Sometimes, life gets hard

First off – yes, I’m alive.

Even though my blogging frequency has been pretty pathetic recently, I still get a steady trickle of emails from concerned readers who miss me. It’s an odd feeling knowing total strangers want to make sure I’m okay and miss my writing, but I do sincerely appreciate it (even if I don’t reply, sorry). It also makes me realize that not everyone follows my twitter feed, so many of you have no idea what has been going on in my life.

No, it’s not just grad school that’s been keeping me busy. These have been the hardest months of my life.

On March 15th, my mom called me. My family knows I hate talking on the phone, so when my phone is ringing and it’s not a holiday, I assume something is wrong. Usually that’s just my irrational anxiety talking, but unfortunately this time it was right. It was news I never wanted to hear – my mom had cancer again.

She had been cancer free for 8 years, after winning her battle against breast cancer during my senior year of high school. I hate to say this, but I had never been truly worried during that time. Part of it was knowing they caught it soon and that she had wonderful doctors, but part of it was definitely being a naive 17 year old. At the time I didn’t realize it, but my parents had painted a rosy picture of the situation to keep me from worrying. What I remember is my mom scheduling her chemo appointments around my high school golf matches, because she didn’t want to miss them for the world. The worst of it was kept behind the scenes.

But now I was a little bit older and wiser. In this case, being a geneticist was not very comforting. I was more aware of the realities of a cancer diagnosis, especially when cancer had come back. But I tried to stay cautiously optimistic, since there was still no official diagnosis.

A week later one morning, I was laying awake in bed worrying about my mom. My phone rang, and this time it was my dad. Getting a phone call in the morning is even more terrifying, and I knew instantly from his voice that something was horribly wrong.

He told me my mom was going to die within hours.

Hearing that out of nowhere, while stuck thousands of miles away across the country, was… I don’t even have an adjective that can describe that. Horrifying? Devastating? I was literally in hysterics, sobbing and shaking for hours. It felt like a nightmare come true. I’m so glad my boyfriend had been there, because I don’t know what I would have done without his immediate support. In the span of a week my mom had gone from perfectly healthy, living the stereotypical retired life golfing in Florida, to “going to die.”

A couple of days earlier, my mom had fluid (caused by the cancer) removed from her abdomen, and that change in pressure had caused massive blood clots to move from her legs to her lungs. “Why didn’t the doctors check for that ahead of time?” I asked myself. She couldn’t breathe. She had a 10% chance of making it, but thankfully our hometown hospital is one of the top 50 in the nation and had a cardiologist present that specialized in dealing with this problem. Also thankfully this happened at 7am on a Sunday morning, so the emergency room was empty. Who knows what would have happened to her if she hadn’t been the only patient there.

She survived. I flew out the next day to be with her.

Even though the clots had been removed, there was little emotional relief. When I got there, we were bluntly told that she may never wake up from sedation at all, or if she did she could be a vegetable. The first thing I saw when I arrived was that her tongue had swollen to grotesque proportions, filling her whole mouth and spilling out. The doctors still have no idea what was going on there and originally blamed the tape holding her breathing tube in, though my dad and I suspect they accidentally gave her antibiotics that she’s allergic to and wouldn’t admit it. When I noticed her face was starting to swell as well, they ignored me…until we had come back from lunch and her whole head had swollen up. It was devastating seeing her like that – seeing someone you love and thinking “that can’t be my mother.” Once her whole head was ballooning up, they finally admitted I had been right, and maybe they should start trying to reduce the swelling. Yeah, you’d think.

(I wish the tongue thing was the only time we dealt with incompetence from doctors and nurses… They constantly ignored call buttons for 30 minutes to an hour and I had to go run and find nurses in emergencies, they tried to give her medicine for other patients which thankfully my dad caught, they tried to give medicine in her left arm despite signs everywhere saying not to do so, some wouldn’t use gloves and were obviously not using sterile technique, doctors fought in front of her which destroyed her confidence in them… Yes, they saved her life, but at the same time my faith in doctors has definitely been shaken.)

Thankfully again, my mom beat the odds. After a couple of days she woke up. We talked by her first pointing to letters on a sheet, then by her writing, and after weeks she was able to barely speak. I can now say that months later, she can talk fairly normally and has all of her mental faculties. I feel like I can’t even thank science or medicine here – she got lucky.

The problem was, you know, my mom still had cancer. And the equivalent of a massive heart attack followed by aggressive weekly chemotherapy is not exactly a good situation. She was getting chemo even when she was still bedridden and unable to walk. She was in the hospital for 90 days, but thankfully has been home for about a month now (and is still getting chemo). Just imagine not being able to leave a hospital room for three months – no sunshine, no idea if it’s day or night, no food (thanks to the swollen tongue)… You don’t even realize the little things you take for granted, like being able to cuddle with your pet or wear your own pajamas.

