Scientific Integrity of the U.S. Government

From time to time since 2008, these GEITP pages have discussed scientific facts, versus “government policy,” based either on such facts or ignoring such facts.

One excellent example has been the Linear No-Threshold (LNT) Theory — developed during the 1950s on inaccurate data — realized by the minority opinion of several members on the BEAR I Committee, and other scientists later, but nothing has ever been undertaken to correct those errors. Consequently, the government has wasted billions of dollars over the past six decades of risk-assesssment research. This topic has been thoroughly investigated by Ed Calabrese, and these GEITP pages have shared at least ten publications about uncovering the fraud [cf, e.g., genewhisperer.com]. We would rank the LNT fraud #2 on the wasted-money list.

Number #1 on the wasted-money list has to be the anthropogenic global warming (AGW) / climate change hoax — which has resulted in trillions of dollars in wasted government (taxpayer) money over the past four decades. There is no “climate crisis,” there has been no “climate crisis,” and no “climate crisis” is predicted in the future; of course, it remains important to continue searching for any trends that might suggest a threat. Below are the comments that the S.E.P.P. recently sent to the Biden Administration’s task force on Scientific Integrity.

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Comments On Federal Scientific Integrity
By Kenneth Haapala, President
The Science and Environmental Policy Project (SEPP)
July 28, 2021 (slightly edited)

“It is one thing to impose drastic measures and harsh economic penalties when an environmental problem is clear-cut and severe. It is quite another to do so when the environmental problem is largely hypothetical and not substantiated by careful observations. This is definitely the case with global warming.” – Frederick Seitz, 17th president of the United States National Academy of Sciences

This paper addresses the scientific integrity involved in the fear that human additions to atmospheric carbon dioxide will cause significant global warming. To comprehend how carbon dioxide influences the globe’s temperatures, one must comprehend the greenhouse effect, how different greenhouse gases influence the loss of heat to space, how different greenhouse gases influence the effectiveness of other greenhouse gases in the atmosphere, and how increasing the greenhouse effect influences climate. Further, to comprehend how human emissions of greenhouse gases affect climate — requires separating the greenhouse effect from other human impacts on climate, such as urbanization. Also, it requires separating human impacts from natural climate change, including changing ocean circulation and changing solar influences which we do not fully understand.

This brief paper is divided into six basic sections: One, the importance of the scientific method for understanding the physical world; Two, the changing climate; Three, the importance of the greenhouse effect, including carbon dioxide, for life on this planet; Four, problems with global climate models used to predict dire consequences from increasing greenhouse gases, particularly carbon dioxide; Five, modern physics evidence supporting an alternative analysis of the greenhouse effect; and Six, a suggested policy for going forward with steps the nation needs to take.

Section 1, The Scientific Method: The scientific method is a process of eliminating error in thinking and concepts by constantly subjecting concepts to rigorous testing using all available physical evidence that is appropriate. As physical evidence changes, the concepts must be changed accordingly. The 20th century began without theories of relativity or quantum mechanics, which upset classical physics, and belief that continents did not move. Today, we make use of these concepts and are experiencing constant change in communications, electronics, and similar technologies. Who knows what new developments may bring?

With dramatic change in our knowledge of the physical world, including science and science-based technology, such as nuclear weapons, scientists acquired political influence and responsibility. There should be no issue as to the rigorous application of the scientific method, particularly by scientists employed or sponsored by the US government, who are responsible to the American public. Political beliefs need to be set aside. As Steven Koonin (the Chief Scientist of the Department of Energy under the Obama Administration), who is familiar with complex mathematical physics, mathematical modeling, and the IPCC process, wrote:

“Philip Handler, a former president of the National Academy of Sciences, identified the problem in a 1980 editorial that resonates eerily four decades later:

‘With scientists’ unique role comes a special responsibility. We’re the only people who can bring objective science to the discussion, and that is our overriding ethical obligation. Like judges, we’re obligated to put personal feelings aside as we do our job. When we fail to do this, we usurp the public’s right to make informed choices and undermine their confidence in the entire scientific enterprise. There’s nothing at all wrong with scientists as activists, but activism masquerading as The Science is pernicious.’” [Endnote (EN) #1, p 10, Introduction]

Since the 1970s there has been a dramatic increase in evidence (data) on the greenhouse effect and how increasing greenhouse gases influence the earth’s atmosphere, thus the climate. It is incumbent on government scientists and government sponsored scientists to apply the scientific method and incorporate these new data (evidence) in their reports, so that they do not mislead the American public.

Section 2, The Changing Climate: Atmospheric physicist Richard Lindzen is noted for his work in dynamic meteorology, atmospheric tides, ozone photochemistry, quasi-biennial oscillation, and the Iris hypothesis. Lindzen described the generally accepted view of the earth’s climate system as circulation of two fluids (atmosphere and oceans) interacting with each other and the uneven land, made turbulent by the rotation of the globe – exposing the fluids and the land to uneven heating by the sun. (The energy flow from the sun to the earth varies as well.) The entire system involves fluid dynamics which is not fully understood. As such,

“The fact that these circulations carry heat to and from the surface means that the surface itself is never in equilibrium with space. There is never an exact balance between incoming heat from the sun and outgoing radiation generated by the Earth. This is because heat is always being stored in (and released from) the oceans. Therefore, surface temperature is always varying somewhat.” [Punctuation slightly changed.] [EN #2]

After discussing the substantial energy transfers from the phase changes of water, Lindzen brings up the greenhouse effect and states:

“…that the two most important greenhouse substances by far are water vapor and clouds. Clouds are also important reflectors of sunlight.

“The unit for describing energy flows is watts per square meter. The energy budget of this system involves the absorption and reemission of about 200 watts per square meter. Doubling CO2 involves a 2% perturbation to this budget. So do minor changes in clouds and other features, and such changes are common….” [Boldface are italics in the original.]

Lindzen concludes the section by discussing “unforced” natural variation that may take 1,000s of years to appear. Thus, climate change involves two parts of physics for which we have no comprehensive theories established by physical evidence: 1) fluid dynamics and 2) the greenhouse effect.

Section 3, The Greenhouse Effect: The greenhouse effect makes the earth inhabitable. Developing laboratory experiments starting in 1859, John Tyndall recognized that greenhouse gasses warm the atmosphere by slowing heat loss from the surface to space. This slowing of infrared energy to space makes the earth inhabitable, with the principal greenhouse gas being water vapor. Tyndall noted that the influence of some greenhouse gases is not proportional to their concentrations. [EN #3]

Decades of laboratory experiments show that carbon dioxide is an effective greenhouse gas only at extremely low concentrations. Its effectiveness is exhausted at less than one-half of the concentration it was when humans began using fossil fuels. Humans increasing the concentration of carbon dioxide is like adding a thin sheet on top of a thick quilt, it does little or nothing.

In the 1970s, with parts of the world undergoing economic development and carbon dioxide concentrations increasing, surface temperatures indicated the earth shifted from cooling to warming. The National Research Council formed an influential panel which asserted that even though laboratory experiments demonstrate that carbon dioxide has a modest effect on temperature, the slight warming caused by carbon dioxide – less than 3 percent of the total atmospheric warming effect – would be greatly amplified by increases in water vapor. This was a guess, without physical evidence. The guess managed to turn a modest 2-degree Fahrenheit (°F) maximum increase due to a doubling of carbon dioxide alone into a speculative 6 °F total increase. [EN #4]

The UN Intergovernmental Panel on Climate Change (IPCC) and many US scientific bodies have incorporated the guess into unstated assumptions. However, starting in 1979, the US developed a significant body of observations of the atmosphere using satellites. Forty years of measured atmospheric temperature trends, the only comprehensive global temperature dataset existing, confirm a century of laboratory experiments. The effect of increasing carbon dioxide is small, much less than natural variation. At the surface, it is difficult to separate the increase in the greenhouse effect from natural variation.

Further, the speculated amplification from increased water vapor cannot be found. For over 40 years the US has compiled data on the greenhouse effect itself, supporting the atmospheric temperature trends – increasing carbon dioxide will produce a modest warming. The current warming of the atmosphere is 0.25 °F per decade since January 1979, or about 1 °F since January 1979, or about 2.5 °F per century. It is in the middle of the lowest set of estimates of warming currently developed by the IPCC, which assumes little increase in carbon dioxide. This includes all greenhouse gases and natural variation. It is well within the range of natural historic warming. [EN #5]

Based on observations by NOAA at Mauna Loa, Hawaii, each year the maximum atmospheric carbon dioxide concentration occurs in May. Using May measurements grew from 339 parts per million in volume (ppm) in 1979 to 419 ppm in 2021. This is an increase of 80 ppm or 24%. Yet the increase in atmospheric temperatures from all sources was only 1°F. The most appropriate physical evidence does not support the fear that increasing carbon dioxide is causing dangerous warming. [EN #6]

For increasing carbon dioxide to cause surface warming, the atmosphere must warm at a greater rate than the surface, but the opposite is happening. The probable causes of surface warming are urbanization, changes in ocean circulations, and solar variations that we do not fully understand — not greenhouse gases. In general, those using surface data to claim dangerous warming ignore such changes. They use models which have never been validated (using physical evidence from the atmosphere) to speculate 30 to 80 years into the future.

Section 4, Problems with Global Climate Models: In his book “Unsettled,” Steven Koonin identifies numerous deficiencies in the IPCC process that need to be addressed its finding are used for public policy. Among the more serious deficiencies Koonin discusses are:

A) a confusion in scale between Celsius and Kelvin when estimating the influence of doubling carbon dioxide resulting in significant error, and

B) IPCC models do not track the warming trend in the surface temperature record between 1910 and 1940, which was greater than the warming trend between 1980 and 2000.

Koonin also points out the complexity of the climate models, which divide the surface and the atmosphere into various hypothetical boxes called cells. Accurate measurements are needed for all the cells, but the measurements don’t exist. Further, the cells are so large that important weather events may be missed. Most important, the IPCC conclusions are political not scientific:

“And—a very key point—the IPCC’s ‘Summaries for Policymakers’ are heavily influenced, if not written, by governments that have interests in promoting particular policies. In short, there are many opportunities to corrupt the objectivity of the process and product.” [Boldface added]

A book by Japanese climatologist and former NASA researcher Mototaka Nakamura shows the deficiencies in Earth’s surface temperatures and considers them unreliable before 1980.

A quasi-global observation system has been operating only for 40 years or so since the advent of artificial satellite observation. Temperature data before then were collected over extremely small (with respect to the Earth’ s entire surface area) areas and, thus, have severe spatial bias. We have an inadequate amount of data to calculate the global mean surface temperature trend for the pre-satellite period. This severe spatial bias in reality casts a major uncertainty over the meaningfulness of “the global mean surface temperature trend” before 1980. [EN #7]

Nakamura also discusses efforts to discredit his views which failed. Unlike Koonin, who accepts global mean surface temperature trends before 1980, Nakamura states these trends are highly questionable. For example, for over 2,000 years changes in land use, such as draining wetlands, clearing forests, irrigation, urbanization, etc., have been recognized to change local climate temperatures. Nakamura states that global surface temperature trends are based on a few, highly localized measurements, and the entire record on which global climate models are based may be highly biased. Indeed, when comparing the results of global climate models to what is occurring in the atmosphere, where the greenhouse effect occurs, the models are highly biased in overestimating the warming effect of carbon dioxide and other greenhouse gases. Both authors express major difficulties in the approach used by the UN IPCC and US government in assessing the effect of greenhouse gases.

The atmospheric temperature effects of greenhouse gases are far less than what the models show. Christy, et al., compared four different satellite datasets, four different weather balloon datasets, and four sets of weather reanalyzes with the average of model simulations used in the Fifth Assessment Report of the IPCC. The researchers found the models grossly overestimate actual atmospheric temperature trends and that the disparity is increasing. Global climate models may be useful teaching tools, but they are not useful for government policy on greenhouse gases. [EN #8]

Section 5, Modern Physical Evidence Supporting an Alternative Analysis of the Greenhouse Effect: During the 20th century great changes occurred in physics such as relativity and quantum mechanics. which describes the physical properties of nature on the molecular, atomic, and subatomic level. Quantum mechanics led to the field of physics called Atomic, Molecular, and Optical Physics (AMO), which enabled the development of databases that can be used to directly calculate the greenhouse effect in the atmosphere. [EN #9]

Using the HITRAN database, AMO authorities W. A. van Wijngaarden and Will Happer have estimated the influence of water vapor, carbon dioxide, ozone, nitrous oxide, and methane in a cloud free atmosphere to increase global temperatures. Under current atmospheric conditions, increasing water vapor and carbon dioxide have a minimal effect on temperatures. At last, we have calculations that agree with measurements of what is occurring in the atmosphere. [EN #10]

Section 6, Going Forward: Scientific integrity requires that the Biden Administration employ the most rigorous application of the scientific method.

As shown above, observations using 21st century technology support certain concepts of the 20th century and demonstrate others to be false. Scientific integrity requires that, the administration should not use long-range models for policy until the models reach the high standards for verification and validation met for modeling the reliability of nuclear weapons by Sandia National Laboratories; or the standards required by the Apollo Team of scientists and engineers for manned lunar exploration. [EN #11 & #12]

Since there is no current physical evidence of dangerous global warming from greenhouse gases or their effects, and no physical evidence of a climate crisis, the administration should use atmospheric temperature trends and the MODTRAN and HITRAN databases to estimate the effects of increasing greenhouse gases in the atmosphere. Further, the government should continue to:

• Monitor atmospheric temperatures, as has been done for 40 years and
• Monitor outgoing electromagnetic radiation, as is being done by the CERES project.

Above all, the Biden Administration should inform the public that there is no current threat, and that it is using the best science possible to monitor the situation to assure that a threat is not developing.

