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?

What if science and faith were no longer at war?

All these things are not only possible, but a present reality.

I know that’s a pretty bold statement. But by now you’re probably used to that from me. Once again I invite you to relax, hear what I have to say, and consider the information that is presented. See if this makes sense for you.

I really do have a new theory of evolution.

Not only that, in future installments I will use this new theory of evolution to make predictions about what we will discover in the next 3-20 years.

And: after today, you may never think about this question the same way again.

Darwin predicted that the fossil record would show a gradual and steady progression from simple to complex forms of life. It’s now well known that what we see instead is long periods of stability interrupted by sudden leaps forward.

Stephen Jay Gould called this “punctuated equilibrium.” He was at a loss to explain exactly how this worked at the time. But today we have many clues pointing to the answer.

Darwin said that evolution is driven by random variation combined with natural selection.

Today I invite you to consider:

Darwin was half right.

And Darwin was half wrong.

Darwin was definitely right about natural selection.

To be fair, being right about that is no Nobel Prize winning accomplishment. The weaklings die and the strong survive. I think our cave man ancestors were familiar with that one.

(Rog hits Grog over the head with a rock and kills him, then they both get eaten by a hungry tiger. Survival of the fittest… nothing profound about that.)

Seriously, natural selection does not have any kind of creative power at all. All it does is kill of the runts.

The secret to evolution, then, has to be in the “random variation” part.

Darwin, in his time, believed that random variation in heredity produced all manner of species. He said: most of the time it’s harmful, but occasionally it’s helpful and from these variations come all kinds of beautiful forms that appear to be designed.

What is meant by “random variation”?

Thousands of biology books say it’s accidental copying errors in DNA.

They say, essentially, that it’s corrupted data that occasionally turns out to be beneficial instead of harmful.

This is where Darwin and the biology books were wrong.

As a communication engineer I know – with 100.000000000% certainty – that this is impossible.

Nowhere in the vast field of engineering is there any such thing as “the percentage of the time that corrupted data is helpful instead of harmful.”

It’s ALWAYS harmful. Always. Copying errors and data transmission errors never help the signal. They only hurt it.

Now please do not misunderstand me:


Nope…. I’m suggesting: Evolution just happens a different way than Darwin said. Way different than you were told.

I’ll get to the details of that in a minute. First I need to explain why randomness only destroys information.

Evolution Through the Lens of Information Theory: Random Mutations and Noise
More Videos Here

If we start with the sentence

“The quick brown fox jumped over the lazy dog”

And randomly mutate the letters, we get sentences that look like this:

The 6uHck brown fox jukped over the lazyHdog
Tze quick bro0n foL juXped over the lazy doF
Tae quick browY fox jumped oGer tgePlazy dog
The iuick brown fox jumped lver the lazy dog
The quiikQbKowSwfox .umped oveh the lazy dog

You can apply all the natural selection to this in the world and you’ll never accomplish anything besides destroying a perfectly good sentence. You can go to www.RandomMutation.com and try for yourself.

Why doesn’t this work?

Because it’s impossible to evolve a sentence one letter at a time – even if you deliberately TRY.

Technically, this is because random mutation is noise and noise *always* destroys a signal. Claude Shannon called it information entropy. Entropy is not reversible. Noise never improves a signal. It only mucks it up.

The only way for this to work is:
Evolution has to follow the rules of language.

So…. successful evolution for this short sentence would look something like this:

The fast brown fox jumped over the slothful dog.
The dark brown fox jumped over the light brown dog.
The big brown fox leaped over the lazy dog.
The quick black fox sped past the sleeping dog.
The hot blonde fox sauntered past the sunbathing man.

In English, successful evolution requires precise substitution of verbs and nouns and following the rules of speech.

DNA is no different. DNA has its own language. In fact thousands of linguists have made huge contributions to the Human Genome project by helping to decode the layers of the genetic code. Dozens of linguistic books describe the eerie similarity between DNA and human language.


There is a mutation algorithm that makes intelligent substitutions when species need to adapt to their environment.

It works very much like the sentences I just showed you. DNA actually re-arranges itself like a computer program that rewrites itself on the fly.

Now here’s the kicker:

This is not new. It’s actually more than 60 years old!

A New Theory of Evolution: Cellular Genetic Engineering

Some errors: Shapiro’s work was with bacteria, not protozoa. Splicing a single protein under starvation stress increased the mutation rates at least 100,000-fold. Dr. Shapiro was not able to determine how many incorrect evolution mutation attempts were made vs. successful mutations.

