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
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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.

cancer-cell
Source

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.

best-doctors-established-by-doctors-used-all-around-the-world_image715_292
Source

 

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

calculator
Source

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
Source

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

New Research Suggests T-Rex is Unable to Hug AND Run

Cody Wolf

Most everyone has probably seen at least one installment of the Jurassic Park series. For those of you in the small population, the main plot of each movie is running away from a ferocious predator, usually a Tyrannosaurus Rex or some similar carnivorous dinosaur. The protagonist typically has the job of running, driving, or otherwise hiding to avoid being eaten alive.

Much like in the movies, the world of dinosaurs, at least in the research of dinosaurs, has thought that a T-Rex had the capability to run and catch fast prey.

Certain research articles suggest that dinosaurs like a T-Rex could run upwards to 50-60 kilometers per hour, or about 37 miles per hour(Paul, 1998). That’s pretty damn fast.

However, a recent study published in Peer J suggests that a T-Rex was actually incapable of running. In this particular study, running was defined as a gait that would be running without having both feet off of the ground at the same time, for example a horse gallop.

So with Velociraptors being the actual size of our modern turkey, and a T-Rex being unable to run, Jurassic Park may not be such a bad idea after all….Just kidding.  

But how in the world can a T-Rex be incapable of running?

The study that previously mentioned a high speed for the T-Rex suggested so due to their long and strong legs and specialized hip structure. This new study indicates that the legs of a T-Rex was actually the reason why they couldn’t run. In fact, their top speed reached about 12 mph.

How can two studies contradict each other when they are looking at the exact same information?

The answer of course, is in the details.

 

If you get a chance to read the Peer J article (which I always recommend), the introduction focuses on previous studies and the various mechanisms used to determine speed. While we don’t have enough time to go over all of them, I figured one may be beneficial to our readers.

Blog #2 T-Rex Can't Run

Gregory S. Paul published an article in 1998 suggesting that a T-Rex, with its specialized pelvis and leg structures being similar to modern tetrapods (four legged creatures), would be able to run at a reasonable pace. In case you are unfamiliar with the running patterns of different species (which I was until researching for this article), it’s important to note that a Rhinoceros, having a similar pelvic and leg structure is able to run at a reasonable pace. They are also quite large. Meanwhile, an elephant, which is more comparable in weight to a large T-Rex has a very different bone structure and is designed specifically for walking (see figure above). Elephants also have an ankle that prevents mobility (which differs from ours, a Rhino’s, and a T-Rex) and have a “flat” pelvis more similar to humans. In addition, examining the shape and orientation of the hip bones of Tyrannosaurus suggests that it is better suited to maintain the weight of its owner and can give it the ability of running.

Paul continues to discuss the correlations of femur bone length and speed where there appears to be a positive correlation between speed and the length of your thigh bone. He also goes on to discuss how bone shapes and certain structures can suggest how fast an animal is able to run.

He then focuses on other studies that suggest a T-Rex is unable to run. One in particular highlights the frailty of the leg bone, and how running could not be possible with the average weight of these gigantic creatures. Paul points out that the femur of a T-Rex may be able to support more weight than expected with these models, largely due to the thicker walls of the femur. He also mentioned discrepancies with the weight they predicted and the fossils analyzed have damage that would confound the data.

As I am sure you have noticed by now, there appears to be a slight conflict in regard to the speed of our beloved dinosaur.

So what does this new study have to say?

The Paul study we just previously mentioned, and other studies that conflict with it all have one thing in common. The research is focused only on bone morphology. All of these scientists spent time studying fossil structures and comparing them to bones of modern animals to “tweak out” clues of what life being a T-Rex was like.

But there is one aspect missing; the tissue.

Blog #2 T-Rex cant run pic 2

 

Bone alone cannot work to move our limbs. Soft tissues like muscles are needed to let our bodies twist and turn. And these soft tissues can have an impact of how we can move.

Recent advances in technology have given scientists the opportunity to estimate how muscles connected to bone, and how they affected movement in extinct species. This technique is what the Peer J article primarily utilizes.

The figure above shows an estimation of various muscle structures and limb interactions might have been like for the T-Rex. By scanning the bones and calculating joint positions and range of motion, muscle structure could then be predicted.

After this, computer models can be simulated. The output from the computer simulations were able to give a maximum velocity. The answer? Eh, about 8 meters per second. The data also calculated the estimated stride of the dinosaur (at its peak about 8 meters), and the Froude number (used to compare speeds with other animals) that suggested a T-Rex can only reach a walking stride.

Additional data that focuses on the change in kinetic and gravitational potential energy also confirms that a T-Rex could not gain the energy differences to achieve a running speed.

