Biology

Dire Wolves: Have we brought them back from extinction and at what cost?

Biology, Science / By

Introduction:

For the past week, the world has been going wild about an announcement by Texas-based company Colossal Biosciences. On April 8th, they announced that by using gene-editing and cloning, they have created three new dire wolves. The thing is though, dire wolves went extinct between 10,000 and 13,000 years ago. According to Colossal, they currently have three pups. Two of these pups, named Romulus and Remus, are six months old. There is also a female pup named Khaleesi who is just two months old. 

This could be a huge step in genetics, helping endangered species, and much more. However, it does raise ethical questions, questions about the future, and, with such a fantastical headline, one has to wonder just how faithful it is to reality. 

How is this possible?

Ben Lamm, the CEO of Colossal, refers to what they did as “indistinguishable from magic.” Of course, they didn’t wave magical wands and just create once-extinct wolves out of thin air. In order to achieve this “magical” task, they extracted DNA from ancient dire wolf fossils: a skull that is 72,000 years old and a tooth that is 13,000 years old.

One of the main things they used was cloning technology. Cloning has been happening for the past 29 years, starting with the cloning of sheep and moving on to the cloning of gray wolves, horses, and more. To do this, scientists use a tissue sample from the animal they want to clone to obtain just one cell. 

The next step is one that many animal rights groups question because it is very invasive. In this step, a single cell’s nucleus is taken out and put into an ovum of an animal of the same species. This animal also has had its nucleus removed. This ovum then grows into an embryo. After this, the embryo is moved into a surrogate’s womb. Finally, from this womb, a duplicate of the original animal the cell was extracted from is born. 

This is just the typical cloning technique though. For the dire wolves, they had to change it up a bit. To start their process, scientists studied the dire wolves’ genome in the skull and tooth. Then, they looked at the genetics of their closest living relative, the gray wolf, and compared the two. They claimed to have found 20 differences located in 14 genes. These few differences were the causes of dire wolves’ most prominent characteristics, such as how large they are and their different vocalizations. After the scientists identified these differences, they took some of the cells that line gray wolves’ blood vessels (endothelial progenitor cells, also called EPCs), and changed the fourteen genes. 

This editing had its issues because each gene usually does several things. For example, dire wolves have three different genes that serve the purpose of giving them their well-known light coat. However, in gray wolves, these genes can cause blindness and deafness. To solve this problem, the scientists had to make two new genes that stopped red and black pigmentation. This was able to give the wolves their signature light coat without hurting them. 

After they had done all of this, they took the edited nuclei from the cells and put them in a gray wolf’s ova that had already had its nucleus taken out. In total, this made 45 embryos that were moved into two domesticated hounds’ wombs. 65 days later, they gave birth to Remus and Romulus.

Ethical Conundrums and a Potential Hoax for Fame

Despite the fact that Colossal says that no animals were injured in this whole process, there are a lot of debates about the ethics of this development. There are also fierce debates about if the dire wolf actually has been brought back from extinction or not. 

For the ethics debate, there are a lot of factors. For example, there is the question of location. All humans know is that before dire wolves went extinct, they lived somewhere in the plains and mountains of North and South America. Currently, the pups are living on a 2,000-acre preserve that is secure and in a secret location. While this may sound like a lot of land, usually wolves live in much larger areas which lets them migrate to follow their food. It is also unknown where the wolves will live for the rest of their lives. While a lot of people are against them becoming a tourist attraction, it could be harmful to ecosystems if they were put into the wild since the environment is very different from when the wolves had gone extinct. In addition to all of this, the newly created wolves had no clue how to survive on their own and, because they went extinct so long ago, scientists don’t know much about their behaviors or even their past diets. 

Another side of the ethics debate has to do with human behavior. People are scared because this technology gives humans a chance to think that we can let any animal go extinct because we assume we can just bring them back in the future. These concerns have been furthered because, after Colossal’s announcement, the Trump administration suggested taking away endangered species’ legal protections. This whole situation has created a fear that this could give people the feeling that we can “play God” in a way. This all leads into the question of if humans actually have the ability now to de-extinct animals. 

In this debate, a lot of professors say that, while impressive, these pups are not truly dire wolves. Duke University professor Stuart Pimm called them a “designer dog” and said that the “dire wolf is not really closely related to a regular wolf.” While some people agree with him that they aren’t related, others claim that, even though they’re related, they are not closely related enough that changing 20 genes would create dire wolves. To that end, paleontologist Ric Rawlence says, “the gray wolf genome is 2,447,000,000 individual bases (DNA letters) long. Colossal has said that the gray wolf and dire wolf genomes are 99.5% identical, but that is still 12,235,000 individual differences.” He goes on to say that only making 20 edits still makes this species “very much a gray wolf.” With this, people are wondering if this is just a wild headline to make money or if it is a legitimate thing done to improve science. 

O, T. (2008, January 19). Woolly Mammoth like the one Colossal could create in the next few years. Flickr. https://commons.wikimedia.org/wiki/File:Wooly_Mammoth-RBC.jpg

The Future of Colossal Gene-Editing

A lot of experts also question why scientists are spending so much time bringing animals back to life when they could be focusing on saving endangered species instead. According to Vox, the reasoning behind Colossal’s decision could be because de-extinction is a very difficult challenge and beating this challenge could lead to developments in technologies that could help future breakthroughs, like creating an artificial womb. Now that they have cloned the dire wolves, they have been working more on conservation. 

