All A-Twitter

I finally broke down and opened a Twitter account. You'll find me there at @BenJMcFarland. Still learning the rules of etiquette there, but it seems to be a great format for passing around science news and quick conversations. I'll focus on science and books on Twitter, while here I have the space to hold forth at more length. From this starting point, let's see what evolves ...

Before and After at the Nanoscale

On this picture (a sideways triptych?), the bottom panel is how we draw the atomic model for a covalent-bond-forming reaction in organic chemistry class. The triple bonds, shown as extra lines on the left, can react with each other and share electrons to form the multicycle molecule on the right. The top two panels are actual pictures of the molecules, shown before and after heating it up. Looks like our models are pretty good representations of reality, no? Read more here.

Before I took chemistry classes I thought that pictures like this would be easy to take. After all, those models are easy to draw. But it's very hard to see on the atomic scale -- atoms are so small that (in a sense) light waves shine right around them. It's nice to see that technology is catching up to my "when I was a child I thought as a child" perceptions. It's kind of pretty too.

Indiana Jones Biochemistry: The Prevenge of the Black Death

The Black Plague had a prequel.

It's clear that Yersinia pestis was the microbe behind the Black Plague in the 14th century, and there was a worldwide sequel pandemic in the 19th/20th century. But in the 6th-8th centuries a plague swept the Byzantine empire, called Justinian's plague. Now a DNA analysis of the remains of plague victims shows that this plague was caused by Yersinia pestis as well -- and it originated in Asia like the other two pandemics.

This biochemical archaelogy isn't exactly like the Indiana Jones movies, but I find it pretty exciting to see the recurrence of this insidious enemy throughout human history. (Maybe it's more like Doctor Who?) Read the paper here.

Rocks from the Bottom of a Martian Lake

Here's the data that shows what was in the rock that Curiosity dug up from Mars (after the rock was blasted with heat into a gas and then molecules of the gas "weighed" with mass spectrometry, that is).

The most amazing part is all the water it implies. It's a perfect clay that was probably deposited at the bottom of an ancient lake, meaning, holy cow, there was a whole LAKE on Mars. Since water is the most probable sine qua non for life, then this is exciting news for possible Martian microbes. Assuming existence is an exciting thing for microbes.

With all the evidence for water, Mars has just become a fascinating test case of how easy it is for simple life to emerge. If it didn't happen there, then it must be very hard. Looks like Mars was playing with a rather full deck, chemically speaking. Was it enough? Was the game rigged to win or lose? The question is still open, and it's the open questions that keep us moving forward.

The other things I note include that the red oxidized iron is not present below the surface, so most of Mars is gray, sulfur-rich rock without much oxygen. Life must have been simple and not photosynthesizing or oxygen-using.

Where did all that water go? What forms of life were able to take hold in those Martian lakes? Times like this I half think they shouldn't have called the rover Curiosity ... they should have called it Patience, because that's what we need to wait for these tests to be done ... which is a virtue, I know, I know ...

Turning a Video Camera into a Stethoscope

This is the coolest thing I've seen all week (and justifies a third post of the day). Here a simple computer program magnifies motions and hue changes in video so that we can see the blood flow (pulse) and breathing movements in patterns that could even be diagnostic, without touching the patient at all:



The best part? The code is open and the idea is simple, so I too cannot wait to see what people across the world do with this. It's like a Neal Stephenson novel in real life ...

Could this be used to identify overly stressed people by video? At TSA checkpoints? Is that an invasion of privacy? In court? Let's not get ahead of ourselves, but I do think this has a lot of potential.

You are a Transformer

You know how there's always this character on the comic-book superhero teams, the character who can change the shape of his or her body, and they make these cool shapes out of their hands to whack supervillains with? Well, in a small way, you can do that. Change the shape of your fingers to accomplish a certain task, that is. Not whack supervillains. But that's OK as long as you aren't presently being harrassed by supervillains.

All this from the humble beginnings of wrinkly, bath-soaked fingers. It used to be described as an accident -- that your outer skin would swell up by absorbing more water, making wrinkles. This is wrong. It is actually a specific, encoded, nerve-driven response, not a swelling accident at all. Now the purpose of this specific response has been made clear. This paper shows that winkled fingers can grip wet, slippery things much better, and so you can hold onto surfaces and tools without losing them in the mire.

Ergo, you have your own superpower. Soak your fingertips in water and non-slip pads develop. That's not quite Mr. Fantastic but it's a lot more interesting that an accidental swelling of the skin. The moral of the story: wait a little while before calling something an accident. Purpose is still purpose even if it's unseen.

A Home Experiment with Hot Chocolate

Do indeed try this at home: Make some hot chocolate, and put some in an orange cup and another in a white cup. The orange cup should taste better. Now, I've heard this in a recent report, but you should be skeptical. Don't take my word for it. Try it for yourself. And remember, repeated trials are the only way to be truly scientific about it. I think a few dozen should get your error bars down to a reasonable level.

If all science labs were like this we would have quite a few more students.

