Rosa Rubicondior: Refuting Creationism - A Cheesy Tease For Creationists

Saturday, 13 September 2025

Refuting Creationism - A Cheesy Tease For Creationists - Observed Evolution in Cheese-Rind Fungi

Cheese Fungi Help Unlock Secrets of Evolution | Tufts Now

Bayley Hazen Blue

Scientists have found a textbook example of evolution in progress—in the very mould used to mature cheese in caves.

“Show me an example of witnessed evolution!” is one of the stock demands from creationists in online debates. But it’s a trick request. No sooner is an example given than they hurriedly shift the goalposts, redefining evolution into a childish caricature. Instead of the real scientific process, they demand to see a cow turn into a whale overnight, or a mouse suddenly grow wings—some grotesque parody of “macro-evolution” that no biologist has ever claimed happens. Ironically, if such nonsense did occur, it would actually falsify the theory of evolution rather than confirm it.

This intellectual dishonesty is the lifeblood of creationist rhetoric. Their arguments only work by preying on scientific illiteracy in their audience, peddling strawmen and false definitions to cover the absence of any evidence for their own claims.

Meanwhile, science continues as it always has, with evolution properly defined as a change in allele frequency in a population’s gene pool over time. And right on cue, another clear demonstration has just been published in Current Biology.

The researchers studied the fungus Penicillium solitum, which is used to ripen cheese, by following its population over eight years in the controlled cave environment of Jasper Hill Farm. By comparing samples collected in 2016 with those taken more recently, they were able to track both visible and genetic changes in the mould over time.

What they found was striking. The rind colour, once a leafy green, had shifted to a chalky white. Genetic analysis showed this was due to repeated mutations in a pigment-producing gene called alb1, which is responsible for melanin production. In the dark, cave-like conditions, melanin offered no advantage, so natural selection favoured lineages that conserved energy by not producing it. The loss of pigment arose independently several times, through different mutations—including both point mutations and the disruption of the gene by mobile DNA elements.

This is evolution at its most direct: heritable changes in the genetic make-up of a population, producing visible differences in response to environmental conditions. It illustrates a well-known principle called relaxed selection—when a trait is no longer useful, natural selection no longer preserves it, and the trait may fade away. In this case, the shift also altered the appearance and sensory qualities of the cheese, underlining how evolutionary change can have immediate, practical consequences.

How Cheese Rinds Form. The rind of a cheese is not just a protective skin — it’s a living ecosystem. During the ageing process, the outer layer of the cheese is colonised by microbes, most often fungi and bacteria, that thrive in the controlled conditions of cheese cellars or caves.

In bloomy cheeses (like Brie or Camembert), surface-ripening moulds such as Penicillium camemberti are deliberately introduced. These fungi grow across the surface, forming the familiar white, velvety rind. In washed-rind cheeses, the surface is repeatedly brushed or washed with brine, beer, or spirits, encouraging the growth of reddish or orange bacteria such as Brevibacterium linens. In natural-rind cheeses, the surface flora develops spontaneously from microbes present in the environment, including caves, maturing rooms, and even the cheesemaker’s own tools and hands.

As these microbial communities grow, they break down proteins and fats, softening the texture beneath the rind and shaping the flavour profile of the cheese. In the case of the cave-aged cheeses studied in the Tufts research, Penicillium solitum was the dominant mould, producing a rind that initially appeared green but, through evolution, shifted to white.

The rind, then, is not just decorative: it’s an edible record of microbial activity — and, as this research shows, a window into evolution itself.

The story of how this discovery was made is outlined in an article by Mike Silver in TuftsNow — the online news magazine of Tufts University, Medford, Massachusetts, USA.

‘These Cheeses Have a Life, They Have a Story’
Color changes in fungi on cheese rinds point to specific molecular mechanisms of genetic adaptation—and sometimes a tastier cheese
Many scientific discoveries are serendipitous—the result of chance. Seeing evolution in action in a cheese cave turned out to be exactly that for Benjamin Wolfe, associate professor of biology, and his colleagues.

