Saturday, March 17, 2018

What is a Chemical Element?

Periodic Table Armtuk3.svg
Source: Wikimedia Commons

The periodic table of the elements organizes all the chemical elements.  Elements are, in most ways, the fundamental building blocks of the kind of matter that we are most familiar with.  You can go smaller than an element and find protons, neutrons, electrons and quarks (and possibly go smaller/more fundamental and find strings).  You can go bigger as well and find molecules built of several elements.  Most of the matter we interact with is made up of molecules containing multiple elements.  But in order to have water or wood or a zebra you need atoms of various chemical elements. 

While most of the stuff around us on Earth is made of compounds, often quite complex compounds when it comes to what makes up living things, we do have some experience with stuff made from single elements.  This is known as a "natural state."  Graphite, the stuff we use to make pencils write, is pure carbon arranged in layers that can easily slip off the tip of the pencil and onto the paper.  Diamond is actually one giant carbon molecule.  Oxygen, while we have a less tangible relationship with it, is perhaps the most important substance to us for, y'know, not dying. 

We also have experience with some metals as single element substances.  Aluminum is used to make foil and cans, silver has been used to make well...silverware and other household items, gold is used in jeweler and wires.  While these metals are often found naturally occuring in a larger compounds we have figured out how to use chemistry to remove the atoms of just the metal.  Natural state metals are extremely useful because they tend to be extremely malleable (you can mash them into a shape, like clay...though, this may require some pretty extreme heat) and conductive (these properties are why gold is so useful for wires). 

Though it may be a bit indirect, we also may have some experience with neon in the form of neon lights or signs.  We use several other gases that are chemically similar to neon to make these lights.  When excited with electricity, these gases will produce different colors.

But these are all experiences of substances at a gross macro level.  We can talk about malleability of metals or how neon glows when excited by electricity.  The factor that makes an atom a given element, though, is the number of protons.  You can change the number of neutrons (and get an isotope) or the number of electrons (and get an ion) but if you change the number of protons in an atom, you change the element.  Thinking about how that translates to the macro level can seem...a little strange. 

Take carbon again as an example.  Right next to carbon on the periodic table is nitrogen which, among other things, makes up most of Earth's atmosphere.  It seems, for lack of a better word, weird, that adding a proton to the nucleus of an atom would make carbon into a gas.  But that exact thing happens all the time!  Well, in geologic terms.  All elements have what is called a "half-life."  This is the time it takes for half of a given sample to undergo a transformation into another element.  Energy is required to hold even many smaller atoms together and so they do not last forever.  In the case of carbon, carbon 14 (which has 6 protons and 8 neutrons) "decays" over time and becomes nitrogen 14 (7 protons and 7 neutrons). 

What we more commonly think of as "radioactive" substances are substances that do this much, much more quickly.  Larger atoms like thorium, plutonium and uranium also tend to decay in a way that involves particles being shot out of their nucleus.  It is these particles, along with the much faster rate (carbon 14 decays in about 6,000 years, the most stable isotope of thorium in just around 18 days) that makes these isotopes dangerous. But it also means they actually turn into other elements.

The alchemists quest to turn lead into gold may not really have succeeded, but humans have found ways using particle accelerators to ram protons into atoms so fast that they stick, changing one element into another.  While experimenters have succeeded in turning other elements, like bismuth, into gold, this is only at the level of about a thousand atoms in a given trial.  This is about a billionth of a billionth of gram of gold.  So while it may not be what the alchemists were looking for, it does experimentally show that what we think of at the macro level as a fairly stable, concrete thing, is changeable and just comes down to the number of protons found in the nucleus. 

So what is a chemical element?  Like many things in the natural world, it depends on what scale you're asking.  At the macro level gold is a shiny metal substance that's really good for making things like rings and wires and such.  But at the atomic level it's just the number of protons in the nucleus.  If you add a proton to gold it becomes mercury and, at least at room temperature, it melts. 


Saturday, November 4, 2017

I Don't Think This is a "Post-Truth World"

I keep hearing about the challenges of science communication in a “post truth world” and I think that framing our challenges in this way plays into a false narrative.  I think simply saying that we do live in a "post truth world" says that on some level we agree.  I would actually wager that on average understanding of science is better now than it’s ever been.  Sure science education in the US needs work.  But it's not like we existed in some Eden where everyone understood statistics and uncertainty and p values and we’ve all been kicked out.  The default truth telling devices for the vast majority of human history have been and still tend to be myths and metaphors (see what I did there with the Eden reference?).  Yes, information moves faster, and misinformation is more readily available but propaganda has always been a tool of the powerful. 

