Two quotes for thought

Science is built up of facts, as a house is with stones. But a collection of facts is no more a science than a heap of stones is a house. (Henri Poincaré)

 

At some point the mind must grammaticize facts and convert them to narratives. The facts of the world do not for the most part come in narrative form. We have to do that. (Cormac McCarthy on the Origin of Consciousness)

Nuance in Two Parts

Here are some thoughts about using accurate words in two different contexts.

When nuance is lost to brevity

A few months ago, a feminist Instagram account that I followed posted a picture with some saying about how “Men are trash.” Quickly this person received many critical comments and backlash, and this person followed up defensively with a response post. This post no longer exists, but my recollection of her response is: when she says “men,” she is referring not to “your boyfriend or your dad,” but instead to patriarchal systems of oppression. (Again for the record, this is my own paraphrasing.)

The original poster certainly is justified in wanting to criticize patriarchal systems of oppression. But the problem with using synecdoche—referring to a whole by using one of its parts—in discussing complex phenomena in sociology or science is that in many cases it does not accurately convey intended meaning and can very easily be misunderstood. Saying that “men” are trash, but not actually referring to “men” as we commonly use the word, seems unwise. (And, if one is going to make clarifications in follow-up posts anyway, one might as well just have been accurate the first time. But anyway.)

Unfortunately, synecdoche sometimes is the only way to work within media that are character-limited, like Twitter. There must be a solution to reach audiences which primarily use these media and still convey complex messages—but I don’t know what it is yet.

When nuance is intentionally sacrificed to approachability

I’ve written before about the necessity of unpacking phrases and literary devices when writing about science or social issues, but I have also been recently thinking about how emotional appeals are sometimes the most effective way to convince a person of facts. These two things collided the other day when I was having a discussion about using the phrase “global warming” vs. “climate change.”

The person I was talking to clearly had a disgust for the phrase “climate change”—saying that it is vague and means nothing. I understand this. A changing climate could mean anything, from an ice age to the warming planet to a season changing. But the person also said that climate change was a cop-out on the part of the left-wing to avoid naming a real problem. This, I feel, is not entirely true.

Global warming is indeed an urgent and frightening problem. Yet nearly half of Americans—48%—are neither extremely certain that global warming is happening nor extremely certain that it is not happening. I have not done enough research to understand why so many people fall into categories of uncertainty, but I would personally guess that it has something to do with a lack of a feeling of their own scientific expertise, combined with the loud swath of right-wing politicians who claim that global warming is inconsequential, combined with some degree of fear of a planetary-scale problem.

If this guess is true, how do we get these people to feel more certain in the facts of global warming? There are certainly many answers, but I suggest that the use of the phrase “climate change” helps the subject feel more approachable. If “climate change” as a phrase offers a better gateway to discussions that will lead to a more-informed public about human-caused global warming, then I see no reason to have disgust towards it. Is it nuanced? No! Does it provide an approachable conversation starter to getting into nuanced discussions with non-scientists? Yes? Then let’s use it.

Of course, these are just my own initial thoughts and I am more than happy to discuss them and hear other arguments.

One last thing—the aforementioned person believed that using “global warming” as a phrase is necessary for “scaring” people into “believing” in climate change. But I will discuss fear and science communication in a separate post.

Facts and Feels

When I was in middle school we used to go to Lake Arrowhead and play in a small cordoned-off bay for swimmers. Almost 10 years later I returned to find the bay almost completely drained, docks left high and dry, grasses growing on land that was once deep under water.

The California drought became real to me at that moment. As much as I had seen the statistics—maps in dark red and orange indicating severity, urging shorter showers—I didn’t feel them.

We now live in a time when facts aren’t always enough. The fact that clean energy jobs outnumber coal and gas jobs five-to-one in the United States did not stop the President from renouncing the Paris climate accord. And though the president is an especially idiotic anomaly amongst all Americans, about 40% of normal everyday people are unsure about climate change despite the consensus of an overwhelming majority of scientists.

