Digitalis Press

The Digitalis Press writes and publishes on life sciences, health technologies & services, and animal health.

We believe that accurately identifying and articulating the most critical unmet needs in health is the first and most fundamental step in deriving solutions that positively impact health at scale. A meaningful understanding of such needs requires a broad view, one that embraces how questions of science and technology are tied inextricably to economic, policy, and social circumstances and histories.

Engineering Biology: Announcing Fresnel

Jacob Oppenheim, PhD

Jacob Oppenheim, PhD

April 9, 2024

The hardest problem in biopharma today is picking the right targets. Our ability to modify biology has increased exponentially over the past decades. No longer is it a question of if we can hit a target (or a pathway) with some compound. Today, we can hit nearly any biological target with multiple different modalities from traditional small molecules to antibodies to interfering RNAs to cell and gene therapies and beyond. The key questions today are what should we hit and how.

Engineering Biology

Notes on Engineering Health, March 2024: Notes on Providers

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

March 28, 2024

As medicine has grown more complex and costly, the way to organize its delivery has had to adapt. How has the work of delivering care evolved, how has it been integrated with the health insurance system, and what trends have emerged that point to ways in which hospitals may continue to evolve?

Notes on Engineering Health

Over at the new OpenProtein.ai blog, Tristan Bepler and I wrote about the seemingly mysterious power of Deep Protein Language Models. Not only do they identify related proteins, they predict functionality, stability, and immunogenicity, in many cases “out-of-the-box.” Why should this be?

Engineering Biology

Engineering Biology: Podcast—Data in Biotech

Jacob Oppenheim, PhD

Jacob Oppenheim, PhD

March 14, 2024

Ross Katz from CorrDyn generously hosted me on the Data in Biotech podcast last week.

Engineering Biology

Notes on Engineering Health, February 2024: Notes on Academic Publishing

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

February 29, 2024

Scientific publications have been the lingua franca of scientific discovery and knowledge, the edifice on which trust is built. To understand how academic publishing got to the structure we know today and think of ways to improve it, it is helpful to understand the story of scholarly publishing, the technological advances that occurred along the way, and the forces and incentives that shape current behaviors and challenges.

Notes on Engineering Health

Notes on Animal Health, February 2024: A Matter of Heart

Cindy Cole, DVM, PhD, DACVCP

Cindy Cole, DVM, PhD, DACVCP

February 9, 2024

The difference in the prevalence of coronary artery disease (CAD) between dogs and humans is particularly striking when one considers that the dog has been proposed to be a model for human aging and mortality.

Notes on Animal Health

Notes on Engineering Health, January 2024: Notes on Pharmacy Benefit Managers

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

January 30, 2024

For this third installment of our series about the American healthcare system, we cover the pharmacy benefit managers (or PBMs), an idiosyncratic and opaque player unique to the American system.

Notes on Engineering Health

Stranded airplanes, packages arriving months late, organizations caught in endless spin unable to make decisions. Stories like these expose broken systems and paradigms that have failed to scale and reveal a quiet truth: the world is not as digitized as it seems.

Engineering Biology

Notes on Engineering Health, December 2023: ICYMI 2023 Edition

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

December 27, 2023

As is now a tradition, our last missive of the year is an opportunity for us to reflect on the topics we covered earlier in the year in our Notes on Engineering Health and see if any updates are in order.

Notes on Engineering Health

Notes on Animal Health, December 2023: Pets vs. Pests

Cindy Cole, DVM, PhD, DACVCP

Cindy Cole, DVM, PhD, DACVCP

December 19, 2023

For many of us, our pets truly are part of our family. They share our homes, our beds, go to work and on vacation with us. They entertain us and protect us. They will be by our sides and on our laps as we celebrate this holiday season with family and friends. We keep our pets close with little concern that they might share fleas, ticks, and intestinal parasites with us. That, however, has not always been the case.

