Genomics is a forum for describing the development of genome-scale technologies and their application to all areas of biological investigation.They claim that all submissiosn are subjected to rigorous peer review and only 25-30% of submissions are accepted for publication.
As a journal that has evolved with the field that carries its name, Genomics focuses on the development and application of cutting-edge methods, addressing fundamental questions with potential interest to a wide audience. Our aim is to publish the highest quality research and to provide authors with rapid, fair and accurate review and publication of manuscripts falling within our scope.
The composition of genomes is important so it's no surprise that the journal is interested in publishing articles that address the junk DNA debate. In fact, it is so interested that it is going to devote a special issue to the subject for publication in February 2016.
That's the good news. Now for the bad news ....
Special issue on the functionality of genomic DNAsSome of you will recognize the names of the guest editors. Jim Shapiro is one of the poster boys of Intelligent Design Creationism because he attacks evolutionary theory. He's one of the founders of the "The Third Way."
Prof. Shi Huang
State Key Laboratory of Medical Genetics
Central South University , China
Prof James Shapiro
Department of Biochemistry and Molecular Biology
University of Chicago
The field of genome evolution and population genetics has for the past half of a century assumed that genomic DNA can be divided into functional and non-functional (“junk”) regions. Experimental molecular science has found little evidence for this assumption. A majority of the noncoding parts of the human genome are transcribed, and numerous experimental researchers have now recognized an important functional role in the so called junk DNA regions, such as syn sites, lncRNA, psudogene transcripts, antisense transcripts, microRNA, and mobile elements. In fact, evidence for functional constraints on noncoding genome regions has long been recognized. New theoretical frameworks based on less arbitrary foundations have also appeared in recent years that can coherently account for the reality of far more functional DNAs, as well as all other major known facts of evolution and population genetics. Nonetheless, there still remains a large gap in opinions between bench scientists in experimental biology and those on the theory side in bioinformatics and population genetics. This special issue will aim to close that gap and provide a view of evidence from a perspective that all genome regions have (or can easily acquire) functionality.
The special issue on the functionality of genome will focus on the following tentative topics:
- Theoretical foundation for all genome regions to be functional. It will cover both the theory and all major features of genome evolution.
- Functional studies on junk DNA regions, including lncRNA sequences, viral DNAs and mobile elements
- Functionalities associated with genome spatial organization in the nucleus
- Isocores and compositional constraints on genomes
- Genetic basis of complex traits and diseases focusing on the collective effects of normal genetic variations
- Cancer genomics
- Roles of repetitive DNA elements in major evolutionary transitions
- Correlations of genome composition and organismal complexity
- Evo Devo and extended synthesis
First submission date: July 1, 2015
Deadline for paper submissions: October 1, 2015
Deadline for final revised version: December 1, 2015
Expected publication: February 2016
You may be less familiar with Shi Huang. He is also part of the Third Way movement but we've recently learned a lot more about him because he posts comments under the name "gnomon." You can see some of his comments in this thread: Ford Doolittle talks about transposons, junk DNA, ENCODE, and how science should work. Shi Huang appears to have a great deal of difficulty expressing himself in a rational manner.
Those guest editors will publish papers that "... provide a view of evidence from a perspective that all genome regions have (or can easily acquire) functionality." In other words, skeptics need not apply.
The controversy is over the amount of junk DNA in genomes. There are two sides in this controversy. Many scientists think there is abundant and convincing evidence that most of our genome is junk. Other scientists think that most of our genome is functional. It looks like Genomics is only interested in hearing from the second group of scientists. That's why they appointed guest editors with an obvious bias. Those guest editors also happen to be skating very close to the edge of kookdom.
This is not how a credible science journal is supposed to behave.