large language model
: a type of mathematical system, inspired by the network of neurons of the human brain, that finds statistical patterns in very large datasets to predict and generate the most probable content following an initial prompt
Flagship Flashcards
generative biology
: the use of vast computational power to create biological designs with desired properties by inferring the principals of biology from large datasets
somatic genomics
: the study of genetic variation found within each cell of a multicellular organism
genetic chemistry
: the use of genetic code to discover the foundations of small molecule medicines
Network Medicines鈩�
: a new class of therapeutics that reprogram diseased cells to release a defined array of signals that precisely coordinate multicellular networks to drive disease resolution
reinforcement learning
: an artificial intelligence (AI) training technique based on trial and error that uses positive and negative feedback to teach the AI to perform a desired task in accordance with maximizing positive feedback
inverse protein folding problem
: the computational challenge of determining the amino acid sequence that produces a desired protein structure
Gene Writers鈩�
: a genome engineering technology based on mobile genetic elements that consists of a protein and an RNA or DNA template to effect a therapeutic change
bioplatform
: biotechnologies that enable intentional and repeatable generation of medicines across many diseases or products for agriculture and sustainability
programmable medicines
: therapeutic modalities based on biological building blocks that can be rationally designed and arranged to achieve a desired effect
human microbiome
: the trillions of microorganisms, including bacteria, viruses, archaea, protozoa, and fungi, that are found within and on the human body
transfer RNA (tRNA)
: an RNA molecule that decodes mRNA and transfers the appropriate amino acid to the growing polypeptide chain
stop codon disease
: any genetically driven disease that stems from a premature termination codon mutation, which prevent the formation of a complete and functional protein
preemptive health and medicine
: protecting, maintaining, or improving people's health before they get sick by providing interventions targeted to pre-disease states for those that are seemingly healthy but at risk
scope 3 emissions
: greenhouse gas emissions from sources not owned or controlled by an organization, occurring upstream or downstream in its supply chain.
carbon farming
: farming practices that leverage nature-based methods to increase atmospheric carbon sequestration in plant biomass and soil and decrease greenhouse gas emissions.
regenerative agriculture
: farm management practices that restore soil health, encourage biodiversity, safeguard water resources, and increase climate resilience while reducing greenhouse gas emissions and increasing productivity and profitability.
nature-positive agriculture
: growing practices that protect, maintain, and enhance ecosystems.
carbon insetting
: nature-based sustainability initiatives upstream or downstream of a company鈥檚 operations that reduce greenhouse gas emissions and increase carbon storage, enhancing the carbon emissions reduction capacity of a supply chain.
agricultural carbon credit
: a permit representing one metric tonne of carbon dioxide that is generated by quantifying and verifying the impact of nature-based methods in either avoiding carbon emissions or increasing the amount of carbon stored in the land.
large language model
: a type of mathematical system, inspired by the network of neurons
of the human brain, that finds statistical patterns in very large
datasets to predict and generate the most probable content following an
initial prompt
Models can be trained using biological datasets to
infer the complex and highly dynamic 鈥渓anguage of biology.鈥� For
example, from a protein sequence, a model could predict protein
structures, or from a genetic sequence, predict a relevant promoter
region.
generative biology
: the use of vast computational power to create biological designs
with desired properties by inferring the principals of biology from
large datasets
The future of drug development will be defined by
the ability to generate, rather than discover, drugs with desired
therapeutic effects, optimized costs, and reduced or eliminated
off-target effects.
somatic genomics
: the study of genetic variation found within each cell of a multicellular organism
All
cells accumulate random genetic changes in their DNA. As a result, an
individual鈥檚 genome is not a single genome but trillions of unique
genomes throughout the body. While variations may have no apparent
impact, some impart disease resistance and others cause or increase
vulnerability to disease. It is as if clinical trials for these
mutations are being conducted at the cellular level. Tapping into this
trove of information opens up new opportunities to cure, prevent, or
reverse disease.
genetic chemistry
: the use of genetic code to discover the foundations of small molecule medicines
Enzymatic proteins encoded in genes make and modify bioactive small molecules. From human samples, we can pinpoint the biosynthetic gene clusters that give rise to these molecules, revealing the instructions for small molecule drug leads that can be matched to disease-relevant targets.
Network Medicines鈩�
: a new class of therapeutics that reprogram diseased cells to release a defined array of signals that precisely coordinate multicellular networks to drive disease resolution
Diseased cells can send pathologic signals to other cell types in their network, perpetuating a cycle of dysfunction and disease progression. Yet drug development has traditionally focused on affecting only one cell type in the network. Network Medicines are designed to have both a direct effect by targeting the diseased cells themselves and a network effect by reprogramming diseased cells to release therapeutic signals that coordinate other key cells in the network to restore health.
reinforcement learning
: an artificial intelligence (AI) training technique based on trial
and error that uses positive and negative feedback to teach the AI to
perform a desired task in accordance with maximizing positive feedback
This
machine learning paradigm has been used to famously train AI to beat
the world鈥檚 foremost Go and chess champions but it can also be applied
to teach machines to pursue other goals, such as optimizing biomolecular
designs.
inverse protein folding problem
: the computational challenge of determining the amino acid sequence that produces a desired protein structure
The
structure of a protein impacts how it functions and behaves in an
environment, particularly how it binds with other molecules. If
scientists could determine the amino acid sequence that would provide a
desired structure, it would take much of the guesswork out of developing
biologic medicines.
