Palindromes & nucleotides (or how to edit genes with the syntax of life)
The CRISPR/Cas system (Clustered regularly interspaced short palindromic repeats) is a prokaryotic immune system that confers resistance to foreign genetic elements such as those present within plasmids and phages, and provides a form of acquired immunity. [Image via. Text via]
We’ve discussed the chemical nature of life; which is all about molecules capable of forming an increasingly complex–and almost infinite–set of bio-machines. In other words, the stuff of life is all about the right chemistry–for example, polymers that can store and manage information.
All life on Earth can do this, thanks to nucleic acids. The following 16 minute film shows what these molecules have been doing for millions of years, in order to defend bacteria from their oldest foe–which is ours as well–the virus. Scientists have harnessed this bio-molecular immune system, and used it to edit, remix, and shuffle our own nucleic acids.
Keep in mind that many things about this video will become clearer during the 2nd semester of AP Bio. Nevertheless, I highly recommend watching the film with everything we have said about bio-molecules–especially nucleic acids & polypeptides–in mind:
LUCA, the ancestor of all living things (via NYT)
Welcome to the 2016-2017 school year.
As part of your AP Biology course, you’ll read, comment, and participate in a community moderated by me, your Biology teacher. This virtual community–which exists since early 2013–has a very important mission: the development of scientific literacy, via the proper use of the Internet.
Given that this is a blog for a Biology course, and this is the first blog post of the school year, I’ve decided to share with you the following New York Times article: Meet Luca, the Ancestor of All Living Things. A brief excerpt from the piece is posted below:
“Deep sea vents are surrounded by exotic life-forms and, with their extreme chemistry, have long seemed places where life might have originated. The 355 genes ascribable to Luca include some that metabolize hydrogen as a source of energy as well as a gene for an enzyme called reverse gyrase, found only in microbes that live at extremely high temperatures”
– Read the NYT article.
– Access your Edline page and read the rubric posted in the Assignment folder.
– Write your first intervention in this community (i.e. comment), following the guidelines of the aforementioned rubric .
Camanchango: a short film about myths, love & nature
The following blog post was designed and written by students from The Science Club (class of 2017 students):
Camanchacas are cloud banks that form on the Chilean coast, by the Earth’s driest desert, the Atacama Desert, and move inland. (via)
This film was based on an ancient Chilean myth and it explains a natural phenomenon: the result of the Chilean coastline meeting with the driest place on Earth, the Atacama Desert. Ancient people explain natural phenomena with myths. The following animation tells the beautiful and poetic story–a love story–of how these cloud banks formed. But we know that jealousy cannot account for natural phenomena. Without science, the ancients had to rely on mythology to make sense of nature, which can be both beautiful and terrifying.
Exoplanets and Kepler’s Legacy
The artist’s concept depicts Kepler-186f , the first validated Earth-size planet to orbit a distant star in the habitable zone. Via NASA Ames/SETI Institute/JPL-Caltech
This post was written by Honor’s Bio student, Isabel López Molini.
Exoplanets are found outside our Solar System. They revolve around a different star. The NASA Kepler Space Telescope discovered the first near earth sized planet, marking the journey to finding another “Earth”. This planet was called Kepler-186f, dedicated to the astronomer Johannes Kepler for his laws on the idea that the planets orbited the sun and the orbits were not perfect circles, but ovals. Although it is not yet determined whether or not the planet is habitable, it is within a habitable zone. The problem is not the exoplanet itself, but the star it revolves around. Scientists believe the star might not provide enough sunlight or heat towards the planet, meaning that life may not be possible. Nevertheless there have been other discoveries of exoplanets.
Kepler-186f is known not as Earth’s twin but as Earth’s cousin; it is about 10X bigger than our Earth. The discoveries of these new exoplanets suggest that life may be possible somewhere else, which is a huge step for human kind. This video provides information and facts about kepler-186f:
A quote from Johannes Kepler:
“The diversity of the phenomena nature is so great, and the treasures hidden in the heavens so rich, precisely in order that the human mind shall never be lacking in fresh nourishment.”
