Contamination

I’ve had contamination on my mind, contamination as in substances getting into places they don’t belong . . . and screwing up scientific research (if not a whole lot more).  Perhaps, as this post may show, it's been more like a longstanding obsession.

News about scientific research where contamination is an enormous threat has become my reading staple.  This includes such research as the analysis of Neanderthal DNA with its various claims about interbreeding with Homo sapiens, and the research on the remnants of soft tissues in dinosaur fossils.  (See, for instance, New Method Rescues DNA From Contaminated Neandertal Bones, e! Science News, January 27, 2014; and Molecular Analysis Supports Controversial Claim for Dinosaur Cells, Kate Wong, Scientific American, October 22, 2012.)  But, as fascinating as I find those two topics, I leave the planet for my current favorite example of scientists wrestling with contamination.

Before the Mars Curiosity rover's launch, a drill bit was added to its drill, an act that occurred outside of NASA’s stringent protocols designed to keep Earth’s germs from contaminating another planet.  When that break from accepted procedure came to light in 2012, it exercised some folks.  But NASA’s planetary protection officer Catherine A. Conley discounted the potential impact, not because contamination hadn’t occurred, but because Curiosity wasn’t going to be anywhere on the Red Planet where ice would be found.  Said Conley, “The requirement for sterility is in order to be able to touch ice, and we don't expect there to be ice at the equator of Mars.”  (Science Friday, Mars Rover May Be Contaminated With Earth Microbes, September 14, 2012.)  Hmmm, “we don’t expect” ice at the equator.  But . . . we don’t know.

Then, last year, astrobiologists Alberto G. Fairén and Dirk Schulze-Makuch trashed most of the planetary protection protocols that NASA follows in its interplanetary program, deeming them unnecessary because Earth’s microbes have almost certainly already made the trip to Mars naturally (i.e., not on devices engineered by humans, but rather on ejecta from impact events on Earth), and costly by raising the expense of missions and, indeed, by diverting them from visiting the very sites where Martian life is thought to have a chance to exist currently (i.e., the sites potentially most vulnerable to the consequences of contamination).  Contamination be damned, they asserted.  (The Overprotection of Mars, Nature Geoscience, July 2013.)

Conley and biologist John D. Rummel responded to Fairén and Schulze-Makuch in no uncertain terms.  As reported in Astrobiology Magazine, the most persuasive (to me) of their counter-arguments was that non-contamination was essential for those aspects of the missions designed to detect traces of life on Mars.  We don’t go to Mars to detect life that might have simply hitchhiked on our interplanetary probes.  As Rummel is quoted as asserting, we have to make sure that we “don’t end up studying [our] own contamination when searching for extraterrestrial life.”  (Andrew Williams, The Overprotection of Mars?, Astrobiology Magazine, November 18, 2013.)  (To be fair, the fact that Curiosity was in an area that Conley considered merited lesser protection (so, don’t worry about a contaminated drill bit) seemed to be making some of Fairén and Schulze-Makuch’s points for them.)

Okay, that was a very long winded way of reaching the crux of the issue – to do the science, we need to keep from introducing things to where they don’t belong.

So, why am I worried about this?  Well, even in the amateurish science that I do in pursuit of microfossils, I try to avoid contaminating the matrix I’ve collected at various sites.  I want to be sure that the fossils I find in each sample actually rode in with that matrix and weren’t introduced by a “dirty” tool or instrument (i.e., a consequence of not following my “stringent” non-contamination protocols).  Or I want to know they weren’t added to the matrix by some unthinking or unscrupulous miscreant.  I’ll come back to this last at the end of this post.

A specific instance triggered a heightened attention to contamination.  Pictured below are the two sides of the same tiny microfossil, a foraminifera.  It’s about a fifth of a millimeter (200 microns) in diameter – small in the foraminifera scheme of things (and just at the limit of what I can photograph, well, maybe a bit beyond that limit).

Its morphology is common.  I believe the shape is planispiral, that is the foram added new chambers all on the same plane.  The specimen is too small, worn, and obscured by matrix, for me to be absolutely sure.  Regardless, I was excited when I spotted it, not because of its purported genus or species, but because of where I found it.

