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Tuesday, December 21, 2021

Omicron variant: lessons from Denmark

Danish scientists have looked at the first 785 cases of Omicron variant in Denmark. The most important lesson is that 83% of the cases were fully vaccinated. (Mostly two doses of an mRNA vaccine). This includes 7% of the total cases that had also received a booster shot. 76% of the Danish population are fully vaccinated.

Espenhain, L., Funk, T., Overvad, M., Edslev, S.M., Fonager, J., Ingham, A.C., Rasmussen, M., Madsen, S.L., Espersen, C.H. and Sieber, R.N. (2021) Epidemiological characterisation of the first 785 SARS-CoV-2 Omicron variant cases in Denmark, December 2021. Eurosurveillance 26:2101146. doi: [Eurosurveillance: Full Text]

This is similar to the results in other countries where a large percentage of the population are vaccinated. The spread of Omicron in those countries is largely driven by infection of the vaccinated group and the only way to blunt this spread is to limit contacts among vaccinated people. That means lockdowns or partial lockdowns for everybody and that seems to be working.

As usual, the United States is going to serve as a good control on these measures since the dominant message from American government, media, and health officials is that you are pretty much okay if you are vaccinated and you just have to be a bit more carefeul. No need to change your holiday travel plans.

The cases in Denmark cover all ages groups but the 20-29 age group had the highest number of infections. Quite a few of the cases could be traced to a "seasonal gathering" of 150 people and a large concert but most others seem to be due to community transmission once the variant became established. The original cases came from people who had travelled from South Africa and other countries.

Since the identification of the first Omicron case in Denmark, a steep increase in the number of cases has been observed. A major driver of this development was a large party with young adults – a population group with more social and close connections than adults and children.

We find several reasons for concern: (i) the rapid spread shortly after introduction despite extensive contact tracing efforts, (ii) the occurrence of several superspreading events with high attack rates and (iii) the high proportion of fully vaccinated Omicron cases.

So far, there haven't been many hospitalizations or deaths due to infection with the Omicron variant but that could come later.

Sunday, December 19, 2021

The omicron variant evades vaccine immunity but boosters help

Scientists are very interested in the omicron variant and why it is so dangerous. Since vaccinated people are getting infected, it must mean that the omicron variant isn't effectively neutralized by vaccine-induced antibodies. Several preprints on this topic have been posted and they all reach the same conclusion. I'll discuss one of them.

Garcia-Beltran, W.F., St Denis, K.J., Hoelzemer, A., Lam, E.C., Nitido, A.D., Sheehan, M.L., Berrios, C., Ofoman, O., Chang, C.C. and Hauser, B.M. (2021) mRNA-based COVID-19 vaccine boosters induce neutralizing immunity against SARS-CoV-2 Omicron variant. medRxiv. doi: 10.1101/2021.12.14.21267755

Recent surveillance has revealed the emergence of the SARS-CoV-2 Omicron variant (BA.1/B.1.1.529) harboring up to 36 mutations in spike protein, the target of vaccine-induced neutralizing antibodies. Given its potential to escape vaccine-induced humoral immunity, we measured neutralization potency of sera from 88 mRNA-1273, 111 BNT162b, and 40 Ad26.COV2.S vaccine recipients against wild type, Delta, and Omicron SARS-CoV-2 pseudoviruses. We included individuals that were vaccinated recently (<3 months), distantly (6-12 months), or recently boosted, and accounted for prior SARS-CoV-2 infection. Remarkably, neutralization of Omicron was undetectable in most vaccinated individuals. However, individuals boosted with mRNA vaccines exhibited potent neutralization of Omicron only 4-6-fold lower than wild type, suggesting that boosters enhance the cross-reactivity of neutralizing antibody responses. In addition, we find Omicron pseudovirus is more infectious than any other variant tested. Overall, this study highlights the importance of boosters to broaden neutralizing antibody responses against highly divergent SARS-CoV-2 variants.

Friday, December 17, 2021

On the effectiveness of vaccines

I've learned a bit of immunology from hanging out with immunologists so I'm going to try and explain how vaccines protect you from the worst consequences of an infection and why booster shots aren't as necessary as you think. This will be an illustration of how difficult it is for the media to keep you correctly informed about real science and why we should have more scientists explaining these things instead of doctors

Dozens of papers on this topic have been published over the past year or so and they all say the same thing. SARS-CoV-2 vaccinations induce an immediate production of antibodies in response to the spike protein antigen whether it's presented on the surface of a viral vector such as adenovirus or synthesized in your cells by mRNA. The antibodies are produced by a small number of B cells that just by chance happen to recognize the viral protein. These cells multiply rapidly so that within a few days you have enough antibodies being produced to fight off any infection.

Over time, the antibody production declines if there's no infection but some of the B cells become memory B cells that lie in wait for the next infection when they can be rapidly stimulated if you get infected months, or years, later. There's another type of cell called a T cell that also forms memory T cells that are very long-lasting and help fight off future infections.

Imagine that you encounter the virus several months after you've been vaccinated. As soon as the virus enters your body the memory cells are activated and the virus is attacked. You may have a mild case of COVID-19 for a few days but you are protected against the most severe forms of the disease. The point is that a reduction in antibody levels is perfectly normal. What's important is whether you have a robust level of memory B cells and memory T cells that can be activated. The hype in the media has convinced people that the vaccines are no longer effective after six months and you have to get a booster shot to protect you from COVID-19.

Here's a very recent paper that presents the data. It was published in Science on December 3, 2021.

Goel, R.R., Painter, M.M., Apostolidis, S.A., Mathew, D., Meng, W., Rosenfeld, A.M., Lundgreen, K.A., Reynaldi, A., Khoury, D.S. and Pattekar, A. et al. (2021) mRNA vaccines induce durable immune memory to SARS-CoV-2 and variants of concern. Science 374:eabm0829. doi: 10.1126/science.abm0829

Vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has proven highly effective at preventing severe COVID-19. However, the evolution of viral variants, and waning antibody levels over time, raise questions regarding the longevity of vaccine-induced immune protection. Goel et al. examined B and T lymphocyte responses in individuals who received SARS-CoV-2 messenger RNA vaccines. They performed a 6-month longitudinal study of individuals who never had SARS-CoV-2 infection compared with people who had recovered from SARS-CoV-2. Humoral and cellular immune memory was observed in vaccinated individuals, as were functional immune responses against the Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.2) viral variants. Analysis of T cell activity suggested that robust cellular immune memory may prevent hospitalization by limiting the development of severe disease.

The authors looked at the immune reaction in three different groups. The first was the naive group of people who have never had COVID-19 but got the vaccine (blue). The second group was people who had already survived COVID-19 and then got vaccinated (red). The third group was composed of people who had mild cases of COVID-19 and never got vaccinated (purple).

This is a long paper with lots of experiments but the data can be summarized in the figure below. The authors looked at antibodies to the spike protein and to its specific ACE2 binding site. They also looked at neutralizing antibodies or the abiity of circulating antibodies to neutralize whole virus particles. The results are summarized in the first graph and they show that the antibody levels rise to maximum levels about one week after receiving the second dose of vaccine (administered four weeks after the first dose).

