Muffins, Demystified

A glimpse into the chemistry of baked goods and an experiment with {Butternut Squash Sourdough Muffins} with {Caramel Swirls} and {Crumble Topping}

There comes a liberating moment in every cook’s development when you realize that you don’t need a recipe anymore. At least not for everything. You can make marinara by taste, and you no longer feel compelled to google whether or not it’s OK to put eggplant in a curry. You start inventing dishes—why not put lentils, quinoa, and kale into a pot and slow cook a stew? Why not roast thinly sliced vegetables and pile them high with layers of white bean hummus in between? Why hadn’t you thought of the possibilities before?!?

In your excitement, your attention might turn to desert, and to baking, and suddenly, all bets are off. The mysterious nature of the transformation of batter in a bowl into the graceful delicacy of finished baked goods is enough to undermine the confidence of the most seasoned home cook. What kind of inscrutable alchemy goes on inside those little muffin cups and that innocuous cake pan?

Often, the caprice of the baking process can cause us culinary explorers to falter even among the well-worn pages of our cookbooks, relegating us to the dreary realm of tried and true baking mixes. Sometimes, we go barreling ahead into unchartered territory, our ignorance notwithstanding, with underwhelming results. I confess that I did this yesterday. In preparing for this post, I thought I would just whip up some muffins, with some significant changes to my standard recipe. What emerged was a gooey, structureless—albeit delicious—excuse for a muffin. I was planning to write about the chemistry of baking, but this gave me an added incentive: I needed to figure it out just to make something edible out of my good idea!

The Constitution of Confections

The basic components of cake are fat, sugar, flour, and leavening agents. Fat and sugar make the cake moist and soft, while flour and leaveners give it structure and rise. The former prevent long chains of gluten from forming by binding to the proteins, which keeps the dough from becoming chewy. Low protein or cake flour also provides assistance in this department, as there is less protein to deal with in the first place.

A less obvious role for fat and sugar is their strong control over texture. It turns out that the “crumb” is almost entirely driven by how many microscopic air bubbles the fat contains. Just like in bread, the gas inside these pockets will expand when heated, making the resulting baked good light and airy. And as with bread, an even distribution is important for a uniform result. Evenness is attained by kneading in bread, and by creaming the butter and sugar for sweet doughs. This is often the first step in a baking recipe, but its importance usually goes unstated. In reality, this is probably the most crucial part!

Appropriately creamed butter

But why do you need the sugar? The grains of sugar actually supply and help incorporate air into the fat during mechanical mixing. The best fats are those that are solids at room temperature, because these can trap and retain bubbles. Butter is the traditional choice, but shortening is commonly used now because it comes with pre-incorporated nitrogen bubbles! However, I still prefer the taste of butter, and I’m always a fan of less-processed food.

Eggs serve a dual role as an emulsifier (the yolk) and leavener (the white). Lecithin in the yolk helps ingredients to mix more thoroughly, improving the consistency of the cake and elevating it to melt-in-your-mouth moistness. The proteins of the white, on the other hand, defy logic by becoming more organized after beating rather than less (take that, entropy!). They help increase the volume of the dough and give it some shoulder. Using fresh eggs is paramount to their leavening ability as the proteins break down the longer the egg sits on the shelf.

When it comes to proportions, cakes should follow the honorable example of the French quatre quarts cake—meaning four quarters. This contains a pound each of butter, sugar, flour, and eggs. These ratios can be tweaked slightly depending on the kind of cake you are after, but the basic relations apply: equal weight of flour and sugar, eggs and fat, and liquid and flour.

Lastly, I want to touch on that age-old question: what the heck is the difference between baking soda and baking powder? It’s pretty simple really. Baking soda is pure sodium bicarbonate. When it reacts with acidic ingredients, it produced CO2, forming bubbles and causing the batter to rise. This reaction starts immediately, so it’s important to bake goodies with baking soda immediately after mixing the wet and dry ingredients!

