Category Archives: Transhuman News

Stanford, which consistently ranks among the top U.S. colleges and universities, is one of the great research institutions in the world. But it is also the source of profound paradoxes superb science in academic departments, but often uncritically defaulting to embrace trendy, socially attractive notions that actually contradict its well-earned reputation as a cutting-edge, science-grounded institution.

Hardly a month passes without news of a genuinely significant breakthrough in some field of science or technology. One week it might be the discovery of an unorthodox arrangement of wind turbines that increases energy output; the next, a new healing and antibiotic compound from scorpion venom or the application of artificial intelligence to enable people who are paralyzed to communicate by text. But too often, the university allows its relentless virtue signaling to overwhelm rationality and a commitment to science.

Consider the issue of sustainable agriculture, a fungible, feel-good term that allows anyone of any ideological persuasion to endorse enthusiastically; after all, who doesnt want an ecologically healthier world?

Stanford is all in with the symbolism. Its created a website, Sustainable Stanford, where it extols the university as living laboratory for environmental action focused on food and farming. The university even offers the ODonohue Family Stanford Educational Farm, for hands-on-learning in sustainable agriculture where students, staff, and faculty grow organic produce. And one of the universitys top initiatives is to support a sustainable food system through its purchasing practices and menu options. How does Stanford do that? It buys and serves organic foods whenever possible.

Whats so striking about these initiatives is the disconnect between Stanfords heavily promoted good intentions and the fast-evolving science surrounding sustainability. Universities are supposed to be a place where faculty and students seek hard truths, a respite from the mob of misguided, feel-good populism, but thats becoming less attainable all the time. In fact, when it comes to the issue of agricultural sustainability, Stanford lives in an unreal green cloud.

What could be more important to sustainability than climate change? Yet, from a climate change perspective which is front and center at Stanford innumerable studies show organic farming is actually a laggard compared to conventional agriculture. Its yield lag tops 30%; tilling the soil (which is not required with farming using genetically modified seeds that provide weed control) results in huge releases of CO2 (5% of all carbon releases); and methane gas release from livestock, which is used to generate fertilizer for organic farming, is the single biggest agricultural contributor to greenhouse gases.

While Stanford wallows in sustainability wokeness, the Massachusetts Institute of Technology (my undergraduate alma mater) gets it right. A 2019 article in MIT Technology Review, headlined Sorry, organic farming is actually worse for climate change, details the myriad ways organic farming, beyond its trendy populism among the chattering classes, is a sustainability red herring. The article summed up extensive research on this issue, included a now iconic UK study that showed organic farming, if widely instituted in England, would lead to increased imports of food, clear-cutting of rainforests and overall increase greenhouse-gas emissions by 21%.

But Stanford students are not exposed to any of that on the Sustainable Stanford website or at the ODonohue sustainable farm. Nor are there informed scientific discussions at the dorms organic farms that use boutique agroecological farming practices (vide infra). That approach to farming might be a gratifying pastime for wealthy students and farm-rich countries like the United States, but it would devastate developing countries if the Stanford sustainability model were to become the global norm. The fact is, Stanford embraces a view of agricultural sustainability that came into fashion in the 1980s and 1990s, was flawed then, and is even more obviously so, now. The university is all about science for academic research, but when it comes to digging below the surface and challenging their students to think out-of-the-box, political correctness reigns.

Consider Stanfords invitation last year to Vandana Shiva, a so-called environmental activist, to present the prestigious 8th Annual Stephen H. Schneider Lecture. Shivas talk, Soil not Oil: Biodiversity-based Agriculture to Address the Climate Crisis, called for an end to large-scale industrial agriculture because of the effects she claimed these methods have on climate change, biodiversity, and food security. All three of her assertions are demonstrably wrong.

In a 2014 article for The New Yorker, Seeds of Doubt, investigative journalist Michael Specter called into question a number of Shivas repeated claims regarding genetic engineering, as well as her ethics and judgment. Specter writes:

At times, Shivas absolutism about [modern genetic engineering] can lead her in strange directions. In 1999, 10,000 people were killed and millions were left homeless when a cyclone hit Indias eastern coastal state of Orissa. When the U.S. government dispatched grain and soy to help feed the desperate victims, Shiva held a news conference in New Delhi and said that the donation was proof that the United States has been using the Orissa victims as guinea pigs for genetically engineered products. She also wrote to the international relief agency Oxfam to say that she hoped it wasnt planning to send genetically modified foods to feed the starving survivors. When neither the U.S. nor Oxfam altered its plans, she condemned the Indian government for accepting the provisions.

These very same products are widely consumed in the U.S. and elsewhere, which perfectly illustrates Shivas blatant dishonesty and disingenuousness.

Others have criticized Shiva in (appropriately) blunter terms. The Genetic Literacy Project describes, in detail, her anti-science history:

Vandana Shivas advocacy focuses on opposition to intellectual property rights, capitalism, free trade, and corporations. Shiva is noted for making extreme statements linking the use of GMOs to rape; calling for criminal destruction of GMO crops and research and, prosecution of corporations that develop GMOs. Her claims of harms associated with GMOs, particularly claims they are failing and causing farmers to commit suicide, have consistently been debunked as false by independent academic peer-reviewed published research.

They add that Shiva openly supports, defends, and has encouraged acts of eco-terrorism and sabotage against GMO plants and research justifying them by claiming one can only commit violence against people, not against things.

In December 2019, scientists and bioengineers from around the world issued an open letter criticizing Stanford for inviting Shiva to speak on campusdespite her constant use of anti-scientific rhetoric to support unethical positions. The university group that invited her stood their ground, remonstrating that The goal of this lecture was not, and is not, endorsing a single individual, ideology, or solution. On the contrary, we aimed to provoke critical thoughtto spur nuanced conversations that help students examine their own values. That response is, as the Brits would say, thin gruel, indeed. The reality is that Stanford invited to the campus a notorious liar and anti-science advocate to spew her venom, and with a handsome honorarium, to boot.