Sincerely yours,
Kenneth Haapala, President
The Science and Environmental Policy Project (SEPP)
P.O Box 1126
Springfield, VA 22151,
Ken@SEPP.org, 703-978-6025

END NOTES:
1. Steven E. Koonin, Unsettled: What Climate Science Tells Us, What It Doesn’t, and Why It Matters, BenBella Books, Inc, 2021 Kindle Edition,
https://www.amazon.com/Unsettled-Cl…

2. Global Warming for the Two Cultures
By Richard Lindzen, GWPF, October 2018
https://www.thegwpf.org/content/upl…

3. Heat, a Mode of Motion
By John Tyndall, (p. 359, fifth edition, 1875)
https://www.amazon.com/Heat-Mode-Mo…)

4. Ad Hoc Study Group on Carbon Dioxide and Climate
By Jule G. Charney, Massachusetts Institute of Technology, Chairman, et al. to the:
Climate Research Board, Assembly of Mathematical and Physical Sciences, National Research Council, National Academy of Science, 1979
https://www.bnl.gov/envsci/schwartz…

5. UAH Global Temperature Update for June 2021: -0.01 deg. C
By Roy Spencer, His Blog, July 2, 2021
http://www.drroyspencer.com/2021/07…
Link to: Global Temperature Report
Earth System Science Center, The University of Alabama in Huntsville, June 2021
https://www.nsstc.uah.edu/climate/…
http://www.drroyspencer.com/2021/07…

6. NOAA, Global Monitoring Laboratory
Mauna Loa, Hawaii, Data Accessed July 26, 2021
https://gml.noaa.gov/webdata/ccgg/t…

7. Confessions of a climate scientist: The global warming hypothesis is an unproven hypothesis
By Motokaka Nakamura, Kindle Edition, October 2019
https://www.amazon.com/s?k=.+Confes…

8. Examination of space-based bulk atmospheric temperatures used in climate research
By John R. Christy, Roy W. Spencer, William D. Braswell & Robert Junod, International Journal of Remote Sensing, March 8, 2018.
https://www.tandfonline.com/doi/ful…

9. The HITRAN Database
By Iouli E. Gordon, Harvard-Smithsonian Center for Astrophysics Atomic and Molecular Physics Division, Accessed July 12, 2019
https://www.cfa.harvard.edu/hitran/…

10. Dependence of Earth’s Thermal Radiation on Five Most Abundant Greenhouse Gases
By W. A. van Wijngaarden and W. Happer, Atmospheric and Oceanic Physics, posted June 4, 2020
https://arxiv.org/abs/2006.03098…
Link to prepublication version: https://arxiv.org…

11. Verification, Validation, and Predictive Capability in Computational Engineering and Physics
By William L. Oberkampf and Timothy G. Trucano, Sandia National Laboratories and Charles Hirsch, Department of Fluid Mechanics, Vrije Universiteit Brussel, Feb 2003
https://digital.library.unt.edu/ark…

12. One More Mission, The Right Climate Stuff Team
https://www.therightclimatestuff.co…

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New recommendations on human genome editing

This Position Paper might be of interest to some of you.

The recent application of tools — such as CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats; Cas9 nuclease), to edit the human genome with the intention of treating or preventing disease and the gaps in our scientific understanding, in addition to some of the proposed applications of human genome editing — raise ethical issues that highlight the need for robust oversight in this area. The COVID-19 pandemic has clearly demonstrated the importance of using new tools and methods to combat serious diseases and highlighted the potential benefits of human genome editing research; it also reminds us of the need to develop technology carefully, with robust testing and quality assurance measures in place to maximize benefit and minimize harm. The balance between benefit and harm, safety and speed, and innovation and access is relevant to all of human genome editing.

In December 2018, the World Health Organization (WHO) established a global, multidisciplinary expert advisory committee (the Expert Advisory Committee on Developing Global Standards for Governance and Oversight of Human Genome Editing, hereafter called The Committee) to examine the scientific, ethical, social and legal challenges associated with human genome editing (somatic, germline and heritable).

The Committee was tasked to advise and make recommendations on appropriate institutional, national,regional and global governance mechanisms for human genome editing. Its remit did not include a review of matters to do with safety and efficacy. Committee members were drawn from each of the WHO regions — Africa, the Americas, South-East Asia, Europe, Eastern Mediterranean and Western Pacific.

The 18 members of The Committee worked for two years and developed several products and new initiatives. The governance framework on human genome editing, along with the recommendations of The Committee, form a set of two publications that provide advice and recommendations on appropriate institutional, national, regional and global governance mechanisms for human genome editing. A position paper on human genome editing provides a summary of these two publications.

During its work, The Committee reviewed the current literature on human genome editing research and its applications, considered existing proposals for governance and relevant ongoing initiatives, and gathered information on a range of topics relating to the different uses of this technology. The Committee consulted widely with individuals and representatives of organizations including, but not limited to, United Nations (UN) and other international agencies; academies of science and medicine as well as other national or professional bodies; patient groups and civil society organizations.

The governance framework and the recommendations on human genome editing form a pair of reports that have been developed by the WHO Expert Advisory Committee on Developing Global Standards for Governance and Oversight of Human Genome Editing. This position paper provides a summary of these two publications.

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SCIENTIFIC MISCONDUCT BY THE U.S. NATIONAL ACADEMY OF SCIENCES

In this 2.5-hour presentation, Professor Ed Calabrese goes through the steps by which the research record was altered by the BEAR Genetics Panel. This led to the Linear No-Theshold (LNT) “government policy,” back in the 1950s, based on this fraudulent research record. These GEITP pages have shared at least a dozen papers by Calabrese on this scandal.

Ed has also documented other significant and highly problematic decisions of this Panel that were used to support their recommendations of the LNT. Just to take one example: strictly speaking, according to LNT, a physician should not prescribe warfarin to prevent a stroke — because it really is rat poison, which will kill a rat in large doses and will also kill you (because of the linear no-threshold model). However, in small doses, it might save your life.

Likewise, according to LNT, even if a nuclear power plant contributes only the tiniest amount relative to normal background radiation (which actually has been shown statistically significantly to increase longevity), the plant should be shut down. And many plants have therefore been shut down. Consequently, we are forced to use fossil fuel energy — which is a constant source of energy but it is not nearly as “clean” as nuclear energy. And we are being pushed to use wind and solar energy, which is not a constant source (always intermittent) and never will take care of any more that 8 to 12 percent of human population requirements.

LINK HERE

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Scientists develop simple blood test for early detection of Alzheimer disease

This article might be of interest to many GEITP-ers who have family members and loved ones — at various stages of dementia. ☹ We would judge this article to be a likely big-time breakthrough in this field — involving proteomics (ultrasensitive and high-throughput protein measurement technology) — and we expect to see many related follow-up studies appearing rapidly in the medical literature.
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Scientists develop simple blood test for early detection of Alzheimer disease

Date:
June 28, 2021
Source:
Hong Kong University of Science and Technology
Summary:

An international research team has developed a simple but robust blood test from Chinese patient data for early detection and screening of Alzheimer’s disease (AD) with an accuracy level of over 96%.

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FULL STORY

An international research team led by HKUST has developed a simple but robust blood test from Chinese patient data for early detection and screening of Alzheimer’s disease (AD) for the first time, with an accuracy level of over 96%.

Currently, doctors mainly rely on cognitive tests to diagnose a person with AD. Besides clinical assessment, brain imaging and lumbar puncture are the two most commonly used medical procedures to detect changes in the brain caused by AD. However, these methods are expensive, invasive, and frequently unavailable in many countries.

Now, a team led by Prof. Nancy IP, Vice-President for Research and Development at HKUST, has identified 19 out of the 429 plasma proteins associated with AD to form a biomarker panel representative of an “AD signature” in the blood. Based on this panel, the team has developed a scoring system that distinguishes AD patients from healthy people with more than 96% accuracy. This system can also differentiate among the early, intermediate, and late stages of AD, and can be used to monitor the progression of the disease over time. These exciting findings have led to the development of a high-performance, blood-based test for AD, and may also pave the way to novel therapeutic treatments for the disease.

“With the advancement of ultrasensitive blood-based protein detection technology, we have developed a simple, noninvasive, and accurate diagnostic solution for AD, which will greatly facilitate population-scale screening and staging of the disease,” said Prof. Nancy Ip, Morningside Professor of Life Science and the Director of the State Key Laboratory of Molecular Neuroscience at HKUST.

The work was conducted in collaboration with researchers at University College London and clinicians in local hospitals including the Prince of Wales Hospital and Queen Elizabeth Hospital. The discovery was made using the proximity extension assay (PEA) — a cutting-edge ultrasensitive and high-throughput protein measurement technology, to examine the levels of over 1,000 proteins in the plasma of AD patients in Hong Kong.

As the most comprehensive study of blood proteins in AD patients to date, the work has recently been published in Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association, and has also been featured and actively discussed on different scholarly exchange platforms on AD research such as Alzforum.

AD, which affects over 50 million people worldwide, involves the dysfunction and loss of brain cells. Its symptoms include progressive memory loss as well as impaired movement, reasoning, and judgment. While patients often only seek medical attention and are diagnosed when they have memory problems, AD affects the brain at least 10-20 years before symptoms appear.

Story Source:

Materials provided by Hong Kong University of Science and Technology. Note: Content may be edited for style and length.

Journal Reference:

Yuanbing Jiang, Xiaopu Zhou, Fanny C. Ip, Philip Chan, Yu Chen, Nicole C.H. Lai, Kit Cheung, Ronnie M.N. Lo, Estella P.S. Tong, Bonnie W.Y. Wong, Andrew L.T. Chan, Vincent C.T. Mok, Timothy C.Y. Kwok, Kin Y. Mok, John Hardy, Henrik Zetterberg, Amy K.Y. Fu, Nancy Y. Ip. Large‐scale plasma proteomic profiling identifies a high‐performance biomarker panel for Alzheimer’s disease screening and staging. Alzheimer’s & Dementia, 2021; DOI: 10.1002/alz.12369

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Origin of SARS-CoV-2 Virus — Following the Clues

For those interested “the origin of the Wuhan virus,” these data — just sent to me today — are interesting and very relevant
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From: Anonymous
Sent: Thursday, June 24, 2021 5:35 AM

The article by Nicholas Wade [below] is not accurate when he states that “CGG for Arg (common codon usage in the human genome) has never been seen in any coronavirus genome.” In an article publishes last year [10.1016/j.virusres.2020.197976], it was shown that CGG is used by the SARS genome (frequency=0.09) and the MERS genome (0.43); in fact, the frequency is even much higher in MERS than it is in the SARS-CoV-2 (0.2) genome, which has caused the COVID-19 pandemic [see Table 1 of 10.1016/j.virusres.2020.197976].

Codon-usage differences like these (half or double in frequency) are very commonly seen — even in closely related bacterial or viral strains. The “double-CGG” feature also is present in the MERS genome. I did not find the polybasic insertion (Pro-Arg-Arg-Ala-Arg) in the COVID-19 reference genome. There will always be some unique genomic features that one might find in any organism. These features can always be interpreted by “conspiracy theorists” as “genetically-engineered,” but they are just as likely to be found in a Martian genome or in some genome from another galaxy.

[You can use this web site (http://hive.biochemistry.gwu.edu/review/codon) to find codon usage tables for different organisms, but this does not include virus genomes.]

Sent: Sunday, May 9, 2021 3:38 PM

For those interested in the possible origin of the coronavirus that causes COVID-19 — Nicholas Wade offers the best analysis yet (without any political agenda). Some of you might recognize the name; Wade has written scientific fact and opinion articles for Nature, Science and many for the New York Times over the years. He writes very well, and this is an EXCELLENT summary.
DwN

Origin of SARS-CoV-2 — Following the Clues

Did people, or Mother Nature, open Pandora’s box at Wuhan?

Nicholas Wade

The Covid-19 pandemic has disrupted lives the world over for more than a year. Its death toll will soon reach three million people. Yet the origin of pandemic remains uncertain: the political agendas of governments and scientists have generated thick clouds of obfuscation, which the mainstream press seems helpless to dispel.

In what follows I will sort through the available scientific facts, which hold many clues as to what happened, and provide readers with the evidence to make their own judgments. I will then try to assess the complex issue of blame, which starts with, but extends far beyond, the government of China.

By the end of this article, you may have learned a lot about the molecular biology of viruses. I will try to keep this process as painless as possible. But the science cannot be avoided because for now, and probably for a long time hence, it offers the only sure thread through the maze.

The virus that caused the pandemic is known officially as SARS-CoV-2, but can be called SARS2 for short. As many people know, there are two main theories about its origin. One is that it jumped naturally from wildlife to people. The other is that the virus was under study in a lab, from which it escaped. It matters a great deal which is the case if we hope to prevent a second such occurrence.

I’ll describe the two theories, explain why each is plausible, and then ask which provides the better explanation of the available facts. It’s important to note that so far there is no direct evidence for either theory. Each depends on a set of reasonable conjectures but so far lacks proof. So, I have only clues, not conclusions, to offer. But those clues point in a specific direction. And having inferred that direction, I’m going to delineate some of the strands in this tangled skein of disaster.

A Tale of Two Theories

After the pandemic first broke out in December 2019, Chinese authorities reported that many cases had occurred in the wet market — a place selling wild animals for meat — in Wuhan. This reminded experts of the SARS1 epidemic of 2002 in which a bat virus had spread first to civets, an animal sold in wet markets, and from civets to people. A similar bat virus caused a second epidemic, known as MERS, in 2012. This time the intermediary host animal was camels.

