Manic Fringe


The personal blog of the one and only Luc Gendrot. Internet Superhero. Not really.

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Glowing organs: rats transfected with a luciferase gene reveal circadian secrets.

We've all seen these guys

Whaaattt? Glowing organs? Well, "glowing" not so much, but "emitting detectable light" for sure!

Even though I see cool stuff like this all the time. And glowing rats are nothing new it's still really cool to see these technologies used in practical applications outside of just making people say "Ohh look a glowing rat".

For example take this group of researchers in Geneva who had the gene for luciferase transfected behind several genes which are expressed in cycles throughout the day and could quantify their precise levels.

They also apparently partnered with some engineering/physics group to make a "device" the mouse could I in (the article's not all too specific)? And it can detect the slight luminescence from the genes tagged with luciferase across the entire rat while it's inside. Thus the researchers could detect levels of certain gene products in a rat all over its body for months on end based on whether or not the rat was glowing.

My dad once said of glowing rats: "well what's the point? Now you have a glowing rat, so what?". Well here you go dad.

So that article I linked to above isn't the most descriptive and I was still curious about the circadian rhythm stuff so I went to google and looked up the technique they talked about and the University of Geneva and it came up with this paper which talks about using the luciferase gene to track circadian rhythm genes in response to actin-inhibiting drugs.

I also found this paper which shows certain gene fluctuations in response to body temperature changes.

So apparently this technique is rather common, and this group in Geneva is doing a whole bunch of circadian rhythm stuff which is great because we don't seem to know much about it from what I remember of the biopsych class I took that one time.

A quick YouTube search yielded the video below, which shows the assay process for what I presume to be a small mammalian cell culture.

Science in ACTION. Enjoy.

I hate the quarter system. Here's why.

I feel frustrated a lot of the time when I’m studying. I feel frustrated because I feel like there’s this ever-present, looming pair of eyes behind me scrutinizing how efficiently I work with my time. I think this self-consciousness stems from the fact that I procrastinate a lot...but beyond than that I think it also stems from how quickly I am expected to gain mastery at the things that I am learning in class. It’s not impossible mind you, it’s just overly stressful and (I think) non-conducive to me learning effectively.

At the university I am attending we go through classes in a 10 week period. These classes are fully-fledged and are completely analogous to the classes I would attend were I in a semester system, they’re just condensed into 10 weeks instead of 16. Think about that for a moment if you would. That means students learning on the semester system have 6 extra weeks to study presumably the same amount of material (or procrastinate on the same material, as it were).

Even some of my most interesting classes haven’t left the sort of impression on me the classes I took at my community college (which runs on the semester system) have. Take for example the sociology class I took as a high school senior over 3 years ago. I still remember most of the things we learned in that class, like that many of the students in my class supported the death penalty and the 3-strikes rule, despite all the statistics we learned about wrongful conviction in the US. I remember being shocked that some of the students thought buying highly pollutive things like Hummer Limousines (the example we used in class) was a god-given right for rich people. They had no qualms with polluting the environment because in their minds, they earned the money and that gave them the right to do anything with it that they wanted. You should have seen the look on the teacher’s face during that discussion...incredulity couldn’t begin to describe it.

I loved that class. Not only did we spend 2 or 3 weeks on the topic of income inequality but the discussions we had were better than any I’ve had at the 4 year university now attend.

2 or 3 weeks on one topic? The thought seems almost ludicrous to me now, considering that in my cell growth and oncogenesis class we spent one day on the topic of senescence and apoptosis, a very complex and intricate topic.

On the flip side, if you asked me anything about what I learned in the microbiology class that I took just 2 quarters ago at my university I would be hard pressed to give you any specifics about...well...anything we learned except maybe the teacher’s name. Maybe. Think about what that means for the classes I took and the things I “learned” at the beginning of my college career? The thought does not inspire confidence.

“But Microbiology is your major!” You might cry with all the incredulity of my old sociology teacher “Shouldn’t you love to learn the subject?!”

Why yes! I do love microbiology, and everything that comes with it. Bacteriology, virology, cell biology, all of it. I love it all. But I’m also taking all of those classes at once, and each has its own textbook from which the teachers pull nearly all of the information for their classes. Trust me I would LOVE to read my textbooks from cover to cover, I would love to take notes on every page and jot stuff down in the margins to look up later. I simply don’t have the time. Not if I want to be doing the other things that are important to me and that I should be doing in college: Socializing with my peers and future colleagues, searching for a lab position so that I can get started on my career, writing this blog, or reading the Wheel of Time series (Yeah, I haven’t finished yet, don’t judge me).

