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.

 

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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.

Dinosaurs! (Or, How to Make a Fossil)

Guess who turns 30 this year? (No not me, that was last year.) It is the Royal Tyrrell Museum. (Pronounced TEER-uhl not tie-RELL) Now, 30 years old might not sound that impressive when you are showcasing exhibits that can boast 30 MILLION years old but none-the-less, still a pretty big deal.

The Royal Tyrrell Museum is nestled down in Alberta’s badlands, in the lovely City of Drumheller. You go from the beautiful canola covered prairies and end up in the desert, where a very different geological landscape awaits you. What makes the Royal Tyrrell Museum one of Canada’s treasures is that it is THE Dinosaur Museum. And who doesn’t love dinosaurs? Seriously, to say you don’t love dinosaurs, weren’t completely fascinated by them as a kid, don’t have a kid that isn’t fascinated by them, and don’t find them remotely interesting now, you are either lying or have no sense of whimsy. Dinosaurs are awesome-that is why Jurassic World it all its terrible-ness still made money hand over fist: dinosaurs are awesome.

And on the other side is a lush prairie field.

And on the other side is a lush prairie field.

For me (and my fiancé), going to the Royal Tyrrell Museum is like being a kid in a proverbial, allbeit science-themed, candy store. Exploring the world, not as we know it, but starting from over 570 million years ago in the precambrian period. What other place can you go where you can you travel in time, going from the Permian, to the Triassic, round a corner, end up in the Jurassic period, walk a little further on and hit the Cretaceous period, see a mass extinction event (one that wasn’t influenced by human activity nor threatens your current safety) and live to see the Rise of the Mammals?

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Dimetrodons from the Permian period.

Stegasaurous (my personal favourite) from the Jurassic period.

Stegasaurous (my personal favourite) from the Jurassic period.

Triceratops from the Cretaceous period.

Triceratops from the Cretaceous period.

Just another thing that makes Alberta a pretty special place to live is the fact that it seems the land in which we now call Alberta was once a hot bed (now fossil bed) for dinosaurs. This shouldn’t be a huge surprise, considering that our economy is oil-based. Petroleum hydrocarbons are what happens to plants and animals millions of years and thousands of tonnes of pressure after they die. What is surprising to me is that we are able to find so many dinosaur fossils at all. What we dig out of the ground are not animals that existed 10s to 100s of millions of years ago themselves, but rather pieces of those animals (and plants) that just happened to die under just the right conditions where their decay wasn’t stunted and they were then turned to stone. This becomes even more remarkable when we are able to find evidence of soft tissues.

So let’s take  a look at how to make a fossil:

The first thing that has to happen is that the animal has to die. Now when you die, there are lots of things that happen. There are always scavengers that are looking for a quick meal. There are also bacteria that start breaking down all of the organic matter through a bunch of biochemical reactions. Then there is the environment: wind, rain, fire, it can all affect the body of a decaying organism. But I haven’t told you anything that you didn’t already know: animals die, their bodies decay. That process doesn’t necessarily lead to fossilisation. To make a fossil, the carcass needs to be buried, and pretty quickly, before too many things have eaten it or capricious weather has destroyed the remains. Now, the speed at which an animal needs to be buried depends on environmental factors such as humidity and temperature. The key is for the animal to be buried before too much of the carcass, specifically bone, is destroyed by the natural degradation processes.

The skeleton known as

The skeleton known as “Black Beauty” at the Royal Tyrrell Museum. The bones of this T-rex are a striking black. This is due to manganese being incorporated into the skeleton during fossilisation.

Now that we have buried the carcass, the bacteria, naturally present, get to work. Animal bones are not inert, hard structures that our bodies hang off of. Bones are a matrix of living organic tissue where the mineral hydroxyapatite has been grafted up around it. Hydroxyapatite is a mineral comprised of calcium and phosphate ions. Over time and under pressure, the hydroxyapatite can change, incorporating ions from the surrounding sediment, such as iron, uranium, even (rarely) manganese. The biggest change, however, comes from the bacteria “eating” the organic part of the bone. As these bacteria metabolise the organic material from the bone, the produce mineral by products, depositing these minerals into the spaces of the bones previously occupied by the organic matter. The most common mineral deposited is calcium carbonate. The bacteria use calcium ions from the surrounding water and sediment to capture the carbon dioxide that is produced as waste product of their metabolism. Calcium carbonate is better known as limestone. The bacteria may also incorporate other ions, like iron, into these mineral deposits. After many years, the bacteria will have successfully transformed bone into stone.

2015-07-29 22_29_38

When I think about this process, how an animal has to die, be buried quick enough and deep enough that degradation processes don’t completely destroy the skeleton, I can help but be amazed that we even have fossils, let alone the stunning array of fossils that we do have. We have managed to piece together some pretty amazing details about the life on earth millions of years ago. This has allowed us to take a glimpse into our own evolution. This is what the science of palaeontology gives us: a passport into the past, a pastport if you will. So if you have ever wanted to travel back in time, I encourage you to visit the Royal Tyrrell Museum.