Despite all the virtue-signaling about sustainability a search for the word on Stanfords website yields no fewer than 103,00 hits the fact of the matter is that university is rather selective in its commitment to it. For instance, housed in one of the oldest dormitories, Roble Hall, is an initiative called the Roble Living Laboratory for Sustainability at Stanford (ROLLSS), which includes undergraduate seminars, a graduate-student speaker series, and activities intended to engage the dorms residents in curbing their natural-resource waste.

So far, so good, but a central part of the initiative is an organic garden, meaning the students of this world-class research institution are being schooled in the myth that organic agricultural methods are sustainable. That sophistry is by no means limited to one dorm; at least up until students departed during the COVID-19 pandemic, all eight of Stanfords major dining halls maintained an organic dedicated teaching garden. In 2014, thanks to a generous gift from two New York-based benefactors, one of whom owns an organic farm, the university turned the nearly six acres adjacent to Stanfords historic Red Barn into the ODonohue Family Stanford Educational Farm, to produce a bounty of edibles as well as a new generation of leaders in sustainable food systems. These programs, as Ive described before, are anti-scientific and otherwise flawed.

Although the organic movement touts the sustainability of its methods, its claims do not withstand scrutiny. For example, in a 2014 study published in the journal Hydrology and Earth System Sciences, researchers found that the potential for groundwater contamination can be dramatically reduced if fertilizers are distributed through the irrigation system according to plant demand during the growing season. Unlike conventional agriculture, organic farming depends on compost, the release of which is not matched with plant demand. Surprisingly, the study found, intensive organic agriculture relying on solid organic matter, such as composted manure that is implemented in the soil prior to planting as the sole fertilizer, resulted in significant down-leaching of nitrate into groundwater. With many of the worlds most fertile farming regions in the throes of extreme drought and aquifer depletion, increased nitrate in groundwater is hardly a mark of sustainability.

Moreover, although composting gets good PR as a green activity, at large-scale, it can generate significant amounts of greenhouse gases. Composting can also be a source of pathogenic bacteria applied to crops. In 2009, a study published in the Journal of Food Protection sampled non-sludge recycled organic matter composts produced in Washington, Oregon, and California and found a wide range of fecal coliform results for all regions.

Organic farms also produce far less food per unit of land and water than conventional ones, making them a huge waste of arable land. Plant pathologist Dr. Steve Savage analyzed the data from USDAs 2014 Organic Survey, comparing various measures of productivity from most of the nations certified-organic farms to those at conventional farms, crop by crop, state by state. His findings are extraordinary. Of the 68 crops surveyed, there was a yield gap (poorer performance of organic farms) in 59. And many of those shortfalls were impressive: strawberries, 61% less than conventional; fresh tomatoes, 61% less; tangerines, 58% less; and so on.

The implications are sobering. As Dr. Savage observed, To have raised all U.S. crops as organic in 2014 would have required farming of 109 million more acres of land. That is an area equivalent to all the parkland and wildland areas in the lower 48 states.

The low yields of organic agriculture impose a variety of stresses on farmland, especially on water consumption. A 2012 British meta-analysis found that ammonia emissions, nitrogen leaching, and nitrous oxide emissions per product unit were higher from organic systems, as were land use, eutrophication potential, and acidification potential per product unit.

Organic production disfavors the best approach to enhancing soil qualitynamely, the minimization of soil disturbance (e.g., avoidance of plowing or tilling), combined with the use of cover crops. Such farming systems offer multiple environmental advantages, particularly with respect to limiting erosion, the runoff of fertilizers and pesticides, and the release of CO2 from tilling. Organic growers frequently plant cover crops, but in the absence of effective herbicides, they often have to rely on tillage (or even labor-intensive hand-weeding) for weed control.

The destructive tilling in organic agriculture was the subject of a recent blockbuster National Public Radio story, entitled, A Giant Organic Farm Faces Criticism That Its Harming The Environment. Giant is right: the organic Gunsmoke Farm, near Pierre, South Dakota, covers 53 square miles. Harming the environment is also right: tillage breaks down parts of the soil that are richest in carbon and nutrients and shakes soil loose from the plant roots that help to keep it together. That makes the soil vulnerable to being carried away by rain or wind, which is exactly what happened at Gunsmoke Farmit became a dust bowl.

One prevalent green myth about organic agriculture is that it does not employ harmful chemicals such as pesticides. Organic farming does, in fact, use insecticides and fungicides: dozens of synthetic chemicals are permitted in the growing and processing of organic crops under USDAs arbitrary rules. Copper sulfate, the most popular pesticide used in organic farming, is a carcinogen, kills beneficial insects, decimates soil, and is persistent.

Perhaps the most illogical and least sustainable aspect of organic farming in the long term will turn out to be the systematic and absolute exclusion of genetically engineered plantsbut only those that were modified with precise and predictable modern molecular techniques. (Except for wild berries and wild mushrooms, virtually all the fruits, vegetables, and grains in our diet have been genetically improved by one technique or another.)

Therefore, the exclusion from organic agriculture of organisms simply because they were crafted with superior molecular techniques makes no sense. Over three decades, the newest, most precise techniques have yielded advances in agriculture, such as plants that are drought- or flood-resistant, that have been more environmentally friendly and sustainable than ever before. Shiva, in a response to Specters New Yorker article she called Seeds of Truth, dismissed these advances as mechanistic thought and manipulated facts.

The irony of all this is that a 1973 co-discoverer of recombinant DNA technology, the prototypic, iconic molecular technique for genetic engineering, was Stanford biochemist Dr. Stanley N. Cohen, who is still a professor of genetics and medicine at the university. (I wonder how many of those involved in the ROLLSS program have even heard of him.) One person who has heard of him is Stanfords president, Marc Tessier-Lavigne, a neuroscientist who was previously Chief Scientific Officer at Genentech, one of the worlds foremost biopharmaceutical companies. And yet, Dr. Tessier-Lavigne knowingly perpetuates this pro-organic, anti-science, reactionary nonsense on his campusto say nothing of permitting Vandana Shiva to speak.

