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:

I AM *NOT* SAYING EVOLUTION DID NOT OR DOES NOT HAPPEN.

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.

NEW THEORY OF EVOLUTION:

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???

Imagine……

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?

Also…

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”

Download The First 3 Chapters of Evolution 2.0 For Free, Here – https://evo2.org/evolution/

Where Did Life And The Genetic Code Come From? Can The Answer Build Superior AI? The #1 Mystery In Science Now Has A $10 Million Prize. Learn More About It, Here – https://www.herox.com/evolution2.0

419 Responses

  1. Jamaalw says:

    Hey Mr. Marshall,

    I commend you for all the work you have done. Really nice job!

    I don’t have a question. The reason why I am posting here is to show you videos that contains evidence that the Earth really is young, there was a Global Flood, one language etc. Basically what is written in Genesis is literally true. I ask you to please watch all the parts of the videos and please leave feedback on what you think.

    http://www.youtube.com/watch?v=dceMA5JdcJo

    There are 11 parts.

    Thank you.

    • Unfortunately I cannot commit to watching the 11 videos. I can probably guess the argument they make for this though. Quick answer:

      I take Genesis pretty much literally, but I interpret just a few details slightly differently than some people. See http://www.evo2.org/genesis1

      As far as I can tell it’s impossible to say that science points to a young earth unless you literally run the laws of physics through a meat grinder. I’ve been exploring this question for many years and I’m dead serious about this. The speed of light alone proves beyond a shadow of a doubt that the universe is very, very old.

      The good news is, I don’t think the Bible says the earth is young at all. With a few very simple assumptions, the Bible and modern cosmology and the fossil record match tit for tat. Atheists and skeptics are usually somewhat shocked when I point this out. See the above link.

  2. Jamaalw says:

    Hey Mr. Marshall,

    You said that you don’t think the Bible says the Earth is young at all. But the information in the videos provides a lot of evidence that in fact the Earth is around 6,000 years old. There is a lot of information scientists or the media is not releasing to the public that supports a young Earth.

    I ask you to please watch the videos. I know it is long but trust me, it is very rewarding. In fact, I think it is one of the most important videos I found on Youtube.

    • Jamaal,

      The media is not hiding any information about the age of the earth. Anyone who tells you anything of this sort, however well meaning, is giving you a snow job. If this video is convincing you that the earth is young, it is giving you a desperately incomplete and misleading picture of science. All you need to understand is the speed of light (which is one of the most practically verifiable facts in science) and it becomes impossible for the universe to be young. As an Electrical Engineer I can assure you this is 100% true.

      Unless you think God made it appear to be old when it is really young – which introduces horrendous philosophical, theological and epistemological problems.

      • GMEstes1 says:

        Mathmatical models and the speed of light prove the universe is approximately 15 billion years in age. Newtonian laws keep the universe in balance.
        The 6000 years for the age of the universe and earth most likely came from a misunderstanding of bibical philosohpy. Please remember the Bible was written after the facts and greatly embellished. The Bibical account of everything is metaphorical.

  3. Felix Rocha Martinez says:

    Please read my interpretations about the the biblical times in http://www.cicatrices.com.mx in my response in three parts to Richard Dawkins’s article “The Angry Evolutionist”. Read Richard Dawkins’s article and my response in three parts to get the whole picture. There is a lot more information in this site including my response to Perry Marshall’s article “7 Biology Myths an Electrical Engineer, Would Never Tolerate.”

  4. Howie47 says:

    The meaning and purpose of life.