 

My Opinion

While I think this study makes valid points, and uses technology that can estimate at a much higher efficiency than previous analyses, there is still much to weed out. Unfortunately, soft tissue does not preserve well and we most likely will not find a perfectly preserved T-Rex. However as technology increases in power, and as we work to understand how other tissues might have impacted the movement of the large dinosaurs, much more is left to be discovered. I do think this study is moving in the right direction, and gives us more information than we had previously. If you are interested in either of the articles I discussed today, the links are below. Attached here is also a link to videos the scientists produced with their program of the simulated T-Rex walking!

If you have any questions, or comments about this article or others, please do not hesitate to email us directly at copernicuscalledblog@gmail.com. You can also reach us through social media, at our Facebook and Twitter pages.

 

Remember to always be curious, and stay mindful!

 

Sources:

1.May, Ashely. Sorry, ‘Jurassic Park’ fans: The T. rex couldn’t run, new research says. USA Today, July 19, 2017. https://www.usatoday.com/story/news/nation-now/2017/07/19/t-rex-couldnt-run-new-research-says/491122001/

2. Paul, Gregory. Limb Design, Function, and Running performance in Ostrich-Mimics and Tyrannosaurs. Gaia 15. December, 1998. http://gspauldino.com/GaiaLimbdesign.pdf

3. Sellers, William. Investigating the running abilities of Tyrannosaurus rex using stress-constrained multibody dynamic analysis. Peer J. July 18,2017. https://peerj.com/articles/3420/.

4. Title picture source- https://www.pinterest.com/pin/474003929501926665/

 

 

Cannibal Caterpillars

 Cody Wolf

Plants, like many other life forms, have to adapt in order to combat the many predators that threaten their existence. Several varieties of plants have developed various techniques to prevent becoming insect feces. A brief communication published in Nature Ecology & Evolution highlights a….. unique way plants evolve to fight their little enemies.

Although most people are fascinated by plants, many are unaware of just how amazing they really are. Many plants are able to halt insects and other potential predators by developing weapons to prevent or delay consumption.

There are several types of mechanisms plants have developed, but here are a two quick examples:

Mechanical defenses– Plants utilize this mechanism by producing thorns, needles, or perhaps other other specialized structures such as waxy resins to make feeding difficult. I am sure most of you are thinking of plants like a cactus, or perhaps a thorny rose bush. Mechanical defenses are the most common type of herbivore defenses among plants

Chemical Defenses– Another technique for defense is chemical warfare. Literally. Many plants have developed complicated chemicals with complicated names (such as terpenoids, phenolics, and nitrogen compounds like alkaloids, benzoxazinoids, and many others) that specialize in destroying/inhibiting potential threats.

These molecules work to either deter the insect from eating (like inhibiting enzymes important for digestion, making consumption extremely difficult) or can possibly destroy DNA repair mechanisms in these little buggers and render them completely helpless (aka death from weird insect cancer).

Obviously, some of these chemicals are dangerous to ingest, but there are quite a few that have inserted themselves into our everyday culture, and are relatively harmless. Caffeine, morphine, cocaine (okay, cocaine isn’t exactly harmless), and nicotine all fall into this category.

Biologists call these defense mechanisms Host-Plant-Resistance or HRP for short.

Note: There are other mechanisms of defense considered in the HRP category that we will not be discussing today.

So..let’s get back to the current article. Recently scientists at the University of Wisconsin in Madison have discovered a completely novel HRP in Solanum lycopersicum or better known as the tomato plant.

In short, when the plant was exposed to a chemical secreted normally by plants in distress (yes, they can indeed “warn each other” so to speak), and then exposed to an arch nemesis, the small mottled willow moth, they found that plants who were exposed to the warning chemical had overall more biomass compared to the control plants or those who were not “cued” as well.

Plant biomass is a fancy way biologists explain how badly plants were eaten. The research team measured biomass by clipping the visible part of the plant (aka without the roots) and weighed the shrubs to compare biomass. Plants who received the highest dose of the “warning” chemical had as much as 5x the biomass compared to the non treated plants.

Interesting……

This data suggests that those plants who get warned properly have a mechanism to ward of those evil moths. So what exactly did the plants do?`

In case you happened to miss the title, the team in Wisconsin determined that cannibalism was at play.

Further experimentation is used to highlight the relationship between plant and insect.  

Tomato plants were once again warned with the various concentrations of the chemical (or not at all), but this time they removed the leaves and fed them to the caterpillars. The team noticed that those insects fed with warned plants tended to eat dead larvae planted inside their containers sooner than the control plants.

It is important to mention at this point, that herbivores such as the lovely small mottled willow moth, will eventually eat their friends if food becomes scarce. It really is a moth-eat-moth world. But for the first time, scientists are actually seeing that plants have the possibility to trick the caterpillars into eating themselves even when they have an abundance of food.

