Epigenetic Regulator CoREST Controls Social Behavior in Brain of Ants

Eusocial insects (showing an advanced level of social organization, in which a single female produces offspring, and nonreproductive individuals cooperate in caring for the young) are among the most successful taxa (taxonomic group such as a species, family, or class) on Earth, because of their ability to segregate tasks among different (often morphologically or behaviorally distinct) individuals within a colony. Because of this extreme phenotypic and behavioral plasticity, ants have emerged as experimental models for asking questions about complex social behavior and investigating epigenetic mechanisms that program expression of the same genome into disparate individual phenotypes. An important example of this “division of labor” involves differentiation of individuals into sterile (worker) and reproductive (queen) physiological castes. Another striking manifestation — in many eusocial insect species — is the allocation of distinct colony roles among worker groups.

Often summarized in these GEITP pages: Multifactorial traits in animals involve genetic (DNA sequence) differences, epigenetic factors, environmental effects, endogenous influences, and contributions from the microbiome. Epigenetic alterations (chromosomal manifestations that are not caused by DNA sequence differences) are associated with differential morphology and behavior among ant castes — involving distinct patterns of chromatin modifications including histone posttranslational modifications (hPTMs) and possibly DNA methylation. hPTMs result in a diverse set of epigenetic signals that typically occur on histone-protein N-terminal amino acid tails and alter transcription, via several mechanisms.

Another emerging mediator of caste division of labor — in multiple eusocial insects — is the metamorphosis-associated hormones, juvenile hormone (JH) and ecdysone (20E). These small-molecule hormones play important roles in both the developmental and behavioral division of labor. The Florida carpenter ant, Camponotus floridanus, has two distinct worker castes: Major and Minor workers. These worker castes display diverse morphology and behavior: the smaller Minor workers perform foraging and nursing of brood; the larger Major workers defend the nest as soldiers and very rarely forage.

Authors [see attached article] discovered that innate chromatin regulation via the corepressor for element-1-silencing transcription (CoREST) factor mediates the natural programming of foraging behavior in Minor workers; moreover, reprogramming of Major workers to forage uses this same CoREST epigenetic pathway. Authors found that CoREST is upregulated, upon reprogramming,

and is required for the epigenetic switch to foraging. CoREST was shown to repress expression of enzymes that degrade JH, a hormone that is elevated upon reprogramming. High CoREST levels, low JH-degrader expression, and high JH levels are seen in natural Minor workers, revealing parallel mechanisms of natural vs reprogrammed foraging. These data demonstrate chromatin regulation via CoREST is a central process to programming of ant social behavior, and these results have potential implications for other manifestations of behavioral epigenetics. 😊

DwN

Mol Cell Jan 2020; 77: 1-14

Posted in Center for Environmental Genetics | Comments Off on Epigenetic Regulator CoREST Controls Social Behavior in Brain of Ants

Effect of tolerance on evolution of antibiotic resistance — under drug-combination therapy

Antimicrobial resistance clearly fits our theme (gene-environment interactions) in these GEITP pages. The environmental signal (to the bacterium) is a drug that threatens its survival; genes in the genome (along with epigenetic effects) respond to this threat by inducing a set of biochemical pathways that will neutralize the drug’s mechanism of action. Prior to development of antimicrobial

resistance, bacteria frequently develop enhanced antimicrobial tolerance (i.e. diminished response to a drug — which occurs when the drug is used repeatedly, and the genome ‘adapts’ to continued presence of the drug). [Antimicrobial resistance is the ability of a microbe to grow in an inhibitory concentration of a drug (usually an antibiotic), whereas drug tolerance denotes a reduced rate of antimicrobial killing.]

Combinations of antibiotic are often used to improve efficacy, as well as to prevent emergence of antibiotic resistance. However, it remains unclear if antibiotic combinations prevent the emergence of tolerance. Authors [see attached article & editorial] studied

sequential Staphylococcus aureus isolates — from patients treated with daptomycin (a cyclic lipopeptide that disrupts bacterial cell membrane function, causing rapid depolarization and loss of membrane potential, leading to inhibition of protein, DNA, and RNA synthesis, and microbial death) plus rifampin (inhibitor of bacterial DNA-dependent RNA polymerase, which blocks the polymerase subunit, deep within the DNA/RNA channel, facilitating direct inhibition of bacterial elongating RNA).

Evolution experiments have shown that drug tolerance evolves quickly under cyclic antibiotic treatments, and subsequently promotes evolution of antibiotic resistance. In contrast to drug resistance mutations — that decrease effectiveness of the antibiotic and elevate the minimum inhibitory concentration (MIC), tolerance mutations increase the minimum time to kill the population — without altering the MIC. To understand whether the evolutionary trajectory of evolving tolerance — and thereafter resistance — occurs in patients, authors [see attached article] followed sequential isolates of life-threatening methicillin-resistant Staphylococcus aureus (MRSA) blood infections, in which bacterial infection persisted for at least 2 weeks, despite antibiotic treatment.