Gene Writers鈩�
: a genome engineering technology based on mobile genetic elements
that consists of a protein and an RNA or DNA template to effect a
therapeutic change
By only nicking the DNA, rather than making a
double-stranded break, Gene Writers can substitute a single base pair;
delete or insert short DNA sequences; or write in entire genes into the
human genome.
bioplatform
: biotechnologies that enable intentional and repeatable generation
of medicines across many diseases or products for agriculture and
sustainability
The power and value of a bioplatform relates to
the degree with which it serves a diversity and breadth of applications
and can be universally applied.
programmable medicines
: therapeutic modalities based on biological building blocks that can
be rationally designed and arranged to achieve a desired effect
The fusion of computation and biology is enabling the development of new medicines with predictable outcomes.
human microbiome
: the trillions of microorganisms, including bacteria, viruses,
archaea, protozoa, and fungi, that are found within and on the human
body
These microbes play important roles in human health.
Interventions can target imbalances in these communities to restore
homeostasis and affect the progression of a wide variety of diseases.
transfer RNA (tRNA)
: an RNA molecule that decodes mRNA and transfers the appropriate amino acid to the growing polypeptide chain
Beyond
properly positioning amino acids in the final protein product, tRNA is
involved in an entire biological framework for coordinating
multicellular life.
stop codon disease
: any genetically driven disease that stems from a premature
termination codon mutation, which prevent the formation of a complete
and functional protein
Reclassifying patients based on their
shared mutation, rather than individual mutated gene or traditionally
defined clinical presentation, could unify treatment for seemingly
disparate diseases.
preemptive health and medicine
: protecting, maintaining, or improving people's health before they
get sick by providing interventions targeted to pre-disease states for
those that are seemingly healthy but at risk
Interventions protect health from external threats (i.e., health security) and prevent or delay the onset of diseases (i.e., preemptive medicine).
scope 3 emissions
: greenhouse gas emissions from sources not owned or controlled by an
organization, occurring upstream or downstream in its supply chain.
While
organizations do not have direct control over these emissions sources,
they can influence reduction by selecting suppliers with a low carbon
footprint or lengthening the useful lifespan of a product.
carbon farming
: farming practices that leverage nature-based methods to increase
atmospheric carbon sequestration in plant biomass and soil and decrease
greenhouse gas emissions.
Plants convert carbon in the atmosphere
to a form they can use via photosynthesis. When the plant biomass
decomposes, microbes convert that material into soil organic carbon.
Farmers can work with nature to prevent carbon from leaching into the
atmosphere and increase the amount that is stored in their land.
regenerative agriculture
: farm management practices that restore soil health, encourage
biodiversity, safeguard water resources, and increase climate resilience
while reducing greenhouse gas emissions and increasing productivity and
profitability.
Soil health is a primary concern for farmers who
adopt regenerative practices as healthy soils resist erosion, maximize
water infiltration, and improve nutrient cycling. This increases
profitability by producing higher yield with fewer inputs.
nature-positive agriculture
: growing practices that protect, maintain, and enhance ecosystems.
Instead
of depleting natural resources, food production can be a vehicle for
delivering positive outcomes for nature, people, and the climate.
carbon insetting
: nature-based sustainability initiatives upstream or downstream of a
company鈥檚 operations that reduce greenhouse gas emissions and increase
carbon storage, enhancing the carbon emissions reduction capacity of a
supply chain.
While offsets compensate for excessive emissions by
funding external sustainability projects, insets proactively look for
opportunities to reduce emissions within a company鈥檚 sphere of
influence. The focus is on embedding practices with a positive
environmental impact in the supply chain rather than removing practices
with negative impacts.
agricultural carbon credit
: a permit representing one metric tonne of carbon dioxide that is
generated by quantifying and verifying the impact of nature-based
methods in either avoiding carbon emissions or increasing the amount of
carbon stored in the land.
Growers who adopt farming practices
that reduce or avoid emissions can produce carbon credits for the
voluntary market once the impact of these practices are quantified and
verified. Companies or individuals can purchase credits to mitigate the
impact of emissions from their operations that cannot be reduced,
removed, or avoided.
From the CEO 01.08.2024
Navigating the Polycrisis
In Flagship鈥檚 2024 Annual Letter, Founder & CEO reflects on navigating the polycrisis and how to harness uncertainty and disequilibrium to propel progress and make the impossible possible.
Watch:
Three Questions with Flagship Leaders
Three Questions with Armen Mkrtchyan, Flagship Origination Partner & Head of Pioneering Intelligence
Three Questions with Craig Williams, Flagship Operating Partner & President of Apriori Bio
