Everyday Erinyes #305

 Posted by at 10:36 am  Politics
Feb 132022
 

Experts in autocracies have pointed out that it is, unfortunately, easy to slip into normalizing the tyrant, hence it is important to hang on to outrage. These incidents which seem to call for the efforts of the Greek Furies (Erinyes) to come and deal with them will, I hope, help with that. As a reminder, though no one really knows how many there were supposed to be, the three names we have are Alecto, Megaera, and Tisiphone. These roughly translate as “unceasing,” “grudging,” and “vengeful destruction.”

We have through this column looked at facial recognition before, and, while it can certainly have some positive uses, I personally prefer to be identified by what’s inside my head rather than what’s outside it. (Then there’s the little issue that I do not own, nor do I plan to own, a phone which is capable of downloadding an app or anything else. Nor do I own or plan to own a webcam …even assuming the technology could be downloaded to a desktop.) If the IRS wants to identify me by a body part, I’d be amenable to a fingerprint … provided it hadn’t been taken from a hand which was subsequently amputated. But that’s the problem. Body parts are not set in stone. So I was very happy to read that the IRS had backed off on making this mandatory.
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Government agencies are tapping a facial recognition company to prove you’re you – here’s why that raises concerns about privacy, accuracy and fairness

Beginning this summer, you might need to upload a selfie and a photo ID to a private company, ID.me, if you want to file your taxes online.
Oscar Wong/Moment via Getty Images

James Hendler, Rensselaer Polytechnic Institute

The U.S. Internal Revenue Service is planning to require citizens to create accounts with a private facial recognition company in order to file taxes online. The IRS is joining a growing number of federal and state agencies that have contracted with ID.me to authenticate the identities of people accessing services.

The IRS’s move is aimed at cutting down on identity theft, a crime that affects millions of Americans. The IRS, in particular, has reported a number of tax filings from people claiming to be others, and fraud in many of the programs that were administered as part of the American Relief Plan has been a major concern to the government.

The IRS decision has prompted a backlash, in part over concerns about requiring citizens to use facial recognition technology and in part over difficulties some people have had in using the system, particularly with some state agencies that provide unemployment benefits. The reaction has prompted the IRS to revisit its decision.

a webpage with the IRS logo in the top left corner and buttons for creating or logging into an account
Here’s what greets you when you click the link to sign into your IRS account. If current plans remain in place, the blue button will go away in the summer of 2022.
Screenshot, IRS sign-in webpage

As a computer science researcher and the chair of the Global Technology Policy Council of the Association for Computing Machinery, I have been involved in exploring some of the issues with government use of facial recognition technology, both its use and its potential flaws. There have been a great number of concerns raised over the general use of this technology in policing and other government functions, often focused on whether the accuracy of these algorithms can have discriminatory affects. In the case of ID.me, there are other issues involved as well.

ID dot who?

ID.me is a private company that formed as TroopSwap, a site that offered retail discounts to members of the armed forces. As part of that effort, the company created an ID service so that military staff who qualified for discounts at various companies could prove they were, indeed, service members. In 2013, the company renamed itself ID.me and started to market its ID service more broadly. The U.S. Department of Veterans Affairs began using the technology in 2016, the company’s first government use.

To use ID.me, a user loads a mobile phone app and takes a selfie – a photo of their own face. ID.me then compares that image to various IDs that it obtains either through open records or through information that applicants provide through the app. If it finds a match, it creates an account and uses image recognition for ID. If it cannot perform a match, users can contact a “trusted referee” and have a video call to fix the problem.

A number of companies and states have been using ID.me for several years. News reports have documented problems people have had with ID.me failing to authenticate them, and with the company’s customer support in resolving those problems. Also, the system’s technology requirements could widen the digital divide, making it harder for many of the people who need government services the most to access them.

But much of the concern about the IRS and other federal agencies using ID.me revolves around its use of facial recognition technology and collection of biometric data.

Accuracy and bias

To start with, there are a number of general concerns about the accuracy of facial recognition technologies and whether there are discriminatory biases in their accuracy. These have led the Association for Computing Machinery, among other organizations, to call for a moratorium on government use of facial recognition technology.

A study of commercial and academic facial recognition algorithms by the National Institute of Standards and Technology found that U.S. facial-matching algorithms generally have higher false positive rates for Asian and Black faces than for white faces, although recent results have improved. ID.me claims that there is no racial bias in its face-matching verification process.

There are many other conditions that can also cause inaccuracy – physical changes caused by illness or an accident, hair loss due to chemotherapy, color change due to aging, gender conversions and others. How any company, including ID.me, handles such situations is unclear, and this is one issue that has raised concerns. Imagine having a disfiguring accident and not being able to log into your medical insurance company’s website because of damage to your face.

Facial recognition technology is spreading fast. Is the technology – and society – ready?

Data privacy

There are other issues that go beyond the question of just how well the algorithm works. As part of its process, ID.me collects a very large amount of personal information. It has a very long and difficult-to-read privacy policy, but essentially while ID.me doesn’t share most of the personal information, it does share various information about internet use and website visits with other partners. The nature of these exchanges is not immediately apparent.

So one question that arises is what level of information the company shares with the government, and whether the information can be used in tracking U.S. citizens between regulated boundaries that apply to government agencies. Privacy advocates on both the left and right have long opposed any form of a mandatory uniform government identification card. Does handing off the identification to a private company allow the government to essentially achieve this through subterfuge? It’s not difficult to imagine that some states – and maybe eventually the federal government – could insist on an identification from ID.me or one of its competitors to access government services, get medical coverage and even to vote.

As Joy Buolamwini, an MIT AI researcher and founder of the Algorithmic Justice League, argued, beyond accuracy and bias issues is the question of the right not to use biometric technology. “Government pressure on citizens to share their biometric data with the government affects all of us — no matter your race, gender, or political affiliations,” she wrote.

Too many unknowns for comfort

Another issue is who audits ID.me for the security of its applications? While no one is accusing ID.me of bad practices, security researchers are worried about how the company may protect the incredible level of personal information it will end up with. Imagine a security breach that released the IRS information for millions of taxpayers. In the fast-changing world of cybersecurity, with threats ranging from individual hacking to international criminal activities, experts would like assurance that a company provided with so much personal information is using state-of-the-art security and keeping it up to date.

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Much of the questioning of the IRS decision comes because these are early days for government use of private companies to provide biometric security, and some of the details are still not fully explained. Even if you grant that the IRS use of the technology is appropriately limited, this is potentially the start of what could quickly snowball to many government agencies using commercial facial recognition companies to get around regulations that were put in place specifically to rein in government powers.