Notes on Animal Health

Notes on Engineering Health, November 2023: Notes on How We Drug The Brain

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

November 30, 2023

The late neurologist Oliver Sacks had his fair share of experience with experiments on chemical compounds altering brain functions. He wrote beautifully in books and articles about how he experimented on himself both to relieve pain and to explore unvisited corners of his self. He was a keen observer of how mental diseases work and what is available to treat them. How did we get to produce such neuro-active compounds? Are the nervous system and the brain like any other organs? Where is neuropharmacology going?

Notes on Engineering Health

Notes on Engineering Health, October 2023: Notes on Payers

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

October 31, 2023

The leaves are falling in the northeast, which can only mean one thing—it's open enrollment season. Time to wade through excruciating details in order to choose the level of health coverage that you deem necessary, covering every possible (high) price point. Why do people in the United States do it this way?

Notes on Engineering Health

Engineering Biology: Big Data—A Path Forward

Jacob Oppenheim, PhD

Jacob Oppenheim, PhD

October 27, 2023

The combination of years of “Big Data” hype and obviously flawed inferences, of overpromising and under-delivering, has led to pervasive online tracking and a miasma of distrust. It is simultaneously too difficult to deploy novel consumer-facing information technology and avoid the sale or at least use of personal information.

Engineering Biology

Notes on Animal Health, October 2023: One Health

Cindy Cole, DVM, PhD, DACVCP

Cindy Cole, DVM, PhD, DACVCP

October 20, 2023

It is particularly easy these days to find ourselves focusing on our differences as humans—different political beliefs, cultures, religions, and diets, to name just a few. However, one thing almost all of us share across the globe is interaction with animals.

Notes on Animal Health

Engineering Biology: Big Data—A False Panacea

Jacob Oppenheim, PhD

Jacob Oppenheim, PhD

October 6, 2023

The story goes that an angry father confronted Target employees after his daughter was mailed coupons for maternity products unnecessarily, only to find out later that she was pregnant. A triumph of big data combined with statistical learning, and a creepy portent of the future, right? That’s how the story went at least.

Engineering Biology

Notes on Engineering Health, September 2023: Notes on Frailty

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

September 29, 2023

In the US, the number of people alive aged 65 or older increased from 4.9 million (4.7% of the total U.S. population) in 1920 to 55.8 million (16.8%) in 2020. While this demographic shift is a testament to progress in healthcare, and a decrease in fertility rate, it also presents unique challenges, including the increasing prevalence of frailty among older adults…

Notes on Engineering Health

Engineering Biology: Software is Management Technology

Jacob Oppenheim, PhD

Jacob Oppenheim, PhD

September 22, 2023

My focus in writing over the past three months has been the interplay between powerful new computational methods, digital technologies, and operational processes. It began with the observation that successful Machine Learning (ML) integrated biopharma companies have a moat in data generation and the scientific application of computation to these data—not in machine learning itself. Operational excellence is requisite for these companies, not merely a nice-to-have.

Engineering Biology

Notes on Engineering Health, August 2023: Notes on Seeing Biology

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

August 31, 2023

From the organism to the organ, the cell to the organelle, the molecule to the atom, biologists have descended into the living matter not only describing it but seeing and photographing it. Whether to convince by their explanatory power or compel by their beauty, images of biological phenomena have transformed how we approach the field.

Notes on Engineering Health

The Age of Engineering Biology

Jacob Oppenheim, PhD

Jacob Oppenheim, PhD

August 15, 2023

I was on a panel about digitization and the data revolution at the annual Academy of Management meeting last weekend. My co-panelist and I were there to give an operational perspective on how data are used in biopharma for everything from R+D to commercialization and how it compared to the empirical studies from a variety of industries presented earlier in the session.

Engineering Biology

Notes on Engineering Health, July 2023: Notes on Heat and Humidity

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

July 31, 2023

While we have written about other aspects of climate change in these notes before, we have not yet addressed the core aspect of climate change: the heat itself. What are the consequences of too much heat on humans, animals, and societies? In other words, how hot is too hot?

