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Posts Tagged ‘microbiology

“There are few creatures more remarkable than the lowly slime mold”*…

… nor, perhaps, more beautiful…

We’ve looked before at the at the “intelligent” accomplishments of the humble slime mold, and wondered what they might mean and what they might teach us. Photographer Barry Webb invites us to appreciate their spendor…

Blown wildly out of proportion in large format, the slime molds that British photographer Barry Webb captures seem atmospheric and sculptural. Stemonitis, for example, looks like dozens of thin pieces of wire with their ends coated in colored wax. But this fungi-like form is one of hundreds of kinds of slime mold, and it typically only reaches a height of about two centimeters at the most. Thanks to Webb’s macro photos, we glimpse a phenomenally beautiful world up-close that is otherwise virtually invisible.

Scientists have documented hundreds of these organisms, which aren’t actually related to plants, fungi, animals, or molds—despite the name. They comprise a unique group unto themselves, more closely related to amoebas. And new discoveries are being made all the time. From mottled gray bulbs that look like snow-covered trees to pink, coral-like tendrils, Webb chronicles a huge array of colors and shapes. He also consistently submits images to local and national botanical records so that researchers have access to high-resolution imagery…

Barry Webb Documents a Marvelous, Macro Array of Colorful Slime Molds,” from @thisiscolossal.com.

More of Webb’s portraits of slime mold on his site.

* Brandon Keim (in “Complexity Theory in Icky Action: Meet the Slime Mold“)

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As we get small, we might send microscopic greetings to William Ian Beardmore (W. I. B.) Beveridge; he was born on this date in 1908.  A microbiologist and veterinarian who served as  director of the Institute of Animal Pathology at Cambridge, he identified the origin of the Great Influenza (the Spanish Flu pandemic, 1918-19)– a strain of swine flu.

WIB Beveridge

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Happy Shakespeare’s Birthday!

While there is no way to know with certainty the Bard’s birth date, his baptism was recorded at Stratford-on-Avon on April 26, 1564; and three days was the then-customary wait before baptism. In any case, we do know with some certainty that Shakespeare died on this date in 1616.

Written by (Roughly) Daily

April 23, 2026 at 1:00 am

“Whoever oppresses the poor shows contempt for their Maker, but whoever is kind to the needy honors God”*…

A rural scene depicting two traditional huts made of mud and thatch, with a woman standing nearby, surrounded by a dry landscape and iconic baobab trees in the background.
From the piece featured below: “GDP per capita in Madagascar is about the same today as it was in 1950. As a consequence, the number of people in extreme poverty increased in line with the country’s population growth” (image source)

It’s easy to feel hope in the advances that the world has made in eraditcating extreme poverty over the last several decades. But as Max Roser writes, unless the poorest economies start growing, this period of progress against the worst form of poverty is over…

In the last decades, the world has made fantastic progress against extreme poverty. In 1990, 2.3 billion people lived in extreme poverty. Since then, the number of extremely poor people has declined by 1.5 billion people.

This means on any average day in the last 35 years, about 115,000 people left extreme poverty behind.1 Leaving the very worst poverty behind doesn’t mean a life free of want, but it does mean a big change. Additional income matters most for those who have the least. It means having the chance to leave hunger behind, to gain access to clean water, to access better healthcare, and to have at least some electricity — for light at night and perhaps even to cook and heat.

Can we expect this rapid progress to continue?

Unfortunately, we cannot. Based on current trends, progress against extreme poverty will come to a halt. As we’ll see, the number of people in extreme poverty is projected to decline, from 831 million people in 2025 to 793 million people in 2030. After 2030, the number of extremely poor people is expected to increase.

To understand why the rapid progress against deep poverty will not continue into the future, we need to know why the world made progress in the past.

Extreme poverty declined in the last three decades because, back in the 1990s, the majority of the poorest people on the planet lived in countries that subsequently achieved very fast economic growth. In Indonesia and China, more than two-thirds of the population lived in extreme poverty. But these economies then grew rapidly, so that by today, the share has declined to less than 10%. Other large Asian countries — including India, Pakistan, Bangladesh, and the Philippines — also achieved strong growth, and as a consequence, the share living in extreme poverty declined rapidly. Much of the progress happened in Asia, but conditions in other regions improved too: the share living in extreme poverty also declined in Ghana, Cape Verde, Cameroon, Panama, Bolivia, Mexico, Brazil, and many other countries.