Colossal works to save endangered species from extinction by editing genes to maximize the genetic diversity of the remaining population. They have partnered with a lot of conservation organizations to make these breakthroughs possible. These organizations include the American Wolf Foundation, Save the Elephants, the Mauritian Wildlife Foundation, and more. They are also working with the native MHA Nation tribes, which are the Mandan, Hidatsa, and Arikara. These tribes have said that they want the dire wolves to be moved to their lands in North Dakota, where they will live in the wild. Colossal also says that it could be possible for them to use their cloning techniques to put species’ blood samples into a biobank to prevent any species in the future from becoming endangered.

While they do plan to do this conservation work, they also plan on using their cloning technology to bring back even more animals from extinction. In March, they announced their most recent development in bringing woolly mammoths back. They showed that they created woolly mice, which are mice that they modified to have woolly mammoths’ traits. After this achievement, they say that they plan to edit Asian elephants’ nuclei to create baby woolly mammoths in 2028. In addition to this, Colossal also wants to bring back Tasmanian tigers and dodo birds.

Conclusion

Whether or not those 20 edits brought back dire wolves from extinction may be up for debate, but this announcement most assuredly could change the future of conservation and gene-editing. Even if they’re mostly gray wolves, this technologically impressive feat is a milestone in history. We now get the chance to shape history and try to navigate this challenge ethically.

As it currently stands, it is putting endangered species at risk of having their protection taken away. Maybe, in this new Jurassic Park-esque world, it’s not the new animals that kill us, but us that kill them and take down whole species because we feel like we can play God. We could do this, or we could use this technology to protect species while respecting animals’ rights by doing our part to protect their ecosystems and help them thrive. 

Figuring out the path forward will be complicated, but, with these dire wolves, we have accepted this responsibility. There may be no truly correct answer on what to do next. We just have to go step by step, always keeping our eyes on doing the next right thing. Then, instead of a sign of a potentially scary future, these unmistakably adorable wolf pups could be a sign that humans can reverse a few of our environmental wrong-doings. 

There is one question that only time and people’s decisions will answer: will we use this technology to redeem or to destroy?

References

Bolotnikova, M. (2025, April 10). The new dire wolves explain everything wrong with “de-extinction”. Vox. Retrieved April 16, 2025, from https://www.vox.com/future-perfect/407781/dire-wolves-deextinction-colossal-biosciences

Kekatos, M. (2025, April 11). Should we be bringing back extinct species? Ethical concerns raised after dire wolf allegedly resurrected. ABC News. Retrieved April 16, 2025, from https://abcnews.go.com/US/bringing-back-extinct-species-ethical-concerns-raised-after/story?id=120674068

Kluger, J. (2025, April 7). The Science Behind the Return of the Dire Wolf. Time. Retrieved April 16, 2025, from https://time.com/7275439/science-behind-dire-wolf-return/

Tardigrades: microscopic animals that can survive space, and now can they help treat cancer?

Biology, Editors Pick, Science / By

What are Tardigrades?

Tardigrades, also known as water bears, are microscopic, aquatic animals that are only about .5 mm long. They thrive in mosses and lichens, but they can survive in any environment, from temperatures near absolute zero to being near volcanic ocean vents. 

They were discovered in 1773 by Johann August Ephraim Goeze, a German zoologist, who called them “little water bears” due to their appearance. Shortly after that, Lazzaro Spallanzani, an Italian scientist, named them “tardigrada,” or “slow steppers.”

These little creatures may look cute and squishy, but they have a hard cuticle around them, like grasshoppers do, that they have to shed in order to grow. Additionally, they’re something between an arthropod and a nematode, so their classification is often debated amongst scientists.

One thing is for sure though, and that is that these creatures are very strange, between having a hydrostatic skeleton instead of bones and ventral nervous system instead of a spinal cord. Another thing we know is that they will probably outlast humans, as they’ve been around since about 400 million years before the dinosaurs and the species has also been able to survive every one of the five mass extinction events that have happened. 

Scientists have only just started researching these little creatures to see what makes them so tough, and they’re making surprising discoveries about this almost unkillable creature and how it could have life-saving impacts. 

Their “Superpowers”

Scientists have really been putting tardigrades to the test over the last few decades. For example, they have had them survive at .05 Kelvin and at temperatures as high as 150 degrees Celsius. Also, they’ve survived 40,000 kilopascals of pressure. That’s as much pressure as 80 elephants! When scientists shot them out of a high speed gun, they also survived speeds of about 3,000 feet per second. 

Despite their ability to survive these environments, they don’t thrive there. In fact they are far from immortal and only live for a few months while they are in their active state. However, they usually have long periods where they “die.” This is called their “tun” state and it happens when they are away from water. In this state, they stop metabolizing and shrink. Whenever they are exposed to water again, they then go back to their metabolizing state.

This process where they suspend their metabolism for only a period of time is called cryptobiosis. Tardigrades can stay in their “half-dead” state for over 30 years. There is also a debate over if this “half-dead” state is actually them being dead because in their “tun” state, they are no different from dead matter.