The U.S. stands at the edge of a slippery slope, and while that doesn’t mean facial recognition technology shouldn’t be used at all, I believe it does mean that the government should put a lot more care and due diligence into exploring the terrain ahead before taking those critical first steps.The Conversation

James Hendler, Professor of Computer, Web and Cognitive Sciences, Rensselaer Polytechnic Institute

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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Alecto, Megaera, and Tisiphone, I think I am even more nervous about the possibilities of false negatives than false positives. I do not take kindly to being told I am not who I am. I realize the government has a legitimate interest in being able to verify people’s identity, and I also realize that people as a whole are pretty stupid about passwords. That’s why there is a trend toward two-step verification (after inputting your password the site gives you an option of getting a one-time code by text or voice phone to a number which is already on record with them, and you input it when you receive it.) I assume we have all done that at one point or another. One of my banks has always had a two-step process where you had to have both a password and a PIN to get in (and now also has the phone/text option.) My credit union has for over a decade has a system where, upon opening an account, you select a picture from a library and then enter a pass phrase to go with it, and each time I log in they show both to me, and if either one is not right, then I don’t even enter my password (not that that has ever happened. In fact, it seems to be working.)

The Furies and I will be back.

 

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Everyday Erinyes #304

 Posted by at 5:50 pm  Politics
Feb 062022
 

Experts in autocracies have pointed out that it is, unfortunately, easy to slip into normalizing the tyrant, hence it is important to hang on to outrage. These incidents which seem to call for the efforts of the Greek Furies (Erinyes) to come and deal with them will, I hope, help with that. As a reminder, though no one really knows how many there were supposed to be, the three names we have are Alecto, Megaera, and Tisiphone. These roughly translate as “unceasing,” “grudging,” and “vengeful destruction.”

There has been, and has been building, a lot of concern about the future of our nation. Even if democracy survives this round of the fight, how will it fare in the next round, or the one after that, if our nation’s schools are churning out the poorly educated? And how will those students become well educated, even if they want to and have the ability to do so, if they cannot get their hands (and eyes) onto the books which contain the material they need?

This artice is addressed to those of us who have the energy, ability, and inclination to invest in the future by serving on a school board – or even on a library board. If that isn’t you, don’t immediately eliminate the possibility that it might be someone you know.
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More than masks and critical race theory – 3 tasks you should be prepared to do before you run for school board

School board elections are increasingly contested.
Nathan Howard/Getty Images

Casey D. Cobb, University of Connecticut

When people run for school board these days, they often are motivated to campaign on a controverisial topic. That’s according to Ballotpedia, a nonprofit that tracks political elections in the U.S.

In an analysis of school board elections in 463 school districts in 2021, the organization found elections that were once uncontested had drawn candidates who were “galvanized by one issue or another.”

Three issues came up the most. The most oft-cited issue was race in education, more specifically, the teaching of critical race theory. The second most frequently cited issue was school policies on the pandemic – that is, requirements to wear masks or get vaccinations, or school reopening. The third most-cited was sex and gender in schools, such as gender-specific facilities.

As of January 2022, Ballotpedia discovered 287 school districts in 25 states where candidates took a position on race in education; 199 school districts in 23 states where candidates took a position on responses to the coronavirus pandemic; and 144 school districts in 18 states where candidates took a position on sex and gender in schools.

A worrisome trend

As a former school board member – and as a researcher who studies educational leadership and policy – I find it worrisome when polarizing issues generate so much attention from candidates. The reason I worry is that I know from firsthand experience that being an effective school board member is never just about taking a stance on a few hot-button topics. Rather, it’s about much broader issues, such as meeting the educational needs of all students in the school district.

Too often, support for candidates hinges on the positions they take on the most controversial issues. For instance, in Florida, Gov. Ron DeSantis, speaking on behalf of his state’s Republican Party, pledged to withhold support from “any Republican candidate for school board who supports critical race theory in all 67 counties or supports mandatory masking of schoolchildren.”

As impassioned as people may be about issues like mask requirements, keeping schools open or confronting issues of race in the curriculum, running a school district is about much more than any one of those single issues. With that in mind, here are three actions that future school board candidates should be prepared to take.

1. Set district policy

A primary function of the school board is to develop, review and approve district policy. These policies can include implementing state mandates – such as establishing high school graduation requirements – or formulating a plan to evaluate teachers.

Some policies take on broad issues that affect all students. For instance, a policy might express a goal to make sure all students have access to the internet at home. Other policies might deal with smaller matters, such as whether home-schooled students can participate in extracurricular activities at the local public school.

2. Make tough budget decisions

One of the most difficult tasks that school board members must do is decide how to spend the school district’s limited revenue.

The vast majority of a district’s budget – about 80% to 85% – goes to personnel costs, such as salaries and benefits for school staff. Paying for these employee expenditures is becoming more challenging because of the rising cost of health insurance.

To stay within budget, school board members may have to cut positions or programs. It’s usually a matter of assessing tradeoffs: Do we cut our gifted and talented program to keep our school safety officer? Do we cut teaching positions to make the budget, and if so, which ones?

Each decision comes with consequences. For instance, cutting a gifted and talented program would make some families upset. Continued funding of a night school program might require a series of budget reductions in other areas, such as field trips or late buses.

A tough budget choice I remember facing as a school board member was deciding whether to renovate an outdated and undersized school theater. The board members all agreed the theater was in desperate need of an upgrade but decided to put off the theater upgrade to deal with other needs. The high school would soon need a new roof and boiler that ultimately took priority.

3. Select a superintendent

Selecting a district leader is critically important. So is deciding whether to keep or get rid of one. A good superintendent can make or break a district. The superintendent is the face of the school community and the district’s instructional leader.

Superintendents work with the school board to set the vision and goals for the district and then make sure they are achieved. They also hire and manage principals and other district leaders. Superintendents are expected to provide for the safety of children and staff and be good stewards of district finances.

Finding a good superintendent involves looking for leaders who have a proven track record in the areas of importance. Do they have a history of improving student achievement? Have they created a positive school climate and culture? Are they effective communicators?

If a school board chooses an ineffective superintendent, it usually sets a district back and the board ends up having to spend time and money to replace them.

A key distinction of American democracy is that candidates can develop platforms as they see fit, and it’s up to voters to decide if a particular candidate will represent their concerns. But when it comes to running a school system, it’s important to keep in mind that it involves much more than taking a stance on a few controversial issues. It’s also about making sound financial decisions and implementing policies that ensure all students get the education they deserve.

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Casey D. Cobb, Neag Professor of Educational Policy, University of Connecticut

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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Alecto, Megaera, and Tisiphone, I’m not sharing this article to be discouraging. I truly believe that any progressive, even if they need to learn in the trenches, would do a far superior job of setting policy, balancing budgets, and hiring superintendants that RWNJs, even though the latter might be more experienced. Even if only because the goals of progressives, and the directions in which they want to go, are healthier and wiser than anything RWNJs can even imagine. But all three areas are definitely something to think about. And the time to start thinking about them is, yes, before starting a campaign. Not only the district, but the campaign itself, will profit from that thought.

The Furies and I will be back.

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Everyday Erinyes #303

 Posted by at 12:41 pm  Politics
Jan 302022
 

Experts in autocracies have pointed out that it is, unfortunately, easy to slip into normalizing the tyrant, hence it is important to hang on to outrage. These incidents which seem to call for the efforts of the Greek Furies (Erinyes) to come and deal with them will, I hope, help with that. As a reminder, though no one really knows how many there were supposed to be, the three names we have are Alecto, Megaera, and Tisiphone. These roughly translate as “unceasing,” “grudging,” and “vengeful destruction.”