As for the cancer, the chemo does seem to be working very well, which makes me rejoice. We were glad to find out it wasn’t breast cancer again, because that would have been the worst prognosis. Unfortunately, it was ovarian cancer, which is scary in its own right. We have no family history of breast or ovarian cancer, but having both occur independently in the same individual is a huge red flag that the cancer may be heritable – that is, that her genome has some mutation that predisposes her to that type of cancer. If correct, that means I would have a 50% chance of having that same mutation.

My mom could honestly care less what her genome is, since it wouldn’t really change her treatment (“Yep, you still need chemo”). But she wanted to get genetic testing for my sake. Thankfully her results said she has normal copies of BRCA1 and BRCA2, the two main breast cancer genes. Having a mutant copy of one of those greatly increases your odds of getting cancer, so hearing that news was a relief. But to a geneticist, it was a minor relief. I knew there were dozens of genes that could contribute to cancer, and dozens more that we probably haven’t even figured out yet. This just ruled out the common problems.

After my parents told her genetic counselor that I was getting my PhD in genomics, the counselor decided she would just rather talk to me directly. We chatted on the phone and she discussed how she wanted to test a larger number of genes, especially since gastrointestinal cancer runs in my mom’s family and may be related to her case. She told me her current problem – getting my mom’s insurance company to okay the test. She explained how insurance companies don’t like tests that utilize modern technology like next generation sequencing, because they rather have you pay a deductible on each individual gene than have one test that covers the whole genome.

(Yeah, they rather squeeze more money out of their dying cancer patients than do an efficient test. I never had any faith in the insurance industry to be able to say I lost it, but let’s just say my rage against them has grown. At least my parents have insurance, because after a month of treatment alone the bill was at one MILLION dollars. It’s horrible enough worrying about my mom’s health; I’m glad I don’t have to worry about their sudden bankruptcy as well.)

But I knew something this genetic counselor did not. I told her that Mary-Claire King, the scientist who discovered BRCA1 & BRCA2, worked in my department and did a cancer gene panel that was twice as large as the one the counselor was considering. After the counselor got done fangirling and squeeing over Mary-Claire (no, really, nerd glee), she asked if I could try to get my mom enrolled in MCK’s study. All it took was one email, and minutes later MCK had said yes. My mom no longer had to worry about insurance, she would learn more about her genome than from some company’s test, and she’d contribute to a growing body of knowledge about cancer genetics.

While I’m relieved to know I’ll have this information, it has been an emotional process. Part of me is terrified for myself. I’ve seen how cancer has affected my mom. The physical weakness, the loss of hair (which can really hurt a woman’s self-esteem), the inability to eat (how I wish Indiana had medical marijuana, or that I could smuggle some from Seattle). Not to mention the giant cloud of doom reminding you that, yeah, you may die from this. It really scares me wondering if I’ll have to go through the same thing when I’m her age, or if I’ll get unlucky and it’ll strike me sooner.

And at the same time, I feel guilty for worrying about myself at all. I feel selfish worrying about what might happen to me in 30 years, compared to what’s happening to my mother right now. I feel guilty that I can only visit her a little bit before I have to come back to work, even though she’s told me that me finishing my PhD is the most important thing to her. I feel guilty that my dad has to be her full-time caretaker and home nurse now, while I get to go “back to normal.” I feel guilty every time I have a moment of happiness when I’m back in Seattle, because I feel like I should always be worrying about her.

I’ve never been good at prioritizing taking care of myself, but now it feels damn near impossible.

And that’s partly why I’ve been so depressed the last couple of months. Worrying about my mom, worrying about myself, feeling guilty about worrying about myself… I wish those were the only things stressing me out, because I could barely handle those. My boyfriend is graduating with his PhD this year (yay!) but that means we’re worried that he won’t be able to find a job in Seattle and will have to move far away (not yay). Grad school has been rough (which is a redundant statement, right?). I’ve been feeling very lost and without guidance for a while now, since my project is very unique and I’ve basically created it from the ground up (or as another grad student told me, I went straight from undergrad to a postdoc). My current experiments aren’t working, and even though troubleshooting lab work is totally normal, it can be crushing when you’re already down. It makes me feel like a failure and an imposter who shouldn’t even be in grad school. My lab is also having some funding woes, so I feel a lot of pressure not to screw anything up or waste supplies because we may not have the money for a round two. The cherry on top is that the two other grad students in my lab are graduating in the next month, so I will be the only graduate student left. I already felt lost and alone, but now it’s just going to be me, my adviser, and our research scientist.

