Will Genetics Be Neo-Darwinism’s Downfall?

The Institute for Creation Research is gearing up for a multi-year GENE project to look for evidence for design (and against evolution) in the genome.  They may not need to work very hard.  Secular scientists, by continuing to find things not all that helpful for neo-Darwinism, are doing yeoman’s work for them.
    While the few pro-evolutionary articles usually focus on mere sources of variation in the genome as fodder for natural selection (such as this Molecular Biology and Evolution paper on retrotransposons), or try to infer phylogeny by molecular comparisons, they usually do not attempt to apply the variations to actual functions except at a trivial level (see 04/06/2006).  Most genetics papers, by contrast, are finding degrees of order, regulation and coordinated action in the cell that challenge gradualistic explanations.  Here are some examples from the past two months:

• Rapid Gradualism?  New Scientist reported that many human genes must have “evolved recently” – even as recently as within the last 15,000 years.  While some of the 700-odd genes they studied, they claim, appear to have been targets of natural selection after the human line diverged millions of years ago, “some of the newly identified genes fall into categories not previously known to be targets of selection in the human lineage, such as those involved in metabolism of carbohydrates and fatty acids.”  (Ker Than at Live Science took this to mean humans are still evolving.)
• Transcript Complexity:  PLoS Genetics had a special issue about the complexity of the “transcriptome,” the body of all transcribed DNA.  The lead article’s teaser sounds pretty dramatic:
  

  Besides revealing staggering complexity, analysis of this collection is providing an increasing number of novel mRNA classes, expressed pseudogenes, and bona fide noncoding variants of protein-coding genes.  In addition, new types of regulatory logic have emerged, including sense-antisense mechanisms of RNA regulation.  This high-resolution cDNA collection and its analysis represent an important world resource for discovery, and demonstrate the value of large-scale transcriptome approaches towards understanding genome function.

  After the human genome was deciphered, scientists were puzzled by the seeming small number of genes – about 30,000.  Now, it appears that the exons of genes can be assembled and reassembled in a modular way by alternative gene splicing (09/23/2005), yielding many protein variants from one gene.  Not only that, the DNA “negative” on the opposite (antisense) strand can play a role in regulating the gene.  These articles speak as if a whole new world of complexity is coming to light.

• Who Regulates the Regulators?  Nature March 23 reported on important pathways that regulate the fate of RNA transcripts of genes.  David Tollervey wrote in the introduction,
  

  Cells alter their rates of mRNA transcription to change mRNA levels, and so rates of protein synthesis, in response to many stimuli.  To adjust mRNA levels, cells must be able to rapidly get rid of normal mRNAs that were previously synthesized (turnover).  In fact, different mRNAs differ radically in their rates of degradation, and this is subject to both metabolic and developmental regulation.  In addition, cells must guard against the synthesis of abnormal mRNAs (surveillance), which can produce defective, potentially toxic, protein products.

  The mechanisms described in the article, including “go/no-go” checkpoints unveil a higher level of complexity beyond the information contained in the genes themselves.

• Ring Job:  The copies during cell division must be accurate.  Many protein parts cooperate to ensure high levels of quality control.  Nature reported March 23 on a discovery of a ring that slides along the microtubules in the all-important stage of separation of the paired chromosomes.
• High Fidelity Proofreading:  Albertson and Preston talked about quality control of the DNA copying process in an article in Current Biology March 23:
  

  Proofreading is the primary guardian of DNA polymerase fidelity.  New work has revealed that polymerases with intrinsic proofreading activity may cooperate with non-proofreading polymerases to ensure faithful DNA replication.

  This means that some polymerases (copy machines) have better fidelity than others, but they cooperate to ensure a precision product.  A low-fidelity machine might be necessary to get past a bad break, for instance – like when a heftier wrench is needed (09/19/2005).  How good is the system?  Orders of magnitude better than a human copyist:

  Normal cells replicate their DNA with remarkable fidelity, accumulating less than one mutation per genome per cell division.  It is estimated that replicative DNA polymerases make errors approximately once every 10⁴-10⁵ nucleotides polymerized.  Thus, each time a mammalian cell divides approximately 100,000 polymerase errors occur, and these must be corrected at near 100% efficiency to avoid deleterious mutations.  This is accomplished through the combined actions of… exonucleolytic proofreading and post-replication mismatch repair.