I think that we expect that whenever we're very close to certainty about any scientific finding then everyone should just automatically understand.  I keep seeing references to the idea that people don't question gravity in the same way they do evolution.  Exactly.  Evolution questions belief systems that have existed for thousands of years.  Science doesn't just get to come along and overturn all that in less than a hundred (I'm counting from the discovery of DNA, the real understanding of the mechanisms of evolution).  Gravity is something we all experience every day.  Evolution takes place over generations and isn't something most people actually get to see unfold.  

I do agree that we need to get better at explaining uncertainty and statistics but we cannot come at this from the perspective that if we just explain these things in the best way then suddenly people will be able to understand the world from a scientific perspective.  A lot of the phenomena we're trying to educate people about (climate change, again, evolution) take place over the course of more than one human life and tell stories that run counter to both people's lived experience and deeply held worldviews.  

I think we owe ourselves the chance to revel in the fact that we live at a time where we have the best understanding of the natural world humans have ever had.  We get to look across the universe with the best telescopes we've ever had.  We get to peer inside cells and understand the mechanisms of mass.  We freaking observed gravitational waves!  This stuff is incredible!  And yes, deeply challenging to communicate effectively about.  But I think we ought to stop wringing our hands over a supposed "post truth world" and remember that humans have always been much better at talking in myth.  And I am hopeful that we can collectively find ways to talk about statistics in a way that helps more people understand how they work.  

Saturday, July 15, 2017

A Response to "The Uninhabitable Earth" by David Wallace-Wells

To start, I fundamentally agree with Mr. Wallace-Wells.  Climate change is the largest environmental challenge humans have ever faced and we should be deeply concerned.  It's important to keep in mind that we can make change, generally at the town, city or state level.  We can manage our shared resources more responsibly through practical, step-by-step processes.  Your neighborhood probably needs safer cycling and pedestrian infrastructure to help take gas-burning cars off roads.  Your city needs more renewable energy and bigger batteries to generate electricity without fossil fuels.  Your state, most likely, needs to reassess how it trades goods and gets food so we can reduce shipping distances and the carbon dioxide that comes with trucks traveling our highways.  There are a multitude of ways of reducing the amount of carbon dioxide that goes into the atmosphere, which adds to the heat trapping blanket that gas creates. By talking to your friends and neighbors, and possibly more importantly, communicating with state and city civic leaders, we get closer to making those possible futures a reality.  These kinds of changes are happening all over the country and the world, like in my city, Boston.  We have become a safer biking city over the last several years and city leaders are currently legislating more renewables in our electrical mix.

OK, now that that's out of the way.  You've probably read or at least heard about the article, The Uninhabitable Earth by David Wallace-Wells.  It was published in the New York Magazine last week and since its publication has created a flurry of conversation online and in real life.

A lot of the response has been about how it's OK to talk about how scary climate change is.  I think that's true, but I think the thing that everything I've read in the last few days misses is: it depends on a) who you're talking to and b) what your communication goal actually is.  I think that, again, what I have in common with Mr. Wallace-Wells is that we both care deeply about this issue and want to see more change and at higher levels.  I have had a lot of conversations about what can feel like a very grim future with colleagues.  But my communication with the public is generally never about the impacts.  It's about solutions.  This is something the article never actually gets to, except at the very end leaving a vague notion that some scientists somewhere are maybe working on carbon capture or something.  Oh, and Elon Musk wants to build a city on Mars.  He doesn't empower you, the reader, to know what to do with all this fear you now have.

While I think we agree on some basic premises, there's a lot I disagree with about the article.

1. The premise that we're not afraid.  Research shows that the majority of Americans are concerned about climate change and believe that climate change will harm Americans generally.  The issue is that we believe others are not concerned and that climate change will not harm us directly.  This is a communication issue not a matter of understanding that there is a huge problem that we all face.

Though a lot of the supporters of this article seem to have a very low opinion of social science, there also have been numerous studies done on how fear is generally an inhibitor to taking action, not the opposite.  Here's just one paper and one article from the Guardian.

