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Accelerating Photosynthesis

Photosynthesis Powers Life on Earth

It's responsible for almost all the air we've ever breathe and almost all the food we've ever eaten. We should accelerate it.

Less than 12k years ago, we couldn't farm and so there were fewer than 1m people on earth. From 1800 to the present day, the population on earth grew 10x, the economy grew 100x, and the price of wheat fell by 15x. However, even if we maintained the extraordinary pace of improvement of the last fifty years for the next fifty years, we would undershoot demand by 30%. And, the max potential yield of wheat plateaued in 1982.

At the same time, photosynthesis and breathing are natural complements - the former removes co2, chains carbons and releases oxygen; the latter burns chained carbons using oxygen and releases co2. Unfortunately, photosynthesis as currently constructed is very wasteful. It's only 0.1-2% efficient at converting light energy is converted into bioavailable energy and removing co2 from the atmosphere.

If successful, accelerating photosynthesis could increase food production to support as many people as we like while gaining the ability to safely shape our climate to optimize human well-being.

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The right hand side represents all respiratory life (humans, other animals, respiratory bacteria).

Even a single photon contains 3x as much energy (180 kJ/mol) than is generated by life's most fundamental energy reaction: hydrolysis of a single ATP (60kJ/mol). A bacteria with cubic micron volume requires roughly 107 ATP/s and yet 3*109 photons hit that bacteria each second. A 1000x energy difference. As co2 levels rise, photosynthesis is becoming more efficient but not quickly enough to balance our burning of stored chained carbons and support the further expansion of our species.

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Earth breathing year after year. NASA.

Photosynthesis: A Living Dynamical System

At the human visual system's spacetime resolution, watching the grass grow is boring. Increase the resolution and it's anything but.

Under the hood of a plant, growth dynamics are changing significantly second by second. Every few seconds, a plant will quickly open its pores thereby increasing co2 and nutrient availability but reducing temperature and humidity. A watch that only counts seconds doesn't even tell the whole story. A plant's optimal light-dark cycle is not necessarily continuous light but rather a duty cycle of roughly 1 millisecond of light (harvest electrons from photons) and 10 milliseconds of darkness (chain carbons). Even a complicated state machine of environmental variables ignores the interplay of regulatory networks.

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A small subset of the state machine interactions.{kaiser2014dynamic}

At its core, photosynthesis can be an exponential process. Chloroplasts generate chained carbons which in turn generate chloroplasts. When its substrates are abundant (no competition for photons from other plants, full water + nutrient availability, co2 availability), it does grow exponentially until reaching maturity. The best growers in the world increase their exponential coefficient by 47% leading to 5-10x higher yields. As such, small improvements in subcomponents in photosynthesis are extremely meaningful.

Accelerating Photosynthesis

To accelerate a process, one must first measure it well and quickly. For example, a wind tunnel creates a variety of wind conditions and measures aerodynamic efficiency against them at a far lower cost than iteratively crashing planes. Similarly, our photosynthetic wind tunnels evaluate photosynthetic efficiency against every possible climate on earth as well as determine the optimal environmental dynamics for a particular genotype.

Measuring photosynthesis

To photosynthesize well, a plant must chain carbons efficiently and then allocate the resulting biomass well. For the latter, segmentation neural nets measure photosynthetic leaf area every few hours. For the former, we count fluorescent photons emitted by chlorophyll. When photons hit a plant's chloroplast, some number of electrons are excited. Some percentage of said electrons are harvested, but others drop an energy level and emit photons at 695nm. By precisely probing the plant with varying LED light levels and counting the fluoresced photons, one can determine photosynthetic efficiency.

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Top Left: Black & white photo of an orchid - flowers in white. Top Right: Same Orchid. Image of photosynthetic efficiency - notice the flowers are black (representative of no photosynthesis). Bottom Left: A cut leaf. Location where leaf was cut (extreme right hand side) has near zero photosynthesis - far fewer chloroplasts inside leaves - can also see traces of lower photosynthetic efficiency along veins of leaf. Bottom Right:Raw measurements

Our current optics enable 30um resolution measurements - enough to recognize the photosynthetic efficiency of individual cells in every plant. Transferring control logic to software reduced the cost from 30k$ to 2.5k$. Mounting these sensors onto a robot means we can now measure the photosynthetic efficiency of every cell in every plant every few minutes. We're working to increase the spatiotemporal resolution to measuring chloroplasts every 30 seconds.

Motivation for Environmental Control & Optimization

Why bother with environmental control and especially environmental optimization when the goal is accelerating photosynthesis genomically?

