Archive for the ‘science’ Category

The riot at Middlebury College over Charles Murray.

Saturday, April 1st, 2017

Recently, Charles Murray, author of the book, “The Bell Curve,” a study of intelligence in the population, was invited to speak at Middlebury college, a liberal arts college in Vermont. His attempt to speak was interrupted by a riot which injured a professor at the college.

Inside Higher Ed’s story on the event explains that college officials admonished the students prior to the talk that they could protest but not disrupt Murray’s talk, which was to be about the way white America is coming apart—the title of his latest book—along class lines. Unfortunately, that admonition did no good. “As soon as Murray took the stage,” we read, “students stood up, turned their backs to him and started various chants that were loud enough and in unison such that he could not talk over them.

The confrontation continued after he had left the stage and attempted to move to another location.

And then matters turned worse. Fearing that there might be a raucous, disruptive mob instead of an audience of students willing to listen and consider Murray’s arguments, school administrators had set up a contingency plan. Once it became clear that the mob had killed the lecture, they moved to another location where Murray would give his talk, which would be live-streamed to students.

Sadly, that location was soon beset by the mob, with banging on windows and pulling of fire alarms. Murray and Professor Allison Stanger, who was the moderator for the talk, tried their best to continue a rational discussion.

Finally, Murray, Professor Stanger, and a few others tried to leave campus.

Mayhem resulted when Professor Stanger, who had been willing to state her agreement that Murray should not have been invited, was injured.

Why did this happen ? Tribalism ?

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Judith Curry resigns from Georgia Tech

Thursday, January 5th, 2017

The world of Climate research lost a great academic figure as Judith Curry resigns her tenured faculty position at Georgia Tech.

She has figured largely in the climate debate as a skeptic in global warming.

I have retired from Georgia Tech, and I have no intention of seeking another academic or administrative position in a university or government agency. However, I most certainly am not retiring from professional life.

Why did I resign my tenured faculty position?

I’m ‘cashing out’ with 186 published journal articles and two books. The superficial reason is that I want to do other things, and no longer need my university salary. This opens up an opportunity for Georgia Tech to make a new hire (see advert).

The deeper reasons have to do with my growing disenchantment with universities, the academic field of climate science and scientists.

She has endured considerable abuse from the alarmist side. She is called a “heretic” in the alarmist circles.

over the past year or so she has become better known for something that annoys, even infuriates, many of her scientific colleagues. Curry has been engaging actively with the climate change skeptic community, largely by participating on outsider blogs such as Climate Audit, the Air Vent and the Black¬board. Along the way, she has come to question how climatologists react to those who question the science, no matter how well established it is. Although many of the skeptics recycle critiques that have long since been disproved, others, she believes, bring up valid points

So, she might have a point. However:

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Genetics and Archeology

Monday, May 9th, 2016

Neanderthal

I recently read a book titled, The 10,000 Year Explosion.

Its premise is that evolution did not stop or “pause” with the development of modern man 40,000 years ago.

A few basic facts about genetics. Genes are sets of nucleotides that encode proteins by encoding RNA. This is all in my book, A Brief History of Disease, Science and Medicine. One key fact is that:

Genes can acquire mutations in their sequence, leading to different variants, known as alleles, in the population. These alleles encode slightly different versions of a protein, which cause different phenotype traits.

I discussed this at some length two years ago and then, because it stirred a hornets nest at Ricochet, I posted some of the nasty replies here.

Mutations occur at random or under the influence of outside influence like UV radiation. Some are harmful, like cancer, and are not continued in the “gene pool.” Some are beneficial and may persist as they provide an advantage to the individual who may live longer, have more children and have more of the children survive to reproduce.

Humans evolved in Africa and spread outside of Africa before 50,000 years ago. There have been successive waves of modern humans that were better adapted to life, especially in areas that were new and often inhospitable like Ice Age Europe. One such group was called the “Neanderthal, as they were found in the Valley of the Neander River in Germany.

