Book Review: The Bobiverse Trilogy by Dennis E. Taylor

Recently, I have come across a fiction series known as The Bobiverse Trilogy. As a fan of all things science, I could not resist reading the series. The first book in Bobiverse, We Are Legion, was recommended to me. I was not disappointed. Following is a quick review on the trilogy (no spoilers).

The series revolves around a quirky character known as Bob Johansson, who recently sold his software company for a small fortune. Now with the ability and funds to live a life of relaxation, Bob has little cares in the world.

Part of his new fortune is invested in cryogenics, and has chosen to be frozen upon his death. Unfortunately for Bob, his death occurred more recently than he hoped, getting hit by a car during a sci-fi conference.

Bob awakes a century later, to discover that his brain has been downloaded into a computer. As a corpsicle (term for cryogenically frozen individuals; mix between corpse and popsicle), he has no rights in the new world, and his new purpose is to operate AI probes for interstellar space discovery.

Bob’s probe however, is no ordinary space ship. His task is not only to seek out the mysteries of the universe, but also to generate additional ships during his travels using the resources he finds, and 3-D printers (self replicating).

These ships in turn would be operated by clones of Bob who would then search out other areas of the universe and repeat the process, thus having the potential to discover much more space one probe could do alone.

Of course, Bob is not the only space probe in development. Other countries are working diligently to launch a probe and claim galaxies before anyone else has a chance. And they will not hesitate to destroy Bob in the process.

All three books are immensely entertaining, and difficult to put down. The concept of the series should make any science fiction fan water at the mouth, and the character Bob is hard to dislike. Dennis E. Taylor is a grea

Not only are the book’s suspenseful and interesting, but are hilarious. The books are littered with sci-fi references that provide necessary comedic relief.

The last two books in the series revolve around Bob, his clones, and the shenanigans they get into while discovering the universe. All three books are worth reading, and if you are like me, you will be depressed there are only three in the series. 

I give the series as whole, 4.5 stars out of 5 and will recommend to anyone interested in science fiction.

Thank you for reading! Stay tuned for upcoming blogs, one of which will be discussing the technique of space exploration that was utilized in this fiction series (called Von Neumann Probes)

As always, you can reach us via email directly at copernicuscalledblog@gmail.com, or you can visit with us via Facebook, Twitter, or Tumblr.

Remember to always be curious and stay mindful!

 

Here is a link to Dennis E. Taylor’s website to learn more about him and other books he has written. 

Photo Source: https://www.space.com/23747-earth-radiation-belts-fast-electrons.html

 

 

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Chemistry: Learning a New Language

 

Many of us are intimidated by chemistry. For those of us who don’t look at chemistry journals everyday, or examine molecular structures very often,  it can be daunting trying to understand chemical structures. 

Nature recently published a quick guide to establishing consistent rules for drawing molecules and understanding what they mean. If you have a basic understanding for how chemist’s draw structures, you can see Nature’s recommendations for particular structures here.

For the rest of us, we have provided a guide to quickly and efficiently see a structure and understand what it is telling us.

 

Chemical Bonds:

I am sure that many of us are familiar with drawing basic bond structures. For example, when you need to draw a small molecule, you can connect two elements with a line, signifying a bond. For example; Carbon (C) bonding with Hydrogen (H) would look like C-H

If we want to draw a full molecule, we can show the bonding between the elements that would represent a molecule.

Methane, a very simple molecule, has one Carbon atom bound with four Hydrogen atoms, as shown below.  In the simplest of terms, a molecule can be described by a chemical equation. This simply lists what elements are in the molecule, and how many of them there are.  The chemical structure of methane is written as CH4 (meaning one Carbon atom, and four Hydrogen atoms). 

003-methane_formula
Source

The image above is a two-dimensional representation of what methane looks like. The drawing does give us more information that the chemical equation. We now know that that the four Hydrogen atoms each bind to Carbon, but what does the molecule look like in reality?

Chemist’s have spent a long time analyzing how molecules look in a 3-D space, and a more accurate representation of methane is below.

Methane-3d
Source

This representation of methane shows that two hydrogen atoms and the carbon atom are in the same plane as the article you are reading. However, two of the hydrogen atoms are out of plane. The black bar indicates that the hydrogen is sticking out of the page (or computer screen), and the dotted lines indicate that the hydrogen is sticking into the page. This is how chemists commonly draw a 3-D structure of molecules.

With modern advancements, software programs can now show molecules in a slightly different way.

molecule_methane_275

Very similar to the previous figure, we see a three dimensional structure of methane. These computer representations however, are not drawn by chemists, and can become extremely complicated for larger molecules that involve several atoms.

 

Basic Drawing:

Now that we understand how bond are normally represented, we can expand our knowledge of drawing molecules.

For simple molecules with a small amount of atoms, it is easy to draw representations the way we have already explored. However, when you need to draw a structure with several atoms, it can take a significant amount of time.

Take for example, octane. The chemical name for octane is C8H18.

octane
Source

While this structure is still relatively simple, it can take a little bit longer to draw.