This chart shows the economic change in these countries over the past decades. As incomes increased, the share of people in extreme poverty declined.

A line graph showing the decline in the share of extreme poverty across various countries from 1990 to 2024, plotted against GDP per capita.
Share of population living in extreme poverty vs. GDP per capita, 1990 to 2024 (World Bank, Eurostat, OECD, IMF)

What is different today is that the majority of the world’s poorest people are stuck in economies that have been stagnating for a long time.Consider the case of Madagascar. In the long run, the country has not seen any growth at all: GDP per capita in Madagascar is about the same today as it was in 1950. As a consequence, the number of people in extreme poverty increased in line with the country’s population growth. In richer countries, it is possible to reduce poverty by reducing inequality through redistribution, but a country like Madagascar cannot reduce its share of people in extreme poverty through redistribution. This is because the mean income is lower than the poverty line; if everyone had the same income, everyone would be living in extreme poverty.

The situation is similar in other countries, as the chart below shows: in the Democratic Republic of Congo, Mozambique, Malawi, Burundi, and the Central African Republic, more than half of the population lives in extreme poverty. As their economies have stagnated, the deep poverty that most people live in has remained largely unchanged for decades.

This is why we have to expect the end of progress against extreme poverty based on current trends. If the poorest economies remain stagnant, hundreds of millions of people will continue to live in extreme poverty.

Line graph depicting the percentage of the population living in extreme poverty in five countries: DR Congo, Mozambique, Malawi, Burundi, Central African Republic, and Madagascar, from 1992 to 2022.
Share of population living in extreme poverty, 1992-2022 (World Bank)

I’m always skeptical when people say that we are at a juncture in history where the future looks much different than the past. But when it comes to the fight against extreme poverty, I fear it is true. Today, the majority of the world’s poorest people are living in economies that have not achieved economic growth in the recent past… Based on current trends, we have to expect the end of progress against extreme poverty…

… It’s no news that we should expect an end to progress against extreme poverty. This article is an update of an article I published in 2019, in which I wrote the same: the fact that the poorest economies are not growing means that the rapid progress against extreme poverty seen in the last decades will end.

Although this prospect has been known for years, it has hardly received the attention it deserves. Progress against extreme poverty was one of humanity’s most outstanding achievements of the past decades — the end of it would be one of the very worst realities of the coming ones.

Importantly, however, these projections are not predictions; their purpose is not to describe what the world in 2030 or 2040 will certainly look like. These projections describe what we have to expect based on current trends; they tell us about our present world rather than the reality of tomorrow. Current trends don’t have to become future facts: many countries left extreme poverty behind in the past, because they had a moment at which they broke out of stagnation.

What these projections tell us, however, is that if the poorest countries do not start to grow, a very bleak future is ahead of us: a future in which extreme poverty remains the reality for hundreds of millions for many years to come…

Eminently worth reading in full– and acting on: “The end of progress against extreme poverty?” from @maxroser.bsky.social and @ourworldindata.org.

* Proverbs 14:31, NIV

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As we put our shoulders to the wheel, we might spare a thought for a man who contributed mightily to our capacity to feed humanity, Kenneth V. Thimann; he died on this date in 1997. A microbiologist, he was a pioneer in plant physiology (especially the hormones that control the development of plants). Building on the thinking of Frits Went, he identified the first plant hormone to be discovered– the first auxin, a class of growth hormones, and revealed its chemical structure– which proved very important to agriculture and its yields.

A black and white portrait of a smiling elderly man wearing a sweater vest and a collared shirt, with shelves of books in the background.

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“The study of taxonomy in its broadest sense is probably the oldest branch of biology or natural history as well as the basis for all the other branches, since the first step in obtaining any knowledge of things about us is to discriminate between them and to learn to recognize them”*…

Seal of the Holotypic Occlupanid Research Group (HORG), featuring a stylized image of a bread clip with the group's founding year, 1994, and the motto 'Fiat Divisa Panem'.

