Part the First: The Healthcare Costs of Fossil Fuels.<\/strong>\u00a0 One would think this is a no-brainer.\u00a0 Nevertheless, the Current Administration has its stone cold heart set on gutting the Office of Research and Development in the Environmental Protection Agency<\/a>.\u00a0 I suppose it would be churlish once again to note the EPA is one of the signal achievements of the last liberal Administration in the US \u2013 that of Richard Nixon.<\/p>\n I have not had the chance to discuss this with my oldest friends, who are now mostly MAGA Men and MAGA Women.\u00a0 We grew up in the 1960s, when our air was unfit to breathe whether we could smell it or not.\u00a0 At one time the Spanish moss disappeared from our live oak trees because of the foul air.\u00a0 When the local industries were required to curb their releases because of the Clean Air Act (Johnson, 1963; Nixon, 1970), the moss came back, after 1970 Amendments:<\/p>\n Required EPA to determine which air pollutants posed the greatest threat to public health and welfare and promulgate National Ambient Air Quality Standards (NAAQS) and air quality criteria for them. \u00a0The health-based standards were called \u201cprimary\u201d NAAQS, while standards set to protect public welfare other than health (e.g., agricultural values) were called \u201csecondary\u201d NAAQS.<\/p>\n<\/blockquote>\n The fish came back to our tidal rivers as a consequence of the Clean Water Act<\/a> (Nixon, 1972).\u00a0 The healthcare costs of polluted water require little explication.\u00a0 The healthcare costs of bad air are often ignored, but as this article at SBM<\/a> notes:<\/p>\n Burning fossil fuels releases sulfur dioxide, nitrogen oxides, particulate matter, carbon monoxide, and mercury into the atmosphere. \u00a0The cumulative effects of these pollutants exacerbates respiratory illness such as asthma and COPD, increases the risk of cardiovascular disease and cancer.<\/p>\n A recent study<\/a> confirms that these effects are not just theoretical, but can be directly measured. They looked at the rate of ED and hospital admissions for asthma and other respiratory illness for the three years prior to and after the closing of the Shenango coking plant located on an island in the Ohio River near Pittsburgh, PA. They found that after the closing there was an immediate 20% decrease in weekly respiratory ED visits, and a 41% decrease for pediatric asthma ED visits. This was following by a 4% decrease per month for the duration of the study. So there are both short- and long-term benefits to respiratory health.<\/p>\n At the high end of estimates is a study <\/a>(pdf) by The Medical Society Consortium on Climate and Health, who estimated the annual cost to the US at $820 billion. \u00a0This includes the direct effects of pollution and the resulting climate change. \u00a0This does not include non-healthcare related costs. \u00a0This does include 107,000 premature deaths each year. \u00a0On average this costs each American $2,500 in increased medical bills annually. \u00a0While it\u2019s possible to quibble about the methods used and what exactly should be included, the estimate is not unreasonable when trying to account for the total societal cost. It is also likely an underestimate for the factors it\u2019s including due to incomplete reporting.<\/p>\n<\/blockquote>\n Of course, coking plants and other polluters such as my first employer during my days as a heavy chemical worker have simply been moved to other countries with lax environmental laws<\/a>, but the point remains.\u00a0 The effluents we continue to release into our environment, not the environment, make us sick.\u00a0 And the point of closing the EPA Office of Research and Development is to make the problem \u201cdisappear.\u201d\u00a0 This is no different from reducing pandemic reporting or to be a bit more prosaic, turning up the car radio so the strange knocking from the engine compartment goes away.\u00a0 But back to my many MAGA friends from our formative years, have we really come to this?\u00a0 Rhetorical question.<\/p>\n Part the Second: The Attack on Scientific Research Continues.<\/strong>\u00a0 The Food and Drug Administration (FDA) will soon be unrecognizable.\u00a0 The current director, Dr. Marty Makary, late of Johns Hopkins University School of Medicine but still a member of the National Academy of Medicine, has done his research.\u00a0 Last year he published much of this in his book Blind Spots: When Medicine Gets It Wrong, and What It Means for Our Health<\/a>.<\/p>\n I read it with the intention of discussing it here, but it was not worth the trouble, especially after doing the same for Casey Means MD, still the Surgeon General nominee last night, and her book Good Energy<\/a> that has become MAHA holy writ (for the rich and famous and rich and not so famous).\u00a0 Dr. Makary is not wrong at the most superficial level, but his blind spots have been covered better by others.<\/p>\n SBM<\/a> is on the case once again.\u00a0 Dr. Jonathan Howard quotes Dr. Makary:<\/p>\n We have a lot of data and it may not necessarily be the traditional 50 year randomized control trial follow up. \u00a0It\u2019s data from families that say their kids have been acting with bad behavior\u2026and they eliminate the petroleum-based food dyes and the behavior improves. \u00a0That is data.