The problem with depression is that even if you have understandable reasons to be depressed, it can make you unreasonable about everything else. I have particularly bad anhedonia – nothing really give me any pleasure. When asked to list my hobbies, I list things I used to enjoy. I have no motivation to do anything, even “fun” things.  Getting out of bed in the morning is a chore. I haven’t had an appetite in weeks, but I just keep feeding myself because I know I have to. I had convinced myself I had no friends who actually cared about me or wanted to hang out with me, which turned me into an even more lonely hermit. I’ve lost all of my goals and dreams, and when I think about the future I just despair. Every news article or opinion piece I read just makes me think how fucked and unfixable the world is, and I feel hopeless to do anything to make the world better.

And the fucked up thing about depression is that it convinces you that all of this is true, and you are the problem. Depression is like having sunglasses glued to your head and insisting the world is dark, even when you rationally know its bright. I was literally convinced for months that there was no hope in the future and that I would never feel happy again. Right now I can’t remember what it feels like to be happy. It wasn’t until yesterday that I had a small moment of clarity when I realized that my brain was lying to me. Not only that my brain was lying to me, but that I had gone through this exact thing before! There have been many times in my life where I’ve felt this way, but happiness and motivation and normalcy always came back eventually. I need to remind myself that this too shall pass.

I’m attempting therapy again (thank you, Secular Therapist Project). At least this time I’m pretty sure they won’t suggest Buddhism and spirituality as the solution (no thank you, University of Washington mental health services). Unfortunately the health insurance they give us grad students is kind of crap, so it looks like I’ll be paying mostly out of pocket for it. But thankfully I have a good amount of savings and just got a raise (thank you, National Science Foundation) so it won’t be a huge issue, and I’m trying to start viewing my mental health as something worth investing in. This isn’t a pity call for money – if you feel the urge to donate, pick your favorite cancer research charity and that will make me happy.

I don’t really have a take home message or wrap up for this post. I simply realized that writing has always been therapeutic for me, and when I quit blogging I threw away that therapy along with a social support network (you guys!). I’ve been meaning to get this off my chest, so here it is.

Dear life: Please stop sucking soon.

kthx,

Jen

Pokébiology 101: “Evolution” and the enigma of Eevee

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(Click here for the introductory post to Pokébiology 101)

You know I had to start my Pokébiology 101 series with the most famously scientifically inaccurate part of Pokémon: evolution.

In the Pokémon world, “evolution” means something different from what you might have learned in your biology classes. …Well, what you should have learned in your biology classes, assuming the religious right failed to push their agenda into your science classroom. Pokémon evolution is when a Pokémon transforms into a different looking creature once some criterion is met. Most often this means reaching a certain level (levels increase as you gain experience, experience comes from participating in battles). Some Pokémon evolve under weirder circumstances like being exposed to a particular item, being traded to another player, reaching a certain level of happiness, and so on.

For example, a Bulbasaur evolves into an Ivysaur at level 16, and an Ivysaur evolves into a Venusaur at level 32.

BulbasaurEvolution

This is not evolution. This is metamorphosis.

What’s the difference? Why are Pokémon actually metamorphosing, and not evolving? They both imply some sort of change is taking place, which is why the terms are so easily confused. But there’s a major difference in when and where that change happens:

  • Metamorphosis is the change in body structure of an individual that happens conspicuously and abruptly during their lifetime. The most common real world example is a caterpillar turning into a butterfly. This is exactly what happens in the Pokémon world. Well, instead of forming a cocoon, Pokémon flash a bright light and make cheery beeping noises…but I’m going to chalk that up to the games being from the point of view of a ten year old with an overactive imagination. Wee, shiny!
  • Evolution is the change in heritable characteristics of a population over successive generations. A characteristic is heritable if it is genetic, and thus will get passed on from parent to offspring, and from that offspring to its offspring, and so on. The key here is that this change happens over many generations and affects the whole population.

What would be a hypothetical example of actual evolution in the Pokémon world? Let’s say we’ve stumbled upon a population of Venusaurs in some jungle untouched by Pokémon trainers. Most  Venusaurs have pink flowers, but a rare individual has a gold flower because of a mutation. In case you’re wondering, this alternative color scheme exists in-game and is known as a “shiny,” and shiny Pokémon are incredibly rare. Like, “I’ve probably played 1000 cumulative hours of Pokémon games and I only found one shiny Sentret a decade ago” rare.

