For sale: One castle. Three bedrooms, three bathrooms, one ghost.

I've said for ages that I would love to spend a night in a haunted house.

I would prefer not to spend said night alone, because I may be a skeptic, but I'm also (1) highly suggestible and (2) a great big coward.  I'd like to think that my generally rational view of the world would inoculate me against jumping to conclusions in scary situations, but the reality is that I adopted skepticism as a worldview largely because the other option was letting my anxiety drive me completely batshit crazy.

Anyhow, this all comes up because yesterday I stumbled upon a haunted house for sale.  Actually, not a haunted house; a haunted castle.  Better still, it's right here in the United States, obviating the need for my obtaining a resident visa from one of your usual castle-having nations.  (Although in all honesty, given the current administration, I've been considering emigrating to a small uncharted island off the coast of Mozambique anyhow, even though small uncharted islands rarely have castles, haunted or otherwise.)

This particular haunted castle is Beckett Castle, in Cape Elizabeth, Maine.  Cape Elizabeth is right on the Atlantic Ocean -- another appealing point -- and is an easy drive from Portland.  This is a definite advantage, because for much of Maine, the only thing you're in an easy drive from is a shitload of spruce trees.  So the site is pretty much ideal.

Beckett Castle was built in 1874 by the eponymous Sylvester Beckett, who was a lawyer, writer, and publisher.  It has 1,981 square feet of living space, which strikes me as a little small for a castle, but after all, Maine is not generally considered castle country, so I guess you take what you can get.  It has three bedrooms, three bathrooms, and -- best of all -- a three-story tower.  It's built of local gray fieldstone, but has been recently "extensively remodeled," so it doesn't feature the usual downside of castles, which is lack of indoor plumbing.

It also has a huge rose garden and a "carriage house" that would be perfect as an artist's studio, so Carol would be happy.

Of course, there's the "haunted" part.  Paul Seaburn, over at Mysterious Universe, says that the "primary ghost" is Sylvester Beckett himself, which brings up an interesting question; how do you get appointed "primary ghost?"  Does the class system transfer directly into the afterlife?  Because that hardly seems fair.  You spend your whole life working your ass off as a servant, then you die and become a ghost, and damned if you're not still scrubbing the floors in spirit form.  If that happened to me, I'd say, "fuck it," and leave.  I mean, what are they going to do?  Withhold my ghostly paycheck?  Write a bad letter of reference for the next place I'm planning to haunt?  They could get as mad at me as they want.  I mean they couldn't even kill me, because I'm already dead.

Seems like a nice position to be in.

But I digress.

The previous owner, Nancy Harvey (who died in 2016; her family is handling the sale) was interviewed prior to her death and went on record as saying that she'd never had any paranormal experiences in the place, despite Sylvester's reputation for appearing as a "radiant blue orb" and pulling the sheets off you while you sleep.  Harvey, however, didn't attribute this lack of ghostly goings-on as evidence that the place wasn't haunted; she said that Sylvester didn't disturb her sleep because he was happy about the renovations she'd done.

I guess even when you're a ghost, you care that people are keeping your house in good shape.

Unfortunately, I don't think I'm going to put an offer on Beckett Castle, as attractive as it seems, for the very good reason that the asking price is $2.5 million.  I just don't have that kind of cash lying around.  Plus, I'm not known for my housekeeping skills.  Most of the time, my approach to housekeeping can be best summed up as "There appears to have been a struggle."  One friend said the interior of my house looks like "a museum maintained by toddlers."  So buying Beckett Castle seems to me to be asking for Sylvester to come back and rip the sheets off my bed at one AM and demand to know why I didn't do last night's dinner dishes.

It's a pity, because the place is beautiful, and it's a great location.  But I think for the foreseeable future, we're going to stay here in upstate New York.  If our current house is haunted, I've seen no evidence of it.  Or maybe the ghosts were people who, when they were alive, were also terrible housekeepers, and are happy the place is owned by kindred spirits (as it were).  That'd also explain it.

