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Anthropogenic Global Warming: the Basic Argument

2015-06-12
  • Rycke Browne said in a comment to an article in Science News:

    “According to this video, global warming and cooling are real, and so is climate change. What is not real is trace gases causing such warming, rather than following it.

    Warming definitely increases CO2 and methane, from increased decomposition. What is not proven and is contradicted by the graphs, is that these trace gases cause warming. Correlation is not causation, especially backward correlation.”

    This part caught my eye: “What is not proven… is that these trace gases cause warming.”  Since the basis of the whole Anthropogenic Global Warming argument is that “trace gases” (CO2) do indeed cause global warming, and that the increase in CO2 concentrations has caused increasing warming that will disrupt the climate, I felt that this assertion had to be contravened if AGW is to be supported.
    My reply to this comment:

    In fact, this was proven by Arrhenius back in the nineteenth century and can be confirmed by simple lab experiments: take a glass container and fill it with air, with concentrations of CO2 varying (the independent variable)… shine a “sunlight” beam through it and measure the transmission of infrared light. Keep the concentration of water vapor the same, as that greatly affects the results. You will find that air with low concentrations of CO2 will transmit more infrared light (the dependent variable) than air with high concentrations of CO2… and this is readily measurable when you take concentrations of 280 ppm versus 400. This simple experiment showed, and reproducibly will show, that CO2 in the air absorbs infrared light, even at “trace gas” concentrations.
    As mentioned above, water vapor also absorbs infrared light, and this is a very important effect. Naturally, as temperature rises, the air can hold more water vapor, so this affects the results as well.
    Bottom line: AGW has been proven to my satisfaction by simple, reproducible experiments, starting with the one above. A lot of people, careful scientists, agree with me. Not very many people disagree.
    My question is: what part of this do you not understand?
    In reference to the article that started this comment thread, a lot of observations, complex math and adjustments have been done to try to demonstrate that the effect predicted by these simple experiments is actually happening now.
    Instead of doing these multiple observations, complex experiments, and mathematical adjustments, we could just wait 50 or 100 years and measure the temperatures, to see if it got warmer or not. By then, if the predictions are accurate, there will be some major problems. If predictions are wrong, then there won’t be. Wouldn’t you like to know now what the weather will be in 50 years, in case you should move away from the coast, increase the power of your air conditioner, retrofit your house with a tornado resistant roof, etc.?– or, if the predictions say things will be good in your area, you can relax.

     In a later post I hope to extend the AGW argument with more simple experiments.

 

Irreproducible PreClinical Research Estimated to Cost $28 Billion/Year in US

2015-06-11

A new paper in PLOS Biology discusses the topic of non-reproducible research.  First, an estimate of the total cost of preclinical research in the United States:

“Extrapolating from 2012 data, an estimated US$114.8B in the United States [ref. 18] is spent annually on life sciences research, with the pharmaceutical industry being the largest funder at 61.8%, followed by the federal government (31.5%), nonprofits (3.8%), and academia (3.0%) [ref. 20]. Of this amount, an estimated US$56.4B (49%) is spent on preclinical research, with government sources providing the majority of funding (roughly US$38B) ”

Second, an estimate of irreproducible research is about 50%, based on a half-dozen studies with rates ranging from 51% to 88%, with 50-54% being the most likely:

” Using a conservative cumulative irreproducibility rate of 50% means that approximately US$28B/year is spent on research that cannot be replicated [see fig. 2]. Of course, uncertainty remains about the precise magnitude of the direct economic costs—the conservative probability bounds approach reported above suggest that these costs could plausibly be much smaller or much larger than US$28B.”

Third, academic research in drug development is typically repeated by the pharmaceutical industry before clinical research can begin:

” Academic research studies with potential clinical applications are typically replicated within the pharmaceutical industry before clinical studies are begun, with each study replication requiring between 3 and 24 months and between US$500,000 to US$2,000,000 investment [ref. 23]”

Improved reproducibility would improve the pharmaceutical industry’s return on investment by allowing clinical research to follow a larger percentage of preclinical studies, meaning more positive studies would result in eventual drug development.

The first aspect of improvement would involve adoption of standards for conduct of research and reporting of results:

” … one issue that has shown demonstrable impact on similar challenges in other settings is the expanded development and adoption of standards and best practices [ref. 13].”

The second improvement would be in training of scientists to include these best practices in their research.  The PLOS paper gives a list which provides a framework for improvement in standards and training, including the allocation of funding for these practices.

Here is an example of a practice that is not followed that could save money by reducing false results in the use of cancer cell lines:

“An illustrative example is the use and misuse of cancer cell lines. The history of cell lines used in biomedical research is riddled with misidentification and cross-contamination events [ref. 29], which have been estimated to range from 15% to 36% [ref. 30]. Yet despite the availability of the short tandem repeat (STR) analysis as an accepted standard to authenticate cell lines, and its relatively low cost (approximately US$200 per assay), only one-third of labs typically test their cell lines for identity [ref. 31].”

The process of validating reagents to prevent misidentification and cross-contamination, and the identification of cell lines to likewise avoid contamination and wrong identification, would eliminate a large proportion of primary errors in the performance of research, but it will be necessary to train, fund, and regulate in order to establish these basic procedures among the entire research community.  An outline of these procedures for training and so on is given as part of the conclusion of this paper.

This type of development is important for reducing errors and making research more reproducible.  Whether this can be done depends on the motivation of the groups that have the most investments in making research accurate: the funding bodies and the administrations of the institutions that do research.  Public awareness of the need for accuracy and reproducibility will improve the motivations of these groups.  Everyone wants to save money by doing things in the most efficient manner possible; what is required is the motivation to do the right thing from the beginning.