Notes on Engineering Health

Engineering Biology: ML as Process Efficiency

Jacob Oppenheim, PhD

Jacob Oppenheim, PhD

July 31, 2023

The integration of Machine Learning (ML) into scientific work exists on a continuum between whole-scale replacement of human processes and providing inputs to complement the judgment of a human arbiter. As I’ve argued previously, current models are insufficient at best for fully substituting human knowledge in biology for all but base-level tasks…

Engineering Biology

We have heard stories about how computation and Machine Learning (ML) are poised to change medicine for well over a decade now. Conferences, press reports, promising results – yet little has changed…

Engineering Biology

Notes on Engineering Health, June 2023: Notes on Women’s Health

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

June 28, 2023

“On the Diseases and Cures of Women” is considered the oldest surviving medical text by a woman. Written by Metrodora (meaning gift of the uterus), a physician and medical writer, the document dates from the 5th century AD and is kept in the Laurentian Library…

Notes on Engineering Health

The past weeks have seen a flurry of articles debating the efficacy (and proof thereof) of “AI” in drug discovery and biotech writ large, kicked off by a large layoff at Benevolent, an “AI” drug developer. I would argue the lesson of the recent AI boom in biopharma is a simple one: If you don't have novel and effective science in the first place, no amount of data science will save you: Data Science and Machine Learning* (hereafter ds/ml) will be most successful in biology where they sit atop transformative science that needs no special analytics.

Engineering Biology

Back in 2017, when I was just starting to build out data science at Indigo, Tristan Bepler joined us as a summer intern. We had a large and growing amount of sequencing data from microbial communities both their composition from marker genes and whole genomes of organisms of interest. Both of these datasets resisted conventional methods. The mathematical modeling of microbial communities remains underdeveloped with heuristic methods that produce nonsense and potentially more correct ones that are difficult to implement.

Engineering Biology

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

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…

Notes on Engineering Health

Notes on Engineering Health, April 2023: Notes on Xenotransplantation

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

April 28, 2023

“Xenotransplantation is the future, and always will be”. The apocryphal quote by the late Stanford surgeon and heart transplantation pioneer Norman Shumway highlights the hopes and difficulties of this endeavor. Xenotransplantation, or transplanting an organ from one species to another, concentrates many biological challenges and some thorny ethical considerations.

Notes on Engineering Health

The hope with Machine Learning has long been that we can eliminate complex, slow, and expensive physical processes with accurate predictions, inferred directly from data. As I’ve written previously, the complexity and scarcity of data make supervised learning like this less relevant in problems of biology. Unlike internet companies, generating reams of labeled data daily, our experimental throughput is orders of magnitude lower and our data modalities considerably more complex.

Engineering Biology

Where does Machine Learning belong in biology? Nearly all successful efforts fall into one of three categories: Exploration—Summarizing large complex datasets that cannot be fathomed by the human mind: gene sequences, chemical structures, images, etc and enabling scientists to explore them. Scaling—Automating, standardizing, and debiasing heuristics and calculations. Prediction—Estimation of how a complex process will perform on a new element.

Engineering Biology

Notes on Engineering Health, March 2023: Notes on Employer-Sponsored Health Insurance

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

March 31, 2023

Decisions in times of crisis can have long-lasting effects on an entire system, and be hard to change when incentives created by short-term decisions then become deeply entrenched. One perfect example of this phenomena is the health insurance system in the United States. Why does your employer pay for your health insurance? Is this a good thing?

Notes on Engineering Health

How do we build models under resource constraints? We almost never have enough data to adjust for every possible confounding factor, nor do we know what all those factors are.

Engineering Biology

We don’t know what the hard problems are going to be. Most of us were trained as academic scientists in a culture of finding winding paths through the dark forest of the unknown. Today, we are much closer to engineers — using data and computation to industrialize the production of knowledge. Biology presents an endless series of learning and inference problems for us to solve.

Engineering Biology

Notes on Engineering Health, February 2023: Some Notes on Fermentation

Steve Allen
Jonathan Friedlander, PhD
Geoffrey W. Smith

Steve Allen, Jonathan Friedlander, PhD & Geoffrey W. Smith

February 28, 2023

“The role of the infinitely small in nature is infinitely large.” Louis Pasteur. Fermentation is the first example of biotechnology in human history. While spontaneous fermentation predates the human species, the earliest human efforts at fermentation date from the Neolithic period (7,000 to 1,700 BCE)…

Notes on Engineering Health

Engineering Biology: Whither Data Science?

