A New Theory of Evolution

I invite you to consider…

What if evolution were true, but it wasn’t quite like Darwin said?charles_darwin_vegan_soldier_c

What if there were a new evolutionary model that could explain why fossils show almost no change for millions of years…. then suddenly the Cambrian Explosion: Thousands of new species emerge intact, virtually overnight.

What if this new theory pointed the way to new innovations in artificial intelligence and adaptive computer programs?

What if “Evolution vs. Design” wasn’t an either/or proposition – but both+and?

What if, instead of arguing endlessly about fossils, we could precisely track evolutionary history with the precision of 1’s and 0’s?

Read more »

Can Anybody Actually Win The Evolution 2.0 Prize?

evonne_crayonsCan Anybody Actually Win The Evolution 2.0 Prize?

Science, God, and

Happy Chemical Accidents


There’s a million codes out there. HTML, bar codes, zip codes, Java, English and Chinese.

Out of a million codes, 999,999 are designed by humans.

There’s one code we don’t know the origin of – and that’s DNA. We don’t know of any codes that are not designed. This implies design in DNA.

That’s an unsolved science mystery. So I and a group of Private Equity Investors have formed a company, Natural Code LLC, to offer a multi-million dollar technology prize for Origin Of Information.

Read more »

Evolution: The Untold Story, Part 1

There are two kinds of evolution:

1) There’s the version that you read about in the bookstore. It’s two-thirds science fiction.

2) Then there’s the version that PhD biologists, cancer researchers and genetic engineers use to do their jobs.

The two are entirely different.

Popular books tell you evolution works like this: Read more »

Francis Collins on Faith vs. Science

FRANCIS COLLINS, U.S. DIRECTOR OF THE HUMAN GENOME PROJECT: “Will we turn our backs on science because it is perceived as a threat to God, abandoning all the promise of advancing our understanding of nature and applying that to the alleviation of suffering and the betterment of humankind?

“Alternatively, will we turn our backs on faith, concluding that science has rendered the spiritual life no longer necessary, and that traditional religious symbols can now be replaced by engravings of the double helix on our altars?

“Both of these choices are profoundly dangerous. Both deny truth. Both will diminish the nobility of humankind. Both will be devastating to our future. And both are unnecessary. The God of the Bible is also the God of the genome. He can be worshipped in the cathedral or in the laboratory. His creation is majestic, awesome, intricate and beautiful—and it cannot be at war with itself. Only we imperfect humans can start such battles. And only we can end them.”

Photo by: National Center for Advancing Translational Sciences

Nassim Nicholas Taleb on Synthetic Life

“At the time of this writing, the biologist Craig Venter is engaging in the creation of artificial life. He conducted experiments and stated them in a famous paper titled “Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome.”

“I have an immense respect for Craig Venter, whom I consider one of the smartest men who ever breathed, and a “doer” in the full sense of the word, but giving fallible humans such powers is similar to giving a small child a bunch of explosives.

“If I understand this well, to the creationists, this should be an insult to God; but further, to the evolutionist, this is certainly an insult to evolution. And to the probabilist, like myself and my peers, this is an insult to human prudence, the beginning of the mother of all exposures to Black Swans.”
-Nassim Nicholas Taleb, from his book “Antifragile.”


How Trees Talk To Each Other – Suzanne Simard

“A forest is much more than what you see,” says ecologist Suzanne Simard. Her 30 years of research in Canadian forests have led to an astounding discovery — trees talk, often and over vast distances. Learn more about the harmonious yet complicated social lives of trees and prepare to see the natural world with new eyes.

Is Intelligent Design really just Old Earth Creationism?

I got this astute blog comment from Frank Morris:

“I was so impressed by your debate with Stephen Meyer 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.

“Cells 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. Thanks for the article.”

I replied back to Frank:

Bingo, Frank, 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, so therefore life cannot be understood in purely reductionist terms. One would have thought that the ID crowd simply wanted the world to embrace an holistic understanding of nature. And that they would be happy for us to have done that.

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

What this debate shows is that Intelligent Design a la Discovery Institute is actually Old Earth Creationism. Also, 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.

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. A scientist must discover natural processes using the scientific method. That is his job. Otherwise, no paycheck.

One time I said to one of the Discovery Institute employees: “James Shapiro at the University 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.”

In November the Royal Society Meeting showed that Shapiro, Noble, Jablonka and the other Third Way scientists are making admirable headway in getting their program accepted by the mainstream.

But at the end of the day the Discovery Institute, instead of healing the war between science and religion, is actually perpetuating it.

Yes, Frank, your understanding of cells is very much the same as mine.

