Invariably you hear this retort:

“Aw, that’s just a god-of-the-gaps argument.”

For many, that’s the end of the discussion.

The retort usually comes with a sneer: “Don’t be stupid. People used to think that weather came from God. Now we know it comes from heat, cold, moisture and chaos. People used to think God hung the stars on a sphere in the sky. Now we know about gravity and orbits. People used to think God created man. Now we know man came from primates.”

You know the drill.

It’s not always obvious that this retort is a tacit admission that the person making the god-of-gaps argument did score a point. Some god-of-gaps arguments are quite persuasive.

I’ve been making a god-of-gaps argument right here on this website since 2005, in the form of a syllogism:

1. The pattern in DNA is a code.
2. All codes we know the origin of are designed.
3. Therefore we have 100% inference that DNA is designed and 0% inference that it is not.

Regardless of what position you take in the debate, I have some things to say about this which might surprise you. I hope you’ll stick with me for a few minutes because this goes to the very roots of how we practice science, and what science is capable of in the first place.

Let’s start with my syllogism. It doesn’t say “designed by who.” The genetic code could have been designed by aliens. It could have been designed by some entity or process we have no knowledge of. However it doesn’t take a genius to connect the metaphysical dots.

So far in 8 years nobody’s punched a hole in this argument. As god-of-gaps arguments go, it’s pretty sturdy. It’s rooted in the fact that codes require specific choices to be made which you cannot derive from the laws of physics. It is different than most god-of-gaps arguments because it’s an ontological argument: Coded information is not even known to exist without an act of intelligence.

When I presented this to my skeptical brother Bryan, he immediately disliked it. He said to me, What do you expect scientists to do, Perry… throw up their hands and say ‘Gee, I guess God did do that. Time to go home, there’s nothing else for us to investigate!’?

If you don’t have a strong scientific orientation, if you’re a fairly religious person, you might say “Yes, I think scientists should rein in their bloated egos and give God some credit for the amazing world He made.”

But if you do have a strong scientific orientation, you know the scientist would be abdicating his responsibility. “God did it” takes a scientist’s job away. If there’s any possibility that a naturalistic explanation might be found, the scientist’s job is to find it.

I shouldn’t have to explain the benefits of sticking to these rules. Almost all scientific discoveries have practical applications. Sooner or later we get better medicine, smarter doctors, better computers, better cars, and a better life, because we understand the laws of nature better with each passing year.

Modern science has no earthly idea where life came from and anyone who suggests otherwise is either deluded or picking your pocket. But these rules still apply even with utterly daunting questions like the Origin of Life.

Personally I think the evidence we have points to the Origin of Life being a “second singularity,” an event as unique and miraculous as the Big Bang itself. In fact I’ve never seen any evidence to the contrary.

Nevertheless I must respect any scientist who endeavors to bridge the gap between life and non-life. That gap, after all, may someday get filled. If and when it is, countless valuable insights and new technologies will ride along as a bonus.

Someone may overturn my syllogism. In the spirit of science I will celebrate when they do. Why? Because the universe once again turns out to be even more impressive than we’d previously thought.

OK, then what about God?

To answer this question we have to go back to the roots of “methodological naturalism” itself. Methodological naturalism is the scientific practice of always assuming the laws of nature are consistent. It assumes they’re sufficient to explain the normal and customary operation of the world.

To my knowledge, the earliest statement of naturalistic thought in ancient times comes from Wisdom of Solomon 11:21, which was written 2,500+ years ago, says, “Thou hast ordered all things in weight and number and measure.” This is found in the apocrypha, i.e. the books of the Catholic Bible.

This came from Jewish theologians who believed that God made a world that was self-sufficient. It didn’t require His constant tinkering in order to operate.

This was not seen to conflict with the assertion that God is also present in the world and does miracles. On the contrary, naturalism itself is defined in terms of miracles. Naturalism is the regular and customary order of things. Miracles are when God shows up and does something that is not the regular and customary order of things.

I’ve witnessed many miracles up-close and in-person. I document a half dozen here, with links to peer reviewed papers that report healing of blind and deaf people in controlled studies. I see no conflict between the job of a scientist and the active exercise of the supernatural by real human beings in past and the present.

What if a scientist does witness a miracle? If he’s working in his professional capacity, he’ll start by searching for a naturalistic explanation. On the other hand as a whole human being he is also free to say, “I conclude that it was a miracle.” If he believes a miracle has happened, then by definition he can’t reduce what happened to scientific process.

