Search the KHIT Blog

Wednesday, November 24, 2021

Science and scientific research publication

Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern

Whenever my latest print edition of Science Magazine shows up, it's a "drop-what-you-were-doing" moment whenever possible (I'm a member). 
to wit, in the snailmail yesterday:

This one arrived packaged in a loose clear plastic outer container, within which was a companion volume.
44 pages of glossy 4-color media Icahn School of Medicine "sponsored content."
“Medical research is advancing at breakneck speed. From the creation of infrastructure and tools that can generate and capitalize on enormous datasets, to the ability to edit genetic material, to a more granular and nuanced understanding of the immune system, we now find in the lab and the clinic what was not that long ago found only in science fiction. But what will the future of medicine look like? The articles in this supplement provide a glimpse. Clinicians and researchers at the prestigious Icahn School of Medicine at Mount Sinai offer their insights on the increasing use of artificial intelligence, on pandemic responsiveness, and on drug discovery and development, and highlight systemic changes needed to improve medical education and address health inequity. They are working collaboratively to break down silos, integrate emerging technologies, and advance personalized treatments to ensure that the needs of today’s and tomorrow’s patients will be served.”
[This collection is brought to you by the Science/AAAS Custom Publishing Office.]
"The excitement and optimism around the remarkable progress in medical research and treatment is what inspired the creation of this supplement. The Icahn School of Medicine at Mount Sinai, in partnership with Science/AAAS, is spotlighting just some of the extraordinary work being done by researchers and clinicians at the frontiers of medical research. Their hard work and innovative spirit will continue to drive advancements in patient-centered health care, now and into the future."
Sean Sanders, Ph.D.
Custom Publishing Office
Notwithstanding my reflexive dubiety toward "sponsored content" (marketing stuff posing as neutral, objective content) this material, given the AAAS credibility rep, was not to be dismissed out of hand, in particular given that this blog commenced with a focus on medical/healthcare infotech. Much of the content set forth above remains of abiding interest to me. 
Become a Partner
To publish as a Science Partner Journals (SPJ) member, an organization must apply and undergo an evaluation process, regardless of whether that organization seeks to create a new journal or bring to the program an existing title with a prestigious background.

Partner proposals are evaluated based on research quality, scope, and organizational fit with the American Association for the Advancement of Science (AAAS). The program welcomes all scientific disciplines but places an emphasis on new and important scientific research in growing or emerging fields.

Once AAAS and a potential partner organization both decide that a title belongs in the SPJ program, AAAS will act as contractual publisher and service provider for that partner organization. This includes providing editorial training, platform access, and marketing services.

Partners participating in the program will be editorially independent and responsible for the content published in each journal. However, AAAS is highly selective about partnerships and strongly recommends that each partner adopt the Committee on Publication Ethics and the Council of Science Editors or equivalent guidelines to establish a baseline set of practices and standards to which a partner is expected to adhere.
We shall see.

This morning I made my customary priority online rounds. A mandatory early stop is that of "Science Based Medicine." Today's post:

Okeee dokeee, then...
The entire scientific enterprise might be viewed as an attempt to systematically weed out bias from our view of reality. At least, this is a critical component of the scientific method. But bias can be subtle, and can creep in at many stages from conception to citation of published research. The subjects of research may have bias, research methods can be biased in terms of how measurements are made or reported, which comparisons are looked at, the statistical methods used, and how data is [sic] collected. The publication process also may introduce bias, as can the way in which researchers access, evaluate, and cite published studies.

All of these sources of bias can distort the scientific literature and therefore the academic process and the conclusions that scientists and practitioners come to, with downstream effects in many aspects of how we run our society. But the key strength of science is that it can be (when done properly) self-reflective and self-corrective. This self-corrective process should apply not only to the findings of science, but to the process and institutions of science as well. This is one of the main missions of SBM, to examine and reflect upon the relationship among how science is practiced, the findings of science, and the practice and regulation of medicine…

Now we can add one more phenomenon to the list of possible journal biases – nepotistic journals.

In a massive review of publications in 5,468 biomedical journals indexed in the National Library of Medicine between 2015 and 2019, Scanff et al. examined the distribution of authors in each journal. They used two measures to quantify this: the Percentage of Papers by the Most Prolific author (PPMP), and the Gini index (level of inequality in the distribution of authorship among authors).

The authors found that the median PPMP for the journals examined was 2.9%, meaning that a typical journal may have around 3% of the papers they publish have the same author. They also used the two standard deviation model, determining the 95% cut-off for PPMP. They found that 95% of journals had a PPMP less than 10.6%, or that 5% had a PPMP of 10.6% or more. A high PPMP also correlated with a high Gini index, which indicates a highly unfair or biased distribution of authors. Further, and perhaps very significantly, they also found a correlation between the specific most prolific authors and a reduced time to publication, such as the percentage of papers that are published within three weeks of submission. This might indicate an expedited or even inadequate review process.

But the most significant correlation they found was that among that 5% of journals with the highest PPMP, in 60% of the cases the most prolific author was a member of the editorial board. This pattern held true when only research papers were considered (therefore not counting letters or editorials that might be disproportionately written by the editors). These were the journals considered “nepotistic”…

…there seems to be a subset of nepotistic journals that cater to one or more members of their editorial staff, allowing them to publish a large number of papers with little editorial barrier. This can be a method of gaming the system, affecting academic promotion and the awarding of grants. These editorial authors can also use these same papers to deliberately reference other papers in the same (or a sister) journal, therefore gaming the impact factor measure also.