The antibody levels fall to about 10% of the maximum value over the next six months. (The x-axis is a log scale.) This is exactly what you expect for a typical vaccine. Note that the levels for people who had already been infected were higher to begin with but the rate of decline was similar to the naive group. This suggests that booster shots will have a similar effect on antibody levels.

The levels of memory B cells and memory T cells rise to a maximum at four months, right at the time of the second dose. They remain high at the end of six months.

Taken together, these data demonstrate that mRNA vaccines induced a population of memory B cells that was durable for at least six months after vaccinaton, and these cells were capable of rapidly producing functional antibodies against SARS-CoV-2, including neutralizing antibodies against VOCs [variants of concern], upon stimulation....

Taken together, these data indicate that mRNA vaccination generates durable SARS-CoV-2-specific CD4+ T cell memory in individuals who were not previously infected with SARS-CoV-2 and only transiently boosts these responses in SARS-CoV-2-recovered individuals.

What this means is described by the authors in the concluding remarks,

These data may also provide context for understanding potential discrepancies in vaccine efficacy at preventing infection versus severe disease, hospitalization, and death. Declining antibody titers over time likely reduce the potential that vaccination will completely prevent infection or provide near-sterilizing immunity. However, the durability of cellular immunity, here demonstrated for at least 6 months, may contribute to rapid recall responses that can limit initial viral replication and dissemination in the host, thereby preventing severe disease.

In other words, if you are fully vaccinated (two doses of mRNA vaccine) then you are well-protected against severe disease although you may suffer mild symptoms for a few days. You may be able to avoid the mild symptoms if you have gotten a recent booster shot but that effect is likely to decline in a few months.

The hype about booster shots is extremely misleading. The media is making it sound like all of your vaccine protection declines after six months and you need the boosters to have any chance at all against the omicron variant. How many times have you heard that your vaccine protection drops to 33% after six months?

You could argue that boosters aren't even necessary but that ignores the possibility that even a mild infection may be harmful to some people. It also ignores the possibility that by preventing even a mild infection you could be blocking the spread of the virus. I don't know of any data on viral loads after vaccination but I suspect that a booster offers some protection against spread.

Image Credit: The coronavirus figure is from Alexy Solodovnikov and Wikmedia Commons.

Thursday, November 18, 2021

"Has Science Killed Philosophy?"

This is a debate sponsored by the Royal Institute of Philosophy on the question "Has science killed philosophy?" It suffers from one of the main problems of the philosphy of science and that's an unreasonable focus on theoretical physics. What's interesting is that the question even arises because that suggests to me that there's some reason to suspect that philosophy might not be as important as most philosophers think.

Watch the debate and decide for yourselves whether philosophy is still useful. Frankly, I found it very boring. I didn't learn anything that I didn't know before and I didn't find the defense of philosophy compelling. The philosopher's best answer to the challenge is that their discipline has complete control over rational thinking so every time you are thinking seriously about something you are doing philosophy. Ergo, philosophy will never be killed by science.

What do you think of Eleanor Knox's description of the differences between your right hand and your left hand? Is she on to a deep metaphysical question that science can't address? Or is this an example of why scientists are skeptical of the value of philosophy?

All three panelists were asked to identify a modern philosopher who made a significant contribution to science. Alex Rosenberg immediately identified someone named Samir Okasha whom I've never heard of. Apparently, Okasha made a significant contribution to the levels of selection question in evolution. According to Alex Rosenberg, the philosophers that he listens to tell him that if anyone has settled these question it's Okasha. Perhaps he should listen to evolutionary biologists to get their view on the subject?

Monday, November 15, 2021

The first review of "Viral" is out and it ain't pretty

Michael Hiltzik is first off the mark writing for the Los Angeles Times: These authors wanted to push the COVID-19 lab-leak theory. Instead they exposed its weaknesses.

Hiltzik is one of the few science writers who know what they'r talking about.1 You should read his entire review—here are some excerpts to tempt you.

... “Viral” is a laboratory-perfect example of how not to write about a scientific issue. The authors rely less on the scientists doing the painstaking work to unearth the virus’ origin than on self-described sleuths who broadcast their dubious claims, sometimes anonymously, on social media. In the end, Chan and Ridley spotlight all the shortcomings of the hypothesis they set out to defend....

“Viral” is built on vague innuendo, dressed up with assertions that may strike laypeople as plausible but have long since been debunked by experienced virologists. An entire chapter, for example, is devoted to the “furin cleavage site,” a feature of the virus’ structure through which the enzyme furin makes the spikes on its surface — which it uses to penetrate and infect healthy cells — more effective.

The furin site was originally described by lab-leak advocates as so unusual that it could have been placed there only by humans. Virologists have since determined that the feature is not all that rare in viruses similar to SARS2, and in any case, it could have emerged through natural evolutionary processes well known to experts. Chan and Ridley place a heads-I-win-tails-you-lose gloss on these findings, writing that if the site “proves to have been inserted artificially, it confirms that the virus was in a laboratory and was altered. ... If, on the other hand, the furin cleavage site proves to be natural, it still says nothing about where the virus came from.” Why write about it at all, then?

Alina Chan's reputation is already about as low as it can get and now it looks like she's dragging Matt Ridely down with her. He was already part way there so he didn't have far to go.

The book is published by HarperCollins. Should American lawmakers look seriously at regulating the publishing industry for spreading misinformation since they're already investigating Facebook for the same crime?

1. See: Is the media finally realizing that they have been duped into promoting the lab leak conspiracy theory?.

Saturday, November 13, 2021

Alina Chan teams up with Matt Ridley to promote the lab leak conspiracy theory

Harper is set to publish Viral: The Search for the Origin of COVID-19 in just a few days. The authors are Alina Chan, a postdoc at the Broad Institute of MIT and Harvard, and Matt Ridley, a science journalist who has written several respectable books.

The book promises to reignite discussion of the lab leak conspriracy theory with a focus on Alina Chan's role in promoting it. In preparation, you should read this article about her: They called it a conspiracy theory. But Alina Chan tweeted life into the idea that the virus came from a lab.

Monday, November 08, 2021

The origin of SARS-CoV-2 and gain-of-function research

I'm currently discussing the meaning of "function" with a small group of scientists and philosophers and it's not easy to come up with an acceptable definition. Imagine how much more difficult it is to identify research that results in a gain of function!

Gain-of-function research has been in the news recently because there are a group of conspiracy theorists who accuse the scientists at the Wuhan Institute of Virology of conducting gain-of-function research on bat caronaviruses leading to the creation of SARS-CoV-2 which then escaped from the lab to cause the pandemic. Some of these conspiracy theorists even accuse the American NIH of funding this gain-of-function research.

How do you define gain-of-function research in a meaningful manner? That's the question posed by Amber Dance in a recent Nature article. (Amber Dance is a freelance science journalist.) The first reference below is the title and subtitle of the article that was published in the magazine and the second reference is the online version.

