Category: Web/Tech
New CRISPR-based COVID-19 test uses smartphone cameras to spot virus RNA
This one brings us closer to the Star Trek medical universe:
Scientists at UC Berkeley and Gladstone Institutes have developed a new CRISPR-based COVID-19 diagnostic test that, with the help of a smartphone camera, can provide a positive or negative result in 15 to 30 minutes. Unlike many other tests that are available, this test also gives an estimate of viral load, or the number of virus particles in a sample, which can help doctors monitor the progression of a COVID-19 infection and estimate how contagious a patient might be.
“Monitoring the course of a patient’s infection could help health care professionals estimate the stage of infection and predict, in real time, how long is likely needed for recovery and how long the individual should quarantine,” said Daniel Fletcher, a professor of bioengineering at Berkeley and one of the leaders of the study…
The new diagnostic test takes advantage of the CRISPR Cas13 protein, which directly binds and cleaves RNA segments. This eliminates the DNA conversion and amplification steps and greatly reduces the time needed to complete the analysis.
“One reason we’re excited about CRISPR-based diagnostics is the potential for quick, accurate results at the point of need,” [Jennifer] Doudna said. “This is especially helpful in places with limited access to testing or when frequent, rapid testing is needed. It could eliminate a lot of the bottlenecks we’ve seen with COVID-19.”
In the test, CRISPR Cas13 proteins are “programmed” to recognize segments of SARS-CoV-2 viral RNA and then combined with a probe that becomes fluorescent when cleaved. When the Cas13 proteins are activated by the viral RNA, they start to cleave the fluorescent probe. With the help of a handheld device, the resulting fluorescence can be measured by the smartphone camera. The rate at which the fluorescence becomes brighter is related to the number of virus particles in the sample.
And:
Now that the CRISPR-based assay has been developed for SARS-CoV-2, it could be modified to detect RNA segments of other viral diseases, like the common cold, influenza or even human immunodeficiency virus. The team is currently working to package the test into a device that could be made available at clinics and other point-of-care settings and that one day could even be used in the home.
“The eventual goal is to have a personal device, like a mobile phone, that is able to detect a range of different viral infections and quickly determine whether you have a common cold or SARS-Cov-2 or influenza,” Fletcher said. “That possibility now exists, and further collaboration between engineers, biologists and clinicians is needed to make that a reality.”
I recall once asking Silvana Konermann: “What am I going to buy at the CRISPR store?” Well, this is what you are going to buy at the CRISPR store.
Here is the article. And funded by Fast Grants, I am happy to say. Quite the week for science, yes?
Computational sentences to ponder
From a very smart correspondent:
“incidentally forgot to say that this is
basically the death of the
“extended Church-Turing hypothesis”
which roughly states that all reasonable computational models can be simulated on a Turing machine with only polynomial cost. but it now sure looks like quantum computers are physically realisable and are non-polynomially faster
– in other words we now almost certainly know that computational complexity does depend on laws of physics”
The indentation was his, and with reference to this earlier reported quantum computational result from China.
American Ph.Ds are failing at start-ups
We document that since 1997, the rate of startup formation has precipitously declined for firms operated by U.S. PhD recipients in science and engineering. These are supposedly the source of some of our best new technological and business opportunities. We link this to an increasing burden of knowledge by documenting a long-term earnings decline by founders, especially less experienced founders, greater work complexity in R&D, and more administrative work. The results suggest that established firms are better positioned to cope with the increasing burden of knowledge, in particular through the design of knowledge hierarchies, explaining why new firm entry has declined for high-tech, high-opportunity startups.
Here is more from Thomas Åstebro, Serguey Braguinsky, and Yuheng Ding.
This was a thing, yes it was, that was then, this is now
Initially founded in 1962, the Anti-Digit Dialing League quickly became the premiere sensible dialing association organization in the United States of America. Nearly 60 years later, the problems this country’s phone network faces are direr than ever. While we continue to espouse the use of 2L+5N dialing over all-number calling whenever possible, our primary aim today is to publicly oppose the proliferation of 10-digit dialing, which is fast becoming a public nuisance and dialing nightmare for ordinary people everywhere in this country.