The decoding of the virus’s genome showed it belonged a viral family known as beta-coronaviruses, to which the SARS1 and MERS viruses also belong. The relationship supported the idea that, like them, it was a natural virus that had managed to jump from bats, via another animal host, to people. The wet market connection, the only other point of similarity with the SARS1 and MERS epidemics, was soon broken: Chinese researchers found earlier cases in Wuhan with no link to the wet market. But that seemed not to matter when so much further evidence in support of natural emergence was expected shortly.

Wuhan, however, is home of the Wuhan Institute of Virology, a leading world center for research on coronaviruses. So the possibility that the SARS2 virus had escaped from the lab could not be ruled out. Two reasonable scenarios of origin were on the table.

From early on, public and media perceptions were shaped in favor of the natural emergence scenario by strong statements from two scientific groups. These statements were not at first examined as critically as they should have been.

“We stand together to strongly condemn conspiracy theories suggesting that COVID-19 does not have a natural origin,” a group of virologists and others wrote in the Lancet on February 19, 2020, when it was really far too soon for anyone to be sure what had happened. Scientists “overwhelmingly conclude that this coronavirus originated in wildlife,” they said, with a stirring rallying call for readers to stand with Chinese colleagues on the frontline of fighting the disease.

Contrary to the letter writers’ assertion, the idea that the virus might have escaped from a lab invoked accident, not conspiracy. It surely needed to be explored, not rejected out of hand. A defining mark of good scientists is that they go to great pains to distinguish between what they know and what they don’t know. By this criterion, the signatories of the Lancet letter were behaving as poor scientists: they were assuring the public of facts they could not know for sure were true.

It later turned out that the Lancet letter had been organized and drafted by Peter Daszak, president of the EcoHealth Alliance of New York. Dr. Daszak’s organization funded coronavirus research at the Wuhan Institute of Virology. If the SARS2 virus had indeed escaped from research he funded, Dr. Daszak would be potentially culpable. This acute conflict of interest was not declared to the Lancet’s readers. To the contrary, the letter concluded, “We declare no competing interests.”

Peter Daszak, president of the EcoHealth Alliance

Virologists like Dr. Daszak had much at stake in the assigning of blame for the pandemic. For 20 years, mostly beneath the public’s attention, they had been playing a dangerous game. In their laboratories they routinely created viruses more dangerous than those that exist in nature. They argued they could do so safely, and that by getting ahead of nature they could predict and prevent natural “spillovers,” the cross-over of viruses from an animal host to people. If SARS2 had indeed escaped from such a laboratory experiment, a savage blowback could be expected, and the storm of public indignation would affect virologists everywhere, not just in China. “It would shatter the scientific edifice top to bottom,” an MIT Technology Review editor, Antonio Regalado, said in March 2020.

A second statement which had enormous influence in shaping public attitudes was a letter (in other words an opinion piece, not a scientific article) published on 17 March 2020 in the journal Nature Medicine. Its authors were a group of virologists led by Kristian G. Andersen of the Scripps Research Institute. “Our analyses clearly show that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus,” the five virologists declared in the second paragraph of their letter.

Kristian G. Andersen, Scripps Research

Unfortunately, this was another case of poor science, in the sense defined above. True, some older methods of cutting and pasting viral genomes retain tell-tale signs of manipulation. But newer methods, called “no-see-um” or “seamless” approaches, leave no defining marks. Nor do other methods for manipulating viruses such as serial passage, the repeated transfer of viruses from one culture of cells to another. If a virus has been manipulated, whether with a seamless method or by serial passage, there is no way of knowing that this is the case. Dr. Andersen and his colleagues were assuring their readers of something they could not know.

The discussion part their letter begins, “It is improbable that SARS-CoV-2 emerged through laboratory manipulation of a related SARS-CoV-like coronavirus”. But wait, didn’t the lead say the virus had clearly not been manipulated? The authors’ degree of certainty seemed to slip several notches when it came to laying out their reasoning.

The reason for the slippage is clear once the technical language has been penetrated. The two reasons the authors give for supposing manipulation to be improbable are decidedly inconclusive.

First, they say that the spike protein of SARS2 binds very well to its target, the human ACE2 receptor, but does so in a different way from that which physical calculations suggest would be the best fit. Therefore, the virus must have arisen by natural selection, not manipulation.

If this argument seems hard to grasp, it’s because it’s so strained. The authors’ basic assumption, not spelt out, is that anyone trying to make a bat virus bind to human cells could do so in only one way. First, they would calculate the strongest possible fit between the human ACE2 receptor and the spike protein with which the virus latches onto it. They would then design the spike protein accordingly (by selecting the right string of amino acid units that compose it). But since the SARS2 spike protein is not of this calculated best design, the Andersen paper says, therefore it can’t have been manipulated.

But this ignores the way that virologists do in fact get spike proteins to bind to chosen targets, which is not by calculation but by splicing in spike protein genes from other viruses or by serial passage. With serial passage, each time the virus’s progeny are transferred to new cell cultures or animals, the more successful are selected until one emerges that makes a really tight bind to human cells. Natural selection has done all the heavy lifting. The Andersen paper’s speculation about designing a viral spike protein through calculation has no bearing on whether or not the virus was manipulated by one of the other two methods.

The authors’ second argument against manipulation is even more contrived. Although most living things use DNA as their hereditary material, a number of viruses use RNA, DNA’s close chemical cousin. But RNA is difficult to manipulate, so researchers working on coronaviruses, which are RNA-based, will first convert the RNA genome to DNA. They manipulate the DNA version, whether by adding or altering genes, and then arrange for the manipulated DNA genome to be converted back into infectious RNA.

Only a certain number of these DNA backbones have been described in the scientific literature. Anyone manipulating the SARS2 virus “would probably” have used one of these known backbones, the Andersen group writes, and since SARS2 is not derived from any of them, therefore it was not manipulated. But the argument is conspicuously inconclusive. DNA backbones are quite easy to make, so it’s obviously possible that SARS2 was manipulated, using an unpublished DNA backbone.

And that’s it. These are the two arguments made by the Andersen group in support of their declaration that the SARS2 virus was clearly not manipulated. And this conclusion, grounded in nothing but two inconclusive speculations, convinced the world’s press that SARS2 could not have escaped from a lab. A technical critique of the Andersen letter takes it down in harsher words.

Science is supposedly a self-correcting community of experts who constantly check each other’s work. So, why didn’t other virologists point out that the Andersen group’s argument was full of absurdly large holes? Perhaps because in today’s universities — speech can be very costly. Careers can be destroyed for stepping out of line. Any virologist who challenges the community’s declared view risks having his next grant application turned down by the panel of fellow virologists that advises the government grant distribution agency.

The Daszak and Andersen letters were really political, not scientific statements, yet were amazingly effective. Articles in the mainstream press repeatedly stated that a consensus of experts had ruled lab escape out of the question or extremely unlikely. Their authors relied for the most part on the Daszak and Andersen letters, failing to understand the yawning gaps in their arguments. Mainstream newspapers all have science journalists on their staff, as do the major networks, and these specialist reporters are supposed to be able to question scientists and check their assertions. But the Daszak and Andersen assertions went largely unchallenged.

Doubts about natural emergence

Natural emergence was the media’s preferred theory until around February 2021 and the visit by a World Health Organization commission to China. The commission’s composition and access were heavily controlled by the Chinese authorities. Its members, who included the ubiquitous Dr. Daszak, kept asserting before, during and after their visit that lab escape was extremely unlikely. But this was not quite the propaganda victory the Chinese authorities may have been hoping for. What became clear was that the Chinese had no evidence to offer the commission in support of the natural emergence theory.

This was surprising because both the SARS1 and MERS viruses had left copious traces in the environment. The intermediary host species of SARS1 was identified within four months of the epidemic’s outbreak, and the host of MERS within nine months. Yet some 15 months after the SARS2 pandemic began, and a presumably intensive search, Chinese researchers had failed to find either the original bat population, or the intermediate species to which SARS2 might have jumped, or any serological evidence that any Chinese population, including that of Wuhan, had ever been exposed to the virus prior to December 2019. Natural emergence remained a conjecture which, however plausible to begin with, had gained not a shred of supporting evidence in over a year.

And as long as that remains the case, it’s logical to pay serious attention to the alternative conjecture, i.e., that SARS2 escaped from a lab.

Why would anyone want to create a novel virus capable of causing a pandemic? Ever since virologists gained the tools for manipulating a virus’s genes, they have argued they could get ahead of a potential pandemic by exploring how close a given animal virus might be to making the jump to humans. And that justified lab experiments in enhancing the ability of dangerous animal viruses to infect people, virologists asserted.

With this rationale, they have recreated the 1918 flu virus, shown how the almost extinct polio virus can be synthesized from its published DNA sequence, and introduced a smallpox gene into a related virus.

These enhancements of viral capabilities are known blandly as gain-of-function experiments. With coronaviruses, there was particular interest in the spike proteins, which jut out all around the spherical surface of the virus and pretty much determine which species of animal it will target. In 2000 Dutch researchers, for instance, earned the gratitude of rodents everywhere by genetically engineering the spike protein of a mouse coronavirus so that it would attack only cats.

The spike proteins on the coronavirus’s surface determine which animal it can infect. CDC.gov

Virologists started studying bat coronaviruses in earnest, after these turned out to be the source of both the SARS1 and MERS epidemics. In particular, researchers wanted to understand what changes needed to occur in a bat virus’s spike proteins before it could infect people.

Researchers at the Wuhan Institute of Virology, led by China’s leading expert on bat viruses, Dr. Shi Zheng-li or “Bat Lady”, mounted frequent expeditions to the bat-infested caves of Yunnan in southern China and collected around a hundred different bat coronaviruses.

Dr. Shi then teamed up with Ralph S. Baric, an eminent coronavirus researcher at the University of North Carolina. Their work focused on enhancing the ability of bat viruses to attack humans so as to “examine the emergence potential (that is, the potential to infect humans) of circulating bat CoVs [coronaviruses].” In pursuit of this aim, in November 2015 they created a novel virus by taking the backbone of the SARS1 virus and replacing its spike protein with one from a bat virus (known as SHC014-CoV). This manufactured virus was able to infect the cells of the human airway, at least when tested against a lab culture of such cells.

The SHC014-CoV/SARS1 virus is known as a chimera because its genome contains genetic material from two strains of virus. If the SARS2 virus were to have been cooked up in Dr. Shi’s lab, then its direct prototype would have been the SHC014-CoV/SARS1 chimera, the potential danger of which concerned many observers and prompted intense discussion.

“If the virus escaped, nobody could predict the trajectory,” said Simon Wain-Hobson, a virologist at the Pasteur Institute in Paris.

Dr. Baric and Dr. Shi referred to the obvious risks in their paper but argued they should be weighed against the benefit of foreshadowing future spillovers. Scientific review panels, they wrote, “may deem similar studies building chimeric viruses based on circulating strains too risky to pursue.” Given various restrictions being placed on gain-of function (GOF) research, matters had arrived in their view at “a crossroads of GOF research concerns; the potential to prepare for and mitigate future outbreaks must be weighed against the risk of creating more dangerous pathogens. In developing policies moving forward, it is important to consider the value of the data generated by these studies and whether these types of chimeric virus studies warrant further investigation versus the inherent risks involved.”

That statement was made in 2015. From the hindsight of 2021, one can say that the value of gain-of-function studies in preventing the SARS2 epidemic was zero. The risk was catastrophic, if indeed the SARS2 virus was generated in a gain-of-function experiment.

Inside the Wuhan Institute of Virology

Dr. Baric had developed, and taught Dr. Shi, a general method for engineering bat coronaviruses to attack other species. The specific targets were human cells grown in cultures and humanized mice. These laboratory mice, a cheap and ethical stand-in for human subjects, are genetically engineered to carry the human version of a protein called ACE2 that studs the surface of cells that line the airways.

Dr. Shi returned to her lab at the Wuhan Institute of Virology and resumed the work she had started on genetically engineering coronaviruses to attack human cells.

Dr. Zheng-li Shi in a high safety (level BSL4) lab. Her coronavirus research was done in the much lower safety levels of BSL2 and BSL3 labs.

How can we be so sure?

Because, by a strange twist in the story, her work was funded by the National Institute of Allergy and Infectious Diseases (NIAID), a part of the U.S. National Institutes of Health (NIH). And grant proposals that funded her work, which are a matter of public record, specify exactly what she planned to do with the money.

The grants were assigned to the prime contractor, Dr. Daszak of the EcoHealth Alliance, who subcontracted them to Dr. Shi. Here are extracts from the grants for fiscal years 2018 and 2019. “CoV” stands for coronavirus and “S protein” refers to the virus’s spike protein.

“Test predictions of CoV inter-species transmission. Predictive models of host range (i.e. emergence potential) will be tested experimentally using reverse genetics, pseudovirus and receptor binding assays, and virus infection experiments across a range of cell cultures from different species and humanized mice.”

“We will use S protein sequence data, infectious clone technology, in vitro and in vivo infection experiments and analysis of receptor binding to test the hypothesis that % divergence thresholds in S protein sequences predict spillover potential.”

What this means, in non-technical language, is that Dr. Shi set out to create novel coronaviruses with the highest possible infectivity for human cells. Her plan was to take genes that coded for spike proteins possessing a variety of measured affinities for human cells, ranging from high to low. She would insert these spike genes one by one into the backbone of a number of viral genomes (“reverse genetics” and “infectious clone technology”), creating a series of chimeric viruses. These chimeric viruses would then be tested for their ability to attack human cell cultures (“in vitro”) and humanized mice (“in vivo”). And this information would help predict the likelihood of “spillover,” the jump of a coronavirus from bats to people.

The methodical approach was designed to find the best combination of coronavirus backbone and spike protein for infecting human cells. The approach could have generated SARS2-like viruses, and indeed may have created the SARS2 virus itself with the right combination of virus backbone and spike protein.