Authors detected rapid emergence of “tolerance” mutations, followed by the emergence of resistance — despite the combination treatment. This study, on clinical strains in vitro, revealed a new way by which (initial) tolerance promotes evolution of resistance under combination treatments. Further experiments under different antibiotic classes (see attached article] revealed the generality of the effect. Authors concluded that tolerance is an important factor to consider — in designing combination treatments that

prevent the evolution of drug resistance. Although this combination of antibiotics delayed emergence of tolerant populations, once tolerance was established, benefits of combination therapy in preventing resistance were lost. ☹

DwN

Posted in Center for Environmental Genetics | Comments Off on Effect of tolerance on evolution of antibiotic resistance — under drug-combination therapy

Chinese Scientist Who Gene-Edited Babies Is Sent to Prison

This article pasted below (Wall Street Journal, Dec 30th) is a follow-up on a GEITP news article we shared last April — on the Chinese scientist who genetically-engineered twin embryos in utero (via CRISPR/Cas9 technology) so that the twin girls might be resistant to the human immunodeficiency virus (HIV) and subsequent acquired immunodeficiency syndrome (AIDS), if exposed later in life.

Besides the world medical community’s concerns about the bioethics of such an experiment (without going through a medical review board and proper legal channels), Dr. He (a PhD physicist with no clinical expertise) has been charged with “illegally practicing medicine” and, along with two accomplices, has been sentenced to 3 years in jail. For anyone who cares to ‘freshen up’ his knowledge on this news, the April 2019 article from GEITP [and attached pdf file] is pasted below this WSJ article. 😊

DwN

By Philip Wen

Dec. 30, 2019 8:18 am ET

BEIJING—The scientist who created the world’s first known genetically modified babies, stunning the global scientific community, has been sentenced by a Chinese court to three years in prison, state media reported.

He Jiankui said in November last year he had engineered twin girls—offspring of a healthy mother and an HIV-positive father—to be resistant to HIV, the virus that causes AIDS, using a nascent gene-editing technology called CRISPR/Cas9.

China was able to race ahead of the U.S. on testing gene-editing technology, because it had few regulatory hurdles to human trials, while the U.S. has stringent rules.

But Dr. He’s revelation drew immediate condemnation from bioethicists and fellow scientists in China and beyond, including the inventors of the gene-editing technology. Chinese authorities said in January they were investigating Dr. He, and he was fired from his post as an associate professor at Southern University of Science and Technology, based in the southern city of Shenzhen.

On Monday, a Shenzhen court convicted Dr. He and two accomplices on charges of illegally practicing medicine related to carrying out human-embryo gene-editing intended for reproduction, the official Xinhua News Agency reported.

The court said Dr. He hoped to profit by commercializing the technology and that he forged documents and concealed the true nature of the procedures from both the patients he recruited and doctors who performed them, according to Xinhua. The report said all three defendants pleaded guilty.

“In order to pursue fame and profit, they deliberately violated the relevant national regulations, and crossed the bottom lines of scientific and medical ethics,” the court said, according to the report.

Dr. He also received a lifetime ban from working in the field of reproductive life sciences and from applying for related research grants, Xinhua said, citing local health and science authorities.

Dr. He couldn’t be reached for comment, and the identity of his lawyer isn’t known. A former spokesman for Dr. He didn’t immediately respond to a request for comment.

Editing the genes of embryos is considered more contentious than editing those of terminally ill patients because any changes would pass on to future generations. Unintended consequences might not surface for several years, meaning a tiny blip could have far-reaching effects.

In what turned out to be one of his last public appearances in November last year, the Chinese scientist sprang another surprise at a scientific conference in Hong Kong, announcing a second woman was pregnant with a gene-edited baby.

Monday’s Xinhua report confirmed the birth of a third gene-edited baby from a second pregnancy but provided no other details. Previous state-media reports had said the newborn twins and people involved in the second pregnancy would be monitored by government health departments.

Dr. He, the son of rice farmers, graduated with a physics undergraduate degree in China and got a doctorate from Rice University, before switching to studying biology.

As earlier reported by The Wall Street Journal, people who know Dr. He have said he wanted to make history and address what he saw as an injustice in China against HIV-positive people, who are barred from getting fertility treatments. They said Dr. He had expected plaudits from Beijing for helping in its goal of making China a force in genetic science.

In much of the Western world, it is illegal to implant a genetically modified human embryo. The U.S. forbids the Food and Drug Administration, whose signoff is needed for such an experiment, from considering it. China doesn’t have a law, and although a 2003 guideline prohibited the genetic manipulation of human embryos, it didn’t outline penalties. In February, China’s National Health Commission drafted new rules governing “high-risk” biotechnology, including gene-editing, that would introduce criminal charges and lifetime research bans if breached, but they have yet to come into effect.

—Fanfan Wang and Preetika Rana contributed to this article.

From: Nebert, Daniel (nebertdw)
Sent: Monday, April 1, 2019 1:19 PM
Subject: The bioethical dilemmas surrounding “the Creation of CRISPR Babies”

These GEITP pages feel “obliged” to help make everyone aware of this recent bioethical dilemma, i.e. for everyone to ponder (if you so wish). The topic [see attached editorial] is “the Creation of CRISPR Babies” — meaning that it is now <> to remove or insert a human allele (one of the two copies of a gene in the developing very-early embryo), just as has already been done successfully in mice for the past 5+ years. A Chinese scientist (biophysicist He Jiankui) reported 3-4 months ago the birth of twin girls with edited genomes (at least, he says that the gene has been altered in these babies); this announcement has created a firestorm in the scientific and ethical communities. By engineering mutations into human embryos (which were then used to produce babies), Dr, He has leaped recklessly into an era of controversy.

