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

Yet another example of how microbiology is important

When people say they have gut feelings, they usually mean that they are going on instinct.

However, it turns out that your instinct, or behavior, could actually be coming from your gut. Microbes that is.


Over at Scientific American, an excellent article summarizes a study by Rebecca Knickmeyer on just that.

She followed a group of developing infants to determine if their guts really are altering their behavior.

Check it out!


(almost as cool as Microbes on Mars)


Biology is Has a Public Relations Problem

Here on NiB we often mention the problems that science is having with public perception. From controversies over biological collections, to finding extra terrestrial life in the octopus , to more basics like teaching evolution and vaccinations.

We as a group have trouble relating to the public what we do and why we do it. And it truly is a shame.

In response a recent post on Yale Climate Connections made a desperate call for scientists to do just that. 

The article also introduces “Grad Slam“. Started in the University of California system, it asks graduate students to take years of academic toil and work and to present it free of jargon or technical lingo. In just three short minutes. It’s like a Ted talk, an exit seminar and an elevator speech had a love child. Check it out below, and consider throwing one of your own.


Classic ecology in charmingly animated rhyme

Ecomotion Studios has been working with the Ecological Society of America to produce short animated films about some of the most influential papers of modern ecology — they’re calling it “The Animated Foundations of Ecology.” Here’s the film about Robert Paine’s famous experiment in removing the top predator of tidal pool communities, sea stars, which led to dramatically reduced diversity in the other species that shared the pools.

There’s a handful more, including on one of my favorite classic ecology papers, David Simberloff and EO Wilson’s experimental demonstration of the process by which species colonize new habitats. Go check ’em out!


Paine, R. T. 1966. Food web complexity and species diversity. American Naturalist, 65-75. doi: 10.1086/282400.

Simberloff, D. S., & Wilson, E. O. 1969. Experimental zoogeography of islands: the colonization of empty islands. Ecology, 278-296. 10.2307/1934856.

Stomach acid to pathogens: YOU SHALL NOT PASS

Did you know you’re walking around with a little vat of super acid in your belly? Human stomach acid registers 1.5 on the pH scale, making it more acidic than pure lemon juice. And we have to invest energy into not only making the powerful stuff, but then also into making sure we don’t accidentally kill ourselves with it. Why do we do that?

A recent paper by Beasley et al. (in open access PLOS ONE) hypothesizes stomach acid in vertebrates is used to protect our bodies from pathogens – and the more dangerous your diet, the more acidy your acid. “Obligate scavengers”, as defined in this paper, are animals that eat (and only eat) carrion – aka the decaying flesh of dead animals. Delicious? I guess they think so. But sanitary? Definitely not. These species should have the lowest stomach pHs because they need an acid “filter” to kill all the pathogens they’re ingesting with their diet. Herbivores, on the other hand, have plant-based diets with a much lower associated risk for pathogens. These species should have a higher stomach pH because they don’t need a “scorched earth” policy for their digestive tracts.

They further suspect that animals with a phylogenetically close diet might have a higher pathogen risk than animals that eat more phylogenetically distant organisms (and thus lower stomach pHs). The theory here is that eating something related to you means that their pathogens are potentially well-suited to also infect you.

Beasley et al. conducted a literature search and found pH data for 68 species of birds and mammals – which according to them was “far fewer than expected”, given its importance in digestion. They then categorized the species as “obligate scavenger”, “facultative scavenger”, “generalist carnivore”, “omnivore”, “specialist carnivore”, “hindgut herbivore” or “foregut herbivore”. The data show that obligate scavengers have the lowest pHs (average ~1.3) and foregut herbivores have the highest (average ~6.1, all seen in the very cool figure below from their paper). Omnivores and carnivores had the most variable stomach acid levels.

The authors conclude that these results are in line with their expectations – that organisms that eat “high risk” diets have lower stomach pHs. They leave room for the influence of other factors (like how much work it is to break down one’s diet once it’s been ingested) but note that all things being equal, a scavenger’s diet shouldn’t be more difficult to digest as a regular carnivore’s – the only difference being the – er – fact that it’s dead and rotting.

