What is a gene?

Now: The Rest of the Genome
by Carl Zimmer

In this jungle of invading viruses, undead pseudogenes, shuffled exons and epigenetic marks, can the classical concept of the gene survive? It is an open question, one that Dr. Prohaska hopes to address at a meeting she is organizing at the Santa Fe Institute in New Mexico next March.

In the current issue of American Scientist, Dr. Gerstein and his former graduate student Michael Seringhaus argue that in order to define a gene, scientists must start with the RNA transcript and trace it back to the DNA. Whatever exons are used to make that transcript would constitute a gene. Dr. Prohaska argues that a gene should be the smallest unit underlying inherited traits. It may include not just a collection of exons, but the epigenetic marks on them that are inherited as well.

These new concepts are moving the gene away from a physical snippet of DNA and back to a more abstract definition. “It’s almost a recapture of what the term was originally meant to convey,” Dr. Gingeras said.

A hundred years after it was born, the gene is coming home.

Genome 2.0: Mountains Of New Data Are Challenging Old Views
by Patrick Barry

This complex interweaving of genes, transcripts, and regulation makes the net effect of a single mutation on an organism much more difficult to predict, Gingeras says.

More fundamentally, it muddies scientists’ conception of just what constitutes a gene. In the established definition, a gene is a discrete region of DNA that produces a single, identifiable protein in a cell. But the functioning of a protein often depends on a host of RNAs that control its activity. If a stretch of DNA known to be a protein-coding gene also produces regulatory RNAs essential for several other genes, is it somehow a part of all those other genes as well?

To make things even messier, the genetic code for a protein can be scattered far and wide around the genome. The ENCODE project revealed that about 90 percent of protein-coding genes possessed previously unknown coding fragments that were located far from the main gene, sometimes on other chromosomes. Many scientists now argue that this overlapping and dispersal of genes, along with the swelling ranks of functional RNAs, renders the standard gene concept of the central dogma obsolete.

Long Live The Gene

Offering a radical new conception of the genome, Gingeras proposes shifting the focus away from protein-coding genes. Instead, he suggests that the fundamental units of the genome could be defined as functional RNA transcripts.

Since some of these transcripts ferry code for proteins as dutiful mRNAs, this new perspective would encompass traditional genes. But it would also accommodate new classes of functional RNAs as they’re discovered, while avoiding the confusion caused by several overlapping genes laying claim to a single stretch of DNA. The emerging picture of the genome “definitely shifts the emphasis from genes to transcripts,” agrees Mark B. Gerstein, a bioinformaticist at Yale University.

Scientists’ definition of a gene has evolved several times since Gregor Mendel first deduced the idea in the 1860s from his work with pea plants. Now, about 50 years after its last major revision, the gene concept is once again being called into question.

Theory Suggests That All Genes Affect Every Complex Trait
by Veronique Greenwood

Over the years, however, what scientists might consider “a lot” in this context has quietly inflated. Last June, Pritchard and his Stanford colleagues Evan Boyle and Yang Li (now at the University of Chicago) published a paper about this in Cell that immediately sparked controversy, although it also had many people nodding in cautious agreement. The authors described what they called the “omnigenic” model of complex traits. Drawing on GWAS analyses of three diseases, they concluded that in the cell types that are relevant to a disease, it appears that not 15, not 100, but essentially all genes contribute to the condition. The authors suggested that for some traits, “multiple” loci could mean more than 100,000. […]

For most complex conditions and diseases, however, she thinks that the idea of a tiny coterie of identifiable core genes is a red herring because the effects might truly stem from disturbances at innumerable loci — and from the environment — working in concert. In a new paper out in Cell this week, Wray and her colleagues argue that the core gene idea amounts to an unwarranted assumption, and that researchers should simply let the experimental data about particular traits or conditions lead their thinking. (In their paper proposing omnigenics, Pritchard and his co-authors also asked whether the distinction between core and peripheral genes was useful and acknowledged that some diseases might not have them.)

Jeff Biggers on Thomas Paine

Thomas Paine’s Truth-to-Power Message in 1776
by Jeff Biggers

“Without the pen of the author of Common Sense,” John Adams begrudgingly admitted, “the sword of Washington would have been raised in vain.”

Rarely in history has the extraordinary power of writing galvanized such an armed resistance. Paine was a living icon in his own age, an 18th-century romantic figure as reviled and revered as Argentinian revolutionary Ernesto “Che” Guevara in the 1960s; Paine would go on to play a key role in the French Revolution. While he was tried in absentia for treason in Britain, his Rights of Man book on the natural rights of people over monarchy would become a global literary phenomenon and upend England’s social order.