Should scientists be able to “revise” the gene pool of future generations — by altering the human germ line? Dr. He has also ignored established norms for safety and human protections along the way. There is still no definitive evidence that this biophysicist actually has succeeded in modifying the girls’ genes — or those of a third child expected to be born later this year. However, the experiments have attracted so much attention that the incident could alter this type of obstetrical research for years to come. Chinese authorities are still investigating Dr. He, and US universities are asking questions of some of the scientists with whom Dr. He had consulted before proceeding recklessly ahead, on his own.

Meanwhile, there are calls for an international moratorium on related experiments — which could affect basic molecular biology research for a long time. This news has motivated some scientists to encourage further discussion “sooner, than later”, in favor of genome editing. Some are concerned about how public perception might now affect the future of the field. The attached article is worth reading, for those who might be interested.

DwN

Nature 28 Feb 2o19; 566: 440-442

Posted in Center for Environmental Genetics | Comments Off on Chinese Scientist Who Gene-Edited Babies Is Sent to Prison

Recurrent functional misinterpretation of RNA-Seq data caused by sample-specific gene length bias

These days, researchers can easiy analyze profiles of entire tissue, or even one-cell, transcriptomes (sum total of all messenger RNA molecules expressed from all genes in the sample). This used to be carried out by expression microarrays, but now RNA-sequencing (RNA-Seq) is a method that has transformed biological research over the last decade — from a formidable task to one that is readily accessible to most small laboratories. Consequently, RNA-Seq is one of the most widely used techniques in biological and medical research and is routinely applied for multiple goals — including elucidation of key transcriptional networks that drive different biological processes, and identification of diagnostic and prognostic expression signatures for many diseases, to monitoring the effects of a drug or environmental toxicant on individual tissues or cell-types.

Data normalization is critical in RNA-Seq studies, allowing for accurate estimation and detection of differential expression. The aim of normalization — is to remove any artifactual effects that occur in the data (so as to ensure that technical bias has minimal impact on the results). Numerous normalization methods are now standardized for RNA-Seq data — including reads per kilobase of transcript length per million reads (RPKM), edgeR’s Trimmed Mean of M values (TMM), DESeq’s relative log expression (RLE), and upper-quartile (UQ) normalization.

A well-known inherent technical effect in RNA-Seq experiments relates to gene length and stems from the fact that in standard RNA-seq protocols, RNA (or cDNA) molecules are fragmented prior to sequencing — in such a way that longer transcripts are sheared into more fragments than shorter ones are. Therefore, the number of reads for a given transcript is proportional not only to its expression level but also to its length. Thus, RPKM divides gene counts by gene length (in addition to library size), aiming to adjust expression estimates for this length effect. A well-known consequence — [of the fact that longer genes tend to get more counts than equally expressed shorter genes] — is over-representation of long genes among the ones that pass statistical tests for differential expression (termed “length bias”), because of their increased statistical power.

This stochastic sample-specific effect is not corrected by common normalization methods. Authors [see attached article] show that this bias causes recurrent false-positive calls (i.e. calling something significant when it actually is not) by gene-set enrichment analysis (GSEA) methods, thereby leading to frequent misinterpretation of data. Gene sets characterized by markedly short genes (e.g. ribosomal protein genes) or long genes (e.g. extracellular matrix genes) are particularly prone to such false calls. This sample-specific length bias is effectively removed by the conditional quantile normalization (cqn) and EDASeq methods, which allow integration of gene length as a sample-specific covariate.

Consequently, authors [see attached article] show that, using these normalization methods, their studies led to substantial reduction in GSEA false results while retaining true ones. Further, authors found that application of GSEA tests that take into account gene–gene correlations attenuates false-positive rates caused by gene length bias, but statistical power is decreased, as well. These results [a] emphasize the inspection and correction of sample-specific length biases as default steps in RNA-Seq analysis pipelines and [b] reiterate the need to account for intergene correlations when performing gene-set enrichment tests to lessen false interpretation of transcriptomic data.

DwN
COMMENT:
This ongoing discussion needs one more opinion — from someone knowledgeable and working “in the trenches” — which should now bring closure to this topic. 😉

DwN

PLoS Biol Nov 2019; 17: e3000481

Posted in Center for Environmental Genetics | Comments Off on Recurrent functional misinterpretation of RNA-Seq data caused by sample-specific gene length bias

‘Cancel Culture’ Comes to Science

These GEITP pages continue to discuss the various aspects of fraud and corruption in science. Pasted below a Wall Street Journal article written by the President of the National Association of Scholars. He describes an incredible story about simply trying to organize a meeting of Scholars next month — with the goal of discussing/looking for solutions — to the problems of fake science, faulty science, the irreproducibility in science, and incomplete studies that still get published as “science.” And others, by way of social media, are determined to stop the workshop from ever occurring…!!

This excessive politicization of science has become incredible during these last few years. Somehow it must be addressed and turned around; otherwise,”old-fashioned science, based on The Scientific Method” will be lost forever. At least in the (politically correct) Western World… ☹

DwN

‘Cancel Culture’ Comes to Science
A scholar with an agenda targets as ‘dangerous’ – our conference on filtering out faulty research.

By Peter W. Wood

Jan. 12, 2020 5:22 pm ET

An unhappy side-effect of the digital age is “cancel culture.” Anyone with an attitude of moral superiority and a Twitter account can try to shut down an event where opinions he dislikes are likely to be spoken. For several years, the National Association of Scholars has criticized this infantile form of protest, which undermines free expression of ideas and legitimate debate. Now the cancel caravan has arrived at our door.

