Social Justice and Science: Sexual Education in the United States

Hello, dear readers.

I’m sorry about the lack of entry in September. I’m new to freelancing, which is what I’m doing now. Also, job-hunting, which I’m also doing, is its own full-time job. Also, my research for what was supposed to be my September entry didn’t pan out. Much to my frustration, there wasn’t enough information out there for a full entry. I had planned on doing a Social Justice and Science entry on “female” and “male” cancers (breast cancer, ovarian cancer, prostate cancer, etc.) in transgender people. All I was able to find was some information on breast cancer and how HRT for transfeminine people increases the risk for breast cancer and elective double mastectomy for transmasculine people lowers the risk for breast cancer. I could probably go on at length about how unfair that is, but that’s not particularly scientific.

I suppose this entry won’t be as scientific as most either. Well, it is in a way; it’s related to social science. Let’s start with some statistics from the CDC:

  • In 2015, the teen birth rate in the United States fell to 22.3 per 1,000 teenaged people with egg-producing reproductive systems
    • This is a record low, but still higher than other industrialized countries
    • There are still significant disparities between ethnic groups and certain regions
  • Rates of chlamydia, gonorrhea, and primary, secondary, and congenital syphilis have increased since 2015
    • Young people (15-24) accounted for a disproportionately large portion of new cases of chlamydia, gonorrhea, and syphilis
  • Sexual minority youth are more likely to have certain sexual health problems
    • Young men who have sex with men* have unusually high rates of STDs compared to young cishet people
    • Sexual minority adolescent women** are more likely to have been pregnant than their cishet peers (yes, really)

Where am I going with this? I’m about to heavily criticize sexual education in this country. Let’s start out with discussing how abstinence-only or abstinence-focused sex ed fails everyone.

I’m going to use the state of Georgia as an example. Georgia isn’t the worst state in the nation for sexual health, but it is close; it ranks fourth out of all fifty states in HIV and syphilis infection rates, ninth for chlamydia infection rates, and thirteenth for teen pregnancies. I’m bringing up Georgia because its terrible sexual health (sorry, Georgia) is definitely connected to its abstinence-focused sex ed. Georgia also makes a nice microcosm for the American South and, indeed, any place in the US where poor sexual health is the result of poor sex education.

I’m not claiming that Georgia’s sex ed is poor because it’s my opinion; the CDC agrees with me that Georgia’s sex ed is severely lacking. In 2015, the CDC issued a report decreeing that over 67% of Georgia schools fail to teach all the sex ed topics that the CDC recommends be taught in school. This failure is due to Georgia’s state law, which mandates that sex ed focus on abstinence until marriage and allows local school systems to decide what information to share on contraception and safe sex. About half of those schools use the “Choosing the Best” curriculum, which disseminates information about the risks of contraception without emphasizing the importance of correct and responsible contraception use. Certain counties that use “Choosing the Best” even deliberately bar students from gaining information about contraception, including how to access it or other services like family planning counseling.

I know that correlation does not imply causation, but in the case of this topic, it has been demonstrated that the worse the sex ed in any given location, the worse the sexual health of its young people is likely to be. Teen pregnancies are 50% less likely among people who receive comprehensive sex education as opposed to those who suffered through “Choosing the Best” or similar programs. These programs are actively harmful, leading young people to believe misinformation about the negatives versus the positives of contraception, and they increase risk of teen pregnancy and STI transmission. In short, abstinence-only and abstinence-focused sex ed programs not only don’t work, they are antithetical to sexual health.

Even so-called comprehensive sex ed fails young LGBTQIAP+ people. Sex ed curricula that erase or stigmatize LGBTQIAP+ students can create an unsafe school environment and lead to bullying. Bullying isn’t the only negative effect of heteronormative sex ed, either; here are some more facts about LGBTQIAP+ students who don’t receive inclusive sex ed compared to their cishet peers:

  • More likely to have sex under the influence of illicit substances or alcohol
  • More likely to experience intimate partner violence
  • More likely to contract STIs
  • More likely to have more sexual partners and be sexually active at a younger age
  • Less likely to use barriers or contraception

So how many LGBTQIAP+ students out there are being failed by heteronormative sex ed? Too many. According to the CDC, as of 2015, only 19% of high schools in the US provided any sex ed curricula—ordinary or supplementary—that was LGBTQIAP+ inclusive (and I would lay odds that none of those curricula used as many letters in that acronym as I did). A devastatingly low 5% of health classes included positive representations of topics related to LGBTQIAP+ issues.

The data are clear: sexual education in the United States needs to change. It needs to be consistently comprehensive in regards to contraception and it needs to be LGBTQIAP+ inclusive. To allow sex ed in this country to remain as it is now is to do a serious disservice to the country’s young people.

 

* I don’t know if the CDC is including trans men in this, so I’m irritated at cissexism for the second time in this entry
** I don’t know if the CDC means “cis women” or “all people with egg-producing reproductive systems” here

What Do Scientists Actually Do?: PCR

Hello, dear readers, and I’m sorry for the wait between entries! Job-hunting is a full-time job, and then I went on vacation. In any case, welcome to the first “What Do Scientists Actually Do?” entry of Immortal Amaranthe.

If I were honest (and snarky), I would say that what biomedical researchers actually do is pipette. A ton. And that would cover about 80% of what I am going to write about in this and future “What Do Scientists Actually Do?” entries, at least when I’m talking about what biologists do. What is pipetting? Using a pipette (shown below) to move small amounts of liquid around. And…that’s how you do a lot of experiments. Pipetting. So much pipetting.

Immortal Amaranthe Pipette

https://www.coleparmer.com/i/labnet-biopette-p3940-10-autoclavable-pipette-adjustable-vol-0-5-10-0-ul/2460102

Image description: a medium blue laboratory pipette with a tip

This is definitely true for the procedure I’m going to discuss today: PCR. Thankfully, I used to love pipetting, but from now on, I’m going to talk mostly about the theory behind PCR, as well as some of the history. Oh, and what PCR actually is.