It cannot yet be stated that Dr. Shi did or did not generate SARS2 in her lab because her records have been sealed, but it seems she was certainly on the right track to have done so. “It is clear that the Wuhan Institute of Virology was systematically constructing novel chimeric coronaviruses and was assessing their ability to infect human cells and human-ACE2-expressing mice,” says Richard H. Ebright, a molecular biologist at Rutgers University and leading expert on biosafety.

“It is also clear,” Dr. Ebright said, “that, depending on the constant genomic contexts chosen for analysis, this work could have produced SARS-CoV-2 or a proximal progenitor of SARS-CoV-2.” “Genomic context” refers to the particular viral backbone used as the testbed for the spike protein.

The lab escape scenario for the origin of the SARS2 virus, as should by now be evident, is not mere hand-waving in the direction of the Wuhan Institute of Virology. It is a detailed proposal, based on the specific project being funded there by the NIAID.

Even if the grant required the work plan described above, how can we be sure that the plan was in fact carried out? For that we can rely on the word of Dr. Daszak, who has been much protesting for the last 15 months that lab escape was a ludicrous conspiracy theory invented by China-bashers.

On 9 December 2019, before the outbreak of the pandemic became generally known, Dr. Daszak gave an interview in which he talked in glowing terms of how researchers at the Wuhan Institute of Virology had been reprogramming the spike protein and generating chimeric coronaviruses capable of infecting humanized mice.

“And we have now found, you know, after 6 or 7 years of doing this, over 100 new sars-related coronaviruses, very close to SARS,” Dr. Daszak says around minute 28 of the interview. “Some of them get into human cells in the lab, some of them can cause SARS disease in humanized mice models and are untreatable with therapeutic monoclonals and you can’t vaccinate against them with a vaccine. So, these are a clear and present danger….

“Interviewer: You say these are diverse coronaviruses and you can’t vaccinate against them, and no anti-virals — so what do we do?

“Daszak: Well, I think…coronaviruses — you can manipulate them in the lab pretty easily. Spike protein drives a lot of what happen with coronavirus, in zoonotic risk. So, you can get the sequence, you can build the protein, and we work a lot with Ralph Baric at UNC to do this. Insert into the backbone of another virus and do some work in the lab. So you can get more predictive when you find a sequence. You’ve got this diversity. Now the logical progression for vaccines is, if you are going to develop a vaccine for SARS, people are going to use pandemic SARS, but let’s insert some of these other things and get a better vaccine.” The insertions he referred to perhaps included an element called the furin cleavage site, discussed below, which greatly increases viral infectivity for human cells.

In disjointed style, Dr. Daszak is referring to the fact that once you have generated a novel coronavirus that can attack human cells, you can take the spike protein and make it the basis for a vaccine.

One can only imagine Dr. Daszak’s reaction when he heard of the outbreak of the epidemic in Wuhan a few days later. He would have known better than anyone the Wuhan Institute’s goal of making bat coronaviruses infectious to humans, as well as the weaknesses in the institute’s defense against their own researchers becoming infected.

But instead of providing public health authorities with the plentiful information at his disposal, he immediately launched a public relations campaign to persuade the world that the epidemic couldn’t possibly have been caused by one of the institute’s souped-up viruses. “The idea that this virus escaped from a lab is just pure baloney. It’s simply not true,” he declared in an April 2020 interview.

The Safety Arrangements at the Wuhan Institute of Virology

Dr. Daszak was possibly unaware of, or perhaps he knew all too well, the long history of viruses escaping from even the best run laboratories. The smallpox virus escaped three times from labs in England in the 1960’s and 1970’s, causing 80 cases and 3 deaths. Dangerous viruses have leaked out of labs almost every year since. Coming to more recent times, the SARS1 virus has proved a true escape artist, leaking from laboratories in Singapore, Taiwan, and no less than four times from the Chinese National Institute of Virology in Beijing.

One reason for SARS1 being so hard to handle is that there were no vaccines available to protect laboratory workers. As Dr. Daszak mentioned in his December 19 interview quoted above, the Wuhan researchers too had been unable to develop vaccines against the coronaviruses they had designed to infect human cells. They would have been as defenseless against the SARS2 virus, if it were generated in their lab, as their Beijing colleagues were against SARS1.

A second reason for the severe danger of novel coronaviruses has to do with the required levels of lab safety. There are four degrees of safety, designated BSL1 to BSL4, with BSL4 being the most restrictive and designed for deadly pathogens like the Ebola virus.

The Wuhan Institute of Virology had a new BSL4 lab, but its state-of-readiness considerably alarmed the State Department inspectors who visited it from the Beijing embassy in 2018. “The new lab has a serious shortage of appropriately trained technicians and investigators needed to safely operate this high-containment laboratory,” the inspectors wrote in a cable of 19 January 2018.

The real problem, however, was not the unsafe state of the Wuhan BSL4 lab but the fact that virologists worldwide don’t like working in BSL4 conditions. You have to wear a space suit, do operations in closed cabinets and accept that everything will take twice as long. So, the rules assigning each kind of virus to a given safety level were laxer than some might think was prudent.

Before 2020, the rules followed by virologists in China and elsewhere required that experiments with the SARS1 and MERS viruses be conducted in BSL3 conditions. But all other bat coronaviruses could be studied in BSL2, the next level down. BSL2 requires taking fairly minimal safety precautions, such as wearing lab coats and gloves, not sucking up liquids in a pipette, and putting up biohazard warning signs. Yet a gain-of-function experiment conducted in BSL2 might produce an agent more infectious than either SARS1 or MERS. And if it did, then lab workers would stand a high chance of infection, especially if unvaccinated.

Much of Dr. Shi’s work on gain-of-function in coronaviruses was performed at the BSL2 safety level, as is stated in her publications and other documents. She has said in an interview with Science magazine that “The coronavirus research in our laboratory is conducted in BSL-2 or BSL-3 laboratories.”

“It is clear that some or all of this work was being performed using a biosafety standard — biosafety level 2, the biosafety level of a standard US dentist’s office — that would pose an unacceptably high risk of infection of laboratory staff upon contact with a virus having the transmission properties of SARS-CoV-2,” says Dr. Ebright.

“It also is clear,” he adds, “that this work never should have been funded and never should have been performed.”

This is a view he holds — regardless of whether or not the SARS2 virus ever saw the inside of a lab.

Concern about safety conditions at the Wuhan lab was not, it seems, misplaced. According to a fact sheet issued by the State Department on January 15,2021, “ The U.S. government has reason to believe that several researchers inside the WIV became sick in autumn 2019, before the first identified case of the outbreak, with symptoms consistent with both COVID-19 and common seasonal illnesses.”

David Asher, a fellow of the Hudson Institute and former consultant to the State Department, provided more detail about the incident at a seminar. Knowledge of the incident came from a mix of public information and “some high-end information collected by our intelligence community,” he said. Three people working at a BSL3 lab at the institute fell sick within a week of each other with severe symptoms that required hospitalization. This was “the first known cluster that we’re aware of, of victims of what we believe to be COVID-19.” Influenza could not completely be ruled out but seemed unlikely in the circumstances, he said.

Comparing the Rival Scenarios of SARS2 Origin

The evidence above adds up to a serious case that the SARS2 virus could have been created in a lab, from which it then escaped. But the case, however substantial, falls short of proof. Proof would consist of evidence from the Wuhan Institute of Virology, or related labs in Wuhan, that SARS2 or a predecessor virus was under development there. For lack of access to such records, another approach is to take certain salient facts about the SARS2 virus and ask how well each is explained by the two rival scenarios of origin, those of natural emergence and lab escape. Here are four tests of the two hypotheses. A couple have some technical detail, but these are among the most persuasive for those who may care to follow the argument.

1) The place of origin.

Start with geography. The two closest known relatives of the SARS2 virus were collected from bats living in caves in Yunnan, a province of southern China. If the SARS2 virus had first infected people living around the Yunnan caves, that would strongly support the idea that the virus had spilled over to people naturally. But this isn’t what happened. The pandemic broke out 1,500 kilometers away, in Wuhan.

Beta-coronaviruses, the family of bat viruses to which SARS2 belongs, infect the horseshoe bat Rhinolophus affinis, which ranges across southern China. The bats’ range is 50 kilometers, so it’s unlikely that any made it to Wuhan. In any case, the first cases of the Covid-19 pandemic probably occurred in September, when temperatures in Hubei province are already cold enough to send bats into hibernation.

What if the bat viruses infected some intermediate host first? You would need a longstanding population of bats in frequent proximity with an intermediate host, which in turn must often cross paths with people. All these exchanges of virus must take place somewhere outside Wuhan, a busy metropolis which so far as is known is not a natural habitat of Rhinolophus bat colonies. The infected person (or animal) carrying this highly transmissible virus must have traveled to Wuhan without infecting anyone else. No one in his or her family got sick. If the person jumped on a train to Wuhan, no fellow passengers fell ill.

It’s a stretch, in other words, to get the pandemic to break out naturally outside Wuhan and then, without leaving any trace, to make its first appearance there.

For the lab escape scenario, a Wuhan origin for the virus is a no-brainer. Wuhan is home to China’s leading center of coronavirus research where, as noted above, researchers were genetically engineering bat coronaviruses to attack human cells. They were doing so under the minimal safety conditions of a BSL2 lab. If a virus with the unexpected infectiousness of SARS2 had been generated there, its escape would be no surprise.

2) Natural history and evolution

The initial location of the pandemic is a small part of a larger problem, that of its natural history. Viruses don’t just make one time jumps from one species to another. The coronavirus spike protein, adapted to attack bat cells, needs repeated jumps to another species, most of which fail, before it gains a lucky mutation. Mutation — a change in one of its RNA units — causes a different amino acid unit to be incorporated into its spike protein and makes the spike protein better able to attack the cells of some other species.

Through several more such mutation-driven adjustments, the virus adapts to its new host, say some animal with which bats are in frequent contact. The whole process then resumes as the virus moves from this intermediate host to people.

In the case of SARS1, researchers have documented the successive changes in its spike protein as the virus evolved step by step into a dangerous pathogen. After it had gotten from bats into civets, there were six further changes in its spike protein before it became a mild pathogen in people. After a further 14 changes, the virus was much better adapted to humans, and with a further 4 the epidemic took off.

But when you look for the fingerprints of a similar transition in SARS2, a strange surprise awaits. The virus has changed hardly at all, at least until recently. From its very first appearance, it was well adapted to human cells. Researchers led by Alina Chan of the Broad Institute compared SARS2 with late stage SARS1, which by then was well adapted to human cells, and found that the two viruses were similarly well adapted. “By the time SARS-CoV-2 was first detected in late 2019, it was already pre-adapted to human transmission to an extent similar to late epidemic SARS-CoV,” they wrote.

Even those who think lab origin unlikely agree that SARS2 genomes are remarkably uniform. Dr. Baric writes that “early strains identified in Wuhan, China, showed limited genetic diversity, which suggests that the virus may have been introduced from a single source.”

A single source would of course be compatible with lab escape, less so with the massive variation and selection which is evolution’s hallmark way of doing business.

The uniform structure of SARS2 genomes gives no hint of any passage through an intermediate animal host, and no such host has been identified in nature.

Proponents of natural emergence suggest that SARS2 incubated in a yet-to-be found human population before gaining its special properties. Or that it jumped to a host animal outside China.

All these conjectures are possible, but strained. Proponents of lab leak have a simpler explanation. SARS2 was adapted to human cells from the start because it was grown in humanized mice or in lab cultures of human cells, just as described in Dr. Daszak’s grant proposal. Its genome shows little diversity because the hallmark of lab cultures is uniformity.

Proponents of laboratory escape joke that of course the SARS2 virus infected an intermediary host species before spreading to people, and that they have identified it — a humanized mouse from the Wuhan Institute of Virology.

3) The furin cleavage site.

The furin cleavage site is a minute part of the virus’s anatomy but one that exerts great influence on its infectivity. It sits in the middle of the SARS2 spike protein. It also lies at the heart of the puzzle of where the virus came from.

The spike protein has two sub-units with different roles. The first, called S1, recognizes the virus’s target, a protein called angiotensin converting enzyme-2 (or ACE2) which studs the surface of cells lining the human airways. The second, S2, helps the virus, once anchored to the cell, to fuse with the cell’s membrane. After the virus’s outer membrane has coalesced with that of the stricken cell, the viral genome is injected into the cell, hijacks its protein-making machinery and forces it to generate new viruses.

But this invasion cannot begin until the S1 and S2 subunits have been cut apart. And there, right at the S1/S2 junction, is the furin cleavage site that ensures the spike protein will be cleaved in exactly the right place.

The virus, a model of economic design, does not carry its own cleaver. It relies on the cell to do the cleaving for it. Human cells have a protein cutting tool on their surface known as furin. Furin will cut any protein chain that carries its signature target cutting site. This is the sequence of amino acid units, proline-arginine-arginine-alanine, or PRRA in the code that refers to each amino acid by a letter of the alphabet. PRRA is the amino acid sequence at the core of SARS2’s furin cleavage site.

Viruses have all kinds of clever tricks, so why does the furin cleavage site stand out? Because of all known SARS-related beta-coronaviruses, only SARS2 possesses a furin cleavage site. All the other viruses have their S2 unit cleaved at a different site and by a different mechanism.

How then did SARS2 acquire its furin cleavage site? Either the site evolved naturally, or it was inserted by researchers at the S1/S2 junction in a gain-of-function experiment.

