If the first, time to let that dead dog lie. It's a tired trope.
Any given group of humans will have a mixture of deceptive and trustworthy participants. Singling one group out for constant castigation, held against an impossible standard, makes it easier for dishonest members of other groups to avoid the spotlight.
How much of the reporting from the media revealed that Theranos was a fraud? Anything that wasn’t was fucking useless because it’s just a megaphone for corporate PR, despite what they think.
The entire concept of a weekly news is risible, let alone daily news. A fully investigated story actually worthy of the term journalism requires probably 2 employee years worth of actual work.
Look at how many articles the NYTimes publishes daily, multiply it by 700, and then compare that number with the actual number of journalists they have. It’s a complete farce.
They could do better, but until they do, it makes sense to castigate them when they err, because avoiding that reputational harm is their incentive to do better. Or, if they fail to do better, the thing that should ultimately kill them so they can be replaced with something that can do better.
While media companies have indeed "eroded their own credibility", in that there's a steady stream of falseness alongside truth, I would add with equal measure that "their credibility has been undermined by others". The loudest voices that castigate the media, in America at least, tend to be the ones that profit the most from being the sole arbiter of truth for their own audiences.
The business model of having an autonomous news room that holds itself to factual standards and is largely sequestered from advertising is shrinking and shrinking. I mourn its death, for I see no replacement coming along.
Since these journalists are spending their time on Twitter and never put a foot outside on the real world, no, I dont trust anything they say.
In large corporations it's effectively already dead, because many of the "trusted" names have already abandoned it, and you can't even tell which ones they are without being inside the newsroom to know if stories there get spiked on behalf of advertisers.
Where you can still get this is the likes of Substack, where you're paying a subscription to someone who doesn't have advertisers.
> The loudest voices that castigate the media, in America at least, tend to be the ones that profit the most from being the sole arbiter of truth for their own audiences.
That's to be expected when it benefits them. But their criticisms would sure have a lot less weight if they weren't accurate.
I think there's too much focus on advertising and corporate interests as the thing that undermines journalism. There's such a thing as to little focus, but right now there's too much focus.
For example, I have seen people lionize particular doctors, or researchers, or climate scientists, or what-have-you, who hold contrarian opinions on particular subjects. Clearly those people, in the minds of those who lionize them, have fewer conflicts of interest than advertising-driven journalists or powerful government officials.
The problem is that there are powerful motivations for people to lie or deceive that are equal in power to advertising money. Power through influence. Power through self-righteousness.
For example: I've looked into various vaccine conspiracy theories that have been touted online, and some of them come from highly credentialed people, sometimes with excellent historical track records in medical fields, who none-the-less are playing fast and loose with the data, or drawing conclusions that cannot be backed by research. The people who tout those theories look to those originators, those highly credentialed people, and say, "Look, there's Dr. So and So, they aren't part of Big Pharma, so they must be on to something". Then I look into Dr. So and So's blog, and look at the research they're citing, realize they're misinterpreting, or exaggerating, or what-have-you. In short, they are deceiving the public. They aren't financially motivated to do so. So why do they do it? Well, there's plenty of reasons. A desire to be right. A desire to be relevant and respected. A desire to have an audience. I think these things are easily as powerful, and often more powerful, than advertising money held over a journalist at a large media company.
And I see benefits to journalists working in groups with editorial control. I've seen great authors go astray in terms of quality when they start self publishing, or somehow become influential enough that they can shrug off their editors. I believe any journalist would be subject to the same forces of ego, influence, etc. If a journalist is making their money through Substack subscriptions, that may be even more of an existential threat than one faced by a journalist at the NYT, who can more readily absorb the financial hit of a story that goes nowhere. The subscribers, after all, now have expectations of what they will get from that journalist. Juicy stories -- at any cost?
35 years ago: https://www.nytimes.com/1987/12/13/magazine/the-genome-proje...
33 years ago: https://www.nytimes.com/1990/06/05/science/great-15-year-pro...
29 years ago: the competition gets fierce https://www.nytimes.com/1994/02/22/science/scientist-at-work...
24 years ago: the race is alive! https://www.nytimes.com/1999/03/23/science/who-ll-sequence-h...
23 years ago: draft is complete https://archive.nytimes.com/www.nytimes.com/library/national...
20 years ago: https://www.nytimes.com/2003/04/15/science/once-again-scient...
2 years ago: https://archive.nytimes.com/www.nytimes.com/library/national...
The celera approach using shotgun was tricky because assembling the bits required a great deal of computational finesse and horsepower; "The final assembly computations were run on Compaq’s new AlphaServer GS160 because the algorithms and data required 64 gigabytes of shared memory to run successfully."
At the time the GS160 was the monster machine, a classic big iron UNIX, which could be tightly clustered- unified IO/filesystem between all the machines. The primary author of the shotgun assembly was Gene Myers, who previously had written BLAST, and invented the Suffix Array with Udi Manber.
