Where did the first fish evolve? The Answer may be shallow

Sunday Ladas

Mr. Ippolito

AP Biology C-EVEN

26 October 2018

Citation:

St. Fleur, Nicholas. “A Shallow Hypothesis for Where Fish First

Evolved.” The New York Times, The New York Times, 25 Oct.

2018,

www.nytimes.com/2018/10/25/science/fish-evolution-shallow-co

asts.html?rref=collection%2Fsectioncollection%2Fscience&acti

on=click&contentCollection=science®ion=rank&module=package&v

ersion=highlights&contentPlacement=1&pgtype=sectionfront.

Where did the first fish evolve? The Answer may be shallow

By: Nicholas St. Fleur

Believe it or not, there used to be fish with a bony body, spikes, had tails, and lacked jaws. REcently scientists have discovered that more than 400 million years ago, there used to be all different types of fish in the ocean that could have looked like there would be no such thing in today’s world. After researching more about this topic and finding fish fossils, scientists have reason to believe that fish used to swim in areas that were closer to the coastlines of the continents rather than deep in the ocean.  Today scientists are wondering where the extinct fishes relatives have evolved. When researching this topic, the fish fossils keep bringing the scientists farther and farther back into time. They have now discovered the origins of the vertebrates who were our ancestors, when they first came to the new land. A vertebrate paleontologist from the university of chicago stated that, with the new fossil database scientists have put together, “Previously we thought the early reef systems would be the cradle of diversification. But no, it seems that these early armored forms were in much nearer shore environments”. Scientists are closer and closer to discovering the where fish today have evolved, they have established two main fish groups, the bony fish and the cartilaginous fish group.  

Discovering the evolution of fish and how they have evolved over time is a major discovery that could be made one day. We already have little bits and pieces of the puzzle and are close to figuring out what fish today have evolved from the jawless and spiked fish. From the fish that scientist have discovered that have evolved they have been shocking discoveries, and the continuous discovered is just a reminder of the evolution in the world. EVerything evolve, maybe humans will evolve even more, what will humans look like in 400 million years from now?

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 the point of view he favoured. It was evident that the author was interested and really liked the topic he was writing about. However, I felt that Nicholas St. Fleur (the author) could have done a better job looking out the other side of this topic, I felt that he just continued to state how amazing the discovery was and there was nothing to refute it the point or a lot more evidence to back up his argument. Lastly, I thought that he could have included more information about how the new pieces of evidence that has been discovered rather than just touching on a few pieces with not explanation.  Overall, I felt this piece was very well written, however, it could have been looking at the other side of the argument.

“Solving the Complex Mysteries of the Microbiome.” Neuroscience News, NeuroscienceNews.com, 25 Oct. 2018, neurosciencenews.com/microbiome-mystery-10091/.

The reactions that take place among the many tiny bacteria in the gut microbiome affect much of our wellbeing as humans, including our mood and even our risk of autism. “Solving the Complex Mysteries of the Microbiome” published in Neuroscience News describes how new research by Jason Papin, PhD, and Greg Medlock at the University of Virginia will provide the first step in actually understanding what each individual reaction of specific bacteria does in the microbiome. This will allow for a much more accurate assessment of what these processes ultimately contribute to human health and disease beyond the correlative information scientists currently have, namely the presence of the bacteria and a vague assessment of their functions without truly understanding the individual mechanisms. The researchers wanted a concrete answer as to which bacteria participate in which reactions and how the molecules generated in those reactions are used by other bacteria, as well as the effects of these populations existing in the system. The format of the experiment was to examine six species of bacteria individually and then to examine 15 pairs of various combinations of these species to determine how molecules were made and used in the system. The data obtained from this experiment was then used to create a computer simulation attempting to predict what would happen with the bacteria in the system. By testing these predictions, the first hard data was generated, supporting the success of a new method of experimentation in the microbiome called the “experimental and computational pipeline.” With hard data, scientists can actually manipulate and control the microbiome by increasing or decreasing levels of certain bacteria.

