AP Biology class blog for discussing current research in Biology

Author: samuelosaurus

Dark Side of the CRISPR

CRISPR-Cas9 editing of the genome
In the bright glow of rapid scientific advancement, CRISPR-Cas9 gene-editing techniques stands out as hope for many people, achieving a future where genetic diseases are no longer an issue to consider about. Awarded the Nobel Prize in Chemistry, biochemists Jennifer Doudna and Emmanuelle Charpentier‘s discovery of CRISPR has shocked the world with the potential to “fix” genetic diseases and malfunctions. However, beneath the surface of this fascinating technique is a complex ethical dilemma: the potential to erase diversity when preventing genetic diseases from occurring

The Promise and Danger of CRISPR

CRISPR offers abilities to edit genes with accuracy, having the power to treat or even eliminate diseases that have plagued humanity for thousands of years. However, this powerful technology also brought up an ethical challenge. It is a risky path that cures diseases but might end up eliminating genetic traits that is undesirable by societal standards, which will decrease the diversity of genes. 

Disability studies scholars, especially those who have genetic conditions, express deep concerns over CRISPR’s application. They fear that perhaps one day humanity will use this technology to “edit out” genetic conditions like cystic fibrosis (CF) and syndactyly, not just from the patient, but from the entire human gene pool. Such result raises the question: Who decides what gene is “normal” or what gene is “bad”?

CC BY 2.0, Link

For many, genetic conditions are closely related to their identity and life. Considering these conditions just as errors results in overlooking the richness and diversity of human life. Lives like those of Sandy and Rosemarie, authors of “The Dark Side of CRISPR”, who navigate daily life with CF and syndactyly respectively, points out the value of diverse experiences and perspectives, even if they are often considered “undesired”. They remind us that difference is not always a negative thing and that the quest for a “perfect” genetic makeup is flawed.

Humanity is at a crossroad of genetic editing, we must recognize the significance of decisions we make today on the future. CRISPR technology have the potential for unprecedented medical abilities, but it also have ethical questions that require careful consideration. We must balance the benefits of gene editing while also accounting for genetic diversity and the rights of individuals that live unedited lives.

Connections to AP Biology
In our AP biology class, we’ve learned about the mechanics of genetics, exploring how DNA sequences determine traits and how mutations can lead to genetic disorders. CRSPR-Cas9 gene editing technology ties closely with these topics, demonstrating a real-world application of the knowledge we’ve learned. The vast majority of genetic disorders are due to mutations or errors on the DNA, there is a very small chance that mutations or errors might occur, and even if there is one, most of the time it would have no effect. However, occasionally, it is still possible for a critical place of DNA to have a mutation, which can result in various genetic diseases that seemed impossible to prevent. This is where CRISPR comes in to save the day, its ability to precisely edit these genes brings up closer from being able to correct genetic mistakes that lead to diseases, preventing patients from getting an genetic disease.

Lets Discuss!
The ethical implications of CRISPR technology are topics that deserve our attention and thoughts. How do you perceive the balance between the health benefits of CRISPR and the ethical dilemmas it presents? How can we use this technology in a way that respects and preserves the diversity of all human experiences? Please feel free to share your thoughts in the comments below and we can dive further in this topic! For more information, go for latest research and updates!



Memory Card Plugged in for Future Generations of Bacteria?

E. coli BacteriaHave you ever thought about the ability of being born with knowledge? It sounds like a plot out of a science fiction novel, yet recent research discovered that Escherichia coli (E. coli) bacteria, despite not having a brain, are able to remember past encounters with nutrients and pass this information down to their future offspring. This discovery not only surprises microbial behavior scientists but also reveals the challenge behind the fight against antibiotic resistance.