Kepler was amused by the discoveries that Earth provided, but outer space was his biggest source of amazement. Kepler was an extraordinary scientist because had an open mind; wonder was an important part of his scientific mind. This is what scientists need in order to stand out. He not only thought of the impossible but, most importantly, he stayed true to his scientific beliefs and that’s how scientists encounter new discoveries.
They fight for what they believe in.
Geocentrism vs Heliocentrism (revisited)
The following text is a comment that Arnaldo Franco, an AP Bio student, wrote about the post titled Science Club Post: Geocentrism vs Heliocentrism:
This is one of the few posts–if not the first–that contains no writing at all, and yet with only a GIF we are able to find a relation between two scientific discoveries and their processes: the correction of the solar system model and the discovery of DNA as the genetic material. For starters, Ptolemy’s model stated that the center of the universe was the Earth itself; we now know that this was an erroneous thought, just like thinking that proteins were the most important molecules of genetic inheritance due to the uncertainty of DNA. Actually, both reasons for these thoughts are similar: there was not enough evidence and no way to think that the Earth was not the center of the universe and that proteins were not the genetic material. It made sense to many because the sun and planets seemed to revolve around the Earth while proteins were present in almost every biological aspect.
However, there are always great minds that think alike. Both Copernicus and the Hershey-Chase duo knew that there was something wrong: there was a center to both ideas, but the centers that were accepted at the time just did not click. And so, as any scientist would do, these people tested their hypotheses with experiments–Copernicus with astronomical observation and the Hershey-Chase duo with laboratory procedures.
In the end, all of their experiments came to prove them right. For Copernicus’ case, the model of the solar system evolved from this—
As for the Hershey-Chase duo, their famous bacteria-phage experiment
came to show that the central figure of genetic material was indeed DNA. This way, many conflicts involving these two situations were solved, and the road to new scientific discoveries was paved.
P.S.: Do these look similar? If so, how?
If you answer the aforementioned question on the comment section below, your comment will be counted as double.
The Antibiotic Apocalypse (via Kurzgesagt)
Coloured transmission electron micrograph of a deadly cluster of methicillin-resistant staphylococcus aureus (MRSA) bacteria, which are resistant to antibiotics. Via
Aulonia hexagona–studied by Ernst Haeckel, with microscopes from the 18th century.
Using handcrafted microscopes, Antonie van Leeuwenhoek was the first to observe and describe microorganisms, which he called animacules. He was the first microbiologist. His skills as a lens manufacturer allowed him to observe a world that no one imagined possible. This happened during the 1670’s. His findings were not met with enthusiasm by his peers:
“Despite the initial success of Van Leeuwenhoek’s relationship with the Royal Society, this relationship was soon severely strained. In 1676, his credibility was questioned when he sent the Royal Society a copy of his first observations of microscopic single-celled organisms. Previously, the existence of single-celled organisms was entirely unknown. Thus, even with his established reputation with the Royal Society as a reliable observer, his observations of microscopic life were initially met with both skepticism and open ridicule. Eventually, in the face of Van Leeuwenhoek’s insistence, the Royal Society arranged for Alexander Petrie, minister to the English Reformed Church in Delft, Benedict Haan, at that time Lutheran minister at Delft, and Henrik Cordes, then Lutheran minister at the Hague, accompanied by Sir Robert Gordon and four others to determine whether it was in fact Van Leeuwenhoek’s ability to observe and reason clearly, or perhaps the Royal Society’s theories of life itself that might require reform. Finally in 1677  Van Leeuwenhoek’s observations were fully vindicated by the Royal Society.” — Via
Almost 350 years later we have been able to observe chemical reactions. We can see atoms with very powerful microscopes. But, does this mean that everyone has seen a cell? Like Leeuwenhoek before us; Science Club and Biology students were able to observe specimens using self-made microscopes at more or less the same magnification: between 50 and 200 times the original size. For this we used: 1) bobby pins, 2) lenses (taken from key chain laser pointers), 3) and a mobile device camera:
[H/T] for the photos to: Adriana, Gerardo & Gustavo (Science Club); Ana & Lorenzo (10-5); Sofía, Diego, Bianca, Christian & Andrea (10-4).