At a high level, the two are inextricably linked. Environments are a primary selection mechanism for genomes and can change the genome itself. Genomes are tailored to environments and small changes in photosynthetic genomics change the environment. The development of carbon concentrating mechanisms in cyanobacteria coincides with a fall in Earth's co2 atmospheric content from 100,000 ppm co2 to 10,000 ppm.

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Development of various species represented by horizontal bars. Historical CO2 levels in black. Historical O2 levels in checkered line. (TODO add citation)

Determining optimal environmental conditions for a given genotype leads to better understanding of the phenotype. For instance, a 59bp change in a cyanobacterial strain led to a 3x increase in photosynthetic efficiency only under 1000mmol/m^2/s of light. By probing light levels, the improvement was traced back to the electron transport chain. (TODO citation) For such an essential living process, many parts of photosynthesis are very poorly understood. In order to make the requisite improvements, it's very important to vary and optimize a much broader & representative set of parameters affecting plant physiology.

Environment control is most associated with indoor growing however every form of human overseen plant growth involves environmental control. In field agriculture, farmers control water, fertilizer, hormones, microbiomes, planting timing and even weather through cloud seeding. Even in carbon sequestration forests, governments have large areas of different weather, ecologies and environments to select from in siting these forests. Environment and genomics are always deeply tied but especially so in plants.

Photosynthetic Wind Tunnels

Reinforcement learning is a challenging technique to apply and often not appropriate for many problems it’s suggested for. However, the paradigm of sensed environment, controlled actions and optimizes rewards is a natural factoring for dynamics problems.

Reward

Since the goal is accelerating photosynthesis, our reward is growth speed which we measure at two time resolutions. One, we measure the photosynthetic efficiency of every cell in every plant every few minutes. Two, we measure the growth in photosynthetically active leaf area every few hours.

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Left:Field of strawberries Right:Results of strawberry segmentation

Actions

The goal with our action space is to capture every environmental factor that regulates plant growth. Air properties: temperature, humidity, carbon dioxide, pressure, oxygen etc... Water properties: temperature, pH, micronutrient ion contents. Nutrients are applied at the roots and on top of leaves (some nutrients like Ca2+ are harder for plants to pull from their roots). We are building towards control over soil-bound microbiome.

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Bank of PLCs for environmental control & control. NVIDIA Jetson JTX2 for inference.

State Space

The state of the plant & its environment is our environment includes all of the above environmental information and adds detailed celllular-level plant physiology information. As mentioned above, we capture real-time photosynthetic efficiency photos of with 30um resolution. At a similar resolution, thermal cameras determine whether plants' pores are open - when open, the leaf's surface is being evaporative cooled. Periodically, we capture 3d spectral images - since plants respond physiologically to most visible light, near & far infrared is very useful to receiving clearer signals of plant structure & water retention.

Fixing Photosynthesis' Leaky Funnel

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The photosynthetic pathway can be decomposed into 5 major subparts. Capturing photons, converting photons into electrons, transporting electrons, converting electrons into energy intermediates, and chaining carbons.

The overall process has 0.5-2% efficiency. Some transitions are remarkably efficient (83% quantum yield of photons to electrons); while others (Rubisco turnover rate) are not. In any chain process, addressing the current limiting factor yields a new one. In our repairman's tour of photosynthesis, we'll detail potential fixes & refactor for each transition as well as consider possibilities of cutting entire steps. TODO add more quantitative information

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Photosynthetic Energy Conversion Funnel (Joules at each step indicated on right). The ABCs of Photosynthesis: Always be Chaining.

Photon Capture

Photons are created via fusion in the sun and propelled against the Earth's surface. Within a plant's leaf, a hall of light-harvesting 1 nm2 antennae greet those photons. Each antenna is excited via the photoelectric effect within a narrow band of wavelengths - resulting excitons "hop" into a central reaction center via a quantum walk. {fassioli2014photosynthetic} 50-350 antennae feed each reaction center.

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Photons hit antennae proteins that select for their wavelength. Since blue light has higher energy, antennae that select for blues are further from the reaction center (RC). Every exciton enters the reaction center with roughly the energy of 1 red photon. organism.

Converting Photons into Free Electrons

This first reaction center (Photosystem II) concentrates energy from said excitons to shard water into a proton, an electron and O2. The O2 is released for us to breathe. The proton creates a proton gradient for downstream ATP energy synthesis. Process is very remarkable - only biological process to oxidize water and generates the largest potential difference found in nature at 1.2V-1.8V. Due to amount of intensity of solar & electrical stress, the core protein (D1) must be replaced every 19 min.

