Archive for December 2010
For most people, the new year is a time to look forward and think about how they will change their behavior in the coming year. I certainly have goals for my own future – but I tend far more towards reflection than anything else. So here, instead, I’ll present something that I’ve learned in the past year.
It all started with a blog post, obviously. In March, I wrote about invasive salamanders and, with a traditional view of invasive species replacing the human-defined idea of “nature,” I ended the post, rather naively, with the line, “How can we save our planet?” I got in a comment argument with Matt Chew about conservation, nativeness, and evolution, and while I still believe much of what I argued, the line of thinking in that thread (including my own obtuseness) set off a chain reaction that altered the way I viewed the world.
From then on, much of the focus of my mind has centered around the place of humans in the natural world. I started shifting my view from a standard anthropocentric view to one in which we are just animals, arguing with myself and friends about whether we really are special, if our consciousness really elevates us above nature, and the factors in society that makes us believe we are the pinnacle of evolution.
For a concrete example, I have since had many conversations with my philosopher queen bestie, Erinrose, about altruism and selfishness. I argued that we are all inherently selfish – that we feel warm and fuzzy when we help someone else because a gene that makes us feel that way has been preserved. And it would only be preserved if it helped individuals survive, passing the gene along the line.
But despite these arguments I make to myself, there is one kicker that always fails my logic: my little brother, Jonah.
Jonah has Fragile X syndrome, a genetic mutation that can cause autism. Jonah himself is not autistic; my mom’s analogy is that he is the opposite of autistic. While a common feature of autism is an inability to detect emotion or differentiate between faces, Jonah has the opposite problem. The world around him is so overwhelming that he cannot help but cower in the presence of most types of stimulation. When he is excited about something, such as when we were riding the trolley around Memphis yesterday, he makes a lot of non-lingual noise as if to block out some of the stimulation and excitement from his joy of the ride. The overstimulation spreads to his limbs, flapping and flopping as if he cannot hold all the energy inside of him but has to do something with it. Let’s just say he draws a lot of attention to himself because he is so overwhelmed with emotion.
The night before the trip, my family sat down to watch some old home movies that my dad had transferred to DVD. (Most of the memories had, unfortunately, been taped over by my middle school-aged brother and his friends recording their slumber parties. THANKS A TON, JACOB!) Part of the film we saw was of three-year old Jonah working with his speech therapist. He could not pronounce vowels at this point, but, working as hard as he could, would spit out the first consonant of a word, causing the therapist to erupt in applause. This was after his teachers at school told us that he would never talk. Now you can’t shut him up.
When my mom found out about his diagnosis, she wept because, as a book-lover with a PhD in english literature, she could not bear the thought that he would never find joy in reading. But on our trip, he could not stop reading. We went on a hike in old growth forest in Mississippi. While he usually is strictly the leader on hikes, he was lagging hundreds of feet behind us, nose buried in a book, unable to keep up because he was so absorbed.
Here he is, evolutionarily some useless runt who cannot take care of himself, who takes up far more resources than a normal person, for whom we were told life would be non-verbal and institutionalized. In nature red in tooth and claw, he would be dead, with the 3 of us other siblings competing successfully for his resources and not worth the parental investment of my darling progenitors. But look at him now! I think he’s even smarter than we suspect. He makes friends wherever he goes. Sure, he still can’t tell a joke for his life, but our human society has allowed for him to survive and grow despite his relative incompetence.
I care about him more than anyone or anything in the world. If you know me, you know this to be pure fact. When I was fuming in the backseat of my parents’ van yesterday because the airline had lost my luggage, I watched him engaging my family about the trip and I started crying just to behold him. I would do absolutely anything for him. The worst thing you could do to me is to take him from me. (Oh lordy, I’m crying again.)
This fact makes zero sense biologically. Sure, he has half of my genes so I have an investment in his survival. But, let’s face it – he’s unlikely to ever pass those genes on. Nonetheless, I would give up 100% of my own genetic heritage to allow his 50% to dead end.
Surely this feeling – this “love” or whatever – has evolved to cause me to protect those close to me who, in turn, help me survive, whether they be family, friends, or potential caretakers of my potential children. Maybe I feel so strongly because, while he is my brother, I also feel like he is my son in many ways. I’m eight years older than him, but emotionally and developmentally the gap is much wider. So maybe I have double the chemical reactions going off when I look at him, part fraternal and part maternal. Or maybe it’s just a mistake in the biological machinery that my knowledge and logic cannot penetrate.
