A World from Dust (Plus): What are the Microbes a Mile Deep Missing?

Scientists drilled down through more than a mile of underwater sediment and, very carefully, isolated the microbes that live in the coal seams down there. Just finding these microbes (while avoiding contamination) was impressive, so we don't know everything about them yet. But we do find them much more abundant in the coal layers, where they can eat the carbon-rich rocks.

Most of the characteristics of these extremely deep microbes are what we expected. For reasons discussed in Chapter 6 of A World from Dust, these microbes use nickel and heme to process their food, and they emit tiny clouds of methane. They seem slightly out of place, because a limited genetic analysis finds they look more like surface soil bacteria than shallow sediment bacteria, but they made have been carried there from when the sediments were first laid down.

The only real surprise so far is how few of these microbes live down there. There's plentiful food, including hydrogen that, for some reason, they eschew, leaving it on their plate like uneaten broccoli. Something else is holding life back down there. The authors note that proteins and DNA fall apart more readily at high temperature and suggest that the hot, high-pressure environment makes the constant repair too costly. If this is so, then a deep underwater coal seam would be like a planned community in Las Vegas after the housing bust of 2008: plenty of rooms but no one willing to move out there because of the heat.

What this says to me is that the limits on life look a little more stringent than we thought. Whether it's the cost of repair, or something else related to high pressure, or something else entirely, what we have here is a reasonably good environment for methanogens that they don't fully exploit. With more investigation, maybe we can find out what's missing, and that will help us figure out just how prevalent life may be in extreme environments, both on this planet and on others. If life can't live well in this environment, then the same thing may be wrong with other environments that right now look OK to us. This one clue makes the universe seem a bit more lonely.

Reference: Science, July 24, 2015, "Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor." DOI: 10.1126/science.aaa6882
   

Genomes for Africa

This link tells the story of how the Mars company (yes, that Mars-bar company) has decided to fund the sequencing of several plant genomes and post the information online. That's cool enough, but look at the list of included genomes: yam, finger millet, tef, groundnut, cassava and sweet potato, among others. These are staple crops in the developing world, and therefore they have eluded sequencing money, until now.

How this could really help is probably not in detailed gene manipulations, but in more mundane areas: grafting/cross-overs to make stronger crops and investigations into the plants' defenses against fungi. It's already helped with the cacao genome, funded and implemented in the same way a few years back.

Wouldn't this make a great project for undergraduates to investigate, using biochemistry in a way to help farmers across the world? I for one can't wait for these to come out. Biochemistry students of the future, you may have a lab exercise in this area. 

Harry Potter and the Genetic Hypothesis

So if you're a best-selling author, by the name of, for example, "J.K. Rowling," and you create an incredibly detailed universe of hidden magic, and you want to link that universe to our real universe, then you may be tempted to explain the magical universe in semi-scientific terms. I understand the temptation ... but the results can cause Pottermaniacs great consternation.

Case in point: Rowling described the wizarding gene as "dominant," which explains why Tom Riddle is a wizard (with one Muggle parent), but runs into big problems because it does not explain why Hermione Granger can do magic (with two Muggle parents) or why Argus Filch cannot (with two wizard parents).

What to do? Deploy the science wing of the Pottermaniacs! They will produce a detailed, footnoted explaination involving trinucleotide repeats that will establish once and for all how Rowling is right but Hermione and Filch can still exist. Whew.

Now, we just need some DNA from a few wizards to track down this gene, and a few gene therapy events later we can all be wizards. And maybe someone can fix poor Filch.

By the way, if someone can write a similar guide to Quidditch strategy that explains how Quidditch could actually be a strategic game and not just a vehicle for exciting writing (150 points for one event in the game? Come on!) ... well, I'd read that too.

[UPDATE: Thanks to Deanna from Deanna's Corner for the link.]

Genetic Evidence for the First Temple?

Some Ethiopian genes look suspiciously like Israeli genes. And the shared genes appear to be 3000 years old. Just about the time a certain Queen of Sheba and her entourage visited a King Solomon, according to an ancient text or two. It's a small thing, but it's very interesting.

Does that mean that we can identify some of Solomon's genes? This is like some kind of weird mash-up of Raiders of the Lost Ark with GATTACA.

The Genes of the Jews

The journal Nature just published "The genome-wide structure of the Jewish people," a large-scale analysis of the genes of Jewish people from around the world, from India to Ethiopia to Europe to Iraq ... and it reminds me why I'm so excited about genetic analysis.

Two of the most interesting findings (in my view!):

1.) Despite large geographical and historical differences, the two major groups of Jews (Ashkenazim and Sephardim) are genetically extremely similar to each other. This is similar to the recent finding that Irish and Scottish genes are very similar. It is biologically accurate to refer to the Jews as, well, Jewish, whatever their history, and the biological evidence is that they have been a separate people for a long, long time. (This also shows that they rarely intermixed the people around them -- except in India and Ethiopia. Ethiopia is such a unique nation ... )

2.) The New York Times reports that the Iraqi and Irani Jewish communities branched out from the other Jewish communities 2500 years ago, correlating with the Babylonian exile and destruction of the first temple. So we can read that part of the Bible in the genes.