Swarming of Bacteria
George O’Toole, a microbiologist at Dartmouth College, explains that while “we typically think of microbes as single-celled organisms,” they actually operate in collective units or swarms. Interestingly, when they move in swarms, they become stronger against Antibiotics because there are more of them close together. According to this article from Missouri Department of Health and Senior Services that explain what is Antibiotic resistance, the reason E. coli bacteria become stronger against antibiotics when they are close together in swarms is due to their biological mutations, DNA exchange, and rapid reproductions. Mutations are essential to evolution, they can bring genetic variation (good or bad) to a specie. Because of the vast number of bacteria present and their high reproduction rate, many mutations can occur in a swarm of bacteria. Through random mutations and selection, bacteria can develop defense mechanisms against antibiotics. After some bacteria have developed some anti-antibiotic genes, bacteria will actively swap bits of DNA among both related or unrelated species. Thus, antibiotic-resistant genes will spread rapidly among a swarm of bacteria and can can even be incorporated into other species of bacteria. Finally, given the fast reproduction speed of bacteria, it does not take long for the antibiotic-resistant bacteria to fill up a huge portion of the bacteria population, therefore disabling/nerfing the effects antibiotic drugs.

Collective Memory of E. coli
A team of scientists, as reported in the Proceedings of the National Academy of Sciences USA, found that E. coli bacteria swarms have a form of memory that correspond to their exposure to nutrients. This experiment, led by Souvik Bhattacharyya from the University of Texas at Austin, observed unusual patterns in E. coli colonies. Through deeper examination with his science team, they concluded that these bacteria acted differently because of their previous experiences. Specifically, bacteria from colonies that had swarmed before were more likely to swarm again. This behavior was passed down to their descendants for four generations, suggesting a genetic memory of past actions in the bacteria.

Diagram of a gene on a chromosome CRUK 020.svg
By Cancer Research UK – Original email from CRUK, CC BY-SA 4.0, Link

Genes that are Responsible for this Behavior:
Further investigation was conducted to this phenomenon concluded that two genes responsible for iron uptake and regulation is the keys to bacteria’s memory. Bacteria with lower levels of iron, an essential nutrient for them, are more likely to move collectively(in swarms) to find environments with higher level of iron concentration. In addition to the past research that shown that many bacteria can remember and pass to their offspring of the description of their physical surroundings, this study suggests that bacterial can also remember and pass to their offspring about nutrients’ presence. This ability of bacteria to remember and pass on knowledge about physical surroundings and nutrient existence demonstrates bacteria’s evolution journey. 

This research increases our understanding of microbial life, showing that bacteria like E. coli can remember more the physical environments and can also recall the presence of nutrients. These memories will affect their decisions on where to settle and can increase their chances of surviving and fitness. O’Toole believes that this mechanism of bacterial memory is probably not exclusive to E. coli; it can actually be a common mechanism that exists among many different types of bacteria. The insights gained from studying these E. coli at a molecular level can provide valuable context for the development of antibiotics, offering new approaches as traditional antibiotics will eventually lose their effectiveness. 

Connection to AP Bio
In AP Biology, we’ve learned about Cell Signaling molecules and mechanisms used by organisms. Bacteria can also communicate amongst them when they are close together through a process called Quorum Sensing. Bacteria will secrete small chemical signaling molecules which will be detected by other bacteria nearby using their receptors. Through Quorum Sensing, bacteria are able communicate with others of their kind, sharing information about bacteria density and adjust gene expression accordingly. In addition, we will also be covering information about DNA, Heredity, and Evolution during this year in AP biology, which are also significant themes in this post. Numerous mutations will occur in swarms of bacteria due to their large number, this mutation of their DNA can occasionally cause significant change. If this change is extremely positive and can do this bacteria good, through natural selection, this gene will be kept and pass on to future generations of bacteria so that more and more bacteria will have this trait. This is the reason behind my antibiotics are slowly losing their functions. More and more bacteria have mutated and can resist the effects of antibiotic drugs.

What are your thoughts?
A couple of years ago, I often watched cartoons that portrays a type of technology that can give knowledge and pass memory to a newborn baby. I thought that it was a fascinating and unrealistic idea. However, during my research, I surprisingly found out that bacteria seemed to have this ability to pass on their memories to their offspring. What are your views about bacteria’s ability to memorize and pass their memories on to future generations? Do you think this experiment is helpful to future development of antibiotics? Feel free to leave a comment below and we can discuss more about this topic! For more information on this post, go to for the latest research and updates.

COVID-19 Vaccine Going Retro?