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Now, let’s say that shiny Venusaur is very successful in producing a lot of baby Bulbasaurs for whatever reason. Maybe gold flowers attract more prey, so shiny Venusaur is well fed and can have more babies (directional selection). Maybe other Venusaurs find the rare gold flower extra sexy, so shiny Venusaur has more mates and thus more babies (sexual selection). Maybe it’s all due to random chance and shiny Venusaur just gets lucky (genetic drift). When that generation of Bulbasaurs grows up, the new generation of Venusaurs might look something like this:

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If we’re still around to observe this population many generations later, it may look like this:

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The shiny trait has now become “fixed” in the population – that is, every individual now has the gold flower. Now the population of Venusaurs looks different than it used to – and that is evolution! If this population is isolated from other Venusaurs and continues to evolve novel traits, one day this population might be so different that it can’t even mate with other Venusaurs anymore. And that, folks, is when you have a new species.

But back to metamorphosis. The common caterpillar example is linear: a caterpillar makes a cocoon and becomes a butterfly. But not all Pokémon have a set fate. I give you the most enigmatic example, Eevee.

eevee-evolutions

Eevee is special in the world of Pokémon because it has the largest number of ways it can evolve depending on your actions. Want a Flareon? Give Eevee a Fire Stone. Espeon? Make Eevee very happy and level up during the morning or day. Leafeon? Level up while near a mossy rock.

It seems like this couldn’t possibly exist within the confines of our natural world, right? How does an Eevee have the ability to metamorphose into such different creatures just from what its exposed to in the environment? How can a Vaporeon, Jolteon, Flareon, Espeon, Umbreon, Glaceon, and Leafeon all have the same genome as their starting Eevee, but such different traits?

Not to erode Eevee’s specialness, but this happens right here on Earth.

This is known as polyphenism: when multiple discrete phenotypes (a set of observable characteristics) can come from the same genetic background because of differences in the environment. The most common example is different castes in bees. You may know that within a hive, one female gets to be the queen bee, and the other females are worker bees. A queen bee is made by feeding a larvae what’s known as “royal jelly,” which contains chemicals that alter the larvae’s development. If that larvae has a twin sister that didn’t get a special meal, sis will grow up to be a worker. They’re genetically identical, but very different thanks to their environment.

The only thing distinguishing bees from Eevees are the number of choices in development.

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In which I speculate on what would happen if you gave a bee a Fire Stone or Macho Brace.

It will forever irritate me that the game designers chose the term “evolution” instead of a totally accurate, also cool-sounding alternative word. My best guess is that “Bulbasaur is metamorphosing” took up too many pixels, so “evolving” won out. Sadly, this kind of sloppy terminology can cause a lot of misconceptions about what evolution really means. But hopefully now that you’ve learned some Pokébiology, you’re less confused.

EvolveMankey

 

So confused.

Welcome to Pokébiology 101

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Hello there! Welcome to the world of Pokémon! My name is Jen! People call me the Pokémon Grad Student!

…Okay, I don’t think anyone has actually called me the Pokémon Grad Student. But I’m a PhD candidate studying evolution and genomics who has been playing Pokémon since its release in 1998. My friend showed me his Red version, and soon after I owned my first video game – Pokémon Blue. I’ve been hooked since then.

As I progressed through my training as a biologist, I started to look at the Pokémon world in a new light. At first, it was irritation. Everything seemed wrong. They confused metamorphosis for evolution. Breeding didn’t make any sense – different Pokémon species could interbreed, but the offspring were always the same species as mom. Gender ratios didn’t reflect biological mechanisms, but rather a game designer’s attempt to keep certain Pokémon rare. Why, it was if they were trying to design a fun game with no regard to biological accuracy

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darwin heart piplup by claudetc

But as I learned more biology, I started to realize nature isn’t as simple as it seems. There are all sorts of strange biological phenomena that result in counter-intuitive mechanisms, traits, and organisms. Nature is really, really weird. So I started viewing the Pokémon world as a puzzle. If I were Professor Oak, what experiments would I be doing? Are there any natural processes in the real world that could explain Pokémon biology?

Bulbasaur Anatomical Study by JoshuaDunlop

Some of you must be thinking, “Jen, it’s just a game. It’s not supposed to make sense. Chill.” I know, I know. I don’t expect all games to be 100% scientifically accurate at the expense of fun. But I like daydreaming about how the biology of Pokémon could “work.” It’s as if I’ve discovered a whole planet of alien life to study, and what biologist wouldn’t want that?

But more importantly, I see the Pokémon world as a great way to teach people about actual biology. And I’m hardly the first person to think this – the creator of Pokémon originally conceived of the game as a way to share his childhood hobby of collecting insects with the children of a modern, urbanized Japan. But I’ll be discussing what I know best: evolution and genomics. How do Pokémon species differ from species here on Earth? What does genomic imprinting have to do with breeding? Can an organism like Eevee actually exist? I’ll be exploring these topics in future PokéBiology 101 posts.