Neanderthals came to Europe some 300,000 years ago. They hunted big game with stone tools. Their territory spanned Europe and Asia. They left distinctive “Mousterian” artefacts.

There were other groups and we are starting to find out who and what they were from their DNA.

We know that modern humans first arrived in Europe about 45,000 years ago when the continent was still a Neanderthal stronghold. Over the next 30,000 years – archaeological work has revealed – a procession of different cultures, each associated with different artefacts and lifestyles, rose in Europe.

Archaeologists tend to think these sort of cultural shifts reflect the spread of new ideas through an unchanging population. But a new analysis of nuclear DNA taken from 51 ancient Eurasians tells a different story. They actually reflected the spread of different peoples.

The Neanderthals were gone earlier than recently believed.

“Until recently, I and many with me had thought that Neanderthals survived until 30,000 years ago, or perhaps even slightly later,” says Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. “The new dates make it clear that they disappeared 10,000 years earlier.”

What happened ?

For Pat Shipman of Penn State University, this supports her theory that modern humans acted like an invasive species in Europe, beating the Neanderthals in a competition for resources. That’s a “distinct possibility”, Higham says.

But that does not mean we murdered our cousins. There is no evidence humans ever killed Neanderthals, and they probably didn’t meet often, says Higham.

So what role did we play? Many now suspect we were the last straw for an already fragile species. Genetics suggests Neanderthal numbers dropped sharply around 50,000 years ago. This coincides with a sudden cold snap, hinting climate struck the first blow.

The Ice Ages were a huge stress.

Over the next 30,000 years – archaeological work has revealed – a procession of different cultures, each associated with different artefacts and lifestyles, rose in Europe.

Archaeologists tend to think these sort of cultural shifts reflect the spread of new ideas through an unchanging population. But a new analysis of nuclear DNA taken from 51 ancient Eurasians tells a different story. They actually reflected the spread of different peoples.

Some of this change involved breeding with Neanderthals, and many of us (including me) have some Neanderthal DNA. Why ? The Neanderthals might have been better adapted to Ice Ages which waxed and waned.

During this period, there were several changes between glacier advance and retreat. The Last Glacial Maximum, the maximum extent of glaciation within the last glacial period, was approximately 22,000 years ago. While the general pattern of global cooling and glacier advance was similar, local differences in the development of glacier advance and retreat make it difficult to compare the details from continent to continent (see picture of ice core data below for differences).

From the point of view of human archaeology, it falls in the Paleolithic and Mesolithic periods. When the glaciation event started, Homo sapiens were confined to Africa and used tools comparable to those used by Neanderthals in Europe and the Levant and by Homo erectus in Asia. Near the end of the event, Homo sapiens spread into Europe, Asia, and Australia.

Maybe Neanderthals were better adapted to glacial epochs.

The Aurignacian culture was dominant between about 45,000 and 35,000 years ago. This culture produced fine bone and stone tools, and some of Europe’s oldest and most beautiful art – for instance at Chauvet cave in southern France.

By about 33,000 years ago a new culture that began in south-east Europe was beginning to spread across the continent: the Gravettian. This is famous for big-game hunting of mammoths and bison.

And later, at the height of the Ice Age about 19,000 years ago, yet another culture swept across west and central Europe. This Magdalenian culture is famous for its reindeer hunts and for its artwork, carved into bones and antlers.

One of the oldest individuals examined by David Reich at Harvard Medical School in Boston and his colleagues is represented by a thigh bone found at a site called Goyet cave in Belgium. Radiocarbon dating shows it is 35,000 years old, meaning the Goyet individual is associated with the Aurignacian industry.

Now, it appears that these people were quite different genetically.

the Aurignacians were pushed aside by an expanding wave of Gravettians.

“It is exciting and striking how a relatively homogeneous population sweeps across large parts of Europe between 33,000 and 26,000 years ago, displacing the populations that were there before,” says Reich.

But that’s not the full story. The genetic analysis also looked at six Magdalenians: they are descendants of the displaced Aurignacians.