Chemists have come up with a way to draw long chains of carbon and hydrogen atoms, by simply drawing zig-zag lines (officially dubbed bond-line structures).

octane kink

Each “kink” and “end” in the molecule, represents a Carbon atom. The lines just as before, still represent bonding. In this case we directly see the bonding between the eight Carbons of the molecule (in chemistry, long strings of Carbon are called the ‘Carbon backbone’)

As already mentioned, Carbon is able to make four bonds with other molecules. When drawing a zig-zag representation, the Hydrogen atoms are omitted from the drawing, even though they are present. For example, looking at the far left of the molecule, we see an end that represents carbon. We also see that this Carbon is bonding with another Carbon, that is represented by the first kink.

The Carbon at the end therefore has 3 more bonds to form. Therefore we can assume that 3 Hydrogen bonds are bound to the terminal Carbon molecule.

The Carbon atom located at the first kink has 2 bonds already formed; one with the terminal Carbon, and one with the Carbon in the next kink. There are still two more bonds for Carbon to form, and we can assume that hydrogen will be binding.

The zig-zag method is extremely common in chemistry journals and texts. While drawing octane by showing each atom may not take an abundant amount of time, with larger complex structures however, this can be a real lifesaver.

 

Complex Structures:

Chlorophyl20B
Source

The figure above (depicting chlorophyll, a molecule that gives leaves their green color) shows all of the rules we discussed above, with a few additives. Looking at the molecule, we see that there are 5 carbon ring structures (again each kink represents a Carbon atom unless replaced by another symbol) and some double bonds (representing two bonds between molecules). We also see a few more elements, such as Oxygen (O), Nitrogen (N), and Magnesium (Mg).

Understanding how chemist’s draw is crucial to understanding their research. Now that you have had a crash course in drawing chemical structures, you should be able to apply this knowledge in chemistry classes, and in reading chemistry papers.

If you have any questions on this topics, or other scientific topics, please feel free to comment below or email us directly at copernicuscalledblog@gmail.com. You can also reach us via social media on Facebook, Twitter, or Tumblr.

Note: The information above primarily came from my own experience in my undergraduate and graduate education. Listed below are links that can provide additional information and videos I find helpful. 

And as usual, remember to always be curious and be mindful!

Written by: Cody Wolf

Additional Sources:

  1. https://www.nature.com/articles/d41586-017-05898-6
  2. https://www.khanacademy.org/science/organic-chemistry/gen-chem-review/bond-line-structures/v/bond-line-structures-new
  3. https://socratic.org/organic-chemistry-1/ways-to-draw-and-represent-molecules/bond-line-notation
  4. https://www.wikihow.com/Draw-Organic-Molecules-in-Bond%E2%80%90Line-Notation
  5. https://www.youtube.com/watch?v=ohA3dMqDOqY
  6. Featured Image source: http://aschoonerofscience.com/drugs/mac-for-3d-molecular-visualisation-apple-makes-drug-design-sexy/attachment/scientist-drawing-molecule-structure/

Must-Read Books for Science Nerds & Newbies

03-woman-reading-book-lgn

For those of you who are extremely interested in science and science related topics, non-fiction books can be a great way to inform yourself of a particular topic, without having to read complicated papers.

Here are a few quick selections we think our fans might enjoy. Periodically, we will do book reviews on non-fiction (or fiction books) and will update our list as often as we can.

Hidden Figures by Margot Lee Shetterly

hidden figures

Most should be familiar with this title, as it was transformed into a spectacular Hollywood hit that featured black women as scientists and math geniuses rather than slaves or maids.

Unlike the film, the book follows four (not three) ‘human computers,’ how they used their intellect to benefit not just the country, but their own lives as well. They were living in the Jim Crow era and trying to break both racial and gender barriers. While there is still racism and sexism in the workplace today, the tenacity and brilliance of these seldom-recognized women is truly inspiring.

 

Sally Ride: America’s First Woman in Space by Lynn Sherr

sally-ride

A lot of people know that Sally Ride was the first woman in space, but are we really taught much else about her? I definitely wasn’t.

This biography gives the reader a much closer look at her as a person, rather than a neat factoid for trivia.  Not only did she go to space, but she helped investigate the failures of NASA that caused both the Challenger and Columbia tragedies. Sherr has interviewed family members, including her partner, as well as friends and co-workers to give a much more in-depth look at the first American woman to go to outer space.

 

The Glass Universe: How the Ladies of Harvard University Took the Measure of the Stars by Dava Sobel

1015870_1_112816-glass-universe_standard

If Rise of the Rocket Girls is a good place for beginners to start, The Glass Universe is recommended for readers who enjoy reading material that is more dense (or a little dry).

It explores the lives of women employed as ‘calculators’ who interpreted the observations made by male astronomers at the Harvard College Observatory. Through advancing technology and their own interest in studying the stars, they made ground-breaking discoveries about the stars.

 

Chasing Space: An Astronaut’s Story of Grit, Grace, and Second Chances by Leland Melvin

Chasing Space

This is a memoir about an astronaut with quite the career history. Previously a wide receiver, Melvin faced many challenges to make it to space, including an injury that made him deaf. Through his perseverance in continuing to work with NASA and eventually made it to space! Through his vast experience in many different areas, from chemistry to football, he recounts how he was able to succeed.

