Nature’s Batman Utility Belt: The Genome

A trilogy and controversial main-character bait-and-switch later, the Dark Knight has resurfaced as a new age hero, bent on brooding and fighting crime from the rooftops of Gotham City. However, one of the greatest mysteries in the story of this powerful vigilante is how his utility belt, which usually stands out bright yellow against his otherwise matte black body armor, always seems to have the right tools on hand for saving the world from someone that day.

"Coolest Belt Ever Made" (credit: House of El. Retrieved February 25, 2014)

“Coolest Belt Ever Made” (credit: House of El. Retrieved February 25, 2014)

Since I am not Batman, I cannot provide an answer to those questions, but it may be useful to think of another daily occurrence to serve as an analogy for B-man’s belt: genomics. Throughout my time participating in research, I have been fortunate enough to have mentors who always taught me techniques with an eye permanently fixed on the scientific future. Their guidance helped me gain insight into what I saw as nature’s utility belt: a series of codes (genomic DNA), complete with a printer (RNA synthase), that allowed any cell to print out the exact instructions it needed (messenger RNA) for the tools (proteins) exactly when they were needed. In that sense, nature and Batman are not all that different.

Alignment of DNA sequences across species. Each color represents a successful alignment of DNA elements, and each block of the same pattern represents successful alignment of a section of DNA, which may signify a conserved protein. (credit: Retrieved February 25, 2014)

Alignment of DNA sequences across species. Each color represents a successful alignment of DNA elements, and each block of the same pattern represents successful alignment of a section of DNA, which may signify a conserved protein. (credit: Retrieved February 25, 2014)

However, genomics and genetic expression do have some quirks of its own. One reoccurring theme in nature is the reappearance of the same gene during development in completely different organs! One of the most notable is the prevalence of messenger RNA sequences coding for a class of proteins known as claudins. Claudins act like the nails in a wall, sticking the membranes of adjacent cells together to form a water-tight junction between them.

During development, we can locate where these specific mRNA sequences are expressed by a process known as whole mount in situ hybridization, abbreviated WISH. By exposing whole zebrafish embryos to sequences of RNA directly opposite the normal sequence found in the embryos, these two sequences stick together within a cell in a process known as hybridization, where two separate sequences become one joint sequence. A protein carrying a dye can then attach to these pieces of hybridized RNA, which will deposit the dye in the cell upon exposure to a particular mixture of chemicals. Using this process, we can see that in early stages of zebrafish development, the sequences coding for members of the claudin family are expressed in many areas of the developing brain and surprisingly in the developing kidney as well!

Who would have thought that the organs used to produce thoughts, feelings, and memories would share structural similarities with an organ used for less glorious purposes on a molecular scale? Our genome is filled with such examples of multipurpose tools, expressed in organs that perform completely different functions. From junction proteins used to hold organs together to sodium channels (also coincidentally conserved between the brain and the kidneys), these structures, derived from the codes which unite all of us, form a powerful example about how intricately connected the structures of our bodies are.

However, this is where we must diverge from Batman. His utility belt may be all-purpose for him, but Mother Nature takes that concept a step further. This code, this natural utility belt, is replicated with striking similarity across all living organisms! They all function with a similar premise: From DNA to RNA to protein; manual to instruction to tool. However, every student with any fleeting interest in modern biology has known this fact, so I will attempt to illustrate the impact of this knowledge in a more concrete way.

Imagine, if you will, a world in which all living systems had a different form of molecular tool creation. In such a world, it would be likely that we would not nearly have the miracle cures of today, such as insulin for those afflicted with diabetes. The great strides or progress made through the use of animal models would never have happened. Almost all of modern progress in the biological sciences would never have been justified with medical relevance as an underpinning factor if this toolkit were not conserved between living species.

The remarkable functionality of the cells which constitute all living beings, and the degree to which they share commonalities, in and among organisms, is an amazing fact that breathed life into all fields of the biological sciences today. The ability to only synthesize the necessary components to our survival from second to second makes our cells extremely energy-efficient, and it also makes our genetic toolkit even more versatile than those dreamed up by the brains they initially created. On the off chance that you may be feeling a little less than super, it may be comforting to remember that at any given moment, every living cell in your body is performing feats beyond the capabilities of the richest superhero ever created.

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Why Every Science Student Should Attend a Conference


Illustration by Yoo Jung Kim

This is a guest post by Dartmouth senior Yoo Jung Kim. 

Last week, the American Association for the Advancement of Sciences (AAAS)–the world’s largest general scientific society–held its annual meeting in Chicago. Among other globally recognized science conferences, the AAAS general meeting is unique in that it represents a broad spectrum of the sciences:  the conference hosts over 150 scientific symposia with topics ranging from science to technology to education to policy. AAAS also offers a wide range of opportunities that it offers to undergraduate students.

“At the Annual Meeting Student Poster Competition, undergraduate and graduate students present their research to other attendees, and scientists from many different fields provide feedback and advice,” said Tiffany Lohwater, the Director of Meetings and Public Engagement at the AAAS.

On top of the deeply discounted trainee registration rate, student attendees can take advantage of career development workshops and networking opportunities. The Student Poster Competition, featuring around 160 to 180 students presenting their research.

According to Michelle Oberoi, a junior at Univerity of California Irvine who won the best poster for “Brain and Behavior” category last year, “Competing in the 2013 AAAS poster competition against both graduate and undergraduate students as an undergraduate sophomore was intimidating and challenging, but overall rewarding. I was asked interesting questions regarding my research, which have ultimately benefited my current findings in the lab.”

AAAS is by no means unique in providing educational opportunities to college students. Many other scientific societies and associations–particularly those in the basic sciences–feature a number of programs to get student involved in their disciplines. For instance, the combined undergraduate/graduate poster session during the American Society of Cell Biology Annual Meeting drew in nearly student 200 presenters during its December 2013 meeting in New Orleans, many of whom were also registered to present in the general poster session. Over 1,200 students are expected to present at the special undergraduate poster session for the upcoming American Chemical Society National Meeting & Expo in Dallas, Texas, and thousands more will be participating in the 2.5 days of programming designed specifically for college students. Given these student-oriented learning opportunities that many scientific societies provide, every student researcher should consider attending a professional science symposium during their undergraduate career.

Despite the popular media depiction of scientists as antisocial individuals, academia is an inherently collaborative profession. At the undergraduate level, it may be hard to see the exchanges across laboratories, but the accretion of knowledge requires the communication of complex ideas from one scientist to another. Although the advent of the e-mail has largely supplanted the necessity of face-to-face conversations, this cross-fertilization of ideas still takes place during academic conferences, where researchers present their projects, discuss their findings, network with potential collaborators, and socialize with their peers. Other sort of interactions occur during meetings as well; graduate students look for post-doc positions, post-docs look for post-post-doc opportunities, principal investigators look for ideas to take back to their lab, science reporters look for interesting scoops, and vendors look for attendees to hawk their services and convention tchotchkes. Seeing these exchanges first-hand will help students to get a feel for a component of scientific research that is not readily observable in the laboratory.