Now, there are some things in the Pokémon Universe that are above my pay grade. I’m not even going to attempt to explain how a tiny mouse generates thunderstorms or how some Pokémon have psychic abilities. I have no clue how a Pokéball can transform Pokémon into pure energy and back again (maybe a bored Physics grad student can hazard a guess). And there’s certainly no explanation for how Onix, a ground/rock type, suddenly becomes vulnerable to electric attacks because a sprinkler system came on (yes, I am still bitter about that episode).

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 I have no idea how this works.

For all of those things, I’m willing to suspend disbelief. But when it comes to the biology of the Pokémon world, I’ve found it’s not necessary to invoke “magic!” as an explanation. Because oddly enough, that bizarre biology is already happening here on earth.

Welcome to PokéBiology 101!

Next in series: “Evolution” and the enigma of Eevee

Republican lawmaker wants to criminalize aborting your rape baby because it’s “tampering with evidence”

I’d say it’s a new low for Republicans, but really, it’s their usual low:

A Republican lawmaker in New Mexico introduced a bill on Wednesday that would legally require victims of rape to carry their pregnancies to term in order to use the fetus as evidence for a sexual assault trial.

House Bill 206, introduced by state Rep. Cathrynn Brown (R), would charge a rape victim who ended her pregnancy with a third-degree felony for “tampering with evidence.”

“Tampering with evidence shall include procuring or facilitating an abortion, or compelling or coercing another to obtain an abortion, of a fetus that is the result of criminal sexual penetration or incest with the intent to destroy evidence of the crime,” the bill says.

Third-degree felonies in New Mexico carry a sentence of up to three years in prison.

But don’t worry, Cathrynn Brown! I know you’re not a geneticist so this wouldn’t have occurred to you, but I have the solution to your problem. You can do paternity analysis using the DNA from an aborted fetus, the placenta, or (thanks to new technology produced from my very own department) fetal cells that are circulating in the mother’s blood. Why, you don’t need a live baby at all! It’s a win win situation. Women aren’t forced to give birth to and raise their rapist’s child as some sort of bizarre punishment for being raped, and evidence is still obtained to identify rapists.

I’m sure Rep. Brown will rescind the bill now that science has come to the rescue. It’s not as if this is actually some underhanded attempt to outlaw abortions, right?

Nazis, genetically modified babies, Mothman, and Jesus

I didn’t think those topics could be combined, but I’ve been proven wrong. No, it’s not the next hit superhero movie. One of the “perks” of being an atheist blogger is that I get signed up to all sorts of wacky mailing lists for creationists, woo peddlers, and conspiracy theorists. I suspect they think this annoys me, when really it usually goes straight to my spam folder to die with all the penis enlargement ads. But sometimes things slip through to my inbox, and sometimes their insanity is hilarious.

I present for your entertainment, “V Blast: THE BEAST REVEALS THEY CREATED GENETICALLY MODIFIED BABIES”