The Holotypic Occlupanid Research Group (HORG) is a tongue-in-cheek non-profit organization founded in 1994 by John Daniel (a visual effects artist with a background in invertibrate zoology). It playfully researches and classifies plastic bread clips, calling them “occlupanids,” as if they were a species in a scientific taxonomy (Kingdom: Plasticae), documenting their diverse forms from around the world. They treat these common, often-ignored objects as fascinating organisms, collecting specimens and creating a taxonomy and a database of their shapes, colors, and “species”…

This site contains several years of research in the classification of occlupanids. These small objects are everywhere, dotting supermarket aisles and sidewalks with an impressive array of form and color. The Holotypic Occlupanid Research Group has taken on the mantle of classifying this most common, yet most puzzling, member of phylum Plasticae…

Occlupanids are generally found as parasitoids on bagged pastries in supermarkets, hardware stores, and other large commercial establishments. Their fascinating and complex life cycle is unfortunately severely under-researched. What is known is that they take nourishment from the plastic sacs that surround the bagged product, not the product itself, as was previously thought. Notable exceptions to this habit are those living off rubber bands and on analog watch hands.

In most species, they often situate themselves toward the center of the plastic bag, holding in the contents. This leads to speculation that the relationship may be more symbiotic than purely parasitic.

Their stunning diversity and mysterious habits have entranced many a respectable scientist into studying, collecting, and cataloging specimens late into the night.

This site contains several years of research in the classification of occlupanids. For those of you who do not consume sliced bread, occlupanids do not form an important part of your life. For the rest of the world, These small objects are everywhere, dotting supermarket aisles and sidewalks with an impressive array of form and color.

The Holotypic Occlupanid Research Group has taken on the mantle of classifying this most common, yet most puzzling, member of phylum Plasticae.

They’ve even created a handy, free print-your-own set of cut-out identifcation placards “for the excitable amateur scientists out there who want to start their own collection!”

Ready, set, browse: HORG- Holotypic Occlupanid Research Group

For more on HORG, see here and here.

Richard E. Blackwelder

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As we contemplate classification, we might send insightful birthday greetings to a man who revolutionized the understanding of the taxonomy of his field, Harold Varmus; he was born on this date in 1939. A microbiologist and medical doctor, he shared (with J. Michael Bishop) the 1989 Nobel Prize in Physiology or Medicine for discovery of the cellular origin of retroviral oncogenes— a discovery that led to great strides in the understanding, diagnosis, and treatment of a variety of cancers.

Portrait of a smiling man wearing glasses and a suit with a light-colored shirt and patterned tie, against a wooden background.

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Written by (Roughly) Daily

December 18, 2025 at 1:00 am

“It’s not a bug, it’s a feature”*…

Microscopic image of plant cells exhibiting a blue hue, showcasing their structure and texture.
Blue-stained serpentine Neotyphodium coenophialum mycelia inhabiting the intercellular spaces of tall fescue leaf sheath tissue. Magnified 400x.

Anna Marija Helt reports that, as global warming challenges tradtional agriculture, scientists are looking to “probiotics” for crops as a new green revolution in agriculture…

Potatoes contain something about which most people are entirely unaware: endophytes, which means “within plants.” Endophytes can also be found in other vegetables, fruits, and grains. In fact, all plants harbor endophytes in the form of bacteria, fungi, and other microbes.

Endophytes eat plant-derived nutrients but typically don’t cause disease. Instead, they bolster plant growth, disease resistance, antioxidant status, or tolerance to stressors such as drought, heat, and cold. Endophytes enable plants to respond quickly to such stressors by expanding their genetic repertoire, according to a review by ecologist Christine Hawkes and colleagues. To improve crop health and sustainability, Hawkes studies how plants, their fungal residents, and such stressors interact.

