Synthetic Genetics Is ID, not Darwinism - Evolution News & Views

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Synthetic Genetics Is ID, not Darwinism

Why does Darwin get credit for designed things? How can geneticists engineer unnatural molecules -- intelligent design, without doubt -- and call them examples of Darwinian evolution? It happened this month in the journal Science.

The Science

An international team of 11 scientists found ways to replace the sugars on the backbones of DNA molecules. "With the use of polymerase evolution and design, we show that genetic information can be stored in and recovered from six alternative genetic polymers based on simple nucleic acid architectures not found in nature," they said in Science.1 (Emphasis added in all quotations.) They called their designed molecules XNAs, where X stands for one of six alternative backbone sugars in the polymers. Using threose, for instance they got TNA; using arabinose, they made ANA, etc.

So did these molecules evolve by a Darwinian mechanism? Did they grow skeletons, eyes and wings? Not even close. Yet here's the basic claim:

We also select XNA aptamers, which bind their targets with high affinity and specificity, demonstrating that beyond heredity, specific XNAs have the capacity for Darwinian evolution and folding into defined structures. Thus, heredity and evolution, two hallmarks of life, are not limited to DNA and RNA but are likely to be emergent properties of polymers capable of information storage.
Right off the bat, we notice several examples of sneaking design into the experiment:

  • The scientists selected the aptamers.
  • The scientists selected the targets.
  • The scientists selected the defined structures.

Wishful thinking is also present in abundance:

  • A capacity for Darwinian evolution is not a demonstration of it.
  • The likelihood of emergent properties is not a demonstration of it.
  • The capability for information storage is not a demonstration of it.

The researchers' bullish sentence, "Thus heredity and evolution, two hallmarks of life, are not limited to DNA and RNA but are likely to be emergent properties of polymers capable of information storage" is a colossal non sequitur. They didn't see any evolution of information. They simply imagined it.

Best of All Possible Genetic Materials

Did the team of scientists rescue any credibility for Darwin? No. They begin with a statement agreeable to ID proponents: "The nucleic acids DNA and RNA provide the molecular basis for all life through their unique ability to store and propagate information." In fact, they admit that their designed alternatives have limitations, that the "chemical polymerization" of these unnatural polymers "remains relatively inefficient." They acknowledge that "most unnatural nucleotide analogs are poor polymerase substrates at full substitution, as both nucleotides for polymer synthesis and templates for reverse transcription."

These studies have revealed the profound influence of backbone, sugar, and base chemistry on nucleic acid properties and function. Crucially, only a small subset of chemistries allows information transfer through base pairing with DNA or RNA, a prerequisite for cross-talk with extant biology. However, base pairing alone cannot conclusively determine the capacity of a given chemistry to serve as a genetic system, because hybridization need not preserve information content. A more thorough examination of candidate genetic polymers' potential for information storage, propagation, and evolution requires a system for replication that would allow a systematic exploration of the informational, evolutionary, and functional potential of synthetic genetic polymers and would open up applications ranging from biotechnology to materials science.
So are "biotechnology" and "materials science" examples of Darwinian evolution or intelligent design?

Assuming the Subsequent

Even worse, their engineering tests required transcription to and from DNA. What on earth could such experiments have to do with the origin of life?

Here, we describe a general strategy to enable enzymatic replication and evolution of a broad range of synthetic genetic polymers based on: (i) a chemical framework [generically termed xeno-nucleic acid (XNA)] capable of specific base pairing with DNA, (ii) the engineering of polymerases that can synthesize XNA from a DNA template, and (iii) the engineering of polymerases that can reverse transcribe XNA back into DNA.
This scenario, in other words, presupposes the existence of DNA. Take away the DNA, and what happens? Nothing! The various XNA alternatives, therefore, cannot be stepping-stones to the DNA code. The whole experimental approach here was "discovery of polymerases capable of processive XNA synthesis" (back and forth with DNA), helped every step along the way by hands acting as the expression of intelligent design. We read a lot about engineering in the paper, but very little about unguided, aimless, purposeless processes of nature.

Even the research team's best candidate, TNA, "allowed polymer synthesis and evolution in a three-letter system but only limited reverse transcription." On January 9, Science Daily reported that Chaput's team had to exclude guanine to get TNA to bind to DNA or RNA. A three-letter code with 27 permutations has far less information-coding capacity than DNA's four-base system with its 64 permutations.