Resistance to changes of this nature can be expected from some individuals, particularly those who have been short-cutting the process of doing good research and those who are used to the situation as it now stands.  Those who want to read good research and those who want to do good research will be forced to put their livelihoods on the line to require improvements in research practices.

Here’s a link to the paper: http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002165

 

 

Scientists Who Cheat and What to Do About It

2015-06-09

Cheating in scientific and academic papers is a longstanding problem, but it is hard to read recent headlines and not conclude that it has gotten worse.

from: http://www.nytimes.com/2015/06/01/opinion/scientists-who-cheat.html

The New York Times (NYT) has today recently (June 1, 2015) published an editorial “wringing its hands” at the seeming epidemic of cheating in scientific research that has come to light, partly thanks to the efforts of the writers of “Retraction Watch”, a blog that is only a few years old.

The editorial concludes that part of the answer to the problem of cheating in research is more research, that is studies to determine how common the problem is, “how much harm it causes, and how best to combat it.”

The editorial also recommends, as a starting point, the release of all underlying data of every research project that comes to publication– to peer reviewers, for a start.  Underlying data should be available to interested parties, preferably in a central repository of data points for all relevant research.

The editorial recommends increased funding for the Office of Research Integrity (ORI) to allow it to investigate “all major cases that come to its attention” and to give it “sufficient independence.”  Other authors have cited the ORI for its lack of transparency and its delay in making investigations.  Still others have objected to the ORI’s lack of stringent sanctions; typically the penalty for irregular research is a three-year suspension of research grants.  Some suggest that offenders should be forced to pay back all or a portion of the money granted for the offending research, possibly a harsh penalty when the grant involves payments for multiple grantee’s salaries and equipment as well as fees for outside surveys and so on.

The proposal to perform more research into the prevalence of cheating, its causes (whether “publish or perish”, career promotion, or simple dishonesty) and the degree of harm that is done to real research, is a good way to determine what is really going on and how serious the problem is.

Finally, the proposal to “do more research” is a good one in any case.  Our budgets for research of all kinds should be dramatically increased.  There is little that cannot be improved by performing more research into all areas of science, and a great deal to be learned everywhere.  The only caveat is that we need to have a clear idea of what we do not know in order to turn our questions towards what we can learn that will make our lives better and longer.

J. Dennis Hastert, a Bad Man Caught by a Bad Law

2015-06-09

Here’s a story that will warm the hearts of Democrats and left-wing ideologues: J. Dennis Hastert, now 73  years old, who was speaker of the House from 1999 to 2007, was indicted in Chicago on federal charges of “structuring” and lying to FBI agents.  He is accused of making withdrawals from his bank accounts of less than $10,000 to avoid having to make specific reports about those withdrawals.  In the case in which he is charged, he made 106 such withdrawals, all for the purpose of payments to one individual, and all apparently for the purpose of preventing that person from publicly making statements about their relationship when Mr. Hastert was a high school wrestling coach in central Illinois from 1965 to 1981.   The relationship apparently involved “sexual abuse”, a crime because the individual was under eighteen years old at the time; the statute of limitations has long passed.

Mr. Hastert was the standard-bearer for the Republican Party and second in line, behind the vice president, in the succession to president in case of death or infirmity.  Some Democrats found his positions and behavior to be unfriendly and unsportsmanlike, while others were able to work with him.  In any case, there was no scandal surrounding him while he was Speaker.  After leaving Congress, he naturally became a lobbyist and was expected to take home two or more times as much money as he did while in Congress.

Unfortunately, an indictment was released on May 28; he was not taken into custody because he was “not considered a flight risk.”   However, the charges are potentially serious; he could be fined $250,000 and face five years in prison on each of the two counts.   In the indictment, it is stated that Mr. Hastert has paid $1.7 million over the last four years to “Individual A” as part of an agreement in which he has promised to pay a total of $3.5 million.

Anonymous individuals who have been “briefed” about the FBI investigation have said that the agreement is the end result of a relationship in which Mr. Hastert “sexually abused” Individual A while Mr. Hastert was a wrestling coach and teacher in Yorkville, a suburb 50 miles from Chicago. The agreement stipulates that Mr. Hastert is to pay a total of $3.5 million in exchange for Individual A’s silence about the relationship, or more properly, repeated episodes of sexual abuse.   This relationship must have been concluded at least 30 years ago.

The judge who is currently handling the case is  Thomas M. Durkin of the Federal District Court for the Northern District of Illinois.  Judge Durkin donated $1,500 to Mr. Hastert’s campaigns years ago before he became a judge.  The judge’s brother is Republican leader of the House for the Illinois State Legislature.  The judge has refused to comment on the case, in particular on whether he will recuse himself.

Mr. Hastert’s Washington lobbying outfit, Dickstein Shapiro, announced that he was resigning shortly after the indictment was announced.  In addition, the  CME Group of Chicago, a company which runs futures and derivatives exchanges, announced Mr. Hastert’s resignation from its board.  Mr. Hastert also saw his name removed from his alma mater Wheaton College at their “J. Dennis Hastert Center for Economics, Government, and Public Policy.”

One of Mr. Hastert’s former students took his sister into his confidence in about 1979 and told her that he was gay.  He died of AIDS in 1995.  At the same time he came out to his sister, he told her that, when he had been the wrestling team’s equipment manager, Mr. Hastert (his wrestling coach) had “sexually abused” him.  The sister said she did not know Individual A, and he wasn’t her brother.