Prehistoric vs. Modern Miracles

If every species of plant and animal was the result of a miraculous act of God thousands or millions of years ago, then we cannot investigate how antelopes evolved into giraffes.

However, if life evolved from a single cell, and if the process of evolution was not guided by God, then there is an evolutionary algorithm at the heart of living things that is truly astounding. However antelopes evolve into giraffes, we ought to get busy and find out how it works.

I’ve shown in other parts of this blog that evolution cannot possibly be the result of random accidents. Evolution is engineered. Therefore I cannot think of any field of study ripe with more promising discoveries than evolution itself.

I believe God wants to use science to teach us as much about Himself as possible. Most theologians would agree. And I believe the way we make those discoveries is through naturalistic investigation via the scientific method.

It’s deeply ironic that many modern evangelical Christians believe that plenty o’ miracles happened 2000+ years ago and 6000+ years ago, but they don’t believe miracles happen today. (They sure didn’t get that from the Bible.)

What if you flip that around? The way you prove miracles exist is by doing what Jesus said: Laying hands on people and healing them. (Most American evangelical churches do not do this.) I think miracles began in earnest with the ancient prophets, and in the meanwhile, God had granted life its own amazing natural engineering capabilities long before.

After all, which is harder?

1) Building a zebra and beaming it onto the savannah, Star-Trek style,

or

2) Designing a cell that builds an ecosystem for a zebra to live in – then builds the zebra too?

or even

3) Designing a universe that gives birth to a cell that builds an ecosystem for a zebra to live in – then builds the zebra too?

An accurate understanding of evolution – one that acknowledges the engineering capabilities of cells, the ability for organisms to adapt to their environment – offers a far more impressive view of God than anything the Young Earth Creationists ever envisioned.

Many religious people have taken the bait from the atheists who claim evolution got rid of God. Now they’re forever selling from their heels.

What a con. Every organism that has the ability to self-replicate and evolve exceeds anything humans know how to engineer. The real question is: Why is it even possible for a universe to even give rise to such things? Why is the universe so incredibly orderly? Why does it obey mathematical laws? Why is it logical?

There’s a huge difference between proximal explanations and ultimate explanations. Science is incapable of disproving or eliminating God, because science cannot even explain itself. In science we have to take on faith the assumption that the universe is logical and consistent. Surely it must be that way for a reason.

So I’ve come to these conclusions:

1. Any theory that takes a job away from a scientist is probably wrong.
2. Any theory that attempts to eliminate God as an ultimate explanation is probably wrong.

These two statements stand forever in tension with each other. The solution to the God of the Gaps problem is for us to always assume ultimate intentionality and order. Yet at the same time we can never announce we’ve reached the end of the scientific rabbit hole. There’s always another layer of order to discover.

Robert Boyle, the world’s first modern chemist, said this around 1675: “… the universe being once framed by God, and the laws of motion settled, and all upheld by his perpetual concourse, and general providence; the same philosophy teaches, that the phenomena of the world, are physically produced by the mechanical properties of the parts of matter; and, that they operate upon one another according to mechanical laws.”

In closing, I want to point out that there is one time-honored assumption in science that is currently failing:

Materialism.

Materialism insists that the fixed laws of physics explain everything. In Darwinism, it is assumed that blind physical processes combined with natural selection explain the diversity of life.

What we know from bioinformatics and the last 50 years of genetics is, every cell in the world is purposeful, teleological, and has built-in DNA self-programming and adaptive features. Non-living things are not teleological; living things are. Evolutionary processes are. We see purposeful direction and natural engineering in living things.

The prevailing scientific paradigm has no room for this. The old guard resists new research because materialists had been assured for 150 years that Darwin got rid of God. Darwin accomplished no such thing. Darwin uncovered an even bigger mystery that is only beginning to come to light now. Darwin thought cells were blobs of goo; he had no idea they’re tiny supercomputers armed with sensors and equipped with digital signal processing.

“There are more things in heaven and earth, Horatio, Than are dreamt of in your philosophy.” -Hamlet

I vehemently disagree with Neo-Darwinists who insist evolution is a simple process of random mutation + natural selection + time. Their theory of randomness is anti-scientific.