PCR stands for “polymerase chain reaction”. “Chain reaction” is one of those phrases I kept hearing when I was growing up and never really understood, and was glad to finally hear what it really meant in college. In case you share my childhood curiosity, a chain reaction is a reaction whose products contribute to the continuation of the reaction, or even speed it up. So what is a polymerase? A polymerase is an enzyme that makes long chains of RNA or DNA. So polymerase chain reaction—at least in a laboratory setting—is a method for amplifying small amounts of DNA several orders of magnitude.

PCR has been around since the early 80s, but a major development in PCR technology came in 1985 when a DNA polymerase that was stable at extremely high temperatures—Taq polymerase—was synthesized in a laboratory setting. (Fun fact: it was initially discovered in bacteria that live at extremely high temperatures.) This was useful because high temperatures are required to cause DNA strands to uncouple from each other so they can be copied, so it is advantageous to have a polymerase that can work at similarly high temperatures. PCR became much more easily usable in 1991, when the heat cycler—a machine that can rapidly bring its contents to extremely high temperatures—was put into production. Since then, PCR has become a staple of most molecular biology labs.

The polymerase chain reaction happens in three stages: denaturation, annealing (binding of short DNA sequences called primers to the DNA to be amplified), and extension of the DNA strands. In an actual PCR experiment, each cycle consists of the three stages, and a given experiment can take anywhere between 35 and 80 cycles to complete (usually).

Here’s a diagram from my master’s thesis depicting the first few cycles of a PCR experiment:

Immortal Amaranthe PCR Diagram

Image description: a diagram of the results of first four cycles of PCR, depicting the exponential increase in copies of DNA each cycle

So the amount of DNA increases exponentially (for a while, until what is called the “pseudolinear” stage, when the reaction can no longer be 100% efficient). Needless to say, PCR is a quick and efficient way to get from a tiny amount of DNA to a very large amount of DNA.

There are many different variations on PCR, but that’s probably not very interesting. I’m guessing you’re probably thinking something more along the lines of “Okay, but why would a scientist want to take a tiny amount of DNA and amplify it to make tons of DNA?” Well, for one, to analyze it. That’s what I did in my master’s thesis.

The idea behind my thesis was to use a tool called a molecular beacon probe to identify small amounts of mutant DNA among a much larger amount of wild type (normal) DNA. In order to do this, I used a type of PCR that amplified more of one DNA strand than the other. DNA’s two strands are called “sense” and “antisense”, with the sense strand being the one that actually codes for a protein; molecular beacon probes bind to the sense strand. The probes work better when there are less antisense strands competing with them for binding to the sense strand, so I used a type of PCR that made more sense strands. When the probes bind to their targets, mutant pieces of DNA, the probes light up, and the experimenter can measure the amount of fluorescence that they give off.

So what was the point of my thesis? Why is it useful to use PCR and molecular beacon probes to identify a mutation? Well, the idea behind the thesis is that molecular beacon probes can be used to identify cancer-related mutations in a human blood sample. When a person has cancer, they may have circulating tumor cells in their blood, and a PCR-and-molecular-beacon-probe test would be able to identify the mutant DNA from the tumor cells even though there is also a large amount of normal DNA in the blood sample.

I hope that wasn’t too complex; I just really wanted to talk about my thesis. I’m very proud of it. A slightly less complicated application of PCR is forensics-related genetic fingerprinting. If you have ever watched any crime procedural show, you’re probably at least vaguely familiar with genetic fingerprinting; you may have heard a character say that someone’s blood was a match for what was found at the crime scene. Have you ever wondered how forensic scientists on the show (and in real life, for that matter) can tell such a thing from a drop of blood or a tiny amount of saliva? Well, the answer is PCR. Forensics experts isolate small amounts of DNA from the evidence and amplify it with PCR before analyzing specific sequences to compare the sample to DNA from a suspect or a DNA database. Similar techniques are used in paternity testing.

Like I mentioned earlier, many molecular biology labs use PCR. In fact, I’ve used PCR in cancer research in a context other than my thesis. During my first laboratory experience, I was tasked with doing PCR on samples from chronic lymphocytic leukemia patients before the DNA could be sequenced. The results of the DNA sequencing were then given back to me so I could look for mutations in a particular gene that is often mutated in solid cancers. (There weren’t any. I was disappointed, but such is science. Hypotheses are frequently wrong.)

PCR-based procedures are also used in the following procedures or experiments:

-Tissue typing (testing to determine whether or not a potential organ donor is a match to the patient who needs a new organ)

-Genetic testing for heritable diseases

-HIV testing

-Testing for antibiotic resistance in TB

-Early diagnosis of leukemia, lymphoma, and other cancers

I think PCR is a pretty cool technique. Yeah, that’s incredibly nerdy, but if I weren’t a nerd, I wouldn’t be running a science blog, would I?

Well, This Is Cool: Amaranthe’s Five Favorite Species Discovered in 2016

Content note: snake (for anyone out there who has ophidiophobia)

Hello, dear readers, and welcome to the first “Well, This Is Cool” entry of Immortal Amaranthe. I will be the first to admit that this is not the timeliest of entries, because today I want to talk about some of the new species that were discovered in 2016. I was surprised at how many new species were discovered last year, both prehistoric and extant, so I have chosen to discuss my five favorites.