Jacob Oppenheim, PhD

Jacob Oppenheim, PhD

February 27, 2023

How does data science fit into the biopharma tech stack? The analytical operations involved are certainly more complex than the transformation and aggregation of data. This might suggest that data science is an artisanal, intellectual operation built off of the core data repository; in essence, an extension of laboratory science to computation. While tempting, this pattern only leads to confusion, frustration, and a misuse of human and silicon capital. Just as we are industrializing biological discovery and drug development, so must we with data science.

Engineering Biology

Engineering Biology: Systems, Tools, and Technology

Jacob Oppenheim, PhD

Jacob Oppenheim, PhD

February 7, 2023

Technology in a biopharma company tends to grow by accretion rather than design. Tools and systems are brought in house as functions are brought on line. LIMS comes with the establishment of a lab, a compound registry with the first experiments with small molecules, a chem informatics tool when it’s time to start digging into SAR. Growth reflects staffing and capabilities — much as you don’t hire a medicinal chemist until it’s time to design small molecules, you don’t bring in the systems they would use until the function is present

Engineering Biology

Notes on Engineering Health, January 2023: This Text Was NOT Written by AI

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

January 30, 2023

The subject du jour is undeniably the emergence and rapid progress of generative AI models such as ChatGPT. While a lot has already been written on the topic, both by humans and robots, the increasing role of AI…

Notes on Engineering Health

Capturing and recording all relevant data is only half the battle. We then need to make it useful. In practice, we will have a deluge of information, much of which will be hard to parse without the relevant context: high throughput instrumental recordings, metadata tables, and the tracing of samples throughout laboratory workflows.

Engineering Biology

What do we need to generate data at scale? Practically, we need tools to allow us to run experiments: laboratory informatics, automation, and data capture. More is needed in order to always be performing the key experiment. We need to be able to design new experiments based on results as they come in, not laying out ten thousand in advance and waiting a month. These are fundamentally data problems, yet we do not have systems designed to enable their solution.

Engineering Biology

Engineering Biology: Case Study I—Genomics

Jacob Oppenheim, PhD

Jacob Oppenheim, PhD

January 10, 2023

In mid 2017, my data science team was tasked with building out a new genome assembly and annotation pipeline that could cover the vast expanse of fungal and bacterial diversity to support our development of novel microbial products. Our company was engaged in bioprospecting of microbes from sites across the US. Back in the lab, we were isolating, identifying, and then assaying a previously unmeasured wealth of biological diversity.

Engineering Biology

So where do we begin? With a hypothesis and a key set of experiments. From there, we must process the data, analyze them, and make decisions. If we are lucky enough to have seized on a real insight, there will be the immediate paired questions of replication and scale. How do we confirm these results and generalize beyond? To properly modify a system, as in drug development, we will need to move from science to engineering, and work with a myriad of slightly different experiments to arrive at the one we can use to, say, improve human health.

Engineering Biology

Engineering Biology: Data and Bio—Are We Learning?

Jacob Oppenheim, PhD

Jacob Oppenheim, PhD

January 2, 2023

There’s been an exceptional amount of talk about and investment in learning from data in biology, especially with the advent of effective ML systems. The ability to quantitatively model and learn from data at scale is real: look at the continued progress in protein structure prediction in CASP. Every biopharma company now has a data science org with diverse operational models from centralized to distributed, and there is continual talk of innovation and AI.

Engineering Biology

Notes on Engineering Health, December 2022: ICYMI 2022 Edition

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

December 30, 2022

As is now a tradition, our last missive of the year is for us an opportunity to reflect on the topics we covered in our Notes on Engineering Health during 2022 and see if any updates are in order.

