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 »

The Royal Society’s Evolution Meeting: James MacAllister / Why Neo-Darwinism was the Biggest Mistake in the History of Science

James MacAllister, curator of the Lynn Margulis archive at the University of Massachussetts Amherst. He wrote a thorough review of the London 2016 evolution conference at the Royal Society.

James MacAllister is the volunteer archivist for the Lynn Margulis archive at the University of Massachussetts-Amherst.

Jim runs, the Environmental Evolution website. Lynn Margulis was the champion of Symbiogenesis theory.

She fought tremendous opposition from Neo-Darwinists to get the theory accepted. Today she is widely regarded as one of the greatest evolutionary biologists of all time.

I met Jim at the Royal Society evolution meeting in London, and in a very brief conversation discovered much in common. Jim runs, the Environmental Evolution blog.

He wrote a fantastic synopsis of the Royal Society meeting. I encourage you to read his entire report. Meanwhile, some highlights:

“The Modern Synthesis, while undoubtedly productive for a time, is a misconception of reality that has reached the limits of its explanatory power. The problems are fundamental. No amount of cosmetic surgery is going correct them.”

“Most of these ‘new trends’ are not new nor are they trends. They have been known and studied quite apart from neo-Darwinism for a long time. Symbiosis and symbiogenesis, for example, have been investigated for over a century while being dismissed and discouraged by proponents of the Modern Synthesis.” 

“Awareness or mentions of these processes by neo-Darwinists fall far short of serious investigation. It is true that these processes have been bolstered or confirmed by evidence from molecular biology, but that evidence generally contradicted the view of the Modern Synthesis. The Modern Synthesis is no longer synonymous with evolutionary biology, molecular biology, or any of the multiple disciplines currently contributing to our understanding of evolution.”

“Martin Brasier, the late Oxford paleontologist, defined science not as the revelation of underlying simplicity, laws or ideals, but as “a unique system for the measurement of doubt.”  This is a helpful conception because it explains why science must be skeptical, but also measured in its skepticism. It avoids the temptation of certainty and leaves the mind open to surprise. Science measures. It compares tests to controls. Experiments and analyses are designed to minimize bias and expose logical fallacies. Results must be reproducible. Science questions unquestioned assumptions. Its theories must be predictive. It does not ignore anomalies, but acknowledges and investigates them.” 

[Jokingly] “Now, through the of magic of we-have-long-known-about-this, symbiogenesis is claimed to be part and parcel of the Modern Synthesis.” (Referring to the Neo-Darwinists who were at the conference saying ’Awww, we’ve known about this stuff for decades!” Well it was the exact same research they’d been downplaying, not funding, denigrating and sidelining for 50 years, which can no longer be ignored.)

 “There is also the current HBO series West World where the character of Dr. Robert Ford (played by Anthony Hopkins) explains to his assistant Bernard (played by Jeffrey Wright) that “evolution forged all of sentient life on this planet using only one tool, the mistake.””

“The Modern Synthesis toolbox holds only one tool: the mistake, the blind random mutation. The organism is acted upon by the environmental elimination process: natural selection. No mention of new trends.

“Let’s not forget that Darwin himself had a better selection of tools in his On the Origin of Species toolbox.  Now we are presented with a toolbox that holds many tools. Some vintage ones, such as symbiogenesis. And long recognized ones, such as horizontal gene transfer, that couldn’t be swept under the rug. But wait there’s more: interspecific hybridization, whole genome duplications, the movement of mobile genetic elements (natural genetic engineering), plasticity, and niche construction. Magically, we are told that all these fit in the The Selfish Gene toolbox. What ever happened to that little toolbox that only held one tool, the mistake?”

John Hands has reported on the meeting in the BBC online Science Focus. During the first Round Table audience discussion, Hands introduced himself as the author of Cosmosapiens: Human Evolution from the Origin of the Universe (outstanding book by the way) and made the following comments.

“It’s appropriate that this meeting is being held at the Royal Society, whose motto, we were reminded yesterday, is “Nullius in verba”: Accept nothing on authority.  The current paradigm in evolutionary biology, NeoDarwinism, also called the Modern Evolutionary Synthesis, has been the authority for some 65 years.  It is, of course, a mathematical model based on several unquestioned assumptions, whose proof was given by 1940s game theory borrowed from economics.