 

 

An Astronaut’s Guide to Life On Earth by Chris Hadfield

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You might be familiar with this astronaut without realizing it. He went viral with his video of singing ‘Space Oddity’ while literally floating in space.

For deeper insight into the training he underwent and a lot of unbelievable stories, Hadfield imparts the wisdom he learned from becoming an astronaut. Even without accomplishing the same daring feats he has, you will learn the mindset it takes to do so and can apply that to life as an Earthling, for the better.

 

Rise of the Rocket Girls by Nathalia Holt

Holt_RiseoftheRocketGirls

This is a good place to start for those who aren’t heavy readers, in science or otherwise. Similar to Hidden Figures, this book looks at the women who made it possible for America to send someone to space and the moon.

The women are explored more broadly, rather than focusing on a select few. The author includes quite a bit of social and personal details about the women, such as their social life and clothing styles, details which might make this an easier transition for fiction readers. Half of those who read this book felt it was dramatic and patronizing towards the women while others felt they were well-characterized.

Thanks for reading!

If you have any questions, comments, or even book suggestions, please do not hesitate to email us directly at copernicuscalledblog@gmail.com. you can also reach us on Facebook, Twitter, and Tumblr.

 

Remember to always be curious and stay mindful!

Written By: Jane Neal 

Homo Naledi, The New Ancestor

H. naledi cover photo
Source

After the relatively recent discovery of Homo naledi, much has been released about their habits and lifestyle.

For those of you that have not heard about this wonderful fossil excavation, here is some background.

In 2015, a remarkable collection of fossils were found in South Africa(1). These bones were quickly categorized as human-like. While several other human-like species have been discovered (Homo habilis, Homo erectus, just to name a few),non resembled the bone structure of the new specimens. Thus, these bones have been classified as a new addition to our ancestral map.

Cross-section_of_the_Rising_Star_Cave_system_Dinaledi_Chamber.svg
Diagram of Rising Star cave system and Dinaledi Chamber where 15 Homo naledi specimens were discovered. Source

They were given the name Homo naledi. Homo refers to the genus of the species (which we are apart of) and naledi translates to “star” in english (named after the cave where they were found). The unique quality of these fossils was not just the knowledge of a new species, but also what we have learned from them. This particular excavation gave scientists a unique understanding of the behavior of the species. Within the Rising Star cave network, 15 different specimens were located in the same cave, making it the largest assembly of human like fossils discovered in Africa (1).

Note: The original study, located here, discusses the specifics of the fossils found. If you wish to learn more about cranial size, hand shape, and how they compare to other Homo and non-Homo descendents, I recommend reading the article. If you are curious on how H. naledi fits into the current model of human ancestry, stay tuned. This whole topic will be covered in a future blog.

Part of the mystery of H. naledi is the placement of the bodies. Having 15 of the same species within such a small cave structure begs the question of how they got there in the first place.

This has been a hot topic since the discovery, and currently there are two bodies of thought:

The first, suggests that the bodies of the dead were placed as a sort of burial (although the bodies were not actually buried). There are no other fossil types within the cave (except a lone owl), which eliminates the hypothesis of a predator’s cave, and no signs of water or dirt to suggest body movement through river systems or mud slides. Dr. John D. Hawks, a prominent anthropologists, suggests that the bodies were indeed placed deliberately (5).

Another school of thought, related to the first, believes that body placement may have been related to a ritualist demonstration (in this case, not a religious ritual). This hypothesis however, has been placed under scrutiny. At the time of this blog post, no tools or other materials suggest a ritual of any kind, and no evidence on fossils suggest violent deaths that may be associated with rituals (6).

In addition to learning about burial rituals, there is also much left to learn from H naledi as far as their lifestyle, i.e. their diet.

Since the stomach of naledi has been decomposed for an extremely long period of time, we can gather much information from their teeth.

It may seem weird, but teeth have been used extensively to gain insight on the lifestyle of extinct species. A recent study has been released doing just that with H. naledi.

Scientists in the UK first looked at the naledi teeth, and immediately discovered a unique quality; they were chipped. But this didn’t occur from damage over time, rather the chipping occurred before the specimens died (called antemortem)(2).

TEETH
Example of  the “chipped” teeth of H. naledi. Source

What makes this unique is that this has never been seen in other fossils of ancestral species, or even in primate species. 44% of the teeth recovered had damage to the enamel occurring before death. These rates by far surpass other teeth examined from our lineage.(2)

Interestingly, scientists have determined that the chipping has occurred due to their diet. By determining which type of teeth have the most chips (incisors, premolars, etc), the researchers were able to infer that a high “grit” diet from roots or tubers that were commonly eaten.(2,4)

While it may not be “front page news” on what H. naledi ate specifically, it does provide another piece to the puzzle. As we continue to learn and discover more about these extinct ancestors, we will be able answer other questions related to evolution and the development of life on our planet.

As always, thank you for reading. If you have questions or comments, please email us directly at copernicuscalledblog@gmail.com. You can also reach us on Facebook, Twitter, and Tumblr.