Notes on Engineering Health

We do not count often enough the blessings public health has brought to the world in general and the US in particular. Public health’s greatest successes in the 21st century include things like…

Notes on Engineering Health

We’d be remiss not to feature in this month’s newsletter a recent positive development at the firm. Specifically, last week we announced the closing of our fourth fund, totaling $300 million in commitments…

Notes on Engineering Health

Notes on Engineering Health, September 2022: Nature, Nurture, & Good Luck

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

September 29, 2022

The role of scientists, and biologists in particular, has been to describe possible futures, predict the likeliest path to get there (through deterministic models, for example), confront the reality of where those paths actually lead, then revise their hypotheses and carry on…

Notes on Engineering Health

Notes on Engineering Health, August 2022: Risky Business

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

August 31, 2022

Since the onset of the Covid-19 pandemic in March 2020, the march of crises across the front pages of the world’s newspapers has been relentless. Myanmar. Afghanistan. Ukraine. Omicron. Monkeypox. Drought. Recession. We have reached the point where crisis seems to be an endemic state of affairs. Is this the result of an increase in communication via digital tools, or are the risks we are facing today of a different nature than before?

Notes on Engineering Health

Notes on Engineering Health, July 2022: On Creativity

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

July 31, 2022

In order to capture the awe-inspiring photographs recently taken by the James Webb Space Telescope, NASA scientists and engineers spent 30 years and $10 billion figuring out how to tightly pack dozens of mechanical limbs and instruments into a package that could be safely delivered to the second Lagrange Point, almost one million miles from the Earth in the exact opposite direction from the sun, and then carefully unfolded and deployed…

Notes on Engineering Health

Notes on Engineering Health, June 2022: Abortion is Healthcare

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

June 30, 2022

At its core, abortion is a healthcare procedure. While its ethical dimension is undeniable, it is worth spending some time on the data collected and the experiments conducted to understand how abortion has evolved in the US since 1973.

Notes on Engineering Health

Notes on Engineering Health, May 2022: Life, the Universe, and Everything

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

May 31, 2022

Ideas of the symbiosis between biological life and information provide a provocative new way to explore more deeply not just the intersection of life sciences and data sciences, but also our understanding of social, economic, and cultural determinants of health. These are themes we expect to continue to explore in our work for years to come.

Notes on Engineering Health

Notes on Engineering Health, April 2022: The Time of Your Life

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

April 30, 2022

Aging can be defined by sequential or progressive changes in an organism that lead to an increased risk of debility, disease, and death. It is actually the major risk factor for most pathological conditions that limit health span and promote chronic disorders including immuno-senescence, cardio-metabolic disorders, osteoporosis, sarcopenia, arthritis, cataracts, neurodegenerative diseases, and most cancers…

Notes on Engineering Health

Notes on Engineering Health, March 2022: Lampposts and Genomics

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

March 31, 2022

Although Watson and Crick famously solved the structure of DNA in 1953 from groundbreaking crystallography work by Rosalind Franklin and Maurice Wilkins, the ability to “read” or sequence DNA was not scalable until the invention of the Sanger sequencing method in 1977. Sanger’s innovation and the ones that followed slowly paved the way to today’s large-scale genome sequencing, with the current state of technology at each step largely determining the problems the scientific community was then able to focus on.

Notes on Engineering Health

Notes on Engineering Health, February 2022: Some Random Thoughts

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

February 28, 2022

The idea of a fully deterministic world held sway in the West until very recently. While tools to describe the unknown were developed in the 16th century when Italian mathematicians began to formalize the odds associated with various games of chance, it was not until the early part of the 20th century that the formal analysis of randomness and the mathematical foundations for probability were introduced, leading to their axiomatization in 1933…

Notes on Engineering Health

Notes on Engineering Health, January 2022: On Human Breastmilk & Personalized Nutrition

Steve Allen
Jonathan Friedlander, PhD
Geoffrey W. Smith

Steve Allen, Jonathan Friedlander, PhD & Geoffrey W. Smith

January 31, 2022

Human breastmilk is a living, dynamic fluid that supports the optimal nutrition of infants. It has an incredibly wide range of nutrients, immune factors, hormones, and metabolites. While many of these components are stable during lactation, some vary significantly in response to maternal diet, infant health, time of day, or whether the meal is starting or ending. In many ways, human milk is the ultimate personalized nutrition.