Circa 1962-64 (those were the days), here is the web site. Web site? Wait, it still is a thing!:
Although 771 is scheduled to be overlaid on D.C.’s 202 area code in 2021, forcing residents of our nation’s capitol to dial 10 digits forevermore, the A.D.D.L. objected to the use of an overlay as a matter of principle. According to NANPA, splits are unlawful when the majority of the area code is in the same rate center (as is D.C.) (see pg. 12 of Sept. 1 Community Hearing Transcript). That doesn’t mean overlays are inevitable in other areas, though. Overlays continue to remain a public nuisance, and although splits have not been commonplace since 2006, we will continue to urge the use of splits over overlays whenever possible, because splits better serve the public interest, a finding which is well supported by empirical data.
Don’t let them tell you money illusion is not a problem. Via Anecdotal.
Is the Great Stagnation over?
– A working mRNA vaccine (first ever in humans!),
– Apple M1 chip,
– SpaceX rocket launch,
– GPT-3,
– Tons of cool companies IPO’ing and tons more getting started,
– V-shaped recovery
– Electric cars
– Crypto going mainstream
That is from a tweet by Nabeel S.Qureshi. One could add warp speed, affordable solar power, the eggplant, and distanced work to that list, the latter also implying significant rent declines and child care cost declines for many people.
Around the time The Great Stagnation came out in 2011, I predicted that it was most likely to end within the next twenty years. We are not there yet, but that claim is no longer looking so absurd.
Note that the vaccine-driven recovery will measure as a rise in labor inputs, but in reality it will be pure TFP. In 2021 (but which quarter?), true TFP will be remarkably high, maybe the highest ever?
Why conspiracy theories are on the rise
There are certain ideas that are highly seductive, so much so that even “WEIRDOS” occasionally dabble in conspiracy theories. So why weren’t conspiracy theories a bigger part of life in the late 20th century? I believe this is because the media was almost completely controlled by WEIRD people. The news desks at ABC/NBC/CBS stuck to the mainstream version of events, unless they had clear evidence that the official were lying (say after the Ellsberg Papers came out.) So there was no major institution to form and disseminate conspiracy theories. These theories did exist back then, but never gained enough traction to have a big impact on society.
The internet changed everything. More specifically, it democratized information sharing all over the world. There are no more “gatekeepers”. Because less that 10% of the world’s population is truly WEIRD, the internet has made conspiracy theories the dominant epistemic style of the 21st century. Just as the 21st century will be a low interest rate/high asset price century (as I predicted years ago), it will also be a century of widespread conspiracy theories. I doubt whether I’ll live along enough to see another president who is generally accepted as legitimate.
That is from Scott Sumner, there is more at the link.
My Conversation with Jimmy Wales
It was excellent throughout, here is the audio, video, and transcript, here is part of the summary:
Jimmy joined Tyler to discuss what happens when content moderation goes wrong, why certain articles are inherently biased, the threat that repealing section 230 poses to Wikipedia, whether he believes in Conquest’s Law, the difference between “paid editing” and “paid advocacy editing,” how Wikipedia handles alternative accounts, the right to be forgotten, his unusual education in Huntsville, Alabama, why Ayn Rand is under- and over-rated, the continual struggle to balance good rules and procedures against impenetrable bureaucracy, how Wikipedia is responding to mobile use, his attempt to build a non-toxic social media platform, and more.
Here is an excerpt:
COWEN: I’m the rare person who actually has no sock puppets. Why not allow sock puppets? What exactly is wrong with them? So what if a person has more than one identity out there, as long as you can monitor the identity that is operating on Wikipedia?
WALES: That’s a great question. In fact, we do try to make a distinction between a sock puppet and a legitimate alternate account. We actually have procedures whereby you can declare a legitimate alternate account to the arbitration committee so that you’re insulated from any bad harms if it’s found out. Some of the keys are that we rely on trust.
One of the things that is really important to us — we do a lot of what we call “not voting.” It’s voting, but it’s really a straw poll. The votes — typically, they’re not the final word, and if somebody comes into a discussion and pretends to be five different people, arguing that something should be deleted, and there are two actual different people arguing that it should be kept, that’s deceptive. It kind of skews the balance.
People who are reviewing that say, “Well, I think we should keep it, but I see there are five people here with a different opinion, so maybe I’m wrong.” That bulking up your impact by double-voting on something, by pretending to be different people, is super problematic.
