Respectful Insolence

A crank attacks the Human Genome Project

The Human Genome Project (HGP) was one of the most massive scientific undertakings in recent years and, from a basic science and technology development standpoint, one of the most productive. The data gained formed the basis of the genomic revolution. And “revolution” is the right word. A mere 12 years after the human genome sequence was first published in papers in Nature and Science, we now have petabytes of sequence data pouring out of universities, research institutes, and genomics institutes. Sequencing a genome, which took several years to do for the HGP and cost billions of dollars, can now be done in days and costs in the tens of thousands of dollars. Before too long, it could cost less than $1,000, or at least well under $10,000, which would put it in the range of the costs of some tests and interventions that health insurance will pay for.

We now have the capability to measure simultaneously the level of expression of every gene in the human genome; in fact whole genome expression profiling seems like quaint technology. Seven years ago, when I published a paper that incorporated cDNA microarray data, it was cutting edge. Now, we have next generation sequencing (NGS) techniques, such as RNAseq, which is the common name for whole genome shotgun sequencing (WTSS). RNAseq overcomes the major limitation of cDNA microarrays, which is that it is only possible to measure the mRNAs whose sequences are known and therefore have been placed on the gene chip. Consequently, cDNA microarrays can’t discover previously unknown transcript and in general do not cover noncoding RNAs, such as microRNAs and long noncoding RNAs (lncRNAs). RNAseq does. As a result, using RNAseq it is possible to identify every sequence of every mRNA transcript, coding and noncoding, being made by the cell and how much. These sorts of techniques were recently in the news with the publication of a new set of results from the ENCODE project, which has led to breathless news stories about how “junk DNA” really isn’t “junk” at all and that 80% of it has function. This is a surprise only to creationists, who attack a straw man version of genetics and genomics, and, in fact, I might blog about ENCODE next week because, well, it’s fascinating stuff, and there’s been a lot of misinformation about it.

I am, however, tired. It’s late in the week, and it’s been a busier than usual week for me, particularly in the OR; so for now I think I’ll slum a bit. (Please forgive me.) And when I’m looking for something easy to blog about, there’s one website that almost always comes through. Well, actually, there are multiple websites that usually come through, but in this case, I’m going to look at NaturalNews.com, specifically a little rant not by Mike Adams himself (a.k.a. the Health Ranger, although in reality he should be called the Health Danger), but rather one of his minions, S. D. Wells, who decided that the HGP was a massive boondoggle. Now, disappointment with the HGP is not new. A round of stories asking “Where are all those cures the HGP promised us?” popped up in 2010, which was the tenth anniversary of the reporting of the HGP, and I duly commented on them. Basically, the HGP was necessary starting point, something that had to be done, before we could really dig into how the human genome works and figure out ways to intervene in diseases with a genetic component. Ten years was too short a time to expect a lot of “cures,” and in fact, as someone who is involved in this sort of research, I still find my mind boggling at how fast genomic techniques have progressed just over the last few years. Even so, it’s hard not to admit that there was some over-promising, but even so I feel the HGP was totally worth it.

Not Wells. In fact, Wells sees a vast conspiracy:

“To ferret out the genetic roots of common diseases like cancer and Alzheimer’s and then generate treatments” was the true goal of the 10-year, $3 billion human genome project, or was it? Geneticists who were paid a very pretty penny to study the genetics of disease are claiming they are “back to square one” in knowing where to look for the roots of these diseases, including heart disease and diabetes. But are any of them really diseases at all?

Cue ominous music.

Or was it? What was the real goal of the HGP, according to Wells? I’m beginning to wonder if Adams has found a protege, a potential successor, because Wells can lay it on almost as thick as Adams, and a quick Google search reveals numerous rants on not just NaturalNews.com, but Gary Null’s website, and numerous conspiracy websites about how The Man is trying to crush alternative medicine. With that background, it’s not surprising that Wells considers the HGP a complete failure, but not necessarily in the way you think, as Wells thinks it’s also a success in one way:

The National Institute of Health (NIH), an organization which actually does publish real findings, embraced the idea [of using the HGP to look for genes associated with disease]. But it looks as though the quackery of Western medicine took on the whole project in an effort to once again find cures just so it could bury them, before someone else comes along and claims they’ve found the same. This has been the trend since the United States hired Nazi scientists after WWII to design food additives and medicine (mustard gas chemo) which fuel cancer. (http://www.naturalnews.com/036484_Bayer_Nazi_war_crimes.html)