We are holding a conference — co-sponsored by the Independent Institute in Oakland, Calif., in early February. It is intended to be an exchange among scholars on the problem of “irreproducibility” in the sciences — i.e. fake science, or failed science, or something-is-missing science. It’s a big problem these days, but there’s no agreement on what to do about it. Our goal is to bring together experts who have diverse, and often conflicting, views — to see if they can come to some agreement about how to improve the situation. The conference is titled Fixing Science: Practical Solutions for the Irreproducibility Crisis.

But one scientist, armed with a keyboard and contempt for contrary opinions, has set out to cancel our conference. Leonid Teytelman has busied himself — writing to the speakers at the event to warn them to stay away. And he has found fellow censors who agree “the conference is problematic.” Our critic calls us “clever and dangerous.”

How so? Once a Twitterstorm starts, the reasons multiply. Our list of speakers includes no women. (All declined our invitations.) Our initials share three letters with the National Academies of Science, Engineering, and Medicine, or Nasem, therefore we are “deceptive.” Wikipedia describes us as a “conservative organization.” We are also accused of “climate denialism,” and of having invited some climate-change skeptics to speak.

The truth is that we are a traditionalist group of scholars who hold to a rigorous standard of open-mindedness on controversial issues in the sciences. We welcome critiques from anyone who agrees to play by the rules of rational argument, openness and scrupulous use of evidence. That’s clever, I suppose, but dangerous only to those who balk at giving the “other side” a voice. Our Twittering critic sees our conference as a sneaky way to legitimate views that he regards as akin to blasphemy — which is ironic for a man accusing us of politicizing science.

So far, the conferees have held fast. Some of the responses are inspiring. One scientist wrote: “The science fields badly need whatever we can accomplish at this conference in the way of understanding and solving the HUGE problem of irreproducibility.” Another batted away the critic by explaining: “If conservatism means antipathy to post-modernism, identity politics, political orthodoxies, and assaults on Enlightenment values and the Rule of Law, then count me in.”

We may lose one or two speakers who are unwilling to defy the mob. We can bear that. The real story here is the degree to which intellectual intolerance and political dogmatism have found a home in the natural sciences. Mr. Teytelman — who holds a doctorate in computational and experimental biology and who works in the area of replication — is someone who does worthy science and deserves to be taken seriously on matters within his competence. But he becomes unhinged at the thought of “conservatives” or “climate skeptics” getting a seat at the table. And he is far from alone.

Cancel culture in various forms is taking root in American science and elsewhere. Last July, Francis Collins, director of the National Institutes of Health, announced that he would decline invitations to speak on panels at scientific conferences where women are not among the speakers. That idea has spread rapidly, and several organizations have begun to penalize conferences that don’t meet a quota of women. The Third International Brain Stimulation Conference held in Vancouver last February took steps to find additional female neuroscientists, so that six of its 20 featured talks were by women. A software conference scheduled for October in Dresden was canceled for failure to attract female speakers.

These may sound like small matters, but they are the drawing board for how science is willingly subjecting itself to the yoke of political orthodoxy. The gender, or race, of scientists has no bearing on the quality of their work. What does have bearing is the openness of science to vigorous intellectual dispute.

Our conference in Oakland — the Twitterstorm notwithstanding — deals with the difficulty the sciences have in recognizing and filtering out faulty research. The effort to cancel it demonstrates the timeliness of the topic. We are under attack by those who would like to maintain groupthink by demonizing dissent, and go still further by compromising science in favor of identity politics.

Mr. Wood is president of the National Association of Scholars.

Posted in Center for Environmental Genetics | Comments Off on ‘Cancel Culture’ Comes to Science

How should we define a “predatory journal”… ????

Below is more correspondence, plus a “confession of one who was recently duped.” For any “journal” (that has been launched since ~2010), one should check its credentials on multiple internet sites (I’ve seen sites in which comments of those who have been duped can register their complaints — much like complaining online about a bad restaurant or poor-quality vacuum cleaner). Many predatory journals also post “fake impact factors” In addition, check the internet address for the “journal”; e.g. if it is @peertechz.us @ptechzoa.net @gmail.com @aol.com @yahoo.com, this is a dead giveaway! You can google an email address, e.g. on google I found:

Flaky Academic Journals: Peertechz Journals

flakyj.blogspot.com › 2017/01 › peertechz-journals

Jan 22, 2017 – Peertechz’s “vision is … to promote qualitative research publications for Science … with an un-restricted access.” The “about us” page explains …

I do believe there MUST soon be an international committee set up, and why not base it in Geneva?

The World Health Organization (WHO) is a specialized agency of the United Nations that is concerned with international public health. It was established on 7 April 1948, and is headquartered in Geneva, Switzerland. The WHO is a member of the United Nations Development Group …

And then each “questionable journal” (that has been established, since, say 2010?) must expect a SITE VISIT from a qualified scientist on this W.H.O. Committee, to interview the publisher and the chief editor. The Inspector must also be allowed to peruse “all reviewed manuscripts submitted (at least) during the previous 2 years”, and be allowed to see the “journal’s” records of how many accepted vs how many rejected (and accepted or rejected … on what grounds).

