Tag: biotech

Destroy agriculture

After 12 ka of feeding humankind, all farming except fruit and veg production is likely to be replaced by ferming, brewing microbes through precision fermentation. Dairy farming in the United States will be “all but bankrupt by 2030”. The American beef industry’s revenues will fall by 90% by 2035.

2022-06-02:

Formo is trying to do the same for cheese. They use genetically modified microorganisms to produce milk protein rather than alcohol. They then “brew” them in a bath of nutrients and plant-based feed, and after it has finished, they strain out the milk proteins.

By combining these proteins with water, plant-based fats and carbs, and a pinch of salt, they have created a completely lab-grown milk. This can be processed just like cow’s milk to make all sorts of cheeses. Formo says its process also uses orders of magnitude less land and produces far fewer CO2 emissions than dairy farming. What’s more, their cheese tastes like normal cheese and has near identical nutritional value.

Life In Our Phage World

The world of phages is more than a little scary. They have been evolving for billions of years, their numbers are so vast every writer in this anthology resorts to scientific notation, and their generation time is as low as minutes, making for dizzying amounts of selection pressure and optimization – phages seem to have explored every possible way of attacking, subverting bacteria, replicating faster, compacting and making themselves more efficient, and won every arms-race bacteria started with them.

2023-01-12: And the reverse

A species of plankton that populate freshwater worldwide is the world’s first known organism that survives and thrives by dining on viruses alone, an advance that sheds new light on the role of viruses in the global food web. This virus-only diet – “virovory” – is enough to fuel the growth and reproduction of a species of Halteria, a single-celled organism known for the minuscule hairs.

2025-09-18: Viable AI-mutated phages

the researchers mixed all 16 AI-generated phages with ΦX174 and then threw them into a tube with E. coli cells. Because the phages were forced to compete for the same host cells, the variants that reproduced fastest would dominate. By sequencing the phages over time, the researchers could track which phages were gaining ground and which were falling behind. Several of the AI phages consistently outperformed wild ΦX174, with one variant (called Evo-Φ69) increasing to 65x its starting level.

Ultimately, these 16 AI-generated phages were not only viable; in many cases, they were more infectious than wildtype ΦX174 despite carrying major genome alterations that a human would be unlikely to rationally design.

Multiplex editing

Enhancing Organs for Cryonics, Space and Transplants

They are able to multiplex edit on the repeating gene sequences. The repeating gene sequences are key to many aspects of antiaging and cancer and other diseases. They are working to multiplex editing for enhancing organs. The can make the organs more resistant to cryopreservation and disease immunity. They can make people better able to travel in space and be more radiation resistant

Cross-organelle response

The problem with serial repitching has beer makers and cell biologists scratching their heads. Clearly, something about the fermentation process is making new generations of yeast less able to ferment. But what? Heat shock response is a complex process because cells are capable of making 1000s of different proteins. But only a subset of these proteins are expressed at any one instant, and the subsets differ inside each organelle in the cell. So maintaining the function of these proteins—proteostasis—requires a complex signaling mechanism that switches on the relevant genes in each organelle. This switching process must be coordinated across the cell, since organelles depend on each other. The process of communication and coordination is called cross-organelle response, or CORE, and it is poorly understood. But this is an important emerging area of cell biology: biologists are beginning to realize that CORE plays a crucial role not just in heat shock response but in metabolism in general, and even in processes such as aging.

Seeing The End Of Oil

The end of petroleum is in sight. The reason is simple: the black goo that powered and built the 20th century is now losing economically to other technologies. Petroleum is facing competition at both ends of the barrel, from low value, high volume commodities such as fuel, up through high value, low volume chemicals. Electric vehicles and renewable energy will be the most visible threats to commodity transportation fuel demand in the short term, gradually outcompeting petroleum via both energy efficiency and capital efficiency. Biotechnology will then deliver the coup de grace, first by displacing high value petrochemicals with products that have lower energy and CO2 costs, and then by delivering new CO2 negative biochemicals and biomaterials that cannot be manufactured easily or economically, if at all, from petrochemical feedstocks.

2021-11-22: Here’s one approach:

Biologists have devised a way to engineer yeast to produce itaconic acid—a valuable commodity chemical—using data integration and supercomputing power as a guide. Yeasts and other microbes are commonly used to produce useful chemicals. While it is easy to get them to produce some chemicals in high yields, like ethanol, other chemicals may provide more of a challenge. Kumar hopes that this system of combining machine learning with metabolic modeling and multiomics datasets will help overcome these production challenges. “Though we still need more testing on this model, there is an amazing potential to expand this computationally guided bioengineering to other systems. This strategy could open up a new era in biosystem design for the production of eco-friendly chemicals.”

Automated Discovery

To what extent can scientific discovery be automated? Where are the areas where automation can make the biggest contribution to human efforts? These questions and a number of others are addressed in a very interesting 2-part review article on “Automated Discovery in the Chemical Sciences”. As the authors say, “The prospect of a robotic scientist has long been an object of curiosity, optimism, skepticism, and job-loss fear, depending on who is asked” I know that when I’ve written about such topics here, the comments and emails I receive cover all those viewpoints and more. Most of us are fine with having automated help for the “grunt work” of research – the autosamplers, image-processing and data-analysis software, the plate handlers and assay readers, etc. But the 2 things that really seem to set off uneasiness are (1) the idea that the output such machinery might be usefully fed into software that can then reach its own conclusions about the experimental outcomes, and (2) the enablement of discovery through “rapid random” mechanized experimental setups, which (to judge from the comments I’ve gotten) is regarded by a number of people as a lazy or even dishonorable way to do science.

GMO Eggplant

Conventionally grown brinjal is one of the most heavily sprayed crops in South Asia. Historically, farmers have sprayed as many as 84x in a growing season to protect their crops. Genetically modified insect-resistant eggplant (Bt brinjal) had a 39% reduction of pesticides and a 51% reduction in the number of times that farmers applied pesticides.

2020-11-19:

Bt eggplant offers a 51% increase in yield, a 37.5% decrease in pesticide use, increased farmer profits and decreased farmer sickness. Wow!

Speed Breeding

Combining speed breeding with gene editing and other technologies is the best way to improve crops. We already have test fields with 3x yield. Getting another 2x would feed more than 20B people. They trick the crops into flowering early by using blue and red LED lights for 22 hours a day and keeping temperatures between 16 and 22 degrees Celsius. They can grow up to 6 generations of wheat, barley, chickpeas and canola in a year instead of only 1-2 crops each year using old farming methods.