Learn some real archaeology

A bunch of archaeologist and other online creators have come together to do an online event where they teach real archaeology – they call this initiative real archaeology:

Real Archaeology was started by a collective of online creators who produce fact-based content about the past. Our goal is to collaborate in creating, promoting, and sharing entertaining and educational media with the wider public on the wonders of our shared history.

We use peer-reviewed sources and our experience as researchers, teachers, archaeologists, historians, and more to bring history to life and make it accessible to as wide an audience as possible. As a part of our efforts to spread our message, we have created the Real Archaeology online event that spans three days in October.

During this time, our speakers will be releasing a myriad of archaeology-related content across multiple platforms including YouTube, TikTok, and Instagram. Follow our creators (list below) or search #realarchaeology to find and engage with our material.

The event started yesterday, but there is still time to catch the schedule today and tomorrow

Lazy linking

Here are a few links that might be of interest

Lady Gaga Never Spoke Out Against Rumors Claiming She’s a Man ‘Because I Didn’t Feel Like a Victim With That Lie’: ‘I’m Used to Lies Being Printed About Me’

Lady Gaga explains why she would not fight against these rumors, since she thought her fighting against them might harm someone else.

—

A graph exploration method for identifying influential spreaders in complex networks

The problem of identifying the influential spreaders – the important nodes – in a real world network is of high importance due to its theoretical interest as well as its practical applications, such as the acceleration of information diffusion, the control of the spread of a disease and the improvement of the resilience of networks to external attacks. In this paper, we propose a graph exploration sampling method that accurately identifies the influential spreaders in a complex network, without any prior knowledge of the original graph, apart from the collected samples/subgraphs. The method explores the graph, following a deterministic selection rule and outputs a graph sample – the set of edges that have been crossed. The proposed method is based on a version of Rank Degree graph sampling algorithm. We conduct extensive experiments in eight real world networks by simulating the susceptible-infected-recovered (SIR) and susceptible-infected-susceptible (SIS) epidemic models which serve as ground truth identifiers of nodes spreading efficiency. Experimentally, we show that by exploring only the 20% of the network and using the degree centrality as well as the k-core measure, we are able to identify the influential spreaders with at least the same accuracy as in the full information case, namely, the case where we have access to the original graph and in that graph, we compute the centrality measures. Finally and more importantly, we present strong evidence that the degree centrality – the degree of nodes in the collected samples – is almost as accurate as the k-core values obtained from the original graph.

An interesting paper from 2017.

—

Five Russian GRU Officers and One Civilian Charged for Conspiring to Hack Ukrainian Government

Defendants Are Alleged to Have Committed Cyber Attacks in Advance of Russia’s Invasion of Ukraine; Also Targeted 26 North Atlantic Treaty Organization Countries

It is the official release of the charge against Tenet and the Russian paymasters that was release a couple of weeks ago. For a good overview of the case, I recommend this article from the Columbia Journalism Review: The Tenet Media Incident

—

A rare link in Danish: OPLEVET ETNISK DISKRIMINATION I DANMARK (pdf)

Denne rapport udgør den hidtil mest omfattende undersøgelse af racisme i Danmark
med udgangspunkt i oplevet diskrimination og fordomme. Mens enkeltpersoners egne
oplevelser ikke kan give et præcist billede af det faktiske omfang af diskrimination
og fordomme, så kan oplevelser i kombination med den omfangsrige forskning, der
henvises til i rapporten, tydeliggøre, at der er problemer, der skal løses.

Undersøgelsen tager udgangspunkt i voksne minoritetsetniske personer med
opvækst i Danmark – dvs. personer der enten er født i Danmark eller kommet hertil
som børn (herefter betegnet som minoritetsetniske personer). Overordnet viser
besvarelserne i undersøgelsen, at over 8 ud af 10 minoritetsetniske personer angiver,
at de har oplevet diskrimination eller fordomme inden for det seneste år. Over 6 ud af
10 minoritetsetniske personer angiver, at de har oplevelser, man som udgangspunkt
kan karakterisere som ulovlig diskrimination. For mange er der ikke tale om en enkelt
hændelse, men gentagne negative oplevelser på tværs af bl.a. arbejdsmarkedet, i det
offentlige rum og i kontakten med myndigheder.