Whatever the reason, he is the stymie in my thinking. He is the puzzle piece that doesn’t fit into my newly-acquired worldview of people as inherently selfish machines. We probably all have such a piece in our lives, something that escapes purely biological explanation or logic.
So this new year, think back on the people in your life that you care for, defying biological explanation. At this point in my thinking, this is what makes us human.
And when Jonah will inevitably force the entire party to raise a toast to the new year as they gaze upon him with pure love, he’ll be toasting a bit to you.
Happy New Year.
PS: Don’t cry, Mom!!
UPDATE: She cried.
Throughout this arsenic-life NASA saga, I’ve been trying to pinpoint the fundamental reasons to explain why this story got out of hand. Why did NASA feel the need to uber-hype this research? Why the rush to publish research even if it may not have been ready?
I’ve drawn the conclusion that the primary cause is the need to be PURPOSEFUL while performing scientific research. For an example, I’ll take the research I currently work on. I study the aging process in yeast cells, focusing on how the cells’ epigenome changes as a cell gets “older.” We do this research under a federally-funded grant, for which our purpose is to study the aging process to help us better understand cancer and other age-related diseases.
But, to be honest, I don’t really care about cancer. I mean, I am someone who is perhaps a bit too comfortable with my mortality, but even beyond that: I actually just think the idea of different proteins and other factors manipulating what sections of DNA are translated and expressed is fascinating. I want to understand this process better – what proteins do what? how is this different in different cell types? how did this system evolve? – and this “aging grant” is really just an excuse for me to do so.
I doubt I’m alone here. I think a lot of scientists are more interested in uncovering the various processes, not for the good of mankind, but simply because we want to understand. (Correct me if I’m wrong, scientists.) I’d be happy to cure cancer along the way if I can, but in terms of my own goals and what is possible during my brief stint in this field, I just want to understand this system a little bit better than when I started.
Science wasn’t always done with a purpose. Think about Charles Darwin. Sure, he was interested in natural history, but he was on the Beagle to provide friendship to the captain. Along the way, he collected a bunch of samples of mockingbirds and finches and other organisms, and it wasn’t till decades later that he put the pieces together and formulated his theory of selection of the fittest. He didn’t collect specimens on his travels for any real purpose, but used the data he collected to draw conclusions later.
Of course, back then science was primarily done by rich men with too much time on their hands. Now science is the forefront of innovation and progress; we need more people than bored rich men to be studying it and, hell, anyone should get a chance to do so! But with greater knowledge and technology, we need more money. And since I’m not a rich bored man, I don’t have any money.
That’s where the government comes in: grants to fund research. But since it is taxpayers that are funding this research, it should have goals that will benefit those taxpayers. Thus I study aging and cancer. And these grants do keep us on task. If I find a cool mutation that alters the epigenome of my yeastie beasties and it’s not related to the aging process, I will not be following up on that project.
I go back and forth on whether this is a good thing. On the one hand, it keeps us accountable to the government and taxpayers, who give us our funding. But on the other hand, does research for a purpose help us really advance in biology, help us better understand how life works?
One of my bosses, a great scientist, doctor and philosopher king, recently emailed this quote to our lab from Carol Greider, a recent Nobel Prize winner for her work on the discovery of the aging-related enzyme telomerase:
“The quiet beginnings of telomerase research emphasize the importance of basic, curiosity-driven research. At the time that it is conducted, such research has no apparent practical applications. Our understanding of the way the world works is fragmentary and incomplete, which means that progress does not occur in a simple, direct and linear manner. It is important to connect the unconnected, to make leaps and to take risks, and to have fun talking and playing with ideas that might at first seem outlandish.”
This idea burns me to my very core. Purpose-based science assumes a certain knowledge of the systems we’re studying. But, let’s face it: we still have so much to learn. We’re all still flailing toddlers, trying to find a surface to hoist ourselves upon so that we can actually get somewhere. While scientists are often conceived to be smart and have all the answers, we actually don’t have many. The more you know, the more you know that you don’t know anything at all.
