Happy Anniversary, Planet Earth! Episode 9: Shallow Seas

The 9th installment of the series, “Shallow Seas” opens with the statistic that 8% of world’s ocean volume contains a majority of its marine life.

I’m in the middle of reading Hope Jahren’s “Lab Girl right now (a fantastic, inspiring book about her life as a scientist that I highly recommend). In the opening paragraph of the Prologue, she mentions a reason why she is not interested in studying the ocean: there is six hundred times more life on land than there is in the ocean. This is true! I don’t think I’ve ever read someone’s reason for not being interested in studying the ocean, having studied and worked for marine-focused institutions for the past 10 years while also living in beach and island cultures with students clamoring to be marine biologists. While Dr. Jahren’s point has more to do with her own interests in land plants, in the broader sense I agree that there is much to be studied and managed on land because terrestrial ecosystems have indeed produced more life than in the ocean. As a result, activities on land have the ability to negatively affect the diverse ecosystems of the “shallow seas”.

Over half of the world’s human population lives within 60 km of a coastline. These are remarkable ecosystem areas surrounding coastlines, separating the land from the ocean.

I lived on Yap Island in the Federated States of Micronesia as a Peace Corps Volunteer from 2004-2006, working with counterparts at the Yap State Environmental Protection Agency. I learned so much from my hard-working colleagues, far more than they probably gleaned from me.

(Left to right, top to bottom) Me (2006), view returning to the MicroSpirit ship with coconuts from an outer island (2004), traditional Yapese dance (2005), lunch on the boat (2004).

DSCN4257 coconuts DSCN3853Elato Ship Wrec

Small island nations are deeply connected to their environmental resources, in both cultural and economic senses. Future climate change and accompanying sea level rise is affecting island societies more than other societies. The President of Palau has spoken prolifically on this topic, and was at the International Coral Reef Society meeting in Palau last month (June 2016).

Regina and Larry Raigetal, of Waa’gey.org recognize this in their efforts to confront challenges: “Extreme isolation, limited economic opportunity and climate change are big problems for the small atolls of Micronesia’s outer islands.” Waa’gey focuses on fostering pride in traditional culture, which has worked to sustain the population in the past, including traditional sailing navigation. Small island nations like Micronesia have populations less then a fraction of some developed countries, yet live entirely in coastal areas.

On the mainland of the U.S., Florida has over 1,000 miles of coastline and is becoming more and more affected by land-based activities. Beginning in the 1900s, land use changes were abundant in the state of FL. Miami was built out by developers and the sugar cane industry moved into the Everglades, a natural wetland area. Originally, water from Lake Okeechobee at the center of the state would naturally drain through wetland areas in south Florida eventually reaching the Gulf. Today, the Army Corps of Engineers has diverted the water out through a series of canals to the east and west, with significant freshwater discharge into estuarine areas and onto sensitive coral reefs causing an ecological disaster.

Economic benefits of the Indian River Lagoon resources were valued at more than $3.7 billion in 2007.

There is a lesson that Floridians and coastal US citizens can learn from the efforts of Waa’gey and other small coastal nations. (Teamwork in Ulithi atoll, outer islands of Yap):


We can team together to place renewed value on practices that were common before development. This means supporting efforts to restore water flow in wetland ecosystems back to their original state. Buying undeveloped land to prevent further land use changes and damage. Lawmakers should encourage sustainable lifestyles by requiring homeowners near and on coastal areas to preserve and restore their shoreline vegetation, slow development and not use fertilizers. Provide more sustainable funding to long-term scientific studies, such as those in Dr. Joshua Voss’ lab at Harbor Branch Oceanographic Institute at Florida Atlantic University, investigating the effects of discharge on near-shore coral reefs.

A well-balanced ecosystem brings long-term benefits. 

The Planet Earth episode ends by focusing on the charismatic macrofauna that depend on the shallow seas: the octopus mimics a moving/rolling rock, a gurnard fish with pectoral fins camouflaging its shape, a jawfish hides underground. Plants manage to take root, which are then pruned by sea turtles. Marine mammals such as dugongs and manatees are the largest herbivores in sea, eating nothing but fleshy rhizomes of sea grass. Dolphins discover a shoal of bait and are shown surfing, riding a wave. Fish refuge close to shore water only few cm deep. Sea birds, cormorants. Shallow temperate seas contain greatest concentration of fish on planet. Huge shoals migrate to feed in rich waters. Cruising back and forth between equator and poles, humpback whales – among the largest inhabitants of the ocean – are shown migrating between the shallow seas where life proliferates so abundantly on our planet.