Base-Stealing by Team Darwin

Despite the attention given to Darwin, ID is ubiquitous in the paper. The scientists "developed a selection strategy called compartmentalized self-tagging" and made libraries "created from both random and phylogenetic diversity targeted to 22 short sequence motifs within a 10 Å shell of the nascent strand." They synthesized polymers "long enough to encode meaningful genetic information." This is no more indicative of a Darwinian origin of information than stating that they designed a memory chip capable of storing a software program, without finding the software in it.

As for "evolution," here's what they did. They got an HNA strand to develop by random mutation, then (by screening the mutants with ID), were able to transcribe it, mutation and all, back into DNA. More ID was required at every step: "As no available polymerase displayed this activity, we engineered an HNA-RT [HNA reverse transcriptase] de novo." Don't look for that happening in primordial soup.

Using further engineering techniques, the team found a few more cases where unnatural polymers could reverse-transcribe their "information" back to DNA. "Together, these engineered polymerases support the synthesis and reverse transcription of six synthetic genetic polymers and thus enable replication of the information encoded therein."

Hopeful Errors

Well, believe it or not, the researchers found the seeds of Darwinism after all. Where? In the capability of these unnatural molecules to make errors! "As previously observed for TNA, noncognate polymer synthesis can come at a cost of reduced fidelity as polymerase structures are poorly adapted to detect mismatches or aberrant geometry in the noncanonical XNA•DNA (or DNA•XNA) duplexes." By this logic, clunky error-prone copy machines hold the promise of authoring new books.

In living cells, the rare DNA copy errors are scrutinized and repaired by a host of error-correcting machines and processes. In the real world, mutations are the scourge of DNA, but to a Darwinian, errors are the seeds of progress.

After engineering heredity for their polymers, the team turned on the Darwin switch to watch them evolve. But again, they had simply taped "Darwin" on top of the "ID" switch. Everything they did involved ID: selecting a target, and screening the mutants for matches to the target. This is ID by definition, not Darwinism. They observed "eight rounds of selection" for a match. They "observed" and "selected" the results they desired.

Team Darwin Steals Home

To perform a true Darwinian experiment, these scientits would have had to pour the building blocks into a tank, let them interact naturally, and take notes without interference. As realistic experiments repeatedly show, even with sparks or heat, the molecules tend to clump into useless globs that sink to the bottom of the tank and go nowhere.

Here's the last sentence of the paper:

Our work establishes strategies for the replication and evolution of synthetic genetic polymers not found in nature, providing a route to novel sequence space. The capacity of synthetic polymers for both heredity and evolution also shows that DNA and RNA are not functionally unique as genetic materials. The methodologies developed herein are readily applied to other nucleic acid architectures and have the potential to enable the replication of genetic polymers of increasingly divergent chemistry, structural motifs, and physicochemical properties, as shown here by the acid resistance of HNA aptamers (fig. S17). Thus, aspects of the correlations between chemical structure, evolvability, and phenotypic diversity may become amenable to systematic study. Such "synthetic genetics" -- that is, the exploration of the informational, structural, and catalytic potential of synthetic genetic polymers -- should advance our understanding of the parameters of chemical information encoding and provide a source of ligands, catalysts, and nanostructures with tailor-made chemistries for applications in biotechnology and medicine.
Tornadoes in junkyards do not develop strategies, routes, functions, methodologies, architectures, systematic study, or exploration of informational potential. If anybody found "applications in biotechnology and medicine" resulting from a tornado-in-the-junkyard process, he or she would be justified in suspecting an intelligent cause was guiding the tornado.

Did you notice, finally, that since "DNA and RNA are not functionally unique as genetic materials," this is more evidence of intelligent design? It means that a designer had a choice of which genetic material to use. DNA is contingent, not predetermined as the only possible genetic storage molecule. Fortunately, it is the best of all known informational macromolecules (see this article from Vanderbilt University).

