Paul Ebert wrote:

You probably don’t know John personally. He is not only a tremendous scientist, but he is also a superb communicator. He enjoys interpreting science for audiences at all levels. Sometimes use of the term junk DNA is an appropriate communication device. He certainly is aware that people spoke of possible functions of “junk DNA”. Text books even mentioned the possibility of functions even though they also used the term “junk DNA”. John spent many years running two research programs. One was mainstream science and the other was an extended effort to discover the function of non-coding RNA. The work on non-coding RNA was carried out under the stigma of working on “junk DNA”.
There was a nearly 30 year span between the “common sense” quotes above and the breakthroughs associated with understanding the roles of regulatory RNAs. I have heard John use the term “intellectual laziness” to refer to the time during which the term “junk DNA” was used. John is certainly not scientifically illiterate as suggested above.
By the way, if you really wanted to rubbish John for his comment, you would have referred to the following:
Science 165: 349-357, 1969.
That paper was much more that a throw-away “common sense” comment. Instead it was a complete description of a possible role for regulatory RNAs. The thinking presented in that paper was displaced by the model of gene regulation provided by bacteria.

Could ‘Advanced’ Dinosaurs Rule Other Planets?

New scientific research raises the possibility that advanced versions of T. rex and other dinosaurs — monstrous creatures with the intelligence and cunning of humans — may be the life forms that evolved on other planets in the universe. “We would be better off not meeting them,” concludes the study, which appears in the Journal of the American Chemical Society.

In the report, noted scientist Ronald Breslow, Ph.D., discusses the century-old mystery of why the building blocks of terrestrial amino acids (which make up proteins), sugars, and the genetic materials DNA and RNA exist mainly in one orientation or shape. There are two possible orientations, left and right, which mirror each other in the same way as hands. This is known as “chirality.” In order for life to arise, proteins, for instance, must contain only one chiral form of amino acids, left or right. With the exception of a few bacteria, amino acids in all life on Earth have the left-handed orientation. Most sugars have a right-handed orientation. How did that so-called homochirality, the predominance of one chiral form, happen?
Breslow describes evidence supporting the idea that the unusual amino acids carried to a lifeless Earth by meteorites about 4 billion years ago set the pattern for normal amino acids with the L-geometry, the kind in terrestial proteins, and how those could lead to D-sugars of the kind in DNA.

“Of course,” Breslow says, “showing that it could have happened this way is not the same as showing that it did.” He adds: “An implication from this work is that elsewhere in the universe there could be life forms based on D-amino acids and L-sugars. Such life forms could well be advanced versions of dinosaurs, if mammals did not have the good fortune to have the dinosaurs wiped out by an asteroidal collision, as on Earth. We would be better off not meeting them.“

But wait! That must just be a bizarre misinterpretation and hypification by the author of the press release, right? Nope. That last part in the quote above is taken right from the concluding paragraph of the paper.

A new hypothesis posed by a University of Tennessee, Knoxville, associate professor and colleagues could be a game changer in the evolution arena. The hypothesis suggests some species are surviving by discarding genes and depending on other species to play their hand.

Yeah. We knew about this. Endosymbionts have provided a clear example for decades.

According to the hypothesis, evolution pushes microorganisms to lose essential functions when there is another species around to perform them. This idea counters popular evolutionary thinking that living organisms evolve by adding genes rather than discarding them.

I see.

“A common assumption about evolution is that it is directed toward increasing complexity,” said Erik Zinser, associate professor of microbiology. “But we know from analysis of microbial genomes that some lineages trend toward decreasing complexity, exhibiting a net loss of genes relative to their ancestor.”

Before you change the game of evolutionary theory, maybe you should try to understand it first?

Interested applicants are requested to submit the following (merged into a single PDF): CV, unofficial transcript, contact information for two referees, and a 500-word statement of research interests. They must also identify one or more potential advisors of interest (see faculty profiles at http://ib.cbs.uoguelph.ca/index.shtml).

Candidates must be Canadian citizens or permanent residents.

Click to download PDF.

_________________________

*

Making something of junk earns geneticist top award

When Sydney geneticist John Mattick suggested junk DNA was anything but rubbish he was challenging an assumption that had underpinned genetics for 50 years.

”The ideas I put forward 10 years ago were quite radical but I thought I was right,” Professor Mattick said.

He was. And tomorrow he will become the first Australian honoured with the Chen Award for distinguished academic achievement in human genetic and genomic research, awarded by the Human Genome Organisation.