I will also be the first to admit that I chose these species were chosen mostly because of their names. I am still a scientist at heart, and scientists have…interesting ideas about names. The thing you have to understand about naming conventions in science is that scientists are nerds, and that we’re weird. For example, there exists a mushroom named Spongiforma squarepantsii after the character Spongebob Squarepants. The worst offenders when it comes to weird names are the Drosophila melanogaster (fruit fly) biologists. Check out some of these fruit fly gene names:

-Ken and Barbie (mutation leads to lack of external genitalia)
-Lush (mutation leads to unusual attraction to ethanol, propanol, and butanol)
-Halloween genes: disembodied, spook, spookier, shade, shroud, phantom (code for P450 enzymes involved in synthesis of steroid hormones; mutations result in spooky-looking embryos)
-Tinman (mutations result in no heart)
-Van Gogh (mutations result in swirling of hair on wing, resembling a Van Gogh painting)
-Swiss cheese (mutations cause brain degeneration, leading to holes in the brain)
-Sonic hedgehog (one of a set of three genes that were already called two kinds of hedgehog based on mutations causing the appearance of spiny projections)

Now that I have firmly established how weird naming conventions are in science, let’s continue. I want to mention that saying these species were “discovered” may be inaccurate. For some of these organisms, it might be more accurate to say “the locals were aware of these species but they weren’t catalogued by Western scientists”. However, it is also possible that the locals knew about these critters but weren’t aware of their taxonomical significance. (Taxonomy is the science of classification.)

You know what, I’m going to go further into the idea of “discovering” new species at this point in time, because when I decided to write this entry, I had no idea how many new species are discovered every year. I thought I would have trouble finding five, but according to several sources I found while researching, between fifteen and eighteen thousand species are discovered a year. (Interesting note: about half of these new species are insects.) I know that numbers that large are usually not written out, but I had to write them out so I could italicize them. This does include corrections of previous taxonomical errors and paleontological discoveries, so that number doesn’t reflect the number of totally new and existing critters that are stumbled across for the first time by any human being, but still. Wow.

Here are common ways new species can be “discovered”:

  • New species were in museums but not examined closely enough to be correctly identified
  • Two or more species look so similar that they were mistakenly identified as the same, but DNA sequencing has realized that they are dissimilar enough to be classified as separate species
  • Scientists looking to “discover” species that have not previously been classified don’t want to look in areas where the political climate is unstable
  • Paleontologists uncover new skeletal remains
  • Researchers explore areas where there is an unusual amount of biodiversity

With that sorted, let’s get down to my favorite five species that were “discovered” in 2016.

The first species I want to discuss is Grammatonotus brianne, called “Brianne’s groppo”, which is surprisingly colorful (at least to me) for living in such deep water. Brianne’s groppo lives in on a reef in the Philippines’ Verde Island Passage known as a “twilight zone” reef, so called because the waters—at a depth between 150 and 500 feet deep—are murky, but there is some light. Brianne’s groppo can be found a depth that is almost out of the “twilight zone” range: 490 feet (150 meters). Why do I think that Brianne’s groppo is so cool? Because it is the deepest-dwelling fish that humans have ever collected…with their own hands. Literally. Previously, humans had only been able to collect such deep-dwelling fish with remote-control submarines, but divers collected this colorful groppo with the help of new diving technology.

Here it is:

Screen Shot 2017-07-14 at 2.21.25 PM

https://reefs.com/2016/10/04/grammatonotus-brianne-spectacular-new-species-mesophotic-groppo/

Image description: small, mostly bright yellow fish with a reddish pink back and a large spade-shaped tail

The next new species discovered in 2016 is my favorite because of my interest in Star Trek: the Tylototriton anguliceps, called the “Klingon newt”. It is so named because of the projections on its forehead, which somewhat resemble the forehead ridges on the Klingons from Star Trek (specifically, The Next Generation, Voyager, and Deep Space Nine).

Here’s a Klingon:

Screen Shot 2017-07-20 at 6.26.24 PM

http://memory-beta.wikia.com/wiki/Worf,_son_of_Mogh

Image description: a broad-shouldered man with medium brown skin and well-defined mountain range-like ridges on his forehead wearing a red Starfleet uniform and long, wavy dark brown hair pulled back into a ponytail

And here’s a Klingon newt:

Screen Shot 2017-07-20 at 6.26.48 PM

https://www.usatoday.com/story/news/world/2016/12/22/southeast-asia-species-discovery-newts/95752938/

Image description: a tiny newt with an extremely dark brown body and bright orange limbs, tail, and three ridges on its back, and projections on its head that resemble the forehead ridges of a Klingon

The Klingon newt lives in northeastern Thailand. Its habitat is part of the Greater Mekong region, a large area that includes Vietnam, Laos, Myanmar, Thailand, and southern parts of China. The Greater Mekong area is extremely biodiverse, and a large number of previously un-catalogued species have been found recently. That “recently” doesn’t just include 2016, either; since 1997, over 2,200 new species have been described in the region, even in the urban areas. The World Wildlife Federation is paying close attention to this region because the ecosystem there is incredibly intricate and delicate, and many species there are threatened or endangered. For example, the Greater Mekong region is home to the world’s largest tiger habitat, but in the past decade, tiger population numbers have plummeted by 70%.

Speaking of the Greater Mekong region, the third new species that I want to discuss was also found there, this time in Laos: the “Ziggy Stardust” snake. Its scientific name is Parafimbrios lao, but its colloquial name was chosen because of its colors; it is also called the “rainbow-headed” snake, and for good reason.

Here’s the rainbow-headed Ziggy Stardust snake:

Screen Shot 2017-07-22 at 2.46.07 PM.png

https://www.theguardian.com/environment/gallery/2016/dec/19/ziggy-stardust-snake-and-klingon-newt-among-163-new-species-discovered-in-mekong-in-pictures

Image description: medium gray-brown snake with iridescent rainbow scales on its head

The Ziggy Stardust snake is unusual because it is visibly different from any other species that has already been catalogued, no DNA sequencing required. The Klingon newt, with its distinctive forehead structures, is similarly unusual. And I think both the newt and the snake are cute. Yes, I think snakes are cute. We have established that scientists are weird.

Continuing with the trend of weird/interesting names, the next species I’m going to discuss is the “devil orchid”. Even the scientific name sounds demonic: Telipogon diabolicus. (Not as good as “Spongiforma squarepantsii”, but I like it.) The flower has a reproductive structure in its center that looks like a devil’s face.