As an electrical engineer, I sympathize with the Intelligent Design movement in its insistence that design is detectable and that design is a proper scientific discipline. Every university in the world has multiple departments that teach design, after all.

But I disagree with the ID movement’s tendency to ascribe everything we don’t understand to direct divine agency. Like many other areas of theology, we have no choice but to live in the tension between the natural and the divine.

Einstein said, “There are only two ways to live your life. One is as though nothing is a miracle. The other is as though everything is a miracle.” I submit to you, dear reader, that even the regularities and natural systems of science are, themselves, enduring miracles.

Perry Marshall

P.S.: The worst way to counter a god-of-gaps argument is with dodges and shell games. Example: Richard Dawkins, on radio station WBUR in Boston, glibly proclaimed that life was a “happy chemical accident.” This statement, and many theories that are much more substantive than that, still engage in wholesale avoidance of the question. When there’s a gap, the honest thing to do is admit it.

“Where I’m not buying evolution in large scale, again goes back to the collection (or lack) of “transitionals” to prove this happened on a grander scale. All need to be in place for the large scale to have existed.

It’s one thing to make claims on microorganisms (and I can see it justified). It’s a far greater stretch to make the other areas fit.

This is not to say they can’t (God has that intellect), but proof that they did is very sparse at best call.”

My reply:

There are few transitional forms because they don’t exist. That’s because evolution is not usually gradual. Just like in human technologies, it’s almost instantaneous.

The proof of evolution is not the fossil record, it’s in the lab.

We can and do observe new species in real time – in the lab and in the field, in micro organisms and plants and animals. This happens through large leaps where you get a new species in 1-2 generations (through Horizontal Gene Transfer, Whole Genome Duplication and Inter-Species Hybridization). These mechanisms are well understood today, and they are very much purposefully adaptive and quite non-Darwinian.

Darwinists are in no hurry to tell you about any of this stuff, because once you take this into account they’re no closer to getting rid of God than they were 200 years ago. (These things don’t prove God, but what they do prove is that evolution is teleological. None of these things occur through random copying errors of DNA – far from it!)

And sadly, ID people aren’t in a hurry to tell you about these mechanisms either, because many of them deny common descent. The truth is in the middle, and the truth is 100% compatible with a theistic view. I submit to you that a God who creates an entire evolutionary process is far more impressive and inspiring than a God who merely creates a plant or an animal.

PDF Handout

HUNTSVILLE ALABAMA - NASA has announced their choice of evolutionary biologist, Dr Richard Dawkins to head the team that will be studying and analysing the UFO that landed intact in the Arizona desert six months ago.

Why Professor Dawkins? His research program came cheaper than all the other candidates for the post. The aerospace experts, quantum physicists and cosmologists were rejected because high on their research agenda was the costly question, “Where did it come from?”

Professor Dawkins will be saving the American tax payers millions of dollars in wasteful research by bringing his scientifically verified answer to this question from the outset, “It’s origins were just a Happy Chemical Accident.”

An un-named though reliable source at the CIA told our reporter, “We already know where the alien space craft came from, but that must remain classified information. National security could be endangered. With Dr Dawkins, we can be sure that he won’t go prying in forbidden areas. He has a world class reputation as the man who has a peer-reviewed aversion to origins. That’s why our official line is, and will remain, “Source – a Happy Chemical Accident.”

Dr Dawkins has made it work for evolution. He’ll make it work here. In the good old Cold War days we could have said it was a Soviet hoax, but times have changed, alas. Conspiracies are out, accidents are in. They are more scientific.”

PHOENIX ARIZONA - Starbucks Corporation will be presenting their new coffee in Arizona next week. It will be served free throughout the state between 6 and 8pm in what they are calling their new “Happy Chemical Accident Hour.”

Samir Rahis, head of Starbucks secretive R & D section revealed that the coffee’s ingredients are selected on a random basis from a massive selection of coffees from all over the world. He explained, “Thanks to our ground-breaking Random Coffee Percolator, nobody will know the origins of their coffee. Each cup will be a unique Happy Chemical Accident and the FDA can go jump in a lake.”

WASHINGTON DC - A new defense is being tried before the Supreme Court next month. Hundreds of prisoners on Death Rows throughout the country have been grouped in a unique class action by the New York lawyer, Ricardo D’Occins. His defense argument will be unique in judicial history, “Not guilty by reason of a Happy Chemical Accident”.

