Notes on Engineering Health, May 2023: Notes from Jacob Oppenheim & Travis Hughes

Jacob Oppenheim, PhD
Travis Hughes, MD, PhD

Jacob Oppenheim, PhD & Travis Hughes, MD, PhD

May 20, 2023

Jacob N. Oppenheim, PhD
I’m excited to announce I’m joining Digitalis Ventures as an Entrepreneur-in-Residence.

The arc of my career has been driven by a fundamental belief that we can identify emergent simplicity from the complexity of biology, provided enough data and algorithms that model the underlying science. At each step along the way, however, it has become clear that we lack the tools, systems, and processes to consistently collect, manage, organize, and learn from these data.

Our ability to manipulate biology is qualitatively different than two decades ago. We are seeing further with radically improved instrumentation in dozens of types of sequencing and imaging. For any target of interest, it is no longer a question of “can we” but rather “how” and “which way.” Biology is rapidly becoming an engineering discipline.

And yet, our digital tools are failing.

We have barely profited from cheap cloud storage and computation, let alone Machine Learning. Digital technology is built on a firm by firm basis in disconnected pieces, lacking focus, generality and the ability to scale. Third party tools suffer from bloat, scope creep, and all too often are designed with contempt for the end user in mind.

It does not feel like we are learning much from data either. Successes are isolated and come about where decades of data have been curated by professional communities. Computational and data scientists spend their time rebuilding elementary software and pipelines, distant from the underlying biology and a company’s core thesis and IP.

Underlying scientific processes are too often those of a scaled-up academic lab, because we lack the technology and systems that will let us be engineers — and to profit from acting like them.

We need modularity. We need product scientists love. We need scale. We need to engineer biology.

We’re not going to get there if we spend our time only with technologists. We need to work directly with scientists across a wide span of modalities, targets, and scientific hypotheses. We need to spend time in the complexities of the problem and identify commonalities. The biopharmaceutical industry has brought us a century of miracles — even those processes that are broken have delivered for decades and we cannot pretend ignorance thereof will deliver meaningful technology.

We are only going to get to product market fit if we begin in the weeds and abstract from there.

At Digitalis, I’m joining a wide-ranging, early stage fund, focused on engineering biology and health more generally. A fund with a deep scientific focus and involvement in portfolio companies. In short, the right place to begin to build the digital technologies, data tools, and yes the machine learning, that will power the future of our ability to engineer biology.

Curious? Want to help? Working on something similar?

Feel free to reach out and connect.

The future is modular — we will need a diversity of people, technologies, and solutions to get there.

Travis Hughes, MD, PhD
I'm thrilled to announce that I'm joining Digitalis Ventures as an Analyst on the Life sciences investment team. I am excited to invest in the next generation of transformative technologies and companies working to develop novel therapies to improve the lives of patients and their families.

In this role, I will be able to explore the latest research across the academic and biopharma ecosystem - vetting, developing, and refining ideas with multiple avenues for execution: Venture investment (DV Investments), company creation (DV Proving Grounds), impact investing (Digitalis Commons), and publication (Digitalis Press). Many thanks to Geoff, Misti, Sam, and Jonathan for the unique opportunity to join the Digitalis team.

I am deeply grateful to my family and the countless friends, colleagues and mentors from Oklahoma to Harvard, MIT, nference, Duke and beyond who have supported my journey through science, medicine, biotech and now VC. I am looking forward to reconnecting with old friends and meeting new people working to expand the boundaries of the possible in science and medicine.

First Five
First Five is our curated list of articles, studies, and publications for the month. For our full list of interesting media in health, science, and technology, updated regularly, follow us on Twitter or Instagram.

1/ Golden (genetically programmed) Retriever
A large study published in Cell pinpointed many of the genes associated with the behaviors of specific dog breeds. The analysis of over 4000 DNA samples from over 200 dog breeds and nearly 50,000 pet-owner surveys shed some new light on the mechanisms underlying breed-specific behaviors and the key role of non-coding regulatory regions. Searching why sheepdogs are so excitable may help us reveal the genetic origins of behavioral diversity.

2/ Food deserts and swamps are hurting Americans

Researchers publishing in JAMA Oncology looked at 3038 counties in the US and showed that those with the highest food swamp score had a 77% increased odds of high obesity-related cancer mortality. This matters a great deal as obesity-related cancers account for 40% of all cancers in the US. Healthy food consumption is known to reduce obesity-related cancer mortality, and residing in areas with less access to grocery stores (food deserts) or higher access to fast food (food swamps) causes excess death.

3/ Harder than adamantium?
A new study in Science reveals the profound properties of a simple metal alloy. While investigating a metallic alloy made of chromium, cobalt, and nickel, researchers stumbled upon what looks like the strongest material ever recorded. The new metal is strong, ductile and opens a myriad of potential applications (though, at this point, none of them include bionic skeleton replacement).

4/ The perfume to extend life?
A recent study published in eLife demonstrated the role of exposure to female odors and pheromones. The lifespan of female mice was increased significantly by odors from adult females administered transiently. Female lifespan was not modified by male odors, nor was male lifespan susceptible to odors from adults of either sex. Another prime example of the difference in biology between males and females. The translation to human biology is still unclear, but it taps into a fantasy about the female scent.

5/ With a little help from my students
For three years at the height of the COVID-19 pandemic, a group of nearly 1,000 students spent an estimated 56,000 hours analyzing the behavior of hundreds of solar flares. The combined work and analysis were published in The Astrophysical Journal and could help astrophysicists understand how the sun's corona reaches temperatures of millions of degrees Fahrenheit.

Digitalis Commons
Public-Interest Technologies for Better Health

Digitalis Commons
is a non-profit that partners with groups and individuals striving to address complex health problems by building public-interest technology solutions that are frontier-advancing, open-access, and scalable.

In reaction to the frightening rise in misinformation during the COVID pandemic, multiple efforts aimed at establishing and presenting degrees of scientific consensus emerged. Tackling the problem with different methodologies, The Institute for Ascertaining Scientific Consensus (IASC), the Clarity Foundation, and comCensus poll experts and present the findings in a compelling and understandable way in the hope of improving public debate and policymaking.

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