Intentional or not, the conviction of Paine’s writing underscored the role of writers in the resistance. He was a truth-teller, contentious and bold, and adamant about holding accountable the brokers of authorized versions of history, calling out their hypocrisy, omissions, and mistruths—and the betrayal of an American credo of “we the people.”

Paine had not cornered the market on this literary tradition, of course. And his own select vision, especially in recognizing a more perfect vision of “we the people,” would be challenged in the process.

The Literary Instigator of the American Resistance
by Jeff Biggers

His letter to the abbé sought to define the transformative impact of the resistance movement on Americans in the aftershock of their triumph. “Our style and manner of thinking have undergone a revolution more extraordinary than the political revolution of the country,” he explained to the French. “We see with other eyes; we hear with other ears; and think with other thoughts, than those we formerly used. We can look back on our own prejudices, as if they had been the prejudices of other people. We now see and know they were prejudices and nothing else; and, relieved from their shackles, enjoy a freedom of mind, we felt not before.”

High-minded perhaps, but hardly delusional, Paine claimed this new way of thinking had “opened itself toward the world” and brought Americans into the world of nations. He didn’t trumpet the military triumph of Washington and his French allies; nor did Paine make an inventory of the natural resources and wealth now at American disposal. The future of the United States of America—and consequently the world—rested in the hands of “science, the partisan of no country, but the beneficent patroness of all,” which served as the great “temple where all may meet.”

Paine’s message to the abbé reflected the ongoing negotiations in Paris—and a clear admonition to its leaders. Instead of pursuing that “temper of arrogance,” he warned, “which serves only to sink” a country in esteem and to “entail the dislike of all nations,” Paine called on all leaders to find a way for the world to live in peace.

Here’s an excerpt from the letter:

Letters, the tongue of the world, have in some measure brought all mankind acquainted, and by an extension of their uses are every day promoting some new friendship. Through them distant nations became capable of conversation, and losing by degrees the awkwardness of strangers, and the moroseness of suspicion, they learn to know and understand each other. Science, the partisan of no country, but the beneficent patroness of all, has liberally opened a temple where all may meet. Her influence on the mind, like the sun on the chilled earth, has long been preparing it for higher cultivation and further improvement. The philosopher of one country sees not an enemy in the philosopher of another: he takes his seat in the temple of science, and asks not who sits beside him.

REAL Democracy History Calendar: June 25 – July 1

This is another example of the ruling elite re-creating the conditions that caused the American Revolution. It was public outrage against this exact kind of corrupt abuse of power in usurping local self-governance that inspired the Declaration of Independence and the original constitution, The Articles of Confederation.

Is there some reason those in power want to start a second American Revolution? Or are they as clueless as the British ruling elite were, in not being able to imagine the people would revolt and could win?


June 30

2008 – Publication of Gaveling Down the Rabble: How “Free Trade” Is Stealing Our Democracy by Jane Anne Morris, corporate anthropologist and former POCLAD principal

“The several themes in this book all connect around the subversion of unrepresentative government democracy by the U.S. Supreme Court. The Court has usurped from Congress the role of making public policy, with judicial decisions based on the U.S. Constitution’s Commerce Clause. These rulings have built a body of law favoring large corporate interests over the rights of states, municipalities, labor, minorities, and the environment.”

As of 2008 according to Morris, 219 state laws had been overturned by Supreme Court just on commerce clause grounds. A complete list of state laws held to be unconstitutional is at http://law.justia.com/constitution/us/047-state-laws-held-unconstitutional.html
Info on the book is at https://rowman.com/isbn/9781891843396

June 25

1975 – Release date of the film “Roller Ball”
“In the film, the world of 2018 (referred to in the tagline as “the not too distant future”) is a global corporate state, containing entities such as the Energy Corporation, a global energy monopoly based in Houston which deals with nominally-peer corporations controlling access to all transport, luxury, housing, communication, and food on a global basis. According to the tagline, in this world, ‘wars will no longer exist. But there will be… Rollerball.’

“The film’s title is the name of a violent, globally popular sport around which the events of the film take place. It is similar to Roller Derby in that two teams clad in body armor skate on roller skates (some instead ride on motorcycles) around a banked, circular track. There, however, the similarity ends…

“The various global corporations own Rollerball teams, named after the cities in…

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