By presenting at a conference, students can gain soft-skills that will be valuable at every level of their academic careers. Students participating in a poster presentation must prepare a visual representation of their work and present the summary of their findings clearly and concisely to other attendees. The poster-making process requires students organize their data and to delve into science writing at a deeper level than allowed by class lab reports. Many undergraduate poster symposiums pair presenters with scientist judges who have some degree of expertise on the topic at hand. This requires the student to be well versed on the paradigms and the methods used in his or her field. The entire process of preparing and presenting a poster necessitate a significant amount of sustained effort and helps student researchers to internalize their research and to build skills that will come handy in the future.

Students also have the opportunity to explore the leading edge of the discipline, and making connections in the scientific community can be of huge benefit for an undergraduate interested in embarking on a scientific career. Walking around the general poster session and attending oral presentations will allow students to get acquainted with the most important recent discoveries circulating in the field. This can help students to identify potential projects, laboratories, and institutions that they would like to work with in the future.

“The AAAS conference reminded me that I’m not alone and that there were lots of other people who were interested in science. I’ve kept pursuing research opportunities and I’ll be participating in the Princeton REU [Research Experiences for Undergraduates] in the summer,” said Christopher Luna, an Arizona State University junior and winner of the “Math/Technology/Engineering” category in 2013.

Any undergraduate who is interested in academia should identify a conference or a meeting of interest–especially those that offer programming for college students–by asking their research advisers. Science is a cooperative endeavor, and conferences allow undergraduate researchers a chance to explore their field outside of their laboratories and to gain skills early in their scientific training.


Yoo Jung (Y.J.) Kim is a senior at Dartmouth College in Hanover, NH. She is a former editor-in-chief of the Dartmouth Undergraduate Journal of Science and is currently working on a book to be published by the University of Chicago Press in Fall 2015. You can find Y.J. on her website at

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Building Button 2.0: The Open Access Button

David Carroll, co-lead of the Open Access Button gives an update on the Open Access Button, with some news and plans for the future.

The Open Access Button is a bookmarklet that lets users track when they are denied access to research, then search for alternative access to the article.  Each time a user encounters a paywall, they simply click the button in their bookmark bar, fill out an optional dialogue box, and their experience is added to a map alongside other users.  Then, the user receives a link to search for free access to the article. The Open Access Button hopes to create a worldwide map showing the impact of denied access to research and to push for a more open scholarly publishing system. The second version of the Button is currently in development but we need you to make it happen – read on to find out why.

We launched the Open Access Button Beta after 7 months of hard work at the Berlin 11 Student and Early Stage Researcher Conference in November 2013, with coverage in the Guardian, Scientific American and beyond.

Open Access Button

Over 5000 paywalls have been marked since launch.

To date, the response has been overwhelming. Over 5000 paywalls have been mapped since launch (just the tip of  the iceberg) and we’ve had people from all over the world sending us messages to tell us the Open Access Button has helped them get access to the research they need. What’s currently at is just a taste of what we are now building and since November, the team has been hard at work building Button 2.0.

The next version of the Button will be more powerful, better and more useful than the Beta. In order to build and launch Open Access Button 2.0, we’re seeking input from a variety of stakeholders to shape the Button project’s future. We want to be community centered and this survey will be the first of many opportunities in which the community can input and shape the Button they want to see in the future. This survey will form a key part of our consultation work and we encourage anyone interested in the Open Access Button to complete this. You can find the survey here.

The Open Access Button Team with Nick and Nicole from SPARC

As we build the bigger, better Button 2.0, were going to need a bigger team to make it all happen. Do you love Open Access and want to be part of the creation of Button 2.0? Then it’s your lucky day, we’re recruiting. You can find out more details including the application form here. The new team members will expand the already global team, reflecting the very nature of the Internet that we’ve grown up with. The people that make up the team embody the system we’re working towards, a world in which every single person on the planet is given free access to the sum of all human knowledge.

If you’re not a student but you love Open Access, there will be opportunities coming up soon, promise! You can follow the latest updates on @OA_Button.

We are best when standing on the shoulders of giants, we’re better when those shoulders are openly available to read and re-use. The Open Access Button hopes to make the problems of paywalls impossible to ignore, get yours at Get involved in building Button 2.0 here.

Screen Shot 2013-11-07 at 16.57.44

David Carroll is a medical student at the Queen’s University Belfast. He is co-founder and co-lead of the Open Access Button. You can find him on Twitter @davidecarroll and the Open Access Button @OA_Button



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All the Small Things

Humans are always trying to breach the boundaries of the unimaginable. In recent years, thinking big has meant thinking significantly small, 10-9 meters small. Nanotechnology has fascinated many scientists from diverse backgrounds with its possible applications. From medicine to everyday electronics, our capabilities have enabled us to build atom by atom and thus, make enormous strides in science. Yet, this trend should come as no surprise. In 1959, Richard P. Feynman gave what could be seen as the catalyst of the nanotechnology age. In “Plenty of Room at the Bottom” he describes a bottom up way of thinking, building bottom up. Feynman expressed his surprise in the lack of nano scale work while simultaneously providing a waterfall of possible methods and applications.

Now, forwarding to the present day a significant amount of work has been done with nanotechnology. When we play with atoms themselves, we must account for weird outcomes. Probably the most popular example is the carbon nanotube. Imagine a monolayer sheet of carbon rolled into a cylinder. Depending on the parameters of the tube, the strength to density ratio can be quite impressive. This strength is due to the covalent sp 2 bonds between each carbon atom. Moreover, the electrical and thermal properties of these tubes also make it an exciting material. Recently, a research team at Rice University led by professors Junichiro Kono and Matteo Pasquali created wet-spun nanowires out of trillions of carbon nanotubes. These wires have proven superior to copper wires in electrical current carrying capacity, stiffness, and convenience, as it is extremely light and thinner than a strand of human hair. Overall, these fibers can carry four times more current than copper wiring of the same mass.

Scanning electron microscope images of carbon nanowires produced by the Rice group in different gases.

Scanning electron microscope images of carbon nanowires produced by the Rice group in different gases. (Credit: Kono Lab/Rice University)

Scientists have also turned towards nanoribbons composed of graphene, a 2D crystal lattice one atom thick. This material can be considered the “star” of the nanotechnology world, with many scientists working on maximizing the material’s capabilities. Recently, a study led by Georgia Institute of Technology professor, Walt de Heer, presented epitaxial graphene nanonribbons grown on silicon carbide that actually conducts electricity at room temperature ten times better than theoretical predicted. Moreover, compared to exfoliated grapehene, we see an increase in conduction length by 1000 times at an impressive >10 micrometer distance. Interestingly, the nature of the flow of electrons along the sides of these ribbons resembles that of photons through an optical fiber. Sleek when you think of the scattered electron paths inside a standard conductor.

