Testable Hypothesis for Intelligent Design, Part 1

A common belief is that Evolution and Intelligent Design are an either/or proposition.

Today I’m going to tie the two together in an elegant way and show that they compliment each other beautifully.

A common criticism of Intelligent Design is that it offers no testable hypothesis.

Today I’m going to lay that accusation firmly to rest with a whole series of predictions about what evolution research will show us in the next 3 to 20 years.


You may or may not have noticed, but Information is always written top-down, not bottom-up. You may or may not have noticed that information also has to be modified or re-written top-down.

Random mutation assumes information is bottom-up. That is the most fundamental reason why that theory is failing. Evolution is a top-down process.

The highest layer of information is intent. All coded information is driven by intent. Intent results in meaning which results in sentences which dictate words which dictate letters.

(Not the other way around.)

Everything I predict in this series, then, comes from a proposition that evolution is an engineered process and is programmed to happen; and that the program itself is intelligent and operates in a top-down fashion.

Onward with my testable hypothesis:

1) Evolutionary adaptation is the work of a “Mutation Algorithm.”

Cells employ a built-in algorithm, which engineers re-arrangement of Mobile Genetic Elements (as observed by McClintock and Shapiro).  Genes and Chromosomes are re-arranged in a fantastically beautiful process which produces useful adaptations and new species.

I call this the Mutation Algorithm. It is a program which attempts to evolve when necessary and computes the optimal path to a desired result. This algorithm is described as exhibiting some form of intelligence.

This Mutation Algorithm, in combination with natural selection, explains what random mutation and natural selection cannot.

Hypothesis: DNA systematically tests skin color and patterns, hair, limbs and other features like blades on a Swiss army knife

Hypothesis: DNA systematically tests skin color, fur patterns, hair, limbs, claws and other features much as you would switch out blades on a Swiss army knife

2) The Mutation Algorithm tests design options like blades on a Swiss army knife. DNA has a huge “bag of tricks” and is able to mix and match combinations of eyes, feet and claws, joints, digits, hair, skin and fur colors and patterns, switching out different “blades” as environments change.

It builds animals on a common chassis of head, spine, heart, lungs, stomach and limbs.

It ferociously defends this core chassis from being corrupted by random mutations, while switching out different variables in the head, spine, heart etc.

3) The Swiss army knife “blades” include variables that adjust the structure of incredibly complex systems with simple changes.

For example the length of a giraffe neck could be “dialed in” by a single gene which controls the length of nerve fibers, muscles, esophagus and number of vertebra, all at the same time.

This explains both small and large variations in species. DNA fills the ecosystem with every imaginable variety of life because it’s designed to.

It adjusts these variables until the creature is maximally adapted to its environment.

4) The Mutation Algorithm is normally at rest. It goes to work whenever the population is under extreme stress. This is why we see the pattern of “punctuated equilibrium” in the fossil record.

There are long periods of stability where there is no change, because the Mutation Algorithm is dormant. When there is a crisis, it activates and begins to test novel features.

5) The Mutation Algorithm operates within populations, not just individuals.

The Mutation Algorithm catalogs past mutation attempts so that it does not get “stuck” repeating past failures. Organisms somehow share information so that they can collectively test a wider variety of mutations than any one organism could attempt.

Efforts to find a mechanism by which organisms share this information will eventually be rewarded. And the mechanism that is discovered will be as surprising and revolutionary to biology as Einstein’s theory of relativity was to physics.

6) Evolutionary pathways are not random and purposeless, they are mathematically optimized in advance to reach desired destinations in the smallest possible number of steps.

An analogous process is the Taguchi method used in Quality Control, which creates a very small set of manufacturing experiments, which represent a very large number of possible manufacturing combinations.

It systematically tests them via a “design of experiments” process, then generates a new design which is a nearly optimal combination.

Thousands of possible design combinations are evaluated with only a few dozen tests.

Then more inputs are gathered, new designs are generated and the test is run again.

I invite you to consider that DNA does something very similar with arrangements of modular biological components, literally calculating and anticipating possible evolutionary steps. It senses inputs from its environment and optimizes the experimental process.

(The Taguchi hypothesis and related concepts from Quality Control, Kaizen and Six Sigma also help explain the phenomenon of punctuated equilibrium.)

Imagine for a moment, if you will – that same process that DNA uses can be quantified and adapted for use in manufacturing and process control.

Comparisons to Quality Control and manufacturing are very useful when considering evolutionary theories. The theory of Neo-Darwinism, which is now fighting for its very life, always insisted that evolution proceeded as a function of random mutations combined with natural selection.

A direct analogy in manufacturing would be if we made a production line where incoming parts were randomly and carelessly modified; then a QC check simply discarded all unsuitable assemblies at the end of the line.

Can you even think of a more wasteful and inefficient quality control system? Soon it would also result in the most wasteful and inefficient factory imaginable. The employees would be laid off and the plant would close.

You may or may not have noticed…. there is no manufacturing facility in the world that makes products that way. Quality Control is always an extremely deliberate set of inputs combined with rigorous analysis of the outputs.

My hypothesis is that DNA operates much the same way as a Kaizen / Six Sigma manufacturing operation. DNA not only actively participates in the mutation process, it also monitors the natural selection process.

I hypothesize that the genome got from single cells to humans in an incredibly short period of time – that 3 billion years from cells to mankind is an engineering feat of the highest order. That such a feat required the most advanced forms of optimization and as little waste as possible.

We’ve only begun. Stay tuned for future installments, where I’ll discuss “Junk DNA”, show you the layers of information in DNA and new discoveries that await us in computer science.

In later parts I’ll also talk about human genetic engineering, the Human Genome Project, and a new Anthropic Principle that specifically applies to DNA.

Perry Marshall

Further reading: Swine Flu Virus Mutations and the Evolution of Google Ads

A 21st Century View of Evolution by James A. Shapiro

Evolution as Computation by Laura F. Landweber and Erik Winfree

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JohnM says:

Hello Perry,

How could we not have noticed the pink elephant in the living room all this time? This is very exciting! May God keep you humble Perry, :) but reading all this information reminds me of how the two walking on the road to Emmaus must have felt!

Leave it to man to touch, handle, and thoroughly investigate the mind boggling wonders of creation only to stand there looking like a cow chewing it’s chud!!! The pearls have surely been cast before the swine! If we wont glorify God, creation itself will! Gods glory back to it’s rightful owner!

