IQ Biology

BioFrontiers Institute and IQ Biology alum, Joey Azofeifa (Arpeggio Bio), Raises $3.2 Million in Seed Funding and is Named to the 2020 Forbes 30 Under 30 List in Healthcare

Anonymous — Wed, 15 Jan 2020 23:51:42 +0000

BioFrontiers Institute and IQ Biology alum, Joey Azofeifa (Arpeggio Bio), Raises $3.2 Million in Seed Funding and is Named to the 2020 Forbes 30 Under 30 List in Healthcare Anonymous (not verified) Wed, 01/15/2020 - 16:51

Arpeggio Bio, a preclinical company whose technology provides a mechanistic understanding of how drugs work, today announced that it has closed a $3.2 million seed financing round, which was oversubscribed by over $2 million. Funding will support the ongoing development of a nascent RNA drug screen.

“We’re excited to have the support of our investors to allow us to continue our mission of helping bring new therapies to patients with epigenetically-driven diseases,” said Joey Azofeifa, Ph.D., Founder and CEO, Arpeggio.

Since inception in 2018, Arpeggio has partnered with over twenty biotech and pharmaceutical companies — including four of the world’s top ten — to uncover new insights into their therapeutics. Arpeggio’s early market traction and progress led it to be selected for the prestigious Y Combinator’s (YC) Summer 2019 batch, which provides emerging startups with funding and mentorship. Following a successful program tenure, Dr. Azofeifa’s YC Demo Day pitch attracted distinguished investors to lead a funding round, including Khosla Ventures, FundersClub, Fifty Years, TechU, and YC.

Arpeggio has built an automated system that collects information about which genes turn on or off for hundreds of time points beginning in the minutes following drug treatment in preclinical models. Using algorithms originally developed for financial forecasting, Arpeggio reconstructs the biological network a drug affects and identifies the genes critical for the success or failure of a drug. This new kind of data allows for the elucidation of novel drug and disease mechanisms, supporting development of safer, more effective therapies by understanding drug effects before they’re given to patients.

The company's platform analyzes its time-series RNA profiles using proprietary machine learning algorithms developed by Dr. Azofeifa. Driven by Arpeggio’s success, Dr. Azofeifa was recently named to the 2020 Forbes 30 Under 30 List in the Healthcare category, recognizing him as one of the country’s top young entrepreneurs.

Arpeggio's technology combines a proprietary biological assay and machine learning algorithms that, together, enable rapid, high-resolution snapshots of cellular dynamics following drug treatment. These snapshots are then analyzed to reveal the biological networks that determine a drug’s function and guide therapeutic development. To learn more, www.arpeggiobio.com

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A Summer Internship Where Only the Cows Obey Traffic Signals

Anonymous — Wed, 13 Nov 2019 20:37:08 +0000

A Summer Internship Where Only the Cows Obey Traffic Signals Anonymous (not verified) Wed, 11/13/2019 - 13:37

Lindsay Diamond

IQ Biology graduate student, Taisa Kushner, spent her summer as a Microsoft Research intern in Bangalore, India, working on a global mental health platform.

Can you tell us about your internship experience at Microsoft Research?

I interned at Microsoft Research (MSR) in Bangalore, India this past summer. MSR is under the umbrella of Microsoft, but it is separate from Microsoft corporate, where they do product development and engineering. The work that comes out of MSR does influence products at Microsoft, but MSR is focused on basic research and functions more like academia than industry. MSR has multiple labs throughout the world, and each lab focuses on a different broad area. The Bangalore lab houses their "Tech for Emerging Markets" (TEM) group, which does computational social science, fieldwork, and tech development focused on working with and for individuals in developing countries. I have been interested in the work coming out of the TEM group for a couple of years and applied to be a Ph.D. intern at the lab. Luckily, after a few rounds of interviews, I got the position!