<\/p>\n<\/blockquote>\n Actually, no.\u00a0 That is \u201canecdata.\u201d\u00a0 As an aside, my lesson for my graduate students was always this: Once is an anecdote.\u00a0 Twice is data.\u00a0 Three times is a result, but if and only if your subsequent experiments build on this particular result.\u00a0 In any case, this Dr. Makary\u2019s trope is no different from \u201cpost hoc ergo propter hoc<\/em>\u201d reasoning.\u00a0 This \u201cthinking\u201d has been responsible for much of the vaccine hesitancy we see today, especially after the pump was primed by the former Dr. Andrew Wakefield with his publication of a spurious link between MMR and autism in one of our leading medical journals, The Lancet<\/em>.<\/p>\n A bit later:<\/p>\n I personally know of people who have been injured by the vaccine. \u00a0I personally know of friends who have lost a loved one from the mRNA COVID vaccine\u2026People have a right to be angry. \u00a0They have been deceived \u2026 I would ask people to be patient with us as we do this the proper scientific way.<\/p>\n<\/blockquote>\n To which I could also retort, \u201cI personally know someone who was the \u201cone-in-a-million\u201d injury caused by the attenuated polio vaccine.\u00a0 Her \u201cmild\u201d childhood polio left her with a limp and other problems that have made her life difficult at times.\u00a0 But not once has she ever lamented the polio vaccine.\u00a0 I asked.\u00a0 She is a very good young friend who is now an outstanding urologist and soon-to-be a professor in a leading medical school.\u00a0 She does not consider herself the object lesson for the proscription of the polio vaccine.\u00a0 And neither to his credit is Senator Mitch McConnell<\/a>, who was the only Republican Senator to vote against confirmation of the current Secretary of Health and Human Services due to his fulminate vaccine denialism.<\/p>\n Director Makary goes way too far in his ridiculous statements about viral pathophysiology:<\/p>\n While Dr. Makary spreads rumors regarding vaccine-harms, when it comes to viruses, he does the opposite. Instead of telling tall tales, he rejects reality. \u00a0Nearly identical examples about measles and COVID are below. \u00a0Compare the casual way he dismisses dead children with the seriousness and concern he showed for supposed vaccine injuries. Hoping to numb parents to potentially grave threats, he claims that viruses don\u2019t kill healthy children. \u00a0This obviously false<\/a>, healthy children have died from COVID and measles. Moreover \u201csoft eugenics<\/a>\u201d is appalling, and viruses can hurt kids without killing them.<\/p>\n<\/blockquote>\n Of the millions who have died of viral illness over the course of human history, most of them were healthy before their viral infection \u2013 measles in post-European contact America, for example.\u00a0 But we do not have to go back that far to remember.\u00a0 One of my best friends, a swimmer and diver and brilliant landscape architect who could have been the model for Adonis, was perfectly healthy, that is until HIV destroyed his immune system and he died at the age of 39 \u2013 four years before HAART became available.\u00a0 I would go further and say the \u201csoft eugenics\u201d of the current madness has hardened considerably and is likely to become much harder before it relents.<\/p>\n Regarding food additives, yes, remove them.\u00a0 But this will not Make America Healthy Again any more than replacing high-fructose corn syrup with cane sugar will make soft drinks \u201chealthy\u201d (the problem of dietary fructose is complicated, and I hope to get to it one of these days).\u00a0 Soft drinks will never be anything more than a treat.\u00a0 The problem is not the sugar, wherever it comes from.\u00a0 The problem is the serving size.\u00a0 When I was a kid, that was 6.5 ounces in a returnable bottle that was reused as many as twenty times.\u00a0 Now the serving size can be a 32-ounce plastic cup that often comes with free refills.<\/p>\n Part the Third: AI Works, When the Training Set Is Valid.<\/strong>\u00a0 Thirty years ago, when I was the oldest postdoc in the oldest Department of Biochemistry in the United States, the dream of protein structure prediction from the primary sequence of amino acids was just that.\u00a0 But many of the scientists around me were working hard on the project.\u00a0 The Wednesday morning Biophysics Seminar was more than an opportunity to eat doughnuts and bagels for free.<\/p>\n This weekly Clash of the Titans was both educational and entertaining.\u00a0 Much of the discussion came directly from what had happened at the most recent CASP meeting.\u00a0 CASP<\/a> is the \u201cCommunity Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction.\u201d\u00a0 CASP<\/a> led directly AlphaFold<\/a>, for which three scientists were awarded the Nobel Prize in 2024.\u00a0 AlphaFold<\/a> has made previously unimaginable research possible.\u00a0 So naturally, the National Institutes of Health plans to discontinue support for CASP.