Bottle with Coronavirus Vaccine and syringe with Novavax logo on white background
Have you ever wondered why the world started to use mRNA vaccines all of a sudden ever since the COVID-19 pandemic? Where did the traditional methods of vaccination go? This sudden shift in vaccine technology didn’t just happen by chance but was a result of years of scientific research and experiments. As the world faced an unprecedented pandemic, the traditional method of vaccination, while reliable, was slower and less effective to adapt to mutating virus than the mRNA vaccines, which is faster and more flexible when combating COVID-19 viruses. However, the traditional methods have returned! The new Novavax COVID-19 vaccine is an old-fashioned, protein-based approach to vaccination, a contrast to the mRNA technology used in Pfizer and Moderna vaccines. The Novavax vaccine especially targets the SARS-CoV-2 variant XBB.1.5, which is a descendent of Omicron. 

Novavax’s Differences: A Protein-Based Approach
Unlike the mRNA vaccines, which use modified viral genetic materials to cause an immune response, Novavax relies on a more traditional approach which injects proteins that resemble SARS-CoV-2 directly into the body. This method has over 30 years of application in vaccines such as the Hepatitis B Vaccine. The Novavax Company also uses insect cells, such as moth cells, to produce SARS-CoV-2’s unique spike proteins. The reason why Novavax researchers use moth cells is because of its efficiency in producing spike proteins. They first select the desired genes that create the spike proteins, and then they put these kinds of genes into a baculovirus, which is basically an insect virus. The baculovirus will then infect moth cells and replicate rapidly inside them creating lots of spike proteins. Finally, the researchers will extract and use the spike proteins for vaccines. Additionally, Novavax’s formula also includes Matrix-M, a compound from Chilean Soapbark Trees, which will further enhance our immune system’s response to the spike protein.

Targeted Variants and Efficiency:                                                                    Novavax vaccines are developed specifically for the XBB.1.5 variant, and they are not optimized for the newer Eris and Pirola variants. However, vaccinologist Gregory Poland notes that all vaccinations, including Pfizer and Moderna, have all been “chasing the tail” of the emerging variants all over the pandemic, so Novavax is not alone in this situation. Additionally, all of the vaccine boosters seem to be able to provide some protection against new variants, but protein vaccinations are way slower to adapt to the new variants than mRNA vaccines. In terms of efficiency, according to infectious disease researcher Kirsten Lyke, Novavax stands on par with other mRNA vaccines. It is 55% effective in preventing COVID-19 symptoms and 31% effective at preventing infections, and this is very similar to the mRNA vaccines.

Protein Synthesis Elongation.png (mRNA coding protein)

Side Effects and Availability:
When it comes to side effects, the Novavax booster demonstrates a lower risk of myocarditis(inflammation of heart muscle) or pericarditis(inflammation of the outer lining of the heart) compared to mRNA vaccines, but of course, it is not entirely risk-free. It also tends to have fewer side effects like muscle fatigue and nausea post-vaccination. A huge advantage of the Novavax vaccine is its availability, it can be stored in a typical refrigerator, making it considerably more accessible than mRNA vaccines, which require subfreezing storage. The Novavax booster is now available in pharmacies across the country, with the CDC recommending having two doses that are eight weeks apart for unvaccinated people.

Which one should I get?
Both the protein vaccines and the mRNA vaccines can help you fight against the SARS-CoV-2 virus, and neither is better than the other. The mRNA vaccine has a faster efficiency in preventing COVID and has a higher adaptability to new variants, while the Novavax vaccine uses a more familiar technology, has a more accessible storage requirement, and has a lower risk of side effects post-vaccination. But no matter which kind of vaccine you think is better, Lyke suggests that the most important thing is to “pick one and get it.”

Novel Coronavirus SARS-CoV-2 (SARS-CoV-2)

Connecting to AP Biology:
In AP Biology, we’ve learned about how our bodies fight bacterial and viral infections and specifically talked about how the spike proteins on SARS-CoV-2 work to attack our bodies. When our body first recognizes the SARS-CoV-2 virus, white blood cells like Macrophages and Dendritic cells will engulf the virus, breaking it down into small pieces and displaying it to Helper T cells on their MHC proteins. The Helper T cells will then release Cytokines which will trigger both the Cell-mediated response and the Humoral response of your immune system. These responses will ultimately kill most of the bacteria/viruses in your body. Additionally, your immune system will then remember the SARS-CoV-2 virus, and if you ever get affected again, your immune system will immediately respond to it. Understanding how vaccines help your body defend against real viruses links directly to our studies on the human body’s defense mechanisms against foreign pathogens.