Media Goes Wild

So that's it -- that's what the paper was all about. Gerald Joyce, summarizing the work in the same issue of Science,2 basted himself in its Darwin-flavored gravy:

Genetics provides a mechanism for molecular memory and thus the basis for Darwinian evolution. It involves the storage and propagation of molecular information and the refinement of that information through experience and differential survival. Heretofore, the only molecules known to be capable of undergoing Darwinian evolution were RNA and DNA, the genetic molecules of biology. But on page 341 of this issue, Pinheiro et al. expand the palette considerably. They report six alternative genetic polymers that can be used to store and propagate information; one of these was made to undergo Darwinian evolution in response to imposed selection constraints. The work heralds the era of synthetic genetics, with implications for exobiology, biotechnology, and understanding of life itself.
The popular science media re-Joyced in this hymn to Darwin, dumbing it down for the readership. The latter are assumed to be oblivious to the fact that anything "made to undergo Darwinian evolution in response to imposed selection constraints" is ID, not Darwinism.

National Geographic announced, "Synthetic DNA Created, Evolves on Its Own." Reporter Christine Dell'Amore even used the occasion to take a jab at ID, linking her report to NG's contrived debate, "Evolution vs. Intelligent Design: 6 Bones of Contention." The 6-part "debate" presents caricatures of six intelligent design arguments, then gives evolutionist Donald Prothero the last word to accuse ID proponents of lying or ignoring the evidence.

PhysOrg reported that the work "sheds new light on questions concerning the origin of life" (Darwinism) but also "provides a range of practical applications for molecular medicine that were not previously available" (intelligent design). Better hope these intelligent designers have enough sense not to turn something loose that could attack DNA, like a software virus.

A Pre-RNA-World World?

A dark secret is revealed in the article (actually a press release from Arizona State promoting its local young champion, John Chaput,3 a co-author of the Science paper). Chaput unveiled his personal doubts about the plausibility of the popular "RNA World" hypothesis:

Nevertheless, the spontaneous arrival of RNA through a sequence of purely random mixing events of primitive chemicals was at the very least, an unlikely occurrence. "This is a big question," Chaput says. "If the RNA world existed, how did it come into existence? Was it spontaneously produced, or was it the product of something that was even simpler than RNA?"

This pre-RNA world hypothesis has been gaining ground, largely through investigations into XNAs, which provide plausible alternatives to the current biological regime and could have acted as chemical stepping-stones to the eventual emergence of life. The current research strengthens the case that something like this may have taken place.

When a scientist tells you something is plausible without any math to support it, you are free to use your own judgment. It appears from this paragraph that Chaput and his colleagues undertook their ID-saturated work because the "RNA world" scenario is highly implausible.

If so, all they did was imagine pre-RNA-world scenarios that "could have" or "may have" taken place. This begs multiple questions. How did non-natural XNA polymers emerge? What was the source of their genetic information? If they had genetic information that produced function, how did these simpler molecules avoid error catastrophe without proofreading machines? And finally, how did the simpler molecules transfer their information to DNA without polymerases and transcriptases? How many "chemical stepping stones" (actually, genetic revolutions) can the Darwinian scenario afford without incurring charges of contrivance?

Playing Ball Against Uncalled Fouls

This is what ID is up against. Darwinists take our strengths and use them against us. They steal intelligent design and call it Darwinism. Then they employ rhetorical tricks (like "chemical stepping stones") and imaginary scenarios to dream up what "may have" taken place in an unobservable prehistoric world where unguided processes are allowed to work miracles.

They get free rein in scientific journals that exclude ID responses (see this ENV article by Granville Sewell). They have Darwin-saturated public relations departments to write press releases, which are dutifully picked up by the popular science media, who are only too happy to celebrate anything that honors Darwin.

It's an unfair game when the umpires are corrupt, but scientific integrity demands keeping at it.

References:

1. Pinheiro, Taylor et al., "Synthetic Genetic Polymers Capable of Heredity and Evolution," Science, 20 April 2012: Vol. 336 no. 6079 pp. 341-344, DOI: 10.1126/science.1217622.

2. Gerald F. Joyce, "Evolution: Toward an Alternative Biology," Science, 20 April 2012: Vol. 336 no. 6079 pp. 307-308, DOI: 10.1126/science.1221724.

3. Ironically, John Chaput works for Arizona State's "Biodesign Institute's Center for Evolutionary Medicine and Informatics."


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