The research process, and a preliminary answer
Preface: “AUGHH, SO BORING!” is probably the first response I expect from this post. I can hear the sound of dozens of laptop screens shutting or browsers navigating away to avoid reading this post. It delves into the daunting world of academic and scientific literature, where the English language is changed into some strange, twisted version of itself, lengthened in sentence and peppered with weird acronyms that are meaningless to all but the most entrenched in the field. But reading research literature is absolutely essential to how we arrive at answers, especially in academic fields like the science. And it’s getting easier to do; academic researchers have realized the importance of making their work accessible to everyone, and have pushed to make the language they use easier to understand.
So if you want to get your feet wet in the academic literature, you want a glimpse into what a lot of grad school is about, or you’re just curious about what researchers in the sciences do for MUCH of their time, this post will tell you.
In the last post I defined our question, which was “What is the smallest self-sustaining ecosystem that we could send to space?”. Now I’ll cover where and how to look for an answer to that question in the scientific literature and give a preliminary answer to our question. By the end of this post, you’ll know how to use scientific literature to answer questions of you own!
Diving into scientific literature
Scientific literature can be daunting because it looks unlike anything else we read, but it is the fount of all scientific information. It is the original source of all the information and data, which is collected by news articles and websites to deliver to you, the reader. As with anything involving interpretation, news articles and websites can leave out important information or get things outright wrong when they report on information from the scientific literature, but the only way for you to know is to go read the original scientific article or research report yourself. So if you want to truly know something, read the scientific literature.
We’ll divide our dive into the scientific literature into three sections: searching the scientific literature for research articles, sorting out which research articles in the literature are useful, and analyzing research articles to answer your question. Doing these three steps successfully is difficult and will be slow, especially if you’re new to the scientific literature. Give yourself time when searching the scientific literature and write your question at the top of your page or next to your computer to keep yourself on track.
Step 1: Searching for research articles that might hold answers
In this step I collect several research articles that might have answers to my question to search through in depth later. The best ways to search the scientific literature are Google Scholar and NCBI’s PubMed. Google Scholar searches research articles and primary literature instead of webpages, but works in a similar way to the standard Google search engine so we won’t cover it. NCBI’s PubMed is also a search engine, but it searches all of the primary literature indexed vetted by the National Institute of Health to create a customizable, highly-specific, extensive output. It is the go-to site when I need to find research articles.
Try PubMed by clicking here and typing in something you want to search.
Like Google, you’ll see that a search will yield research articles. Clicking on an entry pulls up the PubMed page, which contains the research article information, including the title, author, journal it was published in (which, like magazines have varying degrees of prestige and veracity), and a super-useful summary of the paper called an Abstract that will help you determine if the paper is useful. I prefer to cast a wide net in this step, saving anything that might be useful or interesting to read to answer my question.
If you read the Abstract and think this research article has answers, your next goal is to get the full research article, which is easiest through the “Full Text Links” in the upper right of the PubMed entry. This can get…uh…tricky. In the best cases, the article is free either from NCBI or the journal that published it and the box under “Full Text Links” will say “free full text” or “free final version”, which you can click to get to an HTML or PDF version of a research article. If a full version isn’t available for free (you’ll know because the link you clicked on will say ask for $$ to access an article), then there are a few ways you still might be able to get a research article for free. The first is to check the lab website, which can be done by Googling the name of the last author (here, Pace) and the article’s title–some professors will post PDFs of their research articles on their lab website. A second option is Kopernio, which searches a few websites to determine if the article is freely available. If you don’t find a PDF using these methods, you can also contact an author through ResearchGate or via email and ask for a copy of the article; most authors are happy to share. And the last option, one of dubious legality, is to pirate it from the Russian repository Sci-Hub. Whichever way you choose, save the research articles you can as PDFs into a folder to use in step two.
Step 2: Sorting out which research articles matter
Now you have a pile of PDFs in a folder, one (or some) of which may have the answer to your question. But most PDFs won’t and there are more papers in the world than hours you have to read them, so it’s time to start sorting.