This is a real surprise, says team member Cosimo Posth at the Max Planck Institute for the Science of Human History in Jena, Germany. It shows that the Aurignacian lineage didn’t disappear when the Gravettians swept across Europe.

“In fact from the end of the Last Glacial Maximum some 19,000 years ago, its genetic component reappeared in Spain. From then to around 14,000 years ago this nuclear signal spread in Europe again,” he says.

They may have been pushed into a cul de sac in Spain but returned as the glaciers retreated. Why ?

We know a few things, such as why white skin evolved. As humans moved from Africa to Europe and faced cold climates, they needed Vitamin D which is synthesized in the skin.

Dark skin is useful and provides and evolutionary advantage in tropical settings. It also has some protective effect on sun burning and skin cancer. One negative consequence of inadequate Vitamin D is Ricketts, a disease of bones.

Rickets is defective mineralization or calcification of bones before epiphyseal closure in immature mammals due to deficiency or impaired metabolism of vitamin D,[1] phosphorus or calcium,[2] potentially leading to fractures and deformity. Rickets is among the most frequent childhood diseases in many developing countries.

This provides a strong feedback for selecting beneficial mutations.

Some of this will lead to modern therapy and that is why I wrote that I would not recommend a student for medical school who did not believe in evolution. Here is some of the negative response I got. I quit Ricochet when my subscription expired.

The Next Step from Craig Venter.

Thursday, March 24th, 2016

cell

I have previously posted about Venter’s work with synthetic organisms.

While I was digesting this new material, Craig Venter was making the Gene VII book obsolete. He set up a new company to compete with the Human Genome Project The result is well described in The Genome War by James Shreeve who was given access to Venter but less to the government funded project. This year, Venter’s autobiography was published and his plans for the future are described.

The links are at the original article which is from 2007.

Now, his group has progressed to a synthetic bacterium.

Using the first synthetic cell, Mycoplasma mycoides JCVI-syn1.0 (created by this same team in 2010), JCVI-syn3.0 was developed through a design, build, and test process using genes from JCVI-syn1.0. The new minimal synthetic cell contains 531,560 base pairs and just 473 genes, making it the smallest genome of any organism that can be grown in laboratory media. Of these genes 149 are of unknown biological function. By comparison the first synthetic cell, M. mycoides JCVI-syn1.0 has 1.08 million base pairs and 901 genes.

A paper describing this research is being published in the March 25th print version of the journal Science by lead authors Clyde A. Hutchison, III, Ph.D. and Ray-Yuan Chuang, Ph.D., senior author J. Craig Venter, Ph.D., and senior team of Hamilton O. Smith, MD, Daniel G. Gibson, Ph.D., and John I. Glass, Ph.D.

THis is huge news and will take years to develop.

The most surprising result of their work—and perhaps the most sobering one for the rest of the field: The team still doesn’t understand what 31 percent of the essential genes do in even the simplest organism, to say nothing of a human genome. It’s a development Venter called “very humbling.”

“We are probably at the 1 percent level in understanding the human genome,” said Clyde Hutchison III, a distinguished professor at the Venter Institute.

That lack of knowledge isn’t standing in the way of entrepreneurs. Biology has been “hot and heavy” since the development of a molecular tool that makes gene editing easy, Hutchison explained. Scientists might be able to remove disease-causing genes or even determine a baby’s eye color. This technology, known as CRISPR/Cas-9, has alarmed many inside and outside the research community, who fear it may be used on the human genome before its effects are understood, with unforeseen results.

If he does another public seminar, I hope Bradley can get me a ticket. I am now reading “Lewin’s Genes XI,” although he seems to be no longer the editor.

I hope I can wade through it. Sometimes, as knowledge progresses, it becomes simpler. I hope so.

“These cells would be a very, very useful chassis for many industrial applications, from medicine to biochemicals, biofuels, nutrition, and agriculture,” said Dan Gibson, a top scientist at both Venter’s research institute and his company, Synthetic Genomics Inc. Ultimately, the group wants to understand the tiny genetic framework well enough to use it as a biological foundation for more complex organisms that could address many of the world’s ills. Once each essential gene’s function is identified, scientists can build an effective computer model of it; from there, they can simulate how best to go about “adding pathways for the production of useful products,” they wrote.

