Rewinding Paley’s Watch (Part 2)

The Spectacular Spliceosome

Likely the most powerful example of programmed, irreducibly complex design within living things comes in the form of a spectacular splicing code that controls the selection of specific genetic information on demand. And it does so to facilitate the assembly of numerous and variable biological “products”—all from a limited amount of DNA sequencing.

If what I just said seemed a little confusing, allow me to explain the big concept I’ll be driving home with a brief analogy before I get into the details of a marvelous mechanism called the spliceosome.

Let’s say I wanted to have the ability to create, store, later copy, and then deliver numerous messages to various people whenever I wanted. However, I don’t want to have a whole library of books that contain each and every individual message I might want to send. Because I have so many messages, it would take up way too much space.

So, instead of writing out and storing each individual message in a whole bunch of separate volumes, I’ll instead create just one master book, that contains all the individual components for all the messages, and then create a code system I can apply to that book that will allow me to assemble all these unique messages whenever I want. And how might I do that?

Well, just like a spy might send a secret message to another agent using a code that designated page numbers within a specific book to look up (via a numeric system), they could create an almost endless number of messages simply by indicating different code combinations.

For example, if the spy passed on a slip of paper to a cohort that had 12+19 on it, and the receiver knew the book it related to and understood the code meant that they should read the first word found on each of these page numbers, they could figure out the message being sent.

They would do so by opening the book to page 12 and noting the first word (let’s say) is “This,” combined with then turning to page 19 and finding the first word there which just happens to be “Friday.”

Putting the two words together would reveal the simple message “This Friday,” which, of course, might just be a portion of a much longer message that could be expanded upon simply by giving additional coordinates and applying them to the same book (such as “Meet me this Friday behind the old bridge and deliver the secret plans the enemy has.”).

Now, even with this crude analogy, one can see how one source code could provide the ability to create an almost limitless number of messages, as long as there was forethought, agreement, and planning put into the system from the beginning.

And note that the message 12+19 only uses a total of 5 spaces, but it codes for a message (This Friday) that uses 11 spaces, so it’s more compact.

One could make this code even more sophisticated by adding a color to each number that might designate whether it should be the first or last word on the page to be read or perhaps use a specific font for each number that indicates whether entire sentences or paragraphs should be chosen and combined, instead of just single words. This would make each set of symbols far more compact compared to the message it was conveying upon its decoding.

However, it should be obvious that a coded message made up of random numbers, colors, and/or fonts would likely provide no benefit to anyone. If an agent was given a message containing incorrect or nonsensical information, it could prove disastrous should the intel be important for the survival of the recipient.

Codes Within Codes

So, how does this relate to the issue of design and irreducible complexity? Well, first, we need to understand that a human’s DNA contains a similar number of genes that directly code for proteins as a lot of simpler life-forms do.

Proteins are complex molecules and do most of the work in cells. They are important to the structure, function, and regulation of the body of whatever organism they belong to. And when I’m mentioning genes that directly code for these proteins, I mean that the organism’s DNA contains complete and uninterrupted sequences of DNA letters that directly relate to the construction of unique proteins found inside each individual creature.

For example, the thale cress plant I mentioned in Part 1 of this blog has about the same number of directly coding protein genes as we do (around 25,000). However (and here is where it gets very interesting), their overall genome only has approximately 125 million DNA base pairs (letters) whereas humans have 3 billion!1 However, if you sort through the three billion letters that make up the human genome, only about 1% of those letters directly code for proteins,2 which is why we have a similar number of directly coding protein genes as these plants, which are far less sophisticated than we are in terms of functionality/ability.

Now, in an attempt to decode the entire human proteome (the full set of proteins in the human body), research from Matthias Mann from the Max Planck Institute of Biochemistry has shown our vastly more sophisticated bodies are represented at least partially through the expression of a significant number of proteins that are not directly coded within our DNA.

It is now estimated that the human body contains between 80,000 and 400,000 proteins.3

So, where is the information for all these extra proteins stored? Well, just like our analogy earlier, it’s been shown to be stored throughout our DNA (the master book) but is picked out from several different places and then assembled into unique sequences, somehow accessed by a code that directs the biological machinery within us to do so when needed.

