Month: January 2020

Biodiversity Evolution

Biodiversity alters strategies of bacterial evolution

a paper published in Nature found that when a bacterial species resides in even a very simple ecological community — one that includes just a few other kinds of microbes — it evolves very different defense strategies against a predatory bacteriophage virus than it does when it’s left alone with the phage. The research is expanding these ideas into the context of the microbiome, where bacteria exist alongside loads of other species. The finding not only elevates the value of biodiversity as an evolutionary factor in its own right, but suggests that some earlier conclusions about the behaviors and capabilities of microorganisms, drawn from laboratory studies of species in isolation, may be seriously incomplete. It also sounds a note of caution about some contemplated strategies for beating drug resistance in bacteria.

MuZero

MuZero learns a model that, when applied iteratively, predicts the quantities most directly relevant to planning: the reward, the action-selection policy, and the value function. When evaluated on 57 different Atari games – the canonical video game environment for testing AI techniques, in which model-based planning approaches have historically struggled – our new algorithm achieved a new state of the art. When evaluated on Go, chess and shogi, without any knowledge of the game rules, MuZero matched the superhuman performance of the AlphaZero algorithm that was supplied with the game rules.

Napoleon’s Rome

There were plans for the emperor and the King of Rome to visit the city and they wanted to welcome them into a modern imperial capital with wide boulevards, green spaces and grand buildings. Prominent Roman architects like Giuseppe Valadier and Giuseppe Camporese and French ones like Louis-Martin Berthault and Guy de Gisors were commissioned to design urban renewal projects — parks, bridges, new monuments, securing the banks of the Tiber to prevent flooding — and just outside of the city, new cemeteries to comply with Napoleon’s 1804 edict prohibiting burials within city walls

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.

Soleimani’s Death

General Soleimani was the commander of the Quds Force, an external unit of the Islamic Revolutionary Guard Corps, whose primary activities were outside Iran’s borders. He was particularly adept at creating militias manned by recruits from across the Middle East and South Asia. The model was Hezbollah in Lebanon, where in the early 1980s Iran organized the local Shiite community and created a lethal terrorist organization that would commit acts of violence on its behalf. This policy had 2 major advantages. First, it gave Iran a unique ability to assert its influence over disorderly politics in Iraq, Lebanon, and Syria while maintaining a kind of plausible deniability. Second, it allowed Iran to wage through proxies a campaign of violence responsible for the deaths of 100s of US troops during the civil war in Iraq. Iran’s position in all those countries was already precarious. The regime could ill afford the vast imperial project that it undertook since the US invasion of Iraq. It is struggling to meet its domestic budgetary needs and has been reducing its subsidies to its militias. The assassination of Soleimani is unlikely to reverse any of those trends.

Trustable Hardware?

I’ve concluded that open hardware is precisely as trustworthy as closed hardware. Which is to say, I have no inherent reason to trust either at all. While open hardware has the opportunity to empower users to innovate and embody a more correct and transparent design intent than closed hardware, at the end of the day any hardware of sufficient complexity is not practical to verify, whether open or closed. Even if we published the complete mask set for a modern billion-transistor CPU, this “source code” is meaningless without a practical method to verify an equivalence between the mask set and the chip in your possession down to a near-atomic level without simultaneously destroying the CPU.

So where does this leave us? Do we throw up our hands in despair? Is there any solution to the hardware verification problem?

I’ve pondered this problem for many years, and distilled my thoughts into 3 core principles:

  1. Complexity is the enemy of verification
  2. Verify entire systems, not just components
  3. Empower end-users to verify and seal their hardware

2023-03-11: The next step, inspecting the hardware itself

The Infra-Red, In Situ (IRIS) inspection method is capable of seeing through a chip already attached to a circuit board, and non-destructively imaging the construction of a chip’s logic. Each pixel corresponds to 1.67 micron. While these images cannot precisely resolve individual logic gates, the overall brightness of a region will bear a correlation to the type and density of logic gate used. With a reasonable amount of design-level hardening, we may be able to up the logic footprint for a hardware trojan into something large enough to be detected with IRIS. Fortunately, there is an existing body of research on hardening chips against trojans, using a variety of techniques including logic locking, built in self test (BIST) scans, path delay fingerprinting, and self-authentication methods