Dance, A. (2021) The Truth About Gain-of-Function Research: Granting new abilities to pathogenic microbes sounds dangerous, but what has the research told us? Nature 598: 554-555. [doi: 10.1038/d41586-021-02903-x]

Dance, A. (2021) The shifting sands of ‘gain-of-function’ research: The mystery of COVID’s origins has reignited a contentious debate about potentially risky studies and the fuzzy terminology that describes them. Nature 598: 554-555. [Nature website]

The only relevant gain-of-function research is the type specified by NIH as "gain-of-function research of concern" (GOFROC). This is research that makes a potential pathogen more likely to cause disease in humans. This is the kind of research that would be carried out in a lab devoted to biological warfare but it could also apply to some research that was carried out in the past, as described in the article. There is no evidence to support the accusation that scientists in China, or anywhere else, were doing such research on coronaviruses.

There are other kinds of research that involve constructing chimeric viruses in order to test whether they have the potential to cause a pandemic. This is perfectly normal, even necessary, research but conspiracy theorists have claimed that this is forbidden gain-of-function research. The article does a good job of explaining this research and why it's not a problem.

Image Credits: The coronavirus figure is from Alexy Solodovnikov and Wikmedia Commons.

Wednesday, November 03, 2021

What's in your genome?: 2021

This is an updated version of what's in your genome based on the latest data. The simple version is ...

about 90% of your genome is junk

Sunday, October 31, 2021

On the importance of active learning

I'm on the editorial board of an education journal so I've been following the pedagogical literature for many years. The idea of active learning, or student-centered learning, has been around for decades and there's solid evidence showing that it's way more effective than traditional lecture-style learning. If you are a teacher and you haven't adopted some form of active learning in your class then you need to change as soon as possible. There's no scientific justification for sticking with the traditional ways of teaching.

Saturday, October 30, 2021

Will Ontario parents vaccinate their children?

COVID-19 vaccinations are soon going to be available for children in Ontario, Canada. Will parents vaccinate their children?

The Toronto Star recently published a poll where parents of at least one child under 12 were asked this question and 69% said yes, they were going to get their children vaccinated [Nearly 70 per cent of Ontario parents of kids 5 to 11 planning to get them vaccinated, poll says]. Only 11% said they were not going to vaccinate their children. (19% were unsure.)

It's interesting to see the reasons parents gave for not vaccinating their children. 82% of these parents say that they don't trust the vaccine because it's too new and/or not enough research has been done. That's an illogical excuse because public health officials all over the world are recommending children's vaccinations and they wouldn't be doing it if there were any serious doubts about safety. The reluctance of these parents stems from the mistrust in public health officials and science that has been fostered by the media over the past eighteen months. The Toronto Star has been one of the worst offenders.

Some of the skepticism over decisions made by public heath officials is justified but the overall effect of constant criticism and nitpicking has been to undermine the authority of the very people we rely on to get us out of the pandemic. That's unfortunate.

The other problem for Canadians is that we are inundated with news from our neighbor to the South and that country really does have a bad track record. The somewhat more justified criticism of American public health officials spills over into Canada and taints our own physicians and scientists. That's also unfortunate.

Note that only 23% of these parents can be counted as vaccine deniers and since this group only represents 11% of the total surveyed, it means that the total number of those who don't believe in vaccines is less than 3% of the parents of children under 12. This is consistent with other surveys suggesting that the hard-core vaccine deniers represent less than 5% of the population.

A substantial percentage of those who say they aren't going to vaccinate their children think that vaccinations aren't really necessary for children under 12. Some of those people are probably going to change their minds when most of their children's friends get vaccinated. They will certainly change their minds if vaccinations are required for school.

I think the survey is very encouraging. It looks like most children will be vaccinated over the next few months. There will be holdouts but most of them will eventually give in to public pressure.

Friday, October 29, 2021

Science writing in the age of denial

Here's an interesting presentation by Sean B. Carroll, the evolutionary biologist and author of several books on evolution. He's also written a fascinating book on Jacques Monod and he gave a talk at the University of Toronto a few years ago on the role of chance in evolution—I have a signed copy of his book (see the photo and my blog post: Biologist Sean Carroll in Toronto).

Sean likes to emphasize the importance of storytelling in science communication and education. By this he sometimes means stories about individual scientists and sometimes stories about the history of a subject. As Vice President for Science Education at the Howard Hughes Medical Institute in Washington DC (USA) he has helped craft some short videos for high school students and the presentation contains an example of one on evolution. I'm not sure I fully agree with his emphasis on storytelling—as least not to the extent that he promotes it—but some version of it can be useful as long as it doesn't get in the way of understanding important concepts.

I leave it to you to decide whether the short HHMI video is the best way to teach high school students about evolution. I personally don't like the undue emphasis on natural selection and natural history.

The reason for drawing your attention to an old 2012 presentation is to remind you about the charactieristics of science denial. Sean explains the six rules of denialism.

  1. Doubt the Science
  2. Question Scientist's Motives and Integrity
  3. Magnify Disagreements among Scientists and Cite Gadflies as Authorities
  4. Exaggerate Potential Harm
  5. Appeal to Personal Freedom
  6. Acceptance Would Repudiate Key Philosophy

His examples are the denial of evolution by creationists and the rejection of vaccinations by chiropractors. Today, we see how the same rules apply to those who reject COVID-19 vaccinations and to the Lab Leak Conspiracy Theory.

Do scientists write books for the "casual reader"?

I just read a review in Science of Douglas Futuyma’s new book How Birds Evolve: What Science Reveals About Their Origin, Lives, and Diversity. [Contextualizing avian origins and evolution]. Many of you will be familiar with Futuyma because he’s the author of one of the best textbooks on evolution.

Right after reading the review, I signed on to Amazon intending to buy the book but when I saw the price ($95 Cdn) I had second thoughts. Much as I’d like to see how Futuyma handles a complex topic like bird evolution, I don’t think I want to spend that much money.

But there are parts of the review that I find intriguing enough to address because they relate to my concern about science writing. Here’s the first thing that caught my eye. The reviewer, Alan Feduccia, writes,

Although casual readers might find the text somewhat advanced and laborious, the chapters are composed in well-written conversational prose, with expositions on multifarious evolutionary phenomena that are infused with scientific explanations.

This highlights an issue that I’ve been writing about recently. "Casual readers" are not going to buy this book and I’m confident that Futuyma is not writing for casual readers. What’s the point of saying that such readers might find the book "advanced and laborious"? What I want to know is whether the actual intended audience would find the book laborious.

The reviewer goes on to describe some of things that are in the book.

Futuyma’s discussion begins with a section that explains Charles Darwin’s transformative ideas—from natural selection and fitness to brood parasitism to gene flow and genetic drift—and thematic chapters elaborate on the relationship between these ideas and bird lineages. The book describes complex evolutionary issues in understandable terms, ...

That sounds like the kind of science writing that I admire. We should aim for explaining complex issues in terms that are understandable to an audience that is prepared to buy the book. This may mean that the casual readers - who will never buy the book - are left out but that’s okay. It may mean that Futuyuma’s book is not going to win a Pulitzer Price for general nonfiction but that’s okay too since good science books are not high on the list of previous award winners.1 I’m pretty sure that scientific accuracy isn’t a prominent criterion in selecting award winners (in any category).