Here is the devil orchid:

Screen Shot 2017-07-22 at 1.07.25 PM

https://blogs.scientificamerican.com/extinction-countdown/devil-orchid/

Image description: white translucent orchid with bright pinkish red veins and a dark maroon center that looks ridiculously like a pointy-eared devil

Unfortunately, only about 30 of these flowers are known to exist, in a tiny stretch of Colombian forest. Worse, that forest could soon be cut down so a new road can be laid down. It may not be the only Colombian orchid that is at risk for this particular fate. I don’t know about you, but I’d be willing to put that road in a slightly different place to preserve these cool-looking flowers.

I saved perhaps my favorite name for last: the prehistoric Muppet-faced fish. Yes, you read that right.

Look at this thing’s mouth:

Screen Shot 2017-07-22 at 2.10.37 PM

https://www.livescience.com/53660-muppet-faced-fish.html

Image description: artist’s rendition of two large gray-scaled fish with enormous mouths that resemble the mouths of Sesame Street Muppets in shape and proportion

I know it’s an artist’s rendition, but don’t those mouths look so much like Muppet mouths? Those mouths were big, too; these fish were about 2 meters (6.5 feet) long, including a head that measured half a meter (1.5 feet). Their mouths were about 0.3 of a meter (1 foot) in diameter. I know they look (and sound, knowing how big they were) a bit freaky, so if this helps, those gaping mouths were actually designed to consume plankton.

Up until recently (about February of 2016), only one species of this fish had been discovered. A new study, though, helped paleobiologists realize that there are more of these Muppet-faced fish species, which belong to the genus Rhinconicthys. How did they figure this out? Skulls from three separate global regions. Remarkably, only one skull was found per region, but a wealth of information was gleaned from those single skulls. Species currently identified include Rhinconicthys purgatoirensis, found in the Purgatoire River valley in Colorado, and Rhinconicthys utenyoi, found in Hokkaido, Japan, and Rhinconicthys taylori, found in England.

Well, I learned a lot writing this entry, and I hope you did too, dear readers! If nothing else, you now have a solid idea of how weird scientists are in our naming conventions.

Tales From the Bench: Why I Left Laboratory Science

Hello, dear readers. First of all, I want to say that this isn’t going to be a standard “Tales From the Bench” entry. Most of my “Tales From the Bench” posts are going to be interesting (I hope), but be about events slightly more mundane than me deciding to leave bench work forever. Yes, that’s what I’m going to talk about today: why I left the bench.

There’s an expression that I have found useful many times in my life: the straw that broke the camel’s back. I had been miserable for a long time at my job and was doing such a tremendous job putting up a happy front that I was not entirely in touch with how unhappy I was. I was commuting four hours a day—two hours there, two hours back—and when I felt run-down, I said the commute was getting to me.

It wasn’t just the commute. Bench science has an extremely high-pressure environment.

One of my coworkers at my last job (no, I’m not giving a name; I’ll call her N) was far more experienced than I was, so while she was not technically my supervisor, she often acted as such. N frequently told me that there was a lot of pressure on her, which is why she put pressure on me; she acted like it was entirely fair that she took her frustration out on me. This frequently took the form of speaking to me in a tone that screamed “Oh my God, I don’t think you have a brain; what is wrong with you?”, requiring absolute perfection even when I was still learning a new procedure, acting like mistakes meant incompetence, and blaming me for problems in our research that might have been either of our faults. I had to spend a lot of emotional labor responding to N in ways that she would find acceptable despite my instincts that she was being unfair. Not to mention it took a lot of energy to build myself back up after her behavior chipped away at my self-esteem. When I finally worked up the courage to tell N that her teaching style was not always conducive to my learning style, she shut me down, telling me I was too sensitive and comparing me to a child who didn’t understand why her parents were disciplining her. Instead of listening to me, she delegitimized my experiences and infantilized me. That was not the first day she made me cry.

And my experience with that coworker? That was nothing. I’ve been through way worse. I don’t know if I have had a single laboratory experience that didn’t involve a superior who was somehow callous, unfair, or outright nasty.

I don’t know what it is about lab science, but that field seems to have an abundance of people who are difficult to work with. The high percentage of scientists who have acerbic personalities at work seem to be about half the problem; the other half is money. The primary investigator is almost always either applying for funding or waiting to get funding or getting applications for funding rejected, which puts them under pressure and makes them cranky. They are then cranky to their subordinates, who are then cranky to their subordinates, and the people at the lowest level get it the worst. (Not that the stress of being a PI isn’t also a different kind of unparalleled stress; by “it”, I refer here to being the target of crankiness.) This exacerbates the fact that—at least to me—many scientists don’t seem to have good people skills. (I definitely include myself in this statement.) The result is people tearing each other down when they should be building each other up (I’m not saying every scientist does this, just that in my experience, it happens way too much in laboratory settings), and I can’t handle that. I’m sure there are labs out there where everyone is decent to each other and the higher-ups are skilled, patient teachers to students and newer researchers, but I wasn’t about to spend my life looking.

Bench work is also emotionally exhausting unless you have a certain temperament. You can spend two days on a complicated procedure, make a tiny mistake, and ruin everything. You can spend two days on a complicated procedure, make no mistakes, and the procedure can still not work, because that’s how science goes. You can spend months on a project and your refrigerator can break and ruin all your samples. You can spend years on a project and have everything ruined by someone from another lab putting a mouse cage back in the wrong place, flooding the mouse room, and drowning your mice. (This happened to another PI while I was working at my last laboratory job.) You can spend a decade and hundreds of thousands of dollars on a project and your hypothesis turns out to be wrong. You have to not care about these extremely frequent setbacks, or at least you have to be amazing at picking yourself up, dusting yourself off, and continuing, especially when there are people yelling at you for things that went wrong that may have not even be your fault. It takes a toll. Even N, who had been in science for decades, told me she had nightmares about experiments not working. (I had nightmares too. Usually about her.)

When it comes to laboratory bench work, I have the skills. But I do not have the temperament. I am too affected when procedures don’t work.

