Tag Archives: science

Evolution Can Be More Random Than You Think

Posted on December 2, 2015 by julia | Leave a comment

Charles Darwin’s Origin of Species postulated that evolution takes a directed approach toward increasing fitness. A recent discovery suggests that evolution doesn’t always need to have a direction. Dr. Matthew Pennell’s findings suggest that evolution on a chromosomal level can have a high degree of randomness.

Dr. Matthew Pennell, an evolutionary biologist specializing in Computational Biology at the University of British Columbia, recently wrote a paper that gives more insight on evolution, entitled Y-Fuse? Sex Chromosome Fusions in Fishes and Reptiles. In this paper, Dr. Pennell uses software and algorithms to determine the factors that drive sex chromosome fusions. Unlike traditional biologists, Dr. Pennell does all of his work on his MacBook instead of using pipettes and microscopes.

Source: Wikimedia Commons, Dr.Pennell uses computational approaches, such as Mathematica for his research.

This video, courtesy of universityofbc via Youtub, introduces UBC Killam and NSERC postdoctoral fellow, Dr. Matthew Pennell and talks about his research

“The simple fact that Y autosome fusions are way more common than W or X or Z, suggests it’s probably just random, which is a kind of interesting and cool result that this huge thing in our genome and across all genomes is just random chance, and this random chance explanation is the most consistent with our data.”

-Dr. Matthew Pennell

During his graduate studies, Dr.Pennel was part of a team that integrated chromosomal information of thousands of species into an electronic database called “The Tree of Sex“, which we describe in further detail in our podcast below.

Now that we know randomness is involved in sex chromosome evolution another question arises: Is sex determination an absolute process?

As we will soon see there are species, such as the Stickleback fish that change their sex determination system from XY, to ZW, to temperature controlled and so on. However, does this mean that we humans might experience such a change in the future?

Source: Flickr Commons, Huamns have 22 pairs of autosomes and 1 pair of sex chromosome

Source: Flickr Commons, humans have 22 pairs of autosomes and 1 pair of sex chromosome

“They keep reinventing how they make males and females and this is really interesting and crazy because making males and females is the most basic thing animals do….But they keep switching around how they make males and females, which I think is pretty cool.”

-Dr. Matthew Pennell

In addition, we were fortunate enough to have the opportunity to interview Dr. Pennell:

https://youtu.be/9obgQ7mI5Ac

Before the interview with Dr. Pennell, our group had a lot of difficulty understanding the premise and messages of the paper. Dr. Pennell provided us with simple insights on the different facets of the evolution of sex chromosomes – from the creative variety of ways that nature determines sex in species, to the mechanisms which drive sex chromosome fusions. Although a lot of these concepts were hard to understand at first, the premise of the paper is very simple to understand – computational biologists often work with real world data sets (ie. “The Tree of Sex”, and try to fit their models to them to determine the relationships between the scientists’ predictions and what’s really happening. In this specific paper, Dr. Pennell and his team concluded that the different models did not relate to the given dataset and the explanation for the real data is attributed to randomness.

We would like to give a special thanks to Dr. Matthew Pennell for his time and explanation of his paper.
Authors: Justin Yoon, Julia He, Radu Nesiu, and Matt Golf (Group 2)

The CRISPRs Fever

Posted on November 16, 2015 by sainan liu | 1 comment

You may remember from biology textbook that we can edit genetic material using restriction enzymes, a DNA-cutting protein structure. Using this we can learn about gene functionalities, search for disease treatments or increase yields of crops. Controversially, it also made unnatural creations possible. However, different gene targets require different enzyme structures, just like to open different doors you need different keys, and making these “keys” turns out to be complicated, expensive and time-consuming, which might have kept most of the “fantasies”, such as “super human” or other wired things, away from reality for now for better or worse.

by PuraVida_Fotografie from Google Image "genetic mutation" Labeled for reuse

by PuraVida_Fotografie from Google Image search “genetic mutation”, labeled for reuse.

However, what if all the “doors” also have the same type of “digital locks”, and all you need to change is the password? CRISPRs (clustered regularly interspaced short palindromic repeats) turns out to be this “lock”. It contains repeated sequences sandwiched with spacers (unique genetic information) in between. The spacers are external virus genes kept in bacterias and served as the “criminal records” so that when invasion happens again, the bacteria can send an “army” of gene-cutting enzymes, called Cas9, to cut the recognized viruses’ DNA apart.

“Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA” by Hiroshi Nishimasu, F. Ann Ran, Patrick D. Hsu, Silvana Konermann, Soraya I. Shehata, Naoshi Dohmae, Ryuichiro Ishitani, Feng Zhang, and Osamu Nureki – Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA http://dx.doi.org/10.1016/j.cell.2014.02.001. Licensed under CC BY-SA 3.0 via Commons

In 2012, scientists have proven that instead of making restriction enzymes for different genes, we can simply replace these “criminal records” and use the same Cas9 “armies” to cut desired genes with much less time and cost. You can find the details in this following video.

[by McGovern Institute for Brain Research at MIT]

Nature , Science and many major media have unanimously deemed CRISPRs to be a revolution. Radiolab has discussed its ethical controversies as if the realization of the technology is right around the corner. It has been portrayed as such a simple and approachable method that people even claim to provide CRISPR DIY kit for experiments at home.

However, I think despite these attentions, the reality is that we are still far from ready to harness CRISPRs. Although many researches has already been using it to edit genes in a variety of bacterias, plants, and animals within a short 3-year period, few studies focused on the limitations and functions of CRISPR itself. Some research was done too early without waiting for the technology to mature, such as the research using human embryos, which has resulted in a less satisfactory result. Some researchers commented that CRISPR can be less accurate than expected and may not be the most efficient and cost-effective solution for certain problems on Quora. Scientist Konstantin Severinov on Quanta Magazine also pointed out that it is still unknown whether defending invaders is the major usage of CRISPRs since many of these spacers appear to be genes of viruses that are long gone. It might be a good time now to slow down and maybe build the technique from ground up concretely first.

by Sainan Liu

1 Comment

Posted in Biological Sciences, Science in the News

Tagged Biology, CRISPR, CRISPRs, genetic engineering tool, molecular biology, molecular cloning, science

Brains and games in 21st century – How do video games affect us?

Posted on November 9, 2015 by Radu Nesiu | 3 comments

There is a lot of debate regarding how video games influence our brains development and whether or not games are beneficial or damaging. Scientists have examined both sides and the question that needs to be answered is whether games are beneficial or they are transforming us into machines.

credits: http://guardianlv.com/2013/08/researchers-develop-mind-control-using-the-internet-video/

Some studies show that prolonged exposure to video games has negative effect both on the body and the brain. Games decreases attention span, increase the risk of obesity and violent games decrease sensitivity towards aggression. The implications are troubling since decreased attention implies lower academic performance and obesity is a health risk factor. Furthermore it is shown that decreased sensitivity towards aggression not only makes us consider aggressive behavior acceptable but it also increases the chance that we will become aggressive.

credit to: http://yoursinglesourcefornews.com/ academics-debunk-theory-linking-violent-video-games-with-aggression/1379/

Another fact that must be considered is repetitive tasks in games. Because there are lots of games that become repetitive and have reward systems that encourage that behavior gamers are exposed to lose of creativity. Since repetitive tasks are better suited for a computer we could ask ourselves if our mind is encourage to become a basic processing unit.

However, there is another side of games which was investigated by researchers and the findings encourage people to become casual gamers. The benefits from games are as follow: better cooperation skills, adaptation to new challenges, fast reaction time and better attention to details.

credits: http://www.jklmgames.co.uk/how-games-can-train-the-brain

Besides the standard types of games we should also consider games that involve movement (e.g. some Nintendo Wii games) which are shown to motivate exercise. Those type of games should become encouraged in populations with increased risk of obesity, where the reward system should be tailor for the customers.

The tricky part of the games is the reward system which acts as a drug since it releases dopamine which is the hormone for excitement. Using this we can develop games that can stimulate people to learn and train. A study done on surgeons showed it is possible to increase job performance via gaming. Here is a TED talk about games and how we can use them to construct a better world.

Based on what we seen so far casual consumption of non-violent games have beneficial effects, however one must take extra care since crossing the line and becoming an addict can severely impact us.

Radu Nesiu

3 Comments

Posted in Biological Sciences, Issues in Science, Science Communicators, Science in the News, Uncategorized

Tagged benefits from video games, brain, brain functions, excessive gaming, science, Science Communication, TED talk, video games

Work-life Balance

Posted on November 2, 2015 by Luxi Xu | 6 comments

Nowadays, more and more people are working long hours and taking less and less vacations. According to this article, employees in the United States only use 51% of their eligible paid vacation time, and for Chinese the number is even lower. If you calculate the number, that’s nearly 50 billion dollars left unused annually by workers in the states. But does longer working hour reflect a greater amount of work done? The answer might be “no”.

source: Wiki Commons

Working hour and productivity

Longer working hours leads to a fall in labour output per hour, as indicated by the graph below.