Back in 2016, Wolfe convinced his former post-doc advisor to drive with him to Jasper Hill Farm in Vermont to get samples of a special cheese called Bayley Hazen Blue, a ruse for her boyfriend to propose marriage at the spot where they first met. Wolfe ended up keeping that cheese in the freezer in his lab.

I’m notorious for not throwing samples away just in case we might need them.

Benjamin E. Wolfe, Corresponding author.
Department of Biology
Tufts University, Medford, MA, USA.

But when graduate student Nicolas Louw picked up recent samples of Bayley Hazen Blue from the Jasper Hill caves—large, damp rooms built into the side of steep hills—he discovered the cheese, previously coated with a leafy green layer of fungus, was now chalk white on the outside.

This was really exciting because we thought it could be an example of evolution happening right before our eyes. Microbes evolve. We know that from antibiotic resistance evolution, we know that from pathogen evolution, but we don’t usually see it happening at a specific place over time in a natural setting.

Benjamin E. Wolfe.

Wolfe and his colleagues reported the finding in Current Biology.

Understanding how fungi adapt to different environments can help us in areas of food security and health, too, says Louw.

Somewhere around 20% of staple crops are lost pre-harvest due to fungal rot, and an additional 20% are lost to fungi post-harvest. That includes the moldy bread in your pantry and rotting fruit on market shelves. The biggest threat to global food security is just rot from mold.

Nicolas L. Louw, first author.
Department of Biology
Tufts University, Medford, MA, USA.

Understanding how to control this problem while preventing fungal adaptation is an agricultural priority.

A Small but Key Mutation

When wheels of cheese are placed to ripen in natural or artificial cave environments, they form microbial rinds on their surface made up of communities of bacteria, yeast, and filamentous fungi (molds). These wild microbes are picked up from soil, plant, and marine environments and end up colonizing and adapting to the environments of the cheese caves.

What caused the Penicillium solitum fungi on the Jasper Hill cheeses to change color? A student in one of Wolfe’s advanced microbiology laboratory courses on microbiomes found the answer. Jackson Larlee, A24, discovered that the change was prompted by the disruption of a gene called alb1.

Alb1 is involved in producing melanin. You can think of melanin as an armor that organisms make to protect themselves from UV damage. For the fungi, it creates the green color that absorbs UV light. If you are growing in a dark cave and can get by without melanin, it makes sense to get rid of it, so you don’t have to expend precious energy to make it. By breaking that pathway and going from green to white, the fungi are essentially saving energy to invest in other things for survival and growth.

Nicolas L. Louw.

It’s a process called “relaxed selection,” when an environmental stressor is removed, and that happens to many organisms when they adapt to dark conditions, from Mexican cave fish to salamanders to some insects. It’s almost always a loss of pigments and melanin. Some creatures become blind, then increase their ability to sense food in other ways.

The fungi gave the Wolfe lab an opportunity to identify the genetic mechanisms that led to a small evolutionary change.

We found that the change was not just one mutation that swept through the whole colony, but the color shift came about through many types of mutations independently.

Nicolas L. Louw.

Some of the fungi had point mutations—single DNA base pair changes—at different locations in the genome. Others had a large insertion of DNA caused by something called a transposable element. Transposable elements, once called “jumping genes,” pop out of one location and insert themselves into another in the genome.

In this case, transposable elements were inserting themselves ahead of the alb1 gene, which disrupted its expression, effectively knocking it out. Transposable elements can cause a lot of damage, but this time, it was an advantage for the fungi to forego production of melanin—allowing it more energy to grow. Thus, the white wheels of cheese in the Jasper Hill cave.

Aspergillus fungi are in the same family as Penicillium. They are found in the soil, on decaying plants, in household dust and ventilation systems and in massive quantities in the air. Most of the time they are harmless, but some strains can cause severe lung infections. Understanding how they become locally adapted and lodged in the lung environment could help researchers understand and prevent these infections.

For now, the Wolfe lab, in collaboration with Jasper Hill Farm, is exploring another benefit of evolving and domesticating fungi—creating new types of cheese with improved aesthetics, taste, and texture. They inoculated fresh brie cheese with the novel white mold and let it grow and ripen the cheese for two months.

The result:

It’s slightly nuttier and less funky. I think it’s delicious.