The 100,000 breaks come in ciliated protozoa as demonstrated by David Prescott, Laura Landweber, Martin Gorovsky and many others. These edits are highly non-random and RNA-guided, but in this case, there was no change in adaptations. These genome acrobatics go on at each episode of starvation and sexual reproduction. They convert the germline nucleus into a restructured simplified somatic nucleus.
More Videos Here

It’s only new to those who are hearing it for the first time.

It’s not just a wild hypothesis, either. It was discovered by geneticist Dr. Barbara McClintock in 1944.

The Barbara McClintock U.S. Postage stamp includes a diagram that shows how genes are intelligently transposed by the Mutation Algorithm in DNA

Dr. Barbara McClintock’s U.S. Postage stamp includes a diagram that shows how genes are intelligently transposed by the Mutation Algorithm in DNA

She was decades ahead of her time and she received the Nobel Prize for this discovery in 1983. Her picture is now on a U.S. Postage Stamp and she’s one of the greatest scientists in the history of biology.

But even now, people ask me, “Why didn’t they ever teach this to me in biology class?”

Maybe Barbara McClintock could answer that question.

Her discoveries were so radical, so contrary to Darwin, that for most of her career she kept this to herself. She she described the reception of her research as “puzzlement, even hostility. ” Based on the reactions of other scientists to her work, McClintock felt she risked alienating the scientific mainstream, and from 1953 stopped publishing accounts of her research.

Why don’t they teach this in most biology classes now?

I’ll just say, it’s not because her findings haven’t been verified.

And it’s also not because the “random mutation” model works. You may or may not have noticed, but it actually doesn’t work at all. I’ve been publicly debating this online for 5 years and I have yet to have one person send me a link or refer to a book that says, “Here is the actual experiment that proves random mutations drive evolution.”

There is no such paper or book, so far as I know. The random mutation theory, sadly, is an urban legend.

INTERESTING FACTOID: This same process of intelligent evolution is how your immune system learns to fight off germs it’s never seen before: It systematically tries different combinations and once it’s ‘cracked the code’ on the invading disease, it passes those changes onto daughter cells. Your own immune system is a miniature model for evolutionary biology.

Dr. James A. Shapiro of the University of Chicago is one of the leading researchers in this field. Let me share with you about what he’s discovered about protozoa.

What I’m about to pass along is profound, almost miraculous. I want you to read and re-read this a few times before you go on:

A cell under stress will splice its own DNA into over 100,000 pieces. Then a program senses hundreds of variables in its environment and then re-arranges those pieces to produce a new, better, evolved cell.

Again I ask you to re-read that short paragraph and really consider the significance of it. A protozoa re-programs its own DNA and evolves. Intelligently.

What if your computer were able to do… that???


Did you ever use a computer from the 1980’s? Remember Microsoft MS-DOS? Remember turning on your computer and seeing

courtesy winhistory.de

courtesy winhistory.de

Now imagine for a moment that DOS 1.0 was never modified by any Microsoft programmers. Imagine that after 1981 the boys in Redmond, Washington never touched DOS again.

Instead, by analyzing the programs it ran, by sensing changes in hardware, DOS “grew” new parts, all by itself. Imagine that it added icons and a mouse, automatically, and after a process of evolution, Windows emerged.

Imagine that after a time, Windows developed Internet Explorer – all by itself – just by adapting to the changing environment of the computer. By re-writing and re-arranging its own lines of code.

Imagine that it then developed networking features. Imagine that, sensing that it needed an email client, evolved Outlook Express. One day the Outlook icon was suddenly there on your desktop. You clicked on it and as you began to use it, it added and subtracted features to suit you.

Imagine that, sensing that it needed virus protection, that it adaptively developed defenses for those viruses.

Sometimes the viruses would take out some computers, but the computers that survived were even more resistant.

Imagine that the viruses also self-adapted and continued to try to worm their way in, in a never-ending competition of dueling codes.

Imagine that ALL of this adaptation happened over a period of years without a single software engineer ever touching it. Imagine this happening automatically just because it got installed on billions of computers.

Oh, I almost forgot: imagine that the very latest version of Windows could still fit on a single 750 megabyte CD-ROM.

If DOS 1.0 evolved into the Windows of today without any engineer touching it, would you say:

-That accidental file copying errors, culled by natural selection, were responsible for these evolutionary changes?

(When have you ever seen a software program or computer virus that accidentally evolved new features through a accidental copying errors?)

OR would you say…

-That the original engineer who wrote DOS 1.0 was so incredibly skilled that he actually devised a program that could self-adapt? That it could upgrade itself without downloading another friggin’ Service Pack?


If you met the engineer who wrote this, wouldn’t you want to ask him how he pulled off this amazing feat? Would you want his autograph?

Wouldn’t you want to ask him a ton of questions…

How did he lay it all out at the very beginning? What were the design priorities? How does the program sense changes in its environment? How does the program perform its computations? Does the program keep a database of unsuccessful mutations so it can avoid trying them again?

