That seven Nobel Prizes were awarded directly or indirectly for work in tumor virology illustrates the impact of the field on biomedical understanding. (p. 273)
We've entered a new era in the field of molecular biology. Almost all of the emphasis and excitement these days is based on studies of mammals, especially humans. Most of the big bucks are for studying some aspect of medicine so that even if you are interested in basic science you have to slant it toward curing some disease.
We've known for 60 years that some non-coding DNA has a function but the latest generation of scientists thinks this was only discovered in their lifetime. Writer Kara Mason posts an article on the Department of Biomedical Informatics website at the University of Colorado.
I AM the LORD thy God. Thou shalt have no other gods before me. Thou shalt not make to thyself any graven images. Thou shalt not take the Name of the Lord thy God in vain.
The most fascinating part of the interview is when he goes out of his way to say that such a possibility doesn't require a conspiracy theory. Really?
The New York Times goes all in on “lab leak”
Earlier this week, the New York Times op-ed page ran an article by Alina Chan, Queen of lab leak conspiracy theories. How is it wrong? Let me count the ways…
This is a Reuters report about misinformation spread by the United States military in order to discredit China's Sinovac vaccine. It was directed at the Philippines and other countries who were purchasing the China vaccine.
Reuters suggests that by undermining public trust in government health initiatives the US military might have cost thousands of lives in the Phillippines.
A REUTERS INVESTIGATION: Pentagon ran secret anti-vax campaign to undermine China during pandemic
The U.S. military launched a clandestine program amid the COVID crisis to discredit China’s Sinovac inoculation – payback for Beijing’s efforts to blame Washington for the pandemic. One target: the Filipino public. Health experts say the gambit was indefensible and put innocent lives at risk.
It shouldn't surprise anyone that nations engage in propaganda wars in order to destabilize or demonize their perceived enemies. The world is a complicated multinational environment and meddling in the affairs of other countries is a routine part of modern international relations. It's important to emphasize that it's not only the "bad guys" who do this sort of thing. Your own country and your friends and allies also spread misinformation in order to convince you that you are one of the "good guys" (e.g. defenders of morality, decency, democracy, and freedom).
I emphasize this for two reasons. One, here in Canada there's a lot of pearl-clutchng these days about foreign interference and the main focus is on China and India and how they might have influenced our elections. I think this is pretty minor stuff compared to what else is going on and the foreign influence from other countries, including the United States.
Second, as mentioned above, we all need to be aware of the fact that misinformation is rampant and that doesn't just include misinformation spread by Russia, China, Iran, and Hamas. We also need to be skeptical about information being spread by the governments of Ukraine, Israel, and the United States. Do not assume that everything they say is truthful.
These days, I find that it's almost impossible to hear, read, or watch any "authority" who convinces me that they are critical thinkers without an agenda. Almost all of them seem to be victims of propaganda.
Note: I'm aware of the fact that this report may not be accurate—it may, in fact, be misinformation. I'm mostly using it as a vehicle to point out that you can't trust anyone these days, including your friends. That's very upsetting because I grew up thinking that the mainstream news outlets (TV, radio, newspapers) could be (mostly) trusted.
I suspect that some people at the NYT might have been somewhat embarrassed by the response to their reckless behavior so they prepared a response. It was written by David Leonhardt who identifies himself as "a senior writer at the New York Times who runs "The Morning", our flagship daily newsletter." He published his article on the website that he runs and the title sounds like it might be an objective appraisal of the evidence in favor of a natural origin of COVID-19 originating in the Wuhan market: Two Covid Theories.
Don't be fooled by the title. Leonhardt makes no attempt to summarize the massive amount of evidence in favor of a natural origin. Instead, he treats the scientific view and the lab leak conspiracy theory as equally probable.
Do you find both explanations plausible? I do.
As I’ve followed this debate over the past few years, I have gone back and forth about which is more likely. Today, I’m close to 50-50. I have heard similar sentiments from some experts.
“No one has proof,” Julian Barnes, who covers intelligence agencies for The Times, told me. “Everyone is using logic.” Julian’s advice to the rest of us: “Be wary, keep an open mind, rule nothing out.”
The latest opinion piece looks to me like an attempt to defend the NYT against accusations that it is anti-science. You would think that in such a defense, the author would be able to present good scientific evidence for the lab leak conspiracy theory, right? Here's the three arguments advanced by David Leonhardt in support of this massive conspiracy.
I think we are fully justified in claiming that the NYT is anti-science. I think the newspaper owes the scientific community an apology for ignoring the evidence of a natural origin and disparaging the reputations of reputable scientists who reject the lab leak conspiracy theory in favor of a natural origin.