If I had 6 extra weeks to learn the things expected of me...well...I think I would be in a lot better shape both knowledge wise. And grades wise. Go figure.

I do not care for the quarter system, not one bit.

Stop demonizing scientists and research. You just look ignorant.

At least one person in the video above (a supporter of the ridiculously ill-informed anti-GMO movement that has gained so much media attention lately) claims not only that all of the world’s research and health organizations are being paid and are “all liars frankly” but that EVERY SCIENTIST IN THE WORLD is a liar being paid.

I would be hard pressed to make this stupid shit up.

Look. I’m just a 3rd year biology student whose obsession with genetics stems back to the 7th grade, and even I realize how absolutely, stupendously, outrageously stupid these people look and sound. And might I add that more than a few of them look fairly overweight or unhealthy to my eyes? But I’ll not resort to ad-hominem attacks, because I don’t know these peoples’ home lives and I could care less.

What I do care about is the fact that these people are demonizing science and scientists in blanket-statement judgements about how they THINK the scientific community works, without actually being a part of it. The very thought that all scientists, everywhere, are being paid to give an opinion that these people believe is 100% wrong? Well it’s just ludicrous.

Let me break down how people come to be research scientists for these people, because they seem to be woefully misinformed.

1) Have an interest in science

2) Become knowledgeable in your field of research (in this case? Biology) This step probably involves a higher education institution of some form.

3) Spend years building up the knowledge and critical thinking skills needed to be an informed and active member of an ever-evolving field, by keeping up with the current research around the world, and by keeping your ear to the rest of the scientific community.

4) Do research (often in a university laboratory or at non-profit or private research labs) based on your years of accrued knowledge, this research is necessarily based on years of prior research, done by other members of your field. Rinse. Repeat. Learn.

That’s it. Really. I promise. There’s no secret “scientist overlord” who hands down proclamations to the board of “scientist overseers” to ensure that everybody is playing by the same game. There’s no megacorporation that grabs undergraduates out of college and makes sure that they are pro-GMO by handing them wads of evil-fairydusted cash. So when there's a consensus in the scientific community on the validity of a claim it would be wise to think "gee, maybe they're right!"

I hate the sweeping demonization of all science. I seethe with hatred and anger whenever I encounter it. I mostly see it in the equally as stupid anti-vaccine movement (which I will wager overlaps quite nicely with the crowd depicted in the video above), but this just reaches a whole new level of face-palm stupidity.

How do these people think society as they know it functions? With magic? With mother nature’s divine glow as a power source? No. The very same scientific knowledge that brought them the cancer therapy I’m positive some of their aging parents are going through, has brought us GM foods.

The double-think, cognitively dissonant nature of these peoples’ arguments makes me want to tear my eyes and ears out so I never have to see or hear this stupidity ever again.

God I’m so mad I could kick a puppy. Not really though.

How stupid are we going to look to our grandchildren?

“A society grows great when old men plant trees whose shade they know they shall never sit in.”

This old greek proverb is surely something you’ve seen bandied about when people are considering how we should make policy decisions. It also raises the question of how our great grandchildren will judge the era we live in.

In just the last 100 years institutions and ways of living that seem archaic indeed even barbaric to us now were the norm. Technologies that were once completely unknown have become second nature to many of us. Society has changed and is still changing at an accelerated rate compared to generations past.

Take as an example the invention of the telephone. The first telephone company (AT&T) was started in 1878, 2 years after the invention of the telephone by Bell. It wasn’t until the 1970s that cordless phones (a la this dinosaur) were introduced, nearly 100 years later and by 1987 the number of cell phone service subscribers exceeded 1 million. In 2003 the first blackberry smartphone was introduced, and in 2008 the first generation of iPhones hit the market.

The point I’m trying to make in detailing this (very simplistic) timeline, is that it only took 30 years for mobile devices to go from the bricks we attached to our cars to the tiny all-in-one personal computers we carry around in our pockets and that we all practically depend on to function, and those 30 years have brought changes in our society that nobody could have predicted.

Many have rightly pointed out the tremendous impact technologies that we now take for granted can have on our society. So if the ubiquity of technology in just the timespan it has taken Generation Y to grow up has created such a massive change in our group-think in such a short amount of time, think of how much future generations social norms will change with the amount of advancements that are yet to come.

