Yesterday, I discovered that our blog’s commenting system it being discontinued by WordPress. At the moment, it still works, except that every comments has to be approved by an administrator or editor. That’s not necessarily a bad thing. because something has also happened to the spam preventer, and some atrocious things are getting into the moderation queue,, and they need to be DISapproved by an editor or administrator. I spent hours searching through 51 pages of plugins (although I searched for “commonet systems,” most weren’t, which made it more tedious) without finding much. I want to find one that has all the features we are accustomed to and love, including nor requiring a login to comment, and that is being hard to find. I don’t want to jump in on anything we’ll hate, so I hope you’ll all bear with me.
NPR – Desmond Tutu’s laugh was contagious. His fight for freedom was deadly serious
Quote – Yet time and again, Tutu, dressed in his flowing clerical robe, would appear at a potentially explosive scene and invoke his gift of gab to defuse a crisis, often sending the crowd home with a smile on their faces. His impish grin, laughter and amusing stories were always employed in the service of nudging South Africans to retreat from the precipice of a racial confrontation. Click through. What a devastating loss!
Democratic Underground – The Mousetrap
Quote – A mouse looked through the crack in the wall to see the farmer and his wife open a package. “What food might this contain?” The mouse wondered – he was devastated to discover it was a mousetrap. Retreating to the farmyard, the mouse proclaimed the warning. “There is a mousetrap in the house! There is a mousetrap in the house!” Click through for story – nothing to do with the Agatha Christie play but a parable about karma, and a caution.
Food For Thought (from a tweet sent by David Corn):
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
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?
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.
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.
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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.
Glenn Kirschner – Time for the Military Leadership to Return Mike Flynn to Active Duty and Court-Martial Him (I might just add that retirees and active duty military are paid out of the same budget. I’m not saying that that [Dod] budget is not inflated – just that retireepay is a huge chunk of it, and why DoD doesn’t use that fact as a public selling point is beyond me. But it does bolster the military’s ability to recall retirees to active duty at will.))
Don Winslow – #JoeManchinsBrotherSuedHim
Robert Reich – The Oligarchy’s Ultimate Political Weapon
VoteVets – Maj.Gen.(Ret.) Paul Eaton Discusses WaPo Op-Ed & 2024 Insurrection Threat With Wolf Blitzer on CNN
Yesterday, I visited Virgil. It was special to be able to see him on Christmas, and he returns all greetings including special holiday greetings. The Sergeant who heads up the visitation team got the day off (and I really can’t think of anyone who deserves it more. For part of the time, the warden personally filled in for him. Don’t get me wrong – prison is still prison and no one wants to be there.. But there are some employees who have hearts and consciences. Although the time of sunset hadn’t changed (or rather it changed and then changed back) I left a little later and it didn’t work badly. There are still some (and one in particular) dangwr spots, but with proper equipment most of the drive is much better. The mast ten minutes of my drive were in “civil twilight,” which is when the sun is over the horizon, but there is still enough light to see by – you don’t need your lights on to see better, but you do to be seen better.) I can handle that. It only lasts a half hour, though (both morning and evening). Then there’s another half hour of “nauticak twilight” where there is still some reflected light but you need headlights. There might be more light reflected off of a water surface, but on land it’s not the best time to driver. Sunrise is still getting later, abd some of the drive out is becoming a bit more hazardous, but it should start getting earlier soon, which will also help.
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Short Takes
Crooks and Liars – HERO: All In A Day’s Work For Sixth-Grader Davyon Johnson
Quote – His principal, Latricia Dawkins, told the local paper, “He is just a kind soul and well-liked by his peers and staff alike.” His mom, LaToya Johnson, is proud but not surprised. She said her son wants to be an EMT, just like his uncle Wendell Johnson. Click through for story. One more good news story can’t hurt.
Mother Jones – The Mother of All Vaccines May Be Closer Than You Think
Quote – Now, after three coronavirus-sparked health crises in the last 20 years—SARS, MERS, and COVID-19—researchers are working to develop so-called universal coronavirus vaccines for the next outbreak. While COVID-19 vaccines are an incredible feat of science—they were created faster than any vaccine in history—researchers say it wasn’t fast enough. Kevin Saunders, the director of research at the Duke Human Vaccine Institute, points out that hundreds of thousands of Americans died from COVID-19 infections while vaccines were being developed and approved. If we have a universal coronavirus vaccine ready to go in the future, even if it isn’t perfect, he says, it could cut down on hospitalizations and deaths, and buy researchers time to hone a virus-specific vaccine. Click through for much more. The Walter Reed team has gone the farthest to date, but they are not alone, and others are also getting close. Now THAT’s good news.
Glenn Kirschner – Rep. Scott Perry Refuses to Provide Information/Evidence to the Jan. 6 Committee; Subpoena Time
politicsrus Manchin 2 HD
Robert Reich – The Columbia University Strike: My Son Gives an Insider’s Look
Caffeinated – What To Do with Joe Manchin & Krysten Sinema…
The Lincoln Project – Who GAF About Christmas?