According to the bank, Mr. Hastert had started making withdrawals of $50,000 in cash every six weeks in 2010.  After the bank, which is required to file “transaction reports” with the feds for every cash transaction over $10,000, questioned Mr. Hastert, he began making smaller withdrawals, and made a total of 106 such withdrawals.  The law, which makes it a crime to “structure” withdrawals and deposits so as to evade the reporting requirements, has been used against completely innocent individuals who, for example, had saved large amounts of cash through tips and were depositing it in the bank, and who, being unable to physically carry a full $10,000 in small bills on their person, had made multiple smaller deposits.  The law is written so that the prosecutor can confiscate the money without having to prove anything and the individual is forced to hire a lawyer to prove his/her innocence, a case of “guilty until proven innocent.”  In their zeal to protect the public against criminals who want to launder their money, the prosecutors have dragged in many people who are completely blameless, and in typical prosecutor fashion, they refuse to believe perfectly reasonable explanations for the “structuring”; the way the law is written, it is a license for prosecutorial misconduct.

In addition to “structuring”, Mr. Hastert is accused of one count of lying to an FBI agent.  When initially interviewed by the FBI, Mr. Hastert had made a statement to the effect that he didn’t trust banks and was withdrawing the money to keep at home.  This turned out not to be true; in fact, he was making cash payments to Individual A.

J. Dennis Hastert is a bad guy; he pushed for laws that were retrogressive, Republican-inspired, and served the purposes of one of our nation’s less memorable presidents, George W. Bush.  He also, it seems, was a homosexual abuser of minors in his care (whether that represented pedophilia is open to question.)  Finally, he used his position as a leader in Congress to transition to a very highly paid job in which he could trade on his influence with his former colleagues.  To see him be stripped of his powerful positions is a good thing.

However, the law which was used against him is a bad law which has entrapped many perfectly innocent people and forced them to pay (outrageously high, by definition) legal fees just to get their money back.  So having him lose his money in this way is not a good thing, even if the end result is well deserved.

To read more details of this incident, read the story in today’s edition of the New York Times:  http://www.nytimes.com/2015/06/10/us/politics/dennis-hastert-chicago-court-appearance-for-arraignment.html

Epigenetic DNA tags Mostly, but not all, Removed in Embryos | Science News

2015-06-04

In the first weeks after conception, some of the cells in human embryos get their genetic blueprints scrubbed clean, conclude three new studies published June 4 in Cell. Those cells, the ones that become sperm or eggs, could beget the tiny embryos’ future offspring.

via DNA tags mostly deleted in human germ cells | Science News.

I previously wrote a post about epigenetic tags that are placed on DNA to alter the activity of genes– tags that record responses to environmental factors such as childhood abuse and differences in diet.  These tags appear to be related to a number of human diseases and characteristic responses.  For example, children raised in an extremely high stress environment grow up with an increased sensitivity to stress.  These children, as adults, have greater hormonal responses to stressful events: higher levels of cortisol and norepinephrine in response to stress, for example.

One of the common epigenetic markers is methylation; methylated DNA at the right location will shut down or enhance the activity of the associated gene.  Wikipedia describes methylation, occurring on cytosine or adenine nucleotides, as “suppressing the expression of endogenous retroviral genes and other harmful stretches of DNA…methylation is essential for normal development and is associated with…genomic imprinting, X-chromosome inactivation [in female cells], suppression of repetitive elements, and carcinogenesis.”

Now, as reported in these publications in Cell magazine, studies find that most, but not all, of these epigenetic tags are removed from germ cells (those that are destined to become sperm or egg cells) during embryo development.  It had been previously found in mouse embryos that virtually all epigenetic tags are erased from germ cells.  The new studies find that, in human germ cell embryonic precursors, about 4 percent of epigenetic tags are retained (as compared to 37 percent in another embryonic cell type.)  Some of the tags that are retained (“escapees”) relate to tendencies to schizophrenia, obesity, and multiple sclerosis, conditions that are known to run in families.   One of the Cell papers states: “Notably, many of the escapee-associated genes are expressed in brain, with potential links to neurological and metabolic disorders in humans.”

These studies show a significant difference between epigenetic inheritance in mice and humans.  Some things are epigenetically inherited in humans that are not in mice.  This opens the way for further study of epigenetics, a new area of research.

Drug-poisoning Deaths Involving Opioid Analgesics: United States, 1999-2011. – PubMed – NCBI

2015-06-04

Data from the National Vital Statistics System, Mortality File. The age-adjusted rate for opioid-analgesic poisoning deaths nearly quadrupled from 1.4 per 100,000 in 1999 to 5.4 per 100,000 in 2011. Although the opioid-analgesic poisoning death rates increased each year from 1999 through 2011, the rate of increase has slowed since 2006. Natural and semisynthetic opioid analgesics, such as hydrocodone, morphine, and oxycodone, were involved in 11,693 drug-poisoning deaths in 2011, up from 2,749 deaths in 1999. Benzodiazepines were involved in 31% of the opioid-analgesic poisoning deaths in 2011, up from 13% of the opioid-analgesic poisoning deaths in 1999. During the past decade, adults aged 55-64 and non-Hispanic white persons experienced the greatest increase in the rates of opioid-analgesic poisoning deaths. Poisoning is the leading cause of injury death in the United States (1). Drugs-both illicit and pharmaceutical-are the major cause of poisoning deaths, accounting for 90% of poisoning deaths in 2011. Misuse or abuse of prescription drugs, including opioid-analgesic pain relievers, is responsible for much of the recent increase in drug-poisoning deaths (2)

via Drug-poisoning Deaths Involving Opioid Analgesics: United States, 1999-2011. – PubMed – NCBI.

Yes, you read that correctly: the rate of opioid related poisoning deaths in the United States quadrupled from 1999 to 2011.  What’s more, benzodiazepines were also used in 31% of deaths in 2011, up from 13% in 1999.  So, while the rate of killing yourself with narcotic pain killers increased four times and the use of benzodiazepines in combination with narcotic pain killers also dramatically increased.  An epidemic of pain killer and tranquilizer-induced deaths.  Why?