I currently have an internship at the Amen Clinic, which does high-tech brain scans of people who have ADHD, ADD, various symptoms of Cranial Cervical Syndrome, autism among other disorders. A specific example of the relative expertise the Amen Clinic has compared to conventional psychiatrists and neurologists is its knowledge on Cranial Cervical Syndrome. Whereas many neurologists and psychiatrists would just be puzzled if a patient walks in claiming that his or her “brain hurts,” the Amen Clinic psychiatrist I am shadowing understands that this is often caused by trauma to the head misaligning the ligaments at the base of the skull, impeding the flow of cerebrospinal fluid out ot the foramen magnum and allowing for the accumulation of various toxic proteins in the brain. However, despite being relative experts in neuroscience and various disorders, the references to the gut microbiome often made when he is describing it to the patients are comparatively vague, suggesting that this area is just relatively unknown. The ability to elucidate the specific ways in which the gut microbiome are affected by and affect the brain would likely allow for an even stronger treatment for many kinds of patients across the spectrum of neurological disorders. As the Amen Clinic and this new research has already shown, this kind of knowledge is power.

This article was very strong in describing to laymen the exact significance of the research, which is important for keeping attention and interest: it is very clear that this experiment provided a new model for generating hard data that will allow scientists to directly manipulate the gut microbiome with certainty, whereas until now the data was just correlative, making it very dangerous to attempt to manipulate specific populations and reactions. That part was extremely clear. However, one weakness of this article was that it described the actual experimentation in far too vague of a matter. For example, one still does not understand after reading how the computer simulation allows for Papin and Medlock to make predictions. This is important since the data came from evaluating predictions. A sentence or two on how exactly the computer model allows for predicting further outcomes would improve the article by giving a more clear picture of why the experiment was designed this way.

Researchers Explore a Cancer Paradox

Aiden Hiller

Mr. Ippolito

AP Biology

26 October, 2018

Zimmer, Carl. “Researchers Explore a Cancer Paradox.” The New York Times, The New York Times, 18 Oct. 2018, Link

Our understanding and perceptions of cancer are constantly changing, it's seemingly impossible to form a general definition of the disease with our current knowledge. For instance, cancer is commonly associated with mutation, but new research shows that this definition is somewhat misleading. Research that set out to identify the principal cancer-causing mutations ended up uncovering a surprising number of mutations in healthy cells. Additionally, many of the mutations that were believed to be a source of cancer were present in normal cells. The discovery, made by Dr. Martincorena and his research team, utilized new gene sequencing techniques to pinpoint mutations in epithelial (the top layer of skin) cells. In 234 samples from four patients, they discovered that a fourth of all the cells contained a mutation on a gene that had been connected to cancer. The researches expected these cells to be somewhat mutated as skin cells are commonly irradiated by ultraviolet rays, but not mutated to this extent. Furthermore, when the experiment was repeated in esophageal cells, there was an unanticipated prevalence of the same mutations; these cells are untouched by ultraviolet rays, and the researchers were able to eliminate other common causes for cancerous mutations like alcohol and cigarette smoke. The mutations cause cancer-like growth, but they were not cancer cells. Yet, it seems that these mutated cells naturally arise through aging, with Dr. Martincorena noting that they "colonize more than half of your esophagus by middle age."
The research raises many more questions that it answers, and it may come to change our definition of cancer altogether. However, first we must ask why these mutations are present in healthy cells. Dr. Martincorena offered one possible explanation: that cells in the body operate like an ecosystem, they compete for resources, and the cells with advantageous mutations outcompete others. If this theory holds true, we will have to examine the potential health cost of heavily mutated cells. It probably varies based on cell type, but in esophageal cells for example, even if they aren't cancerous, they could cause health problems by reproducing at an increased rate. This could mean it's much harder to slow aging than we currently believe. The modern approach to cancer is preventing it from taking hold in the first place, but it might prove to be more difficult to apply the same philosophy to aging. It's certainly the most efficient method for treating any disease, but this research suggests mutations could be inevitable with age. However, this is all just speculation, and the mechanisms that gives rise to specifically cancerous mutations are still unknown.
Overall, the article is well written, I liked Zimmer's incorporation of quotes from other researchers in the field. They served to contextualize the research being done, and helped the reader understand the magnitude of the results. My issue with the article is the conclusion, it's quite weak, and has the same problem as the other Zimmer article I reviewed. In both cases, he concludes with an interesting point that makes a connection and summarizes the content, but then tacks on an unrelated quote. The article would be much stronger if he just deleted the quote and ended with the piece that connected back to the main idea.

Deep in Human DNA, a Gift From the Neanderthals.