I worked with Dr. Amit Sharma in the TEM group, whose primary research focus is on causal inference and the societal impact algorithmic interventions can have. My project centered around a global mental health platform, Talklife, which seeks to provide a peer-to-peer support network for individuals suffering from psychological distress. When considering interactions on this platform, some end up being helpful, while others are not. Broadly, my work this summer focused on answering the questions, "What makes a certain series of interactions helpful to users?" And, "Are there actions individual users can take to improve their experience on the platform?"

What surprised you about the experience?

I knew MSR functioned more like academia than industry, but I was surprised by the extent to which there is not any hierarchy. Everyone is very humble despite being brilliant. The lab director, Sriram Rajamani, is very kind and collaborative. Despite being busy, he takes time to get to know everyone, including all the interns. I was able to have lunch with Sriram and discuss research ideas for my work back here in Boulder. I appreciated being treated as a research equal by all the full-time researchers.

Did your IQ Biology experience play a role in this experience?

Yes! It is such an interdisciplinary environment. For my project, in particular, we had to communicate with the company Talklife, which provided us with data, physicians from both the US and India, and other researchers who work on societal differences in mental health care and communication across the US and India. Through IQ Biology, I have gained a skill set of being able to effectively communicate with people from different backgrounds and also critically think through all of the aspects of a research problem. For this project, I had to consider how to identify causal relations within the data (math), identify and understand biases that might be present in the data (health care, social science), how to think about and handle them, and how to bridge computational work with medical care. With mental health, in particular, the stigmas are very different in the US and India, and people utilize different words and descriptions to discuss symptoms and how they manifest. You need to understand the human aspect of these nuances to deal with the data effectively.

Would you recommend doing a summer internship as part of grad school? Why/Why not?

Yes, 100%. Working at MSR is still very academic-focused rather than a traditional industry internship, so I can only speak to my experience. Still, I appreciated the opportunity to branch out from my doctoral research, which focuses on artificial pancreas controllers for individuals with type-1 diabetes. I had a lot of freedom to explore the data, and I learned techniques in causal inference, natural language processing, and I learned about how mental health care differs across the globe, which I feel will be beneficial to future work I do.

I would also recommend doing research in an eastern setting, if possible. I thought the experience provided a critical exposure to have as a researcher. I appreciated the opportunity to hear about the differences in culture and opinions and the needs of people in India. MSR brings in a lot of collaborators, and the Bangalore lab does a significant amount of social science focused on working with impoverished people across India, in their language. MSR identifies the needs they have in terms of life stressors and how technology may help rather than taking research done in the west and assuming other people want the same thing.

Did anything happen during your internship outside of the research/work experience that made an impression on you? Any lessons learned while abroad?

MSR brings in lots of researchers and doctoral interns from across the world. As a result, I was able to befriend people who come from different backgrounds. I appreciated embedding into the Indian culture through working and living there rather than just as a tourist. One of the other interns, who is a professor at the University of Cincinnati, is originally from the Indian state of Kerala. I visited her family's rubber and pineapple farms and experienced parts of India that I don't think I would otherwise get to see.

What will happen to the work you were doing during your experience?

We have submitted a paper on the work, and we have a second paper in progress. Related work on the project is being continued at MSR now, and I'm assuming they will have new interns on the project in the future. If anyone wants to talk more about the project or my experience, I'd be happy to connect!

Did this experience affect your current career plans?

It was very helpful in making me feel more competent as a researcher, which is nice to be able to say. I feel like I was able to approach a pretty loosely defined project and complete a substantial amount of work on it. I had a lot of independence in the process, along with excellent mentoring, which made it a great experience overall. In terms of working at MSR again, I would love to work at MSR Bangalore, though there is a lot about living in India that would be tough long-term. It's also a challenging position to obtain.

What is your favorite memory from this experience?

Oh, so many! All of the people I was able to meet and befriend. Everyone was so kind and welcoming. I learned so much about India, the local politics, climate problems, and social structure. It was fascinating to see US news from the Indian perspective and to listen to the thoughts and opinions of people who are not from the west.