Artist's representation of  electrons (blue) traveling impeded through the graphene, which was grown on silicon carbide (yellow steps). (Credit: John Hankinson/Georgia Tech)

Artist’s representation of electrons (blue) traveling impeded through the graphene, which was grown on silicon carbide (yellow steps). (Credit: John Hankinson/Georgia Tech)

At Notre Dame we have our own Nanofabrication Facility, complete with those flattering clean room gowns. I am currently working on growing my own recipe for a novel semiconductor material using MoS2 and WS2. Though it may seem like graphene has a monopoly on the hearts of scientists and engineers working on nanoelectronics, its lack of a band gap, and subsequent leaking current, restricts its use as semiconductor material. Thus, transition metal oxides and sulfides have come onto the seen due to the band gaps they possess. This results in a decrease in the amount of energy lost as well as the size of the electronics the material will be used in. The most successful method for growth has been chemical vapor deposition, which includes precursors and a substrate. Generally, the precursors are vaporized to combine and depose on the substrate to form the desired substance. One can control the shape and the thickness of the crystals by altering the temperature, pressure, amount of precursor, and time.

University of Notre Dame Nanofabrication Facility. (Credit: University of Notre Dame)

University of Notre Dame Nanofabrication Facility. (Credit: University of Notre Dame)

Even the government has begun to praise the value of wide band gap semiconductors. Earlier this year, President Obama announced the Department of Energy’s new manufacturing innovation institute focused on the proliferation of WBG semiconductors. The main motivation of the institute lies in the environmental benefits that result from the reduction, approximately 75-80%, in electronic heat waste. This is a significant stride in the enthusiasm for nanelectronics as it now resides within the intersection of science and government.

Illustration of the energy efficiency benefits and other implications of wide band gap semiconductors. (Credit: U.S. Department of Energy)

Illustration of the energy efficiency benefits and other implications of wide band gap semiconductors. (Credit: U.S. Department of Energy)

Nanotechnology obviously has an outstanding future in electronics, but I should also mention some of its medical promises. Scientists have worked with nanoshell solutions and lasers to replace traditional suturing as well as with nanowires that can electronically identify the proteins present during the early signs of cancer. Though I could list many medical studies in this one post, and I encourage the interested reader to look through the many online papers, I believe it is better to highlight a recent development that is both amazing and creepy. A group at the Pennsylvania State University has, for the first time, succeeded in placing gold-ruthenium nanomotors into living HeLa cells. Through the use of ultrasonic waves, the team was able to magnetically control the motors and watch as they interact with the cellular membranes. As uncomfortable as it is to think of several of these tiny bots constantly playing bumper cars with your cells, the ramifications of this breakthrough are actually quite inspiring. Using this nanotechnology we have better chances of targeting and destroying cancers cells, improving patient diagnosis, delivering noninvasive drugs, and even performing cellular surgery.

Scientists at Pennsylvania State University were able to insert nanomotors into living HeLa cells and guide their movements for the first time.

Scientists at Pennsylvania State University were able to insert nanomotors into living HeLa cells and guide their movements for the first time. (Credit: Mallouk Lab/ Penn State)

Scientists and engineers are often asked to predict the future of technology. Where will we be in 50 years? Will science fiction become a norm? Even companies have taken it upon themselves to give the public a taste of their compelling, though somewhat ambitious future predictions. Samsung has been boasting their flexible screens for a little over a year now and yet; none of these products have come onto the market. Ultimately, we have not refined these products well enough. Time is still needed to make these tech dreams come true.

As a junior physics major, still dreaming of a lab of my very own, I am excited with where science and engineering is headed. We now have the capabilities to manipulate atoms; we can now be more creative than ever. The brilliant minds before us were able to combine materials into products that advanced our lifestyles as well as our knowledge of the surrounding Universe. With nanotechnology the current generation of scientists and engineers can use the inventions of the past to create new and better materials. Combine child like curiosity and imagination with mature scientific knowledge and mankind experiences ingenious discoveries.



  1.  Baringhaus, J., & Ruan, M. (2014). Exceptional ballistic transport in epitaxial graphene nanoribbons. Nature, Retrieved from
  2. Feynman, R. P. (1959). Plenty of room at the bottom. Retrieved from
  3. Gibney, E. (2014, February 06). Graphene conducts electricity ten times better than expected. Retrieved from
  4. Kahn, J. (2006, June). Nano’s big future. National Geographic, Retrieved from
  5. U.S. Energy Department. (2014, January 16). Next-generation power electronics: Reducing energy waste and powering the future. Retrieved from
  6. Weidner, K. (2014, February 10). Nanomotors are controlled, for the first time, inside living cells. Retrieved from
  7. Williams, M. (2014, February 13). Rice’s carbon nanotube fibers outperform copper. Retrieved from




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Genome editing just got a lot easier

This post is cross-posted with Berkeley Scientific Journal

If you’ve recently taken a glimpse at the front page of any major science news outlet, it is likely you are no stranger to an emerging genome editing technology known as CRISPR/Cas9. With the help of RNA, Cas9 (a bacterial enzyme) can be programmed to target specific locations within the human genome, enabling scientists to delete, modify, or insert sequences that may treat, or even cure patients with genetic diseases. Although the CRISPR/Cas9 field is still in its early stages, major breakthroughs have been made recently, paving the road for a new line of gene therapy.

Just a couple weeks ago, researchers at Nanjing Medical University and Yunnan Key Laboratory reported successful usage of Cas9 in monkeys, thereby progressing toward the exciting possibility of editing human genomes. They injected Cas9 into monkey embryos and impregnated female monkeys with the resulting eggs; quite

These set of twins were born with targeted deletions in their DNA as a result of Cas9.

These set of twins were treated with Cas9 as embryos and as a result, born with targeted deletions in their DNA.

remarkably, the newly born monkeys had deletions in the targeted gene of interest. In the world of science, where expected results sometimes never come to fruition, this marks an important stepping-stone in Cas9 technology. Targeting genes with this high degree of specificity could potentially lead to therapies that will prevent individuals from developing genetic diseases.

Cas9 looks for PAM sequences (gold) and matching sequences before cutting the DNA (picture by KC Roeyer)

Cas9 searches for PAM sequences (gold) and matching sequences before cutting the DNA (picture by KC Roeyer)

In the same week, a paper published in Nature revealed the mechanism by which Cas9 finds target DNA sequences tens of base-pairs in size within a genome that contains three billion base pairs. Interestingly, the researchers showed that Cas9 searches for a specific sequence known as the PAM – if the target doesn’t carry this short DNA tag, the sequence is neither recognized nor cut. Samuel Sternberg, lead author on the paper, explains that the presence of PAM sequences “accelerates the rate at which the target can be located, and minimizes the time spent interrogating non-target DNA sites.”