Sunset in Micronesia:


Pumpkin Beer 101

By Lisa Cohen and Peter Cohen

It’s fall, and many tasty options for pumpkin beers are available on tap and in bottles. If you don’t like sweet beers, no problem. Pumpkin beers come in all flavors and types, dark, spicy, light, hoppy. Some examples include: Dogfishhead’s Punkin Ale, Southern Tier’s Warlock and Pumking, and  Ninkasi’s Imperial Pumpkin Sleigh’r. We would like to shout out to our neighborhood favorites in Florida: Intracoastal Brewing Company (Melbourne, FL) for Pumpkin Ain’t Easy and Hourglass Brewery (Orlando, FL) for Stupid Pumpkin Face.

We were wondering, what are pumpkin beers? It seems that there are more options for pumpkin beers these days compared with the past. Like many scientists, we’re fascinated by beer. We thought we’d explore with you all what beer is, then look at where pumpkin flavoring comes from.

History of beer

Reports of fermented alcoholic beverages date back over 9000 years evidenced from chemical analysis of jars found in Neolithic Jiahu, Henan, China. European breweries are famous for their history of beer, Bohemian monks in what is now known as the Czech Republic cultivated yeast and methods for brewing beer for hundreds of years, passing down secrets from one generation of monks to the next. Each monastery was known for their own special flavors and can still be visited today.

Today, it’s pretty easy for anyone to make their own beer. If you’re considering making your own, there are many books and references on the topic (some listed at the end). People are getting creative! Brewmasters with small craft beer businesses are popping up everywhere with some tasty beers. In 2014, craft brewers reported an 18% increase in volume and another increase by 16% already in 2015. There is a market for unique and flavorful craft beers, and pumpkin beers are no exception.  While the craft beer industry is on the rise, overall beer consumption has decreased.

Beer Styles

Beer comes in many styles and flavors. Just like a good wine, we don’t want to make the mistake of ordering a palate-wrecking IPA before a pilsner to pair with our tres leches dessert.

Lagers are stored for long times at cold temperatures with bottom-fermenting yeast cultures. The result is a clean and crisp taste with with a smooth finish. Lagers can be anywhere from light to dark, usually low in alcohol content.  A pilsner is a light and hoppy version of a lager. Hotter than Helles from Cigar City, Baba Black Lager from Uinta are a few of our favorite lagers, along with the pilsner Mama’s Little Yella Pills from Oskar Blues.

Ales are produced quickly using a top fermenting yeast at warm temperatures. The result is sweeter with higher alcohol content. The bitterness from hops can be used to balance the sweet malty backbone. Ales come in many forms: brown, pale, scotch, golden, each with a variety of bitterness, sweetness, alcohol content. A variety of flavors can be imparted with different hops, delivery, malts, yeasts, water, and culture parameters. The possibilities are endless.

What is fermentation?

“Beer” with us, there’s some chemistry. Ethanol fermentation is the conversion of sugar into ethanol and carbon dioxide. Behold, the chemical structure of simple carbohydrates, e.g. glucose (C6H12O6):

Sugar comes in many forms, including being stuck together with glycosidic bonds over and over in long chains of cellulose and starch (n = number of repeating units):


Many researchers are coming up with ways to break down cellulose, which plant cell walls are made of, into sugar for various downstream uses. The most common polysaccharide used for beer comes from the barley plant, which is malted (wetted, grown and dried), breaking down into simpler fermentable components (glucose-maltose-maltodextrins). Proteins are broken down during the malting process. Then, when the malted barley is boiled and reduced down into a thick syrup that looks like molasses, it contains tons of simple sugars. The degree of malting and drying can impart wonderful flavor to the final beer product.

We need lots of glucose to make beer. Now, we need to break down the glucose into alcohol. This is the part where we conveniently call upon our friends, the yeast microorganisms.