This is a report about experienced/perceived ethnic discrimination in Denmark, made by the Danish Institute for Human Rights in 2023

Lockdowns and Teen girl brains

There is currently some news going around that Covid lockdowns prematurely aged girls’ brains more than boys’

Adolescent girls who lived through Covid lockdowns experienced more rapid brain ageing than boys, according to data that suggests the social restrictions had a disproportionate impact on them.

MRI scans found evidence of premature brain ageing in both boys and girls, but girls’ brains appeared on average 4.2 years older than expected after lockdowns, compared with 1.4 years older for boys.

This certainly sounds like something we should be worried about, even if it is not clear what the effect of these differences are.

There are two things that should make you stop up, before getting two worried. It is the fact that the study is based on “MRI scans” and that it is about COVID political measures. MRI studies are rife with problems – as explained in Annual Research Review: Current limitations and future directions in MRI studies of child- and adult-onset developmental psychopathologie

The widespread use of magnetic resonance imaging (MRI) in the study of child- and adult-onset developmental psychopathologies has generated many investigations that have measured brain structure and function in vivo throughout development, often generating great excitement over our ability to visualize the living, developing brain using the attractive, even seductive images that these studies produce. Often lost in this excitement is the recognition that brain imaging generally, and MRI in particular, is simply a technology, one that does not fundamentally differ from any other technology, be it a blood test, a genotyping assay, a biochemical assay, or behavioral test. No technology alone can generate valid scientific findings. Rather, it is only technology coupled with a strong experimental design that can generate valid and reproducible findings that lead to new insights into the mechanisms of disease and therapeutic response

The subject the review focus on is not the one that the prematurely aged brains study fall under, but the same general problem exist.

And then there is the fact that the study is linked to COVID political measures. Any time this is the case, we have to stop up and be extra careful. There are a lot of biases related to this subject, both from the scientists and by the people reporting on the study.

Unsurprisingly this is also the case here. As epidemiologist Gideon Meyerowitz-Katz, the Health Nerd, explains:

Lockdowns Didn’t “Prematurely Age” Teen Girl’s Brains

Why the new viral study is extremely misleading

…

The study in question is a neurological examination of teen brains. The researchers put a bunch of adolescents aged 9-17 into MRIs before the pandemic, and then looked at their brains again a few years later. They used this data to look at what had happened to the brains in the interim using a variety of statistical techniques.

The Health Nerd goes through the study, explaining the setup and limits of the study. Unsurprisingly, it is a small study, and it is hard to make broad conclusions based on it. And when it comes to the effect of lockdowns?

Which brings us to an interesting point – what does any of this have to do with lockdowns?

Simple answer, really: nothing. The study does not, in any way, examine the effects of lockdown on teen brains.

Rather, the study shows that teen girls’ brains after the pandemic were different to the expected trends from brains before the pandemic. This could be caused by many things. Maybe the virus itself, which can cause some changes to brain chemistry, is to blame. Perhaps it was the global disruption brought about by a novel pandemic. Maybe the girls were more vulnerable than boys to things like relatives dying of COVID-19. We have no idea, because the authors didn’t do anything to investigate these myriad explanations. They don’t even report that the children in the study were present in Washington State for the lockdowns, nor whether they experienced similar lockdown impacts (i.e. school closures).

To make any inferences about lockdowns, the authors would’ve had to find some control group who’d had a different exposure to their intervention. Perhaps MRIs from kids in Florida, which had different COVID-19 restrictions, or a longitudinal sample from before the pandemic. These would all be inadequate samples for one reason or another, but they would’ve at least given some insight into whether lockdowns were associated with the cortical thinning seen in the research. As it stands, the study tells us nothing at all.

So, this is a somewhat doubtful study, which doesn’t tell us what is claimed about the study. The claims however are not sensational reporting by the press, but directly made by the scientists:

You can’t just blame the media here – the authors put the word “lockdown” into their study. It’s the second word of the title of their paper. Despite the paper having nothing to do with lockdowns.

This is, in a word, bad. Bad science. Poorly thought-through. Inadequate in a very serious way.

The Health Nerd  explains how such a paper could be published in PNAS.

Speaking of spices and science

Bharat B. Aggarwal was until recently the leading expert in the curative effects of curcumin.