Burke and Hare, anatomy, the founders of modern obstetrics as callous murderers, and dissection as class warfare

2015-06-03

The names of William Hunter and William Smellie still inspire respect among today’s doctors, more than 250 years since they made their contributions to healthcare. Such were the duo’s reputations as outstanding physicians that the clienteles of their private practices included the rich and famous of mid-18th-century London.

But were they also serial killers? New research published in the Journal of the Royal Society of Medicine (JRSM) claims that they were. A detailed historical study accuses the doctors of soliciting the killing of dozens of women, many in the latter stages of pregnancy, to dissect their corpses.

via Founders of British obstetrics ‘were callous murderers’ | UK news | The Guardian.

Here’s a “cold case” that’s really cold: between 1749 and 1774, with a pause between 1755 and 1764 due to suspicion about how they procured their specimens, the two obstetricians had between 35 and 40 pregnant women killed and their bodies delivered to them for anatomical dissection.  The historian Don Shelton built a circumstantial case for murder based on the rarity of natural or accidental deaths of women who were pregnant near to term, that is eight to nine months along.

Don Shelton names Dr Colin Mackenzie and John Hunter, William Hunter’s brother and a celebrated anatomist, as their accomplices.  The author of the Guardian article states that William Hunter had links to powerful families that allowed him to avoid any investigation despite the fact that suspicion had fallen on them both by 1755.  Hunter apparently resumed ordering the killings in 1764 but limited the “take” to one victim a year and stopped in 1774.

The “resurrection” business– the trade in corpses used for anatomical dissection– was described as “very lucrative” during the 18th and 19th centuries in particular.  Two notorious killers, Burke and Hare, gave the name “Burking” to the murder of individuals specifically so that their corpses could be sold to doctors in need of specimens for dissection.  They were said to have murdered 17 citizens of Edinburgh in 1827 and 1828.  Large cities were poorly policed, and London was described as “unhealthy and semi-anarchic.”  The practice of “grave robbing”, or obtaining recently deceased individuals for dissection, was popular and well-compensated, although the bodies normally obtained in this way were usually old or in a state of extremely poor health before death, making them weak subjects if one’s purpose was to look at (“autopsy” means “to look for one’s self”) healthy bodies and organs.  Thus, Burke resorted to the much more risky practice of murder for the purpose of obtaining healthy specimens.

Burke and Hare sold their victims to Dr Robert Knox, a popular anatomist of the time who gave lectures in which he dissected corpses and identified their organs for medical students as well as the interested public.  They were allegedly assisted by Burke’s mistress and Hare’s wife.  They became so notorious that a word for their activities was coined: “burking”, which originally meant to smother a victim, leaving no marks of violence, specifically for the purpose of using the corpse for anatomical dissection.  “Burking” was extended from its original meaning of “to suffocate a victim so as to leave no evidence of violent death” to a more general meaning of “to hide wrongdoing or cover-up misdeeds”.

“Burking” was popularized when Burke and Hare were captured and put on trial; their testimony on the stand was discussed and repeatedly endlessly by morbidly fascinated citizens.  The degree of interest in such grotesque subjects is difficult for modern people to understand, but until the mid-eighteen hundreds, execution by public hanging was the rule and was attended by huge crowds.  Burke was attended by an estimated crowd of 25,000 at his execution and was himself delivered up for dissection afterwards.  Hare escaped execution by turning “state’s evidence” and Knox, who kept his mouth shut, was not charged.

Before the Anatomy Act of 1832 (see below), the fear of grave-robbing led to extreme measures to prevent digging up fresh corpses.  At some cemeteries, guards were set to watch at night to observe any unauthorized digging; small houses were built for these guards, with fireplaces to keep warm, windows to observe the graveyard, and loop-holes to fire potshots at any trespassing grave violators.  At other cemeteries, heavy stones were placed over fresh graves to inhibit digging; when robbers simply dug at the end of the stone to extract the body through the top of the coffin, solid collars were added to keep the body from sliding out.  Heavy stone temporary dwellings were also built to store coffins containing fresh corpses until they had decomposed to the point beyond which dissection was unrewarding.  After a couple of months, the coffin could be removed and the remains safely buried in the normal fashion.

“Grave torpedoes” were even invented that would explode if someone attempted to dig up the coffin beneath.  Naturally, the torpedo was designed to explode upwards to avoid scattering the remains when activated.  Through Wikipedia and a Scottish website detailing methods of discouraging grave robbers I viewed the text from a patent for a grave torpedo that dated to the end of the nineteenth century (Google has scanned the text of numerous old patents).  Apparently there was still sufficient concern about one’s grave being dug up nefariously at that late date.

In a movie released in 1945, “The Body Snatcher”, Bela Lugosi and Boris Karloff take up where Burke and Hare left off; the movie’s story was loosely based on a short story by Robert Louis Stevenson published in 1884.  The movie adds an idealistic young medical student who is forced into the practice of buying corpses by his older, cynical and entrapped doctor mentor.  The young student rebels when he discovers  a poor young woman he has seen on the street dead in the doctor’s basement, another corpse to be dissected.  The perpetrators are killed in a carriage crash at the end of the movie when one of their victims turns out to be still alive and kicking, and has mysteriously turned into one of the killers, supposedly a victim.  Of course the killer is trapped in an out of control horse buggy in the pouring rain, with the reanimated corpse crowding him on the carriage seat.

Another film, “The Flesh and the Fiends” (1960), retold the Burke and Hare story with Peter Cushing as Dr Knox, Donald Pleasance as Hare, and George Rose as Burke.  This movie, while more faithful to the original Burke history, also includes an idealistic young medical student; this time, the student and his girlfriend are killed by Burke, but the killers are arrested.