I like to sort into three categories: useful, less useful, and not useful. To figure out which papers are useful, I’ll open the file and skim the Abstract, figures, and figure captions — 90% of the time, this is enough for me to figure out if a paper isn’t useful. If I still can’t decide, I’ll read the paper’s Discussion section. If it doesn’t have my answer or any useful related info, it goes into the “not useful” folder. If it doesn’t clearly have my answer but might have some useful info, it goes into the “less useful” folder. And if I think it’s useful, I leave it in the main folder.
If you happen to find the answer to your question while skimming a paper, that’s awesome! It does happen, especially if you’re looking for a specific fact or statistic. But for more complex questions, you’ll probably need another step.
Step 3: Finding your answer by analysis and synthesis
In this step, you’ll read the articles you’ve found in depth to piece together the information you need to answer your question. This step takes the longest – while the last two may have taken hours, reading through all the papers you think are relevant and synthesizing an answer can take days, or if the question is really big or you’re really new to this process, weeks.
Since this is the long haul, it’s best to start by getting organized. Pick a method of keeping notes, be it on paper or digitally, and stick with it. If you have more than five or six papers, you’ll likely want to keep track of your notes by paper. I use Mendeley to organize my papers, and OneNote to keep track of all my notes on them, including quotes and excepts from papers I’ve read.
Now, down to the actual reading. It will take time for you to read a research paper, especially if you’re new at it. Be patient with yourself and start with small steps, maybe reading only one paper a day. If you’re also new to the field of your question, then doubly so– you’ll be learning new words and vocabulary as well as how to read a paper. Look up definitions, write down acronyms on a sheet of paper next to you, and take notes somewhere on things relevant to your question. Try to rephrase the findings of a paper in your own words, which tests how well you understand it. Be patient and steadfast and the papers will grow easier to read.
The last part of this step is synthesis, using what you’ve learned from the research and your brain to make an answer. It’s difficult and will also take practice. Try to answer your question after each paper you read; write it down, read it, and see if there are still missing pieces in your answer. This isn’t a research paper, so your answer need not and should not be a whole essay unless that is what you need to answer your question. A sentence, three sentences, or a paragraph is better if that’s all it will take.
The true test of whether you’ve answered your question is to give the answer to someone else. Take your question and answer to a teacher or friend or family member. Tell them the question and explain the answer to see if you can help them understand. If you’re successful, congratulations! You just taught someone something they might not know. If you’re not or they disagree with you, try to be humble and ask for advice. If they disagree, ask where they get their answer and go look it up. If they ask questions, you can return to the research and dig for more answers. Like an adventurer, keep following the threading trail until you find the answer. It might be something no one has ever answered before.
A preliminary answer to our question, or one is the loneliest number
Phew! The above was an essay I hadn’t originally intended to write, but I started it and it seemed to matter so much in a day and age where there seem to be so many questions that need answers. Thank you if you read through all of that.
I promised a preliminary answer this week and an answer you shall receive! An early answer to “What is the smallest self-sustaining ecosystem that we could send to space?” is….drumroll please….
ONE (Chivian et al., Science, 2008). Yes, a ecosystem of one was discovered deep in the Earth’s crust. It was found in a mine shaft in South Africa at 2.8 km deep, or around 933 floors if you take a floor as about 3 meters tall. If you were taking a standard elevator down to this depth, you’d be on waiting in it for a little over two and a half hours.
The lonely microbe’s name is Delsulforudis audaxviator (we’ll call it D. audaxviator), which as far as I can tell with Google means “the bold traveler of the sulfur lineage.” And it’s capable of living alone because it carries a complete toolkit of genes that help it do everything it needs to survive – helping it ‘eat’ carbon dioxide, carbon monoxide, and formate, ‘drink’ the nitrogen it needs from out of the air as nitrogen gas, and ‘breathe’ sulfate compounds as we breathe oxygen. While we breathe out carbon dioxide, it breathes out hydrogen sulfide gas, which smells of rotten eggs. It’s a one-microbe jack-of-all-trades, do-it-yourself word down there, and D. audaxviator is well-prepared.
