Category Archives: Uncategorized

Math isn’t just something to do with numbers

Perhaps contrary to our believes, science is a work in progress, it always has been. The right ideas don’t just pop up in people’s dreams , serendipity is not here to save the day every day. Paradigm shifts don’t happen all the time, more than often hypotheses after hypotheses are proven wrong before a right one will come up. Wrong science is not necessarily bad science, and this paper, although in the wrong, will prove the point.

In 2015, Prof. Daniel Coombs , a mathematical biologist, and his research team at the University of British Columbia published a paper regarding a mathematical model. This model aims to predict the time take for a T-Cell  to reach an Antigen Presenting Cell (APC)  within a Lymph Node. Although the model failed to do it’s intended job, none of the works will be wasted. Many of the works still provide a solid foundation for future works such as an even simpler models to help better understand our immune system

Before we continue, we have to understand the basics of the human immune system.  A T-cell is a type of a white blood cell  that goes out and searches for pathogens. During an infection, APCs such as Dendritic Cells  will take up parts of a pathogen (antigen) and move to the lymph node to wait for a matching T-cell. A T-cell will get activated by binding to an APC  and proceed to activate B-cells which produce antibodies, subsequently destroying the pathogens. Thus, for our immune system to start functioning, a T-cell must come in contact with the APC that has the matching antigen.

The following video will help explain how Coombs and his colleagues devised their model for predicting the time a T-cell needs to find an APC.

Visual Representation of the T-cell. Wikimedia Commons by BruceBlas.

Visual Representation of the T-cell. Wikimedia Commons by BruceBlas.

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Source : SCIE300 Group 2

Credit to: Daniel Coombs, Alana Lee, Ivan Fong, Ryan Tran and Shayini Kanageswaran

To recapitulate, this model is characterised by having only four parameters:

  • Radius of the lymph node – R
  • Radius of APC – r
  • Diffusive constant – D
  • Boundary trapping parameter K.

r is very small compared to R, larger D equals faster the T-cell movement, and K ranges from 0-1.

This is very impressive since according to Coombs, previous models rely on at least 15 parameters to predict the exact same biological phenomenon. Were this model to correctly predict the time a T-cell will take to reach an APC, it would be at the forefront of its field. But as we have not-so-subtly hinted previously, this was not the case. The predicted time was too long compared to reality.

However, the simplicity of this model is where it excels. While other models which gave more accurate results were very complicated to compute with top of the line machines, this model can be hand computed. This model also managed to do this without losing its integrity on explaining the mode of action of a T-cell when finding an APC within a lymph node with only 4 parameters.

The following podcast contains information on the limitations, further research and improvements and our personal questions about the study.

Credit to: Daniel Coombs, Ivan Fong, Alana Lee, Ryan Tran and Shayini Kanageswaran

-Shayini Kanageswaran, Ivan Fong, Alana Lee and Ryan Tran

The Changing Field of Stroke Medication

Strokes are the fifth leading cause of deaths in North America. If one is fortunate enough to survive a stroke, the rehabilitation process is long and painful depending on the amount of damage done to the brain. There are two types of strokes – ischemic and hemorrhagic. Ischemic strokes are the result of a clot forming in an artery and preventing blood flow, whereas hemorrhagic strokes are the result of an artery bursting and and the brain literally bleeding out.

Many researchers have worked towards improving and developing treatments to reduce the amount of brain damage a patient suffers during a stroke. One of the events that takes place during a stroke is called excitotoxicity, where brain cells literally excite themselves to death.

Receptors like NMDA as well as calcium are key culprits in causing damage to brain tissue. NMDA is a protein that is present on nerve cells and binds to the neurotransmitter glutamate. When a stroke occurs, nerve cells release large amounts of glutamate which bind to these NMDA receptors. The binding of glutamate to an NMDA receptor causes it to open. Calcium which is present in excess on the outside of the nerve cell, enters the cell. The calcium alongside with glutamate go on to wreck havoc in the nerve cell ultimately leading to its death. 

Courtesy of Khashayar.