This requires a bit of background.  I recently tried to pass myself off as someone who knew a bit about microfossils and finding them in my home state of Maryland.  It was clearly false advertising since I know a fair amount about only two (foraminifera and ostracodes) of the many different kinds of microfossils that might be found and I’ve collected those specific microfossils from only a handful of sites around the Chesapeake Bay (hardly all of Maryland).

That said, I have collected “macro” fossils from many different sites in the state, and some of these are impressions left in pieces of different kinds of sedimentary rock such as sandstones or mudstones.  Maybe, I thought, I wouldn’t even need to leave the house to search for microfossils elsewhere in the state.  Pictured below is a chunk of Oriskany Sandstone from a site near the town of Hancock in the western reaches of Maryland, up in the state’s panhandle.  This material is from the Devonian Period (416 to 359 million years ago).  (I wrote a post several years ago on this and other material I collected from Western Maryland.)

According to paleontologists Howard Armstrong and Martin Brasier, in their great book Microfossils (2nd edition, 2005), limestones, sandstones, and shales are candidates for what they call the “scrubbing-brush method” of extracting microfossils from matrix.  Their key instruction is:

Take a fresh piece of the rock and scrub it under the water with a hard bristle toothbrush or a scrubbing brush.  The action should be as gentle as possible to obtain a residue without damaging the microfossils.  (p. 274)

Straight forward enough.  So I took pieces of this sandstone, submerged them in a pan of water, and scrubbed.  I then poured the water through a sieve to collect the sandy residue, let the residue dry, and I was in business, with a total of about 1/8th teaspoon of sandy matrix to explore.

The first hour or so of searching yielded not a trace of a fossil.  Then I turned up a small cylindrical piece of material that broke apart into very tiny little disks.  Crinoid?  Perhaps.  A bit later, I spotted it – the foraminifera pictured above – an oasis in a wasteland.

I was thrilled.  That is, until I started to research the foraminifera that were around during the Devonian.  Does this specimen fit?  The British Geological Survey has a nifty little table showing the major events in the evolution of foraminifera.  The problem isn’t that foraminifera don’t go back to the Devonian, they do.  In fact, they predate the Devonian with the earliest examples appearing in the Cambrian.  The problem is that, if one were to rely solely on the British Geological Survey’s table, this particular morphology and shell composition smack of later stages of evolution.

Armstrong and Brasier offer an extensive table that describes the wall structure, arrangement of chambers, and geological age range of major foraminiferal suborders and superfamilies (p. 161-163)  Working from that table and with Alfred R. Loeblich, Jr. and Helen Tappan’s Treatise on Invertebrate Paleontology, Part C, Protista 2 (1964,  5th printing in 1985), I found a genus that offered some hope – its geological age encompasses the Devonian and its general morphology is similar to my specimen.  But Loeblich and Tappan’s illustrations and text leave a something to be desired, they are mostly silent as to relative size, and some of the critical distinguishing characteristics are hard to discern on a small, worn specimen.

Nevertheless, I grabbed the sanctuary they offered and speculated that this shell might, just might be from Nanicella, Henbest 1935.  This is a decidedly Devonian inhabitant with chambers in a planispiral coil and calcareous walls.

The article in which Lloyd G. Henbest of the U.S. Geological Survey named this genus appeared in 1935 in the Journal of the Washington Academy of Sciences (Volume 25, Number 1.)   He explained that the name he gave the genus reflected “the reduced shape and size of the chambers and their subordination to the general architecture of the shell (Latin nanus, dwarf, +cella, chamber).” (p. 34)  He described Nanicella in terms of the other genera it’s similar to or differs from, which means his description of the new genus smacks of frustrating origami instructions that tree backwards:  “Step 1:  From a bird base, . . . .” and, unless you remember, you’re off for instructions on how to fold the bird base, and so on.  Perhaps that’s not surprising, given that taxonomy’s always relative, but there’s precious little in his description that tells the reader what it actually looks like.  Sadly, he offered no illustration of the new genus.