One other concern that this paper could not examine is the scientific quality of nepotistic papers. Given the favorable bias and reduced editorial review, there is concern that low quality science is finding its way into the literature via this method….

The simplest partial fix to this problem (like many things in science) is transparency. Journals might be required to publish alongside their impact factor (a measure of how often they are cited) their PPMP and Gini index. Because prolific journals may mask their nepotistic practices by their high number of publications, publishing the raw number of publications by their most prolific author also helps. Further, the number and/or percentage of papers published in the journal by an author on the editorial staff is critical. At least with this transparency fellow researchers and academics on promotion committees can easily detect blatant nepotistic practices, reducing the benefit of this practice.
Yeah. One minor pedantic pick. It's "cronyism," not "nepotism." The latter is a Registered Trademark of the Donald J. Trump family.
"Cronyism is the practice of partiality in awarding jobs and other advantages to friends or trusted colleagues, especially in politics and between politicians and supportive organizations. ... Whereas cronyism refers to partiality to a partner or friend, nepotism is the granting of favour to relatives." Wiki
I will certainly give "The Frontiers of Medical Research" a good go. At least we have "transparency" here, given that it's overtly noted as sponsored ("in partnership with") material.
BTW, apropos, see my prior riffs on "the 'science' of science communication.
Noted at the end of the supplement: A book in the oven (Feb 15, 2022 release). 

The author. Sounds like a cool person.


Ahmaud Arbery murder trial prosecutor Linda Dunikoski. When you want it done right, send in a woman. Her closing arguments M.O. in this case will be taught in law school. Four hours of summation, all forcefully, methodically delivered without once looking down at notes.


From the Supplement:
Integrating exposomics into precision medicine and public health

Robert O. Wright*, Kecia N. Carroll, Rosalind J. Wright

Precision medicine, which now primarily utilizes genomic and electronic health record data, holds the potential to transform medical practice. Recent calls to expand the field’s purview to encompass all factors that predict health (1–3) underscore the need to include environment (4, 5), as human health and disease are shaped by a range of lifelong exposures and their resultant biological responses. The emerging exposome concept addresses this complexity by studying the effects of all health-relevant environmental factors over the life course (6–8). The 20th-century concept of “nature versus nurture” needs to be tossed aside, as genetics and environment do not compete—they work hand in hand through interactions in which our environment (i.e., where people are born, live, develop, learn, work, play, and age) triggers biological responses that are determined in part by our genetics in a lifelong, iterative process. However, there is not yet a systematic plan to integrate exposomics into precision medicine. Advances in computational science, medical informatics, remote sensing, geographical information systems, and analytical chemistry now provide powerful research tools to facilitate the incorporation of exposomics into precision medicine and public health (9–11).

Understanding our environment is critical to advancing human health and eliminating health inequities. The broad-ranging effects of climate change consequent to rising global average temperatures, increasing atmospheric carbon dioxide (CO2), associated extreme weather events (i.e., heat waves, droughts, floods, and hurricanes), and altered ecosystem functioning and biodiversity, have alarming potential to magnify toxic environmental exposures and amplify consequent health disparities (Figure 1) (12). Climate affects the exposome both directly and indirectly to influence the spatial and temporal distribution of infections, asthma, allergies, mental health, and dozens of other chronic diseases. Also, rates of cancer, diabetes, heart disease, and neurodegenerative diseases, among other complex diseases, continue to rise with minority groups such as Blacks, Latinx, Native Americans, and Asian Americans experiencing increased disease morbidity and/or severity. Structural racism, including redlining, has segregated minoritized groups to live in low-income communities where increased exposure to psychosocial stressors, air pollution, physical environmental toxicants, and reduced access to healthy food and green spaces are concentrated. The systematic segregation of persons of color through redlining policies has significant public health implications (13). These environmental disparities go beyond pollution, particularly for indigenous populations, as cultural practices commonly involve local food and water, further exacerbating social inequities. Health inequities arise from variable—and too often predictable—imposed environments that link to social determinants of health. The geospatial diversity of the exposome underlies its key role in explaining health inequities. Broad categories of the human exposome include nutrition, infections, chemicals, physical environment, and sociocultural conditions that act as psychosocial stressors. Because exposomics encompasses the interconnections among our social, nutritional, and chemical environments, it holds great promise for elucidating root causes of recalcitrant health disparities…
Department of Environmental Medicine and Public Health and the Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
*Corresponding author:

Yeah. Add one to the Omics riffs. We used to call some of this stuff "The Upstream."

Click to enlarge.
And, "Anthropocene," anybody?
I would think all of the foregoing map to my draft list.
I've begun taking these up on my relatively infrequently used Medium site.
Heavily mutated Omicron variant puts scientists on alert
Researchers are racing to determine whether a fast-spreading coronavirus variant poses a threat to COVID vaccines’ effectiveness.
Researchers in South Africa are racing to track the concerning rise of a new variant of the SARS-CoV-2 coronavirus that causes COVID-19. The variant harbours a large number of the mutations found in other variants, including Delta, and it seems to be spreading quickly across South Africa.

A top priority is to follow the variant more closely as it spreads: it was first identified in Botswana earlier this month and has since turned up in a traveller arriving in Hong Kong from South Africa. Scientists are also trying to understand the variant’s properties, such as whether it can evade immune responses triggered by vaccines and whether it causes more or less severe disease than other variants do…
Swell. 2024 headline? "Z.9.9.999 SARS-Cov2 variant emerges, concerning WHO officials."