Dr. Nicolas Weilinger investigated what happens at a cellular level during a stroke and the mechanism which works to damage brain cells. While researching, Dr. Weilinger discovered a new signalling pathway that had broad reaching implications for brain physiology and pathology.

YouTube Preview Image Courtesy of Harnoor Shoker

The findings of this study are important because current treatments in place to protect the brain during and after a stroke are not as effective as they should be. One of the main findings of Dr. Weilinger’s paper was that another channel much bigger than NMDA called pannexin gets activated during a stroke. Pannexin is physically connected to the NMDA receptor so when the NMDA receptor opens it signals pannexin to open as well. The opening of another channel therefore allows more calcium and glutamate to enter at an even faster pace. Using this information, a new drug was designed that would prevent the NMDA receptor from communicating with pannexin – in other words it would block the physical connection between the two proteins.

The wider implications of Weilinger’s paper is to hopefully improve stroke treatment. Future research into Dr. Weilinger’s findings could potentially be the first step in discovering a new drug type that can be used to reduce brain damage suffered during a stroke.

**We would like to thank Dr. Nicholas Weillinger for his time and the SCIE 300 team for guiding us and providing feedback.**

Harnoor, Khashayar, Matthew.

Hybrids: the good, the bad, and the … natural?

What do you think about when you hear the phrase ‘genetically engineered crops’? Do you think they’re inherently bad because they’re not ‘natural’?

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Zebroid – hybrid of zebra and donkey.  Image from Wikimedia Commons

Well, maybe you should think twice before answering, because hybridization is a process commonly found in nature. Basically, hybridization is cross-breeding between two species with different genes. In animals it’s pretty distinct in appearance, but in plants the main changes are on a chemical level. These changes are what affects the taste, smell, or defence mechanisms of the plants. Therefore, people might find a useful application to them, as hybrids may be grown as crops with better qualities, such as stronger resistance against diseases and insects. That’s why researchers are interested in exploring the genes of various plants to find the benefits, which humanity can use.

How the mystery unveiled

Dr. Celine Caseys in her lab. Photo by Alex B.

Dr. Celine Caseys in her lab at UBC. Photo by Alex B.

For example, Dr Celine Caseys and her colleagues at the University of Fribourg, Switzerland, examined the hybridization process between two types of trees from the Poplar family. Their methods involved collecting poplar leaves in three European regions and then looking for certain chemicals, responsible for defending trees from insects. More details on this research in the video below.

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Video: Benefits of Hybridization in plants by Henry Liu and Jan Jenko, Group 5

Practical use

The research revealed that hybrids are capable of creating better defence mechanisms by more efficiently producing chemicals against insects. This might have a practical application for productional growing of plants (like for biofuel) and, furthermore, for farming purposes, since the plants will require less pesticides, therefore growing crops will cost less. More on the benefits and potential drawbacks of hybridization in the podcast.

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Podcast: Benefits and drawbacks of hybridization by Alex Budkina, Group 5

As we learned from above, studying the effects of hybridization is really important, because despite all potential benefits, there are still some danger behind the artificial modification of genes, such as  endangering wild populations. Therefore, humanity must consider the  “ecological consequences”, according to Dr.Caseys, of creating genetically engineered plants. We still know too little about the process, so more studies of natural hybridization will help us to unveil the mysteries behind it.

~ Group #5: Alex Budkina, Henry Liu, Jan Jenko

Visions of a Greener Earth

Have you ever been watering plants and wondered just how much water was being absorbed by plants? Is the water you’re using to soak your garden even being put to good use by the plants? It turns out, plants contain an extensive system with complicated processes which allows them to “drink” water via osmosis. A little known fact, plants have an inner and outer layer which they use to filter water. Dr. Jetter, a researcher in the department of botany at the University of British Columbia, completed a study that aimed to figure out the function of each of those layers. He did this by examining eight different species of plants and studying the chemistry of each individual inner and outer layer.