Jordan Hoang

Mr. Ippolito

AP Biology C Even

10/22/18

Zimmer, Carl. “Deep in Human DNA, a Gift From the Neanderthals.” The New York Times, The

New York Times, 4 Oct. 2018,

www.nytimes.com/2018/10/04/science/neanderthal-genes-viruses.html?action=click
&module=Associated&pgtype=Article®ion=Footer&contentCollection=Matter.

In recent years, scientists discovered something surprising: many people of Asian or
European descent actually share a common ancestor with the nethandrals. They believe
that this phenomenon may be attributed to humans mating with them around 40,000 years
ago. But considering that this group of people have been extinct for many years, scientists
tried to look further into why their DNA are still present today in our genetic code.
What they uncovered was astounding: neanderthal DNA may have helped us fight off certain
diseases. According to scientists however, this immunity was acquired quite unconventionally.
Through breeding with one another, nethanderals actually spread new diseases to humans,
some of which could have been ancient forms of “influenza, herpes and HIV”. Consequently,

this may have left some of the first encounters with nethandrals to end in death. But through
eventual adaptation of genes and exposure, humans were able to form a shield against some
of these diseases and survive. Specifically, Dr, Enard from the University of Arizona studied
over 1,000 different proteins and uncovered that over “one-third of the adaptive changes in
our proteins have occurred among those that interact with viruses”. In short, by interaction
and mating with nethanderals, the ancestors of humansmay have acquired traits to be able
to fend off certain diseases.

These findings were particularly interesting to read about, considering that much of ancient
history is relatively unknown to us. Additionally, it was intriguing to hear how such large
groups of people today could share the same codes of DNA. Although it mentions in the
article that nethanderals only accounts for about 1 to 2% of our total DNA, the number
is actually quite significant considering how long ago these interactions were. Furthermore,
with just this one fraction of DNA from this group, we adapted a form of immunity against
some serious illnesses. I believe that these findings are a great advancement into learning
more about our ancient ancestry and how much it still affects humanity today. I believe
this specific discovery will interest more people to research more about what makes up
our complex genetic code.

In light of the article, I enjoyed how the author used visuals to interest the readers. I also
liked the simplicity of his writing and straightforward descriptions throughout the piece.
However, I would have wanted to see more information regarding the ancient viruses and
diseases he mentioned at the beginning of the article. It would have been interesting to read
more about how individuals exactly gained immunity from these specific diseases. Besides
that, I throughly enjoyed how the article was organized and written.

“'Lifeboats' Amid the World's Wildfires”

Charlotte Cagliostro

Ippolito

C Even AP Biology / Current Event #5

10/18/18

Zimmer, Carl. “'Lifeboats' Amid the World's Wildfires.” The New York Times, The New York Times, 12 Oct. 2018, https://www.nytimes.com/2018/10/12/science/wildfire-biodiversity.html?rref=collection%2Fsectioncollection%2Fclimate&action=click&contentCollection=climate&region=stream&module=stream_unit&version=latest&contentPlacement=5&pgtype=sectionfront.

In Carl Zimmer’s New York Times article, “Lifeboats’ Amid the World’s Wildfires”, he focuses on forest fires and their effects on biodiversity. Recently, wildfires have been occurring quite rapidly across the globe in areas such as California, Greece, Portugal, and Colorado. Fires in these locations have burned and destroyed many forests; however, “islands” of trees, shrubs, and grass were able to survive. The species living in these regions are known as fire refugia and are incredibly important in the survival of forest ecosystems. Fire refugia can provide shelter and food for animals. Additionally, their seeds can travel through the wind to the surrounding charred areas of forest and begin a period of growth and renewal. Today, scientists hike through forests and observe the ecosystems through satellites in order to construct detailed and accurate studies of fire refugia. To conclude his article, Zimmer discusses how climate change will affect wildfires, stating that as temperature increases and fires become more intense, fire refugia may become rarer.

The topics in which Zimmer focuses on, wildfires and fire refugia, are important factors in the overall health and continued prosperity of forests. Without any fire refugia, it will become quite difficult to maintain biodiversity in forests since animals will not have available shelter or food following a fire. While climate change and wildfires are pressing issues that influence many individuals’ lives, Zimmer’s article focuses entirely on the effects on forest organisms.

