The Genes That Make Parrots Into the Humans of the Bird World

Sunday Ladas

Mr. Ippolito

AP Biology C-EVEN

26 October 2018

Citation:

Klein, JoAnna. “The Genes That Make Parrots Into the Humans of

the Bird World.” The New York Times, The New York Times, 7

Dec. 2018,

www.nytimes.com/2018/12/07/science/parrots-genes-longevity.h

tml.

The Genes That Make Parrots Into the Humans of the Bird World

By: JoAnna Klein

Have you ever wondered how it is possible for a parrot to talk? What part of the brain aligns with the human brain for the parrots to have the ability to repeat the words that humans say?  A team of scientists took a trip to Brazil to study what aspects of a Blue-fronted Amazon parrot aligns with humans. After lots of research, the scientists came to the conclusion that the blue-fronted Amazon parrot are like the humans of the avian world. They came to this conclusion from comparing the blue-fronted Amazon parrots genome to other parrots in the same family and their basic knowledge of evolution. There research has also indicated that the birds can live an average of 66 years old. This is a revolutionary finding because it leads to the new question how are parrots able to live this long. To put more context to this question, science has proved that smaller birds are more likely to live five to eight years and larger birds can live a few decades. Scientists have found that in some cases parrots outlive their human companions! Another finding scientists found was that the changes in the parrot genome is surprisingly similar to the human genome. The genes are similar in different parts of the of the genome. They are similar along regions of the genome that regulate the expression of nearby genes that seem to play a role in brain development and intelligence.

Interestingly enough, the new findings about the blue-fronted Amazon parrot is relevant to understand the parrots and humans relation. These new findings provoke other scientists to research the brains of the parrots. Dr. Mello, one of the scientists that went to Brazil to study the blue-fronted Amazon parrot stated that “they’re really, really smart animals, and the brains are particularly big.” Scientists are now researching how the parrots are the parallel to humans of the avian world. This discovery could make advances in science in the evolution and avian area of science.

I thought that this article was constructed in a exceptional manor, I feel that the author made very good points and the authors tone showed her attitude towards the topic. It was evident that the author was interested and really liked the topic he was writing about. However, I felt that JoAnna Klein (the author) could have done a better job emphasizing why this is such a revolutionary idea  I felt that she just continued to state amazing the discovery was and there was nothing to refute it the the facts about how amazing this discovery was rather than providing an argument for how it furthered science. Lastly, I thought that she could have included less information about how the new pieces of evidence that has been discovered rather than touching on multiple pieces with no explanation. Overall, I felt this piece was very well written, however, I thought the author could have emphasized the new findings relativity.

Lava Lamp’ Proteins May Help Cells Cheat Death.

Moskvitch, Katia. “‘Lava Lamp’ Proteins May Help Cells Cheat Death.” Quanta Magazine, Simons Foundation, 26 Nov. 2018, www.quantamagazine.org/phase-separating-proteins-may-protect-and-regulate-cells-20181126/.

        In her scientific review, Katia Moskvitch explores the breakthrough discoveries of biophysicist Clifford Brangwynne and his team concerning the existence of liquid-liquid phase separation in cells. Liquid-liquid phase separation is best visualized by the liquid components of a lava lamp which cluster and separate into shifting blobs due to their different densities and incompatible polarities. Recent work in cellular biology suggests that such a phenomenon has been harnessed by evolution to manipulate the metabolism and functioning of cells via proteins in the cytoplasm. Experimentation and imaging indicate that when cells are deprived of nutrients, or otherwise under severe stress through temperature or acidity changes, non membrane-bound metabolic components aggregate and solidify--essentially putting the cell into a hardy condition of stasis. The state change is orchestrated by specific proteins in the cell, whose “identifiable domains” allow the associated cellular matter to shift between its normal fluid state and more gel-like clusters.

        This breakthrough has extensive repercussions for the way we study cell functioning and molecular biology. Streamlined through cleanly cut curriculums, the average science student’s understanding of cell anatomy, metabolism, and normal operations is inherently flawed and oversimplified. Investigation of the manipulation of physical phases by proteins in the cytoplasm is just one example of how the scientific community is looking to enrich its understanding of the most basic unit of life through a different lens. Moreover, this discovery has sparked the interest of scientists around the world who are suggesting other fields where protein liquid-liquid phase separation could take place. For example, neuroscientists have posited that vesicle deployment at neurotic synapses may be purposefully delayed by aggregation, effectually controlling the reception of neurotransmitters.