 

Remember to always be curious, and stay mindful!

Written By: Cody Wolf

Sources

  1. Berger, Lee R. Homo naledi , a new species of the genus Homo from the Dinaledi Chamber, South Africa. eLife, eLife 2015;4:e09560 DOI: 10.7554/eLife.09560  https://elifesciences.org/articles/09560.
  2. Towle, Ian. Behavioral Inferences from the high levels of dental chipping in Homo naledi. American Journal of Physical Anthropology. 2016. DOI: 10.1002/ajpa.23250. http://onlinelibrary.wiley.com/doi/10.1002/ajpa.23250/abstract;jsessionid=C151DCA7FF6D8C04BBBD29023969E3F8.f02t02
  3. https://en.wikipedia.org/wiki/File:Cross-section_of_the_Rising_Star_Cave_system_Dinaledi_Chamber.svg
  4. Belgastro, Giovanna. Continuity or discontinuity of the life-style in central Italy during the Roman imperial age-early middle ages transition: Diet, health, and behavior. American Journal of Physical Anthropology. 2006. DOI: 10.1002/ajpa.20530.http://onlinelibrary.wiley.com/doi/10.1002/ajpa.20530/abstract
  5. Drake, Nadia (15 September 2015). Mystery Lingers Over Ritual Behavior of New Human Ancestor. National Geographic News.http://news.nationalgeographic.com/2015/09/150915-humans-death-burial-anthropology-Homo-naledi/
  6. Ghosh, Pallab (10 September 2015). New human-like species discovered in S Africa. BBC News. http://www.bbc.com/news/science-environment-34192447

Life on Titan? Farewell to Cassini

Cody Wolf

Researchers have recently discovered evidence for a molecule that may indicate potential life on Saturn’s moon; Titan.

There has been immense interest in regard to Titan. With it being the largest of Saturn’s 62 moons, and a nitrogen based atmosphere, scientists have been trying to understand it further. Part of our interest has stemmed from the famous Cassini orbital that has been orbiting around Saturn gathering data about the planet and its many moons.

Now, an article published in Science Advances further elucidates the potential this moon has on fostering alien life.

Life  would be challenging…well impossible….living on Titan due to its extremely cold temperature. By cold we are talking about -178 degrees Celsius ( -350 Fahrenheit). At this temperature, surface water is frozen. However, Titan happens to have another liquid source that makes up its lakes and seas; methane.

Methane on Earth cannot exactly support life, considering it is gaseous and highly flammable. With the freezing temperatures on the moon however, methane is present in liquid form and acts similar to what water does here on Earth.

These liquid methane pools provide an excellent source for other other molecules, even ones that might promote life formation.

 

Previous studies have suggested that vinyl cyanide (also known as acrylonitrile) might be present on Titan.

This molecule is has been shown through computer models to hold potential for forming membrane-like spheres able to protect molecules….like DNA for example. These membranes are important for early life, due to their capabilities of protecting and preserving genetic information and forming barriers to provide selective entrance and exit of molecules.

saturn 4
Source

Studies have shown that vinyl cyanide is also present in the “methane seas” to create millions of cell like bubbles per centimeter.

This data is very exciting, however it is still far away from confirming life on other planets.

And while we have learned a substantial amount about Titan, there is much left to learn.

 

How did scientists discover all of this information?

A good portion of the discoveries were made by a beautiful piece of equipment; the Cassini Orbiter.

In 1997, Cassini was launched from Earth, destined to reveal the great mysteries of our outer solar system. One of the major targets was, of course, Saturn. Cassini’s first picture of the planet was October 31st 2002, at approximately 177 million miles away (about twice the distance of the Earth from the Sun).

Saturn 1
This is not the first picture Cassini took of Saturn. Source: https://saturn.jpl.nasa.gov/science/overview/caption

Cassini then spent the next 16 years evaluating Saturn extensively. From examining the  famous ring structures, analyzing the surface of Titan, and even discovering two previously unknown moons, Cassini has enlightened and excited the human population with data and beautiful photographs.

saturn 2
Surface of Titan. Taken in 2005 Source:  https://www.jpl.nasa.gov/spaceimages/details.php?id=PIA08113

 

saturn 3
Picture of Earth taken from Saturn. The arrow indicates Earth Source: https://saturn.jpl.nasa.gov/resources/5868/

A major part of Cassini’s contribution to science was not just snapping amazing photographs, but also to analyze the atmospheres and states of Saturn and its moons. It is partially from Cassini that we can thank the research done in the article mentioned above.

Unfortunately however, all good things must come to an end. After 20 years, Cassini is (as I am typing this blog) beginning its descent towards Saturn for its final mission. Eventually it will vaporize and be destroyed by Saturn’s atmosphere. While it goes down, it will collect and transmit every ounce of data it can about the atmosphere and the innermost rings of Saturn. The spacecraft will also degrade in such a way that it will not damage any moons that could harness life (Titan for example).

We at Copernicus Called would personally like to thank the craft Cassini for everything it has done for science and science communication. It is through these wonderful experiments that we understand just how expansive the universe is, and how much the human population has left to learn. We highly recommend that you visit NASA’s website and see all of the incredible accomplishments scientists have made with Cassini and other spacecrafts.  