Zimmer did a great job constructing his article. He takes quite challenging scientific topics and explains them in a simple, straightforward manner. Zimmer also presents the information in a thoughtful way; he first explains what fire refugia are, then transitions into how ecologists research the topic, and then finishes with the future effects of climate change on wildfires. Additionally, Zimmer includes many pictures, which serve to further reinforce the ideas discussed in his article. The dramatic images show forests during and after fires. The pictures showing the “islands” of surviving plant life help the reader visualize what fire refugia are. Overall, Zimmer was able to craft a thought-provoking article that truly makes the reader think about the future of Earth.

Clara DeMagalhaes

AP Biology C Even

October 16, 2018

Current Event #5

Klein, Joanna. “Plants Can't Talk. But Some Fruits Say 'Eat Me' to Animals.” The New York Times,
The New York Times, 9 Oct. 2018,
www.nytimes.com/2018/10/09/science/fruit-color-evolution.html?rref=collection%2Fsectioncollection%2Fscience.

Over time, fruit-bearing plants have evolved different ways to communicate with animals to make their
fruits appeal to them. This way, when the animal eats the fruit and expels the seeds, the seeds will grow
somewhere other than the original location, thus furthering the survival of the species. How exactly plants
have been able to do this has been debated about for a long time,  though the most commonly accepted
hypothesis is that fruits adapt different traits depending on the preference of the animal that eats them, like
their color, shape, or location on a tree branch. Kim Valeta studied this by testing with her team of
researchers how a fruit’s color contrasting against background foliage appeals to different animals in
Madagascar and Uganda. The resulting conclusion is that the way the fruits contrast with the background
is designed to appeal to the visual capabilities of animals. For example, red berries against green foliage
could be easily seen by certain birds and monkeys, but when the colors blue and yellow were contrasted,
then animals who were red-green colorblind were able to see those clearly. Meanwhile, Valeta’s colleague,
Omer Nevo, wanted to test how fruits alter their odor depending on the animal that eats them.
He collected a hoard of ripe and unripe fruits from Ranomafana and hypothesized that fruits eaten by only
lemurs would have a greater distance in odor than the fruits eaten by birds. The odors of the fruits were
extracted by a technique called the “semi-static headspace technique” in which the fruits were sealed in
oven bags, allowing the odors to build up. These odors could then be pumped out of the bags and
analyzed. The team concluded that the fruits whose seeds were spread by lemurs had stronger chemicals
when they were ripe compared to when they weren’t. They recognized that this may only be the case in
remote, specific scenarios, but researchers also suspect a similar relationship is happening between
elephants in Uganda and a tree called the Balanites wilsoniana. The seed of the Balanite wilsoniana
cannot grow into a new plant until the elephant expels it. This type of mutualism is common with
flower-pollinator relationships, but not with relationships between fruits and their seed dispensers.
Other plants, such as the traveler’s palm whose fruit is consumed by aye-ayes in Madagascar, contain
a laxative that causes the consumer to expel the seeds as quickly as possible. Like the Balanites
wilsoniana, the traveler’s palm’s survival depends on their seed dispersers for survival.

The question of why animals choose specific fruits to eat based on characteristics is something that has
intrigued biologists for over a century at this point. This type of information is useful because it helps
scientists specify the niche of a particular species. For example, if it is known that a certain species of
lemur is red-green colorblind, then it will most likely avoid fruits of those colors, and instead consume
fruits that are of a different color. Also, knowing which animals spread which seeds could potentially
help biologists track or estimate the population of the plant by tracking their consumers and finding out
how many seeds are typically released by the plants as well as figuring out where an individual plant’s
location may be. Lastly, if a population of a certain plant or animal species needs to grow and they have
this type of relationship with another species, then researchers could introduce more of the other
species in order to help the other one grow. For example, if the population of a fruit-bearing plant runs
too low and it has a mutually beneficial relationship with a type of animal of this type, then more of that
animal could be introduced. Therefore, more of the plant’s seeds will be spread, which in turn helps
boost the population.

The article was written in a very intriguing way and always brought up new tidbits of information in
order to keep the reader interested. It was moderately paced, but because there was a lot of different
information and many experiments that it talked about, the overall pace of it matched the topic well.
And while there were many different scenarios observed, they were still all explained in a way that
ensured any reader, no matter how well versed they are with biology, could understand. However, one
of the flaws has to do with how each of the experiments and pieces of information were presented. It
felt like the author wanted to talk about a lot of stuff but had a word limit, so many of the tidbits felt
rather rushed. There was also a question that was presented in the article that wasn’t really elaborated
on. Namely, “how can you pin a fruit’s particular traits to an animal when many different animals, with
their own evolutionary adaptations, interact with the same fruits?” I thought this question was what the
experiments were supposed to answer, but it seemed like they were only trying to prove that fruits
adapt certain characteristics to appeal to a specific set of animals. In order to improve the article, I
suggest that the author could maybe cut out one of the sections, like when they were talking about the
diets of aye-ayes, and instead focus on elaborating on another portion that wasn’t explained fully.

