Today, scientists apply similar principles in the lab through a technique known as directed evolution. Researchers use it to improve proteins such as enzymes and antibodies that play important roles in medicine, industrial manufacturing, and even everyday products like laundry detergents.

Limits of Traditional Directed Evolution

Despite its success, standard directed evolution methods have a key limitation. They usually impose a constant selection pressure that favors proteins that remain highly active all the time. However, real biological systems rarely function this way. Many proteins serve as signals, molecular switches, or “logic gates” (proteins that combine multiple inputs to make a yes-or-no decision), meaning they must change states as conditions shift.

For example, a protein might briefly activate, then turn off, and later switch on again. When evolution experiments only reward a single state, other necessary states can degrade. As a result, proteins may lose the ability to switch properly, which can be harmful for cells (e.g. kill a cell). Because of this challenge, creating proteins with complex multi-state behavior has proven difficult with existing directed evolution approaches.

A Light-Based Strategy for Protein Evolution

Researchers led by Sahand Jamal Rahi at EPFL’s Laboratory of the Physics of Biological Systems have introduced a new approach called “optovolution.” This method uses light to steer the evolution of proteins that can perform dynamic functions and even carry out simple computational tasks that follow yes-or-no rules.

The study, published in Cell, helps bring directed evolution closer to how cells naturally operate. In living systems, timing and switching between states are just as important as the strength of a signal.

Engineering Yeast Cells to Select the Best Proteins

To build their system, the researchers used the budding yeast Saccharomyces cerevisiae, an organism widely used both in brewing and scientific research. They redesigned the yeast cell cycle so that cell division depended on the behavior of the protein being evolved. The protein needed to switch cleanly between active and inactive states for the cell to survive.

The scientists connected the protein’s output signal to a regulator that controls the cell cycle. This regulator is essential during one stage but becomes toxic during another. If the protein remained on or off for too long, the yeast cell would stall or die. Only cells containing proteins that switched at the correct time continued to divide.

Using Light to Control Evolution in Real Time

Light provided a way to control this process with precision. The researchers used optogenetics, a technique that activates or deactivates genes using light. By delivering timed pulses of light, they forced the protein to alternate between states.

Each yeast cell cycle lasts about 90 minutes, creating a rapid pass or fail test of whether the protein switched at the correct moment. Proteins that performed best allowed the cell to survive and reproduce, while poorly switching variants were eliminated. This allowed optovolution to automatically select proteins with better dynamic behavior without manual screening or repeated adjustments.

New Protein Variants and Expanded Color Sensitivity

Using optovolution, the team evolved several different types of proteins. They first improved a commonly used light controlled transcription factor. The researchers generated 19 new variants that showed greater sensitivity to light, reduced activity in darkness, or the ability to respond to green light rather than only blue light. Engineering proteins that respond to warmer colors than blue has long been considered extremely difficult because of how these proteins absorb light.

The scientists also evolved a red light optogenetic system so that yeast cells no longer required an added chemical cofactor. Evolution produced a mutation that disabled a normal yeast transport protein. This unexpected change allowed the system to use light sensitive molecules already present inside the cell, making the system easier to use in experiments.

Proteins That Act Like Tiny Computers

The study also demonstrated that optovolution can extend beyond light sensing proteins. The researchers evolved a transcription factor that functions like a single protein computer. It activated genes only when two different inputs appeared at the same time – one light signal and one chemical signal.

Dynamic protein behavior is essential for many biological processes, including sensing environmental changes, making decisions inside cells, and controlling cell division. By enabling these behaviors to evolve continuously within living cells, optovolution offers new possibilities for synthetic biology, biotechnology, and fundamental research.

The technique may help scientists design smarter cellular circuits, create optogenetic tools that respond independently to different colors of light, and better understand how complex protein behaviors arise through evolution.

Other contributors

• EPFL Laboratory of Protein and Cell Engineering
• University of Bayreuth
• Lausanne University Hospital (CHUV)

Martindale and her research team, including Stéphane Bodin of Aarhus University, were exploring the rugged valley to study the ecology of ancient reef systems that once existed there when the area lay beneath the ocean. Reaching those reefs required crossing numerous layers of turbidites, sediments formed by dense underwater debris flows. Ripple patterns often appear on these deposits. However, Martindale noticed small ridges and wrinkles layered on top of the ripples that seemed unusual.

