Saturday, December 14, 2013

Science (fiction?)

Novel Way Discovered to Decode and Read DNA: Scientists
According to a new report, scientists have discovered a new way to read and decode DNA. Scientists are suspecting this research could forever change the ways on how doctors uncover, diagnose and treat various diseases.

Researchers said the main aim of this research is to understand the process of storage of biological functions in the human genome.

The research, published in the journal Science, states how genomes use genetic code to write information about proteins and that too in two separate languages. Researchers believe that the second language lies below the first and instruct the cell to control the genes.

Dr. John Stamatoyannopoulosm, lead researcher, said: "For over 40 years we have assumed that DNA changes affecting the genetic code solely impact how proteins are made".

Researchers said this novel research has thrown light on the fact that the DNA is an incredibly powerful information storage device, which has been fully exploited by nature.
Don't Be Duped By 'Duon' DNA Hype
I can only hope that Stamatoyannopoulos didn’t really say that. The authors report that changes in a single DNA sequence can influence both the protein it encodes and the place where other proteins bind to initiate copying. So evolutionarily, a single change could influence two endpoints–copying the sequence and what gets made using the same sequence. That’s cool, but not actually new.

With today’s headlines hyping “Second Code Uncovered Inside the DNA,” you might think that scientists are running around in circles in their labs, tearing out their hair, and screaming. But the real reaction of scientists to these headlines is more along the lines of this Twitter conversation among several scientific experts and science writers. They have good reason to be snarky.

The hype began with the way hype often begins: an institutional news release offering us the holy grail/huge breakthrough/game-changing finding of the day. This kind of exaggeration is the big reason any science consumer should look well beyond the news release in considering new findings. A news release is a marketing tool. You’re reading an advertisement when you read a news release; it’s also scientifically garbled and open to all kinds of misinterpretation, as the comments at the link to the release make clear.

Scientists have not assumed that the genetic code “was used exclusively to write information about proteins,” or even ever assumed that it “writes information about proteins,” whatever that means. A quick primer: Proteins are molecules that do the work of an organism, and that includes the work of copying DNA for protein production and cell division. Even nonmajors biology textbooks cover the fact that the DNA sequence both contains code for proteins and serves a regulatory purpose, making it possible to copy that code into a form the cell can read, recipe-like, to build the proper protein.

(edited in article) I’d be stunned if UW scientists were genuinely “stunned” to discover this dual use of DNA sequences to “write” “two separate languages” because what they really describe is the use of a single language, the language of nucleotides, for two known purposes. They themselves noted that “the potential for some coding exons to accommodate transcriptional enhancers or splicing signals has long been recognized.”

The release also contains gems such as “The genetic code uses a 64-letter alphabet called codons.” This sentence makes me sad. Codons consist of three nucleotides–which we designate with the letters A, C, G, and T/U–and there are 64 of these triplets, 61 of which serve as molecular code words for 20 amino acids (here is a DNA nucleotide codon table, too; these are the codons the authors address). Some amino acids get more than one word to designate them. The cell “reads” these code words and uses the amino acids they designate to build proteins.

The other problem is the ubiquitous use of the phrase “second code” in so many of the headlines related to this story when the authors themselves state: “ Although nearly all codon biases parallel TF recognition preferences genome-wide…” with the arginine codon as an exception. That’s not a “second code,” even though the news release describes it that way. It’s a different (but already recognized) use of an existing code, now identified as occurring at a greater than previously recognized frequency in areas that use the same code for proteins.

So what was the real import of the study that warranted its publication in Science, a “glamor” science publication? The authors (whose paper I enjoyed) seem to have found that the genome contains more of these dual-use triplet DNA sequences than previously thought, which might make them more relevant when examining some aspects of evolution (see “Single change could influence two endpoints”). And, it seems, the authors wanted the opportunity to, um, codify their own term for these dual-use sequences: duons. I wonder if they realized that the name had already been taken?
Ah, science. Guambat wonders why Mrs Guambat spends so much time watching all the "Housewives of..." shows, when they hardly know the meaning of the term "bitchy". Academic "science" (so often commercial "innovation") could open a whole new realm of reality show in way it never imagined.

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Blogger Vest said...

Very interesting, I hope your knowledge is being put to good use. Sadly most of this info will flow from one ear and out of the other read by most bloggers with a 'C' in science.
Was in Guam on Gab Gab beach late May 45 after op/ iceberg. R N.

22 December 2013 at 6:07:00 am GMT+10  
Blogger Davoh said...

Um, just thought t let ya know that my 'companion'? drank herself to death about 10 years ago. (Long story; Already 'married'. Roman church indoctrination. Couldn't be with me who made her happy. Too many conflicting mental problems).

15 March 2014 at 4:38:00 pm GMT+10  

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