#131 – Cell Biology 101 (essential background for ID talks)

Before hearing from Intelligent Design advocates, we thought we’d give our listeners some useful background information about how cells work …. it turns out it’s all about making shapes out of string.

Before we present our interviews with Drs. Michael Behe and Jonathan McLatchie (both leading proponents of Intelligent Design), we feel we should give our listeners a quick Cell Biology 101 to explain some of the concepts that will frequently come up in those interviews, and which easily mislead non-experts. So, in this episode we’ll talk about how cells make proteins, and how it’s the sequence of amino acids (which is directly decoded from the gene sequences) which determines the 3-dimensional (3D) shape of the protein, and that in turn gives the protein its functionality.

In this casual conversation, given at a NON-EXPERT level, Scott and I talked about:

• the string of DNA gets decoded into a long string of amino acids (we came up with two metaphors for this long string: toothpaste being squeezed out of a tube, and “Silly String” being squirted from an aerosol can at a party)
• that string of amino acid is called a protein; protein adopts a 3D shape that directly gives it its functionality
• the toothpaste / Silly String forms a long strand which flops all over itself, forming loops and folds and a completely disorganized mess; the strand of protein would also form a disorganized mess, except for the fact that the amino acids themselves begin to interact with each other and generate attractive/repulsive forces that cause it to fold and compact the loops into a particular 3D shape
• force #1: electrostatic attraction … a series of positive and negative charges which strongly attract each other, kind of like a sock sticking to a towel when you pull them out of the dryer, and have to peel the sock off
• force #2: electrostatic repulsion … a series of positive versus positive charges (or negative versus negative charges) which push each other apart, kind of like your hair standing on its end when you put your hand on a van de Graf generator at a science museum
• force #3: hydrophilic/hydrophobic attraction … a series of “water-loving” amino acids want to stick together (like sticking a piece of paper to a window just by making it wet); in the same way, “water-hating” amino acids want to stick together
• force #4: hydrophilic/hydrophobic repulsion … a series of “water-loving” amino acids and “water-hating” amino acids push away from each other (like oil and water not wanting to mix)
• force #5: atomic bond sharing … two amino acids both grabbing on to a hydrogen (like two people fighting over a trophy) or both becoming physically connected to a shared sulfur atom (like two people being hand-cuffed together)
• force #6: peg-and-socket connections …. groups of amino acids clumping together like a ball, and then inserting themselves into another group of amino acids which have formed into a doughnut shape (like buttoning up your shirt, or putting a jigsaw puzzle together)
• force #7: each type of amino acid holds its two arms out at different angles (both forward; or one backward and other forward; or both at 90 degrees from forward [or 60 degrees, or 45 degrees, or ….]), and as you connect these different types together (by getting them to hold hands), the angles of their arms begins to make the straight strand of protein kink up and loop in certain predictable ways
• we discussed how the sequence of the amino acids in the protein uses these forces and interactions to constrain the protein strand into specific and predictable 3D shapes, like: filaments, poles, tubes, beams, sheets, planks, pegs and sockets, and other shapes
• we did a mental exercise of creating a screw or a bolt using these forces and interactions, and also building an ion channel that you might find in a nerve cell!
• other intricate, complex and beautiful things can also be explained by naturalistic mechanisms: the Grand Canyon was created by simple geochemical and geophysical forces, or the beauty of a sunset against a stormy sky with a rainbow off to the side is mathematically explained by optical physics and gradients of air pressure, temperature and humidity
• reducing such complicated cell biology to “just chemistry and physics” doesn’t need to diminish “the Creator,” any more than showing that Leonardo DaVinci is “only” working with simple paints and a stick/brush; one is still free to invoke a Creator … or to deny the same.
• this raised questions about teleology and the processes being goal-directed, and science tending to be too reductionist
• a second VERY important topic we discussed was how these inanimate protein parts can self-assemble. Yes: SELF-ASSEMBLY! It sounds like magic, but it’s a common feature in cell systems, and it’s relatively easy to explain (we did this by having Scott jiggle a drawer full of spoons). No need for a little technician with a screw-driver and hammer in hand to put those parts together
• and a third VERY important topic: changes in the genetic information do not have to be simply a single change at one point in the strand of DNA or one single amino acid at a time (as YEC and ID advocates want listeners to believe). Instead, cells will commonly move and reorganize large segments of DNA at a time, coming up with entirely new combinations, which in turn leads to new genes.
• duplication (of parts of genes, of whole genes, or even of whole chromosomes!) accounts for the problem that YEC and ID advocates frequently raise: the original copy can still fully take care of the originally intended cell function, while the duplicated copy can go on to enhance its function, or even become adapted for a completely new purpose. Yes, you CAN have your cake and eat it too!
• duplication and re-shuffling of genetic information explains the evolution of proteins (we showed how easy it is to change a spoon/shovel into a knife/axe, or a stiletto/poker, a fork, a hammer). The immune system routinely takes this shuffling/re-building to a whole new level.
• coaptation: a protein can remain intact and serve more than one function, even in entirely different systems, or it can be slightly modified to now serve a new function

As always, tell us your thoughts on this topic …

If you enjoyed this episode and/or if you want to learn more about the genetic aspects of this discussion, you should check out Episode #70, where we talked to Dr. James Shapiro (an Emeritus professor with decades of hands-on experience with genetics at several world-renowned universities) about how cells routinely move large chunks of DNA around.

Episode image by Milada Vigerova at Pixabay.

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