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Junk DNA and really bad timing

The NYTimes has an article about a “flotilla of papers” that are coming out on Junk DNA.  Junk DNA was, up until recently, thought to be just irrelevant pieces of DNA that hitched a ride with the real genes in your body.  As it turns out, they’re much more important than that:

As scientists delved into the “junk” — parts of the DNA that are not actual genes containing instructions for proteins — they discovered a complex system that controls genes. At least 80 percent of this DNA is active and needed. The result of the work is an annotated road map of much of this DNA, noting what it is doing and how. It includes the system of switches that, acting like dimmer switches for lights, control which genes are used in a cell and when they are used, and determine, for instance, whether a cell becomes a liver cell or a neuron.

In one of the Nature papers, researchers link the gene switches to a range of human diseases — multiple sclerosislupusrheumatoid arthritisCrohn’s diseaseceliac disease — and even to traits like height. In large studies over the past decade, scientists found that minor changes in human DNA sequences increase the risk that a person will get those diseases. But those changes were in the junk, now often referred to as the dark matter — they were not changes in genes — and their significance was not clear. The new analysis reveals that a great many of those changes alter gene switches and are highly significant.

“Most of the changes that affect disease don’t lie in the genes themselves; they lie in the switches,” said Michael Snyder, a Stanford University researcher for the project, calledEncode, for Encyclopedia of DNA Elements.

So, you might ask how we missed the importance of junk DNA while we were doing all that sequencing and stuff.  To understand how junk DNA functions, we have to stop thinking about DNA as a 1 dimensional string of letters (A, T, G, C) and start thinking about it as a three dimensional object.  Picture a spiral telephone cord, if you’re old enough.  Remember what happened to that sucker when it got twisted?  It kind of bunched up?  Imagine that cord wrapped around an octet of soccer balls called a histone.  And then those octets are twisted and assembled into a chromosome and we all have 23 pairs of chromosomes.  Here’s a pic from the EMBL (European Molecular Biology Laboratory) blurb on the ENCODE papers:

When a cell has to transcribe or duplicate a gene, it has to unwind parts of that structure to locate the string of nucleotides to work on.  That part everyone knew.  But there were long strands of material that didn’t seem to perform any function in the gene sense- until they were twisted.  Then, the location of the junk DNA to the gene that was actually transcribed made sense.  The Junk DNA can affect the transcription of the gene because it is functional when the DNA strand is twisted and puts it proximal to the gene of interest.  Proteins work in a similar way.  In a 1 dimensional sense, the sequence of amino acids is meaningless.  It’s only when a sequence is twisted into its 3 dimensional shape that the right amino acids come in contact with or form functional relationships with each other.  When the amino acids are stretched out, the important amino acids may be far apart from each other on the string and do not look like they relate to one another.  It’s only when you compare sequences of related proteins that you see the patterns that indicate the active site of the protein.

Anyway, this is kind of a big deal and I will probably scoot on down to Princeton’s library to read some papers on the whole thing.  There will be reams and reams of data.  This could be very important to cancer research because recently, we have been looking for biomarkers, genes that are common for a particular cancer, and the results have been ambiguous.  But if junk DNA can explain why some genes get switched on inadvertently and others don’t, that might open up a whole new area of drug research.  It’s the kind of thing that people like me and my former colleagues could probably be retrained to do pretty easily.

Unfortunately, industrial R&D has been laying us off left and right and upside down and academia does not have the funds to absorb us.  So, here we are, all kinds of data and no place to go.

I suppose we *could* just work without pay and be selfless and shit.  But there are already people doing that and besides, at some point, our kids need caloric intake as much as any banker’s brats.

Anyway, this discovery comes at a really bad time for the life sciences professional.  It’s not like we’re not out here.  Structural unemployment is NOT the problem.  And this kind of research can be done from the home office so no one even has to move.  It’s just that no one wants to pay for it.

I love this bit of the article:

The new result “is a stunning resource,” said Dr. Lander, who was not involved in the research that produced it but was a leader in the Human Genome Project. “My head explodes at the amount of data.”