The other problematic sock puppeting is a sock puppet to conceal your conflict of interest. I remember we had one notorious case of a PR firm that had engaged in quite a lot of problematic editing.
One of their accounts — it made a lot of edits and pretended to be a retired fellow who was a car collector. There were all these pictures of old cars and so on. They had a whole persona created that seemed like a lovely chap who just liked to edit Wikipedia, but in fact, it was just somebody at the PR firm who was giving a cover, and I think that kind of deception is problematic.
The good examples of multiple accounts would be someone who wants to edit in a controversial area. As an example, let’s say you’re a well-known person, and suppose you took an interest in our entries on pedophilia, not because of any prurient interests but simply because you think this is actually an important topic of social impact.
Well, you probably wouldn’t necessarily want to be known at your university as the guy who edits the pedophilia articles on Wikipedia. That’s just not easy for people to be open about, even if you’re doing all the right things. So you might say, “Yes, I actually want to edit in some areas of World War II history under this identity, but I’m going to do some work over here, and I really prefer it not to be tied back to my real-life identity.” And that’s kind of okay, as long as you’re not voting in elections with two accounts and things like that.
Definitely recommended.
Post-Covid, is the U.S. falling behind China?
I don’t think so, as I argue in my latest Bloomberg column, here is one bit:
If you are wondering whether China or the U.S. with its allies is more likely to make a big breakthrough, in, say, quantum computing, ask yourself a simple question: Which network will better attract talented immigrants? The more that talent and innovation are found around the world, the more that helps the U.S.
And:
Perhaps most important, the European Union has evolved from seeing China primarily as a customer to seeing China primarily as a rival. Even Germany, a longstanding advocate for closer ties with China, has become more skeptical. Furthermore, most European nations have ended up agreeing with the U.S. that Chinese telecom giant Huawei be kept out of the critical parts of their communications infrastructure.
It is also worth noting that GPT-3 came out of the Anglosphere, not China, even though we have been hearing for years that China may be ahead in AI.
Is AI centralizing research influence?
Increasingly, modern Artificial Intelligence (AI) research has become more computationally intensive. However, a growing concern is that due to unequal access to computing power, only certain firms and elite universities have advantages in modern AI research. Using a novel dataset of 171394 papers from 57 prestigious computer science conferences, we document that firms, in particular, large technology firms and elite universities have increased participation in major AI conferences since deep learning’s unanticipated rise in 2012. The effect is concentrated among elite universities, which are ranked 1-50 in the QS World University Rankings. Further, we find two strategies through which firms increased their presence in AI research: first, they have increased firm-only publications; and second, firms are collaborating primarily with elite universities. Consequently, this increased presence of firms and elite universities in AI research has crowded out mid-tier (QS ranked 201-300) and lower-tier (QS ranked 301-500) universities. To provide causal evidence that deep learning’s unanticipated rise resulted in this divergence, we leverage the generalized synthetic control method, a data-driven counterfactual estimator. Using machine learning based text analysis methods, we provide additional evidence that the divergence between these two groups – large firms and non-elite universities – is driven by access to computing power or compute, which we term as the “compute divide”. This compute divide between large firms and non-elite universities increases concerns around bias and fairness within AI technology, and presents an obstacle towards “democratizing” AI. These results suggest that a lack of access to specialized equipment such as compute can de-democratize knowledge production.
That is a new paper by Nur Ahmed and Muntasir Wahed.
Emergent Ventures winners, eleventh cohort
Andrew Dembe of Uganda, working on the “last mile” problem for health care delivery.
Maxwell Dostart-Meers of Harvard, to study Singapore and state capacity, as a Progress Studies fellow.
Markus Strasser of Linz, Austria, now living in London, to pursue a next-generation scientific search and discovery web interface that can answer complex quantitative questions, built on extracted relations from scientific text, such as graph of causations, effects, biomarkers, quantities, etc.
Marc Sidwell of the United Kingdom, to write a book on common sense.
Yuen Yuen Ang, political scientist at the University of Michigan, from Singapore, to write a new book on disruption.
Matthew Clancy, Iowa State University, Progress Studies fellow. To build out his newsletter on recent research on innovation.