The method of the murders, smothering, is said to be the one that leaves the corpse in the best condition and avoids any bloodshed, which could leave tell tale evidence behind.

The problem that doctors and researchers faced for hundreds of years has always been how to see for one’s self how the inside of the human body looks and works.  To look at the inside of one’s body usually requires cutting it open; if done before death, it is painful and destructive.  If done after death, the body has stopped functioning and much is likely to be missed.  Equally important, religious strictures get in the way because it is thought that the body must be retained as intact as possible in order to be raised at the Day of Judgement.  Such issues as how the blood circulates could not be settled until it could be seen where the blood comes from, where it goes, and how it returns to its starting point, in a living subject.

The problem of obtaining specimens became acute when Vesalius (1514-1564) popularized the dissection of human bodies to learn anatomy.  He discovered that the standard anatomical text of the time, published by Galen of Pergamon (Greece) in the second century CE (Common Era, better known as AD–Anno Domini), had been based on the dissection of Barbary macaques (a sort of baboon) because dissection of humans had been banned.  Vesalius began to perform dissections himself and encouraged his students to do the same.  He documented his work in his first publication with detailed illustrations that were published as a set of six large woodcut posters in 1538.

Galen had assumed that arteries carried blood to the brain and lungs from the left ventricle, while veins carried blood to the stomach and other, lesser organs from the right ventricle.  For this circulation scheme to work, there would have to be a series of holes that interconnected the ventricles; these holes didn’t exist, but until Vesalius began his work, all anatomists agreed that they had found them.  Vesalius stated that he couldn’t find these essential holes.

Galen made a number of other notorious errors; for example, he thought that the mandible was two bones, while in fact there is only one mandible bone, joined at the center.  He also thought that the sternum had seven separate bones, which is true in apes; Vesalius showed that the human sternum only has three bones.  Galen mistakenly thought that the bones of the lower leg were smaller than the bone of the upper arm, also probably as a result of dissecting ape cadavers.

Vesalius corrected some of Galen’s errors, which made him suspect for heresy in the eyes of the Roman Catholic Church, and became famous for his publications.  The most important of these works was called “De humanii corporis fabrica”,  published in Basel by Johannes Oporinus; it consisted of seven volumes and had 273 highly detailed illustrations, probably created by multiple artists, all of whom must have personally witnessed complete dissections. Vesalius was only 28 when the first edition was published.  The book made him famous, and shortly afterward, he was invited to be the Imperial Physician to the Court of Emperor Charles V (of the Holy Roman Empire.)

Envious rival physicians mocked him as a barber (the surgeon was often a barber as well) but he served the court for eleven years and had many opportunities as a result to learn by postmortems, treating battle injuries, and observing the results of medications used at that time.  His work was attacked as heretical, but an investigation by the Salamanca Inquisition cleared him of heresy.  One of Vesalius’ rivals, his main detractor, claimed that the human body had changed since Galen studied it, and this was why Vesalius’ findings were different.

“In 1564 Vesalius went on a pilgrimage to the Holy Land after being accused of dissecting a living body.” (Wikipedia)  On his return voyage, he was shipwrecked and died on the island of Zakynthos; he was buried on Korfu.  Apparently the accusation of vivisection, resulting in condemnation by the Inquisition and a forced pilgrimage, was a fabrication.  It’s not clear from Wikipedia whether the fabrication occurred before or after his death.

As a consequence of Vesalius’ work, dissection of human cadavers became extremely popular among physicians, and came to be thought of as essential to a doctor’s training.  At one point, a medical student was required to dissect three cadavers in the course of sixteen months’s training before he could become a surgeon.  Soon there was a serious shortage of material for this purpose, and “Burking” arose to fill this need.

According to Wikipedia, Vesalius freely allowed that he did not have any pregnant cadavers to work with and therefore was unable to fully explain the anatomy of the female reproductive organs.  The work of Hunter and Smellie was to correct this gap in medical knowledge, apparently at a cost of nearly forty murdered pregnant women, if this new analysis as reported in the Guardian is to be believed.

The work of William Harvey (1578-1657), who studied mostly animals, contradicted Galen’s explanation of blood circulation.  Through many experiments performed on animals from shrimp to pigeons all the way to humans(who were not cut open), Harvey was able to establish that blood circulated from the veins, through the right side of the heart to the lungs and back again to the left side of the heart, and then out to the peripheral circulation through the arteries, finally returning through the veins to the right side of the heart.

Harvey’s work on humans was limited to observations of the results of temporary compression of the upper arm or leg.  Lack of blood flow became obvious (and painful) after a few moments of compression to above 200 mm of mercury equivalent.  The actions of the veins, and their valves, could be demonstrated with slight compression and “milking” of blood towards the torso; venous valves prevented back-flow of blood when it was stripped through the vein with finger pressure.

Galen’s theory of the circulation had postulated two separate systems, arterial and venous, which came together through invisible pores in the wall of the left ventricle.  This theory was contradicted by Arabic scholar Ibn al-Nafis, who saw a circulation of blood from heart to lungs, mixing with air, returning to the heart, and then going out to the rest of the body; his work was not publicized in Europe, however.

Harvey’s book, “De Motu Cordis”, showing how blood actually circulated, caused controversy and accusations of blasphemy.  The agreed-upon system, based on Galen, had two separate circulations, as noted above: venous blood, which originated in the liver, and arterial blood, the “vital system”.  The arterial blood was thought to contain “spirits” which came from the heart and distributed heat and life to the body.  The lungs were supposed to cool the “vital blood.”  Pulmonary circulation of the blood was also described by Vesalius, among others, before Harvey completed the circuit.