My Las Vegas music podcasts have been offline for several years now. I just remounted them. Miss my friends.

Friday, November 19, 2021

#COVID19: And, here we go yet again

We'll easily get to more than 800,000 US Covid-19 deaths by year's end. New case incidence is again bounding back up in other nations as well.
Cheryl and I got our Moderna booster shots yesterday at Kaiser. Just have to continue to lie low. This is all getting real old, I'm sure you agree.

Then, there's this crap.

See my 2019 post "In Pain."
Still wondering whether this category of acute social/public health malaise should get its own top "Exigencies" line item?


Imagine waking up tomorrow, feeling a bit under the weather. An annoying pain in your throat, your nose is runny, you cough a bit. All in all, not bad enough to skip work, you think, as you step into the shower, pretty annoyed about how hard your life is. While you are totally not being a whiny little baby, your immune system is not complaining. It is busy keeping you alive so you can live to whine another day. And so, while intruders roam your body, killing hundreds of thousands of your cells, your immune system is organizing complex defenses, communicating over vast distances, activating intricate defense networks, and dishing out a swift death to millions, if not billions, of enemies. All while you are standing in the shower, mildly annoyed.

But this complexity is largely hidden.

Which is a real shame because there are not many things that have such a crucial impact on the quality of your life as your immune system. It is all-embracing and all-encompassing, protecting you from bothersome nuisances like the common cold, scratches, and cuts, to life-threatening stuff from cancer and pneumonia to deadly infections like COVID-19. Your immune system is as indispensable as your heart or your lungs. And actually, it is one of the largest and most widespread organ systems throughout your body, although we don’t tend to think about it in these terms.

For most of us, the immune system is a vague and cloud-like entity that follows strange and untransparent rules, and which seems to sometimes work and sometimes not. It is a bit like the weather, extremely hard to predict and subject to endless speculations and opinions, resulting in actions that feel random to us. Unfortunately many people speak about the immune system with confidence but without actually understanding it, it can be hard to know which information to trust and why. But what even is the immune system and how does it actually work?

Understanding the mechanisms that are keeping you alive as you read this is not just a nice exercise in intellectual curiosity; it is desperately needed knowledge. If you know how the immune system works, you can understand and appreciate vaccines and how they can save your life or the lives of your children, and approach disease and sickness with a very different mindset and far less fear. You become less susceptible to snake oil salesmen who offer wonder drugs that are entirely devoid of logic. You get a better grasp on the kinds of medication that might actually help you when you are sick. You get to know what you can do to boost your immune system. You can protect your kids from dangerous microbes while also not being too stressed-out if they get dirty playing outside. And in the very unlikely case of, say, a global pandemic, knowing what a virus does to you and how your body fights it, might help you understand what the public health experts say...

Dettmer, Philipp. Immune (pp. xi-xii). Random House Publishing Group. Kindle Edition.

News you can use. Stay tuned.

 GOP "Conservative Political Action Committee."



Sunday, November 14, 2021


Kyle Rittenhouse. He was 17 when this photo was taken. It was illegal at the time for him to buy, own, or possess the depicted assault type weapon. He had a friend buy it for him in Wisconsin (an illegal "straw purchase") and stash it for him. During his trial testimony, he said he chose it because "it looked cool."
On the evening of August 25th, 2020, he shot two people to death with it (events recorded on video by others present), and seriously wounded a third person—all during the Kenosha WI riots resulting from the earlier police shooting of Jacob Blake, which was also caught on smartphone video.
Rittenhouse has pleaded innocent to all charges, citing "self-defense," that he "reasonably feared for his life" that night. Notwithstanding that he willfully deputized and inserted himself into a dangerous, chaotic situation brimming with angry people. 
Many other armed self-appointed "militia" citizens were present in Kenosha those nights. None of them shot anyone. 
Kyle admitted on the stand that he'd told other armed participants that he was 19 and a Certified EMT. He was neither.
He has numerous supporters, who call him "a hero" and "a patriot." To others he's an immature, delusional "vigilante murderer."
His case is now scheduled to go to the jury (Nov 15th). The Wisconsin National Guard is reported to be mobilized and on standby. 
I watched most of this trial. It was a depressing, chaotic mess. Mercurial, frequently befuddled judge, and recurrently bumbling prosecutors. I had watched all 15 days of the prior George Floyd murder trial, which was extremely well conducted. What a contrast.
I really don't have a good feel for how the Rittenhouse jury will rule (and that assumes they get the case; a mistrial could still be declared by the judge, who has threatened it). I just hope no more violence ensues in the wake of this, whatever the outcome.

KENOSHA, Wis. [NBC News] — This city on Lake Michigan was quiet, calm and peaceful on Sunday, and many residents want it to remain that way as closing arguments in the trial of Kyle Rittenhouse get underway Monday.
“Monday is coming, so, I mean, it’s kind of a little nervous,” said Kenosha resident Mike Lipp, 35.

Wisconsin has dispatched 500 National Guard troops, and hundreds of nearby police officers will also be available as a precaution to ensure public safety during the conclusion of the trial.

But the increased attention and the additional presence of law enforcement have taken a toll on the city, which isn’t as vibrant as it once was, said downtown resident Max Lewis.

“It’s affected the energy of the city in a negative way. It’s not the same. Everyone is trying to avoid the situation as well as keep an eye out on the situation,” Lewis said. “We’re a little dismayed by the situation. This case should have been cut and dry. You kill two people in the street, you get punished for it, end of story.”