At any rate, I still have a few questions. How do all the genetic mistakes fit into all this? What about all the what would seem to be “evil” designs fit into all this? Such as Viruses, wasps laying eggs inside a living host only to eat it’s way out killing the host etc? I mean some creatures just look right out evil! Use deception and all that. I know these are more theological in nature. After all, it is quite obvious even evil designs are designed, such as torture chambers etc.

How do you deal with all these yourself? Im very interested to know.

God Bless you,


JohnM says:

The way I have dealt with these questions myself is that after the fall, predation and aggression become much more severe, seeing the earth no longer would give it’s increase like it once did. Hense God allowing us to eventually eat meat etc.

The original plan and order of things changed. Would this be considered noise in the original signal so to speak? Something to that effect?


This is pretty much the first question everybody asks. In my article “Design in the Universe + Evil + Suffering = ?” I attempt to address this question as scientifically as possible.

I would encourage you to read it, but the short answer is:

-The reason we have birth defects, aging, extinction and death is: Random mutation. Information Entropy. A slight corruption of the signal is all it takes for the design to degrade over time and malfunction.

There is a very very deep irony, which is that Darwinism gives those things credit for the miracle of evolution.

Those things don’t deserve any credit for evolution at all! Random Mutation is noise, noise is entropy, entropy is irreversible.

Entropy causes birth defects, aging, extinction and death. NOT eyes, ears, new limbs and superior new features. The Random Mutation Theory of Evolution is an inversion of the most ludicrous kind.

It is far and away the most widespread, most absurd, most damaging urban legend in the 1000 year history of science. To a communications engineer it’s more ludicrous than a flat earth.

The fact that millions of scientists still believe it only shows us how easily we human beings can be conned.

I think people believe this because it’s the most convenient way to omit God from the discussion. We become completely BLIND to the elephant in the room, even when it sits down at our breakfast table and belches. When it comes to anything with spiritual implications we human beings are supremely gullible.

But you hit the nail on the head: What a revelation is when you finally see this! You can never un-see it again. It’s a revelation.

So yes, random mutations do exist. Entropy does exist. Information does degrade over time.

And then there is a further twist: Why is nature, as Darwin put it, “red in tooth and claw”? Why parasites and malaria and viruses? Why are some animals so predatory, so ferocious?

Why did God create a universe where that happens?

Now we’re the age-old question of evil. The one every human being has been grappling with since the beginning.

Why did God create a universe where evil is allowed to happen?

That, my friend, is a moral and theological question.

I do address that question, however briefly, in the article “Design in the Universe + Evil + Suffering = ?”.

But what I want to say right here is:

1) The very existence of this question and the fact that we ask it says something very profound about us, about information, and about the existence and importance of theological questions. This is not a ridiculous question. It’s the most important question anyone ever asks. It’s the biggest philosophical question you and I will ever struggle with. We have an imperative to face this question, not run from it.

2) ALL worldviews MUST deal with this question, and all worldviews DO deal with this question.

The atheist worldview is peculiar in this regard. It says, “Shit happens because of random mutation and natural selection and survival of the fittest. Like it or not, it’s what got us here, so deal with it. But at least we got rid of God so don’t have to worry about some Divine Megalomaniac Sadist who left us stuck in this awful hell-hole. So let’s take charge of our own evolution and free ourselves from the shackles of organized religion.”

It initially seems like a great relief to just accept this. It feels like a burden has been lifted from your shoulders when you don’t have to “explain” evil anymore.

I was almost completely ready to accept this myself five years ago, until I realized that the random mutation theory didn’t have any ability to explain why there was anything good.

Random mutation doesn’t explain why anything WORKS.

It only explains what DOESN’T work.

All other religions do deal with this question in various ways.

Leszek Kolakowski, the famous Polish philosopher who lived through the holocaust, said: “I can understand people who do not believe in God, but the fact that there are people who do not believe in the devil is beyond my comprehension.”

The Judeo-Christian worldview suggests that there is a literal battle between Good and Evil. That we have chosen Evil, and thus Evil rules in the world – even though Evil is lesser than and inferior to Good.

Just about every book and story you have ever read, and movie you have ever watched, is about some aspect of that battle between good and evil.

St. Paul said,

“For all creation is waiting eagerly for that future day when God will reveal who his children really are. Against its will, all creation was subjected to God’s curse. But with eager hope, the creation looks forward to the day when it will join God’s children in glorious freedom from death and decay. For we know that all creation has been groaning as in the pains of childbirth right up to the present time.

“And we also groan, even though we have the Holy Spirit within us as a foretaste of future glory, for we long for our bodies to be released from sin and suffering. We, too, wait with eager hope for the day when God will give us our full rights as his adopted children, including the new bodies he has promised us. We were given this hope when we were saved. (If we already have something, we don’t need to hope for it. But if we look forward to something we don’t yet have, we must wait patiently and confidently.” (Romans 8:19-25)

One last comment about Judeo-Christian theology: Nowhere does it ever say the world was created PERFECT. It says it was GOOD. Then evil entered in the world and a huge struggle ensued.

In the book of Job, which deals with the question of evil and suffering more than any other book in scripture, God describes the wildness and ferocity of Leviathan, which appears to be a dinosaur or some kind of other fierce, un-tameable creature:

His chest is hard as rock,
hard as a lower millstone.

When he rises up, the mighty are terrified;
they retreat before his thrashing.

The sword that reaches him has no effect,
nor does the spear or the dart or the javelin.

Iron he treats like straw
and bronze like rotten wood.

Arrows do not make him flee;
slingstones are like chaff to him.

A club seems to him but a piece of straw;
he laughs at the rattling of the lance.

His undersides are jagged potsherds,
leaving a trail in the mud like a threshing sledge.

He makes the depths churn like a boiling caldron
and stirs up the sea like a pot of ointment.

Behind him he leaves a glistening wake;
one would think the deep had white hair.

Nothing on earth is his equal—
a creature without fear.

He looks down on all that are haughty;
he is king over all that are proud.”

-Job 41

JohnM says:


Thanks, the information entropy explanation helped.

But the second part of God allowing evil didnt quite address my second part.

My question was why did God create creatures “designed” to do evil. Creatures that use deception, slavery, mind control etc. If I accept God created life, then he also created these creatures to do what they do.

I have come up with a few ideas myself..