One of the most recent discoveries came out last week in Science magazine: two structural biologists at UC Berkeley, Jennifer Doudna and Eva Nogales, published the structure of Cas9 from two different organisms, providing key insights into the mode of DNA recognition and cleavage by the RNA-guided enzyme. Fuguo Jiang, one of the lead authors on the paper, said, “although the two Cas9s are from different organisms, and overall they look very different, when you superimpose the two structures, their functional domains are very similar. This suggests all the Cas9s have a similar mechanism to make cuts in DNA.” Additionally, the paper revealed an important loop within Cas9 is responsible for recognizing the PAM. As for what this means for the future of CRISPR/Cas9 technology, Jiang elaborated, “The original Cas9 recognizes one particular PAM, but if you can engineer it to recognize a different PAM sequence through mutagenesis, that would be great. The genome sequence is usually fixed. But what you could do is change the PAM sequences that Cas9 recognizes and tailor it to target more genomic loci. In this way, we can expand our Cas9-based genome-editing toolbox.” This discovery, along with the physical mechanism by which Cas9 locates target sequences, may help improve the efficiency of targeted gene editing.

And that’s not all. Editas Medicine, a new company co-founded by some of the leading scientists studying Cas9 aim to translate its genome engineering technology into a novel class of human therapeutics. These therapies are destined to make significant medical advances for people with genetic diseases including, but not limited to, Huntington’s disease, cystic fibrosis, and Alzheimer’s. Since modern sequencing technology has produced a massive amount of human genome sequences, mapping diseases to certain genomic coordinates is becoming faster and easier. With this valuable sequence information, the CRISPR/Cas9 system can simply be engineered to make positive changes in specific diseased DNA sequences and restore normal function.

Editas Medicine's goal is to further develop CRISPR/Cas9 technology into a novel class of human therapeutics. Pictured from left: Jennifer Doudna, Feng Zhang, Keith Joung, and David Liu

Editas Medicine’s goal is to further develop CRISPR/Cas9 technology into a novel class of human therapeutics. Pictured from left: Jennifer Doudna, Feng Zhang, Keith Joung, and David Liu

Genome engineering earned researchers a Nobel Prize in 2007, but with Cas9 speeding ahead, I wouldn’t be surprised if one is awarded to a Cas9-er in the near future.


**While writing this article, a paper was published in Cell that reveals another structure of Cas9, but now bound to its target DNA. This structure provides more information about the molecular mechanisms by which Cas9 cuts its targets and will further aid researchers in improving genome-editing tools**

If you want to learn more about how Cas9 functions, check out this video produced by a student in Eric Greene’s lab at Columbia University:

Cas9: The Enzyme, The RNA, & The Virus

Cas9: The Enzyme, The RNA, & The Virus (video by Myles Marshall)

Cas9: The Enzyme, The RNA, & The Virus (video by Myles Marshell)










photo (1)Prashant is a senior undergraduate student studying biochemistry and molecular biology at the University of California, Berkeley. He currently is Editor-in-Chief of Berkeley Scientific Journal, where he became interested in science journalism and its propensity to motivate general audiences.  Read the current issue here. Follow BSJ on Twitter.

Category: Bacteria, Cancer, Genetics, News, PLoS, PLoS Biology, PLoS Blogs, PLoS Genetics, PLoS Medicine, PLoS Medicine Week by Week, PLoS Medicine's Daily Click, ResearchBlogging, Science, science journalism, The Student Blog | Tagged , , , , , , , , , , , , , , | 10 Comments

Shedding Light on Dark Energy

Dark energy and the nature of the universe are two of the most exciting discoveries of the past couple decades, but can be some of the most difficult concepts for non-physicists to grasp. More often than not, dark energy is just a futuristic-sounding prop in a science fiction novel. But while it may make for a fantastical plot tool, the real discoveries in dark energy are even more exciting. I’m going to do my best to explain a bit of the history of dark energy and some of the experimental evidence that helps to constrain the theory.

The History of Dark Energy

The original concept of dark energy was proposed by Einstein in his field equations in the 1910s, which essentially describe the behavior of matter due to gravity. A good analogy for Einstein’s Theory of General Relativity is a linen sheet, stretched tight – this represents the universe. Let’s scatter a few marbles across the sheet. Each will create a small dimple in the sheet. These represent mass in the universe – galaxies. Now we can observe the effect of gravity: each marble is going to start to roll towards nearby marbles due to each other’s dimples, as gravity causes massive bodies to attract to each other. This is the problem Einstein encountered: the universe couldn’t remain the same size if gravity were the only force to act on massive objects. To keep the size of the universe static, Einstein needed a repulsive force to counteract gravity, and essentially added a “fudge factor” to his field equations, which he called the “cosmological constant.” This constant would be a property of space itself.

When Hubble discovered that the universe was expanding in 1928, Einstein quickly abandoned the idea of a cosmological constant, purportedly calling it his “greatest blunder.” An expanding universe is no longer static, and therefore Einstein didn’t need a force to counteract the contraction due to gravity. Essentially, the expansion of the universe wouldn’t contradict his theory, provided that the expansion was slowing from gravitational pull.

However, in 1998, it was discovered that the expansion of the universe was accelerating. This no longer agreed with a model that only included gravity – the cosmological constant would have to be reintroduced. This accelerating expansion is the first piece of modern evidence that points towards the existence of dark energy.

Type Ia Supernovae

In 1998, Type Ia supernovae provided the first indication of the accelerating expansion of the universe. The explosions of these particular supernovae occur consistently enough that they can be used as a basis for a brightness measurement, referred to as a “standard candle.” Astronomers measure the amount of light received from a particular supernova, and, by tracking the supernova over several days, can estimate how much light the supernova emits at its source. This provides a measurement of how far away the supernova is. Then, by looking at the colors the supernova emits, astronomers can determine how quickly the star is moving away from Earth, using the Doppler shift, or “redshift” (the change in frequency as a result of velocity). Since it takes time for light from these supernovae to reach Earth, light from more distant supernovae was emitted longer ago, and similarly, light from closer supernovae was emitted more recently. Distant supernovae can thus give a measure of the expansion of the universe via their redshifts, and this is where the accelerating expansion was observed: closer supernovae are receding far faster than distant supernovae.

The model of the universe mentioned earlier dictates that there are four parameters that govern cosmology: matter (or mass), the radiation (or light), the cosmological constant (or dark energy), and curvature (or the shape of the universe). We can think of these as “fractions” of what make up the universe, as they add up to 1. (However, the curvature can be positive or negative.) So, if we don’t know anything about dark energy, we should still be able to make measurements of the other parameters and figure out whether or not the dark energy fraction is zero, i.e. if it actually exists.


Results of the Supernova Cosmology Project and BOOMERanG, the cosmic microwave background experiment. Numbers represent fractions, so 0.5 on the dark energy axis would indicate 50% of the universe is dark energy. Source: Supernova Cosmology Project, Lawrence Berkeley Laboratory.

