Beyond the many examples of irreducible complexity, the cell offers a profound example of both irreducibility and specified complexity in one.

Transcription

1 Session 11 Part III Intelligent Design (cont.) 3. Irreducible Complexities (cont.) Signature in the Cell Beyond the many examples of irreducible complexity, the cell offers a profound example of both irreducibility and specified complexity in one. Stephen Meyer s book, Signature in the Cell, uses considerable space to describe these various processes and entities as the focal point for Intelligent Design. This has not been a key research emphasis in creationists groups in recent decades. Irreducible complexity is the state in which no further breakdown of components or features would be functional for evolution because they would not benefit the organism individually or in a smaller collection of fewer parts. Group A might be seen as evolving from group A 1, but A 1 cannot function without the rest of A, or bestows no advantage or benefit to the organism by itself. Therefore, Group A is irreducibly complex. Specified complexity is a state in which a feature or process requires highly specific instructions to bring about the feature or complex combinations of timing and sequence. As in blood clotting, all the factors and their inactive states must be available simultaneously and controlled in the proper sequence for the process of clotting to be beneficial. Without all components or with components out of order, clotting doesn t occur and the organism is lost either through persistent clotting everywhere, or no ability to clot during an injury. In the cell, we have a large number of integrated entities, organelles, and molecular machines which have to arrive at the proper time in the right sequence to allow the key processes of the cell (manufacture of proteins) to occur. It is irreducibly complex in that none of these features would benefit the organism if coming by themselves independently (their benefit is only realized when the other features are present and coordinated). It is specifically complex in that all features must be coordinated in a finely tuned co-dependent process. Processes must be controlled by very specific instructions pertinent to the thing being made, i.e. instructions for other features cannot be applied for dual use. 1

2 The one process in the cell that demonstrates these characteristics is protein synthesis the making of proteins. Proteins are the chief business of every cell. So making them is Job One. Protein synthesis includes DNA copying by means of transcription, translation and gene expression to enable manufacture of proteins from sequenced amino acids. Requirements of Protein Manufacture Proteins are made from chains of amino acids. Amino acids arise and exist in cells separately and are available for building proteins. But amino acids have no internal instructions or programmed functions that guide them to the specific arrangements needed for specific proteins. Something else in the cell must capture and arrange the amino acids in the required configurations. It must not only capture all the required amino acids but must move them into the right positions. Transfer RNA (explained later) is the machine, but it needs information to operate transfer RNA (trna) The information for such configurations or sequences resides in the DNA, specifically in genes in the DNA dedicated to making certain proteins. Thus, the information for sequencing amino acids must be gotten from the DNA and translated into actions that capture each amino acid and also move the acid to its proper position in a chain, called a polypeptide chain. The Process Unwinding DNA The first task is to find the correct section of DNA in the chromosomes for a specific gene. Molecular machines must be available at the proper time to identify which chromosome holds the needed gene, then its beginning and end positions. The machines then stretch out the DNA at that gene location to gain access to the DNA strand for copying. 2

3 In DNA, the actual DNA itself is never used in a process, but a copy is made when the information is needed. In our film clip, the process began here, after the DNA had already been pulled out of its layered position in the chromosome. A molecular machine begins unwinding the DNA double helix to form two unwound strands, each having their half of the information units or base pairs of chemicals. A molecular machine called helicase performs this unwinding on the twisted DNA so as to separate its two strands and the information units bonded to them. Thus, each separate strand pulls away with half the DNA information it has when combined. The separated strands are essentially RNA. helicase (a protein acting as an enzyme) Separated RNA strands Combined DNA Copying DNA - Transcription Once separated, one strand of RNA is selected for copying the genetic instructions for a protein. A molecular machine called RNA polymerase then copies not only the information units (chemical bases) but also the backbone strand. This machine however needs other molecular machines to mark the starting and ending positions of the gene to be copied. The resultant copy is then called messenger RNA. 3

4 The messenger RNA contains half the information contained in DNA (both strands and base pairs). A question might be: why isn t the other half of the information copied at the same time? In fact, the process deliberately excludes the second half of the information because that happens to be the very key to how the components of proteins are sequenced to make the right protein. If the other half of the DNA information is not made available at copy time, it must come from somewhere else in the cell. As it happens, the matching information is available in the very machines that help assemble amino acids. The making of such machines must be coordinated with the making of messenger RNA so that they are available when RNA is used to build the protein. Imagine a series of well-known phrases cut in half as two pieces of paper. The first halves of all sayings are pinned onto a clothes line with additional clothespins glued to the bottom of each page. All around the grass under the clothes line are sheets containing the second half of the phrase. The phrases are things like: - Mary had a little lamb - Like father like son - Feed a cold starve a fever - He who laughs last laughs best In DNA analogy, the second half of these phrase pages must be created so as to be available to match the first half. As human agents, we can pair these up and attach each to the correct first part. In DNA there is no mind familiar with how the phrases go together. Instead, there are chemicals which only match up with their partner chemicals in the RNA. As will be seen later, this chemical pairing is the key to moving amino acids into the correct assembly positions for a protein. 4