Well my friend, so far as we can tell, that’s exactly what DNA has done over the last 3.5 billion years. Instead of degrading and crashing like computer programs and hard drives, it has efficiently adapted and evolved from a single cell to occupy every ecological niche imaginable.

From the frozen ice sheets of the Antarctic to the punishing heat of the Sahara. From the ants under your kitchen sink to glorious singing birds in the Amazon rain forest.

This did not happen through accidental random mutation.

If life evolved from a single cell, this happened through an ingenious algorithm that engineers its own beneficial mutations.

This is an engineering feat of the most amazing proportions imaginable.

Consider this….

If evolution is true, then God is an even more ingenious programmer than the old-school creationists ever imagined Him to be.

This new theory has HUGE implications for the future discoveries of biology. It re-frames the entire evolution debate as a software engineering problem! We have all kinds of tools that can help.

In the next installment I’ll put my balls on the line and describe a half dozen predictions that this New Theory of Evolution makes. Predictions that will be either confirmed or overturned in the next 3-20 years.

Stay tuned.

Perry Marshall

Read more about this fascinating New Theory of Evolution:

Newsweek Magazine: “Was Darwin Wrong About Evolution?”

“Darwin: Brilliantly Half Right, Tragically Half Wrong”

“A 3rd Way” – James Shapiro’s alternative to “Creation vs. Evolution”

Technical Paper (college level, peer reviewed, clearly written, highly recommended): Shapiro’s “A 21st Century View of Evolution”

418 Responses

  1. Jim Payne says:

    Perry, in your book “Evolution 2.0”, which I haven’t read yet, are you espousing a “molecules to man” macroevolution, or “microevolution? Other words are you a “theistic evolutionist?” I can accept microevolution within a species/kind, but can’t accept macroevolution,
    one species/kind evolving into a new species

  2. ananta kedari says:

    It is true that world is evolved(50%right), but actually world is created & creator puts an ability in universe to evolve itself. He is a good engineer. you see all the universe is working like it was managed & operated by someone. but We can not see him. he done his work & stay aside.
    I.e. A software Engg. create & install software. after finishing the work he goes. but work on his created software still going on while the creator is not present there. When problems occurs software has its own ability to reset programs by restarting. even when major problem comes then the creator (Engg) makes necessary changes through networking. there is no need of creator to come front of software users. He comes once in thousands year.
    All the formulas , equation present in universe are all unique. you cannot makes changes in them. you can only use these formulas, equations to verify the result (not for see the result or change the result) of that formula or equation. many more to write …
    Next time…..

  3. Hi Perry, please consider the following view:
    Blind Physics Intelligent Evolution
    Standard physics is blind because it does not envisage the physical properties and laws which distinguish life from nonlife, so it infers that biological evolution is blind random process. Now quantum bio-information theory reveals the evolution physical intelligent guiding principle which maximizes bio-intelligence. Bio-intelligence, evolution target criterion, is the capacity to generate functional structures and has the dimensions of action, information and time.

  4. Dave says:

    Hey Perry. Great work. Here’s an article that may be of interest about the debate within the Evolution community.


  5. Dave says:

    Hi Perry.

    There are friends of mine that I try to explain your Evo 2.0 position to, and yet they get lost — even with the explanation of basic Darwinism. Here’s the challenge: Is there a way to easily summarize Evo 2.0 in a way that anyone can understand? E.g., “Darwinism says …” yet evidence shows…”

    In other words, I think a certain audience, needs it memorable, simple, pictorial, etc.

    In history, some of the best and most powerful arguments are of the this, such as the famous trilemma: who is Christ: Lord, Liar or Lunatic? And then people can try to add attempted escape complications, (that have already been rejected by most serious scholars), such as “Legend” etc. [Essentially, Lewis is simply repeating the easy question that Jesus asks Peter “Who do you think that I am?”]

    I’m basically looking for a similar summary for Evo 2.0 that will stick in the mind, perhaps even with a marketing byline or an unforgettable image.

    Paley’s watch and Behe’s mouse trap are examples. At this point I don’t even care if counterarguments are presented against the analogy — I’m just looking for quick ways to get a person so “see” what the issue is. The point is for the person to first understand what the picture is, and what it is not.

    Maybe I’m just asking for two pictures: a false old one, and a new true one.


    • Dave,

      I would start with the opening chapter “The Young Earth Creationist and his Curious Daughter” – I think that encapsulates the main idea rather concisely. I consider that the elevator speech of the book.

      Or the story of McClintock’s plants editing their own DNA and directing their own evolution. Her audience laughing at her, her winning the Nobel Prize 40 years later, but still most people have never heard this.