The alternative to this being a Nanicella, the possibility I really didn’t want to contemplate, was that I’d contaminated my sieves or pans or slides with a specimen from a different matrix.  What had gone through the process most recently?  Material from the Lee Creek mine in North Carolina, specifically from the early Pleistocene’s James City Formation.  This material had harbored a few foraminifera of a similar shape, though they were significantly larger and had smooth external walls.  A voice in my head nagged, “Hey, your specimen could have been a juvenile, and the shell might have recrystallized.  Besides this is the only microfossil to show up.  Damned suspicious, if you ask me.”

At this juncture, I have no answers to the questions:  Contamination or not?  A Devonian foraminifera, hundred of millions of years old, or a youngster of a couple of million or so years?

Does it make much difference?  Not in the larger scheme of things, but I would be very disappointed if I were guilty of contamination.  Hey, I’ll own up that, after scanning matrix from the Lee Creek mine for fossils, I’ve spread some of this phosphate rich material over my flower beds.  I’ve done it only after a serious internal debate about contaminating a site for a future paleontologist (yes, it's gone that far).  Fairén and Schulze-Makuch said contamination was a fact of life.  But, it’s not always a good thing.

Writer Elizabeth Kolbert had a two part article on extinctions that ran in the December 16 and December 23 & 30, 2013 issues of the New Yorker (which hide behind a paywall), taken, I presume, directly from her new book The Sixth Extinction:  An Unnatural History (coming out later in February, 2014).  The first part was titled The Lost World:  The Mastodon's Molars; the second, The Lost World:  Fossils of the Future.  I was puzzled by the two parts – they differed so much in voice, structure, and tone.  The first was history; the second was a first person narrative.  Perhaps they reflect the structure of the book – a chapter on a past exploration and explanation of extinctions alternating with a chapter on Kolbert’s travels around the world to see current exploration of past extinctions and the unfolding sixth extinction that we humans have precipitated, and so on.

What irritated me the most about this article was an act of contamination that she just laughed off.

In England, with biostratigrapher Jan Zalasiewicz, Kolbert went in search of graptolites.  As she wrote, Zalasiewicz “has more or less invented a new discipline, which might be called the stratigraphy of the future.  It is based on a simple, if disturbing, premise:  humans are so radically refashioning the planet . . . that we may well end up producing a catastrophe comparable in scale to the one that laid waste to the graptolites.”  (December 23 & 30, 2013, p. 48, 49.)  He has been campaigning for a change in the name of our present epoch.  Rather than Holocene, this should be called the Anthropocene because this geological epoch is marked, for better or worse (more the latter), by what human beings have done to the planet.

Zalasiewicz is a graptolite expert, and from the fossil record of these organisms, he and others have teased out important insights into ancient climate change.  Graptolites were decimated by a mass extinction at the end of the Ordovician (444 or so million years ago) though they themselves did not go extinct then; rather, they died off later in the middle of the Devonian.  The organisms lived in colonies and what is fossilized are the connected chambers each individual built.  In his compelling book, The Goldilocks Planet (2012), Zalasiewicz described the fossils as looking “like miniature flattened fretsaw-blades.”  (p. 67.)  An Ordovician specimen is shown below.  (The image was downloaded from Wikipedia.  It was taken by Mark A. Wilson of The College of Wooster’s Department of Geology and he has released the image into the public domain.)

At the conclusion of the second installment of her article, Kolbert really disappointed me.  Yes, it will become clear that I’m making a mountain out of a molehill, but the issue is real.

After spending time with Zalasiewicz in the field, Kolbert had amassed a collection of pieces of shale with the imprint of graptolite colonies gracing them.  But she discovered, as she packed for her flight out of Heathrow, that her suitcase came in over the weight limit.  Something had to go, and the expendable was what she described as “the least impressive examples” of her graptolite specimens.  So, she wandered through the lobby of her hotel, came out to the parking lot, and, in the dirt border of the parking lot, made a small pile of the over 400 million year old pieces of shale and their traces of ancient life, and left them.  Of this act, she wrote:

I tried to imagine a geologist in the year 100,000,000 A.D. stumbling onto the site.  It was hard for me to picture what he (or it) would look like, but I got a certain satisfaction thinking about how puzzled he would be when he came upon my Silurian graptolites nestled amid the wreckage of the Anthropocene.  (December 23 & 30, 2013, p. 56.)

I found it sadly ironic that she laughs off her little transgression in an article (and book) about how humans are polluting and contaminating the planet.