We did have one very ridiculous series of events where we almost got stuck in the Indian Himalayas and, as a last resort effort, ended up going to Kashmir during the peak in military occupation and unrest surrounding the split of the state and removal of article 370. This adventure involved classic Indian twelve-passenger van travel for 17 hours straight with people I had never met. The van was a classic sight: completely falling apart, the exhaust poured in from the gear shift, yet it was decorated with LEDs and cheesy phrases. We had tea in the middle of nowhere in Kashmir at 2:00 am. I genuinely thought we would fall off the mountainside on this incredibly steep and narrow dirt path, and we had a run-in with the Indian Army 30km outside of Srinagar when our driver didn't have his driver's license. Thankfully, they let us through because we all had our proper documents.

I miss being in Bangalore with its almost 13 million people living there. It was overwhelming at times, but by the end, I loved it. I enjoyed being able to safely walk around at any time and see people congregated around tea shops and street food at all hours of the day. It's a lively city. The cows wandering the streets are also very fun. They are the only ones who obey traffic signals.

The Interdisciplinary Quantitative (IQ) Biology Ph.D. Certificate is designed for students interested in gaining interdisciplinary quantitative skills, while also joining a network of interdisciplinary faculty and peers across our eleven partner departments.

IQ Biology graduate student, Taisa Kushner, talks about her summer as a Microsoft Research intern in Bangalore, India, working on a global mental health platform.

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Mimicking the heart's microenvironment

Anonymous — Wed, 11 Sep 2019 06:00:00 +0000

Mimicking the heart's microenvironment Anonymous (not verified) Wed, 09/11/2019 - 00:00

Trent Knoss

CU Boulder engineers and faculty from the Consortium for Fibrosis Research & Translation (CFReT) at the CU Anschutz Medical Campus have teamed up to develop biomaterial-based “mimics” of heart tissues to measure patients’ responses to an aortic valve replacement procedure, offering new insight into the ways that cardiac tissue re-shapes itself post-surgery.

Aortic valve stenosis (AVS), a progressive disease characterized by heart valve tissue stiffening and obstructed blood flow from the heart, is known as a “silent killer,” affecting 12.4 percent of the population over 75 years old with a mortality range of 2-5 years if left untreated. Transcatheter aortic valve replacement (TAVR) procedures, which place an artificial valve at the site of the blockage, have been widely and successfully adopted as a remedy in recent decades.

Details of the broader biological reaction to the valve replacement have remained largely unknown, but nevertheless hold significant ramifications for quantifying the quality of recovery, the risk of complications and the assessment of overall patient outcomes.

During AVS disease progression, tissue-specific cells known as fibroblasts transition into myofibroblasts, which promote tissue stiffening. The researchers were interested in understanding how and why, post TAVR, myofibroblasts revert to the more benign fibroblasts.

“Previous studies have shown significant remodeling of cardiac tissues post-intervention,” said Dr. Brian Aguado, lead author of the study and a post-doctoral researcher in CU Boulder’s Department of Chemical and Biological Engineering. “Our hypothesis was that perhaps there are biochemical cues in a patient’s blood that may revert myofibroblasts back to fibroblasts.”

Modeling such a transformation in the lab is one thing, Aguado said, but the key to the new study was obtaining blood samples from real AVS patients and then using biomaterials to replicate the microenvironment of the heart.

“The heart is not made of plastic like a petri dish is,” he said. “We needed to engineer materials that could reflect the various stiffnesses of both healthy and diseased valve and cardiac tissue.”

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Chris Smith (IQ Biology): Evolution Meeting

Anonymous — Wed, 26 Jun 2019 20:47:51 +0000

Chris Smith (IQ Biology): Evolution Meeting Anonymous (not verified) Wed, 06/26/2019 - 14:47

Chris Smith

I just got back from the Evolution Meeting in Providence and I’m full of information and ideas for research. I had the opportunity to reconnect with past colleagues and meet some new people. Other CU Boulder folks attended, including the labs of Dan Doak, Nancy Emery, Nolan Kane, Stacy Smith, and Scott Taylor (sorry if I missed any others).

