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There’s a lot of chatter out there about the waning antibody titers in vaccinated people over time. Of course, survivors of infections also see their antibody titers fall with time, too, but the focus has been on the vaccines, for obvious reasons. And circulating antibodies do matter for protection from COVID-19. Together with the innate immune response, they represent the frontline response in a viral challenge. But often forgotten in the durable immunity response are the memory B- and T-cells. The assays for their activities are much harder to monitor, but ultimately, this part of the adaptive immune system plays and increasingly important role over time. And for vaccinated people, the memory cells are continuing to perform well: “‘Neutralizing’ antibodies that can intercept viruses before they infiltrate cells might not have much staying power. Levels of these molecules typically shoot up after vaccination, then quickly taper off months later. “That’s how vaccines work,” Doria-Rose ...

I’m still awaiting approval of the Moderna booster. But this preprint suggests that approval may be forthcoming soon: From the abstract: “Antibody neutralization titers against B.1.351 and P.1 variants measured by SARS-CoV-2 pseudovirus neutralization (PsVN) assays before the booster vaccinations, approximately 6 to 8 months after the primary series, were low or below the assay limit of quantification, although geometric mean titers versus the wild-type strain remained above levels likely to be protective. Two weeks after the booster vaccinations, titers against the wild-type original strain, B.1.351, and P.1 variants increased to levels similar to or higher than peak titers after the primary series vaccinations .” From the Discussion: “Prior to the boost, neutralization titers of 198 and 304 in the Part B and Part C cohorts remained significant, at levels predicted to be protective against the original Wuhan-Hu-1 isolate . . . all trial participants, including those that had undetec...

The current population of the US is a little north of 330 million. Even if we took in 3 million refugees and immigrants, that would be less than 1% of the US population. In what sense is that "replacement?" What's being replaced is the privileges of white Protestant heterosexual men. That's not happening because of immigration, it's because a new generation of Americans has come of age without the prejudices of the past, and is not afraid to call out the previous generations that had weaponized those prejudices against Americans who weren't white Protestant heterosexual men. White nationalism and Trumpism (but I repeat myself) have captured the GOP. Too many Republicans, like the "good Germans" who went along with the Nazis* and turned a blind eye to their hatred, are unwilling to reject the overt racist claims of their leaders. They are complicit in a party that is pitting Americans against Americans. Shame. *Yes, I know; Godwin's law https://ta...

I got my genome sequenced a few years back. It cost me $199 for the sequencing (30-50 fold coverage) and an initial report. I paid an additional $100 for my variant call file, which is now annotated so I can look for any newly discovered risk alleles. Of course, most single-gene genetic disorders already evidence themselves clinically by the seventh decade. Indeed, most become symptomatic within the first two decades. I was mainly interested in risk alleles for dementia (e.g., ApoE4), thrombotic disorders or cancer, since my parents had one or another of these conditions. A major promise for the clinical application of genomics was the “thousand dollar genome.” We’re pretty much there, now, and yet genomic sequencing for neonates isn’t routine. Why not? “About one in five extremely ill infants lacking a clear diagnosis benefited from whole genome sequencing, researchers found in a randomized trial. Clinical management shifted for 34 of 161 evaluable patients whose full genomic sequenc...

  I've never understood the racist "replacement theory" being used by the GOP to attack refugees. Apart from being overtly racist, it doesn't make sense mathematically: " . . . let's say the U.S. allowed every one of those Haitians to apply for asylum, you wouldn't get kicked out of the country. It's not the way it works. America is not a night club where people have to come out before other people can come in. It's actually a really big country with nearly 330 million people. So a few thousand people are not replacing anyone." Also too: "These people have done one of the most difficult, ambitious things a human being can do. They left their homes at great personal cost and risk. They crossed thousands of miles to a completely foreign land where most don't know anyone and don't speak the language in the slim hope of a better life. Whatever you want to call that, that's the opposite of obedient. Whatever you want to say abo...

