Sixty years have passed since Watson and Crick unveiled the structure of the DNA double helix and tentatively explained how it encodes hereditary information. The Central Dogma of genetics soon followed: that "DNA makes RNA makes protein" makes cells and organisms. Once this "River out of Eden" was flowing, the story of life was deemed to be essentially understood. Genes were considered to provide the blueprint of life and the task of filling in the details had begun. The blueprint motif was prominent in media coverage of the Human Genome project - any who questioned its veracity were regarded as subverting science. But is the consensus position robust? At least one commentator (Philip Ball in Nature) is prepared to say that it is misleading.
"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." (page 419)
In 1953, Francis Crick and James Watson described the double helix structure of DNA. (source here)
Numerous discoveries have been "unsettling old assumptions". First, the ENCODE project has put the spotlight on regulation rather than transcription. Not only are genes transcribed (about 1% of the human genome) but so also is at least 80% of the human genome. Numerous regulatory roles have been determined for many of these RNA transcripts, and every week brings more examples of functionality to our attention. Not only do these findings challenge "the old idea that much of the genome is junk", they also show us that we are only beginning to understand the genome's role in the cell.
"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." (page 420)
Second, the field of epigenetics has introduced previously unsuspected constraints, whereby environmental factors influence the phenotype without affecting the genotype.
"For example, epigenetic molecular alterations to DNA, such as the addition of a methyl group, can affect the activity of genes without altering their nucleotide sequences." (page 420)
Third, positional information is not revealed by the documenting of amino acid sequences within the DNS molecule, but this information, when recognised, is significant for development.
"Genes can also be regulated by the spatial organization of the chromosomes, in turn affected by epigenetic markers. Although such effects have long been known, their prevalence may be much greater than previously thought." (page 420)
And there are more evidences to throw into the melting pot. Ball refers to the way gene networks are structured: the genes are the same, but differences in organisation of these networks can result in differences in phenotype. Similarly, changes in regulation could be more significant than changes in the genes themselves. There are big questions about the role of natural selection at the molecular level and it is by no means agreed that natural selection is the dominant driver.
"In short, the current picture of how and where evolution operates, and how this shapes genomes, is something of a mess. That should not be a criticism, but rather a vote of confidence in the healthy, dynamic state of molecular and evolutionary biology." (page 420)
Whilst saying this is not a criticism, there are nevertheless aspects of these developments that should be criticised. Notably, it is necessary to vigorously critique the evolutionary consensus that dominates education and the media. Take education first - and recall how vigorously evolutionists have opposed all attempts to introduce critical, evidence-based thinking about evolutionary theory. They have portrayed this as religiously motivated anti-science lobbying, and have ensured that the consensus positions have prevailed. In this they have betrayed a whole generation of biology students.
"A student referring to textbook discussions of genetics and evolution could be forgiven for thinking that the 'central dogma' devised by Crick and others in the 1960s - in which information flows in a linear, traceable fashion from DNA sequence to messenger RNA to protein, to manifest finally as phenotype - remains the solid foundation of the genomic revolution. In fact, it is beginning to look more like a casualty of it." (page 419)
Furthermore, it is a scandal that the whole spectrum of contemporary thinking in genetics is largely hidden from the broader scientific community. The media provides a welcoming stage for celebrity scientists to pronounce on their outdated views, but dissenters find it hard to present on a science platform. When reading the following quotation, it is worth noting that Prospect magazine has honoured Richard Dawkins as the "world's top thinker" as a result of a recent poll of its readers.
"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." (page 420)
Philip Ball does suggest some reasons why there has been a reluctance to acknowledge biological complexity. Whilst not disputing the various points he makes, the analysis is not deep enough. The closest he gets is in the last paragraph:
"When the structure of DNA was first deduced, it seemed to supply the final part of a beautiful puzzle, the solution for which began with Charles Darwin and Gregor Mendel. The simplicity of that picture has proved too alluring." (page 420)
It is not just that simplicity is too alluring; it is that the worldview of the scientists demands simplicity. They are predisposed to look for simplicity and they fall into a trap of confirmation bias. It happened in Darwin's day, when the cell was conceived as a simple building block, and organisms were portrayed as assemblages with varying degrees of complexity (see here). This worldview derives from Deism or Atheism, where everything has to assemble itself: from the cosmos to organisms. The only way that people can imagine this happening is incrementally, deriving complexity from simple building blocks. This is Richard Dawkins explaining the point.
"Darwinian evolution is the only process we know that is ultimately capable of generating anything as complicated as creative intelligences. Once it has done so, of course, those intelligences can create other complex things: works of art and music, advanced technology, computers, the Internet and who knows what in the future? Darwinian evolution may not be the only such generative process in the universe. There may be other "cranes" (Daniel Dennett's term, which he opposes to "skyhooks") that we have not yet discovered or imagined. But, however wonderful and however different from Darwinian evolution those putative cranes may be, they cannot be magic. They will share with Darwinian evolution the facility to raise up complexity, as an emergent property, out of simplicity, while never violating natural law."
Ultimately, then, we have worldview issues to evaluate. Those with a naturalistic mindset interpret all complexity as emergent from natural law with a sprinkling of chance. However, their approach is testable - they require ultimate simplicity and blind (tinkering) processes. Arguably, this approach has been falsified in innumerable areas of science. What we find is ultimate complexity and an extraordinary richness of information. This finding is consistent with, and predicted by, advocates of intelligent design. To move the debate in science forward in a meaningful way, both these avenues of inquiry need to be fully and fairly evaluated.
DNA: Celebrate the unknowns
Nature, 496, 419-420 (25 April 2013) | doi:10.1038/496419a
On the 60th anniversary of the double helix, we should admit that we don't fully understand how evolution works at the molecular level
Watson J.D. and Crick F.H.C. Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid. Nature, 1953, 171, 737-738. (also here)
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