Although most of the research represented at Evolution is empirical research on understanding and preserving biodiversity, many attendees were excited to discuss methods. In particular, producing large amounts of DNA sequencing data - both empirically, and using computer simulations - is no longer limiting in many cases. Therefore, the challenge of developing theory and methods for analyzing these data has received more attention in recent years.

Highlighting a couple of talks I thought were memorable: Paul Hohenlohe (U. Idaho) described the array of reduced representation sequencing approaches that are available and important trade-offs among them. Adam Jones (also U. Idaho) used simulations to see if and how pleiotropy and epistasis affect scans for loci involved in adaptation; he reported that pleiotropic effects don’t really affect outlier scans and that some important loci are still detected in the presence of genetic interactions. Zach Gompert (Utah State) presented a cool approach for quantifying fluctuating selection.

My presentation was part of the session on Population Genetics Theory, which is too broad of a name for the session because the talks were each focused specifically on inferring historical population sizes and admixture. Multiple speakers used ancient DNA to infer population history and used computer simulations to validate their approach. Other speakers, including myself, were trying to “break” commonly used tools that infer population history, to understand which parameters and data work best, or worst.

On a fun note, we got to see the “WaterFire” event in downtown Providence next to the convention center. This event is a big deal. There were thousands of attendees packed onto bridges and standing in the park along the river. Leading up to, and during the event, large amplifiers played music covering a range of- and alternating dissonantly between- intense classical music, tribal music, country music, and horns. At dusk, they lit small bonfires floating on the river. That’s it.

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Do all networks obey the scale-free law? Maybe not

Anonymous — Mon, 04 Mar 2019 23:22:48 +0000

Do all networks obey the scale-free law? Maybe not Anonymous (not verified) Mon, 03/04/2019 - 16:22

Daniel Strain

As Benjamin Franklin once joked, death and taxes are universal. Scale-free networks may not be, at least according to a new study from CU Boulder.

The research challenges a popular two-decade-old theory that networks of all kinds, from Facebook and Twitter to the interactions of genes in yeast cells, follow a common architecture that mathematicians call “scale-free.”

Such networks fit into a larger category of networks that are dominated by a few hubs with many more connections than the vast majority of nodes—think Twitter where for every Justin Bieber (105 million followers) and Kim Kardashian (60 million followers) out there, you can find thousands of users with just a handful of fans.

Key takeaways

A popular theory claims that all networks are “scale-free”—meaning that the patterns of connections coming into and out of nodes follows a precise mathematical structure called a power law distribution.
CU Boulder researchers set out to test that idea, analyzing more than 900 networks from the realms of biology, technology, transportation and more.
They found that only about 4 percent of networks met the strictest definition for being scale-free—and close to half didn’t fit the bill at all.

In research published this week in the journal Nature Communications, CU Boulder’s Anna Broido and Aaron Clauset set out to test that trendy theory. They used computational tools to analyze a huge dataset of more than 900 networks, with examples from the realms of biology, transportation, technology and more.

Their results suggest that death and taxes may not have much competition, at least in networks. Based on Broido and Clauset’s analysis, close to 50 percent of real networks didn’t meet even the most liberal definition of what makes a network scale-free.

Those findings matter, Broido said, because the shape of a network determines a lot about its properties, including how susceptible it is to targeted attacks or disease outbreaks.

“It’s important to be careful and precise in defining things like what it means to be a scale-free network,” said Broido, a graduate student in the Department of Applied Mathematics.

Clauset, an associate professor in the Department of Computer Science and the BioFrontiers Institute, agrees.

