapiro take on the religion of neo-darwinism.

                • There is nothing about “third way” or extended evolutionary synthesis that is inconsistent with the Christian idea of God. It’s not compatible with YEC of course, but in my opinion if you want to inoculate your children against Richard Dawkins and the New Atheists, all you have to do is teach them evolution – the way it really happens.

                  Many of the ID guys are still trying to prove that common descent is impossible which I see as a mistake.

                  This creationist obsession with “kinds” does not serve Christianity. First of all, the Bible doesn’t even begin to define what a “kind” is and secondly it doesn’t say whether this is a hard rule or simply a generalized pattern or principle. If you read my book Evolution 2.0 (or even just click on the links in this article) you’ll discover that you can absolutely get a bacteria to become something other than a bacteria (symbiogenesis) or a dog into something other than a dog (hybridization and genome duplication) and if Christians started talking to atheists about how you prove evolution in the lab instead of how to disprove it, you would make a LOT more progress.

                  Watch the arguments in the comments on my blog and see how the atheists are constantly back pedaling, realizing that their Blind Watchmaker pop religion doesn’t work. Yes it makes them angry and it makes them doubt.

                  Also see

              • Joe Terrell says:

                The ability to reproduce seems to be the definition of kind for God instructed Noah to bring in two of every kind. The obvious goal was to preserve the genetic definition of the various kinds. The creation account seems to imply the same thing: kind signifies a group of creatures with sufficient genetic similarity that that could successfully produce offspring.

                From my understanding, there is no modern taxanomic delineation that corresponds exactly to the Biblical “kind.” I recently read one of the more prominent Creationists who said it most closely aligns with “family” but that it was not a perfect match by any means.

                • Being that “kinds” is extremely vague at best; and given that strict conservative Young Earth Creationists ostensibly believe that every animal on earth necessarily evolved from Noah’s ark, then you have to do the math: Earth went from X species that could fit on the ark to Y species that we have today. X is hundreds or thousands and Y is millions.

                  Therefore it puzzles me that creationists are still telling me that there’s never been an observation of new species evolving (which is manifestly false, see the links above) when in fact they should be showing the world empirical evolution. Such as the organizers of this conference were doing.

                  They’ll get a lot more traction with that, than fighting evolution. Besides, real-time real world evolution is fascinatingly impressive.

                  • Scott Harwell says:


                    As you know, the Bible does not purport to be a biology textbook but the “kinds” mentioned in the Bible are most likely closely akin to “family.”

                    As for your assertion claiming that there has never been an observation of a new species “evolving,” this can be either a true or false statement depending on how you want to define evolution. If you mean microevolution, this has been observed and empirical science has verified that DNA can essentially reprogram itself to meet changes in the environment. Your example of Noah’s ark is actually a good example for how fast microevolution can occur and it would not take millions of years. Rather, this type of microevolution could literally occur in thousands of years for the various “kinds” or “families” of animals which has resulted in the number of species we observe in 2016.

                    However, there is no real science that supports a life form evolving in to a more complex life form. A bacteria may “evolve” in to a new kind of …. bacteria but it is still ……… bacteria.

              • Richard C. says:

                Perry, don’t change the subject to “scripture.” Bass was talking about ID.

                Your statement in the post was: “This demolishes creationist / ID arguments that macro-evolution is impossible. It’s not only possible, you can witness it in real time. Including complete speciation events in microbes and plants and animals. Building and re-building of entire systems.”

                As others here have pointed out, ID explores whether the evidence establishes that life forms change (evolve) via undirected mutation and natural selection. In principle, ID would have no objection to life forms changing via directed mutation — with “natural selection” meaning that the successfully changed organisms prevailed (survival + reproduction) in the population over the unchanged organisms.

                Personally, I find the evidence does not support “common descent” at all – Meyer’s Darwin’s Doubt argues that well, and there are other lines of analysis that way too. But if the cells contain sufficient intelligence to morph from bacteria to other kinds of animals, then that morphing (call it evolution) is intelligently directed change. ID is consistent with that.