    I was reading a post by an atheist who was insisting that there is no meaning to life. In his words, “the only meaning to life is that their is no meaning”. The only meaning, he insisted, is the meaning we find inside ourselves. Which doesn’t relate to any thing out side ourselves! That is of course the madness of atheism. They insist their is no God, creator, or first cause. Who is communicating a message through His creation. Communication to creatures that are designed to be able to receive and understand that message. Like Satan, this atheist insist, that we can go any direction we want, do what ever we want. Because there is no guiding principles written in the creation. Since our atheist and maybe Satan, cannot see God the Creator face to face. But are forced to relate to him through His creation, in bits and pieces. They insist they will not believe (take in) or extrapolate, any such message.
    The Universe is certainly vast. The forms of life are vast, and ever changing. But changing to what degree! Is it like Darwinist and atheist insist, unlimited morphing into Jaba the Hut, and the Blob. Or is life just changing within set perimeters, that still proclaim the message of the Creator. Like beauty, genteelness, mind, order, renewal, love, everlasting life, eternity. etc.
    People of various religions believe they can or have interpreted part of the message the creator has proclaimed in His Creation. While atheist and agnostics say they are blind or to blurry eyed to make out any sense of any message. On the other hand these same atheist insist they can see good enough to extrapolate a common ancestor to all life, from the diversification of life they observe! That sure sounds like the case of the individual, “swallowing camels, but straining at gnats”. It is true that humans all are egotistical, and tend to exaggerate their own understanding. As we see various religions insisting that they own the largest portion of ultimate truth, meaning and purpose. So that they know the path that every individual should take. Isn’t atheism just the opposite extreme to these arrogant religions practitioners? Aren’t atheist these same arrogant religious people looking in a mirror and seeing them selves with rose colored glasses. That glosses over their faults and imperfections with a sheen of, “I think I’m perfect, therefore I Am”. Aren’t atheist just replacing religious guides with, “I am the master of my own fate, my head is blooded, but unbowed” (because there is none greater then I, and if there is, I’ve never met him.)
    What we all should really know and admit is our own frailty, weakness and limited abilities. But never loose our aw or wonder of the unfolding Universe and the truth it reveals right before our eyes. To deny that revelation, by continuously plastering it over with our own human conceived, “narrative gloss”. So we never have to bump into any sign post, that say, “destruction ahead, do not enter”. Or so we never have to change a single step in our comfortable but fear restricted lives. Fear is good when it makes us pay attention to the warning signs ahead. It is not good when it stops all movement and progress. That is the problem in mankind. That problem of confronting and adapting to new lessons learned. That problem has reached it’s zenith in the atheist, agnostic and dogmatic religion, mindsets.

  5. Moshe says:

    I am enjoying your series, but there are a few points that I would like to make [see these points as exceptions to what I think is a very well done argument/series]

    Darwin said that evolution is driven by random variation combined with natural selection. I believe, actually, that this is the neo-Darwinian point of view. Either way, I think it’s worthwhile to differentiate between Darwin’s theory of evolution and the neo-Darwinian theory of evolution.

    The theory that is widely taught or assumed today is, I believe, based on the neo-Darwinian theory of evolution. Dr. Spetner talks about this briefly in his
    book Not By Chance (which is, IMHO, an important book on this subject and which ties into many of the things that you are talking about).

    In short, I think that much of what you are talking about relates to the neo-Darwinian theory of evolution, not to Darwin’s theory that he put forward. It may be a technical point, but often times technical points have real rammifications – try sending any email without the . in .com (that’s about as techincal a point as you will get – pun intended).

    “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.”

    I think we should give the idea of natural selection a bit more credit. It’s power lay in combining this notion with the fact of reproduction – it was how he applied the idea that was novel (not necessarily right, but definitely novel). The notion that the natrual forces of life could combine with another element to create a more sophisticated form of life. It may not be true (my sense is that it is greatly lacking for a number of reasons, some of which you have mentioned), but it wasn’t a no-brainer.

    It’s ALWAYS harmful
    This is actually a form of a debate that Dr. Spetner had with Dr. Edward E. Max. From what I understand, the debate is as follows: there are those who will argue that they have witnessed increases in information from random mutations. Dr. Spetner argues that they are witnessing a LOSS of information that has a protective side effect. For instance, imagine that the lock on your door got corrupted and a thief who stole your keys couldn’t break in – we would not say that the lock improved, rather it’s degradation had a beneficial side-effect. That is what Dr. Spetner wants to argue with mutations which protect against diseases and the like. Here are the relevant links (you could probably understand the science in the discussion better than I can:

    * http://www.talkorigins.org/faqs/fitness/spetner.html
    * http://www.trueorigin.org/spetner1.asp
    * http://www.trueorigin.org/spetner2.asp
    * http://www.talkorigins.org/faqs/information/spetner.html

    It would be wonderful if you could summarize this debate for us :).

    The growing new parts idea – with DOS as an example…
    I believe that the simplest cell has 500,000 nucleotides and the more advanced organisms have around 3,000,000. The

    Theory of Evolution is not just a theory which requires THE REWORKING of existing DNA, but also a theory which requires the CREATION OF new DNA (again, this is based on Dr. Spetner). Rearranging chromosomes won’t accomplish this – you need a mechanism for the creation of new, not-yet-existing DNA to move a single-cell organism to a complex organism.