Bharat B. Aggarwal is an Indian-American biochemist who worked at MD Anderson Cancer Center from 1989 to 2015. His research focused on potential anti-cancer effects and therapeutic applications of herbs and spices. Aggarwal was particularly drawn to curcumin, a non-toxic compound found in turmeric that has long been staple in Ayurvedic systems of medicine. He authored more than 120 articles about the compound from 1994 to 2020. These articles reported that curcumin had therapeutic potential for a variety of diseases, including various cancers, Alzheimer’s disease and, more recently, COVID-19. In his 2011 book Healing Spices: How to Use 50 Everyday and Exotic Spices to Boost Health and Beat Disease, Aggarwal recommends “taking a daily 500 mg curcumin supplement for general health”.

The above quote is from The King of Curcumin: a case study in the consequences of large-scale research fraud

As the title says, it turned out that Aggarwal committed research fraud

MD Anderson Cancer Center initially appeared to be fully on board with Aggarwal’s work. At one point, their website’s FAQ page recommended visitors buy curcumin wholesale from a company for which Aggarwal was a paid speaker (see “Spice Healer”, Scientific American). However, in 2012 (following observations of image manipulation raised by pseudonymous sleuth Juuichi Jigen), MD Anderson Cancer Center launched a research fraud probe against Aggarwal which eventually led to 30 of Aggarwal’s articles being retracted. Only some of these studies were about curcumin specifically, but most concerned similar natural products.

Retractions rarely number this high for a single author; according to the Retraction Watch leaderboard, only 26 other people have authored this many retracted studies. Aggarwal’s retracted articles feature dozens of instances of spliced Western blots and duplicated images, as well as several instances where mice were implanted with tumors exceeding volumes considered ethical. PubPeer commenters have noted irregularities in many publications beyond the 30 that have already been retracted. Aggarwal retired from M.D. Anderson in 2015, but has continued to author articles and appear at conferences.

I predict that more articles will be retracted in the future – not only because of Aggarwal being the author, but also because the field of study seems to be a magnet for frauds

Despite curcumin’s apparent lack of therapeutic promise, the volume of research produced on curcumin grows each year.  More than 2,000 studies involving the compound are published annually. Many of these studies bear signs of fraud and involvement of paper mills. As of 2020, the United States National Institutes of Health (NIH) has spent more than 150 million USD funding projects related to curcumin. Funding increased drastically in the 2007 fiscal year, shortly after Aggarwal began to publish in earnest about the compound and the same year he declared curcumin “the Indian solid gold”.

A obvious reason for this is the big money connected to this sort of fraudulent research

This proliferation of research on curcumin has fueled its popularity as a dietary supplement. Grand View Research estimated the global market for curcumin as a pharmaceutical to be around 30 million USD in 2020. Manufacturers are routinely scolded by the United States Food and Drug Administration for making false claims about the health effects of these supplements.

Spices don’t cure cancer

When you look at so-called alternative medicine, one of the remedies that is often pushed is using different spices against different disease, and quite frequently using spice as a cancer cure. Every time anyone have looked into any of these spices as a cure for something, they have of course turned out to be mostly worthless, though a few have turned out to have some effect.

This of course, leads to the claim that spice consumption is an ancient remedy against cancer. Unfortunately, a study from last year has shown that this is not likely to be the case.

No evidence that spice consumption is a cancer prevention mechanism in human populations by Antoine M Dujon et al

Abstract

Background

Why humans historically began to incorporate spices into their diets is still a matter of unresolved debate. For example, a recent study (Bromham et al. There is little evidence that spicy food in hot countries is an adaptation to reducing infection risk. Nat Hum Behav 2021;5:878–91.) did not support the most popular hypothesis that spice consumption was a practice favoured by selection in certain environments to reduce food poisoning, parasitic infections, and foodborne diseases.

Methods

Because several spices are known to have anticancer effects, we explored the hypothesis that natural selection and/or cultural evolution may have favoured spice consumption as an adaptive prophylactic response to reduce the burden of cancer pathology. We used linear models to investigate the potential relationship between age-standardized gastrointestinal cancer rates and spice consumption in 36 countries.

Results

Patterns of spice are not consistent with a cancer mitigation mechanism: the age-standardized rate of almost all gastrointestinal cancers was not related to spice consumption.