2. There's a premise that we (all Americans, let's say) need to understand the science better.  If we just knew more about climate science and climate change, then we'd act.  Again, the research doesn't support this and often shows the opposite.  The more science you understand, the more polarized you become about acting on climate change.  There are, again, a  number of resources for this but I think one of the clearest is this video by Katherine Hayhoe.  What the article says is that all the scientists talk about climate change in a way that is statistical and muted and we really need to envision what the world might be like and get freaked out.  This also holds the premise that scientists are the best climate communicators.  They can be, like Hayhoe.  But they're not always.

3. More so in the responses, there has been a premise that when people are exposed to the more measured, hopeful kind of climate communication they're not going home and installing solar panels.  That's true, but not the point.  We should not be inflicting the solution on individuals for two reasons.  One, individual actions do not fit the scale of this global problem.  Two, this can lead to what's known as single action bias: where you buy a reusable water bottle and consider your environmental good deed done and then go back to living your life as is.  We live in a system that runs on fossil fuels.  It's the system that must change, not our behavior.  At the beginning of this post I attempted to show what solutions look like.  Communicating with each other and our civic leaders is currently leading to changes all over the country and the world.  Solar panels at home are great but they are not the solution.

4. There is a premise that we haven't seen enough change in the last 30+ years of measured, hopeful climate communication so the whole project must have failed.  However, it's only within the last several years that more concerted efforts to research, test and retest various ways of communicating about climate change have really taken off.  There's Yale, of course, FrameWorks Institute and NNOCCI, Union of Concerned Scientists and others.  Again, the cheerleaders of this article seem to have their minds made up about social science but I'm a firm believer in the scientific method, even when it comes to the very challenging world of human brains and groups of human brains.  Another major reason that we haven't made more change is that the fossil fuel industry is incredibly powerful and it has taken time and concerted effort to find ways to build political capital to oppose them.  It's still a work in progress.

5. The one premise that I do find somewhat intriguing to talk through is that we're missing the forest for the trees.  That is, a fear based communication strategy may cause paralysis in an individual but that if this sentiment, that climate change is real and it's scary, gets accepted on a collective level then this is what will really shift the cultural zeitgeist and create the political will to make change.  I don't want to get into the weeds on this one because I think it's a new argument and I don't have a good sense of its implications.  But, I will reiterate that part of this challenge still lies in the fossil fuel industry itself, and that a million more scared citizens does not take their power away.  I also think that a group of paralyzed citizens is still paralyzed.

I sincerely hope that those that are saying "this is good, people are talking" are right.  I will concede that part of what we need to do is open lines of dialogue and actually get talking about this giant problem that, data show, we are mostly all pretty concerned about.  I'm still not one bit convinced this is the right way to go about it.

Thanks for reading.  I look forward to hearing from you if you have anything to debate or add in the comments.

Thursday, March 23, 2017

Through the Pedantic Looking Glass

I realize that since coming back to writing this blog basically all I've written about is the use of technical language and when and how to use it.  There's two big reasons for that: one is that science and words are probably my two favorite things and right there at the nexus is the world of technical language.  The other is that as a science educator science words are integral to my everyday work and I think about these ideas a lot.

As I have voiced in slightly different words before, as I got closer and closer to the looking glass of being pedantic I found myself falling through into a world where nothing quite makes sense and "technically correct" is no longer the best kind of correct.  I'm writing about this again because of two examples that came up for me recently, both having to do, naturally, with cephalopods.

I have discussed many, many times the difference between "tentacle" and "arm" as it pertains to cephalopods. On a squid it's somewhat straightforward: tentacles are longer and have suction discs only on the clubs at the ends while arms are shorter and have suction discs all the way down.  However there are some problems with this.  First when you look outside the cephalopods this distinction no longer makes any sense.  Snails, polychaete worms, star-nosed moles all have tentacles.  They are often chemosensory but not always, they are often used for grabbing or holding food but not always.  Generally the only other appendage that gets called an "arm" are human arms.  So these are not definitions (which in science, technical words are generally thought to have definitions) but rather conventions.  That is, it is convention to call a cephalopod appendage with suction discs only on the club at the end a tentacle but this is not the definition of the word "tentacle."