    Also, in your example, the protozoa has demonstrated that it can rework it’s DNA into a new model of itself. It may be a better, more adapt protoza, but is it something other than a protozoa? You still need to observe and/or demonstrate that an organism is capable of and actual does rework itself into a new, different entity. Not stronger, more adapt, faster, etc., but different. Perhaps this is a promising indication, but at this point it is not more than that.

    What I think we can rightfully conclude from here is that there is a great amount about DNA and the fundamental heart/engine/code of living organisms that we do not know and that cracking as much as possible the code of the DNA is the key. But let’s not second guess what that key will reveal and what doors it will open until we’ve opened them.

    Yes, we can have hypothesis and have a sense of where this is heading, but let’s understand what this hypothesis is based on and what it is not. It is based on new observations of a protozoa – it is not based on more extensive research in this line on a wide variety of life forms in a wide variety of settings with a more detailed understanding of the DNA code.

    I think this is an important point – I think there is a tendency to generalize and come up with grandiose theories of everything from a limited amount of evidence (I think the Theory of Evolution is a case in point). I think it is healthier to be more conservative in one’s inductive conclusions from the evidence at hand.

    Keep up the good work,

    Moshe

    • GMEstes1 says:

      I’ve been looking over human embryology, you’re correct in approaching cellular life and bacteria with care. We just can’t say with certainity how life begins, other than life is reproductive and genetic traits are passed on to offspring. We can’t change what happens to us in early development of major organs; blood vessels, heart, eyes, lungs, brain, limbs, skin the largest body organ. . We get blood and oxygen from our mother until birth.
      Since life requires life to develop from, on this week of prolife or prochoice, we come to parternity issues and marriage problems…especially for me, Mary and Joseph weren’t married when Jesus was born. That being recorded history, why is there so much to do about children being born out of wedlock. Tradition?
      Fantasys were develpoed to explain the birth of Jesus in relation to parternity.
      Jesus himself seemed to be confused about his parents and John 8:9. He spoke about protocol at a well with a woman about relationships with men.

  6. nuke777 says:

    I’m sorry Mr. Allen but I have been following your conversation and I have to say that Perry has covered his bases well within the limits science places on us. extending Godel’s theory through inference is logically consistent with the scientific process. and he has proven that Godel’s theory does in fact apply to the universe as argued. Now I must grant you the medium is not perfect. It is possible that some things got lost in the printed page. I must also state that neither you or Perry is perfect and may not have responded with 100% of the weight of the evidence that was possible. From what was proven here Perry has proven his point with good reasoned arguments. You have not responded to his reasonable question (Can mathematics accurately model the universe or not?). This is the crux of the conversation. If science is valid and the universe is a logical ordered system, and formal logic does apply and has been used to describe and accurately model the universe then it does follow that Godel’s theory applies to the universe.

    Back when they use to actually teach formal logic in text books and universities everywhere they actually explained that the existence of God as Perry says is 100% inferable with cold logic, but not provable. I do not mean to offend but you have not added anything to the debate that seems to have changed this well known fact. The book was “Principle of Logic” written by George Joyce. It is available free of the net in pdf form the quote is found on pg 4. (book page 4 not PDF page 4)
    and is as follows.

    Whatever displays the harmonious ordering of many
    parts is due to an intelligent cause ;
    The world displays the harmonious ordering of many parts ;
    Therefore : The world is due to an intelligent
    cause ;
    (printed in 1908)

    Yes Perry has updated the idea with new information we as a species have gained. He did not invent the argument. Thomas Aquinas did not invent the argument, Augustine did not invent the argument.

    1 further humble thought. I may be wrong. I have been before and I will be again and I don’t know you good sir, but it seems to me from what I have seen written hear that you sir have more to win or loose in this discussion then Perry Marshall and his ten thousand clams.

  7. kenkoskinen says:

    The big bang theory is speculative in the early stages. The assumptions include: the initial singularity, the high energy Planck era, cosmic inflation. We do not have any direct detection for these elements. A theory of scientific genesis must account for the known detections (these come from later periods) and observed features of our universe. The Steinhardt/Turok Cyclic Universe Model, for example, also meets this bar; so you cannot say the “big bang” per sec was a planned event; never mind the most planned one.