Notes on Engineering Health

Notes on Engineering Health, December 2021: ICYMI 2021 Edition

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

December 31, 2021

Another year ends and instead of writing about the many challenges in front of the world at the moment which we thought did not carry a very positive message for the festive season, we decided to look back on the subjects we covered in the opening section of these Notes during 2021 and see if any updates on them were in order.

Notes on Engineering Health

Accounts of absurd or tragic interactions with the American healthcare system are common. A growing sub-genre of these stories involves surprise billing—many such overwhelming experiences have been recounted from trips to the ER to the result of routine medical testing. Today, on the eve of Thanksgiving, I am sharing a personal story that encapsulates some of the most infuriating idiosyncrasies of our current American system.

Notes on Engineering Health

We sat down with Michael Retchin, a graduate student in New York and the co-founder of the Nucleate program. Digitalis is an early partner of Nucleate, dedicating time and resources to the program and its students.

Notes on Engineering Health

The ubiquity of electronic health records (EHRs) has supported the creation of transformative digital tools to better monitor, diagnose, and treat patients. But, EHRs also pose serious privacy and security concerns. How big of a problem is it? Why should we care? And what types of opportunities will open up to make sure EHR data is treated appropriately?

Notes on Engineering Health

Notes on Engineering Health, August 2021: Evolution and Public Health

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

August 31, 2021

What does it take for a virus to create new variants and to evolve into a more deadly foe?

Notes on Engineering Health

Notes on Engineering Health, July 2021: Some Notes on Model Organisms

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

July 31, 2021

If every organism has a shared origin, then there must be some basic biological principles that are at play in humans as well as in much “simpler” organisms. The idea that certain organisms can be studied and used to acquire knowledge on other organisms led the way to new fields of research and the development of a myriad of the models (zebrafish, yeasts, bacteria, phages, and, of course, mice and monkeys to name a few) that drive much of modern biology.

Notes on Engineering Health

Notes on Engineering Health, June 2021: XX Versus XY

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

June 30, 2021

Does having two X chromosomes set one back when it comes to being understood and treated by the medical profession? The answer seems to be yes in many instances. Here are five striking examples where there are clear differences between diseases men and women get, as well as the way they are treated.

Notes on Engineering Health

Notes on Engineering Health, May 2021: The Ends, Not the Means

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

May 31, 2021

The idea that organisms, organs, tissues, and even cells can generate a desired outcome on their own if you create the proper incentives is a powerful one. It has led to important basic discoveries and could possibly be used in the near future to solve complex problems.

Notes on Engineering Health

Notes on Engineering Health, April 2021: A Fertile Ground for AI Companies

Victoria Perweiler
Jonathan Friedlander, PhD
Geoffrey W. Smith

Victoria Perweiler, Jonathan Friedlander, PhD & Geoffrey W. Smith

April 30, 2021

While machine learning may deliver clinical benefits, the work to understand mechanistic insights is key to not only predict but prevent and treat underlying conditions. We hope that all these innovations will serve couples trying to conceive and lower the cost barriers to reproductive technologies, but recognize that the real impact of the financing gold rush in this area is yet to be seen.

Notes on Engineering Health

Notes on Engineering Health, March 2021: A Short History of the EMR

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

March 31, 2021

In the late 1960’s, the idea to record patient information in electronic form rather than on paper emerged. The goal of the first EMR, presented by Lawrence “Larry” Weed, was to allow a third party to independently verify a diagnosis in order to improve patient outcomes. The first EMR was developed in 1972 by the Regenstrief Institute and was welcomed as a major advancement in healthcare / medical practice.

Notes on Engineering Health

Notes on Engineering Health, February 2021: Climate and Health

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

February 28, 2021

Measuring the effects of climate change and pollution on health is hard but the consensus is that they are overwhelmingly negative. To understand the ramifications of a worsening climate crisis, it is useful to make a distinction between the impact on health and on healthcare delivery.