The reviewer is somewhat critical of the science in the book and takes Futuyma to task for promoting “just-so” stories and for not fully explaining the speculative nature of some of his conclusions. The reviewer notes that “controversy, not consensus, is grist to the mill of good science” and that strikes me as insightful. The problem is that writing about controversy and attempting to explain both sides of an issue are very hard to do and often in conflict with the emphasis on style that is promoted by science writers and editors.

1. Previous Pulitzer Prize winning books that might be counted as science books are: The Emperor of All Maladies by Siddhartha Mukherjee (2011); Guns, Germs and Steel: The Fates of Human Societies, by Jared Diamond (1998); The Beak Of The Finch: A Story Of Evolution In Our Time, by Jonathan Weiner (1995); The Ants, by Bert Holldobler and Edward O. Wilson (1990); and On Human Nature, by Edward O. Wilson (1979).

Thursday, October 28, 2021

Science reviews a creationist book

You can't get much more anti-science than a book about Adam and Eve. Nevertheless, Stephen Schaffner—a computational biologist at the Broad Institute of MIT in Boston—decided that such a book was worthy of a mostly favorable review in one of the most prestigious science journals in the world [Adam. Eve, and the evolution of humankind].

Schaffner is reviewing a book by William Lane Craig whom he describes as "a widely published philosopher, theologian, and Christian apologist." There are others who would dispute that laudatory description including Richard Dawkins in a ten-year-old essay published in The Guardian [Why I refuse to debate with William Lane Craig].

I won't bother to mention all of the issues with the review since Jerry Coyne has covered them on his website but I would like to quote part of the second-last paragraph of the review.

Craig’s goal in writing this book, of course, is not a scientific one, and it cannot be judged on scientific grounds. I suspect that for many scientists, including religious ones, the exercise will be seen as misguided or simply incomprehensible.

Having followed Craig's anti-science crusade for several years, I have no difficulty in understanding why he would write such a book. What I find truly misguided and incomprehensible is why Science would publish such a review. Perhaps it's because AAAS, the publisher of Science, has a history of accommodating religion?

Wednesday, October 27, 2021

They can smell dead people

Dogs can be trained to detect fresh cadavers but can they detect bodies that have been buried for months or years? Can they detect places where a dead body has rested for a short period of time, such as the trunk of a car, during commission of a crime? Can the odor linger for months or years?

These are the questions addressed by Peter Andrey Smith in a recent article in a special issue of Science devoted to criminal injustice [The Sniff Test]. The article asks whether juries can understand science, You will not be surprised to find out that the answer is "no."

Tuesday, October 26, 2021

The case for a natural origin of SARS-CoV-2

Lots of people seem to be confused about the origin of SARS-CoV-2, the virus responsible for the COVID-19 pandemic. The investigating committee ot the World Health Organization (WHO) concluded last winter that a natural origin is the most likely scenario but there still seems to be a substantial percentage of the population who think that the virus was being studied at the Wuhan Institute of Virology (WIV) and leaked from there to start the pandemic. This belief in a lab leak scenario persists in spite ot the fact that 21 expert scientists have discounted it and concluded that a natural origin is the best hypothesis. The lab leak speculation persists even when the United States intelligence agencies reached the same conclusion as the scientific experts and said that a natural origin was more likely.

I've published several posts on this topic over the past year trying to emphasize four points: (1) the evidence strongly favors a natural origin, (2) there is no scientific evidence to support the claim that the WIV scientists were working on SARS-CoV-2 before the pandemic started, (3) the most knowledgeable science experts agree that a natural origin is the most likely scenario, and (4) the media is misrepresenting the science and treating the two competing explanations as equivalent.

In this post I want to describe the case for a natural origin in as simple a manner as possible so that people can refer to the main lines of evidence and so that opponents of a natural origin can explain why they dismiss that evidence. I also want to briefly explain why we need to listen to the experts instead of arbitrarily dismissing their views as a argument from authority and assuming that our own research trumps the experts.

Monday, October 25, 2021

Electron transport supercomplexes in the mitochondria

The generation of ATP in mitochodrial membranes is driven by the energy from a protonmotive force caused by the movement of protons from a high concentration in the space between the inner and outer membranes and a low concentration on the inside of the mitochondria. The discovery of this mechanism, called the chemiosmotic theory, is due to Peter Mitchell, who won a Nobel Prize in 1978. It's one of the classic examples of a real paradigm shift because the mechanism completely changed the way biochemists looked at chemical reactions [Ode to Peter Mitchell].

The creation of the proton gradient is due to a series of oxidation-reduction reactions that involve the transfer of electrons from one molecule to another. The electrons pass down a chain of reactions from a relatively high energy molecule such as NADH to successively lower energy molecules and end up in water. As the electrons lose energy, the excess energy is coupled to the pumping of protons from the inside of the mitochondrion to the inner membrane space, creating a proton gradient. This gradient is what drives ATP production.

The chemical reactions are catalyzed by three large enzyme complexes: Complex I (NADH-ubiquinone oxidoreductase); Complex III (Ubiquinol-cytochrome oxidoreductase; and Complex IV (Cytochrome C oxidase). The electrons are transported between the complexes by ubiquinone (Q) and cytochrome C.

The structure and function of each of these complexes are usually described in separate sections of a biochemistry textbook because they are so complex but we've always known that they function together as an electron transport chain. When I first started writing this section of my textbook it was obvious that the three complexes would cluster together in the inner mitochondrial membrane and there was even some evidence to suggest that they were in close contact. The idea that they would form a well-defined supercomplex was hypothesized in the 1990s but the evidence was weak so it didn't make it into most textbooks.

The structures of Complexes I, II and III were eventually solved by X-ray diffraction studies of the isolated complexes but isolating any supercomplexes was difficult. With the advent of high resolution three dimensional electron microscopy one could finally see the predicted supercomplexes. The latest result, just published in Nature, characterizes the CI-CIII-CIV supercomplex from mammalian mitochondria (Vercellino and Sazanov, 2021).

The nice thing about this result, and the earlier studies on supercomplexes in yeast and plants, is that it confirms earlier speculations that such complexes must exist even though the evidence was weak. It shows you that a deep understanding of biochemistry structure and function can lead to reasonable hypotheses than can be tested when the technology improves.

Image credit: The first image is a modified version of Figure 14.6 from Moran et al. Principles of Biochemistry, 5th edition. The second image is from Vercellino and Sazanov (2021).