Source: OECD and Economist

There has been a lot of paper published on the topic, demonstrating that reduced working hour may higher productivity. This more recent paper shows that working longer hour doesn’t mean quality work. In fact, it is probably the opposite. It all comes down to how people work smart instead of work long hours.

Unlimited Vacation Policy

License: CC0 Public Domain

There is an increasing tendency for companies to offer unlimited vacation as compensations or a way to encourage workers to recharge. Companies that offer unlimited policy includes Netflix, Evernote, Chegg, Prezi and other technology-based firms at Silicon Valley. LinkedIn is the latest to join the group. According to the Society for Human Resource Management survey, even though only 2% of employers on the market offer such benefit, it’s evident that other industries are following the trend.

Having an unlimited vacation policy might sound attractive at first glance but does it really benefit the employees? It’s undeniable that there are a lot of benefits:

Trust and flexibility: Having an unlimited vacation policy implies company’s trust on their employees and it provides high flexibility for employees’ work-life balance.
Higher Productivity: Research shows that working over 40 hours per week without vacation leads to reduced productivity; Being able to relaxed and off-work for a longer period of time might bring higher productivity.
Selling point for recruitment: Such policy will make the company more appealing in the job market and attract like-minded candidates.

However, that’s not the whole story. Employees whose income relies heavily on commissions may not take advantage of the policy, makes it redundant. In fact, this has happened in real life. Majority of the employees won’t go on vacations as much as employers anticipated. In addition, an unlimited vacation policy is not “unlimited” in the sense that workers still need to request from his/her boss for a leave. If the worker hasn’t done the work, there is high probability that the policy doesn’t apply to him/her.

It’s also important to keep in mind that corporation, good ones and bad ones, all share a same common goal — get the most out of the employers given the salaries they pay. To achieve a work-life balance, it is truly up to workers to choose between working long hours or more time with family, friends or one’s self. Most importantly, workers should start by working smart and improving efficiency/productivity for a better balanced life.

Here’s a TED talk that elaborate on how to achieve a better work-life balance.

Credit to: Ted Talk x PSU

Luxi Xu

Comments:

Katherine’s Effects of Sleep Deprivation

Sainan’s Can we predict the future

Esther lo’s Embalming Rosalia Lombardo

6 Comments

Posted in Science Communicators

Tagged balance, life, people, Public Engagement, science, Science Communication, TED talk, undergraduate, Universal Blood, working

How Do We Evaluate Scientific Claims?

Posted on October 31, 2015 by inhye kim | 2 comments

What criteria do you use to judge the validity of scientific claims? Scientific writing should objectively give out information to readers rather than attempt to persuade them. As the roles of scientific claims are answering research questions and serving as the main point of a report, it must be reviewed with reasons and criticality rather than with opinionated arguments. Thus, a good scientific claim should include objectivity, validity of reasons, and authenticity of the evidence; these criteria help the claim to stand without bias or subjectivity, to be proven with validity and the credibility of the claim.

Source: David Wood via Google Image

Objectivity is one of the important components of a good scientific claim because it allows readers to take the claim without bias or subjectivity. If a scientific claim contains any particular bias, it can lead the claim subjugated to prejudice. For example, it is recommended to research and to refer to a variety of information sources that embrace different opinions towards the topic in the discourse. Without objectivity, readers are often misguided that one-sided opinion is a valid criticism.

Without valid reasons, scientific claim would not be able to prove anything. Scientific writings always have to include valid reasons that justify the claim’s position amongst many others. For example, if your claim argues that garbage patch has adverse effects to seawater, you should provide a constructed reason that plastic, the majority of the garbage patch, releases toxins into the water, instead of arguing without the valid reason that garbage pollutes water.

Overview of scientific method Source: David Wood via Google Image

Furthermore, the reasons that support the scientific claim have to be validated by empirical evidences. The reasons cannot stand alone without the evidences that prove the credibility of the claim. Authors can authenticate the reasons by using data or statistics as reliable sources of evidence. For example, if you write a report about the negative effects of Pacific Garbage Patch on environment, a published data on the toxic chemical concentration of seawater would successfully support the claim.

