You'd Prefer An Argonaute

Extreme Tissue Regeneration

Posted in MIT, Science Journalism, Uncategorized by YPAA on May 26, 2014

Read my recent piece on the fantastical flatworm planaria here, in OZY magazine.

The neoblasts (pink) of a planarian.

The neoblasts (pink), a type of stem cell, of a planarian.

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The Animated Life of A.R. Wallace (NYT)

Posted in Evolution, Media, Science Journalism by YPAA on December 29, 2013

The Animated Life of A.R. Wallace (NYT)

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Great Adaptations

Posted in Evolution, Science Journalism, YPAA Journal Club by YPAA on November 10, 2012

great-adaptations

An article that I wrote, Great Adaptations, has just been published in the September/October issue of Natural History Magazine. It’s about the research of Dianne Newman, Lars Dietrich, and their colleagues. Read it to learn about how bacteria and us are really just two peas in a pod, evolutionarily speaking.

“Eden in a Test Tube”

Posted in Evolution, Media, Science Journalism by YPAA on July 28, 2011

A lovely video from The New York Times about the RNA world, and the state-of-the-art in ribozyme evolution from Gerry Joyce’s lab.

Click the link below.

http://graphics8.nytimes.com/bcvideo/1.0/iframe/embed.html?videoId=100000000937455&playerType=embed

Opposing a non-religious attack on science

Posted in Science Journalism by YPAA on March 28, 2011

Humans have always sought answers to nature’s most basic questions, like what are we made of? What surrounds us? What governs this existence? This experience has been manifested most discretely in scientists, who attempt to breakdown the complexity of the natural world into formulas, observations, and theories. With increasing frequency, our curiosities about the world are yielding new solutions, such as medicines and technologies, to old problems, like human disease and energy consumption. Sometimes these solutions make our lives more comfortable, and while there is no doubt that the promise for such outcomes helps sustain science economically, at its core still burns our curiosity and creativity. Science is essential to us.

This brings me to Wendell Berry, and a piece he wrote for Harper’s entitled Faustian Economics: Hell hath no limits. In his piece, Berry, a highly respected American writer/essayist, characterizes our beloved scientific enterprise as utterly wasteful.

Berry’s arguments that I want to highlight aren’t the thesis of his essay, but they emerge in support of it. I encounter his thesis, actually, to be one of great moral significance–to shed our long-held assumptions of limitlessness in the world, with respect to growth, wealth, natural resources, and debt. In Berry’s words:

The normalization of the doctrine of limitlessness has produced a sort of moral minimalism: the desire to be efficient at any cost, to be unencumbered by complexity…

Our national faith so far has been: “There’s always more.” Our true religion is a sort of autistic industrialism. People of intelligence and ability seem now to be genuinely embarrassed by any solution to any problem that does not involve high technology, a great expenditure of energy, or a big machine…

Focusing on economic matters, in one example Berry points out the oxymoronic notion of “free market,” which by definition imposes great economic inequalities, such as in the pharmaceutical industry where there exists

… an absolute discontinuity between the economy of the seller of medicines and the economy of the buyer…

This is because the industry can wield total control over the health and survival of some patients, while the patients themselves usually have no control over the price of drugs. I believe this is an argument worth engaging, but not without careful separation of science from business, which Berry neglects.

Therefore I was disturbed when he generalized these sorts of examples to say that most scientists have been completely naive in the goals of their work.

It is this economy of community destruction that, wittingly or unwittingly, most scientists and technicians have served for the past two hundred years. These scientists and technicians have justified themselves by the proposition that they are the vanguard of progress, enlarging human knowledge and power, and thus they have romanticized both themselves and the predatory enterprises that they have served.

I find this statement ludicrous, and a kind of dangerous anti-science rhetoric that doesn’t advertise ignorance of what we do necessarily (like many forms do), but rather why. In this respect Berry is totally off, it seems he hasn’t listened to any scientists speak about why they are scientists. Or it’s possible he hasn’t sampled a fair cross-section, either way, attacking the scientists cannot help his cause.

Returning to the problem of limitlessness, Berry then contrasts scientists to artists to try to advance his point.

To deal with the problems, which after all are inescapable, of living with limited intelligence in a limited world, I suggest that we may have to remove some of the emphasis we have lately placed on science and technology and have a new look at the arts. For an art does not propose to enlarge itself by limitless extension but rather to enrich itself within bounds that are accepted prior to the work.

