As David Klinghoffer noted the other day, a well-known science journalist has had it with evolutionary pretensions. It’s time to stop the “scientists now know” show and, rather, honestly “Celebrate the Unknowns.” This article deserves special emphasis — it’s that good. Writing in Nature on the 60th anniversary of the elucidation of the DNA molecule’s double-helix structure, Ball observes:
Sixty years on, the very definition of ‘gene’ is hotly debated. We do not know what most of our DNA does, nor how, or to what extent it governs traits. In other words, we do not fully understand how evolution works at the molecular level. (Emphasis added.)
He’s excited about the challenge, but frustrated by the misleading “narrative” or “rhetoric” that portrays scientists as having evolutionary genetics all figured out. He doesn’t like it when “the public continues to be fed assurances that DNA is as solipsistic a blueprint as ever.”
The more complex picture now emerging raises difficult questions that this outsider knows he can barely discern. But I can tell that the usual tidy tale of how ‘DNA makes RNA makes protein’ is sanitized to the point of distortion. Instead of occasional, muted confessions from genomics boosters and popularizers of evolution that the story has turned out to be a little more complex, there should be a bolder admission — indeed a celebration — of the known unknowns.
How will that admission fly at the headquarters of the National Center for Science Education?
Philip Ball assures Nature readers that he still believes in evolution. “Although it remains beyond serious doubt,” he says, “that Darwinian natural selection drives much, perhaps most, evolutionary change,” he follows up with this admission: “it is often unclear at which phenotypic level selection operates, and particularly how it plays out at the molecular level.” That doesn’t leave much room for knowledge about how evolution plays out at any level, or how Darwinian natural selection would drive much of any evolutionary change.
Now Circular RNAs, Too
Well might Philip Ball have expressed intimidation at the complexity of DNA. Last week Science Magazine unveiled new findings about “circular RNA” transcripts of DNA that, as the name implies, fasten into loops. Only now are geneticists realizing that these oddballs outnumber linear RNAs some ten to one. Evolutionists are less apt to dub these pieces of “junk” after having gotten burned with “junk DNA.” It turns out these circular RNAs appear to act as “sponges” that attract certain linear RNAs which might otherwise bind to messenger RNAs, preventing transcription. But a regulatory function might not be their only role. They might, for example, join up with large RNA-protein complexes.
It’s just the latest in a plethora of discoveries that began around 2001 regarding small RNAs (transcribed from non-coding DNA) that function in other ways than just ferrying DNA transcripts to the ribosome. Since then, whole classes of RNAs that had escaped detection (or had been ignored) have been discovered — lncRNA, siRNA, microRNA and more — each with vital regulatory roles in the cell. The Science article about circular RNAs ends,
The discovery of such a large class of previously unknown RNAs also raises the question of what other RNAs might have been missed. Considering that RNA structural elements, such as triple helices, efficiently prevent degradation from RNA termini, it is becoming increasingly clear that the cell uses a myriad of distinct ways to process and stabilize RNA molecules.
ENCODE vs. Junk
As examples of trends that are complicating the story of evolution, Philip Ball specifically refers to the demise of the “junk DNA” concept and the findings of the ENCODE project. Even if we don’t know all the roles of transcribed non-coding DNA, there are indications that a good bit of it is involved with regulatory functions — so much so that it might take the focus off the gene:
ENCODE researchers even propose, to the consternation of some, that the transcript should be considered the basic unit of inheritance, with ‘gene‘ denoting not a piece of DNA but a higher-order concept pertaining to all the transcripts that contribute to a given phenotypic trait.
According to evolutionary biologist Patrick Phillips at the University of Oregon in Eugene, projects such as ENCODE are showing scientists that they don’t really understand how genotypes map to phenotypes, or how exactly evolutionary forces shape any given genome.
ENCODE is just one of several projects that are “unsettling old assumptions,” Ball says. The new science of epigenetics, too, has added more layers of complexity. The methylation of histone tags on DNA bases, for instance, can affect activity of a gene without altering its sequence. Other epigenetic tags affect the structure of chromosomes, or the accessibility of DNA sequences. The linear “central dogma” of the 1960s (gene DNA -> messenger RNA -> protein) is long gone; it has become clear that multiple players — DNA, RNA, proteins, splicers, epigenetic factors, post-transcriptional modifiers — interact in complex networks we can barely fathom.
Natural Selection a Wimp?