So now that we have an answer, are we done? Uh, no. This is a bad answer to our question because it doesn’t meet the rules we set out! Look again at the description of D. audaxviator above. What do you notice? Well, it makes hydrogen sulfide gas like we make carbon dioxide. That’s a waste product. Where is that waste product going? If it just hung around, it would build up. And where are carbon dioxide, carbon monoxide, format, nitrogen gas, and sulfates coming from? If D. audaxviator uses them all up, does it starve? Does it suffocate? This systems fails to meet our criteria of self-sustaining.
If you read the source paper (linked here), you’ll find two things of note. One, many of the things D. audaxviator needs to survive are made from chemical reactions in the earth and somehow either make it to D. audaxviator or D. audaxviator finds them. This same method might be used to sweep away any waste products made, so D. audaxviator doesn’t’ have to worry about them. Unfortunately, we don’t have the luxury of shunting off waste like this while in space. We won’t have the comfort of earth.
The second thing to note in the paper is that while researchers found more than 99.9% of the genetic info from the mine sample comes from D. audaxviator, that is not 100%. There could be some few other microbes living down there, taking the waste products of D. audaxviator as food and turning them into something else. Or maybe they’re taking other compounds and turning them into the compounds D. audaxviator needs to survive. It’s hard to tell for now, and we may not get an answer anytime soon. The researchers couldn’t clearly identify what these other microbes were because there was so much D. audaxviator down there. It’s the majority, and finding the other microbes would be like playing a game of Where’s Waldo, except imagine your book is now more than 2 km deep in the earth and the only chance you get to look at it is through a grainy photograph that’s been fed into a shredder and then put back together again. It might be a while before we get an answer.
So we found an answer to the question, but it’s not a very good one. Let’s follow the trail of research using Step 3 to find a better answer.
Life on Earth is complex and if we want to live out in space, it’s unlikely that we can take every species with us. Our ventures off-planet have carried only the bare necessities and due space constraints (pun intended), that’s unlikely to change in the near future. But constraints breed creativity, so to honor that spirit let’s look at what we small groups of species we can send off into space that would continue to survive without the umbilical cord of earthly supplies. Specifically, our question is:
“What is the smallest self-sustaining ecosystem that we could send to space?”
That’s a tough one, so we’ll start by defining what we mean in this question. First, let’s tackle the meaning of ‘ecosystem’. This is the word we use to encompass many different species living and interacting with each other and the nonliving components of their environment. This is the mix of all the microbes and trees and animals in a rainforest, combined with who eats who and conditions like the amount of rainfall or sunlight available. It is the tiger that eats the deer that eats the leaves, who dies to be eaten by the worms and microbes, who make the dirt to feed the leaves to feed the deer to feed the tiger. This isn’t merely poetic, it’s the literal passing of matter and energy, physical stuff and the power to move it, between individual parts that comprise the ecosystem.
Now, let’s move on to ‘self-sustaining’, the hardest part of our question. We want our ecosystem to continue without supplies from Earth. Is that even possible? Hypothetically yes, but it depends what you mean. Earth itself survives without supplies from elsewhere, passing matter between the living and nonliving in ecosystems – in this sense, Earth is a closed-loop system, moving physical stuff, matter around without gaining or losing matter from an outside supply*. But that’s just matter. Energy is a different story; the sun constantly supplies Earth with energy that flows through ecosystems and eventually dissipates back out to space, mostly as heat. So if we’re talking energy, Earth is an open-loop system, constantly being supplied more energy.
While it would be amazing to make an ecosystem that is both closed-loop for matter and energy, the problem with energy is that it decays into ‘useless’ energy like heat that cannot be used by life. Yes, I feel that irony writing from -10C temperatures in Boston, but it’s scientifically true. So for our question, we’ll aim to find an ecosystem that’s closed-loop for matter, but gets an energy supply from elsewhere. Even this is a hard problem; Earth is huge and while individual ecosystems are mostly ‘closed-loop’ for matter, they’ll shunt waste products off to other ecosystems to use. In space, we won’t have that luxury. Any waste made in an isolated, spacebound ecosystem must be used by something else in that same ecosystem.