Consider natural origin first. Two ways viruses evolve are by mutation and by recombination. Mutation is the process of random change in DNA (or RNA for coronaviruses) that usually results in one amino acid in a protein chain being switched for another. Many of these changes harm the virus but natural selection retains the few that do something useful. Mutation is the process by which the SARS1 spike protein gradually switched its preferred target cells from those of bats to civets, and then to humans.

Mutation seems a less likely way for SARS2’s furin cleavage site to be generated, even though it can’t completely be ruled out. The site’s four amino acid units are all together, and all at just the right place in the S1/S2 junction. Mutation is a random process triggered by copying errors (when new viral genomes are being generated) or by chemical decay of genomic units. So it typically affects single amino acids at different spots in a protein chain. A string of amino acids like that of the furin cleavage site is much more likely to be acquired all together through a quite different process known as recombination.

Recombination is an inadvertent swapping of genomic material that occurs when two viruses happen to invade the same cell, and their progeny are assembled with bits and pieces of RNA belonging to the other. Beta-coronaviruses will only combine with other beta-coronaviruses but can acquire, by recombination, almost any genetic element present in the collective genomic pool. What they cannot acquire is an element the pool does not possess. And no known SARS-related beta-coronavirus, the class to which SARS2 belongs, possesses a furin cleavage site.

Proponents of natural emergence say SARS2 could have picked up the site from some as yet unknown beta-coronavirus. But bat SARS-related beta-coronaviruses evidently don’t need a furin cleavage site to infect bat cells, so there’s no great likelihood that any in fact possesses one, and indeed none has been found so far.

The proponents’ next argument is that SARS2 acquired its furin cleavage site from people. A predecessor of SARS2 could have been circulating in the human population for months or years until at some point it acquired a furin cleavage site from human cells. It would then have been ready to break out as a pandemic.

If this is what happened, there should be traces in hospital surveillance records of the people infected by the slowly evolving virus. But none has so far come to light. According to the WHO report on the origins of the virus, the sentinel hospitals in Hubei province, home of Wuhan, routinely monitor influenza-like illnesses and “no evidence to suggest substantial SARSCoV-2 transmission in the months preceding the outbreak in December was observed.”

So — it’s hard to explain how the SARS2 virus picked up its furin cleavage site naturally, whether by mutation or recombination.

That leaves a gain-of-function experiment. For those who think SARS2 may have escaped from a lab, explaining the furin cleavage site is no problem at all. “Since 1992 the virology community has known that the one sure way to make a virus deadlier is to give it a furin cleavage site at the S1/S2 junction in the laboratory,” writes Dr. Steven Quay, a biotech entrepreneur interested in the origins of SARS2. “At least eleven gain-of-function experiments, adding a furin site to make a virus more infective, are published in the open literature, including [by] Dr. Zhengli Shi, head of coronavirus research at the Wuhan Institute of Virology.”

4) A Question of Codons

There’s another aspect of the furin cleavage site that narrows the path for a natural emergence origin even further.

As everyone knows (or may at least recall from high school), the genetic code uses three units of DNA to specify each amino acid unit of a protein chain. When read in groups of 3, the 4 different kinds of DNA can specify 4 x 4 x 4 or 64 different triplets, or codons as they are called. Since there are only 20 kinds of amino acid, there are more than enough codons to go around, allowing some amino acids to be specified by more than one codon. The amino acid arginine, for instance, can be designated by any of the six codons CGU, CGC, CGA, CGG, AGA or AGG, where A, U, G and C stand for the four different kinds of unit in RNA.

Here’s where it gets interesting. Different organisms have different codon preferences. Human cells like to designate arginine with the codons CGT, CGC or CGG. But CGG is coronavirus’s least popular codon for arginine. Keep that in mind when looking at how the amino acids in the furin cleavage site are encoded in the SARS2 genome.

Now the functional reason why SARS2 has a furin cleavage site, and its cousin viruses don’t, can be seen by lining up (in a computer) the string of nearly 30,000 nucleotides in its genome with those of its cousin coronaviruses, of which the closest so far known is one called RaTG13. Compared with RaTG13, SARS2 has a 12-nucleotide insert right at the S1/S2 junction. The insert is the sequence T-CCT-CGG-CGG-GC. The CCT codes for proline, the two CGG’s for two arginines, and the GC is the beginning of a GCA codon that codes for alanine.

There are several curious features about this insert but the oddest is that of the two side-by-side CGG codons. Only 5% of SARS2’s arginine codons are CGG, and the double codon CGG-CGG has not been found in any other beta-coronavirus. So how did SARS2 acquire a pair of arginine codons that are favored by human cells but not by coronaviruses?

Proponents of natural emergence have an up-hill task to explain all the features of SARS2’s furin cleavage site. They have to postulate a recombination event at a site on the virus’s genome where recombinations are rare, and the insertion of a 12-nucleotide sequence with a double arginine codon unknown in the beta-coronavirus repertoire, at the only site in the genome that would significantly expand the virus’s infectivity.

“Yes, but your wording makes this sound unlikely — viruses are specialists at unusual events,” is the riposte of David L. Robertson, a virologist at the University of Glasgow who regards lab escape as a conspiracy theory. “Recombination is naturally very, very frequent in these viruses, there are recombination breakpoints in the spike protein and these codons appear unusual exactly because we’ve not sampled enough.”

Dr. Robertson is correct that evolution is always producing results that may seem unlikely but in fact are not. Viruses can generate untold numbers of variants, but we see only the one-in-a-billion that natural selection picks for survival. But this argument could be pushed too far. For instance, any result of a gain-of-function experiment could be explained as one that evolution would have arrived at in time. And the numbers game can be played the other way. For the furin cleavage site to arise naturally in SARS2, a chain of events has to happen, each of which is quite unlikely for the reasons given above. A long chain with several improbable steps is unlikely to ever be completed.

For the lab escape scenario, the double CGG codon is no surprise. The human-preferred codon is routinely used in labs. So, anyone who wanted to insert a furin cleavage site into the virus’s genome would synthesize the PRRA-making sequence in the lab and would be likely to use CGG codons to do so.

“When I first saw the furin cleavage site in the viral sequence, with its arginine codons, I said to my wife it was the smoking gun for the origin of the virus,” said David Baltimore, an eminent virologist and former president of CalTech. “These features make a powerful challenge to the idea of a natural origin for SARS2,” he said.

A Third Scenario of Origin

There’s a variation on the natural emergence scenario that’s worth considering. This is the idea that SARS2 jumped directly from bats to humans, without going through an intermediate host as SARS1 and MERS did. A leading advocate is the virologist David Robertson who notes that SARS2 can attack several other species besides humans. He believes the virus evolved a generalist capability while still in bats. Because the bats that it infects are widely distributed in southern and central China, the virus had ample opportunity to jump to people, even though it seems to have done so on only one known occasion. Dr. Robertson’s thesis explains why no one has so far found a trace of SARS2 in any intermediate host or in human populations surveilled before December 2019. It would also explain the puzzling fact that SARS2 has not changed since it first appeared in humans — it didn’t need to because it could already attack human cells efficiently.

One problem with this idea, though, is that if SARS2 jumped from bats to people in a single leap and hasn’t changed much since, it should still be good at infecting bats. And it seems it isn’t.

“Tested bat species are poorly infected by SARS-CoV-2 and they are therefore unlikely to be the direct source for human infection,” write a scientific group skeptical of natural emergence.

Still, Dr. Robertson may be onto something. The bat coronaviruses of the Yunnan caves can infect people directly. In April 2012 six miners clearing bat guano from the Mojiang mine contracted severe pneumonia with Covid-19-like symptoms and three eventually died. A virus isolated from the Mojiang mine, called RaTG13, is still the closest known relative of SARS2. Much mystery surrounds the origin, reporting and strangely low affinity of RaTG13 for bat cells, as well as the nature of 8 similar viruses that Dr. Shi reports she collected at the same time but has not yet published despite their great relevance to the ancestry of SARS2. But all that is a story for another time. The point here is that bat viruses can infect people directly, though only in special conditions.

So who else, besides miners excavating bat guano, comes into particularly close contact with bat coronaviruses? Well, coronavirus researchers do. Dr. Shi says she and her group collected more than 1,300 bat samples during some 8 visits to the Mojiang cave between 2012 and 2015, and there were doubtless many expeditions to other Yunnan caves.

Imagine the researchers making frequent trips from Wuhan to Yunnan and back, stirring up bat guano in dark caves and mines, and now you begin to see a possible missing link between the two places. Researchers could have gotten infected during their collecting trips, or while working with the new viruses at the Wuhan Institute of Virology. The virus that escaped from the lab would have been a natural virus, not one cooked up by gain of function.

The direct-from-bats thesis is a chimera between the natural emergence and lab escape scenarios. It’s a possibility that can’t be dismissed. But against it are the facts that 1) both SARS2 and RaTG13 seem to have only feeble affinity for bat cells, so one can’t be fully confident that either ever saw the inside of a bat; and 2) the theory is no better than the natural emergence scenario at explaining how SARS2 gained its furin cleavage site, or why the furin cleavage site is determined by human-preferred arginine codons instead of by the bat-preferred codons.

Where We Are So Far

Neither the natural emergence nor the lab escape hypothesis can yet be ruled out. There is still no direct evidence for either. So, no definitive conclusion can be reached.

That said, the available evidence leans more strongly in one direction than the other. Readers will form their own opinion. But it seems to me that proponents of lab escape can explain all the available facts about SARS2 considerably more easily than can those who favor natural emergence.

It’s documented that researchers at the Wuhan Institute of Virology were doing gain-of-function experiments designed to make coronaviruses infect human cells and humanized mice. This is exactly the kind of experiment from which a SARS2-like virus could have emerged. The researchers were not vaccinated against the viruses under study, and they were working in the minimal safety conditions of a BSL2 laboratory. So, escape of a virus would not be at all surprising. In all of China, the pandemic broke out on the doorstep of the Wuhan institute. The virus was already well adapted to humans, as expected for a virus grown in humanized mice. It possessed an unusual enhancement, a furin cleavage site, which is not possessed by any other known SARS-related beta-coronavirus, and this site included a double arginine codon also unknown among beta-coronaviruses. What more evidence could you want, aside from the presently unobtainable lab records documenting SARS2’s creation?

Proponents of natural emergence have a rather harder story to tell. The plausibility of their case rests on a single surmise, the expected parallel between the emergence of SARS2 and that of SARS1 and MERS. But none of the evidence expected in support of such a parallel history has yet emerged. No one has found the bat population that was the source of SARS2, if indeed it ever infected bats. No intermediate host has presented itself, despite an intensive search by Chinese authorities that included the testing of 80,000 animals. There is no evidence of the virus making multiple independent jumps from its intermediate host to people, as both the SARS1 and MERS viruses did. There is no evidence from hospital surveillance records of the epidemic gathering strength in the population as the virus evolved. There is no explanation of why a natural epidemic should break out in Wuhan and nowhere else. There is no good explanation of how the virus acquired its furin cleavage site, which no other SARS-related beta-coronavirus possesses, nor why the site is composed of human-preferred codons. The natural emergence theory battles a bristling array of implausibilities.

The records of the Wuhan Institute of Virology certainly hold much relevant information. But Chinese authorities seem unlikely to release them — given the substantial chance that they incriminate the regime in the creation of the pandemic. Absent the efforts of some courageous Chinese whistle-blower, we may already have at hand just about all of the relevant information we are likely to get for a while.

So, it’s worth trying to assess responsibility for the pandemic, at least in a provisional way, because the paramount goal remains to prevent another one. Even those who aren’t persuaded that lab escape is the more likely origin of the SARS2 virus may see reason for concern about the present state of regulation governing gain-of-function research. There are two obvious levels of responsibility: the first, for allowing virologists to perform gain-of-function experiments, offering minimal gain and vast risk; the second, if indeed SARS2 was generated in a lab, for allowing the virus to escape and unleash a world-wide pandemic. Here are the players who seem most likely to deserve blame:

1. Chinese virologists

First and foremost, Chinese virologists are to blame for performing gain-of-function experiments in mostly BSL2-level safety conditions which were far too lax to contain a virus of unexpected infectiousness like SARS2. If the virus did indeed escape from their lab, they deserve the world’s censure for a foreseeable accident that has already caused the deaths of 3 million people.

True, Dr. Shi was trained by French virologists, worked closely with American virologists and was following international rules for the containment of coronaviruses. But she could and should have made her own assessment of the risks she was running. She and her colleagues bear the responsibility for their actions.

I have been using the Wuhan Institute of Virology as a shorthand for all virological activities in Wuhan. It’s possible that SARS2 was generated in some other Wuhan lab, perhaps in an attempt to make a vaccine that worked against all coronaviruses. But until the role of other Chinese virologists is clarified, Dr. Shi is the public face of Chinese work on coronaviruses, and provisionally she and her colleagues will stand first in line for opprobrium.

2. Chinese authorities

China’s central authorities did not generate SARS2 but they sure did their utmost to conceal the nature of the tragedy and China’s responsibility for it. They suppressed all records at the Wuhan Institute of Virology and closed down its virus databases. They released a trickle of information, much of which may have been outright false or designed to misdirect and mislead. They did their best to manipulate the WHO’s inquiry into the virus’s origins, and led the commission’s members on a fruitless run-around. So far they have proved far more interested in deflecting blame than in taking the steps necessary to prevent a second pandemic.

3. The worldwide community of virologists

Virologists around the world are a loose-knit professional community. They write articles in the same journals. They attend the same conferences. They have common interests in seeking funds from governments and in not being overburdened with safety regulations.

Virologists knew better than anyone the dangers of gain-of-function research. But the power to create new viruses, and the research funding obtainable by doing so, was too tempting. They pushed ahead with gain-of-function experiments. They lobbied against the moratorium imposed on Federal funding for gain-of-function research in 2014 and it was raised in 2017.