“The idea of scale-free networks has been a unifying but controversial theme in network theory for nearly 20 years,” he said. “Resolving the controversy has been difficult because we lacked good tools and broad data. What we’ve found now is that there is little evidence for classically scale-free networks except in a few specific places. Most networks don’t look scale-free at all.”

Power law

Deciding whether or not a network is “scale-free,” however, can be tricky. Many types of networks look similar from a distance.

But Scale-free networks are special because the patterns of connections coming into and out of nodes follows a precise mathematical form called a power law distribution.

“If human height followed a power law, you might expect one person to be as tall as the Empire State Building, 10,000 people to be as tall as a giraffe, and more than 150 million to be only about 7-inches-tall,” Clauset said.

Beginning in the late 1990s, a handful of researchers made a bold claim that all real-world networks follow a universal structure represented by such giraffe- and inch-sized disparities.

There was just one problem: “The original claims were mostly based on analyzing a handful of networks with very rough tools,” Clauset said. “The idea was provocative, but also, in retrospect, quite speculative.”

To take scale-free networks out of the realm of speculation, he and Broido turned to the Index of Complex Networks (ICON). This archive, which was assembled by Clauset’s research group at CU Boulder, lists data on thousands of networks from every scientific domain. They include the social links between Star Wars characters, interactions among yeast proteins, friendships on Facebook and Twitter, airplane travel and more.

Their findings were stark. By applying a series of statistical tests of increasing severity, the researchers calculated that only about 4 percent of the networks they studied met the strictest criteria for being scale free, meaning the number of connections that each node carried followed a power-law distribution. These special networks included some types of protein networks in cells and certain kinds of technological networks.

A multitude of shapes

But not all researchers use those exact requirements to decide what makes a scale-free network, Broido said. To account for these alternative definitions, she and Clauset adapted their tests to account for each of the variations.

“Wherever you’re coming from, one of our definitions should be close to what you’re thinking,” Broido said.

Despite the added flexibility, most networks still failed to show evidence even for weakly scale-free structure. Roughly half of all biological networks and all social networks, for example, didn’t look like anything close to a scale-free network, no matter how flexible the definitions were made.

Far from being a let-down, Clauset sees these null findings in a positive light: if scale-free isn’t the norm, then scientists are free to explore new and more accurate structures for the networks people encounter every day.

“The diversity of real networks presents a mystery,” he said. “What are the common shapes of the networks? How do different kinds of networks assemble and maintain their structure over time? I’m excited that our findings open up room to explore new ideas.”

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Barn swallows may indeed have evolved alongside barns, humans

Anonymous — Tue, 30 Oct 2018 06:00:00 +0000

Barn swallows may indeed have evolved alongside barns, humans Anonymous (not verified) Tue, 10/30/2018 - 00:00

Cay Leytham-Powell

As humans evolved and expanded, so too did barn swallows, new research from CU Boulder suggests

The evolution of barn swallows, a bird ubiquitous to bridges and sheds around the world, might be even more closely tied to humans than previously thought, according to new study from the University of Colorado Boulder.

Chris Smith (left) and Rebecca Safran (right) re-examined the evolution of barn swallows and found that they may indeed have evolved alongside barns. Photographs courtesy of Rebecca Safran and Patrick Campbell/University of Colorado Boulder.

The research, published this week in Molecular Ecology, offers preliminary insight suggesting that the barn swallow and its subspecies evolved alongside—but independently from—humans. These new results make it one of the only known species, in addition to microscopic organisms like bacteria or viruses, to have developed in such a way, upending previous assumptions that barn swallows evolved prior to human settlement.

“Humans could be a really big part of the story,” said Rebecca Safran, a co-author of the study and an ecology and evolutionary biology (EBIO) associate professor at CU Boulder. “There’s very few studies that can point to the exact influence of humans, and so here, this coincidence of human expansion and permanent settlement and the expansion of a group that relies really, really heavily on humans is compelling.”