The other real problem with arm vs. tentacle within the cephalopods is that the nautilidae have "tentacles" but lack suction discs entirely.  So again, these terms, both "arm" and "tentacle" appear to be conventions and not definitions.  That's fine, we use language in this way in colloquial life all the time.  It generally leads to only minor confusion.  The thing is that in science, we have tricked ourselves into believing that the words we use always have a very precise meaning.  The truth is, this is only sometimes true.  Planet, continent, species are all examples of very common terms that really lack a precise definition.  But there's fun to be had here.  The natural world is tenaciously difficult to put into the boxes our human brains want to put it in.  The fun is figuring out what other sorts of containers we can use.  Turns out these imperfect conventions are fairly useful.

The other example around technical language that came up recently was around the word "octopi."  In a lot of the scientific community this is regarded as an "incorrect" plural of "octopus."  This is because the word "octopus"is a Greek route word and not a Latin route word and the -us to -i pluralization is not used in Greek.  So the "technically" correct pluralization of "octopus" is "octopuses."  But here's the rub: a lot of people use the word "octopi."

And this is the argument that I think we all, myself included, need to do better at remembering: if people use a word and you understand it, it probably means it's a word.  If we only obey the "dictionary definitions" of words or the "technical" definitions of words we're saying that a whole section of language is completely off limits: slang.  Even though it might not be "good grammar" you know perfectly well what I mean when I use the words "a'int," "dope," "cool" (I don't mean temperature), etc.

This might be where we all fall into the looking glass of pedantry and "technically" correct:  I'll introduce the character of the Merriam-Webster dictionary.  They include "octopi" among their plurals for "octopus." So does this mean that "if the dictionary says it's a word, it's a word"?  Kind of.  Dictionaries change, words change, usage change and with this example that's the real point.  A lot of us think about the dictionary as being some kind of Platonic codification of our language.  Sorry, though, language refuses to play that game.  So if you understand when someone says "octopi" that they mean "more than one octopus" why correct them?

These rules morph and flex depending on your audience.  Should I use "octopuses" when I'm addressing marine biologists and "octopi" if my eight year old student has just used that word and not "octopuses?"  Yeah probably yes to both of those.

As I was developing this post I came across this graph on Twitter and thought about not even writing this post at all.  As you can see, I did write the post but I wanted to include it here, because, well, I still think it sums up what I just said a bit better than I said it.

click to embiggen.  Courtesy  

As usual I'll invite you to disagree, yell, berate and complain in the comments.  

Thursday, November 17, 2016

The Word "Worm"

It's no secret that I think common names are a problem.  They would be great if they were as systematized as scientific names but that's simply not the way language works.  Common names are a product of colloquial, everyday speak and therefore they are the antithesis of scientific names.  They lead to situations where we have a blue crab, a lesser blue crab, a red blue crab (seriously!?) and an ornate blue crab all inside the same genus.  Common names give us such taxonomically frustrating linguistics as the electric eel (a knifefish more closely related to catfish than eels), the bearcat (something like a civet), and the flying lemur (in a branch of mammals separate from all the primates).  

It also creates situations like when I get a video of some insects milling around on top of a tidal pool from a friend, she asks what they are, and I reply "Anurida maritima," and there is no common name.  The fact that we typically understand organisms only through their common names means that when we're faced with a situation when an organism doesn't have a common name we don't have the hooks to hang new information on much of the time.  I'm not suggesting we give up on common names, again, they are part of colloquial language and you cannot stop the indomitable force that is the evolution of language.  But there's one name that's always deeply frustrated me: "worm."

If you use the word "worm," people typically think of an earth worm, which is a land-living oligochaete in the phylum annelid, one of the closest living families to the arthropods.  But when you bust out a list (I got on this rant when I was once in a middle school science room and saw a poster of major animal phyla) of all animal phyla you start to see how little this name means: spiny headed worms, Acoelomorpha, segmented worms (Annelid), arrow worms, goblet worms, gastrotrichs ("worm-like"), jaw worms, acorn worms and roundworms, horsehair worms, ribbon worms, flatworms, peanut worms strange worms, velvet worms.  The number varies from source to source and also starts to get even more garbled when you descend to the subphylum and lower levels.  