To me, the scariest part, these days — is that the LINE between “scientifically sound” and “scientifically dubious” has become extremely VAGUE; 5-10 years ago, this line was not nearly so ambiguous… Another factor I look for is the volume number. These days, a predatory journal (that began in 2012, with two “fake volumes” per year) can be “up to volume no. 16”. Find out when the journal began. And where. And why. And with what publishing company.

How can such a Scientific Institute of Integrity be set up? As with most things, of course “this is easier said than done.” 😊

FROM EARLIER
Over the past decade, these GEITP pages have often discussed the problems with “online open-access predatory journals,” which have increased from a few in ~2008 to more than 20,000 today. Many of us receive several hundred emails per week, requesting that we “submit a manuscript within the next 1-2 weeks, it can be one page or 30 pages long, we just need one more paper to satisfy our quota for the current issue.” Many of us also receive dozens of email requests to “become a part of their editorial board”, or “be a keynote speaker at a meeting/symposium/workshop” (often in exotic locations), “following which we’ll publish the proceedings of the meeting in our prestigious journal.” Honest scientists often will have sufficient data to prepare for publication, and are puzzled/challenged in their decision as to which journal it might be best to submit the manuscript.

There is no question that these predatory journals are a global threat. They “accept” articles for publication — along with hundreds of dollars in publication fees — without performing proper quality checks for such matters as plagiarism or ethical approval. Naïve readers are not the only victims; many naïve researchers have been duped into submitting articles to predatory journals, only to find out their work can subsequently be overlooked. One study suggests predatory publishers collect millions of dollars in publication fees that are ultimately paid out granting agencies such as the US National Institutes of Health (NIH). One example of fraud (discussed previously in these GEITP pages) was a family of four living in Turkey had earned more than $1 million in “publishing fees” in one year, just by pretending to be a legitimate “publishing company.”

What is needed is consensus on a definition of predatory journals; this would provide a reference point for research into their prevalence and influence, and would help in crafting coherent interventions. To agree on “a consensus” and to map solutions, authors [of the attached editorial] and others met in Ottawa, Canada, in April 2019. Participants hailed from 10 countries and represented publishing societies, funding agencies, researchers, policymakers, academic institutions, and libraries. Their focus was on biomedical sciences, but their recommendations should apply broadly. Some of their conclusions included:

Predatory journals are driven by self-interest (usually financial), and at the expense of scholarship. They are characterized by the following:

False or misleading information. (They pretend to have “official impact factors” when they actually do not).

Deviation from best editorial and publication practices. (They promise an honest “peer review” by at least two experts in your field, but then accept the paper, as is, within 48 hours so as to meet their deadline of “publishing another issue”).

Lack of transparency. (The name of the soliciting editor might be “Mary George” (i.e. common English names) and a fake address on a street in some town in New Jersey — when in fact the “journal” represents one or a few people living in Pakistan or China).

Aggressive, indiscriminate solicitation. A clear warning sign is that the invitee’s expertise is outside the journal’s scope (e.g. I’ve been invited to speak at nurses’ conventions, global economics summits, particle physics workshops, and geochemical symposia).

Other criteria — such as journal quality, and intent to deceive. The bottom-line today is that there is a very blurry gradient [e.g. see the diagram on p 211 of attached], showing how problematic it can be to distinguish between a predatory journal and an honest journal that is “becoming under-resourced” (caused perhaps precisely by these predatory journals taking over their domain). The attached article is highly recommended to be read carefully. 😊

DwN

Nature 12 Dec 2019; 576: 210-212

Posted in Center for Environmental Genetics | Comments Off on How should we define a “predatory journal”… ????

The Great Oxidation Event and the Lomagundi Event might have both occurred by tectonic plate movements about 2.5 billion years ago

These GEITP pages have often discussed events during evolution — which in fact occurs because of gene-environment interactions. Once the original nucleic acid formed “the first gene” (more than 4 billion years ago), all genes ever since have diverged and mutated in response to environmental and climate changes — in order to improve survival (i.e. need to find food, avoid predators, and reproduce) of the species. Carbon dioxide (CO2) and atmospheric oxygen (O2) are two gases essential for aerobic life on Earth. [This fact flies in the face of today’s eco-environmentalists — who erroneously claim that existing levels of CO2 are undesirable and dangerous.] These two gases are linked via photosynthesis: CO2 + H2O = CH2O + O2

This important link between CO2 and O2 is evident in the geological record from association of the most dramatic events in the histories of both gases. The Great Oxidation Event (GOE) — during which time Earth’s O2 levels increased by several orders of magnitude — and the Lomagundi event (LE) — when carbon-isotope ratios of marine carbonates [(CO3)2- or (C=O)(O-)2] increased as much as ~10% — both occurred between ~2.5 and ~2.0 billion years ago. The temporal association of the two events suggests that both may be attributed to a single mechanism, such as enhanced organic carbon (organic C) burial; this is because increasing the fraction of carbon buried as organic C (forg), relative to carbonate, will increase the amount of O2 that is produced and allowed to accumulate (CO2 + H2O = CH2O + O2).

Despite the apparent temporal association of the GOE and LE, and the conceptual consistency of explaining both events via increased forg, its role as the driver of the GOE and LE remains uncertain. There is evidence that photosynthesis evolved at least a half billion years before the GOE, so why would O2 have remained low for so long?. In addition, other studies have suggested that the GOE may have preceded the LE by ~100 million years. If the onset times of the GOE and LE were indeed temporally different — it becomes difficult to explain both events via a single mechanism; this has led researchers to propose mechanisms invoking decreased sinks of O2 as the main driver of the GOE. Whereas decreased O2 sinks would allow atmospheric O2 to accumulate, it is unclear how they would drive the associated positive C-isotope excursion.

