Cooking from Scratch

cucumber and turnip

Everything that comes out of our kitchen is made from scratch, start-to-finish. We are committed to 100% scratch cooking for many reasons. The food tastes amazing, of course, but this style of cooking also gives us complete control over ingredient quality and freshness. We are able to make sure that absolutely zero cross-contaminants enter our food.

We also pay very close attention to each of our ingredients once they come into the kitchen— we store each item properly and we never pre-slice, chop, or grind anything until right before we’re about to use it. Why? Pre-prepped produce and protein is far more susceptible to microbial spoilage than in its whole state. Produce comes fully equipped with protective outer layers, and it is silly to just throw that away. When it comes to protein, the more surface area exposed to oxygen, the faster the meat will spoil. We put so much effort into sourcing great ingredients that it would be a shame to see any of them go to waste!

Many of our steps are easy to implement at home, and we want to encourage you to start cooking from scratch as frequently as possible. Below, we’ve added some tips for maximizing your time and energy in the kitchen.We also recognize that many of you simply don’t have the time to cook elaborate meals during the week—that’s where Mission: Heirloom comes in! We’ve done the safe preparation and storage so you don’t have to.

We confit our octopus in beef fat. It's delicious, trust us!

Seal off meat and vegetables with a layer of fat to keep oxygen out and goodness in.


Shop wisely: The first step to quality cooking is careful shopping. Seek out the best products you can afford, and purchase only whole ingredients. Organic and biodynamic produce is the best choice; if you’re on a budget, take a look at the Dirty Dozen to maximize your dollar. Look for pastured, organic, and grass-fed meat. Skip the pre-chopped veggies and pre-ground meat. Remember: the fresher your ingredients, the better the dinner!

Chop to order: Avoid slicing, peeling, and chopping ahead of time. Produce is much better at protecting itself from spoilage when it is in its whole state than when it is chopped. If you absolutely need to pre-peel or chop (like for make-ahead lunches), be sure to eat the food within a day.

Seal out oxygen: If you plan to batch cook meals ahead of time, make sure you’re taking the proper steps to seal out oxygen. You don’t actually need to use plastic to do so—fats are a great way to protect food. Store cooked food in glass jars or storage containers and cover completely with a layer of melted butter, ghee, tallow, or coconut oil. The fat will form a solid layer over the food. Remove (or don’t) before reheating and serving.

Utilize your freezer: While there are countless detrimental microbes that can grow at safe refrigerator temperatures, there aren’t many that can survive the freezer. Store meat and even fully cooked meals in the freezer for super safe keeping.

Whole, organic or biodynamic vegetables will have a higher nutrient content than commercial, pre-cut veggies.

Swap out baby carrots for young, whole varieties—bonus points if they’re colorful!


Starting from scratch takes much of the uncertainty out of cooking. Think about it—you end up with 100% control over the ingredients making it into your dinner. Making bone broth from scratch and avoiding convenience products like canned food are obvious steps, but there are also other considerations to keep in mind.

Food Storage and Spoilage

It is fairly common knowledge that foods like ground beef will spoil more quickly than a whole steak. Likewise, meats packed in vacuum bags will keep fresh longer than those in looser containers and wraps. But it may be less obvious that this rule applies to fruits and vegetables as well.

In their whole, unpeeled state, produce will remain unspoiled for five days to several weeks in a properly chilled fridge. Why? Produce comes “packaged” in its own protective coat. Even the millimeter-thick skin on carrots keeps bacteria, molds, and yeasts from reaching the sweeter flesh within. Peel and remove that skin and microbes will flock. Of course, there is no sense in worrying about the minutes or even hours after peeling a carrot or cutting a peach and adding it to a pot (or into your tummy). The far bigger concern with peeled and sliced produce has to do with the grocery store.

As American shoppers have become more and more preoccupied with saving time in the kitchen, a proliferation of pre-peeled and pre-cut vegetables packed into their own neat little packages have made their way onto grocery shelves. What started with “baby” carrots now encompasses pre-packed salads, chopped squash, and even sliced apples. Some have preservatives added (take a good whiff of a bag of baby carrots and you’ll smell the extra chemicals) while others are relatively “pure.”

These preservative-free prepared fruits and vegetables may sound like a good, timesaving solution, but just because they’ve been refrigerated and look fresh doesn’t mean they are free of pathogenic microbes.


Raw vegetables keep best when they’re whole and unpeeled.

