New life

New from the "Don't You People Even Watch Science Fiction Movies?" department, we have: bioengineers at Cornell University recently created a DNA-based material that has three of the main characteristics of life -- metabolism, self-assembly, and organization.

Oh, and they pitted different versions of the material against each other, and triggered two more: competition and evolution.

The research was published last week in Science: Robotics, in a paper called, "Dynamic DNA Material With Emergent Locomotion Behavior Powered by Artificial Metabolism," authored by a team led by Cornell bioengineer Shogo Hamada.  Working with substances they call DASH (DNA-based Assembly and Synthesis of Hierarchical) materials, they ended up creating something so close to a living thing that even the most ardent life-is-unique-and-unquantifiable proponents are sitting up and taking notice.

What they did is start with 55-nucleotide pair DNA fragments, which were then injected into a machine that provided raw materials (free nucleotides) and a source of energy.  The DNA fragments began to extend, adding new bases to the front end while slowly losing them from the back end, so the entire fragment crept along.  The addition process was faster than the degradation, so eventually there were fragments a few millimeters long -- corresponding to tens of thousands of base pairs.

"The designs are still primitive, but they showed a new route to create dynamic machines from biomolecules. We are at a first step of building lifelike robots by artificial metabolism," said Shogo Hamada, who led the research.  "Even from a simple design, we were able to create sophisticated behaviors like racing. Artificial metabolism could open a new frontier in robotics."

The fragments then began to compete against each other in terms of speed and growth rate, something that has never been seen before in an artificially-created DNA-based material.  "Everything from its ability to move and compete, all those processes are self-contained," said study co-author Dan Luo.  "There’s no external interference.  Life began billions of years from perhaps just a few kinds of molecules.  This might be the same...  [T]he use of DNA gives the whole system a self-evolutionary possibility.  This is huge."

The researchers are currently trying to design ways to have the DNA fragments move toward sources of light, warmth, or sources of nutrients, and away from dangers, not to mention ways to speed up the process to create new generations within seconds.  "We are introducing a brand-new, lifelike material concept powered by its very own artificial metabolism," Luo said.  "We are not making something that’s alive, but we are creating materials that are much more lifelike than have ever been seen before."

Hamada added, "Ultimately, the system may lead to lifelike self-reproducing machines."

Okay, now, just hang on a moment.

I'm not really buying Luo's comment that they're "not making something that's alive," because we don't really have a good working definition of life to start with.  Viruses, commonly referred to as "alive," have no metabolism, are not made of cells, do not respond, and outside of the host do not use energy.  Honestly, they're more like self-replicating chemicals than they are living things.  Then there's the life characteristic "has a limited life span," which doesn't seem to apply to some plants (such as the essentially immortal bristlecone pines) and cancer cell lines (such as the famous HeLa cells).  There's a lot of speculation on whether life even has to be carbon-based -- speculation that's been around for a long time (remember the original Star Trek episode "The Devil in the Dark," about a silicon-based life form that has hydrofluoric acid instead of water as the solvent in its blood?).

So don't tell me the new Cornell DASH-material isn't alive because it's missing a couple of characteristics of life from the canonical list.  The number of naturally-occurring exceptions is long enough.

And I'm right up there with the folks who think this is amazingly cool -- my background is in evolutionary genetics, after all -- but for cryin' in the sink, doesn't this concern anyone?  Especially if you design DASH-materials that avoid danger and seek out sources of nutrients?  Because I can think of one really great source of nutrients they'd probably be attracted to:

They're called "us."

And the problem is, we don't set up a good immune response to DNA fragments.  Up till now, this has been a good thing; we take in DNA fragments in our food every time we eat.  If you eat a carrot, you're swallowing carrot DNA.  If you eat a steak, you're swallowing cow DNA.  If you eat Slim Jims, you're swallowing...

... well, the DNA of some kind of organism.  I think.  Who the hell knows what those things are made of, anyhow?

But my point is, you have one shot at breaking these foreign DNA strands down into their component nucleotides, and that's using the nuclease enzymes in your small intestine.  If they get past that...

Cf. my earlier comment about the new artificial DNA fragments learning how to "avoid danger."

Okay, maybe I'm being alarmist, here.  But -- and I mean this with all due affection -- humans have a really good track record of fucking things up royally, sometimes out of the best of intentions.  So I'm not sure that creating a self-replicating, competitive life form that can evolve to become more efficient at seeking out sources of nutrients is really all that great an idea.

But that's not gonna stop 'em.

Oh, and did I mention that I live ten miles from Cornell University?  At least I'll be amongst the first people to get devoured, and won't have to sit around wondering when the DASH-monsters will arrive.

But I'm gonna try not to worry about it.  After all, we've got enough other things to worry about, such as climate change, the threat of war, and whether today'll be the day Donald Trump decides to open the Seventh Seal of the Apocalypse.

Maybe that's what Michele Bachmann meant by saying Trump was "highly biblical."