Notes on Engineering Health

Notes on Engineering Health, January 2021: Health Equity

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

January 31, 2021

The global COVID-19 pandemic caused an unprecedented number of challenges for our health systems during 2020. Many of these health challenges, however, have been persistent problems for years. For example, according to data released by the Center for Disease Control and Prevention (CDC), almost one-third of COVID-19 infections in the U.S. have affected black Americans though they represent only 13% of the U.S. population…

Notes on Engineering Health

Notes on Engineering Health, December 2020: 2020 and Lung Inflammation

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

December 31, 2020

2020 has been the year of airway inflammation. Everyone became an immunologist in record time with a specialization in infectious disease and a fellowship in lung damage. Words like cytokine (storms) and R0 have become common lingo in households. The difficulty of understanding and treating airway inflammation, however, was no stranger to the medical community, despite lengthy efforts to better understand targeted therapies to ameliorate its effects.

Notes on Engineering Health

Notes on Engineering Health, November 2020: Thoughts for Food

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

November 30, 2020

Although the maxim “Let food be thy medicine, and let medicine be thy food” is generally agreed to be an apocryphal quote by Hippocrates, there are good reasons why it still resonates as an immutable truth. Looking at the healthcare industry from a standpoint of health—as we try to do at Digitalis—regularly brings us back to nutrition as a key pillar of a healthy life. In particular, our attention this month was attracted by a number of studies carefully looking at large datasets that highlight again the key importance of diet and nutrition.

Notes on Engineering Health

Notes on Engineering Health, October 2020: Show Unfinished Work

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

October 31, 2020

This month we are introducing a new section of the newsletter, First Five, a curated list of topics that we are working on along with a bit of commentary and links to some of the content (scientific papers, books, podcasts, video, etc.) that is motivating our work. Our hope is that this new format will add some additional openness about our unfinished work, and will further facilitate the free flow of ideas with our readers.

Notes on Engineering Health

Notes on Engineering Health, September 2020: Can We Learn How to Control Fat Metabolism?

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

September 30, 2020

While our understanding of fat metabolism has evolved considerably since the nineteen-thirties, blockbuster agents have yet to be developed to help curb the obesity epidemic. We focus on three areas of current interest in the search for control over fat metabolism.

Notes on Engineering Health

Notes on Engineering Health, August 2020: Some Notes on Metabolism

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

August 31, 2020

While a lot of research has been focused on understanding the genetic causes of disorders in the hope to fix problems at the gene level, a number of disorders cannot be solved using this method alone — whether because they are multigenic or of unknown genetic cause. As a response, a growing trend has been to characterize pathologies according to their metabolic phenotypes. New techniques have allowed clinicians and researchers to measure more accurately a wider array of metabolites and nutrients, shedding new light on biology and disease.

Notes on Engineering Health

Notes on Engineering Health, July 2020: Why Are Some Foods More Allergenic Than Others?

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

July 31, 2020

The choreography of immune cells continues to be better understood, the reasons why we seem to be developing more allergies are being plumbed (from the hygiene hypothesis to the role of the microbiome), the way to treat symptoms are being advanced, but there is still a deep lack of understanding why some foods or common allergens are more prone to excite the immune system than others. Uncovering these differences will open the door to understanding the root causes of allergic reactions and engineer ways to modulate the immune response which is critical as the number of people worldwide with allergies is increasing.

Notes on Engineering Health

Notes on Engineering Health, June 2020: A Quick Look at Vitamin D & COVID-19

Casey Brooks
Jonathan Friedlander, PhD
Dac Nguyen, MD, PhD
Geoffrey W. Smith

Casey Brooks, Jonathan Friedlander, PhD, Dac Nguyen, MD,PhD & Geoffrey W. Smith

June 20, 2020

There are numerous studies correlating low levels of vitamin D in plasma to increased risk of varying health maladies. Cancer, autoimmune disorders, general innate immunity, hypertension/other cardiovascular events, diabetes types 1 and 2, neuropsychiatric function, pregnancy outcomes, and all-cause mortality have all been cited as conditions potentially mediated by a patient’s Vitamin D status.

Notes on Engineering Health

We cannot standby and avert our gaze from what is happening in the United States. The need for change, systemic and immediate, is as clear and inarguable in our health industry as it is in our political arena.