Scientific writings play an important role in informing and educating the public. Hence, they have to present their positions with objectivity, validity of reasons, and authenticity of the evidence. Without accomplishment of these three conditions, a scientific writing becomes null.

“Social Complexity and Scientific Validity” by Dave Wiley

YouTube video courtesy of: TEDx Talks

InHye(Lisa) Kim

2 Comments

Posted in Issues in Science, Science Communicators, Science in the News

Tagged empirical evidence, objectivity, Public Engagement, science, Science Communication, scientific communication, scientific validity, valid reasoning

The Promising Near Future of Blood Transfusions

Posted on October 20, 2015 by jookyung yoon | 1 comment

Rendering of red blood cells. Source: Flickr Creative Commons – Nocturnal lust

Have you ever donated blood? Canadian Blood Services is always looking for more blood, because they need lots of it. For example, here’s a table of the required donations per single procedure.

Required amount of blood donors per case. Source: Canadian Blood Services – Who does my donation help?

As you can see, a single car crash can require blood from up to 50 donors. Such events can cause a shortage of blood. In fact, just last year, Canadian Blood Services issued an appeal for more blood donations, as blood supplies hit an all-time low, especially for type O universal donors.

What are universal donors? Donors of blood type O can donate to every other blood type, because they have no antigens (molecules that can cause severe and harmful responses by immune system on the recipient of the transfusion). The video below explains the concept of blood types and why some people can flexibly donate to all others blood types. Credit for this video goes to user nafis A on Youtube.

The problem with blood donations is that we can’t simply take many donations and stop worrying about blood reserves. This is because, just like milk, blood is perishable. Blood Centers Organization states that red blood can only be stored for 42 days before going bad. This creates a need for a continuous supply of blood donations to account for any emergencies.

On the bright side, the future of blood supplies look promising due to a recent publication by a research group at the University of British Columbia (UBC) at the Centre for Blood Research. They discovered a method to genetically enhance an enzyme which removes the antigens from blood. To do this, they used a genetic manipulation method called directed evolution.

David Withers’ Research Group at the Centre for Blood Research. Source: UBC Centre for High-Throughput Biology

This process introduces step-wise mutations in the DNA that encodes the enzyme. They use a multi-pronged approach by introducing many random mutations to the gene, and select the best performing mutants and do this for multiple rounds. The researchers at UBC claim that after five rounds of directed evolution, the enzyme which removes antigens from red blood cells is 170 times faster than the original enzyme. The original enzyme, although functional, was never fast enough to be a feasible way of removing antigens from blood. This genetically enhanced enzyme, however, can be used practically in the medical setting.

This discovery could potentially eliminate the shortage of antigen-specific blood by converting all donated blood to donor types! I think this has great potential for saving lives. From what I know about Biology, once the DNA of this hyper-enzyme has been sequenced, it can be easily generated from protein farms – where bacteria produce large quantities of the protein which can be purified and extracted for clinical use. I think it’s amazing to hear that my university is at the frontier of such impactful discoveries!

Blog by Justin Yoon

Commented on the following blogs:

Electronic cigarettes by Brian Cheng

Bioethics dilemma by Paul Yi

Imposter syndrome by Luxi Xu

1 Comment

Posted in Biological Sciences, Issues in Science, Science in the News, Uncategorized

Tagged Biology, Blood transfusion, Breakthrough, Chemistry, Discovery, science, Science Communication, Universal Blood

Image

The future of wound healing

If today you cut your hand accidentally, what would you do? I would put some pressure on the wound and a Band-Aid to stop the bleeding! However, what if you are an military doctor operating on someone who has been shot on the battlefield, and is bleeding profusely on the operating table?

Surgery, Author: Army Medicine Source: Flickr Commons

Modern blood clotting agents do exist, but they are slow to action and may pose health risks later on. This is where Vetigel^™ comes into the spotlight! Created by Joe Landolina and his company Suneris, this new invention has the possibility to revolutionize the medical field.

Before we find out what Vetigel^™ does, I will first explain how our body heals that simple paper cut on our hand. It may be surprising to know that the healing mechanisms behind a paper cut and a gunshot wound is strikingly similar. The major difference is the size of the wound, which means your body has less time to self-heal with more blood being lost every second.