1. [The New York Times promotes the lab leak conspiracy theory] [Real scientists destroy the Alina Chan lab leak conspiracy theory] [The New York Times goes all in on “lab leak”] [No, gain of function research did not cause COVID-19]
The main issue in this field concerns the number of non-coding genes in the human genome. I cover the available data in my book and conclude that there are fewer than 1000 (p.214). Those scientists who promote the importance of RNA (e.g. Tom Cech) would like you to believe that there are many more non-coding genes; indeed, most of those scientists believe that there are more non-coding genes than coding genes (i.e. > 20,000). They rarely present evidence for such a claim beyond noting that much of our genome is transcribed.
Although most scientists now agree on RNA's bright promise, we are still only beginning to unlock its potential. Consider, for instance, that some 75 percent of the human genome consists of dark matter that is copied into RNAs of unknown function. While some researchers have dismissed this dark matter as junk or noise, I expect it will be the source of even more exciting breakthroughs.
Let's dissect this to see where the bias lies. The first thing you note is the use of the term "dark matter" to make it sound like there's a lot of mysterious DNA in our genome. This is not true. We know a heck of a lot about our genome, including the fact that it's full of junk DNA. Only 10% of the genome is under purifying selection and assumed to be functional. The rest is full of introns, pseudogenes, and various classes of repetitive sequences made up mostly of degraded transposons and viruses. The entire genome has been sequenced—there's not much mystery there. I don't know why anyone refers to this as "dark matter" unless they have a hidden agenda.
The second thing you notice is the statement that 75% of the genome is transcribed at some time or another and, according to Tom Cech, these transcripts have an unknown function. That's strange since protein-coding genes take up roughly 40% of our genome and we know a great deal about coding DNA, UTRs, and introns. If you add in the known examples of non-coding genes, this accounts for an additional 2-3% of the genome.1
Almost all the rest of the transcripts come from non-conserved DNA and those transcripts are present at less than one copy per cell. As the ENCODE researchers noted in 2014, they are likely to be junk RNA resulting from spurious transcription. I'd say we know a great deal about the fraction of the genome that's transcribed and there's not much indication that it's hiding a plethora of undiscovered functional RNAs.
Photo credit: University of Colorado, Boulder.
1. In my book I make a generous estimate of 5,000 non-coding genes in order to avoid quibbling over a smaller number and in order to demonstrate that even with such a obvious over-estimate the genome is still 90% junk.
Scientists have been actively investigating the origin of SARS-CoV-2 for the past four years. The evidence strongly favors early transmission from infected animals in the Huanan seafood market in Wuhan, China (Worobey et al., 2022; Alwine et al., 2023; Dwyer, 2023; Holmes et al., 2021; Holmes, 2024). The virus probably originated in bats in China or southest asia. [The case for a natural origin of SARS-CoV-2] [Real scientists discuss the lab leak conspiracy theory]
Some people have suggested that the infectious virus, SARS-Cov-2, escaped from a lab in the Wuhan Institute of Virology in spite of the fact that there's not a shred of evidence that the scientists there ever worked with such a strain before the pandemic and all the scientists deny that they had ever seen the pandemic virus before the pandemic began. Such suggestions have all the characteristics of a conspiracy theory (Lewandowsky et al., 2023; Goodrum et al., 2023).1
The New York Times has just published an opinion piece that promotes the lab leak conspiracy theory. It just happened to coincide with a Republican witch hunt investigation into Dr. Fauci and the origins of SARS-CoV-2. The article is written by Alina Chan who wrote a book on the subject with co-author Matt Ridley [Alina Chan teams up with Matt Ridley to promote the lab leak conspiracy theory].
This is just about the only thing in the lab leak conspiracy theory that is true.
The year before the outbreak, the Wuhan institute, working with U.S. partners, had proposed creating viruses with SARS‑CoV‑2’s defining feature.
This is extremely misleading. The researchers at WIV worked in collabortion with scientists in other countries, including the United States, on investigating the features of coronaviruses that could lead to infection of humans. That's exactly what you would expect them to do. They never created a virus that could be infectious.
The Wuhan lab pursued this type of work under low biosafety conditions that could not have contained an airborne virus as infectious as SARS‑CoV‑2.
The labs followed all the standard procedures for work of this type and passed an international inspection.
The hypothesis that Covid-19 came from an animal at the Huanan Seafood Market in Wuhan is not supported by strong evidence.
That's a lie. There is strong evidence that the outbreak began in the market.
Key evidence that would be expected if the virus had emerged from the wildlife trade is still missing.