So what, then, is a worm?  Etymologically speaking the word comes form the Latin "vermis:" vermin.  This is a great colloquial word with no real scientific meaning.  It's kind of like...anything gross or small so flies, maggots, earth worms, but even rats and snakes can be vermin.  Moving forward into Middle English you get "wyrm" which means a snake or a worm (and as I hope you all know, a snake is not a worm).  When you start poking around in other languages "wyrm" sometimes means "dragon" as well.  

So biologically what is a worm?  Well, the online OED says that a "worm" is "Any of a number of creeping or burrowing invertebrate animals with long, slender soft bodies and no limbs."  That is basically it, except for Onycophora, which does have limbs.  But we get to call anything that is bilaterally symmetrical and longer than wide a "worm."  Which is, as we've seen, a huge chunk of the animal world.  

So I'm not suggesting we get rid of the word.  But next time you call something a "worm," maybe remember how unspecific the word really is.

Friday, September 30, 2016

How We're Related to Other Four Legged Vertebrates

I'm doing battle with common misconceptions in biology, a lot of which we were all taught in school and people still being taught in school.  I'm not exactly sure the level of importance of this one but I think I can handle it fairly quickly.  As always, please correct any misconceptions or feel free to argue with me in the comments.

There is a common misconception, or rather a set of misconceptions, around the relationship of the groups in Tetropoda.  Tetropoda, or the tetropods, are amphibians, mammals, reptiles (really non-avian reptiles) and birds (which are reptiles, technically).  These are the major groups that are still around today.  When you look at a lot of cladograms for these groups they look something like this:
image by me, click to embiggen
What the cladogram actually looks like is something more like this:
image by me, click to embiggen
This is a minor difference, but it's an important one and there are several misconceptions that are portrayed by the first one.  First, and I've glibly added an explosion to humans at the crown in the first one to reinforce this, it portrays evolutionary time as always going from "less advanced" to "more advanced" with us humans at the very peak of...advanced-ness.  Evolution is not a movement towards more advanced.  Natural selection doesn't have any conceptions about what is more or less advanced, only what organisms are best at getting their genes to keep going.  Just check out the bacteria.  They're the polar opposite of what most would probably call "advanced" but they're darn good at making their genes survive for billions of years (and yes, a Domain is very different from these much smaller clades).  

Second, and I may be projecting here, but I think this also portrays the misconception that amphibians "evolved into" reptiles and then reptiles "evolved into" mammals.  But if that were true, wouldn't there only be mammals?  If reptiles evolved into mammals, why are there still reptiles?  

Partly because mammals did not evolve from reptiles, rather the two groups share a common ancestor.  Millions of years ago there was a population of animals that weren't mammals or reptiles.  As this population evolved it diverged into (at least) two distinct groups.  One is what we today call mammals and the other is what we call reptiles and birds.  You'll sometimes hear people use the term "mammal-like reptiles."  There's no such thing.  There are animals that came before the common ancestor of reptiles and mammals which are neither and there are animals after that common ancestor which are one or the other (sort of, this is a bit of a simplification).  There's a group of animals called Synapsids, which mammals are a part of, and early Synapsids didn't really look or behave much like modern mammals and maybe they were kind of reptile-ish (in that they were tetropods that weren't amphibians) so we've gotten stuck in the habit of calling those animals "mammal-like reptiles" even though they're really a lot more mammal than reptile.  

Third, this also may portray the misconception that reptiles have been around longer than mammals.  So again, it gets a bit complicated, but the two lineages that have led to what we currently call "mammals" and "reptiles" have actually existed for exactly the same amount of time.  That's because they share a common ancestor, they diverged from the same population of animals millions of years ago.  So what we might recognize as a "modern mammal" didn't appear until much later, these two clades have existed alongside one another since they both evolved from a common population.  

Let me know what I got wrong, what's confusing and what you're disagree with.  This was actually a bit harder to write than I thought and I hope that my simplifications make this understandable and fairly accurate.   

Friday, September 23, 2016


I recently finished the book Unseen City by Nathanael Johnson and rather than write a formal review (the upshot is that if you're knowledgeable about natural history, especially urban natural history you likely won't learn a ton but it's a good read, I would recommend it) I wanted to address a specific few sentences in the book about invasive species.  Johnson writes: "Immigrant species often do reduce native populations, sometimes significantly.  But the ecologist Mark Davis has pointed out that they rarely cause extinctions, and when they do it's of populations in isolated habitats like lakes or islands.  All this mixing may yield more biodiversity by producing more combinations, hybridization, and new species."  And in the book's conclusion: "These invasive species are not nature's destroyers, but rather its creators.  They begin setting up food webs, they evolve and diverge into new species."