Those who are aware that conspiratorial practices have already wildly exceeded even the most fantastic speculations were not surprised to hear that scientists have now admitted that genetically modified babies have already been born. Although the mainstream, or the so called “ethical” medical community is now publicly acknowledging they’ve mixed genes from multiple parties to produce designer babies all the way back to the late 1990’s, the reality is genetically engineered babies were probably born as far back the 1940’s in one of Joseph Mengele’s Nazi laboratories.
Generally speaking, secretive “black” science significantly precedes the allegedly legitimate version, in which the mainstream commonly lags behind by decades. In fact, the recent mainstream media exposure in the Daily Mail periodical, reignited interest in a subject which was actually covered, albeit rather quietly, years earlier.
It turns out that In Vitro Fertilization (IVF) clinics have been using a technique now for years that “rejuvenates” the eggs of women who are having trouble conceiving, by injecting components of another woman’s egg. This component is called cytoplasm, and it contains the mitochondrial DNA from the donor – thus making the resultant baby the product of 3 parents – the father, and two mothers.
It turns out this has been publicly known since 2001 and, by tracing the research (and the scientist who developed the technique), we learn that babies with more than 2 parents were born at least as far back as 1997. Once again, once such things go public, it virtually always means it’s been going on for quite a bit longer, and has gone much further than is generally acknowledged.
Time for a science break! It’s actually true that scientists are trying to develop methods that use a third individual’s mitochondria during IVF, but it’s not to make abominations or super babies. It’s to cure diseases caused by malfunctioning mitochondria. Mitochondria are the “powerhouse” of the cell, making lots of energy so your cells can actually function.
They also have their own genomes because they were once a separate organism! They were engulfed by another type of cell and the two formed a symbiotic relationship, and now every eukaryote (anything that’s not bacteria or archaea) has mitochondria. Mitochondria are passed from mother to child, not father to child. This is because egg cells have the room to store mitochondria, but sperm don’t.
So if you have a disease that’s caused by a mutation in the mitochondrial genome, you could technically suck out all the “defective” mitochondria and replace them with “healthy” mitochondria from another person. And people are going nuts at the ethics around this, because yes, technically you’d have a third genetic “parent.” If you want to learn more, read this great article in The Guardian.
For instance, there is nothing to indicate these maniacs have stopped at 3 parents, as they could have, theoretically, added the cytoplasm of a dozen women – each selected for what are perceived as desirable characteristics – i.e. blue eyes from mom #4, physical speed and agility from gymnast mom #5, a very high IQ from mom #6, and so forth.
Yeah, theoretically you could add all sorts of mitochondria. But mitochondrial genomes are tiny and don’t really contribute to any distinguishing traits. Things like eye color would still be determined by nuclear DNA (the ones egg and sperm contribute to).
To put it another way, this is the stuff the Nephilim were made of.
I’m not even going to touch that.
What happens if they try to splice in the mitochondria of another father is anyone’s guess, but such outcomes could look like something out of a horror film. And it gets worse.
Actually, nothing different would happen if you took the mitochondria from a man. The only reason mitochondria are transfered maternally is because eggs have the room to do so. There are rare examples of mitochondria being transmitted paternally, with no real consequences.
Now we’ve learned the key research embryologist who pioneered this technique left the fertility clinic work he was doing, and was hired by a US military medical institution. This chilling fact begs the question, is there anyone who seriously doubts the military establishment will seek to engineer a super-soldier, and will not be deterred by any of those messy moral or ethical considerations?
Christian Media, the ministry which fields the V Channel output such as the V Blast Internet letter, the Eclipse printed periodical, and the Exotica TV and radio show, has previously produced material on the efforts to create robo-soldier. In what looks like a Marvel Comics fiction, hardly anyone knows military scientists have already succeeded in growing (with spider DNA) a dense, Kevlar like compound, directly into the skin of solders, so they can withstand a bullet wound (see the Exotica TV episode on the subject).
Military scientists are talking about using spider silk to make structures that are stronger than Kevlar…but they can hardly hardly make enough with the current technology, and they definitely haven’t started breeding genetically modified soldiers. We don’t have that technology. We hardly understand how spider silk production works.
With such efforts, one can only wonder if these madmen will eventually produce a modern version of the mothman, replete with wings that can quietly transport the organic killing machine behind enemy lines. Furthermore, it is certain the Biblical prophets described just what is occurring.
Oddly this was probably the paragraph that offended my brain cells the most. Mothman? Not…you know, Spiderman? I…I just don’t understand why they wouldn’t go with the obvious if they were going to invoke genetically modified superheroes.
For instance, the prophet Joel described military men that were unstoppable in very scary terms:
 “a great people and a strong: there hath not been ever the like…A fire devoureth before them; and behind them a flame burneth…and nothing shall escape them. The appearance of them is as the appearance of horses [centaurs]; and as horsemen, so shall they run. “They shall run like mighty men; they shall climb the wall like men of war; they shall march every one on his way, and they shall not break their ranks: Neither shall one thrust another; they shall walk every one in his path: and when they fall upon the sword, they shall not be wounded” (Joel 2:2-8)
For those unfamiliar with the prophetic texts, the manipulation of genetics is a primary theme found in the numerous descriptions of the end of the age. Jesus Christ said the last generation would be “…as it was in the days of Noah, so shall it be also in the days of the Son of man” (Luke 17:26)
The primary description of the days of Noah was focused on what is sometimes called the “first incursion,” wherein the fallen angels tampered with the genetics of men and women, and the offspring became “mighty men” – a population which was quickly catapulted into leadership within the old world order.
The book of Genesis tells us the whole world was “corrupt” and the LORD saw nothing but “violence” everywhere, so He purposed to destroy the world (Genesis Chapter 6). This is what Jesus used as a template for the last generation – a time of massive destruction, preceded by violence and genetic manipulation.
When coupled with the descriptions of world war, famine, and pestilence, to say nothing of the massive fraud of the so called pre-tribulation “rapture” in which millions of deceived believers “know not” that they are about to be “taken away” to the grave in a violent judgment (Matthew 24:39),  this tribulational devastation could occur at any moment.
– James Lloyd
Jesus blah blah blah.

The only other thing worth highlighting is their unique instruction on how to remove yourself from their mailing list:

Of course, if you have been convinced Christians should never send an Email to someone without permission (Did the Disciples of Jesus ask people for permission to tell them the Good News?), then we will cheerfully delete your name from our database.

Woah, gettin’ a little defensive there. Of course I want to stay subscribed! I love getting a good laugh at conspiracy theorists with no solid grasp of science.

The tale of Taq

One donor requested that I talk a little bit about polymerase chain reaction, or PCR.