The public project had its own issues, as many of the teams assigned to work on it still had the "cottage industry/artisinal/academic" approach, then Eric Lander came along and turned it into an industrial process, and parlayed that into running the Broad Institute, a privately funded MIT/Harvard research institute in Boston.
These days petabytes of sequence data are generated every day and stored in clouds. The genome has been a fundamental tool for shaping our studies of humans, although its true potential for understanding complex phenotypes remains elusive.
So... um... BLAST processing?
As someone who is in the genomics world now as a software person, I find it amusing that I've gotten more into perl over the last year or so. It has its place, in the way that grep/sed/awk/etc does.
IMHO the person who "saved the genome project" was WJ Kent, who developed the assembler, BLAT, that the public project needed. I strive to point out that he wasn't a sole hero, nor was Lincoln. What I really like about BLAT is that while Celera was using Big Iron UNIX (massive 64-bit 64GB machines with 10s of terabytes of central high performance storage), BLAT ran on a cluster of linux machines, right around the time that people were waking up to the fact that linux was becoming a useful tool for scientific data processing. BLAT's design allowed it to work on a cluster of cheaper/smaller machines, while celera's algorithm really needed a massive shared memory single machine. it was sort of a microcosm of the larger battle being fought between Big iron UNIX and little intel linux at the time.
smaller organizations were realizing they could get slower computers power pretty cheap, and they could get a whole lot of them. There was a little flurry of activity with flocking algorithms, objective-c had a little renaissance due to swarm computing. probably the most famous and lasting was map-reduce, from alphabet, but they were called google back then.
there were a bunch of clever little tricks, like channel bonded network cards to make multiple cards look like one fast card, so you could double or triple bandwidth.
The beowulf cluster joke was kind of the spirit of the scrappy, make something cool out of junk approach while calling companies like sun, hp, compaq dinosaurs. and it continued for a while with people building stuff like this - https://ncsa30.ncsa.illinois.edu/2003/05/ncsa-creates-sony-p... I think there was some weirdness with export controls of ps2's for this kind of stuff.
I don't remember what pc chip was the new hotness back then, it was a good 20 years ago and my memory is dim.
but that, I think, captures the gist of the meme.
However, I got into the genomics world in the early aughts, and the perl hung on and on and on. I remember starting a new job in the mid-teens, and one of the first tasks I had was to port over a legacy perl script. Such is the world of scientific software. 99% of the people I know who have touched perl since ~2003ish are in the bioinformatics space.
And if I remember correctly BLAT was so useful because it could be run on machines with less cpu power by loading more data into memory…or was it the other way around?
> The primary author of the shotgun assembly was Gene Myers
And it is worth noting that despite all the critiques of shotgun sequencing at the time as "cheating", chromosome walking sequencing is dead, and shotgun is what we use today. If anything replaces that it will be long read technology like that done by Oxford Nanopore sequencing, although we aren't really there yet (you still need to assemble that data and don't really get end-to-end sequences yet).
And the cost of a T2T using a combination of these technologies is already well under $10,000 in reagent costs. The assembly is still a complex art especially for a messy chromosome like Y.
Does that mean that every possible polymorphism is accounted for?
Does that mean that 100% of possible polymorphic sites are known?
What about weird edge cases. You have a tandem repeat that is known, but in some small population of humans, there's two tandem repeats with an island of something else in there.
Imagine it like putting together a jigsaw puzzle, except that the picture on the front of the puzzle has lots of repeating motifs, so you end up with multiple pieces that look identical. You won't be able to tell how the whole thing fits together, but you can assemble the bits that are well-behaved and unique.
Modern technology gives us larger jigsaw pieces, which allows us to distinguish between almost-identical parts of the puzzle better. But I would note that the project linked did a huge amount of sequencing using very expensive methods to be able to resolve the whole thing.
Modern sequencing techniques allow us o read 200 to 500 bases at a time. So after hat we need do find a way o arrange these short sequences into a single sequence. And this can be prety hard, especially when you are doing 'de novo' assembly[0].
Besides that, there is the fact that some regions of DNA are repeated[1].
[0] - https://en.wikipedia.org/wiki/Third-generation_sequencing#De...
My knowledge cut-off period in this domain is around 2018. So it's not suprising that things moved on.
Because the sequencing uses short reads, it will not be able to resolve parts of the genome that are repetitive with a repeat unit longer than ~150bp. You'll have all the jigsaw pieces from the puzzle, but you won't be able to reconstruct some parts of the picture. Long read sequencing can help with those, but that's more expensive.
> The decoding is now close to 100% complete. The remaining tiny gaps are considered too costly to fill and those in charge of turning genomic data into medical and scientific progress have plenty to be getting on with.
OP is being silly. Nobody was fooling anyone.
http://news.bbc.co.uk/2/hi/science/nature/2940601.stm
> The remaining tiny gaps are considered too costly to fill and those in charge of turning genomic data into medical and scientific progress have plenty to be getting on with.
Ref: https://www.technologyreview.com/2007/09/04/223919/craig-ven...