Rittenhouse, 18, is charged with reckless homicide, intentional homicide and attempted intentional homicide after he shot two men and wounded a third during a night of protest and civil unrest in Kenosha in August 2020.

The unrest was a response to the shooting of Jacob Blake by a Kenosha police officer after a domestic disturbance. Blake was paralyzed from the waist down…
The case is now before the jury. The one misdemeanor count (illegal possession of the AR-15 rifle) has been dropped by the judge. Five felony counts remain. If I had to place a bet, it would be acquittal on "reasonable doubt" grounds—that the defendant's "right of self-defense during deadly circumstances" prevails, however marginally.
We'll see. Declaration of "mistrial" remains a possibility in the event of intractable jury deadlock (on a count-by-count basis).

He probably walks.

As the Kyle Rittenhouse trial comes to a close, two things are becoming clear at once. First, absolutely no one should be surprised if Rittenhouse is acquitted on the most serious charges against him. And second, regardless of the outcome of the trial, the Trumpist right is wrongly creating a folk hero out of Rittenhouse. For millions he’s become a positive symbol, a young man of action who stepped up when the police (allegedly) stepped aside...
No verdict through Thursday. It is now Friday morning.


Not guilty on all counts.
“We have moved from castle doctrine protections that allow you to defend yourself in your home to laws that allow you to shoot in self-defense anywhere you feel unsafe. Once we are there—or, rather, here—your gun both protects and endangers you, because you need lethal force to protect against those who would use your own lethal force against you. The “good guy with a gun” can reasonably assume everyone else is bad, or at least could be trying to kill them. The analytical circle is complete, and that circle is closing in on us all…

The Rittenhouse jury should not be held responsible for the ways in which gun owners may be emboldened to vigilantism by the outcome of this trial. You can provoke violence and reasonably be afraid of violence at the same time. The jury should not be held responsible for the potential proliferation of armed citizens taking it upon themselves to enforce the law, or the defenses those citizens will increasingly feel entitled to use to explain their actions once things go wrong. The jury must confine itself to the facts of this case. The Supreme Court, on the other hand, is poised to ensure that in the future, juries will be asked, again and again and again, to decide how things should go when everyone had a gun, everyone else wanted to use it, everyone knew their intentions were good, but suspected everyone else was a danger. How do we act as a society when absolutely everyone is always in fear of their life? Welcome to the future. It’s already here.”
Dahlia Lithwick

Thursday, November 11, 2021

COP26: Progress, or platitudes?

While the world debates how best to reverse the trend of anthropogenic global warming (AGW), scientists continue to refine their data on historical global temperatures. A recent study published in Nature adds to this a high resolution picture of average surface temperatures over the last 24,000 years, since the last glacial maximum. The study reinforces the conclusion that the last century of warming is unprecedented over this time frame, and does not reflect any natural cycle but rather the effects of human forcing.

To construct their map of past temperatures, the researchers combined two methods. They used a dataset of chemical analysis of marine sediments, which are affected by local average temperatures. They combined this with a dataset based on computer-simulated climate models. The idea was to leverage the strengths of each approach to arrive at a map of historical surface temperatures that is more accurate than either method alone.

Of course, no one study is ever the final word, but this reconstruction is in line with other research using independent methods and data. The authors also draw two other main conclusions from their data. There has been a debate about whether or not the last 10,000 years had a small warming trend, and this graph supports that conclusion. Further, the authors conclude that the main driver of the large warming trend starting around 17,000 years ago is the retreat of the glacial ice sheets, but that the main driver of the rapid warming over the last 150 years is increasing green house gases. The rate of this recent warming is also out of proportion to any natural cycle detected in the last 24,000 years.

Those who refuse to accept the overwhelming scientific consensus on AGW will likely not be moved by this new study. It’s easy to find reasons to dismiss data if you are motivated to do so. For AGW, that motivation appears to be solution aversion – concerns about proposed steps to mitigate AGW and its consequences. For the fossil fuel industry, this motivation is obvious. They have massive assets in the ground they want to capitalize on, and will push back against any policy that deprives them of those assets. But they have successfully financed a disinformation campaign and turned it into a political ideology. Now denying AGW is a matter of tribal identity for some.

This denial takes many forms, but they tend to flow into each other. There are “stages” of denial: the Earth is not warming, the Earth is warming but its part of a natural cycle, human activity is causing the warming but it won’t be harmful (and may even be beneficial), human activity is causing warming and it will be bad but there’s nothing we can do about it or need to do about it. The one thing that all these positions have in common is the conclusion that we need not do anything about AGW – solution aversion. In practice deniers tends to flow up and down the list of positions depending on the situation, using a Motte and Bailey defense strategy. They will deny that warming is even happening when they think they can, but otherwise will retreat to more defensible positions when necessary, only to sally forth later to again deny even that warming is happening…

The Neurologica Blog

Click here.
OH, BOY...