As genetic engineerings successes continue to emerge, the gap between modern, high-tech agriculture and organic methods is becoming a chasm. Genetically engineered potato varieties already in the marketplace are bruise-resistant and contain 50-70% less asparagine, a chemical that is converted to acrylamide, a probable carcinogen, when heated to high temperatures. The advantage of lower levels of acrylamide is obvious, but the bruise resistance is important to sustainability: according to Simplot, the developer of the genetically engineered Innate varieties, with full market penetration for its varieties sold in the U.S., Innate will reduce annual potato waste by an estimated 400 million pounds in the food service and retail industries and a significant portion of the estimated 3 billion pounds discarded by consumers.

Genetically engineered potatoes that are resistant to bruising and to the late blight fungus represent the very essence of sustainabilityevery serving of French fries or mashed potatoes made from them represents less farmland used and less water consumed. But none of these varieties can be used by organic farmers.

How could one of the worlds preeminent research universities, which regularly produces breakthroughs across virtually the entire spectrum of science and technology, embrace and endorse anachronistic, destructive practices?

A 2012 New York Times article entitled The Organic Fable, by columnist Roger Cohen provides the answer. In it, he offered some pithy observations about the popularity of organic food:

Organic has long since become an ideology, the romantic back-to-nature obsession of an upper middle class able to afford it and oblivious, in their affluent narcissism, to the challenge of feeding a planet whose population will surge to nine billion before the middle of the century and whose poor will get a lot more nutrients from the two regular carrots they can buy for the price of one organic carrot.

Sustainable farming should mean maximizing and capitalizing on the ability of human ingenuity to invent processes, products, and approaches that are more efficient, less costly, and at the same time, less harmful to the environment. In other words, exactly the kinds of advances that come from university chemistry, plant science, artificial intelligence, engineering, and molecular biology labs. But organic farmers, including Stanfords, can forget about using them.

The organic movement and green sensibility have become rooted in society over the past quarter century or so, and Stanford has uncritically gone along. Its both unscientific and unbecoming.

Acknowledgement: The author thanks Michelle Sheldon and Jon Entine for excellent suggestions on the text.

Henry Miller, a physician and molecular biologist, was a research associate in molecular genetics at the NIH and the founding director of the Food and Drug Administrations Office of Biotechnology. Find Henry on Twitter @henryimiller

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Viewpoint: Stanford is a world-class science institution except when it comes to critical thinking about the 'sustainability myth' of organic...

Jul 28th 2021

DOGS CAN smell things at concentrations of one part in a trillionequivalent to a single drop in a pond the size of 20 Olympic swimming pools. That ability is put to good use by human beings. Trained dogs can sniff out explosives and drugs, track missing people, and even guide truffle-hunters to their prizes. They can also detect illnesses, including cancer, malaria, Parkinsons disease and covid-19, before obvious symptoms appear. A study published in 2019, for example, suggested that trained dogs were able, 97% of the time, to identify blood samples taken from patients with lung cancer. A group of researchers in Germany recently trained dogs to pick out saliva samples collected from those infected with SARS-CoV-2, the covid-causing virus, from uninfected samples, with a success rate of 94%.

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Training dogs, however, takes time. Handlers must be paid. The animals themselves get tired and bored. In past studies on cancer detection, less than half of canines entered for training made the grade. Dogs are not, then, a practical answer to the question of how to detect illness quickly, before it gets a grip.

But fruit flies might be. And so might tiny nematode worms called Caenorhabditis elegans. And so, indeed, might bees. Unlike dogs, all are cheap and expendableand their senses are just as good. Along with technology tailored to their talents, they could provide economical, easy and non-invasive ways of detecting cancer, and also offer an alternative to laboratory tests for covid that might be welcome in countries with limited budgets.

At the moment, only four cancersof the breast, cervix, colon and rectum, and sometimes the prostateare screened for routinely, and only in places that can afford it. Between them they account for only a quarter of the worlds cancer deaths. For many unscreened-for tumoursfor example, cancers of the pancreas, stomach and oesophagusearly detection is vital. Animal-based diagnostics could extend the range of screening tests available.

Fruit-fly-wise, one leading researcher is Giovanni Galizia of the University of Konstanz, in Germany. Fruit flies smell things using their antennae, and Dr Galizia has genetically modified his flies so that when they detect odiferous molecules, the resulting brain activity generates fluorescence under a microscope.

The exact pattern depends on what the fly is smelling. With the help of machine learning, Dr Galizia can recognise the patterns generated by odours from healthy cells and those generated by cancerous ones. Indeed, he can now tell between cells from different types of breast cancer.

For his experiments, Dr Galizia is using cancerous cells grown in a dish. Collecting such cells from people would require a biopsy. That would only be done if there was already suspicion that something was wrongrather defeating the point of a screening test. Dr Galizias ambition is therefore to detect cancer in urine rather than cells. He is also keen to dispense with the flies, for looking at fly brains down a microscope is fiddly. Instead, he hopes to find combinations of chemical-receptor proteins that can distinguish between urine from people with and without cancer. Those proteins could be integrated into sensors on silicon chips. If Dr Galizia can make this work for breast cancer, it will probably work for other cancers, too.

Detection by worm, by contrast, relies on whole organismsthough the detection itself is automated. In 2015 Hirotsu Takaaki, then a researcher at Kyushu University, in Japan, tested whether C. elegans could distinguish between the urine of people who had cancer and those who did not. He found that the worms tended to crawl towards urine from cancer patients and shy away from urine from the healthy. The following year Dr Hirotsu founded a company to automate the process.

Five years on Hirotsu Bio Science has three test centres around Japan. In each of these, robots drop spots of urine onto the edges of Petri dishes, and then add clusters of worms at the centre. This process is repeated dozens of times per patient. If most of the worms crawl towards the urine, then the patient in question is likely to have one of 15 kinds of cancerthough Dr Hirotsu cannot yet say which. The firm hopes to change that by using genetic engineering to tweak the worms senses. Eric di Luccio, its head of research and development, says the company plans to offer a test specific to pancreatic cancer next year.