The truth of the matter is that the genome project was a huge success. Every gene and control element can now be mapped to its correct site on the genome, enabling all the working parts of the human system to be related to one another. But according to modern “disease-curing” science, it has turned out to be a dead end, a waste of time and money, a labyrinth with no exit, a boondoggle. Scientist who are paid off by the FDA, the CDC, and Big Pharma are very skilled at confusing the general public, with comments about the Genome Project like, “The only intellectually honest answer is that there’s no way to know.” This is the ultimate example of total intellectual property domination, where the answers are right there in our hands, but the chronic care industry won’t release them.

I do so love a totally unnecessary and unconnected argumentum ad Nazi-ium. Actually, I don’t. It’s the very reason I created the Hitler Zombie, lo those many years ago. However, Wells’ brain is far too thin a gruel to sate the hunger of the undead Führer; so I didn’t see this post as a suitable vehicle to resurrect His Undeadness again. This particular Nazi analogy feels too “tacked on,” anyway, as though Wells is trying too hard to find a way, however tenuous, to liken conventional medicine to Nazis.

It is a rather amusing idea, though. Think of it. Wells thinks that the government spent over $3 billion, used the efforts of hundreds, if not thousands, of scientists, and a spent a decade in order to sequence the human genome and then, having succeeded at that task, “buried” the results. Why would the government do that? It makes no sense, except in the fevered brain of a Mike Adams acolyte, who seems to think that the results were buried in order to keep people from finding out about “natural cures” for cancer and Alzheimer’s disease. Again, given the burden that these diseases cause in terms of care and lost productivity, it boggles the mind why the government would acquiesce to such a scheme, even if you believe that big pharma actually wanted it. In fact, there is a hint of an implication in Wells’ rant that in reality the HGP was a huge success for reasons other than using the information to find the causes of and cures for diseases with a major disease component. What could Wells mean? Well, there is an undercurrent in the alt-med crankosphere that the HGP is going to be used as a tool of eugenics. For example:

An even greater threat to mankind is that this technology will not merely be used passively to document existing genetic makeup but will be used actively and aggressively to create new sub—races of human beings specialized to perform certain tasks. Naturally—created children will find themselves competing against genetically—modified people that are stronger, faster, smarter, less constrained by feelings of empathy and more disease and stress resistant.

Although Wells doesn’t say this explicitly, I’m sure he knows about these sorts of paranoid conspiracy theories about the HGP. They’re all over the crankosphere.

I’ve written about the HGP before and how perhaps its potential for immediate cures was overhyped. Science is messy and doesn’t yield up its secrets that easily, particularly given how massively, incredibly complicated the human genome is, a complexity that the ENCODE project has reminded us of once again. Twelve years after the results of the HGP were published, only now are we starting to see the potential for uses of the fruits of the HGP.

Comments

  1. #1 mimi
    September 14, 2012

    Creationists could take a page from Francis Collin’s book. Francis Collins being the director of the Human Genome Project and a Christian.

    http://articles.cnn.com/2007-04-03/us/collins.commentary_1_god-dna-revelation?_s=PM:US

    In essence, God is the why, and science is the how.

    There seems to be, an alarming number of people who prefer to believe fantasy over science. Even in this country, the relative success of Rick Santorum attests to this frighteningly. Why was this man able to get so far when he stated that he could not believe that the earth was not the center of the universe? We have this candidate who believes that science is made up by the government control our way of life. (not trying to be political, but I think the success of the politician attests to the widespread mindset)
    http://www.freewoodpost.com/2012/03/15/santorum-tells-supporters-that-all-science-is-make-believe-and-the-sun-revolves-around-the-earth/

    Even among those who are not religious in evangelical christian terms have a deep fear Dr. Moreau style. Compound everything with the completely unethical scientific experiments that an insane totalitarian dictator (Hitler and the Nazi’s) coupled with a growing fear of “big brother” and we have seeds for disaster.

    This is fertile ground for cranks of all types. As many are ignorant of the truth, and as they receive it piecemeal are quick to dismiss it via cognitive dissonance.