Science. Science deniers. This is not new. The two kinds of people have existed side by side for literally thousands of years. Taking one fact as an example, consider the “flat earth.” Scientests have known the earth ws not flat, but instead a more of less spherical shape, as early as the 5th century B.C.E. I say scientists have known, not that everyone has known. Galileo ws threatened with excommunication and improsonment as recently as the 1600s C.E. for suggesting that the earth mpved around the sun. (Yet 200 years earlier, Dante’s Inferno/ Purgatorio/ Paradiso was based on the premise of a spherical earth, through which he descended to the lowest levels of Hell at the center (he did get the temperature wrong – he pictured it as frozen – he wasn’t a scientist himself, but he must have listened to some) and then ascended through the levels of purgatory to come out into paradise on the other side. Today most people have grasped at least the concept of the solar system, and yet some still have not, and consider th earth to be flat.

Medical advances have a bad name in some circles because testing advances can be problematic. Of course no one would consider trying an idea on humans before doing animal testing, which brings up the question of how do you get informed consent from a frog? There might be a way, but we certainly don’t know what it is.

But I really find it exciting what this particular group of scientests is trying to do – and I have to believe that TC also would be excited – peersonally. Of course they are not going to get results usable by humans in my lifetime – nor in the lifetime of anyone here – and, discouraging as it is I have to wonder if the human race itself will last long enough to get results usable by humans.

But it’s still exciting.
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A new treatment helped frogs regenerate their amputated legs – taking science one step closer to helping people regrow their body parts, too

Reactivating the signals cells use to regenerate could help patients regrow lost limbs and damaged tissue.
George Jones/Stockbyte via Getty Images

Michael Levin, Tufts University; David Kaplan, Tufts University, and Nirosha Murugan, Algoma University

Our bodies connect us to the world. When people lose parts of their bodies to disease or traumatic injury, they often feel that they’ve lost a part of who they are, even experiencing a grief akin to losing a loved one. Their sense of personal loss is justified because unlike salamanders or snarky comic book characters like Deadpool, adult human tissues generally do not regenerate – limb loss is permanent and irreversible.

Or is it?

While there have been significant advances in prosthetic and bionic technologies to replace lost limbs, they cannot yet restore a sense of touch, minimize the sensation of phantom pains or match the capabilities of natural limbs. Without reconstructing the limb itself, a person won’t be able to feel the touch of a loved one or the warmth of the sun.

We are researchers in regenerative and developmental biology and biomedical engineering. Our recent study in the journal Science Advances showed that just 24 hours of a treatment we designed is enough to regenerate fully functional and touch-sensitive limbs in frogs.

Kickstarting regeneration

During very early development, cells that will eventually become limbs and organs arrange themselves into precise anatomical structures using a set of chemical, biomechanical and electrical signals. In considering ways to regenerate limbs, we reasoned that it would be much easier to ask cells to repeat what they already did during early development. So we looked for ways to trigger the “build whatever normally was here” signal for cells at the site of a wound.

One of the major challenges in doing this, however, is figuring out how to create an environment that encourages the body to regenerate instead of forming scars. While scars help protect injured tissue from further damage, they also change the cellular environment in ways that prevent regeneration.

Axolotls are known for their powerful regenerative abilities.

Some aquatic animals such as the axolotl have mastered regeneration without scar formation. And even in early human development, the amniotic sac provides an environment that can facilitate regenerative mechanisms. We hypothesized that developing a similar environment could override scar formation at the time of injury and allow the body to reactivate dormant regenerative signals.

To implement this idea, we developed a wearable device made of a silk hydrogel as a way to create an isolated chamber for regeneration by blocking other signals that would direct the body to develop scars or undergo other processes. We then loaded the device with a cocktail of five drugs involved in normal animal development and tissue growth.

We chose to test the device using African clawed frogs, a species commonly used in animal research which, like humans, does not regenerate limbs in adulthood. We attached the device onto one leg stump for 24 hours. We then removed the device and observed how the site of the lost limb changed over time. Over the course of 18 months, we were amazed to find that the frogs were able to regenerate their legs, including fingerlike projections with significant nerve, bone and blood vessel regrowth. The limbs also responded to light pressure, meaning that they had a restored sense of touch, and allowed the frog to return to normal swimming behavior.

Frogs that were given the device but without the drug cocktail had limited limb regrowth without much functional restoration. And frogs that weren’t treated with the device or the drug cocktail did not regrow their limbs, leaving stumps that were insensitive to touch and functionally impaired.

Interestingly, the limbs of the frogs treated with the device and the drug cocktail weren’t perfectly reconstructed. For example, bones were sometimes fragmented. However, the incompleteness of the new limb tells us that other key molecular signals may be missing, and many aspects of the treatment can still be optimized. Once we identify these signals, adding them to the drug treatment could potentially fully reverse limb loss in the future.

Person putting on prosthetic leg
While prosthetic and bionic limbs can help amputees regain their independence, they do not fully restore function.
Nadia Ramahi/500px Prime via Getty Images

The future of regenerative medicine

Traumatic injury is one of the leading causes of death and disability in Americans. And limb loss from severe injury is the most frequent source of lifelong disability. These traumatic injuries are often caused by automobile accidents, athletic injury, side effects of metabolic diseases such as diabetes and even battlefield injuries.

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The possibility of decoding and awakening dormant signals that enable the body to regenerate parts of itself is a transformative frontier in medical science. Beyond regrowing lost limbs, regenerating heart tissue after a heart attack or brain tissue after a stroke could extend life and dramatically increase its quality. Our treatment is far from being ready to use in humans, and we only know that it works when applied immediately after injury. But uncovering and understanding the signals that allow cells to regenerate means that patients may not have to wait for scientists to really understand all the intricacies of how complex organs are constructed before they can get treated.

Making a person whole again means more than just replacing their limb. It also means restoring their sense of touch and ability to function. New approaches in regenerative medicine are now beginning to identify how that may be possible.The Conversation

Michael Levin, Professor of Biology, Tufts University; David Kaplan, Professor of Biomedical Engineering, Tufts University, and Nirosha Murugan, Assistant Professor of Biology, Algoma University

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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Alecto, Megaera, and Tisiphone, perhaps unleashing your fury on the science deniers – even if only those in denial cults who are destroying science and truth for the rest of us – that might help. I don’t know what else could.

The Furies and I will be back.

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Everyday Erinyes #302

 Posted by at 11:22 am  Politics
Jan 232022
 

Experts in autocracies have pointed out that it is, unfortunately, easy to slip into normalizing the tyrant, hence it is important to hang on to outrage. These incidents which seem to call for the efforts of the Greek Furies (Erinyes) to come and deal with them will, I hope, help with that. As a reminder, though no one really knows how many there were supposed to be, the three names we have are Alecto, Megaera, and Tisiphone. These roughly translate as “unceasing,” “grudging,” and “vengeful destruction.”