It's true that the exact infectious animal carrying SARS-CoV-2 has not been identified but the circumstantial evidence is strong—just as strong as the circumstantial evidence that sends some people to jail. It's crazy to say that evidence for animal transmission is missing when ALL the evidence for the presence of SARS-CoV-2 at WIT is also missing.
1. The researchers at WIV are highly respected international experts on virology, especially coronaviruses. They published in the best international journals. Since they all deny that they were working with SARS-CoV-2 before the pandemic, the lab leak hypothesis absolutely requires that several hundred reseachers are lying and covering up the fact that the virus leaked from their labs. In other words, a conspiracy is an essential part of the lab leak conspiracy theory [see Most scientists dismiss the lab leak conspiracy theory].
2. It's amazing how many media personalities have assumed that there must be some element of truth in this opinion piece just because it was published in the New York TImes. It's even more amazing that these media personalities couldn't find any real scientists to interview.
Alwine, J.C., Casadevall, A., Enquist, L.W., Goodrum, F.D. and Imperiale, M.J. (2023) A critical analysis of the evidence for the SARS-CoV-2 origin hypotheses, Am Soc Microbiol. 97: e00365-00323. [doi: 10.1128/jvi.00365-23]
Dwyer, D.E. (2023) The origins of severe acute respiratory syndrome-coronavirus-2. Seminars in Respiratory and Critical Care Medicine, Thieme Medical Publishers, Inc. [doi: 10.1055/s-0042-1759564]
Goodrum, F., Lowen, A.C., Lakdawala, S., Alwine, J., Casadevall, A., Imperiale, M.J., Atwood, W., Avgousti, D., Baines, J. and Banfield, B. (2023) Virology under the microscope—a call for rational discourse. Journal of virology 97:e00089-00023. [doi: 10.1128/jvi.00089-23]
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 184:4848-4856. [doi: 10.1016/j.cell.2021.08.017]
Holmes, E.C. (2024) The emergence and evolution of SARS-CoV-2. Annual review of virology 11. [doi: 10.1146/annurev-virology-093022-013037]
Lewandowsky, S., Jacobs, P.H. and Neil, S. (2023) Leak or Leap? Evidence and Cognition Surrounding the Origins of the SARS-CoV-2 Virus. Covid Conspiracy Theories in Global Perspective, ed. Michael Butter and Peter Knight:26-39. [PDF]
Worobey, M., Levy, J.I., Malpica Serrano, L., Crits-Christoph, A., Pekar, J.E., Goldstein, S.A., Rasmussen, A.L., Kraemer, M.U., Newman, C. and Koopmans, M.P. (2022) The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic. Science 377:951-959. [doi: 10.1126/science.abp8715]
Telomeres are just one of many functional DNA elements in the human genome. The average length of human telomeres was long thought to be about 10 kb and since there are 24 distinct chromosomes in the human genome this amounts to about 480 kb of telomere sequence or about 0.015% of the human genome. With the advent of new sequencng technology it is now possible to generate long reads of DNA sequence and this has led to a somewhat shorter estimate of telomere length (Karimian et al., 2024). The figure from thier paper shows that the average length of telomeres gets shorter with age but the starting length in newborns (cord DNA) is about 8 kb instead of 10 kb. The authors explain why their sequencing technique is likely to give more accurate results than the earlier estimates.
If we use 8 kb as the average length, then that means a total of 8 × 2 × 24 = 384 kb or 0.012% of the standard human genome, which includes 22 autosomes and both sex chromsomes.
Image Credit: The image shows human chromosomes (blue) labelled with a telomere probe (yellow), from Christopher Counter at Duke University.
Karimian, K., Groot, A., Huso, V., Kahidi, R., Tan, K.-T., Sholes, S., Keener, R., McDyer, J.F., Alder, J.K., Li, H., Rechtsteiner, A. and Greider, C. (2024) Human telomere length is chromosome end–specific and conserved across individuals. Science 384:533-539. [doi: 10.1126/science.ado0431]
The President of the University of Toronto, Meric Gertler, has responded to these demands with a letter sent to the members of Occupy for Palestine [President Meric Gertler’s response to members of Occupy for Palestine].
With respect to the first demand, President Gertler points out that the university has a history of opposition to academic boycotts.
Such demands are antithetical to the University’s firm conviction that the best way to protect human rights is by staunchly defending and promoting academic freedom, freedom of expression, and the unfettered circulation of ideas within the global scholarly community. We have consistently emphasized that it is both inappropriate and, ultimately, counterproductive to single out academics working or studying in a particular country, and to hold them accountable for the actions or policies of their country’s government. Faculty and students are often among the most trenchant critics of their own government’s policies or actions. Events over the past year confirm that Israeli academics – as well as university leaders – have been amongst the most vociferous critics of the current government and its policies.