The benefits of the research in preventing future epidemics have so far been nil, the risks vast. If research on the SARS1 and MERS viruses could only be done at the BSL3 safety level, it was surely illogical to allow any work with novel coronaviruses at the lesser level of BSL2. Whether or not SARS2 escaped from a lab, virologists around the world have been playing with fire.

Their behavior has long alarmed other biologists. In 2014 scientists calling themselves the Cambridge Working Group urged caution on creating new viruses. In prescient words, they specified the risk of creating a SARS2-like virus. “Accident risks with newly created ‘potential pandemic pathogens’ raise grave new concerns,” they wrote. “Laboratory creation of highly transmissible, novel strains of dangerous viruses, especially but not limited to influenza, poses substantially increased risks. An accidental infection in such a setting could trigger outbreaks that would be difficult or impossible to control.”

When molecular biologists discovered a technique for moving genes from one organism to another, they held a public conference at Asilomar in 1975 to discuss the possible risks. Despite much internal opposition, they drew up a list of stringent safety measures that could be relaxed in future — and duly were — when the possible hazards had been better assessed.

When the CRISPR technique for editing genes was invented, biologists convened a joint report by the U.S., UK and Chinese national academies of science to urge restraint on making heritable changes to the human genome. Biologists who invented gene drives have also been open about the dangers of their work and have sought to involve the public.

You might think the SARS2 pandemic would spur virologists to re-evaluate the benefits of gain-of-function research, even to engage the public in their deliberations. But no. Many virologists deride lab escape as a conspiracy theory and others say nothing. They have barricaded themselves behind a Chinese wall of silence — which so far is working well to allay, or at least postpone, journalists’ curiosity and the public’s wrath. Professions that cannot regulate themselves deserve to get regulated by others, and this would seem to be the future that virologists are choosing for themselves.

4. The US Role in Funding the Wuhan Institute of Virology

From June 2014 to May 2019 Dr. Daszak’s EcoHealth Alliance had a grant from the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health, to do gain-of-function research with coronaviruses at the Wuhan Institute of Virology. Whether or not SARS2 is the product of that research, it seems a questionable policy to farm out high-risk research to unsafe foreign labs using minimal safety precautions. And if the SARS2 virus did indeed escape from the Wuhan institute, then the NIH will find itself in the terrible position of having funded a disastrous experiment that led to death of more than 3 million worldwide, including more than half a million of its own citizens.

The responsibility of the NIAID and NIH is even more acute because for the first three years of the grant to EcoHealth Alliance there was a moratorium on funding gain-of-function research. Why didn’t the two agencies therefore halt the Federal funding as apparently required to do so by law? Because someone wrote a loophole into the moratorium.

The moratorium specifically barred funding any gain-of-function research that increased the pathogenicity of the flu, MERS or SARS viruses. But then a footnote on p.2 of the moratorium document states that “An exception from the research pause may be obtained if the head of the USG funding agency determines that the research is urgently necessary to protect the public health or national security.”

This seems to mean that either the director of the NIAID, Dr. Anthony Fauci, or the director of the NIH, Dr. Francis Collins, or maybe both, would have invoked the footnote in order to keep the money flowing to Dr. Shi’s gain-of-function research.

“Unfortunately, the NIAID Director and the NIH Director exploited this loophole to issue exemptions to projects subject to the Pause –preposterously asserting the exempted research was ‘urgently necessary to protect public health or national security’ — thereby nullifying the Pause,” Dr. Richard Ebright said in an interview with Independent Science News.

When the moratorium was ended in 2017 it didn’t just vanish but was replaced by a reporting system, the Potential Pandemic Pathogens Control and Oversight (P3CO) Framework, which required agencies to report for review any dangerous gain-of-function work they wished to fund.

According to Dr. Ebright, both Dr. Collins and Dr. Fauci “have declined to flag and forward proposals for risk-benefit review, thereby nullifying the P3CO Framework.”

In his view, the two officials, in dealing with the moratorium and the ensuing reporting system, “have systematically thwarted efforts by the White House, the Congress, scientists, and science policy specialists to regulate GoF [gain-of-function] research of concern.”

Possibly the two officials had to take into account matters not evident in the public record, such as issues of national security. Perhaps funding the Wuhan Institute of Virology, which is believed to have ties with Chinese military virologists, provided a window into Chinese biowarfare research. But whatever other considerations may have been involved, the bottom line is that the National Institutes of Health was supporting gain-of-function research, of a kind that could have generated the SARS2 virus, in an unsupervised foreign lab that was doing work in BSL2 biosafety conditions. The prudence of this decision can be questioned, whether or not SARS2 and the death of 3 million people was the result of it.

In Conclusion

If the case that SARS2 originated in a lab is so substantial, why isn’t this more widely known? As may now be obvious, there are many people who have reason not to talk about it. The list is led, of course, by the Chinese authorities. But virologists in the United States and Europe have no great interest in igniting a public debate about the gain-of-function experiments that their community has been pursuing for years.

Nor have other scientists stepped forward to raise the issue. Government research funds are distributed on the advice of committees of scientific experts drawn from universities. Anyone who rocks the boat by raising awkward political issues runs the risk that their grant will not be renewed and their research career will be ended. Maybe good behavior is rewarded with the many perks that slosh around the distribution system. And if you thought that Dr. Andersen and Dr. Daszak might have blotted their reputation for scientific objectivity after their partisan attacks on the lab escape scenario, look at the 2nd and 3rd names on this list of recipients of an $82 million grant announced by the National Institute of Allergy and Infectious Diseases in August 2020.

The US government shares a strange common interest with the Chinese authorities: neither is keen on drawing attention to the fact that Dr. Shi’s coronavirus work was funded by the US National Institutes of Health. One can imagine the behind-the-scenes conversation in which the Chinese government says “If this research was so dangerous, why did you fund it, and on our territory too?” To which the US side might reply, “Looks like it was you who let it escape. But do we really need to have this discussion in public?”

Dr. Fauci is a longtime public servant who served with integrity under President Trump and has resumed leadership in the Biden Administration in handling the Covid epidemic. Congress, no doubt understandably, may have little appetite for hauling him over the coals for the apparent lapse of judgment in funding gain-of-function research in Wuhan.

To these serried walls of silence must be added that of the mainstream media. To my knowledge, no major newspaper or television network has yet provided readers with an in-depth news story of the lab escape scenario, such as the one you have just read, although some have run brief editorials or opinion pieces. One might think that any plausible origin of a virus that has killed three million people would merit a serious investigation. Or that the wisdom of continuing gain-of-function research, regardless of the virus’s origin, would be worth some probing. Or that the funding of gain-of-function research by the NIH and NIAID during a moratorium on such research would bear investigation. What accounts for the media’s apparent lack of curiosity?

The virologists’ omertà is one reason. Science reporters, unlike political reporters, have little innate skepticism of their sources’ motives; most see their role largely as purveying the wisdom of scientists to the unwashed masses. So, when their sources won’t help, these journalists are at a loss.

Another reason, perhaps, is the migration of much of the media toward the left of the political spectrum. Because President Trump said the virus had escaped from a Wuhan lab, editors gave the idea little credence. They joined the virologists in regarding lab escape as a dismissible conspiracy theory. During the Trump Administration, they had no trouble in rejecting the position of the intelligence services that lab escape could not be ruled out. But when Avril Haines, President Biden’s director of National Intelligence, said the same thing, she too was largely ignored. This is not to argue that editors should have endorsed the lab escape scenario, merely that they should have explored the possibility fully and fairly.

People round the world who have been pretty much confined to their homes for the last year might like a better answer than their media are giving them. Perhaps one will emerge in time. After all, the more months pass without the natural emergence theory gaining a shred of supporting evidence, the less plausible it may seem. Perhaps the international community of virologists will come to be seen as a false and self-interested guide. The common-sense perception that a pandemic breaking out in Wuhan might have something to do with a Wuhan lab cooking up novel viruses of maximal danger in unsafe conditions could eventually displace the ideological insistence that whatever Trump said can’t be true.

And then let the reckoning begin.

Nicholas Wade

April 30,2021

Acknowledgements

The first person to take a serious look at the origins of the SARS2 virus was Yuri Deigin, a biotech entrepreneur in Russia and Canada. In a long and brilliant essay, he dissected the molecular biology of the SARS2 virus and raised, without endorsing, the possibility that it had been manipulated. The essay, published on April 22, 2020, provided a roadmap for anyone seeking to understand the virus’s origins. Deigin packed so much information and analysis into his essay that some have doubted it could be the work of a single individual and suggested some intelligence agency must have authored it. But the essay is written with greater lightness and humor than I suspect are ever found in CIA or KGB reports, and I see no reason to doubt that Dr. Deigin is its very capable sole author.

In Deigin’s wake have followed several other skeptics of the virologists’ orthodoxy. Nikolai Petrovsky calculated how tightly the SARS2 virus binds to the ACE2 receptors of various species and found to his surprise that it seemed optimized for the human receptor, leading him to infer the virus might have been generated in a laboratory. Alina Chan published a paper showing that SARS2 from its first appearance was very well adapted to human cells.

One of the very few establishment scientists to have questioned the virologists’ absolute rejection of lab escape is Richard Ebright, who has long warned against the dangers of gain-of-function research. Another is David A. Relman of Stanford University. “Even though strong opinions abound, none of these scenarios can be confidently ruled in or ruled out with currently available facts,” he wrote. Kudos too to Robert Redfield, former director of the Centers for Disease Control and Prevention, who told CNN on March 26, 2021 that the “most likely” cause of the epidemic was “from a laboratory,” because he doubted that a bat virus could become an extreme human pathogen overnight, without taking time to evolve, as seemed to be the case with SARS2.

Steven Quay, a physician-researcher, has applied statistical and bioinformatic tools to ingenious explorations of the virus’s origin, showing for instance how the hospitals receiving the early patients are clustered along the Wuhan №2 subway line which connects the Institute of Virology at one end with the international airport at the other, the perfect conveyor belt for distributing the virus from lab to globe.

In June 2020 Milton Leitenberg published an early survey of the evidence favoring lab escape from gain-of-function research at the Wuhan Institute of Virology.

Many others have contributed significant pieces of the puzzle. “Truth is the daughter,” said Francis Bacon, “not of authority but time.” The efforts of people such as those named above are what makes it so.

https://nicholaswade.medium.com/origin-of-covid-following-the-clues-6f03564c038

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HGNC 2021 Spring NewLetter

New HGNC search application is live!

Readers of the Winter newsletter will remember being asked to test the beta version of our improved search. Thanks so much to all who did this and provided us with feedback. On April 1st we switched over to this new search on genenames.org. We have been enjoying the improved search ever since and we hope you have too! We are always happy to receive your feedback, both positive and negative…
MANE transcripts now on genenames.org

You can now find MANE (Matched Annotation from NCBI and EMBL-EBI). Select transcripts on our Symbol Reports and in our REST service. The MANE project aims to provide a set of standard transcripts for human protein-coding genes annotated by both RefSeq and Havana-Ensembl, for which there has been agreement between annotators from both teams on the entire sequence, including 5’ UTR, coding region and 3’ UTR. Please read our recent guest blog post, ‘Transcripts are the MANE attraction’ by Jane Loveland of the Havana-Ensembl team to learn more. Here is an example from our MTOR Symbol Report showing a MANE Select transcript in the ‘Nucleotide Resources’ section:

Note that MANE transcripts have both RefSeq and Ensembl IDs, and these are versioned, i.e. the MTOR gene report shows both the RefSeq ID NM_004958.4 and the Ensembl ID ENST00000361445.9. These IDs link through to transcript pages in NCBI Gene and Ensembl, respectively.
All about HCOP

We are delighted to announce that we recently published a paper in Briefings in Bioinformatics ‘Updates to HCOP: the HGNC comparison of orthology predictions tool’ describing the current version of our HCOP tool (to see the full citation for this paper, please see the ‘Publications’ section of this newsletter).

The original version of HCOP (HGNC Comparison of Orthology Predictions) was created nearly 20 years ago and initially collated orthology calls between human and mouse from a number of orthology prediction resources, in order for the HGNC and the Mouse Genomic Nomenclature Committee to identify cases where gene nomenclature could be aligned between the two species. Two decades later, the current tool presents orthology predictions between human and the following 19 different species: chimp, rhesus macaque, mouse, rat, dog, cat, horse, cow, pig, opossum, platypus, chicken, anole lizard, xenopus, zebrafish, Caenorhabditis elegans, fruit fly, Saccharomyces cerevisiae and Schizosaccharomyces pombe using 14 separate orthology prediction resources (please see Table 1 in the new paper to view the full resource list). As many of our readers will know, we still use HCOP to align nomenclature; we now use the tool to auto-approve appropriate gene nomenclature for each VGNC full species gene set (chimp, rhesus macaque, dog, cat, cow, horse and pig). We have a software pipeline that searches the HCOP data to identify high confidence ortholog sets between human and each VGNC species, as predicted by Ensembl, NCBI Gene, OMA and PANTHER. These VGNC genes are then auto-assigned the same gene symbol as their human ortholog, provided the symbols pass rules devised by curators to ensure that the human nomenclature is suitable for transfer across species. Genes not identified in this pipeline are not given auto-approved symbols and need to be assigned nomenclature manually by a curator – a huge task which we are still working towards for each core VGNC species!

In addition to orthology calls, HCOP displays approved nomenclature from HGNC, VGNC, MGNC (mouse gene nomenclature from MGI), Rat Genome Database (RGD), Chicken Gene Nomenclature Consortium (CGNC), Xenbase, ZFIN, WormBase, Saccharomyces Genome Database (SGD) and PomBase.