    I do like the McClintock/Shapiro “cellular genetic engineering model.” However one cannot say the process does not include any randomness. If Shapiro puts a “zillion” cells in a hostile environment many/most would or could die. However it would only take one to successfully do the 100,000 or so needed internal re-arrangements. The cell with the new defensive mechanism would proliferate in the population via natural selection.

    It is also speculative to say the “all of this” was coded per sec in the primal cell. Who has cracked this “big daddy biological code?” Even the “primal or progenitor” cell could have been the first successful survivor from an initial group that was challenged in an early toxic environment. You can only say the primal cell and its offspring had the potential to survive such threats due to versatility and this increases with successes over time. In any case some randomness must still be part of the “cellular genetic engineering” scheme.

    The arrival and survival of cellular life is only one part of the history of the human story. The other part is that cellular life appeared and took hold in a life evolving friendly environment like earth. Life could have originated here or arrived from elsewhere; we do not know. However our earth/solar system features, as I have indicated in other posts, are not designed and we lucked out. Randomness, although not necessarily of the neo-Darwinian kind, is still a huge feature in the overall story of how we got here.

  8. SamThompson says:

    Perry;
    I’m curious as to why you feel the need to incorporate evolutionary possibilities into your argument at all. Isn’t doing so a compromise that opens the whole “undirected mutation” argument again. From what I understand, both the triggers for and the mechanisms that facilitate the transposition of 100,000 segments of DNA (and only specific segments in specific increments, otherwise the organism would self destruct) in a distressed paramecium, for instance, is blindingly undeniable evidence of sophisticated programming and consequently, design.
    That being said, the transposition process is still random to some degree, isn’t it? Aren’t we talking about millions of distressed single celled organisms (a container of paramecium being denied food or having their tolerance for temperature pushed, for instance) each accelerating what Darwin thought was random chance, but in a very controlled way? They’re all making random transpositions inside of certain guidlines and the winners get to survive and reproduce.
    If I’m correct, this scenario still doesn’t account for speciation. I don’t think we have any evidence in either biology or paleontology of any organism making a clean jump to becoming another species. It would seem to me that the odds of rearranging DNA through transposition might be a better possible avenue, but the odds would still have to be staggeringly high.
    My point is this. Regardless of who’s willing to face it, Darwinism and NeoDarwism look to me to be on the ropes. It’s just a question of time (perhaps too much time) before this is conceded and we can begin to expunge it and it’s horribly deleterious effects from the popular culture. Why create any argument that might prop it up?

    • Entire new species of plants are well known to be produced by blending of different species. This is called inter-species hybridization. Good example: http://en.wikipedia.org/wiki/Salsify

      This usually causes a doubling of genomes (polyploidy) in which one of the two genomes is largely silent and which then becomes a playground for transposition to do its work within the domain of silent genes – which later can be switched on.

      Hybridization is also commonly seen in small reptiles.

      Symbiogenesis also creates new species. For example Lichen = Algae + Fungus. This is not a gradual “Darwinian” adaptation, this is a merger that generates sudden and completely new species. Symbiogenesis is like putting a Starbucks in a Hilton hotel or one company buying another. It creates a whole new business.

      Transposition is a smaller scale evolutionary mechanism that generate adaptations after these larger-scale speciations have occurred.

      Transposition of mobile elements is not random, it’s linguistic. It’s hit and miss but it’s not random in the strict mathematical sense. It’s algorithmic. There’s no guarantee which combinations are going to survive but that’s not anywhere near the same as saying it’s accidental.

      Strictly, neither transposition nor hybridization nor symbiogenesis are “Neo-Darwinian” concepts. They’re rival theories. Which are very well documented, by the way. In fact it’s almost impossible to deny their prevalence. But atheist Darwinists are VERY reluctant to talk about them because they fly in the face of the “evolution = random accident” paradigm and its intellectual poverty. They’re all teleological.

      Dawkins, in his book “Greatest Show on Earth” barely breathes a word about any of this in 450 pages. Intelligent people should ask why.

      You are right sir, Neo Darwinism is on the ropes. It’s got less than 5 years, my friend.

      • levgilman says:

        “For example Lichen = Algae + Fungus. This is not a gradual “Darwinian” adaptation, this is a merger that generates sudden and completely new species. ”
        Totally wrong. “Sudden” is not given, it’s your point to be proven.
        By default, there IS gradual “Darwinian” adaptation. Algae and fungus gradually become more and more adapted to each other, beginning from very loose association.