                • I had a recent email exchange with Casey Luskin who used to work for the Discovery Institute. Some ID people believe in common descent (Behe for example) and others do not (Paul Nelson for example.)

                  A significant problem is that ID is generally perceived by the public and scientists as “anti-evolution.” But clearly not all ID people take that view at all.

      • Sean Davis says:

        Hi Perry,

        First, thank you for your response. I read what you had posted about your personal concerns regarding the ID movement. Thank you- that was helpful as far as knowing your personal reservations.

        At the same time, I’ve been routinely reading posts from the Discovery Institute over the last 3-4 years, as well as following some of their most ardent supporters on YouTube (Meyer, Behe, Axe, Dembski, Gauger Denton, Jay Richards) and I don’t really agree with your conclusion and feel that you’re really making the same case, albeit launching from a specific trajectory that you specialize in.

        If you listen to Meyer, in particular, with any consistency you’ll realize that he is consistently fighting against the “Creationism” stereotype (as well as “God of the Gaps” arguments against him, and reinforces His theory solely from a scientific perspective- scientific method, research, experimentation, and empirical evidence.

        He does not sugarcoat or hide from the potential implications that his theory could point towards, nor does he hide from the philosophical implications surrounding the “blind-watchmaker” thesis. And I would say that their #1 goal is to refute that thesis until Design is a more commonly accepted alternative to publicly acknowledge and review.

        I also think beliefs, emotional biases, and passions are at the heart of scientific explorations. Meyer doesn’t hide from that, neither does Dawkins/Hitchens, and neither do you (I’ve read what motivated you to dive into this research). And why shouldn’t it? At the heart of the human condition is a core question: How did we get here? And in pursuit of that question you have two options that cannot be mutually exclusive: Naturalism/Chance or the work of Design

        They also invest a lot of time in epigenetics. So much that I feel someone has sold you a false impression of their work. Perhaps Meyer didn’t invest in your particular areas enough to your pleasing, but that doesn’t undermine or discredit his other research (and I definitely don’t think he’d disagree with your findings, b/c it does nothing to discredit their cause, but support it).

        Finally, I do realize that the ID movement has a broad spectrum, but which key ID figures would you classify as pushing forward a no “common descent” agenda? From my experience, most acknowledge “common descent” as uncontroversial when it’s defined that “many different varieties of similar organisms within different species, genera, or even families are related by common ancestry”. Note that it is possible for some scientists to accept evolution when defined in this sense without necessarily accepting evolution defined as universal common descent— the idea that ALL organisms are related by a single common ancestor.

        Universal common descent is still in question by the majority of the ID community but not outright refuted (although things appear to be leaning more in that direction). However, the “Blind Watchmaker” thesis (the idea that all organisms have not only descended from a universal common ancestor, but that that the mechanisms of natural selection, random variation and mutation, and perhaps other similarly naturalistic mechanisms, are completely sufficient to account for the appearance of design in living organisms) has garnered enough scientific evidence to reject its theoretical conclusion.

        Do you agree when “common descent” is defined under those terms, or no? Thanks.

        • When I say “common descent” I mean universal common descent from a single cell, not a common designer or some other such idea.

          I spoke to Stephen Meyer personally a month ago at the London conference and he said that he is very skeptical about common descent. His co-author Paul Nelson who did much of the research behind Meyer’s books is even less favorable to CD than Stephen is.

          The whole point of Darwin’s Doubt is to say that the Cambrian requires intelligent design as in “outside influence.” A great deal of that book argues that the evidence FOR common descent is poor, that there are all kinds of missing steps and that the genetic records don’t match up well etc.

          You are absolutely right that we are both arguing against “natural selection = blind watchmaker” and blind materialistic forces, bottom-up view of the universe, reductionism and scientism. We agree about a great number of things.

          However ID, as commonly understood, absolutely positively IS a God-Of-Gaps argument.

          I am at best neutral towards whether God is the answer to the gaps. I greatly prefer the position that there are no gaps, that it’s all pre-loaded from the big-bang on. I also freely admit that Origin Of Life has every appearance of being a true singularity event. (But in time we may discover otherwise.) You can’t prove one way or the other, really, but the no-gaps position is more honoring to scientists and the jobs they do and it’s more productive towards the enterprise of science itself.