Authors [see attached article] propose a single mechanism for the GOE and LE. Modeling shows that their proposed mechanism can simultaneously explain both increased O2 production and a positive C-isotope excursion in marine carbonates. Authors show that their proposed mechanism is consistent with a delay between the evolution of photosynthesis and increased O2 levels, as well

as a delay between the build-up of O2 in the atmosphere, and the positive C-isotope excursion observed in marine carbonates.

Authors demonstrate that ~2.5 billion years ago, a tectonic transition — that resulted in increased volcanic CO2 emissions could have led to increased deposition of both carbonates and organic C via enhanced weathering and nutrient delivery to oceans. Increased burial of carbonates and organic C would have allowed the accumulation of atmospheric O2 while also increasing the delivery of carbon to subduction zones. Coupled with preferential release of carbonates at arc volcanoes, and deep recycling of organic C to ocean island volcanoes, authors report that such a tectonic transition can simultaneously explain the Great Oxidation Event and the Lomagundi Event — without any change in fraction of carbon buried as organic C relative to carbonate (which is often invoked to explain carbon isotope excursions). Authors therefore suggest that the first substantial burst of O2 on Earth was added by a wave of volcanic eruptions — brought about by tectonic plate movements. Their study offers a new theory to help explain the Great Oxidation Event of ~2.5 billion years ago, from which Earth began an explosion of evolution of many aerobic-metabolism organisms — in addition to the predominance of anaerobic metabolic organisms from ~4.2 billion to ~2.5 billion years ago. 😊

DwN

Nature Geoscience; Dec 2019; https://doi.org/10.1038/s41561-019-0492-6

Posted in Center for Environmental Genetics | Comments Off on The Great Oxidation Event and the Lomagundi Event might have both occurred by tectonic plate movements about 2.5 billion years ago

The University’s New Loyalty Oath

This EXCELLENT article appears in the Wall Street Journal online evening of Dec 19, out in print morning of Dec 20.

THIS (very sad) story is what I’m seeing more and more of, at the University of Cincinnati. And it is TOTALLY rampant at other colleges and universities such as Oregon State University. Some of my former graduate students and postdoctoral fellows have complained to me about these (political indoctrination) requirements — “getting in the way of seriously looking at a faculty position…”

DwN

Seven decades ago, the University of California introduced a loyalty oath, requiring employees to swear they were “not a member of the Communist Party.” After a contentious period in which 31 faculty were fired for refusing to sign, the requirement was reconsidered. An eventual consequence was the current Standing Order of the Regents 101.1(d): “No political test shall ever be considered in the appointment and promotion of any faculty member or employee.” This is a statement of principle. No one will be denied a position at the University of California based on political beliefs. No communist, no conservative, no progressive, no liberal.

Now the university appears to be abandoning this principle. In the past few years “Diversity, Equity and Inclusion” statements, in which applicants for faculty positions profess their commitment to these social goals, have become required on eight UC campuses and at colleges across the country. These requirements are promoted as fulfilling worthy goals: to help redress the historic exclusion of underrepresented groups, to ensure that candidates from all backgrounds apply for and are given fair consideration for faculty jobs, and to make sure faculty respect and support all students in their teaching and mentoring.

There are many constructive ways to pursue these admirable aims. For example, professors can reach out to underrepresented communities at every level. We can enact family-friendly policies that help young faculty balance family life with jobs. We can encourage students from all backgrounds to explore and succeed in academic careers.

The mathematical community, my own discipline, has widely embraced the ideals of inclusiveness. But I have become increasingly uneasy with the use of DEI statements in faculty hiring. This spring the university issued guidelines instructing each campus to develop and use a scoring system, called a “rubric,” for applicants’ diversity statements. No longer will faculty hiring committees use their own judgment about how best to create a diverse and inclusive environment in their fields.

Instead, each candidate’s commitment to diversity will be assigned points. To score well, candidates must subscribe to a particular political ideology, one based on treating people not as unique individuals but as representatives of their gender and ethnic identities.

A rubric from the Berkeley campus, singled out because it is available online, specifies that job applicants who describe “only activities that are already the expectation of Berkeley faculty (mentoring, treating all students the same regardless of background, etc)” will score poorly (1 or 2 points out of 5). A low score in this or other areas will disqualify a candidate. This system specifically excludes those who believe in a tenet of classical liberalism: that each person should be treated as a unique individual, not as a representative of an identity group. Rather than helping achieve inclusion, these DEI rubrics act as a filter for those with nonconforming views.

Earlier this year, I was invited to submit an essay to the Notices of the American Mathematical Society, the most widely read journal in mathematics. I decided to express my view that these required statements have become political litmus tests, and that this should worry us all. My submission provoked an intense controversy—confirming that this has become a dangerously politicized issue.

Social media posts called my views disgusting, condemned the American Mathematical Society for publishing the essay, and called for my public shaming. Mathematicians were urged to steer their students away from studying at UC Davis, where I teach, and to contact the university to question my fitness as chair of the math department.