While it's true that you can find examples, as Johnson sites, of stories where invasions are followed by an increased biodiversity I found it odd that he brings up this incredibly complex issue but only writes a little more than two sentences about it.  One of the big issues here is that we don't all agree on what an invasive species actually is.  I'll illustrate with three marine invertebrates that have been introduced to New England through human activity.  

One: Hemigrapsus sanguineus, the asian shore crab.  Introduced in 1988, this crab is considered a significant concern to local ecosystems primarily due to its voracious feeding.  This has two major impacts, one, it can easily out-compete local species like Cancer irroratus and borealis, two, it specifically has been correlated with a decline in juvenile lobsters (presumably it eats the post-larvals).

Two:  Carcinus maenas, the green crab.  Introduced in the early 1800s this larger crab species purportedly has an "insatiable" appetite and, unfortunately for us, seems to like many of the same animals we like such as clams and mussels.  It's also theorized that it may be contributing to salt marsh decline.  Which, I will point out right now, we think is bad.  I could ramble all day about salt marshes but the two highlights are that they are more productive than rain forests and sequester more CO2 than rain forests (which is why we should have been learning about them growing up in the 80s).

Three: Littorina littorea, the common periwinkle.  We have no idea when the common peri got to New England, and it could have been as long ago as circa 1000 AD when Vikings first came to North America.

Here's the rub: almost no one considers L. littorea an invasive.  Indeed, a NY Times article describing the research of Prof. Mark Bertness who has done some of the most robust work on the impact of periwinkles on New England coasts as far as I can tell, describes them as a keystone species.  You might call that the opposite of invasive.

And yet, when you put the present day ecological data on how periwinkles feed together with historic maps that show where there used to be salt marsh it seems very likely that periwinkles ate through a huge amount of algae and reduced much of that historic marsh to rocky shore.  And remember, we agreed above that salt marshes are good.

What's the difference between these three species?  Time.  There are a couple ways an invasive can be defined as such.  It's always non-native but to be invasive it's generally agreed that it has to have some negative impact on ecosystems and/or the economy.  For H. sanguineus and C. maenas it's easy to check those boxes but as soon as you look at the whole story for L. littorea you are forced to check the same boxes.  Struggling to define invasive (vs non-native, and why we don't call periwinkles invasive) I've often said "well, no one is suggesting any kind of management for periwinkles."  But no one is suggesting that for the others either.  At least when it comes to marine inverts, the plan is monitoring, education and the hopeful prevention of new invasives but there is no plan to manage the established invaders.  And while there are management plans in place for invasive terrestrial plants they will likely need to continue indefinitely.  So as far as I can tell, really the only difference is that periwinkles have been around for about a thousand years and no one remembers a New England ecology without them.  Heck, they might even be a keystone species!

So the weird thing is that when it comes down to it I do agree with Johnson that we shouldn't be losing our hair over invasives.  They are, in a lot of ways, just another example of the biological world moving and evolving and changing.  However, I'm hesitant to say, with such simplicity, that invasives (writ large) generate biodiversity.  Sure, you can find examples of that happening, but you can also find examples of invasives out-competing local species, close to extinction or completely altering huge swaths of ecosystems (and again, I'm going to make a value claim that salt marsh is more important than rocky shore, we can debate that in the comments if you like).

Through writing this I've been thinking about another book: Out of Eden by Alan Burdick.  In this book he doesn't so much argue that invasives are a good thing but that, well, there's not a heck of a lot we can do about them so...why freak out?  Again, I think that's where I land.  That's also a whole book, not a few sentences in a book that's not really about this complex and often really interesting issue.  They might be a problem but our relationship with invasive species is a huge part of the story of how we humans are forever changing the biosphere.  Maybe it's not great, I'm still not sure how to make a value claim about such a big, complex issue, but there's some really neat science going on there.

Also, kudzu stinks.


Johnson, Nathanael. (2016). Unseen City. New York, NY: Rodale Inc.