1) creatures may actually be more intelligent than we think, thus actually being creative enough to devise new ways of surviving. But this doesnt explain actual pysical designs such as stingers using poison etc.

2) Original design and purpose has been lost since the fall. An example would be machines that are designed to cut wood and metal, out of there original context and purpose they can also destroy life. A knife designed to cut tomatoes can also cut throats etc.

3) A more theological one. That many of these creatures are used as spritual analogies. Many creatures lie and wait for innocent victims. Hense “sin lieth at the door.” Many creatures poison their victims, hense sin poisons our lives and minds and hearts. Many creatures entangle there victims, such as spiders. Anyone that understands the effects of sin can surely see the comparison here.

Anyway theres a few explanations I have come up with, whats your take?

In Christ,



I think God designed a predatory world. This is true even “before the fall.” If you read the passages in Job God talks about this and doesn’t refer to any of it as bad. Just wild – not tame – dangerous. God takes credit for it and challenges Job’s authority to question it. Of course this STILL does not sit well with modern intellectuals. BTW I personally interpret the Garden of Eden as being a less predatory place than locations outside the garden. That’s just one possible interpretation. But it does make sense. God did force Adam and Eve to leave. Then there is the tree of life which God did not permit them to eat from.

Whether you take this story literally or allegorically, the lesson remains the same. We live in a hostile world and we have chosen to participate in evil, and we are responsible for our choices.

I think we also have the spiritual word, ie the demonic, which is clearly a consequence of free will. And yes the spiritual world and the physical world are very analogous to one another.


JohnM says:


So there was death and predation “outside” of the Garden before the fall? And entropy and all that was already at work in the rest of creation excluding man? Was the glory man had before he fell the “absense” of entropy?

So let me see if I got this right. Entropy and death and predation existed before man fell. And basically man was the only part of creation not subject to it? No entropy in the human DNA etc? And the after the fall, once man partook of the evil in nature, now he himself became subject to it? Hence entropy in the human DNA?

JohnM says:

But if man came via evolution, then entropy must have already been at work in the primates.

Unless once the suitable frame for man was ready, is when God breathed His own life in Him thus man aquired Gods own glory of immortality, no longer subject to entropy?


Not sure I have a position on that question. Was adam physically immortal? Or was “death” a spiritual thing in the promise of what would happen if they sinned? I don’t know.


Qqccho says:

John’s questions appointed here are the important ones to resolve; After the Fall the Creator changed already designed human’s DNA? and gave us Free Will?
You wrote ” Not sure I have a position on that question. Was adam physically immortal? Or was “death” a spiritual thing in the promise of what would happen if they sinned? I don’t know.”
Well I think you should know for your theory to have no open holes. It cannot be said this is theological because the fundamentals of your theory lays on Creator’s design. It’s all in the Genesis and yes it says We were created perfect as his image and inmortals. You take it or not. There’s no space in between. Bible readers won’t agree with you that spiritual beings dye, will them?
We would like to know how your communication theory applies from the very beginning of all creation- Heaven & Universe, so we can follow from it.


We ALWAYS had free will. Would be surprised if Man’s DNA began to degrade after the fall.

Genesis never says we were perfect, or that anything was perfect. It says it was “good.”

ramkumar says:

perry ,

Good that you are having listeners who considers evolution and natural selection in a artistic ,spritual sense … ”but reading all this information reminds me of how the two walking on the road to Emmaus must have felt! ”.
Readers digest captioned an article ‘they lived with God ‘regarding the population that lived in that 200 Km area where Jesus is said to have roamed around .The two on the road where picked up by jesus ..or random selection ..there is also a myth that they become some Bishops after that
and where killed .. But this mixture of a religious concept/story and evolution has no meaning and is idiotic.

Information is written in top down not bottom down … (pm)
Note: this means that in the beggining itself the first protoplasm knows about the end product .. or in cosmological terms singularity where once every thing was there knows about the divergent complex and marvellous universe that is going to be the result after big bang .Then why failed mutations and failed genes .. dinosours ,extinct classes, species .Fact is that failed ancestors are more than sucessful one . Failed stars are more , wasteful pulsars ,neutron stars ,M-dwarfs (even though they found some planets orbiting it also) , Gene centric view of evolution points out to survival of fittest for only a rare few amoung genes survive . The fraction of sucessfull and failed scenarious
nearer to 1/10000 .To be more clear in cosmology .. to assume that there is no life any where in our obervable universe . sucess rate of universe in generating a earth like planet is 1/ trillion , trillion,trillion.a rare event … But we are here …

1)Mutation alorithm …this term was coined after Jems cricks decoded gene structure .. you had mentioned that a future change is encoded in the program it self .But here the alogorithm changes in accordence with the environment not on the basis of a pre-conceived program coded depending upon conditons , environments , adapatability and various other factors .(Not to mix this with normal alogrithms encoded in DNA like ,sperm ovary genetics pregenency ,birth of a child , growing up and death )
There is a conditional selection done by man also .. (Heike crabs with their heads that resembles a samurai warrior is not killed by Japan’s fisher man and hence they have more chances of survival .

2)Incredible changes occur not by simple changes .giraffe neck dialed in …(pm)but it took again a billion years for a protoplasm to evolve into a giraffe .not day’s or life time work like shuffling of cards that in one lucky step will give u a desired combination of numbers (even this is rare ) .

3)Mutations happens under stress , to be clear changes occur when the existence or lively hood of the animal or species is at risk (pm) . yet to be proved .. but we can accpt the fact there there are long periods of stabillity ..
But these are really periods unnoticed variations .

Evolution is the correct prespective to look at regarding the origin of man . This might be out of context ..there has to be some thing with out beggining or end for the whole universe to occur (even if we beleive in cyclic nature of universe ). a singulariy bsed on what the big bang concept is all about .. that has no shape ,weight, quantity,that is in no palce,in no time ..

Jon says:

Your “top down” infomation theory doesn’t match with what we know. For most of Earth’s history, life evolved no futher than algae. The world was filled with very simple organisms. Then after several events (ex: Cambrian Explosion) you start seeing more and more complex organism. Over the millions of years you then see even more complex creatures, plants and finally animals and us.

So from that point of view, it would seem that the information is bottom up. Because we know that those early life forms we very basic and simple. It’s that accumlation (Something Dawkins suggested) of those random mutations that gives us the incredible diversity today.