    I don’t know if it’s the fact that I am growing older and so my perception is changed with each disillusionment, but it seems as if a growing number of people are believing the lie they want to hear above the truth.

  2. #2 Fragallrocks
    London, UK
    September 14, 2012

    Orac – I thought that the Encode project stated that upto 23% of the genome might have functionality. 3% genes and upto 20% regulatory regions? This article states upto 80% of the genome may have a function.

    Have I misread something in the ENCODE project or have the figures got mixed up in the article??

    The HGP was a massive multi national project that successfully delivered the outcomes that they initial went after. It brought together many research institutes and people so has an intrinsic value over and above the scientific value of the project itself.

    To many people have a utopian ideal that if something does not provide benefits (or ME with benefits) right now it is not worth doing. A very small minded idea that holds us back.

  3. #3 Dangerous Bacon
    September 14, 2012

    People like Wells are a sort of human genome project themselves.

    With appropriate recombination and gene therapy, perhaps their conspiracy-riddled brains could be adjusted into productive, critical thinking (cue ominous music).

  4. #4 Antaeus Feldspar
    September 14, 2012

    mimi, Santorum may be quite anti-science, but that article is satire. If you look at the site it appears on, that becomes quite clear. Headlines of other articles on the site include “Texas Bigfoot Sighting Turns Out To Be Shirtless Rick Perry” and “Paul Ryan Tells Crowd ‘Obamacare HERP DERP DERP'”.

  5. #5 palindrom
    September 14, 2012

    mimi @ 7:22 — As Antaeus pointed out, that Santorum article is satire, although like much great satire it’s plausible because it’s soooo close to reality.

    You also beat me to the Dr. Moreau reference. As I read that last paragraph, the 7/8-time intro to Devo’s “Are We Not Men?” burst into my consciousness.

    (As a memorable Onion “community voices” character said, “I have an I-pod ….. In my mind!”)

  6. #6 palindrom
    September 14, 2012

    The headline of another on the satirical Free Wood site: A TV listing that reads:

    Next Dr. Oz Episode: Are Your Oranges Full of Acid?

  7. #7 mimi
    September 14, 2012

    Oh dear! I have fallen victim to believing satire. How utterly embarrassing. Just proves my point about believing the lie you want.!

    I guess it wasn’t too far off from his beliefs on global warming and his statements about man and stewards of the earth.

    Now I must go remove the foot from my mouth..

  8. #8 Heliantus
    September 14, 2012

    @ Mimi

    Don’t feel too bad. I call Poe on this article. As you say:

    I guess it wasn’t too far off from his beliefs on global warming and his statements about man and stewards of the earth.

    Actually, is it really that far off? We are talking about people who literally believe that the planet Earth, and more precisely Man, is the center of God’s creation.
    I am tempted to argue that these types of anthropocentric science deniers do indeed believe that Earth is at the center of everything.

    Re: genome project

    Back on topic: a colleague gave me last week an article (from the journal Science) on the ENCODE project.
    We are specialized in protein identification (“proteomics”) and people from our field are regularly headbutting with people from the genomics field – in essence, people from my field think that genomics people are missing half the picture.
    But after reading this paper, I was not jealous that the spotlight went back on genomics. Actually, I’m giggling like a bunch of teenagers on nitrous oxide. Finding out that all this “junk” DNA is actually doing something, and having RNA strands suddenly involved in half a dozen new regulation systems, in the cell nucleus and outside? The potential implications are enormous.
    We may be talking about a revolution in our understanding of how a cell is working.

    Science. It works, poppyheads.

  9. #9 qetzal
    September 14, 2012

    Meh, I’m not that impressed with Wells. He does OK, but his conspiracy doesn’t really hang together well enough to have any staying power. He’s a bit like a schizophrenic who’s obviously very earnest about his conspiracies, but it’s too easy to see that they don’t make sense.

    I mean seriously. His thesis is that NIH wanted to ‘bury’ all the potential new cures hiding in the genome, so their brilliant plan was to sequence the genome and publish the whole thing where anyone could access it for free? Oh yeah, and then fund ENCODE to look at every single stretch of the genome for evidence of possible function, and then publish all of that data too. That’s his idea of burying it all?

    He should play up the genetically modified sub-humans conspiracy. I think that one might have some legs.