Conclusions

Direction other than foodborne pathogens and cancers should be explored to understand the health reasons, if any, why our ancestors developed a taste for spices.

I appropriate the effort to understand why spice was introduced into food in some parts of the world, and am looking forward to future research results

Computer models advancing science

Computer modeling has become a more and more important tool for science. We have seen it in Climatology for decades, as well as in a number of other fields. People who have a poor understanding of science, or who are trying to deny science, such as creationists and climate change deniers, will often claim that it isn’t really real science, but that is of course pure nonsense, as empirical evidence has demonstrated it again and again.

Now, there is a new great example of how a computer model is advancing our understanding of science. As ScienceDaily reports:

First hominin muscle reconstruction shows 3.2 million-year-old ‘Lucy’ could stand as erect as we can

A Cambridge University researcher has digitally reconstructed the missing soft tissue of an early human ancestor — or hominin — for the first time, revealing a capability to stand as erect as we do today.

Dr Ashleigh Wiseman has 3D-modelled the leg and pelvis muscles of the hominin Australopithecus afarensis using scans of ‘Lucy’: the famous fossil specimen discovered in Ethiopia in the mid-1970s.

…

Wiseman was able to use recently published open source data on the Lucy fossil to create a digital model of the 3.2 million-year-old hominin’s lower body muscle structure. The study is published in the journal Royal Society Open Science.

The research recreated 36 muscles in each leg, most of which were much larger in Lucy and occupied greater space in the legs compared to modern humans.

For example, major muscles in Lucy’s calves and thighs were over twice the size of those in modern humans, as we have a much higher fat to muscle ratio. Muscles made up 74% of the total mass in Lucy’s thigh, compared to just 50% in humans.

Paleoanthropologists agree that Lucy was bipedal, but disagree on how she walked. Some have argued that she moved in a crouching waddle, similar to chimpanzees — our common ancestor — when they walk on two legs. Others believe that her movement was closer to our own upright bipedalism.

Research in the last 20 years have seen a consensus begin to emerge for fully erect walking, and Wiseman’s work adds further weight to this. Lucy’s knee extensor muscles, and the leverage they would allow, confirm an ability to straighten the knee joints as much as a healthy person can today.

The paper can be found at the Royal Society Open Science: Three-dimensional volumetric muscle reconstruction of the Australopithecus afarensis pelvis and limb, with estimations of limb leverage

Abstract

To understand how an extinct species may have moved, we first need to reconstruct the missing soft tissues of the skeleton, which rarely preserve, with an understanding of segmental volume and muscular composition within the body. The Australopithecus afarensis specimen AL 288-1 is one of the most complete hominin skeletons. Despite 40+ years of research, the frequency and efficiency of bipedal movement in this specimen is still debated. Here, 36 muscles of the pelvis and lower limb were reconstructed using three-dimensional polygonal modelling, guided by imaging scan data and muscle scarring. Reconstructed muscle masses and configurations guided musculoskeletal modelling of the lower limb in comparison with a modern human. Results show that the moment arms of both species were comparable, hinting towards similar limb functionality. Moving forward, the polygonal muscle modelling approach has demonstrated promise for reconstructing the soft tissues of hominins and providing information on muscle configuration and space filling. This method demonstrates that volumetric reconstructions are required to know where space must be occupied by muscles and thus where lines of action might not be feasible due to interference with another muscle. This approach is effective for reconstructing muscle volumes in extinct hominins for which musculature is unknown.

The paper is an interesting read and in my opinion fairly accessible.

Science Vs limiting their output

I have listened to the Science Vs podcast for a while, but had somehow missed the fact that they had become exclusive to Spotify. This is not a good situation to be in for a podcast promoting the understanding of science, and the host/producer Wendy Zukerman and the editor Blythe Terrell have taken the consequences and are now limiting their output to shows that debunk stuff released on the Spotify platform

Zukerman, the host and executive producer for “Science Vs,” and Terrell, an editor for the science podcast, plan to limit their production on new episodes because they do not believe Spotify’s rules regarding misinformation go far enough.

“Until Spotify implements stronger methods to prevent the spread of misinformation on the platform, we will no longer be making new Science Vs episodes, except those intended to counteract misinformation being spread on Spotify,” they wrote in a letter to Ek, posted on Twitter on Monday.