I will be following this story closely, if I can only understand it.

Schizophrenia’s cause ?

Thursday, January 28th, 2016

nature13595-f1

Today there is an article in the Washington Post that describes a genetic site that may be the source of schizophrenia.

The researchers, chiefly from the Broad Institute, Harvard Medical School and Boston Children’s Hospital, found that a person’s risk of schizophrenia is dramatically increased if they inherit variants of a gene important to “synaptic pruning” — the healthy reduction during adolescence of brain cell connections that are no longer needed.

In patients with schizophrenia, a variation in a single position in the DNA sequence marks too many synapses for removal and that pruning goes out of control. The result is an abnormal loss of gray matter.

For years that has been a search for the reason why this mental illness appears in adolescence in people who seemed normal until that stage of development. It is known that adolescence is the time for”pruning” of excessive neuron synapses. Now, it seems that this may be the target f the genetic defect.

The fact that the answer might come from genetics has been known for a while.

To date, around 30 schizophrenia-associated loci10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 have been identified through GWAS. Postulating that sample size is one of the most important limiting factors in applying GWAS to schizophrenia, we created the Schizophrenia Working Group of the Psychiatric Genomics Consortium (PGC). Our primary aim was to combine all available schizophrenia samples with published or unpublished GWAS genotypes into a single, systematic analysis24. Here we report the results of that analysis, including at least 108 independent genomic loci that exceed genome-wide significance. Some of the findings support leading pathophysiological hypotheses of schizophrenia or targets of therapeutic relevance, but most of the findings provide new insights.

The new paper, just out yesterday in epub, has narrowed the search to the C4 gene on chromosome 6.

After conducting studies in both humans and mice, the researchers said this new schizophrenia risk gene, called C4, appears to be involved in eliminating the connections between neurons — a process called “synaptic pruning,” which, in humans, happens naturally in the teen years.

It’s possible that excessive or inappropriate “pruning” of neural connections could lead to the development of schizophrenia, the researchers speculated. This would explain why schizophrenia symptoms often first appear during the teen years, the researchers said.

This is huge news. I have a chapter on my own experiences in treating schizophrenic men in the early 1960s in my book, War Stories: 50 years in medicine.

My teacher, George Harrington, told me he thought schizophrenia had to be organic in origin and he speculated that it could be deficiency of an unknown vitamin. Genetics were very primitive in those days. The discovery of the number of human chromosomes had only recently been announced when I began medical school. The number was only discovered in 1956, six years before I began medical school.

Using postmortem human brain samples, the researchers found that variations in the number of copies of the C4 gene that people had, and the length of their gene, could predict how active the gene was in the brain.

The researchers then turned to a genome database, and pulled information about the C4 gene in 28,800 people with schizophrenia, and 36,000 people without the disease, from 22 countries. From the genome data, they estimated people’s C4 gene activity.

They found that the higher the levels of C4 activity were, the greater a person’s risk of developing schizophrenia was.

The researchers also did experiments in mice, and found that the more C4 activity there was, the more synapses were pruned during brain development.

This is not therapy by any means but it is a huge step toward something that may prevent the disease is susceptibles.

What the black college students are rioting about.

Monday, November 16th, 2015

Ithaca

Power line has a post today that seems to me to be right on the topic of what these students want, which is freedom from accountability. They are afraid they are overmatched against white colleagues. They can’t hack it and want a pass. It is called “Mismatch.”

The biggest change since Grutter, though, has nothing to do with Court membership. It is the mounting empirical evidence that race preferences are doing more harm than good?—even for their supposed beneficiaries. If this evidence is correct, we now have fewer African-American physicians, scientists, and engineers than we would have had using race-neutral admissions policies. We have fewer college professors and lawyers, too. Put more bluntly, affirmative action has backfired.

Why is this ? We know that the normal distribution of IQ is a standard deviation lower for blacks than whites.