If you have any questions, as always, do not hesitate to email us directly at copernicuscalledblog@gmail.com. You can also contact us through Facebook, Twitter, and Tumblr.

 

Remember to always be curious, and stay mindful!

 

Sources:

  1. Palmer, Maureen Y. ALMA detection and astrobiological potential of vinyl cyanide on Titan. Sciences Advances. 2017; 3:e170002. http://advances.sciencemag.org/content/3/7/e1700022
  2. Saey, Tina Hesman. Potential ingredient for alien life found on Titan. ScienceNews. July 28, 2017. https://www.sciencenews.org/article/potential-ingredient-alien-life-found-titan
  3. https://saturn.jpl.nasa.gov/the-journey/timeline/#launch-from-cape-canaveral
  4. Cover photograph-https://saturn.jpl.nasa.gov/

A Quick Guide: How to Read A Scientific Paper

Cody Wolf

One major aspect to truly understanding science news is reading the articles the news items are derived from. This may be daunting for those who aren’t used to reading scientific papers, so we at Copernicus Called decided to post a guide on the best way to read scientific papers.

Before we get started, we need to introduce exactly what a scientific paper is and their relevance.

Scientific papers are the main way scientists convey their research, not only to colleagues  across the world, but also to the general public. With that in mind, research papers are usually very dense with terminology and complex research methods that can be quite a challenge for someone outside of the field of study.

Most papers are also not submitted in magazines you find at your local doctor’s office. Papers are typically submitted by the researcher (usually for a fee), peer-reviewed for quality assurance by colleagues in the same field, and then if deemed worthy, are accepted and published in a journal specifically for research articles. For example, someone who researches plant cells and how they interact to make complex tissue structures would likely seek a journal that is well known for publishing articles on plant cells or plant development.

In addition to picking the right type of journal, researchers also prefer to publish in journals that are considered high quality. If you spend years working on research that is long and complicated, you do not want it to be placed in a journal that is hardly read by scientists in your field.

Therefore, journals themselves are usually given a number that correlates with the “quality” of the journal and the impact this journal has on the scientific or general population (i.e. how many people read it). This number is called an impact factor.

To give you a little context,  journals Nature and Science currently have the highest impact factors (40[2] and 37[3] respectively). Most journals however fall into a much lower range (my experience is to say 5-10 impact factor is within a decent range). So if you happen to be a researcher, receiving a submission in Nature is like winning an olympic gold medal.

The impact factor can also indicate the value of research that must be done in order to be included in the journal. If a researcher does low quality work, and does not prove the point they are trying to make with their research accurately, it will most likely not be in a high impact factor journal. This however does not always mean that the research is fantastic in Nature, but crappy in an impact factor journal of 3. Most researchers in universities or other learning institutions are judged off of the work they have done and the impact factor journals they have had paper submissions in. If you have done high quality of work that is in a decent impact factor journal, you likely get to keep your job. However, if you are constantly submitting to impact factors of 1 or 2 (or not publishing papers at all) then your time teaching at an institution may be short. In the world of academics, we call this publish or perish.

It is also important to note, that papers typically published in Nature and Science are groundbreaking in nature, and tend to answer scientific questions that have been asked for a long time.

 

Types of Scientific Papers

Most people who discuss scientific papers (especially media outlets) refer specifically to primary articles. These articles include research that the scientists and their team have worked on and collected new and unique data in their lab. Primary articles discover new things in science and provide us with new insights than what we had previously. These articles typically have several authors, and most show collaboration efforts from multiple labs, even spanning across countries.

The other main type are called review articles. These articles typically have no “new” data, but rather discuss and combine several primary articles on a specific topic. These articles are typically written by a few people within the same lab, and are a good way to inform readers of  current literature that focuses on a specific topic.

Note: While these are the most common types of scientific papers, there are other versions that we will not discuss today.

 

Parts of Scientific Papers

Now that we have talked about what scientific papers are, and how they differ from regular news items, we are going to go through the individual areas of a scientific paper. We will present the areas in the order in which they typically appear, but they may not be in the same order that you want to read each piece of the paper.

 

Title & Author List

Picture 1
Typical layout of a title and author page (source below)

 

This may seem obvious, but the very first thing you should read is the title of the paper. If you are researching a specific topic, the title will give you clues on whether or not this paper is relevant to your literature search.

If you are reading your paper due to a news item, or were otherwise instructed to read the specific article, then the title will tell you what you are about to get into. I recommend that if you are new to reading scientific articles,  take a moment to read the title very thoroughly. If you do not know understand a word or two in the title, look them up. This will give you some insight to what specifically the paper is focusing on.

Additionally, the author list will provide you with all the members of the team, and which institution they work in. The first author is considered to have contributed the most work and is likely that scientists main subject of interest. This person may be an undergraduate student, graduate student or a post-doc. The last author is usually a PI (principal investigator). This person usually is a tenured professor at an institution and most likely is the mentor for the first author. When looking at authors, the first and last authors are usually the most relevant.

