Cavalcade of Mammals

Keying off Kevin Drum’s The lessons of COVID, which is a good start but too limited in imagination.

What the US did right: the CDC has great world-wide infectious disease monitoring.

What the US did poorly: the US had spotty local infectious disease monitoring. And lack of data–ignorance–was used as an excuse for inaction. With post-COVID wastewater monitoring, the US is doing better, let’s keep the funding high for it.

Biggest mistake: the federal government responded slowly and ineffectively in the first two months. Faster response that seems like an over-reaction at the time is the best response. If the response is effective, and a disease is slowed or stopped, it should always feel like an over-reaction. Hoof-and-mouth disease is the model.

What qualities will make an AI a person?
-General intelligence, not just a special ability to solve a particular class of problems.
-General ability to learn from interacting with the environment.
-Can communicate with people.
-The AI needs a sense of self, needs to see itself as a person.
-General ability to reason abstractly, reason about problems in general.

The various types of machine learning that exist today can and likely will be a part of a human-level AI, but as a module or subcomponent that gets applied to learning tasks. Another level of AI will need to exist on top of that, applying general knowledge storage, modeling / conceptualizing problems, dealing with overarching direction and goals.

The basic problem with carbon capture is energy, and energy is cost. When coal or oil is burned, heat and CO2 are produced. CO2 is a pretty low energy form of carbon. Turning it into something solid (calcium carbonate, graphite or coal) requires a lot of energy. Also, when CO2 is made by burning fossil fuels it disperses, and re-concentrating it requires energy. That’s why carbon capture proposals often include using exhaust gas, grabbing the CO2 before it disperses. The other main type of capture I’ve seen proposed takes the CO2, concentrates it to high pressure, and pumps it underground (and hopes it stays there). Compressors take a lot of energy, and so do pumps if the CO2 needs to be piped hundreds of miles to a place where it can be pumped underground.

The key number for carbon capture is, how much energy is required relative to the amount generated by burning the fossil fuel? I’ve never seen articles about it touting this number. A quick look shows one assessment being 30% – 35% of the energy (Zhang et al, 2014), another figures the production cost of electrcity with carbon capture being 62% – 130% higher (White et al, 2012, Table 6) Another article looks at the harder case, CO2 capture from air, and estimates the cost at $1000/ton CO2 (link). Burning the coal to generate a ton of CO2 (1/3 of a ton coal) generates about $80 of electricity.

So the best case cost of carbon capture–from power plant exhaust gas–is dismal, 25%, 75%, maybe over 100% of the value of the electricity. This number will translate directly to increased fossil fuel energy costs (+30%, +100%, etc.) if fossil fuel companies are required to capture the majority of the CO2 pollution they generate.

All the carbon capture projects are basically stalling actions. The fossil fuel companies pay small $$ to put together a pilot plant (or better yet, get the govt to fund it), run tests for years, but never implement CO2 capture on a coal or gas energy plant. This had been a very successful approach for the fossil fuel industry, they’ve managed to stall things for 50 years already!

The CRISPR gene editing system is a major technical advance. It does open up the near term possibility of making a few small changes to a human embryo’s DNA, but I don’t find that particularly interesting or alarming.

What makes CRISPR better than previous tech for gene modification is that it works at high efficiency–1% to 60% with very high specificity. I read a recent paper testing CRISPR on human embryos that reported 50% effectiveness. Given a handful of embryos to work with, there is a very good chance of making a single change in one embryo.

We have very little knowledge or technology for making positive changes to animals which is a huge limitation to genetic ‘engineering’. Mostly what is understood are disease causing (or predisposing) genetic variants. So a single change (maybe in a few years, a handful of changes?) can be made to a human embryo. There are other limits to modifying human embryos apart from lack of knowledge. The more time an embryo or human embryonic stem cell is cultured, the more it is manipulated, the greater the chance of something going wrong, and the child being born with problems. This tech is great for manipulating animals in the lab. If many or most of them have the genetic change, great! If some are born with defects, cull them, or breed another generation and use those in experiments (often the first generation has non-genetic defects that breed away). But these are huge problems if you are working on humans, because things that increase the risk of getting a damaged child are not desirable.

Long term (100-1000 years), when increases in understanding of biology make improvements (or significant changes of any sort) in humans possible, I think what we’ll see is that the people with the least concern for child welfare will be the most willing to experiment on them.