And lastly, what do we mean by ‘simplest’? We could say that ‘simplest’ just refers to the fewest number of different species in our ecosystem. After all, fewer moving parts that can have something go wrong is better, right? Or we could say that ‘simplest’ refers to how complex the species in our ecosystem are, meaning we’re looking to work with the simplest parts we can get. This would be microscopic life like bacteria, amoebas, fungal yeasts, cyanobacteria, and single-celled algae, which have the benefit of being small as well as ‘simple’.
Finally, we could take a step back and erase species from the equation and instead say the ‘simplest ecosystem’ is just the fewest number of chemical reactions to keep matter moving through the environment when you add energy. This is like cutting away all of the walls and membranes on cells and just looking at their metabolism, what chemical reactions they are running to convert starting reactant A into finished product B. Another reaction then need to take B and make C, and a third reaction then takes C and makes A. For now, we won’t settle on a specific definition of ‘simplest’, but will keep all of these in mind as we look for the simplest self-sustaining ecosystem.
Speaking of, where are we going to look?
Good question! Stay tuned for Part II, in which we’ll speculate on where to start looking for the simplest self-sustaining ecosystem.
I start my first consulting job this Monday, working with a healthcare consulting firm to help companies solve real-world problems. Before this, I was PhD student working in a research lab and my consulting experience was only pro-bono projects with a graduate consulting club. Nor was I terribly close to the healthcare field—my lab doesn’t do research on anything directly related to healthcare of pharmaceuticals. Given this background, you might be asking how I can possibly work in healthcare consulting. There’s so much I don’t know, how can I possibly succeed? Where do I possibly start learning?
When faced with a huge field containing a lot of information, I’ve found the best way to start learning is to build stories. The human brain is wired for stories because it naturally creates or attributes agency to things. It finds causes and effects. So we can use this innate understanding of stories to go into a field and build a narrative that helps us understand. Think of the story of Newton and the apple during discovery of gravity. Whether or not it’s true, we remember that an apple fell onto Newton’s head and he realized gravity exists. There’s a cause – the apple – and effect – Newton suddenly ‘getting’ gravity as a force that pulls things toward the Earth. In learning this story, we remember more than if someone had simply told us “Gravity pulls things toward the Earth.”
But in a new field, it’s not enough to simply hear the story. It’s the act of making that makes you remember. To truly understand something, build the story yourself. As an example, this isn’t my first field switch; before my PhD in synthetic biology, I got a B.S. in Environmental Science. But the those two fields are far apart, so I built stories that covered the major breakthroughs in synthetic biology. I looked at who had done what and when and who built on that research afterward. It helped me rapidly catch up and graduate on time with my peers. Science also backs me up on this one: writing, or more broadly just interacting with information beyond reading it silently helps you remember it (Sources: PopSci article, Hardcore paper source from recent literature).
So if you’re jumping into a new field or subject, don’t just passively read stories, make them. How? There’s always pencil and paper, where you can draw a timeline or write a paragraph-long story summarizing what you’ve learned. But if you want something searchable, try making your story digitally. I’m currently using Sutori, which lets you create timelines for free using any kind of mixed media (text, image, video). There are also several other timeline builders listed here, and you can even organize information beyond the timeline and make a flowchart or sketch on Google Docs, Microsoft Office, or wherever else you can find the tools to sketch and write. Get creative, because the more you create, the more you’ll remember.
So feeling lost in a new field? Start making a story out of it.
It’s been a while since I updated, thanks to the hectic nature of moving to a new state, driving across the U.S. for a third time, and getting settled before I start work. Here’s a cross-post from a project inspired by my friend Cindy Nguyen. She runs Haptic Press, a creative arts labspace for anyone to looking to experiment with creativity. Especially those people who haven’t done something ‘creative’ in ages like *cough* me. Graduate school was an eternal summer for my mind, but it was a long, dark winter for the creative self.