Abstract

Scientists do not care about plot twists. We do not make you wait for our grandiose conclusions. In fact, the very first paragraph of the paper, the abstract, gives away everything that a research team did over the project and the conclusions that they can draw from it. This may seem weird to many of you, but for scientists who need to read  hundreds of papers in order to work on their own project, this provides a quick way for them to favorite articles that are necessary for their research, or pass to read articles more relevant.

For those of you who are not trying to read hundreds of papers for your Ph.D dissertation, this paragraph may provide you with some interesting information, but it will likely be too dense with terminology and data analysis to completely understand. This section can really be skipped for new article readers. Everything in the abstract will be discussed in the rest of the paper.

Introduction

This section may also be described as background. If you are new to the topic, I recommend that you begin with this section. It is here that you will learn acronyms and important terms that will likely be discussed throughout the whole paper. The introduction will also provide knowledge on the topic as a whole, and will likely highlight the “hole” missing in the scientific body of knowledge (and the paper usually tries to fill that hole). The intro will give you an idea of why the researchers decided to pursue this particular project.

If you are an experienced reader and are familiar with the topic, glazing over the introduction for any new information is recommended, but all in all may not need to be read in depth.

Materials & Methods

As you probably guessed, the methods section focuses on the experiments (sometimes called assays) that were performed in the research. A procedure for the experiments is typically discussed, as well as a list of the materials purchased. High quality papers usually list explicitly what was done and what reagents or tools were used. I recommend that this section saved for last. Once you have gone through the data and have developed specific questions on how a particular experiment is achieved, you should then refer to this section as a reference. You will also find in this section how the scientist performed the data analysis that is crucial for the next section.

Results

Picture 3
Example of a figure in a scientific article (source below)

The results section is arguably the most important in the paper, and thus is typically the largest.  Within this section you will find results from the experiments performed and it is here where the scientists will tell you a story. Most papers have several figures (ranges from maybe 1-2 at the bare minimum to upwards of maybe 10-12) each with several components.

The example above gives you an idea on the typical size, layout, and components of a scientific figure. Most of them will have some pictures (of cells under special microscopes, diagrams, etc…) and then you will typically see a variety of graphs that are actual data. The graphs will likely show a trend that fits with the scientists narrative and supports their hypothesis. Each figure also has a legend explaining what every piece of data was collected from (what experiment was performed) and now many times an experiment was replicated.

In science, one experiment performed once is not enough to prove a trend. For research paper, an experiment must be replicated at least 3 times before it can be accepted (sometimes shown as an n=3, or n=x; x being the number of time the experiment has been replicated). If the results show a significant difference between the control group (the group that has been untreated) and the treated group, the graph will usually be marked by a star. This star in most cases means the p value is below 0.05, indicating that the trend we are seeing is not occurring by random chance.

I personally recommend that you spend the most time in this section. Look at every graph and every figure. Read the figure legends to understand what experiments are being performed. If you do not understand the experiment, then you can look it up online or read the methods section.

As you read through how the scientists are explaining the data and why they decided to follow the path they were on during the research, ask yourself questions. Is what they are saying make sense? Are their claims matching up with the data? Is there something they are missing that they should have done? It is in this section that you can judge whether a paper is legitimate or not. If the data does not make any sense, or does not seem to match up with their claim, something is likely wrong. Although researchers specifically write to remove bias from their work (that’s why these aren’t entertaining) there will most likely be some sort of over exaggeration. Make judgments from yourself. Just because it is a scientific paper does not mean that it is flawless. If you are uncertain whether or not you can trust the article, I recommend trying to read other articles discussing the same topic, and doing a search on Google to see what is known, and what remains to be discovered with the topic.

Discussion

The discussion is a section that I typically read after the results. Once you have looked at the data for yourself and determined if the research is legitimate or not, you can move on to the discussion and see what more they have to say.

In this part of the paper, a summary of the most important figures is typically common. This is where the researchers can truly extrapolate from their data and determine what needs to be done further within their specific field.

Most of the time, scientists will discuss future directions for the project and any pitfalls that may have occurred during the whole project. Once you have finished this section, you can re-read anything that may not make sense, and determine if the scientists proved their hypothesis to be true.

References

If you are interested in the topic discussed, or just want to learn more, browsing the references for articles that may relevant to you is not a bad idea. Typically there can be up to a hundred or more articles. Reading all of them is probably unnecessary, but there are likely a few gems to enhance your knowledge, including previous work done by the first and last authors.

Other tips: Here are a few more tips for reading scientific papers in general

 

  1. Read and re-read: It is likely that you will not understand every piece of data and comprehend every step the researchers took in their work. True understanding can only come from reading multiple times
  2. Highlight important items: highlight what the scientists main points are in the text. This will help you take a step back and see the big picture for the research.
  3. Google: As I have already mentioned, you will probably have to Google a few terms. Don’t be afraid to. Even though you may not be experienced now, if you take the time to learn the language and the purpose for experiments; it will help you understand the results that much better.
  4. Don’t be afraid to criticize: If you feel like the paper is exaggerating, don’t be afraid to think so. Unfortunately, some studies are just plain wrong. When this happens, look up the authors and the journal to determine if it there have been discrepancies in the past. If it turns out to be true, then the paper is unreliable.
  5. Read review articles: For research topics new to you, it may be beneficial to read a review article on the subject. These provide great background information and will give you a little history on what scientists have done previously. It’s not uncommon for topics to evolve and change over the years. Informing yourself of what is known, and what isn’t, is never a bad option.
  6. Read other articles written by the author: Most of the time, authors are continuously releasing articles on the same overall topic, except with new information (for example someone who focuses on the growth and reproductive cycle of sagebrush most likely has already written previous studies on this topic.