Now, no doubt when somebody mentions the ubiquity of technology and how it has changed our culture, images of teens sitting around with their faces glued to their twitters, instagrams, and facebooks leap into your mind. It’s doubtful that the images that came to your mind had much to do with public policy, governmental practices, or world building of any kind. And it’s that fact that scares me.

It scares me because it is this humble student’s firm belief that we have, and have had, the capability to solve many of the worlds issues for a dozen years now. Without politicizing it too much, the failure of our policymakers to fully utilize and apply the scientific advances of the past few decades is staggering. Our collective (potentially world altering and beneficial) actions are marred by bloated bureaucracy and selfish political maneuvering of the sort that our children and theirs will surely look down on.

The rate of advancement seen in the tech sector is colossal, and dwarfs the analogous amount of change in the government sector. And unlike the young’uns whose entire social existence has morphed, the government is still People have long demanded a more open-source government, and in the wake of the NSA leak by Edward Snowden recently the implications of such a shift should be on everybody’s mind as an important and far-reaching issue to be discussed.

Our culture may be changing rapidly in the social realm, but our government seems to be only a reactionary one, attempting to solve only the short-term and petty problems that affect us right now, with little to no regard for the future of the planet and the people who inhabit it. In determining our place on this planet, and in living up to the obligation we have to ourselves as humans we have failed to adapt as quickly or as effectively to the changing technological landscape as the generation whom we laud for their reliance on technology. We need to start taking a page from their book, embrace the technology we have. Not only that but we need to look to the future of technology and plan accordingly.

The whole topic leaves me worried about just how incredibly stupid and wasteful and selfish we’re going to look as our story is inscribed in the annals of history. We have massive capability at our fingertips, and yet it seems only profit margins and the bottom line color the lense through which those in power see the future.

I am yet hopeful that as the older generations are slowly but surely filtered out of their positions of power, the young usurpers who have grown up in the communications age can, with their completely different worldview, fix what problems their short-sighted predecessors have wrought. Until then I guess I’ll just tweet about it.

Discretion is the better part of valor: militant atheism re-examined

So silly

I have a new addition to the repertoire of my overused phrases: “Discretion is the better part of valor”.

I like this saying because it embodies a lot of how I think civil people should act. Too often people are preemptively hostile, coming out with guns blazing no regard to whom, or in what context they are speaking. Too often people act too soon, too harshly, they fail to take into account a milieu of variables that are key in determining the outcome of a situation. People who lack discretion fail to see the big picture, seeing only what’s in front of them.

I used to be a militant atheist, I would enter into conversations about religion with my fists out and swinging, hitting as hard and as fast as I could. I can’t say this approach did anything for convincing anybody (just as those door to door Mormons don’t convince you of jack squat) but it did serve to alienate me from people who would otherwise loved to have had a civil discourse. I planted no seeds of skepticism, or inquiry, merely ones of cognitive dissonance and reactionary shouting matches.

I even got into a rather large fight with one of my very good friends because she claimed me talking about my lack of faith was belittling her actual faith. A terrible premise for an argument on her part, but nonetheless I can sympathize with her now, looking back. No, not because I actually agree that I was actively belittling her faith, but because I was doing absolutely nothing for fostering a rational conversation by shouting to the high heavens about how there is no god.

Recently I had the pleasure of being interviewed by a couple of men who were taking a survey surrounding spirituality and religion. Now, I don’t want to cast the light of suspicion too brightly on these upstanding gentlemen, but I suspect their primary motive was to proselytize a bit, but that’s okay I suppose, as they didn’t really try and convert me or anything. The fact that I identified myself as an atheist right away may have done something to deter that, but I digress.

They wrote down my answers to their questions so I have a vague, but probably misguided, hope that they were actually doing a survey.

Incidentally I gave them my blog address (what can I say, I’m enterprising). Hey fellas!

Anyway I posted about the experience on Reddit’s /r/atheism and received..well...not the reception I remember receiving for similar posts in the past. I urged people in the title of my post to remember that not all christians deserve the kind of derision, contempt, and blatant prejudice. What I received was a slew of frankly non-constructive comments such as “Fuck them all” and “Yes they do” (deserve our derision and hatred).

Let’s look really quickly at the etymology of Prejudice:


from prae- "before" + -iudicium "judgment"

So, as everyone knows, “to judge before knowing”. Isn’t this exactly what everyone on /r/atheism rails about constantly? Being presumed to be a satanist, a debaucherous heathen, or worse yet a rapist or a murderer?