(I do wonder about the studies reported in which blue drinks quench thirst better than red ones ... are we talking a light blue or the Tid-y-Bowl blue of certain Gatorade flavors? Because I cannot abide the latter, even if it will quench thirst more efficiently. Just not natural.)

Two Concrete Ideas: Glow-in-the-Dark Roads and Self-Healing Bacterial Concrete

What's better than a good idea? Two good ideas in one blog post! Both have to do with concrete or asphalt, so I thought they'd go together.

1.) Even when I mentioned the long-lasting glow-in-the-dark pebbles for driveways earlier, I didn't think of this use for them: embed them in roads for glowing directional signals, even without streetlights. They can even be made temperature sensitive, so when the road gets icy, big glowing snowflakes could appear on it. This is a great idea (although implementing it could run into some problems in Seattle given our infamous lack of sun in the winter months).

2.) Instead of glowing pebbles, mix in something much smaller into concrete: bacteria. Bacterial spores can survive a long time without water or nutrients. When the concrete is cracked, the water will wake them up (like Sea Monkeys) and they'll start making carbonate. Deposits of calcium will react with this to make calcium carbonate (calcite) which is a little bit of mortar that will fill in the crack. The result is self-healing concrete.

The problem is keeping the bacteria alive in the concrete for a long enough time, but they're working on that. Given how long some spores can survive, this might just work.

Realize that this shows that you can use bacterial spores as dormant little chemists waiting to control their environment through chemistry: in this case, ejecting carbonate and making concrete in a newly formed crack. Life is a powerful thing, if you can keep it alive in the place where you want it to work.

Are We in a Goldilocks Zone in Time as Well as Space?

A recent finding has just blown my mind and I'm not sure if anyone else has put it together with other results yet. To me at least, putting it together, it makes the universe look much different than I thought at the beginning of the day, so I'd like to share it with you and see what you think. It also suggests that Earth is that much more special. Let me explain.

The Kepler space telescope is exciting stuff, because it's looking for planets around distant stars and finding them all over the place. Here's an orrery of the planets found by Kepler (and even this is more than 18 months old now!):



The real key is to find a planet in the habitable zone (the "Goldilocks zone"), which is the right distance away from a sun so that ice melts and steam condenses, giving liquid water. Note that even this is only one element in the recipe for life, but it's got to be one of the most important ones. Here's one planet recently discovered to be "in the zone."

But, like I mentioned, you need more than liquid water for life. For instance, you need metals far down on the periodic table like iron, molybdenum, etc., to build a rocky planet out of, and to provide important catalysts for life. Basically, you need a decent portion of the periodic table built in order to do complex chemistry. After the Big Bang you start with the simple stuff, hydrogen and helium, and have to build up to iron and company. That's takes a while, past the first generation of stars, at least, according to this article, "a few billion years."

I've been aware of that for a while, and that some people say you need more than "a few" billion years, you need something more like 7 or 8 billion years. (You need at least three because the oldest stars of this type are about 10 billion years old, and our sun's right in the middle of that.) The universe is 13.7 billion years old and the earth is 4.5 billion years old, so by that logic, there's a "few billion"-year window in which an earth-like planet could have been built and produce complex life. Kind of like a "Goldilocks zone" in time rather than space. I've always wondered if the reason why we're not hearing much through SETI or seeing many aliens coming down from the sky (well, I haven't seen them, have you?) is if we're kind of the first kids on the block, because it's taken this long for the periodic table to form and then a planet to form and gestate life. I've assumed there's plenty of time for more planets and stars to form in the universe. I may have assumed wrong.

So, you need water and you need metals. But don't forget, you also need a star to have formed at the same time as the planet. The "photo" part of the whole photosynthesis thing is kind of important. That's why I was shocked to hear that a recent comprehensive study of star formation has suggested that the universe is almost done making new stars. By looking at star formation rates, the astronomers concluded that the golden age for star formation was 11 billion years ago and has been declining ever since, and recently it's just dropped off the table. Check out this graph:

It's not that the universe's biological clock is ticking ... it's more like it's wheezing its last. The universe is not just out of childbearing age, it's close to collecting retirement. [Insert bad "my universe is so old/how old is it?" joke here.] This -- if it holds up, and it looks solid to me -- is one of the most mind-boggling things I've read. It also means that complex life is that much more likely to be rare and precious. If it ain't happened yet, it ain't happening.

Maybe complex life can form in 3 billion years rather than 4 (maybe the "boring billion" didn't have to happen ... but my impression is that it did). Maybe a star has formed 2 billion years ago that will have complex life in 2 billion years. But it looks like the constantly-expanding universe combined with limited energy and matter would suggest that if something hasn't happened yet it will not have much more of a chance to happen. That's a "few billion"-year window that may have already closed. The numbers are adding up to be surprisingly restrictive in time, even in a universe that is huge in space beyond comprehension.

As my physics colleague likes to quote, "There are two possibilities: either we are alone in the universe or there are others like us out there. Either way it blows your mind." For me, the likelihood of the former just got raised, and my mind is suitably blown.