Our wounds heal with special mechanisms that involve our cells, and a microscopic mesh that exists between these cells called the extracellular matrix. This matrix is also what holds your cells in place, help cells communicate with each other, and assist in nutrient transport. When a wound heals, the human body is simply recreating this matrix with the help of other specialized cells from the immune system (Enoch & Leaper, 2005). Unfortunately, I don’t think the human body has the one type fits all kind of extracellular matrix. Instead, our bodies has to slowly recreate this extracellular matrix specifically for the site of injury.

Extracellular matrix, Author: Alejandro Porto Source: Wikimedia commons

In my opinion, this problem of slow self-regeneration is what Vetigel^™ tries to resolve. Vetigel^™can spontaneously assemble into the same “configuration” of extracellular matrix wherever it’s applied. It speeds up your own body’s ability to heal wounds by removing the need to slowly recreate the extracellular matrix. If you put Vetigel^™ on your skin, the gel will self-assemble into a mesh similar to your skin`s extracellular matrix; if you apply Vetigel^™to your heart, the gel will assemble into a mesh similar to your heart’s extracellular matrix. I was truly amazed at the speed at which traumatic bleeding can be stopped, here is a video demonstrating Vetigel^™ in action (blood warning):

Joe Landolina`s genius is that he realized certain polymers derived from plant cell wall have self-assembling properties. Therefore, by basing Vetigel^™ on these plant polymers, Vetigel^™ can automatically assemble in a similar fashion as the micro-environment it is applied on. Here’s his TED talk giving a more detailed introduction of his product:

The future of emergency and military medicine sure looks bright, but FDA approval of this amazing product is still a few years away. For now, Joe Landolina has started producing Vetigel^™ for veterinary medicine, and maybe one day your beloved dog will be saved because of innovative science!

Saving man’s best friend! Author: Austin Community College, Source: Flickr Commons

By Yu Chieh (Brian) Cheng

Your Password is TOO Short

How many times are you forced to change your password on CWL and get constantly annoyed by the restriction rule? You are not alone, most people experience difficulty with strict requirements for their new password. According to this study, Only 18 percent of the population are able to create a password that meets all the requirements on their first attempt; 25 percent simply give up.

It is human nature not to feel threatened by thefts they don’t see, and we feel confident about all the passwords we created. Unfortunately, most of us have weak passwords, which can be “guessed” by computer within few minutes, even seconds.

Source under: Creative Commons CC0

How do they crack your password?

© User:Colin / Wikimedia Commons, via Wikimedia Commons

There are numbers of ways for a cracker to get your password. This post by Dorothy Ordogh from 2014 Term 2 explained it pretty well. In addition to trick you for passwords/personal informations over network, A cracker can:

guess your password online using the common passwords every 24 hours to avoid lockup of the account
try every word offline from a dictionary using software tools
try Brute-force attack: test every combination of letters and symbols(for example, Enigma)
hack into a vulnerable security system, get the hash of your password and then run tools to find matches

Nowadays, most systems have encryptions/hash implemented to secure clients’ passwords. However, such implementations doesn’t guarantee the safety of your data. The best way to keep you safe from any attack is to use strong ones.

If there are millions of passwords waiting to be matched, you want to your password to be the hardest to crack.

This scientific study reveals that passwords with a 16-character minimum requirement is the hardest to attack compared to other groups, including a 8-character minimum group with upper/lower case and dictionary check requirements. Another interesting finding is that adding a number to a password doesn’t decrease the predictability of the password.

So How long should my password be?

In 2010, a study by the Georgia Tech Research Institute suggested that a good password should be long, complex and easy to remember such as a sentence with numbers or symbols. The minimum length should be 12 characters.

If you would like to test the strength of different passwords, here is a website that calculates the time to crack your password under different attack scenario.(keep an eye on the offline fast attack scenario)

Given the processing speed and the capability of computers nowadays, short and simple passwords won’t survive even the simplest attack. Extensive use of internet and mobile devices make us easy targets for online thefts. To protect yourself from being a potential victim, it is important to be aware of the danger and take actions. Remember, a longer password won’t hurt.

Here is an interesting TED talk by Professor Lorrie Faith Cranor. She also talk about how hashing passwords works:

YouTube video courtesy of: Ted Talk

Time to change passwords!

Posted by: Luxi Xu

Tag Archives: science

Evolution Can Be More Random Than You Think

The CRISPRs Fever

Brains and games in 21st century – How do video games affect us?

Work-life Balance

How Do We Evaluate Scientific Claims?

The Promising Near Future of Blood Transfusions

The future of wound healing

Your Password is TOO Short

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