The Early History of Counting

Curated on Posted on by Stefaan Verhulst

Essay by Keith Houston: “Figuring out when humans began to count systematically, with purpose, is not easy. Our first real clues are a handful of curious, carved bones dating from the final few millennia of the three-​million-​year expanse of the Old Stone Age, or Paleolithic era. Those bones are humanity’s first pocket calculators: For the prehistoric humans who carved them, they were mathematical notebooks and counting aids rolled into one. For the anthropologists who unearthed them thousands of years later, they were proof that our ability to count had manifested itself no later than 40,000 years ago.

In 1973, while excavating a cave in the Lebombo Mountains, near South Africa’s border with Swaziland, Peter Beaumont found a small, broken bone with twenty-​nine notches carved across it. The so-​called Border Cave had been known to archaeologists since 1934, but the discovery during World War II of skeletal remains dating to the Middle Stone Age heralded a site of rare importance. It was not until Beaumont’s dig in the 1970s, however, that the cave gave up its most significant treasure: the earliest known tally stick, in the form of a notched, three-​inch long baboon fibula.

On the face of it, the numerical instrument known as the tally stick is exceedingly mundane. Used since before recorded history—​still used, in fact, by some cultures—​to mark the passing days, or to account for goods or monies given or received, most tally sticks are no more than wooden rods incised with notches along their length. They help their users to count, to remember, and to transfer ownership. All of which is reminiscent of writing, except that writing did not arrive until a scant 5,000 years ago—​and so, when the Lebombo bone was determined to be some 42,000 years old, it instantly became one of the most intriguing archaeological artifacts ever found. Not only does it put a date on when Homo sapiens started counting, it also marks the point at which we began to delegate our memories to external devices, thereby unburdening our minds so that they might be used for something else instead. Writing in 1776, the German historian Justus Möser knew nothing of the Lebombo bone, but his musings on tally sticks in general are strikingly apposite:

The notched tally stick itself testifies to the intelligence of our ancestors. No invention is simpler and yet more significant than this…(More)”.

Philosophy of Open Science

Curated on Posted on by Stefaan Verhulst

Book by Sabina Leonelli: “The Open Science [OS] movement aims to foster the wide dissemination, scrutiny and re-use of research components for the good of science and society. This Element examines the role played by OS principles and practices within contemporary research and how this relates to the epistemology of science. After reviewing some of the concerns that have prompted calls for more openness, it highlights how the interpretation of openness as the sharing of resources, so often encountered in OS initiatives and policies, may have the unwanted effect of constraining epistemic diversity and worsening epistemic injustice, resulting in unreliable and unethical scientific knowledge. By contrast, this Element proposes to frame openness as the effort to establish judicious connections among systems of practice, predicated on a process-oriented view of research as a tool for effective and responsible agency…(More)”.

AI tools are designing entirely new proteins that could transform medicine

Curated on Posted on by Stefaan Verhulst

Article by Ewen Callaway: “OK. Here we go.” David Juergens, a computational chemist at the University of Washington (UW) in Seattle, is about to design a protein that, in 3-billion-plus years of tinkering, evolution has never produced.

On a video call, Juergens opens a cloud-based version of an artificial intelligence (AI) tool he helped to develop, called RFdiffusion. This neural network, and others like it, are helping to bring the creation of custom proteins — until recently a highly technical and often unsuccessful pursuit — to mainstream science.

These proteins could form the basis for vaccines, therapeutics and biomaterials. “It’s been a completely transformative moment,” says Gevorg Grigoryan, the co-founder and chief technical officer of Generate Biomedicines in Somerville, Massachusetts, a biotechnology company applying protein design to drug development.

The tools are inspired by AI software that synthesizes realistic images, such as the Midjourney software that, this year, was famously used to produce a viral image of Pope Francis wearing a designer white puffer jacket. A similar conceptual approach, researchers have found, can churn out realistic protein shapes to criteria that designers specify — meaning, for instance, that it’s possible to speedily draw up new proteins that should bind tightly to another biomolecule. And early experiments show that when researchers manufacture these proteins, a useful fraction do perform as the software suggests.

The tools have revolutionized the process of designing proteins in the past year, researchers say. “It is an explosion in capabilities,” says Mohammed AlQuraishi, a computational biologist at Columbia University in New York City, whose team has developed one such tool for protein design. “You can now create designs that have sought-after qualities.”