 

Most of these tips were derived from my personal experience as a scientists and a student. However, some of the resources below are worth mentioning. If you would like other opinions on how to read scientific papers, please follow the links below.

Additional Resources

  1. http://www.huffingtonpost.com/jennifer-raff/how-to-read-and-understand-a-scientific-paper_b_5501628.html
  2. http://www.sciencemag.org/careers/2016/03/how-seriously-read-scientific-paper

 

Works Cited

  1. Segonzac C, Newman TE, Choi S, Jayaraman J, Choi DS, Jung GY, Cho H, Lee YK and Sohn KH (2017) A Conserved EAR Motif Is Required for Avirulence and Stability of the Ralstonia solanacearum Effector PopP2 In Planta. Front. Plant Sci. 8:1330. doi: 10.3389/fpls.2017.01330http://journal.frontiersin.org/article/10.3389/fpls.2017.01330/full
  2. http://www.nature.com/nature/about/index.html -Nature Impact Factor.
  3. https://en.wikipedia.org/wiki/Science_(journal)- Science Impact Factor.
  4. Title photo- https://www.sciencenewsforstudents.org/article/study-drugs-can-be-dangerous

To Treat or Not to Treat; That is the Question – At Least for Prostate Cancer

Cody Wolf

I’m sure that many of our readers know (or at least you will in a few moments) that I am a cancer researcher. It of course makes sense then that one of my first blog posts is on cancer. I also happen to study prostate cancer. This article came across my desk recently and I could not help but share it with the Copernicus Called Family.

So….Here Goes.

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Cancer is by far one of the largest threats that currently looming over societies head.Prostate cancer is especially worrisome, being the third leading cause of cancer deaths in the United States for males; behind lung and colorectal (colon) cancer [1]

That being said, being diagnosed with prostate cancer does not necessarily indicate a painful or tragic death. In fact, a recent article in The New England Journal of Medicine sought out to study exactly when treatments are necessary for prostate cancer patients……and when watching without conventional treatment may be the best option.

Although prostate cancer still is high on the list for mortality in men, many patients are diagnosed at a very early stage. Currently Stage 1 and stage 2 prostate cancer (tumor contained within the prostate, no lymph node metastasis, no metastasis to other organs) has a 5 year survival rate of 99%. That’s pretty great. And  later stages of prostate cancer have a high survival rate (nearly 100%) even though the cancer has potentially spread to nearby areas (regional lymph nodes)

So, I mean, this is all pretty good news right? The only downside is of course cancer that has spread to distant areas of the body (brain, liver, bones), which has a survival rate of 29%. Not the best. [2]

But, fortunately many men who are diagnosed usually fall into the Stage 1 to Stage 2 category. About 4 out of 5 cases actually. [2]

Therefore, medical doctors are faced with the question on how to treat early stage prostate cancer.

Back in the good ole’ days, prostate cancer was considered a major issue, even at Stage 1.

Men would get checked, blood and pee would be analyzed, and then prostates would be cut. Pretty routine procedure that did indeed prevent cancer. The official term is radical prostatectomy (removing the whole prostate and neighboring tissues). There are various methods for surgery. If you would like to read more about the subject, please follow this link.

But…there’s a small problem. Side effects from a radical prostatectomy aren’t the best. These include incontinence (leaking of urine from the urethra) and incompetence (do I need to explain this one?). For a man potentially in his 40’s, the downsides of surgery are just a little bit daunting.

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So what can physicians do?

The best way to determine whether or not surgery should be performed regardless of the consequences, is to study whether or not it has a major effect on survival for patients.

Turns out… for the early stages of prostate cancer, we may want to hold the scalpel.

The study previously mentioned supports the hypothesis that a radical prostatectomy is just a bit overkill.

At this time it’s important to note that this study is not the only one to propose this idea. In fact, the authors of this current study published something similar four years ago.

And there have been a few other sources that favor this hypothesis.

Let’s get into this study.

731 lucky patients with localized prostate cancer were divided into 2 groups. One group received radical prostatectomy surgery, and the other received nothing but observation (medical doctors call this active surveillance or watchful waiting).

Now you may be wondering how long the study lasted. 5 years? 10 years? Well in reality, it was more like 15-16 years. Patients were randomly assigned from 1994-2002 (do not confuse this with the length of the study, this is how long they were selecting patients), and then all patients were observed until August of 2014. Quite a long time.

The Data

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Well, after the study, 64% of the men had died. This may sound devastating, but we must remember that the majority of males diagnosed with prostate cancer are older, and this study has the average age at 67 years. Not spring chickens.