  What's wacky is the whole idea of having to vote on raising the debt ceiling. The trillion dollar platinum coin is a paragon of sobriety by comparison. https://www.cnn.com/2021/09/24/economy/trillion-dollar-coin-debt-ceiling/index.html

  "A monthslong hand recount of Maricopa County's 2020 vote confirmed that President Joe Biden won and the election was not "stolen" from former President Donald Trump, according to early versions of a report prepared for the Arizona Senate," The Arizona Republic reported Thursday evening, one day before the findings were scheduled to be released. "The three-volume report by the Cyber Ninjas, the Senate's lead contractor, includes results that show Trump lost by a wider margin than the county's official election results," the newspaper noted. "The hand count shows Trump received 45,469 fewer votes than Biden. The county results showed he lost by 45,109." Now they're pushing a fraudit in Texas. Wonder if they'll find more Biden votes there, too. https://www.rawstory.com/arizona-cyber-ninjas-fraudit/?fbclid=IwAR3wXlaqRPypdyg7ZieodJKjj0wtaLbnvaE3vg5tp9qBXKHgIcQ-3wIrNno

  Been seeing a lot in the news about a pretty blond white woman on social media who went missing and then was found dead. This is certainly a tragedy, but: "The story has also further highlighted the tens of thousands of missing persons stories that do not garner such intense interest; there were nearly 90,000 active missing person cases as of the end of 2020, according to the National Crime Information Center." https://www.cnn.com/2021/09/22/us/gabby-petito-brian-laundrie-update-wednesday/index.html?fbclid=IwAR2ooW3hJRe6NJvVxNTPrgweNJLSuvMV-lDvzQjdtHG-xDXN1x2hFY4xz5s

  The bleat of the anti-vaxxer is "my body, my choice." Uh, no, not for a contagious disease during a pandemic. If your "choice" means someone else loses access to health care, it's not just you who is affected. Nevermind all the other people you infect when you exercise your choice, and that you may end up incubating the next COVID-19 variant. "Idaho public health leaders announced Tuesday that they activated "crisis standards of care" allowing health care rationing for the state's northern hospitals because there are more coronavirus patients than the institutions can handle. The Idaho Department of Health and Welfare quietly enacted the move Monday and publicly announced it in a statement Tuesday morning — warning residents that they may not get the care they would normally expect if they need to be hospitalized. The move came as the state's confirmed coronavirus cases skyrocketed in recent weeks. Idaho has one of the lowest vaccination...

Of course, I'm over 365 days out, so I'd be happy to get a booster while I wait for the one-year data. But I'm glad I enrolled in the Moderna trial (and was lucky to be in the vaccine arm of the trial). "After 120 days from the time of vaccination, however, Moderna's VE against hospitalization only dipped to 92%, a non-significant decline, while Pfizer's dropped to 77% (P<0.001). "Differences in VE between the Moderna and Pfizer-BioNTech vaccine might be due to higher mRNA content in the Moderna vaccine, differences in timing between doses (3 weeks for Pfizer-BioNTech versus 4 weeks for Moderna), or possible differences between groups that received each vaccine that were not accounted for in the analysis," Self and co-authors suggested. No data were shown for the J&J shot after 120 days due to the limited number of patients who received the vaccine, but the VE rate dipped to 68% for the single-dose vaccine after 28 days." https://www.medpa...

  Looks like the GOP is once again threatening to vote against raising the debt ceiling, since the president is a Democrat. The national debt only matters with Democratic presidents, doncha know. But ultimately, this is just political posturing and both parties know it. From a comment over at Angrybear blog: "If the US defaults on its sovereign debt, then that would end the dollar’s exorbitant privilege causing the dollar’s foreign exchange rate to plummet and eliminating trade deficits along with most of the US economy. Republican’s threat to default is only a negotiating tactic like extortion. A dead hostage cannot be ransomed."

