"Form Follows Function"

The title of this post, a phrase often associated with architecture, is a concise way of saying that the appearance or aesthetics of a functional object often is constrained by its ultimate use. Synthetic sediment can be thought of in this way.  Its composition and to a lesser extent its appearance may be constrained by its specific application.  This might be a good working assumption for those developing synthetic sediment: decide a batch’s functionality and work backwards to develop a formulation to achieve that functionality. 

We think up many possible uses or functions for sediment in a laboratory setting: aquarium decoration, substrate for testing interactions between chemicals and sediment components, substrate for growing aquatic plants or culturing aquatic macro-invertebrates, a clean reference sediment to control test variables associated with physical properties of test sediment, a chemical-spiked positive control to confirm the observed response to a test sediment, and others.  Each of these uses, and others we might imagine, requires a different “minimum” level of detail or complexity of the sediment substrate; a substrate cannot be too complex for a given use, but complexity less than the minimum will not work.  We could think of natural sediment as having the highest level of complexity, so any sample of natural sediment will work for any use.  The accuracy of that statement might be debatable, but for our purposes the complexity of natural sediment is the benchmark to shoot for and to which synthetic substrate complexity is compared.

The first response might be to develop one, universally-complex synthetic substrate and use it for all possible functions and applications.  In practice, that might be an ambitious approach because of the difficulty in assuring that the complexity of the synthetic material matches the natural.  Secondly, replicating that level of complexity by multiple labs in multiple locations throughout the world would require a lot of time and expense by the participating labs.  For many applications, such effort would be over-kill.  Lastly, regional differences in natural sediment characteristics, or organism differences in micro-habitat requirements, would make a single universal synthetic substrate inappropriate.  This is one of the drawbacks with current synthetic sediment formulations.

So thinking of synthetic substrates as use-specific can simplify how specific labs might approach formulating it.  Recipes and components (type, number) would be specific to end-use, regional environment, data quality objectives and organism habitat needs.  To apply this approach requires a clear understanding of what components can or should be used for which end-use substrate.  This means knowing how each individual component affects and contributes to the characteristics of the whole, and how each interacts with the other components.

Most of my work with synthetic sediment so far is focused on researching, documenting and testing how individual components affect characteristics of the whole material.  This knowledge will help end-users of synthetic sediment select appropriate components and recipes for their specific needs.  Some components have little influence on substrate characteristics; large particle-size sand (silica; quartz) is an example.  Most have a strong affect on the characteristics of the whole material.  Examples include small particle-size geochemical clay (layered alumina-silicate minerals), geochemical silt (simple oxides, simple silicates, carbonates, feldspar and granite minerals), all types of organic matter, and mineral components like metal-sulfides.  One set of experiments, presented at a technical conference in Long Beach, California, demonstrated how the type and amount of mineral oxides included in a mixture can have a profound effect on pore water pH and on the cohesion and compaction properties of whole substrates.  You can find the summary of that presentation on page 313 of the 2012 conference abstract book, found online HERE. 

More tests will be done with other minerals and organic matter.  Stay tuned for more posts to this blog. 

In-house testing with organisms.

Well, I'm back.
After over a year of attempts (and $$), I've finally succeeded in starting and maintaining a healthy culture of Hyalella organisms.  This is an enormously important milestone!

The dark spots on the white gauze are Hyalella..

 Here's what they look like really up close:

[I did not take this one... photo was borrowed from an online source]

In fact, it's been so successful... they're proliferating rather quickly.  I went from one small bag of 100 organisms, to this:

and now I'm up to this:

We start excavation in the backyard for the pool later this summer... just kidding.

I now will be able to more frequently test synthediment recipes on real live biological organisms, the type that live in natural sediment, and get feedback information much quicker.  This is the break I've been needing to make quicker progress.  My wonderful Partner-Labs have gone above and beyond their everyday work to provide me with some very good data-feedback.  I will continue working with them because they have access to biological species that I do not.  But this Hyalella culture breakthrough will help things move along at a faster pace.

I have worked out a certain combination of fine particles (in terms of types and amounts) that make the material "sticky" or cohesive.  This is very important to some organisms who need that kind of sediment for successful construction of their "burrow" habitats.  They do not like sediment that is loose and flowing (like sand) because their excavation only collapses as quickly as they dig.   I'm presenting this work at a scientific conference in November.