Vercellino, I. and Sazanov, L.A. (2021) Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV. Nature 598:364-367. [doi: 10.1038/s41586-021-03927-z]

Characteristics of COVID-19 in the United States during 2020

An interesting paper on COVID-19 infections in the USA during 2020 was recently published in Nature. The take-home lessons are:

  1. about 78% of infections were probably undocumented so the actual number of people with COVID-19 is almost twice the number that's been reported
  2. about 31% of the population was infected during 2020 giving rise to a considerable level of natural immunity
  3. by the end of 2020 the case fatality rate (CFR = number of deaths per estimated cases) fell to about 0.30% due to better reporting of cases and better patient care
  4. the case fatality rate of 0.30% is about four times higher than that of seasonal influenza (<0.08%)

Sen, P., Yamana, T.K., Kandula, S., Galanti, M. and Shaman, J. (2021) Burden and characteristics of COVID-19 in the United States during 2020. Nature 598:338-341.
[doi: 10.1038/s41586-021-03914-4]

The COVID-19 pandemic disrupted health systems and economies throughout the world during 2020 and was particularly devastating for the United States, which experienced the highest numbers of reported cases and deaths during 2020. Many of the epidemiological features responsible for observed rates of morbidity and mortality have been reported; however, the overall burden and characteristics of COVID-19 in the United States have not been comprehensively quantified. Here we use a data-driven model-inference approach to simulate the pandemic at county-scale in the United States during 2020 and estimate critical, time-varying epidemiological properties underpinning the dynamics of the virus. The pandemic in the United States during 2020 was characterized by national ascertainment rates that increased from 11.3% (95% credible interval (CI): 8.3–15.9%) in March to 24.5% (18.6–32.3%) during December. Population susceptibility at the end of the year was 69.0% (63.6–75.4%), indicating that about one third of the US population had been infected. Community infectious rates, the percentage of people harbouring a contagious infection, increased above 0.8% (0.6–1.0%) before the end of the year, and were as high as 2.4% in some major metropolitan areas. By contrast, the infection fatality rate fell to 0.3% by year’s end.

Sunday, October 24, 2021

Style vs substance in science communication: The role of science writers in major science journals

Science writers have always had articles published in the leading science journals such as Science and Nature but over the past few decades their role seems to have increased so that now even lesser journals employ them to write articles, commentary, and press releases. I recently posted an example of where this can go horribly wrong [Society for Molecular Biology and Evolution (SMBE) spreads misinformation about junk DNA].

The role of science writers has come to dominate the pages of Science and Nature so that we now have a situation where only two thirds of the pages in a typical issue are devoted to actual science publications and most readers are concentrating on the news and opinons in the front part of the journal. In some cases, the science writers control the image of these journals as happened at Nature during the ENCODE publicity campaign in 2012. Over at Science, Elisabeth Pennisi has done more to spread misinformation than any scientist in the field of molecular biology.

These are cases where science writers have sacrificed sustance for style. They write nice readable articles that promote the image of their journal but are scientifcally incorrect.

Let's look at a specific example. Back in 2005 Science celebrated its 125th anniversary by publishing "125 Questions: What We Don't Know." One of those questions was "Why Do Humans Have So Few Genes?"—a question that scientists had adequately answered in 2005 but you wouldn't know that from the short article written by Elizabeth Pennisi [SCIENCE Questions: Why Do Humans Have So Few Genes?]. The article was full of untruths and misinformation. There were lots of other questions in that issue that were just as ridiculous if you knew the topics.

Now, you might imagine that these questions were posed by the leading researchers in their fields but you would be wrong. The list of questions was drawn up by editors and science writers as described in the anniversary issue [SCIENCE Questions: Asking the Right Question].

We began by asking Science’s Senior Editorial Board, our Board of Reviewing Editors, and our own editors and writers to suggest questions that point to critical knowledge gaps. The ground rules: Scientists should have a good shot at answering the questions over the next 25 years, or they should at least know how to go about answering them. We intended simply to choose 25 of these suggestions and turn them into a survey of the big questions facing science. But when a group of editors and writers sat down to select those big questions, we quickly realized that 25 simply wouldn’t convey the grand sweep of cutting-edge research that lies behind the responses we received. So we have ended up with 125 questions, a fitting number for Science’s 125th anniversary.

Isn't it remrkable that editors and writers are being asked to evaluate science (substance) as if their opinions were more important than those of the scientists?

Has Science learned from these mistakes? No, because a few months ago they published a new list of 125 questions in collaboration with the 125th anniversary of Shanghai Jiao Tong University: 125 Questions: Exploration and Discovery. The list of questions hasn't gotten any better; it includes questions like, "How do organisms evolve?"; "What genes make us uniquely human?"; and "How are biomolecules organized in cells to function orderly and effectively?" Many of you can imagine what the short accompanying explanation looks like and you would be right.

Pennisi's original question has disappeared but there's a very similar question in the 2021 list.

Why are some genomes so big and others very small?

Genome size, which is the amount of DNA in a cell nucleus, is extremely diverse across animals and plants, and varies more than 64,000-fold. The smallest genome recorded exists in the microsporidian Encephalitozoon intestinalis (a parasite in certain mammals), and the largest genome belongs to a flowering plant known as Paris japonica, which has 150 billion base pairs of DNA per cell (50 times larger than that of a human). Plants are interesting in that their genome size plays an important role in their biology and evolution. But as the authors of a 2017 paper in Trends in Plant Sciences wrote: “Although we now know the major contributors to genome size diversity are non-protein coding, often highly repetitive DNA sequences, why their amounts vary so much still remains enigmatic.”

Sandwalk readers know that knowledgeable scientists came up with good answers to that question about 50 years ago. One answer is that different species have different amounts of junk DNA because some species don't have large enough populations to eliminate it by natural selection. In other cases, the differences are due to polyploidization.

You would think that after all the criticism of Science over their past coverage of genomes and junk DNA that the writers and editors would know this. But they don't, and that's because science writers and editors seem to be remarkably immune to scientific criticism. (The topic probably doesn't come up when they get together at their science writers' conventions.) I'm making the case that they are so focused on style (science writing) that they just don't care about substance (scientific accuracy).

The major journals have a serious problem that they don't recognize. A lot of the stuff that appears in their journals is not scientifically accurate or, at the very least, is misleading. They're not going to fix this problem if their editorial staff is dominated by science journalists.

Tuesday, October 19, 2021

Society for Molecular Biology and Evolution (SMBE) spreads misinformation about junk DNA

The Society for Molecular Biology and Evolution (SMBE) is a pretigious society of workers in the field of molecular evolution. I am a member and I have attended many of their conferences. SMBE sponsors several journals incucluding Genome Biology and Evolution (GBE), which is published by Oxford Academic Press.

The latest issue of GBE has a paper by Stitz et al. (2021) that describes some repetitive elements in the platyhelminth Schistosoma mansoni. The authors conlcude that some of these elements might have a function and this prompts them to begin their discussion with the following sentences.

The days of “junk DNA” are over. When the senior authors of this article studied genetics at their respective universities, the common doctrine was that the nonprotein coding part of eukaryotic genomes consists of interspersed, “useless” sequences, often organized in repetitive elements such as satDNA. The latter might have accumulated during evolution, for example, as a consequence of gene duplication events to separate and individualize gene function (Britten and Kohne 1968; Comings 1972; Ohno 1999). This view has fundamentally changed (Biscotti, Canapa, et al. 2015), and our study is the first one addressing this issue with structural, functional, and evolutionary aspects for the genome of a multicellular parasite.

It is unfortunate that the senior authors didn't receive a good undergraduate education but one might think that they would rectify that problem by learning about genomes and junk DNA before publishing in a good journal devoted to genomes and evolution. Alas, they didn't and, even worse, the journal published their paper with those sentences intact.