In another experiment, they sent tardigrades to space and put them into space’s vacuum for ten days. Once they returned to Earth, they only had to be rehydrated to become reanimated again. Through experiments like this, researchers have found that tardigrades can survive 2,000 to 3,000 times more radiation than humans.

Applications

These “superpowers” that tardigrades have can be applied to people’s everyday lives, although a lot of ideas are still under development. First of all, because they can survive very low temperatures, scientists are looking to use their hardy proteins for vaccines because, as many people learned during the pandemic, a lot of vaccines have to be stored at low temperatures, which makes distribution difficult. 

Researchers also think that they can use tardigrades that have been mashed into a paste to make a kind of sunscreen. They were inspired to do this in 2020 when they found that tardigrades can survive a lot of ultraviolet radiation because they emit the longer wavelengths of light while absorbing the shorter ones. So, scientists made tardigrades into a paste which they put on worms. This paste made the worms able to survive a lot more ultraviolet radiation than normal.

Some other applications span from creating more drought resistant crops to protecting astronauts from radiation damage. However, the focus of recent tardigrade research has been treating cancer. 

In all, about 60% of cancer patients in America use radiation therapy as a means to help them beat their cancer. However, this radiation can harm the DNA inside the cancer cells and inside healthy cells too. This can hurt patients’ quality of life by making basic tasks such as eating difficult due to swelling. Because of these damaging side effects, a lot of patients either stop or delay treatment.

A team supported by the National Institutes of Health was inspired by tardigrades’ hardiness, especially their protein that suppresses damage called Dsup. Dsup is able to keep DNA strands from breaking, so researchers made nanoparticles with mRNA that carry instructions to make the Dsup protein. They used mRNA instead of DNA because it only expresses the Dsup protein temporarily instead of incorporating it into the genome of a cell. 

In February of 2025, this team published what they found, which was that with this mRNA, Dsup was brought to healthy tissues to minimize the damage of radiation treatment. To test this method, scientists used mice. In these mice, they found that the production of Dsup peaked six hours after it was injected and this peak was followed by a decline that ended about four days after injection, leaving no Dsup behind in the mouse. In mice where they injected the Dsup into them before radiation therapy, there was significantly less DNA breakage. 

In the mice, the amount of DNA that was broken by radiation was reduced by 50%. Thankfully, these effects were contained to the place that was injected, which means that these particles are not likely to accidentally protect tumor cells. The problem that scientists will have to solve now is how to not cause an immune response in humans because using tardigrade’s original protein could do that. Despite this problem, it shows promise as a way to protect patients while they are getting treated for cancer.

Conclusion

Tardigrades are an example of how even the smallest creatures can be the toughest and have the greatest impact. So, next time you are looking at moss on a log, think about how there could be thousands of lifesaving creatures right there. Overall, tardigrades really are wonders of the microscopic world, and hopefully, someday, they will make space travel more possible and cancer more treatable. 

References:

National Institutes of Health. (2025, March 25). Tiny tardigrades may hold clues to cancer care. National Institutes of Health. Retrieved March 30, 2025, from https://www.nih.gov/news-events/nih-research-matters/tiny-tardigrades-may-hold-clues-cancer-care#:~:text=Researchers%20found%20that%20a%20protein,radiation%20therapy%20to%20treat%20cancer

Robertson, L. (2022, October 18). Everything you need (and want) to know about tardigrades. Front Line Genomics. Retrieved March 30, 2025, from https://frontlinegenomics.com/everything-you-need-and-want-to-know-about-tardigrades/

Trafton, A. (2025, February 26). A protein from tiny tardigrades may help cancer patients tolerate radiation therapy. MIT News. Retrieved March 30, 2025, from https://news.mit.edu/2025/tiny-tardigrades-protein-may-help-cancer-patients-tolerate-radiation-therapy-0226

Chel Snakehead Fish Rediscovered After 85 Years

Biology / By

In the proceedings of rather remarkable events, the Chel snakehead fish (Channa amphibeus), previously deemed extinct, has lately been rediscovered in India following a period longer than eighty years. This surprising discovery not only brings about hope to conservationists but also shows the need for more exploration to preserve the earth’s biodiversity.

The Chel snakehead is a freshwater fish that is known for its bright green scales and unique yellow stripes. It has a large size, being the largest known snakehead species. Historically, it was collected between 1918 and 1933 in the Himalayas, after which the species “disappeared,” leading to scientists assuming its extinction.

It was in 2024 that scientists and researchers began an expedition across the banks of Chel River in West Bengal. They began this expedition after they heard about the species being spotted through contact with a local indigenous tribe in the region. The expedition led to the collection of three specimens of the species and photographs that proved that the species was not extinct.

Indigenous groups made important contributions to a re-discovery of species based on their understanding of freshwater species found locally. Their knowledge helped scientists make the identification of the Chel Snakehead.

The rediscovery of Chel snakehead fish species after over eight decades shows how much has been unexplored on the earth. This shows the importance of exploration to discover new species to help conserve the biodiversity of our planet. 