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This week's book recommendation is the biography of one of the most inspirational figures in science; the geneticist Barbara McClintock.  A Feeling for the Organism by Evelyn Fox Keller not only explains to the reader McClintock's groundbreaking research into how transposable elements ("jumping genes") work, but is a deft portrait of a researcher who refused to accept no for an answer.  McClintock did her work at a time when few women were scientists, and even fewer were mavericks who stood their ground and went against the conventional paradigm of how things are.  McClintock was one -- and eventually found the recognition she deserved for her pioneering work with a Nobel Prize.

Take my hand

Today I'm going to take a detour from my usual fare and tell you about a former student of mine, a young man named Justin.

I first met Justin in my Critical Thinking class, almost two years ago.  He struck me right away as the thoughtful type (in both senses of the word).  He was quiet, friendly, and kind, and always was the first one to laugh at my jokes (which may speak to his kindness as well).  As the semester progressed, he was more and more willing to contribute to class discussions, and what he said never failed to be articulate, interesting, and well-considered.

He tuned in right away on my obsession with UFOs and Bigfoot (not that hard to discern, really, considering the various Roswell-and-Sasquatch-related paraphernalia strewn about my classroom).  He started ferreting out good examples of goofy paranormal claims -- I used more than one of his finds as a basis for a Skeptophilia post -- and I still remember when he took me up on my offer to the class of an optional assignment to use PhotoShop to make the most convincing fake paranormal photograph they could.  His submission -- a wildly creepy double exposure that looked like a ghost floating over a country road -- stayed on my wall for the rest of the year.

So I was glad to see that he'd signed up for my AP Biology class this past school year.  He continued in much the same fashion, participating in a quiet, understated sort of way, coming in early to discuss the latest science fiction movies, asking good questions.  Not a boy who was a splashy presence, but someone who was steady, smart, and pleasant, the kind of student most teachers would love to fill a class with.

Justin graduated from high school six days ago.  I saw him that Thursday evening, laughing with some friends in their caps and gowns, and he asked me to take their picture with his cellphone.

That was the last time I saw him.  Three days ago, Justin committed suicide.

My first thought, when a colleague called me up at 9:30 Monday night to tell me the news, was, "How could I have missed the signs?"  Justin never exhibited the slightest sign of depression to me.  No moodiness, no sudden disinterest in classwork, no distancing himself from friends.  All year long, he was the same constant, easy-going person, almost always with a smile on his face.

Of course, I know from first hand experience that my reaction was ridiculous.  Since his death, I've heard from a couple of colleagues that he'd had bouts of depression, had contemplated suicide, but in the past months had seemed so much better.  One friend, who was especially close to him, said, "I honestly thought he was in the clear."

So did we all.  But we depressives are chameleons.  It's what we do best.  And I use "we" deliberately; I've had serious depression and anxiety as long as I can remember, and until I went public with it -- I first blogged on my own personal struggles about four years ago -- I'd bank on the fact that no one knew.  I never missed work, never seemed down, never did a sudden radio silence.  If anything, people described me as dependable and reliable, and most of all, competent.  I never acted as if I needed help.

The truth, of course, is that a good part of the time, it was a struggle even getting myself to work.  Once there, I put the happy-mask on -- because I was expected to.  Taking charge is part of my job.  Even when I was at my lowest, during the breakup of my (all things considered) disaster of a first marriage, hardly anyone knew what was going on.  To admit it, in my depressive state, was somehow to give it more reality.  Easier to pretend it didn't exist, that my life was just hunky-dory, thank you very much.

So it's not to be wondered at that a lot of us didn't know what was going on with Justin.  Still... I wish I had.  Maybe had someone known, we could have made a difference.  I know hindsight is 20/20, and all that, but suicides always leave the survivors playing out what-if scenarios, as pointless as they are, as unfair as they are to everyone concerned.

But it does highlight that it's absolutely critical we look after each other.  Our society has taught us that going it alone is some kind of virtue, that to ask for help is to appear weak or needy.  We pretend we're fine when we're falling apart, and our closest friends often don't know.

So reach out to the people around you.  Treat people with compassion, even those who don't seem to deserve it; sometimes those are the ones who need it most.  Don't forget to check in with the strong ones, the competent ones, the quiet-but-steady ones, who may not be showing you what they're really feeling -- not until you push them to dig deeper.

And don't forget the Suicide Prevention Lifeline Number, 1-800-273-8255.  If you're hurting, and it seems like you can't keep going, give them a call.  If you have a friend or family member who is in crash-and-burn mode and don't know how to help them, give them a call.  Don't go it alone.  You don't need to.