PCR is now a super common laboratory technique for people doing any sort of molecular biology. It’s a way of amplifying a specific section of DNA so it’s present in millions of copies. This is really important if you want to, for example, sequence a specific gene. You want that gene to be present in such high quantity compared to the rest of the genome so nothing else is sequenced.

As for how it works…I’m not sure if I’m able to explain that in a coherent way right now, so here’s a handy dandy video!

Most PCR uses a specific type of DNA polymerase known as Taq. Taq is an enzyme that was originally isolated from Thermus aquaticus, a thermophillic bacteria that lives in hot springs and hydrothermal vents. Taq is special because it can withstand high temperatures without losing its function. Since PCR requires DNA polymerase to be functional at higher temperatures, this makes Taq super important. The one downside to Taq is that it’s not very good at proofreading, which makes it error prone. Thankfully DNA polymerase has been isolated from other thermophillic species. Pfu is an example of a thermophillic DNA polymerase with proofreading ability.

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How important will genomics be for future healthcare?

Short answer: Not very.

Biologists are stuck in an unfortunate situation. Most major funding sources in the US come through the government, and it’s essential to stress the impact your research will have on humans. Basic research for the sake of understanding the unknown just isn’t enough to secure funding nowadays. Everything has to be spun to make it appealing to humans since taxpayers are the ones funding the research, and the research needs to seem “justified” in their eyes. Want to study primate microRNAs to study how primates evolved? You better mention how microRNAs are involved in cancer, even if you have no interest in studying that. Want to figure out how spider silk proteins evolved to fulfill different biological tasks? Better mention how spider silk is stronger than Kevlar even though it’s practically impossible to mass produce.

The same is true for human genomics. When the human genome project was first announced, scientists made endless promises about how sequencing the human would lead to immense advances in human health. They had to say that to get funding for this basic research project. Years have passed and we’ve learned a great deal about the human genome, but we still haven’t had the medical revolution we were promised.

Frankly, we probably never will. For most people, getting their genome sequenced is going to be a novelty. You’ll be able to learn about your ancestry, but that’s about it. Sure, you may learn you have a 10% increase in your chance of getting heart disease, but is something that small going to change your diet and exercise routine? Only a tiny fraction of people will have diseases with very high penetrance (likelihood of showing the trait if you have the gene) that can be identified by genomics. And of those diseases, few are going to have preventative treatment or cures.

And right now that knowledge is only available to the very rich, who are more likely to have better preventative health care anyway. Yes, prices of genome sequencing are dropping rapidly, but we’re eons away from every person on the planet being able the afford their genome. Even if they could afford it, it’s not really worth it. The health of people around the world would most improve by increasing exercise and by having clean water and healthy food available. I mean, diarrhea is one of the leading causes of death in developing nations…are they really going to benefit from knowing their exact risk for diabetes? There are more basic problems that we need to fix first.

The field of human genomics is still incredibly important to study in order to learn more about our species and about disease…but it’s not going to be the panacea scientists had to promise in order to receive funding.

(I should add this isn’t just a personal opinion of mine, but one that is frequently voiced by a number of professors and other scientists during various panels I’ve attended)

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My research part 4: How did microRNA convergently evolve?

How could microRNA have evolved to have such similar structure and function in plants and animals after evolving independently? You must be thinking, “What are the odds?!”

If evolution boiled down to nothing but random chance, the odds seem staggering indeed. No, I’m not about to say God guided evolution. What happens is there are certain traits about the system that constrain it to act in a certain way, making similar outcomes more likely.

To understand more fully, I have to teach you a little bit about microRNA biogenesis. Awww yeeeaaah!

Adapted from Berezikov 2011

In animals, a microRNA gene is transcribed to make what’s called “primary microRNA.” This pri-microRNA forms a hairpin structure – that is, it folds over and complementarily base-pairs to itself, forming a step and loop. This pri-microRNA is trimmed by the protein Drosha and is then shipped out of the nucleus as an ~80 nucleotide precursor microRNA. In the cytoplasm, the protein Dicer cleaves the pre-microRNA to form the mature ~22 nucleotide microRNA, which will go on to be involved in gene regulation.

In plants, pri-microRNA still forms hairpins, but their size can be far more variable. Plants also lack Drosha – all of the processing is done by a Dicer homologue.