          If you read my book “Evolution 2.0” you’ll find that the Discovery Institute doesn’t give nearly enough credit to mechanisms like horizontal gene transfer, epigenetics, symbiogenesis, hybridization and transposition and viruses to account for the entire evolutionary story. This approach is consistently delivering answers and tremendously useful insights for medicine, treatment of disease, technology etc.

          I think arguing against evolution itself at whatever level is a fool’s errand. Evolution such as it actually operates in real time experiments speaks to a level of sophistication in the universe that creationists and Richard Dawkins fans have scarcely dreamt of.

          In Chapter 17 I take both Dawkins and Meyer to task for never really explaining the empirical evolutionary toolbox at all.

          I am not throwing Meyer under the bus. But I am saying that ID as normally formulated has missed the biggest story in the entire history of science, which is the discoveries of McClintock, Margulis and the like. And ID by nature irritates scientists by pitting science against theology.

          If you really ‘get’ the import of what those women figured out, it will tilt your world.

          • Sean Davis says:

            Hey Perry,

            I have a stronger hold on theology and philosophy than I do physics/engineering, but I am trying to learn more about the science surrounding “origin of life” theories and their philosophical implications. So my comments and questions are less to argue, but more a humble attempt to find out more about where you’re coming from in relation to Intelligent Design and Naturalism in hopes of learning a little more and sharing some things I know.

            Maybe I’m wrong, but while I’m familiar with the widespread perspective surrounding ID, fundamentally doesn’t it come down to whether the epistemological framework of dna, a cell, body plans,etc display elements of design or whether it can be proved through random occurrences and natural causes? The information you provide regarding the transformative power of epigenetics are compelling and fascinating, but I don’t think they do anything to undermine the essential argument surrounding ID.

            There are a few things that came to mind following your reply that I’d like to discuss:

            1) Epigenetic information is still transcribed from DNA, correct? Therefore, the question is still begged, where does that information come from? You get there and ultimately you still have an “either/or” scenario that the scientific community is not willing to address-> Random or Design?

            2) Historical science will never be completely exact-> you must continue to explore, test, prod, review, and examine, but ultimately there are challenges to recreating exact environments without error, bias, or guesswork. That’s why historical science can never be exact. In fact, no science can be exact outside of the laws that govern them-> Godel’s Theory, if correct, demonstrates that). Having said that, scientific inquiry into “origin of life” type questions do require some inference to the best explanation. Rigorous testing of that best explanation should be permitted. I do recognize that ID mostly pursues a negative argument, but I also believe that Demski has attempted to lay a framework (CSI) that permits a positive argument for ID Theory. Here is a more comprehensive argument reflecting on how ID is not “A God of the Gaps” argument: Furthermore, the “God of the Gaps” argument bears no weight. John Lennox states, “If you define the God to be the explanation for what science has not yet explained, then you have to choose between God and science as a logical trajectory. But the God of the Bible doesn’t just fill gaps, He’s the God of the whole show-> The bits of we understand and the bits we don’t.”

            3) Bias comes from all perspectives. Its unavoidable. The science has philosophical implications to “Meaning of Life” type questions, but ultimately those philosophical biases are foundational to the scientific theory, methodology, and conclusions. Having said that…science isn’t blind exploration but it starts with a conceptual idea or belief that is then studied and examined. Often our biases cloud judgment-> It’s a psychological consequence known as “Cognitive Dissonance”-> We ignore or dismiss what’s otherwise obvious to an unbiased observer b/c our finding our filtered towards what we hope to find (see Einstein on his initial mistakes before uncovering his Theory of Relativity). The growing conflict within the scientific community regarding issues with naturalism as an explanation for “Origin of Life” questions is flipping a script on this new epigenetic research (one that used to be denied emphatically, b/c the more complexity provided more questions to a naturalistic explanation through random occurrence) and trying to now fuse it with a naturalistic explanation.