  Arguably *the* transformative scientific innovation of the past two years was the development and deployment of mRNA vaccines against SARS-CoV-2. But like any innovation, there is a long unsung history, with lots of players nobody heard of. Since the Nobel Prize in Medicine is likely to go to mRNA vaccines next month, there's plenty of chatter about who will be named (maximum of three). Here's a history of mRNA vaccines that appeared in this week's Nature. It highlights both the key enabling discoveries and the many stumbles along the way. You'll also learn where "Moderna" got its name. This quote resonated with me: "“RNA was so hard to work with,” says Matt Winkler, who founded one of the first RNA-focused lab supplies companies, Ambion, in Austin, Texas, in 1989. “If you had asked me back [then] if you could inject RNA into somebody for a vaccine, I would have laughed in your face.”" I've been working with mRNA and gene expression for over 40...

  Yom Kippur begins at sundown today. I was raised Roman Catholic, not Jewish, although according the Israel's law of return, I'm Jewish. In practice, I'm an atheist. But there are certainly worthwhile practices framed in religious terms that we all can endorse. This is one for Yom Kippur: "You don’t have to be Jewish to recognize how much harm is done by the sins we commit against one another — above all, by the words we use in talking (or texting or tweeting or posting or e-mailing) to and about one another. You don’t have to be a believer to know that no good can come of our vanishing ability to find common ground. You don’t have to observe a Day of Atonement to wish there were more forgiveness in our world. But the world won’t change unless we change ourselves. However much it goes against the grain, we must learn to communicate more sympathy and less anger, to balance our own passionate convictions with greater forbearance toward others. It isn’t an easy aspiratio...

  I was directed to a post on the nakedcapitalism blog authored by someone called Yves Smith entitled “US as failed state: COVID bosster shot mess.” The post is a farrago of snark, innuendo and misdirection. When you don’t know your topic, the wise thing to do is either research it or shut up and listen to people who have. Sadly, Smith chooses self-indulgence over wisdom. Here are some facts: • thanks in large part to the Trump Administration, the US was ill-prepared for the COVID-19 pandemic. When it did arrive, Trump lied about it (“hoax,” “it will be gone by summer,” “just like the flu”) and his administration bungled efforts to supply masks and respirators; • for the NIH and CDC, dealing with the virus and the novel mRNA vaccines was like the fog of war with continuous sniper fire from the American right. Mistakes occur in the fog of war, and of course, members of the 86th Chairborne will generously offer their unsolicited advice after the smoke clears; • getting the American ...

  “I have never killed any one, but I have read some obituary notices with great satisfaction. ~Clarence Darrow During my ca. 40 year career as a research scientist, I arrived at something I called “the vengeful god hypothesis.” In developing testable hypotheses about the various research problems I tackled, I had to acknowledge that there was an alternative outcome that would falsify my assumptions. In fact, this is how all scientific hypotheses work: they must be testable by experiments that are capable of falsifying the hypothesis. But I jokingly referred to this outcome as “the vengeful god hypothesis,” as only a vengeful god would visit this outcome on me. The God of the Old Testament is a vengeful god, smiting humans by the millions. Definitely not a “pro-life” god. But it appears that there is a vengeful god in operation in the age of COVID, as several anti-vaxxer pandemic denialists have been smitten. I don’t exactly rejoice when I read this, but I shake my head at the eter...

  When I was in junior high and high school, I often had to prepare dinner while my parents were at work. For a family of seven, meat was a significant expense, so I would add textured vegetable protein to the hamburger. In a mix, it wasn't really noticeable. When I was a cook at the Pizza Inn, textured vegetable protein was also in the sausage we spread on pizzas. Recently, we've been experimenting with faux hamburger, and the household consensus is that the Impossible Burger makes a pretty good substitute for ground bison, which is what we were using after Rebecca weaned us off of beef. Here's an article about meat substitutes that considers in detail the alleged health benefits. "The bottom line: switching to plant-based meat alternatives may or may not confer some health benefits; it all depends on their composition, individual health needs, and one's overall diet. More than that, they're part of a bigger food system, the realities of which are often what p...