        I enjoyed Moskvitch’s article because of her ability to put complex microbiological topics in layman's terms. However, I felt that at times, she avoided scientific jargon to the extent that the specific procedures used by the scientists and the types of proteins involved in aggregation were unclear. Reading this article has left me with many unanswered questions: is aggregation a physical or chemical process and why are specific proteins able to regulate it? What is “the domain” of a protein that determines its ability to regulation phase change? What are the long-term effects of solidifying organelles and proteins and are they able to recover their functions? I look forward to seeing liquid-liquid phase separation explored in future scientific discussions and perhaps in the future, it could be manipulated by humans to treat disseminating diseases by delaying spread between cells.

Chinese Scientist Who Says He Edited Babies’ Genes Defends His Work

Aiden Hiller
Mr. Ippolito
Current Event #10
5 December, 2018

Belluck, Pam. “Chinese Scientist Who Says He Edited Babies' Genes Defends His Work.” The New York Times, The New York Times, 28 Nov. 2018, Link

In a bizarre turn of events, a Chinese scientist has revealed that he successfully created the world’s first genetically modified babies. Should his claims be legitimate, He Jiankui used CRISPR to modify a pair of embryos for resistance to H.I.V. The modification disables a gene known as CCR5, which is responsible for the production of a protein that must be present for H.I.V. to enter cells. Many nations, including the United States, have outlawed the use of CRISPR on humans, asserting that it is an unethical and irresponsible practice. In China it is legal to modify embryos, however they are not permitted to remain viable for more than 14 days. Dr. He’s trial involved eight couples in which the male was positive for H.I.V. and the female was not. After modifying the embryos, he used in vitro fertilization to further reduce the risk of H.I.V. At a human genome editing conference at the University of Hong Kong, He maintained that the participants were informed of the procedure and potential risks involved. Yet this failed to alleviate discomfort in the room, with many of his colleagues making accusations of deliberate secrecy due to the controversy surrounding the project.  
Many fear that the birth of the first genetically modified humans will open the floodgates for gene editing. They claim that with the barrier broken, we will soon be living in an era of designer babies and superhumans. This seems somewhat reactionary, and with new reports that Dr. He has gone missing and is allegedly under house arrest, the scientific community and the Chinese government have made it abundantly clear that this kind of activity is still unacceptable. Many have also taken issue with the fact that there are alternative and much simpler methods, especially when only the father is infected with H.I.V. Additionally, only one copy of the CCR5 gene was disabled in one of the twins, and both were disabled in the other, which just adds another variable for potential issues in the future. Past efforts to edit embryos have brought some unintended effects such as off-target mutations and mosaicism, where the altered gene only appears in some cells. The scientific community can continue to shun and denounce his work, but it’s important that we allow responsible hands to monitor development of the twins.

I appreciated that the author was able to condense the story leading up to the new developments into one short paragraph. This made it easy to follow while simultaneously acting as an effective starting point for the rest of the article. She provided quotes from many voices of authority that creates an accurate representation of the tensions during the conference. She also gave many examples of faults that Dr. He’s colleagues have found with his work that further display the resentment within the community. However, I don’t agree with how she structured the article. For example, she discusses the genome editing summit and uses quotes from after the conference criticizing Dr. He’s work, but then back peddles and uses a line that more closely resembles a hook: “When Dr. He, 34, walked onstage in an open-collar shirt carrying a tan briefcase, it was clear this would be no ordinary conference presentation.” However, my main problem with the article is that the author limits discussion of the actual process to one short paragraph. I understand that it’s only a New York Times article and she doesn’t want to get tangled in some of the technicalities, but her explanation of Dr. He’s experiments is a little too simple. Additionally, she brushes over the research he had presented on mouse and monkey embryos prior to conducting human trials that would have been interesting to see.

Gutierrez, Graciela. “Microbial Based Treatment Reverses ASD's Social Deficits: Mouse Study.” Neuroscience News, Neuroscience News, Baylor College of Medicine, National Institutes of Health, Sammons Enterprise , 4 Dec. 2018, neurosciencenews.com/asd-microbial-treatment-120204/.