NormalCurveSmall

This is the over all curve with the distribution around an average of 100, by definition.

IQ_Bladk_White

The curve for blacks has a peak at IQ about 80. White peak at 100 to 104. Asians peak at around 106. What this means is that the average IQ is lower for blacks but this does not mean that all blacks are less intelligent than whites. At an IQ of 110 there is a large difference but the number of blacks who will do well in certain academic fields like Medicine is still significant. It would seem important to identify those blacks who will do well in fields requiring higher than average intelligence but the present system of affirmative action ignores this truth.

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A Few Timid Questions on “Climate Change.”

Sunday, October 18th, 2015

The discussion on Global Warming, has shifted to “Climate Change” as the warming has slowed or stopped, depending on your politics. Now there are a few rather timid questions being asked about this highly charged topic.

“Doubt has been eliminated,” said Gro Harlem Brundtland, former Prime Minister of Norway and UN Special Representative on Climate Change, in a speech in 2007: “It is irresponsible, reckless and deeply immoral to question the seriousness of the situation. The time for diagnosis is over. Now it is time to act.” John Kerry says we have no time for a meeting of the flat-earth society. Barack Obama says that 97 per cent of scientists agree that climate change is “real, man-made and dangerous”.

This is the consensus of politicians. Scientists ? Read the resumes of the people pontificating on Climate Change. How many are real scientists ?

A Member of Parliament with a Physics degree, was ridiculed by the BBC for questioning Climate Change.

Peter Lilley, a long standing member of the energy and climate select committee, has made a formal complaint to director general Lord Hall after discovering that mandarins had issued an apology following claims he made that the effects of climate change were being exaggerated.

Appearing on BBC Radio 4’s ‘What’s the Point of The Met Office’, Mr Lilley stated that, while he “accepted the thesis that more CO2 in the atmosphere will marginally warm up the earth”, he questioned the assertion that global warming would be as dramatic as is being portrayed in some scientific circles.

Mr Lilley, who graduated with a degree in natural sciences at Cambridge University, said: “I’m a ‘lukewarmist’, one who thinks that there won’t be much warming as a result of it, and that’s the scientifically proven bit of the theory. Anything going on the alarmist scale is pure speculation.”

Sounds mild to me.

Mr Lilley was horrified to discover that the BBC later placed “health warnings” on the programme’s website, and issued an apology for “giving voice to climate sceptics” and failing to “make clear that they are a minority, out of step with the scientific consensus.”

The apology was written to listeners who had complained, including academic Dr Andrew Smedley, of Manchester University, and then re-stated on the BBC Rado 4’s programme Feedback.

That sounds like “Trigger Warnings” in American university life. This sort of thing has gotten more common the past 20 years. Why ?

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The Medical History of the American Civil War.

Wednesday, September 2nd, 2015

Slide01

This is a lecture I have given a few times and am converting to a long blog post. The American Civil War was the first major war since a number of major advances of medicine had occurred. Sanitation had been studied by John Snow and Florence Nightingale. Anesthesia had been discovered by two Americans, Morton and

Unfortunately, antisepsis would not be described until, 1867, after the war. Infection than was the great scourge of the wounded.

Slide02

The state of medical art before the war was limited.

Slide03

Baron Larrey was the greatest army surgeon of the Napoleonic Wars. He invented the ambulance and pioneered some sanitary advances but the cause of infection was still obscure.

Slide04

Benjamin Rush was a famous American physician but little of what he knew or advocated was of use.

Slide05

The discovery of Ether anesthesia was momentous but it did add the factor that more operations would be attempted before infection was understood.

Slide06

Semmelweiss was tragic figure who realized that infection was transmissible from physicians’ hands to patients but he was unable to convince his colleagues. His discovery of the uses of hand washing were ignored.

Slide07

Florence Nightingale discovered the use of hand washing in caring for the wounded but she did not know why it worked. She is a great hero of the British Army and her apartment in Scutari Barracks in Istanbul is preserved in a shrine.