Given climate-related drought and temperature extremes, declining soil quality, and a decrease in arable land, endophytes, argue Pankaj Trivedi, Chakradhar Mattupalli, Kellye Eversole, and Jan E. Leach, might undergird a sustainable “green revolution” to improve agricultural productivity while lessening reliance on environmentally damaging and health-threatening agricultural chemicals. Endophytes can have an impact, says plant biotechnologist Julissa Ek-Ramos, on “climate change, recovering the soil, and having more healthy food to eat.”…

… “It’s really amazing how strongly these endophytes can combat the fungal pathogens of crops,” [microbiologist Sharon] Doty says. And she notes regarding their growth-promoting effects, “It works in maize, in rice, in tomatoes, in bell peppers, and strawberries.” Her team has also isolated endophytes from sweet potatoes that improve the rooting of poplars, a promising biofuels crop.

Endophytes confer additional traits useful for a changing planet. For example, those from geothermal habitats can confer heat tolerance, based on studies led by geneticist Regina Redman. And crop physiologist K. M. Manasa demonstrated salt-tolerance in rice plants inoculated with an endophyte from seaside plants. Rice is salt-sensitive and one of the world’s main food crops. But increasing soil salinity is impacting a fifth of farmable land globally due to climate change and human water and land use practices…

Nitrogen is often the most limiting soil nutrient for crops, something nineteenth-century farmers recognized. Agronomist and Nobel Prize nominee Johanna Döbereiner discovered nitrogen-fixing endophytes in non-legume plants in the twentieth century that, like rhizobia, might reduce the need for financially and environmentally costly synthetic fertilizers. Many of the endophytes Doty has characterized over twenty-five years fix nitrogen and promote growth in lab, greenhouse, and field trials but have a much broader host range than rhizobia, extending from farm lands to forests…

… Developing real-world endophyte applications is a complicated challenge, but a necessary one given the need for more productive and sustainable agriculture. In the meantime, skeptical farmers are getting onboard.

“There’s a lot of conversations going on between researchers and farmers,” says Friesen, to “move the needle on our understanding of these processes that are so important for soil health but also plant health and the stability and security of our food supply.”…

More at “Better Farming Through Endophytes,” from @ahelt.bsky.social in @jstordaily.bsky.social.

common phrase

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As we muse on microbes, we might send healthy birthday greetings to John Boyd Orr (1st Baron Boyd-Orr); he was born on this date in 1880. A teacher, medical doctor, biologist, nutritional physiologist, politician, businessman, and farmer, he was awarded the Nobel Peace Prize in 1949 for his scientific research into nutrition and for his work as the first Director-General of the United Nations Food and Agriculture Organization.

A black and white portrait of John Boyd Orr, a distinguished man in a suit, looking directly at the camera with a serious expression.

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“But somewhere, beyond space and time / Is wetter water, slimier slime”*…

Close-up of a vibrant yellow slime mold, _Physarum polycephalum_, spreading across a textured brown log.
Physarum Polycephalum

Scientist’s have long marvelled at the “intelligent” accomplishments of the humble slime mold (and here). Noting that certain slime molds can make decisions, solve mazes, and remember things, Matthew Sims ponders what we can learn from the blob…

During the COVID-19 pandemic, some people took up baking, others decided to get a dog; I chose to grow and observe slime mould. The study in my partner’s flat in Edinburgh became home to two cultures of Physarum polycephalum, an acellular slime mould sometimes more casually referred to as ‘the blob’.

I began a series of experiments investigating how long it would take for two separated cell masses from the same bisected Physarum cell to stop fusing with one another upon reintroduction. Hours turned into days, and days into weeks, and, due to time constraints, the experiment eventually fizzled out around six weeks. This, however, was only the beginning. Over that following year (unbeknown to our unsuspecting neighbours), I conducted several more experiments. Although none of them were published, each inspired new philosophical questions – which to this day continue to shape my thinking. One of the core questions was: what can the behaviour of slime mould teach us about biological memory?