        • You may be right about lichen. In the case of inter-species hybridization, the new species emerges in one generation. This is a proven fact.

          If you have a model that explains how evolution can happen rapidly, why hang on to a bias that says it only happens gradually?

          • kenkoskinen says:

            NeoDarwinism may well be too slow to explain rapid spurts of life. However, if the McClintock/Shapiro model works the way it is presented, evolution should be more rapid than we detect/observe. Something must be reigning it in or controlling it. You have not proven the existence of the “overlord code” you postulate existed from the 1st cell (a top down arrangement) and connected to the idea of the 2nd singularity. It seems to me that something or even much is still missing.

            Evolution is not about the survival of the fitest. It is about the continuance of the able. Also natural selection does not kill the runts. It passes on advantageous traits that increase an organisms efficiency. I think the mechanisms question of what creates traits is still unfinished work.

            Further the idea expressed as the first cause is only valid in a finite system. If our universe originated from a prior infinite system then the initial causality argument falls. The big bang with its cosmic singularity is speculative and cannot be used to prove any god exists outside of space/time. There are other scientific genesis models (that also account for known detections and features of our universe)that do not have the initial singularity.

            The appearance of life is still a mystery and even though it probably only happened once, (with DNA or some precursor to it), nothing you have said on this blog proves the biblical god exists.

            • Evolution is rapid. Bacteria developing resistance to viruses is proof enough.

              In just the last 100 years we have observed speciation through hybridization and genome duplication; the evidence overwhelmingly points to rapid evolution through symbiogenesis events, ie algae+fungus=lichen and Protozoan + Cyanobacteria = Alga. We observe transposition and epigenetics in the lab. Yes, my hypothesis something IS reigning it in and controlling it. Within the limitations of current human language, a very crude, inadequate description of this thing would be “an algorithm of extraordinary elegance.”

              This is something so utterly opposite of the randomness of Neo Darwinism that the random mutation component of the current theory is nothing less than the biggest mistake in the history of science. An appalling disaster that has costs us hundreds of millions of lives through its vandalism to medical research, immunology and aging research. You need look no further than the failed “Junk DNA” hypothesis and 30 years of impeding research.

              You are right, the first cause scenario is only valid in a finite system. There is a necessity for something infinite but according to Gödel’s incompleteness theorem it cannot be a system of component parts because that invokes infinite regress. I discuss this in great detail at http://www.perrymarshall.com/articles/religion/godels-incompleteness-theorem/ I encourage you to read the article, the discussion and the comments that follow.

              • kenkoskinen says:

                Well okay … something much be reigning in evolution but much is still missing in the mechanisms issues. What it is, is a mystery.

                I disagree with the evils of Neo Darwinism … I also fail to accept that all modern biological research, medicine etc. makes any direct connection to the theory. I’m sure many will disagree and point to the evil theory as being the overlord. However scientists still observe, adjust, add, delete and invent what is in the “test tubes” and experiments. Also there has been great advances in medicine as a result.

                Something of necessity had to have been eternal. We exist in “All That Is” i.e. ATI and we are here because of fairly recent changes (i.e. the last mere billions of years) within ATI. However changes will continue within ATI and humans will someday no longer live on earth or in the universe or our neck of the woods within ATI.

                Nothing prevents ATI from having components as without them changes are impossible. Infinite regress is the norm within ATI since that is also part of infinity.

                I have read your article on Godel and think you and others are misapplying the inferences. For starters I suggest you download “Godel and Physics” by physicist/writer John D. Barrow. The search for the TOE does not need to be impeded by Godel’s theorem. He even escued its application to physics. I will prepare a more detailed response when time permits. The theorm is not what you and others think/claim it is.

                • Infinite regress is almost universally rejected by philosophers. I encourage you to inquire into the reasons for that.

                  • kenkoskinen says:

                    I am well aware of the limiting power of an infinite regress to reason. However I was discussing the necessity of infinity. If there weren’t any changes which require components; then our universe and us would not be here. I encourage you to think about that.