Because -- as I found out in my case, having attempted suicide twice, once when I was 17 and once when I was 20, when things looked completely hopeless -- the only thing suicide ensures is that things won't get better.  Whatever's gone wrong for you, you can survive it, if you're willing to put out your hand and say, "Please help me up."

[Image is in the Public Domain]

I always try to remember the adage that a family friend told me when I was six.  I was whinging about some classmate that I didn't like, and this friend -- instead of commiserating -- bowled me over by saying, "Always treat people with more kindness than you think you need to, because everyone you meet is fighting a terrible battle that you know nothing about."  I've never forgotten it.

And to Justin, who lost his terrible battle three days ago: I will always remember you as a kind young man with a fine mind and a ready smile.  I, and your friends and family, will miss you dearly.  I wish I could have helped you, but perhaps, if your life and death push someone else to reach out for help, it won't have entirely been in vain.

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This week's book recommendation is the biography of one of the most inspirational figures in science; the geneticist Barbara McClintock.  A Feeling for the Organism by Evelyn Fox Keller not only explains to the reader McClintock's groundbreaking research into how transposable elements ("jumping genes") work, but is a deft portrait of a researcher who refused to accept no for an answer.  McClintock did her work at a time when few women were scientists, and even fewer were mavericks who stood their ground and went against the conventional paradigm of how things are.  McClintock was one -- and eventually found the recognition she deserved for her pioneering work with a Nobel Prize.

The devil on my shoulder

Me, trying to find a topic for today's Skeptophilia post:  Hmm.  Let's see, what do we have in the news today.  *sips coffee*  Science news, political news, religious news...

Diabolical voice from on my left shoulder:  How about Alex Jones?

Me:  No, everyone knows that Alex Jones is a certifiable wingnut.  Why would I want to...

Diabolical voice:  No, really.  You need to check out what Alex Jones just said.

Me (scowling angrily):  Why?  Everything that comes out of the man's mouth is either complete lunacy, or a desperate plea for attention, or both.  It's total clickbait.  I don't want to...

Diabolical voice:  C'mon.  You know you want to.

Me:  I'm sure there are much better things for me to be reading, not to mention writing about.

Diabolical voice (alluringly):  Alexxxx Jonnnessss...

Me:  Well, I don't know, it seems like a waste of time, but maybe...

Diabolical voice (in a whisper):  Take the bait, little mouse... take the bait...

Me:  Oh, fine, I guess one quick look won't hurt me.

Alex Jones:  Atrazine does have the same effects in mammals as it has in frogs.  And it changes areas of the brain associated with the olfactory nerve.  That's the nose, my friend.  That's the part of your brain that hooks to your nose.  And everything else that make men feel attracted to other men...  The Pentagon developed a Atrazine-type spray that they would spray.  They tested it actually in Iraq.  That's classified but it was -- it got leaked.  You can pull it up.  Gay bomb!  They always take like a clip of me going gay bomb, baby!  And then I show BBC, but they cut the BBC, and it's basically a chemical cocktail, not just of Atrazine.  They add some other chemicals.  It's classified.  But the word is, it's like, what's ecstasy's compound?  I forgot.  MDMA!  They mix that with Atrazine and stuff.  And then they spray that on you and you'll start having sex with a fire hydrant...  I mean, the point is, is that sex is all based not even on visual, men it's mainly -- but it's smells with women particularly.  But they can flip that on.  It's like perfume.  You know, everybody knows about that?  Well, they've got weaponized perfumes, basically that will make men attracted to other men and they want you to do that so you don't have kids.

Me (eyes spinning):  Yes... gay bombs... weaponized sex perfumes... mixed with atrazine and stuff...  "olfactory" means "nose," my friend...  guys humping fire hydrants...  It all makes so much sense, now!

Diabolical voice:  See, isn't this better than some silly story about new advancements in science?

Me:  ... thank heaven for Alex Jones, for having figured all this out!  Otherwise I might have inhaled some atrazine mixed with MDMA, and suddenly gotten the hots for that guy who lives down the street, which would make my life all higgledy-piggledy!  And if he turned me down, I'd have to look for a fire hydrant!