Speaking on the Daily News he explained, “Everybody accepts that Life came about by a Happy Chemical Accident. Our Supreme Court judges need to recognise that what’s good for the Origins of Life is good for the Cause of Death. My clients are all on Death Row on account of a Happy Chemical Accident. I believe they will all be free men by next week.”

“Without science art would become a crude mess of folklore and emotional quackery. The truth of art keeps science from becoming inhuman, and the truth of science keeps art from becoming ridiculous.”

-Raymond Thornton Chandler, writer, 1888-1959

What most people think they know about evolution is 30 to 70 years out of date.

The most popular books (even recent ones by very famous authors) make it sound as though the last five decades of scientific research never happened.

That’s a tall claim, I know. But James Shapiro’s new book “Evolution: A View From the 21st Century” is the first to spell it all out in a comprehensive way.

This is not in any sense a religious book. Nor does it indulge in any of the mud-slinging that is typical of creation-evolution arguments.

Shapiro is a bacterial geneticist from one of the world’s great research institutions, the University of Chicago. The late Nobel Prize winner Barbara McClintock mentored him and he discovered DNA transposition in bacteria. He has an Order of the British Empire medal from the Queen of England. Impeccable credentials.

In this new book, endorsed by two Nobelists, Shapiro sets the record straight.

I first encountered Shapiro’s work six years ago, when guy sent me a link to one of his papers. I had become fascinated with the question of evolution from the perspective of an Electrical Engineer.

I designed speakers for Honda, Mazda, Chrysler and Acura in the 1990′s. Then sold networks for manufacturing and robotics for 7 years; in 2002 wrote an Ethernet book. In e-commerce, I consulted in 200+ industries, optimizing sales processes on the web. As a specialist in Google advertising, I saw that Google’s #1 job was to accurately simulate natural selection.

Because of my work in communications, control systems and the web, in DNA I saw an utterly remarkable communications protocol. Something vastly superior to anything humans had ever designed. I found myself increasingly frustrated with the Darwin-design debate. One side charged that evolution was a fraud; the other claimed it happens by accident. I doubted both.

I couldn’t help but wonder: “If random mutation and natural selection are all you need to produce the most amazing machines, how come they never uttered a single word about these things in engineering school?”

And furthermore: “If evolution is true, what design principles should they be teaching in engineering school that they’re not teaching now?”

This really was THE question that drove me. I guessed all that “junk DNA” might possess some evolutionary function. I figured that once we understood exactly how evolution produces novel features, we’d be able to produce miraculous new technologies.

Shapiro’s work was a revelation. He described how cells, like wireless routers, militantly guard against copying errors. He lifted the hood on the splendid information processes of the cell. He described how the genome is like an operating system, organizing information, cleaning up files, repairing damage, regulating activity.

He even had the humility to point out that sexy new 21st century computer metaphors are dangerous because they limit our thinking. The truth of mother nature, he said, is even more amazing than that.

He referenced the Nobel Prize winning work of Barbara McClintock. I was surprised her name wasn’t a household word in biology, because her discoveries had radical implications for evolutionary theory.

He defined an alternative to both creationism and Darwinism, a “Third Way.” In this view, the information capacities of the cell are the real star of the show. He recounts how molecular geneticists showed a protozoan under stress splicing its own DNA into 100,000 pieces, re-arranging them to produce a new functional nucleus, freshly adapted to its environment.

As I probed further, I discovered that thousands of PhD’s are aware of this. Any cell biologist worth his paycheck knows that bacteria exchange genes with each other, much the same way musicians trade guitar riffs. This is how germs battle antibiotics. They do this very deliberately, and at tremendous speed.

But John Q. Public knows nothing of this. He’s been told it happens so slowly that it can hardly even be replicated in the lab. He’s been led to believe it all happens by accident.

Until now.

In his book, “Evolution: A View from the 21st Century,” Shapiro outlines the adaptive systems of evolution in detail:

• “Natural Genetic Engineering” refers to cells’ innate ability to re-organize their genomes in response to hundreds of kinds of inputs. This is the star of the show. Not natural selection.
• Horizontal Gene Transfer, cells exchanging segments of DNA to instantly gain new features;
• Inter-species hybridization – new species form when unlikely mates cross from two different species;
• Symbiogenesis, when completely different organisms merge to form a new species;
• Epigenetics, switching genes on and off without altering the DNA sequence;
• Whole Genome Duplication – DNA doubling to expand “hard drive space” and make room for novel features.