For this reason, the university rejects the Occupy for Palestine's first demand.
The second demand is unreasonable because the University does not directly control the pension fund; those investments are controlled by a Board of Trustees, some of whom are appointed by staff and faculty because a large percentage of the pension fund is their money. Also, the pension fund is a joint fund with the University of Guelph and Queen's University. Similarly, with respect to the endowment fund, the University does not directly control direct investments in companies so it cannot comply with the demand even if it wished to.
However, notwithstanding those practicalities, there are fundamental principles at stake that need to be addressed.
... the University’s Policy on Social and Political Issues with Respect to University Divestment notes in its opening Preamble that “As a general matter, the University does not take positions on social or political issues apart from those directly pertinent to higher education and academic research.” Accordingly, “the University will not consider proposals for restrictions on its investments that require the institution to take sides in matters that are properly the subject of ongoing academic inquiry and debate.” It further notes, as a corollary, that the University’s response to any requests for divestment “must be governed by the fundamental place of diversity of opinion within its community. Except in those situations in which the University must settle on an answer to controversial questions about how best to achieve its academic mission, the University risks abandoning its core values if it takes sides in ongoing debates and is perceived to be advancing a specific political or social position.”
This is consistent with the Chicago Principles on free expression and the Kalven Report on the University's role in political and social action. Meric Gertler does not specifically mention the Kalven Report from the University of Chicago but it's clear that it forms the basis of the University of Toronto's position. For that reason, and because that position is not widely understood, I quote from the report.
A university has a great and unique role to play in fostering the development of social and political values in a society. The role is defined by the distinctive mission of the university and defined too by the distinctive characteristics of the university as a community. It is a role for the long term.
The mission of the university is the discovery, improvement, and dissemination of knowledge. Its domain of inquiry and scrutiny includes all aspects and all values of society. A university faithful to its mission will provide enduring challenges to social values, policies, practices, and institutions. By design and by effect, it is the institution which creates discontent with the existing social arrangements and proposes new ones. In brief, a good university, like Socrates, will be upsetting.
The instrument of dissent and criticism is the individual faculty member or the individual student. The university is the home and sponsor of critics; it is not itself the critic. It is, to go back once again to the classic phrase, a community of scholars. To perform its mission in the society, a university must sustain an extraordinary environment of freedom of inquiry and maintain an independence from political fashions, passions, and pressures. A university, if it is to be true to its faith in intellectual inquiry, must embrace, be hospitable to, and encourage the widest diversity of views within its own community. It is a community but only for the limited, albeit great, purposes of teaching and research. It is not a club, it is not a trade association, it is not a lobby.
Since the university is a community only for these limited and distinctive purposes, it is a community which cannot take collective action on the issues of the day without endangering the conditions for its existence and effectiveness. There is no mechanism by which it can reach a collective position without inhibiting that full freedom of dissent on which it thrives. It cannot insist that all of its members favor a given view of social policy; if it takes collective action, therefore, it does so at the price of censuring any minority who do not agree with the view adopted. In brief, it is a community which cannot resort to majority vote to reach positions on public issues.
I am a University of Toronto retired professor and I fully support the position of the University President. The university cannot and should not take a position on social issues. I fully support the rights of students and faculty to express their personal views on such issues. For example, we may protest the behavior of the Israel government, of Hamas, the governments of Russia or Ukraine, and even, especially, our own government. Those are all legitimate targets of protest. The university is not a legitimate target. The university is not our enemy.
Here's a link to the junk DNA debate between Dan Stern Cardinale and Casey Luskin. The debate took place on May 2, 2024.
I mentioned in a previous post that Luskin should have been called out on his repeated attempts to equate junk DNA with non-coding DNA. This allowed him to portray all non-coding functions as evidence against junk DNA. [Casey Luskin posts misleading quotes about junk DNA].
There are several other things that I would have done differently. I would have made it clear that 10% of the genome is functional and we don't know the function of some of that fraction. Thus, all newly discovered functional regions could still fit into the 10% and 90% of the genome is still junk. Every time Casey mentions a new function he should have been challenged to specify exactly what percentage of the genome he is referring to. (Dan tried to do this but he was too nice, and let Casey off the hook.)
The idea here is to make it clear to viewers that recent discoveries of functional regions do not affect the idea that most of our genome is junk.
