“Data is not information, information is not knowledge, knowledge is not wisdom, wisdom is not truth,” —Robert Royar (1994) paraphrasing Frank Zappa’s (1979) anadiplosis

I also found it interesting that they quoted T. R. Gregory who is critical of ENCODE, but for completely different reasons. According to Gregory, we supposedly knew about function decades ago and that this should be so no big surprise. Of course as I had to remind him that maybe one of the problems laid in the fact that many scientist ignored this data (as they should have just stuck to science and not get involved in the culture war) as it is well document that many instead, held this useless junked DNA paradigm as a poster child for bad design with all this supposed empirical evidence to back it up. Like many others, Gregory is of the sort that follows the logic, that if the data is incongruent to the theory, then the data must be wrong as he speaks of his “onion test” concerning C Value paradox below.

“The onion test is a simple reality check for anyone who thinks they can assign a function to every nucleotide in the human genome. Whatever your proposed functions are, ask yourself this question: Why does an onion need a genome that is about five times larger than ours?” —T. Ryan Gregory”
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Dan Graur

”playing fast and loose with the term “function,” by divorcing genomic analysis from its evolutionary context and ignoring a century of population genetics theory”….

Dan maybe its time to update these 80 year old constructs. As this paper below which is one of many indicates……
The new biology: beyond the Modern Synthesis Michael R Rose1* and Todd H Oakley2 . The last third of the 20th Century featured an accumulation of research findings that severely challenged the assumptions of the “Modern Synthesis” which provided the foundations for most biological research during that century. The foundations of that “Modernist” biology had thus largely crumbled by the start of the 21st Century. This in turn raises the question of foundations for biology in the 21st Century. .
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Dan Graur

”There are two almost identical sequences in the genome. The first, TATAAA, has been maintained by natural selection to bind a transcription factor, hence, its selected effect function is to bind this transcription factor. A second sequence has arisen by mutation and, purely by chance, it resembles the first sequence; therefore, it also binds the transcription factor. However, transcription factor binding to the second sequence does not result in transcription, i.e., it has no adaptive or maladaptive consequence. Thus, the second sequence has no selected effect function, but its causal role function is to bind a transcription factor”

Here is what ENCODE’s lead analysis coordinator E. Birney says about this….
”Rather than being inert, the portions of DNA that do not code for genes contain about 4 million so-called gene switches, transcription factors that control when our genes turn on and off and how much protein they make, not only affecting all the cells and organs in our body, but doing so at different points in our lifetime. Somewhere amidst that 80% of DNA, for example, lie the instructions that coax an uncommitted cell in a growing embryo to form a brain neuron, or direct a cell in the pancreas to churn out insulin after a meal, or guide a skin cell to bud off and replace a predecessor that has sloughed off”
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Dan Graur 

“The human genome is rife with dead copies of protein-coding and RNA-specifying genes that have been rendered inactive by mutation. These elements are called pseudogenes (Karro et al. 2007). Pseudogenes come in many flavors (e.g., processed, duplicated, unitary) and, by definition, they are nonfunctional”

Not according to paper below…..
PSEUDOGENES: Are They “Junk” or Functional DNA? Annual Review of Genetics
Vol. 37: 123-151 (Volume publication date December 2003)
First published online as a Review in Advance on June 25, 2003
DOI: 10.1146/annurev.genet.37.040103.103949″Pseudogenes have been defined as nonfunctional sequences of genomic DNA originally derived from functional genes. It is therefore assumed that all pseudogene mutations are selectively neutral and have equal probability to become fixed in the population. Rather, pseudogenes that have been suitably investigated often exhibit functional roles, such as gene expression, gene regulation, generation of genetic (antibody, antigenic, and other) diversity. Pseudogenes are involved in gene conversion or recombination with functional genes. Pseudogenes exhibit evolutionary conservation of gene sequence, reduced nucleotide variability, excess synonymous over nonsynonymous nucleotide polymorphism, and other features that are expected in genes or DNA sequences that have functional roles”…..

It seems the biggest criticism in this paper is in how the the word function is used, as its definition of function is used broadly, but it also seems kind of silly to not expect such a broad definition when the findings themselves are so broad. And again just because the findings seem incongruent to how we view selection based on the modern synthesis (and or what Stewart Newman refers to as these old entrenched dogmas) it does not mean the theory should trump scientific revelation & the discovery of new and empirical data. Maybe it’s the theory that needs changing. One very well known scientist once told me. Scientist don’t change their minds, they just die.