References:

https://www.facebook.com/peoplemag. (2024). One of the “World’s Rarest” Fish, Thought to Be Extinct, Rediscovered After 85 Years. People.com. https://people.com/one-the-world-rarest-and-presumed-extinct-fish-rediscovered-after-85-years-11684608/

Jacobo, J. (2025, February 17). Fish species thought to be extinct for 85 years rediscovered. ABC News. https://abcnews.go.com/International/researchers-rediscovered-elusive-fish-species-thought-extinct-85/story?id=118895751/

Magazine Desk. (2025, February 22). Long Lost Fish Species Resurfaces After 85 Years Shocking Scientists. Tribune.com.pk; The Express Tribune. https://tribune.com.pk/story/2530213/long-lost-fish-species-resurfaces-after-85-years-shocking-scientists

McCormack, C. (2025, February 19). Chel snakehead, fish species believed to be extinct, spotted in India after 85 years. New York Post. https://nypost.com/2025/02/18/world-news/chel-snakehead-fish-species-believed-to-be-extinct-spotted-in-india-after-85-years/

Breaking the Mold: the Slime Mold That is Forcing Researchers to Rethink What it Means to Think

Biology, Medicine / By

Meet the Blob:

In 1958, the horror movie classic The Blob took the world by storm, depicting a large blob that had intelligence and had a hunger for people. What if that blob exists, intelligence and all, and its favorite food is oatmeal? This blob is called slime mold, and it is changing scientist’s very idea of intelligence. Not only can this unicellular organism make decisions, but it can learn from its mistakes. With new revolutionary discoveries being made with it, the possibilities of what we can do with it are endless, from having it solve problems it took humans decades to figure out, to computing, and even to medicine. 

Despite the name, slime mold is not mold at all. Instead, it is a protist. Protists are kind of the junk drawer of classifications since it is what something is classified if scientists have no clue what else to call it.  

There are more than 900 types of slime mold and over 720 sexes. Its scientific name, Physarum polycephalum, means “many headed slime,” which is fitting given how the slime mold branches out to traverse its environment. It’s also fitting because it is made up of thousands of individual nuclei who come together to make a super-cell that makes decisions to benefit the whole group. They are also extremely versatile creatures and can live in almost any environment, from jungles to the arctic and even to outer space on the International Space Station.

Slime Mold in Technology and Engineering:

At Hokkaido University in Japan, a team put slime mold in a maze and put food at two points. The slime mold made a connection between these two points and retracted itself from areas where there was no food. Even though there were several ways to get through the maze, the smile mold always found the shortest route.

To expand this experiment, they put oats at every major city on a map of Japan. They then put slime mold on this map, and within two days the slime mold had created a route that was nearly identical to the transportation network it had taken engineers more than 100 years to figure out. Now, civil engineers can use slime mold to figure out the most efficient routes faster than any human could. 

In the UK, scientists created Plasmobot, a computer that runs on oak flakes and slime mold. This computer can do math problems and pull or push objects all by the power of slime mold. 

Another application to technology is using slime mold to create accessible biosensors that enable citizen scientists and students to be able to gain access to and use sensors affordably. In Europe, the project PHYSENSE made a prototype biosensor that does exactly that. The prototype uses slime mold’s response to stimuli to control the sensor. In the future, these sensors could be applied to security, the discovery of drugs, food safety, and monitoring the environment. 

Slime Mold in Physics and Medicine:

Even NASA has “hired” slime mold to help it tackle the challenging physics problems. They found that there could be a cosmic web throughout the universe that is mainly made of dark matter, a mysterious substance that can’t be seen. When observing this cosmic web and slime mold, NASA claimed that “there is an uncanny resemblance between the two networks: one crafted by biological evolution, and the other by the primordial force of gravity.”

So, NASA made a slime-mold inspired computer algorithm that they applied to data about nearby galaxies. This created a 3-D map of dark matter filaments in the surrounding universe.

For medicine, biophysicists in Singapore and Germany looked at slime mold’s patterns and found that the way it grows is remarkably similar to a tumor, allowing them to study how tumors supply themselves with blood. This lets them create new solutions that will cut off a tumor’s blood supply, stopping it from growing and eventually killing it. 

Source: Murugan, N., Levin Lab, Tufts University, & Wyss Institute at Harvard University. (2021). Slime mold sample exploring a petri dish. Harvard Magazine.

Rethinking Intelligence:

When you think about the word intelligence, what comes to mind? Is it the ability to make decisions? To remember? To problem solve? Maybe you think that the most inherent part of intelligence is the ability to think, most likely with a brain. Before slime mold, almost everyone, including scientists, believed that to be intelligent something had to have a way to think. Now, slime mold is sparking debates because it can do everything listed above without a brain or even neurons.

For example, slime mold was once exposed to the cold every half an hour. When it encountered the cold, it would slow its growth to conserve energy. Then, scientists stopped exposing the slime mold to the cold, but it had remembered the timing and anticipated it, showing that it has some sort of memory.

Harvard also found that slime mold can sense objects before even coming into contact with them. To discover this, they put three glass disks on one side of a petri dish and one glass disk on the other. The majority of the time, the slime mold strongly favored the side with three glass disks, but only when the disks were put side by side. When stacked, the slime mold showed no preference, leading the scientist to determine that slime mold decided where to go in this instance based on the amount of the horizon the glass disks took up. This begs the questions: how does the sightless slime mold make these decisions and why?

In the end, there is a lot more research to be done about this confusing protist. Whether you think that it is intelligent or not though, one thing is for certain, and that is that this unicellular organism is changing society for the better.

