Muscles are extraordinarily complex biological machines. Made of elastic tissue, there are three main types: cardiac, smooth, and skeletal. Cardiac and smooth muscle groups are not under voluntary control — these muscles are responsible for the contractions in your heart and digestive system, respectively. In contrast, skeletal muscles are the only muscles that can be consciously manipulated. They also happen to be the most important muscle type for meat production.

Skeletal muscles' primary function is to contract, allowing you to make the thousands of small and large movements that get you through your day. To do so, muscles depend on chains of thousands—or tens of thousands—of myofibrils, the basic tube-like unit of a muscle cell. Myofibrils themselves are made from proteins, including actin and myosin, which are organized into thin and thick filaments. When you try to move a muscle, electrochemical signals are sent from the brain to motor neurons. These release a neurotransmitter called acetylcholine, which creates an electric potential across the membrane of the desired muscle's cells, causing calcium ions to flow into them and the filaments to slide. When thick myosin filaments slide along thin actin filament, muscles contract. Coordinating all this to produce movement requires a lot of energy, so muscle cells are also packed with mitochondria, the powerhouse of cells.

Muscles also contain other kinds of tissue. Muscle cells are bundled together and enclosed in a sheath of connective tissue, called the endomysium, which surrounds each individual muscle cell. Woven through the endomysium are nerve fibers and capillaries, which provide sensory feedback and supply the muscles with nutrients from the blood stream. Another common type of structure found in muscles is collagen—an important structural protein which regulates the firmness and elasticity of a given tissue.

As the protein filaments in muscle cells can be very long, muscle cells are organized in an elongated shape. Unlike other cells, muscle cells are produced during a process called myogenesis during neonatal development—which means that, after you're born, you almost never generate new muscle fibers. Instead, existing cells grow in size when the need arises. 

Muscle generation begins during embryonic development when stem cells—a unique type of cell that can develop into many types of specialized tissue or organ—start to differentiate into myoblasts, which are the precursor to muscle cells. During myogenesis, some of these myoblasts eventually mature into myobtubes, tubular structures with multiple nuclei (ordinarily, most cells only have one nucleus)—while the rest of the myoblasts continue proliferation to protect against future muscle damage. As muscle-generating myoblasts stop their cell division process and align themselves on a tubular axis, neighboring myoblasts start to fuse their cellular membranes, forming a muscle cell, known as myocytes. Even into adulthood, myosatellite cells (stem cells or myogenic cells, those with capability to make muscle) reside in the skeletal muscles of our bodies. Their most important task is muscle regeneration after damage. For example, if you pull a muscle while exercising, these stem cells can act as building blocks to repair the damage, fusing with the injured muscle cell.

Muscles, of course, can vary widely in size and strength from person to person. That's because muscle cells grow in size in response to mechanical tension, like regular exercise (although the total number of muscle cells stays the same.) This process is called muscle hypertrophy. It's still unclear how this growth is actually achieved, but there are (at least) two hypotheses: The first is known as "sarcoplasmic hypertrophy," which is where an increase in a carbohydrate called glycogen increases the volume of the muscles' storage areas, known as the sarcoplasmic reticulum. This increases the  total volume of the muscle. The second is called "myofibrillar hypertrophy," which is where muscle cells try to adapt to external tension—for example, by exercising, which increases the number and size of myofibrils. 

Most likely, both processes occur in parallel. In livestock, the same rules for muscle growth apply. The more animals move and exercise their muscles, the larger their number of muscular fibrils which may be associated with more juiciness and a stronger meat flavor. (An alternate hypothesis suggests there's no such benefit.) But there's an argument that's why the exercised meat from free-ranging cattle has a stronger flavor and texture than meat from fenced cattle, while cooped up chickens produce a tender meat from muscles which were hardly used during their lives. 