Harvey’s work was limited by his ability to magnify only with a simple hand lens; he did not have available to him a microscope, although this was developed by Antonie van Leeuwenhoek(1632-1723) shortly after Harvey’s death.  Leeuwenhoek, who was primarily a businessman rather than a scientist, kept his method of developing powerful magnifying lenses a secret because he wanted to be remembered for his role in developing microscopy rather than simply lensmaking.

He had discovered a powerful and extremely simple method of creating tiny glass spheres by heating a the center of a long piece of soda lime glass over a flame; pulling the piece apart while it was soft created two thin whiskers of glass.  Reheating the end of the whisker made it collapse into a tiny glass sphere which was smooth enough to serve as a powerful magnifying lens.  Combining two such spheres would make a microscope.  This bypassed the tedious method of grinding a larger piece of glass on a careful pattern and then smoothing the surface with finer and finer abrasives.

Leeuwenhoek’s method of building microscopes didn’t create a demand for cadavers, but it satisfied a demand for close examination of tissues and opened up a new world of “animalcules”– single-celled organisms too small to be observed with the naked eye or a hand lens.  At the same time, microscopic examination of animal and plant tissues revealed that they were built up of billions of individual cells that were separated by thin walls.  While he is thought of as an amateur due to his orientation towards business, he was able to build microscopes that magnify to at least 275 times (the nine surviving microscopes) and may have reached 500 times magnification(some twenty to thirty were lost over the years).

The resurrection business was slowed down in 1832, at least in the United Kingdom, by the Anatomy Act, which provided for the legal dissection of those cadavers whose relatives did not object to the work.  Prior to this Act (which was not universally acclaimed) the supply of bodies for dissection had been drying up, at the same time that the demand was increasing, by the reduction in the number of executions that gradually occurred at the end of the eighteenth century.  The Act allowed for persons whose corpses were unclaimed by relatives after death to be “anatomized”, especially those who died in prison or in the workhouses.  A person could even donate the body of a next of kin or his own body, in exchange for burial at the expense of the anatomy school.

Dissection was still discouraged by the Church because of a widespread belief that the body had to be intact in order to be resurrected at the End of Days.  For the same reason, cremation was thought to prevent one’s rising again to be judged by Christ at the Apocalypse.

In addition, popular revulsion was shown by the actions of “angry mobs”; in particular, Wikipedia mentions the vandalism of an anatomy theater in Cambridge, England late in 1833.  People believed that the Anatomy Act failed to prevent the sale of pauper’s bodies for medical research without the individual’s consent.  For this reason, the anatomy laboratory was kept under wraps even after the Anatomy Act.

Finally, the passage of the Anatomy Act was hindered by the opposition of the poor for the following reason: the well-to-do would be the primary beneficiaries because, first, they would be free of the fear of their graves being dug up, and second, the advances in medical science would be to their benefit and not to the benefit of the poor, who could not afford medical treatment and doctor’s fees.  The poor would be the worse off for the Act because they would be the ones whose bodies would be dissected after they died in the workhouse or without any relatives to claim their bodies.  The poor were probably also more likely to believe that they needed to have an intact body to be resurrected and to go to heaven, rather than wander in limbo for eternity.

Thus, even body-snatching can be seen as a class struggle.  Not that I endorse that way of thinking: it’s really tortuous and distorted and even silly.  In the end, everyone benefits from advances in medical science, and all developed countries other than the United States have universal “free” (insured) health care.  No-one is worried about grave-robbing, although there is still a shortage of cadavers for dissection: medical students are assigned, four students to each cadaver, in the first year of medical school.

Nonetheless, poor people distrusted the Anatomy Act and resented the provisions which allowed the government to claim any body that could not be buried at the expense of the family.  Thus, if there was no money to pay for interment,  “after six weeks” (often in practice, less than one week) the body could be sold for dissection.  The body was supposed to be buried after such procedures, with the parts reassembled in a coffin; in practice, often six bodies were combined in one coffin, which was then buried under a numbered crucifix.

Poor people’s resentment of government and distrust of the Anatomy Act’s provisions was, to repeat, based on religious belief: those whose bodies were cut apart in the process of dissection could not rise from their graves intact on the Day of Judgement.  To prevent dismemberment, families pooled their resources, purchased insurance policies, or did whatever they could to finance “proper burial.”

This reflects a low opinion of the medical profession in general: the attitude that doctors prefer to work for wealthy people, only do what they get paid to do, and have a habit of covering up unethical practices when they are witness to misdeeds.  To stretch a slang term, the poor see doctors as guilty of “burking” their victims.

A Climate-Modeling Strategy That Won’t Hurt the Climate – NYTimes.com

2015-06-02

Dr. Palmer said the case for the required investment should be self-evident.

“It’s a trivial amount of money when you think of climate impact being in the trillions of dollars,” he said. “It’s actually an existential question. If it’s at one end of the spectrum, we can adjust, but if it’s at the other end of the spectrum, we’re not going to come out of it unless we cut emissions in the next decade.”

via A Climate-Modeling Strategy That Won’t Hurt the Climate – NYTimes.com.

This article appeared in the May 11, 2015 online version of the New York Times (NYT) and the quote is from the very end of the article.   The primary thrust of the article from its first paragraph was that new computing techniques will be needed to solve the problems of climatology– specifically the scientific question of how quickly global warming will occur and, in general, what is likely to be the trend of the climate over the next hundred years.  The new computing techniques will be required because a sufficiently fine-grained model of the earth for climatological purposes– say one kilometer on a side as the pixel size– would require 200 million cells to be computed per cycle, suggesting a 30 megawatt power consumption by the computer used to run the simulations.  Large numbers, to be sure, and calculating the climate may be very expensive and will generate a lot of heat!