      All this is utterly and entirely different from “time and chance.”

      How about this 5-minute video?


      This is an important question and I value your feedback.

  6. Farah,mo says:

    Evolution as narrated by the creator’s own words is recently uploaded… please visit my site and own a copy of the eBook in English or Arabic; decoding the procedure of human creation. …this new presentation is superseding the global knowledge in this matter. don’ miss out, please tell a friend. Link: http://tinyurl.com/cqoaqqd

  7. Otangelo Grasso says:

    I wrote a comment at :


    Perry Marshall was a pioneer in educating people about
    DNA and information. His website Cosmicfingerprints was where i first learned about this fundamental issue and one of the pillars of intelligent design. Stephen C. Meyers book , Signature in the Cell, came afterwards. So i regard Perry amongst Werner Gitt , Stephen C.Meyer et al as one of the pioneers of the ID movement, and he deserves credit for it.

    As about Evolution 2.0, it has some interesting things like information entropy. And so other issues like communication of bacterias etc.

    As for his 5 mechanisms of evolution that lead to macro evolution , body form and cell differentiation, histology and development, i think the arguments and explanations are too superficial and not enough indept researched.

    Irreducible complexity is a barrier of evolution to many molecular mechanisms and biosynthetic pathways, and epigenetics involves far more than just gene regulatory networks. That is not well exposed in Perry’s book.

    In that regard, Stephen’s Darwins doubt is a far better educational book about the real mechanisms of biodiversity.

    I have made a little list, which is certainly incomplete, but shows the real mechanisms of complex life forms, and the mechanisms that are involved :

    Where Do Complex Organisms Come From?


    Meyer, Darwins doubt, page 212:

    According to neo-Darwinism, new information, form, and structure arise from natural selection acting on random mutations arising at a very low level within the biological hierarchy—within the genetic text. Yet both body-plan formation during embryological development and major morphological innovation during the history of life depend upon a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. If DNA isn’t wholly responsible for the way an embryo develops— for body-plan morphogenesis—then DNA sequences can mutate indefinitely and still not produce a new body plan, regardless of the amount of time and the number of mutational trials available to the evolutionary process. Genetic mutations are simply the wrong tool for the job at hand.

    Even in a best-case scenario—one that ignores the immense improbability of generating new genes by mutation and selection—mutations in DNA sequence would merely produce new genetic information. But building a new body plan requires more than just genetic information. It requires both genetic and epigenetic information—information by definition that is not stored in DNA and thus cannot be generated by mutations to the DNA. It follows that the mechanism of natural selection acting on random mutations in DNA cannot by itself generate novel body plans, such as those that first arose in the Cambrian explosion.

    Cell and body shape, and organism development depends on following :

    Membrane targets and patterns
    Cytoskeletal arrays
    Ion channels, and
    Sugar molecules on the exterior of cells (the sugar code)
    Gene regulatory networks

    Various codes and the encoded epigenetic information is required:

    The Genetic Code
    The Splicing Codes
    The Metabolic Code
    The Signal Transduction Codes
    The Signal Integration Codes
    The Histone Code
    The Tubulin Code
    The Sugar Code
    The Glycomic Code

    ” Junk DNA ”

    MicroRNAs–“Once Dismissed as Junk”–Confirmed To Have Important Gene Regulatory Function

    In 2008 Scientific American noted that microRNAs were “once dismissed as junk” and said the following:
    Tiny snippets of the genome known as microRNA were long thought to be genomic refuse because they were transcribed from so-called “junk DNA,” sections of the genome that do not carry information for making proteins responsible for various cellular functions. Evidence has been building since 1993, however, that microRNA is anything but genetic bric-a-brac. Quite the contrary, scientists say that it actually plays a crucial role in switching protein-coding genes on or off and regulating the amount of protein those genes produce.

    Transposons and Retrotransposons

    striking evidence has accumulated indicating that some proviral sequences and HERV proteins might even serve the needs of the host and are therefore under positive selection. The remarkable progress in the analysis of host genomes has brought to light the significant impact of HERVs and other retroelements on genetic variation, genome evolution, and gene regulation.

  8. Otangelo Grasso says:

    Furthermore, micro adaptation or micro evolution depends not on mutaton and natural selection, but is a DESIGNED process, as Shapiro states :

    Non random mutations : How life changes itself: the Read-Write (RW) genome 2 3


    And all available scientific evidence also indicates that evolution is an engineered process. In engineering and computer science, evolution never happens by accident. It’s always the result of a deliberate act. A program that can self-evolve is always considered an engineering marvel. 6

    The genome has traditionally been treated as a Read-Only Memory (ROM) subject to change by copying errors and accidents. 7 I propose that we need to change that perspective and understand the genome as an intricately formatted Read-Write (RW) data storage system constantly subject to cellular modifications and inscriptions. Cells operate under changing conditions and are continually modifying themselves by genome inscriptions. These inscriptions occur over three distinct time-scales (cell reproduction, multicellular development and evolutionary change) and involve a variety of different processes at each time scale (forming nucleoprotein complexes, epigenetic formatting and changes in DNA sequence structure). Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences.