Thanks for buying Evolution 2.0, I believe you will enjoy it. Welcome to the blog and don’t be a stranger.

Richard Rohr on Evolution

“The universe really is “inspirational matter,” we now know, and is not merely inert. Now we might call it instinct, evolution, nuclear fusion, DNA, hardwiring, the motherboard, healing, growth, or just springtime, but nature clearly continues to renew itself from within.

“God seems to have created things that continue to create and recreate themselves from the inside out. It is no longer God’s one-time creation or evolution; rather, God’s form of creation precisely is evolution.”

-Fr.Richard Rohr, from his book Falling Upward

Are Cells Intelligent?

I had a great exchange with a gentleman, Matthew Taylor, on the Unbelievable discussion board, following my debate with Stephen Meyer.

Matthew said:

I was intrigued by the suggestion by one of the guests that cells might have some form of intelligence.

I’d like to know what experiments and tests have been proposed so that evidence of this intelligence can be shown and measured. It’s all well and good coming up with far out ideas like that, but if they can’t be demonstrated there is little point is trying to build an idea based on the hypothesis. It would be far more honest to prove the claim before trying to build an idea on it.

I replied:

Bonnie Bassler’s TED talk “How Bacteria Talk” is a great start:

Nobel Prize winner Barbara McClintock had a lot to say:

“The ability of a cell to sense these broken ends, to direct them toward each other, and then to unite them so that the union of the two DNA strands is correctly oriented, is a particularly revealing example of the sensitivity of cells to all that is going on within them. They make wise decisions and act upon them.

Time does not allow even a modest listing of known responses of genomes to stress that could or should be included in a discussion aimed at the significance of responses of genomes to challenge.

In addition to modifying gene action, these elements can restructure the genome at various levels, from small changes involving a few nucleotides, to gross modifications involving large segments of chromosomes, such as duplications, deficiencies, inversions, and other more complex reorganizations.

The responses of genomes to unanticipated challenges are not so precisely programmed. Nevertheless, these are sensed, and the genome responds in a discernible but initially unforeseen manner.

A goal for the future would be to determine the extent of knowledge the cell has of itself, and how it utilizes this knowledge in a “thoughtful” manner when challenged.

Induction of such reprogrammings by insects, bacteria, fungi, and other organisms, which are not a required response of the plant genome at some stage in its life history, is quite astounding… It is becoming increasingly apparent that we know little of the potentials of a genome. Nevertheless, much evidence tells us that it must be vast.

The stimulus associated with placement of the insect egg into the leaf will initiate reprogramming of the plant’s genome, forcing it to make a unique structure adapted to the needs of the developing insect. The precise structural organization of a gall that gives it individuality must start with an initial stimulus, and each species provides its own specific stimulus. For each insect species the same distinctive reprogramming of the plant genome is seen to occur year-after-year.”

From Barbara McClintock’s 1984 Nobel Prize paper

“Life requires cognition at all scopes and scales. The critical factor in evolution was the moment of instantiation of the self-referential cell. How that occurred is unknown, but the fact that cells are self-aware problem-solving agencies cannot be reasonably disputed. I offer that it is best to consider it as a phase shift derivative of the thermodynamic scale as a state function. As a result, the cell acquires critical participant/observer status, by which physical data becomes information that can be used to solve problems through the attachment to the larger information space.

It proceeds then by differing means. This is best understood as engineering in the sense that Shapiro indicates with his concepts of natural genetic engineering. However, in this circumstance, it is natural cellular engineering (acknowledging the vital importance of all aspects of the crowded, active cellular environment including the cell membrane). It is clear then, that genes are tools and not a dominating agency. This process of cellular engineering is conceptually just like humans making a city though competition and collaboration wherein every individual (cell) is serving its own interests which are then reciprocally linked to all other participants. This is evolution as successive rounds of niche construction, emanating from the cell as the first niche construction, as John Torday has correctly identified. When we, as humans build we use the tools we have according to our abilities. Cells do the same, and their substrate are bioactive materials.”

-William Miller MD author of “The Microcosm Within”

“Cells are cognitive entities possessing great computational power. DNA serves as a multivalent information storage medium for these computations at various time scales. Information is stored in sequences, epigenetic modifications, and rapidly changing nucleoprotein complexes. Because DNA must operate through complexes formed with other molecules in the cell, genome functions are inherently interactive and involve two-way communication with various cellular compartments. Both coding sequences and repetitive sequences contribute to the hierarchical systemic organization of the genome. By virtue of nucleoprotein complexes, epigenetic modifications, and natural genetic engineering activities, the genome can serve as a read-write storage system.”