You’re probably thinking, “So they’re processed differently. This doesn’t really convince me of the odds.” But what’s important to notice is that both of these systems share a couple of key things, which make convergent evolution more likely:

  1. Both use the protein Dicer to process mature microRNA. This is thought to be an exaptation – where a trait initially evolved to have one function, but has subsequently come to have another. Dicer is thought to initially be used to cleave foreign RNA particles, for example from viruses. There’s also evidence that suggests Dicer plays a role in repairing double stranded breaks in DNA. Since Dicer was already present in plants and animals because of these more ancestral functions, it was available in both lineages to be used for something else. Plants and animals didn’t have to evolve a totally new protein to process microRNA – they used the machinery they already had sitting around.
  2. Both process microRNA from hairpins. RNA hairpins spontaneously occur all the time, and some of these spontaneous hairpins give rise to new microRNA. That’s because if a hairpin happens to process into a mature microRNA that conveys a fitness advantage to an organism, natural selection will act to perpetuate it. If a hairpin results in an unfavorable outcome like disease, purifying selection will purge it from the population. Because RNA hairpins spontaneously occur and Dicer was already around, natural selection would act favorably on a system where processing hairpins leads to a fitness benefit.
I have only one thing left to say:

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My research part 3: MicroRNA in plants

Since my research focuses on primates, I don’t exactly work with plant microRNAs. But they’re still fascinating enough that I wanted to touch on them. Plant and animal microRNAs are very similar – they’re approximately 22 nucleotides in length, they’re processed from larger hairpin structures, and they function by downregulating messenger RNA. But they have a number of differences because microRNA in plants and animals evolved independently.

Yes, this similar system arose separately in the plant and animal kingdoms. No, this is not proof for God. This is an example of convergent evolution, where the same trait is acquired independently in different lineages. Think of the ability to fly in insects, birds, and bats. The evolution of microRNA is the same, it’s just more molecular instead of having an obvious effect like flight, which is visible to the naked eye.

Why do we think plant and animal microRNA evolved independently? One major piece of evidence is that there are no homologous microRNAs between plants and animals (homologous meaning shared through a common ancestor). This is especially striking when you compare it to microRNAs within animals, a number of which are homologous. There are some animal microRNAs present throughout the whole animal kingdom, from sponge to fruit fly to orangutan, that just don’t exist in plants. Plants have their own set.

Another thing supporting independent evolution is that plants and animals have different processes for generating mature microRNA. In plants, microRNA is fully matured in the nucleus before being shipped out to the cytoplasm for use. In animals, much of the processing takes place out in the cytoplasm. Animals have additional proteins that are involved in processing – I’ll touch on it a little more in my next post. Also, plant and animal microRNA differs in how it targets messenger RNA. In plants, the whole ~22 nucleotide microRNA is involved in complementary base-pairing with the messenger RNA. In animals, only a 7 nucleotide “seed region” of the ~22 nucleotide mature sequence determines which messenger RNA it’s supposed to match up with.

A final piece of evidence is that microRNAs are missing in other forms of life. They’re absent in fungi, placozoans (the most basal animal lineage), and choanoflagellates (the closest living relative to animals). It’s more likely, especially considering the other evidence, that microRNA arose twice independently, rather than microRNA being lost multiple times in the specific lineages that happen to make it look like it arose twice independently. The latter would be getting into “Satan buried the dinosaur bones to make it look like a natural process” territory!

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My research part 2: MicroRNA evolution

Like I said previously, microRNA is typically highly conserved (have the same sequence) across animals because it’s involved in such important biological processes. But some microRNA isn’t conserved, which makes it particularly interesting. Is it not conserved because it just doesn’t have an important function? Is it not conserved because the divergent microRNA confers a specific fitness benefit to an organism? Or is it a rare mutation that leads to a disease like cancer?

That’s where my particular research comes in. I’m investigating microRNA variation within human populations and across the primate lineage. Here are some examples of interesting trends I may find:

  1. A microRNA is totally conserved across primates and other animals. This microRNA is likely involved in a really important biological process, like making a type of tissue.
  2. A microRNA is totally conserved within primates, but differs from other animals. This microRNA could confer some primate-specific trait.
  3. A microRNA is totally conserved within humans, but differs from other primates. This could be an example of “what makes us human.”
  4. A microRNA is not conserved at all. The more likely explanation is that this isn’t a functional microRNA at all. That’s the risk with working with such new data. Other types of small RNA can be erroneously labeled as a microRNA. MicroRNA is a specific class of small RNA because it’s processed in a very distinct manner and has a specific function.
We already know that there are some differences in microRNA between primates. In 2011, Svante Paabo’s group found a number of microRNA that were upregulated (present in higher amounts) in human brain, but not in chimpanzee brain. When they validated which messenger RNA these microRNA were targeting, they found the targets were involved in neural development. This is an exciting possibility for what shaped human brain evolution, but obviously still needs further testing.
The way my research differs is that I’ll be looking at how the sequence of microRNA differs rather than the amount. A sequence difference could totally change which messenger RNA is targeted, which is what ultimately affects the organism. I’ll be experimentally validating the effects of these sequence changes in a number of primates, including humans.

This is post 7 of 49 of Blogathon. Donate to the Secular Student Alliance here.