    Ever since the formulation of the neo-Darwinist Modern Synthesis evolutionary theoryin the 1930s and 1940s, it has been an article of faith that hereditary variation results from stochastic copying errors and unavoidable damage to the genome

    In the past 60 years, since the structure of DNA was elucidated, molecular biologists have studied the basic mechanisms of long-term genome change. They have discovered a wide array of proofreading and damage repair biochemical systems that remove copying errors and correct DNA damage. At the same time, they have revealed an amazing and wholly unanticipated array of cellular and molecular systems that operate to generate genome variability, both temporary and structural. As we begin the second decade of the 21st century, accumulating empirical evidence has thus shifted the perspective on genome variation to that of an active inscription process changing the information passed on to future generations.

  9. Hi Perry, I just blazed through your Evolution 2.0 book and found it very fascinating, especially as a software engineer and committed Christian who was raised on YEC but is now open to more perspectives, thank you for putting this together.

    I really wanted to get your take on an aspect of Evolution 2.0 that *seems* to disagree with Michael Behe. On the face of it you and Behe are natural partners – both Christians who accept common ancestry but not Darwinian evolution, with Behe arguing for the impossibility of random mutations but not proposing any actual scientific mechanism, and you providing the mechanisms via adaptive mutations – in fact your book explicitly highlights this in your brief mention of Darwin’s Black Box.

    However I would love to know if you have read Behe’s second book Edge of Evolution. He criticizes scientists who describe things like bacteria resistance as an “arms race” via random mutation, going into details about random mutations in humans and malaria regarding malaria infection and resistance, arguing that all the “advantages” provided by random mutation are really just each side breaking their own machinery to keep the other side from using it against them. Trench Warfare, not Arms Race.

    But now you come along and claim that bacteria resistance really is an Arms Race – just via Evolution 2.0 / natural genetic engineering instead of random mutation. Behe briefly mentions Shapiro in his book – discussing non-random theories of how “unintelligent forces may mimic intent” so “evolution doesn’t have to proceed in a Darwinian manner by tiny random changes.”

    Similar to you, he says “in many ways Shapiro has a higher, more respectful view of the genome than Darwinists do… it’s like a computer that contains not only specific programs, but an entire operating system.” But since it doesn’t explain where those tools came from, “if anything, he is pointing the way to a possible mechanism for the unveiling of a designed process of common descent.” OK so far so good.

    But here’s the kicker that I’d love to get your thoughts on – Behe says “the fact that natural genetic engineering processes are indeed quite active… yet malaria and HIV have made no good use of them in 10^20 tries, strongly suggests they have very limited utility.”

    So how should I harmonize these competing claims about Trench Warfare vs the Arms Race? Do you disagree with Behe? Or are you just looking at different examples – he focuses on malaria which for some reason hasn’t done any apparent Evolution 2.0 despite enormous pressure, while you’ve focused on other examples which do – and it all just comes down to details about how the swiss army tools get activated and used in some cases but not others that we are still just starting to understand? Would love to know ANY of your thoughts on this.

  10. edward Enz says:
  11. Tufail Dhana says:

    Rewriting of life in crisis by language of genome. It is interesting and convincing to understand evolution on basis of algorithm theory. The species which fails to re wright life, fails to survive test of Natural selection. God is not concerned. God does not stand in need to create and change to save.

  12. Mr. Marshall,

    I just now finished your book. I bought it as a result of your debate with Stephen Meyer, in which some of your doubts about I.D. echoed my own. Your book – the details therein – cleared up a lot of the ‘fog’ of my problems with Meyer et al (The Discovery Institute).

    In fact, just prior to my reading (just two days reading time, always a good sign) I’d published on my blog ‘An Open Letter to Michael Behe, Stephen Meyer, and Douglas Axe’ (as you know, all Discovery Institute ‘names’), in which I thanked them for their work (via their books/lectures/debates) in exposing the fatal flaws in Neo-Darwinism; in subtext I also challenged them for the lack of clarity/specificity in defining ‘how the world really works’ (HTWRW); here I was referring to not only the specific processes of ‘evolution’ (in the change over time sense) but also regarding the simple though critical question of ‘how we got here.’

