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Empiricism and Anecdotes from a Creative Scientist

Marine Genomics

5/22/2018

 
  1. Avocado mole
  2. Lawn chair hyperbole
  3. Marine genomics

When people get to the third, their reaction is very similar to that from the first two:
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“What do those have to do with each other?”
 Yes, what indeed DO genomics, or the study of genomes, have to do with the ocean or fish or whatever? But first:
 
-If you’re familiar with genetics and gene editing, skip down to the next divider. 
​-If you need a brief review or are new to this, read on: 


GENETICS 101
DNA to RNA to proteinIf you're interested in how DNA makes us "us," click to go to thinglink and check this out.
A genome is all of an organism’s DNA, and DNA is the how-to manual for creating every cell and protein that perform every single function in all living things.
 
If you think of us humans as a house, with different rooms serving different purposes, filled with appliances, plumbing, wiring, etc., our genome includes not only the house’s layout and construction plan, but also how to manufacture the appliances, and even make pipes and grow trees for lumber. Our genome is us.
 
As biotechnology (the term for studying and manipulating genomes) has advanced, we’ve been able to do increasingly fancy things with DNA. We’ve gone from being able to isolate it (“Oh look! DNA!”), to nailing down what individual sequences of DNA, or genes, do (“This gene dictates what color hair a person has.”), to actually being able to “edit” genes (“I’m going to add this gene to my cat’s genome so it’ll glow green.”).
 
That last one—changing/subtracting/adding onto the genome—is a big deal. If our genome is us, and we can change our genome, well shoot, we can do everything from cure deadly diseases to choose the gender of our babies.
 
I’m not going to delve into the ethical implications of editing genomes, because that’s its own quagmire of a post; however, maybe listen to this podcast if you want a glimpse of the moral implications of gene editing.

NOW BACK TO OUR REGULARLY SCHEDULED PROGRAM

Genomes and biotechnology are all well and good, but why bother gathering information and examining the genomes of marine organisms? What purpose does it serve?

MUCH PURPOSE. MUCH. ​

marine genomics mind blown
Brace for purpose.

Here are some examples of how marine genomics is revolutionary. 

marine genomics cures cancerPeriwinkle flower says, "I cure cancer. What do you do? NOTHING."
You may know that rainforests, despite covering a tiny portion of the earth, contain most of our world’s plants and animals. What’s more, a massive number of important prescription medicines have been discovered by studying rainforest flora and fauna[ii]. The biodiversity of rainforests makes them a veritable pharmacy.  

Rainforests comprise about 6% of the earth, but the ocean covers more than 70%, and we’ve only explored around 5% of it. Some scientists are now theorizing that the sheer breadth of the ocean means it is the most biodiverse place ever, far outstripping even rainforests, especially because the deep sea isn’t devoid of life like everyone used to think[ii]. Just imagine what kind of medical discoveries await among the bajillions of critters we haven't yet discovered! Marine genomes have already provided important human health breakthroughs (as with the creation of a non-opioid painkiller from cone snail venom), and as we delve deeper, I’ve no doubt we’ll keep finding novel treatments for what ails us.

The utility of marine genomics doesn’t stop at its human health implications. No siree. It’s also being used to help us figure out what fish are really doing because, as Dr. John Shepherd said, “Counting fish is just like counting trees—except that they’re invisible and keep moving.” If we don’t know how many fish there are, or how they’re behaving, it’s hard to regulate fisheries effectively and fairly. 

​State and federal government base decisions of when folks can and can’t catch fish on “the best available science”;  but even the best available science, and the best intentions, can get it wrong. Oftentimes, openings and closings are set by counting how many fish are in the water, and estimating their age; if the managers think the fish are too young, they’ll close an area so that the fish have a chance to grow and reproduce before they’re caught. But… how you be sure those fish are too young?  How, then, are we supposed to make the right calls about opening and closing fisheries? The wrong call costs people their livelihoods, or causes a species of fish to go commercially extinct. 

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If only it were this easy...
Enter marine genomics: the bester available science.
otoliths for aging fish
Image credit: NOAA NEFSC
You can tell the age of bony fish by examining their ear bones (called otoliths). Yay! Some otoliths have rings like a tree, showing how old a fish was riiiiiiight before you sliced open the back of their head so you could pull out their otoliths...
By sampling a fish’s DNA, you can tell how old it is, which is particularly useful when your fish’s age is otherwise unverifiable. Or, by measuring the amount of fish DNA free-floating in the water, you can theoretically get a decent idea of the total population. If there are many “island” populations of one kind of fish, like cod that live in Northern Maine and Southern Massachusetts, a fish’s genome shows how the groups are breeding together, or not, and which are adapting best to their environment. We can also compare the DNA of similar species to see which has a better chance at surviving our warmer, more acidic ocean, and so could still be commercially fished without tanking the species.