These purposeful systems, in combination, generate the huge diversity we see on planet earth. Not random copying errors.

At last count, I have 114 books that address the question of evolution in some way, shape or form. They span a century and a half.

Dr. Lynn Margulis, for example, does an outstanding job of explaining symbiogenesis in “Acquiring Genomes” – but symbiogenesis is only about 15% of the story. Other books describe Horizontal Gene Transfer but that too is only part of the story.

Shapiro’s book is head and shoulders above the others. No other text assembles the picture as completely and coherently as this.

Remarkably, he accomplishes all this in 150 pages. This thing is dense. It’s like the richest chocolate cake you’ve ever eaten. You can spend a week digesting one page. Most evolution books are cotton candy.

For example, Richard Dawkins’ “The Greatest Show on Earth” asserts that evolution is driven by random changes in genes. Then, in 450 pages, Horizontal Gene Transfer is briefly mentioned once. Epigenetics is dismissed as a confused theory that will enjoy 15 minutes of fame. Symbiogenesis and transposition are never discussed at all. Nor is whole genome duplication.

When it comes to the exact mechanisms of evolution – the systems that make it possible – many books have almost no content at all.

Last year I attended a lecture at Fermilab by Dr. Shapiro. After his talk, a group of people huddled around him in the cafeteria, peppering him with questions. One guy suddenly ‘got’ what he’d been saying all night long.

“You mean the mutations aren’t random?” he asked.

“No sir. They’re not random at all. “When bacteria are comfortable and well-fed, certain DNA changes occur at a frequency of less than one per billion cells. But when they’re starving, the mutation rate skyrockets by a factor of 100,000. They develop new adaptations so they can survive.”

The man looked to be in his fifties and I imagine he’d bought into the random mutation myth decades ago and never questioned it since. I watched the guy’s face. You could see the gears grinding inside his head.

So will it be for many readers of this book. It challenges widely accepted dogmas and replaces them with systems. If you doubt Shapiro, consult the 1162 references he provides. Then decide for yourself.

In any case, be prepared to discover things nobody else told you. Be prepared to ask yourself why the “evolutionists” never bothered to show you how evolution really works.

This book is written at a college level. Lay readers may only be comfortable with a third of it, and he has suggestions for what portions to read first. But you’re far better reading 50 pages of real research from the University of Chicago than 500 pages of “evolution thru random copying errors” by the Darwin lobby.

If you are remotely interested in the “behind-the-scenes” truth of evolution and its systematic mechanisms, you must own this book.

In future installments I’ll peer inside its pages and share more with you. Meanwhile . . . pick up a copy for yourself.

Perry Marshall

Get Evolution: A View from the 21st Century by James A. Shapiro on Amazon

Richard had a radical conversion experience in 2008. Not only did it rock his world in an instant, it incited a riot on the Dawkins Internet discussion board. Despite his mannerly approach, he was quickly banished from the forum.

In this video, Richard tells you his strange yet wonderful story. (It’s featured in the book “The Dawkins Letters” by David Robertson, 2nd edition.)

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He asked me to offer citations from the literature showing that evolution is non-random. This is what I sent him:

1. Genomic evolutionary change is a systematic response to the environment, not a result of random copying errors:

From James A. Shapiro, “A 21st century view of evolution” http://shapiro.bsd.uchicago.edu/21st_Cent_View_Evol.html. Emphasis mine:

“…the prevailing theory of biological evolution postulates a random walk to each new adaptation. In the last 50 years, molecular genetics has revealed features of DNA sequence organization, protein structure and cellular processes of genetic change that suggest evolution by natural genetic engineering. Genomes are hierarchically organized as systems assembled from DNA modules, which themselves generally constitute systems at lower levels. Each genome is formatted and integrated by sequence elements that do not code for proteins. These formatting elements constitute codons in multiple genetic codes for distinct functions such as transcription, replication, DNA compaction and genome distribution to daughter cells. Consequently, the genome has a computational system architecture.”

“Natural genetic engineering functions are sensitive to biological inputs, and their non-random operations help explain how novel system architectures can arise in evolution.”

“Moreover, the fact that natural genetic engineering changes are neither random in nature nor restricted to a single site in the genome means that they can create novel distributed (multilocus) systems and new genome system architectures.”