    I made sure Drs. Behe, Meyer, and Axe got the link to my blog post and was disappointed that I did not hear back, especially considering the ‘thought experiment’ I posed them, to better define their ‘meta-view’ of evolution. (My blog post was June 5th so I assume I will not hear from them.) I also sent a link to Discovery’s website, Evolution News; likewise, no response.

    Part of my blog post is my correspondence with Neo-Darwinist Carl Zimmer, a regular science contributor to The New York Times and author of several books on evolution. At the very least I would have thought that the I.D.ers would have found Zimmer’s reply to my mini-essay on irreducible complexity illuminating, for how he displayed his own ignorance of the view he espouses (Neo-Darwinism).

    After reading your book I now sense the logic behind the silence. In your essay (a review response) ‘Intelligent Design’s Blind Spot’ you say, ‘…my impression has always been that Meyer is theologically predisposed against common descent; he’s just not coming right out and saying it.’

    Bingo! Although my problems with I.D. are complex, your observation hit home; in fact, none of the three ‘recipients’ of my Open Letter have ever spelled out HTWRW, evolutionarily, not in their books or in their many online lectures/debates. For me, this is a lie by omission, if a sly and subtle one.

    The ‘thought experiment’ I posed them in my blog post would have forced the issue. Perhaps this explains the lack of response; they just didn’t want to ‘go there.’ (I’m a well-thought of writer with three books in print [Random House/Penguin, with 400 Amazon reviews averaging 5 stars] and over 1,500 active blog subscribers. Google my name for more, but my point is that I’m a bit more than some goofball coming in over the transom.)

    Anyway, I’ll link you to my blog post and hope you’ll respond, however briefly. Your book was a revelation regarding HTWRW and a breath of fresh air in a subject wrought with imprecision, blatant cognitive dissonance, and both subtle and outright dishonestly.


    Please keep in mind that my post was written when I still believed that intelligent design (w/without caps) was the only non-Neo-Darwinian game in town. I’ll put that right in my next post. Again, thank you for Evolution 2.0. As an author I know the effect of Amazon reviews and will soon post one.

    • Allan,

      Thank you for posting this. Sorry for the late reply. I’ve been doing a lot of behind the scenes work with cool stuff coming soon.

      You grasp the issues. Carl Zimmer is disturbingly vague about HTWRW and so are the ID guys.

      I simply know of no other way to approach the issue than to approach the question through coordinated observable processes like Natural Genetic Engineering and to keep digging empirically.

      After much consideration I think that if God designed the world to evolve through natural process, then the world is maximally discoverable which means maximal revelation from God to man. So the evolution 2.0 view takes a higher view of God than either Zimmer or the ID camp.

      BTW Carl Zimmer was at the Royal Society meeting and did a rather lousy job of reporting what really happened. My take:

  13. Dwain Smith says:

    First, I am super impressed by your Evolution 2.0 book. It’s evident that you put an exceptional amount of time and effort into creating it. I’m sure my impression of your effort is much lower that your actual effort, so kudos to you.

    My original collegiate degree was in medical technology way back in 1978, so I know a bit about biology. Or at least I thought I did. I’ve been working in the computer industry since 1981, so I also know a bit about information systems. As a lifelong Christian, I’ve continued to evolve and ponder what I believe and why.

    For many years, I have believed that science and faith can easily coexist. In my opinion, science has been a study of what God created. A few areas have been problematic though because it’s difficult to hear a portion of the Christian community say with assurance that the earth is 6000 years old and listen to scientists claim it is billions of years old. Hugh Ross’ video did a great job of aligning the age of the universe and the Biblical record of creation.

    Similarly, evolution was an issue. I was sure evolution was not the answer but didn’t have sufficient resources to back up my stance. Your book Evolution 2.0 discussed a variety of topics that I was not aware of before I read the book. So many thanks for that. I appreciate your focus between the two extremes of evolution and ID.

    I have a few questions you didn’t address and I suspect you didn’t address them because there is no supporting research on the topics. Here are a few of my questions/comments. Any clarity you can provide would be appreciated.

    1. XYZ axis of matter, energy and information. At first glance, I appreciated the injection of information. I do think that overall it is lacking and needs a fourth axis – intelligence. I understand you approach to categorize DNA as a code. I get that certain molecules can only be inserted in specific places where rules are followed, much as your analogy of grammar states that nouns can replace nouns, verbs replace verbs, etc. But to change a DNA sequence or protein with a better molecule implies some intelligence – actually knowing that the molecule will be better. I don’t remember any references in your book that states that DNA might try every noun combination swap until it finds the right one. That would take a while and like your immune system analogy stated, I might be dead before the right combination is found. The right combination would have to be found in a majority of cells as well for the whole organism to survive. You did state on p169 “…evolving their DNA language first. How might they “know” to do this?” As you know from your IT work, information without intelligence on how to use it is worthless. So, I felt the 3 axis illustration needed a fourth axis.