Barn swallows are found across the northern hemisphere and are characterized by their mud-cup nests that are built nearly exclusively on human-made structures. Despite their prevalence, however, not much is known about their evolutionary history, the timing of their expansion from northern Africa (where they originated) or how the six subspecies evolved so physically and behaviorally different yet remain almost genetically identical.

Previous studies published in the Proceedings of the Royal Society of London and Molecular Phylogenetics and Evolution looked into these questions and found that the different subspecies split early, well before human settlement.

This new study, however, gave the topic a fresh look by examining the whole genome of 168 barn swallows from the two sub-species farthest apart on an evolutionary scale: H. r. savignii in Egypt (a non-migratory species that lives along the Nile) and H. r. erythrogaster in North America (a species found throughout North America that migrates seasonally to South America).

Barn swallow subspecies are found throughout the northern hemisphere. Barn Swallow illustrations courtesy of Hilary Burn, and map courtesy of the Safran lab.

These data—which are on the order of 100,000 times bigger than the previous dataset used—were then analyzed with more sophisticated computational resources and methods than previously available. This allowed researchers to get a more complete picture that places the timing of barn swallow differentiation or speciation (i.e., when the barn swallow subspecies separated) closer to that of when humans began to build structures and settlements.

“The previous studies were playing with the idea of potential impact on population sizes due to humans,” said Chris Smith, a graduate student in EBIO and the Interdisciplinary Quantitative Biology program, and the study’s lead author. “Our results suggest a much more substantial link with humans.”

These new preliminary findings also suggest that this evolutionary link may have been forged through a “founder event,” which is when a small number of individuals in a species take over a new environment and are able to expand their new population there thanks to an availability of resources and an absence of competitors. For barn swallows, this event may have occurred rapidly when they moved into a new, relatively empty environment: alongside humans.

“Everyone is always wondering how do you study speciation? It’s been viewed as this long-term, million-year (process), but in barn swallows, we are not talking about differentiation within several thousands of years,” said Safran. “Things are really unfolding rather rapidly.”

Smith concurred: “It’s interesting to study speciation in the beginning steps.”

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World Congress of Biomechanics – Dublin, Ireland

Anonymous — Wed, 24 Oct 2018 16:53:57 +0000

World Congress of Biomechanics – Dublin, Ireland Anonymous (not verified) Wed, 10/24/2018 - 10:53

Kristin Calahan

This summer, I had the opportunity to present my research at the 2018 World Congress of Biomechanics in Dublin, Ireland. As the premier meeting worldwide in the field of biomechanics, this was an incredible opportunity to network with scientists in this field, both within my subfield of biomechanics and far outside of it. I especially enjoyed this aspect of the conference because as an IQ Biology student I am intrigued by interdisciplinarity and the intersection of biology and mechanics at different length scales.

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Curiosity killed the cat, but it may help you get the Nobel prize

Anonymous — Fri, 17 Mar 2017 06:00:00 +0000

Curiosity killed the cat, but it may help you get the Nobel prize Anonymous (not verified) Fri, 03/17/2017 - 00:00

BioFrontiers Institute

I don't feel frightened by not knowing things, by being lost in a mysterious universe without having any purpose - which is the way it really is so far as I can tell - it does not frighten me.

–Richard Feynman, The Pleasure of Finding Things Out

Doctoral students have a lot of time on their hands. It may appear otherwise, but the unstructured nature of a graduate student’s life lends itself to exploring seemingly endless plains of fascinating information. I am a Materials Science and Engineering Ph.D. student working on developing molecular tools like CRISPR (Clustered Regularly-Interspaced Short Palindromic Repeats used for editing DNA) to make microorganisms that can convert sugar into plastics. And somehow, on a snowy day in early January, I found myself going down a rabbit hole of attention-grabbing references that led from CRISPR to molybdenum.