Let’s face it – we have already gone so far with our abuse of resources that zero emissions is not going to be enough. We are going to need negative emissions if we are ever again going to have a planet capable of living on in even relative comfort. There are people working on ways to go about achiening that. This is the story of one possible method – direct air capture.
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Why we can’t reverse climate change with ‘negative emissions’ technologies

Without rapid and dramatic changes, the world will face a higher risk of extreme weather and other effects of climate change.
AP Photo/Mike Groll

Howard J. Herzog, Massachusetts Institute of Technology (MIT)

In a much-anticipated report, the Intergovernmental Panel on Climate Change (IPCC) said the world will need to take dramatic and drastic steps to avoid the catastrophic effects of climate change.

Featured prominently in the report is a discussion of a range of techniques for removing carbon dioxide from the air, called Carbon Dioxide Removal (CDR) technologies or negative emissions technologies (NETs). The IPCC said the world would need to rely significantly on these techniques to avoid increasing Earth’s temperatures above 1.5 degrees Celsius, or 2.7 degrees Fahrenheit, compared to pre-industrial levels.

Given that the level of greenhouse gases continues to rise and the world’s efforts at lowering emissions are falling way short of targets climate scientists recommend, what contribution we can expect from NETs is becoming a critical question. Can they actually work at a big enough scale?

What are negative emissions technologies?

There is a wide range of opinion on how big an impact these techniques can have in addressing climate change. I became involved in the debate because two of the most prominent negative emissions technologies involve CO2 capture and storage (CCS), a technology that I have been researching for almost 30 years.

Many NETs remove the CO2 from the atmosphere biologically through photosynthesis – the simplest example being afforestation, or planting more trees. Depending on the specific technique, the carbon removed from the atmosphere may end up in soils, vegetation, the ocean, deep geological formations, or even in rocks.

NETs vary on their cost, scale (how many tons they can potentially remove from the atmosphere), technological readiness, environmental impacts and effectiveness. Afforestation/reforestation is the only NET to have been deployed commercially though others have been tested at smaller scales. For example, there are a number of efforts to produce biochar, a charcoal made with plant matter that has a net negative carbon balance.

A recent academic paper discusses the “costs, potentials, and side-effects” of the various NETs. Afforestation/reforestation is one of the least expensive options, with a cost on the order of tens of dollars per ton of CO2, but the scope for carbon removal is small compared to other NETs.

On the other extreme is direct air capture, which covers a range of engineered systems meant to remove CO2 from the air. The costs of direct air capture, which has been tested at small scales, are on the order of hundreds of dollars or more per ton of CO2, but is on the high end in terms of the potential amount of CO2 that can be removed.

A handful of commercial companies are testing direct air capture technology,, which takes carbon dioxide out of the air. This project in Italy will use the CO2 to ultimately produce natural gas to power vehicles.
Climeworks

In a 2014 IPCC report, a technology called bio-energy with carbon capture and storage (BECCS) received the most attention. This entails burning plant matter, or biomass, for energy and then collecting the CO2 emissions and pumping the gases underground. Its cost is high, but not excessive, in the range of US$100-200 per ton of CO2 removed.

The biggest constraint on the size of its deployment relates to the availability of “low-carbon” biomass. There are carbon emissions associated with the growing, harvesting, and transporting of biomass, as well as potential carbon emissions due to land-use changes – for example, if forests are cut down in favor of other forms of biomass. These emissions must all be kept to a minimum for biomass to be “low-carbon” and for the overall scheme to result in negative emissions. Potential “low-carbon” biomass includes switchgrass or loblolly pine, as opposed to say corn, which is currently turned into liquid fuels and acknowledged to have a high carbon footprint.

Some of the proposed NETs are highly speculative. For example, ocean fertilization is generally not considered a realistic option because its environmental impact on the ocean is probably unacceptable. Also, there are questions about how effective it would be in removing CO2.

Academic takes

A 2017 study at the University of Michigan did a literature review of NETs. One the one hand, they showed that the literature was very bullish on NETs. It concluded these techniques could capture the equivalent of 37 gigatons (billion tons) of CO2 per year at a cost of below $70 per metric ton. For comparison, the world currently emits about 38 gigatons of CO2 a year.

However, I think this result should be taken with a large grain of salt, as they rated only one NET as established (afforestation/reforestation), three others as demonstrated (BECCS, biochar and modified agricultural practices), and the rest as speculative. In other words, these technologies have potential, but they have yet to be proven effective.

Other studies have a much harsher view of NETs. A study in Nature Climate Change from 2015 states, “There is no NET (or combination of NETs) currently available that could be implemented to meet the <2°C target without significant impact on either land, energy, water, nutrient, albedo or cost, and so ‘plan A’ must be to immediately and aggressively reduce GHG emissions.” In another study from 2016, researchers Kevin Anderson and Glen Peters concluded “Negative-emission technologies are not an insurance policy, but rather an unjust and high-stakes gamble. There is a real risk they will be unable to deliver on the scale of their promise.”

The bottom line is that NETs must be shown to work on a gigaton scale, at an affordable cost, and without serious environmental impacts. That has not happened yet. As seen from above, there is a wide range of opinion on whether this will ever happen.

Safety net?

A critical question is what role NETs can play, both from a policy and economic point of view, as we struggle to stabilize the mean global temperature at an acceptable level.

One potential role for NETs is as an offset. This means that the amount of CO2 removed from the atmosphere generates credits that offset emissions elsewhere. Using negative emissions this way can be a powerful policy or economic lever.

For example, with airline travel the best approach to net zero emissions may be to let that industry to continue to emit CO2, but offset those emissions using credits from NETs. Essentially those negative emissions are a way to compensate for the emissions from flying, which is expected to rely on fossil fuels for many years.

About 25 percent of our current carbon emissions can be classified as hard to mitigate. This offset model makes economic sense when the cost of negative emissions is less than the cost to cut emissions from the source itself. So if we can produce negative emissions from say BECCS at about $150 per ton of CO2, they can economically be used to offset emissions from aircraft that would cost several hundred dollars per ton CO2 to mitigate by changing how planes are fueled.

The economics of using NETs to correct an “overshoot” are very different.

We as a society seem unwilling to undertake sufficient efforts to reduce carbon emissions today at costs of tens of dollars per ton CO2 in order to keep enough CO2 out of the atmosphere to meet stabilization targets of 1.5 or 2 degrees Celsius. However, correcting an “overshoot” means we expect future generations to clean up our mess by removing CO2 from the atmosphere at costs of hundreds of dollars or more per ton CO2, which is what the future deployment of NETs may cost.

This makes no sense, economic or otherwise. If we are unwilling to use the relatively cheap mitigation technologies to lower carbon emissions available today, such as improved efficiency, increased renewables, or switching from coal to natural gas, what makes anyone think that future generations will use NETs, which are much, much more expensive?