    2. Similar to question 1, I’m curious how cells replicate and understand where they are in 3D space. I’ve lived in two houses, both of which I’ve had built. In both cases, the builders made mistakes reading blueprints and putting doors and windows where they were designed to go. Similarly, I look at my face in the mirror and wonder how DNA can grow my ears in roughly the same size and 3D position, in mirror image to each other on opposite sides of my head. Same with eyes, arms, legs, etc. Understanding that much of this starts in the embryo stage, how does this happen even on a much smaller scale? How do 2 cells in 3D space know that one needs to be skin and the adjoining one needs to be muscle? Again, some intelligence seems to be required here and not just at a “cell neighbor” level. There seems to be some 3D space awareness, i.e., how does one ear know to be a mirror-image of the other and where to position itself on the head?

    3. Last question. The Swiss Army Knife describes how cells can rearrange DNA to address environmental changes or stressors. I get that. The more difficult task, in my opinion, is how would DNA changes that improve how my hand works get updated in a male’s sperm, or in a woman’s eggs so the mutation is available to offspring? On a cellular scale, it’s a long way from where a mutation may have benefits to getting the code updated in the reproductive system. Using an information systems analogy, making bug fixes in a hot fix coding branch still requires updates in the main coding branch (and dot release and service pack branches) so the fix doesn’t get lost in future releases.

    Those are my questions for now. Any insights you can provide would be appreciated.

    Again, kudos for all your research on getting the book written!

    Dwain Smith

    • Dwain, thank for the great questions.

      1. Matter – Energy – Information – Intelligence: This is a graphic which was never put in the book because it was too difficult for most readers to easily grasp:

      Matter Energy Information Consciousness

      The shadow cast by the Chinese characters on the matter & energy is the information.

      But it addresses the exact problem you bring up. Information is not enough. You need what I refer to as consciousness.

      2. You are asking questions about Development, a subject on which I am poorly versed. I suggest this paper as a starting point, and the authors’ related work (Pivar, Edelman) and the many references they give:


      This stuff is VERY INTERESTING.

      3. We know that some epigenetic changes can move from somatic to germline, so that immediate adaptations are genetically passed on. A friend of mine from UCLA, John Torday, who has posted comments here, told me that epigenetics is “the dark matter of biology.” He’s in pediatrics in the evolutionary medicine department there and he researches the effects of smoking on children. There are 300 side effects of smoking and guess what – the #1 most damaging one to children is this: epigenetic markers inherited from a grandmother who smokes.

      In other words the grandmother’s epigenome reacts to deal with the toxins from the cigarettes, for the purpose of protecting her own body, and these changes get passed to offspring and are larger at the 2nd generation than the first.

      The questions about how all of this works are myriad and this is currently at the bleeding edge of science. Torday’s work is impressive and I would encourage you to take a look at his books and papers.

  14. G Lindenbach says:

    Just recently bought Evolution 2.0 and have been enjoying the read. I’ve been looking for a source of information on the topic that is objective and open to whatever the evidence – in it’s entirety- might suggest.
    I wouldn’t necessarily have commented just to say that, however after seeing the number of combative posts on this site, no harm in chiming in with kudos for the effort and the insight.

  15. Prem says:

    Mr. Marshall, I am wondering if you have looked at this new discovery of Dark DNA – See here: https://scroll.in/article/848472/introducing-dark-dna-the-phenomenon-that-could-change-how-we-think-about-evolution

  16. Larry Iles says:

    While it only gets a small mention I find your reference to the way the Immune system works to be a rather elegant and easily understood way to help people understand your rationale. It is an environmental adaptation that is purposefully driven, and one we have all experienced firsthand. I find your intellectually honest treatment of the subject refreshing and the intelligent communication of uncorrupted data presentation very persuasive.

    • Larry,

      This is the subject about which people should be the most reverent. Yet they treat it with scorn and disdain.

      One of the most valuable things we can do is take these very complex processes and do our level best to explain them to ordinary people in ways they can understand.

      Thanks for your appreciation.