References:

Barnett, H. (2014, July 17). What humans can learn from semi-intelligent slime. TED Talks. Retrieved March 11, 2025, from https://www.ted.com/talks/heather_barnett_what_humans_can_learn_from_semi_intelligent_slime/transcript

Bland, E. (2009, September 8). Plasmobot computer runs on slime mold. NBC News. Retrieved March 11, 2025, from https://www.nbcnews.com/id/wbna32736017

Shrourou, A. (2019, April 16). Using slime mold to produce accessible biosensors. News Medical. Retrieved March 11, 2025, from https://www.news-medical.net/news/20190415/Using-slime-mold-to-produce-accessible-biosensors.aspx

Slime Molds Help Show How Cancer Grows. (2012, August 24). WIRED. Retrieved March 11, 2025, from https://www.wired.com/2012/08/slime-molds-cancer-growth/

Slime Mold Simulations Used to Map Dark Matter Holding Universe Together. (2020, March 10). NASA Science. Retrieved March 11, 2025, from https://science.nasa.gov/missions/hubble/slime-mold-simulations-used-to-map-dark-matter-holding-universe-together/Walecki, N. (2021). Can Slime Molds Think? Harvard Magazine. Retrieved March 11, 2025, from https://www.harvardmagazine.com/2021/10/right-now-can-slime-molds-think

Quantum-Inspired AI model helps CRISPR Cas9 Genome Editing for Microbes

Artificial Intelligence, Biology, Biotech, Medicine, Science, Technology / By


A team of scientists at the Oak Ridge National Laboratory (ORNL), have embarked on a groundbreaking venture, leveraging quantum biology, artificial intelligence (AI), and bioengineering to revolutionize the effectiveness of CRISPR Cas9 genome editing tools. Their focus is on microbes, particularly those earmarked for modifications to produce renewable fuels and chemicals, presenting a unique challenge due to their distinct chromosomal structures and sizes.

Traditionally, CRISPR tools have been tailored for mammalian cells and model species, resulting in weak and inconsistent efficiency when applied to microbes. Recognizing this limitation, Carrie Eckert, leader of the Synthetic Biology group at ORNL, remarked, “Few have been geared towards microbes where the chromosomal structures and sizes are very different.” This realization prompted the ORNL scientists to explore a new frontier in the quest to enhance the precision of CRISPR tools.

The team’s journey took an unconventional turn as they delved into quantum biology, a field at the intersection of molecular biology and quantum chemistry. Quantum biology explores the influence of electronic structure on the chemical properties and interactions of nucleotides, the fundamental building blocks of DNA and RNA, within cell nuclei where genetic material resides.

To improve the modeling and design of guide RNA for CRISPR Cas9, the scientists developed an explainable AI model named the iterative random forest. Trained on a dataset of approximately 50,000 guide RNAs targeting the genome of E. coli bacteria, the model took into account quantum chemical properties. The objective was to understand, at a fundamental level, the electronic distribution in nucleotides, which influences the reactivity and stability of the Cas9 enzyme-guide RNA complex.

“The model helped us identify clues about the molecular mechanisms that underpin the efficiency of our guide RNAs,” explained Erica Prates, a computational systems biologist at ORNL. The iterative random forest, with its thousands of features and iterative nature, was trained using the high-performance Summit supercomputer at ORNL’s Oak Ridge Leadership Computer Facility.

What sets this approach apart is its commitment to explainable AI. Rather than relying on a “black box” algorithm that lacks interpretability, the ORNL team aimed to understand the biological mechanisms driving results. Jaclyn Noshay, a former ORNL computational systems biologist and first author on the paper, emphasized, “We wanted to improve our understanding of guide design rules for optimal cutting efficiency with a microbial species focus.”

Graphical Abstract https://academic.oup.com/nar/article/51/19/10147/7279034

Validation of the explainable AI model involved CRISPR Cas9 cutting experiments on E. coli, using a large group of guides selected by the model. The results were promising, confirming the efficacy of the model in guiding genome modifications for microbes.

The implications of this research extend far beyond microbial genome editing. “If you’re looking at any sort of drug development, for instance, where you’re using CRISPR to target a specific region of the genome, you must have the most accurate model to predict those guides,” highlighted Carrie Eckert. The study not only advances the field of synthetic biology but also has broader applications in drug development and bioenergy research.

The ORNL researchers envision collaborative efforts with computational science colleagues to further enhance the microbial CRISPR Cas9 model using additional data from lab experiments and diverse microbial species. The ultimate goal is to refine CRISPR Cas9 models for a wide range of species, facilitating predictive DNA modifications with unprecedented precision.

The study, supported by the DOE Office of Science Biological and Environmental Research Program, ORNL’s Lab-Directed Research and Development program, and high-performance computing resources, signifies a significant leap forward in the quest to improve CRISPR technology. As Paul Abraham, a bioanalytical chemist at ORNL, remarked, “A major goal of our research is to improve the ability to predictively modify the DNA of more organisms using CRISPR tools. This study represents an exciting advancement toward understanding how we can avoid making costly ‘typos’ in an organism’s genetic code.” The findings hold promise for applications in fields ranging from bioenergy feedstock enhancement to drug development, marking a pivotal moment in the evolution of CRISPR technology.