The straw that broke the camel’s back for me, the event that made me realize why I was miserable at work and that I didn’t have the personality to be a lab researcher, was this: I came back after a week-long illness on a Monday, and when I sat down with N and my lab notebook and asked her to catch me up, she told me that almost all of our cells had been contaminated the previous week. Three months of work were gone. There was no way to tell which of us had made the error that contaminated our cells, so of course she blamed me. She said in that voice that screamed “you’re so incompetent I can’t stand it”, “I am telling you very nicely to be careful”. Nicely. Sure, N. Sure.

The misery I had been suppressing for weeks erupted when I arrived home. I burst into tears that didn’t seem to want to stop and poured out all my frustrations to my parents. They cautioned me not to make any snap decisions, as I had been dedicated to the idea of being a biomedical researcher for nearly two decades, but the camel’s back had been broken. I knew the truth: I wasn’t cut out for bench work.

I tried to continue working—I knew the smartest thing to do was find a new job before I quit—but my work quickly started suffering. I had previously pushed forward despite being miserable because I actually enjoyed doing some of the procedures, and I had been motivated to get through the two or three years in the lab before returning to graduate school (and getting away from N). My enjoyment of the procedures was completely gone and I no longer wanted a PhD. Without my motivation, my ability to concentrate—which was required for stretches of six hours at a time for certain procedures—began to deteriorate. I decided to get out before I made a mistake that would seriously impair the PI’s research. I put in my two weeks’ notice.

And here I am today! I’m freelancing to build my portfolio, writing this blog (if not as prolifically as I would like), and searching for a full-time job. As for why I picked writing…that might be a story for another day.

I’m Not Dead!

I’m currently working on a Tales From the Bench entry on why I chose to leave laboratory bench work. But on Thursday the 19th, I developed a painful gum infection and I had my wisdom teeth removed the following Monday. I took a break from writing while I recovered, and right now I’m swamped. I currently am working on two freelance jobs and a writing assessment for a full-time associate medical writer job. In a few days, I’ll be able to write more, and I hope to have my next real entry up next week.

Pseudoscience Be Gone: Climate Change

Welcome back, dear readers, and I hope you’re ready for some inconvenient truths. (Is that reference too dated? I’m still new to this blogging thing.)

This entry is part of a section called Pseudoscience Be Gone, in which I will confront (sadly) common pseudoscientific beliefs with cold, hard facts. In this entry, I won’t be talking about the actual pseudoscientific beliefs much; instead, I will focus on the evidence that exists to support the ideas that 1) global warming is real and 2) humans are having a profound effect on global warming.

I’ll start by discussing what climate change actually is. “Climate” can be described as “the average weather”, and when it comes to “climate change”, the scientific definition of climate change is often different than the political one. The scientific definition is “a change in the statistical properties of the climate system on a large scale over long periods of time”. “Statistical properties” means averages—such as average temperature or average concentration of carbon dioxide in the air—as well as how much those properties vary. The “climate system” is the sum of five zones covering the Earth, including the atmosphere and the biosphere (the portion of the Earth populated by living things). As far as the political definition, when most people talk about climate change these days, what they really mean is anthropogenic global warming: the increase in the Earth’s surface temperature caused by humans. That “large scale and long periods of time” bit from the scientific definition still applies, though; anthropogenic global warming refers to what’s happening to the entire Earth over hundreds of years. So the next time someone brings up El Niño in a discussion about climate change, you can tell them that that doesn’t count; the change doesn’t last long enough.

“Global warming is real! Science shows that!” is something I hear a lot from frustrated people who are in touch with the truth. And they’re right, but how do scientists figure out that the Earth is getting warmer, and what evidence do they actually have? That’s what I’d like to focus on for the rest of this entry. As a cancer biologist, I started research for this entry without much knowledge on how environmental scientists actually gather evidence for climate change. There are a number of sources that scientists can turn to when looking at how Earth’s climate has changed over time: ice cores, fossil records, sediment layers, floral and faunal records, and meteorological stations.

I do love fossils, but my favorite climate change information source to research was the ice cores. Ice cores are cylindrical samples of ice taken with a special kind of drill called a core drill, and they provide some of the best records for investigating past climate conditions. Not only can some of the deeper cores contain information that go back hundreds of thousands of years, they can be used to figure out data on this long list of conditions at a given time:

  • Temperature
  • Strength of air circulation in the atmosphere
  • Precipitation (rain/snowfall)
  • Ocean volume
  • Dust in the atmosphere
  • Volcanic eruptions
  • Solar variability
  • Amount of sea ice
  • Rate at which energy is converted to organic substances by marine life
  • Geographic extent of deserts
  • Forest fires
  • Radioactivity

How is this possible? Well, all of those can be figured out by looking at the levels of materials like dust, ash, and human pollutants in the air. Snowfall captures those things, and in some places (such as the poles), that snow doesn’t melt. Ice cores provide valuable information about the ambient temperature, which has been useful in the hunt for evidence of anthropogenic global warming. Certain molecules—like deuterium, which is hydrogen with an extra neutron—have a known relationship with temperature, so scientists can determine temperatures at specific years from the concentration of deuterium at a particular point in the ice core. Known geological events, such as an extremely powerful volcanic eruption in 1815, can be used as “dating horizons” to figure out approximately what year an ice core layer is from. Increased radioactivity from nuclear bomb testing is also often used as one of these “dating horizons”.

As I mentioned, I also like fossils. One of the things that the fossil record does for scientists is to divide up geologic time, often by showing extinction events. (Well, okay, the division of Earth’s history into periods is mostly based on visible changes in layers of sedimentary rock, but fossils are involved too.) The fossil record currently shows seven mass extinctions, my favorite of which is the Great Dying, when 96% of all marine life and 70% of all land-dwelling vertebrates died due to a possible asteroid impact and one of the most tremendous known volcanic eruptions on Earth. (If you ever want nightmares, look up “formation of Siberian Traps”.) That extinction event ended the Permian period and began the Triassic period. Periods are divided into epochs, which are further divided into ages; more on why that is important later. For now, I want to talk about foraminifera.