Gram-Negative Bacteria and LPS

One microbe that likes to grow on both produce and protein is gram-negative bacteria. Gram-negative bacteria encompasses a large category of bacteria that have an outer cell membrane surrounding an interior cell wall. This membrane protects the actual bacterial cell from antibiotics and other aggressors. Gram-negative bacteria includes both benign species as well as pathogenic groups like E. coli, Salmonella, and Enterobacter. Our guts contain both gram-negative and single-walled gram-positive bacteria. Some of these bacteria, like E. coli, are perfectly harmless when found in the right balance in our guts. However, when they escape the gut, they can wreak havoc.

Why? The outer membrane of gram-negative bacteria is made up primarily of large molecules called lipopolysaccharides (LPS). Each LPS molecule has a long tail called the O-antigen and a lipid head referred to as lipid A. The O-antigen tail sticks out from the bacterial cell, where it can be recognized by antibodies. Lipid A attaches LPS to the outer membrane of the bacterium, and it is the primary reason why gram-negative bacteria can be so problematic. (Not all gram-negative bacteria are pathogenic. Some, like cyanobacteria, are not suspected to cause problems in humans.)

LPS can make its way into the bloodstream in a number of different ways. It can be released by the gram-negative membrane as a normal part of the bacterium’s physiological activity, as a response to an attack, and when the bacterium is destroyed. When LPS makes its way into the bloodstream, it elicits a very strong immune response, causing fever, diarrhea, and even septic shock and death. LPS is classified as an endotoxin, which means that it is a self-contained toxin that is located within a bacterial cell. (LPS is often referred to interchangeably with endotoxin; but there are a few less-common endotoxins, such as the delta endotoxin located in Bacillus thuringiensis.) Endotoxins are only found in gram-negative bacteria. Gram-positive bacteria secrete exotoxins, which are only toxic when released out of the cell.

LPS and the immune system

Much of the body’s response to LPS is mediated by the immune system. Rogue LPS binds to receptors in many different immune cells, setting off a cascade of inflammatory signals. Some species of bacteria contain LPS molecules that look like other, non-pathogenic, molecules in the body, causing the immune system to attack healthy cells. These reactions can happen rapidly with little control and send the body into shock. LPS is strikingly good at sending the body into a tailspin; as little as 1 microgram/kg of pure LPS can induce shock.

As you might be able to imagine, LPS has been implicated in the exacerbation of autoimmune symptoms. Studies have linked increased circulatory levels of LPS with Guillain-Barre syndrome, Miller-Fisher syndrome, rheumatoid arthritis, and multiple sclerosis. In addition, LPS can interfere with insulin tolerance and absorption, and it can bind with endocannabinoid receptors in the brain, blocking the hormones that determine our satiety.

When gram-negative bacteria and accompanying LPS are found in healthy guts, they do not cause problems. But as soon as the gut becomes permeable, LPS can sneak out into the bloodstream. Recent research has consistently demonstrated that patients with IBS, Crohn’s disease, and other inflammatory disorders all have elevated levels of circulating LPS. Even more telling is new work suggesting that LPS could, in fact, increase or even stimulate gut permeability. As this work has only been tested on animals, it is too early to tell if LPS definitively can cause intestinal permeability in humans. Regardless, it doesn’t help.

stone fruit and succlent salad

Eat raw chopped produce when it is still super-fresh to reduce exposure to LPS.

LPS in our food

To return to the topic at hand, it is worth considering how much excess gram-negative bacteria we consume on a regular basis. As we mentioned above, pre-cut produce and proteins are far more susceptible to microbial spoilage than whole items. Some of this spoilage is visible or aromatic, and you’ll likely not want to eat it.

However, the levels of gram-negative bacteria can reach a pathogenic level before foods appear spoiled, especially when they are pre-prepped. A series of studies examined the levels of LPS and related immune stimulators in pre-cut produce and meat products, finding that even something as innocent as a peeled carrot could have clinically problematic levels of LPS after just four days in a typical refrigerator. Un-peeled, whole carrots showed minimal or undetectable levels of LPS. Not surprisingly, ground meat performed much worse; the best way to store meat is frozen in large pieces, stored in well-sealed bags.

An influx of LPS in the diet may not affect healthy individuals, but it could cause problems for those with gut permeability and/or those who have altered their gut flora after taking antibiotics. What’s the takeaway here? Peel, slice, and cook your produce and protein as you need it, and stay away from those containers of pre-peeled squash!


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