NOTES

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Notes on Engineering Health

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

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

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