Click the title. Just watch wingnut heads explode. To them, you cannot even say "Structural Racism." Texas Governor Abbott will probably soon get legislation forbidding the use of the phrase.
For generations, policies of structural racism have systematically undervalued and removed opportunity from non-White communities. From the Black Hills of South Dakota to Boston's formerly redlined communities of Chelsea and Dorchester, such structural racism has limited medical access for communities of color, created cascades of comorbidities, and eroded social safety nets. Therefore, when SARS-CoV-2 landed on our shores, this systematic removal of resources saw Black, Indigenous, and persons of color experience twice the death rate from Covid-19 as White individuals. As healthcare professionals, it is critical that we understand how such a historical removal of opportunity has led to these health inequities. Such an understanding is foundational to achieving the truly equitable solutions that we so desperately need…

As we look towards the climate crisis, we must learn from and avoid the many shortcomings of the US Covid-19 response. Our attempts at buying our way out of social accountability with record breaking vaccine production and mandated masks played into these historic inequities. During the depths of the pandemic in 2020, those who have historically had resources and opportunity could much more easily achieve social distancing and safe pandemic practices. By repeating such a surface level approach for the climate crisis we will assuredly ruin our chances of providing adequate resiliency to frontline communities.

For the climate crisis, we must be skeptical of solutions that rely solely upon innovation and individualism…

To achieve equitable climate solutions, we must look inward to successfully move forward. We must look critically at our institutions of healthcare and government if we want to achieve long-lasting, equitable progress. As structural racism has historically disempowered millions in this country and made so many communities disproportionally vulnerable to climate change, then our healthcare solutions must be centered upon empowerment…

Doing right by marginalized communities across this country will mean prioritizing policy that undoes structurally racist policies, builds community resilience through infrastructure, and mitigates US emissions through revitalizing our energy infrastructure and cutting our emissions in half by 2030. To achieve such systemic change, our united action will be essential…

In my inbox this morning.

Why are so many American children learning so much misinformation about climate change?

Investigative reporter Katie Worth reviewed scores of textbooks, built a 50-state database, and traveled to a dozen communities to talk to children and teachers about what is being taught, and found a red-blue divide in climate education. More than one-third of young adults believe that climate change is not man-made, and science instructors are being contradicted by history teachers who tell children not to worry about it.

Who has tried to influence what children learn, and how successful have they been? Worth connects the dots on oil corporations, state legislatures, school boards, libertarian thinktanks, conservative lobbyists, and textbook publishers, all of whom have learned from the fight over evolution and tobacco, and are now sowing uncertainty, confusion, and distrust about climate science, with the result that four in five Americans today don’t think there is a scientific consensus on global warming. In the words of a top climate educator, “We are the only country in the world that has had a multi-decade, multi-billion dollar deny-delay-confuse campaign.” Miseducation is the alarming story of how climate denialism was implanted in millions of school children.

"Exceptional reporting undergirds the truly shocking facts in this book: the fossil fuel industry is doing all that it can to undermine education about climate change, which will be the most important fact in the lifetimes of kids in school today." —Bill McKibben
Release date Nov. 16th. More info here.
Why I care about these topics. Not the only reason, by any means, but certainly a priority.
I care about the world we are handing off to our progeny. I rather doubt that my list of priority exigent topics will diminish anytime soon.

As I’ve noted before, a lot of this stuff is overlapping and mutually recursive (“feedback loops”). Some of it perhaps transient, some of it “existential“ if not dealt with effectively.

Oh, my current New Yorker just arrived.
For those inclined to see them, there were plenty of bad omens last week as the latest round of international climate negotiations—cop26—got under way in Glasgow. A storm that lashed England with eighty-mile-per-hour winds disrupted train service from London to Scotland, leaving many delegates scrambling to find a way to get to the meeting. Just as the conclave began, Glasgow’s garbage workers went on strike, and rubbish piled up in the streets. Prime Minister Boris Johnson, in his opening speech, compared the world’s situation to that of James Bond, who often finds himself “strapped to a doomsday device, desperately trying to work out which colored wire to pull to turn it off, while a red digital clock ticks down remorselessly to a detonation that will end human life as we know it.” As one commentator pointed out, in his latest movie—spoiler alert!—Bond ends up dead.

Joe Biden’s performance in Glasgow, too, was inauspicious. In his formal remarks to cop26, the President declared that the United States was “back at the table” and “hopefully leading by the power of our example.” Later that day, Biden was undercut by Senator Joe Manchin, Democrat of West Virginia, who announced that he wasn’t quite sure he could support the $1.75-trillion spending package on which Biden’s claims rested. The timing was, as the A.P. noted, “unfortunate.” In separate, unscripted remarks in Glasgow, Biden circled back, acknowledging that the U.S. is not leading by example—or, really, leading at all. “I guess I shouldn’t apologize, but I do apologize for the fact the United States, in the last Administration, pulled out of the Paris accords,” he said, referring to the set of climate agreements negotiated at cop21, in 2015. He added, by way of understatement, that this has “put us sort of behind the eight ball.”

cop26 is a sequel to cop21, which was an attempt to recover from the mess of cop15, held in Copenhagen in 2009. To really appreciate America’s fecklessness, however, you have to go all the way back to the conference that preceded all these bad cops—the so-called Earth Summit, in 1992. At that meeting, in Rio de Janeiro, President George H. W. Bush signed the United Nations Framework Convention on Climate Change, which committed the world to preventing “dangerous anthropogenic interference with the climate system.” At the United States’ insistence, the convention included no timetable or specific targets for action…

—Elizabeth Kolbert

Tuesday, November 9, 2021

"Science: Stay in your lane!"

Or, build some new ones.

New editorial in Science.
A recent Science editorial on the social and political headwinds that have blunted, obfuscated, and confused public behavior in the United States’ COVID-19 response cautioned both politicians who appoint themselves scientists and scientists—including virologists and epidemiologists—to stay in their lanes. The warning raises an important question: Should science add another lane?