These supernova measurements provide information about the mass dark energy fractions, shown on the right. It doesn’t provide an exact answer for each, but instead gives an estimate, shown as the yellow oval to the right. This shows that the values for dark energy fraction and mass fraction fall somewhere inside that oval. Supernova data largely point towards the existence of dark energy, but not definitively. The oval is bisected by the red “flat universe” line, along which the true value would lie if there universe were shown to be flat. Thus, determining the shape of the universe is a key step towards determining the existence of dark energy.

Cosmic Microwave Background

The second experiment we’ll look at is the observation of the cosmic microwave background, which is the residual light left in the universe from the Big Bang. This corresponds to a temperature of 2.7 Kelvins (-455 °F), and gives a direct measure of the radiation fraction, which turns out to be the minute value of 0.01%. It also allows astronomers to determine the curvature of the universe.

The notion of curvature is difficult to visualize. Our linen sheet from earlier describes a flat universe. A closed universe would be a world contained along the surface of a spherical shell, and an open universe is a saddle-like shape.

Representation of closed, open, and flat geometries. Source: NASA, Wilkinson Microwave Anisotropy Probe.

Representation of closed, open, and flat geometries. Source: NASA, Wilkinson Microwave Anisotropy Probe.

The temperature of the cosmic microwave background is remarkably consistent, but small part-per-million fluctuations in it (called “anisotropies”) can be observed, which come from sound waves in the very early universe, just after the Big Bang. Astronomers know what pitch these sound waves should be, so by measuring the residual waves in the sky, they can tell whether or not the observed angle is from a flat or a curved universe. An experiment called BOOMERanG collected data in a balloon above Antarctica, and found that the Universe is flat, and so there is zero curvature. Going back to the graph earlier, the combination of supernova and BOOMERanG data puts the dark energy and mass fractions somewhere inside the green wedge. We’ll need one more experiment to precisely determine what the fractions are.

Baryon Acoustic Oscillations

Returning to the model mentioned at the beginning, we now have values for the radiation fraction and the curvature, and a relationship between the mass and the dark energy fractions. The final piece of our puzzle comes from baryon acoustic oscillations, which are the peaks and troughs in the concentrations of galaxies found in the universe. Essentially, the size of these oscillations gives a number for the mass fraction of the universe, which turns out to be roughly 30% of the universe. Now that we have the mass fraction, we can figure out the dark energy fraction directly.

Putting It All Together

Combination of Type Ia supernova (SNe), cosmic microwave background (CMB) and baryon acoustic oscillation (BAO) data. The combination of the three experiments confines the dark energy and mass fractions of the universe to a very narrow range. Source: Supernova Cosmology Project, Lawrence Berkeley Laboratory.

Combination of Type Ia supernova (SNe), cosmic microwave background (CMB) and baryon acoustic oscillation (BAO) data. The combination of the three experiments confines the dark energy and mass fractions of the universe to a very narrow range. Source: Supernova Cosmology Project, Lawrence Berkeley Laboratory.

Merging the three different experimental data sets, the true story of dark energy surfaces – a whopping 70% of the universe is made up of dark energy. Of the 30% that is mass, it turns out that only 4% is ordinary matter, the stuff we think of being in the universe (stars, planets, interstellar dust, etc.) while the other 26% is dark matter (different from dark energy).

So What?

There’s strong evidence that dark energy exists, and experiments based on different physics come together to support each other. In fact, dark energy comprises most of the universe. However, the nature of dark energy is still unknown – all our evidence is indirect (hence the moniker “dark”). Even though it makes up so much of the Universe, its tendency to “push back” means that it has a very low density (10-26 kg/m3). Theories about the nature of dark energy abound, but, until there is a way to experimentally challenge each, the true identity of dark energy will remain a mystery.

bioDan is a physics Ph.D. student at University of Colorado Boulder and is a graduate research assistant at the National Institute of Standards and Technology. His research involves the development of infrared lasers for the detection of atmospheric greenhouse gases. You can reach him at daniel.maser AT

References / Further Reading

  1. A. G. Riess et al., Astronomical Journal 116, 1009 (1998).
  2. S. Perlmutter et al., Astrophysical Journal 517, 565 (1999).
  3. B. Schwarzschild, Physics Today 60, 21+ (2007).
  4. B. Schwartzschild, Physics Today 54, 17 (2001).
  5. P. J. E. Peebles and B. Ratra, Reviews of Modern Physics 75, 559 (2003).
  6. P. de Bernardis et al., Nature 404, 955 (2000).
  7. D. J. Eisenstein, New Astronomy Reviews 49, 360 (2005).
  8. S. Perlmutter, Physics Today 56, 53 (2003).
  9. J. B. Hartle, Gravity: An Introduction to Einstein’s General Relativity (Addison-Wesley, 2003).
  10. W. Hu, N. Sugiyama, and J. Silk, Nature 386, 37 (1997).
  11. L. Miao, L. Xiao-Dong, W. Shuang, and W. Yi, Communications in Theoretical Physics 56, 525 (2011).
  12. J. A. Frieman, M. S. Turner, and D. Huterer, Annual Review of Astronomy and Astrophysics 46, 385 (2008).
  13. M. Kowalski et al., Astrophysical Journal 686, 749 (2008).
  14. J. E. Lidsey, Temperature fluctuations in the cosmic microwave background, (2003).
  15. Planck Collaboration, P. Ade et al., Astronomy & Astrophysics (2013), arXiv:1303.5076.
  16. Planck Collaboration, P. Ade et al., (2013), arXiv:1303.5075.
  17. H.-J. Seo and D. J. Eisenstein, The Astrophysical Journal 598, 720 (2003).
    S. W. Allen, A. E. Evrard, and A. B. Mantz, Annual Review of Astronomy and Astrophysics 49, 409 (2011).

Category: Physics, The Student Blog | 5 Comments

What we could learn from industry

You have probably heard a lot of articlesblog posts, tweets, and facebook rants lately about the abysmal state of the job market for aspiring academics.  You’ve probably heard stories (the Berkeley Science Review even ran one last semester) about the shifting reality for graduate students, and about the needed focus on non-academic careers for graduate education.

I’m not here to debate any of this, but there’s plenty of material out there if you’re curious.  However, there’s a really important point in this discussion that almost never gets voiced: learning about the non-academic world is not only about getting a non-academic job, it also makes us better scientists. 

Now, I can see you all rushing to your keyboards to rise up in protest, so let me make this clear: I’m not saying that academia should be a “business” in some sense, and I understand the importance of keeping conflicts of interest out of science (though last time I checked the simple desire to publish can be, itself, a conflict of interest).  What I’m saying is that we have a lot to learn from the non-academic world, about how to interact with our peers, how to work together as teams, how to manage projects, and how to communicate with others.