Here are just a few fascinating facts I learned from this search: Did you know that molybdenum, occupying position 42 in the periodic table, has the sixth-highest melting point of any element? And that one of the world’s largest molybdenum mines – the Henderson Mine – is located near Leadville, Colorado, and adjoins a 10-mile railroad tunnel that goes under the Continental Divide? Or that molybdenum is an essential cofactor for nitrogen fixation in plants and arsenic detoxification in the liver? That there are species of archaea – some of the most ancient organisms on our planet – that can survive at pH < 0 (think battery acid) and reproduce at 250° F? And that some archaea have flat square-shaped cells? Oh, and that thing that initially began my search? There are now over 16 different subtypes of CRISPR systems.

So, how did I get from CRISPR to molybdenum mining? Mere curiosity. It may appear like a form of procrastination, but I prefer to think of it as an “idea treasure hunt.” In the process of mental exploration, one thought leads to another through association. Sometimes they flow in a linear pattern, other times they branch, splay and explode into thousands of new connections, forming intricate webs of facts and concepts in our brains. Occasionally an idea might wormhole its way to a distant node in the network, generating a surprising product – or even a revolutionary discovery. The mind theorists call this process the “promiscuous combination of ideas,” and it has led many scientists to come up with new theories and unexpected solutions.

Richard Feynman had the spark for his Nobel Prize-winning idea when he saw a student throw a plate across the cafeteria. Initially, he set out to solve a classical mechanics problem, but ended up in the quantum physics realm: the calculations of the wobbling speed and rotation of the plate transformed into a theory of how electron orbits move in relativity. Of course, that flying dish alone did not inspire the Nobel Prize theory. It involved connecting the dots from a giant constellation of concepts and theories in his mind. In the words of Feynman, “then there's the Dirac equation in electrodynamics. And then quantum electrodynamics. And before I knew it…the whole business that I got the Nobel Prize for came from that piddling around with the wobbling plate.”

One could argue that it was his deep understanding of physical principles and intense concentration that led Feynman to formulate the theory. I bet at least part of it was that Feynman was a man with insatiable curiosity; he was curious about how dreams work, how smart ants are, Japanese culture, or whether jelly can set at a low temperature if continuously stirred. When something grabbed his attention – like the wobbling plate – he chased after it, regardless of whether it was an elusive physics problem or something trivial he simply wanted to know more about. On his curiosity-fueled hunt for interesting things, he acquired a wealth of information and the ability to effectively process it, which enables one to draw surprising connections between distant ideas.

The information age has created a kind of “meta-mind” where people can easily share their ideas and together contribute to solving advanced problems. Most of the scientific discoveries today come not from individual researchers, but from the combined efforts of many people working in a field. For example, initial observations of the effects of CRISPR occurred in the dairy industry, where deliberate exposure to bacterial viruses (phages) was used to protect bacterial cultures against future phage infections¹. A computer search for similar sequences found fragments of phage DNA in the curious spacer-repeat CRISPR patterns, so it was proposed to be the bacterial “immune system”. Later, other researchers realized that CRISPRs could be expressed in different organisms and harnessed to target specified DNA sequences. Thus, CRISPR editing technology emerged from the combined efforts of many different labs and is now being proposed for applications like modifying human embryos – a prospect almost as far removed from its original use for making yogurt as it is from molybdenum mining.

I doubt that any scientist could have single-handedly figured out the application of CRISPR technology for gene editing purposes. Advancements like that take the combinatorial powers of the collective scientific mind. However, smaller discoveries are happening in labs every day, and they also require connecting the dots between quite distant concepts. So, next time you catch yourself procrastinating by reading seemingly unrelated articles on the internet, or by watching ants going about their business, or throwing a Frisbee (while trying to calculate its rotation speed in the air) – don’t be so hard on yourself. After all, you may just stumble upon your Nobel Prize idea.

¹If you are curious, this source provides a great timeline of CRISPR discovery and development.