In fact, the journey from muscle to meat begins even before the slaughtering process. For instance, so-called "pre-slaughter stress" can dramatically affect meat quality. In pigs, this process is referred to as pale soft exudative meat, resulting in meat that is a very pale color and that tastes particularly acidic. In cattle and sheep, the equivalent is the self-explanatory Dark Firm and Dry Meat. Both defects cause the meat to be less valuable and unpopular with consumers. They happens because stress—perhaps caused by handling or stunning—affects the chemistry of the meat after death.

Typically, the reddish color of meat is determined by myoglobin, an oxygen-binding protein in muscle cells, similar to the hemoglobin in your blood. The concentration of myoglobin determines the color of the meat—that's why myoglobin-rich beef is deep red and myglobin-poor poultry characteristically white. When unstressed animals die, lactic acid builds up in the muscle cells, slowing their mitochondria activity. This leaves surplus oxygen (which would normally be consumed by the mitochondria) for myoglobin to bind with. The oxygenated myoglobin then turns a bright red color (think hamburgers). But when stressed animals burn through their glycogen stores, they have none left after death to produce lactic acid. Their mitochondria keep going like gangbusters, using up the muscles' remaining oxygen, and leaving myoglobin unbound—causing the meat to turn an unsightly purplish-pink color. This kind of discoloration costs the U.S. meat industry $1 billion dollars of revenue every year.

Meat undergoes further chemical and structural changes during cooking. As you may have noticed, meat changes both color and texture when warmed, going from red to gray to brown. These color changes are influenced by a few things. What myoglobin—the oxygen-binding protein in your muscles—is doing plays a big role. Myoglobin carries an iron atom which in turn carries oxygen, like your hand carrying a cup which in turn contains tea. Myoglobin that carries a lot of oxygen is a bright pink (like the color of ground beef, which gets mixed with air during grinding). When meat is exposed to air, the iron in myoglobin essentially rusts, spilling its oxygen, causing the meat to turn brown. Heat also denatures meat proteins. When cooked, myoglobin separates from its iron and forms a "hemichrome" pigment, also brown/tan-ish. When myosin and actin, muscle-movement proteins, are cooked, they unfold and form intricate knots—a similar chemical process occurs when you cook an egg. And, like an egg, meat becomes more firm during this denaturation process. After prolonged heat, collagen, the main protein in connective tissue, also breaks down to gelatin, converting cartilage into melting jelly.

Meat's shape is also altered by the loss of water during cooking, which typically causes it to shrink in size. This in itself leads to a drier product—but since fat also melts under heat, the perception of juiciness depends on the cut's proportions of fat and water. In fact, emulsions of fat and water are stabilized by proteins, such as myosin, which are more stable under high temperatures. This higher stability allows more water to remain in fatty meat than in lean meat while cooking. So, a cooked fatty cut of meat will have more water than a lean cut, once both are on the dinner plate.

Beyond these textural changes, meat goes through a series of taste-modifying chemical reactions as temperatures increase. During the Maillard reaction, usually occurring between 140 and 165°C, amino acids (for instance from degraded proteins) react with sugars to form thousands of different compounds, each with its own unique flavor. At higher temperatures, caramelization breaks down the structure of sugars and produces an even greater abundance of flavorful molecules. Finally at extremely high temperatures, pyrolysis, or charring, produces carbon from the complete breakdown of surface molecules. All of these changes contribute to an arguably more complex flavor in cooked food than you can often find in raw food.

Of course, that's only true if the antibodies do what they're supposed to. Biological substances such as poor-quality antibodies are major drivers of scientific studies that can’t be reproduced.

Reproducibility is one of the gold standards of sound science – to be considered trustworthy, a lab's results have to be repeatable by others. But around 36 percent of all research that has been flagged as irreproducible is caused by bad biological substances, making up a good third of the staggering $28 billion wasted every year due to irreproducible preclinical research.