James A. Shapiro, Genome Informatics: The Role of DNA in Cellular Computations

Matthew said:

What I see in your reply are selected quotes which would appear to agree with your assessment. I am pretty sure if I spent some time googling and could find some quote that disagree. We could have a fun game of quote ping pong. Quotes don’t provide demonstrable proof.

I responded:

I don’t think you can “prove” this one way or the other. And I don’t think there’s a lot of value in watching the ping pong of opinions go back and forth.

What you can do is look at what cells, plants and animals actually do in real time and ask yourself, what is the most reasonable explanation?

I would simply suggest that you read with care and detail, Barbara McClintock’s paper “The Significance of Responses of the Genome to Challenge.”

See what her cells and plants did in real time in real experiments and decide for yourself. But in any case, look at the original data. It’s all out there for everyone to examine.

Matthew said:

I would agree that some incredible things happen in cells. My problem is drawing a conclusion that can’t be proven. I also don’t like the suggestion to ‘decide for yourself’.

You might look at it and say it shows evidence on innate intelligence and that means a god put it there. I might look at it and say it’s evolved function and it only looks intelligent because we can’t see all the evolutionary steps that brought the illusion of intelligence.

How does one tell from that evidence if either of us is close to the right answer when what we are doing is deciding for ourselves? Deciding for ourselves tends to bring in our own biases. I would contend that what we should be doing is asking what the evidence suggests and then seek ways to confirm those suggestions.

I don’t think there is enough to be certain that intelligence is the answer. And you still need to make the link from that apparent intelligence to your specific god, which is whole other challenge and discussion.

I responded:


For decades, “anthropomorphic language” has been forbidden in biology. (Except, of course, when talking about things like “selfish genes” – which really just shows you it’s impossible to avoid such language, even for people who are stark materialists.)

But the pendulum is swinging the other way now. So at the present time if you go searching all you’ll find is a lot of disagreement.

When I’ve tried to answer this question for myself, I go to two places: digital communication and genetic algorithms.

Genomes and cells are linguistic (see the paper “Linguistics of DNA” by Ji or Bonnie Bassler’s TED talk “How Bacteria Talk). And the genetic code is a proper code, and DNA transcription and translation are formal encoding and decoding systems. It’s digital communication.

The huge realization I had when I started this was the incredible parallels between DNA and Ethernet, because I had written an Ethernet book. The similarities were almost scary. Encoding, decoding, error detection, error correction, checksums, layers. On and on.

In digital data, information is always encoded top-down, and decoded bottom-up. When you send an email, your intent becomes words which are made of letters which are represented by bits. You press send, the bits go across, and it’s re-assembled in the opposite order.

The start of that process is your own conscious intent.

Even if a computer is automatically generating emails, they always originated from a conscious source.

I have never seen any exception to this.

So whenever I see communication taking place, I see a chain of intentionality that always leads me back to a conscious source.

If it walks like a duck, talks like a duck, and quacks like a duck…. well, I vote for cells being intelligent. At least in some sense.

The other clue is genetic algorithms.

Darwinists tell you that random copying errors and natural selection can evolve anything.

Well if that’s true, where are all the software companies that should allegedly be writing their software that way?

How come there aren’t any? Can you name even one?

How come Genetic Algorithms are little more than a footnote in the software development industry?

Why doesn’t Apple or Google have any use for programs like Tierra or Avida?

How come it usually takes more work to create a fitness function and develop systematic mutation flows for a Genetic Algorithm, than it does to simply sit down and write the code by hand?

If you could write software that evolves the way Darwinists say life evolves, Bill Gates wouldn’t need payroll. He could just buy a million servers and let Genetic Algorithms churn out the next version of Windows.

I’ve started two software companies in my career. I had equity in a hardware company that we sold to a NASDAQ firm for $18 million. And I’ve never seen software that writes itself, let alone develops without significant input from intelligent agents.

Yet cells demonstrably DO program and re-program themselves and evolve in real time. If we knew how cells do this, we could write incredible software.

But the funny thing is, if you read books by old-school Darwinists like Richard Dawkins, Jerry Coyne and Bill Nye, for some reason they never tell you any of this stuff. Nary a word about transposition, symbiogenesis etc. Everything’s just natural selection, natural selection.

The last question I would ask myself is: “Which hypothesis is more likely to lead us to interesting discoveries, new hypotheses and interesting observations? A) the idea that cells are dumb machines created by a series of accidental mutations and selected for survival, or B) the idea that cells are intelligent agents that direct their own development?

Which premise would help you make better antibiotics? Which premise would help you fight cancer better? Under which premise would you be less likely to underestimate your opponent when combating disease?