  When I was a postdoc in the mid-80s, the building I worked in was next door to the Washington University student union, which housed a large bookstore. While waiting for an experiment to run, I would sometimes go over to the union and browse the books. In addition to the science books, I started buying history books, beginning with Stanley Karnow's Vietnam: A history, which later became the basis for a PBS series. The Karnow book not only led me to other Vietnam histories, but to an appreciation of how the Vietnam war--from which I narrowly escaped the draft--was a manifestation of the larger Cold War. This led to books on WWII, which led to books on WWI, along with histories of the Soviet Union and China, all of which shaped the Cold War, my parents’ world and the world I grew up in. In the past couple of weeks, I came more or less back to where I started, with two books recommended to me by Janet Michel. The first was Poisoner in Chief by Stephen Kinzer, which concerns Sidney G...

  "At six weeks into a pregnancy, there is no functional cardiovascular system, let alone a functional heart. The “beat” produced by the ultrasound machine is an artificial sound that corresponds to a light fluttering of electrical activity, not the beating of a pumping heart. “When I use the stethoscope to listen to a patient’s heart, that sound that I hear is that typical bum-bum bum-bum that you hear as the heartbeat is created by the opening and closing of the cardiac valves. And at six weeks of gestation, those valves don’t exist,” Dr Nisha Verma, a fellow at the American College of Obstetricians and Gynecologists and a physician who provides abortion care, told The Texas Tribune." https://www.iflscience.com/health-and-medicine/heartbeat-bill-is-a-misleading-name-for-texass-extreme-abortion-ban-doctors-say/?fbclid=IwAR05duKV7UyKgcWA-tByJZ0vdI4p8Duo8w5Tfzy0ZV_A0FXIi1aX2JnbZDQ

  "The editors of Frontiers in Pharmacology have taken down an article about the use of the antiparasitic drug ivermectin in COVID-19 patients. The paper, which was written by members of an organization called the Front Line COVID-19 Critical Care Alliance (FLCCC), had been provisionally accepted and posted in abstract form by the journal in January, but was ultimately rejected this Monday (March 1). The editors determined that it contained unsubstantiated claims and violated the journal’s editorial policies." https://www.the-scientist.com/news-opinion/frontiers-removes-controversial-ivermectin-paper-pre-publication-68505

You may have read about the trustee's report that Social Security will become "insolvent" when the trust fund runs out in 2033-34. This is nonsense. SS can't be insolvent. Projected benefits may be reduced by 21-23% by then, but as long as there are people people paying SS taxes, SS cannot be insolvent or bankrupt or any of those other scare words. There are also scare stories about tax increases and benefit cuts. Here's the real scoop: "Today Maya MacGuineas, president of the Committee for a Responsible Federal Budget, issued a statement in which she said: “Acting today, we could fix Social Security with a 27 percent tax increase or 21 percent benefit reduction.” What makes this a lie, though technically “true,” is that MacGuineas knows that the “27% tax increase” is 27% of a 6.2% tax…or about a 2% of payroll increase. On the other hand, the 21% benefit reduction is indeed 21% of the whole benefit. An average benefit is about 1500 dollars…so the benefit cut...

  Analogies are imperfect things, but used properly, they can make a valuable point in far fewer words. The COVID anti-vaxxers* today are analogous to drunk drivers. Drunk drivers have a misplaced confidence in their ability to manage the risk of drunk driving to themselves and others. They believe it is their choice to drive while impaired. Yes, if you drive drunk and slam into a bridge abutment, the only person who pays the ultimate price for your bad judgment is you. But if you run a red light and kill a mother of three and her mother on the way home from a church picnic, your “freedom” has destroyed the freedoms of others, living and dead. It’s the same with not getting vaccinated: if you are the only one who dies and you die at home, you are the only one to pay the ultimate price for your misplaced confidence in your judgment. But if you take up a hospital bed that could have been used for an accident victim or cancer patient, or if you infect others who end up hospitalized or...