If what you are saying was true, then those first organisms would be more advanced and evolved than we are. Since they are at the top and information only goes down, then it would seem that all life afterwards would be less evolved. But we know that is not the case because I think we can both agree that humans are more evolved than algae.

Remember, mutation promotes diversity.

The genome had to build an entire ecosystem with simple organisms, before the complex organisms could evolve.

My hypothesis is that it was programmed to do exactly that.

And the Cambrian Explosion itself is the best evidence that my theory is valid. The Wikipedia entry puts it this way: “The long-running puzzlement about the appearance of the Cambrian fauna, seemingly abruptly and from nowhere, centers on three key points: whether there really was a mass diversification of complex organisms over a relatively short period of time during the early Cambrian; what might have caused such rapid evolution; and what it would imply about the origin and evolution of animals.”

A gradual random mutation theory completely fails to explain this. At the same time the pattern perfectly matches what we see in human evolution, which is intelligent: In a span of 50 years, between ~1875 and 1925, we got electricity, automobiles, airplanes, phonographs and movies.

The Internet came along and in a span of 10 years, another quantum leap.

Intelligent Evolution perfectly explains long periods of stability followed by explosive growth. Gradualism does not.

The top-down nature of information is a fact of information theory. People can blindly insist that the Random Mutation theory is valid, but it still has yet to be proven after 150 years. I am still asking you or Dawkins or anyone else to provide factual evidence that evolution is driven by random mutation. Communication theory shows us that noise can only destroy information.

Don’t believe it just because I said it. Read Claude Shannon, James Shapiro, Barbara McClintock, and the book Evolution as Computation – I have provided links to these resources above.

Jon says:

But the top down nature of information is not a fact of random mutation or evolution. Again, if what you are saying is true then those first organisms had all the information. The information on how to breathe, how to walk, how to digest an apple and how to grow an arm. Yet those early organism were nothing more than slime.

How does the information degrade if it’s already at its most basic level? If that was the case then it would seem that humans (since we are very evolved) should have come first in the chain of life, not 4 billion years later.

The only way simple organism evolve to move complex ones are those random mutations. It’s about accumlating those traits that ensure survival.

The first organisms might have had all the information.


They had the ability to COMPUTE the information.

One thing’s for sure: The organisms prior to the Cambrian Explosion were not “slime.” It is an insult to the practice of science and the beauty of nature to even suggest such a thing. Even the simplest organism is vastly beyond the ability of humans to create, and is to be looked upon with respect. You cannot learn from something you have contempt for.

There is no way humans could have survived 4 billion years ago. What would they eat?

You are blindly, dogmatically insisting on random mutation – a theory for which you have never seen proof of any kind.

Jon, I have a question for you:

If it were theoretically possible for science to infer information about the metaphysical, would you be open to that information?

Jon says:

But communication theory is not a proven theory in regards with Evolution and Natural Selection. You produce numbers trying to show incredible and impossible odds but all that it showing to me is that you don’t understand how it works.

As a creationist, you see the world as starting out great and becoming worse over time. Again, Science does not show this as you and me and all life alive today are proof of that. Humans are a much more evolved species that those early organic life-forms that covered the Earth billions of years ago. You say that they were “programmed” that way. Well, lets use computers to represent your theory.

According to you, those first organisms were like the IBM Roadrunner, (A modern day super computer), the fastest, most advanced computer to date. Then, these computer began breaking down or “degrading” their information, which would then result in computers that were not as advanced and organized as that first computer. Then over the billions of years as these computers are growing LESS and LESS organized, that by our time you would probably end up with an abacus.

See, your theory does not support the facts. We know that those early life forms were basic and the only way to create “new” information is to accumulate those traits that ensure survival. Now, many of those mutations are harmful but some are not. When you take into the fact that life has been evolving over billions of years, you get the diversity of life we see today. That is not what would happen, according to your theory.


Communication theory is a proven theory in all respects. If you disagree then I invite you to provide links to peer reviewed scientific literature stating the contrary.

It is clear from what you wrote here that you did not read the article above and I do not feel your assertions merit a response.


Lumpy says:

But you aren’t discussing communication theory or information theory or prob stat. You are discussing biology. They are are not the same things.

It is easy to see that mathematics can be mis-applied to certain equations. I remember in my Calculus I class we did the classic problem of the two trains and the fly travelling between them. Using integration you get that the fly will never be squashed between the two trains. However, a rational person would realize that the answer is not right and know to throw out the answer. Just as only a fool would belienve Zeno’s argument that a shot arrow would never hit you as it would always have to trave another half distance.

You are taking theories from another field of science and mis-applying them to Biology. His reply more than merits a reply from you.

Lumpy, see “Information Theory, Evolution and the Origin of Life” by Hubert Yockey (Cambridge University Press, 2005) http://www.amazon.com/gp/product/0521802938?ie=UTF8&tag=httpwwwperryc-20&linkCode=as2&camp=1789&creative=390957&creativeASIN=0521802938

This book completely and exhaustively addresses your question. As do numerous pages on my site. http://www.cosmicfingerprints.com/faq

Jon says:

AGAIN, I have already answered your question. Science is not out to prove the unproveable. I’m sorry, but you will NEVER be able to prove something Metaphysically with Science. That is not how Science works so why do you keep asking this question?

I’m sorry but Science isn’t dogmatic. How can the search for the truth be dogmatic? (This suggests to me again that you do not trust Science) The first organisms did not have all the information nor did they have the ability to compute it. They were simple organisms but over time, and after many mutations and adaptations, they evolved into more complex organisms. We know this is true; Evolution with Natural Selection is the only way to go from something simple to complex. That accumulation of traits that gives us the complexity.

All the evidence the points towards simple organisms evolving into more complex ones.

I understand why you created this website. To find those “sheep” in the herd and do the thinking for them. Many people are lazy when it comes to things like our origins, which is why so many people say “God did it” and leave it at that.

What you have presented here is a theory that does not support the facts. Only what you have discovered. If you were to try and produce this theory in Science circles, no one would be able to back it up. Because everything what you have shown, is based around two things, Incomplete Data and your personal beliefs that are creeping in to the research.

You come from the position of “knowing” the answers before you test them. (And odds are not tests) Science isn’t about that. Science is about getting through what you don’t know, to get past all the things that we think we know, to get to the truth. Scientists don’t go into the lab and say to themselves “I know this is the truth, but let me go ahead and test it anyway”, no they say “That is interesting, I don’t know how this works so let us find out.” You have to be humble when looking for the truth.