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IQ Biology Blog: SIAM Life Sciences Conference in Boston

Anonymous — Thu, 13 Oct 2016 06:00:00 +0000

IQ Biology Blog: SIAM Life Sciences Conference in Boston Anonymous (not verified) Thu, 10/13/2016 - 00:00

BioFrontiers

By Jacqueline Wentz

This July I attended the Society for Industrial and Applied Mathematics (SIAM) Conference on the Life Sciences in Boston. It was four days long, packed with talks, poster sessions, and unnecessary amounts of coffee. At the conference, I presented a poster on my latest research examining a molecular mechanism that is associated with aging in C. elegans. There were eight other graduate students from CU Boulder who gave presentations on topics, such as, biofilm dynamics, bacterial flocculation, wound healing, and disease outbreaks.

The SIAM Life Sciences conference is geared towards applied mathematicians who are interested in using their mathematical expertise to help answer biological questions, ranging from questions on intracellular dynamics to epidemiology. Thus, the conference is inherently interdisciplinary. At many of the talks I was pleasantly surprised when I realized that the courses I took during my first year of IQ Biology helped me understand the biological problems discussed. For example, several of the talks dealt with microtubule dynamics, a topic that was extensively covered in the biophysics course I took in the spring. Other talks of note included a discussion of how mathematical modeling helped in the development of an artificial heart valve and an exploration into how the extracellular matrix affects sperm dynamics. I even got to see the notable Donald Knuth discuss the topic of satisfiability (i.e., given a formula, is there a model that makes that formula true). Besides making significant contributions to theoretical computer science, Donald Knuth is the developer of TeX, a computer typesetting language used extensively by mathematicians (myself included).

There were also many presentations that directly related to my research. For example, several talks discussed Turing instabilities. This is a type of instability that can explain how patterns arise from random distributions through a reaction/diffusion process. I am currently studying a system in which, I hypothesize, this type of instability leads to spatial expression patterns of a small heat shock protein in C. elegans. I actually met a PhD student who was examining Turing instabilities in C. elegans, but instead of mechanisms related to aging, she was modeling the development of neuronal synapses.

Overall the conference was a great experience. I was introduced to a group of interdisciplinary scientists who, like me, are interested in biological processes and want to use mathematics to enhance our understanding of these processes. I even had the opportunity to meet my academic “grandfather”, Dr. H. T. Banks. Dr. Banks greeted me at my poster session and explained to me that since he had advised my advisor, Dr. David Bortz, he was my academic grandfather and would treat me as such. Some additional bonuses included exploring the nearby Aquarium, visiting my alma mater, and getting to tour around Boston.

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IQ Biology Blog: My experience with Evolution

Anonymous — Tue, 30 Aug 2016 06:00:00 +0000

IQ Biology Blog: My experience with Evolution Anonymous (not verified) Tue, 08/30/2016 - 00:00

BioFrontiers

by April Goebl

Attending Evolution, the premier international conference for evolutionary biology, had a big influence on my recently spawned, yet still vague, choice to pursue a career in evolutionary biology. Held in Austin, Texas this year and the largest conference in its field, Evolution is a joint event for three major societies: the American Society of Naturalists, the Society for the Study of Evolution, and the Society of Systematic Biologists.

By observing well-seasoned Evolution attendees, I noted their strategy for making the most of the busy conference: Attend talks on emerging methods, and spend time re-connecting with old lab mates and collaborators. For those transitioning from undergraduate, this conference was an optimal space to explore the breadth of current evolutionary biology research and to casually meet and chat with potential graduate advisors.

For me (someone recently starting on their PhD journey with broad interests in ecology, evolution and environmental biology) attending this conference felt like a well-timed bonus. I was able to attend talks and posters ranging from genomics, population genetics theory and ecological genetics to speciation and adaptation, biogeography, and conservation biology.

While this breadth of selection was nothing short of overwhelming for someone that struggles with indecision, the payoff of defining where my interests lie was well worth it. The challenge of navigating which talks to attend and how to traverse the conference center in time to make my next session of interest, was balanced by the reward of gaining insight into how to appropriately ask questions in this field and how to try to answer them.

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