Foraminifera are tiny protozoans with carbonate shells. While these little critters are alive, their shells are formed from the elements found in the water where they live. Paleontologists can look at the ratios of elements in foraminifera shells and be able to tell how much of the Earth’s surface was covered in ice when the animals were alive. This is important because it provides valuable information on a time when rapid climate change—that thing that’s happening now—happened before. This rapid climate change, which marked the end of the Eocene epoch and the beginning of the Oligocene epoch, was actually a transition from a “greenhouse” climate to a much cooler one. This rapid cooling led to one of those mass extinction events I was talking about earlier. So rapid changes in the Earth’s overall temperature? Those don’t bode well for the things living here.

So we have all this evidence. What does it show, exactly? One of the things we have learned about climate change is that starting in the Industrial Revolution—let’s say 1750—ice cores show dramatically increasing concentrations of carbon dioxide and methane. To be specific, there has been a 40% increase in the concentration of carbon dioxide since the beginning of the Industrial Revolution. Carbon dioxide and methane are what is known as “greenhouse gases”, or gases that absorb and emit heat. These gases are the main cause of the “greenhouse effect”, which is what happens when a planet’s atmosphere warms its surface to a higher temperature than what it would be without the atmosphere. Higher concentrations of greenhouse gases in the atmosphere cause higher surface temperatures.

The Earth has had atmospheric carbon dioxide levels this high before: in an age called the Pliocene, which the Intergovernmental Panel on Climate Change has called the “benchmark for modern global warming”. Dr. Aradhna Tripati, an assistant professor at UCLA who studies Earth Sciences and is so smart she started university when she was 12 (really), says “Our data from the early Pliocene, when carbon dioxide levels remained close to modern levels for thousands of years, may indicate how warm the planet will eventually become if carbon dioxide levels are stabilized at the current value of 400 parts per million”. What Dr. Tripati is saying is that the Earth is currently on the bullet train to having a climate like the Pliocene’s, which would mean summertime Arctic temperatures 18 to 15 C warmer than they are today. Meteorological station records show that the Earth’s surface temperature had increased a little over half a degree Celsius in the past century, and just that is already causing hotter days, heavier rainfall, stronger hurricanes, and more severe droughts. Now imagine what might happen if the Earth gets 15 C warmer. One thing we can predict is that if the concentration of greenhouse gases in the atmosphere doesn’t change, there could be no sea ice in 50 to 100 years.

Humans have had such a profound impact on the climate that many geologists believe that we have entered a new geological age: the Anthropocene Age. While there is not a consensus in the scientific community regarding the Anthropocene Age, it is still extremely telling that humans have changed our environment so much that some experts are claiming that we have entered a new period of geological time. While we haven’t made a noticeable change in the sediment layers, 12% of land masses are now cropland. On the topic of humans cultivating so much land, Dr. Anna Behrensmeyer, a paleoecologist with the National Museum of Natural History, says “the shift from forest to grassland took millions of years, but the pace and rates were nothing like they are now. With the rates now, you don’t really give the animals and plants a chance to evolve”. Dr. Thomas Lovejoy, the Smithsonian assistant secretary for external affairs, cautions “biological systems can take it, and take it, and take it, then all of a sudden there’s a tremendous reordering”. So it looks like we’re headed for a “tremendous reordering” from all the meddling we’ve been doing with the environment.

So the next time some ill-informed soul tells you climate change is a hoax, tell them about ice cores and foraminifera. And remember: science doesn’t care what you believe.

Credit to my sister-of-the-heart Rocky Blonshine for geology tips and my biological nuclear family for reading.

The History of Science: Dr. Rosalind Franklin

Well, it looks like it’s time for my first entry! Let’s talk about one of my favorite scientists: Dr. Rosalind Franklin.

Dr. Franklin’s name often comes up in high school biology classes when students are first learning about the discovery of DNA’s structure. I would be willing to bet that several of the students in those classes are already familiar with the duo Watson and Crick when they first hear the name Rosalind Franklin and see Photo 51. If you ask those who study biology at higher levels about Rosalind Franklin, you might see their face screw up in anger and hear them snarl that Watson and Crick—or you might hear the name Wilkins—stole Dr. Franklin’s work. You might also hear that Dr. Franklin wasn’t given the credit she deserved due to sexism. Still others might say that the only reason Dr. Franklin is said to not have gotten sufficient credit for her work is because she died prior to Drs. Wilkins, Watson, and Crick being awarded the Nobel Prize, or that Dr. Franklin didn’t actually realize her results indicated that DNA’s structure was helical.

So what’s the real story? Was Dr. Franklin’s work stolen? If she had such definitive results on the helical structure of DNA, why didn’t she publish it before Watson and Crick did? I had to do more research than I expected to find out the answers to these questions, and in this entry, I plan to share those answers with you, dear readers.

But first, I want to share some information on Dr. Franklin herself. As I mentioned above, she passed away before the Nobel Prize for the discovery of DNA’s structure was awarded. She died tragically young; she was only 37 when she succumbed to ovarian cancer. She was born in the United Kingdom in 1920 into a Jewish family. According to Dr. Franklin’s sister, the family supported her scientific endeavors despite the fact that the sexism that exists in STEM fields today was even more rampant in the past.

While most people think of DNA as related predominantly to biology—it is occasionally referred to as “the molecule of life”—Dr. Franklin was primarily a chemist. While her contribution to the study of DNA was recognized posthumously, Dr. Franklin was still a celebrated scientist during her life. Her study of the porosity—the percentage of empty spaces in a material—of coal, which was the subject of her PhD thesis, provided critical information on how different types of coal would perform as fuels. She was a PhD student during World War II, and not only did her work with coal contribute to the design of gas masks with charcoal filters, but she also volunteered as an Air Raid Warden.