Jon says:

I am “comtempt” of Science? That was a good one!

Did I insult you by saying those early INORGANIC lifeforms were nothing more than slime and soup? Those early forms were LESS evolved than a single cell organism, not more.

Please show empirical evidence of these “inorganic life forms.” (Isn’t that an oxymoron?)

Jon says:

Even though you have expressed yourself very well here, I can’t help think see a little Christian Theology in it. That life started out great, Adam and Eve had everything. Then the fall of man, and life and information degrades after that initial perfect source, God.

Oh yes, there is Christian theology in this. Just like there was Christian theology in Isaac Newton and Copernicus and Galileo.

Jon says:

Evolution is better Science than Genesis.

Gary Estes,PhD says:

Yes, anyday…evolution is undiscoverd and challenging…Genesis challenges the human mind even more with smoke and mirrors. The God man has created in Christendom never existed. It’s impossible to prove God. I find intelligent design humanities attempt to explain the unexplainible. If you don’t believe in evolution just look in the mirror, your degenerating body. Look at your own life cycle.
Reverse engineering is all we can do.
And mathmatical solutions don’t drop out of the sky.
DNA generally follows a preset pattern, of course there are mutations.
Spend some time in childrens hospitals! What is wrong with mans created creator?

Jon says:

There is still much we don’t know. Like what happened, why was there an explosion of life. Even though that word “explosion” is a bit misleading. In geologic circles, the Cambrian Explosion happened over like 70 million years, it wasn’t very fast at all.

Jon says:

Evolution isn’t a miracle at all, it’s a relentless and never-ending process. So when a child is born with a birth defect, that is information entropy degradation? When people die of old age, or die from a disease or an entire species is wiped out, that is the same as well?

So God created the information and the rule of entropy as well? Since he is all-knowing then he knew that a little girl was going to be born without a lung or people were going to suffer from aging and death or the extinction of an entire species like the dinosaurs. Again, I can’t help to think about malevolence.

Science is about consensus. When those same millions of scientists come to their own conclusion about something like Evolution, Natural Selection and Random Mutation, then it must be true. It’s not like they are all a part of some global conspiracy about our origins, it’s that they followed the evidence.


Yes, when a child is born with a birth defect, that is information entropy degradation. Same with old age.

God created entropy and God permits evil and suffering. Judeo-Christian theology does not flinch from this reality. God said to Moses: “Who gave man his mouth? Who makes him deaf or mute? Who gives him sight or makes him blind? Is it not I, the LORD?”

Yes Jon you are right, the BUSINESS and the DOGMAS of science are POLITICALLY about consensus.

But the scientific method has nothing to do with consensus whatsoever. And Jon you have now struck at the very heart of the matter! You have said, “Because all these scientists believe this it must be true.” Jon, that is herd mentality. You are letting them do your thinking for you – because they have presented no proof for their hypothesis.

The emperor has no clothes.

Jon, I am challenging you: Stop following the herd and think for yourself.

Jon says:

Now you are insulting me. I’m sorry; I am not letting anyone think for me.

The beauty of Science is that it’s there for everyone. Of course I didn’t do any leg work or experiments but I can read and I can think. Again, Science is for everyone and as Newton said, “We’re standing on the shoulders of Giants.”

Herd Mentality is a product of religion. People don’t stop to ask the questions and think for themselves because they go with what a superior or preacher or priest or Holy Book says. Now if you believe that a book is the source of ultimate information and DON’T question it as many people do, then that is herd mentality.

The Scientific Method is not about consensus BUT when everyone uses that method to uncover the truth about something (In this case, Evolution) then there is Consensus. They go hand in hand.

Lumpy says:

In science, one begins with a Hyptohesis and then attempts to prove it wrong. If you are unable to do so, then you invite other people to prove it wrong. If they are unable to do so then you invite still other people to prove it wrong.

I do not see you doing so here. I do not see an argument from Biology that can be discussed and debated. I see a mis-application of manufacturing theories that have nothing to do with Biology.

You do not reply with refutations of the persons argument. But rather, with personal attacks and a re-statement of your own position.


You are welcome to take on any specific statement I have made and challenge it.

GMEstes1 says:

Excellent reply!
Do your own thinking but offer scientific proof !

PJ Eby says:

What you’re proposing here was already mostly laid out in 1973 or thereabouts by an engineer named William T. Powers, the creator of something called PCT: Perceptual Control Theory.

PCT is mostly about neuron-level negative-feedback control systems, but he noted that even E. Coli use negative-feedback control systems to trigger “reorganization”.

Anyway, Powers speculated that DNA might also have a negative-feedback control system, and the ability to “reorganize”, but his hypothesis doesn’t require reorganization to be intelligent or systematic. E. Coli bacteria actually manage to swim towards food and away from poison by RANDOMLY changing direction. What they do is alter the *timing* of these random direction changes so that, as long as they’re swimming in the right direction, they keep going. If they’re going in the wrong direction, they swirl around and try going straight again.

My point here is twofold: one, the idea here isn’t new, and two, you’re overestimating the usefulness of intelligence. ;-) All you need to get useful work out of randomness (or pseudo-randomness) is a way to use feedback to control it, and the ability to process feedback is really the only difference between living and non-living things.

You might want to check out “Behavior: The Control Of Perception” — as an engineer, you’ll find it interesting. And it agrees with another portion of your thesis here: that is, where living beings are concerned, intention comes before behavior or environmental stimuli.

That being said, I don’t think that there’s any reason why the existence of feedback systems requires an original “designer” to exist. Or, if it did, we could just as easily say that DNA itself must be a God. ;-) The simple truth is: we don’t know how DNA got here, and speculation is pointless unless it leads to a *repeatable* experiment. Since we can’t travel back in time, and praying over a Petri dish and asking God to bless it with some fresh DNA doesn’t seem to work, the speculation seems kind of pointless.

Last, but not least, I still think you are misinterpreting information theory as though it describes something independent of physical reality, when it only describes emergent properties of lower-level physical laws, the way temperature and pressure emerge from more basic concepts like momentum. Temperature and pressure are real phenomena, but they don’t somehow exist independently – they “run on” physics in the same way that . information does. For example, we believe information can’t travel faster than light because *physical changes* can’t travel faster than light. If we ever find a way to make information travel faster than light, it’ll be because we found a way to make physical changes travel faster than light. So the idea that information has an independent existence is an illusion, because you’re ignoring the physical machine (your brain) that your ideas about information are embodied in.