Sources

https://doi.org/10.1093/nar/gkad736

“Synthetic Biology’s Promise and Peril: Shaping the Future of Medicine

Biology, Science / By

Image Credit: https://www.technologynetworks.com/drug-discovery/blog/how-is-synthetic-biology-shaping-the-future-of-drug-discovery-340290

As a recent and ever-changing form of medicine and science, synthetic biology is paving the way for the future of medicine. Defined as a “research and engineering domain of biology where a human-designed genetic program is synthesized and transplanted into a relevant cell type from an extant organism” (A.M. Calladine, R. ter Meulen, 2013), synthetic biology offers possible solutions to some of society’s most pressing medical issues. Through DNA sequence modification and genome editing, scientists have been able to edit genetic material in living organisms with tools such as CRISPR (Clustered regularly interspaced short palindromic repeats). This ability allows scientists to provide organisms with genetic tools that nature has not yet apportioned. CRISPR also allows for the creation of ‘living therapeutics’ and introduction of immunity cells into the human body. 

So, what does this all mean? Well, synthetically creating genetic tools has already allowed for a breakthrough in different areas of production, such as the ability for silkworms to produce spider silk, as well as genetically engineered food, such as cheese, plant-based meat, etc., some of which are already available on a market scale. This provides society with a more sustainable way of creating different materials, which may be necessary as we continue to experience the impacts of consumerism on our planet’s environment. Living therapeutics and immune cells can help treat patients with various diseases, including multiple forms of cancer, providing them with a better chance of recovery and survival. Synthetic biology also assisted in the mass production of certain COVID-19 vaccines by manufacturing the SARS-CoV-2 genome sequence. 

It’s clear that an abundance of benefits derive from the usage of synthetic biology. Consequently, as with most technological advancements, there is also a profusion of risks. A majority of these risks appear to be ethical and extremely dangerous. According to The University of Oxford, synthetic biology, although promising, gives biologists a concerning way of ‘playing god.’ Misusing synthetic biology could potentially destroy existing ecosystems and undermine our crucial distinction between living organisms and machines. The loss of this distinction could be catastrophic for humans’ view on the importance of different organisms and creates an ethical concern of prioritizing machines and technology over nature and living organisms. Synthetic biology also introduces the risk of the synthesization of known human pathogens, such as Influenza or Smallpox, which could be released in much more dangerous forms than what they currently are. Although some of these associated risks are unlikely, the potential danger they inflict could be devastating. 

When considering the sad reality of human greed, it is essential to question whether the findings of synthetic biology will continue to be used for good. If put into the wrong hands, the technology could cause the decimation of multiple existing species, ultimately jeopardizing the balance of our ecosystem. Synthetic biology also poses the genuine risk of bioterrorism, as creating hazardous and genetically mutated organisms could be maliciously and violently released. Control of this technology is seen more in richer first-world countries, creating an inequality regarding access and usage. This gives certain countries, such as the U.S., an extensive scientific advantage over other countries, which could be used at the expense of other nations. 

It is still being determined what the future of synthetic biology holds, but it is imperative that both the benefits and drawbacks are considered. Naturally, we hope synthetic biology continues to be used for the greater of humankind, but that could very easily and swiftly change. Therefore, and when considering that we are already in the midst of multiple ethical, moral, and environmental crises, it is necessary to be aware of the information we consume and promote, specifically regarding the ongoing evolution of technology and science. 

Public sees promise of synthetic biology, but wary | ZDNET

Image credit: https://www.zdnet.com/article/public-sees-promise-of-synthetic-biology-but-wary/ 

Sources

  1. https://www.practicalethics.ox.ac.uk/synthetic-biology 
  2. https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/synthetic-biology#:~:text=Synthetic%20biology%20is%20commonly%20viewed,type%20from%20an%20extant%20organism. 
  3. https://www.gao.gov/products/gao-23-106648#:~:text=Synthetic%20biology%20can%20modify%20or,have%20broadened%20its%20potential%20benefits. 
  4. Image Credit: https://www.technologynetworks.com/drug-discovery/blog/how-is-synthetic-biology-shaping-the-future-of-drug-discovery-340290

Unlocking Limb Regeneration: The Salamander’s Clue to Ending Phantom Pain

Biology, Biomedical, Engineering, Medicine, Science / By

You wake up in the morning with some arm pain. Sounds pretty normal, no? But what if you were told that that pain was all in your head? Alright, well obviously it’s in your head, your brain is what detects the pain, but bear with me. What if your arm wasn’t… there? What if your arm hadn’t been there for years, only for you to still feel it being there despite this objective truth? If all of that applies to you, then you are a victim of phantom pain. 

Over 500 people lose their limbs each day, whether it’s through the brutality of warfare, a freak accident at a job, or otherwise. Of these individuals, approximately 80% of them experience phantom pain. Not to mention that all of them suffer some degree of reduction in quality of life and even mental health for some. For what seems like its conception, limbs and their loss seemed like an unfortunate reality of the world. We all are only given one pair of parts, if we lose them somehow, that’s on us. That’s it. No redos, no replacements, no takesies-backsies. 

But what if there were redos? What if there was a way to replace the irreplaceable? What if there was a way to grow the ungrowable? That may very be possible through researching an animal that most of us have yet to encounter in the flesh: the humble salamander. 