I had a bit of bad timing with that cohesion work: the batches I sent to labs with access to "burrowing" organisms were sent just a few weeks BEFORE I finally worked out the composition and combination.  Here are two photos that illustrate how the early synthetic material failed to function like natural sediment. 

One of my early synthediment recipes...

... looks nothing like the real stuff!!

Those little burrows and tracks in the lower photo are the tell-tell signs of healthy living benthos. They are conspicuously absent from my synthediment batch!  Although these results were "negative" in the sense that these batches were not suitable to the organisms, they were positive in that they provide valuable information to guide future adjustments.  As has been said, "science IS a continuing process..."

So the next stages of development will involve lots of experiments exposing Hyalella to batches of synthediment in my own lab, and will focus on adding organic material to the most successful mineral recipes.  Onward!

Uses for synthetic sediment: Part 2

Happy New Year, dear Readers (... in April?).  I must post more frequently than once per quarter!  Thanks to all who have told me they enjoy reading this blog.  Pass the word on to your friends and family.

Today's post explores another possible use of synthetic sediment: to strengthen the reliability of data generated from samples of natural sediment.

Environmental Data
Environmental samples are collected and analyzed, and environmental professionals interpret that data to guide their decisions about how to manage and steward the environment.  The analyses are done by chemists at environmental laboratories.  Part of the chemists' job is to check that the instruments used to analyze samples are giving them reliable readings, and to report their "instrument reliability" findings to the client who submitted the samples.  There are many types of instrument-checks, but one is to analyze a material (a reference standard) that contains a precisely known amount of what they're measuring.  Doing this isn't to find out what's in the reference standard; it's to "test" the instrument.  By comparing the known amount of material in the reference standard to the reading given by the instrument, the chemists get a sense for how well the instrument is working (... how efficiently and accurately it is detecting the material they're measuring).  This information is the only way the chemists know how much confidence they can put in the instrument's readings, and whether those readings truly and accurately reflect the actual composition of a field sample containing an unknown amount of material.

Natural Sediment is Alive
Natural sediment is an enormously complex mixture of components (living organisms and non-living material) and those components are actively changing all the time.  Very few of those components are stable (almost all components in natural sediment change to some degree, over time).  Because of this, natural sediment makes an extremely lousy laboratory reference standard.  One interesting component of natural sediment is a material that contains sulfur.  It's called acid-volatile sulfide (AVS, for short) because it becomes a gas (volatilizes) when it reacts with acid.  AVS is one of those sediment components that constantly changes: it occurs in different amounts from location to location within a sediment bed, and the amount found at any one location changes at a over time (perhaps seasonally to some degree).  It's created by the activity of micro-organisms in the sediment munching on organic material and "inhaling" dissolved sulfate ions (think, Epsom salts).  The organisms "exhale" sulfide (think, rotten-egg odor), and this sulfide is very reactive and very different than the original sulfate.  Sulfide quickly combines with many types of metals in the water to form a new chemical, one that doesn't dissolve in water very well (a precipitate).  Sulfide is different from the original sulfate also in that sulfide does not tolerate being around dissolved oxygen.  When it reacts with dissolved oxygen in the water, it reverts back to sulfate.. which is again available for those sulfate-"breathing" bacteria to use in their part of the cycle.

One of the most abundant metals in the earth's crust is iron (Fe).  Its presence in natural sediment is not usually considered contamination.  The natural metal iron (and also another natural metal, manganese; Mn) combines with sulfide to form a dark-brown or black precipitate which stays associated with the sediment (iron sulfide - FeS; manganese sulfide - MnS).  In simplistic terms, chemicals like these constitute AVS in natural sediment.

Because of AVS's instability around dissolved oxygen, what happens in natural sediment is that the very thin surface layer of sediment along the sediment bed is in contact with so much dissolved oxygen that almost no FeS or MnS exists.  There is a point within sediment where the migration of oxygen from the water above is just balanced by the biological activity of the sulfate-"breathing" bacteria living and growing in the deeper parts of the sediment.  At this depth, and below, the sulfate is converted to sulfide faster than the oxygen from above can migrate down, and the AVS can persist without being oxidized.