Yes, I’m sure all of our heads will explode.  There are more than enough projects to keep every scientist I know over their heads in work for generations to come.  It’s such a shame that hundreds of thousands of us aren’t doing it because some rich assholes in the finance industry see research only as a money pit.

It’s an even worse shame when the political parties either don’t want to acknowledge or don’t care that our scientific industry is dying in this country.  If there was ever a reason for the government to invest in a jobs program that would put thousands of people back to work, this would be it.

By the way, this article in Slate about how wonderful the job market is for the STEM PhD is total bullshit.  I’m living in ground zero where PhDs are getting laid off all around me on a daily basis and most of them regret they ever chose science as a career.  They love science but they sure don’t like being the new precariats, overworked, overeducated and expected to suck it up when they get laid off.  It tends to cool one’s enthusiasm for the lab pretty quickly.  Many are getting out of science altogether and are training to become teachers (probably expected to work without pay) and lawyers.  That’s in addition to their PhD.  This stupid article is how the structural unemployment crap gets spread and it’s pretty unbelievable to those of us who are living through the nuclear winter of the R&D industry.

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10 Responses

  1. I LOVE this. Do you think they’ll have to come up with a new name for the stuff now?

  2. Many are getting out of science altogether and are training to become teachers (probably expected to work without pay).

    Virtually all of these new, “second-career” teachers will be permanently assigned to high needs schools as well. Their students are dealing with many, many issues in their lives, so these new teachers better clearly understand this, understand that they are working with teenagers, not adults, and understand that their workload will be much heavier than they ever had at their old pharma job.

    Also, due to extremely tight budgets, the science departments of these schools are, with few exceptions, poorly equipped, so these teachers will be expected to spend some portion of their own salaries on laboratory consumables and other supplies for their classes. Every semester.

    • And yet, it sure beats no salary at all. So, you know, there’s that…

      • Oh, no doubt. Honestly, the basic salary and benefits usually are OK in public high schools, because the teachers are unionized, and the salary scale is significantly higher for teachers who come in with a Ph.D. You get even more money for being advisor to an after-school club, or an assistant coach for a sports team.

        What wipes out so many new “second-career” teachers, though, is not low salaries, but the shock of working in a place with poor infrastructure, overcrowded classrooms, and very high-needs students who are “testing” you all the time. Classroom management can be very challenging; it’s very, very easy for a new teacher to lose control of one or more of their classes in such an environment.

        • Again, steady, reliable salaries tend to have an invigorating effect on acquiring classroom management techniques.
          And have you been to an academic lab these days? {{shudder}}

          • They do, but the most important thing to have is real empathy for the overall situation that high-needs students are in. Teaching high-school science to high-school teenagers whose reading and math skills are at the mid-primary school level is…interesting, to say the least. You have to recognize that you have to work with what you’ve got, and plan your lessons, and your methods of evaluation, accordingly. Flexibly respond to the needs of the moment, with humor and empathy.

            That’s the ticket for surviving and thriving as a teacher in a high-needs school

          • I’m fairly certain that many of my former colleagues a.) have adolescents of their own and b.) did a fair amount of science fair and classroom demonstrations.
            Not all of them want to be science teachers but the ones who do know what they’re getting into.
            I should add that my daughter’s 8th grade math teacher was a former engineer for Lucent and he was excellent. Some people just have a knack for it. They just didn’t know it until they were furloughed from their original profession.
            If I were traditionally educated secondary ed science and math teachers, I would be very concerned about the new competition.

  3. It’s misleading hype, compounded by disingenuous obtuseness on ENCODE’s part. 80% is the fraction of the DNA gets transcribed to RNA, irrespsective of whether that RNA ever does anything.

    The actual ENCODE extimate for functional DNA is 9%-20%, which would make the genome between 80% and 91% junk, basically the opposite of how the press is reporting the results.

  4. I spent the last few years believing that this DNA should be referred to as “dark DNA” the way we refer to the mystery matter all over Deep Space which we don’t understand yet as “dark matter”. We don’t know what it does, but we rightfully suspect it does something.

    Same for Dark DNA.

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