    @Fragalrocks

    The 80% figure comes from the abstract of the lead paper in Nature, which stated:

    These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions.

    In fact, it’s only 80% if you count ‘being transcribed into RNA’ as a biochemical function. Of course, just because some stretch of DNA is transcribed doesn’t mean that has a functional effect on the cell or organism.

    Unfortunately, while the ENCODE authors were careful about such distinctions in the body of the paper, they were less so in the abstract and in their discussions with the press. Thus, the general message has been ‘80% (and maybe more!) of the human genome has an important function.’

    That could be true, but their data doesn’t actually show that, and it would conflict with a lot that’s known about repetitive elements, transposons, promiscuity of DNA binding proteins, etc.

    There’s a pretty good discussion of this issue by John Timmer here.

  10. #10 Denice Walter
    September 14, 2012

    Orac notices a trend I’ve seen frequently: Natural News and PRN ( Gary Null) trade articles, the latter often showcases various efforts by reading them aloud amongst his original rants. There is also a Health Ranger show on PRN. Oh joy!
    ( also some sharing with AoA / Mercola/ Sayer Ji’s Green Med Info) Null is expanding his schedule because he seems to have been re-instated at a Washington DC radio station that is desperately in need of fundraising money.

    Wells has another article on Gary Null.com ( from Natural News ) about the “true history” of the AMA which was ” built on racketeering and the pocketing of ‘non-profit’ profits'”.

    Odd how frauds and liars like to point their fingers at others to distract from their own malfeasance and unsavory business operations.
    I see a lot of that. They also like to sue people.

  11. #11 rork
    September 14, 2012

    I’m sorry, but Collin’s ID opinions are an embarrassment. It’s plain old god of the maybe-that’s-a-gap junk. Could leprechauns have made tiny DNA changes in past generations of humans? I can’t disprove it.

    Trivially, second paragraph meant to say whole transcriptome shotgun sequencing rather than genome. Any reader that cared probably caught that though.

    Wells’ “scientists who were paid off” is about as crappy as anything I have ever read. We use that genome daily. Found an odd chunk or protein or mRNA, or found an amplified bit of DNA in someone’s tumor? You can figure out exactly where it came from, today. 20 years ago we had to go out there and clone the region, perhaps spending months to figure such a thing out. Interested in the promotor region for some cistron in humans – compare the region with what it looks like in rat, mouse, dog, chicken, fish, yeast. Holy schmoly can we get work done now.

    Take care in not over-selling RNA-seq. People aren’t saying what it’s problems are, only talking about it’s potential superiority. I’ve been having troubles that I think are due to failures of reproducibility of an amplification step in making the libraries – folks aren’t talking about it much. There are fragmentation steps to worry about too. Also it’s so expensive that I could have run a bigger set of samples on arrays and learned most of what I might have been looking for. There really is not a big problem measuring miRNAs either – several inexpensive methods work fairly well (Iillumina itself has a bead-array trick, or you do RT-PCR on plates). Can single-molecule attacks (Helicos) do better? It seems likely. Right now the experiments being designed also suffer from problems related to the expense – they suck for lack of biological replicates. Many papers make no estimates of their false-discovery rates, or if they do, I do not believe their estimates are accurate, since they ran no damn replicates. If it weren’t so “cool” these papers would get rejected. Also agree with quetzal – there is perhaps not a single base of our genomes that a DNA-directed RNA-polymerase doesn’t stumble over once in awhile, in either direction. People imagine it’s so orderly in there – I think it’s more like drunken sailors, and it’s amazing the ship floats. LINE1’s flying around like loose cannons, transcription factors binding in the deserts.

  12. #12 Bronze Dog
    September 14, 2012

    One thing I always bear in mind when I hear someone crying Gattaca: The conventional method of reproduction is too much fun. Artificial methods are kind of limited on that front.

    The other is that we don’t live in a sci-fi world. You can’t just turn all the dials to maximum to get a superior being. A lot of improvements would probably come with risks. I especially suspect this with regard to attempts at improving the human brain. You might get a genius, but he might have various neurological/psychological problems as a result of tampering with a delicate balance we weren’t aware of. Enhancing pattern recognition too much could lead to rampant apophenia, for example.