Facts are hard to feel. Numbers are hard to relate to even when they’re about people. 37 people died in a Manila terrorist attack this morning, 137 people in the November 2015 attacks in Paris, 1.5 million (1,500,000) million Armenians murdered during the first World War, more than 5 million (5,000,000) Syrians fleeing from their homes. And there are numbers that are possibly too vast to ever feel—7.5*10^18 (7,500,000,000,000,000,000) grains of sand on Earth, 7*10^22 (70,000,000,000,000,000,000,000) stars in the observable universe. What capacity do we have to begin to comprehend any of these numbers? One can only begin to absorb the sorrow and fear of 5 million refugees through one photo of a child alone on a beach. Most people have no context for understanding a CEO’s $46 million yearly salary, but it becomes even more shocking—almost personal—when you realize that it amounts to $180,000 per day.

Facts and numbers are most effective when they can connect with the heart. And thus when writing about science we have to make you feel it. We have to show you a photo of the wondrous and messed up Pale Blue Dot you’re on. We have to tell stories of names and faces. We have to see the bays of our childhood drained and dry.

I used to think that appealing to emotion was cheap; clickbait. But honestly, all I do is feel. Science—all of its simplistic glory and elegant mathematics and long nights and tears and sacrifices—makes me feel a way, makes me act a way, makes me be a way. Now I suppose the point is to make you feel a way, too.

feelings on failure

Being a science writer who was formerly a scientist is hard because it always subconsciously feels like you failed at doing the higher, nobler thing. It feels like you failed at making fundamental discoveries about the universe and now you are just the messenger. And while I think that science writing is important and I think I’m pretty good at it, these “evidences” of failure at pure science are always in the back of my head: The time when I discovered that a very close high school friend had written to the caltech admissions office to say that I should not have been admitted. The time when my research advisor fired me. The time when my grad school admission was rescinded because of low grades.

It’s particularly difficult to accept failure at science because there’s now so much push and motivation to get girls into STEM—and with this new push came, for me, the feeling that any other major, journalism or english or philosophy, anything “less” than science, was so exactly that: lesser; condescendingly expected of a girl. At 17 I really thought I would break all kinds of barriers and norms as a woman in astrophysics at Caltech. But I couldn’t do it. I scraped my way to graduation and exhaled. I couldn’t be the discoverer. Instead I am the messenger. The wingman. The assistant to the regional manager.

It’s hard to break this mindset of being disappointed in myself for leaving (not to mention, it’s probably offensive to other science writers lol) particularly because: writing is “for girls.”* Writing is “supposed” to be what girls are better at and science is “supposed” to be what boys are better at. So I’m not being a revolutionary by being a girl in writing. I’m just a girl that leaked out of the STEM pipeline because science was just too hard—and it makes me feel ashamed. I feel like I failed because everyone knows that girls ARE good at science, girls CAN succeed in science, it’s encouraged and championed and supported in order to overturn those old stereotypes. But I won’t be an example.

I look at the stories that I have published and I’m proud of them. I look at this past year of rapid promotion and growth and I am proud of it. I look at women who are boldly succeeding in science, who are pushing ahead and breaking barriers, and I will stand up and cheer and applaud and support those women. But I am not one of them. And I have to learn to be okay with that, I have to learn that success is not measured by a PhD or by papers published or by other people liking your words. I have to learn.

 

*I don’t actually think this is true

**Edited because some of you haters are real sticklers for proper capitalization damn

Wonder

“Wonder” is such a fabulous word. An expression of curiosity and exploration when used as a verb and an expression of amazement when used as a noun, and often these definitions exist in a wonderful superposition. During field trips to the Galápagos and Indonesia, one of my professors encouraged us to continually make an effort to begin our sentences with “I wonder…” To begin our thoughts with openness, curiosity, and amazement.

As Caltech’s de facto biology writer, I have been reading through a hefty molecular cell biology textbook* trying to understand the basic principles of life. And let me tell you, WOW, this book is hitting me in the face with new wonders on every page. A few examples of some things I’ve learned in the first five pages:

  • Your body is made up of 10,000,000,000,000 cells, all of which originated from one single cell that started to divide. Ten trillion cells—more than the number of stars in our galaxy—from a single cell!
  • If you’re over ~20 years old, you’ll have noticed that the way that computers store information has evolved drastically, from big clunky floppy disks or VHS tapes to miniscule chips in an iPhone. So you would expect that, because cells have been evolving and diversifying for over 3.5 billion years, the way they store information would have evolved too, or you’d expect that you wouldn’t be able to read the information of a seaweed cell the same way you read that of a horse cell. Lol, nope. As from the textbook: “You can take a piece of DNA from a human cell and insert it into a bacterium, or [vice versa], and the information will be successfully read, interpreted, and copied.” That’s some crazy machinery.
  • A single strand of DNA is made up of long sequences of four different chemical compounds (A, T, C, or G). Each strand has a direction in which it is read, symbols interpreted from one direction to another. So when we say DNA is “read…” it’s not a metaphor. DNA is a language.

