It’s the Environment, Stupid!

Hello! Welcome and thank you for joining me in another post in my series Meta-Moments. I had so much fun writing my previous post on The Biology of Belief by Dr. Bruce Lipton (see: Looking Beyond our DNA for Life’s Determinism) that I decided to go ahead and dive into Chapter 2 of this incredibly novel book. Chapter 2 happens to be a little more “pointy-headed” or rather emphasizes several scientific studies regarding the description of DNA and how proteins are built from their constituent amino acids. Nevertheless, I’m going to do my best to explain these pages in a manner that will be easier to understand.

The chapter’s name is funny it’s called “It’s the Environment, Stupid!”. Listen to how Dr. Lipton came up with such a title: “My professor, mentor, and consummate scientist Irv Konigsberg was one of the first cell biologists to master the art of cloning stem cells. He told me that when the cultured cells you are studying are ailing, you look first to the cell’s environment, not to the cell itself, for the cause. [Furthermore], Bill Clinton’s campaign manager, James Carville, who decreed, ‘It’s the economy, stupid,’ for the mantra of the 1992 presidential election.” Thus, Dr. Lipton used this mantra with a slight variation arriving at “It’s the environment, stupid!” and we’re going to get into why.

Since the dawning of the Age of Genetics, we have been programmed to accept that we are subservient to the power of our genes. The world is filled with people who live in constant fear that, on some unsuspecting day, their genes are going to turn on them. Consider the masses of people who think they are ticking time bombs; they wait for cancer to explode in their lives as it exploded in the life of their mother or brother or sister or aunt or uncle. Millions of others attribute their failing health not to a combination of mental, physical, emotional, and spiritual causes but simply to the inadequacies of their body’s biochemical mechanics. Of course, there is no doubt that some diseases, like Huntington’s chorea, beta-thalassemia, and cystic fibrosis, can be blamed entirely on one faulty gene. But single-gene disorders affect less than 2% of the population; that’s mind-blowing! That means that when you are concerned about genetic disorders that are potentially passed on to you, the likelihood of that being the fundamental cause of your disease process is less than the factors like mental, physical, emotional, and spiritual causes. Only 2% of genetic diseases are hereditary without much influence from the environment. Illnesses that are today’s scourges like diabetes, heart disease, and cancer – can short circuit a happy and healthy life. But they are not the result of a single gene. They are the result of complex interactions among multiple genes and environmental factors.

Nevertheless, confusion has reared its ugly head in explaining such a straightforward concept. For example, the media has repeatedly distorted the meaning of the words: correlation and causation and that it’s one thing to be linked to disease, but it’s quite another to cause a disease, which implies directing and controlling the action. For example, if I show you my keys and say that a particular key “controls” my car, you at first might think that makes sense because you know you need that key to turn on the ignition. But does the key actually “control” the car? If it did, you couldn’t leave the key in the car alone because it might just borrow your car for a joy ride when you’re not paying attention. But really and truly, the key is correlated with the control of the car. The person who turns the key is the one who controls the car. Specific genes are correlated with an organism’s behavior and characteristics, but they are not activated until something triggers them. What’s that trigger? It’s the environment, stupid!

The idea that genes control biology is a supposition. It has never been proven, with the latest scientific research undermining it. Nevertheless, “genetic control” has become a metaphor in our society. We want to believe genetic engineers are now the new medical magicians who can cure disease while they’re at it and create more Einsteins and Mozarts. But metaphors do not equate to scientific truth. When a gene product is needed, a signal from its environment, not an emergent property of the gene itself, activates the expression of that gene. In other words, when it comes to genetic control, it’s the environment. Thus, our cells are mainly an assembly of protein building blocks. One way of looking at our trillion cell bodies is that they are protein machines, although as you know, I think we are more than machines. It takes over 100,000 different types of proteins to run our body. And let’s take a closer look at how our cells assemble these 100,000 proteins. Each protein is a linear string of linked amino acid molecules. Think of a child’s pop bead necklace representing a string of amino acids linked together through a polypeptide bond. But it is not a perfect replica of how an amino acid works because amino acids influence the protein by creating a slightly different shape. To be completely accurate, think of a pop bead necklace that got mangled in the factory, so it’s more clumped up in nature.

Twenty amino acids make up proteins. Each protein is comprised of a specific sequence of amino acids, giving the protein its particular function. Proteins can range from only 150 amino acids to thousands of amino acids! The backbone, which connects the amino acids, is known as the polypeptide chain, and the rotation of this polypeptide bond gives a protein its unique shape and confirmation. There are four classes of amino acids, including polar (water-loving), non-polar (water-hating), positive charged (basic), and negatively charged (acidic). A protein containing different types of amino acids constitutes confirmation; for example, non-polar amino acids stay away from water and bury themselves inside the core of the protein. Positively charged amino acids will be attracted to the hydrogens of water and the negative charges (if present) of basic amino acids. Most amino acids have a positive or negative charge which acts like magnets. Like charges cause the molecules to repel each other, two positive charges would repel those beads apart, but opposite charges will bring them together. Therefore, you can imagine that the protein’s backbone will conform based on the amino acids present and their charges. Changing confirmation generates movement, and the movement is harnessed to do work, providing such functions as digestion, respiration, and muscle contraction. When the signal molecule detaches, the protein returns to its preferred extended confirmation. This is how signal-generated protein movements provide for life. A signal comes in, it has an attraction or repellent to it based on its charge, and it makes the protein move in such a way that allows for a specific function. When that signal is removed, the protein goes back to its original state.