Despite the remarkable development of safe and effective vaccines, only about two-thirds of Americans have received their first dose. Even nonmedical actions (social distancing and masking) supported by rigorous evidence are met with widespread indifference, resistance, and rage. Unfortunately, this number is the rule rather than the exception. Broadly, Americans receive about 55% of clinical interventions known to benefit their health.

To address this failing, science needs to add another lane—one called implementation research. Implementation scientists move beyond medication and device development and study how to facilitate their use by clinics, front-line health care providers, patients, communities, and policy-makers. Public health failures that could have been avoided, as well as successes attributable to this science, illustrate the importance of this work... 

...{R]esearch on how to expand the use of proven COVID-19 interventions is underway but must be scaled up substantially to address pressing questions: What strategies lead to vaccine acceptability, feasibility, fidelity, equity, scale-up, and spread? What social marketing messages are most effective? Who are the best opinion leaders? How can health systems overcome delays in identifying mildly ill outpatients eligible for monoclonal antibodies? Data are emerging about how to equip vaccine champions with the resources necessary to train others, build coalitions, and optimize organizations to administer vaccines as widely as possible. But more must be done, especially given the current politicized pandemic response and frayed social fabric.

Society needs a lane of science that studies rapid uptake of proven interventions. Questions pursued in implementation research require cross-disciplinary collaborations among scientists who understand communication, marketing, anthropology, economics, and social psychology—disciplines that have not historically interacted with one another.

...The US National Institutes of Health (NIH) should create an Office of Implementation Research with funding that institutes must compete for, modeled on the Office of AIDS Research. The office would study emerging interventions and address obstacles to their use. Insights would guide health delivery, making learning-while-doing a standard. The office should support innovations that track rates of intervention use (vaccination and effective therapeutics) and capture the strategies leading to their uptake. And the NIH should support networks for implementation research, similar to the AIDS Clinical Trials Group. At least 10% of the NIH budget should be dedicated to this work. If this seems expensive, consider the costs of not taking these steps: Effective interventions that are not used optimally will fail to reap value from existing investments.

COVID-19 has shown the world that “knowing what to do” does not ensure “doing what we know.” It demonstrates that intervention discovery is the start, not the end, of the scientific journey. There is no better time for science to establish a new lane, one devoted to ensuring that our nation’s health discoveries are used to improve population health...
Well, given that we are now apparently going to have all of this federally funded "infrastructure" building and re-building going on pursuant to President Biden's recent legislative victories, I would certainly support rational initiatives via which to increase the effectiveness of the breadth of applied sciences. "Exigencies? Priorities?" Hello?
This open access book provides a broad context for the understanding of current problems of science and of the different movements aiming to improve the societal impact of science and research.

The author offers insights with regard to ideas, old and new, about science, and their historical origins in philosophy and sociology of science, which is of interest to a broad readership. The book shows that scientifically grounded knowledge is required and helpful in understanding intellectual and political positions in various discussions on the grand challenges of our time and how science makes impact on society. The book reveals why interventions that look good or even obvious, are often met with resistance and are hard to realize in practice. [emphasis mine]

Based on a thorough analysis, as well as personal experiences in aids research, university administration and as a science observer, the author provides—while being totally open regarding science's limitations—a realistic narrative about how research is conducted, and how reliable ‘objective’ knowledge is produced. His idea of science, which draws heavily on American pragmatism, fits in with the global Open Science movement. It is argued that Open Science is a truly and historically unique movement in that it translates the analysis of the problems of science into major institutional actions of system change in order to improve academic culture and the impact of science, engaging all actors in the field of science and academia. [emphasis mine]
From the book:
It is truly amazing, that a way to do science and research, that for the majority of its practitioners and the public and policy makers makes a lot of sense, and which has been around for quite some time, has not been embraced to become common practice. To answer this question, we have to delve deep into the science of science and research. We have to understand ‘the idea of science’ that does exist in the plural. We have to analyse why in particular one of these concepts and its corresponding public image has been dominant practically since 1945 and what that has done to science and scientists. That philosophical/sociological idea has been the basis for the ideologic narrative with which science has been internally organized and is being used to claim a unique position, authority and funding for science. With this narrative, the scientific community promised that science would be there to the benefit of society, at least when her autonomy and neutrality are respected. How come that although this legendary image and its narrative by the philosophers, historians and sociologists has no philosophical and timeless foundation, scientists apparently without knowing this demise of their Legend keep using that narrative? It may well be the fear, the insecurity that comes with the awareness that knowledge production in science is based not on a given metaphysical foundation, but rests on a firm social process of a community of inquirers that relentlessly criticize, question, debate what the best knowledge claims are. Knowing very well that the consensus reached may work well but is never absolute and may be replaced by better ones by this same process of inquiry called science. Having said this, we realize that, despite the commonly held views, the ‘method’ of the ‘hard’ sciences and that of the ‘soft’ social science and humanities may not be all that different after all!

In our present-day world of hyper-modernity, where knowledge is everywhere to be found and always contested by some, the process of the production of knowledge cannot be insulated from potential users and interested critical other parties. Clinging to the idea of a unique method for absolute truth and a foundation for science is understandable but a wrong reflex in debates with the public about its problems. Explaining how science really works and produces knowledge would be the best response…
[Open Science, The Very Idea, vii-viii]
Again, "is there a 'science' of science communication?"
Chapter 8
Epilogue: Open Science in an Open Society

Abstract The European Union has chosen Open Science as the way to do science and research based on its cultural and social values. Open Science can only really thrive in democracies and Open Societies to the benefit of humanity. This relationship between science, scientists and society is not trivial and sometimes endangered, therefore we need to continuously engage in research with and for society...
[Page 211].