<\/p>\n But CASP was the catalyst that made AlphaFold possible and will be necessary for future developments to remain in the public domain.\u00a0 So naturally, this is unlikely to matter as the neoliberalization of all science proceeds apace:<\/p>\n For the past several years, CASP has gotten around $639,000 from the National Institute of General Medical Sciences<\/a> at the NIH, which supports two full-time employees. They coordinate the biennial international conference\/competition where computational modelers test their (now largely AI-powered) methods on an even playing field. The grant, administered through the University of California, Davis, is running out with no news of a renewal, and both employees have received termination notices for Aug. 8.<\/p>\n Rather than being part of a targeted defunding, the grant seems to have gotten swept up in the general chaos surrounding biomedical funding in the U.S., according to Moult, a cell biology and molecular genetics professor at the University of Maryland. \u00a0He thinks that the organization will eventually get NIH funding again, especially since the experiment\u2019s bent toward ensuring that scientific claims are backed by evidence fits into the current federal administration\u2019s stated priorities.<\/p>\n \u201cThe emphasis from the administration is we want \u2018gold-standard science,\u2019 which is reproducible, transparent, rigorously [executed], and that\u2019s almost a description of what CASP does in this particular area,\u201d he said. \u00a0\u201cNobody has told us this, but it seems blindingly obvious to me it\u2019s a really good fit for what, at least on paper, the administration wants to achieve.\u201d<\/p>\n If CASP falls apart, it will be hard to get up and running again, he warned. \u00a0It would survive, but \u201cdeeply wounded in a different kind of setup,\u201d he said, and the U.S. would lose its leadership in this area. \u00a0Without U.S. federal funding, a European or Chinese organization would likely pick up the reins in some way.<\/p>\n<\/blockquote>\n The locution \u201cgold-standard science\u201d is false.\u00a0 The \u201cgold standard\u201d is nothing but a fetish, although it does fit in the current White House<\/a>.\u00a0 And there is no doubt leadership in this essential discipline would probably pass to China or perhaps a European consortium if public support for CASP ends.\u00a0 This is no way to run scientific research.\u00a0 But here we are.<\/p>\n Oh, and back to that Biophysics Seminar.\u00a0 The doughnuts and bagels were not exactly free.\u00a0 Regular attendees were required to participate (with personal death being the only excuse not to show up on your scheduled day).\u00a0 My presentation was not about the technical details of protein structure prediction, which were and will remain beyond my ken.\u00a0 So, I went back to the original paper in which Christian Anfinsen, a sometime member of my then department before my time, showed that the amino acid of the small enzyme ribonuclease was necessary to make the active protein.\u00a0 Anfinsen was awarded the Nobel Prize in Chemistry in 1972<\/a>.<\/p>\n My talk made the case that the amino acid sequence was necessary but not sufficient to specify\/determine an active protein structure.\u00a0 Anfinsen successfully \u201crenatured\u201d ribonuclease only when he included a small amount of a common reducing agent in his preparation.\u00a0 These conditions allowed the protein to fold and become active, but only because they mimicked the interior of the cell.\u00a0 I have never had a worse case of stage fright in my life.\u00a0 The audience of 25 or 30 included three or four members of the National Academy of Sciences and one Nobel Laureate.\u00a0 They appreciated my perspective but thought I was making too much of the importance of the cell.\u00a0 Perhaps, but all life is cellular or it is not life.\u00a0 Alas, In Search of Cell History<\/em><\/a> was still twenty years in the future \u2013 highly recommended for all biology nerds in the community, as are any other out-of-print books by Franklin Harold you might find in the used book store.<\/p>\n Part the Fourth: Arsenic Cleanup in Aisle 2010.<\/strong> \u00a0Finally!\u00a0 After nearly fifteen years one of the most remarkable papers to ever have been published in a legitimate scientific journal, in this case Science<\/em> of all places, has been retracted<\/a>.<\/p>\n To summarize, a group led by Felisha Wolfe-Simon<\/a> isolated a bacterium from Mono Lake<\/a> in California.\u00a0 They \u201cshowed\u201d that this bug could grow without phosphorous by substituting it with arsenic (one element below phosphorous in the periodic table<\/a>).\u00a0 There can be few more extraordinary claims about a living organism.\u00a0 We are all, from bacteria to animals, made of oxygen, carbon, hydrogen, nitrogen, sulfur, phosphorus plus an assortment of trace elements.\u00a0 Let us start with DNA.\u00a0 The \u201csugar-phosphate backbone\u201d of DNA forms the legs of the helical ladder with the bases that make up the information-rich codons on the inside.\u00a0 The paper implied that the DNA in this bug is made of a \u201csugar-arsenate backbone.