**********************************

Monday's post, about the institutionalized sexism in scientific research, prompted me to decide that this week's Skeptophilia book recommendation is Evelyn Fox Keller's brilliant biography of Nobel Prize-winning geneticist Barbara McClintock, A Feeling for the Organism.

McClintock worked for years to prove her claim that bits of genetic material that she called transposons or transposable elements could move around in the genome, with the result of switching on or switching off genes.  Her research was largely ignored, mostly because of the attitudes toward female scientists back in the 1940s and 1950s, the decades during which she discovered transposition.  Her male colleagues laughingly labeled her claim "jumping genes" and forthwith forgot all about it.

Undeterred, McClintock kept at it, finally amassing such a mountain of evidence that she couldn't be ignored.  Other scientists, some willingly and some begrudgingly, replicated her experiments, and support finally fell in line behind her.  She was awarded the 1983 Nobel Prize in Physiology and Medicine -- and remains to this day the only woman who has received an unshared Nobel in that category.

Her biography is simultaneously infuriating and uplifting, but in the end, the uplift wins -- her work demonstrates the power of perseverance and the delightful outcome of the protagonist winning in the end.  Keller's look at McClintock's life and personal struggles, and ultimate triumph, is a must-read for anyone interested in science -- or the role that sexism has played in scientific research.

[Note: If you purchase this book using the image/link below, part of the proceeds goes to support Skeptophilia!]

The Higgs boson, uncertainty, and the scientific method

It's begun, just as I predicted it would.

This week, a pair of physicists at Cornell, Joseph Lykken and Gabe Shaughnessy, published a paper calling the Higgs boson finding into question.  (Source)  What was described in the widely-publicized press release from CERN ten days ago could be the Higgs, Lykken and Shaugnessy say -- or maybe not.  The relevant sentence is, "... a generic Higgs doublet and a triplet imposter give equally good fits to the measured event rates of the newly observed scalar resonance."

In other words, there are other possible explanations for the CERN findings other than it having been a Higgs boson.  "Currently the uncertainties in these quantities are too large," Lykken and Shaugnessy say, "to make a definitive statement."

Like I said, I predicted this, and it certainly isn't because I have some kind of ESP regarding scientific discoveries.  Nor is it (more prosaically) because I even understand all that well what the Higgs boson is, and what the CERN findings meant.  My expectation that the CERN results would be challenged came from a more general understanding of how the scientific process works.  And this is why I make another prediction; the paper by Lykken and Shaughnessy will be widely misunderstood by the lay public.

In order to see why, let's imagine that you're at work, and there's a general meeting of staff.  Your boss states that there's a problem, one that will ultimately affect everyone in the business, and it's up to the staff at the meeting to propose a solution.  (S)he assigns all of you to go off, by yourselves or in small groups, and brainstorm a solution to the problem.  You and two others spend the better part of a day hammering out a solution.  You and your pair of friends look at it from all angles, and you are absolutely convinced that your solution will work to fix the problem.  At the end of the day, you bring back your solution to your boss and the staff.

Now, let's envision two possible scenarios of what happens next.

(1)  Everyone looks at your idea, and applauds, and tells you that you clearly have a working solution.

(2)  Each member of the staff takes his/her turn tearing at your idea, stating why it might not work, proposing ways to prove that it won't work, and recommends testing every single one of the ways that your solution could fail.  "Let's beat this solution," they say, "and try to see if we can get it not to work!"

Which one, in your opinion, is the better outcome?

If you said #1, you are in agreement with the vast majority of humanity.  #2 seems somehow mean-spirited -- why would your colleagues want you to fail?

#2, however, is the way science is done.

I see no greater misunderstanding about scientific matters that is more pervasive than this one.  While specific ideas in science are frequently the subject of erroneous thinking, there is no area in which there is more widespread lack of comprehension by the lay public than the general method by which science is accomplished.  When a scientific discovery is announced, when a new theory or model is proposed, the first thing that happens is that it is challenged by every researcher in the field.  Is there another explanation for the results?  Are the data themselves accurate, or did some inaccuracy or bias slip into the experiment despite the researchers' best efforts?  Can the results be replicated?

The last one, of course, isn't always possible -- and the Higgs boson result from CERN is an excellent example.  It took decades, and millions of dollars of equipment and research time, to get this single result -- it would be decidedly non-trivial to replicate it.  This, in part, is why the other physicists are hammering so hard on the data CERN generated -- it's not like they can go home to their own labs and try to make a Higgs of their own. 

So Lykken and Shaugnessy's paper isn't mean, it isn't some kind of bomb launched at the CERN team's reputation in the scientific world -- and it was bound to happen.  This is how science is done -- and why it is so often misunderstood by the lay public.  And now, I'll make a second prediction -- there will be a flurry of stories in the media about how "the CERN results aren't certain," which will cause large quantities of influential non-scientists to bloviate about how those damn scientists don't know what they're doing, for criminy's sake with all of those advanced degrees and all of that money and time you'd think they'd at least be sure what they were looking at.  So, inevitable as this announcement was, it is likely to have the result of further undermining the standing of science itself in the eye of the layperson.

And that's just sad.