These are only the “amazement” types of wonder. At pretty much every sentence in this book, my brain is screaming, “?!??!” How the crap did all these chemicals come together to encode information that directs the production of more molecules? When did any of this happen? Why did these complex processes like replication and transcription evolve this particular way? ARE WE “ALONE” IN THE UNIVERSE?!

I’m sure some of my biochem-y questions are going to be answered as I keep reading. But the bigger questions of life’s existence and context in the Universe are legitimately open ended. They remain to be continually wondered at.

 

 

*Molecular Biology of the Cell, Sixth Edition.

A Tiger-Striped Surprise: Ice Volcanoes on Enceladus

I wrote this piece as part of my grad school applications last fall.

At first glance, Saturn’s tiny moon Enceladus appears to be nothing like its namesake, the giant of Greek mythology whose breath caused volcanic eruptions. Enceladus (the moon) is a frozen celestial body smaller than the state of Arizona. No one would have guessed that its name would turn out to be serendipitously appropriate.

When the Cassini spacecraft arrived at Saturn in 2005, scientists didn’t intend to conduct more than a quick flyby of Enceladus. But any expectations of Enceladus as an inert, cratered moon were soon dismantled as Cassini captured images of four large, hot fissures sliced across the south pole, like the jagged claw marks of a tiger. And so it was revealed that Enceladus truly is living up to its mythological namesake: from these so-called “tiger stripes” spewed at least 100 ice volcanoes, jetting particles and water vapor far out into space.

The discovery of these plumes was a shock. One wouldn’t initially expect moons to have active processes like violent geysers of particles — moons are usually too small and cold to produce much energy. Craters on our own Moon indicate that its surface hasn’t changed for three billion years. For tiny Enceladus to have such vigorous volcanoes, something must be happening internally to generate heat and energy.

The most natural explanation for such a small moon to be producing so much power is a process called tidal flexing. Tidal flexing occurs because Enceladus’ orbit around Saturn is not perfectly circular, so the huge planet gravitationally squeezes and stretches its tiny moon as it orbits. This constant exercise of the moon’s rocky interior causes it to heat up. But scientists expect that this tidal flexing can only generate about 10% of the power that the plumes output, so Enceladus must have some sort of other unexpected internal heat storage.

Chemical analyses of the plumes hint at more subsurface secrets. Samples of the plumes reveal “salty” sodium particles, indicating the presence of silicate rocks. Along with the abundance of water vapor particles, this data paints an image of a deep subsurface ocean with a solid rock bottom.

Liquid water, heat, and a water-rock interface are a crucial combination of ingredients for the chemistry of life that has made the once nondescript Enceladus a prime target in our search for extraterrestrial life. The idea that life could potentially arise under a crust of ice on a tiny moon of Saturn has revolutionized concepts of habitable environments. Enceladus is an embodiment of the surprises of our solar system that we have yet to uncover.

Mars may harbor subsurface liquid water

I wrote this piece as my “Discovery Story” assignment for En84, “Writing About Science,” at Caltech, and got an A. The press release I drew information from is here and the original paper is here.

 

Ancient Mars was a warm and wet place, coursing with rivers and lakes. Though the lakebeds are now dusty and the water long gone, researchers have recently discovered evidence that the present-day Mars may not be as dry as we thought. The evidence suggests that a thin layer of salty liquid water may exist just under the Martian surface, condensing in the cool hours of night and evaporating in the morning.

Conditions on Mars are not favorable for liquid water — Martian temperatures and atmospheric pressures only allow water to exist as ice or vapor. However, the Curiosity rover recently detected a chemical compound in the Martian soil that could make it possible for water to exist in a liquid form.

The compound, called calcium perchlorate, lowers the freezing point of water, acting like an anti-freeze by allowing water to exist in a liquid state even under temperatures where it would normally form ice. Under particular humidity and temperature conditions, perchlorates can also absorb water vapor from the atmosphere, forming salty liquid solutions called brines that can then trickle down into the soil.