Darwinism vs. ID vs. Evolution 2.0



Intelligent Design

Evolution 2.0 (a.k.a. Third Way, Extended Synthesis)

Origin of Life

Presumed to have emerged from random chemical processes

Created by an Intelligent Designer

Information theory says codes require a designer, or else an undiscovered emergent process that generates codes



Instantaneous events of intervention

In real time

Sources of Novelty

Random copying errors; natural selection is the hero

Insertion of information by outside agent

Transposition, Horizontal Transfer, Epigenetics, Hybridization, Symbiogenesis, Niche Construction, Retroviruses

Scientific Status

Randomness impossible to prove; much of the evidence is anecdotal, not empirical; millions of years too long to test

Supported by inference; not possible to experimentally demonstrate; rejects methodological naturalism

Demonstrated in 70-plus years of documented live lab experiments

Implications for Humanity

Chance, luck, and “blind pitiless indifference” of an uncaring universe; social Darwinism

Man is a special creation

Profoundly directional, cooperative process that invites us to humble ourselves and study with care

Implications for Science & Technology

Humans are smarter than nature, so we must now begin to direct our own evolution

Scientists can study designs, but not the design process

Nature is far wiser than we are, suggesting caution; cell research promises tremendous breakthroughs in medicine and engineering




Systems biology: There is no privileged point of causation

Implications for Spirituality

Religion is a myth, a way for “holy men” to wield power over the masses

Most commonly associated with evangelical Christianity

Science points to something beyond itself, far greater than us or the universe


Truth or Market Share? Intelligent Design vs. Evolution 2.0

After my radio debate with Stephen Meyer, the Discovery Institute Volleyed back.

They took umbrage with me defining the debate in terms of “Market Share”:

Perry Marshall: 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.

Sure, I’m talking about eyeballs. But I’m also talking about truth and street cred.

Every year, scientists discover natural systems and processes that creationists and ID people long ago declared to be interventions of an Intelligent Designer.

This does not bother most religious people, because in the end God made everything anyway. But every time this happens, ID gets a black eye.

This makes a world of difference to a scientist, who can only get paid to discover natural processes.

The ID framework may help a scientist see order where others only see randomness. But at the end of the day it still has to be a process.

Otherwise, no paycheck.

Yeah, I know. Paychecks are crass too.

But scientists still have to earn them. And those grant committees can be brutal.

Does my preoccupation with paychecks and empiricism make me less interested in the truth? Absolutely not. Because truth takes many forms.

Suppose DOS evolved into Windows 10 over the last 35 years, all by itself, with no software engineers in Redmond Washington… suppose it developed a Windows desktop, an internet connection, a browser, Word and Excel… all by itself.

Would you be less impressed with Bill Gates? Or would you be more impressed?

And if DOS could evolve into Windows 10, would you accuse Bill Gates of monistic idealism or quantum mysticism? Or would you suspect he was far and away the greatest software genius that ever lived?

And if you’re any kind of engineer or entrepreneur, wouldn’t you want to know how that self-adapting software works in the first place?

Do you think you might find some cool applications for code like that?

What I’m suggesting is: ID sets its sights way too low.

Darwinists underestimate nature. Creationists underestimate God.

I’m not merely theorizing. When I discovered Barbara McClintock’s work in 2006, I said to myself, “HOW COME NOBODY IS TALKING ABOUT THIS???? This is the biggest untold story in all of science – and everybody is just ignoring it!”

In McClintock’s 1984 Nobel Prize paper, she describes the adaptive behavior of genomes. The title of her paper is “The Significance of Responses of the Genome to Challenge.” In this paper, she describes not only threats for which her plants clearly had pre-programmed responses (like heat shock) but also singular responses to unique threats that no plant could possibly anticipate.

Barbara wrote, “Induction of such reprogrammings by insects, bacteria, fungi, and other organisms, which are not a required response of the plant genome at some stage in its life history, is quite astounding… It is becoming increasingly apparent that we know little of the potentials of a genome. Nevertheless, much evidence tells us that it must be vast.”

She continues, “A goal for the future would be to determine the extent of knowledge the cell has of itself, and how it utilizes this knowledge in a “thoughtful” manner when challenged.”

You can label this monistic idealism. You can call it mysticism. I call it empirical scientific observation. I call it not being afraid to ask an incredibly obvious question:

“How do those cells know how to do that???”

The first algorithms I wrote were on my HP calculator in college. For the last 15 years I’ve been advising advertisers who spend tens of thousands of dollars per day on Google AdWords how to deal with Google’s 21st century algorithms.

I know algorithms.

And what a plant does is not an algorithm.