As you might imagine, these statements were seized upon by Intelligent Design Creationists who wasted no time in posting on their creationist blog [Oxford Journal: “The Days of ‘Junk DNA’ Are Over ”].

But that's not the worst of it. The same issue contains an editorial written by Casey McGrath who self identifies as a employee of the Society for Molecular Biology and Evolution in Lawrence Kansus (USA). She is the Social Media Editor for Genome Biology and Evolution. The title of her editorial is "Highlight—“Junk DNA” No More: Repetitive Elements as Vital Sources of Flatworm Variation" (McGrath, 2021). She starts off by repeating and expanding upon the words of the senior authors of the study that I referred to above.

“The days of ‘junk DNA’ are over,” according to Christoph Grunau and Christoph Grevelding, the senior authors of a new research article in Genome Biology and Evolution. Their study provides an in-depth look at an enigmatic superfamily of repetitive DNA sequences known as W elements in the genome of the human parasite Schistosoma mansoni (Stitz et al. 2021). Titled “Satellite-like W elements: repetitive, transcribed, and putative mobile genetic factors with potential roles for biology and evolution of Schistosoma mansoni,” the analysis reveals structural, functional, and evolutionary aspects of these elements and shows that, far from being “junk,” they may exert an enduring influence on the biology of S. mansoni.

“When we studied genetics at university in the 1980s, the common doctrine was that the non-protein coding parts of eukaryotic genomes consisted of interspersed, ‘useless’ sequences, often organized in repetitive elements like satellite DNA,” note Grunau and Grevelding. Since then, however, the common understanding of such sequences has fundamentally changed, revealing a plethora of regulatory sequences, noncoding RNAs, and sequences that play a role in chromosomal and nuclear structure. With their article, Grunau and Grevelding, along with their coauthors from Justus Liebig University Giessen, University of Montpellier, and Leipzig University, contribute further evidence to a growing consensus that such sequences play critical roles in evolution.

There's no rational excuse for publishing the Stitz et al. paper with those ridiculous statements and there's no rational excuse for compounding the error by highlighting them in an editorial comment. The Society for Molecular Biology and Evolution should be ashamed and embarrassed and they should issue a retraction and a clarification. They should state clearly that junk DNA is alive and well and supported by so much evidence that it would be perverse to deny it.

McGrath,C. (2012) Highlight—“Junk DNA” No More: Repetitive Elements as Vital Sources of Flatworm Variation. Genome Biology and Evolution 13: evab217 [doi: 10.1093/gbe/evab217]

Stitz, M., Chaparro, C., Lu, Z., Olzog, V.J., Weinberg, C.E., Blom, J., Goesmann, A., Grunau, C. and Grevelding, C.G. (2021) Satellite-Like W-Elements: Repetitive, Transcribed, and Putative Mobile Genetic Factors with Potential Roles for Biology and Evolution of Schistosoma mansoni. Genome Biology and Evolution 13:evab204. [doi: 10.1093/gbe/evab204]

Monday, September 27, 2021

The biggest mistake in the history of molecular biology (not!)

The creationists are committed to proving that most of our genome is functional because otherwise the idea of an intelligent designer doesn't make a lot of sense. They reject all of the evidence that supports junk DNA and they vehemently reject the notion that 90% of our genome is junk.

I was recently alerted to a video on junk DNA produced by Creation Ministries International in which they quote John Mattick.

A leading figure in genetics, Prof. John Mattick said ...'the failure to recognize the implications of the non-coding DNA will go down as the biggest mistake in the history of molecular biology'.

The creationists are making the common mistake of equating noncoding DNA and junk DNA but the quotation sounded accurate to me since John Mattick makes similar mistakes in his publications. I decided to try and find the exact quotation and reference and the closest I could come to a direct quote was in a paper by Mattick from 2007 (Mattick, 2007). He's referring to introns—here's the exact quotation.

It should be noted that the power and precision of digital communication and control systems has only been broadly established in the human intellectual and technological experience during the past 20–30 years, well after the central tenets of molecular biology were developed and after introns had been discovered. The latter was undoubtedly the biggest surprise (Williamson, 1977), and its misinterpretation possibly the biggest mistake, in the history of molecular biology. Although introns are transcribed, since they did not encode proteins and it was inconceivable that so much non-coding RNA could be functional, especially in an unexpected way, it was immediately and almost universally assumed that introns are non-functional and that the intronic RNA is degraded (rather than further processed) after splicing. The presence of introns in eukaryotic genomes was then rationalized as the residue of the early assembly of genes that had not yet been removed and that had utility in the evolution of proteins by facilitating domain shuffling and alternative splicing (Crick, 1979; Gilbert, 1978; Padgett et al., 1986). Interestingly, while it has been widely appreciated for many years that DNA itself is a digital storage medium, it was not generally considered that some of its outputs may themselves be digital signals, communicated viaRNA.

However, the idea of the biggest mistake in molecular biology predates that reference. Mattick is quoted in a Scientific American article by W. Wayt Gibbs where Gibbs is discssing the "suprising" fact that regulatory sequences are conserved and that some genes are noncoding genes (Gibbs, 2003).

“I think this will come to be a classic story of orthodoxy derailing objective analysis of the facts, in this case for a quarter of a century,” Mattick says. “The failure to recognize the full implications of this—particularly the possibility that the intervening noncoding sequences may be transmitting parallel information in the form of RNA molecules—may well go down as one of the biggest mistakes in the history of molecular biology.”

The discovery of introns in the mid-1970s was definitely a surprise but it's not true, as Mattick implies, that they were immediately assumed to be junk. In fact, as he points out, there was a lot of debate over the possible role of introns in the evolution of protein-coding genes where they could stimulate exon shuffling. Later on, the presence of introns was recognized to be an essential component of alternative splicing.

Once more and more sequences were published it became apparent that neither their size nor their sequences were conserved except for the spliceosome recognition sequences. It soon became obvious that their sequences were evolving at the neutral rate demonstrating that they were mostly junk. Mattick assumes that this conclusion—that introns are mostly junk—is one of the biggest mistakes in molecular biology. I think the opposite is true. I think that the failure of most molecular biologists to understand junk DNA is a huge mistake.

The creationists are misquoting Mattick when they say that the classification of all noncoding as junk is the biggest mistake in molecular biology. In the quotations above, Mattick is specifically referrring to introns but I'm sure he won't be upset to be misquoted in that manner since he firmly believes that most noncoding DNA is functional.

There's a bit of an ironic twist here. If it were true that knowledgeable scientists in the 1970s actually believed that all noncoding DNA was junk then I'd have to agree that this would have been a big (biggest?) mistake. But they didn't and it wasn't a big mistake. As I've said many times, no knowledgeable scientist ever said that all noncoding DNA was junk since they (we) all knew about noncoding genes, regulatory sequences, centromeres, and origins of replication, all of which are functional noncoding DNA. We now know that about 1% of our genome is coding sequences and about 9% is functional noncoding DNA. The other 90% is junk.