Detecting covid with bees, meanwhile, involves a method that goes back to Ivan Pavlov and his dogs. The insects are offered sugar-water alongside SARS-CoV-2-infected saliva samples, but not with uninfected samples. They thus learn to extend their probosces when they sniff covid.

Aria Samimi, boss of InsectSense, the Dutch firm that developed this approach, imagines local apiarists providing armies of bees for the firms training machines, just one of which can train more than 100 bees a day. Potential partners in Zimbabwe and India have expressed interest, Mr Samimi says. And, intriguingly, researchers in both the Netherlands and Denmark are keen to see if bees can detect cancers, too.

Which, if any, of these ideas will come to fruition remains to be seen. Medical regulators will have to be convinced that what may seem wacky at first glance is actually sensible. But doctors have been encouraged to use their noses to assist diagnosis since the time of Hippocrates. Having a little olfactory assistance from invertebrates might be no bad thing.

This article appeared in the Science & technology section of the print edition under the headline "The nose knows"

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Flies, worms and bees could help detect illness - The Economist

Shortly after the outbreak of COVID-19 disease from inside Wuhan, China, when the virus infections had reached numerous people across the world, some people began exploring various possibilities around the origins of the current SARS-Coronavirus, also known as SARS-CoV-2. These people included individuals across diverse sectors from many countries such as Scientists, Politicians, Activists, Lawyers and of course the people from Security and Intelligence fraternity, as they are supposed to inform the policy makers.

Eventually, these efforts at uncovering the truth about the COVID-19 origins began to play out in public domain via various media outlets shaping the public discourse around the subject. Multiple theories began emerging and these theories can be broadly grouped into three categories, namely 1) Natural Origin Theory, 2) Laboratory Origin Theory and/ or 3) Bioweapon Theory.

The theorists advocating natural origin of SARS-CoV-2 contend that it is a result of a bat coronavirus (bat-CoV) undergoing zoonotic transfer after a recombination event inside the Pangolins with another coronavirus. The Pangolins in question were reported to have been smuggled into China from Malaysia and were sold in the Sea Food Market in Wuhan. Therefore, according to Natural Origin Theory, current pandemic is supposed to have emerged from the Wuhan Sea Food Market.

The Lab Origin theorists suggest that a genetically engineered virus from the laboratory escaped and led to the current pandemic. They say that this virus was produced through Gain of Function research or experiments and according to most of them, it escaped from the BSL-4 laboratory in Wuhan, China, also known as Wuhan Institute of Virology (WIV).

The Bioweapon theory is basically a version of Lab Origin theory wherein theorists indicate towards the use of gain of function technology by scientists at WIV to create a highly pathogenic virus at the behest of Peoples Liberation Army (PLA). It is this virus that is supposed to have accidently leaked according to some of the Bioweapon theorists while others have asserted that Chinese Communist Party (CCP) leadership decided to release this virus to wreak social and economic havoc at a Global Level.

It is important to examine the scientific information that underpins these theories, so as to enable an informed public discussion on the subject of COVID-19 origins. So, in the next section we will begin by discussing the basics of this subject to be able to make sense of what is written in the scientific publications that have either been cited or produced by proponents of theories discussed above.

Also important is to review the conduct of Chinese Government during the initial days of the current pandemic. All this would easily suffice to establish that China must be held accountable for the adversities that are being currently experienced across the world because of this pandemic.

BASICS

Coronavirus are a group of viruses that infect mammals and birds to cause respiratory diseases. They can be classified as Alphacoronavirus, Betacoronavirus, Gammacoronavirus and Deltacoronavirus. The SARS-CoV-2, SARS-CoV-1 coronavirus responsible for 20022004 SARS outbreak -and MERS-CoV virus come under the category of Betacoronavirus.

The Betacoronaviruses can be further categorized in terms of lineages A, B, C and D, so SARS coronaviruses are lineage B Betacoronaviruses while MERS coronaviruses belong to lineage C.

Now viruses are either made of DNAs or RNAs. They can be double stranded or single stranded and single stranded RNAs can further be classified as positive and negative. So, the SARS-CoV-2 virus is a positive single stranded RNA.

These DNAs or RNAs are basically chains or a sequence of nucleotides that encode all the components of an organism. Each nucleotide consists of a molecule known as Nitrogenous Base. The RNA is made up of nucleotides, each having different nitrogenous base and there are four different types of nitrogenous bases Adenine (A), Uracil (U), Cytosine (C) and Guanine (G).

Simply speaking, we can refer to nitrogenous bases as A, U, C and G and they are basically alphabets (or codes) that go on to form words (or codons). Every word is formed from a combination of any three out of these four alphabets and this way we can make 64 words. Each word or a codon codes for an amino acid which is the building block of protein and as such there are 20 amino acids. So, a single amino acid can be coded by more than one codon or word.

The RNA strand or viral genome can be represented as sequence of A, U, C and G which is known as nucleotide sequence. Another way of representing them is, as a sequence of amino acids. These two different types of sequences serve different purposes in studying the virus.

STRUCTURE OF CORONAVIRUS

Every virus has a genome which is either a DNA or RNA but never both unlike all other organisms. They have a protein coat called Capsid which are proteins arranged in a symmetrical manner and form a protective shell for the nucleic acid. In case of SARS-CoV-2, this symmetry is helical.

Diagram: Coronavirus Structure

The SARS-CoV-2 is an enveloped virus which has a lipo-protein envelope around the capsid. This envelope is constituted by lipids that are derived from the host cell and proteins that are synthesized using the host cell machinery according to the codons inside the RNA Genome. Now there is certain protein that projects outward from this envelope and it is known as Spike protein (S-Protein).