Dr. Reinhard Jetter from UBC Department of Botany. Image courtesy of Daryl’s Camera

Our group had the pleasure of interviewing Dr. Jetter at the Biological Sciences building where he gave us further insight into his research. When our group first read his paper, we expected similar research had already been completed by scientists at other institutions but surprisingly, that was not the case. In fact, Dr. Jetter told us related research had only been done by one other group of scientists located in Germany in 2001. The video below highlights the most important components of Dr. Jetter’s research and what he found:

https://youtu.be/Ex1gqoDKbEQ

Video – Credit to Dr. Reinhard Jetter, Brian Wong, Daryl Kwok and Ying Yu

Plant cuticles were isolated. Image courtesy of Daryl’s Camera

A specially designed water chamber was used to measure how fast water passes through each layer of cuticles. Image courtesy of Daryl’s Camera

Why is this research significant? Well for one, North America suffered major droughts from 2012-2015 due to record-breaking heat waves. Acres of vegetation died off and as a result, entire ecosystems were disrupted. Additionally, water became an extremely scarce resource and states such as California were so desperate for water, they were buying it from Canada. So what are the nitty-gritty details regarding the composition of how plants control water loss? Furthermore, what are its applications to the general public? We examine this in the podcast below:

Audio –  Credit to Dr. Reinhard Jetter, Brian Wong and Ying Yu

Like all studies done in the name of science, there exist limitations. Each individual plant’s chemical components are not analogous, the water-loss barriers will vastly differ within each species. For example, in Dr. Jetter’s study, some plant species had up to 100 times water-loss prevention effectiveness versus other species. This variation is due largely to the interaction between chemical compounds within the plant itself. As a result, it would be an extremely extensive task to accurately record every individual plant species’ ability to control water-loss.

With Dr. Jetter’s research as a basis, huge potential exists in developing technologies that would drastically reduce the negative effects of drought. In the future, if scientists can fully understand and utilize the level of water loss between plant layers, vast farmlands which are highly dependent on weather conditions could be alleviated of disastrous levels of crop loss. Undoubtedly, Dr. Jetter’s research serves as the pioneering basis for a frontier of unspoken possibilities to benefit our great big green planet Earth.

-Group 3: Brian Wong, Daryl Kwok and Ying Yu

What could global warming bring for our cities?

From the pre-industrial carbon concentration of 240 parts per million, human activities have steadily increased the amount of carbon in our atmosphere to current levels of 400 parts per million. Carbon in our atmosphere interacts with oxygen to become carbon dioxide, CO2, which acts as a greenhouse gas. Greenhouse gasses are effective at trapping heat that is leaving from the surface of our planet. As a result, our planet gets warmer since less heat is able to escape to space and instead linger around in our atmosphere where it is then reflected back to the surface.

What changes could we be expecting?

We are aware that the increase of CO2 is causing global warming and scientists estimate that if we continue to release carbon at the same rate we are emitting now, there could be up to 4.5°C increase in global temperature by 2100.

A 4.5°C increase temperature does not sound like a lot but according to the IPCC report in 2007, this could bring 0.26-0.59 meters increase in sea levels and another study predicted a much higher increase in sea level of 2 meters by 2100.

Climate Central released numerous visualizations of what major cities around the world will look like after carbon emissions have had their affect on sea levels using recently published data.

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City of Durban after 2°C rise (left) and 4°C rise (right). Image from Climate Central

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City of Rio after 2°C rise (left) and 4°C rise (right). Image from Climate Central

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City of Mumbai after 2°C rise (left) and 4°C rise (right). Image from Climate Central

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New York City after 2°C rise (left) and 4°C rise (right). Image from Climate Central

What does that mean for us?

Vancouver, being a coastal city, is not safe from rising sea levels either. To prevent damages done to the buildings and infrastructures in the city, city planners recommend that the flood plains be raised by 1 meter than current height, to a total of 4.6 meters. They think that this change to the bylaws will provide safety net for predicted sea level increase of year 2100.

Lots of CO2 emissions come from fossil fuel combustion from industrial activities, however we could also do our part to reduce CO2 emissions in effort to reduce the impact on climate change we have. Simple steps we could take include reducing usage of personal cars and taking public transportation or biking instead. Remembering to turn off lights in unused rooms also help since producing electricity is also a big source of CO2 emissions.