Diabolical voice:  Lucky you have me around, isn't it?

Me:  Really lucky.

Diabolical voice:  Next up: Rudy Giuliani explains how being loudly booed at Yankee Stadium means everyone loves him.

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This week's book recommendation is the biography of one of the most inspirational figures in science; the geneticist Barbara McClintock.  A Feeling for the Organism by Evelyn Fox Keller not only explains to the reader McClintock's groundbreaking research into how transposable elements ("jumping genes") work, but is a deft portrait of a researcher who refused to accept no for an answer.  McClintock did her work at a time when few women were scientists, and even fewer were mavericks who stood their ground and went against the conventional paradigm of how things are.  McClintock was one -- and eventually found the recognition she deserved for her pioneering work with a Nobel Prize.

Probing the scientists

Because we clearly needed something else to be angry about, today we have: a cadre of four senators who are calling for an investigation into the National Science Foundation's grant program designed to educate meteorologists about climate change.

The four senators are James Lankford (Oklahoma), Rand Paul (Kentucky), Ted Cruz (surprise! -- Texas), and James Inhofe (even bigger surprise! -- Oklahoma).  Inhofe, you may remember, is the knuckle-dragger who doesn't know the difference between weather and climate, and illustrated the fact by bringing a snowball onto the floor of the Senate and presenting it as evidence that the world wasn't warming up.

Along the same lines, every time Inhofe eats dinner, world hunger goes away for a while.

The four drafted a request for a probe into the NSF's Climate Central program, stating that it was "not science -- it is propagandizing."

My question is: what would it take to make the NSF's stance on climate "science?"  Saying that fossil fuels are great for the environment because plants like carbon dioxide?  That dumping coal ash into streams -- now completely legal in states that do not have a standard "maximum contaminant level" for water, and have demonstrated the need for "regulatory flexibilities" -- is perfectly safe?  That we should all be optimistic, because even if it does warm up, it'll make the Alaskan tundra nice and toasty warm?

These four -- and others like them -- have zero respect for science.  Science, to them, is what is expedient for their constituents and (especially) the lobbyists who fund their campaigns.  They've somehow confused "peer-reviewed valid science" with "science that aligns with the way I'd like the world to work."

And anything that doesn't align in that fashion is summarily dismissed.  Can't have the universe be inconvenient to your preconceived biases, after all.

[Image licensed under the Creative Commons Welp.sk, Air pollution, CC BY-SA 3.0]

Ben Strauss, CEO of Climate Central, was (understandably) livid at the impending investigation.  "Climate Central is not an advocacy organization, and the scientific consensus on climate change is not a political viewpoint," Strauss said in an email to NBC News.

Which, I predict, will have exactly zero effect, given that Scott "Fuck Ethics" Pruitt, who said last year that "Science should not be something that's just thrown about to dictate policy in Washington, D. C." is still in charge of the Environmental Protection Agency, despite having amassed more allegations of misconduct in his short tenure than any other appointed or elected official I've ever seen.

So if we shouldn't use science, what should we use to dictate policy?  Astrology?  Divine inspiration?  Thoughts and prayers?

The anti-science bent goes all the way to the top, given that every time any science-related subject is brought up with Donald Trump, he gives evidence of having maxed out his science education when he outgrew My First Big Picture Book of the Universe in second grade.  All you have to do is look at the list of appointments he's made to high government positions to convince yourself that if you're a anti-intellectual young-Earth creationist, you've got a good shot.  (Just to mention one particularly egregious example: Teresa Manning, who was deputy assistant secretary of the Office of Population Affairs, went on record as saying that contraception "does not work to prevent pregnancy."  After making use of the revolving door Trump has installed in all of the government offices, Manning was replaced by Diane Foley, who said that teaching teenagers how to use condoms correctly was "sexual harassment."  Foley's qualification for the post seems to be her tenure as president and CEO of "Life Network," the mission statement of which is to "present the gospel of Jesus Christ.")

I know I'm prone to hyperbole at times, but I don't think it's overstating the case to say that the people in charge right now wouldn't know a valid, evidence-based scientific argument if it walked up and bit them on the ass.