Taking stock of science in the COVID-19 crises, it seems that science and scientists as an international community are committed and more than ready to practice Open Science. However, the open society—with its plurality, economic inequality, the speed and the use and abuse of social media, the higher levels of education, but also the increasing differences in education levels, the populism fueled by politicians—is often felt to make the connection between science and the public no less complex and to some even dangerous. Social media and the role of the tech giants since 1990 have had an enormous impact on how, when and where the debates in the public sphere take place. Fueled by ugly partisan battles, the internet it seems has divided countries and people more than it has resulted in open debates, in which listening to each other’s fears and opinions is being practiced, to reach mutual agreements. This is a major problem for science and society. Recently we have seen the worst of it in the USA, where partisan battle lines already since the 1980s are raging… [Page 217].

The time is long gone that the claims and views of science and experts were automatically accepted because of mythical ‘God given’ authority or a ‘unique scientific method’. As I have argued and demonstrated, the sciences, in their many different communities of inquirers do produce reliable and robust knowledge that has proven successful and has in the past contributed enormously to the quality of life. Much is still to be done and at this very moment scientist around the world are working 24/7 on therapies and vaccines for COVID-19 which are badly needed. To make clear what science has to offer we have to engage tirelessly in continuous conversation, debate and discussions about science and society. With the same energy and perseverance, because of geopolitics, ugly partisan politics and outright suppression we have to keep campaigning for open debates and deliberative democracies, as the stakes for humanity are higher than ever, this needs to be done within our own region, country, in the EU and in global collaborations around the globe…[Page 218]. 
"We have to keep campaigning for open debates and deliberative democracies, as the stakes for humanity are higher than ever..."

"Deliberative democracies?" Hmmm... Is there a "science of deliberation?"
Yeah, and perhaps invest in some off-road vehicles, too. 

After the increasingly toxic environment of modern research culture forced her to nearly abandon her career, astrophysicist Dr Rachael Ainsworth began to question why the subject she loved had become so inhospitable. Identifying some of the pressures placed on her peers that encouraged aggressive competitiveness, unfair benchmarking and shoddy research practices also helped her identify a compelling potential solution.

Dr Rachael Ainsworth is a Research Associate and Open Science Champion at the Jodrell Bank Centre for Astrophysics at the University of Manchester. She has a PhD in Astrophysics, a BSc in Physics and was an intern at NASA’s Jet Propulsion Laboratory. She is an expert in the interpretation of radio emissions from protostellar systems in nearby star-forming regions and her research involves observing jets from young stars with next-generation radio telescopes to investigate the physical processes that assemble stars like our Sun.

She is passionate about openness, transparency, reproducibility and inclusion in research, and organises a women-in-data meetup group in Manchester called HER+Data MCR. Originally from Hampton, New Hampshire, USA, Dr Ainsworth is now based in Manchester. Dr Rachael Ainsworth is a Research Associate and Open Science Champion at the Jodrell Bank Centre for Astrophysics at the University of Manchester. She has a PhD in Astrophysics, a BSc in Physics and was an intern at NASA’s Jet Propulsion Laboratory. She is an expert in the interpretation of radio emission from protostellar systems in nearby star forming regions and her research involves observing jets from young stars with next-generation radio telescopes to investigate the physical processes that assemble stars like our Sun. She is passionate about openness, transparency, reproducibility and inclusion in research and organises a women in data meetup group in Manchester called HER+Data MCR. Originally from Hampton, New Hampshire, USA Rachael now lives in Manchester.
Dr. Ainsworth on Twitter.

Sunday, November 7, 2021

"Lets go, Aaron"


Wednesday, November 3, 2021

"Malign Technologies?"

Added one to my exigencies list.

Yeah, and, again, lots of recursive cause/effect overlap in the foregoing, some of it probably transient. But, a lot of it likely increasing in adverse intensity.
Mulling over adding Fentanyl (etc) to the list (lethally dangerous addictive intoxicants). Might it warrant its own category line item? Or would it suffice to just be implicitly subsumed under Degradation of Human Heaith?
"Malign technologies?" See, for one recent example, my prior post on "synthetic media / deep fakes." I see a decided skew on the "malignancy vs. beneficence" relative potential balance beam. What of "Artificial Intelligence" more broadly? Applications of genomics?

Yeah, blah, blah, blah, "technology is morally neutral." Right.

BTW: I got'cher Malign Disinfo Technology right here. "Threats to Democracy?"

Whenever my Science Magazine arrives, I typically head straight for the book reviews.

Found this yesterday.

Since humankind’s first migration out of Africa, we have trimmed, trained, and reshuffled the tree of life at breakneck speed. In the past 10,000 years, we learned to manipulate the basic building blocks of life through breeding. In the past century, we increased the speed and magnitude of our impact through mass global transportation, industrialized agriculture, and urbanization. In the past decade, we have seen major advances in biotechnology that now allow us to directly rewrite the genetic code of almost any organism to create never-before-seen biological variation.

Our unmatched ability to destroy, reshape, and rebui
ld life to suit our purposes has allowed our species to become an evolutionary force rivaled only by the five major mass extinctions of Earth’s past. Evolutionary biologist Beth Shapiro explores this legacy in her new book, Life as We Made It.