Greenwood, Veronique. “Taming the Groundcherry: With Crispr, a Fussy Fruit Inches Toward the Supermarket.” The New York Times, The New York Times, 5 Oct. 2018, www.nytimes.com/2018/10/05/science/groundcherries-crispr-gene-editing.html?rref=collection%2Fcolumn%2Ftrilobites

The processes of editing or outright replacing genes found in certain plants and animals are becoming more and more common as technology develops. Specifically, a new gene editing technology known as CRISPR has become very useful in allowing gene scientists to edit specific genes in a DNA sequence, as it is able to cut genes with greater accuracy than it's predecessors. One of the ways this new CRISPR technology is being used to improve agricultural yields and properties of certain plants is the Groundcherry, “a small, tart, edible fruit, similar in appearance to a cherry tomato, that is sometimes sold at farmer’s markets”. The article written by Veronique Greenwood on this subject begins by highlighting the market potential in supermarkets of the groundcherry and how this is limited by the fact that the “Groundcherry bushes sprawl untidily and can drop their fruits early”. Since selective breeding of plants to reduce the showing of these traits could take years, Greenwood explains how genetic editing using CRISPR has been the preferred method of achieving these desirable changes in the plant. (The exact results of the first few trials were recorded in this study). Given that groundcherries have a very similar genetic makeup to that of tomatoes, Greenwood explains how the scientists were able to use known gene sequences in the tomato DNA to more quickly identify the specific genes that they had to alter in the groundcherry sequence in order to obtain the desired changes in the plant: “They examined the groundcherry genome for analogs of known tomato genes, and found one: an analog of a gene called “SELF-PRUNING” or SP, that in tomatoes controls the shape of the plant”. By simply using CRISPR to remove this specific gene, the scientists saw “Close to 25% more weight in the fruit”. Finally, this whole process took the scientists about 2 years, significantly less than the predicted five years it would have taken if they had chosen to pursue selective breeding. When this is combined with the fact that these groundcherries would not be considered GMOs under US, Canadian and EU regulations because they only remove genetic material and do not add any, it really rounds off Greenwood’s argument that using CRISPR can be a very effective tool for breeders not just in terms of time, but also in terms of the economic impact this could have.

When seeing the incredibly successful results produced by the scientific study of altering the genes of ground cherries, it becomes quite clear that such continued success could have a significant impact on human agriculture and therefore society as a whole. If breeders are able to use CRISPR in not only a time effective but also economically advantageous manner, it could significantly reshape our ability to change the genetics of our agricultural products to the extent that it could have broad impacts on agriculture as a whole. As demonstrated in this article, the use of CRISPR can significantly reduce the number of years it usually takes to produce a plant with desirable qualities, making the idea of gene editing for agricultural products a lot more financially feasible and advantageous. This could lead to a rise in more resistant plants that could possibly withstand drastic changes to our future environment brought about by climate change.

The major flaw that can be noted in the conclusions drawn from this article, is that the only reason why using CRISPR was so significantly faster than selective breeding in this instance, was because the scientists were able to use previously known information about the genome of tomato plants to more quickly identify the relevant genes in the ground cherry DNA sequence. It is however not guaranteed, that we will always be aware of these genetic similarities when we aim to edit agricultural products with CRISPR. This could that mean that using this new technology, might not be as quick as it was in the instance presented in the article, simply because it will take the scientists longer to identify to corresponding genes. That being said however, one cannot discount the fact that as the technology becomes more commonplace, many small improvements and adaptations will surely be made to help reduce cost and time requirements to use CRISPR effectively. Overall I felt the assertations about CRISPR and its potential uses in the future made by Greenwood were grounded in reason and logic, specifically because she decided to focus on such a seemingly small instance of an application which was so easily applicable to the bigger picture. One thing I felt Greenwood could have improved upon was to give a bit more background information on CRISPR and how it exactly works to better allow us to edit DNA, as this piece of information would have been helpful to aid in the fundamental understanding which this topic requires.