It is the artists, not the scientists, who have dealt unremittingly with the problem of limits. A painting, however large, must finally be bounded by a frame or a wall… Within these limits artists achieve elaborations of pattern, of sustaining relationships of parts with one another and with the whole, that may be astonishingly complex…

It is true that insofar as scientific experiments must be conducted within carefully observed limits, scientists also are artists. But in science one experiment, whether it succeeds or fails, is logically followed by another in a theoretically infinite progression. According to the underlying myth of modern science, this progression is always replacing the smaller knowledge of the past with the larger knowledge of the present, which will be replaced by the yet larger knowledge of the future.

In the arts, by contrast, no limitless sequence of works is ever implied or looked for. No work of art is necessarily followed by a second work that is necessarily better. Given the methodologies of science, the law of gravity and the genome were bound to be discovered by somebody; the identity of the discoverer is incidental to the fact. But it appears that in the arts there are no second chances. We must assume that we had one chance each for The Divine Comedy and King Lear. If Dante and Shakespeare had died before they wrote those poems, nobody ever would have written them.

Scientists constantly deal with the problem of limits, but a “larger” knowledge hasn’t been what we’re after, it’s a refined knowledge. Not greater mass; but greater magnitude. We work towards a more complete understanding of how things are connected in nature, exactly the “sustaining relationships” Berry describes. In refining our understanding of the natural world and its history, all scientists are inspired by work that preceded theirs, as are artists. The capacity for insightful thought and creativity hasn’t really changed for artists or scientists for thousands of years, only the instruments have changed.

And regarding Berry’s assertion that “the identity of the discoverer is incidental to the fact”? This simply isn’t true, and among the numerous exceptions are those that have probably had the most substantial impacts on science. Like Einstein. If you had a very wild imagination, you might imagine several people collectively making Einstein’s quantum intellectual leaps. Had he never existed, the record of science would be very different, like the arts would be different had you subtracted Shakespeare.

We can appreciate art for its often singular nature, resulting from the unique mind and experience of individuals whom create pieces loosely connected by time, medium, or emotion. Science has its own such pieces, together which sustain our curiosity and understanding of life and all matter in the universe. Each new piece can combine with the last, sometimes they join in a unifying way, wholly the result of human creativity in the face of absolute limits. The results have been beautiful, don’t you think?

Exceptions

Posted in Lab Life, Science Journalism by YPAA on January 23, 2011

I don’t read many science blogs these days, but one I definitely recommend is Carl Zimmer’s The Loom. He recently dug up and posted this gem quote:

If I may throw out a word of counsel to beginners, it is: Treasure your exceptions! When there are none, the work gets so dull that no one cares to carry it further. Keep them always uncovered and in sight. Exceptions are like the rough brickwork of a growing building which tells that there is more to come and shows where the next construction is to be.

–William Bateson, in The Method and Scope of Genetics, 1908

Yes! Yes! Wise words for even the non-beginners, like me. In fact, my current project in the lab grew out of an exception, out of which I’ve built something. And when I think about other projects I’ve watched develop in the lab, exceptions have often propelled them. Behind many of them is a story worth telling, no?

CNN=science journalism pretty not good

Posted in Media, Science Journalism by YPAA on October 15, 2009

In my daily (hourly), incredibly narcissistic practice of reading my own blog (the one you’re reading right now), I traveled back to my October 7th post about how Harry Noller got screwed by being overlooked for the Nobel Prize for work on the ribosome. Below the post, under WordPress’s automatically generated “possibly related posts,” was a link to a CNN article with an amusing, although I suppose technically accurate title:

“Chemistry Nobel honors research on life-giving ribosome”

Life-giving” ribosome? Ha. Yes. I remember that’s exactly how Harry Noller introduced it to us in Biochem 100A back in college. So next time you say grace/thanks, thank the ribosome for giving you life. Ok?

Following the title is an underwhelming article. At least there’s a nice picture of Tom Steitz sportin’ his trademark frosty chinstrap beard. I’m not making fun–if  I could pull that off, I would try. And now with a Nobel in his pocket (around his neck perhaps), that look is certified OG.