In my most cynical moments, I view “business” as a relatively simple game: how can the right collection of people make as much money as humanly possible?  This may sound like a critique, but it’s not. It is just a goal (in reality probably only one of many). And guess what businesses are really good at doing?  Making money, and accomplishing that goal.  They’re clearly doing something right, so what is it that we can learn from them?

Let’s take a moment and think about what being part of a successful business generally entails: you need to get a group of people together with a wide range of expertise and experience.  You must define a common goal, and make a plan to accomplish that goal.  Moreover, you need to split up chunks of that plan and assign each of them to people in your group, making sure to pair the right job with the right person.  In so doing, each individual contributes their own skills to the project, and they learn a lot in doing so.  At the end of the day, the team achieves their goal, and everyone shares in the riches gained.

To me, this sounds a lot like a science lab.  Labs tend to be focused on a single “theme” of scientific question (e.g., “we study visual processing in zebrafish”).  They’ve got a bunch of graduate students and post-docs, all of whom bring something unique to the table, and each of which is involved in asking a different question related to the “big picture”.  Finally, you’ve got the PI at the top, pulling the strings and making sure the machine runs smoothly (ideally anyway).

The only problem is that even though the task that academics and businesses must accomplish is quite similar, they take very different approaches to solving it.  The business world has a tendency to emphasize interpersonal relationships and “teamwork” as attributes that it admires.  It gives credit to those who can work with groups, and who learn to share the load and the glory.

“Piled Higher and Deeper” by Jorge Cham

Academia, on the other hand, runs on a sort of “wheel and spoke” model in which each graduate student is expected to be the sole lead in “their project”.  Post-docs may have a few people working underneath them, but it’s rare to find a lab that truly distributes the workload.  And why should they?  Academic publishing incentives encourage the outdated picture of a lone genius toiling away in the lab until the wee hours of the morning.  How many of you remember the last names of all those middle authors?

Another lesson we could all learn from the business world is communication.  What’s the single most important thing that you can do after discovering something amazing about the world?  Tell people about it.  Unfortunately, many academics seem to have an aversion to speaking in “layperson’s” terms, and do little more than pay it lip-service in trying to tailor their writing and speaking to be understandable by the average person.

In the non-academic world, communication skills are one of the most important abilities that anyone can have.  You must be able to make other people understand what you’re talking about, whether this means presenting to others on your team, potential partners, or even your boss(es).  Businesses understand that image and presentation are incredibly powerful tools in persuasion, and academia would do well to take a lesson from this.

To this point, many researchers say “but our job isn’t to speak to the average person, it’s to speak with other scientists who take an inherently objective approach to everything!”  Perhaps they’re right (that’s a point we can debate another time), but at the risk of insulting our fellow academics, there’s a good chance that those fancy experts in the audience are just as swayed by a well-crafted presentation, and that they probably have no idea what you’re talking about.

In reality, scientists are humans just like everybody else.  They don’t have super-human intelligence or the attention spans of an owl, and just like everybody else they respond to material that is clearly presented, well prepared, and above all interesting.  If you’ve ever said to yourself “well, this slide is full of jargon, but the audience is pretty well-versed in this field so it’s OK”, then you should stop right there and read journal abstracts until your eyes bleed.  Then, rewrite your presentation with the goal of not inflicting the same kind of pain on your audience.

So, do I think academia should be run like a business? No. We study far more interesting problems that (for better or worse) most companies are never going to be interested in.  That said, we have a duty to do the best possible work with the resources that we have.  To me, that means looking towards other industries, learning about what they do well, and incorporating this wisdom into our own scientific culture.  I dream of a world in which scientists are viewed like entrepreneurs: masters of many trades, steeped in charisma, making connections where none existed before and forging a path into the unknown.

Author’s Note: Some people have excellently pointed out that my use of “average people” comes across as condescending.  I want to reiterate that by “average”, I do not mean inferior or less intelligent in any way at all.  By “average”, I simply mean people with less specialized, domain knowledge than someone with scientific training in a particular field might have.


Chris studies cognitive and computational neuroscience, attempting to link higher-level theories of the mind with information processing in the brain. He’s also an avid science communicator – check out his posts on the Berkeley Science Review and follow him on Twitter at @choldgraf

Category: The Student Blog | 1 Comment

Not So Ordinary: A Tale of Unsung Science Heroes

Of the 638 Nobel laureates in the sciences (physics, chemistry, medicine, and economics), how many names do you recognize? Einstein, Pierre and Marie Curie, and perhaps Pavlov? Most scientists—even Nobel laureates—do not become household names. However, these “ordinary” scientists are no less brilliant, hard-working, or interesting than the “extraordinary” ones.

Gino Segrè’s 2011 book, Ordinary Geniuses, is the biography of two such “ordinary” figures, Max Delbrück and George “Geo” Gamow, whose contributions to their respective fields of genomics and cosmology were anything but ordinary. Delbrück and his team discovered the mechanism of gene replication, for which they were awarded the Nobel Prize in Physiology or Medicine in 1969, and Gamow and his team were early proponents of the then-controversial Big Bang theory, which provided a theoretical framework that could explain how hydrogen and helium were formed in the baby universe.

Max Delbrück and his team discovered the mechanism of gene replication.

Max Delbrück and his team discovered the mechanism of gene replication. Image sources: left, right.

Gamow and his team were early proponents of the Big Bang theory.

Gamow and his team were early proponents of the Big Bang theory. Image sources: left [in public domain due to expired copyright], right.

Ordinary Geniuses follows Delbrück and Gamow from their humble beginnings as unknown but promising students to their emergence as pioneers in biology and physics. They both began as students in physics, and became friends while studying at the Niels Bohr Institute for Theoretical Physics in Copenhagen. Sometimes, late at night, Gamow would barge into Delbrück’s room, turn on the lights, and announce his latest idea on physics, which they would then discuss over beer and sausages. However, though Gamow’s career was taking off with his work on radioactive decay, Delbrück was not so successful. Bohr convinced Delbrück that the “next big question” would be in the life sciences, and so he began making a transition to biology.

When the two met again as established scientists decades later—this time in the United States—Delbrück had become a giant in genetics research. Gamow’s interest also shifted to biology around that time, and he even started the RNA Tie Club, a scientific “gentlemen’s club” dedicated to discovering how DNA instructs the body to create proteins. With Delbrück’s and Gamow’s careers established, the book concludes by summarizing modern perspectives on genomics and cosmology.

Segrè weaves together Delbrück’s and Gamow’s stories, alternating between them every chapter or two. The descriptions of scientific theories and discoveries are interesting, and can be readily understood by the curious layperson. As a biography, however, the book shines in its descriptions of these two fascinating figures. Here are some of my favourite parts:

1) Young Delbrück as he sought a research specialty.

As a graduate student struggling to carve out my own niche in science, it heartened me to know that even a Nobel laureate once felt lost and confused in his youth. In his own words, “I had not felt that I was doing well in astronomy and I did not feel that I was doing well in physics; and I was just hoping that something would happen that I was doing well and was willing to carry on with.” Even after he switched to biology, it took several years before he established a name and a lab for himself. I enjoyed reading about how his persistence and trust in his instincts led him to pioneer a field.