Therefore, the innovators of the Times article discuss using an inexact computing model to allow for approximate results that would give good enough conclusions with much less power required.  One can imagine the analogy of using a slide rule to get results to two or three significant digits– approximate but close enough to point to a correct conclusion.  The mechanisms of an inexact computation are discussed, and its theoretical advantages pressed, in this article, convincingly I think.

The final quotation refers to something very important that really has not been addressed– the inexact nature of our ability to predict what will happen over the next hundred years.  The climate change may be mild enough, in the best case, for us to adapt to easily– or, in the worst case, the change may be so severe as to threaten the survival of the human species.  We don’t really have an exact answer to the question that says: how bad is it going to be?

Krugman Flogs a Dead Horse (Just Kidding)

2015-05-30

The New York Times’ resident economist, Paul Krugman, has published a new column entitled, “The Insecure American”,

http://www.nytimes.com/2015/05/29/opinion/paul-krugman-the-insecure-american.html ) in which he reports some more statistics that point out the continued, possibly worsening, economic insecurity that plagues middle America.  For example, the Pew Research Center reports that “more than 3/4 of conservatives believe that ‘the poor have it easy’ due to government benefits.”  The same poll reports that “only one in seven [conservatives] believe that the poor have hard lives.”

Krugman claims that “punishing the poor has become a goal in itself”, resulting in the refusal of Republican-run states to accept a Medicare expansion that would be paid for by the federal government; refusing the expansion leads to a group of people caught in the middle, too poor to afford private health insurance, and too “rich” to qualify for Medicaid.  These millions of in-between people are unable to obtain health insurance of any kind and are actually worse off than they were before.

Krugman continues by repeating a contradiction to the widely-held belief that the age for Social Security should be raised because people are living longer.  In fact, only the wealthy are living longer: the average life expectancy for those in the lower half of the income curve has hardly risen at all.  Those who need Social Security the most are worn out by chronic diseases (some of them induced by their work) and die just as young as they did when Social Security was first implemented in the late 1930’s.  The facts of this distribution of life expectancy have been well known for years, and yet it is almost a part of neoliberal dogma to claim that the retirement age should be increased because people are living longer.   People are living longer, but almost the entire benefit of this increased life span is limited to the well-to-do, and the physical battering that poor people suffer in their jobs has not improved.  The average coal miner, janitor, or street sweeper is worn out by age fifty, and lucky to reach sixty-five alive.

This problem is reflected in the rate of people applying for permanent disability, which allows immediate access to one’s Social Security savings; unfortunately, it does not result in eligibility for Medicare for two years after being declared disabled, an absurd restriction which theoretically saves money for the government but usually results in doctor’s visits not made or emergency room bills not paid.  The only exception to the two year waiting period is for people afflicted with Lou Gehrig’s disease, who are not expected to survive the two years.

Krugman also reports on the results of a study run by the Federal Reserve, which reveals that three in ten nonelderly Americans have no retirement savings whatsoever.  That is a surprisingly low figure, and I suspect that the retirement savings reported by the typical survey respondent are minimal when they exist at all.  In addition, 47 percent of respondents stated that they would not have the resources to pay for an unexpected $400 bill, such as a car repair or noncovered medical expense.

Here is a “conservative” commenter’s argument against welfare:

“I am certainly not devoid of compassion. Its a basic human instinct. If you read what I said carefully, it is that permanent entitlements create dependencies, lead to anti-social behaviour and in the end a burden for society to maintain those dependants in a state of managed care that minimises violent “protests”.”

You can see that this person thinks that “permanent entitlements create dependencies” and “lead to anti-social behavior” and a “burden for society” that puts those dependents in “a state of managed care that minimizes violent ‘protests’ ” –surely this is a poor form of reasoning that argues against providing the type of help that is really needed,  that is “permanent entitlements” for fear of “anti-social behavior” in those who are given the help they need.  It seems to claim that those who are helped are actually hurt by “creating dependencies”– as if a “burden for society” does not already exist in the situation in which people who really need help are present.  This is twisted reasoning that creates a specter of entitled, dependent, angry people who demand help as their right and are “anti-social” if they don’t get it, staging “violent ‘protests’ ” and generally causing trouble by asking for help.

In reality, people who need help are suffering and society will be helped by giving help.  There is no reason not to help people by providing paid work, paid health care, and payments for housing, clothing, and food.  Society and the economy are helped because those who are helped will spend all the money they receive; the economy heats up because spending increases, and those who do not appear to need help are benefited by a stronger economy.  The bugaboo of “permanent entitlements” is just that– a fear that functioning people have of people who cannot function.

It is true that poor people are scary.  Just looking at them reminds one of the possibility of one’s self becoming poor and helpless.  Rather than indulge fear by turning away from needy people, we should banish fear by helping them.  All of society will benefit from our help.

Killing Cats

2015-05-28

Killing Cats

When I went back to school in the spring of 1972, my parents handed me an assistantship in a research project that was going on at Massachusetts General Hospital. My parents were friends with a professor whose boyfriend was a medical student; this student had been working in a laboratory there and wanted someone to replace him as an assistant. The research was in neurophysiology, and it involved using very thin electrodes inserted into the brains of cats to pick up activity in certain nerve centers within the brain.

This work was complex and morbid. We would take a young cat that had been raised in a cage at the laboratory animal compound in a big room in the basement that had cages of dogs, rabbits, and a few other mammals that were there to be used in various research projects. The men who worked in the big room were called Dieners, which is German for ‘servant’, and I was told to be very careful to be respectful of them because they were sensitive.