One note: humans have a stomach pH similar to carrion feeders, although we’re technically omnivores. Why would that be? Did we evolve eating a diet that contained more scavenging? (In practical terms, should the Paleo diet include roadkill?) Or does our relatively large number of “fecal-oral pathogens” favor a more acidic stomach? More data on other hominds would be illuminating here.

The paper finally discusses their expectation that when human stomach pH is raised more pathogens are able to become established. Elderly humans have a stomach pH of ~6.6 – a full 5 pH points higher than a healthy adult (wowza!); premature babies have a stomach acid of 4 or higher. Both of these groups suffer more bacterial infections than adults and children. Furthermore, gastric bypass patients have a stomach pH around 6 and may also suffer more bacterial infections. These facts seem to support their main hypothesis – that stomach acid acts as a barrier to pathogens as strong as the risk of infection – but statistical tests remain to be done.

It’s pretty interesting to me to contemplate why animals invest energy into the things that we do. But it seems at this point, stomach acid may be blocking the path of pathogens in the same way Gandalf stopped the Balrog: YOU SHALL NOT PASS. (And it occurs to me – if we stick with this analogy and the caves of Moria are a digestive tract – that would make the rest of the Fellowship that emerges from the caves…turds? Oh geez. I’m sorry, Tolkien…)

The Fellowship does not like being called turds.

Going Viral Against Cancer

We have heard of viruses causing cancer (HPV) or even cancers that act like viruses (devil facial tumor virus).

But now there is a virus that can fight cancer! An engineered herpevirus provokes an immune response against cancer. And after a long hard road, it has been approved to treat certain types of cancer by the FDA!

Read about it over at Nature!

Killer T cells (orange) are recruited to attack malignant cells (mauve) in the viral-based cancer therapy T-VEC.

Killer T cells (orange) are recruited to attack malignant cells (mauve) in the viral-based cancer therapy T-VEC.

The Complicated Legacy of the Mad Scientist

When I was around ten years old, I dressed up as a mad scientist for Halloween. I wore coke-bottle glasses and a lab coat splattered with a mysterious green substance. I carried a (fake) lab rat in my pocket, along with test tubes full of brightly colored solutions. And my mom did my hair, using a comb and A LOT of white hairspray to give me a look that I hoped was reminiscent of Doc Brown (but that probably looked more like Beetlejuice).

I have been fascinated by the mad scientist for as long as I can remember. Growing up, my favorite television shows included Pinky and the Brain, Beakman’s World, and Mystery Science Theater 3000. I loved Back to the Future, and I watched Batman Forever over and over again to see Jim Carrey play Edward Nygma.


Doc Brown in Back to the Future

Once I got a little older, I was able to appreciate some of the more sinister mad scientists in cinematic and literary history; characters like Dr. Moreau, Dr. Seth Brundle, and, of course, Dr. Victor Frankenstein. The mad scientists of movies and books helped to nurture my interest in the natural world, capturing my imagination in ways that the standard, garden-variety scientist sometimes did not.

Though an important and positive part of my childhood, the legacy of the mad scientist is actually quite complicated. The mad scientist archetype has grown out of society’s simultaneous fascination with, and fear of, scientific discovery, and thus it has had both positive and negative effects on the public perception of science.

The good: mad scientists are creative and exciting

One great thing about mad scientists as fictional characters is that they help keep the public engaged in science. Science is commonly perceived as boring. Scientists are generally thought of as generic and unsmiling (even by scientists themselves!) and science is seen as a mind-numbingly mundane process. Mad scientists, in contrast, are anything but boring. The mad scientist is an engaging character that tends to shake things up- when a mad scientist is on the scene, you know things are about to get interesting (and probably a little bit weird, too).

Another positive of mad scientists is that they help to dispel the myth that science is not creative. Science is often viewed as the antithesis of art: people who are good at science aren’t creative, and people who are creative can’t hack it at science. This misconception is particularly frustrating given that successful science actually requires a good deal of ingenuity and innovation. Mad scientists aren’t afraid to think outside the box- in fact, this is one of the hallmarks of their madness. They push the boundaries of scientific discovery, with sometimes spectacular, and sometimes disastrous, results.

The bad: mad scientists are eccentric, greedy, and immoral

The mad scientist has also done a fair amount to negatively impact the public perception of science. In fact, some of the most common misconceptions surrounding present-day scientists share apparent connections with the mad scientist archetype.