2) Gamow as a jovial, kind man with an unmatched joie de vivre.

Whereas I would have been somewhat afraid to meet Delbrück—he was known to have a sharp tongue as well as a sharp mind, frequently declaring seminars to be the worst that he had ever heard—Gamow comes across as far more approachable. A prankster, a joker, and an accomplished artist, he adorned his letters to colleagues with hilarious illustrations. “[a] discussion of the virus that attacks tobacco plants might be accompanied by a drawing of a happy smoker flicking cigarette ashes, and the question of what can be accommodated into the spacing between the bases on a DNA molecule sidetracks Geo [Gamow] into contemplating what fits into the open mouth of a tiger.” A picture of the latter is provided on page 218.

Gino Segrè is a particle physicist with an interest in astrophysics. He has previously written two books, Faust in Copenhagen and A Matter of Degrees.

Gino Segrè is a particle physicist with an interest in astrophysics. He has previously written two books, Faust in Copenhagen and A Matter of Degrees. Image source.

3) The “Copenhagen spirit.”

Bohr created a welcoming and stimulating environment at the Institute for Theoretical Physics. Several of the scientists were permanent members of the institute, but others stayed for a few months at a time. They lived and worked together, united by their interest in physics. The stay at Copenhagen clearly affected Delbrück and Gamow; they later tried to re-create the Copenhagen spirit at the Cold Spring Harbor Laboratory, and at the George Washington University Theoretical Physics Conference. I loved the idea of being surrounded by friendly, like-minded individuals focused on the same topic, and found myself becoming quite envious of the Copenhagen spirit.

What does it mean to be an extraordinary scientist? Despite the title of the book, I got the sense that drawing a distinction between the ordinary and the extraordinary may be misguided. The ordinary geniuses of Segrè’s book are anything but ordinary—they are accomplished, brilliant people in the modern history of science. Ordinary Geniuses entertains and educates, and is highly recommended.



Photo by Karen Meberg

Minjung (“MJ”) is a PhD student at the New York University Department of Psychology, Cognition and Perception Program. She studies the visual perception of light and colour, with a keen interest in material perception (e.g., what makes glowing objects appear to glow?). 

To read more about MJ’s work, please go to her academic site.

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Fruitless remains ever-fruitful: a genetic story of love and aggression

This article is being cross-listed on The Berkeley Science Review. Check out some other really interesting pieces there!

One of the most exciting prospects of biological inquiry lies in its potential to explain the peculiarities of our own lives. Human behavior provides some of the most spectacular examples of the output of a fundamentally biological system, the brain, but despite decades of remarkable research spanning the scale of neurotransmitters, to brain hemispheres, to interactions on the internet, we struggle to firmly explain the biological (and environmental) underpinnings of any given human behavior.

Luckily, some of our behaviors aren’t exclusive to our species. Chimpanzees seem to mourn the death of family members. Ants are capable of organizing into social hierarchies that eerily resemble human social structures.  Even the lowly fruit fly, Drosophila melanogaster, goes through bouts of light and heavy sleep that resemble human sleep cycles. All these examples suggest that the biology of behavior might be conserved in the same way that many genes are conserved from fly to human, and hint that perhaps the same genes control similar behaviors in wildly different organisms – a hint that tantalizes scientists to this day.

Thomas Hunt Morgan, the Nobel-prize-winning biologist who popularized the use of the fruit fly, D. melanogaster, as the model organism of choice for modern genetics.

Thomas Hunt Morgan, the Nobel-prize-winning biologist who popularized the use of the fruit fly, D. melanogaster, as the model organism of choice for modern genetics.
Source: Wikipedia

A century ago, when the fruit fly was popularized as a model organism by the lab of Thomas Morgan, these similarities were fairly well-appreciated, but tools for manipulating fly genetics and observing fly behavior were lacking.  Fifty years later, researchers were better-prepared to manipulate the fruit fly genome, thanks to advances made in prior decades with mutating the fly genome with x-rays. In 1963, a researcher at Yale named Kulbir Gill used this technology to create mutant flies that lacked the typical behavioral program ensuring male pursuit of female partners for reproduction. These mutant male flies courted male and female partners equally, and utterly failed to reproduce. Gill dubbed this mutation ‘fruity,’ a less-than-appropriate pun on the fruit fly and its mating strategy, but limited his observations to a short note in a fly journal, declining to investigate further.

In 1977, the geneticist Jeffrey Hall dug up Gill’s fruity line, and again observed a failure of male flies to properly court and reproduce with female flies. Hall renamed the mutation fruitless, acknowledging Gill’s original name while tactfully shifting its implication onto these flies’ futile attempts at reproduction. With Hall’s resurrection of the fruitless fly line, scientists now had an animal model that could provide insight into how genes influence male behavior – an insight with the potential to explain the root of differences in the behavior of men and women.

We now know that the original fruitless flies possessed a mutation in the fruitless gene, which disrupts the production of the male-specific protein FruM. FruM is expressed in neurons that exist in the male, but not female, fly brain, and some of these neurons are responsible for orchestrating the male courtship ritual. When scientists engineered female flies to express FruM, these female flies began to behave like courting males, despite their lack of the very neurons that guide male courtship. All this raises some of the biggest questions in biology. If sexual orientation and courtship can be influenced by a single gene in flies, might these traits be controlled by a gene, or genes, in humans? If differential gene expression in female versus male flies leads to behavioral differences, does a similar scenario explain behavioral differences across the human sexes? And lastly, how does the introduction of a male protein into a female brain allow that female brain to carry out a male behavior, when the male neural circuitry is not present?

FruM, and the male neurons possessing FruM, obviously deserved further study, as biological mediators of male behavior. Over the course of his career, Hall himself managed to define the FruM neurons responsible for male courtship, but these neurons represented but a fraction of the total of two thousand FruM neurons, suggesting that FruM might control other male-specific behaviors in the fly. High on the list of observable sexually-dimorphic behaviors in the fly is aggression: though both male and female flies are capable of exhibiting aggression, males are measurably more aggressive than females. This is also true for most mammalian species, including humans. Men are broadly more violent than women, and while the causes of human violence are likely more complex than any violence observed in a fly vial, it is tempting to speculate on how biology, and genetics, might be influencing this behavioral sexual dimorphism, just like how FruM neurons enable male flies to perform their courtship song.

Perhaps unsurprisingly, aggression was formally linked to fruitless by the lab of Barry Dickson at Harvard in 2006, with a study that was able to swap male and female modes of aggressive fighting by replacing the fruitless variant of one gender with the fruitless variant from the opposite gender. However, despite the efforts of dozens of additional labs, the identity of the FruM neurons that drove male-specific aggression remained unknown. Furthermore, even though both courtship and aggression in flies seemed to depend on fruitless, this gene was nowhere to be found in higher organisms, including humans. Fruitless, fifty years out, was still puzzling the best of the science community – could further study actually bring us closer to understanding divergent behavior between the sexes?