    And, of course, there’s the fact that genes aren’t destiny. Just because someone has enhanced muscle genes doesn’t mean he’s going to be inclined to exercise and build up those muscles. Likewise, someone with an enhanced brain isn’t going to have much of an advantage if he isn’t raised in an intellectually nurturing environment.

    Frankly, if someone tried to create a superman race, I’d more likely expect most of them to be underachievers with a sense of entitlement and psychological problems when they don’t live up to their parents’ inflated expectations.

  13. #13 kruuth
    September 14, 2012

    Orac, for once i have to disagree with you here…

    Coming out of IT and medicine, I can tell you that genetic sequencing WILL be part of medical insurance coverage and it will most likely, once optimized for mass production, clock in at well under $100 a person.

    Case in point–in WWII a computer with the processing power of a simple pocket calculator was the size of a building. During the 50s and 60s it was the size of a room. Then the size of a bus, then car, then refrigerator. When personal calculators came out they came in at $2000+(Wikipedia says the Friden EC-130 was $2200 and Sharp CS-10A was $2500) and were no way portable…needless to say, pocket calculators come in under 1 dollar today so there’s no reason that can’t happen to human genetic sequencing. The technology will get more and more refined, faster, and simpler to handle to the point where it may be done in the doctor’s office. Just my 2 cents.

    The rest of the article is great BTW.

  14. #14 Composer99
    http://composer99.blogspot.ca
    September 14, 2012

    Bronze Dog @12:50 pm:

    But… but… but… KHHAAAAANNN!

  15. #15 THE ONE TRUE GOD
    September 14, 2012

    ” one of his minions, S. D. Wells,
    who decided that the HGP
    was a massive boondoggle.”

    Hey! Only Craig Venter is supposed to say that!

  16. #16 rork
    September 14, 2012

    Kruuth: quote the part you disagreed with to help me find it, cause I think everyone agrees with what you are saying.

  17. #17 kruuth
    September 14, 2012

    Before too long, it could cost less than $1,000, or at least well under $10,000, which would put it in the range of the costs of some tests and interventions that health insurance will pay for.

    I agree it will be covered. My belief is that the cost will be much, much lower than Orac estimates.

  18. #18 Lawrence
    September 14, 2012

    @kruuth – eventually, but probably not in the short term….

  19. #19 Orac
    September 14, 2012

    Coming out of IT and medicine, I can tell you that genetic sequencing WILL be part of medical insurance coverage and it will most likely, once optimized for mass production, clock in at well under $100 a person.

    Uh, where did I ever say that medical insurance wouldn’t some day cover it? Let’s go to the tape:

    Sequencing a genome, which took several years to do for the HGP and cost billions of dollars, can now be done in days and costs in the tens of thousands of dollars. Before too long, it could cost less than $1,000, or at least well under $10,000, which would put it in the range of the costs of some tests and interventions that health insurance will pay for.

    Yep, that’s me, Orac, saying, to paraphrase myself, that it could well be not too long before the cost of sequencing of a genome is under $1,000 and that, even if it’s around $10,000 (which is the low end of what it is right now) that is within the range of what some tests and procedures cost that insurance companies pay for. I must admit, I’m puzzled at how what I wrote was interpreted that way. True, I did point out that proponents of the HGP overpromised, at least as far as how fast treatments would be developed from the information, and linked to a post that I wrote about that issue two years ago, but I never doubted that the information will one day be used clinically on a much more routine basis.

    Of course, the problem is that we still don’t know what to do with all that information; until the benefits of sequencing genomes and applying the information to personalized patient care are demonstrated in clinical trials, I’m not so sure that insurance companies will be eager to pay for the test.

  20. #20 Beamup
    September 14, 2012

    @ kruuth:

    Are you saying that you’re certain it will be in the $100 range so soon that “before too long, it could cost less than $1000″ somehow understates it so badly as to be “wrong?”

    Nothing in Orac’s quote implies that it will STOP there.

  21. #21 AdamG
    September 14, 2012

    until the benefits of sequencing genomes and applying the information to personalized patient care are demonstrated in clinical trials, I’m not so sure that insurance companies will be eager to pay for the test.

    I’d like to point out that these clinical trials are happening now. I’m involved with 3 of them in the Seattle area alone, all are actively recruiting participants and one already has several subjects enrolled and sequenced.

    This stuff is a reality, folks, and it amazes me every day that I live in such a world.