Notes on Engineering Health

From the 1950s when the double helix structure of DNA was unveiled to the CRISPR editors of the past few years, progress toward being able to engineer biology consistently and at high fidelity has been constant. Our ability to treat biology as an engineering discipline may even be reaching the point where it can be tasked with solving problems such as the current coronavirus pandemic.

Notes on Engineering Health

Notes on Engineering Health, Special Edition: Vaccine Development

Dac Nguyen, MD, PhD
Geoffrey W. Smith

Dac Nguyen, MD, PhD & Geoffrey W. Smith

May 15, 2020

While there are many open questions about managing the current pandemic, there seems to be universal agreement that the best case solution is the creation of an effective vaccine to SARS-CoV-2, the coronavirus that causes COVID-19.

Notes on Engineering Health

Notes on Engineering Health, April 2020: Natural Computing

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

April 30, 2020

As the current coronavirus crisis evolves, the key question will eventually shift from how we should we manage this pandemic to how can we be better prepared for the inevitable next one. What tools can we develop to make us more agile and effective when a virus strikes again?

Notes on Engineering Health

Notes on Engineering Health, March 2020: Apocalypse Now

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

March 31, 2020

In these troubled days, it certainly can feel like we are approaching the end of civilization as we have known it. The Doomsday Clock has never been closer to midnight (currently just 100 seconds away) and the obvious level of unpreparedness of societies facing the ongoing coronavirus crisis has not done anything to reverse the somber ticker.

Notes on Engineering Health

Notes on Engineering Health, February 2020: Medicine & Math

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

February 29, 2020

The fact that the broad population can’t calculate or has poor instinct for statistics such as positive predictive value is one thing, but more serious concerns about public health and safety are raised when the main clinical actors in the medical profession are less than proficient in understanding basic statistical tools.

Notes on Engineering Health

Notes on Engineering Health, January 2020: Mendelian Randomization

Jonathan Friedlander, PhD
Geoffrey W. Smith

Jonathan Friedlander, PhD & Geoffrey W. Smith

January 31, 2020

The search for causal inference when randomized clinical trials are problematic (and even when they are not) has long been a goal of epidemiological research. Taking advantage of the rise of Genome Wide Association Studies (GWAS) and the wealth of data they have produced, epidemiologists have created a clever hack known as Mendelian randomization (“MR”) to untangle correlation from causation.

Notes on Engineering Health

Life expectancy is a metric for the average age of death in a population. In 1800, regardless of place of birth, a newborn could expect to live fewer than 35 years. By 1950, the global average for life expectancy was still only 46 years, but with a much broader distribution spanning from 68 years in the richest countries to only the low 30s in the poorest countries. Today, it ranges from 53 (in the Central African Republic) to 85 (in Japan), with a global average of 71 years.

Notes on Engineering Health

While it is a bit of a truism to say that we live in a time of rapid change, that does not make the fact of it any less challenging. In particular, change at the intersection of technology, social norms, and economics is forcing us to grapple with the meaning and practice of trust in unexpected ways.

Notes on Engineering Health

Recent research has shown that we cannot hide amongst the crowd. In fact, more than 60 percent of Americans with European ancestry are identifiable through their DNA, whether or not they have ever submitted a sample to be sequenced. This potential inability to remain genomically private stems from the fact that by early 2019 an estimated 26 million consumers had been sequenced by the four leading commercial consumer DNA companies.

Notes on Engineering Health

An approach to discovery—answers first, explanations later—accrues what is call intellectual debt. It’s possible to discover what works without knowing why it works, and then to put that insight to use immediately, assuming that the underlying mechanism will be figured out later. In some cases, we pay off this intellectual debt quickly. But, in others, we let it compound, relying, for decades, on knowledge that’s not fully known.

Notes on Engineering Health

Digitalis invests in solutions to complex problems in health. In doing so, we aspire to framing and tackling Hilbert-level open problems in fields relevant to our mission. This newsletter will periodically provide notes on our efforts in an attempt to “show our work.” We invite you to be in touch with your ideas about important problems and potential solutions. And we look forward to working with you to develop the best solutions at scale to deliver better health to all.

Notes on Engineering Health