What makes the salamander so special lies in its capability to regrow its limbs in its entirety. It could lose all of its arms and legs: as long as the stump is not destroyed, it can regrow them again and again without fail. These were only possible through the salamander’s natural capabilities to salvage what was left and prevent the wound from festering. The blood vessels quickly contract and a layer of skin cells swiftly encase the wound site. This wasn’t what made the salamander’s capability to regrow limbs so odd though, it was that it had other parts of its body (namely the opposite side of the missing limb) chip in to regrow the lost part. Although it would sometimes appear in a slightly different place, it would, for all anatomically sound purposes, be a perfectly functional limb. 

Although humans and salamanders are not the same, we both possess some form of a regeneration factor (with the former resorting to healing and the latter resulting in completely regrowing a limb). It is just a matter of time before we transform our natural capability to heal into being able to regrow lost limbs, perhaps indefinitely. No more will those who are missing an arm or a leg through horrid circumstances have to suffer a poor quality of life. No more will they have to make do with painkillers and accept the never-ending pain. No more will they have to live their life to a fraction of their potential all because of an unfortunate sequence of events. With the help of some salamanders, these circumstances may very well become a thing of the past. 

Image Credit: CAS.org, depiction of limbs regenerating.

Sources

  1. https://acl.gov/sites/default/files/programs/2021-04/llam-infographic-2021.pdf
  2. https://www.montefiore.org/limb-loss-facts
  3. https://my.clevelandclinic.org/health/diseases/12092-phantom-limb-pain
  4. https://www.ucl.ac.uk/news/2014/jun/limb-regeneration-do-salamanders-hold-key

Synthetic Biology: A Brave New World of Cures and Cautions

Biology, Biotech, Medicine, Must Read, Science, Technology / By

As a recent and ever-changing form of medicine and science, synthetic biology is paving the way for the future of medicine. Defined as a “research and engineering domain of biology where a human-designed genetic program is synthesized and transplanted into a relevant cell type from an extant organism” (A.M. Calladine, R. ter Meulen, 2013), synthetic biology offers possible solutions to some of society’s most pressing medical issues. Through DNA sequence modification and genome editing, scientists have been able to edit genetic material in living organisms with tools such as CRISPR (Clustered regularly interspaced short palindromic repeats). This ability allows scientists to provide organisms with genetic tools that nature has not yet apportioned. CRISPR also allows for the creation of ‘living therapeutics’ and introduction of immunity cells into the human body. 

So, what does this all mean? Well, synthetically creating genetic tools has already allowed for a breakthrough in different areas of production, such as the ability for silkworms to produce spider silk, as well as genetically engineered food, such as cheese, plant-based meat, etc., some of which are already available on a market scale. This provides society with a more sustainable way of creating different materials, which may be necessary as we continue to experience the impacts of consumerism on our planet’s environment. Living therapeutics and immune cells can help treat patients with various diseases, including multiple forms of cancer, providing them with a better chance of recovery and survival. Synthetic biology also assisted in the mass production of certain COVID-19 vaccines by manufacturing the SARS-CoV-2 genome sequence. 

It’s clear that an abundance of benefits derive from the usage of synthetic biology. Consequently, as with most technological advancements, there is also a profusion of risks. A majority of these risks appear to be ethical and extremely dangerous. According to The University of Oxford, synthetic biology, although promising, gives biologists a concerning way of ‘playing god.’ Misusing synthetic biology could potentially destroy existing ecosystems and undermine our crucial distinction between living organisms and machines. The loss of this distinction could be catastrophic for humans’ view on the importance of different organisms and creates an ethical concern of prioritizing machines and technology over nature and living organisms. Synthetic biology also introduces the risk of the synthesization of known human pathogens, such as Influenza or Smallpox, which could be released in much more dangerous forms than what they currently are. Although some of these associated risks are unlikely, the potential danger they inflict could be devastating. 

When considering the sad reality of human greed, it is essential to question whether the findings of synthetic biology will continue to be used for good. If put into the wrong hands, the technology could cause the decimation of multiple existing species, ultimately jeopardizing the balance of our ecosystem. Synthetic biology also poses the genuine risk of bioterrorism, as creating hazardous and genetically mutated organisms could be maliciously and violently released. Control of this technology is seen more in richer first-world countries, creating an inequality regarding access and usage. This gives certain countries, such as the U.S., an extensive scientific advantage over other countries, which could be used at the expense of other nations. 

It is still being determined what the future of synthetic biology holds, but it is imperative that both the benefits and drawbacks are considered. Naturally, we hope synthetic biology continues to be used for the greater of humankind, but that could very easily and swiftly change. Therefore, and when considering that we are already in the midst of multiple ethical, moral, and environmental crises, it is necessary to be aware of the information we consume and promote, specifically regarding the ongoing evolution of technology and science. 

Sources

Battling Plastic Pollution: Unveiling Nature’s Tiny Heroes

Biology, Ecology, Editors Pick, Science / By

Polyethylene, plastic for short. It’s used everywhere, from the humble water bottle to grand and towering airplanes. We all hear that plastic doesn’t decompose, but many of us adopt an “out of sight, out of mind” thinking process. But, all because you can’t see a problem doesn’t mean that it’s not there. 

Over 170 trillion plastic pieces are in our oceans currently, with that number exponentially skyrocketing. This causes several issues, primarily a negative impact on wildlife and ecosystems within the ocean (colloquially referred to as plastic pollution). 