A letter misrepresenting my views attracted hundreds of signatures. It inaccurately stated that I had equated “actively attempting to include more students in mathematics” with the “Red Scare.” Two supportive letters also circulated, gathering hundreds of signatures. One emphasized the value of open discussion without fear of intimidation if we are to make mathematics a welcoming community for everyone. Another agreed that mandatory diversity statements “undermine faculty governance.”

I received more than 150 emails, overwhelmingly supportive, many from leading mathematicians in the U.S. and overseas. Some recalled similar required statements in Soviet bloc countries, which they encountered earlier in their careers. Some pointed out that the diversity statements tend to be formulaic, with many candidates coached on how to write them, and that the content often emphasizes ideology over accomplishments. Others noted that the statements disadvantage foreign applicants and candidates from low-income groups, who may not have opportunities to participate in voluntary activities that demonstrate a commitment to diversity.

Many emails contained a disturbing theme, typified by this line from one of them: “Some day I, too, hope to speak out on this issue, but it is simply too dangerous at present.” This is a frightening sentiment to hear in academia. If expressing a widespread but controversial view is seen as taking a tremendous personal risk, the university system isn’t healthy. Ideas cannot thrive and mistakes cannot be corrected if people are afraid to speak out.

To its credit, the UC Davis administration has supported my right to speak. I hope that continuing discussion will confirm the vital principle that scholars discuss ideas, they don’t silence them.

Mandatory diversity statements can too easily become a test of political ideology and conformity. “No political test shall ever be considered in the appointment and promotion of any faculty member or employee.” This fundamental principle, forged in one of the most difficult periods the UC system has ever endured, must not be abandoned.

Ms. Thompson is chair of the mathematics department at the University of California Davis.

Posted in Center for Environmental Genetics | Comments Off on The University’s New Loyalty Oath

VDH ~ How America’s Students Need to Get ‘Woke’

This is an incredibly powerful summary of what has happened to our nation’s colleges and universities during the past three decades — eloquently and sincerely written by a Stanford professor who knows what is happening.

Brilliant observations from one who is in the trenches.

How America’s Students Need to Get ‘Woke’

The progressive campus project is a mere veneer. It is a scab of sorts, overlaying a wound beneath of progressive exploitation and class privileges and hierarchies.

By: Victor Davis Hanson

December 1st, 2019

Today’s university students want to “wake” the nation to problems that they and their professors have identified as threatening our very existence. And they issue these periodic alarms in hyperbolic terms: we have just 10, 20—fill in the blanks—years to end fossil fuel use, or else die from global warming.

They warn us that there is a veritable war waged on American women who have been limited to a mere 800,000 abortions on average per year. Sexism must explain why only 56 percent of college students are women.

The woke university lectures us that ubiquitous racism, white privilege, sexism, homophobia, transgender hatred, Islamophobia, nativism, and xenophobia supposedly make life deadly for people of color, gays, immigrants, the transgendered, and women. Apparently, such endemic hatred explains why the United States is the most tolerant, freest, most leisurely and affluent country in history for racial, religious, and gender minorities.

To address these supposedly existential concerns and agendas, the university has radically reinvented itself over the last 30 years. The relative and absolute number of tenured and tenure-track professors on campus has nosedived. In their places, the legions of noninstructional employees and part-time lecturers have soared. The former are mostly highly paid race, class, and gender diversity and inclusion provosts, deans, and czars. The latter are low-paid and largely exploited temporary teachers.

Student aid packages have been front-loaded with federally-guaranteed debt, as tuition in response has naturally soared over the last few decades above the rate of inflation. All sorts of “studies” majors have blossomed—ethnic studies, peace studies, environmental studies, black studies, Latino studies, Asian studies, feminist studies.

The curriculae now expand into popular culture, as if comic books, Hollywood movies, hip-hop music, and cartoons need academic study, professional scholarship, and professorial guidance.

In the university’s zero-sum game, something was lost to provide the needed space for these therapeutic new classes. And what was deleted were precisely those traditional courses in English grammar, composition, literature, foreign languages, philosophy, and history—that sharpened reasoning, honed written and oral expression, developed an aesthetic sense of art and music, and provided the student with the facts-based architecture central to fundamental education.

It was once agreed that reading Sophocles’ Antigone was more valuable for young minds than deconstructing “The X-Men,” and that Dante’s Inferno offered students more insight than did “To Pimp a Butterfly.” Might our 20-year-olds become less self-absorbed, and less ignorant if they knew what Shiloh, Normandy, and Iwo Jima were? Do any think that they could have survived the Oregon Trail, the Meuse–Argonne offensive, or the Schweinfurt raid?

In addition, the university went through one of the most bizarre cultural transformations of any institution in our society—albeit in a completely paradoxical way.

Students were no longer considered young, independent adults—at least sort of. They instead were apparently no longer always mature enough to make their own social and cultural decisions—and live with the consequences, good and bad.

Instead, students were recalibrated as episodic pre-teens who could not hear speakers, read texts, or listen to professors if thosee things challenged their safe spaces and status quo beliefs. Independent thinking apparently could harm such fragile souls and therefore had to be carefully restricted and rationed.

The First Amendment, as we have known it, really no longer exists on college campuses. Speech codes predominate and supersede it, citing the need for censorship as a protection from “hate speech,” a tool that can be used to smear almost any form of expression.

Visiting speakers know that—if they are deemed unapologetically conservative, they either will need guards to speak or are likely to be shouted down, or both—usually with the wink and nod of approval from careerist and itinerant administrators who no sooner arrive on campus than they virtue signal in hopes of advancing to higher paying billets elsewhere.