[Stop Using the Term "Noncoding DNA:" It Doesn't Mean What You Think It Means]

Mattick, J.S. (2007) A new paradigm for developmental biology. Journal of Experimental Biology 210:1526-1547. [doi: 10.1242/jeb.005017]

Gibbs, W.W. (2003) The unseen genome: gems among the junk. Scientific American 289:46-53.

Monday, September 13, 2021

Most scientists dismiss the lab leak conspiracy theory

A recent review in Science has the following subtitle, "Why most scientists say it's unlikely that SARS-CoV-2 originated from a lab leak." The title of that article was Call of the Wild but on the Science website it's The hunt for SARS-CoV-2’s ancestors heats up. The website article is behind a paywall but the original magazine article is open access.

Friday, September 10, 2021

21 experts support a natural origin for SARS-CoV-2

Here's a link to a recent review on the origins of SARS-CoV-2 written by 21 scientists from seven different countries. They are all recognized experts on the subject.

Holmes, E.C., Goldstein, S.A., Rasmussen, A.L., Robertson, D.L., Crits-Christoph, A., Wertheim, J.O., Anthony, S.J., Barclay, W.S., Boni, M.F., Doherty, P.C., Farrar, J., Geoghegan, J.L., Jiang, X., Leibowitz, J.L., Neil, S.J.D., Skern, T., Weiss, S., R, Worobey, M., Anderson, K.G., Garry, R.F. and Rambaut, A. (2021) The origins of SARS-CoV-2: A critical review. Cell. (published online Aug. 19, 2021) [doi: 10.1016/j.cell.2021.08.017]

Since the first reports of a novel severe acute respiratory syndrome (SARS)-like coronavirus in December 2019 in Wuhan, China, there has been intense interest in understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in the human population. Recent debate has coalesced around two competing ideas: a “laboratory escape” scenario and zoonotic emergence. Here, we critically review the current scientific evidence that may help clarify the origin of SARS-CoV-2.

If you are interested in the origin of this virus then you must read this paper, especially if you are a supporter of the lab leak conspiracy theory. The review attempts to put the issues into the proper perspective by looking at the big picture instead of focusing on the kinds of trivia promoted by conspiracy theorists. For example, the review notes that SARS-CoV-2 is the ninth documented coronavirus that has spread to humans and all of the previous ones have zoonotic origins as do the vast majority of human viruses. Four of these viruses are endemic (HCoV-OC43, HCoV-HkU1, HCoV-229E, and HCoV-NL63). They cause minor respiratory illnesses that we classify as common colds. Its interesting to learn about HCoV-HKU1 ...

"These [endogenous] viruses have zoonotic origins, and the circumstances of their emergence are unclear. In direct parallel to SARS-CoV-2, HCoV-HKU1, which was first described in a large Chinese city (Shenzhen, Guangdong) in the winter of 2004, has an unknown animal origin, contains a furin cleavage site in its spike protein and was originally identified in a case of human pneumonia (Woo et al., 2005)."

The authors look at the bat coronaviruses that have been isolated and sequenced before and after the pandemic began. In particular, they examine RaTG13, a bat virus that was identified at the Wuhan Institute of Virology (WIV). They note that this virus is not particularly closely related to SARS-CoV-2 and that three other bat viruses that were identified only last year are more closely related to SARS-CoV-2. The sequences of all these viruses were examined because there has been unfounded speculation that scientists at the WIV created SARS-CoV-2 from RaTG13.

"Collectively, these data demonstrate beyond reasonable doubt that RaTG13 is not the progenitor of SARS-CoV-2, with or without laboratory manipulation or experimental mutagenesis."

Furthermore, the authors note that the RaTG13 virus didn't actually exist. It was just a bunch of sequences assembled in silico from short sequence reads.

The lab leak conspiracy theorists imagine that the WIV was working on SARS-CoV-2 prior to the beginning of the pandemic and they somehow allowed to virus to escape and infect the citizens of Wuhan. The experts examined this speculation and conclude ...

"... there is no data to suggest that the WIV—or any other laboratory—was working on SARS-CoV-2, or any virus close enough to be the progenitor, prior to the COVID-19 pandemic."

This is a very important point. There is no evidence to support the most important part of the lab leak claim. It's just unfounded speculation.

What about the claim that some workers at the WIV were hospitalized with COVID-19 in November 2019? This claim was spread on Reddit and made it's way into some US intelligence briefings in Januray 2020.

"Despite extensive contact tracing of early cases during the COVID-19 pandemic, there have been no reported cases related to any laboratory staff at the WIV, and all staff in the laboratory of Dr. Shi Zhengli were said to be seronegative for SARS-CoV-2 when tested in March 2020 (World Health Organization, 2021), with the laboratory reportedly following the appropriate biosafety protocols during their coronavirus work (Cohen, 2020)."

This is another important point because if it were true that workers had been infected with SARS-CoV-2 then it would support the lab leak theory. But the scientists at the WIV deny that any such infections occurred and reported to WHO that nobody tested positive for the virus. Furthermore, the public version of the American review of intelligence reports on the origin of SARS-CoV-2 published last month failed to mention the speculation that WIV workers were infected [Intelligence Community: Unclassified Report]. The most logical explanation is that the intelligence agencies could not back up the claim. If they had evidence to support the Reddit rumour then you can bet they would have made it public.

What this means is that, in the absence of evidence, the lab leak supporters have to add an additional layer to their accusation. They have to assume that the scientists at the WIV are lying and covering up the fact that they were secretly working with SARS-CoV-2 and allowed it to escape. The speculation becomes a conspiracy theory.

There's another aspect to this false claim that's very interesting. The 21 experts note that in order for there to have been multiple hospitalizations of lab workers in November 2019 there would have to have been widespread circulation of the virus since not all infections result in hospitalizations. However, a close examination of the known cases coupled with extensive modeling indicates that the virus probably started with a single individual around November 1st.

Epidemiological modeling suggests that the number of hypothetical cases needed to result in multiple hospitalized COVID-19 patients prior to December 2019 is incompatible with observed clinical, genomic, and epidemiological data (Pekar et al., 2021).

The conspiracy fans will no doubt claim that this is just part of a massive coverup by the Chinese government. This coverup involves hundreds of patients who were sick with COVID-19 in October and November 2019 and many who were hospitalized. They have all been silenced along with dozens and dozens of health care workers. Not only that, the Chinese government has been clever enough to release just enough information to make it look like the pandemic stated with a few individuals in November and spread slowly until late December as shown in the figure accompanying the review paper.

The available evidence doesn't rule out a lab leak but it's inconsistent with the Reddit rumour that three or four WIV workers were hospitalized with COVID-19 in November.

Nobody can definatively rule out a conspiracy theory—that's why they are so popular. But you can address false claims that presumably support the conspiracy theory. That's why the experts considered whether the scientists at WIV had been working on gain-of-function research or had previously worked with infectious human viruses. They could find no such evidence.

"There is no rational experimental reason why a new genetic system would be developed using an unknown and unpublished virus, with no evidence nor mention of a SARS-CoV-2-like virus in any prior publication or study from the WIV (Ge et al., 2012; Hu et al., 2017; Menachery et al., 2015), no evidence that the WIV sequenced a virus that is closer to SARS-CoV-2 than RaTG13, and no reason to hide research on a SARS-CoV-2-like virus prior to the COVID-19 pandemic. Under any laboratory escape scenario, SARS-CoV-2 would have to have been present in a laboratory prior to the pandemic, yet no evidence exists to support such a notion and no sequence has been identified that could have served as a precursor."

