Image source: By Muhammad Mahdi Karim (www.micro2macro.net) Facebook Youtube (Own work) [GFDL 1.2 (http://www.gnu.org/licenses/old-licenses/fdl-1.2.html)], via Wikimedia Commons.
You know about ENCODE, the project that found 80 percent or more of the human genome is transcribed and appears functional. Now, along comes modENCODE: the ENCODE project for model organisms. Results from the fruit fly are in, and Indiana University shares the surprises (for evolutionary theory, that is): "Study of complete RNA collection of fruit fly uncovers unprecedented complexity."
The paper shows that the Drosophila genome is far more complex than previously suspected and suggests that the same will be true of the genomes of other higher organisms. The paper also reports a number of novel, particular results: that a small set of genes used in the nervous system are responsible for a disproportionate level of complexity; that long regulatory and so-called "antisense" RNAs are especially prominent during gonadal development; that "splicing factors" (proteins that control the maturation of RNAs by splicing) are themselves spliced in complex ways; and that the Drosophila transcriptome undergoes large and interesting changes in response to environmental stresses. (Emphasis added.)
Ten of the 41 researchers from 11 universities working on modENCODE came from IU. They found many genes transcribed only under stress, such as exposure to heat, cold, and toxins. "In total, 5,249 transcript models for 811 genes were revealed only under perturbed conditions," they said. As if the "junk DNA" myth needed any more pounding, the lead author testifies:
"As usual in science, we’ve answered a number of questions and raised even more. For example, we identified 1,468 new genes, of which 536 were found to reside in previously uncharacterized gene-free zones."
The news item notes that "biologists have developed increasing appreciation of how well genes and critical life processes are conserved over long evolutionary distances."
Meanwhile, the transcriptome of another model organism, the sea anemone, was studied by researchers at the University of Vienna. This creature, like the fruit fly, shows a similar unexpected complexity in its gene networks. The news release claims that this creature is "half animal, half plant," but what they mean is that gene regulation for both kingdoms of the tree of life is so similar, it must have already existed in the microbial common ancestor 600 million years ago:
The team led by evolutionary and developmental biologist Ulrich Technau at the University of Vienna discovered that sea anemones display a genomic landscape with a complexity of regulatory elements similar to that of fruit flies or other animal model systems. This suggests, that this principle of gene regulation is already 600 million years old and dates back to the common ancestor of human, fly and sea anemone. On the other hand, sea anemones are more similar to plants rather to vertebrates or insects in their regulation of gene expression by short regulatory RNAs called microRNAs. These surprising evolutionary findings are published in two articles in the journal "Genome Research".
So here is another apparently "simple organism" with "complex gene content." What they found contradicts another evolutionary expectation:
In the last decades the sequencing of the human and many animal genomes showed that anatomically simple organisms such as sea anemones depict a surprisingly complex gene repertoire like higher model organisms. This implies, that the difference in morphological complexity cannot be easily explained by the presence or absence of individual genes. Some researchers hypothesized that not the individual genes code for more complex body plans, but how they are wired and linked between each other. Accordingly, researchers expected that these gene networks are less complex in simple organisms than in human or "higher" animals.
Well, surprise. When they examined the epigenetic mechanisms for gene expression and regulation (the "grammar" of the genetic code), they found that "Gene regulation [is] comparable to higher animal model systems." For instance, they estimate that 30 to 50 percent of genes are regulated by microRNAs, just one of the facets of regulatory processes.
The dominance of complex regulation in such a simple organism leads these evolutionary biologists to postulate that "this principle of complex gene regulation was already present in the common ancestor of human, fly and sea anemone some 600 million years ago." Yet the simple Precambrian animals lacked most of the developmental processes and organ functions of those that emerged fully formed in the Cambrian explosion.
To bolster their story, the researchers claim to have found microRNA activity in these animals that resembles that of plants. Since the discovery contradicts the hypothesis that the regulatory elements arose independently in the two kingdoms, they believe they have uncovered "the first evolutionary link between microRNAs of plants and animals." But then they try to have it both ways:
In summary, while the sea anemone’s genome, gene repertoire and gene regulation on the DNA level is surprisingly similar to vertebrates, its post-transcriptional regulation is plant-like and probably dates back to the common ancestor of animals and plants. This is the first qualitative difference found between Cnidaria and "higher" animals and the findings provide insight on how important levels of gene regulation can evolve independently.
Of course, the identity of the common ancestor was left as an exercise.
In 2013, ENCODE turned the tables on Darwinian evolutionists with their assumptions about junk DNA, showing that the human genome is overwhelmingly transcribed and most likely functional. And it’s not just functional, but regulated with mind-boggling layers of complexity — switches, networks, and codes controlling other codes. Now, the modENCODE project is showing the same pattern for fruit flies. The Vienna study shows the same thing for sea anemones. Both expect that "unexpected complexity" will be the norm for all "higher" organisms.
Yet if all this inter-related complexity has to be pushed back to some mythical common ancestor, it is tantamount to believing multiple miracles happened to a simple organism that had no gut, eyes, sex, limbs, or nerves. The mythical "common ancestor" that possessed these abilities serves only as a placeholder for ignorance — not a scientific explanation.
Intelligent design, which does not rely on such religious premises, knows how to explain the observations. Whenever we see a complex, functioning system (like a rollout of a software system), we know intelligence played a role in its origin. We also know that intelligence can explain multiple, independent instantiations of similar systems. We never see, however, complex, networked systems arising de novo by unguided natural processes.
In 1980, Carl Sagan knew nothing about ENCODE and modENCODE. With all the revelations of genetic complexity coming to light in the past 34 years, these must be hard times for Neil deGrasse Tyson to keep a straight face while sweeping his hand up the cartoon-drawn Tree of Life in Cosmos 2.0 and ascribing "all the beauty and diversity of life" to random mutations. As Casey Luskin noted, it only makes sense if you don’t think about it.