When I tweeted this, I was hoping you’d stop by and post something :^> I always enjoy your views.

The feedback system of DNA of course is not analog, it’s digital. Take Shannon’s encoder > code > decoder and add negative feedback to it and you have a digital control system.

As you know, my central thesis is that all digital communication systems that we know the origin of are designed. That information is not an emergent property of matter.

Our description of DNA as a code or that encoding and decoding take place is not merely a human abstraction or some kind of confusion of territory and map. Rather, DNA has its own map, specifically its pattern of base pairs, and it builds a territory from that map. I assert that is an objective fact and not just a label that humans attach to it.

Subtle but important point: For DNA and evolution to be a digital control system such as we describe, feedback from environment back to genome has to take place. Traditional biology rejected any such notion, i.e. Lamarckian evolution was thrown out decades ago. But in fact I am suggesting that in some sense Lamarck was right: That parents do somehow pass acquired traits to their offspring. This was discussed in a recent Newsweek article.

Finally it’s not pointless to speculate on this question – it’s actually the most important question in biology. Because if information is top-down, then all kinds of assumptions about evolution are reversed. One need not adopt any specific theology or religious doctrine in order to benefit from this. This very article describes a scientific hypothesis that emerges from this view. The hypothesis is testable and provides valuable challenges to the current paradigm.


PS was reading your “SelfHelpMyth” article yesterday. Excellent.

Jon says:

Thanks for the discussions Perry. I think it’s time to remove myself from your site and leave you to your work. Best of luck!

David says:


In regard to this sentence in your article, “Testable Hypothesis for Intelligent Design, Part 1″, in which you say, “For example the length of a giraffe neck could be “dialed in” by a single gene which controls the length of nerve fibers, muscles, esophagus and number of vertebra, all at the same time.”, I’d just like to point out that giraffes have the exact same number of vertebrae as humans and most other mammals; in particular, their necks have 7 vertebrae, just like humans.

I send this only because when I read your sentence, I felt that it implied that giraffes, due to their long necks, have more vertebrae in them than other mammals. So I double checked and found that they don’t.

Respectfully submitted,



I believe in the great architect-great thought-things can not happen randomically
the mycrocosmos and the macrocosmos are under the same law-the planets and
its satellities works like atom and electron-molecules and interstellar space-the
dna is coiled in chromosomes, each cell has more than 2m of dna double strend, we have billions of cells, hundreds times longer than the distance between earth and sun, we can see the gene -dna repair gene,the genes that encode proteins that correct erros in dna sequences,avoiding mutation accumulate in the genome,
dna mismatch repair,the universe works in the united field made by the same architect
regards Leonardo Riva

wency says:

The Big bang theory and the expanding of the universe is in the holy book of the muslims (QURAN), and it was revealed to prophet Mohammad 1400 years ago… what can you say about it?

trowbridge says:

Perry, is there a dumbed down version of what you’re saying? I can’t understand half of your words by I get the general gist of it, I’d just like to understand the details (and terminology) better.

Jim Diamond says:

I can see why you believe ID. You don’t understand evolution. Evolution is basically blind. Using our 90% recessive DNA to create mutations minute and small, these are tested by whether the person survives long enough to breed, so carrying on the mutation. If not, it dies there. If so, then it could prove a survival factor. Eventually all these small changes reach a point where you have a separate species, as with Man and Ape. ID has been proved to be nothing more than creationism in disguise (Dover School trial). So you have god make things, then he experiments to see what works? Duh! He’s supposed to be god. He should know what works. But then again, why should god start off with a less than perfect being, so what point in further changes?


First of all ID and evolution are not mutually exclusive. All things that evolve that we know the origin of (such as adaptive computer programs) are intelligently designed to evolve. Computer programs not designed to evolve do not evolve, they degrade. There are no exceptions to this.

Secondly I do understand evolution, specifically I understand that it is not blind. Jim, please show me a peer reviewed scientific paper that PROVES (and does not just assume or assert) that what drives evolution is random variations.

Shapiro has shown very explicitly that this is not the case: See James A. Shapiro, “A 21st Century View of Evolution”: http://shapiro.bsd.uchicago.edu/Shapiro.2005.Gene.pdf

You are just parroting the familiar Darwinian dogma and that is not sufficient. I am asking you to provide proof that what drives evolution is randomness. There is no such proof.

Your last question is a theological question, not a scientific one.


Jim Diamond says:

First, you prove that you do not understand evolution. There are things which help animals to survive. Running faster, sharper claws, natural camouflage, better eyes and ears, etc. The offspring that has an advantage over others has a better chance of survival and of breeding, so giving those genes to the next generation. It does not need god thinking that Adam was a crap design so god altering him to make him better. Evolution is a natural process.

Go check the internet. Go check talkorigins. Evolution is about survival of the fittest. That says it all. If the environment, climate. predators, prey, etc change, then others must change or face extinction. If the prey is too fast, the predator starves. If the predator is too good, all the prey dies. There are no random variations. It is only what works survives to future generations. Evolution does not experiment like seeing how man would manage with a third arm. If you had a clue about evolution, you would not make such dumb mistakes as claiming that anyone thinks it is randomly driven.

Name me one peer reviewed paper about creationism. Just one. Lots of people with degrees and such, like plumber Hank Morris. Excuse me if I don’t hold my breath while I am waiting.

OK, you think you know how genes work. You have Adam. From him god takes a rib and makes Eve. They produce Cain, Abel and unnamed girl children. They have only the original DNA of Adam and no ancestral DNA. What happens?

The children are exact clones of their parents. The children interbreed, still having only the original DNA of Adam. More clones. How many generations before individual children who aren’t almost complete copies of their parents since this can only happen by mutations. Hundred generations? Thousand generations? What would cause mutations? No harmful chemicals. No harmful radiation.

Qqccho says:

First you wrote ” First of all ID and evolution are not mutually exclusive” and then below you wrote ” Your last question is a theological question, not a scientific one”.
ID- Intelligent Design, is all about Theology and if not mutually exclusive with Evolution then the asked question had to be answered. If wasn’t then there’s an open hole in your theory. You cannot be a christian some times and a science man at others. Not in XXI century. THEY are exclusive.
It seems you’re developing theory as you go answering the posted questions.