“Science Vs,” which is exclusive to Spotify, looks at the science behind topics including pandemics.

They have already started doing this, with their latest episode Joe Rogan: The Malone Interview, which you can listen to here.

I applaud the principled stance that they have taken. You can find their twitter feed here.

Engadget have a few more details in Spotify’s ‘Science VS’ podcast will only fact-check misinformation being spread on Spotify

NASA Webb Telescope is on its way

I am always awestruck about the feats of engineering and science that goes into space exploration, and I love when there is yet another milestone to celebrate.

 


You can follow the news on the Webb Telescope Twitter feed or the blog dedicated to the Webb Telescope over at NASA.

Words have consequences: Hospital drops anti-vaxxer as spokesperson

I don’t follow US sports, and especially not the commercial vehicle claiming to be a sport, that NFL is, so I don’t really know how big a name Kirk Cousins is, but being a quarterback on a NFL team does give you a certain reach, no matter how good you are. This is why it is rather bad that Kirk Cousins has been saying stuff that is clearly anti-vaccination. It turns out that one of his sponsors, the Holland Hospital in Michigan feels the same way.

Michigan hospital ends relationship with Kirk Cousins after anti-vaccination remarks

“While we acknowledge that each person is entitled to their own viewpoints, those who speak on our behalf must support messages that align with the hospital’s position on matters of vital importance to individual and community health,” the hospital’s statement on the matter read. “For this reason, Holland Hospital will discontinue using Kirk Cousins as our spokesperson for now. We are proud of our association with Kirk. He embodies many values we respect and share as part of our work culture. However, we must be certain that our communications about COVID vaccination are consistent and unequivocal.

“Evidence also indicates that vaccinated individuals may be less likely to carry and transmit the virus to others including children, family members and friends,” the statement said. “For these reasons, Holland Hospital has and will continue to strongly recommend the COVID vaccine to those who are eligible to receive it.”

It is a pity that they feel the need to sugarcoat the breakup, instead of just saying that having using Kirk Cousins as a spokesperson was a mistake, given his anti-science and anti-evidence stance on health care and disease prevention.

Kirk Cousins is not the only sportsperson who has made dangerous remarks about COVID-19 and vaccinations, and I hope more companies will take the lead from Holland Hospital, and distance themselves from people promoting dangerous views.

Ancient DNA just became older

Most science news in recent days have been focused on the Perseverance Mars Rover and its landing on Mars. However, that is not the only major science news in recent days. We have also had the publication of the news about million years old mammoth DNA being sequenced.

The Guardian reports on this: Million-year-old mammoth genomes set record for ancient DNA

Teeth from mammoths buried in the Siberian permafrost for more than a million years have led to the world’s oldest known DNA being sequenced, according to a study that shines a genetic searchlight on the deep past.

Researchers said the three teeth specimens, one roughly 800,000 years old and two more than a million years old, provided important insights into the giant ice age mammals, including into the ancient heritage of, specifically, the woolly mammoth.

This is really exciting, and will help create a more accurate picture of the lineage of mammoths, as well as expand the possible range for future sequencing. As the Guardian states:

Dalén said new technologies could allow the sequencing of even older DNA from remains found in the permafrost, which dates back 2.6m years.

For a good look behind the science, Patrícia Pečnerová, the Postdoc involved in the research, has written a great write-up: Pushing the limits with million-year-old DNA

The write-up gives an interesting and humorous look behind the scenes, as the starting paragraph clearly shows:

I had low expectations when we went into the lab to extract DNA from samples that based on geological evidence were 600 thousand to 1.2 million years old. At that point of my PhD, I already knew better than to put faith in high-risk/high-gain projects. And attempting to extract DNA older than has ever been done before topped the list of some pretty funky projects that I have been involved in, like trying to retrieve DNA from rocks from the ocean floor. Such efforts rarely yield results and end up in the invisible section of the CV where dreams go to die. My supervisor, Love Dalén, calls it character building.

The article is unfortunately behind a paywall at Nature: Million-year-old DNA sheds light on the genomic history of mammoths

Further reading: Million-year-old DNA provides a glimpse of mammoth evolution (news write-up in Nature)