That’s why I see the role of NETs as an offset being very sound, with some deployment already happening today and increased deployment expected in the future. By contrast, treating NETs as a way to compensate for breaking the carbon budget and overshooting stabilization targets is more hope than reality. The technical, economic and environmental barriers of NETs are very real. In formulating climate policy, I believe we cannot count on the future use of NETs to compensate for our failure to do enough mitigation today.The Conversation

Howard J. Herzog, Senior Research Engineer, Massachusetts Institute of Technology (MIT)

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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Alecto, Megaera, and Tisiphone, in the Open Thread, I posted a story about IKEA buying land for afforestation. That’s a good thing. But forests alone are not going to do the trick. Neither will direct air capture alone do the trick. Even if the technology were advanced enough to handle the amount of carbon removal which is needed, you can’t get fruit, or nuts, or wood, or habitat for endangered species, from direct air capture. There are other negative emissions technologies being tested or developed, but, at this point, nothing works well enough to actually achieve enough benefit to save the world. Direct ait capture seems to be the most promising – but we are not where we need to be on it either. And ALL possible technologies should be investigated and considered.

The Furies and I will be back.

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Everyday Erinyes #301

 Posted by at 7:07 pm  Politics
Jan 162022
 

Experts in autocracies have pointed out that it is, unfortunately, easy to slip into normalizing the tyrant, hence it is important to hang on to outrage. These incidents which seem to call for the efforts of the Greek Furies (Erinyes) to come and deal with them will, I hope, help with that. As a reminder, though no one really knows how many there were supposed to be, the three names we have are Alecto, Megaera, and Tisiphone. These roughly translate as “unceasing,” “grudging,” and “vengeful destruction.”

When you live with unfettered capitalism, pretty much anything that happens which involves money will also make inequality worse. And inflation is no exception.Without further ado, here are the facts and figures.
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Inflation inequality: Poorest Americans are hit hardest by soaring prices on necessities

Not all baskets are created equally.
Gina Ferazzi/Los Angeles Times via Getty Images

Jacob Orchard, University of California San Diego

The fastest rate of inflation in 40 years is hurting families across the U.S. who are seeing ever-higher prices for everything from meat and potatoes to housing and gasoline.

But behind the headline number that’s been widely reported is something that often gets overlooked: Inflation affects different households in different ways – and sometimes hurts those with the least, the most.

Inflation, as calculated by the Bureau of Labor Statistics, is designed to track the price increases in a typical U.S. household’s basket of goods. The problem is spending bundles differ across households. For example, a family in the lowest 20% of income typically spends around 15% of their budget on groceries – this is nearly 60% more than households in the top 20% of the income distribution, according to my calculations.

The widening inflation gap

On Jan. 12, 2022, the BLS released figures showing that inflation jumped by 7% in December from a year earlier – the fastest pace since 1982. To see how this varied across households, I used the bureau’s own price data and factored in the typical spending habits of different income groups.

I calculate that inflation is running at 7.2% for the lowest income households – higher than for any other group. For the highest income families, the rate of change was 6.6%.

The difference between the two income groups steadily increased throughout 2021, starting the year at just 0.16 percentage point but ending at 0.6 percentage point – near the highest it has been since 2010.

The reason for this widening rich-poor inflation gap, known by economists as inflation inequality, comes down to the typical spending habits of people in each income group.

In times of economic uncertainty and recession, most households tend to hold back on buying luxury goods. But by and large, people can’t cut down on necessities such as groceries and heating – although wealthier consumers are better placed to stock up on these necessities when prices are cheap.

This shift of spending away from luxury items like vacations and new cars, and toward necessities, pushes inflation up for poorer families more than richer ones. This is because lower-income households dedicate a higher percentage of their income on necessities.

My data shows that this inflation gap tends to be widest in times of recession or in the early stages of economic recovery. In the aftermath of the Great Recession of 2008-2009, the gap in inflation rates between the lowest and highest income groups was close to 1 percentage point – higher than it is now.

By contrast, in times of economic growth – for example, from 2012 to 2018 – the gap narrows. It even inverted at one point in 2016; the inflation rate for poorer Americans was almost a half-percentage point lower than that of richer Americans.

The main driver of the growing gap in 2021 was the increases in groceries and gas prices. This has made inflation run hotter for all households. But given the greater proportion of household income that poorer families dedicate to food and energy costs, it has affected them more.

Take out gas and grocery prices, then the inflation gap is reduced significantly.

Going forward, I expect the inflation gap will follow a similar pattern as we saw after the Great Recession – as economic recovery turns into continued expansion, inflation will be lower for low-income households than high-income households.

[More than 140,000 readers get one of The Conversation’s informative newsletters. Join the list today.]The Conversation

Jacob Orchard, Doctoral Candidate in Economics, University of California San Diego

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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Alecto, Megaera, and Tisiphone, the vast differences in spending habits is also why a universal sales tax makes no sense. The poor spend every penny they earn, while the wealthy put much of their income into savings. So a universal sales tax translates to those who can best afford to pay taxes paying very little, while those who can least afford it are paying more than they can afford. So of course those who would impose a universal sales tax claim it is more fair, because “everyone pays the same rate.” No. They don’t. End of rant.

The Furies and I will be back.

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Everyday Erinyes #300

 Posted by at 5:03 pm  Plus, Politics
Jan 092022
 

Experts in autocracies have pointed out that it is, unfortunately, easy to slip into normalizing the tyrant, hence it is important to hang on to outrage. These incidents which seem to call for the efforts of the Greek Furies (Erinyes) to come and deal with them will, I hope, help with that. As a reminder, though no one really knows how many there were supposed to be, the three names we have are Alecto, Megaera, and Tisiphone. These roughly translate as “unceasing,” “grudging,” and “vengeful destruction.”

Walter Shaub writes a newsletter for the Project on Government Oversight, called “The Bridge.” It is only published in emails – there is no link I can give you so you can find it and read it. If I want to share it in full, I have no choice except to reprint it in full. However, I have always thought, and now courts have held, that if you put something into an email it is fair gme to reprint.

Shaub is a specialist in ethics, and that is the focus of The Bridge. This week’s issue (like just about everything else on the ‘net this week) is related to last year’s insurrection, and he has thughts. Thoughts which I consider worth sharing.
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Today is the anniversary of the January 6, 2021, attack on the Capitol. Others will offer analyses of ongoing investigations into the attack. I want to reflect on its significance.

A DAY THAT HAS NOT LIVED IN INFAMY

Former president Donald Trump tried to overthrow American democracy from inside the government. Members of Congress and the vice president fled from a mob. People died. More were injured. The casualties include more than 140 police officers who defended the Capitol against an overwhelming onslaught. The republic was threatened.

You wouldn’t know it, though.

Insurrection sympathizers have celebrated their plot like the storming of the Bastille. Others have labeled it “America’s failed insurrection,” as though a verdict of failure were possible yet. The Department of Justice boasts that it has arrested 725 people, but they are low-level insurrectionists; the vast majority are charged with mere property crimes or obstruction of the investigation. There’s no public indication that DOJ is pursuing those who incited the attack. Even the name DOJ has given its prosecutorial effort downplays the significance of the insurrection: “Capitol Breach Cases.”