I am not embracing traditional ID. I’m defining my own version of ID which is origin of life = 2nd singularity.

Lumpy says:

“It ferociously defends this core chassis from being corrupted by random mutations, while switching out different variables in the head, spine, heart etc.

On what do you base this?

Also, how does your “Swiss Army Knife” theory explain vestigial eyes in cave fish and lizards? Seems to me that God would just turn said organs off in those animals. Why do they still have the vestiges?

Also, you seem to think that individuals Evolve but this is not the case. Only populations evolve.

Oh, and you are partially correct about this part:”Efforts to find a mechanism by which organisms share this information will eventually be rewarded. And the mechanism that is discovered will be as surprising and revolutionary to biology as Einstein’s theory of relativity was to physics.”

The mechanism has been discovered ,it is called DNA, and it was revolutionary in that it completely supported Darwins theory of descent with modification.

Genome ferociously depending against mutations – See James A. Shapiro, “A 21st Century View of Evolution”: http://shapiro.bsd.uchicago.edu/Shapiro.2005.Gene.pdf

You don’t seem to understand what’s really being said here or what the question really is. Please read Shapiro’s paper carefully.

I agree with much of what has been presented here . The Darwinian model is a dismal failure and should have been abandoned decades ago.

However I do not believe creative evolution is any longer in progress. Just as ontogeny terminates with the death of the individual, so phylogeny is now apparently terminating with the present biota which is undergoing extinction without replacement. Both the anti-Darwinian Robert Broom and the Darwinian Julian Huxley pointed out that a new Genus has not appeared in the last two millioin years. I have challenged the Darwinians to produce experimentally verifiable evidence for the production of new true species in historical times. That challenge has gone unanswered.

I believe with Robert Broom that evolution resulted from a Plan, a word he capitalized much to the distress of the atheist Darwinians. I believe the Plan has been realized with the appearance of the present biota with Homo sapiens one of the most recent products.

Ontogeny remains the best model for phylogeny. They are each part of nthe same reproductive continuum and should be considered simultaneously.

The history of organic evolution, like the development of the individual, is the history of the loss of potentiality until today there seems to be no further replacements for the countless creatures that have become extinct. It is questionable if any “evolvers” still remain. I realize this is not an popular view but I believe it is in accord with what we really know about the great mystery of phylogeny.

Pierre Grasse also questioned whether evolution is still in progress.

“Aren’t our plants, our animals lacking some mechanisms which were present in the early flora and fauna?”
Evolution of Living Animals, page 71

Note the contradiction between this statement and the title of his book.


Jim Diamond says:

John A Davidson. Two million years is very little time in evolutionary terms as you would know if you read about it rather than just quoting names to make it look like you had.

Of course evolution is still in progress since we live in a potentially changeable environment. There is no end product other than death of a species.

TPD says:

” I can see why you believe ID. You don’t understand evolution. ”

Typical neo-Darwinian response.

” Evolution is basically blind. Using our 90% recessive DNA to create mutations minute and small, these are tested by whether the person survives long enough to breed, so carrying on the mutation. ”

Natural selection prevents random mutations from occurring acting as a regulatory mechanism. Accumulation of random mutations inevitably leads to extinction, it decreases rather then increases function. No “new” species has been generated with exception to intra-specific varieties. Evolution doesn’t work the neo-Darwinian way, plain and simple. That is, YOU don’t understand evolution.

“If not, it dies there. If so, then it could prove a survival factor. Eventually all these small changes reach a point where you have a separate species, as with Man and Ape. ID has been proved to be nothing more than creationism in disguise (Dover School trial). So you have god make things, then he experiments to see what works? Duh! He’s supposed to be god. He should know what works. But then again, why should god start off with a less than perfect being, so what point in further changes?”

No, they don’t. There is a another mechanism that is responsible for evolutionary change and it is NOT random mutations and natural selection.The position effects of chromosomes lead to new species, these are far from random, in fact they are quite determined. Neo-Darwinism simply fails on all accounts.

I’m waiting for that evidence of “new” species formed by genetic drift, random mutations and natural selection. Lets see if so called “evolved” population y from pre-exising population x could NOT interbreed. Hope you bring me solid concrete evidence for that population y could not rather then would not interbreed (there is a big difference between “would not” and “could not”)

Just because progressive evolution IS no longer going on (which is my conviction) does not mean that it WAS blind in the past. The Designers may be dead but their design persisted and became fulfilled.

Henry Ford invented the automobile assembly line. While Ford is dead, the assmbly line continued without him. I see no reason to insist on a lving God when there is not a shred of evidence for that proposition. That does not mean that God does not exist. As a Roman Catholic, I like to keep my options open!



“Not a shred of evidence” that God is living?

I disagree with that on so many levels. Just one sample of my own personal experience: http://www.perrymarshall.com/travelogue/india/june-12/

Even if we restrict the discussion to medically documented miracles, if we’re going to say there’s not a shred of evidence then we have to take a substantial stack of books off the library shelf and run them through the shredder.

…And then we will still have nice-sized pile of shreds of evidence. Go to Amazon and type in “Lourdes miracles” and that’s just a start.


Jim Diamond says:

Personal delusions are no more evidence of god than presents under a tree are evidence of Santa.

No medical miracles that can be proved. A test with patients who were prayed for and people who weren’t showed that the patients who were not prayed for did best!

Lourdes? What a con game for the gullible.

God to St Peter: I want to send my message to the people of Earth and I can’t decide who to contact. Shall I:

a) Contact the President of the United States?
b) Shall I address the UN?
c) Should I contact the pope?
d) Should I send Mary to a field in the middle of nowhere?

St Peter: I’d go with (d).

D for DOH, that is.


Stacks of evidence have been presented regarding miracles. The documentation is there. You choose to reject all of it. That is your decision.


billy says:

Jim Diamond, you would have to show how Charlie’s computer wrapped as a present under the tree is the result of a fortuitous process. Then you would have show how Santa could have evolved via random mutation. I doubt, in your appeal to Santa, that he would be an atheist, seeing that he appoints elves rather than shuffle the toy parts in a giant mixer.