I'm finding it harder and harder to stay optimistic, here.  The pro-Trump faction, along with their answer to a North-Korea-style state sponsored media (Fox News), have done their job too well.  When we've devolved from respecting the research of the people who actually understand how the world works to accepting whatever Rush Limbaugh and Ann Coulter and Sean Hannity say without question, we've entered a realm where facts -- hell, reality -- doesn't matter.  As I've said before, once you teach people to doubt the data, you not only can convince them of anything, no logical argument you could craft will ever change their minds.

As a long-ago environmental science student of mine said, things are going to have to get a whole lot worse before people will wake up.  We've already seen prolonged droughts, killer storms, blistering heat waves, and various other weather weirdness that (taken together) form a pattern that is incontrovertible.  But for most people in the United States, it hasn't become dire enough yet.  We can still sit in our comfortable homes, go to the grocery store to pick up food, turn on the tap and get clean water, cool things off with air conditioning.

Once those things start being affected by climate change -- when we get jolted out of our complacency, and say, "Hey, maybe the scientists were right after all!" -- I'm afraid it will be too late to do anything.

Which is just what Paul, Lankford, Cruz, and Inhofe want.  They're just counting on it being delayed long enough for them to retire with cocky grins and full bank accounts.

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This week's book recommendation is the biography of one of the most inspirational figures in science; the geneticist Barbara McClintock.  A Feeling for the Organism by Evelyn Fox Keller not only explains to the reader McClintock's groundbreaking research into how transposable elements ("jumping genes") work, but is a deft portrait of a researcher who refused to accept no for an answer.  McClintock did her work at a time when few women were scientists, and even fewer were mavericks who stood their ground and went against the conventional paradigm of how things are.  McClintock was one -- and eventually found the recognition she deserved for her pioneering work with a Nobel Prize.

Prison camps for children

When I considered topics for today's post, the one I was thinking about was so upsetting that I nearly decided to find some cheerful, science-newsy subject to write about instead.  But the more I thought about it, the more I felt like I couldn't leave what was first and foremost in my mind unaddressed.

So here goes.  If you're easily upset, you might want to opt out now.

It all started with Melania Trump's jacket.

Most of you probably know by now that the First Lady went to visit an immigrant shelter in Texas on Thursday while wearing an olive-green jacket that bore the words, "I Really Don't Care.  Do U?" on the back.

On first glance, this is tone-deafness on a level that makes Marie Antoinette's infamous "Let them eat cake" seem minor league.  Melania has given a lot of lip service to the Poor Immigrant Children, so to wear a jacket saying "I Really Don't Care" to a migrant camp is either epic cluelessness, or else...

... deliberate.

For all of the ridicule that Melania's gotten, she is not stupid.  There is no way that jacket choice was an accident.  She was dog-whistling her husband's rabid base -- people like Ted Nugent, who said that immigrants are "rabid coyotes" who "should be shot on sight."  You don't just pick up an item of clothing with a slogan in huge lettering without giving any thought to what it says or how it might be perceived.

And that goes double if you're the First Lady of the United States.

And triple if you're then wearing it on a tour of a migrant shelter.

So the jacket was a big ol' middle finger and "fuck you" to the immigrants and the people who support their humane treatment.  But what makes this even worse is that there are multiple (and credible) allegations of horrific abuse at these shelters, so Melania's tour, and subsequent conclusion that everything is hunky-dory, is a lot of whitewash over a situation that is about as nausea-inducing as anything I've read recently.

Let's start with one fact; these children are not criminals.  They were brought across the border by their parents.  Whether the parents deserve jail and/or deportation is a discussion we can have.  But these children are guilty only of being in the wrong place at the wrong time.  I won't go into all the allegations, but if you check out the link you can read about the charges that are being levied against not just one, but dozens, of shelters.  Here are a few, all of which are from children under the age of 16:

• forcible administration of psychotropic and/or addictive drugs, without the consent either of the child or the parent
• forcible restraint -- including one allegation of a child being strapped hand and foot to a chair and left there for two days
• manhandling that left kids with multiple severe bruises
• ridicule of children for being Hispanic or for speaking poor English
• children being gagged or having a cloth bag put over their heads to silence them (there is already a court case regarding a child who died of asphyxiation during restraint; it's been ruled a homicide)
• children being pepper sprayed in the eyes -- one child says it has happened to him seven times

Workers at these detention facilities say all this happens because the kids are "acting out."  Let me ask you a question that I'd like you to give an honest answer to; if you were fourteen years old, were separated from your parents, kept in unsanitary conditions (many of which have no air conditioning), were ridiculed and abused and drugged, wouldn't you act out?  Wouldn't you fight back?  Wouldn't you try to escape?

