Arguments from design are not faith based guesses about biology in search of hopeful supernatural
comfort. Design is a logical argument about the world that is based upon known processes; tested chemistry and a good understanding of how information is created and used to build and maintain complex structures. In comparison, evolution is not an empirical science. It is historical science and is dependent on philosophical premises; based upon our current knowledge of biochemistry, biology, cellular metabolism, animal behavior and ecosystems. Indeed, the theory of evolution does not answer the hard questions. How did life arise? How did so many species come to be? Why are species distributed the way they are?
Though we laugh at the question, “Which came first the chicken or the egg?” there are many instances in cosmology and biology that require this question be asked and answered. A good example is found in the flow of information from the DNA molecule to the cell. It is the Central Dogma of biology that states cellular control flows from the information molecule of DNA to RNA to protein. When asked the question which came first, DNA (the information) or protein (the functional construct) evolutionary materialism is stuck. This is because the nature of the information flow in the cell is dependent on proteins to read the DNA code in order that those proteins and all other proteins can be manufactured. The conundrum is found in the fact that DNA cannot exist without proteins and proteins cannot exist without DNA. The system of genetic regulation of cellular metabolism is irreducible; neither the chicken nor the egg could have existed without the other.
Inherent in understanding cellular biology are the facts that proteins are not formed from amino acids just “falling together” from random collisions and DNA does not spring out of chemical mixtures spontaneously, no matter the conditions or how much time that the correct biochemicals are given to randomly bump into each other. This is true given any prebiotic conditions and it is certainly true of cellular metabolism. Proteins have specified complexity. They are encoded for by the DNA molecule to be assembled from amino acids in a precise sequence in order to properly fold and carry out their specific role in cellular physiology. They must be assembled with precision. Of the many DNA encoded informational parameters for protein production is their ability to spontaneously assemble to form a complex structure that can read the DNA molecule, to polymerize RNA, to edit the RNA and to shuttle it out of the nucleus into the cytoplasm of the cell. Other multimeric protein structures read the RNA code in order to produce more proteins that are required by the genetic program. Neither proteins nor RNA nor DNA will form without the guidance of the cell (or by human engineering).
Proteins that work as enzymes are able to speed up biochemical reactions (metabolism) in the cell a million times faster than the rate of synthesis or degradation by random chemical collisions. More than this, cells control the manufacture of proteins; when they are produced, where they are localized, what types of proteins and how much of each protein is made are all determined by a
network of regulatory pathways. Such regulation forces biochemical pathways in a particular direction. Proteins and genes receive feedback from the products that they form and from the reactants waiting to enter the reaction. The rigor and robustness of the control strategies found intact in the cell are just beginning to be understood in molecular biology. Furthermore, DNA is now understood to have two languages embedded in its chemical code and some would argue much more than just two. One message specifies the protein sequences and another language regulates protein metabolism through signals in the DNA or the RNA or the protein itself. Remember that the function of any protein molecule is the result of the DNA message, therefore, the DNA determines what regulatory features the protein is endowed with. What is clearly understood is that DNA is useless until proteins recognize its various molecular signals, which act as switches, enhancers, and repressors for the flow of information from the genetic code. To suppose that chemistry has a natural tendency to counter entropy or has advanced knowledge of biological requirements of living systems is a violation of what is known about chemistry, biology, and physics. The biological system of gene regulation is a complex system of interdependence that cannot be reduced further or it becomes nonfunctional; it is irreducibly complex. Which came first the DNA
or the protein that it encodes? Which came first; the cell or the DNA that encodes the biology of the cell?
Irreducible complexity describes many features of life at the cellular and organismal level. The cell possesses many complex structures composed of many components. Each component has a specified function in the overall structure that then supports the function of the whole structure. Michael Behe was the first scientist to define irreducible complexity. He used the bacterial flagellum to show the irreducible complexity of molecular machines. Each of the components that make up this organelle is required for the overall function of the flagellum, which is used to move bacteria through water. No sort of evolution can account for the existence of parts of the flagellum. All of the parts are required to exist for the flagellum to work. Even the construction of the flagellum is coordinated for self-assembly of the proteins that make up this organelle.
Another example is found in the organelle called the ribosome. This molecular machine is able to read the RNA transcripts from a gene and then translate the coded sequence into protein molecules.
The structure of the eukaryotic ribosome is complex, involving 4 RNA molecules (ribosomal RNA or rRNA) and as many as 70 proteins that bind to the RNA or to one another to form the two major units of the ribosomal organelle. Some proteins interact transiently to build and regulate the protein synthesis machinery. The two subunits that form the ribosome are called the large and the small subunits. When an RNA transcript is free for translation into a protein molecule, the two subunits attach to specified sequences on the strand of RNA and the code is read as amino acids are enzymatically linked together, like beads on a string, to form a new protein. As the strand of RNA is shuttled through the ribosome, a termination signal encoded in the molecule ends the synthesis of the new protein. Both the RNA and the new protein are then released.
Assembly of a flagellum in bacteria. Michael Behe’s example of irreducible complexity and my example of proteins that self assemble.
So which came first, the proteins or the ribosome? Once again the conundrum exists between the cell’s need for a complex molecular machine to produce proteins and the proteins required to produce the molecular machine that makes proteins. One cannot exist without the other. The ribosome requires the essence of approximately 72 genes to function and even more to assemble correctly. Ribosomal genes are found in tandem repeats of several hundred identical sequences in mammalian cells. They produce only rRNA.