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Top 10 countries in danger from future sea rise

video by The Daily Conversation

 

Alana Lee

Stop smoking to make a big difference to your health

Nowadays, it’s hard to find a person who hasn’t heard about how harmful smoking is to our overall health. Each year, cigarette smoking is responsible for nearly 20 percent deaths in the United States and more than 6 million of people in the world died from smoking-related diseases. Smoking is harmful to every part of the body and can lead to serious health problems, such as cancer, heart diseases and respiratory problems.

 Smoking-related diseases

Smoking is one of the leading causes of cancer and it accounts for more than 30 percent of all cancer deaths in the U.S each year. The reason behind it is that smoking can trigger DNA mutations and damage the genes that protect us from cancers. Studies have shown that cigarette smoke contains more than 7000 chemicals and more than 69 of them are known to be carcinogens, which can cause varying degrees of DNA damage. As a result, people who smoke are more likely to develop certain types of cancers, such as lung cancer, throat cancer and liver cancer.

Additionally, cigarette smoking can cause heart diseases by damaging the function of your heart and the structure of the blood vessels. First, smoking produces carbon monoxide that can reduce the oxygen level in the bloodstream and hence increase heart rate to supply the body with enough oxygen. Second, some chemicals in cigarette smoke have been shown to cause the fatty plaque build-up inside the arteries. This will increase the risk of getting stroke, heart attack and atherosclerosis.

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The image shows how smoking can affect arteries in the heart. Image from National Heart, Lung, and Blood Institute.

Furthermore, smoking is also the primary cause of chronic obstructive pulmonary disease (COPD), which is a type of progressive lung disease that can cause respiratory problems and lung infections. The main symptoms of COPD include coughing, wheezing and shortness of breath. Cigarette smoking can also cause damage to lung tissues and reduce the airflow in and out of the lungs, resulting in many breathing-related problems.

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Youtube video – Smoking and its effects on Health. By iheedinstitute

Benefits of quitting smoking

Quitting smoking can lower the risk for smoking-related diseases and largely improve our overall health. Recent studies have shown that quitting smoking before the age of 40 can reduce the risk of early death from smoke-related diseases by 90 percent and increase the life expectancy by 10 years.The following graph shows the timeline of recovery effects after quitting tobacco.

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Timeline of health benefits after stopping smoking. Image from http://www.tobaccofreeco.org

In summary, cigarette smoking can cause negative health effects in many ways and it is also a major risk factor for developing cancers and other preventable diseases. Quitting smoking can help regain your health to the same level as those of non-smokers. It is never too late to stop smoking and start a healthy lifestyle!

-Ying Yu

The Okinawan Secrets to Longevity

The island of Okinawa, southwest of Japan’s main landmass, is home to the healthiest and largest population of centenarians in the world. In other words, people who have lived one hundred years or more and have led remarkably healthy lives. The centenarian ratio of Okinawans is 50 per 100,000 people in a given population, almost triple that of Canada’s ratio, and on average, Okinawan males live 78 years whereas Okinawan females live 86 years. Furthermore, the Okinawan people are known for having the lowest rates of age related diseases such as cancer, heart disease, dementia, and osteoporosis.

What is their secret? According to The Okinawan Centenarian Study, apart from possible genetic factors, their stress free lifestyle and nutrient dense diet plays a major role. A few of the key habits are briefly discussed below.

Always Kind

An elderly Okinawan (Image Courtesy Of: Flikr Commons)

“Whew, I’m stuffed!”. This is a phrase you’ll probably never hear on this small island due to the Okinawans having a philosophy of only eating till they’re 80% full, referred to as hara haci bu . Although there is no instinctual way of knowing if you’re 80% full, it is roughly around 1800-1900 calories, the typical amount consumed by Okinawans. It’s important to note that just as the quantity of calories is key, so is the quality of the calories. The diet of Okinawans is heavily plant based, accompanied by oily fish 2-3 times per week, and is limited in refined grains, meats, saturated fats, and dairy. 