Dr. Franklin also did important work on the structures of RNA and viruses. After her work with DNA (which I will discuss later), she made groundbreaking discoveries on the structure of tobacco mosaic virus. Tobacco mosaic virus, often called TMV, is what is termed a model organism: a living thing that provides useful information for biologists on many similar other living things…and is usually easy to study. Dr. Franklin’s discoveries that the proteins in TMV were arranged in a spiral and that the RNA in TMV resides inside a groove in the protein arrangement were crucial to the understanding of several other similar viruses. Dr. Franklin was at the top of her game, cranking out papers on structural virology at an impressive speed, when her life was cut short.

In case you’re impatiently tapping your foot while waiting for me to talk about DNA, dear readers, I’m about to get to it. Dr. Franklin started working at King’s College London in 1950. She had done extensive work with a technique called X-ray crystallography—a method for determining the structure of a material that can form a crystal—after earning her PhD. She was hired to do similar work on proteins, but the department head reassigned Dr. Franklin to study DNA fibers. Dr. Franklin was able to use her past experience with X-ray diffraction to improve the quality of the results her department’s experiments were yielding. She discovered that DNA had two forms, which she called “A” and “B”. She noted that DNA fibers were long and thin when wet (form “B”), and shorter and fatter when dry (form “A”).

Some suggest that Dr. Franklin never realized that DNA was helical, which is why she did not publish that discovery ahead of Watson and Crick. The truth is that Dr. Franklin was a perfectionist who wanted to make absolutely sure that she had correctly interpreted all her data. In lecture notes dated November 1951, Dr. Franklin wrote: “The results suggest a helical structure (which must be very closely packed) containing 2, 3 or 4 co‐axial nucleic acid chains per helical unit, and having the phosphate groups near the outside.” In 1952, asymmetrical images of the “A” form of DNA caused Dr. Franklin to balk at the idea of claiming that both forms were helical. By 1953, she had reconciled all of her data and became convinced that both “A” and “B” forms of DNA were helical. Not only did she now know that DNA was helical, but she had deduced that DNA was a double helix: two helices intertwined with each other like a twisted ladder. She began work on several manuscripts on the subject, and one day before Watson and Crick completed their model of “B” DNA, two of Dr. Franklin’s papers on “A” DNA’s structure reached the headquarters of a journal called Acta Crystallographica. Years later, another manuscript dated March 1953 was found in Dr. Franklin’s files, this one discussing the structure of “B” DNA.

I don’t know about you, dear readers, but I’m pretty convinced that Dr. Franklin discovered the helical structure of DNA independent of Watson and Crick.

You know what, I’m not done gushing about Dr. Franklin’s research. It’s also important to note that not only did she figure out that DNA was a double helix, but she also knew that DNA contained a sequence of nitrogenous bases: key parts of the building blocks of DNA. She also deduced that the sequence of bases provided the genetic code. She even discovered that the nucleotides—the aforementioned building blocks of DNA—were paired with each other. I’m sorry, but that’s impressive. Actually, no, I’m not sorry.

“But what about the controversy?” you might be saying. “Did Watson and Crick steal her work?” Well, all right, dear readers. Let’s talk about the controversy. In 1952, Dr. Franklin’s student, Raymond Gosling, took one of the most famous photographs in science: Photo 51, an image of the “B” form of DNA.

Here it is.
Photo 51.png

https://en.wikipedia.org/wiki/Photo_51#/media/File:Photo_51_x-ray_diffraction_image

Image description: an X-ray crystallography image in grainy black and white showing small horizontal black bars in an “X” shape on a circular gray field

The crux of the controversy is this: Dr. Watson had the epiphany that DNA was helical when he saw Photo 51, which he saw without the permission of Dr. Franklin (or Raymond Gosling). In my research for this entry, I stumbled across at least one person claiming that Watson and Crick would have discovered the helical structure of DNA with Dr. Franklin’s consensual help had Dr. Watson been paying attention during a seminar Dr. Franklin gave on the relative distances of repetitive elements in DNA. (Dr. Watson admits to this inattention in his book The Double Helix: A Personal Account of the Discovery.) However, Photo 51 was taken after this lecture, and regardless of speculation, Dr. Watson had his realization when a colleague of Dr. Franklin’s—Dr. Maurice Wilkins—showed him Photo 51, again, without Dr. Franklin’s permission. I’m pretty certain that at no point in recent history was showing your labmates’ work to competing scientists considered anything but unscrupulous. Well, unscrupulous if not a terrible idea, since it could lead to you getting scooped. (“Scooped” is what scientists call it when someone else publishes results you’ve been working for before you do.)

Why in the world would Dr. Wilkins do this? That isn’t clear. What is clear is the sequence of events: on January 30, 1953, Dr. Watson arrived at King’s College London, bearing a manuscript containing another researcher’s incorrect model of the structure of DNA. He was looking for Dr. Wilkins, who wasn’t in his office, and Dr. Watson instead went to Dr. Franklin’s lab and insisted that they all collaborate before the author of the incorrect paper realized his model was wrong. As part of his insistence, Dr. Watson suggested that Dr. Franklin didn’t know how to interpret her own data, and Dr. Franklin was (understandably, I think) irritated. As he was scurrying away from this confrontation, Dr. Watson ran into Dr. Wilkins, who tried to console him and then showed him Photo 51. Some theorize that Dr. Wilkins did this because he had a terrible relationship with Dr. Franklin, who intimidated him; Dr. Wilkins was shy and retiring. Still others theorize that sexism was a factor in Dr. Wilkins’ actions. I can’t figure out people’s motivations when they aren’t historical figures that I’ve only read about, so I don’t know what Dr. Wilkins was thinking, but I do know he was in the wrong.

At no point was Dr. Franklin aware of her influence on Watson and Crick’s work. In modern science, if someone helps you with your research, you acknowledge their contribution in your paper. In April of 1953, Watson and Crick published their model for the structure of “B” DNA in Nature—a very, very reputable journal—without properly crediting Dr. Franklin. Later in the same issue, several articles by Dr. Wilkins and Dr. Franklin appeared in support of Watson and Crick’s model.