Leave a Comment!
COVID-19 is a years-long pandemic that still hasn’t ended today, I think it is really important for everyone to know how they can protect themselves through modern technologies and minimize the impact of the virus. I am also intrigued by how fast different vaccine technologies have evolved to help mankind to combat the virus. How do you feel about the re-introduction of protein-based vaccines like Novavax? Do you think this will change the public’s preferences on COVID-19 vaccines? Feel free to leave a comment below and we can discuss more about this topic! For more information on this post, go to for the latest research and updates.

Unlock the POV of Pups: How Dogs See the World Beyond Colors.

Madsen the dog, 001

Have you ever wondered how your furry friends recognize the world around them? This question was asked by a group of scientists who recently studied how canines “see” the world not only with their eyes, but also with their nose.

For a long time, the world believed that dogs could only see the world in black and white, or that dogs could only perceive color weakly, if at all. However, this myth was debunked in 1989 by ophthalmologist Jay Neitz and his colleagues, who discovered that dogs can indeed see colors, specifically blues and yellows. They cannot perceive reds and greens, similar to color-blind human.
Assorted Red and Green Apples (deuteranope view)

The reason why dogs can’t process light as well as most human is because they only have two types of color-sensing receptors, called cones, in their retinas, similar to many mammals: cats, pigs, and raccoons. This differentiates them from humans which have three cones. In addition, most dogs have 20/75 vision, meaning that they need to be 2o feet away to see as clear as a human would from 75 feet. Their world may be somewhat blurry compared to ours.

To truly understand how dogs see the world, we must look beyond their ability to process color, as highlighted by Sarah-Elizabeth Byosiere. Dogs rely on various other senses to help them “see,” or identify objects and movements around them. For example, unlike humans who have difficulty seeing in dark environments, dogs’ eyes are made to see in both daytime and nighttime. This is because of their abundance of rods, a type of photoreceptor cell in the retinas, which aids in night vision. Rods are 500-1000 times more sensitive to light than cones which allows dogs to see better in the dark. Dogs also have a unique structure in their eyes called the Tapetum Lucidum(Shown in diagram below), which acts like a mirror that reflects light back onto the retina. This enables them to see in conditions with six times less light than what human requires to see.

This is also the reason why dogs’ eyes will glow in photos in the dark, because their Tapetum Lucidum reflects the light back.

(Structure of eyes)

Mammal eye structure (tapetum lucidum)

Another significant aspect of dogs’ perception is their sense of smell, they are 10,000 to 100,000 times stronger than that of an average human. Dog’s mighty sense of smell plays a crucial role in how they perceive the world, they can even pick up odors from as far as 12 miles. Another study published recently in the Journal of Neuroscience revealed a direct connection between dogs’ olfactory bulb, which processes smell, and their occipital lobe, which processes vision. This integration of sight and smell was not observed to happen on any of other animal species.

While human are good at recognizing different colors, dogs are more into their sense of smell that humans can’t appreciate. Dogs aren’t missing out on anything; they just have their own unique way of exploring the world around them.

In AP Biology, we learned about how neurons transmit signal to the brain when we touch, hear, see, and smell. When vision and smell is received by optic nerve in eyes and olfactory sensory neurons in noses, they will pass the information of the sight and smell to the brain through neurons. Neurons transmit signals simply through a flow of ions across the axon membrane, which reverses the distribution of charges of the neuron compared to when it is at rest. This is how a neuron passes a signal to another neuron, they will repeat this process until they reach the occipital lobe and olfactory bulb in the brain where the information of the sight and smell will be processed and analyzed.

As a biology student, I have always wondered about how canines, mankind’s best friend, and how other animals see the world in their perspective. It is fascinating to find out that all animals have their unique way of sensing the world and collecting information from the area around them. Their “sensing” strategy are often different from ours’s; human primarily uses vision to receive information of the world, but our neighbors on earth could be using their sense of smell, sense of hearing, and even echoing to accomplish the same goal! Let me know in the comments below if you are also curious about how other animals recognize our world or if you are interested in this topic! Share your thoughts with me! If you want further information about this post or on this topic in general, please go to for more information and further research.

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