  22. #22 AdamG
    September 14, 2012

    For more info on some of the studies I’m working on check out this great slide set my one of the PIs involved in the project:

    http://www.genome.gov/Multimedia/Slides/GenomicMedicineII/GMII_GJarvik_ClinicalSequencingUW.pdf

  23. #23 herr doktor bimler
    September 14, 2012

    if someone tried to create a superman race, I’d more likely expect most of them to be underachievers with a sense of entitlement and psychological problems when they don’t live up to their parents’ inflated expectations.

    KIDS TODAY!!

  24. #24 herr doktor bimler
    September 14, 2012

    Wells:
    the roots of these diseases, including heart disease and diabetes. But are any of them really diseases at all?

    I am not going to follow the link and see what he believes heart disease and diabetes REALLY are, if they’re not diseases.

  25. #25 Alan Kellogg
    Way, way northeast of Oz
    September 14, 2012
  26. #26 Denice Walter
    September 14, 2012

    @ Alan Kellogg:

    We should all buy ourselves ear plugs before the shrieking -at AoA, TMR, PRN, Natural News and other woo-infused outlets- begins.

  27. #27 herr doktor bimler
    September 14, 2012

    have you read the story yet?
    Good press release; bad science.

  28. #28 Marry Me, Mindy
    September 14, 2012

    I see 3 problems from the press release:
    1) It calls autism hereditary – that’s of course. Wrong because autism is caused by vaccines
    2) The proposed cause does not involve heavy metals, and therefore cannot be treated by chelation.
    3) Lastly, since we know that no one is actually studying autism, the whole study never even took place in the first place, so it must be crap

  29. #29 Narad
    September 14, 2012

    I see 3 problems from the press release

    4) Funding from Big pHARMa.

  30. #30 Grant
    September 14, 2012

    Fragallrocks,

    I hope you’ve already got the picture, but the 80% is ‘some biochemical activity’ not if that activity is contributing to some higher-level function or not.

  31. #31 Alan Kellogg
    East of the Sun, West of the Moon
    September 14, 2012

    @ Edith

    Dyslexia can be treated, but first you must seek treatment.

  32. #32 Alan Kellogg
    North of the bull ring by the sea
    September 14, 2012

    “Denice! Denice!”

    And here I’m talking about dyslexia.

  33. #33 Mark McAndrew
    September 14, 2012

    Is that all it takes to get published by those clowns – plagiarising a sci-fi script?

    Can’t wait for the follow up: “McDonald’s burgers are made from people…”

  34. #34 Denice Walter
    September 14, 2012

    More on Natural News:
    Today the Health Danger ( good one, Orac!) informs us that because he selflessly provides the Truth about vaccines, chemotherapy, nutritional cures and fluoride, he has been UNDER ATTACK by Russian hackers hired by dastardly pharmaceutical companies and undermined by “internet terrorists” who sully his pristine reputation in an effort to censor him.( Does he mean US? )

    Mikey asks for his fans’ support:
    oh, how can they support him… let him count the ways: well, he outlines quite a few modes of cyber grovelling and arse kissing that will suit his purposes. He goes into detail.

    One of Mike’s claims to fame is ‘inventing’ an e-mail advertising software. I think I can ferret out this weasel’s way of managing the internet.

  35. #35 Johnny
    127.0.0.1
    September 14, 2012

    Today the Health Danger ( good one, Orac!) informs us that because he selflessly provides the Truth about vaccines, chemotherapy, nutritional cures and fluoride, he has been UNDER ATTACK by Russian hackers hired by dastardly pharmaceutical companies and undermined by “internet terrorists” who sully his pristine reputation in an effort to censor him.

    The thing is, it’s sorta true. The Russians are attacking his computer. Mine, too, along with your computer. The Chinese are attacking us, too. However, it’s mostly Romania, at least for me. Sometimes it’s government sponsored, but mostly it’s just hacker script kiddies. Learn to look at your firewall logs, and how to read them, and you’ll see it, too. It’s just what happens when you have a device connected to the Internet.

    Keep your firewalls up, keep your ports locked down, and your OS and virus definitions up to date. Be safe out there.

  36. #36 Narad
    September 14, 2012

    One of Mike’s claims to fame is ‘inventing’ an e-mail advertising software. I think I can ferret out this weasel’s way of managing the internet.