  9. radomir says:

    Hi Perry,
    I run into your writing by looking for the reviews of Prof.Shapiro’s new book on the web. I am as excited by your theory of evolution as I was with his when I first encountered it almost a decade ago as they both agree in so many important points with ours (I have a coauthor), while not being exactly the same. It is great to see how our little band is growing and be your prediction true that in five years we will see the old thinking overturned.
    Our basic idea is: yes, evolution is natural programming, but we differ from you in that for us the unit of life programming is species and nothing else. So speaking metaphorically some closely related species are programatically related as Dos 1.0, Dos 2.0, etc and those a bit further apart as Windows 98, Vista and Mac Os. and life evolves by selection of species programs as wholes. Unfortunately, biology is more complex than Physics or Engineering so you must take above as a teaser and a very incomplete statement. As your readers Moshe and Kenkoskinen have shown, theory that does not cover all angles and facts in its (first) presentation is open to criticism on that alone. I believe we covered all those that they raised including the mechanism and numerous others they did not. On the flip side, this makes our text pretty rough going, or even irritating to an excellent communicator such as yourself, so be forewarned.
    If interested you can find our paper on http://www.evolutionisprogramming.com
    As I am not into blogging you may, but need not publish this on your web site.
    Thanks

  10. Perry – what is the difference between your “mutation algorithm” and the “fundamental organism-building toolboxes” referred to by some genteticists?

  11. Parakletos says:

    What a load of BS. Sorry, but it is. Your conclusion about biology from your experience in communications is laughable. As you are CONFUSING a signal which must be delivered in its perfect state to a being who is able to change and actually be better than the parents. You don’t have that in communications. There is no error that can be introduced to the signal that will BETTER the COMMUNICATION — because the test is whether or not the end communication EXACTLY matches the original communication. With evolution that is NOT the case. With evolution, a sentence with extra data COULD actually turn out to be BETTER than the data which produced it.

  12. pat says:

    “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”

    What you’ve described here in a very self-refuting way is the evolutionary paradigm in miniature. This kind of variability is induced by a process known as somatic hyper-mutation (At least thats what immunologists have called it for years. To Shapiro acolytes it’s been rebranded as NGE)

    Furthermore the natural selection process is still in place. The selective pressure is the particular antigen that very few cells with the proper antigen receptors willrecognize. And what happens to the rest; the “runts” as you would call them? Most of them die.

    • I’m in agreement with what you say. The key phrase in your description is:

      “systematically tries”

      It doesn’t accidentally mutate. It runs permutations. It’s a lot like testing Google ads in online marketing, trying stuff until you find something that works.

  13. Ray says:

    Agh it’s all a load of Hogg wash. If we can’t find the missing link here’s a therory. Apes were around long b4 mankind. Ufo’s have been around for thousands of yrs. one day they landed on earth and seen a creature almost the same as them (apes). And they thought if we can change their DNA. Low and behold along came that of man kind. That’s why there’s no missing link. My thought anyway

  14. Michael Price says:

    “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.”
    No you don’t. In fact an actual communications engineer, or even someone smart enough to become one, would know it’s actually inevitable with enough trials. There is nothing that prevents a random change from making a system more closely approximate a given set of criterion, provided it’s doesn’t already prefecty match said criterion. If there were it wouldn’t be a random change. For instance if you have send a text file copy of “Pride and Prejudice” that I typed up, any typos I made could be corrected by tranmission errors. The percentage chance of that happening is the percentage of wrong characters * the chance of getting a correct character by chance. This is not difficult to determine and in fact shows you’re being dishonest either in theorectical claim or claiming that you are an electrical engineer.

  15. Christopher Easterling says:

    smh. A change in a single base can still make the same protein. A change in a single amino acid can still make the same protein, or it could be slightly different. Occasionally, the slight differences provides the organism with an advantage, AZT anyone? To compare the genetic code with language is absurd. DNA is degenerate, English is not. Not to mention that the suggestion that random noise can’t account for evolution is to completely deny the possibility that life arose through natural processes.

  16. Anthony says:

    Hi Perry, I just read your book and have some constructive comments, if you ever plan on writing a follow up. I know you get all kinds of similar correspondence. If you are interested in an honest constructive criticism, from a theist and a science enthusiast, then I could send a few fair-minded (outsider perspective) ideas your way. My love of science and philosophical outlook have never been in competition.

  17. Carol Sperling says:

    You know, engineers came up with data error-correcting methods before we knew how DNA worked. These methods are just as good, some even better than, what is present in DNA. Are you telling us that your Creator could not come up with anything better than what humans invented on their own? That sounds blasphemous to me.