“You’re building a protein structure customized for a problem,” says David Baker, a computational biophysicist at UW whose group, which includes Juergens, developed RFdiffusion. The team released the software in March 2023, and a paper describing the neural network appears this week in Nature1. (A preprint version was released in late 2022, at around the same time that several other teams, including AlQuraishi’s2 and Grigoryan’s3, reported similar neural networks)…(More)”.

Just Citation

Curated on Posted on by Stefaan Verhulst

Paper by Amanda Levendowski: “Contemporary citation practices are often unjust. Data cartels, like Google, Westlaw, and Lexis, prioritize profits and efficiency in ways that threaten people’s autonomy, particularly that of pregnant people and immigrants. Women and people of color have been legal scholars for more than a century, yet colleagues consistently under-cite and under-acknowledge their work. Other citations frequently lead to materials that cannot be accessed by disabled people, poor people or the public due to design, paywalls or link rot. Yet scholars and students often understand citation practices as “just” citation and perpetuate these practices unknowingly. This Article is an intervention. Using an intersectional feminist framework for understanding how cyberlaws oppress and liberate oppressed, an emerging movement known as feminist cyberlaw, this Article investigates problems posed by prevailing citation practices and introduces practical methods that bring citation into closer alignment with the feminist values of safety, equity, and accessibility. Escaping data cartels, engaging marginalized scholars, embracing free and public resources, and ensuring that those resources remain easily available represent small, radical shifts that promote just citation. This Article provides powerful, practical tools for pursuing all of them…(More)”.

Engaging Scientists to Prevent Harmful Exploitation of Advanced Data Analytics and Biological Data

Curated on Posted on by Stefaan Verhulst

Proceedings from the National Academies of Sciences: “Artificial intelligence (AI), facial recognition, and other advanced computational and statistical techniques are accelerating advancements in the life sciences and many other fields. However, these technologies and the scientific developments they enable also hold the potential for unintended harm and malicious exploitation. To examine these issues and to discuss practices for anticipating and preventing the misuse of advanced data analytics and biological data in a global context, the National Academies of Sciences, Engineering, and Medicine convened two virtual workshops on November 15, 2022, and February 9, 2023. The workshops engaged scientists from the United States, South Asia, and Southeast Asia through a series of presentations and scenario-based exercises to explore emerging applications and areas of research, their potential benefits, and the ethical issues and security risks that arise when AI applications are used in conjunction with biological data. This publication highlights the presentations and discussions of the workshops…(More)”.

How should a robot explore the Moon? A simple question shows the limits of current AI systems

Curated on Posted on by Stefaan Verhulst

Article by Sally Cripps, Edward Santow, Nicholas Davis, Alex Fischer and Hadi Mohasel Afshar: “..Ultimately, AI systems should help humans make better, more accurate decisions. Yet even the most impressive and flexible of today’s AI tools – such as the large language models behind the likes of ChatGPT – can have the opposite effect.

Why? They have two crucial weaknesses. They do not help decision-makers understand causation or uncertainty. And they create incentives to collect huge amounts of data and may encourage a lax attitude to privacy, legal and ethical questions and risks…

ChatGPT and other “foundation models” use an approach called deep learning to trawl through enormous datasets and identify associations between factors contained in that data, such as the patterns of language or links between images and descriptions. Consequently, they are great at interpolating – that is, predicting or filling in the gaps between known values.

Interpolation is not the same as creation. It does not generate knowledge, nor the insights necessary for decision-makers operating in complex environments.

However, these approaches require huge amounts of data. As a result, they encourage organisations to assemble enormous repositories of data – or trawl through existing datasets collected for other purposes. Dealing with “big data” brings considerable risks around security, privacy, legality and ethics.

In low-stakes situations, predictions based on “what the data suggest will happen” can be incredibly useful. But when the stakes are higher, there are two more questions we need to answer.

The first is about how the world works: “what is driving this outcome?” The second is about our knowledge of the world: “how confident are we about this?”…(More)”.