            4) Isaac Newton showed through his principles that a logical sense could be made of a variety of apparently disconnected phenomena, and that the symbolic language of mathematics could account for aspects of reality as diverse as orbiting spheres and falling apples. Newton’s work was grounded firmly in a rational belief that such Order required Divine Orderer, which was foundational to the rationality governing scientific inquiry to begin with and was instrumental to the scientific revolution in the West. But the Enlightenment, and ultimately Modernism, ushered in a glorification of the laws in and of themselves, along with the deification of humanity in its perceived capability of unlocking the mysteries surrounding them (where does humanity’s intelligibility come from to even comprehend and relate with these laws?-> but that’s another topic). The Grand Designer of these laws got lost in the mix. It’s not a unique experience-> Adam and Eve, the Tower of Babel. Both speak to the passion underlying the heart of man-> It’s desire to be like God. That hidden passion is what underlies this controversy today. And it’s exactly why people not only pursue scientific explanation nobly, but also resist or refuse any explanation other than a naturalistic one, even when it’s staring them dead in the face. It’s a naturalism of the gaps b/c the thought of a supernatural explanation outside of space and time has been outright rejected (see Godel’s Theory again). Keep in mind, that status quo has really only been relevant for the last 150 years. It reminds me of a great quote from Ludwig Wittgenstein- “The great delusion of Modernity is that the laws of nature explain the universe for us. The laws of nature describe the universe, they describe the regularities, but they explain nothing.

            Thanks again!

            • I completely agree with John Lennox.

              My view is 100% compatible with intelligent design, lower case i and d, intelligent design writ large. I’m not in agreement with Discovery Institute Intelligent Design, which is a somewhat political movement that does, at the end of the day, present a God of Gaps argument.

              I used to be very similar to them in my approach ie 2005, but have shifted my approach. See When you have an unanswered question you post a big reward for it instead of forcing people to choose between God and science. If you read my God of Gaps article and click the links you’ll see that Origin Of Information is FAR from solved, as you say.

              Your philosophy of science comments are all appropriate. Your #4 is all correct as well.

              The nuance that is important to me is to not put the practicing experimental scientist in the crossfire, and to not disrespect their quest. And yes their quest operates within a philosophical framework which most people don’t know is only possible because Judeo-Christian theists in the middle ages believed, through faith, that God made a universe with fixed discoverable elegant laws.

              • Bass Afrass says:

                I have a hard time conceptualizing how any miracle or supernatural event would not be susceptible to the “God of the gaps” accusation. If it is truly a miracle or truly supernatural then there is no way science can explain it or necessarily reconcile the data before it. If God really did bring everything into existence from nothing then no observer or measuring equipment will be able to find scientific explanation, even if it was there to hypothetically witness it firsthand. Or if a team of scientists were examining the water under Jesus feet as He walked on it, there would be no empirical data to explain it. And yet in cases such as these where science is inadequate then the “God of the gaps” argument can be made. How is that adequate when it comes to handling the actual supernatural? Doesn’t it come down to presuppositions about whether or not the supernatural is even possible, or of course if God exists? If one denies the possibility of the supernatural then every divine explanation for an actual supernatural event will look like a “God of the gaps” explanation to those with those presuppositions right?

                • If you take a look at you will see that I am 100% fine with miracles.

                  I am just greatly biased in favor of miracles you can actually observe, as opposed to miracles that happened 1 billion years ago.

                  I believe that God wants to reveal himself maximally to mankind so that means OBSERVABLE miracles in the present and in the case of nature, nature being self sufficient and not requiring intervention when we were not there to see it.

                  Yes it is possible that origin of life is a literal miracle and intervention from God. And I am personally quite comfortable with that. However scientifically I am biased in favor of there being a naturalistic explanation and I believe we should search for those.

                  As long as we are 100% honest about what we know and do not know then there is no danger in that at all.

                  • Scott Harwell says:


                    You must have a confused theology based on this post. As a follower of Christ, may I assume you believe he turned water in to wine, walked on water, commanded a storm to cease, casted out demons, healed lepers, lame persons and blind men, raised people from the dead and rose from the dead. These would all be supernatural events.