    Oh, dear, this was in my head somewhere, but I had left it in a dusty corner. I will credit him, based on what I have seen of the Arial Software pages, with promoting what seems to be a genuine opt-in model for such mail. Not that I’m convinced there’s no leaking around the cracks.

  37. #37 Narad
    September 14, 2012

    (And it looks like there was a design leak around the cracks.)

  38. #38 Midnight Rambler
    September 15, 2012

    The thing that no one mentions about the cost of sequencing a genome is, yeah you can do it for about $5,000 right now. But that’s just to get a pile of raw data. It doesn’t include the $50,000 you have to pay to hire a bioinformaticist for a year or so to actually pound it into shape. The cost of that part is going down much more slowly than the sequencing itself; in fact it’s going up because the amount of data that can be quickly and cheaply generated is skyrocketing.

  39. #39 Midnight Rambler
    September 15, 2012

    Also, it’s hard to believe so many people missed the joke on the Free Wood Post site, when it has a big banner at the top that says “News that’s almost reliable”. Though what they have Santorum saying is pretty close to what Andy Schlafly of Conservapedia believes, so Poe’s law obviously applies to some extent.

  40. #40 Bob G
    Los Angeles
    September 15, 2012

    The human genome project is an advancement in knowledge that provides part of the developing understanding of how cells work, how cells interact with each other, and how things can go wrong. The deep understanding of how biochemical pathways work in cells, how these pathways interconnect, and how they can generate different kinds of cancers is an outgrowth of the whole collection of developing knowledge bases.

    Compared to the 1970s and ’80s, when there was some developing understanding of regulatory pathways, but only the smallest understanding of genetic composition and regulation, the modern era is hugely different and has come with incredible rapidity.

    I’m not sure why the HGP has to be connected to clinical advancement all over the board in hardly any time at all. It’s like saying that the study of anatomy in Renaissance Italy was a failure because it did not immediately lead to open heart surgery. It’s fairer to say that anatomical understanding was one requirement for the development of modern surgery, and when anesthesia and the ability to avoid infectious contamination came around, anatomical knowledge was already in place.

    The HGP will be like that atlas of anatomy when the appropriate new understandings and techniques come along. Meanwhile, we have a whole new field of microRNAs to sort through. Twenty years ago, the concept didn’t even exist, and as of now, there are something like 120 review articles on microRNAs and breast cancer alone in the peer reviewed literature. This is an incredibly important line of research, and when you look at the literature about how microRNAs have come to be studied, you find that miRNA sequences were compared to the known human genome sequence, and out of that, the chromosomal origins and locations of miRNA genes came to be known.

    In other words, the HGP has allowed for the invention of whole new areas of understanding, and major new advances in older fields. I don’t see why anybody would have also expected it to be a clinical tool right off the bat. If it does happen that way, then this will be good luck. I wonder if the question is really just a matter of time and patience.

  41. #41 Grant
    September 15, 2012

    Midnight Rambler,

    Aside from the cost of bioinformatician [I’m one! – an independent consultant available for hire… ;-) ], and generalising here, at the moment a general-purpose computational screen would mainly only give specifics about particular rare diseases–the diseases that are dominantly predicated on just one or two alterations to genes or regulatory elements, etc.–or make general statements about increased or decreased odds for various things basis on correlations, with the issues correlations have. You could get a computational biologist (what I prefer to call myself rather than a ‘bioinformaticist’) to dig deeper if a person has particular (rare) disease features, etc. and you want to explore candidate genetic differences that might contribute to their disease, but that’s a long-odds game (one that has been done successfully at least once, though).

    Not saying there will be more informative analysis in time, just that I prefer to consider the current offerings a tad limited – there’s sometimes too much hype and I’d rather lean the other way, if anything.

  42. #42 janerella
    September 15, 2012

    My not so cerebral input on the subject – a nice, concise summary of the Encode project has been animated by the storm team and narrated by the awesome Tim Minchin…

    http://www.youtube.com/watch?v=TwXXgEz9o4w&feature=player_embedded

  43. #43 mimi
    September 15, 2012

    Thank you Midnight Rambler for further trying to ridicule me after I have already admitted my mistake and embarrassment..