This "boundary" depth (where the rate of at which sulfide is created (by bacteria) just balances the rate at which oxygen migrates down from the overlying water above) fluctuates wildly based on all sorts of factors and conditions.  An important one is the temperature of the water, which dictates not only how much oxygen can dissolve in the water, but also the activity of the bacteria in the water.  In cold temperatures (fall/winter), water can hold more dissolved oxygen and bacteria are lethargic: that combination favors a net loss of sulfide (more is oxidized than is produced  = low AVS concentrations).  During periods of warm temperature (spring/summer), the combination of lower dissolved oxygen in the water and high bacteria activity favors more production than oxidation (high AVS concentrations).  So not only do AVS concentrations vary from season to season, but it also varies from place to place, depending on available organic material and dissolved sulfate and how easily dissolved oxygen can penetrate into the sediment.

So... how do chemists and environmental professionals ensure that their AVS instrumentation equipment is accurate if it's always changing??  They don't use a natural sediment sample containing AVS.. that's for sure.  They rely on measurements of pure chemical FeS or MnS or other stable metal-sulfide compounds.  That's not very realistic when you consider that the "real" samples being analyzed are soil/mud type materials, whereas the "reference" is a pure chemical scooped from a lab bottle.  Wouldn't it be more relevant to measure AVS that's associated with a sediment sample?

Sediment Alternative for Reference Standard
In theory, synthetic sediment may be constructed to simulate the complexity of natural sediment, without all the complex changes.  In other words, synthetic sediment could be prepared to represent a "snap-shot" in time of a sample of natural sediment.  The materials in the synthetic sediment would be consistent in composition and stable through time.  Such a material would make an excellent reference standard for sediment analysis.  Also, such a synthetic sediment would simulate natural sediment more closely than just measuring a pure sample of the material being measured (which currently is the only way to "instrument-check" for some sediment components).  The stability of synthetic sediment against uncontrolled changes like those experience by natural sediment is only part of the equation for a synthetic sediment reference standard.  The other part is finding a chemical that acts like AVS in all aspects EXCEPT in its instability when exposed to oxygen.  That's the focus of one part of my work: finding a metal sulfide that reacts with acid like natural sediment, but that does NOT oxidize in air or when in contact with dissolved oxygen unlike natural sediment.


Other Stuff.. if you're interested...

Why is reliable data important?
Making an accurate "diagnosis" of the sediment that was sampled depends on how reliable are the lab data.  Here's why...

Reliability in the world of scientific data doesn't exactly mean "dependability" like one might think ("It's critical that you be there on time... I'm relying [depending] on you.").  Reliability of data is closer in meaning to "confidence" in data.  It's the way scientists address the question: "Can I trust this measurement?"  Another way of asking this question is: "Does this measurement REALLY reflect what is actually going on in this sample?"  I think these and other variations of this question are at the heart of science.  We explore the universe by poking and prodding and measuring tiny parts of it, to see what it tells us about itself.  If we want an accurate understanding of that part of the universe, the response we get from our poking and prodding needs to accurately reflect what is there.  On a very basic level, imagine the consequences of reading the temperature of an oven with a broken (inaccurate; uncalibrated) thermometer.  A reading of 70*F on that thermometer may mean the difference between a second degree burn or just a call to the appliance repair shop.

It's the same for scientific endeavors.  A measurement of contamination level in soil from a lot that is slated to be converted into a playground needs to accurately reflect what really is there: the "reliability" of that measurement could be the difference between years of fun and laughter, or years of unexplainable skin rashes.  In a less dramatic example, data from sediment in a river bottom could suggest possible hazard to the ecology of that river (based on the level of contamination present in the sediment), or the data could indicate a self-adjusting/self-attenuating river with no hazard to the ecology.  The interpretation of the data depends heavily on the answer to the question: "How confident are we that those data are accurately reflecting actual conditions in the part of the environment we sampled?"  A lot rides on the level of confidence in scientific data.

How do materials get buried under sediment?
Sediment under water bodies (streams, creeks, lakes, estuaries, bays, oceans) are collections of particles of various sizes and compositions.  The same way late-season snow storms cover the remnants of earlier snow storms, sediment particles continually settle on the bottom, covering "older" sediment particles.  The oxygen and other dissolved material in the water above the sediment surface can migrate into the pore-water between sediment particles.  The sediment bed contains a whole host of components, both living and non-living.  The living part includes bacteria and the non-living part includes organic material and dissolved salts that are food and "oxidants" for the bacteria.  So the more particle material "rains" down onto the sediment surface, the deeper the sediment bed gets, the further away the deeper layers of sediment get from oxygen-rich water.  These deep areas are devoid of oxygen and are called anoxic.