But instead of being allowed to play, to follow up on work because it’s exciting, to take risks, we have to make sure we stay within the limits of our funding and, thus, our purpose. Because “playing” or studying something because we think it’s AWESOME doesn’t provide evidence of “progress.”
I could be entirely wrong: maybe the old adage that progress is made in leaps and bounds (as opposed to baby steps, I suppose) is farcical. Maybe I only believe this because my human soul that thrives on chaos is drawn to it.
Either way: the purpose of research is overemphasized. When I read papers, I am interested in knowing how their discovery fits into “practical knowledge” (“There is hardly anything known about X disease, BUT WE FOUND SOMETHING!”), but more than that, I’m interested in how it fits in with the current model of whatever system they are studying. But that rarely gets as much attention in papers.
And this idea of “purpose” is why science in the media is so often overhyped. News articles often take a definitive stance on how the new study has contributed to the public good. Maybe it’s “eating blueberries will preserve your memory” or “sleeping 8 hours will make you attractive.” This makes the science easy to digest, sure, but it also paints an incomplete picture. These studies are just tiny pieces in a puzzle that scientists will continue to work on for decades. It’s pure hubris to believe that non-scientists cannot understand the scientific process – that they cannot understand that it takes incremental steps. But, nonetheless, if your research cannot be easily hyped, no one will hear about it, so you have to serve a purpose.
So with NASA’s arsenic-based life. The current model, both in funding and the media, of requiring purpose to justify research forced NASA to claim a greater purpose for its discovery: “an astrobiology finding that will impact the search for evidence of extraterrestrial life.”
To give both NASA and the researchers the benefit of the doubt, let’s just say they found this cool bug and wanted to share the news to get help in studying it, as author Oremland suggested. They submitted the paper to officially get the word out. But then they needed to find a “good reason” to have been studying arsenic microbes and NASA decided this was a good opportunity to reinvigorate its reputation of performing “useful science” so called a press conference. You know where it goes from here.
All that is pure speculation – but it probably isn’t too far from the truth. Maybe I’m being too kind, but I really doubt that the researchers or NASA had any ill-intentions. They simply lost control, and the following shitstorm took off.
We can scoff at them all we like: “an astrobiology finding that will impact the search for evidence of extraterrestrial life, my ass!” But it’s really not so different from my lab publishing a paper with the headline, “KEY FACTOR IN CELL AGING UNCOVERED” when, really, we just discovered a factor, and we don’t even know if it’s key.
The idea of “useful science” also dampens my feelings about science: SCIENCE IS COOL! Longing to pry up the corners of current knowledge isn’t enough: we can’t just look, but have to reveal a direct outcome. But if we don’t allow ourselves even to look because of various purpose-based limitations, we could be missing out on something FUCKING AWESOME!
I’m just rambling now – and am very interested in hearing your thoughts on this.
- Does purpose-driven science lead to better science or more innovation?
- Are there ways of judging research as worthy (e.g. for funding purposes) without having to provide a direct purpose?
- How should the media change its model for covering stories? Should every study that comes out get attention, or should we wait for more details and provide more review-like coverage?
- Would larger, field-based studies dampen competition? Would this help or hurt scientific progress?
Etc. etc. If you made it this far, thank you, xox, Hannah.
I never wrote what I meant to here – I simply could not keep up with the rest of the blogs regarding arsenic life! But I’m also aware that outside of the sci-twitter bubble, what went down may not be entirely clear, so here’s the beginning of the draft just in case you need to catch up.
Reactions to NASA’s announcement of “arsenic-based life” have been resounding through the science world these past few weeks. (For more thorough reviews, check out Bora Zivkovic’s link dump, Martin Robbins’s coverage, or the National Association of Science Writers.) For those who haven’t been scouring all the blogs, I’ve illustrated a brief review of events.
The saga began with a NASA press release announcing a press conference about a discovery about “an astrobiology finding that will impact the search for evidence of extraterrestrial life.” This led to speculation about aliens – life on Titan? – and then, when it was uncovered that the study was written by scientists studying the arsenic-rich Mono Lake in California, perhaps the researchers discovered a “shadow biosphere” – a form of life unlike ours, based on different molecules and evidence of a novel evolution of life on earth.