“What we have heard over the last 2 days is empirical evidence that new species arise rapidly, from such mechanisms as symbiogenesis, horizontal DNA transfer, hybridisation, whole genome duplication, interactive systems producing novel emergent properties, and other mechanisms described in Part 2 of my book. These mechanisms contradict the fundamental tenets of neo-Darwinism, namely:

  1. Random gene mutations provide phenotypical characteristics enabling successful Darwinian competition;
  1. These random gene mutations spread through a population’s gene pool by sexual reproduction;
  1. Darwinian gradualism leads to the genetic transformation of populations of individual species members over tens of thousands of generations;
  1. Information flows one-way from a gene to a protein in a cell. Not one whit of empirical evidence shows that new species arise from the neo-Darwinian mechanism.
[Note that John Hands’ remarks above, issued during Q&A at the very end of the 3-day meeting, were the most complete definition of Neo-Darwinism ever offered at the London conference. The Neo-Darwinists avoided using any definition at all, as it would be damning to their cause.] Hands continues:

“To the contrary, Darwinian competition causes not the evolution of species but the destruction of species.  It is collaboration in its various forms that causes biological evolution. Hence I’m surprised by calls for extending the neo-Darwinian Evolutionary Synthesis. You can’t extend something that is broken. Surely what is needed now, after 65 years, is using the empirical evidence to develop a new paradigm for biological evolution.” 

Read Jim MacAllister’s entire report on the London evolution conference here.

To subscribe to Jim’s Environmental Evolution newsletter, send an email to jmacallister {at} with the word “subscribe” in the subject field and please include your name and email address in the body.

Environmental Evolution, the first Big Earth History and Earth systems science course, was taught by Lynn Margulis at UMass from 1986-2010. Margulis was also the principle collaborator with James Lovelock on the Gaia hypothesis, the proposal that the entire earth can be understood as a single macro-organism.

Dance to the Tune of Life: Biological Relativity – Book Review

 World-class heart researcher Denis Noble demolishes Neo-Darwinism – With Grace and Wit

Just as modern astronomy has shown us there is no definite “center of the universe” (and it is most certainly notthe earth), in his book “Dance to the Tune of Life: Biological Relativity,” Oxford Professor Denis Noble shows that in biology there is no “starting point of the organism.” (And it is most certainly not the gene!)

Denis Noble is the man who worked out the details of the cardiac rhythm, which made pacemakers possible, as well as the drug ivabradine.

He received the distinction “Commander of the British Empire” from the Queen of England for his service to the sciences. His heart research involved knocking out genes and altering gene expression.
His heart research (including extensive computer modeling of heart activity) convinced him that the Neo-Darwinian conception of the gene and its role was deeply flawed. This book belongs to a growing category of critiques from “outsiders” – people not originally indoctrinated by conventional evolutionary biologists, whose professional work proves beyond reasonable doubt that Neo-Darwinism is irredeemably flawed.

The book begins with a history of astronomy, where ideas that the earth is not the center, and not even our sun or galaxy are at the center, were met with great resistance.

Noble says making the gene the immortal center of evolutionary biology is at least as great a mistake as earth-centric astronomy!

This is because it has negatively impacted fields as diverse as economics, theology, sociology, politics and literature.

Noble is a strong historian and his book uncovers the detailed history of the language and development of the ideas behind modern evolutionary theory.

He says:

“Neo-Darwinism is a product of nineteenth-century scientific thought in the last decades before the revolutions in physics leading to quantum mechanics and relativity theory.”

“Since Neo-Darwinism has dominated biological science for over half a century, its viewpoint is now so embedded in the scientific literature, including standard school and university textbooks, that many biological scientists may themselves not recognise its conceptual nature, let alone question incoherencies or identify flaws.”

“the language of Neo-Darwinism is itself a powerful barrier to the development of a more inclusive theory… it is the whole conceptual scheme of Neo-Darwinism that creates the difficulty. Each concept and metaphor reinforces the overall mind-set until it is almost impossible to stand outside it and to appreciate how beguiling it is.”

He shows how the entire field has become a prisoner of its own circular reasoning, and of an unjustified antagonism towards teleology, or purpose in nature. He explains how it is manifestly impossible to understand something like a heart if you will not acknowledge that it exists for the purpose of pumping blood, and doing so in a very particular manner.

He shows that you can only understand the behavior of a heart at a certain level of the system and that, at other levels of the system, the same behavior may appear random or invisible or incomprehensible. He shows that biology is systems within systems within systems, and that every system has a relationship to other systems.

He shows that you cannot pinpoint any particular starting or ending point to a living organism. Each effect flows from multiple causes and each cause produces multiple effects.

This reminds me of a statement made by Gary Fugle, an author and biologist who said, “there is no single place in nature where you can say ‘Aha – THERE is the hand of God, you can see it right there!’”