Now I want to know, can genetic analysis find the Lost Tribes mixed in with others? Probably not but ... I have tons of questions. Bring on the genes!

Is Life Simple or Complex? (The Answer is Yes.)

I've read four interesting papers over the last week or so that I keep thinking about. I don't actually have them in front of me but I think together they show what is so great about science.

Paper #1 maps all the genes from a small microbe with compartments. From this it concludes that the first microbe with compartments must have been really complex, more complex than previously believed.

Paper #2 finds that a simple element (silicon) can help piece carbon together to make small sugars, some of the building blocks of life.

Paper #3 addresses a problem in making DNA: because DNA is a long line, it's much easier for it when forming to make small circles rather than large lines. The problem is that large lines are needed to store a reasonable amount of information. By itself, DNA will make small circles. But add a small simple carbon molecule and it lines up in the DNA to push it into a long line, something that can hold enough information to support life. A small molecule makes a big difference and lets DNA fulfill its potential.

Paper #4 finds that the complex molecule tRNA that we use to make proteins might still work if it's reduced to just five RNA bases in a row, much more simple then I would have thought.

Paper #1 = life is complex and wonderful.
Papers #2-4 = some parts of life might be simple (or simplifiable) and wonderful.

If creation is a gift then I want to see that gift clearly and truly. If you're tempted to ignore any of these papers by preconceived notions of how simple (or how complex) life must be, I encourage you to take them on, debate them, and doubt them, as you doubt your jumping to conclusions about them. The one thing I ask is that you don't ignore them. They're just too interesting on multiple levels.

The Red-Headed Caveman

Did you know we have sequenced some Neanderthal DNA? It turns out some Neanderthal remains in Spain were well-preserved enough to pull out some genes. One of the genes they pulled out was one of the genes primarily associated with red hair (see previous post on Red Hair about Aidan, our red-haired boy -- I think it's the same gene, or similar). So they cultured cells, expressed the gene, and found it produces pigment the same way, and therefore, it looks like some Neanderthals had fair skin and red hair. Just like my boy.

Now I can tell him, "Stop acting like a Neanderthal!" And he can say "I can't help it Dad, it's in my genes!" (Never mind that my other son is already prone to saying things like that ...)

Also, I read recently that the red-haired gene is not Irish in origin but reflects a Viking source (by way of the Irish). So Aidan's got a Viking nature and a neanderthal nature. Good thing we have so many more genes than that!

James Watson Does It Again

James Watson was one of the people (I was about to say two people, but it was at least four and really more than that) who figured out the structure of DNA. He did this as a brash young scientist, and doing Nobel-Prize-winning work when you're barely out of high school transformed him into a brash old scientist. Personally, I think his colleague, Francis Crick, handled the transition with a bit more grace, but it is both a blessing and a curse to be a famous scientist. Watson always has seemed to enjoy it, and he's always been ready with a quick, sharp quote.

Recently, Watson's been in the news more for his talk than his walk. For instance, fellow scientists chose to sequence his entire genome to demonstrate new DNA sequencing technology. That's very cool, but he didn't do much beyond the donation process. Yet he got in the news for it. Watson's never shied away from the spotlight. But today's headlines tell a story of how he went too far, gave quotes that were too quick, and too sharp, and hurt a lot of people for no reason at all.

I won't repeat them here, but the executive summary is that Watson's 1.) worried that Africa will never catch up because blacks have less inherent intelligence; 2.) says that anyone who's ever worked with a black knows they're less intelligent on the whole; 3.) implies through all this that intelligence is genetically based and that the intelligent have more value than the unintelligent.

Where do you start to respond to that? Again, I will let the others more qualified than myself deal with the scientific refutation of these arguments, while commenting on the irony that in holding himself out to be an authority on intelligence, Watson has shown very little of that same quality in his comments. Just like with the baseball pitcher John Rocker a whle ago, a love for the spotlight kept Watson thinking that the more outrageous the comments, the wider the coverage. Like Rocker, he stepped way over the line and is feeling the repercussions (he has been suspended from his leadership role at Cold Spring Harbor Laboratory, for one).

What I think about when I hear such easily refutable and reductionistic comments is, where does this stuff come from? We seem to have created a class of scientific provocateurs who are happy to hurt entire classes of people for a quote. You start off making straw men of theists, you end up making straw men of African-Americans. I have always wondered about the neo-atheist writers, what they do with the Christian nature of African-American (and continental African) communities. Their arguments that Christians are dumb feed right into this racism, because many Christians are poor, and many Christians are black or Latino or "other." The general intellectual strategy that Dawkins/Hitchens/Harris/etc. follow is to make caricatures of Christians. This same "oh, look, how outrageous!" strategy led to Watson's comments.

Francis Collins, evangelical Christian scientist (look, I just typed those three words together!!), is a friend of Watson's and was quoted in the article I read, with him stating how Watson's comments were "hurtful" to a large group of people. At first I thought that was just too simple, but stepping back I think that's the best word to use to characterize Watson's speech and to point out a huge rhetorical flaw in the entire public face of science. It's hurtful.