So was Dr. Franklin’s work stolen? I wouldn’t go that far. Was she not given enough credit? Definitely. Watson and Crick are still seen as the primary discoverers of DNA’s double helical structure when Dr. Franklin’s work was just as if not more important, and Watson and Crick likely would not have been able to publish that Nature paper without Photo 51. Was sexism a factor in Dr. Wilkins’ decision to show Photo 51 to Dr. Watson? I think that is possible; it was the 1950s, and as for anyone who doesn’t believe that there has always been sexism in science and that it still isn’t prevalent, I would like to know what life is like on their planet. (I mean, while Dr. Franklin was working at King’s College London, the female scientists were not allowed to eat in the common room. Also, if you read The Double Helix…wow, Watson and Crick have no idea how sexist and arrogant their attitudes were. No idea.) More important than what was in the heads of Drs. Watson, Crick, and Wilkins, though, is the fact that Dr. Franklin still isn’t given enough credit. To this day. I can’t show statistically significant data proving that sexism is a factor in that, but I would still bank on it.

If you take anything away from this entry, dear readers, is that Dr. Rosalind Elsie Franklin was an incredible, brilliant scientist who made many groundbreaking discoveries and who deserves all the credit in the world. Oh, and that the answer to “is sexism a factor in this?” is going to be “yes” 99% of the time if it involves women in science.

Introduction

Hello, dear readers, and welcome to Immortal Amaranthe: A Science Blog! The purpose of this blog is to try to disseminate information on science in a manner that is (hopefully) accessible to all. (Speaking of accessibility, if anyone knows the most disability-accessible WordPress theme, please let me know.) I’ll probably stick to biology at first since that’s where I’m most comfortable; my bachelor’s degree is in biological sciences and my master’s degree is in biomedical sciences.

I’d like to start by sharing how I came up with the name of this blog. My pen name is Amaranthe; I named myself after the flower, not the flour. Amaranth (without the “e”, which I added because…well, if I’m honest, because there exists a Swedish metal band I like called “Amaranthe”) is a genus of plant that plays a minor role in several myths and legends. Its name comes from the Greek “Amarantos”, meaning “unfading”, or in the case of the plant, “un-wilting”. Amaranth’s “un-wilting” nature is what landed it in stories and poems; in Paradise Lost, John Milton wrote “Immortal amaranth, a flower which once/In paradise, fast by the tree of life/Began to bloom”. My blog title is taken from that quote in part because of the nature of scientific research. People go into science for various reasons, so I won’t say every scientist wants their work to go down in history, but significant discoveries will last, and many researchers would love for their work to be remembered—maybe even celebrated—in the future. “Immortal” might be a bit of an exaggerated description to apply to important scientific discoveries, but I liked the quote, so I’m going with it.

I know what you’re thinking, and no, it has nothing to do with The Immortal Life of Henrietta Lacks. Even though I also like the parallel of my blog’s title with immortalized cell lines. I may actually write about Henrietta Lacks later, though, probably in an entry about biomedical ethics. I will also likely write about cell culture and how much I hate it.

Speaking of what I will likely write about, the entries in blog will belong to several categories, which are as follows:

  • The History of Science: anecdotes on researchers or discoveries
  • Well, This Is Cool: entries on recent scientific discoveries that I find interesting
  • Social Justice and Science: confronting bigoted ideas with facts
  • So What Do Scientists Actually Do?: explaining protocols of common scientific procedures
  • Pseudoscience Be Gone: debunking common pseudoscientific claims
  • Found in Translation: summarizing historically important scientific papers
  • Tales From the Bench: anecdotes about what it’s like to do biomedical research
  • Ama-rants: op-ed entries

I’m currently planning to write entries in the order listed above. My first entry after this will be a “History of Science” one, my second entry will be a “Well, This Is Cool” one, etc. I also might sprinkle in some “Well, This Is Cool” entries out of order if a new discovery becomes famous enough that I want to comment on it right away. Right now, my goal is to write one entry per week. I’m not used to being such a prolific non-fiction writer—I often can’t even crank out Star Wars fanfiction that quickly—so that goal probably won’t be a reality for a bit. In all likelihood, I’m going to be posting every other week. The tone of the blog is going to be informal, so I hope you, dear readers, are not bothered by fragments, run-on sentences, and sentences starting with words that don’t ordinarily start written sentences.

What else can you expect from this blog? Well, I already have many entries planned! Here are a few topics I already have chosen to write about:

The History of Science:

  • Rosalind Franklin, especially the controversy over whether or not her work was stolen
  • Social Darwinism
  • The invention of vaccines

Well, This Is Cool:

  • How chocolate might lower chances of atrial fibrillation
  • New species discovered in 2016 (I know it’s May, but new species are still cool)

Social Justice and Science:

  • Genetics is not the weapon of transphobes
  • Medical fatphobia and why it needs to end
  • Darwinian evolution and how it is often twisted to suit ableism

So What Do Scientists Actually Do?:

  • Polymerase chain reaction (I did my thesis on this)
  • The basics of culturing cells

Pseudoscience Be Gone:

  • Vaccines do not cause autism
  • Detox cleanses are heinously misnamed

Found in Translation:

  • Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors by Takahashi K. and S. Yamanaka (about the reprogramming of cell functions…and these people won a Nobel Prize for this work)
  • Detection of specific sequences among DNA fragments separated by gel-electrophoresis by Southern, E. M. (about a useful breakthrough in visualizing DNA fragments)
  • An epigenetic mutation responsible for natural variation in floral symmetry by Cubas, P, C Vincent and E Coen (about epigenetics, which is the study of changes to genes other than changes to the actual bases)

Tales From the Bench:

  • How college did and didn’t prepare me for bench work
  • The first time I lost several months of work

Ama-rants:

  • Eugenics is unethical
  • Women (and sexism) in science

Do you have a science-related topic you would like to see me tackle? Great! Comment on this entry or Tweet your ideas to me at @AmarantheRae. I’m particularly interested in hearing about any scientific concepts that my readers might find hard to understand but that I can hopefully elucidate a little bit.

I think that covers everything I wanted to say. Farewell for now, dear readers!

—Amaranthe