You’ll notice that we did not discuss DNA at all. It’s because of the conformational changes of the protein as a result of the amino acid’s electromagnetic charges that are responsible for behavior generating movement, not DNA. How did we get to the widespread and cited notion that genes control biology? In The Origin of Species, Darwin suggested hereditary factors were passed on from generation to generation and control the traits of the offspring. His influence was so significant that scientists myopically focused on identifying that hereditary material they thought controlled life. Thus, in 1910 intensive microscopic analysis revealed that hereditary information was passed down to subsequent generations, which was found within chromosomes: a threadlike structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes. Additionally, each chromosome is divided into two sections (arms) based on a narrowing (constriction) location called the centromere. By convention, the shorter arm is called p, and the longer arm is called q. The chromosome arm is the second part of the gene’s address.¹

Furthermore, chromosomes are incorporated into the daughter cells’ largest organelle, a smaller portion of the cell called the nucleus. When scientists isolated the nucleus, they dissected the chromosomes and found the hereditary elements comprised of two kinds of molecules: protein and DNA. Somehow the proteins machinery of life was entangled in the structure and function of these chromosome molecules. The understanding of chromosomal function was further refined when Watson and Crick showed that DNA contained hereditary information.

Just what exactly is DNA? Well, for starters, DNA stands for deoxyribonucleic acid, where a single molecule that makes up DNA is termed a nucleotide (or nucleic acids). Each nucleotide is comprised of a phosphate group (which links to other nucleotides through a phosphodiester bond making the backbone of DNA), a ribose sugar molecule with a free hydroxyl group at the 2’-carbon (hence deoxyribose), and a nitrogen base. There are four types of nitrogen bases, which can be classified into pyrimidines and purines. Note that one pyrimidine always hydrogen bonds with one purine. The two pyrimidines in DNA are adenine (A) and guanine (G). The two purines are thymine (T) and cytosine (C). As you now know, adenine hydrogen bonds to thymine, and guanine hydrogen bonds to cytosine. Why pyrimidines hydrogen bond to purines is beyond this post, but if you are interested in learning more, please let me know! These hydrogen bonding patterns between two strands of DNA are what make up the double helix. For the DNA sequence to be expressible, it is first transcribed into a complementary molecule known as RNA (ribonucleic acid). RNA leaves the nucleus into unique organelles known as ribosomes, where polypeptide chain synthesis can begin. Every three nitrogen bases along the RNA sequence (known as a codon) signals for an amino acid to enter the ribosome. Each codon is specific for each of the 20 amino acids. For example, if the codon reads AAG, L-Lysine will be signaled to the ribosome. This process continues until the entire RNA molecule is read and all the corresponding amino acids are linked together through a polypeptide bond. This string of amino acids is what constitutes a polypeptide chain. And once the polypeptide change takes on its correct confirmation, then it will be called a protein.

Genes are specific segments of DNA. Depending on what needs to be expressed, transcription and translation proteins will unwind that specific segment of DNA to produce the proteins needed. The aforementioned explanation is what constitutes the central dogma: DNA -> RNA -> Proteins. The central dogma’s assumption is that there is a one-way flow of information. In addition, since proteins represent the physical body, the dogma implies that your physical body is your life experiences cannot send information back and alter the DNA. Meaning, DNA controls your life, and you cannot influence your DNA. This led scientists to believe that DNA rules the expression of information. The central dogma was so fundamental to modern biology; it was essentially written in stone, the equivalent of science’s Ten Commandments. The central dogma also referred to as “the Primacy of DNA,” is a fixture of almost every scientific text. Nevertheless, as we are seeing, epigenetics is proving this claim wrong.

Now we enter the age of the Human Genome Project. A global scientific effort started in the 80s, and it was an ambitious one from the outset. Conventionally we thought the body needed one gene to provide a blueprint for each of the 100,000 different proteins that make up our body and at least 20,000 regulatory genes which orchestrate the activity of protein-encoding genes. Then scientists concluded that the human genome had to contain a minimum of 120,000 genes to create these 23 pairs of human chromosomes. Geneticists experienced a considerable shock that contrary to their expectations of how many genes humans have, they found that the human genome contains fewer than 25,000 genes, much less than they initially thought. So what’s going on?? Check out my next blog in our Meta-Moments series for answers. Thank you so much for reading! Please comment below if you have any questions!