The public is bewildered by masked and hooded campus protesters breaking the law, storming barricades and trying to disrupt politically incorrect speakers. They suspect that if the police would actually arrest—and district attorneys indict—these barricade braggadocios, the latter would likely curl up into fetal position, crying about “getting an arrest record” and how that might impair their later privileged trajectories.

Who Are the Snowflakes?

“Snowflakes” arose as a term for sheltered students who regressed to needing puppies, coloring books, milk, and cookies to comfort them—even before Donald Trump won the 2016 election. But just when we thought colleges were nursery schools of safe spaces, trigger warnings, and racially segregated dorms, we saw that, in fact, they are incubators also of sketchy adult sex, alcohol and drug use. Courses, lectures, and symposia openly discuss the need for sexual awakening and experimentation, while the university has become a safe space for the use of particular recreational drugs.

So the public has become baffled at the result of these promiscuous Victorians, drunken prohibitionists, and zero-tolerance drug users—not to mention supposedly tolerant intolerant disruptors and social justice warriors fighting for the injustice of denying free expression.

The only possible common-denominator explanation of these radical disconnects is the gratification of the appetites and the paths of least resistance: students still like sex and parties and especially courses that are therapeutic, require less work, and confirm status quo pieties.

In other words, protesting and organizing are preferable to memorizing Latin declensions and physics theorems. Students as adults certainly like to drink, but so often after getting drunk and sickened do not like those who fostered that permissive atmosphere and allowed these sudden adolescents to drink in the first place.

Sexual hook-ups are supposedly transformative and cosmopolitan—but only if later shielded from the age-old crass and unfortunate emotional consequences that result when the male is given free rein to indulge his sexual appetites without commitment or honor or love.

The University House of Cards

But hypocrisy is not the most dangerous paradox of the university. Its entire financial structure is far more hypocritical. And the fix goes something like this: 18-year-olds enter college after being sold a bill of goods that an undergraduate degree is so invaluable that it will more than justify tens of thousands of dollars in aggregate long-term debt.

Often “aid packages” brim with showy fellowships, grants, and tuition waivers to disguise the reality that the discounted, rock-bottom, bargain-based, final total cost of a year at college is still exorbitant.

Students are reminded that at least a B.A. or B.S. degree will provide status that will aid upward economic and social mobility. Sometimes that is true, but when it is not, the results wreck lives.

Woke majors centering on social justice are lauded and promoted on campus as the spear of resistance culture. Yet years later, such campus veterans don’t impress employers. The now-indentured-serf graduate is left to fend for himself, far away the previous reverie and energy of progressive protests and inculcation.

In other words, the next time you see a chanting crowd of woke students shouting down a speaker with a faculty member cheering them on, imagine such protestors five years from now, solitary without good jobs, but with lots of their own private debt and plenty of bitterness and angst.

Who then pays for the tenured full professor who indoctrinates students for 32 weeks of the year? Who pays for the assistant provost for “Diversity, Equity, and Inclusion,” who teaches no classes but monitors those who do? Who helps to subsidize a costly campus that is increasingly disconnected from learning?

Is it not the part-time lecturer driving between campus gigs without job security, retirement or good, if any, benefits?

Is it not the student carrying $100,000 in 6 percent loans, majoring in environmental policy studies?

If students were really “woke” to the abject exploitation in their own landscapes, they would march on the president’s office to protest the lack of transparency in student loaning, the bureaucratic fat that does not contribute to learning or academic excellence, and the disparity between helot part-time lecturers and full-professor overlords. They would demand to know how much they are paying for each class, for office hours, for much on campus that ultimately is leveraged by their own government guaranteed student debt that will be an albatross around their collective necks into their thirties.

Viewed through these lenses, the progressive campus project is a mere veneer. It is a scab of sorts, overlaying a wound beneath of progressive exploitation and class privileges and hierarchies of the exploiters and exploited.

The results spill over from campus and are deleterious for the entire nation, ranging from prolonging adolescence and infantilizing young adulthood, delaying marriage, child-rearing, and home ownership to radicalizing the Democratic Party to the point of near irrelevance—not to mention the cost of defaulted government loans. Many of those indebted who actually graduate will gravitate into low-paying jobs.

And the professors and administrators who damned capitalism to them will be doing the same to each successive generation of naïfs, but always play-acting as radical mentors from tenured and six-figure salary billets.

In sum, today’s students are the most unaware, naïve—and unwoke—generation in our nation’s history. They pose as all-knowing and all-caring. But in the end, they are proving unwoken to the full dimensions of those who have channeled them into a decade or more of crushing debt, left them with unmarketable degrees, nourished both their ignorance of the world, past and present, and their political arrogance—and called it all success.

Posted in Center for Environmental Genetics | Comments Off on VDH ~ How America’s Students Need to Get ‘Woke’

Happy Holiday Season

Happy Holiday Season

THESE GEITP PAGES WISH EVERYONE A JOYOUS HANUKKAH AND A MERRY CHRISTMAS AND A HAPPY NEW YEAR 2020. OUR SHARING OF SCIENTIFIC ARTICLES — WILL RESUME AFTER THE FIRST OF THE YEAR. 😊

DwN

Posted in Center for Environmental Genetics | Comments Off on Happy Holiday Season