  44. #44 fragallrocks
    london, uk
    September 15, 2012

    Qrtzel and grant – Thanks for the responses guys. I thought I must have had it wrong. It has Benn s decade since my biology degree and I am clearly a bit rusty!!

  45. #45 Ken
    Madison
    September 15, 2012

    Naturally-created children competing with genetically modifed children?

    To paraphrase Al Pacino:

    “Gattica! Gattica! Gattica!”

  46. #46 Denice Walter
    September 15, 2012

    OT – but what the hey, it’s Saturday…

    Gary Null and Jeremy Stillman have a new article ( @ Gary Null.com) :
    Shilling for Big Agra: Challenging the Stamford (sic) Report’s Conclusion.

    Are they talking about the town of STAMFORD? Or could there possibly be a STAMFORD University founded by a Mr STAMFORD or named for a Mr STAMFORD Leland ?

  47. #47 Mephistopheles O'Brien
    September 15, 2012

    DW – Doubtless the study was named for Sir Thomas Stamford Bingley Raffles, founder of Singapore. The bar in the hotel named for Raffles was where the cocktail “Singapore Sling” was invented. As the Singapore Sling contains pineapple juice, which is an agricultural product, the report was named after Raffles as well.

  48. #48 Johnny
    127.0.0.1
    September 15, 2012

    More on Natural News:
    Today the Health Danger ( good one, Orac!) informs us that because he selflessly provides the Truth about vaccines, chemotherapy, nutritional cures and fluoride, he has been UNDER ATTACK by Russian hackers hired by dastardly pharmaceutical companies and undermined by “internet terrorists” who sully his pristine reputation in an effort to censor him.( Does he mean US? )

    He might mean us, but I suspect that he’s just managed to take a look at his firewall logs.

    The sad truth of the Internet is that any connected device is going to be probed, often several times a day, by people looking to break into it. Some time it’s just kids, often it’s crooks, but on occasion it’s state sponsored. My firewall logs show Russia, China, Ecuador, and, mostly this week, Romania.

    It’s the equivalent to somebody walking down the street trying every doorknob, hoping one is unlocked.

    Only the truly paranoid would take it personal, but that doesn’t mean you should ignore the threat. Keep your OS and virus definitions up to date, check your firewalls now and again to make sure they are still on and working, and close down any unnecessary ports. Be careful out there.

  49. #49 Grant
    September 15, 2012

    Ken,

    “Gattica! Gattica! Gattica!”

    The Gattaca sequence has mutated to have inosine?? :-)

    Or perhaps they mistook a tRNA for a DNA fragment??

    Sorry, can’t refrain from playing with this…

  50. #50 Kathryn
    Valley of the Superfund Sites
    September 16, 2012

    Regarding the study Alan linked to, it’s another (*^&(#$^ “autistic mouse” study. See Item #8 on science writer Emily Willingham’s list of 10 things to keep in mind when reporting on autism studies.

    http://www.emilywillinghamphd.com/2012/08/writing-about-autism-science-10-things.html

    I maintain, as always, that brain development in humans is subtle enough that efforts to tinker with it are FAR, FAR likelier to cause worse effects than the disorder we are trying to prevent. How do we keep from altering the balance of neuronal growth too far in the other direction? Perhaps something that doesn’t show up in mice, or perhaps researchers weren’t even looking for more than the absence of “mouse autism.” Perhaps something as subtle as taking someone who could be the next Alan Turing and making them a dumb jock instead.

  51. #51 kruuth
    September 16, 2012

    My apologies Orac, I agree with you on tat it will be covered. I’m of the belief that it will be much, much cheaper that’s all.

  52. #52 Denice Walter
    September 16, 2012

    @ Johnny:

    You are, of course, right BUT MIkey Adams does believe that sceptics are trying to make him look in-expert and untrustworthy. Obviously, we have no need to do so because he is quite efficient at producing that effect all on his own.

    In truth, he is often a source of amusement- however when we remember that his bad ideas influence real people to avoid SBM, we know that he isn’t just a joke.

  53. #53 Koen Perdieus
    Belgium
    September 17, 2012

    By the way, Mr.Wells isn’t the only one with a gripe about the Human Genome Project…
    popperfont.net/2012/09/11/angry-words-from-a-gnome-who-to-this-day-continues-to-think-the-human-genome-project-was-actually-the-human-gnome-project/

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