Proteins Are Machine Tools by Design
You Are A Product of Awesome Design Part 2
Up Front — A Quick Summary
What you are about to read is the second of two companion articles intended to awaken you to something obvious but not so widely known!
Up-to-date scientific evidence reveals the seemingly improbable is in fact reality. The numbers, the probabilities, as explained below exquisitely demonstrate this point.
Think about what you read because the evidence from science reverses long held thoughts and concepts taught within the scientific realm. Educators need to inform students of a huge paradigm shift regarding who we are. This is all about following the evidence where it leads!
To summarize briefly, consider this: You are made up of parts including a multitude of proteins that are uniquely shaped and function as molecular tools. These tools are part of a living factory and this applies to all of the cells in your body. Once you see how incredible each protein is, you will again be faced with a marvelous conclusion about how special it is to be alive and to be aware that life is not by chance.
Questions about Proteins as Machine Tools
Question: Is the chemical arrangement of molecules that make life possible simply arbitrary?
Question: How much specificity is necessary for the molecule to work?
Question: Is a discussion about enzymes just a simple observation about life, OR is there some awesome conclusion to be reached?
Answers to these questions are highlighted below by providing the probabilities that a specific functional arrangement exists beyond anything you might imagine as reality!
The answers will awaken you to how your life is supported by something incredible, improbable, and particularly by design.
Life’s Factory, a Look at Proteins: In 1986 a British-Australian biochemist, Dr. Michael Denton (MD, PhD), published a book that included a chapter with paragraphs that described cells functioning as factories.
“Protein molecules are the ultimate stuff of life. If we think of the cell as being analogous to a factory, then the proteins can be thought of as analogous to the machines on the factory floor which carry out individually or in groups all the essential activities on which the life of the cell depends. Each protein is a sort of micro-miniaturized machine, so small that it must be magnified a million times before it is visible to the human eye. The structure and functioning of these fascinating work horses of the cell was a complete mystery until the 1950s.” (Michael Denton, MD, PhD. 1986. Evolution: A Theory In Crisis. Page 234)
Seriously, cells operate like organized factory floor operations. Factories coordinate use of machine tools to do single or multiple functions, step-by-step in series, in a larger process … that sometimes assemble, rearrange, dismantle parts in production. The tools have specified shapes that determine function. For example, a hammer cannot turn a screw, a saw cuts but does not join parts, and a wrench does not cut, but each tool and its specified shape in fact supports specific factory function.
More recent, very detailed descriptions of biochemical and genetic studies reveal that proteins are a cell’s molecular machines and machine tools—tools that make metabolic pathways functional. From the cellular production floor these machine tools support the mechanics to the larger overall C-robot—that is you, a human being (See companion article about carbon-based robots).
Dr. Denton writes about how there is an array of different protein molecules that play additional roles.
“Most proteins consist altogether of some several thousand atoms folded into an immensely complex spatial arrangement. Proteins which perform different functions have completely different overall 3-D structures and functional properties.” (Michael Denton, MD, PhD. 1986. Evolution: A Theory In Crisis. Page 238)
Proteins make up hair, fingernails, are involved in various cell functions, but most interestingly include enzymes—these are the ‘machine tools’ of the cell that are involved in chemical pathways making, breaking, and modifying the chemicals that make physiology and metabolism functional for your being human.
The Specific Shape of the Protein Tool
The place in the enzyme itself that is able to conduct a chemical function is called an ‘active site,’ and that is characterized by a specific location in the molecule that is pictured three dimensionally by the word ‘fold.’ Think of a long chain of subunits (amino acids) that are strung together like a string of beads. Each subunit has a character all its own and when strung together those properties are responsible for the resulting elaborate three-dimensional (3-D) shape of the enzyme including a very specific set of ‘beads’ that make a very specific active fold shape. In other simpler terms, the ‘beads’ are amino acids that can have a charge that attracts or repels other amino acid molecules. Thus the string of ‘beads’ makes an overall folded shape, with a specific fold inside for just the active site.
While the quotation from Dr. Denton’s book, published in 1986, gives us the analogy of proteins as micro-machines, the specificity and improbability that proteins just come about by chance requires added investigation and evidence. The work of a protein biochemist in more recent time, Douglas Axe, PhD, provides the evidence necessary to awaken us, even shock us, into an awareness of the complexity and specificity or each unique protein—especially in the portion of the protein that is the active site.