“One source of this latter view is the conventional theory that evolution occurs by a random walk through adaptive space and produces a virtually endless series of sui generis inventions. One alternative to this conventional view is that there exist design principles and procedures that are used repeatedly in evolution (in other words, evolution occurs as an engineering process).”

“In terms of a 21st Century view of evolution, the major importance of natural genetic engineering is that this capability removes the process of genome restructuring from the stochastic realm of physical-chemical insults to DNA and replication accidents. Instead, cellular systems for DNA change, place the genetic basis for long-term evolutionary adaptation in the context of cell biology where it is subject to cellular control regimes and their computational capabilities.”

“Non-randomness and Regulation of Natural Genetic Engineering Activities

The foregoing discussion and an extensive literature that cannot be cited here make it clear that MGEs and other natural genetic engineering functions have the capacity to reorganize genomes in just the ways needed to reformat modular genome system architectures. This point is increasingly recognized (e.g. 21,22). However, the degree to which these genome reorganization activities are not random is poorly appreciated. Non-randomness is evident at three levels: mechanism, timing, and sites of action.”

“These examples make it clear that natural genetic engineering occurs episodically and non-randomly in response to stress events that range from DNA damage to the inability to find a suitable mating partner.”

“We have come to realize some of the basic design features that govern genome structure. Combining this knowledge with our understanding of how natural genetic engineering operates, it is possible to formulate the outlines of a new 21st Century vision of evolutionary engineering that postulates a more regular principle-based process of change than the gradual random walk of 19th and 20th Century theories.”

“Molecular genetics has amply confirmed McClintock’s discovery that living organisms actively reorganize their genomes (5). It has also supported her view that the genome can “sense danger” and respond accordingly (56). The recognition of the fundamentally biological nature of genetic change and of cellular potentials for information processing frees our thinking about evolution. In particular, our conceptual formulations are no longer dependent on the operation of stochastic processes. Thus, we can now envision a role for computational inputs and adaptive feedbacks into the evolution of life as a complex system. Indeed, it is possible that we will eventually see such information-processing capabilities as essential to life itself. “

2. Jean-Claude Perez’ discovery of the golden ratio in the ergodic patterns of DNA:

Codon patterns in DNA conform to a checksum matrix to a precision of 0.1%. Microorganisms like bacteria and HIV all the way to most human chromosomes follow this unusual mathematical pattern.

Layman’s version http://www.cosmicfingerprints.com/mathematics-of-dna/
Published journal article: http://www.springer.com/life+sciences/bioinformatics/journal/12539
PDF free of charge: http://www.resurgence.be/pdf/ADN-perez.pdf

3. Biologist Lynn Margulis, advocate of the theory of Symbiogenesis:

“Many ways to induce mutations are known but none lead to new organisms. Mutation accumulation does not lead to new species or even to new organs or new tissues… Even professional evolutionary biologists are hard put to find mutations, experimentally induced or spontaneous, that lead in a positive way to evolutionary change.”

-Lynn Margulis and Dorion Sagan, “Acquiring Genomes”

4. I’ve had over 3 million visitors to my Cosmic Fingerprints website over the last 7 years, I have an email list of 200,000 people. I’ve challenged skeptics on my blog email list to come forward with experimental evidence that shows that random changes to DNA produce new features. No one has ever been able to come up with one.

The closest anyone has come is citations of Richard Lenski’s bacteria experiments, where he simply assumes the mutations were random without backing up his statement. And as I’ve said before, it’s mathematically impossible to prove randomness; it’s entirely possible to prove non-randomness.

5. The patterns in DNA are linguistic, they follow the rules of universal grammars.

“The Linguistics of DNA: Words, Sentences, Grammar, Phonetics and Semantics” by  Sungchul Ji of Rutgers University – www.rci.rutgers.edu/~sji/Linguistics%20of%20DNA.pdf In this paper, Dr. Ji explains that human language has 13 linguistic characteristics and DNA has 10 of them. He says cells speak a language called “cellese.”

The opening sentence of his paper says this:

“There are theoretical reasons to believe that biologic systems and processes cannot be fully accounted for in terms of the principles and laws of physics and chemistry alone, but they require in addition the principles of semiotics – the science of symbols and signs, including linguistics.”