The really exciting possibilities CRISPR opens up is in genetic treatment of human disease in the tissues of kids and adults. There is delivery tech (well tested viral vectors, and a host of other methods) that can get CRISPR into a good percentage of cells (10% to 50+%) in many tissues, and once there, CRISPR will edit a good fraction of those cells. For many diseases, fixing a genetic defect in 1%, 10% or 20% of cells is enough to treat the disease, so genetic treatment of host of diseases is now possible. Things like hemophilia, some muscular dystrophy, maybe Huntington’s Disease, metabolic diseases, Parkinson’s disease, and on and on. There will be a lot of exciting advances turning that ‘possible’ into actual treatments for different diseases over the next decade or two.

The other major effect of CRISPR tech is that it makes animal experimentation faster and cheaper, and will accelerate basic biological research. We still don’t know what the majority of indivdual genes do, let alone how they work in complexes and networks in cells.

Picked up a GeneTac 1000, a biochip scanner. Here are teardown pictures:
Here is the unit:

Teardown pictures. The unit has a self-contained lamp module that plugs into the main controller unit (EG&G Optoelectronics, Model # 300mXT-04, lamp module LM-300MX). Can’t find much about it–looks to be a 300W lamp. The center of the unit has a CCD camera, a Nikon lens, and a big custom lens, and two sets of filters. The slide carousel is on the other side.

Recently Gao et. al. published “An Estimate of the Average Number of Recessive Lethal Mutations Carried by Humans”. They studied a Hutterite group in South Dakota, highly inbred (63 founders 13 generations ago). From serious genetic diseases common in this population, they determine the number of deleterious variants present in the founders. They find that 0.29 recessive lethal alleles per haploid genome. Since some lethals manifest before birth, they double the estimate to 0.58.

This gives an expected 1.8% increased chance of a genetic disease from two first cousins.

Gao, Z., Waggoner, D., Stephens, M., Ober, C. & Przeworski, M. Genetics 199, 1243–1254 (2015).

I was sent a link to a blog post, “This Mama Isn’t Scared of the Shmeasle Measles” by Megan Heimer.

I’ll run through the post in a minute, it contains a whole lot of nonsense. First, some links to reliable info:
CDC measles info
CDC Manual for Surveillance of VPD: Chapter 7: Measles
Measles week posts by an immunologist

Now, on to the post…

(more…)

Hybrid balloon / vehicle approaches

Saw a recent news item about JP Aerospace. They are working on a two step to orbit approach. The basic plan is to put a large lighter than air (LTA) craft at 200,000 ft, and then accelerate it using a ion thruster to reach orbital velocity.

So I was interested in how this would work, and what the basic parameters (mass, thrust, time) are for approaches of this type.

The benefit of starting from a high altitude is very low air pressure. A balloon can provide steady support so a low thrust vehicle has time to accelerate.

Orbital velocity is roughly 9500 m/s.

What size solid fuel rocket would be required to put a 10 kb payload into orbit?

OK, this is quite annoying. It was plenty annoying when I was at a univerisity and 90% of the articles were available at publication, but that 10% always included a handful of important articles so it has always been a PITA. So now I’ll start future blogging!

I’ll tag interesting articles when they get published and follow up when I can actually read them. Many journals now are open access, but some release an article six months or a year after publication. Or sometimes the pdf gets posted. So I’ll tag intertesting articles when they hit the news and write a follow up when I can read them. Because titles and abstracts aren’t enough for articles with useful information!

Duration of urination does not change with body size. Patricia J. Yanga, Jonathan Phama, Jerome Chooa, and David L. Hu. PNAS vol. 111 no. 33p11932–11937.

BTW, PNAS used to release articles at publication. When did they go dark?!

Could new measures substantially improve public health?

What would be the effect if, say, 90% of the country wore filter masks for one week, and concentrated on washing hands?

Infection is a chain, one individual infects one or more others, and an infection gets passed on. That is how disease persists–for most infectious agents, not in one person for months on end, but passed serially every few months as an individual gets infected, and over a few weeks mounts an immune response and fights it off.

An infectious agent requires a basic reproduction factor, an R₀, of more than one. If R₀ > 1, an infection is growing more common, if R₀ < 1, an infection is disappearing. For more diseases, for infection to persist it must spread.

Currently there are constant but weak efforts to reduce the spread of infection–encouraging the sick to stay home and hand washing. Vaccines for influenza. But what if a serious effort was made? A big effort could not be sustained, at least not in the US culture.

But what would be the effect of a large, short effort? If infection transmission can be stomped down for a short period, but long enough to break the chain of infection, it might have a large effect on public health. I wonder if this has been modeled?