                    However, when it comes to life, your post appears to read that you believe in “natural” causes. Would this include abiogenesis and the initial chemical and molecule evolution of the first life? Are you a theistic evolutionist or do you believe in “punctuated creationism?” I analogize this to Gould’s theory to explain the absence of any evidence of evolution in the fossil record which, in a nutshell states that evolution is a slow gradual process that we cannot observe in real time but it cannot be observed in the fossil record because is is too fast to observe. At least Gould was honest enough to admit the problem and propose a theory to attempt to explain the lack of fossil evidence.

                    If you believe in macroevolution, how do you explain the increasing information from the “simple” cell and first life when observable science shows loss of information?

                    I am not saying God could not have used a macroevolutionary process but you have to perform mental and spiritual gymnastics to avoid clear teachings in the New testament about Adam.

                  • Scott Harwell says:

                    Brevity did not answer my question as to the miracles ascribed to Jesus of Nazareth. Do you believe these miracles occurred as recorded in the 4 Gospels? Simple question.

                • Scott Harwell says:

                  You are somewhat correct but the God of the gaps argument is the naturalists way to say we don’t know how historical events happened (the universe and life) and theists are just using God as a crutch to explain the unknown. Intellectually honest naturalists admit that they have a “naturalism” of the gaps belief and believe and have faith that everything has to be explained by natural causes. Simple philosophical and scientific principles of cause and effect defy the naturalistic presupposition that everything came from “nothing.” Again, honest naturalists and evolutionists will admit that they have numerous “just so” positions because they must hold to this position to avoid the supernatural alternative. These are the only 2 games in town and the evidence points to a First Cause and the design in the universe and life points to a Designer.

                  If you want to have faith and believe that there is no God and we are all cosmic accidents, you just need to recognize that it is based on faith in “not God.”

                  In my on-line and personal encounters with naturalists, most have never actually studied and researched this issue and have merely been taught that the “just so” theories are fact.

                  There are hundreds of books on this topic by very intelligent theists and not all are Christians. Check out Anthony Flew’s book and why he “converted” to theism. Berlinski’s book “The Devil’s Delusion” shreds the “science” behind naturalism.

                  Behind the curtain that is naturalistic science on origins, the emperor truly has no clothes.

                  • Scott Harwell says:

                    I do not have any intellectual or spiritual qualms with many of your positions. We have “real” scientific examples of species “evolving” in real time to environmental conditions and stimuli. Based on the foregoing, I have no doubt that God “programmed” DNA in cells to be able to quickly adapt and survive to varying conditions. However, until such time that science can prove via observable, repeatable and falsifiable methods that a simple cell like bacteria can change in to something other than bacteria, all I see is micro-evolution and on this both theists and naturalists can all agree on this. Until such time, the naturalists must have faith and just believe it happens and it is a “just so” position for them at this time.

                    As for abiogenesis, do you believe God created the first living cell and it then evolved in to me and you OR do you believe that the first life came in to being via chemical evolution by solely natural processes?

                    • We do know that simple cell-like bacteria can merge with other organisms (experiments by Kwong Jeon for example) and that we see symbiotic relationships all over the place in present nature, like the fact that a chloroplast is actually a blue-green algae living inside a eukaryotic cell.

                      And we know that hybridization produces bona fide new species. We know that both of these things can happen in weeks months or a year or two. Not centuries, not millennia, not millions of years.

                      Both of these examples are more than what most people call “micro” evolution. By definition this is macro.

                      For me personally it’s not too much of a stretch to put together symbiogenesis, hybridization, epigenetics, horizontal gene transfer and transposition and retroviruses and see how you get from one cell to present earth in 4 billion years.

                      I explain my take on origin of life at

          • Richard C. says:

            Perry, there are many of us who have analyzed these issues and conclude that universal common descent is not plausible using the neo-Darwinian processes. Your position suggests that universal common descent is plausible if the cells themselves contain the information and ability to modify themselves (in real time or upon reproduction) intelligently. Your position does not support universal common descent via undirected purposeless physical processes.