One of the biggest strengths of HCOP is that it is updated daily, so the data are always as current as possible. For example, it includes the latest data from Ensembl, OMA and PANTHER, which have all released new ortholog sets in the last few weeks. Please read the full paper to learn more!
Updates to placeholder symbols

The HGNC continues to update placeholder symbols whenever new data becomes available. In the past few months we have updated the following genes based on discussions between an HGNC curator and researchers working on the gene:

C8orf37 -> CFAP418, cilia and flagella associated protein 418
FAM155A -> NALF1, NALCN channel auxiliary factor 1
FAM155B -> NALF2, NALCN channel auxiliary factor 2

The following genes have been renamed following updates to their annotation models, resulting in a change in locus type from protein coding to long non-coding RNA:

C17orf77 -> CD300LD-AS1, CD300LD antisense RNA 1
C9orf147 -> HSDL2-AS1, HSDL2 antisense RNA 1
C9orf106 -> LINC02913, long intergenic non-protein coding RNA 2913
C14orf177 -> LINC02914, long intergenic non-protein coding RNA 2914
C15orf54 -> LINC02915, long intergenic non-protein coding RNA 2915
C11orf72 -> NDUFV1-DT, NDUFV1 divergent transcript

New gene groups

Here are some examples of new gene groups that we have made within the last couple of months:

Methylcrotonyl-CoA carboxylase subunits (MCCC)
Transcription factor AP-2 family (TFAP2)
Tet methylcytosine dioxygenase family (TET)
Adducin family (ADD)
TNRC6 adaptor family (TNRC6)
PARN exonuclease family
TLDc domain containing (TLDC)

Gene Symbols in the News

Babies born with spinal muscular atrophy in the UK can now benefit from gene therapy with an active copy of the gene SMN1. This therapy has been heralded as the ‘most expensive’ drug treatment ever approved and has already been available in other countries, such as the USA. It requires just a single treatment early on in life.

In cancer-related news, the cell surface-expressed gene LRRN4CL has been identified as a biomarker for melanoma following a CRISPR activation screen. There is hope that a drug could be developed in the future to target the LRRN4CL protein in melanoma patients, particularly as it is a cell surface protein and therefore drugs could be extracellular.

Most humans carry a pseudogenised copy of the SIGLEC12 gene, but about 30% of people have a protein coding version. The protein version has been suggested to partially explain why humans have high rates of carcinoma compared to other great apes, as the protein appears to be involved in aberrant cell signalling and its expression has been associated with poor prognosis in colorectal cancer patients.

In COVID-19 news, variants in the following genes have been newly associated with an increased risk of contracting the disease: ERMP1, FCER1G and CA11. The same study corroborated previously-reported variants in the ABO and SLC6A20 genes. Additionally, the study identified variants in the IL10RB, IFNAR2 and OAS1 genes that are linked to patients suffering from a more severe form of the disease.

Finally, we bring you news about a dog gene! A study from Finland has identified the causal gene for nonsyndromic early-onset hereditary hearing loss in Rottweilers as LOXHD1. We have already approved this gene symbol for the dog gene in VGNC via the pipeline described in the HCOP section above. The human ortholog has also been associated with deafness.

https://blog.genenames.org/hgnc/2021/05/27/Spring_newsletter_2021

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What has happened to American education?

This description by a communist defector — is not to be taken lightly. This is very scary. ☹

North Korean defector says ‘even North Korea was not this crazy’ after attending Ivy League school
Yeonmi Park escaped the oppressive regime in 2007 at the age of 13

Teny Sahakian

By Teny Sahakian

You can Click on underlined title to listen to her description (in excellent English):
‘America’s future is as bleak as North Korea’ says defector after attending Columbia

Yeonmi Park was shocked by the oppressive culture within the university, reminding her of the country she fled.

As American educational institutions continue to be called into question, a North Korean defector fears the United States’ future “is as bleak as North Korea” after she attended one of the country’s most prestigious universities.

Yeonmi Park has experienced plenty of struggle and hardship, but she does not call herself a victim.

One of several hundred North Korean defectors settled in the United States, Park, 27, transferred to Columbia University from a South Korean university in 2016 and was deeply disturbed by what she found.

“I expected that I was paying this fortune, all this time and energy, to learn how to think. But they are forcing you to think the way they want you to think,” Park said in an interview with Fox News. “I realized, wow, this is insane. I thought America was different but I saw so many similarities to what I saw in North Korea that I started worrying.”

Those similarities include anti-Western sentiment, collective guilt and suffocating political correctness.

Yeonmi saw red flags immediately upon arriving at the school.

During orientation, she was scolded by a university staff member for admitting she enjoyed classic literature such as Jane Austen.

“I said ‘I love those books.’ I thought it was a good thing,” recalled Park.

“Then she said, ‘Did you know those writers had a colonial mindset? They were racists and bigots and are subconsciously brainwashing you.’”

It only got worse from there as Yeonmi realized that every one of her classes at the Ivy League school was infected with what she saw as anti-American propaganda, reminiscent to the sort she had grown up with.

“’American Bastard’ was one word for North Koreans” Park was taught growing up.

“The math problems would say ‘there are four American bastards, you kill two of them, how many American bastards are left to kill?'”

She was also shocked and confused by issues surrounding gender and language, with every class asking students to announce their preferred pronouns.

“English is my third language. I learned it as an adult. I sometimes still say ‘he’ or ‘she’ by mistake and now they are going to ask me to call them ‘they’? How the heck do I incorporate that into my sentences?”

“It was chaos,” said Yeonmi. “It felt like the regression in civilization.”

“Even North Korea is not this nuts,” she admitted. “North Korea was pretty crazy, but not this crazy.”

After getting into a number of arguments with professors and students, eventually Yeonmi “learned how to just shut up” in order to maintain a good GPA and graduate.

In North Korea, Yeonmi Park did not know of concepts like love or liberty.

“Because I have seen oppression, I know what it looks like,” said Yeonmi, who by the age of 13 had witnessed people drop dead of starvation right before her eyes.

“These kids keep saying how they’re oppressed, how much injustice they’ve experienced. They don’t know how hard it is to be free,” she admonished.

“I literally crossed through the middle of the Gobi Desert to be free. But what I did was nothing, so many people fought harder than me and didn’t make it.”

Park and her mother first fled the oppressive North Korean regime in 2007, when Yeonmi was 13 years old.

After crossing into China over the frozen Yalu River, they fell into the hands of human traffickers who sold them into slavery: Yeonmi for less than $300 and her mother for roughly $100.

With the help of Christian missionaries, the pair managed to flee to Mongolia, walking across the Gobi Desert to eventually find refuge in South Korea.

In 2015 she published her memoir “In Order to Live,” where she described what it took to survive in one of the world’s most brutal dictatorships and the harrowing journey to freedom.

“The people here are just dying to give their rights and power to the government. That is what scares me the most,” the human right activist said.

She accused American higher education institutions of stripping people’s ability to think critically.

“In North Korea I literally believed that my Dear Leader [Kim Jong-un] was starving,” she recalled. “He’s the fattest guy – how can anyone believe that? And then somebody showed me a photo and said ‘Look at him, he’s the fattest guy. Other people are all thin.’ And I was like, ‘Oh my God, why did I not notice that he was fat?’ Because I never learned how to think critically.”

“That is what is happening in America,” she continued. “People see things but they’ve just completely lost the ability to think critically.”

Witnessing the depth of American’s ignorance up close has made Yeonmi question everything about humanity.

“North Koreans, we don’t have Internet, we don’t have access to any of these great thinkers, we don’t know anything. But here, while having everything, people choose to be brainwashed. And they deny it.”

Having come to America with high hopes and expectations, Yeonmi expressed her disappointment.

“You guys have lost common sense to degree that I as a North Korean cannot even comprehend,” she said.

“Where are we going from here?” she wondered. “There’s no rule of law, no morality, nothing is good or bad anymore, it’s complete chaos.”

“I guess that’s what they want, to destroy every single thing and rebuild into a Communist paradise.”

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NORMAL SOLAR MINIMUM vs the MAUNDER MINIMUM

Right now, in the field of atmospheric science — there is an interesting debate going on. We’ve been in our “Solar Minimum” for more than a year now; the usual thing that happens next (in the normal 11-year solar cycle) is that sunspots (solar activity) return on the surface of the sun. However, some scientists are speculating that we might be entering a “Maunder Minimum” — which is a prolonged severely cold time on the planet.

Our last Maunder Minimum occurred between 1645 and 1715 AD (part of the Little Ice Age). We’ve had some evidence of “more extreme cold than usual” during this past year, which is a bit scary. We should know within the next ~2 years which way the sun is planning to go. ☹ 😊

https://canadafreepress.com/article/cold-more-to-come

Solar physicists at the ultra-warmist Potsdam Institute for Climate Impact are warning that Europe may be facing a ‘Mini-Ice Age’ due to a possible protracted solar minimum. For an institute that over the past 20 years has steadfastly insisted that man has been almost the sole factor in climate change over the past century and that the sun no longer plays a role, this is quite remarkable reports Pierre Gosselin.[1]

Little noticed by the mainstream media in their obsession with global warming is an exceptionally chilly 2020-2021 winter in the Northern Hemisphere and an unusually early start to the Southern Hemisphere winter. Low temperature and snowfall records are tumbling all over the globe. [2]

Presently, snow records have continued to be broken around the world

Whether the present frigid and snowy conditions in much of the world are merely a result of La Nina, or the start of a longer cooling trend, we won’t know for several years. Climate, after all, is a long-term average of the weather over an extended period of time, up to decades.

Nonetheless, there’s ample evidence that the current cold snap is not about to let up. At the same time the UK experienced its lowest average minimum temperature for April since 1922, and both Switzerland and Slovenia suffered record low temperatures for the month, bone-chilling cold struck Australia, New Zealand and even normally shivery Antarctica in the Southern Hemisphere. The 2021 sea ice extent around Antarctica is above or close to the 30 year average from 1981 to 2010. [2]

Flashback to 2014, when The New York Times, a charter member of the climate crisis cabal, ran a terrifying article that predicted ‘the end of snow.’ That dire forecast preceded 14 years earlier, in 2000 by the UK Independent, another charter member of the climate crisis cabal, which reported that “Snowfalls are a thing of the past. Children just aren’t going to know what snow is.” [3]

For those who claimed children would not know what snow looked like — global snowfall rates have risen 3% since 1980. [4]

Presently, snow records have continued to be broken around the world. Belgrade, the capital of Serbia, registered its all-time high snowfall for April, in record books dating back to1888; during April both Finland and Russia reported their heaviest snow in decades; and the UK, Spain and several countries in the Middle East saw rare spring snowfalls from March to May. On the other side of the globe, up to 22 cm (9 inches) of snow fell on southeastern Australia mountain peaks a full two months before the start of the 2021 ski season; and southern Africa was also blanketed in early season snow. [2]

Mass deaths of reindeer have been reported across the Yamal Peninsula, Russia

In early January 2018, a powerful blizzard caused severe disruptions along the East Coast of the United States, as snow and bitter cold weather set new records, with Erie, PA shattering its all-time snowfall record. The next month, Chicago tied a longstanding record with nine straight days of snow after chalking up its most frigid New Year’s Day in history. The Plains, Midwest, and Northeast were hit with record setting frigid temperatures, and the Deep South was gripped by sub-zero freezing that dumped snow, even in Florida. [3]

Mass deaths of reindeer have been reported across the Yamal Peninsula, Russia. The animals forage was locked under unusually thick ice this year. Members of a scientific expedition have called for new urgent ideas to rescue herding in the region due to an increase in periodic glaciation. [5]

Twenty-one people, including two of China’s top marathon athletes, died after freezing rain and high winds struck a 62-mile mountain race in northwestern China on Saturday May 22, 2021. The 62-mile mountain race in Gansu Province found athletes in shorts and T-shirts facing freezing rain, hail and high winds.

Hours into the event the weather suddenly deteriorated as the runners were climbing to 6,500 feet above sea level to the 12-mile mark. Runners dressed in shorts and T-shirts were suddenly facing freezing conditions, and rain turned to hail. [6]

One model has projected we are entering another ‘grand minimum,’ which will overtake the sun beginning in 2020 and will last through the 2050s, resulting in diminished magnetism, infrequent sunspots production, and less ultraviolet (UV) radiation reaching Earth. This all means we are facing a global cooling period that may span 31 to 43 years. The last grand minimum event produced the mini-ice age in the mid-17th century. Known as the Maunder Minimum, it occurred between 1645 and 1715, during a longer span of time when parts of the world became so cold that the period was called the Little Ice Age, which lasted from about 1300 to 1850 AD. [7]

References

1. Pierre Gosselin, “U-turn! Scientists at the PIK Potsdam Institute now warning of a mini ice age,” notrickszone.com, June 29, 2016
2. Ralph B. Alexander, “Is recent record cold just La Nina, or the onset of global cooling?”, scienceunderattack.com, May 17, 2021
3. John Eidson, “Al Gore, our melting planet and the blizzard of 2018,” Canada Free Press, May 16, 2021
4. P. Gosselin, “Surprising results: global snowfall rate increases 3% over the past 40 years,” notrickszone.com, May 5, 2021
5. “Unusually thick ice kills thousands of Russian reindeer,” principia- scientific.com, May 13, 2021
6. Alexandra Stevenson and Cao Li, “21 runners dead after extreme weather hits Chinese ultramarathon,” The New York Times, May 23, 2021
7. “Are we headed into another ice age?”, principia-scientific.com, May 3, 2021

Comment from an astrophysicist: My theory holds that reversals of the earth’s poles do not result from solar minima. Just the opposite. The earth’s negative pole is at the north axis because the earth orbits in a predominantly negative solar wind and rotates in the right direction to put the negative pole (south pole) of earth’s magnet at the north axis. We call it the north pole because it attracts the north pole of a compass.

