Western scientists should continue to cooperate with Chinese scientists

China has become a science powerhouse and it achieved this goal, in part, by sending its young scientitsts abroad to train in universities in Canada, Australia, United States, and Europe. Many of these countries have signed scientific cooperation agreements with China but some of those agreements are in danger of lapsing as China is increasingly seen as an untrustworthy enemy.

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Visual guide to airfoils

Bartosz Ciechanowski is at it again with an in-depth explainer that makes heavy use of slider-driven interactive graphics. This time he simulated the patterns of air flowing over and around the wings of an airplane, also known as airfoil.

The length of each article starts to feel kind of long at times, but there’s something to these simple sliders that are useful in keeping you engaged and helping to understand the physics.

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Intelligent design creationists think junk DNA is a placeholder for ignorance

Paul Nelson is a Senior Fellow of the Discovery Institute—the most important source of intelligent design propaganda. Paul and I have been disagreeing about science for many years. He is prone to interpret anything he finds in the scientific literature as support for the idea that scientists have misunderstood their subject matter and failed to recognize that science supports intelligent design. My goal has always been to try and explain the actual science and why his interpretations are misguided. I have not been very successful.

The photo was taken in London (UK) in 2016 at a meeting on evolution. It looks like I'm holding my breath because I'm beside a creationist but I assure you that's not what was happening. We actually get along quite well in spite of the fact that he's wrong about everything. :-)

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Do some IQ data need a ‘public health warning?’ A paper based on a controversial psychologist’s data is retracted

Richard Lynn

A journal has retracted a controversial 2010 article on intelligence and infections that was based on data gathered decades ago by a now-deceased researcher who lost his emeritus status in 2018 after students said his work was racist and sexist.

The article, “Parasite prevalence and the worldwide distribution of cognitive ability’, was published in Proceedings of the Royal Society B, by a group at the University of New Mexico. Their claim, according to the abstract

The worldwide distribution of cognitive ability is determined in part by variation in the intensity of infectious diseases. From an energetics standpoint, a developing human will have difficulty building a brain and fighting off infectious diseases at the same time, as both are very metabolically costly tasks.

Overlaying average national IQ with parasitic stress, they found “robust worldwide” correlations in five of six regions of the globe: 

Infectious disease remains the most powerful predictor of average national IQ when temperature, distance from Africa, gross domestic product per capita and several measures of education are controlled for. These findings suggest that the Flynn effect [which posits that average national IQs increase over time] may be caused in part by the decrease in the intensity of infectious diseases as nations develop.

The study – and a related paper by a different group of authors – caught the attention of the popular science media. The Washington Post covered the research (pointing out some shortcomings), as did Science, and the lead author, Christopher Eppig, wrote about it for Scientific American. In that article, Eppig wrote: 

In our 2010 study, we not only found a very strong relationship between levels of infectious disease and IQ, but controlling for the effects of education, national wealth, temperature, and distance from sub-Saharan Africa, infectious disease emerged as the best predictor of the bunch. A recent study by Christopher Hassall and Thomas Sherratt repeated our analysis using more sophisticated statistical methods, and concluded that infectious disease may be the only really important predictor of average national IQ.

But as the journal notes in the retraction, Eppig and his colleagues based their study on an analysis of data published in 2004 by Tatu Vanhanen and Richard Lynn, who died in 2023: 

Following the publication of this article, Proceedings B was recently made aware of potential problems with the underpinning datasets used in the analyses, which were drawn from published sources [1,2]. The editors’ attention was drawn to the fact that the datasets on between-country variation in IQ had been the subject of several critiques claiming that they contain substantial inaccuracies and biases that throw substantial doubt on inferences made from them, and that these problems had not been resolved in revised versions of the dataset used by Eppig and colleagues. Upon detailed scrutiny, the editors found these claims to be convincing and asked Eppig and colleagues for their response. While the authors acknowledged at least some of the claimed flaws, they maintained that the inferences from the data were nevertheless reliable.

Proceedings B publishes research of outstanding scientific excellence and importance, conforming to recognized standards of scientific procedure in terms of methodology and ethical standards. Journal policy stipulates retraction where editors have clear evidence that the findings are unreliable (and may invalidate the conclusions of the paper). After carefully considering the dataset, the critiques, the authors’ response and the potential harms created by using a dataset that appears to portray human populations in some geographical regions as of below normal intelligence on average, the editors concluded that the manifest problems in the data warranted retraction in order to uphold these standards.