Let's set some Robert Fulghrum-style ground rules here. It's not OK to hurt other people. It's not OK to suggest genetic superiority of the people who are like you. It worries me that these naturalists can't seem to stay away from an implicit social Darwinism. But then again, when you worship the intellect, you denigrate the other aspects of life, and you lose the complexity of what humans really are.

I don't know what really motivates Watson, what was a slip of the tongue and what was a deliberately outrageous comment. I do know that in the intense pressure cooker of academic science, reviewers are encouraged to be hurtful with reason, and that has a place. But it doesn't have a place outside the system of peer review, and it doesn't have a place when dealing with real people. I constantly worry about idolatry with scientists, idolatry of reason and the intellect. I don't know exactly how that applies here, but I take it as cautionary, because saying something that's not just wrong, but hurtful and wrong, is not the way to win any arguments.

The Past and Future of Red Hair

A recent issue of Science magazine included the article "Why I Have Red Hair, Need to Avoid the Sun, and Shouldn't Commit a Crime" by Ingrid Wickelgren. We have now pinpointed the gene that causes red hair. It's called MC1R, which is for a receptor on the surface of skin cells. If a mutation messes up the receptor enough that it doesn't work anymore, you have a defective MC1R gene. If you get defective MC1Rs from both your father and your mother, there's a ~90% chance that you will have red hair, pale skin, and the propensity to broil rather than bake in the sun.

So, I have a child who would have no problem being admitted to Arthur Conan Doyle's red-headed league (let's call him Red Bug). He's even got an Irish name, in the spirit of this mid-March season. His skin is pale white, so different from his older brother's that in the bath they look like two different races. So Red Bug's hair and Red Bug's skin both tell me he's probably got two bad MC1Rs, one from me and one from my wife. Sorry, kid. Still, I wouldn't trade that red mop for anything.

Furthermore, a bad MC1R also means you're at more than a three-fold higher risk for melanoma, even if you carry only one defective gene and have dark hair. Like, say, probably, me! Also, my wife (who has blond hair). What's a little uncanny about all this is that ever since I spent too long in the sun swimming in a Florida lagoon in 10th grade, I've had "redhead freckles" on my shoulders, and I also found a strange spot/mole on my arm a few years later that I never really think about except at times like this.

(The Florida lagoon story involves my adolescent brain not processing the importance of sunscreen, and the fact that That Girl Lindey was floating on a raft in the lagoon and it seemed like a good idea to make conversation for an hour or so out there. Never mind that our summer program was over a week later and I never heard from her again! I have a distinct memory of wearing a very baggy white shirt every day for the remainder of the program.)

Good thing I moved to Seattle, right? Except that the lack of sunlight in these northern latitudes could be a contributing factor to multiple sclerosis. I have a nutrition colleague who disdains all supplements except vitamin D. The reason is, we may not get enough sunlight in Seattle to convert starting materials into vitamin D, and vitamin D deficiency may be implicated in MS, and there's a surprising prevalence of MS cases around Seattle. There's enough vitamin D in milk and butter to prevent rickets, but it may not be enough to completely prevent MS.

As far as I'm concerned, this is reason enough the next time the sun comes out to take a long walking break down by the canal.

So whatever happens, we can't worry too much about increased risk, but we can all be a little more liberal with the sunscreen, especially with our little Red Bug.

My favorite part of the article is the last little throw-away bit: "Spelling out a person's MC1R genes could also help crime-scene investigators, Rees suggests. If the analysis of biological tissue left at the scene reveals two aberrant versions of MC1R alleles, there is a 90% chance that its owner has red hair."

So, little Red Bug, word to the wise: if you ever get in trouble and are tempted to deny it, just know that Daddy has access to a DNA sequencer at work and can tell if that's your tissue or not. I'm not sure if the evidence would be legally admissible, but it certainly would be sufficient for being-sent-to-your-room-until-you're-18 in the most local of courts (the one in my house).

But my little angel would never do anything like that! I do have to be careful. He does have a devious streak, especially when it comes to anything electronic with buttons. Or with wheels. Or animals.*

Uh-oh.

So, in that DNA sequencer, I have access to a powerful instrument that can scry into the past and the future, almost like something out of Harry Potter. I can see the past in the sense of where did this gene come from?, and the future in the sense of am I at a higher risk of cancer because of it?

There are certain teaching lab experiments I've had to disregard, not because of danger or cost, but because in a classroom setting there are some things you just don't want your students to find out. I mean, what would it mean to test for a genetic disorder in class? For Alzheimer's? Or paternity? Theoretically, I could do it, although with a healthy uncertainty. Ethically, I could not. Legally ... ?

The line between the "cool experiment" and the "wrong experiment" is getting very thin.




* Anyone who knows me personally and would like access to the Other Blog where I take time to chronicle everything mildly amusing these kids say, email me for an invite. But be warned -- it's like the Family Circus, only not as edgy.