Baking powder on the other hand, comes with its own supply of acidic compounds, in case your recipe is lacking. Powders dubbed “double-acting” release some of their CO2 immediately, like baking soda, and some only when heated. So recipes with baking powder can wait a little longer before going in the oven, but it is still wise never to delay. The reason to use these leaveners instead of yeast in the first place is because the batter is too weak (too low in gluten) to trap gas for very long before it bubbles out and escapes. The rule of thumb is ¼ tsp. of baking soda, or 1 tsp. baking powder for every cup of flour in your recipe. Invent away!

There you have it: everything I know about baking cakes and muffins. In the recipe below, I experiment with using some sourdough starter in place of flour and adding butternut squash. We can still get frozen local squash at the store, and what better for a rainy March morning? To compensate for the increased water content of these additions, I cut back on wet ingredients, and substituted sour cream for buttermilk or milk, because it conveys the same flavor with less liquid. I give the recipe in it’s full complexity, but the caramel swirl and crumble topping could easily be omitted. The result is a lovely, moist muffin with moments of decadent sweetness and others of hearty sustenance. The flavor of the squash permeates, enveloping all in its subtle, sweet embrace.

Butternut Squash Sourdough Muffins with Caramel Swirls and Crumble Topping
(Makes 18)

½ c. butter, slightly thawed but not room temperature
1 c. brown sugar
½ c. fine baker’s sugar
2 eggs, room temperature
1¼ c. cake or low-protein flour
1 tsp. baking powder
½ tsp. baking soda
½ tsp. cinnamon
¼ tsp. nutmeg
pinch of salt
¾ c. sourdough starter
½ c. sour cream
2 c. cubed butternut squash, pureed

For topping:
½ c. caramel, made ahead and cooled to room temperature
1 c. crumble

*If you do not want to use sourdough, increase the amount of flour to 2 cups and use ½ c. of buttermilk in place of sour cream.

Preheat the oven to 350°F.

Using an electric mixer, cream the butter for several minutes, until peaks form. Add the sugar and mix for 5 minutes more, until the mixture has increased in volume and lightened several shades. Add the eggs and beat until incorporated.

In a separate bowl, combine the flour, baking powder, baking soda, cinnamon, nutmeg, and salt. Mix thoroughly.

Alternate adding the flour mixture, sourdough starter, and sour cream to the wet ingredients, mixing gently. Fold the squash puree into the batter.

Spoon into a greased or lined muffin tin. If making the caramel swirl, drop an almond-sized amount on top of each muffin, then swirl using a few strokes of a knife. Do not over-mix or the swirl will get diluted.

Top with crumble and bake for 30 minutes, or until a toothpick comes out clean.


This was a new adventure for me, and I fear that it is something like learning how easy it is to make popcorn at home: I have a hunch I am going to make it all the time!

½ c. fine baker’s sugar
3 tbsp. butter
A pinch of salt
⅓ c. cream or half & half

Place the sugar in a medium saucepan over medium heat. Watch carefully for the first signs of melting. Using a heat-proof utensil, stir by occasional single strokes, pulling from the outside of the pan to the center. Watch the color carefully, and remove from heat when the sugar reaches a light brown (also known as caramel) color as this will quickly lead to burning.

As the sugar becomes molten, stir more continuously to break up any lumps. When it is smooth and caramel-colored, lower the heat, and add the butter and salt. Stir continuously to prevent lumps from forming.

When the butter is fully incorporated, slowly add the cream, stirring continuously. Remove from heat and let cool.


This seems like a simple concept, combine some butter and sugar into a salty, sweet muffin topping. However, I’ve had numerous failures with crumble, mostly stemming from recipes that instruct you to cut in the butter. This either results an uneven distribution of butter, with large patches of just sugar, or too even a distribution, drenching the underlying muffin. This procedure works well for me, and is simple and straightforward.

½ c. brown sugar
½ c. all-purpose flour
a pinch of salt (optional)
spices (optional)
1/3 c. butter, melted

Combine the dry ingredients in a bowl. Slowly add the melted butter, stirring with a fork as you do. The mixture should form small pebble-sized clumps. Sprinkle on top of muffins for a tasty topping!

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