The cat would be given an intraperitoneal (that is, in the stomach) injection of a fast acting anesthetic like Pentothal. In a couple of minutes, the cat would fall sound asleep and we would then perform a cutdown (cut through the skin to expose a vein) and insert an intravenous line. This line was used to infuse a paralyzing agent, Flaxedil, and a saline/glucose mixture that kept the cat hydrated.
After the cutdown, we would open the cat up at the neck and perform a tracheostomy (insert a plastic breathing tube into the trachea after cutting it open.) The “trach” tube would be connected to an air pump that breathed for the cat, since the Flaxedil stopped the cat’s breathing muscles as well.
Finally, the cat’s head was placed in a large adjustable metal device that supported it on two prongs inserted in the ears and a clamp that held its jaw. The skin over the top of the skull was cut lengthwise and small holes were drilled over the needle insertion sites. The needle was then run on a stereotactic vise (a vise on which precisely measured movements can be made) down into the brain until we picked up a signal from a nerve center that responded to light. The cat was placed in a large box with a translucent screen in front of its eyes and measured lines of light were projected on the screen, moving across in a slow, measured fashion, or moving up and down in the same measured fashion. The light source was adjustable from a long line to a small spot.
The desired nerve centers responded to the light in a repetitive fashion: as the line of light moved across the screen, at a certain spot the nerve would start firing, then after the beam of light had passed, stop firing again. The best nerves we located would respond to the light like a bull’s eye: there would be a round area within which the nerve would fire repeatedly, but in the center of this area the nerve would suddenly stop firing altogether for a moment.
These nerve centers represented cells within the lateral geniculate body, a kidney bean shaped area in the brain within which were the neuron cell bodies that passed along visual impulses from the optic nerve and the eye to centers in the occiput or rear of the brain that processed visual information. These neurons were organized and specialized to fire only at a light impulse that appeared in a small area of the visual field, and the individual neurons collectively built a picture of the cat’s visual field.
We also inserted electrodes into the median raphe, the general activating center of the brain. Small electrical impulses in this area would alert the cat or wake it up.
We recorded the electrical impulses we received from the electrodes that we inserted into the lateral geniculate body onto a large tape recorder that we could play back afterwards to remind us of specific activity that we had picked up at definite times after light beams stimulated it or electrical stimulation of the median raphe occurred.
When we had located a cell that appeared to have the right behavior, a bull’s eye shaped reaction to light, we would infuse LSD-25 into the cat’s vein and record the cell’s reaction, which usually lasted two or three hours. Most often, the cell’s activity would increase but its sensitivity to light would decrease.
In the first few cats we did this procedure on, we did not use any anesthetic. After I figured out what was happening from the cat’s perspective, I realized that it would be awake but paralyzed and possibly suffering. I insisted that they find some sort of anesthetic and they began to use nitrous oxide through an anesthesia machine; a mixture of 80% nitrous oxide and 20 % oxygen was produced by the machine, and this was pumped into the cat’s lungs by the ventilator.
After dosing the cat with nitrous oxide, an inhalation anesthetic that induced a light coma, we would record impulses from the cat’s brain for 24 to 72 hours, depending on how long the cat survived. Eventually the cat would die, from side effects of the anesthesia or malnutrition (we fed them intravenously with glucose but it wasn’t adequate for prolonged survival.)
We then infused glutaraldehyde as a preservative into the cat’s brain, cut it out and sent the preserved brain to be sliced for microscopic examination. This would show us the needle tracts and whether we had reached the desired location within the brain.
Between the fall of 1972 and the spring and summer of 1973, I participated as an assistant in about twenty or thirty of these procedures, each ending with the death of the cat and its preservation in glutaraldehyde for microscopic examination.
In the summer of 1973, our cats started dying prematurely and we discovered that the anesthesia machine had a crack in the output valve that was allowing the cats to be slowly suffocated.
In the fall of 1973 and into 1974, the lab moved into a different building and I didn’t do any more cat procedures. I analyzed the data we had gathered and performed statistical tests on it. Eventually I produced a report which was turned into a paper published in the Proceedings of something or other.
In the spring of 1973, possibly in February or March, I adopted one of the cats from the lab cages and took it back to my dorm room. It promptly took shits randomly all over the place and I had to clean these things up. The next day I took the cat back to the lab and a few weeks later, I used that cat in an experiment where I anesthetized it and cut out its lateral geniculate body for evaluation of the amount of serotonin in it by another laboratory. I then turned up the nitrous oxide to 100% and disposed of the cat a few minutes later after its heart stopped beating.
I was dating a girl named Mei-Ling Ma in the spring of 1973 and I took her on a visit to the laboratory. She took a job in a lab a floor above us where there was a hospital unit.
The lab became a place where I did unauthorized experiments, and in the summer of 1973 I took an ounce of marijuana and extracted the cannabinoids with ether, concentrating them in a smaller portion. I did the experiment late at night and put a sign up on the door to warn the night watchman that I was working that night.
When I went home I forgot to take the sign down. I remembered after I went home and turned around, and went back to the lab and took the sign down. After I took it down, it was already 7 in the morning, and I sat down at the bench to look at some specimens under the microscope. I was looking through the scope when the head of the lab came in, a few minutes before 8 in the morning. He saw me working at the microscope and assumed that I had been there examining specimens for some time. He told me to go home and get some sleep, which I did.
The process of experimenting on cats disgusted me after a while and I think I felt guilty about it too. When I went to medical school I was offered a position in a lab that did experiments on cats; this time they kept the cats alive indefinitely and they seemed to be doing well. They installed plastic domes in place of their skulls and took small samples of cerebrospinal fluid periodically to measure serotonin levels. This was some of the pioneering research that was being done on serotonin in the brain. I turned down the offer to work in that lab in medical school. If I had accepted the offer, I could have paid my way through medical school. Instead I turned to a National Health Service scholarship and obligated myself to serve for four years in an underprivileged area in return for a generous scholarship and stipend.
That was a major turning point in my life, in which I abandoned research in favor of primary practice in an underserved area.