Although people who espouse God-of-gaps arguments take comfort in such things, those gaps have a way of migrating elsewhere in the face of growing scientific knowledge.

Noble is making a complementary statement, but aimed at scientific reductionists instead: There is no one all-encompassing, explanatory, simplistic Final Answer In Nature that says “this is the spot where everything starts.”

Rather, says Noble, goals are contextual, and just like randomness, only have meaning *with respect to something else.* He says, “It is in this context that we can understand why many prominent Neo-Darwinists are also prominent atheists. That also is a statement of faith. Part of that statement of faith is that creative purpose, consciousness and intentionality are all mirages, epiphenomena without significance or effect.”

Thus his argument for “Biological Relativity.” Every system, every goal and behavior is relative to others around it, both smaller and larger scales and levels of systems. This book will be liked by anyone who creates for a living and instinctively knows that nothing in nature is as simplistic as Dawkins’ just-so explanations and stories.

He rigorously demonstrates new models of evolution via the work of several researchers including Conrad Waddington: In direct defiance to Neo-Darwinism, learned traits are inherited, and Lamarck was right 200 years ago: organisms direct the evolution of their progeny.

Noble devotes time to describing the evolutionary toolbox of Horizontal Gene Transfer, Epigenetics, Symbiogenesis and Transposition. He shows that many evolutionary events are grand movements of large-scale sections of DNA.

He gives Neo-Darwinism credit for a number of fields of study such as population genetics but also shows how it has slowed discovery in other fields for 50 years. He blames some of this on the ever-narrowing scope of scientific categories, fragmentation of disciplines, increasingly unable to see the whole for the parts.

Some memorable quotes:

“I saw a film of a living unicellular organism, an amoeba. It could hardly have been more different from the two-dimensional sections of dead cells that I had drawn as a student. Nothing stood still. Everything was streaming this way and that as the organism moved around. When it found an object that was sensed (I assumed chemically) to be food the movements became beautifully co-ordinated as two extrusions called pseudopodia (false feet) encircled the object, eventually allowing it to be taken in as a membrane coated vesicle to be digested.

“This tiny organism had a ‘nose’: the chemical receptors on its membrane surface. It had ‘muscles’: in fact formed of protein molecules, some of them very similar to those in our cells, only not organised into separate muscular organs. It clearly had a ‘nervous system’ to connect the two together, although it had no nerves as we know them. It had a clear goal: to feed itself. As we will see later when we discuss the cell cycle, it knows when and how to reproduce itself in an intricately co-ordinated activity when it makes its genes dance as they and their predecessors have done for at least one billion years.”

“Those working on a systems approach were openly denigrated as not doing ‘real science’, not being ‘where it is at’. Later, in the 1970s when I became a member of research grant committees, I was to hear that phrase often. Being ‘where it is at’ was committee-speak for excluding any other approach. Sadly that exclusion was so successful that very little integrative research remained. Molecular biology and genomics sucked up most of the funding.”

“Neo-Darwinism is incomplete as a theory of evolution. It also suffers from deep conceptual confusions, and is not compatible with the wider range of experimental evidence we now have.”

“Why are scientists like me apparently in such a small minority? There is a simple answer to that question. We are only apparently a minority. I have discussed extensively with evolutionary and other biologists in the course of lecturing to audiences, large and small, all around the world. Exceedingly few of the tens of thousands involved have seriously defended the orthodox Neo-Darwinist view as a complete explanation.”

On the benefits of updating our evolutionary models:

“Whole areas of economics, sociology and philosophy are based on interpretations of selfish gene viewpoints. No field of human endeavour will remain untouched since the implications affect even our concept of humanity.”

This field of “Extended Evolutionary Synthesis” is growing rapidly and it’s great that a person of Noble’s stature has taken the time to write such a careful book. Just as Neo-Darwinism has leaked poison into many fields, Biological Relativity has the potential for bringing new insights into economics, sociology and many other disciplines. Noble is mature enough and well-enough read to speak to these other disciplines.

Noble is no stranger to this debate. He has every qualification necessary to critique evolutionary biology from the outside. Noble organized the first debate about Richard Dawkins’ bestseller “The Selfish Gene” in 1976 and again between Dawkins and Lynn Margulis in 2009. He was on Dawkins’ PhD review committee at Oxford. He’s an Emeritus professor at the University of Oxford.

He’s a Fellow of the Royal Society, the oldest scientific body in the world. He organized the Royal Society’s November 2016 Conference “New Trends in Evolutionary Biology” and chaired the 2nd day of the conference.