An enormous ribosomal manufacturing complex called the nucleolus is found in the nucleus of cells. The rRNA that is transcribed from ribosomal genes requires processing for new RNA strands to be mature and act as the backbone of the ribosome. Over 200 protein factors and 76 small nucleolar RNAs associate transiently with the pre-ribosome to accurately construct the ribosome. While the rRNAs act as the scaffold for the 70-100 or so proteins that will spontaneously bind to the rRNA, the rRNA must first fold back on itself to form a three-dimensional structure with hairpin loops and internal complementary double-stranded binding. The 70 protein-coding genes are transcribed into 70 unique messenger RNA (mRNA) molecules. These must be translated by existing ribosomes into 70 unique proteins in order to form new ribosomal subunits. All ribosomes are made in the nucleus of eukaryotic cells so that all ribosome proteins must be translocated into the nucleus for assembly of the ribosome in the nucleolus. Elaborate mechanisms exist to monitor the formation of correct structural and functional “neighborhoods” of the assembling ribosomes and to destroy pre-ribosomes that fail to assemble properly.
Quite remarkable and a property intrinsic to proteins is the ability for them to self-assemble. For the construction of the ribosome, the proteins for the large subunit and those for the small subunit have been shown to bind to their respective sites in an orderly and sequential manner. In fact, the nomenclature used to follow each protein to its binding site is based upon which protein must bind first for other proteins to bind in sequence to create a functional ribosome. The proteins are numbered as L1, L2 or S1 and S2 for the large (L) or small (S) subunits based upon the sequence of their binding. At least 70 proteins are known to bind in a coordinated way on or around the RNA scaffold. Other proteins may be temporarily associated with the mRNA, transfer RNAs (tRNA), ribosomal complex or are involved in the energetics of powering the ribosome to build the new protein.
In Drosophila melanogaster, disruption of RP genes results in the ‘Minute’ syndrome of dominant, haploinsufficient phenotypes and are typically lethal. The absence or the mutation of any one of these proteins can effectively shut down the functionality of the ribosome. In many cases, defective ribosomes have been found to be an inherited characteristic. The resultant organism develops slowly and incompletely, most often resulting in fatality before complete maturity. These life forms are known as minute (min-uuts) in the fruit fly. This causes prolonged development, short and thin bristles, poor fertility and viability. Fifty-minute loci have been defined genetically and 15 have been characterized as due to mutations in RP genes. Furthermore, the small subunit (SSU) processome is a large ribonucleoprotein (RNP) complex in eukaryotes and is required for the assembly of the SSU of the ribosome as well as for the maturation of the 18S rRNA. Mutations in SSU processome components have been implicated in human diseases. Mutations in three known SSU processome components result in related human diseases: hUTP4/Cirhin, is implicated in North American Indian childhood cirrhosis (NAIC); UTP14, is implicated in infertility, and ovarian cancer, and scleroderma; and EMG1 is implicated in Bowen-Conradi syndrome (BCS). There are other diseases with suggestive evidence for the involvement of the SSU processome and are pathogenic. So how could random mutations and natural selection be responsible for creating a complex system like the ribosome? No amount of guesswork or hypothesizing will fix this real problem for evolutionary scientism. It requires metaphysics; faith in a process that defies what we know about chemistry and biology.
In a nutshell, the complexity of the information flow from the DNA molecule to the cell is so dependent upon a network of regulatory infrastructure and interactions with so many intermediate components like the ribosome, the nucleolus, and existing cellular proteins that no single step in cellular metabolism can be found to be biologically meaningful when isolated apart from the whole of the cellular requirements for life. Evolution does not help either to explain how this system managed to come to be in a step-wise, random, but progressive developmental pathway!
Ribosomal synthesis of protein: Translation of the genetic code.
Evolution assumes too much, explains too little and is counter to what is known in empirical sciences like chemistry, physics, cellular and molecular biology. Only a thinking and rational mind having forethought and purpose could have created life. And this level of genius is far beyond any human capacity to design though it is not beyond the ability of humans to discover. So intelligent design is not a cop out on biology. It is a discovered attribute of biology. It is a fundamental requirement that explains how molecular and cellular biology must have come to be. Biological research leads to a metaphysical answer to materialistic problems but the evidence demands this verdict. To think otherwise is not just absurd it is prejudicial. It is no longer objective. It would be like finding the remains of the Mayan cities in the rain-forests of South America and attributing those buildings, temples, roads, aqueducts, art, and architecture to natural processes. The answer is a metaphysical one. Human intelligence, the mind of man, was responsible for planning, constructing and inhabiting those ancient cities. We know that the current process of creating a city requires a mind or many minds to accomplish such a feat. We do not cross over into religious questions until we begin to ask who the engineers were that designed the city. While we might glean some insights into the character of such an individual through our study of the material world we cannot know whom that engineer was unless some revelation tells us through a written journal that was left behind. No arguments against the reality of design in biology are meaningful. They are faith-based in hopes that a supreme being doesn’t exist who will hold people responsible to what can be known through an understanding of the created order of the world and all that is in it.
Excellent article- I’ve always considered even the lightest study of molecular biology to be eye-opening when considering the legitimacy of evolution theories. And then there’s irreducible complexity which by itself reveals the impossibility of evolution.
I wish universities could return to being a place of debate and curiosity, always seeking truths, always asking questions. We’ve lost this to political agendas. History has proven this to be dangerous and damaging.