Evolution in a Test Tube

Posted in MIT, Science Journalism by YPAA on October 8, 2009

David Bartel’s career as a biochemist began marked by tension between his exceedingly meticulous method and the most careless of biological processes. Evolution, the process in which living things change and diversify from their predecessors, is random, at moments appears illogical, and leads to many dead ends. But in a seminal paper published in 1993, with clear thought and clever technique Bartel, along with thesis advisor Jack Szostak, brilliantly distilled the highly complex nature of evolution literally into a test tube.

Bartel focused on “ribozymes,” a class of molecules composed entirely of ribonucleic acid (RNA) that catalyze chemical reactions. Starting from a synthetic large pool of different RNA molecules of random sequence, he used a technique called in vitro selection to isolate a new type of ribozyme that performed a specific chemical reaction, known as an RNA ligation, otherwise only attributed to natural protein based enzymes. He then evolved these ribozymes by introducing random mutations into their sequence and re-isolating more active versions that outcompeted earlier variants—in effect modeling evolution in a test tube.

Naturally occurring ribozymes are rare—a host of enzymatic activities they may have once possessed have been appropriated to faster and more accurate proteins during evolution—but owing to their structural similarity to DNA, and catalytic potential, they are attractive candidates for the original self-replicating macromolecules, predating more complex life forms.

While generation of a self-replicating ribozyme remains elusive, and would not prove that catalytic RNAs directly preceded life, Bartel’s study was paramount in demonstrating the ability to isolate ribozymes with new activities. He notes, “We’re left with lots of gaps in knowing how RNA based life forms might have emerged, but it is still useful to know what RNA can do.”

Appreciating the highly mutable nature of evolution, Bartel also recognizes that the particular ribozyme he isolated was only one possible outcome of the experiment. “Evolution is the sum of a huge number of chance events, and the biological world is the culmination of all these chance happenings,” says Bartel. “If you replayed a tape of biological evolution, we would all look different.”

Reference: Bartel and Szostak, Science 261, 1993.

I wrote the piece above for another assignment for my science journalism class. The assignment was a “front of the book” magazine piece, written for an audience interested in science, but probably not very knowledgeable about RNA or ribozymes.

We were instructed to pick a paper we are (were, have been, etc.) excited about, and interview one of the authors or an expert in the field. Ribozymes are what first sparked my interest in RNA back in college, so I picked my favorite ribozyme paper. And conveniently, being at MIT, I had the opportunity to interview Professor David Bartel, the first author of the paper.

What are microRNAs?

Posted in MIT, Science Journalism by YPAA on September 29, 2009

MicroRNAs (miRNAs) are tiny molecules composed of ribonucleic acid (RNA) that modulate the expression of genes. In nearly all known cases, these tiny RNAs reduce the level of protein produced by their gene targets.

To accomplish this task, miRNAs chemically pair with messenger RNAs (mRNAs), the molecular intermediates between a gene’s DNA sequence and its protein product. This pairing event essentially sequesters the mRNA, preventing it from being decoded to produce protein.

Recognition of an mRNA by a miRNA is imparted by complementary molecular motifs present in both molecules. These molecular motifs are encoded in the DNA sequence of a genome.

MicroRNAs compose a class of gene regulatory molecules widespread and evolutionarily conserved throughout plants and animals. While miRNAs’ effects on gene expression are modest compared to other modes of gene regulation, en masse their total contribution to gene expression in the cell is significant.

The ~150 word definition of microRNA above I wrote for an assignment in a science journalism class I am taking this semester. (Incidently, you may have noticed the frequency of my contributions to this blog has slowed in recent weeks, resulting from an increased non-blog workload. Sorry.)

The assignment was to write an “explainer” for a key scientific term, like you might see set aside from a longer article (in a Scientific American or Discover type magazine) concerning some scientific idea, that references the term. Thus it is meant for a audience interested in science, but not necessarily familiar with the scientific details of whatever topic is under discussion.

My class had mixed reaction to my explainer. The paragraphs were deemed somewhat disconnected in content from each other, perhaps resembling more of a list of facts in the form of sentences. Some found the voice dry and boring (like that of a scientist’s?).

My goal in writing it was to define microRNAs: (1) What they are; (2) What they do; (3) How they function; (4) Why they are important. I could have started with the importance, but the way I wrote it is the way my brain organizes thoughts. I should learn to think like my reader, and also make the language a little more, um, charming.