We so often scoff at Christians who would ask us “well what stops you from murdering people without the bible?”, as they misinterpret our lack of faith and presume the worst in us. Yet we turn around and accuse all Christians of being bad people? I’m sorry (no I’m not) but despite the delusion we might assume they are under--believing in a magical sky fairy or however you want to put it--shouldn't we at least attempt to elevate the discussion, be the bigger men and women, know...actually voice our opinions in somewhat intelligent ways?


Guess it’s just me then, what with my discretion and what not.

An interesting visualization

I'm one of those people who "loves" certain fields of science despite having a very rudimentary knowledge of them. Data analytics is one of those fields. I love the idea of taking a huge amount of information and parsing it into something useful and analyzable.

So I was looking at google's Ngram viewer, which will show you the relative frequency of words in a selection of same-language books. Just playing around with it for 10 minutes I was able to very easily see the re-appropriation of the word gay by the LGBT community.

Reappropriation of the word

Not exactly a spectacular or novel insight, but still really interesting that google can give us these sorts of insights. Text mining for the masses!

If you go back to the 1800's you can also see what I presume to be the fall of the word "gay" as meaning "happy" and again the re appropriation.

Reappropriation of the word

Interestingly the lowest point on the graph for the word gay, and the point at which it starts rising (what I'm calling the word-appropriation) corresponds pretty well with the years following the stonewall riots (1969).

Obviously I'm not a historian or a sociologist, but this is pretty cool anyway. Someone correct me if I'm egregiously misrepresenting this data. Otherwise play around with the Ngram viewer, and see what you can figure out.

My journey to understanding the Higgs Field. Also, why Kids don't like textbooks.

It’s embarrassing for someone like me who pretends to be way smarter than he is, when understanding of a concept doesn’t come right away.

Particle physics is difficult because there’s really no good way to conceptualize it. Every attempt at explaining some of the more complicated things like the higgs boson is rife with analogy and ill-conceived comparisons that don’t get the point across effectively.

That’s why I was so surprised with these TED Ed videos on the subject. Totally blew me away. If you don’t know much about physics, then this is the place to get your toes wet.

I wrote the other day that science education could use some work, but I didn’t say anything about how that could be accomplished. You know, because I'm just a college student. I think that one of the biggest roadblocks in effective science teaching is boredom. I mean come on, how exciting is it to read that biology textbook you still have from your undergraduate intro courses?

I love things like TED Ed and Khan Academy because they’re very visual resources, and often times they’re made to be fun. Nobody can stand to read a brick full of text and figures that cost $300, but everybody can get down on a bit of video consumption, amirite?

If I were a high school teacher I would absolutely incorporate online video resources like these both into my classroom time, and into homework time. Kids need to be excited about learning, and textbooks do not incite that sort of excitement, but YouTube videos certainly might.

Science Education could be better....a lot better.

HAHAHA...What? But seriously though, this is REAL. As in, the people who made this think they've beaten the stupid "evolutionists" (Is that what the kids call it now?) at their own game! Holy cognitively dissonant fear of science batman!

I am constantly surprised by the fear that arises when new scientific discoveries are made. I’m even more frequently surprised by the fear that arises from OLD and DISCREDITED scientific "discoveries" (I’m lookin’ at you, anti-vaccine movement and climate change deniers).

I really shouldn’t be surprised though. All those after-school specials I watched as a kid and this Macklemore song keep telling me that “people fear what they don’t know”.

Just kidding, after school specials weren't a thing when I was a kid. What am I, 30?

Point being: in general people really don’t know science, so it’s not surprising things like vaccines and the Large Hadron Collider get a lot of flack from and produce a lot of fear in the less informed among us.

So obviously if we take that old adage to be true, then maybe to free our society from the shackles of poor understanding and ignorance of the world around us...we should just provide our children with basic science education. Hell, we should provide our adults with better science education. I know a few people who could use it, frankly.

I’m really tired of getting on facebook and seeing yet another crazy video of, say, Kirk Cameron ranting about Abortion and Gay Marriage. I'm also sick of shit like this entire interview with Wendy Wright.

(BTW It's almost creepy how soft spoken and charismatic Kirk is in that interview, despite the absolute clap trap coming out of his mouth.)

That’s why I’m really glad that President Obama is placing such a high emphasis on projects like mapping the human brain, and on promoting science education, and just generally advocating for science and technology. I want space-race era USA back, even though I never lived there.