The italicized words are his, by the way, not mine. He goes on to say:

“Recently it was postulated that language is more than just a metaphor and that linguistics provides a fundamental principle to account for the structure and function of the cell. The conclusion is supported by the facts that cells use a language, called cell language or cellese, defined as “a self-organizing system of molecules, some of which encode, act as signs for, or trigger, gene-directed cell processes,” and (2) that cell language has molecular counterparts to 10 of 13 design features of human language (humanese) characterized by Hockett and Lyon, thus suggesting an isomorphism between cellese and humanese.”

I challenge you to offer any example of any language that can be subjected to random mutations and not be systematically destroyed. After all, why do computer systems devote so many resources to error detection and correction?

6. Cells actively repair damaged DNA. E. coli reproduces with less than one mistake for every billion new nucleotides. “The extraordinarily low error frequency results from monitoring the results of the polymerization process and correcting incorporation mistakes after the fact, not from the inherent precision of the replication apparatus.” -from the book Evolution: A View from the 21st Century, James A Shapiro, 2011. He goes on to describe two separate error correction mechanisms which monitor for mistakes and correct in real time.

Also see “Revisiting the Central Dogma in the 21st Century” http://shapiro.bsd.uchicago.edu/2008.GenContext.Salbzburg.pdf

7. The genetic code is 2/3rds redundant, mapping 64 combinations to 20 amino acids; ie GGA, GGG and GGC all code for Glycine. This is a form of Forward Error Correction http://en.wikipedia.org/wiki/Forward_error_correction. I quote from “Nanoscale Communication Networks” by Stephen F. Bush, p. 51: “…Forward error correction (FEC) techniques which are clearly used in biological systems such as DNA…”

DNA uses parity to detect errors as well. From the same book, further down in the page: “Each of the DNA bases has a sequence of three connecting structures, either hydrogen donors or hydrogen acceptors. Thus, each nucleotide base can be considered a sequence of three binary values. The fact that the base is either a pyrimidine or a purine appears to serve as the final parity bit.”

Another form of error detection found in DNA is checksums. In most chromosomes of single-stranded DNA, the total number of times each codon appears is controlled to within 0.1% by a checksum matrix. The cell adds up the total number of codons and checks for errors. Checksums are the subject of Perez’ paper, cited above.

One may ask: If there are thousands of books and papers that say evolution is random, why should I pay attention to a minority that say it is not?

Quite simply, because these people methodically proved their assertions and the Neo-Darwinists did not.

The #1 problem is that randomness is not experimentally or mathematically provable. If you think that the sequence of numbers 2905739303023745748 is random, you may or may not be right, but it’s not possible to prove it. However you can calculate the statistical odds of whether the number sequence 111122223333444 is random or not – odds are 99.99+ percent that it is not random.

Those who claim evolution is random have no proven this assertion and it is impossible for them to do so. However those who claim it is non-random offer systematic, documented, predictable mechanisms that produce evolutionary change.

Given a choice between a hypothesis that a process is random vs. a hypothesis that a process is non-random, the non-random hypothesis is always inherently more scientific. Why? Because science is the presumption of discoverable underlying order, not disorder. The “random mutation” paradigm of 20th century biology is contrary to the most basic aims of science.

This has obscured many of the discoveries cited above, because science is the presumption of discoverable underlying order, not disorder. The “random mutation” paradigm of 20th century biology is anti-scientific and has obscured many of the discoveries cited above.

Other blog posts dealing with the non-randomness of evolution:

Evolution: The Untold Story, Part 1

Intelligent Bacteria: Cells are Incredibly Smart

7 Biology Myths No Electrical Engineer Would Ever Tolerate

A New Theory of Evolution

In this video, he defines a half dozen major mechanisms of biological evolution. He also discusses hot new questions raised by 21st century research:

James A. Shapiro – Revisiting evolution in the 21st Century

Here are the slides for this lecture:
shapiro.bsd.uchicago.edu/​2010.WorksOfTheMind.pdf

Dr. Shapiro was mentored by the eminent scientist Barbara McClintock. She won the Nobel Prize for her discovery of Mobile Genetic Elements. He discovered Mobile Genetic Elements in bacteria at UChicago and has carried on McClintock’s work. He backs his research with rigorous experimental data.

James A. Shapiro is a professor at Department of Biochemistry and Molecular Biology at the University of Chicago, Gordon Center for Integrative Science