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Transporting Electrons

Disorganized free electrons would tear apart cellular infrastructure and greatly increase entropy. Instead, electrons are immediately transported down a 30nm biological wire (electron transport chain) to a second reaction center.

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Electron transport chain. In low light, when fewer electrons are being transported the wire shortens to 20nm.

Converting Electrons into Energy

The second reaction center (Photosystem I) also concentrates energy from 50-300 light-harvesting antennae to form a 0.5V potential difference. That energy then re-energizes the electrons flowing out of the electron transport chain which in turn oxidize NADP+ to create NADPH - an energy intermediate for the carbon cycle.

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Converting Energy + Carbon Dioxide into Carbohydrates

The core enzyme of photosynthesis, Rubisco, then consumes the intermediate energy forms (NADPH / ATP) & CO2 in order to chain carbons into sugars. Its' crucial functionality but also its' slow work-rate (3-5 co2 per second vs >100 per second) make it Earth's most abundant enzyme. Not only slow, Rubisco emerged an era with low oxygen and so it also catalyzes a respiratory reaction where the carbon chains just synthesized are torn apart :( Some photosynthetic organisms have developed mechanisms for storing carbon dioxide near Rubisco to increase its efficiency.

Potential Fixes

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Photosynthesis

All efficiency gains are maximal - in the presence of no other limiting factor. Of course, there are always other limiting factors

Improvement Cause of Efficiency Loss Component Potential Gain Notes
Add Green & Infrared Antennae Proteins Unused Solar Radiation Photon Capture 210% 52% of solar energy outside of accceptable wavelengths. Some photosynthetic bacteria (bastochloris viridis & cyanobacteria acaryochloris) have antennae tailored for near-infrared wavelengths (700-1000nm).
Avoid Expensive Antennae Synthesis. Poor resource allocation. Photon Capture 50% Some antennae proteins are expensive to synthesize. Recently, novel cyanobacterial strain was found that reduced doubling time from 4.9hrs to 1.5hrs. Only differed by 59 bps. Didn't use expensive antennae (phycobilisome); instead, key proteins of electron transport chain (plastocyanin, cytochrome b6f, etc...) were expressed at 1.5-2.7 higher levels. 50% improvement in efficiency from photosystem II led to a 3x reduction in the doubling rate.
Modify Photosynthesis Inhibition Regulation. Slow recovery from excessive light. Converting Photons to Electrons 20% Too much light => too many free electrons. Plants respond by quenching new photon energy as heat. Restarting photosynthesis to changed environmental conditions is slow. Recently, 20% photosynthesis acceleration by down regulating slow-response proteins. With LED light control, entire regulatory network can be removed.
Add Carbon Concentration Mechanism Rubisco's Specificity for CO2 vs O2 Chaining Carbons 20% Cyanobacteria and C4 plants disentangle CO2 storage and consumption. CO2 kept at 4000-40000 ppm near Rubisco to prevent respiratory reactions. Substantial improvement: C4 plants make 4% of plant species but 30% of biomass. Higher CO2 => choose fast catalyzing / low selectivity Rubisco => increase turnover rate to 48CO2 / second.
Intra-leaf CO2 Conductance Rubisco's Specificity for CO2 vs O2 Chaining Carbons 30% CO2 levels are 3x lower at Rubisco site => requires slow but highly selective Rubisco.
Express Rubisco in only Nuclear DNA Slow Evolutionary Progress in Rubisco Other ? Currenly 1/2 protein synthesized from chloroplast DNA; 1/2 protein synthesized from nuclear DNA. Single point mutations disable functionality impairing incremental progress. Make CRISPR-based edits simpler to execute. Cyanobacteria and C4 plants disentangle CO2 storage and consumption. CO2 kept at 4000-40000 ppm near Rubisco to prevent respiratory reactions. Substantial improvement: C4 plants make 4% of plant species but 30% of biomass. Higher CO2 => choose fast catalyzing / low selectivity Rubisco => increase turnover rate to 48CO2 / second.
Move Rubisco Synthesis to Nucleus Scientific Process 20% Selectively knock out regulatory networks that regulate photosynthesis inhibition due to excessive light. Too much light => too many free electrons. Plants respond by quenching new photon energy as heat. Restarting photosynthesis to changed environmental conditions is slow. Recently, 20% photosynthesis acceleration by down regulating slow-response proteins. With LED light control, entire regulatory network can be removed.
TODO TODO TODO TODO TODO

Conclusion

We have two subsequent blog posts on the details on training & developing the environmental optimization reinforcement learning algorithms as well as on developing a high-through put plant genomic editing pipeline where the relevant edits are proposed & vetted by ML algorithms.

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