Capitol breach cases? The full name of the 9/11 Commission was “The National Commission on Terrorist Attacks Upon the United States.” By DOJ’s logic, it could’ve been called the “Unauthorized Flight Diversion Commission.” What happened on January 6 was a terrorist attack. Terrorists warrant more than bureaucratic language and slaps on the wrist.

Congress has shown more courage, but its powers are as limited as its capacity for rapid response. Congress took half a year to establish a committee to investigate the attack. News reports suggest the committee has uncovered a trove of information from hundreds of cooperating witnesses. But its initial report isn’t expected until this summer. Complicating the effort, some key witnesses have openly defied the committee and seem determined to stall in the hope of a leadership change in Congress next year.

There’s a reason accountability has been elusive: the movement behind the attack on the republic remains powerful. Just hours after the attack, 147 members of Congress voted to overturn the election because they didn’t like the result. Those who incited a mob to storm the Capitol lost a battle, not the war on democracy. The threat today is as real as it was then.

Seven Days in May

The persistence of the threat isn’t a cause for despair; it’s a call to action. Democracy has always been fragile, and threats to freedom are not new. The 1964 film Seven Days in May offers an instructive reminder of that. This black and white thriller was always a favorite of mine for its artful portrayal of the republic’s vulnerability and the need for vigilance. The film has never felt more relevant than it does now.

In the film, the chairman of the Joint Chiefs of Staff, General James Mattoon Scott, plots with other Pentagon leaders and at least one member of Congress to overthrow the government. The film opens with a protest outside the White House, where the treacherous general’s followers converge with followers of the president. Violence erupts.

Later, when General Scott delivers an inappropriately political speech at Madison Square Garden, it becomes clear that he has been priming the public for a change in leadership. His plot is conceived with military precision, and it fails only due to the intervention of a faithful marine, played by Kirk Douglas, who lives up to the Marine Corps’ motto: Semper Fidelis.

This depiction of democracy narrowly escaping destruction served as a warning about how those with authoritarian ambitions can misuse the government’s own machinery against itself. The fictional General Scott is said to be based partly on two real-life figures. One was the notorious General Edwin Walker, who resigned after being stripped of his command for extremist political activities and was later charged with insurrection for participating in a deadly riot to block Mississippi University’s integration. The other was General Curtis LeMay, who objected bitterly to President John F. Kennedy’s refusal to invade Cuba.

President Kennedy received an advance copy of the book on which the film was based and found it believable. The military’s top brass had earned his distrust by advocating for the tactical use of nuclear weapons and proposing terrorist attacks in Florida to generate support for invading Cuba. Kennedy urged Hollywood to make the book into a movie as a warning about the republic’s fragility.

The particulars of the film’s storyline differ from the events of January 6, but the particulars don’t matter; this is the story of a threat from within the government. In both cases, an attack incited by a demagogue follows a protest outside the White House. The film ends when the plot is foiled. We’re past that point with our insurrection, but Seven Days in May can still serve as a warning about what happens next. In the film, most (not all) of the conspirators are forced out of government, but political circumstances save them from more serious accountability for their treachery. In the absence of accountability, the viewer can’t escape feeling that the republic remains vulnerable. It could happen again.

The same is true now. President Trump and some of his allies are out of government, but they haven’t faced further accountability. Trump’s chief of staff, Mark Meadows, joined him in pressuring DOJ officials and Georgia state election officials to help overturn the election results. Trump used his public platform to incite the attack. His Pentagon appointees did not come to the aid of the hopelessly outnumbered police for hours. Trump and his supporters continue to lie about voter fraud and sow doubts about our election systems. It could happen again.

In the year since the attack on the Capitol, the danger to the republic has only grown. The movement has shifted tactics, focusing now on voter suppression and keeping its adherents primed for future action with lies about voter fraud. We should be pressing our leaders to hold those responsible for the insurrection accountable. We should be pressing them to pass voting rights legislation. We should be active participants in the work of democracy. We must be. The fate of the republic depends on it.

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Alecto, Megaera, and Tisiphone, The 1994 TV movie “The Enemy Within” was more or less billed as an updated remake of “Seven Days in May.” I don’t know how accurate that is, nor how good it is (it couldn’t have JFK’s seal of approval, for one thing), but it is available to stream, whereas I believe “Seven Days in May” would be DVD or BluRay (or of course one could read the book.) I’ve always maintaind that what people learn through storytelling is better learned and more deeply internalized than anything learned through any other method. So any of those possibilities may well be worth a shot.

The Furies and I will be back.

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Everyday Erinyes #299

 Posted by at 12:01 pm  Politics
Jan 022022
 

Experts in autocracies have pointed out that it is, unfortunately, easy to slip into normalizing the tyrant, hence it is important to hang on to outrage. These incidents which seem to call for the efforts of the Greek Furies (Erinyes) to come and deal with them will, I hope, help with that. As a reminder, though no one really knows how many there were supposed to be, the three names we have are Alecto, Megaera, and Tisiphone. These roughly translate as “unceasing,” “grudging,” and “vengeful destruction.”

This article is several months old, but I missed it when it was new. It deals with something I have literally opposed since I was nine – forcing religion into government. I have never grasped why more people don’t recognixe the horrors of losing the separation of church and state – horrors which are even worse for the church than they are for the state (when the church beomoes about nothing but temporal power, it becomes the worst kind of cult.) Of course, now, after seeing the lengths of insanity to which “conservatives” have gove (the latest is that norses are now witches -seriously) – I still don’t understand it, but a least I have a clue why I don’t understand it.
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How ‘In God We Trust’ bills are helping advance a Christian nationalist agenda

Christian nationalists are pushing for ‘In God We Trust’ to be omnipresent.
Joe Longobardi Photography via Getty Images

Kristina M. Lee, Colorado State University

City vehicles in Chesapeake, Virginia, will soon be getting religion.

At a meeting on July 13, 2021, city councilors unanimously voted in favor of a proposal that would see the official motto of the U.S., “In God We Trust,” emblazoned on every city-owned car and truck, at an estimated cost to taxpayers of US$87,000.

Meanwhile, the state of Mississippi is preparing to defend in court its insistence that all citizens, unless they pay a fee for an alternative, must display the same four-word phrase on their license plates. Gov. Tate Reeves vowed last month to take the issue “all the way to the U.S. Supreme Court should we have to.”

“In God We Trust” became the national motto 65 years ago this month. But over the past few years a string of bills and city ordinances has sought to expand its usage and presence. Such efforts include legislation requiring or encouraging the motto be displayed in government buildings and schools, on license plates and on police vehicles.

A sample license plate with 'In God We Trust' on it
Mississippi license plates carry the motto.
State of Mississippi

The rise of bills across the country at this time is no coincidence. It fits with a concerted effort by Christian nationalists who view the motto as a tool to help legitimize an agenda of passing legislation that privileges conservative Christian values.

Christian nationalism is a political ideology that fuses conservative religious beliefs with a – usually white – American identity. Christian nationalists assume that the laws of the land should be based on Christian morals.