Lynn’s career, and views, have been highly visible for many years in the United States in the United Kingdom, where he worked. In 2018, Ulster University, where he was a professor emeritus, agreed to demands from students that the school revoke his academic status – news covered by the BBC among other outlets (including this one).

We emailed the chief editor of the journal, and received a reply from a spokesperson for the Royal Society, who told us: 

In July 2023, the editorial team was made aware of criticism about the dataset used by Eppig et al. in a 2010 paper in Proceedings B. After considering a wide array of evidence, including the original data set, subsequent critiques and the authors’ response, the editors concluded problems with the study were sufficient to call its conclusions into question and warrant retraction.

The decision to retract was made in January 2024, and the authors were informed at that time, the spokesperson added.

Randy Thornill, the last author of the paper, did not respond to our request for comment.

So what about the other paper that used Vanhanen and Lynn’s data? Hassall and Sherratt told us that in light of the retraction, they would ask Intelligence, where they published their paper in 2011, to revisit the research. Hassall, of the University of Leeds, in England, told us: 

Our paper was really focused on statistical issues when looking at spatial patterns in anything, but with IQ data as a case study (prompted by the fact that Eppig et al (and many others) were doing these kinds of analyses). As a result, I’d be hesitant to retract the whole thing as it has value as (and was always intended as) a methodological contribution. 

However, both researchers agreed the journal ought to do something to indicate the work was potentially fraught. Hassall said: 

researchers are clearly using our work to support the idea of an IQ-disease link.

Taken together, it’s a complicated picture:

  1. The point of our paper is the method and the method is sound and important, independent of data
  2. Our analysis yields quantitatively the same conclusions whether based on a problematic dataset (IQ) or on a robust dataset (PISA) that is measuring something similar
  3. Researchers cite our work sometimes for the methods and sometimes for the (potentially questionable) results.

Sherratt, of Carleton University in Ottawa, Canada, added: 

While our paper does a service by educating researchers on why autocorrelation matters and how to address it, at very least there needs to be a “public health warning” on the data set on which our methods paper is based. We should insist on this. A corrigendum might do the trick if it is seen whenever a reader views our paper … The fear is that if we don’t do anything then, now that Epigg et al. (2010) has been taken out of circulation, our paper can still be used to provide general support for the relationship!

Like Retraction Watch? You can make a tax-deductible contribution to support our work, subscribe to our free daily digest or paid weekly updatefollow us on Twitter, like us on Facebook, or add us to your RSS reader. If you find a retraction that’s not in The Retraction Watch Database, you can let us know here. For comments or feedback, email us at team@retractionwatch.com.

Happy St. Patrick’s Day 2024

Happy St. Patrick's Day! These are my great-grandparents Thomas Keys Foster, born in County Tyrone on September 5, 1852 and Eliza Ann Job, born in Fintona, County Tyrone on August 18, 1852. Thomas came to Canada in 1876 to join his older brother, George, on his farm near London, Ontario, Canada. Eliza came the following year and worked on the same farm. Thomas and Eliza decided to move out west where they got married in 1882 in Winnipeg, Manitoba, Canada.

The couple obtained a land grant near Salcoats, Saskatchewan, a few miles south of Yorkton, where they build a sod house and later on a wood frame house that they named "Fairview" after a hill in Ireland overlooking the house where Eliza was born. That's where my grandmother, Ella, was born.

Other ancestors in this line came from the nearby counties of Donegal (surname Foster) and Fermanagh (surnames Keys, Emerson, Moore) and possibly Londonderry (surname Job).

One of the cool things about studying your genealogy is that you can find connections to almost everyone. This means you can celebrate dozens of special days. In my case it was easy to find other ancestors from England, Scotland, Netherlands, Germany, France, Spain, Poland, Lithuania, Belgium, Ukraine, Russia, and the United States. Today, we will be celebrating St. Patrick's Day. It's rather hectic keeping up with all the national holidays but somebody has to keep the traditions alive!

It's nice to have an excuse to celebrate, especially when it means you can drink beer. However, I would be remiss if I didn't mention one little (tiny, actually) problem. Since my maternal grandmother is pure Irish, I should be 25% Irish but my DNA results indicate that I'm only 8% Irish. That's probably because my Irish ancestors were Anglicans and were undoubtedly the descendants of settlers from England, Wales, and Scotland who moved to Ireland in the 1600s. This explains why they don't have very Irish-sounding names.