            Your book establishes that codes (including encoder and decoder devices) have never been shown to arise via undirected physical forces and processes. The DNA code to build a new organism would have had to be modified from the previous code. If the DNA (or some other cell element) contains intelligence sufficient to self modify its own code and build a new organism, that’s fine — but that is not what Neo-Darwinism says happens. Your book thus shows why universal common descent might be plausible only if the code systems were intelligently directed. (Right?)

            • Yes you are right. I reject Neo-Darwinism. It is utterly incapable of doing what it claims. Darwin himself was actually about twice as correct as the Neo-Darwinists. We have to backtrack all the way to the 1940s, and re-frame biology from the standpoint of McClintock, Margulis and the like, then come back forward. Fortunately almost all the experimental data can be reframed in the new view.

  3. Gilles St=Pierre says:

    More than a Century ago, Henri Bergson proposed a radical new theory of evolution without any reference to God. This is not ID. It’s a new definition of matter (matter-image) and a new theory of knowledge based on the reality of time, movement, and memory. Lynn Margulis was right, they have excluded life from biology and this led us in a very dangerous dead-end.
    Dawkins, Coyne and Moran are not defending science, but an outdated biology.

  4. Thanks for this Perry – it’s a really accurate succinct summary of a challenging and revolutionary three days.

    • Thank you. I’ve gotten similar feedback from several other people who were there. I’ve also gotten numerous comments that the Carl Zimmer version did not accurately represent the conversation between Denis Noble and David Shuker.

  5. FredD says:

    If new discoveries show evolution in real time, not requiring “miyons and biyons” of years of the Darwinists, and displaying a core purpose and logic for its changes… then is it logical to assume a “purpose maker”? The dreaded I.D. of some sort? If this real time evolution is fast and therefore no longer requires those “miyons and biyons” of years… does that not give some credence to the “young earth” theorists? Has the evolution karma run over their long held dogma? And like all of us who love our dogma, we will mourn and deny its passing. Oh the “rusty” irony!

    • Use your full name.

      Speed of light precludes any possibility of a young earth. Search “speed of light” on my blog for more.

      The Extended Synthesis raises a great many philosophical questions that the materialists thought they had put to bed a long time ago.

      • Scott Harwell says:

        I am not a young universe/earth advocate. The Bible simply states, “In the beginning, God created ….”

        However, one must assume that the speed of light is and always has been constant. I have read where it has actually changed since it was first measured but this has never been a focus point of any serious study on my part.

        • In a whole bunch of physics equations – equations that experimentally work VERY well – speed of light is a constant. Like E=MC^2.

          If it wasn’t, all of physics would disastrously fall apart. Even conservation of matter and energy falls unravels. The tremendous success of things like cell phones and internet indicates that it really is a constant. So if a star is 100 million light years away, then that light left the star 100 million years ago and the universe is old – and that pretty much settles that.

          I’m fairly dogmatic about this because this is not remotely controversial in physics and engineering, and because YEC is not serving theology or science. If you teach YEC to kids it’s a ticking time bomb, like it was for my brother.

          I apologize if this sounds brusque. It’s certainly not intended that way.

      • Mzungu Mkubwa says:

        Would be interested to know your thoughts on recent cosmological theories that the speed of light is not actually a constant, but has changed over time. I watched a “documentary” on Netflix regarding this “breakthrough” entitled “Einstein’s Biggest Blunder” and it was quite interesting. Ramifications could be quite far-reaching if any truth to it.

  6. Ed Gosnell says:

    Wouldn’t any species that developed a usually dormant survival mechanism that allowed it to adapt or even evolve in a seemingly directed hyper manner to a rapidly changing environment have an advantage over species without such a mechanism? It seems to me that it is the complex mechanisms that initiate such changes rather than basic principal of survival of the fittest that are the mystery here. An example of such a mechanism would be mothers who in a suddenly chaotic violent environment experience hormonal changes that result in male children with higher testosterone levels making the children bigger and meaner.

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