For instance, even the most benign mad scientists in fiction are often portrayed as zany and peculiar. Their laboratories are full of ridiculous rube goldberg-esque inventions, and they spend time developing elaborate and impractical schemes to solve trivial problems. Characters with these qualities include Back to the Future’s Doc Brown and Futurama’s Professor Farnsworth. At first glance, this trope may seem fairly harmless to scientists in the real world. However, politicians like Representative Lamar Smith routinely rely on this trope to argue against government support of academic research, citing seemingly obscure-sounding NSF-funded projects in order to make scientists sound eccentric and irresponsible.

Another common characteristic of mad scientists is that they are doing mad science for some kind of personal gain. Alchemists in 15th century fiction were commonly depicted as being motivated by greed, while comic super villains such as Lex Luthor and Doctor Doom are often in pursuit of power and control. And in this summer’s Jurrasic World, Dr. Wu got the mad scientist treatment when we found out he was creating genetically enhanced super-dinos for the US military, for profit. In the real world, this trope is particularly relevant to the climate change debate. Climate change deniers, seeking to undermine experts in the field, often argue that the researchers have fabricated results in order to increase job security and funding.

Finally, mad scientists in books and movies are frequently portrayed as having a corruptive influence on society. The scientist’s research is itself in direct conflict with morality, resulting in harm to the scientist and those around him. For example, Dr. Victor Frankenstein, Nathan from Ex Machina, and the creator of the Replicants in Blade Runner are all scientists that pursued taboo work, with disturbing results. In the real world, some of the most direct effects of this trope can be seen in the field of evolutionary biology. Evolutionary theory is thought by many to encourage immoral behavior, and this viewpoint is common enough that it continues to affect science education in schools throughout the US.

The future: Princess Bubblegum and diversity in the mad sciences

Mad scientists are exciting and creative. They are also often eccentric, greedy, and morally misguided. The mad scientist’s ambiguity is one of the things that makes him such a compelling character, but the negative characteristics of fictional scientists can have very real consequences for scientists and science educators.

Today, we are entering a new age in the world of the mad scientist. My proof? Princess Bubblegum, of the animated television series Adventure Time.

Princess Bubblegum is a fantastically unique and incredibly interesting character. She isn’t your typical mad scientist- she’s a she, for starters, and she’s a princess! She’s smart, curious, and morally ambiguous. Her science often falls more on the “mad” side of the spectrum. For instance, in an experiment gone wrong she created the Earl of Lemongrab, a lemon-headed creature who terrorizes and cannibalizes the inhabitants of his earldom. So yeah, definitely some mad science going on there.

Princess Bubblegum, doing science

Princess Bubblegum introduces some diversity into the incredibly one-dimensional world of the mad scientist. And her arrival on the mad scientist scene comes at a time when our perception of scientists in the real world is experiencing an overhaul as well.

Historically, we as a society have had a very narrow definition of what it means to be a scientist. Scientists have traditionally been pictured as straight white males, and also as “lone geniuses”- socially isolated, naturally gifted individuals that exhibit a dedication to their work that borders on obsession. In other words, what we commonly think of as the “ideal” scientist is essentially just the archetypal mad scientist, minus the bad hair day. Really, is it any surprise that the line between scientist and mad scientist can sometimes seem so blurry?

Fortunately, we are beginning to move away from this one-dimensional view of what makes a scientist a scientist. Thanks to recent campaigns highlighting diversity in STEM fields, greater recognition that scientific progress tends to be collaborative in nature (rather than the work of a single “genius”), and a push to address the shockingly pervasive “culture of acceptance” surrounding mental health problems in academia, we are closer than ever to dispelling the myth that only certain people belong in the sciences.

As we continue to achieve greater levels of diversity in the sciences, I hope that we also continue to broaden our horizons with depictions of mad scientists in fiction. And as the motivations, backstories, and personality traits of these characters become more varied, the outdated tropes of the archetypal mad scientist will inform our perceptions of real scientists less and less.

So here’s looking forward to mad scientists that shake things up, that break the mold, that play by their own rules push the boundaries of what we already know. Because, really, isn’t that what the mad scientist is all about?

And in honor of the upcoming holiday, please check out our compilation of some of the greatest mad scientists in cinematic history. Happy Halloween!