While perchlorates are abundant in many places on Mars, this is the first time they have been detected along with the right humidity and temperature for brines to form. Additionally, these conditions were detected at the equator — the driest and hottest region of Mars. If the delicate brine-forming conditions can exist even on the harshest region of the planet, it’s likely that milder regions can stably support brines as well.

The authors measured air humidity and temperature at the equator using Curiosity’s Rover Environmental Monitoring Station (REMS) over a Martian year. They describe the brines as “transient” because the proper humidity and temperatures for brine formation don’t last throughout a full Martian day. The salty solutions only have one night to condense before evaporating with the sunlight.

Liquid water is considered a crucial building block for life, but these brines are unlikely to harbor it — they are simultaneously too short-lived, too cold, and too exposed to solar radiation to support terrestrial organisms.

“Conditions near the surface of present-day Mars are hardly favorable for microbial life as we know it, but the possibility for liquid brines on Mars has wider implications for habitability and geological water-related processes,” says the lead author on the study, Javier Martin-Torres of the Spanish Research Council in Spain and Sweden’s Lulea University of Technology. He is also a member of Curiosity’s science team.

Though for now this finding seems to have few extraterrestrial implications, it is part of a collection of Curiosity’s discoveries that are transforming our perception of Mars. Last year, Curiosity measured sharp spikes and drops in atmospheric methane concentration, implying that somewhere on Mars is a source producing the organic chemical. Scientists have also observed dusty geysers of carbon dioxide erupting from the polar ice caps in the warming of spring. Mars is turning out to be a much more diverse and dynamic planet than we thought.

Challenging the Precious Metal Paradigm

This article was originally published in Caltech’s weekly newspaper, The California Tech.

A team of Caltech scientists and students has discovered a groundbreaking new method of synthesizing carbon-silicon bonds—a method that is easier, cleaner, and a thousand times cheaper than the current state-of-the-art. The Tech sat down with graduate student Anton Toutov and undergrad Kerry Betz, members of the Grubbs lab; and postdoc Wen-Bo “Boger” Liu, a member of the Stoltz lab; to hear the story of how they pursued a seemingly improbable reaction to make a cutting-edge achievement in chemistry.

Lori Dajose: First of all, let’s talk about why your new method is so revolutionary to chemistry.

Kerry Betz: Well, carbon-hydrogen (C–H) bond silylation—replacing a hydrogen atom with a silicon group in a molecule—is normally pretty challenging. You have to use these expensive, rare, and sometimes dangerous metals like platinum, palladium, and iridium, as catalysts. But our reaction uses potassium tert-butoxide as the catalyst. Potassium is naturally abundant, making our compound safe and inexpensive—no more need for those precious metals.

Boger Liu: Additionally, replacing a carbon-hydrogen bond with a carbon-silicon bond is really crucial in making important molecules called organosilanes, chemical building blocks valuable in manufacturing basically everything from new medicines to new functional materials, like next-generation liquid crystals for LCD screens. The idea of making organosilanes catalytically without precious metals seemed so naive and lofty—it was unprecedented. This “precious metal paradigm” was like an axiom in chemistry that few scientists had attempted to challenge.

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From left: Kerry Betz (’15), Anton Toutov, and Wen-Bo “Boger” Liu have recently published a paper detailing the use of potassium tert-butoxide as a catalyst in silylation reactions. Photo courtesy of Allison Maker.

LD: What inspired you to challenge it?

Anton Toutov: Two and a half years ago, I noticed organosilanes occurring as unexpected byproducts from my unrelated experiments with biofuels. It was kind of random, but this really provided the crucial proof-of-principle that we didn’t need to use crazy expensive precious metal catalysts for the carbon-silicon reaction to occur. I just decided to run with it.

LD: And you started looking for people to run with you.

KB: Yes. Around the same time that Anton’s project was gaining momentum, I was looking for summer research. I met with several potential mentors, him included. He was just so incredibly excited and animated talking about it, and I thought, “Wow, he seems like a really fun guy to work with!” I was relatively new to this type of chemistry, so I didn’t have the same bias that more experienced researchers had with regards to this precious metals paradigm.

LD: Boger, you teamed up with Kerry and Anton a few months later. What inspired you to join?