At the London conference, the overwhelming consensus from both presenters the 300 in attendance was that Neo-Darwinism is due for a major upgrade and perhaps needs to be replaced entirely.

He’s written over 500 scientific papers and he’s President of the International Union of Physological Sciences, the global umbrella organization for physiology. His keynote talks to physiologists worldwide regularly include critiques of Neo-Darwinism, and he often hears complaints from members that the evolutionary biology clique refuses to publish their papers.

He’s one of the pioneers of the field of Systems Biology and he is also editor of the Royal Society’s cross-disciplinary publication “Interface Focus.”

The book is very readable, it’s in middle-school to high school level English, and the glossary and explanations take pains to explain complex ideas in simple language.

If you’re hot on the trail of new evolutionary developments – the Extended Evolutionary Synthesis and systems like Natural Genetic Engineering and Symbiogenesis; if you’re fascinated by the Post-Dawkins evolutionary frontier, this book is a must-read.

It is part of a growing body of works that provide alternatives to the classical, textbook version of evolution that is repeated ad nauseum in the media. Other books include my own “Evolution 2.0” of course; “Evolution: A View from the 21st Century” by James Shapiro; “COSMOSAPIENS” by John Hands; “The Music of Life” also by Denis Noble, and “Acquiring Genomes” by Lynn Margulis and Dorion Sagan.

Last but not least, don’t miss these two videos by Denis Noble, via Voices From Oxford:
“Rocking the Foundations of Evolutionary Biology” presented at an international conference of physiologists in Suzhou, China

From Creationist to Atheist to Reasonable Faith

Guest Blog by Ryan Ferguson

At the age of 6, I loved my family, my dog, my Lord Jesus, awesome flying kicks and Ankylosaurus. At the age of 6, this was considered perfectly normal and no one batted an eyelid.

At the age of 12, I was told I could love four of those five things, but when it came to the God who loves me and amazing ancient creatures, I had to choose.

Why? Because Ankylosaurus lived approximately 60,000,000 years ago, while the Bible “clearly” states that God created the world 6,000 years ago.

And, as the fundamentalists’ claims went, the Bible is inerrant, so if any of it is wrong, it’s all wrong.

In other words, if I’m not Read more »

Welcome to the DMZ: The Creation-Evolution De-Militarized Zone

Between North and South Korea there’s a “DMZ,” a De-Militarized Zone. A strip of land a couple of miles wide. A buffer between the two sides. A place where people from both sides can go… and not get shot.dmz_myllissa_2

The DMZ has a number of buildings for peace talks between the two sides.

Evolution 2.0 is a De-Militarized Zone for the evolution debate.

We need this desperately. Why?

Because it doesn’t exist anywhere else!

You cannot go to university and have a Read more »

From “God Of The Gaps” to “Let’s Get This Thing Solved!”

Since giving my talk “If You Can Read This I Can Prove God Exists” in 2005, my thinking has evolved tremendously.


This continues to be one of the most argued-about talks on Origin Of Life on the web.

It sparked a 7-year debate on Infidels. At the time, was the largest atheist website in the world. This went on to become the longest-running, most-viewed thread on the site.

No one overturned my argument. Eventually Infidels did their best to make the whole episode disappear.

“If you can read this” has been pounded hard by thousands of skeptics. Every scientific detail and technical fact still stands intact today, more than 10 years later.

However I must be clear: I did not prove God exists. What I proved is Read more »

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 Read more »

Conversations Beyond Science and Religion: Evolution 2.0 interview with Philip Comella

philipcomellaThere’s more to life than just atoms and molecules. And it’s the biggest untold story in the history of science.

Philip Comella is an attorney with a philosophy background and author of the book “The End of Materialism.” On his podcast “Conversations Beyond Science and Religion” Philip and Perry discuss the untold evolution story – the one that bridges the gap between scientific evolution and common sense. Read more »

Geeking on code, DNA and Starbucks with author John Somnez

John Sonmez is a code geek if there ever was one.

He is the founder of and author of Soft Skills: The Software Developer’s Life Manual. John focuses on helping software developers, programmers and other IT professionals improve their careers and live better lives through coaching, podcasting and teaching.

John recently interviewed me after reviewing my Evolution 2.0 book. We cut right to the chase and got into Read more »

Wanted: “I was a Young Earth Creationist” Stories


I was raised a Young Earth Creationist.

Were you?

WANTED: Stories of people who lost or almost lost faith – and only came back because they realized…

There’s more than one way to read Genesis!

I’d love to feature your story here on my blog.

Post a short version in the comments below and if it’s a fit we’ll be in touch with you directly.


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