Apart from their dietary habits, Okinawans remain active individuals throughout their life. Walking, gardening, dance, and tai chi are a few examples that the elderly partake in, which helps maintain their cardiovascular system, in addition to allowing them to maintain their muscle and bone strength.

“So the secret to a longer life is daily exercise and proper nutrition? Lame! How about telling me something I haven’t heard before?”

Not so fast.

In addition, the Okinawans embrace an ikigai. An ikigai is a Japanese concept meaning “a reason for being”. Older Okinawans can readily articulate their purpose in getting up every morning. This definite sense of purpose and a deeper understanding of one’s self provides them with a clear role of responsibility and a feeling of being needed.

It’s clear that apart from healthy eating habits and daily exercise, a positive outlook on life is just as important, as illustrated by the stress free lifestyle of the Okinawans.

Check out the short documentary below for a more in depth review of the lifestyles of the Okinawans!

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Youtube video courtesy of: TheWayPlace

Thanks for reading!

-Sahil Mann

Iron Deficiency: The Quiet Killer

Iron is an “essential mineral”  for humans; this means it is an element that our bodies cannot manufacture independently, and therefore, must be obtained through an external source.  The sad fact of the matter is that many individuals (approximately two-billion people world wide) do not consume an adequate amount of iron, leaving them iron deficient, which can have many adverse effects on our bodies.

Image Source: http://www.medicinenet.com/hemoglobin/article.htm

Image Source: http://www.medicinenet.com/hemoglobin/article.htm

Why is iron so important to us? Iron is essential to the circulatory system as it is a main component of hemoglobin (a compound responsible for binding to oxygen and carbon dioxide) within our red blood cells. Iron deficiency is responsible for nearly 20% of all maternal deaths during pregnancy. Mothers with low iron status can be heavily effected by the loss of blood during labour. As blood is lost, individuals already low in iron will drop to more alarming levels, resulting in an inability to provide their bodies with enough oxygen. Their hearts will begin to pump harder, eventually resulting in cardiac arrest, and subsequent death.

This begs a the question, how much iron does an individual need? The answer varies from person-to-person depending on body composition and lifestyle, however, the average male should be consuming roughly 8 mg of iron daily, and the average woman should be consuming nearly 18 mg per day. The drastic difference between men and women is due to the fact that women loose a large portion of their iron stores as they progress through their monthly menstrual cycle, forcing women to consume larger volumes of iron to compensate for their losses.

If we cant make iron ourselves, where do we get it from? Iron can either be obtained from the food we eat, or through supplementation. The iron in our diets is termed “dietary iron”, and there are two types: “heme Iron,” and “non-heme iron.”

Image source: Michael Collan, inSlideShare

Image source: Michael Collan, inSlideShare

Heme-iron is exclusively obtained through a carnivorous diet, in particular, it is found within the meat’s blood (attached to hemoglobin), and the meat’s muscle (attached to myoglobin). This type of iron is more bioavailable, meaning it is better absorbed through the gastro-intestinal tract into the blood stream. Non-heme iron is found in both animal tissue (representing 60% of the iron present), and is the only type of iron found in plant tissue (100%). This type of iron is comparatively less bioavailable. The implication here is that those who have a herbivorous diet must consume 1.8 times the amount dietary iron (as less of the iron they consume is appropriately absorbed through the GI tract into the bloodstream.) This further implies that vegetarians are more susceptible to iron deficiency.

Image Source: http://geekymedics.com/respiratory-examination-2/

Pale Conjunctiva                 Image Source: http://geekymedics.com/respiratory-examination-2/

Image Source: Rachel Casiday

Ferritin, Image Source: Rachel Casiday

 

 

 

 

 

 

How do we know if individuals are deficient in iron stores? One practical method is to track your dietary intake and calculate your iron consumption. However, a more reliable and specific mode of detection is through measuring “serum ferritin” concentrations within the blood. This is a protein that stores iron, and therefore, low levels of serum ferritin are indicative of iron deficiency. Clinically, the presence of pale conjunctiva of the eyes, or pale red inner lip colour can indicate low iron stores. The symptoms of iron deficiency are not obvious, and often go unnoticed, leading to many deaths that could have been easily avoided.

Ali Lamont

Baked potato chips: Are they actually healthier than fried chips?

Fried potato chips are one of the most common and popular snack around the globe.  Often classified as junk food because of it’s high fat and sodium content, food manufactures have been offering a seemingly “healthier” alternative: baked potato chips.

Baked potato chips manufactured by Lay's Source: Flickr Commons

Baked potato chips manufactured by Lay’s (source: Flickr)

Baked potato chips must be healthy, correct?  They have been prepared without the deep frying process, therefore contain much less fat than the conventional potato chips. For comparison, one cup of conventional potato chips contains about 10 grams of fat while baked chips contain about 6 grams. In addition, baked chips contain much less saturated fat. According to the American Heart Association, saturated fats increases the level of cholesterol therefore the risk of heart diseases.

Since the fat content is lower, baked potato chips may seem like a healthy alternative, but is this really the case?  Studies show that the sodium content of baked potato chips is higher than normal potato chips. Is it suspected that to compensate for less flavour than fried chips, manufactures add more artificial flavouring to baked chips thus increasing sodium content.  Research shows high sodium intake leads to higher blood pressure, which is a leading cause for cardiovascular diseases.

The process of making baked potato chips is very different from fried chips.  Prior to baking potato chips, the potatoes are dried prior to the baking process.  During this drying process, potatoes are heated to high temperatures and releases the chemical compound acrylamide. Acrylamide is a cancer-causing chemical and according to a study by U.S. Food and Drug Administration, baked potato chips contain up to three times the amount of acrylamide compared to fried potato chips. To get an idea of how potato chips are made, have a look at the clip below by NFB:

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Along with the addition of extra flavouring for baked chips, we may even find additional ingredients used such as corn oil. While we are removing the frying process with vegetable oil, the corn oil in baked potato fries are just as unhealthy!

Baked potato chips has its benefits of being low in fat content.  However, consider the other components you are putting into your mouth before you indulge yourself into a bag of baked chips. They may not be so “healthy” after all.

 

Daryl Kwok

 

 

Era of Teleportation is One Step Closer

Teleportation image from quantum-tech.ru

How many of you have heard about teleportation? I assume, this terminology isn’t new for a reader. Everywhere, starting from the sci-fi movies and finishing with the computer games, one may meet the variety of teleportation methods and devices.

The term “teleport” appeared as early as second half of 19th century and described as an “apparatus ‘by which man can be reduced into infinitesimal atoms, transmitted through a wire and reproduced safe and sound at the other end!’”

Through the time, several theories evolved on the possible teleportation methods, such as quantum teleportation, matter/energy conversion, extra dimensional teleportation, etcThe most progressive one and the most popular method is a quantum teleportation, when the exact state of the particles is transferred to another location rather than the matter itself. What does it mean? Instead of measuring and destroying an object and then reconstructing it by using a “printer”, the scientists send the information about the particles’ state from one side and put the particles on another side into the same state without replication via a pair of bounded in space particles. More scientific explanation of the process is in the video below (John Rarity, Physics World):

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The most fascinating part about quantum teleportation is that it recently became a possible reality not only for the world of quantum particles, but also for the “classical” world. Inspired by “beaming technology” of Enterprise from Star Trek and lead by Alexander Szameit from the University of Jena (Germany), the team of scientists encoded some information into a special form of a laser beam and successfully teleported it through the space. The transfer occurred without loss in time, which could be qualified as an instantaneous teleportation. How this experiment is different form the previous experiments with particles? Well, the light particles don’t belong only to the realm of the quantum particles. They also have the classical world properties, described in optics, which means the teleportation is potentially possible for the objects with the regular physical properties. The one current drawback, admitted Szameit, “with this form of teleportation, we can, however, not bridge any given distance.” That means in the nearest future people won’t be able to teleport the information on the long distances.

Despite all drawbacks, this breakthrough opens a real opportunity in teleportation not only the objects of the world of particles, but the objects of the classic world as well. And who knows, maybe within a couple decades a first life form “beaming” will occur.

~Alex Budkina