• New Uses for Junk:  “Just because we don’t know what it does, doesn’t mean it’s really junk,” said Christina Cheng of non-coding DNA (U of Illinois) in an interview for Radio Netherlands.  Her work has found that arctic cod produce antifreeze proteins (05/13/2004) from non-gene regions of DNA, “a gene that appears to have evolved [sic] out of this DNA that supposedly serves no purpose.”  Yet “Preserving this rubbish [sic] seems an inefficient use of time and resources.  Evolutionary pressures [sic] should favour creatures with less junk DNA” said author Marnie Chesterton.  “So its conservation may be because it has functions that we don’t yet know.”  Cheng said, “conventional thinking assumes that new genes must come from pre-existing ones because the probability of a random stretch of DNA somehow becoming a functional gene is very low if not nil.” (see online book).
• No More Mr. Simple Guy:  Embley and Martin in Nature March 30 had some words for those who tell simplistic tales about an ancient prokaryote being co-opted as a mitochondrion in the first primitive eukaryote (see 08/06/2004):
  

  The idea that some eukaryotes primitively lacked mitochondria and were true intermediates in the prokaryote-to-eukaryote transition was an exciting prospect.  It spawned major advances in understanding anaerobic and parasitic eukaryotes and those with previously overlooked mitochondria.  But the evolutionary gap between prokaryotes and eukaryotes is now deeper, and the nature of the host that acquired the mitochondrion more obscure, than ever before.

• Modular Programming:  An article in Nature March 30 by 37 European scientists found an exquisite example of modular programming – in yeast.  They even spoke machine language:
  

  The richness of the data set enabled a de novo characterization of the composition and organization of the cellular machinery.  The ensemble of cellular proteins partitions into 491 complexes, of which 257 are novel, that differentially combine with additional attachment proteins or protein modules to enable a diversification of potential functions.  Support for this modular organization of the proteome comes from integration with available data on expression, localization, function, evolutionary conservation, protein structure and binary interactions.  This study provides the largest collection of physically determined eukaryotic cellular machines so far and a platform for biological data integration and modelling.

  Question is, what evolutionist would want to model 257 novel proteins and 491 complexes, all tightly regulated and “evolutionarily conserved” (i.e., unevolved)?

• Pas de Deux:  We know that we have two copies of each gene, one from the father and one from the mother, but which copy leads and which follows?  As in marriage, this process is surprisingly complicated.  Spilianakis and Flavell explored this important question in a Perspectives article in Science April 14.  They showed how the dance involves the help of many servants:
  

  The genetic information of higher organisms is encoded in DNA that is not randomly dispersed within the cell nucleus, but is organized with nucleoproteins into different kinds of chromatin, the building blocks of the chromosomes.  Each chromosome resides in a specific region of the nucleus when the cell is not undergoing cell division, and usually genes that are actively being expressed loop out from their condensed chromatin territory and localize to a region of transcriptional activity.  These “transcription factory” areas are thus abundant with protein factors that initiate and regulate gene expression.

  The dance gets really wild, but not chaotic, when a gene on one chromosome is regulated by factors on another chromosome.

• The Parallel Universe of RNA:  The title of this article in PNAS hints at previously-unknown complexity: “Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes.”  This article was discussed in more detail here 04/27; see also the 09/08/2005 entry.
• Guardian Spirits:  In today’s Nature (May 4), Paul Megee titled an article, “Molecular biology: Chromosome guardians on duty.”  He begins, “Curiously, in cell division the proper separation of chromosomes into daughter cells needs set periods when they are stuck together.  So how do they come apart at the right time and place?  Their ‘guardian spirits’ intercede.”  Reminding the reader of the importance of high fidelity in cell division, he discusses work by Japanese scientists who “describe how proteins known as shugoshins – Japanese for ‘guardian spirits’ – and an associated regulatory enzyme temporally and spatially control the removal of cohesins from chromosomes.”  Cohesins keep the chromosomes together while they line up on the spindle, but need to be broken at the right time (03/04/2004) in a coordinated way – thanks to their guardian spirits.

These are just samples pouring out of the secular literature on genomics.  Clearly, a great deal more choreographed complexity is being found in the nucleus than Watson and Crick could have imagined when the genetic code first began to be deciphered.  Perhaps creationists will need to do little more than compile and cite.

Darwinists are fond of storytelling with glittering generalities.  When challenged, they retreat into accusations that anything other than 100% pure materialistic Darwinism is religion, not science, and use other shifty-feet tactics.  The answer is to pile on the evidence.  These articles are the tip of a truckload of data-rich, fact-filled laboratory studies that shout design instead of evolution.  Let’s rid secular science of its bad storytelling habit, and let the evidence speak for itself.   The Darwinists are sliding downhill with an avalanche of data racing down against them.  Perhaps a better cartoon of their predicament is to picture Wiley Coyote hanging by his fingers on a cliff.  Jonathan Wells, by debunking the icons of evolution, is like the Road Runner lifting Mr. Coyote’s fingers one at a time, while the genetic evidence is like Tweety Bird simultaneously piling weights on his feet.  Pretty soon he fall down go boom.