BL: Well, one of the key components of the reaction involves breaking a carbon-hydrogen bond in a heteroarene and replacing it with a carbon-silicon bond. I had done some research on the first half of that process—methods for breaking C-H bonds. Anton and I would have coffee every Saturday, and one day he showed me how he had been using a potassium catalyst for this reaction. I couldn’t believe it. I knew this would change the entire field of C-H silylation chemistry. It was natural for me to get on board with him.

AT: I had worked on the problem alone for some time and solved it to an appreciable degree, and then I knew I could use some really talented and passionate people to help improve the reaction further, and broaden its scope. When Kerry and Boger joined the project, it just took off.

BL: Originally, we began by applying the method to a class of molecules called heterocycles, biologically important scaffolds present everywhere in nature. When it became unbelievably clear that it was really working, we each branched out to apply the method to different classes of molecules.

AT: We were each working in our own direction, simultaneously pushing the project forward on several different fronts. Kerry was making molecules that have never been made before, discovering interesting subtleties about the reaction, and developing some sophisticated hypotheses.  She’s now a completely independent research chemist, and a leading world authority on Earth-abundant metal catalysis, working on extending this method to other molecules. I’m so proud of her. And Boger, he is such an amazing talent. He helped me to optimize the reaction to an excellent level, synthesized a large amount of new molecules using our method, and helped me to develop several new methods based on our general concept. He has also been working on elucidating the mechanism of the reaction, which is currently a big mystery that nobody in the world seems to understand! All in all, I had just the best team imaginable with which I could bring my C–H silylation reaction to life.

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Kerry Betz is the third author on the recent silylation paper. She is an undergraduate in the lab of Professor Robert Grubbs, who won the Nobel Prize in Chemistry in 2005. Photo courtesy of Allison Maker.

LD: Your method isn’t just a new way of synthesizing organosilanes—it’s also a better way than the existing state-of-the-art. Tell me about that.

BL: First of all, we found that the reaction could actually occur under pretty mild conditions. We’re talking room-temperature here—the lowest temperatures this reaction has ever occurred at. In addition, there were no harmful or dangerous byproducts, just hydrogen gas—which is valuable itself!

KB: The method is really environmentally friendly. Using precious metals produces toxic metal waste that has to be filtered out from your desired products—our method has no such drawbacks. On top of being green, it is thousands of times cheaper than using precious metal catalysts. And if being clean and cheap wasn’t enough, it is also pretty easy. This is the kind of thing that could probably be taught in an introductory freshman lab, like Ch3a. It’s shocking how it just blows away this precious-metal paradigm that has been around for almost a century.

LD: Your paper was recently accepted and published in Nature. What was it like for you, to be published in such a prestigious journal?

BL: Well, we got the acceptance email on my birthday. It was a fantastic present.

KB: My birthday was a few days before we got our paper accepted, so it was like a birthday present for me too. I was actually having a really bad day. Then I got a card from Anton saying, “Happy birthday… oh and by the way, congratulations on your publication acceptance into Nature.” It has been so amazing; I’ve been able to help this project come from an uncertain, possibly controversial beginning, to an unprecedented and publishable conclusion.

AT: Yes, and it’s really just the beginning. There’s so much to come, and we are the pioneering lab for this research. Our hope is that this discovery will change the way that people think about chemistry, and about the logic of chemical synthesis in particular.

 

The full paper was published in Nature on February 5, 2015, titled “Silylation of C-H bonds in aromatic heterocycles by an Earth-abundant catalyst.”

The Rusted Red Planet

It is a well-known nuisance that when you leave a freshly sliced apple exposed to air, it quickly turns brown. It’s a nuisance of the same kind that must frustrate the Statue of Liberty—her once-coppery skin turned green from only two years of exposure to air. The process that causes these seemingly dissimilar metamorphoses is called oxidation. Oxidation occurs when an atoms in a substance lose electrons, changing the overall chemical makeup and structure. It doesn’t necessarily cause decay; oxidation is essentially just atomic reshuffling. Key to oxidation processes are atmospheric elements like water and oxygen.

Another common kind of oxidation is rust. Rust occurs when iron metals oxidize to form other compounds. Hematite is one of these results of oxidation, rust-red in powdered form and created by the oxidation of other iron-containing compounds, like magnetite. When magnetite rusts, one of its iron atoms loses an electron, chemically changing into hematite. The presence of water is an important catalyst for this reaction—if you’ve ever left an old bike out in the rain, you’ll notice it gets rusty pretty fast.