I don't mention this when I'm in an Irish pub. Instead, I focus on my mother's maiden name, which was Doherty, and her ancestors on her father's side who were O'Doughertys. The O'Doughertys were a prominent Irish clan from Donegal and they were fierce enemies of the English invaders. Unfortunately, my ancestor was Donald O'Dougherty (1760 - 1810) who came to Canada in 1803 from the Isle of Skye in Scotland where his family had been for several generatons after fleeing Ireland in the 1600s. His wife was Anne Stewart and she wasn't Irish.

I don't mention that part either.


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How do proteins move around amidst the jumble of molecules inside a living cell?

I've been reading Philip Ball's book on "How Life Works" and I find it increasingly frustrating because he consistently describes things that he's "discovered" that biochemists like me must have missed. Here's an example from pages 231-232.

He presents a cartoon image of a cell showing that it's full of all kinds of molecules packed closely together, then he says,

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Weekend reads: A paper written by ChatGPT goes viral; the Gino misconduct investigation report; superconductivity scandal

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The week at Retraction Watch featured:

Our list of retracted or withdrawn COVID-19 papers is up past 400. There are more than 47,000 retractions in The Retraction Watch Database — which is now part of Crossref. The Retraction Watch Hijacked Journal Checker now contains more than 250 titles. And have you seen our leaderboard of authors with the most retractions lately — or our list of top 10 most highly cited retracted papers? What about The Retraction Watch Mass Resignations List?

Here’s what was happening elsewhere (some of these items may be paywalled, metered access, or require free registration to read):

Like Retraction Watch? You can make a tax-deductible contribution to support our work, subscribe to our free daily digest or paid weekly updatefollow us on Twitter, like us on Facebook, or add us to your RSS reader. If you find a retraction that’s not in The Retraction Watch Database, you can let us know here. For comments or feedback, email us at team@retractionwatch.com.

Nils Walter disputes junk DNA: (9) Reconciliation

I'm discussing a recent paper published by Nils Walter (Walter, 2024). He is arguing against junk DNA by claiming that the human genome contains large numbers of non-coding genes.

This is the ninth and last post in the series. I'm going to discuss Walker's view on how to tone down the dispute over the amount of junk in the human genome. Here's a list of the previous posts.


"Conclusion: How to Reconcile Scientific Fields"

Walter concludes his paper with some thoughts on how to deal with the controversy going forward. I'm using the title that he choose. As you can see from the title, he views this as a squabble between two different scientific fields, which he usually identifies as geneticists and evolutionary biologists versus biochemists and molecular biologists. I don't agree with this distinction. I'm a biochemist and molecular biologist, not a geneticist or an evolutionary biologist, and still I think that many of his arguments are flawed.

Let's see what he has to say about reconciliation.

Science thrives from integrating diverse viewpoints—the more diverse the team, the better the science.[107] Previous attempts at reconciling the divergent assessments about the functional significance of the large number of ncRNAs transcribed from most of the human genome by pointing out that the scientific approaches of geneticists, evolutionary biologists and molecular biologists/biochemists provide complementary information[42] was met with further skepticism.[74] Perhaps a first step toward reconciliation, now that ncRNAs appear to increasingly leave the junkyard,[35] would be to substitute the needlessly categorical and derogative word RNA (or DNA) “junk” for the more agnostic and neutral term “ncRNA of unknown phenotypic function”, or “ncRNAupf”. After all, everyone seems to agree that the controversy mostly stems from divergent definitions of the term “function”,[42, 74] which each scientific field necessarily defines based on its own need for understanding the molecular and mechanistic details of a system (Figure 3). In addition, “of unknown phenotypic function” honors the null hypothesis that no function manifesting in a phenotype is currently known, but may still be discovered. It also allows for the possibility that, in the end, some transcribed ncRNAs may never be assigned a bona fide function.

First, let's take note of the fact that this is a discussion about whether a large percentage of transcripts are functional or not. It is not about the bigger picture of whether most of the genome is junk in spite of the fact that Nils Walter frames it in that manner. This becomes clear when you stop and consider the implications of Walter's claim. Let's assume that there really are 200,000 functional non-coding genes in the human genome. If we assume that each one is about 1000 bp long then this amounts to 6.5% of the genome—a value that can easily be accommodated within the 10% of the genome that's conserved and functional.