NOTE: There is insufficient space in this article to give a full account of the research and writings of Dr. Axe. A more detailed account, for example, appears in Dr. Axe’s book: Undeniable: How Biology Confirms Our Intuition That Life is Designed. However, a few key points will be presented here.
Key Point: The composition of the ‘strings of beads,’ the order of the stringing of the chains of amino acids, is specific for the entire protein, but highly specific for the functional fold in order to make a functional enzyme.
The example below is a diagram of Glucosidase enzyme with its central active site which is the internal place with a functional fold where one maltose is split into two glucose molecules.
For example, let’s consider the functional section of a protein made up of only 150 amino acids. This functional region of the protein, with one specific active site, opens the way to assessing the probability of that protein originating simply by chance.
In simple terms, if you were to build a string of beads and have 20 different bead types (perhaps all differing in color and shape) to use at any of the 150 locations along the string (e.g., of a unique colorful necklace), then you have an analogy for how to compose a protein active site made from the 20 amino acids that are biologically available to make an enzyme. Also, be aware that some enzymes have more than one functional site, thus adding to further complexity to this scenario.
Awakening #1: The probability to achieve a specified and certain string of 150 specific amino acids requires a probability factor that multiplies a chance of one of 20 possible amino acids at each of the 150 locations along the string. For example, if we had a string of four amino acids, we would multiply 20 X 20 X 20 X 20 which equals 160,000. Simply, the probability of chance arriving at the specific four amino acids in the specific sequence is one chance in 160,000. That is for only four amino acids. What is the probability when it is 150 amino acids? The result is one chance in 10 to the 77th power (in scientific notation = 1077) or 1 followed by 77 zeros!
From the abstract of a peer reviewed scientific journal, Dr. Axe states:
“Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 1077, adding to the body of evidence that functional folds require highly extraordinary sequences.” (Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Fold, published in: Journal Molecular Biology, Volume 341, Issue 5, 27 August 2004, Pages 1295-1315)
Would you buy a lottery ticket where you had one chance in 1077 to win a jackpot?
Awakening #2: How big a number is 1077? One estimation of the number of atoms in our Milky Way galaxy comes to 2.4 × 1067 atoms. To arrive at a protein active site made of only a specified 150 amino acids is way more improbable than if you were to try and by chance locate one specific atom in the galaxy. 1077 is hugely greater than 1067 and it simply defies logic or reason to think life is by chance.
Awakening #3: Particular proteins are tools with specific jobs that perform factory-like operations to sustain life. Your life depends on 1300 different enzymes for metabolism, your body’s physiology. Enzymes work individually or in a series working together like a factory production line. How did that coordination of multiple enzymes come into being? Take the improbability for one enzyme and think of that across the unique nature of over 1000 enzymes … multiply that improbability by the improbability of another enzyme and ask yourself how that supports the notion your existence is by chance!
There is an added writing by Dr. Axe and Dr. Gauger that looks at how many mutations would be required to modify a functional enzyme protein into another relatively similar enzyme. They estimate for one example that some seven steps, or seven mutation changes, would be required to make a full transition from one functional enzyme to another very similar enzyme. Biologists know that mutations would have to be highly specific and sequence coordinated to arrive at another functional result, but also that mutations, even as few as two in series result in a compromised or non-functional result (i.e., lethal and totally compromised). In other words, rather than leading to some evolutionary advancement or advantage, mutations (changes to a protein) predominantly degrade or eliminate function (or otherwise cause change with no effect).
Key Summary Point: Take one highly improbable molecular tool and multiple the improbability by all the improbabilities of all the other such molecular tools and you are faced with the question of how you even came into existence. The activity of each tool is unique and reflects design, not only for the one molecular tool, but the presence of all other required molecular tools in a cell to make life functional for that cell and on the whole for your entire body, your existence, your being alive.
The resultant reflection you are left with is both scientific and theological! Specificity, complexity, and the coordination of what is illustrated here is a revelation of design … which itself leads to questions to the purpose of being alive. Why are you here? What does your existence in this life offer you? The WindowView Harmony Area helps to broaden the view and address other aspects of our lives. Take a look, explore, and view the larger picture to the underlying purpose to why you have a life!