    • I don’t know of any human technology that can preserve and advance data for 4 billion years. Not even close. If you think human technology is superior, I’d be interested in knowing what your evidence is.

      • Carol Sperling says:

        Are you freaking kidding me? Even writing it on paper will preserve it for 4 billion years if it is recopied onto fresh paper every 80 years, as genomes are recopied every generation. Is that the best response you can come up with?

        • I don’t know of a single self-replicating machine that man has ever made. Nature has kept them going for 4 billion years. And no, pieces of paper that someone could copy if they want to don’t count.

          • Carol Sperling says:

            You are adept at moving the goalposts. Nobody is talking about 4 billion years. I am talking about a single generation. People came up with error-detection and correcting methods that can achieve an error rate of zero in copying any quantity of data. DNA accumulates over 100 errors per generation, some due to copying errors. That does not sound like a system that came from some intelligence greater than our own.

            • DNA accumulates errors of 100 base pairs in some situations. More in some situations. Less in others. It would be difficult to make an apples to apples comparison to human technologies because many times human technologies are worse. You don’t even know how many TCP/IP retries it took for your blog comment to safely appear on my website! The larger fact is, the error correction in DNA has kept life going for 4 billion years. That is an established fact. Humans have done nothing remotely approaching that. Unless you know something I don’t?

  18. Kevin says:

    Perry,

    Correct me if I am wrong here, but biological speaking the environment dictates what is deemed “useful” mutation. So, it is not just the organisms that are evolving, but the very environment that the organisms inhabit. If there was no light in our environment then eyes as we know them would not be a useful mutation.

    So, if the rules of our environment are changing and allowing for new useful traits, then couldn’t it be possible for the random mutations to adapt to those rules?

    I’m not disagreeing with you entirely because I am also a believer, and I believe that God does have a plan, and we were created–whatever that means–in His image. But, it seems to me that the “quick brown fox” example could be slightly simplistic, because it assumes that the language (or environment) is still modern American English. But science has shown that our environment is not the same is it was even 100 years ago.

    Granted, I am no scientist; more of a theologian I guess. I believe that the creation narrative mirrors or reflects the “Big Bang” theory of the origins of the universe. Which–if confirmed–would seem to suggest that there was a knowledge of the origins of the universe that was passed down from a source of knowledge to a prescientific society in a way that was “useful” because they could understand it without having access to the same knowledge; the same set of scientific rules that we have.

    If this is the case, then is it not only possible, but likely–in my opinion–that random mutation and intelligent mutations coexist. I believe that being “created in Gods image” refers to our ability to impact evolution in a similar way that God does. Ours being random and indirect because we must operate within the rules of our environment; and God’s being random and direct because He has the ability to change the rules of our environment.

    For example: if we do not do something to change the carbon monoxide levels in the atmosphere then we must pray/hope that some of us have adapted the ability to breath carbon monoxide, because the current rules of our environment state that carbon monoxide is toxic. However, if we are constantly undergoing random mutations that are neither helpful or harmful–in much the same way that rearranging letters wihtin a word does not countreact ones ability to understand the word so long as the first and last letters remain the same–we would not see the benefits of the mutation until the rules of the environment change. it doesn’t matter that I have webbed feet until suddenly the environment reaches a tipping point and causes the ice caps to melt and flood major parts of the world.

    Again this is from a completely non scientific view; purely a rhetorical one. But if the Big Bang is confirmed, and the bible appears to mirror the Big Bang. Wouldn’t it suggest that the knowledge was passed down from an entity who was present? And wouldn’t that entity have to have the ability to affect our environment directly in order to pass down such knowledge? and would that mean that our mutations–random or intelligent–are mimicking the ability of a higher power to directly affect the environment?

    Once again: yes, I am biased; no, I’m not a scientist; and yes, I am very open to the possibility that I am wrong. But, hey! If you aren’t open to being proven wrong, then you aren’t open to learning.

  19. Kevin says:

    I meant “God’s being intelligent and direct.” Not random and direct. This point–I believe–is evident in the apparent transfer of scientific knowledge to a prescientific society in a way that was intelligently designed to be processed and understood by people. The entity passing down the knowledge–whom I would call God–must have had the ability to affect the environment in order to give this society such knowledge.

  20. Derek says:

    In 3 words- Apologetics meets copywriting.

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