Science Club Post: Starstuff
Today we’ll talk about life, stars, music, art & cancer. I’ll play two songs. Then we’ll talk about them. Keep in mind that discussion is encouraged; in other words, disagreements are allowed. The first song is called Solstice. From the album Biophilia (Björk, 2011):
What is a star? Why did the ancients thought of them as musical entities, responsible for time, life & death? Now we know that Sol–our star–is not unique. And it can be the size of an atom, compared to other stars:
“Rho Cassiopeiae Sol VY Canis Majoris” by Anynobody – Own work by uploader.. Licensed under CC BY-SA 3.0 via Commons.
Right to left: VY Canis Majoris compared to Betelgeuse, Rho Cassiopeiae, the Pistol Star, and the Sun (too small to be visible in this thumbnail). The orbits of Jupiter and Neptune are also shown.
The second song is Blackstar. From David Bowie’s last album, Blackstar.
You might be asking yourselves, “What does this song has to do with science? Wasn’t David Bowie the artist that recently died a few days ago?” The aim of this Science Club is to develop scientific literacy, while observing that Science is an interdisciplinary human activity, that accounts for the whole spectrum of the human experience.
This said, I believe that David Robert Jones is a good vehicle to talk about Science. Besides him being one of the most influential artists that has ever existed–a quick Google search will provide a wealth of information on this matter–, he was also a huge Science nerd. His art–which included theater, music and film–was constantly mutating; as if he wanted to escape time itself (Could you think of two topics more related to Science and Art than time and mutations?).
Unfortunately, time and cells behaving badly–aka cancer–caught up to him. He was 69 years old: “A ‘black star’ is a proliferative breast lesion… described as long and thin with radiating radiolucent linear structures, which against a radiolucent fat background gives a black star or dark star appearance”.
Could we as a species win the war against cancer? Or is it something that will forever be a part of our genome? Will Biotechnology, Genetic Engineering, Gene Therapy, etc. cure cancer once and for all? If so, will the 21st century see our favorite artists, our loved ones–pets and family members alike–easily living beyond the age of 100, while looking as young as 60?
“CRISPR overview” by Nielsrca – Own work
“CRISPR has enormous potential application, including altering the germline of humans, animals and other organisms, and manipulating the genes of food crops. By delivering the Cas9 protein and appropriate guide RNAs into a cell, the organism’s genome can be cut at any desired location.CRISPRs have been used in concert with specific endonuclease enzymes for gene editing (adding, disrupting or changing the sequence of specific genes) and gene regulation in species throughout the tree of life. Ethical concerns have been expressed about this nascent biotechnology and the prospect of intentional gene editing by humans.”—Via
Time. Change. Mutations. Stars. Music.
What do these words have in common? How can talking about the largest star ever discovered, and a recently diseased rock star, lead to a discussion about Science?
To put it simply, we are starstuff. And by we, I mean you, me, a plant, a bacterium, etc. The elements of life–SPONCH–were cooked in the piths of ancient stars that spewed their dust on barren celestial bodies. Our planet was one of them. DNA, the language of life, is made from the aforementioned elements. This molecule can make copies of itself, and it can also change. These changes accumulate over billions of years, resulting in what we know as evolution. Sometimes, though, these mutations lead to what we know as cancer.
The very nature of our universe–which is chaotic, leading to disorder, according to entropy–is written in our cells; cells that have information in them, which can lead to cancer, making us face death. But, if enough of these changes are preserved, allowing for brains to get big, and hands develop thumbs, and weird and wonderful animal can get eyes, and those eyes can look at the night sky and hear music, then we have humans: animals aware of their existence; beings that know that one day they’ll return home–to the stars.
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