The 10-step process of glycolysis, where glucose gets broken down into pyruvate for energy production (in the presence of oxygen) or ethanol (absence of oxygen), takes place in all living cells including our own. We could do each step individually in separate vials in a lab, but yeast organisms are way more efficient and happy to perform this service for us under the right conditions. Each step of glycolysis requires a different enzyme, conveniently manufactured by the yeast. All steps are shown below. It looks complicated, but really isn’t. Just think of it as a series of atomic rearrangements where each arrow is facilitated by a different enzyme protein. All of these molecules are present in certain concentrations, moving around in the syrup solution with the yeast, running into each other at a certain temperature, volume, and pressure. For every molecule of glucose, two molecules of pyruvate get produced:

If there were to be oxygen present, the microorganisms would continue respiration to create chemical energy, ATP. But, when there is no oxygen, pyruvate is decarboxylated by the pyruvate decarboxylase enzyme towards the final end-product of ethanol. Therefore, it is really, really important that no oxygen is present during the beer-making process. That is why fermentation must take place in sealed off containers.

Carbon dioxide (CO2) comes off as a by-product along with acetaldehyde, which is then reduced and rearranged by the yeast’s alcohol dehydrogenase enzyme to produce – here’s the big moment – ethanol!

The term “alcohol” is really just a hydroxyl group stuck to a carbon molecule. Ethanol is not to be confused with other alcohols, such as isopropanol (rubbing alcohol).

Microbial fermentation

We love our little domesticated yeast microbes. And they love us. We use these microorganisms for their enzymes, feeding them the glucose from the malted barley syrup. They produce ethanol and flavor, and in exchange we keep them alive in culture for the next batch. We select for batches that are tasty and throw away the batches that don’t work. Micrograph of yeast from a microbiology course lab notebook (2 um scale bar):

Yeast microorganisms aid in common fermentation methods including mead (fermented honey), sake (fermented rice), cider (fermented apples), and beer (barley or wheat fermented with yeast). Whereas cider takes advantage of natural endogenous microbes originating from within the fruit to break down the sugar into ethanol, mead, sake, and beer introduce yeast organisms purposefully cultured to aid in fermentation.

High-throughput DNA sequencing technology is recently allowing us to examine the evolutionary relationship of yeast microbes. Along the way, on the road to domestication, we have been positively selecting for genes in these microorganisms. This has resulted in functional differences between species. In a study of the domesticated fungal species used for sake (rice) fermentation, Gibbons et al. 2012 from the Rokas lab at Vanderbilt University studied Aspergillus sp. in sake, demonstrating that genes associated with flavor and carbohydrate metabolism have been selected for. In addition, production of chemicals that are toxic to humans have been down-regulated.

The Saaz and Frohberg yeast strains used for beer fermentation have been shown to be two separate lineages originating from Bohemia and Germany, respectively. Studies have recently shown that they were domesticated then diverged several different times. They belong to the species, Saccharomyces pastorianus syn. S. carlsbergensiswhich is a hybrid between the common yeast, S. cerevisiae and the cold-tolerant S. eubayanus. The differences between them include temperature tolerance, flavor chemicals and fermentation rates, with Saaz strain producing considerably lower alcohol (~4.5% abv) than the Fohberg strain (~6.5% abv) at 22degC fermentation temperature.

How does beer get its pumpkin flavor?

In short, the pumpkin flavor in beer (usually) comes from actual pumpkins. The meaty squash vegetable is cooked and added along with the malted barley syrup to the fermentation process, allowing the yeast to feast upon the pumpkin in addition to the malted barley. Since the pumpkin is a plant, it contains complex carbohydrates just like the barley. This feeds the yeast more sugar and the flavor molecules from the pumpkin stick around. We did not have a bountiful harvest of pumpkins this year, unfortunately. So, this does not explain why there have been more options for pumpkin beers available in stores than in years past. The reason for the increase in options is likely because of the creativeness of the craft beer industry. You can use canned pumpkin, or pumpkin bread, or even just the spices themselves. Pumpkin beers come in many varieties from bourbon barrel aged stouts that taste like pumpkin pie, to light ales, and even lagers.

That’s it! Hope you enjoyed this exploration. We sure did. :)

Additional References