Nicolas L. Louw.

Based on a taste testing panel, the new cheese has promising attributes that will be further fine-tuned in future batches of cheese at Jasper Hill Farm.

Seeing wild molds evolve right before our eyes over a period of a few years helps us think that that we can develop a robust domestication process, to create new genetic diversity and tap into that for cheesemaking.

Benjamin E. Wolfe.

Publication:
Louw, Nicolas L.; Eagan, Justin L.; Larlee, Jackson; Kehler, Mateo; Keller, Nancy P.; Wolfe, Benjamin E.
Long-term monitoring of a North American cheese cave reveals mechanisms and consequences of fungal adaptation
Current Biology (2025) DOI: 10.1016/j.cub.2025.08.053

© 2025 Elsevier.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

Highlights

A Penicillium solitum population has shifted from green to white in a cheese cave
Multiple mutations in a melanin biosynthesis gene (alb1) are found in white strains
White P. solitum strains outcompete green strains, but only in the dark
This local adaptation may be part of a fungal domestication process

Summary
Previous comparative and experimental evolution studies have suggested how fungi may rapidly adapt to new environments, but direct observation of in situ selection in fungal populations is rare due to challenges with tracking populations over human time scales. We monitored a population of Penicillium solitum over eight years in a cheese cave and documented a phenotypic shift from predominantly green to white strains. Diverse mutations in the alb1 gene, which encodes the first protein in the dihydroxynaphthalene (DHN)-melanin biosynthesis pathway, explained the green-to-white shift. A similar phenotypic shift was recapitulated with an alb1 knockout and experimental evolution in laboratory populations. The most common genetic disruption of the alb1 genomic region was caused by putative transposable element insertions upstream of the gene. White strains had substantial downregulation in global transcription, with genetically distinct white strains possessing divergent shifts in the expression of different biological processes. White strains outcompeted green strains in co-culture, but this competitive advantage was only observed in the absence of light. Our results illustrate how fermented food production by humans provides opportunities for relaxed selection of key fungal traits over short time scales. The local adaptation we observed may be part of a domestication process that could provide opportunities to generate new strains for innovation in fermented food production.

Graphical abstract

Louw, Nicolas L.; Eagan, Justin L.; Larlee, Jackson; Kehler, Mateo; Keller, Nancy P.; Wolfe, Benjamin E.
Long-term monitoring of a North American cheese cave reveals mechanisms and consequences of fungal adaptation
Current Biology (2025) DOI: 10.1016/j.cub.2025.08.053

© 2025 Elsevier.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

So here we have it: evolution, witnessed in real time, written not in fossils but in the rind of a cheese. No sudden monster hybrids, no overnight miracles, just the steady, measurable genetic change that defines evolution.

It’s a reminder that evolution doesn’t need to be spectacular to be real. Most of the time, it works quietly, generation by generation, gene by gene, adapting life to its environment with ruthless efficiency. In this case, it stripped away an unnecessary pigment because, in the darkness of a cave, producing it was a waste.

And that’s the point creationists can’t face: evolution is not a matter of belief, but of evidence. It can be seen in the lab, in the field, and now, even in the cheese on your plate. So the next time a creationist demands to see “witnessed evolution,” you can simply tell them to check their dinner.

Advertisement

What Makes You So Special? From The Big Bang To You

How did you come to be here, now? This books takes you from the Big Bang to the evolution of modern humans and the history of human cultures, showing that science is an adventure of discovery and a source of limitless wonder, giving us richer and more rewarding appreciation of the phenomenal privilege of merely being alive and able to begin to understand it all.

Ten Reasons To Lose Faith: And Why You Are Better Off Without It

This book explains why faith is a fallacy and serves no useful purpose other than providing an excuse for pretending to know things that are unknown. It also explains how losing faith liberates former sufferers from fear, delusion and the control of others, freeing them to see the world in a different light, to recognise the injustices that religions cause and to accept people for who they are, not which group they happened to be born in. A society based on atheist, Humanist principles would be a less divided, more inclusive, more peaceful society and one more appreciative of the one opportunity that life gives us to enjoy and wonder at the world we live in.

Amazon