​There is so. Much. To. Learn. Inside every single marine organism is a literal encyclopedia of useful information, and we only need four letters—A,T, C and G (Ayyyy!)—to spell it out for us.


​Avocado mole and lawn chair hyperbole totally aren’t a thing, but marine genomics totally is. In fact, it’s the best thing: fish + cutting-edge science = solving our most pressing problems.  

Part III: The Evidence

5/11/2017

 
(Excuses: In a job interview I was once asked: "Would you rather be on time, or perfect?"
I said I'd be on time AND perfect, because it's a job interview, and that's actually my preferred format. If I were forced to choose, though, I'd rather be on time. 
...Which is why I'm so annoyed that Part III has taken until now, and! AND! It's still not done. Oh well. Here it is: neither on time, nor perfect.) 

​

Putting It All Together (Parts I, II, & III) for Climate Science


​​I began to write this piece as soon as I saw a statement given by a Trump campaign advisor[1] about putting a stop to politicized science and “politically correct environmental monitoring,” particularly as it pertains to climate science.
 
I want to stop the process of facts becoming partisan, at least in this small corner of the world, and to decouple science from opinion, politics, and media[2].
 
Since Trump has taken office, the issues page on Whitehouse.gov has changed significantly from its previous iteration and as of January 23rd, 2017, there is no official White House policy on climate change. The new administration’s cabinet has varying views on climate change, the danger it poses, and whether or not it’s caused by man.

So let's start from the beginning. 

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The earth is getting hotter, and that’s not good news.
 
The term climate change describes variations, natural or unnatural, in the earth’s temperature and weather. Thanks to fluctuations in the amount of gases that trap heat in our atmosphere (mainly CO2, AKA carbon dioxide), the earth’s climate has always had times when it was warmer or colder, but according to records that stretch back 800,000 years, we’ve reached an all-time high amount of that heat-trapping CO2.
 
We need carbon dioxide in our atmosphere. CO2 is naturally formed by volcanic eruptions and breathing/metabolism in living creatures, among other things, and plants need it to photosynthesize. Tons of ocean animals need carbon to form shells and living structures (and some shelled organisms actually build even tougher shells with more CO2 present). Without CO2, earth would be a lifeless ball of ice. 

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​​CO2 is also created when humans burn fossil fuels like oil and gasoline, and a lot of our modern world relies on fossil fuels to function. While some people say there’s no way human-produced carbon dioxide emissions approach the levels of naturally produced CO2, others say that man-made CO2 emissions are many, many times greater than natural, and our contributions are what’s causing global warming. 

It’s been well documented that 97 percent of the world’s scientists agree that climate change is real and caused by human activities; it’s also been well documented that consensus may have been overstated, and the actual amount could be lower, though still around 80 percent. More recently, a 2016 paper confirms the 97% figure among climate scientists, and several surveys conducted of scientists found that the more experience a scientist has with climate, the more likely they are to cite climate change as driven by human activities.
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According to the makers of SG-20 adhesive, the originator of the graphic, this is what 97% looks like.
63 percent of the American public thinks that global warming is happening, and about half believe it’s caused by human activities. 34 percent think there’s “a lot of disagreement” in the scientific community over whether climate change is occurring. [3]
 

I hear this a lot: “If scientists can’t agree that humans cause climate change, why should I agree?” 


It’s a very frustrating (but unsurprising and understandable) question. (Refer to Part II: FACT DRIFT if you want an example of how people might conclude that there’s a lot of disagreement.)
​

Some people don’t believe the scientific consensus because they distrust scientists’ ability to be impartial
[4], and because there are sources that dispute the human origins of climate change. If a person only pays attention to sources that agree with their personal opinion, they may fall victim to confirmation bias, or believing something is true because they want it to be true.


To be continued. 

​


[1] Bob Walker is a Republican from Pennsylvania who served in Congress from 1977-1997 and was the Chairman for the Committee on Science from 1995-1996. 

[2] Wherever possible, I’ve used primary source materials and have included information presented by both left and right-leaning media sources. I encourage everyone reading this to check my sources. ​
​
[3] Points 1 and 2 come from a study conducted by Yale on US national opinions about climate change: environment.yale.edu/poe/v2014/

[4] A breakdown of who’s reporting on validity of climate change: Science Progress, part of the Center for American Progress, which some would argue has a liberal bent; Skeptical Science is run by the author of one of the papers that arrived at a figure of 97% consensus regarding the anthropogenic origins of climate change; NASA’s Global Climate Change program, which got its start under a liberal government and stands to lose funding; NOAA, another government agency that stands to lose funding for programs; and Science Daily, which collects news about science and research, but does not publish its own material; the National Review Online, a publication of the National Review Institute, is the self-proclaimed “most widely read and influential magazine and website for conservative news, commentary, and opinion.”
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