Sandwalk readers will recognize the issue here. You can't prove a negative so the lab leak conspiracy theorists will always be able to say that their conspiracy theory hasn't been disproven. If that's all you have to go on then I feel sorry for you. You are in the same group as those who believe in all other conspiracy theories.

The 21 experts then go on to address the claim that the virus was "pre-adapted" to humans suggesting that scientists at the WIV had selected the virus for its ability to infect human cells. This speculation includes the ridiculous claim that the furin cleavage site had been deliberately engineered. That particular claim has been debunked but so has the general claim of pre-adaption. In fact, the data shows that the virus was a generalist virus that has gradually become more adapted to humans during the pandemic. This fact, that it was a generalist virus, has been known for more than a year but that hasn't squelched the conspiracy theorists.

"SARS-CoV-2 is also notable for being a host generalist virus (Conceicao et al., 2020), capable of efficient transmission in multiple mammalian species (including mink, tigers, cats, gorillas, dogs, raccoon dogs, and ferrets), and large outbreaks have been documented in mink with spill-back to humans (Oude Munnink et al., 2021) and to other animals (van Aart et al., 2021). Combined, these findings show that no specific human “pre” adaptation was required for the emergence or early spread of SARS-CoV-2, and the claim that the virus was already highly adapted to the human host (Zhan et al., 2020), or somehow optimized for binding to human ACE2, is without validity."

The authors conclude that the lab leak conspiracy theory has no merit because there's no evidence to support it. Thus, the only reasonable hypothesis is a natural origin and there's plenty of evidence to support that hypothesis.

"There is currently no evidence that SARS-CoV-2 has a laboratory origin. There is no evidence that any early cases had any connection to the WIV, in contrast to the clear epidemiological links to animal markets in Wuhan, nor evidence that the WIV possessed or worked on a progenitor of SARS-CoV-2 prior to the pandemic. The suspicion that SARS-CoV-2 might have a laboratory origin stems from the coincidence that it was first detected in a city that houses a major virological laboratory that studies coronaviruses. Wuhan is the largest city in central China with multiple animal markets and is a major hub for travel and commerce, well connected to other areas both within China and internationally. The link to Wuhan therefore more likely reflects the fact that pathogens often require heavily populated areas to become established (Pekar et al., 2021).

We contend that although the animal reservoir for SARS-CoV-2 has not been identified and the key species may not have been tested, in contrast to other scenarios there is substantial body of scientific evidence supporting a zoonotic origin. Although the possibility of a laboratory accident cannot be entirely dismissed, and may be near impossible to falsify, this conduit for emergence is highly unlikely relative to the numerous and repeated human-animal contacts that occur routinely in the wildlife trade. Failure to comprehensively investigate the zoonotic origin through collaborative and carefully coordinated studies would leave the world vulnerable to future pandemics arising from the same human activities that have repeatedly put us on a collision course with novel viruses."

Image credits: The first figure is from the Holmes et al. paper and the second one is from a Scientific American article [A Visual Guide to the SARS-CoV-2 Coronavirus]

Is the media finally realizing that they have been duped into promoting the lab leak conspiracy theory?

I would like to think that the media will eventually wake up and recognize the science behind the origin of SARS-CoV-2. It overhelmingly supports a natural origin and does not support the lab leak conspiracy theory. I was encourgaged by a Los Angeles Times article published a few weeks ago [Column: The lab leak theory for the origin of COVID-19 is fading.]. It was written by Michael Hiltzik who took the time to read some of the scientific papers that have recently been published. He has written an excellent summary of the issues.

Here's the bottom line ....

It would be inaccurate to say that evidence for the lab leak theory is fading. That’s because there never was any evidence for the theory, just conjecture.

Virtually from the outset, the lab leak theory was driven by ideology, not science. It employed the vocabulary of science, but that’s a familiar technique for bamboozling a susceptible public.

"The only evidence for a lab leak, period, is just that the virus emerged in Wuhan, where the Wuhan Institute of Virology is,” Rasmussen told me. “That’s it. Since day one, that has been the only piece of evidence.”

The assertions supporting the lab leak theory are not only conjectures, but in many cases provably wrong conjectures. They’re often based on misinformation, scientific ignorance, or even bad translations from Chinese documents.

Unfortunately, journalists like Michael Hiltzik are rare. Furthemore, there's no evidence that the talking heads on TV are even close to realizing that they have been duped.

Thursday, August 26, 2021

Conversation with Massimo Pigliucci

This is really worth one hour of your time. You will learn about knowledge and abduction and lots of other things.

Friday, July 09, 2021

Mutation, Randomness, & Evolution

I just received my copy of a book by Arlin Stoltzfus on mutation. I haven't finished reading it but I thought Sandwalk readers should know about it so they can order their own copy.

This is not light reading since the topics are complicated and there's a lot of misinformation about evolutionary theory floating around. In order to make his points, Arlin has to explain what's wrong with orthodox thinking and why it needs to change and this isn't an easy task. But it's worth the effort ... buy this book!

Here's a short synopsis from page 13.

The following represents a brief guide to the book, which has three parts that correspond roughly to the three combinations of terms.

  • mutation and randomness—how does the biological process of mutation seem random, or not?
  • randomness and evolution—what role does the concept of "random variation" play in evolutionary thinking?
  • mutation and evolution—what is the role of mutation in evolution, and particularly, the role of mutational tendencies?

Wednesday, June 30, 2021

Richard Dawkins talks about the genetic code and information

This is a video published a few weeks ago where Jon Perry interviews Richard Dawkins. Jon Perry is the author of animations posted on his website Stated Clearly. He (Perry) has a very adaptaionist view of evolution—a view that he got from Richard Dawkins.

The main topic of the interview concerns DNA as information and the genetic code. Both Dawkins and Perry give the impression that the only kind of information in the genome is the genetic code (sensu stricto); in other words, the code that specifies a sequence of amino acids using the sequence of nucleotides in a coding region [The Real Genetic Code]. Dawkins makes the same point he has often made; namely, that this is a real code just like any other code.

Perry points out that most people don't understand this, including many atheists who argue that the "code" is merely an analogy and not to be taken literally. Atheists, and others, also argue that the information content of DNA includes lots of other things such as genes that specify functional RNAs and sites that bind proteins. It's hard to argue that a gene for tRNA functions as any kind of a code and it's hard to argue that the DNA binding sites in origins of replication are codes even though you could argue that they carry information.

I don't get excited about arguments over whether DNA carries "information" because there's not much to be gained by such arguments. Who cares whether the genetic code falls under the definition of "information theory"? However, I do get annoyed when people say that the ONLY information in DNA is in the form of the genetic code.

Watch the video and let me know what you think. Jerry Coyne watched it and he wasn't the least bit bothered by the things that bothered me [A discussion on genetics, evolution, and information with Richard Dawkins].