The spike protein (S-protein) in coronavirus has two sections 1) a receptor binding domain (RBD) and 2) a second section which is made of sequences that facilitate the fusion of virus cell envelope and the host cell membrane.

So, the RBD binds to something called as ACE-2 receptor of the host cell, after which there is an enzyme in the host cell called protease which breaks the protein and this enzyme cleaves (split or sever) the S-protein and the fusion sequences of the second section get exposed and virus envelope fuses with the host cell membrane. Different coronaviruses have different S-proteins and they are severed by different host cell protease.

Also, the S-proteins in some coronaviruses get split during their entry into the host cell while others during their exit from the host cell so that they are ready to enter the next host cell. The site at which this cleavage happens is called cleavage site.

NATURAL ORIGIN THEORY

RATG13

On 3rd February, 2020 a paper authored by Zheng-Li Shi was published in the Nature that identified a previously found bat coronavirus named RaTG13 as sharing 96% identity the closest known so far with the SARS-CoV-2 at a whole genomic level. The scientific publications that support the Natural origin of SARS-CoV-2 base their studies and assertions mainly on this piece of evidence.

According to the database of Global Initiative on Sharing Avian Influenza Data (GISAID), this RaTG13 virus is known to infect the horseshoe bat and it is said to have been discovered in 2013 from a mining cave near the town of Tongguan in Mojiang county, Yunnan, China. However, it has not been mentioned in any of the publications before by Zhengli Shi that were about the bat coronaviruses.

Instead, one of Shis previous studies that was published in 2016, highlights a bat coronavirus strain called BtCoV/4991 whose short region of RNA-Dependent RNA Polymerase (Rd-Rp) gene has shown 100% nucleotide identity with the one that belongs to RaTG13. Basically, this implies that RaTG13 and BtCoV/4991 are the same strain because Rd-RP gene is integral to replicate the viruss genetic material inside the cell. Also, if they were different, Shis report should have separately identified BtCoV/4991 as also having high similarity with SARS-CoV-2 Rd-Rp. However, if they are the same strain then one cant help but wonder, as to what is the rationale behind giving two different names to the same virus strain.

This and many other inconsistencies around the accuracy of RATG13 Genome Sequence and even its actual existence have been pointed out in many scientific publications. However, many of such publications exist only as pre-prints or non-peer reviewed articles because of the alleged censorship against arguments that raise objections to the information supporting the Natural Origin narrative.

Pangolins

Several scientific institutions and experts have suggested Pangolins as being the likely intermediate host for the SARS-CoV-2 after the reports emerged that Sunda Pangolins carrying coronaviruses were smuggled into China from Malaysia.

The reason behind this suggestion was that the S-protein of RATG13 virus was very different from that of SARS-CoV-2 as the amino acids in its Receptor Binding Domains (RBDs) differ hugely at the sequence level with that of the latter but they were similar to the RBD of Pangolin coronavirus. However, a recently published study in Nature that was conducted by scientists in Australia, has shown results that strongly contradict this suggestion.

The scientists in Australia compared the affinity of ACE-2 receptors of human, pangolin, dog, monkey, hamster, ferret, cat, tiger, bat, civet, horse, cow, snake and mouse, towards the RBD of SARS-CoV-2. They found that human ACE-2 (h ACE-2) and Pangolin ACE-2 had highest affinity towards SARS-CoV-2 RBD but most importantly, h ACE-2 had much higher binding potential to the SARS-CoV-2 RBD than that of the Pangolin. Now this is not normal if we assume Pangolin as an intermediate host for SARS-CoV-2 because a zoonotic virus would normally have the highest affinity for its immediate preceding host, as it takes time to adapt to the new host.

LAB ORIGIN THEORY

ZC45 and ZXC21

On 12th January, 2020 Eddie Holmes an Australian virologist who is also a colleague of Professor Yong-Zhen Zhang from Fudan University, Shanghai put out the genome of SARS-CoV-2 and later, a paper based on Professor Zhangs discovery was published by Nature on 3rd February, 2020, alongside the paper authored by Zheng-Li Shi that linked the SARS-CoV-2 with RATG13.

An interesting feature of Professor Zhangs paper was that it did not mention RATG13 or BtCoV/4991 in its paper but found another bat coronavirus named bat SL-CoVZC45 (or ZC45) as sharing high sequence identity of 89.1 % with the SARS-CoV-2 at nucleotide level. The paper also discusses another bat SARS-like virus ZCX21 which is highly identical to ZC45 and suggests possible recombination events between these viruses.

Professor Zhangs paper was picked up by many among the Scientific community and one of them is Dr. Li-Meng Yan, a Chinese virologist who as of now is probably the leading proponent of bio weapon theory. She has fled to U.S. from Hong Kong and has authored multiple papers to substantiate her assertions. Her paper provides some more information corroborating the findings of Professor Zhang.

Dr. Yans paper explains that when SARS-CoV-2 and ZC45/ZXC21 are compared at amino acid level there is a high sequence identity observed for most of the proteins between these viruses. Among those proteins, she highlights the high sequence identity for Orf8 proteins and E protein, simultaneously, between these viruses as one of the definitive evidence that ZC45/ZXC21 is the backbone for SARS-CoV-2. According to her findings, the Orf8 proteins in these viruses are 94.2% identical while no other coronaviruses share more than 58% identity with SARS-CoV-2 on this particular protein. Also, the E proteins in these viruses share 100% sequence identity and this has been observed between the previous SARS-CoV-1 and other SARS-like viruses but none of those pairs simultaneously share over 83% identity on the Orf8 protein.

Therefore, Dr. Li Meng Yan suggests that ZC45/ZXC21 is probably the template used for creating SARS-CoV-2 in the laboratory through genetic gain-of-function modifications.

Receptor Binding Domain (RBD)

According to Professor Zhangs findings there were evidences to suggest that recombination events had occurred between SARS-CoV-2, SARS-CoV-1, ZC45/ZXC21. However, this recombination event was probably limited to the Spike gene and not the entire genome. So, the Receptor Binding Domain (RBD) region of the spike gene in SARS-CoV-2 was highly similar to the SARS-CoV-1 RBD, while the rest of the sequences were most closely related to ZC45 and ZXC21.