I sure as hell would.

One fifteen-year-old, who fled Guatemala to escape an abusive father and child labor, said, "The detention center makes me feel like an animal.  The conditions at the detention center are terrible."  A boy from Honduras said, "I want us to be treated like human beings."  An eleven-year-old named Maricela said, "I do not feel safe here.  I would rather go back to Honduras and live on the streets than be at Shiloh [Treatment Center in Virginia]."

Shortly after giving her sworn statement about the abuse she and others have received, Maricela was transferred from Shiloh to another facility.  Her current whereabouts are unknown.

Elissa Steglich, a clinical professor of psychology at the University of Texas Immigration Clinic in Austin, is unequivocal.  She said, "We've ensured there will be lifelong damage to these children."

Remember what I started with?  The children are not criminals.  But we're treating them like they are.  Worse, actually.  At least there are standards in prison to make sure the guards aren't abusing the prisoners, and the prisoners have at least some recourse if abuse occurs.

Here?  What recourse do these nameless, faceless children have?

What we've heard from the powers-that-be is nothing more than lip service.  The Republican leadership -- which has been shouting "all lives matter" for the last two years, and based their anti-abortion stance on "compassion for the poor children" for a hell of a lot longer than that -- has shown that in their view human rights begin at conception and end at birth.

And if you have brown skin, you probably don't even get that grace period.

It seems to me that we've reached a critical point, where we are establishing who we have become as a nation, whether we will be true to the idealistic "Give me your tired, your poor, your huddled masses yearning to be free" that appears on the pedestal of the Statue of Liberty, or if we've decided that our identity is something darker, more insular, more selfish.  If we choose the latter, there may be no turning back.

So, to go all the way back to what started this post: yeah, Melania, it's pretty obvious you, and your husband, and your husband's hand-picked leadership, "don't really care."  You may as well stop pretending you do.

As for me, I care a lot.  And I can only hope that the fact we are currently being led by a family of lying, cruel, narcissistic grifters is not going to mark the end of America the Compassionate in the history books of the coming centuries.

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This week's recommended read is Wait, What? And Life's Other Essential Questions by James E. Ryan.  Ryan frames the whole of critical thinking in a fascinating way.  He says we can avoid most of the pitfalls in logic by asking five questions: "What?"  "I wonder..." "Couldn't we at least...?" "How can I help?" and "What truly matters?"  Along the way, he considers examples from history, politics, and science, and encourages you to think about the deep issues -- and not to take anything for granted.

The master cookbook

Every year, I look forward to teaching my biology classes the basics of molecular genetics, because it's just so cool.

All organisms on the Earth contain a master recipe book -- DNA -- that contains all of the instructions necessary to create them.  Each of those recipes is deciphered, through a pair of processes called transcription and translation; the first produces a temporary copy of a single recipe (called RNA), and the second takes that RNA and uses it to build a protein of some sort.  So to extend the analogy of DNA-as-cookbook; transcription would be photocopying a single recipe, and translation would be reading that recipe and using it to make lasagna.  (The lasagna, if you don't mind my stretching the analogy to the snapping point, would be the protein.)

The problem is, as with most things in life, it's not quite that simple.

Your DNA contains a lot more than recipes used in a straightforward fashion to the building of a protein.  Between twenty and seventy percent of your DNA -- depending on whom you believe -- is junk DNA, which are essentially evolutionary leftovers.  Genes that got damaged, lost promoters (promoters are, more or less, universal "on" switches), or were moved somewhere in the genome that they couldn't be activated.  Some researchers think that junk DNA provides a sort of backhanded benefit; it gives us a larger target for mutations.  Mutations in the junk DNA have no effect, so it makes it less likely that any given mutation will kill us.