Now let's look at how he frames the actual disagreement. He says that the groups on both sides of the argument provide "complementary information." Really? One group says that if you can delete a given region of DNA with no effect on the survival of the individual or the species then it's junk and the other group says that it still could have a function as long as it's doing something like being transcribed or binding a transcription factor. Those don't look like "complimentary" opinions to me.

His first step toward reconciliation starts with "now that ncRNAs appear to increasingly leave the junkyard." That's not a very conciliatory way to start a conversation because it immediately brings up the question of how many ncRNAs we're talking about. Well-characterized non-coding genes include ribosomal RNA genes (~600), tRNA genes (~200), the collection of small non-coding genes (snRNA, snoRNA, microRNA, siRNA, PiWi RNA)(~200), several lncRNAs (<100), and genes for several specialized RNAs such as 7SL and the RNA component of RNAse P (~10). I think that there are no more than 1000 extra non-coding genes falling outside these well-known examples and that's a generous estimate. If he has evidence for large numbers that have left the junkyard then he should have presented it.

Walter goes on to propose that we should divide non-coding transcripts into two categories; those with well-characterized functions and "ncRNA of unknown function." That's ridiculous. That is not a "agnostic and neutral term." It implies that non-conserved transcripts that are present at less that one copy per cell could still have a function in spite of the fact that spurious transcription is well-documented. In fact, he basically admits this interpretation at the end of the paragraph where he says that using this description (ncRNA of unknown function) preserves the possibility that a function might be discovered in the future. He thinks this is the "null hypothesis."

The real null hypothesis is that a transcript has no function until it can be demonstrated. Notice that I use the word "transcript" to describe these RNAs instead of "ncRNA" or "ncRNA of unknown phenotypic function." I don't think we lose anything by using the word "transcript."

Walter also address the meaning of "function" by claiming that different scientific fields use different definitions as though that excuses the conflict. But that's not an accurate portrayal of the problem. All scientists, no matter what field they identify with, are interested in coming up with a way of identifying functional DNA. There are many biochemists and molecular biologists who accept the maintenance definition as the best available definition of function. As scientists, they are more than willing to entertain any reasonable scientific arguments in favor of a different definition but nobody, including Nils Walter, has come up with such arguments.

Now let's look at the final paragraph of Walter's essay.

Most bioscientists will also agree that we need to continue advancing from simply cataloging non-coding regions of the human genome toward characterizing ncRNA functions, both elementally and phenotypically, an endeavor of great challenge that requires everyone's input. Solving the enigma of human gene expression, so intricately linked to the regulatory roles of ncRNAs, holds the key to devising personalized medicines to treat most, if not all, human diseases, rendering the stakes high, and unresolved disputes counterproductive.[108] The fact that newly ascendant RNA therapeutics that directly interface with cellular RNAs seem to finally show us a path to success in this challenge[109] only makes the need for deciphering ncRNA function more urgent. Succeeding in this goal would finally fulfill the promise of the human genome project after it revealed so much non-protein coding sequence (Figure 1). As a side effect, it may make updating Wikipedia and encyclopedia entries less controversial.

I agree that it's time for scientists to start identifying those transcripts that have a true function. I'll go one step further; it's time to stop pretending that there might be hundreds of thousands of functional transcripts until you actually have some data to support such a claim.

I take issue with the phrase "solving the enigma of human gene expression." I think we already have a very good understanding of the fundamental mechanisms of gene expression in eukaryotes, including the transitions between open and closed chromatin domains. There may be a few odd cases that deviate from the norm (e.g. Xist) but that hardly qualifies as an "enigma." He then goes on to say that this "enigma" is "intricately linked to the regulatory roles of ncRNAs" but that's not a fact, it's what's in dispute and why we have to start identifying the true function (if any) of most transcripts. Oh, and by the way, sorting out which parts of the genome contain real non-coding genes may contribute to our understanding of genetic diseases in humans but it won't help solve the big problem of how much of our genome is junk because mutations in junk DNA can cause genetic diseases.

Sorting out which transcripts are functional and which ones are not will help fill in the 10% of the genome that's functional but it will have little effect on the bigger picture of a genome that's 90% junk.

We've known that less than 2% of the genome codes for proteins since the late 1960s—long before the draft sequence of the human genome was published in 2001—and we've known for just as long that lots of non-coding DNA has a function. It would be helpful if these facts were made more widely known instead of implying that they were only dscovered when the human genome was sequenced.