I hope you are right. Unlike David Springer who “loves being right,” I “hate being right,” especially about God. That is one of several reasons I have postulated a minimum of two Gods, one benevolent, the other malevolent. It makes the world I perceive much easier for me to understand. I guess that makes me a polytheist. Horrors, such blashemy!

“All great ideas originate as blasphemies.”
George Bernard Shaw.

re Two Gods: Leszek Kolakowski who lived through the Nazi invasion of Poland said,
“I can understand people who do not believe in God, but the fact that
there are people who do not believe in the devil is beyond my


I did not mean to offend anyone. I meant only that the existence of God is not subject to experimental verifiction. If God’s existence were verified there would be no atheists! Wouldn’t that be a dull world? Furthermore, I feel that there is no more reason to believe in monotheism than there is in a monophyletic evolution. The Greeks and Romans did fine with several Gods but I know of no great civilization that had none. Does anyone?

“Organisms have developed from tens of thousands of primary forms, i.e, polyphyletically.”
Leo Berg, Nomogenesis, page 406.

If evolution was polyphyletic, and I agree with Berg, why can’t a religion be polytheistic?



Having been a devout student of human behavior for 20 years and having conversed with atheists very closely for 12 years now, I do not think experimental verification would convince all atheists. Some, I’m sure – but NOT all. If experimental verification won’t convince even them that DNA is a code (!!!) – which they deny only because they CHOOSE not to believe in God – why would any other kind of experiment convince them?

I submit to you that a monotheistic theology was required first, before man could formulate a coherent philosophy that would eventually lead to the rise of science. Ostensibly, science emerged from monotheism, not polytheism. I think that’s at least clue.


I am fed up trying to communicate with either atheist or religious fanatics. I have made my position clear enough and it accomplishes absolutely nothing. To be ignored or villified by ideologues has always been standard procedure in every field of human inquiry and it always will be. If anyone chooses to communicate with me they know where to find me.


“All great truths begin as blasphemies.”
George Bernard Shaw

Vishesh says:

Dear Readers and Perry (If you’re reading this),

Now, I’m just a 16 yr. old boy and I don’t have much experience in the world of
philosophy, religion or science, but I do take a keen interest in subjects, I daresay are “beyond my age”. I have been surfing the web looking for theories that can satisfyingly explain the existence and working of our universe and have come across many others trying to prove the existence of antimatter(CERN) as well as parallel universe(s). The one that relates antimatter and the big bang has particularly intrigued me, which states that before the existence of our universe, matter and antimatter were the only things that existed. When matter and antimatter interact physically, they eliminate each other and a huge amount of energy is evolved. Some say that during the big bang, matter somehow prevailed antimatter during their interaction (along with releasing huge amounts of energy) and has developed into the universe we live in today, while the energy released is the cosmic radiation we observe even today as a proof of the big bang’s occurrence. Now, I’ve also been a fan of the Chinese theory of yin and yang and according to it, our universe remains in balance when the forces of yin and yang, good and evil, right and wrong exist in harmony. Throughout our lives, we see patterns almost symmetrical yet believable – like the balancing forces of life and death, good and evil, heaven and hell, man and woman, on this very earth. I for one, personally believe that our universe remains in balance when opposing forces act in harmony and maintain the delicate balance of this world. Now, this is purely my own speculation and the readers are free to point any flaws seen by them, but I believe that before the existence of the universe matter and antimatter did exist, but in equal proportions. I am not satisfied by believing the theory that matter “somehow” prevailed over antimatter, and thus, I put forward my own speculation- What if matter and antimatter still exist today in harmony with each other? What if the parallel universe did exist, but in the form of antimatter? Is it possible that beyond the limits of our universe, a similar, or maybe entirely different universe existed, except for the fact that it would be composed of antimatter entirely?

I’m free to all comments and I’d love to hear from people more knowledgeable and credible than me who would be so kind as to enlighten me with their views on my speculation. My E-mail ID is VCool123@zapak.com, and I welcome anyone and everyone to express their opinion through E-mail or through this very blog.

Thank you for your time.

kooros says:

Dear Vishesh
Regarding the balance you mentioned in your comment, I think it is not right to generalize apparent dualities.
As for good and evil forces, I understand from Holy Quran that evil forces inside and outside mankind are created by The God to provide mental evolution environment for man, struggling against these forces and achieve a quality which would not reach otherwise.
If there was no evil / bad , “good” could not be recognized.
As you have noticed, a kind of balance is kept (by an external will) between bad and good in our social environment throughout the history of mankind.It seems doing good and fighting against bad, is a mental growth process which is planned for human moral evolution. There are several valuable moral qualities (for example, sacrifice) which may not be understood and gained by other means.
Best regards,

VCool123 says:

I agree to your statement that good and evil are relative, but you’re missing the point. I just used it as an example to cite my theory. As I said before, antimatter couldn’t just have prevailed for some unknown reason over matter during the big bang. And if my theory is wrong, I’m perfectly alright with it. But the question still remains- where did the antimatter go? Also, kooros, if you’re interested, try googling “Noetic Science”. The matter available is worth a read, and it has HUGE implications on our existence.

levgilman says:

“Cells employ a built-in algorithm, which engineers re-arrangement of Mobile Genetic Elements (as observed by McClintock and Shapiro)”
OK, if it is a part of the hypothesis to test. But before, you merely stated intelligence of those and other DNA rearrangements intelligent just as fact to start from. No wonder that biologists find no interest in discussion with one who claims such things, what you arrogantly mistake for lack of argumented objections.

Carbon-based Machine says:

QUESTION: If genetics has the ability to experiment with novel mutations (a mutation algorithm), would that take the Intelligent Designer out of the equation? In other words, could your argument be turned around to undermine the premise of intelligent design?

historian186 says:

This is more of a commentary. Perry, wonderful site and insights! As Jesus said to Peter- “…..It is not flesh and blood and blood that revealed this to you, but my Father in heaven.” (Matt 16:17.) However, my concern with Intelligent Design is the title. When a question is posed to me as a follower of Jesus Christ, I try to ask myself the question – How would Jesus answer this question? I believe that He would say it was by GODLY design, and then provide evidence to substantiate this. (Actually, He already has, through the Living Word, His creation and His life while He was physically on earth – but that is another story.) Humans beings are intelligent, and we definitely did not bring creation about. Chimps are reasonably intelligent, they did not either! Let us call it Godly Design, whoever is unhappy with that, we deal with it as it comes.

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