“As we’re walking up these turbidites, I’m looking around and this beautifully rippled bedding plane caught my eye,” says Martindale. “I said, ‘Stéphane, you need to get back here. These are wrinkle structures!'”

What Are Wrinkle Structures

Wrinkle structures are tiny ridges and pits ranging from millimeters to centimeters across. They develop when algae and microbial communities grow in mats across sandy seafloors. These delicate textures are rarely preserved in younger rocks because animals often disturb and destroy them. As a result, wrinkle structures are uncommon in rocks younger than about 540 million years old, when animal life rapidly diversified and began actively stirring ocean sediments.

Today, scientists typically find wrinkle structures in shallow tidal environments where sunlight supports photosynthetic algae.

Why These Wrinkles Should Not Exist

The wrinkle structures Martindale spotted appeared in rocks that formed far below the ocean surface. The turbidites where they were found had been deposited at depths of at least 180 meters, far too deep for sunlight to penetrate. This meant the structures could not have formed from the same sunlight dependent algae that create wrinkle patterns in shallow environments today.

Previous claims of wrinkle structures in deep water turbidite deposits have also been disputed. Another complication was the age of the rocks. At about 180 million years old, they formed during a time when animals were actively disturbing the seafloor worldwide, which normally erases delicate microbial textures. In other words, the wrinkle structures Martindale saw should not have been preserved at all.

Recognizing how unusual the find was, she set out to confirm whether her first impression was correct.

“Let’s go through every single piece of evidence that we can find to be sure that these are wrinkle structures in turbidites,” says Martindale, because wrinkle structures, usually photosynthetic in origin, “shouldn’t be in this deep-water setting.”

Evidence of Chemosynthetic Microbial Life

The research team carefully examined the surrounding rock layers and confirmed that the sediments were indeed turbidites. Next they investigated whether the unusual textures truly formed from biological activity.

Chemical testing provided a key clue. The sediment just beneath the wrinkles contained elevated carbon levels, which often indicate a biological origin. The team also looked to modern ocean environments for comparison. Footage from remotely operated submersibles exploring seafloors far below the photic zone revealed that microbial mats can develop there as well, but they are produced by chemosynthetic bacteria. These microbes obtain energy from chemical reactions instead of sunlight.

How Deep Sea Microbes Created the Wrinkles

By combining geological observations, chemical evidence, and modern examples from the deep ocean, the scientists concluded that they had discovered chemosynthetic wrinkle structures preserved in the rock record.

Turbidite flows likely played a critical role in creating the right conditions. These debris flows transport nutrients and organic material into deep water while also lowering oxygen levels in the surrounding sediments. Such conditions can support communities of chemosynthetic bacteria.

During quieter periods between debris flows, these bacteria can spread across the seafloor and form mats on top of the sediment. As the mats grow, they develop the wrinkled surface patterns that Martindale observed in the rocks of Morocco. In most cases, the next debris flow would erase the mat, but occasionally the structure becomes buried and preserved.

Expanding the Search for Ancient Life

Martindale now hopes to conduct laboratory experiments to better understand how wrinkle structures might develop within turbidite environments. She also hopes the discovery encourages scientists to rethink the long standing assumption that wrinkle structures are created only by photosynthetic microbial mats.

If chemosynthetic mats can also produce these features, geologists may begin searching for wrinkle structures in environments that were previously overlooked in the hunt for ancient life.

“Wrinkle structures are really important pieces of evidence in the early evolution of life,” says Martindale. By ignoring their possible presence in turbidites, “we might be missing out on a key piece of history of microbial life.”

Fibermaxxing refers to consuming at least the recommended daily amount of fiber for your body weight each day. The idea has gained traction across social media and traditional media this year.

Jennifer Lee is a scientist at the Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University. Her research focuses on how shifts in gut health and differences between sexes affect metabolism throughout a person’s life.

Lee says she is not surprised that fibermaxxing has become popular. In fact, she sees it as a sign that more people are recognizing an important distinction between lifespan and healthspan. Living longer does not necessarily mean living those years in good health, so many people are searching for ways to stay healthier as they age.