The actual paper, published in Science, instead announced that the scientists had found a bacterium that, when forced in a lab, could utilize arsenic in place of phosphorus in its molecules, including DNA. After the hype and build-up, it was a disappointing announcement. Due to the massive let-down, a lot of writers and scientists (myself included) chose to accept these findings instead of scrutinizing them. It is a bit embarrassing in hindsight, but after so much hype about a scientific discovery that engaged the public, I wanted to find something to stay excited about, if only to support the idea that science isn’t a complete sham.
Soon after, scientists began to carefully look at the researchers’ methods and found that these findings simply weren’t very well-supported. For the details, I recommend Rosie Redfield’s highly-publicized critique as well as Alex Bradley’s on We Beasties. The researchers’ evidence could easily have been contaminated, and they failed to do some fairly simple tests to definitively show the use of arsenic by these microbes. At this point, most media sources threw up their hands in frustration and stopped covering the story. (For more detail, see Carl Zimmer’s Slate piece, “This Paper Should Not Have Been Published.”)
This series of events led to some interesting reflections around the blogs, including thoughts on the peer review process, the scientific process, and the upside of public scientific debate. The authors’ refusal to engage the bloggy criticisms (even though they used the web to get everyone hyped about their discovery) got everyone into an uproar as well, as described in this open-access Nature editorial.
Ever wonder what benefit clownfish bring to anemones that make it a mutualism? At Sleeping with the Fishes, my marine ecology blog on the Southern Fried Science Network, I wrote about some new research about nutrient transfer in this symbiotic relationship between clownfish, anemones, and zooxanthellae. Excerpt below!
Anemones and clownfish: a true mutualism?
Of course anemones aren’t famous for their symbioses with zooxanthellae, but rather with the brightly-colored clownfish or anemonefish. Although anemones have nematocysts that they use to sting and shock their prey before consuming it, the anemonefish are able to swim among their tentacles unharmed. (We still don’t know how they develop this ability!) These little guys were made famous by the movie Finding Nemo to their own detriment, ironically, considering the message of the film. But I knew about anemonefish before they sold-out and became famous: in 1999, I wrote my 6th-grade research paper on these puppies!
The benefit to the fish in this symbiotic relationship is clear: living amongst tentacles armed with automatic stinging cells provides a lot of protection to this conspicuous (and tasty!) little fish. But what can a little fish do for an anemone? In my 6th-grade paper, I summarized a 1986 study by Dr. Daphne Fautin suggesting that they provide protection to the anemone:
Dr. Daphne Gail Fautin did an experiment in the Great Barrier Reef. She removed clownfish from their sea anemones to discover what would happen to the fish and the anemones. When she checked back the next day, the anemones had disappeared… It turned out that butterflyfish had eaten the anemones and the clownfish had swum away… The butterflyfish were able to feast on anemone because the clownfish weren’t there to protect their anemone by baring and chattering their teeth or making other threatening noises. Dr. Fautin’s experiment proved that the clownfish/anemone relationship is two-sided because the anemone protects the clownfish and the clownfish protects the anemone.
(I haven’t improved much in the past decade.)
Even as an 11-year old, I remember forcing myself to belabor this point. Despite the results of Dr. Fautin’s experiments, the protection of a non-threatening, bite-sized snack of a fish did not seem to be enough benefit to the anemone for this to be a true mutualism. Is teeth-chattering really the only thing that clownfish bring to the table?
Read on here
Things have been a bit quiet around here – and I think I finally figured out the problem last night. I moved a couple months ago and there is a high correlation between this life change and my inability to write. So I rearranged my apartment last night – hopefully having a more legit “desk” will help? I’m pathetic, I know. My space is important to me, ok!!
It occurred to me yesterday that while stressing out about my writer’s block, I totally missed my ONE-YEAR BLOGIVERSARY. Culturing Science and I have been together for a whole year! And while we’ve gotten in some arguments over time, mostly we’ve learned from one another.
I really do want to thank you guys for sticking it out with me this year. I went to a lecture last month and, afterwards, realized that all the topics he covered I did not know a year ago, but now understood because of writing this blog. So thank you for putting up with my learning and stumbling.