Fish (among other aquatic creatures) run the risk of being constricted by plastic rings, eating miniature pieces of them, or even having them cut against their skin. Not only this, but the plastic itself is toxic, with it containing thousands of chemicals that are harmful for aquatic life but also anyone else who comes in contact with contaminated water, humans included.

Image credit: https://www.surfacemag.com/articles/plastic-research-toxins-carcinogens/, depicts a gigantic pile of empty plastic containers. 

Since the dawn of its creation, it was just assumed as an unfortunate reality that we had to accept: gain a powerful, versatile, and cheap material and sentence the oceans and all the life it maintains to the guillotine. After all, it would cost an arm and a leg (upwards of $150 billion specifically) to remove the majority, not even all, of the plastic. 

But what if human hands combined with those of Mother Nature? What if we called upon the meek insects that scurry on the floors we stepped on to remove this pollution? What if we found a solution to this problem, a cheap and readily available cure for this illness? Well, that may just be possible.

October of 2022 brought more than just the welcoming of Halloween, it also was the time of a critical discovery: a type of caterpillar whose spit could decompose plastic. This was oddly enough discovered by a hobbyist beekeeper named Federica, who placed these caterpillars (wax moth in particular) into a plastic bag and found out briefly afterward that they had escaped, leaving multiple holes as their tunnels to freedom. 

But first, let’s review how they were able to do that. They utilized two specific enzymes, or proteins designed to cause a biochemical reaction, named Ceres and Demeter. These were considerably faster at decomposing plastic than traditional means (e.g. fungi or general bacteria), which could take weeks at a time. 

Scientists are currently looking to harvest and mass-produce these enzymes to decompose plastic at a more global scale. Although this is still in the beta phase of testing, it does offer a multitude of questions. How much faster do these enzymes decay plastic than conventional means? Are there other enzymes like this? How long will it take before it can be synthesized and ready for mass engineering? 

But, it does offer something important: a step in the right direction. With the capabilities of science and the will of those who desire clean water free of plastic residue, anything is possible, just maybe with the help of some little bugs by our side. 

AI can now use the help of CRISPR to precisely control gene expressions in RNA

Artificial Intelligence, Bio Chemistry, Biology, Biomedical, Engineering, Medicine, Science, Technology / By

Almost all infectious and deadly viruses are caused due to their RNA coding. Researchers from established research universities, such as NYU and Columbia, alongside the New York Genome Center, have researched and discovered a new type of CRISPR technology that targets this RNA and might just prevent the spread of deadly diseases and infections.

A new study from Nature Biotechnology has shown that the development of major gene editing tools like CRISPR will serve to be beneficial at an even larger scale. CRISPR, in a nutshell, is a gene editing piece of technology that can be used to switch gene expression on and off. Up until now, it was only known that CRISPR, with the help of the enzyme Cas9, could only edit DNA. With the recent discovery of Cas13, RNA editing might just become possible as well.

https://theconversation.com/three-ways-rna-is-being-used-in-the-next-generation-of-medical-treatment-158190

RNA is a second type of genetic material present within our cells and body, which plays an essential role in various biological roles such as regulation, expression, coding, and even decoding genes. It plays a significant role in biological processes such as protein synthesis, and these proteins are necessary to carry out various processes. 

RNA viruses

RNA viruses usually exist in 2 types – single-stranded RNA (ssRNA), and double-stranded RNA (dsRNA). RNA viruses are notoriously famous for causing the most common and the most well-known infections – examples being the common cold, influenza, Dengue, hepatitis, Ebola, and even COVID-19. These dangerous and possibly life-threatening viruses only have RNA as their genetic material. So, how can/might AI and CRISPR technology, using the enzyme Cas13 help fight against these nuisances?

Role of CRISPR-Cas13

RNA targeting CRISPRs have various applications – from editing and blocking genes to finding out possible drugs to cure said pathogenic disease/infection. As a report from NYU states, “Researchers at NYU and the New York Genome Center created a platform for RNA-targeting CRISPR screens using Cas13 to better understand RNA regulation and to identify the function of non-coding RNAs. Because RNA is the main genetic material in viruses including SARS-CoV-2 and flu,” the applications of CRISPR-Cas13 can promise us cures and newer ways to treat severe viral infections.

“Similar to DNA-targeting CRISPRs such as Cas9, we anticipate that RNA-targeting CRISPRs such as Cas13 will have an outsized impact in molecular biology and biomedical applications in the coming years,” said Neville Sanjana, associate professor of biology at NYU, associate professor of neuroscience and physiology at NYU Grossman School of Medicine. Learn more about CRISPR, Cas9, and Cas13 here. 

Role of AI

Artificial intelligence is becoming more and more reliant as days pass by. So much so, that it can be used to precisely target RNA coding, especially in the given case scenario. TIGER (Targeted Inhibition of Gene Expression via guide RNA design), was trained on the data from the CRISPR screens. Comparing the predictions generated by the model and laboratory tests in human cells, TIGER was able to predict both on-target and off-target activity, outperforming previous models developed for Cas13 

With the assistance of AI with an RNA-targeting CRISPR screen, TIGER’s predictions might just initiate new and more developed methods of RNA-targeting therapies. In a nutshell, AI will be able to “sieve” out undesired off-target CRISPR activity, making it a more precise and reliable method.