I would also attempt to get Casey to admit that there's a scientific controversy over junk DNA so there are many papers defending junk DNA and criticizing the arguments of junk DNA opponents. For every quotation from a scientist who opposes junk, there's an equally significant quotation from one who supports junk. Why does Casey only quote scientists who agree with him? Is this cherry-picking? Is selectively rattling off quotations and references from people who agree with you a reasonable way to have a serious scientific debate?
I think the arguments over transcripts should begin with presenting all the scientific evidence that spurious transcripts exist - for example, random DNA sequences inserted into a cell nucleus are transcribed and spurious transcription is easily documented in well-studied organisms such as bacteria and yeast. The characteristics of spurious transcription are that the transcripts are present in very small amounts, that they are rapidly degraded, that they come from regions of the genome that are not under purifying selection, and they are cell/tissue specific. So what is the most reasonable explanation when you look at such transcripts?
Casey Luskin's attempt to avoid the best explanation (spurius transcription) is a classic example ad hoc rescue and it might have been useful to point this out to viewers.
Regulation is not new. There was serious discussion and debate over the amount of the genome devoted to regulation back in the late 1960s when the concept of junk DNA was first proposed. Casey should have been challenged to state what percentage of the genome is devoted to regulation and if he comes up with an unreasonable number he should have to give examples of many well-studied genes that have been shown to have that level of regulation. (Hint: There aren't any.) All of the detailed work on the regulation of dozens of specific human genes has shown that you don't need more than a few transcription factor binding sites to control expression. Is there any reason to suppose that the other genes require ten or a hundred times more regulatory sequences to control expression?
What is the trend line? Ever since the ENCODE publicity disaster of 2012 there has been a flood of papers defending junk DNA and the data supporting junk DNA is now stronger that it has ever been because we now know from hundreds of thousands of human genome sequences that only about 10% is under purifying selection. There have also been a lot of papers fleshing out the 10% of the genome that's functional. There have only been a handful of papers published in the past ten years that seriously attempt to present evidence that most of our genome is functional. I would have challenged Casey to come up with a single scientific publication in the past ten years claiming, with supporting data, that most of the genome is functional.
On Thursday May 2, 2024, Casey Luskin and Dan Stern Cardinale debated junk DNA on the YouTube channel "The NonSequitor Show." David Klinghoffer thinks that this debate went very well for the ID side [Debate: Casey Luskin Versus Rutgers Biologist Dan Cardinale, Thursday, May 2]. I agree with Klinghoffer; Luskin did an excellent job of promoting his case because many of his statements and claims were not challenged effectively.
I'll be putting up a separate post on the debate but for now I'd like to address an article by Casey Luskin that he posted before the debate as preparation for what he was going to say. The article consists of a bunch of quotes from prominent scientists about junk DNA [“Junk DNA” from Three Perspectives: Some Key Quotes]. Here are the three perspectives, according to Luskin.
Some of the quotes represent the actual position of junk DNA proponents but Luskin has also picked out stupid quotes from scientists who think, incorrectly, that all non-coding DNA is junk. This is deliberate as we will see below.
Luskin builds the case for function in non-coding DNA by quoting religious scientists who "predict" that there will be functional DNA in non-coding regions of the genome. This is disingenuous at best because Luskin knows full well that from the very beginning of the scientific debate we knew about functional non-coding DNA. It was never the case that all non-coding DNA was assumed to be junk.
Many of these quotes are from scientists announcing that some non-coding DNA has a function. They support Luskin's false claim that all non-coding DNA was thought to be junk and the discovery of functional regions of non-coding DNA has resulted in a "paradigm shift" in our view of the human genome.
Casey Luskin should not have been allowed to get away with equating junk DNA and non-coding DNA in the debate. He should have been challenged to retract that false claim at the very beginning of the debate and called out whenever he used the term "non-coding DNA" during the debate.
Intelligent Design Creationists are heavily invested in refuting junk DNA because it casts doubt on their model of an intelligently designed human. Over the years they have advanced all kinds of arguments against junk DNA and some ID supporters actually address the real scientific issues (e.g. Jonathan Wells). However, most Intelligent Design Creationists are as ignorant about the scientific dispute over junk DNA as they are about evolution and lots of other science issues that conflict with their underlying religious beliefs.
A few days ago (March 26, 2024), the Discovery Institute's Center for Science and Culture published a short video on "The MYTH of Junk DNA" where they ignored most of the science and appealed to the majority of creationists who don't care about the truth. We have enough data to conclude that the Discovery Institute isn't just ignorant of the real science but is actually lying in this video. We know this because there are prominent Senior Fellows of the Center for Science and Culture who know that the material in this video is wrong and/or mispleading.