A male flies prepares to lunge at a second male fly, a stereotypically aggressive behavior that can be detected by automated software developed in David Anderson's lab.  Source

A male fly prepares to lunge at a second male fly, a stereotypically aggressive behavior that can be detected by automated software developed in David Anderson’s lab. Source: Anderson Lab

Though fruitless retained mystery, the fly field did not rest. Just how did FruM impart aggression in male flies? Researchers at Caltech, led by David Anderson, had spent over a decade developing automated tools for monitoring a variety of fly behaviors, so they undertook a modern version of Gill’s original observational study: manipulate fly genetics systematically, and document the consequences for fly behavior. Other groups had shown the importance of particular hormones, also known as neuropeptides, in fruitless-mediated courtship, which led Anderson’s group to speculate that an unknown neuropeptide could be responsible for male fly aggression.

Harnessing genetic tools for screening many mutant flies at once, the Anderson group created forty fly lines in which small groups of neurons could be activated by heat, depending on which one of twenty neuropeptides they expressed, hypothesizing that some of these lines would display increased aggression. Of these forty lines, two stood out as having increased aggression (for flies, this includes stereotyped lunging and boxing behavior). Both of these lines contained neurons that produced the neuropeptide tachykinin (Tk), also known as Substance P in mammals – a promising early observation for connecting aggression across species. When the researchers obtained high-quality images of these neurons within the fly brain, they noticed that they visually resembled FruM neurons identified in other studies. Digging deeper, lo and behold, this handful of neurons actually expressed FruM, corroborating the earlier work of Dickson’s lab, but refining the aggression-responsible group from two thousand FruM neurons to just four Tk/FruM neurons.

Visualization of Tk/FruM neurons (green), responsible for aggressive behavior, in the male fly brain (left, yellow arrows); for comparison, the female fly brain (right) lacks these neurons.  Source

Visualization of Tk/FruM neurons, responsible for aggressive behavior, in the male fly brain (left, yellow arrows); for comparison, the female fly brain (right) lacks these neurons. Asahina et al., 2014. Source: Caltech

The hunt was on. Anderson’s team characterized how Tk neurons sparked aggression, and found that overexpressing Tk itself, while simultaneously activating the Tk neurons, ramped up aggressive behavior to the point of driving flies to attack inanimate objects (in this case, a fly-sized magnet). Despite also expressing FruM, activating these neurons had no effect on courtship, indicating their specific role in increasing ‘aggressive arousal,’ or the likelihood of engaging in aggressive behavior. These neurons were only observed in males, as expected for FruM neurons, potentially explaining female flies’ low levels of observed aggression. And perhaps most intriguingly, the neuropeptide Tk itself was driving aggression, presenting the first molecular link between aggression in flies and mammals.

With a gene and a neuropeptide pinned down as the factors responsible for male aggression in flies, the Anderson lab, and indeed the entire field studying aggression, now has a new lead on the genetic basis of gender differences in aggression. Will we soon understand why men and women demonstrate different levels and kinds of aggressive behavior? Maybe not for some time. But a similar, aggression-related molecule is present in the mammalian brain, and the fruit fly’s behavior provides the foundation for further study into how sexual dimorphism occurs in higher organisms.The fruitless gene, over forty years since its inception as fruity, continues to bear intellectual fruit, as the grandfather of behavior-regulating genes known to be expressed in a sex-based fashion. Good science takes time, some fumbles with inappropriate names, and some gambles, but the modest fruit fly has yet again proven it is not to be underestimated. Especially when it is up for a fight.

Category: The Student Blog | 1 Comment

My path to graduate school: medicine vs. research

After leaving the California Institute of Technology with a BS degree in biology, I took a relaxed summer in preparation for what is going to be the next 5, 6, or maybe even 7 years of my life – graduate school.

The first step to tackling graduate school starts well before you step through the front doors. It starts in your undergraduate years when you find your passion. For me, that passion was in the sciences. Aided by my parents’ urging towards a career in science, I participated in local science fairs and started research in the latter years of high school at the National Cancer Institute. There, I truly had my first taste of biological research. However, I didn’t expect that I would ever end up in graduate school.

National Cancer Institute at Frederick, MD.

National Cancer Institute at Frederick, MD. Source.

Despite only having experience in research, I never considered it as a career choice. Biology was something that I excelled at, and I knew that I was interested in helping people through medicine. These dreams motivated me to want to become a doctor from a young age. I wanted to make a difference in the lives of as many as I could touch. I was so focused on that path that I never considered any others– blinded to other careers, especially those not in science. To understand how a career in medicine would be, I chose to do an internship at the Huntington Memorial Hospital in Pasadena.

Huntington Memorial Hospital in Pasadena, CA.

Huntington Memorial Hospital in Pasadena, CA. Source.

For 6 weeks, I arrived at 7:00AM to doctors checking on patients and reading charts. I rotated through different wards including pediatrics, neurosurgery, and pathology. I remember that, on several occasions, I had to stand for 6 or more hours watching surgeries. The doctors told me that they had done the same surgery several times that week for many weeks in the month and many months in the year. But, of course, not all the rotations were so repetitive. My experiences in internal medicine were probably most interesting because I was able to meet different patients every day and see doctors’ diagnoses and treatments. However, what I found after the 6 weeks was most telling about the outlook of my future – I wanted to be a scientist.

For the last 3 weeks of my internship, most of my thoughts led to returning to the laboratory bench. I realized that leading up to this point in my life, I was being trained to be a scientist, yet I was so blinded by the goals set by my parents and myself. I realized I yearned for the creativity that comes with research and the flexibility to take projects in whichever direction was most interesting. The natural curiosity I had about the world around me was repressed by, from what I thought, the monotonous routine of being a medical doctor. Even more telling was the fact that I was at one of the world’s leading research institutions. It’s almost as if my actions knew what I was meant to do, but my mind had yet to accept.

As a young student in middle school and high school, I lacked the wisdom to understand that I should question my motives for wanting to be a medical doctor. Equally or even more important than using medicine to treat patients is to discover those medicines, and that is almost exclusively the job of the scientists. It took me several years to realize that researchers could be as helpful to people as a medical doctor.

Now that I’m in graduate school, I’m glad to be where I am. I go to work every day wondering how to take my science to the next level and think about biology in ways that I had never before. Every day seems like a new problem to tackle, and I appreciate that about research. I realized that being a medical doctor was not something that matched my interests, although it can certainly be the right career for those looking for patient contact and a direct impact on patients’ lives.


Marvin is a PhD candidate at Stanford University in Immunology. He was an editor-in-chief at the Caltech Undergraduate Research Journal. See it at Follow on twitter @Marvzipan.

Category: The Student Blog | 11 Comments