Are the mutations that drive evolution random?

I’ve been corresponding with a professional scientist about randomness in biology. I told him that the Neo-Darwinian paradigm of “random mutation” is dead, and most people just haven’t gotten the memo yet.

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://urbanshakedowns.files.wordpress.com/2011/01/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

 

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10 Comments

chris says:

No dictionary, no scientist, no-one anywhere would define science as the search for underlying order. It hasn’t been since we made it a secular subject.

An example; Heisenberg’s Uncertainty Principle states that there is no way in which to determine the properties of a particle. If you know one thing about it you decrease your knowledge of another aspect. Furthermore, when an electron is sent to a location there is no way to determine the route it will take to get there. There is no indication that it will take the same route consecutively even if all other conditions are identical.

This alone renders the presumption of underlying order ridiculous. This is a fundamental property of the universe. Why is Perry not making such a fuss over this? Surely we should scrap this idea as it assumes randomness? Or is the fact that it does not reduce the need for an intelligent designer its saving grace as this means that those with an agenda are not concerned enough to try to come up with an alternative?

Perry has written of several ways in which DNA may engineer itself. However, these “systematic mechanisms” are also highly random. Transposable elements are highly restricted as to where they are able to join a strand of DNA. Why would this be necessary? If a cell is intelligent enough to alter its own code in order to become more productive it would certainly be able to insert scraps of DNA arbitrarily in order to do so. The fact that these failsafes exist cast as much doubt on this paradigm as point 6 above. Cells repair BOTH types of mutation. Why then is one considered non-random?

From dictionary.com: Definition of science. Emphasis mine:

a branch of knowledge or study dealing with a body of facts or truths systematically arranged and showing the operation of general laws: the mathematical sciences.
2.
systematic knowledge of the physical or material world gained through observation and experimentation.

From Wikipedia:

Science (from Latin scientia, meaning “knowledge”) is a systematic enterprise that builds and organizes knowledge in the form of testable explanations and predictions about the universe.

Our limitations in measuring electrons should never be construed as an assumption that they do not exhibit law-like behavior.

You said:

“Perry has written of several ways in which DNA may engineer itself. However, these “systematic mechanisms” are also highly random. Transposable elements are highly restricted as to where they are able to join a strand of DNA. Why would this be necessary?”

Go back and read what you just said. In your second sentence you admitted that transposition is non-random.

It is necessary because the genome obeys syntactic rules, and because it must be repaired and re-arranged according to those rules; otherwise the program is destroyed.

God Chaser says:

Perry,

It seems along time ago the U.S Government stated that DNA is a code, look at what i found…

National Library of Medicine’s Profiles in Science

The Francis Crick Papers
Defining the Genetic Coding Problem, 1954-1957

“James Watson and Francis Crick’s insight that genetic information is embedded in the physical structure of deoxyribonucleic acid (DNA) made possible a new understanding of heredity at the molecular level and opened up new avenues of research into the genetic control of essential biological processes, most importantly the synthesis of proteins. Watson and Crick were the first to realize that the seemingly random sequence of the four bases in DNA formed a code which specified the order of the twenty amino acids that make up most proteins. (It was Watson and Crick who drew up the list of twenty from dispersed and confused information in the biochemical literature.) ”

“Before their discovery of the double helix, the term genetic code had no meaning; afterwards, deciphering the code–putting together the dictionary by which the four-letter nucleic acid language is translated into the twenty-letter protein language–became the most urgent and ambitious undertaking of biologists throughout the world, an effort that defined the classical age of molecular biology”

http://profiles.nlm.nih.gov/ps/retrieve/Narrative/SC/p-nid/153

God Chaser says:

Hello Perry,

It seems atheists have created a newer argument that
“DNA is not a code because there is no symbols in DNA, we just created the symbols at the human level. At the DNA level, they do not use symbols, its just chemicals and physics. humans invented the code. DNA Code dont look up a table.
Show me a symbol in DNA.”

How would you respond to them?

That’s an old argument. They’re saying information only becomes information after we give it a name. This fails to recognize that encoding and decoding was already happening long before humans ever showed up to give it a name.