Once we sort out which transcripts are functional, we'll be in a much better position to describe the all the facts when we edit Wikipedia articles. Until that time, I (and others) will continue to resist the attempts by the students in Nils Walter's class to remove all references to junk DNA.


Walter, N.G. (2024) Are non‐protein coding RNAs junk or treasure? An attempt to explain and reconcile opposing viewpoints of whether the human genome is mostly transcribed into non‐functional or functional RNAs. BioEssays:2300201. [doi: 10.1002/bies.202300201]

Measles Outbreaks Still Occur: How the APHL/CDC VPD Reference Centers Are Working to Identify Them

1981 poster promoting measles vaccination that says, "Make Measles a Memory." Photo source: CDC

By Donna Campisano, specialist, Communications, APHL

A vaccine to prevent measles has been available since 1963. And yet this highly contagious disease, characterized by fever, respiratory symptoms and a telltale body rash, is still with us.

While measles is thought of as a childhood illness, its outcomes can be far from benign.

According to the Centers for Disease Control and Prevention (CDC), 1 in 5 unvaccinated people who contract the virus will be hospitalized. One in every 20 children with the disease will develop pneumonia. And up to 3 of every 1,000 children infected will die from the neurological and respiratory complications measles cause.

Disease Outbreaks and the Role of Vaccine Preventable Disease Reference Centers

Thanks to a robust vaccination program, measles practically disappeared from this country and was declared eliminated in the US by the World Health Organization (WHO) in 2000. But increased vaccine hesitancy and a return to global travel (most cases of measles in this country are imported from elsewhere) following the pandemic have officials concerned.

As of the first week in March, 45 measles cases from 17 jurisdictions have been reported to the CDC in 2024. Compare that to 58 total cases from 20 jurisdictions reported in all of 2023. Florida accounts for 10 of those cases, nine in one county alone. While the vast majority are children and teens, one is an adult. All 10 cases were reported in February, demonstrating how quickly cases can spread. And more cases are popping up every day. The CDC recently sent a team to Chicago to help with a measles outbreak clustered mostly in a migrant shelter. Eight cases have been confirmed in about as many days.

While the number of cases reported thus far in this country isn’t staggering, the same can’t be said for other parts of the world where vaccination rates are particularly dismal. According to WHO, measles cases increased 18% globally from 2021 to 2022 and deaths jumped by 43%.

In 2013, APHL, in partnership with CDC, established four Vaccine Preventable Diseases (VPD) Reference Centers to help reduce the diagnostic load of state laboratories and assist with the pathogen typing that’s necessary to detect the origin and spread of disease outbreaks.

These four centers—located in California, New York, Wisconsin and Minnesota—perform molecular testing for the viruses that cause measles, mumps, rubella (German measles), chickenpox, enterovirus (which can cause diseases like polio and hepatitis A) and MERS-CoV (Middle East respiratory syndrome-related coronavirus). The Wisconsin and Minnesota centers also perform bacterial pathogen testing.

Testing, both diagnostic and characterization, is performed using standardized methods developed by CDC and is available to public health departments free of charge. Submitting sites are assigned to one or two VPD Reference Centers depending on what services they need. Test results are reported to the submitting site and to CDC.

Detecting Outbreaks in Real Time

How do VPD Reference Centers help curb outbreaks?

To reduce vaccine-preventable diseases like measles and the burden they cause, officials—from clinicians to public health professionals to lab scientists—need details about what diseases are circulating where. And the more immediate the information, the more immediate a response.

To that end, APHL will be launching a VPD dashboard in the next few months. The VPD Reference Centers will submit monthly or bimonthly data reports to APHL detailing the number of specimens submitted to them for testing, how many tests were performed per pathogen and the number of positive specimens detected. That information will be fed into the publicly available dashboard.

The dashboard, along with the rapid detection of disease provided by member labs and the outreach conducted by public health officials, will play a pivotal role in responding to disease outbreaks. APHL and CDC will continue to work together to provide training and improve knowledge in identifying and curtailing disease outbreaks, whatever form they take, wherever they erupt.

The post Measles Outbreaks Still Occur: How the APHL/CDC VPD Reference Centers Are Working to Identify Them appeared first on APHL Blog.

Mile-by-mile map along the path of totality

On April 8, 2024, the moon is going to completely block the sun along a designated path. For the Washington Post, Dylan Moriarty and Kevin Schaul use a strip of satellite imagery to show the totality across the United States, with events and time along the way.

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