Recent experiments performed by researchers at Baylor College of Medicine give support to an unconventional idea that could finally allow for the treatment of the core symptoms of Autism Spectrum Disorder. The researchers found in 2016 that mice offspring of mothers fed high-fat diets had social deficits and changes in their gut microbiome characterized by reduction of the gut bacterium L. reuteri. The important revelation of this finding was that the researchers could reverse the social deficits caused by autism by restoring this bacteria. Additionally, since the tested model was only for one of the many underlying mechanisms of autism, the researchers investigated whether this finding applied to other mechanisms of autism with different causes (idiopathic- or spontaneous/unknown occurrence of disorder or condition- genetic, and environmental models), and adding L. reuteri worked in all tested models of the condition. Afterwards the researchers explored the mechanisms that mediate the rescue of social behavior in mice models of ASD with L. reuteri, and they discovered that the bacteria works in vagus nerve, which bidirectionally (in both directions) connects the gut microbiome to the brain. This is interesting because the supplication of a gut bacteria that was deficient would be expected to restore the composition of the gut microbiome, but rather this bacteria is actually restoring proper functionality to a pathway of a specific connection to the brain, which in turn promotes social interaction. Furthermore, when vagus nerve is active, oxytocin- a social interaction promoting hormone that activates “social reward” when it binds to neuron receptors- is released, so researchers tested whether genetically engineering mice without the oxytocin receptors on their reward neurons, blocking those receptors with certain drugs, cutting the connection between the gut and the brain, or interfering with oxytocin’s binding to the receptors would affect the bacteria’s ability to restore proper social behavior in the mice models of autism: in all cases, the bacteria could not restore social behavior in mice. This corroborates the finding that it is the oxytocin released by the vagus nerve that restores social behavior in mice models, not just the presence of this bacteria. These findings are important because not only does it change the way that neuroscientists and psychiatrists think about the treatment of autism and related disorders, but it gives support to the relatively new idea that it may be possible to control or alter specific behaviors through the gut microbiome by selecting specific strains of bacteria.

This final idea is hugely important because the ability to manipulate people’s gut microbiomes is turning out to have a wide variety of implications. The gut microbiome, which consists of trillions of types of bacteria, not only function in the brain, but they digest food, process nutrients, make vitamins B and K (I know personally that vitamin B makes all of the difference in emotional wellbeing), and produce immune system substances to fight inflammation and heal wounds. In addition to all of these functions, the microbiome is in constant, direct contact with the brain through immune and nerve cell pathways collectively known as the gut-brain axis. One of the neuroactive compounds made in the microbiome and sent to the brain is 90% of the brain’s serotonin, which helps stabilize emotions and prevent depression. In addition to autism, shifts in the composition of the gut microbiome through certain bacterias outcompeting other, necessary ones have been linked to inflammatory bowel disease, blood cancers, and dementia-causing conditions. With such a diverse functionality, the ability to alter specific behaviors through a more advanced understanding of the types of bacteria may fix a wide range of health related problems before the ethical and practical concerns of genetic engineering ever have to be considered. In the foreseeable future, the race to discover and study all of the various bacteria in the microbiome could be the modern day version of the race to sequence the human genome, both in the sense that it will be a literal race and that there may be a gold mine of information in accomplishing such a task that could drastically improve the conditions of many people (the citation for the microbiome information is in the footnote).

In conclusion, this article was well-written in the sense that it highlighted the important points, especially in the beginning to grab attention, and synthesized important quotes from the experts in the topic for the analytical side of the research. This use placement of expert quotes gives credibility to the article. However, one weakness of the article is that it somewhat places a positive spin on the research, using only the most optimistic facts about the research to make the reader think that the experimental results were more full proof than they actually were (ie “Surprisingly, they discovered that, indeed, L. reuteri can trigger the recovery of social behaviors in all the models they tested, suggesting that this microbial-based approach could improve social behavior in a wider subset of ASD.”) Indeed, the abstract of the actual paper paints a more realistic view of the findings by stating that, “However, whether the effect of L. reuteri on social behavior is generalizable to other ASD models and its mechanism(s) of action remains unknown. Here, we found that treatment with L. reuteri selectively rescues social deficits in genetic, environmental, and idiopathic ASD models.” Note that unlike the article, the abstract concedes that the tests were limited with respect to the models it used versus all of the possible ASD models that exist, that the way the L. reuteri work in the vagus nerve is still unknown, and that the bacterial treatment only selectively rescued social deficits in the tested models. When writing to a scientifically curious audience, it is important that an article paints a realistic picture of the research so that the average reader won’t just think that one finding can do something as grand as automatically cure an important ASD symptom. The lesson that research is a long, cumulative process is important for any budding scientist to learn.