New Protein Science Publication

Protein Science is one of my favorite journals, so I'm doubly excited to have a publication accepted by it. I'm also happy with the long list of student co-authors on this one; it was really an amazing team effort. The article was accepted only a short while ago and it's already online. Here's the link to the official abstract.

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 Soup vs. The Miracle Mineral Solution

My friends with autistic children have it hard enough without having to deal with fake cures for autism. The most recent, and probably most egregious, treatment is called the Miracle Mineral Solution (MMS), although if there's any truth in advertising they should just call it what it is: bleach. Supposedly the bleach will cleanse the system from the toxins that cause autism.

There's something psychological going on if the idea is that autism is completely caused by the environment and can be scrubbed out with a caustic solution. It's like Lady MacBeth, rubbing her hands to remove the spot that isn't there. Autism is a complex interplay of environmental and genetic factors and it is tied up with the mysteries of brain function, which is the most protected part of the body against external chemical "toxins." It just doesn't make any sense to think you could wash it all out -- it would be like scrubbing your computer to fix the internal wiring!

But all that argument aside, my wife pointed out that the best argument against bleaching out the autism may have been presented on the most academic of all TV shows, The Soup starring Joel McHale. I never thought I'd be citing Jennifer Love Hewitt to cap off a scientific argument, but if it works, it works ... and the lady is right about this:

TV News Interview on BPA

So yesterday I was asked to get up early in the morning, drive in to the local FOX news studio, and answer some questions about BPA and other plastics additives. Those are chemicals, and I'm a chemist, so I said yes. This is the result:

http://www.q13fox.com/videogallery/69481607/News/Plastics-in-Food#pl-62890122

It's funny how much is not able to be said in that context, but I think I was able to squeak out some of the nuance to the issue. I didn't know they were going to use that particular study to open with, so what you see is my on-the-spot reaction on live TV. Hey, as long as I don't get made fun of by Joel on The Soup I think I'll be pretty happy with this result.

(By the way, the one chemical fact I really wanted to get across but didn't is that there's some good science done by Joseph Thornton in Oregon about how the hormone receptors learned to recognize their hormones, and it turns out they bind by exclusion -- that is, the estrogen receptor isn't really specific for binding estrogen, it's more that it's specific for NOT binding testosterone or cortisol or anything else -- and this gives me a little more pause that maybe BPA might be able to bind, if it's never been specifically excluded before. But I'm still only mildly cautious. We aren't all gonna die, I don't think. Well, not from BPA. The bottom line is that mechanisms of receptor development and hormone binding probably do NOT make for good TV!)

Metal Enzymes That Multitask

Here is the heart of a metal-containing enzyme -- see how the two purple irons (marked Fe) are held in place by the network of dashed green bonds. Those iron ions are poised, waiting for a component of DNA (adenine) to bind the enzyme. When the adenine approaches, they will swiftly switch one of its protruding nitrogen atoms for an oxygen, changing the adenine into a hypoxanthine and producing nitrogen for nitrogen-needing processes.

But wait ... there's more. Some researchers (see reference below) had some trouble purifying this enzyme, and when they investigated why, they found out that it's because of an alternate activity; this enzyme does more than one thing with its iron atoms. If peroxide approaches the irons, they can neutralize it into oxygen or water by shuttling electrons around. So this enzyme converts nucleotides, and it also protects against reactive forms of oxygen. This means the enzyme has two names and two jobs: it is not just a "deaminase" (described in the first paragraph), but it's also a "catalase."

It's a useful reminder. When we ask an enzyme what its job is, we shouldn't stop when we get one answer. We should be like that kid in the Coke Zero commercial: "And ... ?" Metal ions in enzyme active sites are powerful enough to do several different things: even in the same enzyme. This is a good example of how the power of metal ions makes enzymes able to do more than we expected. What other hidden jobs are in other enzymes that we don't know yet because we haven't asked the right questions?

This also has important implications for the development of enzymes. If an enzyme can do two things at once, that gives it the freedom to tweak one of its activities while the other one keeps plugging away, earning its worth in the cell. In this way, the second activity might be able to change and do something else entirely. All because of the versatility of the iron ions at the heart of the enzyme.

Source: Kamat et al. (2011). "The catalase activity of diiron adenine deaminase." Protein Science 20:2080—2094.

Simplicity Undergirding Complexity

You never know with science. You can find complexity in simple things (chaos theory/butterfly effect, quantum mechanics) or simplicity in complex things, you just never know. It turns out there is a grid or scaffold of simplicity underlying the arrangement of the brain. This is a wonderful thing to find, like Maxwell's equations relating electricity to magnetism or the gas laws of chemistry; more accurately, it's like a simple coordinate system (or map/address book?) that can be used for future studies of the brain. I'm sure when we dig a little deeper that there will be some maddening complexity that confounds us again, but today let's revel in the simplicity given to us!

Simple 3-D grid structure underlying complexity of primate brain