As a scholar of religious and political rhetoric, I have observed how Christian nationalists are using what I call “theistnormative” legislation – government-endorsed policies, rituals, laws and symbols that use vague religious references, such as “God” – to encourage people to view the United States as a theistic collective – that is to say, as a nation of believers in God.

From coins to national motto

Christian nationalists played a key role in getting “In God We Trust” put on coins during the Civil War and ever since have attempted to use the motto as “proof” that the United States is a Christian nation.

Early Christian nationalists criticized the Founding Fathers for failing to recognize the United States as an explicitly Christian nation in the Constitution. An early Christian nationalist organization, The National Reform Association, pushed for a “Christian Amendment” that would correct what they called the “original sin” of not recognizing Jesus Christ in the Constitution.

Their efforts failed. But Christian nationalists had better success in getting the more ambiguous motto “In God We Trust” put on coins in 1864. It followed a report to the U.S. Treasury by the director of the U.S. Mint, James Pollock, an active member of the National Reform Association, in which he asked: “We claim to be a Christian Nation – why should we not vindicate our character by honoring the God of Nations in the exercise of our political Sovereignty as a Nation?”

A handwritten letter in which Treasury Secretary Salmon Chase amends 'In God is our Trust' to 'In God We Trust' in an 1863 letter to James Pollock, director of the Philadelphia mint.
Treasury Secretary Salmon Chase amends ‘In God is our Trust’ to ‘In God We Trust’ in an 1863 letter to James Pollock, director of the Philadelphia mint.
National Archives and Records Administration

Amid fears of “atheistic communism” during the Cold War a century later, Christian nationalists in the U.S. again tried and failed to pass a “Christian Amendment.” But they again found success in advocating for legislation that used vague religious references, culminating in the adding of “under God” to the pledge of allegiance and making “In God We Trust” the national motto on July 30, 1956.

President Eisenhower at a ceremony introducing a 8-cent Statue of Liberty stamp with the inscription ‘In God We Trust.'
Two years before making ‘In God We Trust’ the national motto, President Eisenhower introduces a stamp carrying the slogan.
Bettmann / Getty Images

Since it became the national motto, conservative Christians have used “In God We Trust” to justify opposing abortion rights and same-sex marriage by suggesting that they violate the principles embedded in the motto.

Earlier this year, Mississippi state Sen. Cindy Hyde-Smith justified legislation that would ban voter registration on Sundays by holding up a dollar bill and saying, “This says, ‘The United States of America, in God we trust.’ … In God’s word in Exodus 20:18, it says ‘remember the Sabbath and keep it holy.‘”

While most Christian nationalists claim to support religious freedom – which would seemingly apply to all faiths – most believe Christianity, specifically white conservative Christian values, should be privileged in the public sphere.

‘Project Blitz’

Christian nationalists have increasingly turned to “In God We Trust” bills as a way to further legitimize their agenda. This is particularly evident in the “Project Blitz” initiative, led by the Congressional Prayer Caucus Foundation, which states its aim as “restoring Judeo-Christian principles to their rightful place.”

Project Blitz started in 2015 with the purpose of “blitzing” the country with legislation advancing Christian nationalism. As David Barton, a leader in the initiative, explained in a 2018 conference call with state legislators: “It’s kind of like whack-a-mole for the other side; it’ll drive ‘em crazy that they’ll have to divide their resources out in opposing this.”

One such success in Project Blitz was in Chesapeake, where the Congressional Prayer Caucus Foundation is based. The organization successfully pushed for the motto “In God We Trust” to be displayed at the City Hall.

After Project Blitz generated negative publicity in 2018, it was misleadingly rebranded as “Freedom for All.” During a recorded strategy meeting that was later circulated by the social justice think tank Political Research Associates, Lea Carawan of the Congressional Prayer Caucus Foundation explained, “As soon as we understood that they knew they were on to us, we changed the name; shifted things around a little bit […] we’ve renamed and moved on but it’s moving just as strong and just as powerfully.”

Up to 2018, the initiative had helped more than 70 bills relating to their agenda get proposed. The group continues to have successes in getting legislation not only proposed, but also passed. According to BlitzWatch, a group tracking Project Blitz initiatives, this includes bills that support Bible readings in schools and policies that allow adoption and foster agencies and health care providers to deny services based on religious grounds. But it is the “In God We Trust” bills that have seemingly been the most successful for Project Blitz.

Pushing America’s ‘Christian heritage’

According to the initiative’s 2020-2021 playbook – which was obtained by the religion news website Religion Dispatches – “In God We Trust” bills aim to recognize “the place of Christian principles in our nation’s history and heritage.”

While those behind “Project Blitz” claim the bills are not about converting people to Christianity, they also argue that the U.S. should be a Christian nation whose laws and policies “reflect Judeo-Christian or biblical values and concepts.”

As such, “In God We Trust” bills set the foundation for more explicitly conservative Christian legislation.

The playbooks suggest “In God We Trust” bills can “shore up later support for other governmental entities to support religious displays” to help America accept its “Christian heritage.” The Congressional Prayer Caucus Foundation also recommends legislators push for other types of bills including, as stated in their 2018-2019 playbook, a resolution to establish policy “favoring intimate sexual relations only between married, heterosexual couples.”

The risk of opposing

What makes “In God We Trust” bills so successful is that they often receive bipartisan support. In Louisiana, for example, it was a Democratic governor who signed the 2019 bill requiring the motto be displayed in all schools. Politicians who do oppose “In God We Trust” bills run the risk of being labeled as “anti-faith.”

Despite its being the national motto for only 65 years, Christian nationalists have framed “In God We Trust” as part of the U.S.‘s founding tradition. Moreover, the motto has become an important rhetorical weapon for Christian nationalists – using it to advance their belief that governments and people are to “trust in God,” and more specifically their perception of a conservative Christian God.

[Explore the intersection of faith, politics, arts and culture. Sign up for This Week in Religion.]The Conversation

Kristina M. Lee, Ph.D. Candidate in Rhetoric, Colorado State University

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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Alecto, Megaera, and Tisiphone, a sweet little phrase like “In God We Trust” sounds so harmless, so innocent. But it isn’t. In the first place, it’s a lie – we don’t all trust in God (least of all those who so loudly claim to do so). In the second place, it’s lazy – and dangerous – to “trust in God” in lieu of doing what you should be doing. I could go on, but all of us probably could. What was the matter with “E pluribus unum“, for the sweet sake of the sweet universe? At least it was pro-diversity, as our national motto should be. “Christian Nationalism” is nothing but a way to destroy Christianity and the nation (whatever nation gets caught up oin it) simultaneously.

(P. S. I just heard Beau define “heritage” as “peer pressure from the dead.”  I could not possibly have said it better.)

The Furies and I will be back.