A Famous Alpha Wolf's Daughter, Spitfire, Is Killed by a Hunter

Clara DeMagalhaes Current Event #10

Robbins, Jim. “A Famous Alpha Wolf's Daughter, Spitfire, Is Killed by a Hunter.” The New York Times,
The New York Times, 30 Nov. 2018,
www.nytimes.com/2018/11/30/science/wolf-spitfire-killed.html?rref=collection%2Fsectioncollection%2Fscience&action=click&contentCollection=science®ion=rank&module=package&version=highlights&contentPlacement=1&pgtype=sectionfront.

Recently, a wolf known as 926F, or “Spitfire”, was shot and killed by a hunter when it wandered a little way outside of Yellowstone National Park. This wolf was part of a pack called Lamar Canyon and
also happened to be the daughter of a well-renowned alpha female that was also killed by a hunter.
Technically, Spitfire had wandered into an area where wolves were permitted to be hunted, but the killing
is still extremely controversial.  There have been attempts to have a buffer zone around the park be
established so that if wolves of Yellowstone, who have little fear of humans, cannot be shot. The buffer
was denied (though hunters are only permitted to shoot two wolves per year), but the uproar about the
general topic of wolf hunting near the national park has yet to quell. A guide for the Yellowstone Wolf
Tracker, Leo Leckie, tracks their family history, and believes that hunting these wolves makes seeing
them more rare. There are debates questioning how moral it is to hunt animals who have long thought
that humans are safe. Spitfire’s ancestry line hasn’t been extinguished, as she left behind a daughter
and her mate. However, the wolf biologist of the park, Doug Smith, says that the Lamar Canyon pack’s
survival may be in danger with the death of its matriarch. Now that its size has been reduced to 7
wolves, competing with other groups of wolves will be considerably harder.

The article mentions that the controversy of hunting wolves near Yellowstone highlights “the clash
between the New West’s ecotourism and the Old West’s hunting to protect game and livestock”. Many
concerns for the park and the survival of the wolves have been expressed throughout the article, and
Leo Leckie talks about how because hunting wolves makes it more difficult to spot them, it hurts the
business of the national park. As mentioned in the summary, killing off the pack’s alpha leader
jeopardizes the survival of the entire group. The incident also brings into question whether its ethical to
hunt animals who have lost their fear of humans, which is a debate that could potentially extend to other
ecological topics. There’s also the effect that killing the daughter of such a beloved wolf has had on the
public. Spitfire’s mother was something of a celebrity and was even the subject of the book American
Wolf: A True Story of Survival and Obsession in the West, and so her popularity extends to her descendents
as well. As a result, public outrage only intensifies the conflict more.

The article as a whole was very interesting and presented its information clearly. It was fast
paced and got straight to the point while providing enough background information for the
reader to fully understand. It also provided a couple of pictures so that the reader has a visual
representation of what the article is about. However, one of the drawbacks was that it
sometimes seemed like the author was trying to incorporate too much information at once and
in awkward places. It was hard to tell if the article just wanted to focus on what the public
response to the death of the wolf was or another subject and it was like the author wanted to
talk about everything the author could entail but couldn’t quite elaborate on why certain tidbits
were important or even necessary. And the order of subjects was also a bit strange, like how the
author had an entire paragraph in the middle of the article talking about the history of the wolves
when background information like that is better at the beginning. To improve, I suggest that the
author first talks about the background before expanding into their main points and making
them the main subject instead of trying to tackle everything at once.

Mosquito-trapping balloons could help us understand one of the world's deadliest diseases

Mock, Jillian. “Mosquito-Trapping Balloons Could Help Us Understand One of the World's Deadliest Diseases.” Popular Science, 3 Dec. 2018, www.popsci.com/balloons-mosquitoes-migration-malaria.

In the article, "Mosquito-trapping balloons could help us understand one of the world's deadliest diseases", Jillian Mock discusses how scientists approaching their attempts to contain malaria in a new way. In a study of mosquitos, scientists discovered that the diseased insects flew at significantly higher hights than they had previously thought, and thus can travel farther. In order to see how many mosquitos are moving and at what altitudes, Tovi Lehmann and his team released these white balloons, each equipped with a sticky net to trap the insects, at different altitudes in the forests of Mali. The data collected suggests that mosquitos migrate far more than scientists had previously expected, but because each of the 3,000 insects collected was not screened for malaria, it is not yet possible to determine how such traveling affects disease transmission between humans.  The researchers hope future studies will reveal how mosquito migration correlates with human and animal travel patterns and with the spread of related diseases. They hope that further conclusive studies may help them discover means of containing and eradicating mosquito-spread diseases.