For decades after James Watson and Francis Crick discovered DNA was a double helix, scientists believed most genes were the written instructions for proteins, the building blocks of all body processes. The assumption was true for bacteria but not complex organisms like humans, said Professor Mattick, the new executive director of the Garvan Institute.

In humans, more than 95 per cent of the genome contains billions of letters that do not make proteins, called non-coding DNA. ”When people bumped into all this DNA that didn’t make proteins they thought it must be junk,” he said. But Professor Mattick felt it was unlikely that useless material would survive hundreds of millions of years of evolution.

He found that the non-protein-coding sections of DNA had a function, to produce RNA.

“The obvious and very exciting possibility was that there is another layer of information being expressed by the genome – that the non-coding RNAs form a massive and previously unrecognised regulatory network that controls human development.”

Many scientists now believe this RNA is the basis of the brain’s plasticity and learning, and may hold the secret to understanding many complex diseases.

Sometimes people would ask what would happen if a publisher asked me to take down my papers. Often I would answer that I would comply, but that I would never have anything to do with that publisher again, either as an author or a reviewer. The fact that this is from the NRC Press is a shame, because I have published a lot with them and have reviewed a large number of manuscripts for several of their journals. I am also working on a special issue for one of them, but I may have to reconsider that now.

Anyway, here’s the message. It’s polite and not threatening at all, but it does make it clear that colleagues outside of Canada will have to ask me for each reprint that they want, which is a huge pain for them and for me.

Hi Ryan,

It has been brought to my attention that the full PDF version of a number of articles published with NRC Research Press have been posted on your website as “Reprints” which can be freely accessed by anyone.

We do have a liberal authors’ rights policy (http://www.nrcresearchpress.com/page/authors/information/rights ) and author benefits (http://www.nrcresearchpress.com/page/authors ), which allow authors to post their submitted and accepted manuscript, but not the final PDF. We also provide authors a free copy of their final PDF, which can be passed around to colleagues for personal use, but they are not to be posted on a website other than the NRC research Press website (http://www.nrcresearchpress.com/). We do not charge our authors page or submission charges, but as a not-for-profit publisher we need to generate revenue through subscriptions to run our operation.

Here is the link to your site where the “reprints” are in copyright violation: http://www.gregorylab.org/cv/. We would prefer that you link to the PDF on our site, which would be freely accessible to all Canadians (content pre-2011) and paid subscribers.

Here is a list of publications in question:

45. Andrews, C.B. and T.R. Gregory (2009). Genome size is inversely correlated with relative brain size in parrots and cockatoos. Genome 52: 261-267.
-Reprint-
39. Gregory, T.R. and J.D.S. Witt (2008). Population size and genome size in fishes: a closer look. Genome 51: 309-313.
-Reprint-
22. Gregory, T.R. (2003). Genome size estimates for two important freshwater molluscs, the zebra mussel (Dreissena polymorpha) and the schistosomiasis vector snail (Biomphalaria glabrata). Genome 46: 841-844.
-Reprint-
21. Gregory, T.R. and P.D.N. Hebert (2003). Genome size variation in lepidopteran insects. Canadian Journal of Zoology 81: 1399-1405.
-Reprint-
18. Prokopowich, C.D., T.R. Gregory, and T.J. Crease (2003). The correlation between rDNA copy number and genome size in eukaryotes. Genome46: 48-50.
-Reprint-
14. Gregory, T.R. (2002). Genome size and developmental parameters in the homeothermic vertebrates. Genome 45: 833-838.
-Reprint-
13. Gregory, T.R. (2002). Genome size of the northern walkingstick, Diapheromera femorata (Phasmida: Heteronemiidae). Canadian Journal of Zoology 80: 1303-1305.
-Reprint-
11. Gregory, T.R. and P.D.N. Hebert (2002). Genome size estimates for some oligochaete annelids. Canadian Journal of Zoology 80: 1485-1489.
-Reprint-
7. Gregory, T.R. (2000). Nucleotypic effects without nuclei: genome size and erythrocyte size in mammals. Genome 43: 895-901.
-Reprint-
2. Gregory, T.R. and C.M. Wood (1999). Interactions between individual feeding behaviour, growth, and swimming performance in juvenile rainbow trout (Oncorhynchus mykiss) fed different rations. Canadian Journal of Fisheries and Aquatic Sciences 56: 479-486.
-Reprint-
1. Gregory, T.R. and C.M. Wood (1998). Individual variation and interrelationships between swimming performance, growth rate, and feeding in juvenile rainbow trout (Oncorhynchus mykiss). Canadian Journal of Fisheries and Aquatic Sciences 55: 1583-1590.
-Reprint-

Thanks.

