I did cringe. This is my field. (I know virtually all of the people he's been talking with.)
The descriptions are accurate, but murky. One huge missing piece is a description of the structure of the genome. There is one mention of the word chromosome. The words haplotype and allele never make an appearance. There is no mention of the fact that we are diploid, nor that one copy of our chromosomes comes from each of our parents. Nor is there any hint as to the way that we share our genomes.
Maybe I'm allergic to assertions of novelty, but I don't enjoy his claim that he's the first journalist to get access to their "raw" genomic data. That's just being fancy. Is it necessary to say that? In any case, what's "raw" changes every few years, so someone else will soon get the chance to say the same thing. (I gripe, but I have to admit that it's nerdy/cool to see someone writing so much about BAM files :) !)
I'm still waiting for the first journalist to mention genome structure in a popular article on genomics. As badly as we need to understand what's going on in the genome, the public, and particularly professionals whose work brings them to articles like this, need to develop an intuition about how genomes work.
>I did cringe. ... The descriptions are accurate, but murky.
I agree that the article does not have the precision that biologists expect; however, I think broad accuracy is important when writing for the general public and sadly lacking in most science reporting.
I attended a conference on evolution and medicine last month where Zimmer spoke about how he approaches reporting science and the struggle to cover important, but complex ideas for a general audience. Having heard his side of the story, I may be a bit biased but I would love to hear recommendations for other science journalists that tend to get the story right.
The article touches or at least hints to ploidy level. The author talks briefly about being a carrier of a disease.
But as you state, it is devoid of the 4D structure leading to the central dogma of molecular biology (DNA->RNA->Protein->function). This might be the natural discourse between science and the public. NGS technology didn't really exploid until 2005. So ten years roughly, to get the media to start talking about re-sequencing experiements. I don't know the normal length of time before trends in scientific literature bleeds into general mass media, but I would think it would be at least several years, if not a decade.
With that being said, structural genomes (which the author technically foreshadows with insertions/deletions) and their spatial effects on RNA expression is still a large mystery in scientific literature - so it wouldn't surprise me at all that it's not included or missed by a journalist.
All the points you're missing I learned at secondary school decades ago. What I did not learned is how people might judge the overwhelming complexity of their own genome in terms of fitness. I found his views appropriate if not foreshadowing.
You did, but if others did they promptly forgot their lessons. These things need to be repeated many times for people to appreciate them. This is an opportunity to do so, and the author apparently found it unimportant.
Would you recommend some resources that might help me more understand genome sequencing and its consequences? I too was thinking that the author could have go deeper and explain more in the article. I am computer scientists with high school biology knowledge.
I wonder about the novelty. He doesn't give very specific dates (was 'mid-January' this January, last January, or the January before that?) but does say
"The process, including my registration at an Illumina-sponsored seminar, cost $3,100."
Hasn't Illumina been at $1k/genome now for at least a year?
Illumina claims they can do $1k/genome using their latest HiSeq X Ten technology. But a miSeq or nextSeq cost more and produce less throughput. The author states ~70GB of data for $3.1k That could be two lanes of a MiSeq or a 1/4 lane of HiSeq (sharing with other samples); prices can vary by sequencing center.
The descriptions are accurate, but murky. One huge missing piece is a description of the structure of the genome. There is one mention of the word chromosome. The words haplotype and allele never make an appearance. There is no mention of the fact that we are diploid, nor that one copy of our chromosomes comes from each of our parents. Nor is there any hint as to the way that we share our genomes.
Maybe I'm allergic to assertions of novelty, but I don't enjoy his claim that he's the first journalist to get access to their "raw" genomic data. That's just being fancy. Is it necessary to say that? In any case, what's "raw" changes every few years, so someone else will soon get the chance to say the same thing. (I gripe, but I have to admit that it's nerdy/cool to see someone writing so much about BAM files :) !)
I'm still waiting for the first journalist to mention genome structure in a popular article on genomics. As badly as we need to understand what's going on in the genome, the public, and particularly professionals whose work brings them to articles like this, need to develop an intuition about how genomes work.