In eight chapters, Shapiro takes readers on a succinct and compelling journey through historical events, inventions, and decisions that have forever changed the course of life on Earth…

Shapiro’s latest literary work makes plain that human intervention will likely be necessary to confront the problems we currently face and that biotechnology has an important role to play across a range of issues, from saving species teetering on the brink of extinction to curing disease to feeding a growing human population…

In what is perhaps the greatest accomplishment of Life as We Made It, Shapiro clearly articulates key questions whose answers will define how we think about and use the power we now yield. In a world that has been remixed and remade by humans several times over, what is “natural”? When and how should we intervene in evolution? Who should make this call?…

In a world where we can engineer life in much the same way we engineer skyscrapers, we are bounded more by imagination than by ability. But while buildings will eventually deteriorate in the sands of time, life will keep on ticking. In Life as We Made It, Shapiro offers readers a history lesson from which to pull both caution and inspiration. In doing so, she sets the table for a needed conversation about our lasting imprint on the tree of life. It is up to us to take a seat.

It's customary in Science book reviews to give 'em the venerable "Praise-Criticism-Praise Sandwich" workover.

Not one disparaging word about this book. Hmmm... "Purchase instantly with 1-Click."

And Off We Go...
THE LAST DECADE HAS SEEN DEVELOPMENT OF POWERFUL BIOTECHNOLOGIES that are at the same time astonishing, encouraging, and pretty scary. Cloning, genome editing, synthetic biology, gene drives—these are words and phrases that promise a different kind of future, but is it a welcome future? On the one hand, technological advance is a good thing. Biotechnology stops us from getting sick, cures diseases that we already have, and makes our food taste better and stay fresh longer. On the other hand, biotechnology creates things that feel weirdly unnatural, like corn with embedded bacterial genes and chickens that lay eggs out of which ducklings hatch.1 In fact, it is increasingly difficult to find anything that hasn’t been sullied by people in some way. And while scientists race to protect the natural things and spaces that remain, crises like offshore oil spills, rising extinction rates, and emerging infectious diseases demand solutions beyond what our existing technologies can achieve. Should we dig in, embrace the power of modern science, and look ahead to a future where bacteria clean up our messes and where hairy elephants roam Siberian fields while sterilized mosquitoes buzz overhead? Or should we resist this future and stop messing with things before it is too late?

For many, a future filled with human-modified plants and animals is bleak. Engineered microbes, mammothified elephants, and mosquitoes that can’t transmit disease would probably benefit people in some way, but creating them just isn’t right, and a world that includes them is somehow false. To those who feel this way, there is a tendency to blame science. Thanks to scientists and their twenty-first-century technologies, our world is on the precipice of a metamorphosis beyond which lies a new nature, one created entirely by and for people, and one that is anything but natural. This nervous narrative assumes, however, that humans have only just begun to meddle with nature—that the border between natural and unnatural is obvious and unblurred. History, however, and archaeology and paleontology and even genomics, tells a different story. In studying the past, we learn that people have been shaping the evolution of the living things around us throughout our history. Within the last 50,000 years, our ancestors hunted, polluted, and outcompeted hundreds of species to extinction. They turned wolves into Boston terriers, teosinte into popcorn, and wild cabbage into kale, broccoli, cauliflower, brussels sprouts, and collard greens (to name a few). As our ancestors learned to hunt, to domesticate, and to travel, their actions and movements created opportunities for species to adapt and evolve. Some species survived their encounters with humans, but many did not, and all were transformed in some way. Living things today are as we made them, shaped in part by the randomness of evolution and in part by less random human intent…

Shapiro, Beth. Life as We Made It (pp. 9-11). Basic Books. Kindle Edition.
Stay tuned. Interesting person. Very impressive.

Over the last 50,000 years, we transformed the plants and animals with which we share our planet into lineages that are exquisitely adapted to today’s world, where the dominant evolutionary force is us.

We are, however, a different kind of evolutionary force. Evolution is a random walk through experimental space. Evolution does not evaluate risk before making decisions about which breeding experiments to perform, but we do. Evolution doesn’t care what the next generation looks like or even if the next generation survives, but we do. Evolution is not guiding horses or wheat or cattle or bison to any particular fate, but we are. And this is where the contradiction in our opposition to our biotechnologies is laid bare. We resist biotechnologies precisely because they give us the control over evolution that humans have continuously worked to achieve. Evolution will not get us to a future that we predetermine. Our biotechnologies, however, can.

The decisions that we make over the next decades will determine our own fate and the fate of other species, perhaps far into the future. We can choose to take advantage of our technologies as they develop, to use synthetic biology to make even more with less, to protect wild species and wild spaces, and to do so in a sustainable way. Or we can reject our new biotechnologies and follow this same path anyway, just more slowly and with less success.

Biotechnologies can be frightening, in particular when they are new. We still have lots of work to do to make our technologies safe, to learn how to assess risk, to collaborate at a global scale. But biotechnologies also give us reason to be hopeful. The world is changing, and people and animals and ecosystems are suffering. Biotechnologies give us the power to help. We can change the evolutionary trajectories of species destined to become extinct. We can clean up our trash and make our farms more efficient. We can cure diseases that afflict us and other species. We can create and sustain a world in which wild species thrive in natural spaces and where people are healthy and happy and decidedly in charge. [Beth Shapiro, pp. 313-314]