The researchers address this by determining the “all cause mortality” or in layman’s terms, dying from anything. What they found is that there was no significant difference in those who received treatment, and those who did not. Note: Statistical significance is extremely important in research, and this will be discussed more thoroughly in another blog.

Another powerful piece of data is the comparison of those who died due to prostate cancer rather than non-related deaths. Death by cancer occurred in 69 men, or 9.4% of those in the study. 65 deaths were attributed to prostate cancer and 4 to treatment complications.

Death due to prostate cancer occurred in 7.4% of those in the surgery group, and 11.4% in the observation group. Again the differences between the two groups are not significantly different.

Another aspect of this study that is interesting, is what the patients thought of different treatment conditions. Subjects were asked to fill out a Medical Outcomes Study 12-Item Short-Form General Health Survey (from what I can gather it’s just a fancy name for a survey to asks how patients feel about their treatment).

Overall, worry about health did not differ between groups. But, the interesting fact is that men who received surgery reported more complications due to prostate cancer or treatment, physical discomfort, and limitations to daily activities. Incontinence also was an issue with those who underwent surgery, and erectile dysfunction occurred in a significant portion of those who visited the surgeon’s table.

There is a touch more to the study, but we will not cover those in the blog today. If you are interested, and want learn more, follow the link to the study.

Now, so far I have talked about this study as if it’s the finality of the topic, but really it’s not.

One of the main issues I have with this study is the statistical significance. As mentioned above, we will discuss this in much more detail at a later time, but I can’t help but get this off of my chest now.

Officially, a set of data is considered significant if the p value is at or below 0.05. In our context, this number would suggest that the probability that those treated with surgery and those not will have different outcomes (i.e beneficial to have surgery). This suggests that there is a 5% chance that the surgery is actually beneficial to patients.

If the p value is higher than 0.05, let’s just take a hypothetical number, 0.45. This hypothetical value suggests that 45% chance that the surgery is beneficial to patients.  So at that point, is it worth having the surgery, if it means that your sexual function is eliminated, or if you are forced to wear a pad due to a leaky urethra?

The p values for the study are just barely over the line of significance. For the overall mortality rates, and the prostate related deaths examined in this study, the p values were 0.06. So 6% of patients who receive treatment will have no difference in outcome based off their treatments.

Technically… by standards set, 0.06 is not a statistical significance. But it’s pretty damn close.

Let me be as clear as I can. I am not trying to change the way science works, or how statisticians evaluate data, and I am not trying to knock what the study suggests here.

But I do want our readers to be thinking. “Is this study really the final word?” I will let you, as the reader make the final decision.

doctor-old man
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That being said, I do not oppose the active surveillance treatment method. I think it’s a perfectly valid method for prostate cancer patients who are in the early stages. As more studies are performed, researchers and clinicians will be able to make the best decisions for their patients.

Thank you all for reading! I have just a few notes to add to today’s blog:

 

If you happen to be reading this, and you have prostate cancer or have recently been diagnosed, please do not take this blog post as medical advice. I will always recommend that you speak to your medical team and discuss the best options for your specific case. If you are seeking answers to questions, I would ask that you visit cancer.org. This website run by the American Cancer Society has fantastic information on all types of cancers (and was a great source for me writing this blog) and can direct you to assistance you may need.

 

And finally, since I am already on my soap box, I would like to remind everyone who is at the age for testing (whether it be prostate, breast, colorectal, or any other type) of various cancers. Please go. It is worth it. A small amount of discomfort now can prevent a lifetime of suffering. Testing is the best way to detect cancer early. 

 

As always, questions can be submitted to our email account copernicuscalledblog@gmail.com, on Facebook (CopernicusCalled), or Twitter (@CopernicusCalled).

 

Remember to always be curious, and stay mindful! 

Works Cited

  1. “Key Statistics for Prostate Cancer.” American Cancer Society. January, 5th, 2017 https://www.cancer.org/cancer/prostate-cancer/about/key-statistics.html
  2. “Survival Rates for Prostate Cancer.” American Cancer Society. May 30th, 2017. https://www.cancer.org/cancer/prostate-cancer/detection-diagnosis-staging/survival-rates.html
  3. “Watchful Waiting or Active Surveillance for Prostate Cancer.” American Cancer Society. March 11th, 2016. https://www.cancer.org/cancer/prostate-cancer/treating/watchful-waiting.html
  4. “Surgery for Prostate Cancer.” American Cancer Society. March 11th, 2016. https://www.cancer.org/cancer/prostate-cancer/treating/surgery.html
  5. Wilt TJ, Jones KM, Barry MJ, Andriole GL, Culkin D, Wheeler T, Aronson WJ, Brawer MK. “Follow-up of Prostatectomy versus Observation for Early Prostate Cancer.” New England Journal of Medicine. 377:132-142. July 13 2017. DOI:10.1056/NEJMoa1615869. http://www.nejm.org/doi/full/10.1056/NEJMoa1615869
  6. Featured image credit-http://www.globalpatientservice.com/prosatate-cancer.php