I'm sorry Ecology! I didn't mean it!

Ecology has a symbol? who knew?

I've been guilty of uttering the words: "Ecology is a joke branch of biology". Now before you jump down my throat and tell me how wrong I am: I've seen the error of my ways. In a way.

A lesson I've learned so far in college is that things are hardly ever as simple as they seem to be in undergraduate biology courses. I recently had this lesson applied to my erroneous views of the field of Ecology, because I learned there can be a whole lot more maths involved than I thought (not that math automatically makes things more credible mind you).

I emailed a professor the other day to see about a lab position (the eternal search continues). What interested me about this lab is that it apparently integrates programming and mathematical modeling heavily into the research they're doing, and while I don't know exactly what that will entail, I am still a (somewhat undeserving) proponent of more math and CS literacy in the biological fields. It's the future folks.

I digress. I found myself reading his doctoral dissertation and in the first chapter he builds a model for analyzing niche breadth in animal populations that exhibit varying reproductive selection methods. It's pretty math-y. I'm not through the whole thing, but I've flipped through the remaining parts and there's a whole lot more where that came from.

I'm excited to read the rest of it, but I felt the need to reconcile my 3 year (somewhat ignorant) hatred of ecology by publicly saying: It's not a joke science, but in my undergraduate ecology courses they portrayed it as such by giving us the most barebones, unattractive, dumbed down, lackluster attempt at even giving a glimpse of what ecology can be. (based on what I can extrapolate from this one dissertation).

I think schools should appeal to the math geeks and hard science enthusiasts in the early undergraduate courses by focusing a little more on the core theory behind the maths that we actually do learn. Then maybe I could have avoided being so mean to a potentially pretty cool branch of science. Provided it's all like this.

Internet privacy pessimism

All rights Fox corporation yadda yadda. I don't own Futurama. I just needed a snappy photo for the top

"Delete that post and let the internet forget about it"

"It's not smart to have your blog tied to your real name, don't you think employers google you?"

Someone I was having a conversation with on Reddit told me those two things in the context of the post I wrote the other day. The post echoed my disgruntled angst surrounding my place in the higher education system.

The conversation I had with that reddit user got me thinking about internet privacy (like everyone else, right?). I especially thought about all the things I put out onto the internet for everybody to see. Do I care if people know my stance on things? Do I care that people know I'm gay? Do I care if they know I dropped the fuck word in one of my posts? (oops?)

It occurs to me that nobody seems to CARE about my opinion no matter how loudly I broadcast it. It also occurs to me that I'm not a radical in any way shape or form, and that my opinions probably don't elicit any rage or offense in people. So in all honesty my internet presence SHOULDN'T be a detriment to me, I'm pretty normal in most respects. I think people are just afraid of the internet

People have been concerned with privacy on the internet probably since its inception, and recently lots of articles written by sites like Mashable and Forbes have highlighted the potential pitfalls that come with a large internet presence. Specifically they bring to light the trend of employers screening potential hires based on those pictures from last weekend, or that status they wrote about the annoying people at the mall, or even for the blog post you wrote about being a disgruntled biology undergraduate in a bubble that's about to pop.

In a world where we're so easily connected to one another, it's not hard to learn somebody's feelings on something by just sifting through their Facebook profiles. Individual people output massive amounts of data in a way that hasn't ever been seen before. I can't shake the feeling that it's a mistake to JUDGE them based on that data.

It's interesting to think that there were no blogs a few years ago, instead of writing a short post and posting it immediately people may have had a self published periodical (probably not), or a personal journal that only they saw, or perhaps they might have been a legitimately published author. There weren't as many avenues to have your voice heard. People couldn't just sit at home on their couch and have their thoughts broadcast to the entire world with the push of a button. It's easier than ever before to set up a blog and start writing. More than ever before people are able to make their opinion known, and not just to a couple people, potentially to anybody with an internet connection.

Shouldn't we love how easy it is now to be a writer now? Even if it's just a hobby?

I don't really want to live in a world where people think that anything connecting me to my online presence is just inherently bad. I especially don't want to live in a world where employers can demand employees' Facebook information.

The world I most don't want to live in though, is the world where my favorite outlet for the creativity I have and the desire I have to write and be heard is what prevents me from getting a job or prevents people from taking me seriously.

F' that. No thank you.

I feed on your attention, so in the spirit of "having your opinion heard": let me know your thoughts on the subject in the comments!