The differences between P polycephalum and humans may seem vast, but slime mould can reveal a remarkable amount about various aspects of how we remember. While many people might assume that our memories are primarily stored within our brains, some philosophers like myself argue that – along with some other aspects of cognition – memory can extend beyond the confines of the body to involve coupled interaction with structures in the environment. At least some of our cognitive processes, in short, loop out into our surroundings. Slime mould is an intriguing candidate to explore this idea because it doesn’t have a brain at all, yet in some cases can apparently ‘remember’ things without needing to store those associated memories within itself. In other cases, memories acquired via learning by one individual can even be acquired by a separate individual through physical contact. The behaviour of this strange form of life suggests that some of our ideas about how memories are acquired may need a rethink…

[Sims explains how slime mold “remembers”– via slime trails– and explores the questions that this raises…]

… So, what can slime mould teach us about biological memory? One lesson is that spatial memory needn’t be confined entirely within an organism (á la HEC). Moreover, what becomes memory traces when used (eg, extracellular slime) needn’t be the result of learning by the external trace-producer. Another takeaway is that, in some cases, an individual can acquire such memory without having engaged in learning itself. This raises an intriguing parallel in the human case. We do, after all, routinely read and act upon instructions, maps and manuals written by others, drawing on information acquired through their experiences, not our own. Although such externalised sources of information are typically declarative in structure – designed to represent facts explicitly – we often act upon them automatically, without needing to consciously recall or reflect on the information they convey. In this way, they guide behaviour in ways that functionally resemble non-declarative memory. While the analogy shouldn’t be pushed too far, both the human and slime mould cases illustrate how memory can become decoupled from individual learning, instead becoming accessible to others through environmental structures.

These conclusions, of course, remain contentious within traditional cognitive science and psychology where memory is often defined as the result of learning on the part of the same individual whose memory it is. Despite important concerns raised by the likes of Francis Crick in 1984, memory storage is still often attributed to synaptic plasticity – changes in strength of connection between neurons – quashing the very possibility of external memory traces. That said, some like the psychologist C Randy Gallistel – who has long argued that memory may also be stored in molecules like RNA within the brain – have remained vigilant in thinking outside the box. However, given the accumulating empirical evidence that memory-guided behaviour is exhibited in non-neuronal organisms like Physarum, then even this outside-the-box thinking remains firmly planted in traditional views about the requirements of brains for memory and the kind of strict internalism HEC suggests needn’t always be the case. Both HEC and memory without learning are not easy pills to swallow, but then again, neither is the very idea that a non-neuronal organism can learn in the first place – an idea that Physarum’sbehaviour unequivocally seems to support.

Whether it’s the subject of experiments carried out in a lab (or in a cramped study of an Edinburgh tenement flat) or it’s the subject of empirically informed, armchair philosophising, Physarum provides a valuable model organism to inspect, challenge and refine some of our most fundamental biological concepts – concepts like memory…

Fascinating: “Memories without brains,” from @philosobio.bsky.social‬ in @aeon.co‬.

Rupert Brooke

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As we reckon with recall, we might send microscopic birthday greetings to Carl Woese; he was born on this date in 1928. A microbiologist and biophysicist. Woese is famous for defining, in 1977, the Archaea (a new domain of life, distinct from the previously-recognized two domains of bacteria and life other than bacteria). To accomplish this feat, he pioneered phylogenetic taxonomy of 16S ribosomal RNA, a technique that has revolutionized microbiology. Microbiologist Justin Sonnenburg of Stanford said “The 1977 paper is one of the most influential in microbiology and arguably, all of biology. It ranks with the works of Watson and Crick and Darwin, providing an evolutionary framework for the incredible diversity of the microbial world.”

Woese originated the RNA world hypothesis in 1967, although not by that name. And he also speculated about an era of rapid evolution in which considerable horizontal gene transfer occurred between organisms. With regard to Woese’s work on horizontal gene transfer as a primary evolutionary process, Professor Norman R. Pace of the University of Colorado at Boulder said, “I think Woese has done more for biology writ large than any biologist in history, including Darwin… There’s a lot more to learn, and he’s been interpreting the emerging story brilliantly.”

A portrait of Carl Woese, a prominent microbiologist and biophysicist, sitting and looking directly at the camera with a thoughtful expression. He has gray hair and is wearing a dark shirt with a multi-colored sweater. A wall filled with scientific charts is blurred in the background.

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Written by (Roughly) Daily

July 15, 2025 at 1:00 am