The paper also stated, Despite these recombination events, which seem relatively common among sarbecoviruses, there is no evidence that recombination has facilitated the emergence of WHCV (SARS-CoV-2). So, if there is no evidence of recombination behind the emergence of SARS-CoV-2 then this opens up an avenue for discussion on genetic engineering as one of the possible reasons.

Dr. Yans paper dwells more into the subject of Spike protein of SARS-CoV-2 and its similarity with SARS-Cov-1. Her findings show that the S2 functional domain of the Spike protein in SARS-CoV-2 shares a high sequence identity of 95% with that of ZC45/ZXC21 but the S1 functional domains the RBDs in these viruses which determine the host that the virus can infect share only 69% amino acid sequence identity. This is because the RBD of SARS-CoV-2 is highly identical to that of SARS-CoV-1.

Also, Dr. Yans paper further examines the bind between the h-ACE-2 and the RBDs of SARS-CoV-2 & SARS-CoV-1. Her findings show that the hACE2 bindings with both the RBDs resemble greatly however they are not exact copy paste. This is perhaps because of the difference in nucleotide sequences between the two as there can be more than one codon used to code for same amino acid. Also, some of the amino acid residues in the RBD of SARS-CoV-1 that are non-essential for the RBD-hACE2 binding are absent in SARS-CoV-2 RBD Which probably helps to obscure the link between the RBDs of these viruses.

Two unique restriction sites EcoRI and BstEII

As we discussed in the previous section that many laboratory origin theorists contend that the SARS-CoV-2 RBD is actually the customized SARS-CoV-1 RBD which is swapped with the ZC45/ZXC21 RBD.

So, Li Meng Yan in her paper provides information to substantiate this contention. Her paper has emphasized on the presence of Restriction Sites on either end of the SARS-CoV-2 RBD that are absent in the ZC45/ZXC21 viruses. The Restriction Sites are those segments of nucleotide sequences that can be cut by Restriction Enzymes, such as EcoRI and BstEII, which happen to be popular choices for everyday molecular cloning, as suggested by Dr. Yan. A particular Restriction Enzyme will only cut a specific sequence of nucleotide bases which means that a Restriction site is unique to a Restriction Enzyme.

Dr. Yans paper states that SARS-CoV-2 RBM has a restriction site on one of its end that can be cut by EcoRI and on the other end there is another restriction site that can be cut by BstEII. Now, the ZC45/ZXC21 viruses originally do not have these restriction sites so Dr. Yan suggests that they could be easily introduced on either end of their RBM by deleting and inserting certain nucleotide bases through a method known as Site Directed Metagenesis. Then they could have been cut by EcoRI and BstEII so as to swap the original RBM with the customized SARS-Cov-1 RBD.

However, this can only be true if ZC45/ZXC21 are indeed the backbone of the current SARS-CoV-2 virus because the RATG13 virus which is currently accepted backbone for SARS-CoV-2 does have these restriction sites. Also, the restriction sites can be naturally present in virus genomes. Which is why Dr. Yan also states, Such EcoRI and BstEII sites do not exist in the spike genes of other coronaviruses, which strongly indicates that they were unnatural and were specifically introduced into this spike gene of SARS-CoV-2 for the convenience of manipulating the critical RBM.

Furin like Cleavage Site

Back in the year 2020, Dr. Francis Boyle, an American Human Rights Lawyer, gave an interview to Geopolitics & Empire where he said that the SARS-CoV-2 is a bioweapon that leaked from the BS4L facility in Wuhan, China. He based his claims on a paper authored by a group of scientists from France and Canada which was published by Elsevier.

Dr. Boyle is known to have drafted the US domestic implementing legislation for the biological weapons convention, known as the Biological Weapons Anti-Terrorism Act of 1989. He has served as a counsel to governments and has advocated for various organisations in the areas of human rights, war crimes and genocide, nuclear policy, and biowarfare.

This paper that was cited by Dr. Boyle highlighted the presence of peculiar furin-like cleavage site in the SARS-CoV-2 that was absent in the other SARS or SARS-like CoVs. This furin like cleavage site is found present in the spike protein of SARS-CoV-2 virus.

As discussed before, once the RBD binds to the receptor of a host cell, the protease in host cell cleaves the S-protein and the fusion sequences of the second section get exposed and virus envelope fuses with the host cell membrane. Now according to what is usually observed, SARS-CoV-1 belongs to the category of coronaviruses whose S-protein gets split during entry into the host cell and MERS-CoV belongs to the second category whose S-protein gets split during exit from the host cell so that it is ready to enter the next host cell.

Therefore, the cutting of S-protein is a very decisively important factor when it comes to cross species transmission of virus because even if the RBD in the first section of S-Protein is able to bind to a receptor of host cell, if the S-protein is not already cleaved or if a protease required to split it is not present in the host cell, the virus genome cannot enter inside it.

The S-protein of SARS-CoV-1 is reported to be cleaved by the protease called TMPRSS2 present in human epithelial cells during its entry. The research presented in the paper cited by Dr. Boyle shows that S-protein of SARS-CoV-2 contains cleavage site for furin protease. Furin is a protease found abundantly in respiratory tract of humans and furin cleavage site is found generally in the S-protein of MERS-CoV which, as mentioned before is known to be cleaved during the virus exit from the host cell. Which is why the presence of a furin like cleavage site in the S-protein of SARS-CoV-2 indicates towards the possibility of cleavage occurring during virus exit which is in contrast to what is generally known and therefore peculiar.

However, the paper does not confirm if this cleavage site actually gets severed or not therefore it is possible that the S-protein of SARS-CoV-2 gets cut during virus entry, just as normally observed. Otherwise, it is also possible that there are two cleavage sites in the S-protein of SARS-CoV-2 that can be cleaved by two different protease in the cell TMPRSS2 and Furin during virus entry and exit respectively. Also important is that the paper does not confirm or deny if this Furin-like cleavage site is the only cleavage site present.