But there are other complications, too.  Some DNA (called "non-coding DNA") doesn't actually produce proteins directly, but acts to control the activity of other genes -- so it's pretty critical even though it's not specifically making your lasagna for you.  Some of these are "riboswitches" -- bits of DNA that are transcribed into RNA, but the RNA then binds to other pieces of RNA and alters the rate at which they're translated.  Another example are the telomeres, which form the ends of the chromosomes and act to protect them from degradation -- the decreasing size of telomeres is thought to play a role in aging.  A third, more mysterious example are the VNTR (variable number tandem repeat) regions, which are regions made of the same pattern of bases repeated over and over -- it's been made useful in the technique of DNA fingerprinting in forensics, but their function in the living organism is unknown.

With all of this complexity, it's been an ongoing source of contention as to exactly how many genes we have.  As you can see from the admittedly brief description I've given, it's not completely clear whether something is a functional gene in the first place, so how could you hope for an accurate count?  Estimates have run up to 6.7 million genes in the human genome -- and it certainly seems like something as sophisticated as we are must surely be the product of a huge number of individual instructions.

But the more people have looked into it -- starting with the Human Genome Project in the 1990s -- the smaller the estimate has become.  Just last week, the most recent revision was released, and it's pretty startling; a team led by Steven Salzberg at Johns Hopkins University has come up with a tally of 21,306 coding genes (ones that directly produce proteins) and 21,856 non-coding genes (bits of DNA that act to control the expression of other genes).

Which, considering that we're made up of trillions of cells interacting in countless different ways, is really a pretty small number when you come to think about it.

Salzberg is up front that these estimates could still be revised.  He, and study co-author Mihaela Petrea, write:

We aligned all human genes from NCBI's RefSeq database to the Ensembl gene set in an attempt to explain the differences, but although the total counts differ by less than 300, there are several thousand genes in each set that do not map cleanly onto the other, many of them representing genes of unknown function.  Our personal best guess for the total number of human genes is 22,333, which corresponds to the current gene total at NCBI.  We prefer this to the slightly higher Ensembl gene count both because the NCBI annotation is slightly more conservative, and because recent compelling arguments support an even lower gene total.  This number could easily shrink or grow by 1,000 genes in the near future.  However, recent analyses make it clear that even if we agree on a complete list of human genes, any particular individual might be missing some of the genes in that list.  The genome sequence is complete enough now (although it is not yet finished) that few new genes are likely to be discovered in the gaps, but it seems likely that more genes remain to be discovered by sequencing more individuals.  Additional discoveries are likely to make our best estimates for this basic fact about the human genome continue to move up and down for many years to come.

So the exact count of recipes in our DNA cookbook is still a matter of contention, but the whole thing is fascinating -- to think that such a (relatively) small number of sets of instructions could produce something as complex as we are.  As for me, this whole discussion has left me hungry, for some reason.

I think I'm going to make some lasagna.

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This week's recommended read is Wait, What? And Life's Other Essential Questions by James E. Ryan.  Ryan frames the whole of critical thinking in a fascinating way.  He says we can avoid most of the pitfalls in logic by asking five questions: "What?"  "I wonder..." "Couldn't we at least...?" "How can I help?" and "What truly matters?"  Along the way, he considers examples from history, politics, and science, and encourages you to think about the deep issues -- and not to take anything for granted.

Tales of contagion

I have to admit to a morbid fascination with things that can kill you in nasty ways.

Tornadoes, hurricanes, earthquakes, mass extinctions from giant meteorite collisions -- and epidemics.  I remember first reading Daniel Defoe's A Journal of the Plague Year, about an outbreak of the Black Death in London in 1664 and 1665, when I was in college, and being simultaneously horrified and mesmerized at the scale of it.  An estimated 100,000 people died in two years -- a quarter of London's population.

But even that is dwarfed by two other epidemics.  First, there's the infamous outbreak of bubonic plague that started in 1347 and, by some estimates, killed one-third of the human population of the Earth -- something on the order of fifty million people.  The worst, though, was the "Spanish flu" epidemic of 1918 and 1919.  Odd that an event only a hundred years ago, and that killed an estimated 75 million people worldwide -- twice as many as World War I, which was happening at the same time -- is much less known.  Mention the Black Death, and almost everyone has an idea of what it is; mention the Spanish flu, and often all you get is a puzzled look.

