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: