Tomatosphere and Epigenetics

Have you heard of Tomatosphere™? This is a really cool program operated in Canada through Let’s Talk Science. It is a free program offered to students from Kindergarten to Grade 12, where these students can study the effects of “space” on the germination of tomato seeds. Participating classes receive two packages of tomato seeds: one is a package of seeds from tomatoes that were sent into space or treated to space-simulation conditions, i.e., the experimental group; the second package contains seeds that spent time on plain old Earth, i.e., the control group. Students the study the germination of these two groups of seeds, expanding on the basic experiment depending on curriculum and grade level.

As a scientist and a gardener, I am in LOVE with this program. But I have a question for Tomatosphere™: I want to know if anyone is looking at the possibility of EPIGENETIC changes to the tomatoes. This begs the next question: what is epigenetics? That’s the question I am hoping to answer for you today.

Tomatospher Question

My tweet to Tomatosphere

 

To begin our understanding of epigenetics, let’s do a quick review of the central dogma of genetics and inheritance. The traits that make us a human (or a gorilla, or a tomato plant) are coded in our DNA. To express the trait, the DNA is transcribed into messenger RNA (mRNA), which is in turn translated into amino acids that are then put together to build the necessary proteins for each trait. We inherit these genes from our biological parents: one gene from the egg and one gene from the sperm. The trait that is expressed is the dominant gene. Differences in expression generally mean differences in the genes, or the specific DNA code.

For example, let’s look at blood types. Let’s say you inherit the “A gene” from your dad and the “O gene” from your mum. Your genotype will be AO. But since the A gene is dominant, you will only express this gene and you will have blood type A. This is called your phenotype. To change your blood type, you would need to change your genotype. That is the basics of inheritance.

Epigenetics throws a wrench into this understanding of genetics and inheritance. Epigenetics means “outside genetics”, and refers to changes in gene expression that are not a result of physical changes to the DNA sequence. In other words, changing our phenotype without changing our genotype. Epigenetic marks control the expression of genes, which ones are turned on, when, and how much. One of the most interesting things about epigenetics is that we can start to see how the environment plays a role in gene expression. Our lifestyles, our preferences, our exposures to certain environmental factors can all contribute to variations in how the same gene can be expressed across individuals. What’s more, is that it has been discovered that these changes in epigenetics can be inherited. What this means is that if you exposed to something in your environment that causes a change in how a gene in your DNA is expressed, this change could be passed on to your child, and even to your grandchild. This is referred to as transgenerational epigenetics. It is an emerging area of research and the exact mechanisms of how this works is being widely studied.

This brings us back to Tomatosphere™ and my question. In the experiment we have tomato seeds that were exposed to space conditions. These conditions may not have changed the gene sequence, the genotype, of the tomato, but they may have caused epigenetic changes. It has been shown that changes in the gene that controls ripening in tomatoes is impacted by epigenetics, so do we see changes in other factors with these space tomatoes? AND, what about the progeny? Do the tomato plants grown from the seeds of the space tomatoes also show epigenetic changes?

Epigenetic tomato experiment

A sketch of my proposed Tomatosphere experiment.

 

For more information on transgenerational epigenetics, check out this Nature article.  I also recommend the website What is Epigenetics for a more detailed description of epigenetics.

 

Advertisements

Bill F*cking Nye?! Seriously?

Last week, March 6th, Canada’s Liberal Party was out promoting Budget 2018. This budget has Canada’s scientific community pretty excited because of the huge investment that the Canadian government is making in fundamental research. I am no exception. So last week, the Liberal politicians were out making the rounds to promote the budget and its impact on Canadian science: there was Navdeep Bains visiting Memorial University; there was Finance Minister Bill Morneau at the Djavad Mowafaghian Centre for Brain Health and Brain Behaviour Laboratory; and there was Science Minister Kristy Duncan was over at the University of Waterloo. But all eyes were on Canada’s mascot, I mean Prime Minister, Justin Trudeau. See Trudeau did his post-budget armchair discussion at the University of Ottawa with none other than Canada’s most prominent scientist and science educator…oh no wait, he sat down with Bill Nye. That’s right, American engineer and television host, Bill F*cking Nye. This pissed me off – so much that I actually had a Twitter rant about it. Bill Nye tweet

I am not one who is usually given to ranting my feelings on social media. I don’t feel that 280 characters is enough to fully express nuanced thoughts, and much of the time it feels like I am trying to talk in a room of 1000 other people all talking at the same time. But here’s my top 3 reasons why I am incredibly disappointed in the PM’s choice to have this discussion with Bill Nye:

1) Bill Nye IS NOT CANADIAN

I don’t think I can stress this enough. Bill Nye isn’t Canadian. He wasn’t born in Canada. He wasn’t educated in Canada. He never worked in Canada. He hasn’t lived in Canada. He has never paid taxes in Canada. Other than clips of Bill Nye the Science Guy showing up in Canadian science classrooms, he doesn’t have a Canadian connection. He is simply not a stakeholder in Canadian federal budgets.

It is deeply disappointing that of the THOUSANDS of Canadian scientists, myself included, that would have happily discussed the benefits of investing in STEM and research, that of the THOUSANDS of Canadian scientists who could have connected to Canadian taxpayers why it is so important for the government to spend their money on research and innovation even if they themselves aren’t scientists, the Canadian Prime Minister chose an American. Trudeau took away an opportunity for a Canadian voice to be on that platform. He allowed an American, someone who doesn’t benefit from the budget, and doesn’t have to answer to the consequences of the budget to speak on behalf of Canada’s scientific community.

That’s the thing about federal budgets: there is only a limited amount of money to spend. I know as a taxpayer that for every dollar the government spends on research and innovation, that is a dollar that isn’t getting spent on health care or infrastructure. Not to mention that with deficit financing, I will also be the one to pay off that debt. For me, that investment is worthwhile. And I am prepared to champion that to my fellow Canadians as to why they should also feel that matters, regardless of whether or not they are a scientist themselves. How can Bill Nye, an American, speak to any of that? He doesn’t qualify for NSERC grants. He doesn’t have to worry about Canada’s deficit. He’s not looking for jobs in Canada’s oil and gas industry. He doesn’t have to worry about under-funding some other Canadian program in order to fund science.

2) Bill Nye is Not the Only Voice

Okay, I know I have come off pretty hard on Bill Nye. I don’t hate Bill Nye. He’s done a lot for promoting STEM. But science has basically had one spokesman (two if you count Neil deGrasse Tyson) for the last 25 years. That’s not a lot of diversity. There are millions of scientific voices out there. I am personally tired of hearing Bill Nye’s perspective on science. I want to hear more of Jillian Buriak’s, Bonnie Schmidt’s, or on the more famous side Jay Ingram‘s. If I am going to hear about science from an American prospective, how about Raychelle Burks? My point here is that there are a lot of different science voices that can offer insight into why investing in STEM is a great choice for Canada. Bill Nye’s isn’t one of them.

Here’s another thing: Bill Nye’s version of science communication has actually done some damage to science itself. His willingness to entertain non-scientific individuals in debates about creationism or climate change, he has given these science deniers an elevated platform that they wouldn’t normally have. It puts creationism and climate change denial on the same level as scientific fact. It suggests that their beliefs they are passing off as fact are on the same level as scientific data. After all, debates are about two perspectives on the same set of facts right? Thanks Bill, but this wasn’t helpful. Actually, it made it harder for every other scientist trying to promote scientific literacy in the fields of climate change and evolution. This Scientific American article basically explains what I am trying to get at here.

3) The Kinder Morgan Thing

Or as Bill Nye called it “Morgan Kinder“. Pipelines and oil – this is contentious. I don’t want to get into all the science about oil or its impact on the environment. Yes, we know it is bad environmentally; yes, we know it is contributing to climate change; yes, we need to regulate and fix this problem. BUT that doesn’t happen by simply turning off the pipes. (Hey Bill, how’d you get to Canada? Did you like that jet fuel keeping the plane in the air? How about that car from the airport to the University of Ottawa? Was that water bottle you were drinking from plastic?) If you’re in Alberta right now, like me, you know that there is a lot going on in respect to the Trans Mountain Pipeline. The fact that this particular issue is so contentious that British Columbia and Alberta are having to go to the federal government to solve the damn issue should probably say to anyone, especially an American outsider, that maybe this wasn’t the best venue for discussing pipelines and what they mean. (Also, where is Bill discussing American shale gas production?) I go back to my point about Bill Nye not being Canadian. The pipeline is more than a scientific issue in Canada, with stakeholders in many sectors of the Canadian economy. Bill Nye is not one of those stakeholders and his woeful ignorance about this issue’s complexity was on display.

Now, I have ranted on Twitter. I have shared my thoughts here. But none of this is really going to create that much action. I am just not that important. But I believe that by taking action we put more meaning into our words. This is why I actually wrote a letter to the Prime Minister. I doubt that I will get a response, but I couldn’t very well complain about his choice on Twitter and not write to him to share my incredible disappointment in his decision to take away a great opportunity for Canadians to meet their amazing scientists and instead give it to the tired voice of science’s mascot, Bill Nye.

*Full disclosure: I have been a supporter of the Liberal Party but my previous political support does not mean an unconditional support of all their choices. That’s the fun part about democracy.

What’s the Deal with Climate Change?

Climate change: it has has been all over the news, especially recently with the Paris Climate Change Conference underway.

I just recently had a client of mine ask me my thoughts on climate change because he was unsure that it is as big of a deal as the media is making it seem. I could understand where he was coming from. One of the biggest issues with climate change is that it is obscured by lobbyists, politicians, private corporations, numerous jurisdictions all pushing through their own agendas, making it difficult for others outside that group (i.e., your average citizen) to understand what exactly climate change is and why we should even care.

The first big problem associated with climate change is jargon. I love this article by the BBC because they actually address the jargon issue. Anything that is too heavy in jargon (and that is pretty much all of science) quickly alienates people because they don’t speak “science language”. I am going to address some of the terms to help you through the climate change jargon mess, but also check out the BBC’s climate change glossary for a more complete list of definitions.

The first thing to understand is the greenhouse effect and greenhouse gases. The greenhouse effect is the insulation of the earth by certain gases in the atmosphere. The result is a rising of the earth’s temperature. In order to support life (as we know it) on Earth, we need some of the sun’s heat to stay on our planet and keep us warm. The atmosphere of the earth helps to trap some of the heat from the sun and keep us at an optimal temperature. The general principle of the greenhouse effect is sketched

Greenhouse-effect

Comparing the natural greenhouse effect to how human actions are influencing climate.

out in this diagram I grabbed from Live Science’s explanation of the greenhouse effect. The gases that trap the heat are carbon dioxide (CO2), methane (CH4), water (H2O). These are natural, but normally present in small amounts.

The atmosphere is comprised of approximately 78% nitrogen, 21% oxygen, 1% argon, and the rest is every other gas. Carbon dioxide only makes up about 390 ppmv (parts per million). With this composition, everything remains in a nice balance and we live happily ever after.

The problem comes in when we (and yes I do mean human activity) start adding more water, carbon dioxide, and methane into the atmosphere. They start trapping more and more heat, which gradually warms the temperature of the earth, and puts us in the predicament we are currently facing.

Why is it now “climate change” and not “global warming”?

Excellent question. The reason that nomenclature was changed is because “climate change” is a much more accurate picture of what is truly happening world wide. Global warming, the gradual increase of the global temperature as a result of the greenhouse effect, is occurring; however, global warming implies that we should all be expecting balmier winters when the true picture of what is occurring means more erratic weather patterns around the world. Any physical scientist can tell you, temperature is extremely important to how chemistry behaves and even more so in the gas phase. The pressure and the volume of a gas is directly influenced by temperature. Since our atmosphere is made up of gases, changing the temperature means that the movement of the gases in the atmosphere is going change, drastically influencing weather patterns. That is why we are seeing more severe droughts in certain areas of the

scientists-clues-print

The signs of climate change.

world, crazy colder winters in other parts. I grabbed this picture from the US Environmental Protection Agency (EPA). It shows some of the ways that we can tell climate change is occurring, and it is more than just a global increase in temperature. Actually, the EPA has a very nice explanation of some of the things going on in climate change.

The biggest issue of climate change is that the Earth exists in balance. Every ecosystem has evolved for specific conditions, conditions that include temperature and weather patterns. The plight of the polar bear and the melting ice caps has become the poster child of climate change, but here is a different example for you: coral reefs. I have had the pleasure of snorkelling on the Great Barrier Reef in Australia. That is an ecosystem that is absolutely breathtaking. From all of the different types of coral to the fish that call that coral home. Coral are actually animals. Their sexual reproduction involves the release of eggs and sperm simultaneously. This release depends on time of year, water temperature, tidal and lunar cycles. The more erratic weather and the increase in water temperature can alter the ability of these animals to reproduce. As they begin to die off, all of the sudden the variety of life that depends on coral reefs as a habitat are now also adversely impacted.

There are many more examples that demonstrate how the Earth has evolved in a balance. Something as seemingly insignificant as an increase in the amount of carbon dioxide in the atmosphere can have long-lasting impacts on the planet.

Our actions do impact the environment. The solutions are certainly not as simple as some environmental lobbyists might suggest. But it is important that we start changing our lifestyles to be more aware of how our actions adversely impact the environment. We can all be better stewards of the Earth.

What small things can you do to help be more environmentally friendly?