Danse Macabre by Michael Wolgemut [image is in the Public Domain]

This all comes up because of a paper by Maria Spyrou et al. that appeared in Nature: Communications last week.  In it, the researchers describe looking for evidence of pathogens in the Bronze-Age burial sites -- and finding evidence that the bubonic plague has been with us for a long, long time.  The authors write:

The origin of Yersinia pestis and the early stages of its evolution are fundamental subjects of investigation given its high virulence and mortality that resulted from past pandemics.  Although the earliest evidence of Y. pestis infections in humans has been identified in Late Neolithic/Bronze Age Eurasia (LNBA 5000–3500y BP), these strains lack key genetic components required for flea adaptation, thus making their mode of transmission and disease presentation in humans unclear.  Here, we reconstruct ancient Y. pestis genomes from individuals associated with the Late Bronze Age period (~3800 BP) in the Samara region of modern-day Russia.  We show clear distinctions between our new strains and the LNBA lineage, and suggest that the full ability for flea-mediated transmission causing bubonic plague evolved more than 1000 years earlier than previously suggested.  Finally, we propose that several Y. pestis lineages were established during the Bronze Age, some of which persist to the present day.

Which is fascinating enough, but it bears mention that there are still a number of epidemics that scientists have no clear explanation for.  Here are three of the most puzzling:

1. "Sweating sickness."  In the late 15th and early 16th centuries, several waves of contagious illness swept through western Europe.  It killed fast -- starting with disorientation, fever, chills, aching joints, and finally progressing to delirium and copious sweating.  Most of the victims died within 36 hours of the onset.  It claimed a number of well-known victims, including Prince Arthur of England -- the son of King Henry VII, and brother of King Henry VIII.  Arthur's death at the age of fifteen put Henry in line for the throne, and set into motion events that would change the world -- such as the English Reformation and the founding of the Anglican Church.  Sweating sickness went as quickly as it started -- the last outbreak was in 1551, and it hasn't been seen since.  Scientists are still mystified as to the cause, but the speculation is it might have been a hantavirus, carried by mice.
2. The Dancing Plague of 1518.  In eastern France and western Germany, people were stricken by a disorder that caused shaking, mania, and... a desperation to dance.  People took to the streets, dancing desperately, many of them until they died of hunger, exposure, heat exhaustion, or stroke.  In Strasbourg alone, at the height of the plague, it was killing fifteen people a day.  It, like the sweating sickness, vanished as soon as it appeared, leaving everyone mystified as to its cause -- although some researchers suspect it might have been caused by ergot, a fungus that grows on wheat and rye and produces lysergic acid diethylamide -- LSD.
3. "Nodding syndrome."  This one is much more recent, having first emerged in the 1960s in Sudan.  It affects children, causing listlessness, stunting of growth (especially of the brain), and a peculiar symptom called a "nodding seizure," often triggered by eating or becoming cold.  The child's head bobs, and (s)he becomes unresponsive, the seizures lasting for up to ten or fifteen minutes.  It's progressive and fatal -- the usual duration being about three years.  To this day no one knows the cause, although some suspect it might be connected to parasitism by the roundworm Onchocercus volvulus, which is endemic in the area and also causes "river blindness."

So this combines my love of horrible things that can kill you with my love of unsolved mysteries.

Anyhow, I realize this is all kind of morbid, and I have no desire to ruin your mood.  After all, we live in an age where most of the worst diseases of antiquity have been vanished; even bubonic plague, if it's caught quickly, can be cured with antibiotics (and yes, there are still cases of it today).  Thankfully, we seem to have gotten rid of sweating sickness and the dancing plague, even if we've replaced them with Ebola fever and chikungunya and West Nile virus.  I'll still take what we've got today over life in the past, which was (accurately) described by Thomas Hobbes as "solitary, nasty, poor, brutish, and short."

Have a nice day.

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This week's recommended read is Wait, What? And Life's Other Essential Questions by James E. Ryan.  Ryan frames the whole of critical thinking in a fascinating way.  He says we can avoid most of the pitfalls in logic by asking five questions: "What?"  "I wonder..." "Couldn't we at least...?" "How can I help?" and "What truly matters?"  Along the way, he considers examples from history, politics, and science, and encourages you to think about the deep issues -- and not to take anything for granted.