Ball reassures Nature readers again that he has faith in neo-Darwinism: “In a sense this is still natural selection pulling out the best from a bunch of random mutations, but not at the level of the DNA sequence itself.” But his next paragraph casts doubt on the usefulness of evolutionary theory to sort out all the complexity:
One consequence of this complex genotype-phenotype relationship is that it may impose constraints on natural selection. If the same phenotypes can result from many similarly structured gene networks, it might take a long time for a ‘fitter’ phenotype to arise. Alternatively, mutations may accumulate, free from selective ‘weeding’, thanks to the robustness of networks in maintaining a particular phenotype. Such hidden variation might be unmasked by some new environmental stress, enabling fresh adaptations to emerge. These sorts of constraints and opportunities are poorly understood; evolutionary theory does not help biologists to predict what kinds of genetic network they should expect to see in any one context.
So while he maintains faith that the “hidden variation” in accumulated random mutations “might” lead to evolutionary novelties, he admits those kinds of opportunities are “poorly understood.” This dismissal of the helpfulness of evolutionary theory contradicts Dobzhansky’s old canard that nothing in biology makes sense apart from evolution.
It gets worse. What if natural selection is less a force for innovation, and more a messy salvage operation? Ball entertains an idea by Michael Lynch that random genetic drift scatters introns randomly into protein-coding sequences. “He has also shown that rather than enhancing fitness, natural selection can generate a redundant accumulation of molecular ‘defences’, such as systems that detect folding problems in proteins,” Ball explains. “At best, this is burdensome. At worst, it can be catastrophic.” Such ideas hardly give neo-Darwinism’s primary mechanism anything worthwhile to do. “In short, the current picture of how and where evolution operates, and how this shapes genomes, is something of a mess.”
Speaking to the Preachers
Philip Ball addresses some well-chosen words to preachers and purveyors of simplistic misinformation, including the current Dr. Evolution himself:
Barely a whisper of this vibrant debate reaches the public. Take evolutionary biologist Richard Dawkins‘ description in Prospect magazine last year of the gene as a replicator with “its own unique status as a unit of Darwinian selection”. It conjures up the decades-old picture of a little, autonomous stretch of DNA intent on getting itself copied, with no hint that selection operates at all levels of the biological hierarchy, including at the supraorganismal level, or that the very idea of ‘gene’ has become problematic.
While some evolutionists or evolution skeptics might quibble with Ball’s assertion that selection operates at all levels, few could dismiss his overall message. Darwinian evolutionists need to abandon their sentimentality and affection for old ways, because those “old arguments, for instance about the importance of natural selection and random drift in driving genetic change, are now colliding with questions about non-coding RNA, epigenetics and genomic network theory.”
But what if the dreaded intelligent design people latch onto honest admissions of ignorance? Wouldn’t the fear of disrobing in public justify maintaining “reluctance to acknowledge the complexity“? That’s no cover, Ball says:
There may also be anxiety that admitting any uncertainty about the mechanisms of evolution will be exploited by those who seek to undermine it. Certainly, popular accounts of epigenetics and the ENCODE results have been much more coy about the evolutionary implications than the developmental ones. But we are grown-up enough to be told about the doubts, debates and discussions that are leaving the putative ‘age of the genome’ with more questions than answers. Tidying up the story bowdlerizes the science and creates straw men for its detractors. Simplistic portrayals of evolution encourage equally simplistic demolitions.
Ball concludes: “For the jubilee, we should do DNA a favour and lift some of the awesome responsibility for life’s complexity from its shoulders.”
DNA: Atlas Unshrugged
That’s not at all to disparage DNA. It’s still an Atlas of molecules that bears a lot on its shoulders. The BBC News celebrated Watson/Crick jubilee year with adoration of DNA as possibly the “smartest molecule in existence.” The article wafts the perfume of awe over DNA’s stability, flexible structure and method of transcription, to say nothing of its phenomenal information storage capacity: two petabytes per gram, enough for three million CD’s.
That’s pretty smart, especially when you compare it to other information-storing molecules. Using the same amount of space, DNA can store 140,000 times more data than iron (III) oxide molecules, which stores information on computer hard drives.
DNA may be tiny but with properties including stability, flexibility, replication and the ability to store vast amounts of data, there’s a reason why it must be one of the smartest known molecules.
Since the authors of the article fail to mention evolution, we’ll move in and gather their facts as evidence for intelligent design. After all, how can a molecule be smart, any more than a hard drive? But if intelligence were impressed into it, that makes sense. That’s how intelligence is impressed into all the information storage devices we know about. Since DNA is rapidly becoming the IT engineer’s storage medium of choice, the logic is complete.