  17. Hi Perry
    Thanks for the email and the interesting story of your little son Zander.
    Please let me draw your kind attention to my recent published book “The new physics revolution – Discovery of the life-organizing principle” , published by:
    In which I revealed that the secret of life, its origin as origin of bioinformation, is embedded in the nature of the phase (Z ), which defines system’s action capacity, of the wave function, in some sort of generalized complementarity of matter waves and bioinformation oscillations.
    Case1: If Z**(0) = 0 , the system is subject to the least or stationary action principle. The physical information associated with such system is a measure of static complexity; it is inactive information the generation of which necessitates an external intelligent source, i.e., sender. For example Shannon type of information.
    Case2: If Z**(0) > 0 , the system is subject to the maximum action principle. The bioinformation associated with such system is a measure of developmental functional complexity, it has the dimensions of energy and physical information since there is no function without energy. Bioinformation is self generating in accordance with biointelligence law, i.e., the evolution physical intelligent guiding principle.
    Case 1 defines the phase of matter wave’s oscillations, while cas2 defines the phase of bioinformation oscillations. Moreover a biosystem is intelligently designed because it possesses biointelligence, i.e., capacity to generate functional structures including abstract functional structures such as languages and algorithms.
    EV2.0 prize’s challenge requires answering the question: where did the information in DNA come from? If by information in this context is meant physical information then it is clear the problem is unsolvable, for the simple reason that neither physical information alone nor energy alone can contain the dynamical essence of living systems. In consequence, as I propose in the above mentioned book, the origin of life is the origin of bioinformation. Bioinformation originates when oligonucleotides and oligopeptides undergo reciprocal autocatalysis (Charles; Carter, 2012) and (Peter; Gulik; Speijer, 2015) subject to the maximum action principle, i.e., arrangement of nucleotides along a path of maximum action and maximum bioinformation. Such subjection is a necessary condition for generating syntactically meaningful genetic code. A genetic code is meaningful if it produces viable functional proteins, (Elsheikh, 2016).


  18. Farshad says:

    I have a new theory of evolution
    how can I present it in a science journal ?

  19. Woodrow A. Francia says:

    Of billions of years and one evolutionary chance and random selection of survivability, where is the amoeba that has grown some limbs and crawling out of the fluid habitat fits in?

  20. Dave Nevins says:

    Hey Perry:

    Great job. I heard your “Unbelievable Justin Brierley” radio debate with Steve Meyer, and something you said at the end intrigued me but neither of you followed up on, perhaps because of time, but I think it’s the key.

    The evidence has been inferring that organisms have a “something” that re-arranges the DNA to preserve life. But many are hesitant to go down that route, perhaps because it falls out of the realm of science and starts to get into meta-science, metaphysics, philosophy or religion. However, most of the classic Western thinkers believed just that — in the “top-down” over the “bottom-up” approach.

    That is, the
    bottom-up approach says “because you have an eye, you can see.”
    Top down approach says “so that you can see, you have an eye.”

    In bottom-up eyesight is the cause; in top-down the eyesight is the effect.

    Traditionally this life force from the top is called the “soul” and we normally use it for all sentient life (e.g., humans, dogs, plants), but not usually for cells.

    You can’t see or measure a soul directly; but you can see and measure many of its effects (and thus infer causation by looking back to it).

    So the question for you: Isn’t it possible we are simply witnessing the effect of cell’s “soul”? — just as you know a person is alive if they exhibit properties of being alive?

    It seems to me this is all just another way of saying the cell has a soul, just like anything living. And it challenges the bottom-up false position. An effect can’t be greater than the cause. Just like your soul has authority over your body. Even though your body has heavy influence on the soul, there is an order. You can override your body’s choices in the majority of cases.

    And when you can’t override your body, yet you need to, you can call on a higher life: God.

    Thx! Dave

    • Dave Nevins says:

      Note: strike out the word “sentient”

    • Dave,

      I personally wouldn’t go so far as to say the cell has a soul… but still you are asking precisely the right question and you are exactly right about why so many people are uncomfortable with it. The bottom line is that all organisms have not just bottom-up but top down (and also system-to-system lateral) causation. The reductionist version of science has no grid for this. A lot of people don’t want to deal with this so they simply make up stories or call people who acknowledge this problem “quacks” etc. But that’s no substitute for proving that you fully understand the system, and the only way to do that is to build one yourself. We’re a long way from doing that.

      This mystery is staring us in the face and it’s darn near the top of the list of most-fascinating questions in science. And philosophy.

      • Dave Nevins says:

        Thanks for the reply Perry. I agree.

        Except though, note that the term “soul” has been used by classical philosophers to describe any life-organizing agent. So in everyday usage we say a dog has a soul, but in the technical sense even a plant has a soul, in that there is an “organizer” acting from outside the system and hold together the organism.

        (And it must be from outside the system, for how could it self-organize from only inside the system? As you say, wouldn’t that be like MS Windows debugging itself w/ zero help from a programmer?)

        That why I think we can say a cell has a soul, because it is alive, and the pattern follows that whatever is living has and needs a life-arranger; an organizer for the organism, etc.

        (And following the clues higher: the Organizer of the entire system of life, I would say is the living God.)

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