Which brings up my next question: WHO ARE YOU? Some famous bloggers sometimes do a roll call to get to meet some of their readers who don’t comment. I think it’s a nice idea, although I’m a little nervous that not even my dad will comment. But I really am interested in learning a little about you … so … will you leave me a comment? I’m nice and friendly, we can be internet friends? Yeah?
Recent news you might be interested in:
- Carnival of Evolution #30! Up at This Scientific Life
- The Molecular Biology blog carnival is up, hosted by the dear Labrat
- Carnival of the Blue #43 is being hosted by Alistair Dove’s Deep Type Flow
You may know that I am attending the Science Online conference, being held in the Science Triangle in January, for the first time! Not only that, but I’m on a panel to moderate a discussion about amateur blogging! (Full program here)
“But it’s just a blog!” – Hannah Waters, Psi Wavefunction, Eric Michael Johnson, Jason Goldman, Mike Lisieski and Lucas Brouwers
Many young people are eager to communicate science despite their lack of scientific and/or journalistic credentials. While all science communicators face challenges, this subgroup has their own set of challenges including cultivating a following of readers from scratch, and high levels of self-doubt, often referred to as “imposter syndrome.” What value does this rapidly-growing group of science communicators bring do the field? How can the science blogging community encourage and mentor young bloggers? How can we hold these individuals accountable to the high standards of science and journalism while simultaneously allowing them to make mistakes as part of the learning process? In addition, established and successful science communicators will be encouraged to share their tips and tricks with their newer colleagues.
And, lastly, I’m an reviewer for the 2010 edition of Open Lab! Open Lab is a yearly collection of the best science blog posts from the previous year, collected together into a physical book (!). This year, Jason Goldman is the editor and faces the monstrous task for sorting through the 900 nominated entries! So I’ll be helping out with some of the ecology posts. It’s a great honor and I’m very happy to support this fine publication.
Thanks for slugging through this poor excuse for a blog post. Don’t forget to check in in the comments! (Please, Dad, will you at least check in so I don’t feel like a total loser?)
Today I bring you something extra special: A guest post from Lucas Brouwers of the world-famous blog Thoughtomics. He loves genomes, I love plankton, and you get a great story involving spaceships, genomic party crashers, and, of course, a planktonic sea squirt. Enjoy!
Just below the surface of the sea, little animals are floating through a universe where the stars are made of plankton. They travel in what can best be described as gelatinous spaceships, which provide both shelter and food. They are Oikopleura dioica (Oikos is ancient Greek for house or household).
Their spaceships are ingenious constructions, made in such a way that every beat of Oikopleura‘s tail brings in a new flow water. The water and all the plankton it contains, is led through different tubings and chambers of the ship, until it reaches the waiting mouths of Oikopleura. The spaceships are not of a durable design and last for only a couple of hours before they are broken down again. Oikopleura spend the largest part of their short lives (5-10 days) repeating a cycle of building, feeding and destruction.
As small and short-lived as they may be, their genomes are evolving at at an extraordinary speed. A large team of scientists sequenced the full genome of Oikopleura recently, and found that its genome has been reorganized and trimmed down on an unprecedented scale.
One of the first things they noticed was the rapid evolution of introns in the genes of Oikopleura. Introns are the genetic equivalent of party crashers who show up at parties uninvited. They hang around inside genes, without coding for anything. Our cell have to force the introns out of messenger RNAs before they can properly be translated into proteins. Despite their apparent lack of use, many genes of distantly related animals have introns in exactly the same places. These introns have been conserved for millions of years, leading some to believe that they provide an evolutionary advantage somehow.
Oikopleura doesn’t care about these million year old traditions though. A staggering 76,2% (or 4.260) of its introns are unique to Oikopleura. Conversely, 3.917 of introns that are present in other animals (including close relatives) have been lost in Oikopleura. Not only do the newer introns outnumber their older peers, they are also good deal shorter than the few introns that have been retained.
But the extensive remodeling of the genome didn’t stop with introns. Normally, genes tend to hang out in similar neighborhoods in different species. There’s a good chance that two genes that are close to one another in mouse, are also close together in the human genome for example. Just like introns, many of these neighborhood relationships have persisted in species that are as far apart as humans and sponges.
Not so in Oikopleura. Its genes have been shuffled and switched around until the point that conventional gene orders are no longer recognizable. For small sets of genes the gene order in Oikopleura is closer to random than the gene order in other species.