Diversity of Expertise is Key to Scientific Impact

Curated on Posted on by Stefaan Verhulst

Paper by Angelo Salatino, Simone Angioni, Francesco Osborne, Diego Reforgiato Recupero, Enrico Motta: “Understanding the relationship between the composition of a research team and the potential impact of their research papers is crucial as it can steer the development of new science policies for improving the research enterprise. Numerous studies assess how the characteristics and diversity of research teams can influence their performance across several dimensions: ethnicity, internationality, size, and others. In this paper, we explore the impact of diversity in terms of the authors’ expertise. To this purpose, we retrieved 114K papers in the field of Computer Science and analysed how the diversity of research fields within a research team relates to the number of citations their papers received in the upcoming 5 years. The results show that two different metrics we defined, reflecting the diversity of expertise, are significantly associated with the number of citations. This suggests that, at least in Computer Science, diversity of expertise is key to scientific impact…(More)”.

Index, A History of the

Curated on Posted on by Stefaan Verhulst

“A Bookish Adventure from Medieval Manuscripts to the Digital Age” by Dennis Duncan: “Most of us give little thought to the back of the book—it’s just where you go to look things up. But as Dennis Duncan reveals in this delightful and witty history, hiding in plain sight is an unlikely realm of ambition and obsession, sparring and politicking, pleasure and play. In the pages of the index, we might find Butchers, to be avoided, or Cows that sh-te Fire, or even catch Calvin in his chamber with a Nonne. Here, for the first time, is the secret world of the index: an unsung but extraordinary everyday tool, with an illustrious but little-known past.

Charting its curious path from the monasteries and universities of thirteenth-century Europe to Silicon Valley in the twenty-first, Duncan uncovers how it has saved heretics from the stake, kept politicians from high office, and made us all into the readers we are today. We follow it through German print shops and Enlightenment coffee houses, novelists’ living rooms and university laboratories, encountering emperors and popes, philosophers and prime ministers, poets, librarians and—of course—indexers along the way. Revealing its vast role in our evolving literary and intellectual culture, Duncan shows that, for all our anxieties about the Age of Search, we are all index-rakers at heart—and we have been for eight hundred years…(More)”.

Harvard fraud claims fuel doubts over science of behaviour

Curated on Posted on by Stefaan Verhulst

Article by Andrew Hill and Andrew Jack: “Claims that fraudulent data was used in papers co-authored by a star Harvard Business School ethics expert have fuelled a growing controversy about the validity of behavioural science, whose findings are routinely taught in business schools and applied within companies.

While the professor has not yet responded to details of the claims, the episode is the latest blow to a field that has risen to prominence over the past 15 years and whose findings in areas such as decision-making and team-building are widely put into practice.

Companies from Coca-Cola to JPMorgan Chase have executives dedicated to behavioural science, while governments around the world have also embraced its findings. But well-known principles in the field such as “nudge theory” are now being called into question.

The Harvard episode “is topic number one in business school circles”, said André Spicer, executive dean of London’s Bayes Business School. “There has been a large-scale replication crisis in psychology — lots of the results can’t be reproduced and some of the underlying data has found to be faked.”…

That cast a shadow over the use of behavioural science by government-linked “nudge units” such as the UK’s Behavioural Insights Team, which was spun off into a company in 2014, and the US Office of Evaluation Sciences.

However, David Halpern, now president of BIT, countered that publication bias is not unique to the field. He said he and his peers use far larger-scale, more representative and robust testing than academic research.

Halpern argued that behavioural research can help to effectively deploy government budgets. “The dirty secret of most governments and organisations is that they spend a lot of money, but have no idea if they are spending in ways that make things better.”

Academics point out that testing others’ results is part of normal scientific practice. The difference with behavioural science is that initial results that have not yet been replicated are often quickly recycled into sensational headlines, popular self-help books and business practice.

“Scientists should be better at pointing out when non-scientists over-exaggerate these things and extrapolate, but they are worried that if they do this they will ruin the positive trend [towards their field],” said Pelle Guldborg Hansen, chief executive of iNudgeyou, a centre for applied behavioural research.

Many consultancies have sprung up to cater to corporate demand for behavioural insights. “What I found was that almost anyone who had read Nudge had a licence to set up as a behavioural scientist,” said Nuala Walsh, who formed the Global Association of Applied Behavioural Scientists in 2020 to try to set some standards…(More)”.