Watson and Crick wrote near the end of their seminal paper - “It has not escaped our notice that the specific pairing we have postulated suggests a possible copying mechanism for the genetic material.”
It is dubbed as the greatest understatement, but what if it followed the norm of scientific reporting of the era? We remember reading the paper of Leon Cooper published in 1956, and from the narrative, it was impossible to guess that the paper had clues to one of the greatest mysteries of condensed matter physics. When we first moved to biology, it took us time to tune our mental compass from physics-style reporting to biology-style reporting. We could not easily accept the speculation in ‘discussion section’. Of course that is difficult to understand in the Ewan Birney world, when publication followed by press release is the norm.
Dan Graur published another witty and hard-hitting piece on latest ENCODE development in his blog -
Imagine a respectable scientific journal publishing an article critical of the general theory of relativity written by Jack Weatherford, Professor of Anthropology and the author of a book on Genghis Khan and one on the history of money. Or a journal publishing an article refuting plate tectonics or the existence of dinosaurs by Elizabeth Owens, whose specialty is spiritualism and clairvoyance, and who pens how-to books on developing ones psychic abilities. I am quite confident such a respectable journal would not be considered respectable for long. I also believe that the readers would know that the editor and its staff took leave of their senses and are currently in dire need of medical attention.
The point Dan Graur makes is so obvious that we are surprised that the ENCODE- backers are still continuing there BS claims. Part of the misguided notion comes from our human-centric view of biology, and especially government’s human-centric funding. In this morning’s coelacanth conference call, someone mentioned about lungfish genome being many times larger than human genome. Nobody challenged the subsequent claim that much of it is filled with junk DNA. Only when it comes to human genome, people start to believe extraordinary claims about 80% genome being functional simply because it is our chromosomes. We have always been critical of human-centric bias of funding and thinking (see here and here).
However, we believe Dan Graur is fighting a losing battle. We were reading another commentary titled “Junk DNA and the C-value Paradox” written by Dr. Merlin Corssely. Everything the author said made sense, but we were shocked after reading the comment section. Not a single reader agreed with the author !! We do have shortage of scientists.
When the argument gets to ‘I haven’t worked out what it’s used for, therefore its rubbish’ you know you’re fast approaching the bottom of the barrel. In keeping with the grand old scientists of yore who experimented on themselves, my suggestion to Dr Corssely would be to take a sample of his own DNA, remove the bits he’s supremely confident serve no purpose, and grow the trimmed-down version and see what eventuates. One suspects the two most likely outcomes are either a Nobel Prize or else first rights to a cracking horror sci-fi movie script. My money’s on the latter.
B. Couple of interesting blog posts on DNA Sequencing Business
Our thoughts -
i) Illumina may not get knocked off the perch very soon.
ii) We heard that SOLiD is coming up with a second adapter near the end of the read so that the reads can be converted from color space to sequence space directly. We do not know whether the technology is already out, but it will give SOLiD-users a leg up in using sequence space-based traditional algorithms. If you are unfamiliar with color-space and do not understand what we are talking about, please check this old commentary.