This piece is in response to Cindy’s most recent theme, “Classification”, merged with what I know to become “Biology x Classification”. This is a tribute to how messy life is, despite our best attempts as scientists to classify. Hope you like it.
An instructional on species
step one: definition
Figure 1: An individual
what is a species?
do you know?
Can you look up the definition?
Go ahead. Do it now.
i’ll wait here.
Figure 2: A lineage
have it? Read it out loud
for both of us to hear.
Figure 3: Two descendants, one ancestor
now, things get fun.
imagine the definition in your mind,
like on a piece of paper.
Take it, tear it up,
And toss it into the wind.
make a mess.
Figure 4: A mess
step Two: mess
The truth is, a species is messy.
it’s messy just like the scattered paper
That now makes up our definition.
you may have looked at animals and thought,
“This duck is different than a cat,
which is different than a deer or a bat.
All different species.”
Figure 5: Shared ancestry
And you’re right.
we can tell very different things apart.
but what about this bat and that?
This lizard and that?
The closer the two animals get together,
The harder to say they’re a different species.
Figure 6: Species complex, wherein ring species interbreed
we biologists like to say if animals don’t breed,
meaning they can’t make offspring together,
They’re different species. Separate.
but there are species of lizards that blend,
from one place to another.
Able to breed with neighbors,
but not neighbors-neighbors-neighbors,
And more distant.
so where does one species start,
And another end?
hard to say.
Figure 7: Interbreeding fails at ring edges
step Three: mix
or look at bacteria,
That make offspring only by dividing.
how do you decide a species
in a thing that does not mate for offspring?
who is to say bacteria A is a species itself,
isolated and separate from bacteria B?
Figure 8: Asexual reproduction
well, we tell ourselves that it’s in the DNA,
The genetic information that makes all life.
we look at two bacteria,
And if the DNA is different enough,
(we say 1%, but where does that come from?)
we say Bacteria A and B are different species.
but it gets even messier in the bacterial world,
like the pieces of our definition swirling in the wind.
because bacteria can mate,
They just don’t make offspring.
They mate across species,
Across close relatives and distant friends
not to make more of themselves,
but to swap DNA,
The very basis of our definition!
Figure 9: Horizontal gene transfer
They share DNA in mating,
Copying and swapping like teenage pirates,
a gene here, sequence there.
Copy, cut, share, paste, repeat.
each action blurring lines:
is the new cell, now carrying a bit of species A
still species B, or something new?
who’s to say.
Figure 10: Which species, none, or both?
step four: matrimony
And then there’s you.
The collection of cells you think you know
All descended from a first.
but beside your human cells are the others,
A collection of millions by millions of bacteria,
on your skin, in your gut,
on every open inch of body.
The unseen multitudes of multitudes,
different between each person.
They make you, become you,
so you are what?
Figure 11: Human and microbiome
And where do you come from?
who are your ancestors,
your mother’s mother’s mothers
stretching back into unconscious unmemory.
A secret, hidden in you
Thousands by millions of years ago.
Chance cast her lot,
As one cell engulfed another.
A normal act of eat to live,
but this time the infinitely unlikely,
Completely unguessable happened.
The devourer did not kill to sate its hunger
And embraced instead the cell within it
As a host would a guest in their home.
The guest, sealed and safe from the surrounding world,
gave energy for life in return.
if you seek within your cells,
you find these once-guests still today.
making, providing, trading
Their energy for a home.
The two working together,
Creating life from mice to men.
That is the strangest thing about you,
descendent of that accidental chance.
you are a marriage of not one form of life,
Figure 12: Endosymbiotic theory
step five: reality
As you can see, the definition of a species
diverges between flat paper and life.
our paperbound sentence is just convenient shorthand
hiding a stout, immovable truth.
for it’s impossible to encompass the chaos of life
of even for an individual in a word.
A name, a handle, a term,
And life’s lineage stretches long.
Figure 13: The lineage of life