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Hematite is the abundant mineral that gives Mars its distinctive reddish color. The planet is covered by a layer of fine red hematite powder, so much so that you can see the hue from Earth on a clear night. But there are no oceans or lakes of water on Mars, and the Martian atmosphere is practically parched. Without water to facilitate rusting and oxidation, the origins of this ubiquitous mineral are unknown. NASA’s Martian rovers have found no indication of rusty Martian bicycle tracks, so there’s one scenario we can rule out.

Mars has a very sparse atmosphere, about 1/100th of Earth’s, and so the surface receives very little protection from solar ultraviolet (UV) radiation. UV light is very powerful: it can split apart molecules to create extremely reactive new molecules called radicals, and it can even interact with our genes to cause mutations. Perhaps the abundance of UV light on Mars, in the absence of water, can facilitate the oxidation of magnetite into hematite.

To test this hypothesis, I placed a few magnetite samples into a chamber with a simulated Martian atmosphere: a very cold, low-pressure CO2 atmosphere with no water vapor. Then I switched on a powerful UV lamp and waited for two weeks. I carried out this research with the Mars Group at the Niels Bohr Institute at Copenhagen University.

There were two possible outcomes.

Possibility 1: Oxidation was detected on the samples at the end of the experiment. This could imply:

  • UV radiation can physically knock electrons off of iron, and alter the ratios of iron and oxygen from magnetite to hematite. No water is necessary. This could mean that the dust on Mars is actively, however slowly, being formed. Mars may not be such a static “dead” planet as we may have thought.
  • UV radiation can interact with CO2 to create an oxidant which then oxidizes iron, changing magnetite to hematite. No water is necessary. Again, this could mean that the dust on Mars is actively, however slowly, being formed.
  • The magnetite in our samples had already been oxidized through exposure to Earth’s atmosphere before we introduced them to our chamber. I’ll explain this more in the results section.

Possibility 2: No oxidation was detected on the samples at the end of the experiment. This could imply:

  • UV radiation cannot induce oxidation alone. It may have no role in converting magnetite to hematite. Alternatively, it may have a partial role combined with mechanical weathering, or other processes. Perhaps the only way UV radiation could have played a role in oxidation is under a completely different set of atmospheric conditions. If Mars previously had an Earth-like atmosphere containing more water and oxygen, UV radiation could photolyze H2O or O2 to create radicals that would steal an electron from iron atoms.
  • UV radiation can indeed induce oxidation without the presence of water, but over very long timescales—the experiment did not run for enough time. This would imply that the dust on Mars could be very old, which suggests that the planet has been unchanging for millions of years.
  • The analysis did not catch the oxidation.

The results are now in.

After the experiment, the samples were analyzed using x-ray photoelectron spectroscopy (XPS). This mouthful is a technique sensitive to the surfaces of materials, giving the chemical composition of the top 10 nanometers. This means that the results we found were only for the surfaces of our samples, not the bulk. XPS can also tell us the chemical environment of an atom, meaning we can determine the oxidation state of elements. The analysis was carried out by Dr. Nico Bovet at Copenhagen University’s NanoGeoScience Center.

The powder samples showed signs of oxidation even before they went in the chamber. The little bump in the graph around 719 eV indicates iron in the oxidized state. After the experiment, they didn’t show any noticeable change.

 

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The spectrum of the powdered magnetite sample before the experiment.

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The spectrum of the powdered magnetite sample after the experiment.

As for the solid samples, neither of them show that same bump around 719 eV — indicating that no iron oxidized after the experiment.

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The spectrum of the solid magnetite sample from Greenland.

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The spectrum of the solid magnetite sample that also included olivine.

So there you have it. Our results indicate that UV radiation cannot, in two weeks, induce the oxidation of magnetite to hematite in an atmosphere analogous to Mars’.

In science, getting “no” for an answer is common, and it’s not necessarily a bad thing. Any result of the scientific process is important, and leads to new questions and new directions of research. It’s possible that UV radiation does play a role in oxidation on longer timescales, or in combination with other Martian processes. We will just have to ask more questions and do more science to find out.