Radical Theory Explains the Origin, Evolution, and Nature of Life, Challenges Conventional Wisdom
Case Western Reserve Theorist Develops Incomparable Model that Unifies Physics, Chemistry, and Biology

CLEVELAND – Jan. 26, 2012 – The earth is alive, asserts a revolutionary scientific theory of life emerging from Case Western Reserve University School of Medicine. The trans-disciplinary theory demonstrates that purportedly inanimate, non-living objects—for example, planets, water, proteins, and DNA—are animate, that is, alive. With its broad explanatory power, applicable to all areas of science and medicine, this novel paradigm aims to catalyze a veritable renaissance.

Erik Andrulis, PhD, assistant professor of molecular biology and microbiology, advanced his controversial framework in his manuscript “Theory of the Origin, Evolution, and Nature of Life,” published in the peer-reviewed journal, Life. His theory explains not only the evolutionary emergence of life on earth and in the universe but also the structure and function of existing cells and biospheres.

In addition to resolving long-standing paradoxes and puzzles in chemistry and biology, Dr. Andrulis’ theory unifies quantum and celestial mechanics. His unorthodox solution to this quintessential problem in physics differs from mainstream approaches, like string theory, as it is simple, non-mathematical, and experimentally and experientially verifiable. As such, the new portrait of quantum gravity is radical.

The basic idea of Dr. Andrulis’ framework is that all physical reality can be modeled by a single geometric entity with life-like characteristics: the gyre. The so-called “gyromodel” depicts objects—particles, atoms, chemicals, molecules, and cells—as quantized packets of energy and matter that cycle between excited and ground states around a singularity, the gyromodel’s center. A singularity is itself modeled as a gyre, wholly compatible with the thermodynamic and fractal nature of life. An example of this nested, self-similar organization is the Russian Matryoshka doll.

By fitting the gyromodel to facts accumulated over scientific history, Dr. Andrulis confirms the proposed existence of eight laws of nature. One of these, the natural law of unity, decrees that the living cell and any part of the visible universe are irreducible. This law formally establishes that there is one physical reality.

Another natural law dictates that the atomic and cosmic realms abide by identical organizational constraints. Simply put, atoms in the human body and solar systems in the universe move and behave in the exact same manner.

“Modern science lacks a unifying, interdisciplinary theory of life. In other words, current theories are unable to explain why life is the way it is and not any other way,” Dr. Andrulis says. “This general paradigm furnishes a fresh perspective on the character and meaning of life, offers solutions to protracted problems, and strives to end divisive debates.”

One debate swirls around the scientific merit of James Lovelock’s popular Gaia hypothesis. By showing that the earth is theoretically synonymous with life, Dr. Andrulis’ paradigm substantiates the Gaian premise that all organisms and their surroundings on earth are closely integrated to form a single self-regulating complex system.

Another legendary quarrel is that between biblical creationists and neo-Darwinian evolutionists. In demonstrating that the origin and evolution of life is a consequence of natural laws and physical forces, this theory synthesizes arguments and dispels assumptions from both sides of the creation-evolution debate.

To test his paradigm, Dr. Andrulis designed bidirectional flow diagrams that both depict and predict the dynamics of energy and matter. While such diagrams may be foreign to some scientists, they are standard reaction notation to chemists, biochemists, and biologists.

Dr. Andrulis has used his theory to successfully predict and identify a hidden signature of RNA biogenesis in his laboratory at Case Western Reserve University School of Medicine. He is now applying the gyromodel to unify and explain the evolution and development of human beings.

For more information, see “Theory of the Origin, Evolution, and Nature of Life,” Life, Vol. 2:1-105 (2012).

Update:

• I have looked at the original paper, and it’s even crazier than the press release would indicate. So I can’t blame the author of the press release as much as the author of the actual paper — but why this was promoted by the institution is a mystery. Seriously, this paper feels like a Sokal hoax.
• Jonathan Badger pointed out in the comments to my post that I am cited in the paper. Here’s what it says: “C-value enigma. The C-value enigma states that less evolutionary developed cell types have greater genome size than more complex cell systems [725].” Of course, the C-value enigma says no such thing, and I would never used a term like “less evolutionary developed”. *Facepalm*
• John Timmer provides a nice summary of the issue at Ars Technica.

Favourite part: the Onion test followed by a Simpsons reference (at 37:00). Can’t ask for more than that! (Incidentally, PZ gets the onion test right — it’s about onions vs. humans AND onions vs. other onions; see also Larry Moran’s summary).

Nazi racial ideology was religious, creationist, and opposed to Darwinism