An issue such as the quality of everyday research substances – one that seems fundamentally mundane – impedes the progress of medicine and costs every one of us dearly, financially as well as personally. Currently, there are no official standards for the quality of commercially available antibodies or evaluations by third-party institutions before commercial availability. As these unreliable preclinical studies, partly caused by poor-quality antibodies, distort entire scientific fields and endanger the lives of citizens relying on future healthcare, distributors of commercial antibodies have to take action by imposing stricter quality standards.

Two studies which comprehensively investigated the quality of commonly used antibodies tell a disconcerting story. In the first, published in 2010 in the journal Nature Structural & Molecular Biology by the group of Jason D. Lieb located at the University of North Carolina at Chapel Hill, all 246 of the commonly used antibodies in the field of DNA-binding protein modifications were tested. Of these, 25 percent bound multiple targets, instead of the one that they're supposed to do. Four antibodies were perfectly specific - yet to the wrong protein. In the second study, published in 2008 in Molecular & Cellular Proteomics by the laboratory of Mathias Uhlén at the Royal Institute of Technology in Stockholm, Sweden, researchers tested the quality of around 6,000 of the most commonly used commercial antibodies. The results were dismal; less than half of the antibodies were sufficiently specific for their supposed target protein. 

Eleftherios Diamandis, a cancer researcher at the Mount Sinai Hospital in Toronto, Canada, is one researcher who fell prey to this widespread issue. He just wanted to contribute to the fight against pancreatic cancer. As in practically every type of cancer, early detection is key, as it can increase the five-year survival rate from 5 percent up to 20 percent. What better way to detect cancer early than by a biomarker, a molecule indicating the presence of cancer if it is present in unusual amounts, measurable by a quick blood test? He and his collaborators found a promising protein from the pancreas, CUB and zona pellucida-like domains protein 1 (CUZD1), which seemed to reliably indicate the presence of pancreatic cancer.

To determine elevated levels of CUZD1, indicating cancer, they used a commercial testing kit, an enzyme-linked immunosorbent assay (ELISA). Briefly put, in an ELISA an antibody specific for the target protein, such as CUZD1, binds to the target protein and then a second antibody (specific for the first antibody) coupled to an enzyme is added. The amount of enzyme is then measured by, say, a color change induced by an enzymatic reaction. With this, the initial amount of CUZD1 can be inferred. Being commercially available from a major distributor of laboratory substances typically indicates standardization and reliability, which is why it is usually preferred to a self-made solution.

But something was rotten in the state of biomarker detection. When Diamandis and his team investigated whether their ELISA truly recognized their protein of interest (something most researchers would never attempt to do with a purportedly reliable commercial product), they found the horrible truth: their expensive product did not even detect CUZD1 at all. Instead, it measured the cancer protein CA125.

No wonder it presented a good biomarker for cancer – it literally was cancer. A poor-quality antibody in the commercial ELISA kit cost the Diamandis lab around $500,000 and many months of hard work. And worst of all, only a hair’s breadth away: if they didn’t question their results, an obvious next step would be a clinical trial to test whether early detection with this novel biomarker led to a better patient outcome. People could have died from the error, as the detection of cancer wouldn't have happened at an early stage but at a later stage where the cancer protein CA125 would be present.

Tackling an abstract problem such as the reproducibility of preclinical research is notoriously hard, as actionable procedures are not immediately obvious. One approach to make this feasible is to apply practical solutions to the much more tangible root causes of this problem. Poor-quality antibodies are one of these root causes for the reproducibility crisis of preclinical research. So what can we do about it?

Every link in the chain of the great human endeavor of research has to play its part to achieve improvement. Manufacturers of antibodies need to fulfill more stringent quality standards, testing their antibodies with multiple methods. These quality standards ideally should be set by an independent organization (at least partly consisting of scientists) that would certify the antibodies prior to their usage. Funding organizations should demand this antibody quality standard prior to the start of a project and editors as well as reviewers of scientific journals should demand them after the end of a project.

We should demand an improvement in the groundwork for clinical trials, starting with mandatory quality controls of commercial antibodies. We all entrust our life and health to these quality standards.