Once every few hundred thousand years, the sun gets super-active. Then the more positively charges in the inner solar atmosphere come all the way out to the earth’s orbit. The positively charged region is has greater charge density because positive particles are 2000 times heavier than electrons. When that happens — the earth’s poles flip, because the rotation of the now-positively-charged earth puts the earth’s negative pole at the south axis.

However, instead of the earth getting hotter with a hotter sun, the opposite happens. Much more water is evaporated from the oceans via Compton Effect evaporation (different from thermal evaporation). Clouds rise higher and freezing occurs; ice falls and cools the lower atmosphere. The excess water precipitates as ice, rather than rain, and a new ice age builds rapidly. A very hot sun causes an ice age. Even on Venus the temperature in the upper atmosphere will freeze water. Earth is no different. When clouds rise to great heights, ice falls to the ground. Falling ice depletes the heat in the lower atmosphere.

Joseph Tomlinson, Physicist

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The decline of mathematics and creative science these past two decades

Attached is the 98-page report by the National Association of Scholars (NAS) — warning the U..S. that our current trend of encouraging mediocrity in science will have disastrous long-term consequences. In fact, it already has. Comparing scientific thought processes and creative science — in the 1950s, 60s, 70s and 80s — to what we’ve seen during the past two decades … I’ve often concluded to my close colleagues that this is nothing short of terrifying.
“Climbing Down: How the Next Generation Science Standards Diminish Scientific Literacy”

Clearly, this obsession with “diversity, equity, social justice, inclusivity, environmental justice, race-baiting, and gender” nonsense — is seriously destroying the true meaning and focus of the quantitative fields of mathematics and science.

If “education in the fields of math and science” is not corrected and turned around VERY quickly, this nation is headed toward disaster. Among all nations, U.S. students in math and science are already ranked below the top-20 countries, worldwide.

Below is pasted the Summary & Conclusions, and the Recommendation — from the attached 98-page report. I encourage everyone to read the entire report. This could be the most important email of my last 12-13 years of GEITP (2008-2021). ☹

DwN

SUMMARY AND RECOMMENDATIONS

The Next-Generation Science Standards for K-12 teaching (NGSS) are the latest iteration in top-down, untested, and disas­trous education reform — touted by progressive activists, bureau­crats, and philanthropists. The botched rollout of the Common Core State Standards generally illustrates the bad track record of such imposed reforms [135]. National Assessment of Educational Progress (NAEP) math scores show the same percentage of 8th-graders scoring profi­cient or better in 2017, as the year before their imple­mentation in 2010. This suggests that the similarly unvetted CCSS mathematics curriculum’s negative effects — entirely undid what should have been a decade of improvement in mathematics education [136]. America’s experience with failed education reforms — suggests it should expect little from the NGSS standards.

135 Peter Wood, ed., Drilling through the Core: Why Common Core is Bad for American Education (Pioneer Institute, 2015).

136 National Center for Education Statistics, NAEP Mathematics Report Card, U.S. Department of Education, https://www.nationsreportcard.gov/math_2017/nation/scores?grade=8.

The NGSS actually do possess some good features. The addition of engineering standards — which introduces students to another field of science — is valuable. While we raise concerns about project-based ed­ucation standards, we too recognize that inquiry-based learning can be beneficial, if used as a pedagogical approach in moderation. Raising questions and encouraging curiosity is good. It appeals to the natural inclination of children to question everything in the world around them, and the naturally curious child may take a keen interest in science as a possible career pursuit. Children enjoy the process of discovery. In fact, some of the most valuable scientific discoveries are the result of curi­osity and the inclination to ask questions. It is the imbalance of this ap­proach that raises concerns, since overreliance on inquiry-based proj­ects may not contribute to long-term memory of what is learned. After all, we’re told that students can “just Google it.”

The poor track record of education standards and outcomes— at the hands of progressive education reformers — should, of course, give us all pause, when we consider the merit of any new set of education stan­dards. For decades, America has put its trust in education bureaucrats, not to mention well-meaning, but misguided, philanthropists like Bill Gates, to decide what is best for American schoolchildren. This has left us with unfulfilled promises of better educational outcomes, frustra­tion by parents and their children, with a de facto national curriculum in the form of CCSS, and consequent flat NAEP score growth since its implementation.

Adopting the new science standards nationwide may offer nothing better. It should come as no surprise that, given the pre­vious failures of constructivist math (“the new math”) in the mid-20th century, America has not fared any better with the constructivist math­ematics of CCSS. The assurances of superior education — resulting from math standards that were never piloted or vetted prior to implemen­tation — were simply hollow. How can the NGSS, without pilot testing or vetting, promise any better? We will not know the outcome of the NGSS until a generation of school children has completed its K-12 education. The potential cost of this educational gamble is much too high. The NGSS are an uncontrolled experiment in how to ruin science education in the name of reform.

Students should be able to engage in thoughtful analysis, sort through evidence, systematically analyze it, and then build arguments based on findings. Moreover, science education should be about discov­ering truth, not just assembling and regurgitating facts. Unfortunately, the NGSS abandon both. The NGSS severely neglect content instruction, politicize much of the content that remains, largely in the service of a diversity and equity nonsensical political agenda, and abandon instruction of the sci­entific method. The NGSS will leave students unable to use the scientific method as a way to approach the truth. Furthermore, content knowl­edge is replaced with group projects, and (it appears, anyway) consensus answers to scientific questions, rather than verifiable evidence, are ac­cepted without challenge. This is not real science, and it will most likely lead to more widespread issues of politicized groupthink and irrepro­ducible science — as described by David Randall and Christopher Welser in their National Association of Scholars (NAS) report, The Irreproducibility Crisis of Modern Science [137].

137 Randall and Welser, The Irreproducibility Crisis of Modern Science.

The NGSS fail to prepare students for undergraduate science coursework and to provide the basic scientific competency that all Americans should have when they graduate from high school, regard­less of whether they proceed to an interdisciplinary Science, Technology, Engineeering & Mathematics (STEM) career. NGSS proponents pre­sume that college professors will compensate for the resulting deficits in K-12 science education. If they do, this will reduce undergraduate science courses to remedial classes. If they don’t, a large number of un­prepared college students, ill-served by the NGSS, will fail out of intro­ductory science classes. Either way, the NGSS will do terrible damage both to college students and to colleges.

The most fundamental flaw of the NGSS is the missing essential sci­ence content. The “Framework for K-12 Science Education”, which was the foundation for the NGSS, summarizes the intended goal of the standards:

The overarching goal of our framework for K-12 science education is to ensure that by the end of the 12th grade, all students have some appreciation of the beauty and wonder of science; possess sufficient knowledge of science and en­gineering to engage in public discussions on related issues; are careful consumers of scientific and technological information related to their everyday lives; are able to continue to learn about science outside school; and have the skills to enter careers of their choice, including (but not limit­ed to) careers in science, engineering, and technology [138]. [Underlining for emphasis added]

138 Framework, p. 1.

This “overarching goal” makes it quite clear that the NGSS func­tion as a set of what Ze’ev Wurman (former senior policy advisor at the U.S. Department of Education and outspoken critic of the NGSS) so aptly calls science appreciation standards rather than rigorous education­al standards [139].

139 Ze’ev Wurman, “Education to Raise Technology Consumers Instead of Technology Creators,” Monolithic 3D, August 4, 2011, http://www.monolithic3d.com/blog/education-to-raise-technology-consumers-in­stead-of-technology-creators.

State education departments and boards of education should avoid adopting the NGSS — and, if they already have adopted it, immediately replace it with superior standards. The price of continuing with this ed­ucational folly is far too high.

The content errors, numerous omissions, imbalance in content, feasibility concerns with the implementation of integrated standards, obvious political dogma, and major shift in pedagogy — should all give deci­sion-makers pause. To adopt an entirely new set of standards — without any evidence of success through pilot testing — is a dangerous educational experiment that is a disservice to all high school students, regardless of whether they plan to pursue STEM careers, but especially so for those who do.

Blanket adoption of the NGSS without careful comparison to oth­er existing science standards — those rated higher than the NGSS by Fordham — is not beneficial. This should never happen, although many states have done so. It is time to engage in careful appraisal and ask questions about the science, or lack thereof, being taught in our schools.

We offer the following recommendations to States and school districts:

1. If a State has not adopted new science standards and wishes to update and improve its existing standards, it should use the science standards graded as ‘A’ by the Fordham Review as a template. It should compare them with and find any helpful additions from the NGSS, such as the engineering standards that will introduce students to a new discipline, but with the understanding that students will likely not have the prerequisite mathematics preparation for true engi­neering standards in the upper grades.

2. States that have already adopted the NGSS should compare them with the other State science standards graded as ‘A’ by Fordham and make changes, additions, and deletions as needed.

3. Chemistry and physics standards should be supplemented with previous existing standards to provide solid, complete high-school level courses for students who plan to pursue STEM in college.

4. States should strongly consider replacing CCSS mathemat­ics with higher-level standards, such as the excellent and highly rated pre-CCSS California mathematics standards, to allow students to begin algebra in 8th rather than 9th grade. This will better prepare STEM-bound students as they enter college-level work.

5. States which choose to incorporate engineering in K-12 science education should adopt rigorous standards that require substantial amounts of mathematics.

6. States should allow, encourage, or require students to begin algebra in 8th grade rather than 9th, so that they may be prepared for rigorous high-school science classes.

7. School districts using the NGSS should encourage science teachers to use pedagogies that emphasize knowledge reten­tion rather than project learning.

8. States should ensure that science instruction focuses its case studies on individual effort, scientific dissent, and para­digm shifts, selected from the most important episodes in the history of science, without reference to the race or gender of the scientists in question — but rather with preference for outstanding representatives of the American scientific and engineering tradition, i.e., Benjamin Franklin, Samuel Morse, Alexander Graham Bell, Othniel Charles Marsh, Josiah Willard Gibbs, Thomas Edison, Edwin Armstrong, Edwin Hubble, Thomas Hunt Morgan, Claude Shannon, William Shockley, Linus Pauling, Richard Feynman, Robert Jarvik, and James Watson.

9. States should remove all political commitments from science education, especially those to diversity, environmentalism, and activism.

10. States should ensure that science standards steer students toward the full range of scientific careers and highlight how science and engineering can and should serve the American national interest.

11. States should ensure that science standards emphasize that devotion to science and engineering is its own reward, with­out reference to any “societal need,” and that all research and design can and should aim, above all, for truth and beauty.

CONCLUSION

The warning issued in 1983 by Dr. Glenn Seaborg and his colleagues in the opening paragraphs of A Nation at Risk could have been a critique of the NGSS:

…the educational foundations of our society are presently being eroded by a rising tide of mediocrity that threatens our very future as a Nation and a people…

If an unfriendly foreign power had attempted to impose on America the mediocre educational performance that exists today, we might well have viewed it as an act of war. As it stands, we have allowed this to happen to ourselves … We have, in effect, been committing an act of unthinking, uni­lateral educational disarmament [140].

140 A Nation at Risk, p. 7.

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Role of Environmental Genetics in Preventive Medicine. An Interview with Daniel W. Nebert

The medical students of Yale University first published The Yale Journal of Biology and Medicine (YJBM), Volume 1, No. 1, in October 1928. Since then, YJBM has been the only internationally recognized medical journal edited and published by students.

In its first year of publication, YJBM presented papers on infectious diseases, embryology, nutritional deficiency diseases, community health, trauma, medical history, and cancer. Today, YJBM continues to cover the breadth of medical science, including the publication of proceedings of international symposia and festschrifts honoring notable Yale medical faculty.

Milton C. Winternitz, dean of the Yale School of Medicine from 1920-1935, founded YJBM for the educational and professional betterment of his students. The son of a Czechoslovakian Jewish immigrant doctor, Winternitz was a Baltimore native who obtained his MD degree from Johns Hopkins in 1907.

Winternitz’s educational mission continues — as student members of the Board of Editors participate directly in the peer review process. Every manuscript reviewed at YJBM is analyzed and scrutinized by a faculty-student team. The faculty is recruited from across the University, and other institutions as needed, on a case-by-case basis to provide an opportunity to work with the best available expert in the field of the manuscript under review. Hypotheses, methods, results, and conclusions are reviewed, questioned, and examined for validity and logical soundness. Each student reports the results of this joint review to the Board of Editors, and thus gains experience in the scientific process from peer review, while maturing into a more confident physician-scientist through his or her interaction with distinguished faculty.

YJBM is, and has been, an internationally distributed journal with a long history of landmark articles. Our contributors also feature a notable list of philosophers, statesmen, scientists, and physicians, including Ernst Cassirer, Harvey Cushing, René Dubos, Edward Kennedy, Donald Seldin, and Jack Strominger. Our Editorial Board consists of students and faculty members from the Yale School of Medicine and the Yale University Graduate School of Arts & Sciences.

YJBM has been divided into a number of sections over time — so as to cover a wide range of functions and topics — which include original articles, medical reviews, scientific reviews, book and software reviews, case reports, and a section for focus on Yale medicine. Yale M.D. thesis abstracts continue to be published annually, documenting student research in the medical literature. Each year, an average of 15 students joins the Board of Editors. A permanent board of medical faculty joins the students in an advisory capacity. The Board meets monthly throughout the year to consider manuscript reviews and other matters of academic publishing.

YJBM has been indexed at the National Library of Medicine (NLM) since 1949 and has been available on PubMed (and its precursors) for 56 years. YJBM is currently an open-access publication through PubMed Central. Yours truly was honored by an invitation last fall to be interviewed by a graduate student, Brian Thompson. Just published in the first quarter issue of 2021, the interview is attached, for your bedtime reading pleasure. 😊

DwN

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