Samarth Athreya, Ontario: “I’m a 17 year old who is incredibly passionate about the advent of biomaterials and its potential to push humanity forward in a variety of industries. I’ve been speaking about my vision and some of my research on the progress of material science and nanotechnology specifically at various events like C2 Montreal, SXSW, and Elevate Tech Festival!”
Applied Divinity Studies, this anonymously written blog has won an award for his or her writing and blogging. We are paying in bitcoin.
Jordan Mafumbo, a Ugandan autodidact and civil engineer studying Heidegger and the foundations of liberalism. He also has won an award for blogging.
Social Media Usage and the Level of Depressive Symptoms in the United States
I find that using Twitter decreases the level of depressive symptoms by 27%.
That is from the job market paper of Qin Jiang from USC. Via Jennifer Doleac.
Blog and Substack contest winners
To date there are three:
1. Anton Howes for his Substack Age of Invention. He is a historian of invention, often but not exclusively focusing on the eighteenth century, here is Anton on Twitter. As a separate matter, don’t forget Anton’s excellent recent book Arts & Minds: How the Royal Society of Arts Changed a Nation.
2. Works in Progress. Here is their About page: “Works in Progress is a new online magazine dedicated to sharing novel ideas and stories of progress, and features original writing from some of the most interesting thinkers in the world.” The major individuals behind Works in Progress are Sam Bowman, Saloni Dattani, Ben Southwood, and Nick Whitaker, all with bios at the previous link, all strong intellectual forces.
Note also: “Works in Progress is always looking for new writers for upcoming issues and our blog. Reach out if you want to talk about writing for us, with a short summary or abstract of your piece.”
3. Alice Evans, lecturer at King’s College London. Here is Alice on Twitter. She is working on “”THE GREAT GENDER DIVERGENCE” What explains global variation in gender relations?” and here is her related blog on that same topic. Here is her famous post on gender relations in north vs. south India. Her home page also links to her podcast.
I do expect there will be further awards, and I will keep you posted (here is the original announcement). If you just started writing a blog and submitted, you may still be in the running for the future. In the meantime, congratulations to these winners!
Vitalik Buterin’s Conversation with me
He is interviewing me, and yes he does close with a bout of Overrated vs. Underrated. Here is the YouTube link, it starts at about 7:00, give or take a few seconds. I thought it was very interesting, on both of our sides, more of a dialogue than an interview, the points of focus being crypto and tech utopianism.
Perhaps the next time we will get to The New Monetary Economics…
Novid — a pre-exposure notification system for Covid (and other things)
I find the (short) video easiest to follow:
https://www.youtube.com/watch?v=WN-dw-45Cwc
Best of all, it is incentive-compatible. The founder Po-Shen Loh, a mathematician from Carnegie Mellon, wrote to me:
…for each positive case, don’t just ask the direct contacts to quarantine; instead, tell everyone how many relationships away COVID just struck (e.g., “3” is a contact of a contact of a contact). Then animate this over time like a weather radar…Keep everything anonymous.
Suddenly, the main purpose of the intervention is no longer to protect others from you (quarantining after being exposed). Instead, it is to directly protect you from others, because that early warning of approaching COVID lets you know it’s a good time to wear a better mask, or to be more vigilant about distancing, because the situation is getting hot. This appeals to self-protection instincts instead of altruistic instincts. Since this app is already in deployment, we know anecdotally, for example, of a person who installed the app because his kid was going to a university that was using the app. Why? So that he could be alerted in case COVID started spreading his way from the university via his kid.
Here is his associated preprint. As economists, ought we not to feel that appealing to self-interest and love of family sometimes works?
Threadhelper, a new method for improving Twitter
Vasco Queirós, from the 7th cohort of Emergent Venture grant winners, has, with Francisco Carvalho, launched ThreadHelper – “A serendipity engine on the Twitter sidebar”. You can get it here.
ThreadHelper is a browser extension that finds you the tweets you need. It shows as a sidebar on the right hand side of your Twitter timeline and instantly and automatically searches bookmarks, retweets, and your past tweets for tweets that are semantically relevant to the tweet being composed. It can be used as a specific search that’s faster than Twitter’s or as a fuzzy search tool.