The authors subtly hint at a potential cause for all this genetic upheaval: Oikopleura‘s genome lacks a full set of DNA repair genes. DNA is a robust molecule, but it can still be damaged. One of the nastier things that can happen is that both DNA strands of a single chromosome break. Cells can repair this type of damage in two different ways. The first way of repair works by taking a close look at the sister chromosome, and see how the damaged strands should be repaired, as shown in the video below. Another way is to directly seal the broken ends.
Oikopleura is lacking the genes for this last type of repair work. This means that every double strand break in Oikopleura‘s DNA can only be repaired via a sister chromosome, increasing the recombination rates (the exchange of genetic material between chromosomes) for Oikopleura. The causal link between the missing DNA repair genes and the accelerated evolution of Oikopleura‘s genome remains to be proven, but it isn’t hard to imagine how their absence could have played a large role in the overhaul of genomic architecture.
In addition to having a fast evolving genome, Oikopleura also has one of the smallest animal genomes (70 MB, compared to 3,174 MB for humans), which still contains some 18,000 genes (compared to ~21,000 in humans). Clearly, we don’t need that extra 3,100 MB for only a couple of thousand genes more. Compared to Oikopleura, our genomes are like attics crammed full of boxes and old furniture. Some scientists think that many features of our genomes (such as introns) are quite unnecessary, while others disagree. The debate boils down to this: are we keeping all the stuff because it is worth a lot, or because we never got around to throwing all the junk away?
Since Oikopleura was successful in redecorating and cleaning out its entire genome, our conserved genomic architecture might be nothing more than a product of historical contingency. In the small and slowly reproducing human population, natural selection might not be strong enough to remove all the unnecessary junk.
Despite the large genomic changes, Oikopleura has remained an animal in every way. While it might not be immediately obvious, they are very closely related to us vertebrates (animals that carry a backbone such as fish, reptiles, birds and mammals). They don’t have a spine, but they do have a lining of tough cells (a notochord) and a neural tube running through their entire bodies.
Oikopleura belongs to a group of animals known as tunicates, or sea squirts. Most sea squirts live a sedentary life on the ocean floor where they filter plankton from seawater. They are basically hollow bags with two siphons – one for drawing seawater in, and the other to expel waste and water. But the solitary and free swimming Oikopleura don’t look anything like these stationary creatures, so what are these familial ties based on?
A different life stage holds the answer: every sea squirt starts its life as a larvae, looking very much like Oikopleura. After swimming around for a couple of days the larvae attach themselves to a comfortable looking outcropping and morph into the sedentary sea squirts. By retaining its larval features and delaying its further development, the ancestor of Oikopleura has permanently avoided the fate of settling down (these processes are known as neoteny and progenesis).
The similarity between vertebrates and sea squirt larvae implies that our own vertebrate ancestor once looked very much like larvaceans such as Oikopleura. Like Oikopleura, we are basically sea squirts that have never grown up. But unlike them, we still carry the baggage of 600 million years of animal evolution. I think there is much that we can still learn from the Peter Pans of the oceans.
Denoeud F, Henriet S, Mungpakdee S, Aury JM, Da Silva C, Brinkmann H, Mikhaleva J, Olsen LC, Jubin C, Cañestro C, Bouquet JM, Danks G, Poulain J, Campsteijn C, Adamski M, Cross I, Yadetie F, Muffato M, Louis A, Butcher S, Tsagkogeorga G, Konrad A, Singh S, Jensen MF, Cong EH, Eikeseth-Otteraa H, Noel B, Anthouard V, Porcel BM, Kachouri-Lafond R, Nishino A, Ugolini M, Chourrout P, Nishida H, Aasland R, Huzurbazar S, Westhof E, Delsuc F, Lehrach H, Reinhardt R, Weissenbach J, Roy SW, Artiguenave F, Postlethwait JH, Manak JR, Thompson EM, Jaillon O, Du Pasquier L, Boudinot P, Liberles DA, Volff JN, Philippe H, Lenhard B, Crollius HR, Wincker P, & Chourrout D (2010). Plasticity of Animal Genome Architecture Unmasked by Rapid Evolution of a Pelagic Tunicate. Science (New York, N.Y.) PMID: 21097902