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Everyday Erinyes #298

 Posted by at 1:51 pm  Politics
Dec 262021
 

Experts in autocracies have pointed out that it is, unfortunately, easy to slip into normalizing the tyrant, hence it is important to hang on to outrage. These incidents which seem to call for the efforts of the Greek Furies (Erinyes) to come and deal with them will, I hope, help with that. As a reminder, though no one really knows how many there were supposed to be, the three names we have are Alecto, Megaera, and Tisiphone. These roughly translate as “unceasing,” “grudging,” and “vengeful destruction.”

This article was posted before the heads-up from Walter Reed (which sent Mother Jones off to investigate, which led to an article included among today’s short takes), but that diesn’t mean it’s “old news.” I doubt that anyoe here has been up close and personal with gene sequencing. If you are into genealogy, or if you have any kind of hereditary medical condition, you may have in some obscure way used the results of the process, but of course that doesn’t make an expert, any more than drinking milk makes one an expert on cattle – much less a cow. As always, The Conversation has taken pains to make what’s in the article clear, and, hopefully, interesting.
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Genomic sequencing: Here’s how researchers identify omicron and other COVID-19 variants

Sequencing the genome of a virus gives researchers information on how mutations can affect its transmissibility and virulence.
catalinr/iStock via Getty Images Plus

Andre Hudson, Rochester Institute of Technology and Crista Wadsworth, Rochester Institute of Technology

How do scientists detect new variants of the virus that causes COVID-19? The answer is a process called DNA sequencing.

Researchers sequence DNA to determine the order of the four chemical building blocks, or nucleotides, that make it up: adenine, thymine, cytosine and guanine. The millions to billions of these building blocks paired up together collectively make up a genome that contains all the genetic information an organism needs to survive.

When an organism replicates, it makes a copy of its entire genome to pass on to its offspring. Sometimes errors in the copying process can lead to mutations in which one or more building blocks are swapped, deleted or inserted. This may alter genes, the instruction sheets for the proteins that allow an organism to function, and can ultimately affect the physical characteristics of that organism. In humans, for example, eye and hair color are the result of genetic variations that can arise from mutations. In the case of the virus that causes COVID-19, SARS-CoV-2, mutations can change its ability to spread, cause infection or even evade the immune system.

We are both biochemists and microbiologists who teach about and study the genomes of bacteria. We both use DNA sequencing in our research to understand how mutations affect antibiotic resistance. The tools we use to sequence DNA in our work are the same ones scientists are using right now to study the SARS-CoV-2 virus.

The first human genome took two decades to sequence. With advances in technology, scientists are now able to sequence DNA in a matter of hours.

How are genomes sequenced?

One of the earliest methods scientists used in the 1970s and 1980s was Sanger sequencing, which involves cutting up DNA into short fragments and adding radioactive or fluorescent tags to identify each nucleotide. The fragments are then put through an electric sieve that sorts them by size. Compared with newer methods, Sanger sequencing is slow and can process only relatively short stretches of DNA. Despite these limitations, it provides highly accurate data, and some researchers are still actively using this method to sequence SARS-CoV-2 samples.

Since the late 1990s, next-generation sequencing has revolutionized how researchers collect data on and understand genomes. Known as NGS, these technologies are able to process much higher volumes of DNA at the same time, significantly reducing the amount of time it takes to sequence a genome.

There are two main types of NGS platforms: second-generation and third-generation sequencers.

Second-generation sequencing marks each nucleotide with a specific color.

Second-generation technologies are able to read DNA directly. After DNA is cut up into fragments, short stretches of genetic material called adapters are added to give each nucleotide a different color. For example, adenine is colored blue and cytosine is colored red. Finally, these DNA fragments are fed into a computer and reassembled into the entire genomic sequence.

Third-generation technologies like the Nanopore MinIon directly sequence DNA by passing the entire DNA molecule through an electrical pore in the sequencer. Because each pair of nucleotides disrupts the electrical current in a particular way, the sequencer can read these changes and upload them directly to a computer. This allows clinicians to sequence samples at point-of-care clinical and treatment facilities. However, Nanopore sequences smaller volumes of DNA compared with other NGS platforms.

Third-generation sequencing detects changes in an electrical current to identify nucleotides.

Though each class of sequencer processes DNA in a different way, they can all report the millions or billions of building blocks that make up genomes in a short time – from a few hours to a few days. For example, the Illumina NovaSeq can sequence roughly 150 billion nucleotides, the equivalent of 48 human genomes, in just three days.

Using sequencing data to fight coronavirus

So why is genomic sequencing such an important tool in combating the spread of SARS-CoV-2?

Rapid public health responses to SARS-CoV-2 require intimate knowledge of how the virus is changing over time. Scientists have been using genome sequencing to track SARS-CoV-2 almost in real time since the start of the pandemic. Millions of individual SARS-CoV-2 genomes have been sequenced and housed in various public repositories like the Global Initiative on Sharing Avian Influenza Data and the National Center for Biotechnology Information.

Genomic surveillance has guided public health decisions as each new variant has emerged. For example, sequencing the genome of the omicron variant allowed researchers to detect over 30 mutations in the spike protein that allows the virus to bind to cells in the human body. This makes omicron a variant of concern, as these mutations are known to contribute to the virus’s ability to spread. Researchers are still learning about how these mutations might affect the severity of the infections omicron causes, and how well it’s able to evade current vaccines.

A screen showing sequences of the letters T, C, A and G.
This image shows a DNA readout of the alpha variant of SARS-CoV-2. A mutation is marked by dotted lines.
Sebastian Gollnow/picture alliance via Getty Images

Sequencing also has helped researchers identify variants that spread to new regions. Upon receiving a SARS-CoV-2 sample collected from a traveler who returned from South Africa on Nov. 22, 2021, researchers at the University of California, San Francisco, were able to detect omicron’s presence in five hours and had nearly the entire genome sequenced in eight. Since then, the Centers for Disease Control and Prevention has been monitoring omicron’s spread and advising the government on ways to prevent widespread community transmission.

The rapid detection of omicron worldwide emphasizes the power of robust genomic surveillance and the value of sharing genomic data across the globe. Understanding the genetic makeup of the virus and its variants gives researchers and public health officials insights into how to best update public health guidelines and maximize resource allocation for vaccine and drug development. By providing essential information on how to curb the spread of new variants, genomic sequencing has saved and will continue to save countless lives over the course of the pandemic.

[Get the best of The Conversation, every weekend. Sign up for our weekly newsletter.]The Conversation

Andre Hudson, Professor and Head of the Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology and Crista Wadsworth, Assistant Professor in the Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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AMT, Genomic sequencing is certainly not something I am an expert on. All I ever knew about it was that in the book “Gödel, Escher, Bach: an Eternal Golden Braid,” Douglas Hofstadter used “dialogues” based on Achilles and the Tortoise because their first latters matched adenine and thymine (he also snuck in a Crab for cytosine and occassionally referred to G for guaritine. Once I believe it was a guitar.) Pretty sophisticated for short pieceswhich were intended to bu humorous (but also to make readers think.)

Thank heaven we don’t need to be experts – that’s what real experts are for. But it’s nice to be a little familiar with a process, and its results, which are going to be dominating medical fields (and not just epidemiology) for decades to come.

The Furies and I will be back.

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