In 2017 alone, there were 212 million cases of malaria in 90 countries, some 435,000 of which resulted in deaths. This has a massive impact on our world, particularly the continent of Africa. Thus, it is absolutely essential for scientists to put every necessary effort into finding ways to cure malaria and prevent its spread. It is important to research and experiment with this new balloon technology because it may hold the key to saving 435,000 lives in the coming year.

Overall the article was beautifully written and very well organized. Mock did an excellent job of providing an effective summary of the new technology and its potential impacts without making it confusing. However, I felt the article lacked in its description of exactly what these balloons are and how they work. A more thorough explanation of the science behind the creation of the balloon rather than just its effects would have aided readers in understanding the subject. Likewise, an image of the balloon would have supplemented the writing well.

Pluridirectional High-energy Agile Scanning Electron Radiotherapy (PHASER): a novel design for radiation treatment of cancer

Maxim, Peter, and Billy Loo . “Pluridirectional High-Energy Agile Scanning Electron Radiotherapy (PHASER): a Novel Design for Radiation Treatment of Cancer.” Stanford.edu, Stanford University, 28 Oct. 2018, biox.stanford.edu/research/seed-grants/pluridirectional-high-energy-agile-scanning-electron-radiotherapy-phaser-novel

After months of research and a lengthy fund obtaining process, researchers at Stanford university, in collaboration with multiple federal agencies, have been going to work on a project named PHASER, revolutionary revision of cancer radiation therapy as we know it. The aim of the project is to change modern radiation therapy which “takes typically about 15 to 90 minutes” to simple  a second-long procedure. They aim to accomplish this while also drastically altering the physical and economical nature of the devices which produce this radiation in order to make them more effective and readily available across the globe. The main issue with the current nature of radiation therapy is that during the lengthy minutes in which the dose of radiation is administered, tissues and organs within the person’s body move, creating a higher risk of destroying healthy cells and it some cases, even turning them cancerous. This would be a significant problem to overcome if we were able to reduce the time of an individual radiation therapy procedure as there would be much less potential for the affected cells to move out of the target range of the highly energized radiation. In addition to significantly reducing the risk of side effects, early trials with the new way of administering the radiation on tumors in mice have revealed that the “extremely rapid radiation delivery may have a more effective biological impact on tumors than the prolonged dosage”. However, it is not only how the radiation is administered that is under question but also how the radiation is produced with in the devices. Currently, x-rays are produced by forcing electrons through an electromagnetic field,causing them to release energy in a beam of x-rays. A new type of procedure however, which involves the acceleration of protons with large magnets, has proven to yield “even more effective results than traditionally produced radiation in regards to treating malignant tissue structures”. Lastly, the article discusses some important statistics regarding the impact of cancer not only of the US population, but the world's population as a whole. After showing that “Of the 1.5 million Americans who are diagnosed with cancer each year ⅔ could benefit from radiation therapy”, the authors conclude with a pretty compelling case as to why their project should receive further funding.

Overall, the nature of the PHASER project is highly promising. If the scientist at Stanford University are able to harness the power of accelerating electrons into a second long beam of radiation, this could have potential very good consequences not only for clinical results in the United States, but also in making radiation therapy more readily available across the globe. A key component of the project was to reduce the size of the machines with which radiation therapy is administered and make them more compatible with existing infrastructure in hospitals around the world. This could allow for hospitals in third world countries or countries which don’t see a lot of usage of radiation therapy to gain access to this potentially very life-saving device.

While many of the goals set by the Phaser program look very promising, one cannot forget that the project itself is still in it’s experimental phase. As of now, they are working with “computer simulation models” to test the effects of generating radiation from protons instead of electrons, meaning they are years away before clinical trials  can even begin. This means that it could take almost another decade for this project to have any real impact in saving people’s lives. Another major hurdle that the team faces is that the radiation they wish to create in their machines often relies on very large magnets moving around the patients, similar to an MRI. This stands in direct conflict with their goal of creating a device that is economically efficient but also convenient to use at hospitals around the world in terms of its size as this clearly presents a large engineering challenge that to be overcome if the project wants to meet the goals it set out to accomplish. Despite the initial shortcomings and the clearly long and winded road that the project has ahead of itself, we should not forget that this team of researchers at Stanford University enjoys the full support of the national Accelerator laboratory as well as significant amounts of federal funding. This, in contrast, paints a more optimistic future of the project’s  potential outcomes. The fact that the project goals appear to be very attainable within the reasonable future, means the only suggested improvement I can offer to the scientists at Stanford is to obtain as much federal funding as possible as this should have greatly help them experiment and accomplish their goals as soon as possible, potentially saving millions of lives across the United States and across the world.