Now, many of you may be wondering; “Why don’t all plants have a defense mechanism such as this?”

The short answer is that it’s not as easy as it seems.

Although plants may benefit from this chemical defense system, HRP mechanisms are extremely costly for vegetation. It takes a ton of energy for plants to make molecules strong enough to make fellow caterpillars look delicious. There are many plants on our planet that lack defense mechanisms. They may be potentially more exposed, but they are able to allocate energy to other important mechanisms (photosynthesis, water uptake, etc..)

As of right now specifics on the properties of these cannibal inducing molecules, and how they actually work towards influencing caterpillars to eat dead comrades is vague, at least from the news article published on Nature.com. It’s also worth mentioning that brief communications piece is not a full-fledged article. The information has not been peer reviewed and there is much left to do to piece out the details of how these species co-exist.

To wrap up: The article mentioned highlights a novel defense mechanism for plants that has previously been undiscovered by biologists. While this article is not the final word on the issue, it does create an interesting starting point for scientists to weed out specifics and potentially (a long time from now) morph this information and create potential pesticide treatments.

But let’s not get ahead of ourselves.

THANKS for reading our humble blog! Please feel free to email the crew at copernicuscalledblog@gmaill.com if you have any questions about this article, previous articles, or anything you may have heard in your own travels.

You can also follow us on Twitter(@CopernicusCalls) , and Facebook.

 

Remember to always be curious, and stay mindful!

 

Sources:

1. Castells,Laura. “Plants turn caterpillars into cannibals.” Nature News. 10, July, 2017. http://www.nature.com/news/plants-turn-caterpillars-into-cannibals-1.22281?WT.ec_id=NEWSDAILY-20170710
2. Orrock,Connelly, and Kitchen. “Induced defences in plants reduce herbivory by increasing cannibalism.”  Nature Ecology & Evolution 1, 1205–1207 (2017) .10,July, 2017.  doi:10.1038/s41559-017-0231-6.https://www.nature.com/articles/s41559-017-0231-6

3. Picture source- http://globe-views.com/dreams/caterpillar.html

 

Welcome to Copernicus Called!

Hello Everyone,

Welcome to the Copernicus Called Blog! We are very excited about this project.

A brief overview of what exactly this blog entails.

The purpose of our blog is to accentuate and discuss current scientific topics. With the steadily increasing amount of information published online, it becomes more challenging to keep up with the times. In the past few decades alone, the various fields of science have grown exponentially. Although it is great for our society, it can be a challenge for the population to stay aware and up to date. We at the Copernicus Called Blog are here to help.

We want to do everything in our power to help the curious. For those who are fascinated by physics, chemistry, biology, psychology, anthropology, and the many other fields of science, we hope to enlighten our audience as best we can with current scientific issues. Gene editing, the cognitive mind, space exploration, the discovery of new hominin species….. all of these will be covered in our blog.

We will also review science-related books and films, and highlight scientists, both past and present (I mean, we are named after the famous Nicolaus Copernicus).

Another aspect of our blog is to consider issues that are currently “topics of discussion” in today’s society. These topics include, but are not limited to, GMO’s, vaccinations, and  global climate change. We hope to highlight the controversial issues of these topics and discuss why the media is misrepresenting what current scientific methods actually suggest.

The Copernicus Crew will also be completely open to feedback from our viewers. If you see a confusing science story, or have questions on any story that you may hear , please do not hesitate to email us at our email copernicuscalledblog@gmail.com or contact us via Facebook, Twitter, or Tumblr.

Now, here is a tiny bit of information on the team behind the Copernicus Called Blog.


pictureCody Wolf: As a young kid, I was always fascinated with living creatures. 99% of my childhood was spent either crawling on the ground examining insects, destroying my back yard looking for dinosaurs, or looking up at the stars and wondering just how big our universe actually is. Once I was introduced to biology in high school, I became officially hooked. Learning about how cells and tissues work together so that we can walk, and talk intrigued me so much that I told myself that I had to learn as much as possible. I recently graduated with a Bachelor’s in Biology, and am now currently working towards my Master’s Degree where I study cancer cells and how they metastasize throughout the body. I hope to eventually earn a Ph.D and teach the next generation of scientists. 

Jane_BlogJane Neal: I’m currently attending school to earn a degree in English with an emphasis on writing creatively. As a kid, I hated reading and much preferred running around outside and pretending to be lost in big forests. When I was introduced to Harry Potter, I became obsessed and re-reading those books on repeat for three or four years (there were only four at the time). Before that, I never had the patience for any stories outside of animated movies and cartoons. I have a lot of opinions on books, movies, animation, and representation in all of the above. Once I earn my Bachelor’s degree, I plan on attending grad school for an MFA.

This blog will be saved in our About us section.