Parody Project – It’s Beginning to Look a Lot Like – Uh-Oh! (I wanted a Chrsimas song here – this wasn’t it. But I’ll get to the other one before New Year’s.)
Beau – Let’s talk about Biden, Hunters, and trophies….
Yesterday, I mostly worked at getting my Christmas geese in a row so there’d be no interruptions. A package came whoch they had told me to expect on Monday, and I almost wish it hadn’t (but not quite) By the time you reat this, I’ll be on the road. It’s expected to be sunny with a high of 56°F, but that doesn’t mean I won’t need gloves on the way there . I’ll comment when I get back – not the instant I walk in the door but as soon as I get to the computer.
Cartoon – I never thought TC was naughty in any way, myself.
Short Takes
The Hill – Flynn suit against Jan. 6 committee dismissed over procedural errors
Quote – A federal judge on Wednesday dismissed former national security adviser Michael Flynn’s lawsuit against the House Jan. 6 select committee for failing to follow procedural rules in filing his case, but said he would have an opportunity to make corrections and re-submit it to the court. U.S. District Judge Mary Scriven said in an order issued just one day after the lawsuit was filed that, among other things, Flynn’s lawyers failed to show that there was an imminent need for the court to intervene against a set of subpoenas from the select committee aimed at the retired general and his phone provider. Click through. I figured from the headline he’d be allowed to resubmit, but that may be OK. It just needs to be dismissed again on more solid ground – like lack of atanding.
The Revelator – What’s Working: The Revelator’s 12 Favorite Solutions Stories of 2021
Quote – Writing about the environment these days can be tough. There’s more bad news than good. Climate-fueled disasters, new extinctions, science denial — we’ve covered some topics this year that will make your heart sink. But there’s a lot of encouraging news, too. As we look back at 2021, we want to revisit the stories that gave us hope, introduced new solutions, and highlighted the people hard at work on some of the most challenging issues of our day. Click through for all twelve headlines with links.
Second Nexus – GOP Rep. Who Opposed Certifying Biden’s Election On Jan. 6 Now Regrets Vote, Calls Trump A ‘Coward’
Quote – But even after their very lives were threatened, more than a hundred members of the House, along with seven Republican Senators, voted to toss out the electoral votes of at least one state. Among them was Republican Tom Rice of South Carolina, but in a recent interview, Rice expressed regret for his vote…. It’s worth noting that, when the House voted a week later to impeach Trump for inciting an insurrection, Rice was one of only 10 House Republicans who voted in favor. Click through. Second Nexus is one of George Takei’s sites (ha has several,) Eric Swalwell speaks for Rice, which carries weight with me (but it’s still pretty much too little – and too late.)
Yesterday, my second cousin Ann, whom I haven’t seen for just over 21 years, phoned to say Merry Christmas. She doesn’t use email, so we have been out of touch for that long, except for Christmas cards, and we havn’t been very chatty in those. I had just finished typing today’s first short take, and I told her about it, and she said that was a wonderful Christmas gift from me. I hope everyone feels that way. I certainly thought it was a BFD. I tried for all good news today, so I have probably left something out … but I hope I can do it again tomorrow.
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Short Takes
Crooks and Liars – WOW: Walter Reed Scientists Develop A Universal Covid Vaccine
Quote – The achievement is the result of almost two years of work on the virus. The Army lab received its first DNA sequencing of the COVID-19 virus in early 2020. Very early on, Walter Reed’s infectious diseases branch decided to focus on making a vaccine that would work against not just the existing strain but all of its potential variants as well. Click through for more. Of course thos would take longer than the strain-targeted vaccines to develop. I’m surprised it’s even possible. WO# indeed.
Law & Crime – Ex-Cop Kim Potter Convicted of All Charges for Shooting and Killing Daunte Wright
Quote – To convince the jury of the highest count, first-degree manslaughter, the state was required to prove that Potter caused Wright’s death during the commission of a lesser offense. Here, the lesser alleged offense was the reckless handling or use of a firearm. That lesser offense had to be proven in full and beyond a reasonable doubt as follows, according to the jury instructions the judge read before deliberations. Notably, the state was required to prove that Potter’s actions were a “conscious and intentional” act: Click through for story. It is a step in the direction of accountability for police. Although it does sound like this one knew from the get-go that she was responsible, which is unusual.
AP News – Tribes Lacking Water see glimmer of hope with massive bill
Quote – Now, there’s a glimmer of hope in the form of a massive infrastructure bill signed last month that White House officials say represents the largest single infusion of money into Indian Country. It includes $3.5 billion for the federal Indian Health Service, which provides health care to more than 2 million Native Americans and Alaska Natives, plus pots of money through other federal agencies for water projects. Click through fpr details and scope. It is a crying shame that native Americans, who as a groupdid more over more centuries to preseve clean and ample water supply are among the groups being cheated out of it. The bill referred to here is the infrastructure bill which already passed and has been signed into law. May it be a lifeline.