Now how does the presence of furin-like cleavage site allude to the possibility of laboratory origin? Interestingly, this furin like cleavage site is not known to be present inside any of the bat-CoVs RATG13, ZC45/ZXC21 that have been suggested as possible backbones for the present SARS-CoV-2 virus by different theorists. This indicates towards the occurrence of an insertion of this furin-like cleavage site into the bat CoV, which allowed it to infect humans. Now such an insertion can either occur due to its recombination with another virus that possessed that site inside an intermediate host or they can be inserted into the backbone virus inside lab.

Variations around the S-protein cleavage site are known to play a role in cellular tropism and pathogenesis. The researchers in the paper say, This furin-like cleavage site, is supposed to be cleaved during virus egress (exit) for S-protein priming and may provide a gain-of-function to the 2019-nCoV for efficient spreading in the human population compared to other lineage b betacoronaviruses. So, Dr. Boyle while citing this paper, specifically emphasized on the use of phrase Gain of Function in this sentence when he made his assertion that this is a smoking gun evidence because GOF technology is DNA genetic engineering which has no other legitimate scientific purpose except make biological weapons and can be carried out safely only in BSL-4 or a BSL-3 facility.

Now, GOF is a result of mutations. Mutations are classified on the basis of their impact on the function of virus or a protein inside it. The GOF mutations have incremental effects on this function and therefore they are also known as activating mutations. These mutations can either occur naturally or they can be carried out in laboratories. There is a discipline of research in virology known as Gain of Function research or studies which involves increasing the ability of a virus to cause disease. While this increased ability of the virus can indeed be used as a bio-weapon, as suggested by Dr. Boyle and therefore he is not completely inaccurate but it is not true that that there is no other legitimate scientific purpose behind GOF research other than making bioweapon.

GOF research are conducted to study the human-pathogen interactions which can enable appraisal of the pandemic potential of emerging infectious agents. Also, GOF studies are required for vaccine development. However, there is a consensus within the Scientific community that GOF research involve grave biosecurity risks if they are not carried out properly.

RISKY EXPERIMENTS, LABORATORY SAFETY AND GENERAL OPAQUENESS

In April, 2020 there was a report in Washington Post by Josh Rogin which claimed to have obtained two U.S. Diplomatic Cables sent from the U.S. Embassy in China to State Department. In these cables, the U.S. Diplomats in China voiced their concerns about the safety and management issues in BSL-4 lab facility of WIV. One of those cables also emphasized on the labs work on bat coronaviruses and their potential human transmission which posed a risk of new SARS-like pandemic. According to those cables, as reported in Washington Post, in their visit to the BSL-4 lab facility, the U.S. officials found serious shortage of appropriately trained technicians and investigators needed to safely operate that high-containment laboratory.

Besides, there have been other previously reported instances of such concerns raised by researchers and scientists about works in which Shi Zengli was involved.

In 2015, U.S. and Chinese scientists which included Shi Zengli, published a paper about a chimeric virus that they developed by substituting or swapping a gene that encoded spike glycoprotein of SARS like virus obtained from bats, with a gene inside the mouse adopted SARS-CoV backbone. The mouse adopted SARS-CoV, means the SARS-CoV was able to replicate in mice after series of passages from mouse to mouse. The scientists found that the chimeric virus produced by them was able to replicate efficiently in primary human airway cells which they described as surprising.

This paper drew criticism from experts such as Richard H. Ebright and Simon Wain-Hobson. Elbright, an esteemed American micro-biologist who is also known for his work on biosecurity said, The only impact of this work is the creation, in a lab, of a new, non-natural risk and Wain-Hobson, virologist at the Pasteur Institute in Paris described this study as the creation of a novel virus that grew remarkably well in human cells and if it escaped, nobody could predict the trajectory.

Also, there have been multiple known instances of laboratory leaks of SARS-viruses in different countries before, which includes China itself. The other known countries are Singapore and Taiwan. Therefore, laboratory leak theory cannot be discounted. It is also important to consider that governments in Singapore and Taiwan had addressed their occurrences of laboratory leak with complete transparency and co-operation with the International Agencies such as WHO. The Chinese government institutions, however, failed to do so.

Even this time in case of the current COVID-19 pandemic as reported by the media outlet Caixin Global, it was discovered as early as December, 2019 that there is an outbreak of a viral disease which has pandemic potential but China tried to conceal it from rest of the world and covered it up by prohibiting further tests and public sharing of test results, etc. This kept the measures such as restrictions on travel or public gathering from implementing. Besides, in 2002-03, the SARS epidemic had originated in China and it spread from China to 37 countries and even then China had not disclosed about the SARS disease until it was too late.

CONCLUSION

The above presented information makes it clear that there is a need for a thorough investigation into the origins of the current SARS-CoV-2 virus and it must be conducted in an unbiased manner. For that to happen, the International Community must exert pressure over the Chinese government to cooperate with absolute transparency. This pressure will have to be exerted by governments through international organisations and agencies that are comprised of them. However, this is not possible unless the public mandate forces their governments to do that which is necessary and this in turn is dependent on the quality of public discourse on this subject. It is therefore important that this debate about the COVID-19 origins, within the scientific community is brought to masses. This article is an attempt towards that end.

Tanmay Kadam is an engineer-turned-geopolitical practitioner.

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Needed, a transparent investigation into origins of SARS-CoV-2 - The Sunday Guardian Live - The Sunday Guardian

Researchers expect to discover new genetic biomarkers relevant to Alzheimers disease.

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Shuiwang Ji, associate professor in the Department of Computer Science and Engineering at Texas A&M University, is one of the principal investigators on a $6 million grant from the National Institutes of Health to develop artificial intelligence-driven methods to automate the process of finding subtle telltale signs of Alzheimers disease in neuroimaging data. Jis team shares $1.2 million of the grant.