“There is a nine-year gap between living to a certain age in good health and then living in poor quality of health at the end of your life,” Lee added. “Behavioral or nutritional strategies that can keep someone healthy are very on trend right now.”

Research shows that consistently low fiber intake can contribute to metabolic and cardiovascular problems, including diabetes and obesity.

“If you’re not consuming a lot of fiber, you’re possibly consuming calories from other macronutrient groups, and they may be high in carbohydrates or fats, which can lead to weight gain,” Lee said. “Then, depending on a number of factors that may impact one’s cancer risk, a fiber deficiency may increase your risk for certain cancers, such as colorectal, breast, and prostate cancer.”

Overall, Lee explained that adding more fiber to your daily diet tends to produce wide ranging health benefits.

How Much Fiber Do I Need?

You can find a detailed recommendation for your personal nutritional intake via the USDA’s National Agriculture Library Dietary Reference Intakes (DRI) calculator.

Meeting Daily Fiber Intake Recommendations

According to the Dietary Guidelines for Americans, 2020-2025, published by the United States Department of Agriculture (USDA) and United States Department of Health and Human Services, adults should consume between 22 and 34 grams of fiber each day, depending on age and sex.

Lee also pointed to a simple guideline. For every 1,000 calories consumed, people should aim for about 14 grams of fiber. As people get older and typically eat fewer calories, their recommended fiber intake decreases accordingly.

“For someone between 19 and 30 years old, a female’s average recommended daily fiber intake would be 28 grams, based on a 2,000-calorie diet,” Lee said. “But for a male in that same age range, the recommended amount of fiber increases to 34 grams because they’re eating a little bit more.”

Soluble vs. Insoluble Fiber

Lee noted that dietary fiber falls into two main categories. Soluble fiber dissolves in water and slows digestion, while insoluble fiber helps move waste through the digestive tract.

“Soluble fiber attracts water into your gut and forms a gel-like substance,” Lee said. “It keeps you full, helps you feel satiated, and once it makes it into the colon, can provide or serve as a substrate for microbiota, meaning your microbiota can metabolize the food that you digest as well. So, this type of fiber serves as a beneficial food source for the microbes.”

Soluble fiber can also help regulate blood sugar by slowing digestion and reducing sudden spikes in glucose levels. It may also help lower cholesterol by preventing some cholesterol from being absorbed into the bloodstream.

Foods rich in soluble fiber include many fruits and vegetables, such as apples, avocados, bananas, cabbage, broccoli, and cauliflower. Legumes, beans, and oatmeal are also good sources. Insoluble fiber is commonly found in whole grains, nuts, and seeds.

“Insoluble fiber, on the other hand, cannot be dissolved and will not contribute to the calories you consume,” Lee said. “The body can’t take up energy from insoluble fiber, but it is critical to consume because it’s the bulk of substrate that helps you have a bowel movement. Because insoluble fiber bulks up your stool, it helps to prevent constipation.”

To maintain a healthy balance, Lee recommends consuming roughly twice as much insoluble fiber as soluble fiber each day. For example, if your daily goal is 30 grams of fiber, about 20 grams should come from insoluble fiber and 10 grams from soluble fiber.

How Can I Eat More Fiber?

The U.S. Centers for Disease Control and Prevention put together a resource on how fiber can help to manage diabetes, which includes tips for adding more fiber to your diet by eating things like fiber-friendly breakfasts.

Fiber Supplements and Potential Side Effects

For people who struggle to get enough fiber through food alone, supplements may help fill the gap. Lee noted that many adults fall short of recommended fiber intake levels, making supplementation a practical option in some cases.

“The majority of adults are not meeting their dietary fiber intake levels, so generally supplementation is a good strategy to meet recommended levels.”

Fiber supplements are available as capsules or powders that can be mixed into drinks. However, Lee cautioned that increasing fiber intake too quickly can cause digestive issues while the body adjusts.

“You could run into the extremes of eating too much, where if you’re not drinking enough water to hydrate and exceed the amount of soluble and insoluble fiber, you can get constipated,” Lee said. “The other extreme is that some people respond differently to fiber and they run the risk of getting diarrhea. You really should check in with your body, since you know how your body is responding to what you’re challenging it with daily.”