“Algorithm” is a useful metaphor, for sure. But whatever a cell does is a living algorithm. Something human engineers have no category or language for. The word algorithm doesn’t begin to capture what the cell actually does.

And please note, McClintock was not theorizing about what might have happened over millions of years. She was describing direct personal observation and experiments.

Is all of this “front loaded”? Is it pre-programmed? Or is nature in some sense truly free to develop as it desires?

I don’t know. But as a person who’s worked with information systems in acoustics, digital signal processing, analog signal processing, digital communication protocols for 35 years, having authored an Ethernet book, the only things that do what living things do are things that possess willfulness and linguistic capability.

Which is exactly what I’m seeing when a protozoan cuts its DNA into 100,000 pieces and radically alters its physiology in response to stress – in 12 hours. And its “program” doesn’t even crash!

You guys are looking for miracles. But there’s one staring you in the face with every symbiogenesis experiment. There’s a natural living miracle in every McClintock paper, every Margulis paper, every Shapiro paper.

So I am pursuing a body of empirical, experimental TRUTH that grows with each passing year.

YES – “where this all came from” is a mystery. Where the information originally came from is a mystery. Absolutely it is.

Günter Bechly said, “Intelligent agents cannot be their own designers, because they have to come into existence before they can design anything.

I agree.

So the larger question is: Where do codes come from in the first place?

My answer is a $3 million technology prize for anybody who can figure it out. Because I’m here to carry empiricism as far as it can be taken.

All these questions about what bacteria “know” only serve to highlight the original origin of information problem. I suspect that the answer to both questions is the same. I suspect it’s got something to do with consciousness.

Maybe my challenge will still be here in 500 years, prize money unclaimed. Like Euclid’s parallel postulate, which stands unproven after 2500 years.

I’m fine if nobody ever solves Origin of Information. I’m also in favor of getting it solved. Maybe someone will solve it tomorrow.

Either way, we won’t have to listen to made-up stories by Richard Dawkins about warm ponds and happy chemical accidents anymore.

And if the problem of chemicals-to-code is solvable, I’m on the side of solving it.

So let’s handle a few objections before I go:

OBJECTION: “Given the lack of any physical basis for such intelligence on the level of simple organisms like bacteria, this intelligence must be based on an immaterial mind.”

ANSWER: Nobody knows why or how bacteria do what they do. Nobody knows what a cell knows about itself.

Barbara McClintock reported: “The stimulus associated with placement of the insect egg into the leaf will initiate reprogramming of the plant’s genome, forcing it to make a unique structure adapted to the needs of the developing insect.”

If one insect burrowing into a plant leaf causes restructuring of the plant’s genome, automatically forming a symbiosis between plant and creature… then what other questions have we not even thought to ask?

Are we in any position to declare what cells can’t do? Especially when most of us are ignoring what cells can do?

QUESTION: “Why do we need brains at all?”

ANSWER: Isn’t it obvious that every organ in your body possesses its own kind of intelligence? Does not the stomach “know” how to digest food? Does not your immune system “know” how to fight pathogens? And isn’t it obvious that your brain does very different jobs than either of those other organs?

And is it not true that nearly every cell in your body has the ability to cut, splice, and re-arrange its own DNA?

What are those editing systems really capable of?

Does anybody know?

I say we stand to find a lot more answers than we’ve gotten so far. I believe in God, but abdicating to God of the Gaps won’t help us in this most important of quests.

DNA, Fitness, Evolution: Perry Marshall flexes mental muscles on muscle head podcast

Why the heck would a bunch of muscle heads want to talk evolution? Simple: because it’s incredibly relevant to every area of our lives, including fitness.

I was just featured on the MindPump podcast, to talk about my work on Evolution 2.0, and the Evolution 2.0 Prize. If you’re not into fitness, you may never find this podcast (or my interview) on your own. So I wanted to make sure you saw it. Because even if you haven’t stepped a foot in a gym in the last decade, you’re still going to love this interview.

We covered a TON in the 1-hour discussion… Read more »

The Iron Curtain of Biology, Junk DNA, and the Protestant Reformation

In 1517, Martin Luther nailed his 95 Theses to the door in Wurms, Germany and started a revolution.

Seven years ago I wrote a piece called “The Iron Curtain of 2010”. There, I predicted that Darwinism would crack in ~2013. That there would be some Berlin Wall tipping-point event.

Well, I was a little early….but definitely in the ballpark.

In 2012, The ENCODE project reported that at least 80% of our DNA has at least some discernible function, in contrast to those before who insisted that 97% is junk.

ENCODE pounded a good solid nail into Read more »

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