Ji will lead the research team tasked with developing advanced deep-learning methods for finding relevant neural signatures lurking within neuroimages taken using different techniques, such as PET scans and MRIs.

I feel very excited with this collaborative opportunity to make scientific discoveries in medical domains using deep learning and artificial intelligence, said Ji, who has extensive expertise in machine learning, deep learning and medical image analysis.

Alzheimers disease affects 5.6 million Americans over the age of 65, and its symptoms are most noticeably the progressive impairment of cognitive and memory functions. It is also currently the most common form of dementia in the elderly. Despite copious amounts of studies on Alzheimers over the years, researchers understanding of the biology and progression of the disease remains limited, so there are limited advances in therapeutics and preventive strategies.

Ji said the research team expects to discover new genetic biomarkers relevant to Alzheimers, which may lead to understanding the molecular basis of the disease, and in turn, uncover a potential new treatment.

Researchers will leverage existing neuroimaging and genetic data resources from the UK Biobank, the Alzheimers Disease Sequencing Project, the Alzheimers Disease Neuroimaging Initiative, and the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium.

Other collaborators on this research areDegui Zhi, associate professor with the UTHealth School of Biomedical Informatics, and Myriam Fornage, professor at the Center for Human Genetics at UTHealth.

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Artificial Intelligence May Find Signs Of Alzheimer's In Neuroimaging Data - Texas A&M Today - Texas A&M University Today

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Simone Biles, the greatest gymnast of all time, will not compete in the individual all-around gymnastics final at the Tokyo Olympics on Thursday.

Biles is the defending champion for the sport's marquee individual event. She won by a huge margin at the 2016 games in Rio de Janeiro.

The announcement comes after she pulled out of the team final after a rocky opening vault on Tuesday, saying she needed to take care of her mental health.

"I've just never felt like this going into a competition before," she said. "I tried to go out here and have fun ... but once I came out here, I was like, 'no, the mental is not there, so I just need to let the girls do it and focus on myself.' "

USA Gymnastics was supportive of her decision to withdraw from Thursday's event and applauded "her bravery in prioritizing her well-being" in a statement. "Her courage shows, yet again, why she is a role model for so many," the organization added.

Jade Carey, who came to Tokyo as an event specialist, will take Biles' place in the all-around individual event. The 21-year-old had an exceptionally strong showing at the qualifying event, placing ninth overall. However, she was not chosen as a member of the U.S.' four-person team and did not compete in the team event on Tuesday after Biles' withdrawal.

The announcement does not mean this is the last we'll see of Biles; she could still compete in the individual event finals. USA Gymnastics said she'd be evaluated every day to determine whether she'll take part. She qualified in all four of the events.

Biles is one of several Olympic athletes garnering praise and support after speaking openly about the stress of the Games and the importance of prioritizing mental health others include legendary American swimmer Katie Ledecky and Japanese tennis star Naomi Osaka.

As Mandalit del Barco reports from Tokyo, Olympic organizers and Team USA brought mental health resources for athletes and staff in an especially stressful year.

"Besides the pressure to be the best, and besides the global pandemic, there's also the fact there are no spectators allowed to watch the Games in person," she explains. "There aren't any family members to hug after they win, there are no friends or family or fans to cheer them on from the stands."

Stress affects all of us, even if we're not Olympic athletes. Here are some more resources and suggested reading:

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Simone Biles And Valuing Mental Health, Mask And Vaccine Guidance, Child Tax Credit Options: Today's Top Stories - NPR

Advanced therapy medicinal products (ATMPs) are a focus for biopharma. The ability to treat disease in a targeted manner, the reduced likelihood of competition, and regulatory support make such products attractive R&D targets.

The revenue potential of ATMPs is another factor. Estimates suggest the global market for ATMPs could grow to $9.6 billion by 2026.

But for the market to reach its full potential, industry must find efficient ways of making ATMPs, according to Maria Papathanasiou, PhD, assistant professor, Imperial College Londons department of chemical engineering, who says mathematical modeling is key.

Mathematical models and/or computer modeling tools can assist decisions throughout drug development from discovery all the way to therapy distribution, she says. In manufacturing, such tools can help with decision making related to selection of units, optimization of processes, identification of optimal conditions of operation, and they can also be used as soft sensors when measurements are not readily available.

For Papathanasiou, the key benefit of building a mathematic model is that it allows for the systematic analysis of the system considering multiple factors at the same time.

The impact of synergetic/antagonistic effects can be better studied. Also, they provide a cost-efficient basis for in silico experimentation, decreasing the time and labor required for wet lab experiments, she tells GEN. Such tools give us the ability to run a very high number of experiments on the computer and then decide which of those we want to validate in the lab. They have a great potential to assist with initiatives such as Quality-by-Design and Design Space Identification as well.

Models can also be used on the factory floor, Papathanasiou says, explaining they prove to be a very powerful tool for in-process monitoring and online control as validated models can be used as soft sensors when online measurements are not readily available.

Papathanasiou, who co-authored a recent study examining the role modeling can play in process development for ATMPs and next-generation vaccines, says choosing the correct type of model on which to base process development is a critical step.

Such models can be mechanistic, data-driven, or hybrid. Each class of models is different with mechanistic models being the most detailed in terms of translating the physicochemical characteristics of the system into mathematical equations (each variable and parameter reflects an actual entity of the system at hand), she explains. Data-driven models sit at the other end where they use input/output datasets to capture the system dynamics, without the need to know what is exactly going on in terms of physicochemical properties, reactions, etc.

Choice of model is important as each require different types of data and process monitoring technology required.

Depending on the class of models one uses the amount of data differs. In our collaborations with companies, we use primarily existing or offline data for the development of such tools and the current analytics tie in nicely, she continues. For an online implementation of such tools that are also known as digital twins advanced PAT would really advance the usability.

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Advanced Therapy Medicinal Products and Next-Gen Vaccine Production - Genetic Engineering & Biotechnology News