The fact is, it doesn’t matter what names we assign to it, because our name is only our symbol for the original symbol which objectively exists independently of our knowing. We call the symbols TCAG but what name we ascribe to them is irrelevant, it doesn’t change the operation of the system. The sequence GGG is instructions to make Glycine. It is very important to note that GGG itself is guanine-guanine-guanine, it is not Glycine. Look up the genetic code table, the relationship between GGG and Glycine is symbolic. It’s still an encoding/decoding table no matter what letters or numbers you choose; and the system operates according to Shannon’s model just the same.

I explain the exact whys and hows of this at http://www.naturalcode.org.

God Chaser says:

Perry,
Georgia State University evidences why DNA is a “real code” with a very simple but powerful illistration. Check out the webpage…

“The sequence of bases in DNA operates as a true code in that it contains the information necessary to build a protein expressed in a four-letter alphabet of bases which is transcribed to mRNA and then translated to the twenty-amino-acid alphabet necessary to build the protein. Saying that it is a true code involves the idea that the code is free and unconstrained; any of the four bases can be placed in any of the positions in the sequence of bases. Their sequence is not determined by the chemical bonding. There are hydrogen bonds between the base pairs and each base is bonded to the sugar phosphate backbone, but there are no bonds along the longitudional axis of DNA. The bases occur in the complementary base pairs A-T and G-C, but along the sequence on one side the bases can occur in any order, like the letters of a language used to compose words and sentences.

To further illustrate what is meant by a true code, consider the magnetic letters fixed to the magnetic board at right. The letters are held to the board by the magnetic forces, but those forces do not impose any specific ordering of the letters. The letters can be arranged to spell out a meaningful message in the English language (code) or to form a meaningless sequence like the one at bottom.”

http://hyperphysics.phy-astr.gsu.edu/hbase/organic/gencode.html

@GodChaser : You say, “Georgia State University evidences why DNA is a “real code” with a very simple but powerful illistration. Check out the webpage…”
Your quote says,”The sequence of bases in DNA operates as a true code…”

You have jumped from “operates as” to “is”. Atheist objectors, who like to object to everything because they are often objectionable, could retort that you can’t reason “X operates as Y, therefore X is Y.”
My reply to them is that it makes no difference. As an obedient husband I sometimes operate as a dish-washer. Now, our dish-washer never operates as a husband, but that is beside the point. The point is the end result – clean dishes.
To say that DNA is a code is more a description of its behaviour that of its intrinsic nature. It makes more of itself and we call the end result Life.

God Chaser says:

P.S- The web page also gives a complete illustration on Shannons communication model and how DNA has syntax, Sematic information. Its a great 3rd party resource. perhaps you can start a page where your fans can post the thousands of references that evidence DNA as a real code!

herrie says:

Hi Perry

I have this funny hypothesis that the laws of thermodynamics were different before and after the fall. Before you make this idea off as crazy, consider this.

As far as i know, time and the concept of entropy is somehow related. If you could stop (or decrease) the increase of entropy, i assume for all practical purposes you have stopped time as well. Now, from the bible it appears to me that before the fall, the concept of the increase of entropy did not apply, first because of the perception of length of time (7days to create everything) and secondly because Adam did not have to labour for his food, as was the case after the earth was cursed. We all know the consequences of the fall and how it is now.

If my hypothesis is true, it would explain evolution as a non-random system as you advocate(if i understand you right), but the only difference is that it happened before the fall. After the fall everything starts to die off.

What is your opinion of this. I will not submit this to a debate about evolution, i mean they will really take me apart, but at least it put me in a neutral posision in investigate the truth regarding evolution and realy focussing on real facts.

pelumi says:

Am sorry but all thoughts here are warped.

We define DNA as we understand codes, other animals, should they be able to, will have a separate definition.

DNA is different from human codes by the fact that computer codes cannot replicate themselves.

Amino acids are known to spontaneously form. Whoever says DNA did not arise spontaneously has a lot of reading and keeping up to make.

God is never an answer to anything. God is a wish.

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