This allows multiple proteins to be assembled from the same source code. In the world of computer technology, this type of coding is known as data compression. And as one online security company describes it,

Data compression is the process of encoding, restructuring or otherwise modifying data in order to reduce its size. Fundamentally, it involves re-encoding information using fewer bits than the original representation. Compression is done by a program that uses functions or an algorithm to effectively discover how to reduce the size of the data. For example, an algorithm might represent a string of bits with a smaller string of bits by using a ‘reference dictionary’ for conversion between them.4

Sound familiar?

This brilliant design concept allows the streamlined optimization of our genome in such a way that it takes up only a fraction of the space it would when compared to those that only code for their proteins independently. And here is a more detailed explanation of how this splicing code and its machinery works.

Snips and Snurps

Most of our genes (and those within many other higher life-forms) are composed of numerous short sequences of DNA called exons, and these sequences are interspersed between longer stretches of noncoding (but essential) DNA sequences called introns.

Now, the coding for proteins doesn’t come directly from DNA itself. Rather, when the information is needed, the DNA is “unzipped” at the specific location where the DNA coding required for the protein’s assembly is found, and a copy of that sequence is made—called messenger RNA.

This mRNA sequence includes both introns and exons, but before this RNA molecule can be used to make a protein, the introns have to be removed and the exons need to be connected to make a new DNA sequence. This process is called RNA splicing, and this is where a structure called the spliceosome plays a key role.

The spliceosome is a complex composition of several small molecules designated as snRNPs, or snurps, as they’re often referred to. Now snurps themselves are made up of protein and small RNA molecules, and the formation of the spliceosome begins when one kind of snurp binds to one end of a chosen intron and a different kind of snurp binds to its other end.

Then several additional snurps engage with this isolated area in a way that brings the two ends of the intron together, causing it to form a loop. This activity also brings all separate snurps together to form the completed spliceosome, which then cuts off the looped intron and joins the now-connected exons together into a new and specific DNA sequence that codes for a protein.

The Master Code

The big takeaway here is that we now know that the majority of our genes are constructed by taking specific parts from one place in our genome and combining them with different parts from other genes in other places in our DNA in order to create proteins that aren’t coded directly.

That is, you take words from different paragraphs and pages in the master book and put messages together that aren’t readily noticeable before specific instructions and operations are performed.

Just like in the case of our spies having a code that is applied to the master code (the book), this logically entails there must be an even higher level of genetic coding above what we currently understand DNA itself to be doing. And this provides a level of sophistication that results in an unsolvable puzzle that simply begs any sort of naturalistic explanation.

Think it through. How does a step-by-step process develop such a result? How could the utilization of a spliced code that requires an incredibly sophisticated mechanism like the spliceosome arise from simple modifications and tweaking over time?

What possible small step in a genome that only has directly coding proteins will (1) provide a survival advantage to the host organism while (2) getting built up toward becoming a splicing code and (3) result in the seeking out of several independent predetermined sections of DNA and then assemble them in anticipation of a useful and functional protein being produced?

What accidental trial-and-error process could possibly be beneficial that would start randomly snipping DNA sequences apart and stitching them back together? How would this process “learn” where to start and where to stop in the correct sequence to produce a correct result for a brand-new functional protein?

Remember, there are infinitely more ways to make mistakes than there are of getting things right.

Paley’s Supercomputer

Metaphorically, “Paley’s watch” can no longer be thought of as some archaic timepiece. It’s now known to be a supercomputer with seemingly unlimited capacity, rich in design, dynamic in ability, and virtually unfathomable in its complexity, which are all the hallmarks one would expect to see if the God of the Bible created the world.

The question of “whodunnit” is a cinch, revealed in the very first sentence of the Bible.

When one simply puts aside their materialistic presuppositions and considers the idea of a master designer, all the clues line up easily, and life’s ultimate mystery is easily solved. The question of “whodunnit” is a cinch, revealed in the very first sentence of the Bible.

In the beginning, God created. (Genesis 1:1)