\u201d<\/p>\n This is complete and utter nonsense, not to mention impossible if our understanding of the evolutionary biology of life on Earth is correct (i.e., there is one common universal ancestor of all life).\u00a0 If this were true, the bacterium would have enzymes that worked on arsenates rather than phosphates in a parallel biological universe.\u00a0 Extraordinary claims require extraordinary evidence, of which there was none:<\/p>\n After the paper was published, chemists and biologists took aim at it<\/a> in journal submissions and on social media. \u00a0Chemists said that if arsenic were incorporated into DNA\u2019s backbone, the bonds would be so unstable that they would fall apart in water in less than a second. \u00a0Microbiologists, including Redfield, pointed out flaws in the work, such as that the bacterium\u2019s growth medium contained enough phosphate contamination that, despite the team\u2019s effort to prove that the organism could live on arsenic, it was probably still phosphate dependent.<\/p>\n \u201cThere were very, very powerful reasons to think that the result must be wrong,\u201d Redfield says.<\/p>\n In May 2011, Science<\/em> published eight technical comments<\/a>, one of them from Redfield, criticizing the paper, alongside a response from the authors refuting the comments. \u00a0The next year, the journal published two studies, including one from Redfield\u2019s laboratory, attempting \u2014 and failing \u2014 to reproduce the results using bacterial samples from the arsenic-life team. \u00a0But Science<\/em> did not retract the paper. \u00a0Until now.<\/p>\n<\/blockquote>\n The authors of the paper disagree with the retraction.\u00a0 Their reasons, perhaps the only reason, the paper has not been retracted until now can be summarized as \u201cthere was no fraud in the paper.\u201d\u00a0 While this may be true, the paper was as mistaken as a biology paper can be.\u00a0 The data were unconvincing to everyone except the authors and the reviewers.\u00a0 Regarding the latter, I would imagine they want to remain anonymous.\u00a0 Regarding the editorial process that allowed this paper to be published in the world\u2019s second-leading scientific journal after Nature<\/em>, the mind fairly reels.\u00a0 But the work was supported by NASA, which has been a bureaucracy in search of a budget since Apollo 18 was cancelled<\/a>.\u00a0 Stuff happens.<\/p>\n What now, wonders Ivan Oransky of Retraction Watch?\u00a0 The scientific literature is filled with papers that turned out to be wrong.\u00a0 Carl Gajdusek<\/a> was awarded a Nobel Prize for identification of \u201cslow-acting viruses\u201d that cause Kuru<\/a> (he was also later identified as a pedophile).\u00a0 It turns out that prions, infectious proteins, are the cause, and for that discovery Stanley Prusiner<\/a> won a second Nobel Prize for the same thing.\u00a0 Prusiner\u2019s results were \u201cheretical\u201d but correct. \u00a0Wolf Simon\u2019s results were heretical and incorrect.\u00a0 It is not necessary that Gajdusek\u2019s papers be retracted; prions are real and behave like slow-acting viruses. \u00a0Egas Moniz<\/a> won a Nobel Prize in 1949 for \u201chis discovery of the therapeutic value of leucotomy (prefrontal lobotomy) in certain psychoses.\u201d\u00a0 His papers do not need to be retracted.\u00a0 No one cites them in support of the return of the lobotomy, and they provide an example of the dangers of what can only be called stupid science.<\/p>\n A case can be made that the retraction of the Wolfe-Simon paper is superfluous.\u00a0 But the case is very weak.\u00a0 Their assumption the bacterium was growing in the absence of phosphate was immediately shown to be wrong.\u00a0 Remember, bacteria are very good at \u201cmaking do\u201d under very harsh, starvation conditions.\u00a0 That the culture medium used was \u201cphosphate-free\u201d was absurd, as any competent biochemist or analytical chemist knew from the start.\u00a0 Neither were the techniques used to prove the thesis were up to the task.\u00a0 Isolating DNA from the organism would have been a trivial task.\u00a0 This was not done but it would have shown that its DNA was no different in content from that of any other living organism.<\/p>\n Not so long ago, a group of structural biologists (x-ray crystallographers) solved several protein structures.\u00a0 It turned out the structures were mirror images of the correct structures because of an error in the program used to analyze the data (something like a negative sign in place of a positive sign).\u00a0 It was an embarrassing error.\u00a0 No fraud was involved but the papers were retracted and the reputations of the authors suffered not.<\/p>\n Still, it is necessary that scientists, reviewers, and editors pay close attention to the business of scientific publication, which in the era of pay-to-publish open-access \u201cjournals\u201d has been polluted, perhaps beyond recovery in the near term.\u00a0 The ultimate problem with such nonsense is that it gives science deniers semi-solid ground to stand on.<\/p>\n Maybe we need a \u201cClean Journals Act\u201d for the twenty-first century?<\/p>\n\n
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