5 Beginning Protein Synthesis Messenger RNA (the new copy with half the gene instructions in the DNA) moves outside the nucleus into the general environment of the cell called the cytoplasm, which is a fancy term for the general medium of fluid material in which objects in the cell exist whether free-floating or stationary. Interesting is how the messenger RNA moves to the exit portal of the nucleus and to its destination in the outer cell. Messenger RNA is not a motor molecule, so there must be additional machines that help transport the RNA. cytoplasm nucleus The messenger RNA locates and attaches to another complex protein the ribosome which is in many ways a small cellular factory, in that it is the site and enabler for the assembly process for proteins. Here is where we answer the question How amino acids get assembled properly into a specific protein. The ribosome is a clamshell-like structure in two parts. While the RNA has yet to arrive at the ribosome, its two halves are separated. When the mrna arrives and attaches to one side of the ribosome, the other half closes loosely over its other half with enough entry space for other assembly machines to enter and perform work on the captured RNA. Elsewhere and in coordinated timing with the exit of mrna from the nucleus, transfer RNA (trna) has been configured with the precise information units (bases) that will properly match up with their partners in the RNA strand now captured in the ribosome. 5

6 messenger RNA inside the ribosome arriving transfer RNA with an amino acid Entering the ribosome, transfer RNA has captured an amino acid and has with it the correct chemical connectors to link up with a position in the RNA. Here then is how DNA directs the building of a protein by containing the chemical links that attract only the correct set of chemical pairs in the correct sequence. The transfer RNA has the chemical connectors for AGT (adenine-guanine-thymine). It will be brought into contract to match up with its pair in the RNA TCA (thymine-cytosine- adenine). The object of this process is to connect together amino acids by simple physical contact. Each transfer RNA transports its attached amino acid into the next position until all acids for the protein have been assembled. Where specified complexity comes into this process is the attempt to explain how a transfer RNA molecule gets the correct chemical connectors in anticipation of the amino acid that will be needed at the match up point. In other words, we might explain how a trna can attach to an amino acid. We can explain when and how a trna acquires the DNA chemical information link matching a section of the messenger RNA. But we can t explain how the chemical connectors acquired happen to match the specific connections needed by the amino acid that will be attached and transported by the trna. That is sequence, timing and information that isn t available in a process created by random, unguided chance. 6

7 Finalizing the Amino Acids into a Protein As amino acids are attached to one another in a chain, the chain is moved out of the ribosome toward a chamber called a chaperone machine. In this machine, the acid chain folds over on itself in very specific motions required to make a particular protein. But another instance of specified complexity is that the acids themselves don t contain complete inherent instructions for how to fold in a particular instance. one combination of acids for a protein a new combination for another protein (using similar acids) How do these same acids know to fold in this new combination? Scientists have observed an essential relationship between the sequence of the acids and a resultant folding outcome. So it is the sequence that not only determines the protein to be made but the folding it will need. That s why a chain folds differently based on which protein is will make. 7

8 But other factors must be present, so it isn t a case that the instructions reside completely in the acids themselves. It is also observed that a number of other factors must be timed and coordinated to enable the folding to complete correctly. These include: the presence of co-factors and the chaperone chamber presence of a solvent the concentration of salts ph factor temperature What is unexplained, as we might expect, is how these elements came together by chance accidents of mutation in the first place. The more complex the precise arrangement of needed components the less likely they arose by chance and the more likely they were designed. Circular Co-dependency What is very difficult for science to explain is the amazing co-dependency of molecular machines and DNA in the manufacture of proteins, given that the machines are proteins also, that need to be made by the same process they serve. Here is the problem: to make a molecular machine, DNA is needed for the instructions, but DAN needs the presence of the machines to translate and transcribe the information and to catalyze or assemble the acids needed to make the protein. How does a process originate for making needed components, but then needs those components already in place to conduct the process? It s a Catch-22. It s similar to the conundrum of looking in a dictionary for the definition of A and it says, see B. When you go to B, it says, see A. Not only is this circular dependency alarming, but it is devastating to any theory of origination by chance. If DNA came first, how would DNA accomplish its purposes while waiting for the machines to evolve? If the proteins for the machines came first, what function would they perform while waiting for DNA to evolve? And how could the machines exist at all as a first step if the DNA needed to make them doesn t exist yet? This whole problem of which came first in a co-dependent system is resolved by a Prime Mover, who can originate both elements of a co-dependent system at the start. The odds of both elements evolving together by chance is astronomically remote. 8

9 The RNA polymerase below must be present with the unwound DNA in order to transcribe DNA into messenger RNA (bottom strand) that would be used to make RNA polymerase. 9