Slide08

The Scutari Barracks from across the Bosphorus.

Slide09

I visited the museum about ten years ago and visited her quarters which the Turkish Army preserves.

Slide13

The history of Military Medicine really begins with Ambrose Pare’ who served several French Kings and who invented the hemostat.

200px-Ambroise_Paré

His methods were a huge improvement on the Greeks but not much else can be said for their efficacy.

Slide14

The American Army in 1860 was tiny and the medical establishment was a joke.

Slide15

The war resulted in many of the army surgeons resigning to join the Confederacy. The lack of military medical texts resulted in Samuel D Gross, professor of surgery at Jefferson Medical College, writing his own textbook.

To be continued.

Metabolic Syndrome and Obesity.

Monday, July 20th, 2015

I spent an interesting day last Saturday at a USC post-graduate course on “premalignant lesions of the GI react.”

Part of the session discussed the question of obesity and diet. “Fatty liver” is a condition related to obesity and metabolic syndrome.

The Wikipedia definition includes.
1. abdominal (central) obesity,
2. elevated blood pressure,
3. elevated fasting plasma glucose,
4. high serum triglycerides, and
5. low high-density lipoprotein (HDL) levels

Central obesity is not the same as subcutaneous obesity, which is what we all think of. Titters out there is a racial factor with blacks more likely to have subcutaneous obesity without the central obesity involving the liver and internal organs.

Metabolic syndrome and prediabetes appear to be the same disorder, with insulin resistance as a major factor.

Other signs of metabolic syndrome include high blood pressure, decreased fasting serum HDL cholesterol, elevated fasting serum triglyceride level (VLDL triglyceride), impaired fasting glucose, insulin resistance, or prediabetes.

Associated conditions include:
1. hyperuricemia,
2. fatty liver (especially in concurrent obesity) progressing to
3. nonalcoholic fatty liver disease,a.so called NAFL
4. polycystic ovarian syndrome (in women),
5. erectile dysfunction (in men), and
6. acanthosis nigricans.

It is generally accepted that the current food environment contributes to the development of metabolic syndrome: our diet is mismatched with our biochemistry. Weight gain is associated with metabolic syndrome. Rather than total adiposity, the core clinical component of the syndrome is visceral and/or ectopic fat (i.e., fat in organs not designed for fat storage) whereas the principal metabolic abnormality is insulin resistance.

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Why Doctors Quit.

Friday, May 29th, 2015

Today, Charles Krauthammer has an excellent column on the electronic medical record. He has not been in practice for many years but he is obviously talking to other physicians. It is a subject much discussed in medical circles these days.

It’s one thing to say we need to improve quality. But what does that really mean? Defining healthcare quality can be a challenging task, but there are frameworks out there that help us better understand the concept of healthcare quality. One of these was put forth by the Institute of Medicine in their landmark report, Crossing the Quality Chasm. The report describes six domains that encompass quality. According to them, high-quality care is:

1) Safe: Avoids injuries to patients from care intended to help them
2) Equitable: Doesn’t vary because of personal characteristics
3) Patient-centered: Is respectful of and responsive to individual patient preferences, needs and values
4) Timely: Reduces waits and potentially harmful delays
5) Efficient: Avoids waste of equipment, supplies, ideas and energy
6) Effective: Services are based on scientific knowledge to all who could benefit, and it accomplishes what it sets out to accomplish

In 1994, I moved to New Hampshire and obtained a Master’s Degree in “Evaluative Clinical Sciences” to learn how to measure, and hopefully improve, medical quality. I had been working around this for years, serving on the Medicare Peer Review Organization for California and serving in several positions in organized medicine.

I spent a few years trying to work with the system, with a medical school for example, and finally gave up. A friend of mine had set up a medical group for managed care called CAPPCare, which was to be a Preferred Provider Organization when California set up “managed care.” It is now a meaningless hospital adjunct. In 1995, he told me, “Mike you are two years too early. Nobody cares about quality.” Two years later, we had lunch again and he laughed and said “You are still too years too early.”

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