A "Junk DNA" Functionality Analogy

I am not a molecular biologist, nor a geneticist, so may be oversimplifying or whistling in the wind here, but I have found the following analogy helpful in better understanding the shifting issue of "junk DNA" in human (or other) cells.

As a quick introduction, the human genome has some 3 billion DNA nucleotide pairs that, taken together include most of the information needed to build and operate a human being, complete from development of a fertilized egg, through to the maintenance of an adult, including the means for ongoing metabolism and eventual reproduction. Back in the 1980's, it was discovered that something like 98% of this DNA does not code for proteins or enzymes, the building blocks of life. Thus, your 20,000 or so genes (instruction for these blocks) make up only around 2% of your genome.

Those enamoured to the neo-Darwinian theory of evolution grabbed onto this factoid and declared that most of the remaining 98% of your genome is simply "junk DNA" left over from millions of years of evolutionary trial and error, just as might be expected from the undirected Darwinian process of random mutation plus natural selection.  This assumption quickly became the received wisdom and researchers did not look for function or purpose in the supposed junk. The same people also made a lot of the fact that, within that 2% coding DNA, almost 99% is the same as for chimpanzees and bonobos, our nearest relatives on the presumed tree of life.

The then nascent Intelligent Design (ID) community responded to this "junk DNA" assumption with their own prediction, that essential functions would be found for most of the 98% "non-coding" DNA if careful testing were to be done. (And some people claim that ID makes no predictions.) Subsequently, the ENCODE project did a series of experiments and found that perhaps 80% of the genome (so far) shows some sort of "activity" in human cells, but did not delve into the nature of the activity and how important it might be for humans. Rather than admit that ID was right, Darwinists attacked the ENCODE results, or simply denied their prior "junk DNA" claims, stating that, of course Darwinism would optimize the genome by throwing out non-functional DNA. (Darwinism is like that; if prediction "X" doesn't pan out as expected, claim that the theory also predicts "not-X".)

In the meantime, assuming that 98% of the genome was indeed "junk" most evolutionary biologists did not bother to look for functionality there, delaying much of our understanding of human cell biochemistry by a decade or so. Now that we know the 98% is NOT all inactive, scientists have begun to explore its varied functions and have found all sorts of purposes for some of the "junk": regulatory, developmental, quality control, etc. And since then, most Darwinists have quietly stopped using the term "Junk DNA".

Notwithstanding all this, my purpose in this post is not to delineate these new-found DNA functions. Rather, I will offer up a simple analogy to explain why there has to be much more to the human genome than just codes for proteins and enzymes. As an aside, I used to ask people who passed on the meme that "we only use 10 % of our brains", whether they would like to have the other 90% removed to improve their thinking efficiency. Similarly, I wonder if those who claim that 98%, 50%, or even just 20% of their DNA is "junk" would like to have that removed from their cells - not that it would be possible to do so, of course, but just in principle. After all, if it truly is junk, then having a smaller genome would make for more efficient cell division (less DNA to copy and sort through), and possibly a longer life or more energy for other things.

Anyway, on to my analogy, which is to compare the building of a human being to the construction of a house or some larger building, or even an entire city. Of course, a human is far more complex than any building, and buildings do not self-replicate, so the analogy is limited, but I hope it will serve to elucidate potential "functionality" for the non-coding parts of our own DNA.

In this analogy, the house to be constructed has a stack of blueprints, or a hard drive full of all the design information needed to construct the house. This information is, of course, analogous to our DNA. The coding parts of the DNA (genes) would then be analogous to the instructions for making bricks, two-by-fours, shingles, glass, cabling, pipes, etc. (the "protein" materials needed for the house). Given that the information for the house has to start from available materials, we cannot assume that bricks, lumber and tools are readily available to the house (or the fertilized cell in the biological case). Some of them may be available initially (in the womb as it were), but later on, once the house (baby) has begun to grow, it will have to make its own materials out of simpler ones (e.g. metabolism of digested food in the human context).

In addition to materials (proteins), the house plans will need instructions for making the tools (or parts of tools) required to build the house (the enzymes, as it were). In the context of the house construction, these tools will have to be more complex than those usually employed as we cannot assume people are available to use them. Thus, some of the instructions will have to include how to make robots to use the tools to build the house. And of course, the "parent house" (maybe a model home?) will be available to supply the first robots, tools and materials, until the new house can take over its own construction.

If you have not entirely given up on me as having concocted a bizarre analogy, we can move on to the next part. A house cannot make itself just from instructions on brickmaking and sawing up lumber. Even with some capable robots, tools and materials, the house cannot be constructed without detailed plans or instructions. The hard disk or blueprints will have to contain step-by-step instructions for where to start, what to do next, and how to perform each step, which materials to use, where to find them (in a pile somewhere after they were made), how to prepare them, and precisely where to put them. None of those instructions create materials or tools, so would not be considered as coding information (genes) in the genome context, yet they are essential to the project.

Moreover the construction robots are probably not handy-man generalists. As there are usually many subcontractors needed to finish a house, so there will be many robots required, or perhaps it would be better to have one type of very simple robot, with lots of detailed instructions (an expanded version of the "how to" guides from Home Depot?). So already we have some detailed functional (necessary) "non-coding" instructions: instructions for how to use tools and what to do with materials.

For efficient construction, the building plans would also need a lot of control instructions, both positive (enable process X) and negative (disable or suspend process Y) to avoid piling up bricks before they are needed, or delivering lumber before the hole is dug, and to make sure that when the roof goes on, the shingles are available, the roofing tools are ready and the robots know how to use them. Oh by the way, there will doubtless be other "protein" codes for temporary items such as scaffolding, concrete forms, etc. at certain times during construction (or child development in the womb). These must also be specified, along with when they are needed, and what to do with them after they are no longer needed; e.g. discarded, or dismantle so bits can be reused.

The instructions would need to be very detailed to get the house built right. You cannot just tell the robot to "lay bricks", it would need to be told where to start, how to hold the brick and trowel, how to spread mortar, what to do at corners, how to handle half-bricks or broken ones, how to finish a row and start another, when to stop, and so on. Lots of instructions are needed to build a house (or a human). There would also be a need for "what if" instructions for unexpected things or random errors. Something would have to check the work as it progresses (supervisory or inspection robots?), make corrections (more specific tools?), and allow the work to proceed once each inspection passed. The cells in your body have analogous processes that also follow coded instructions.

All of this work would also require some sort of schedule or timeline, with complex start/stop instructions and checks/balances to ensure a timely and accurate result. There would also be a need for sensing and feedback mechanisms as noted above for quality control, repairs and rework. Once the house was completed, there is still a need for operating instructions - how to: open/close windows, adjust thermostats, regular checking and cleaning, and so on. In the human context, each cell has to monitor itself and its cell boundary for conditions around and within it, and make adjustments to protein and enzyme synthesis to keep itself and its surroundings healthy (this is called homeostasis in biology). Thus, cells, humans and self-constructing houses all need "non-coding" instructions in order to grow and exist properly.

If a house can be likened to a cell, then perhaps a human organ can be like an apartment building, with specialized rooms, and a human being can be analogous to a whole city, with many different buildings, along with infrastructure requirements. Indeed, a human cell has itself been likened to a city, given its internal complexity, so a human must be far more complex than even a big city. In that respect, some might consider it remarkable that a human being can be constructed using only 3 billion nucleotide bits of information! In any case, the building instructions would have to include plans for many types of buildings as well as the interfaces between them, in order to get everything in the right place and working together harmoniously.

Consider now, that many different buildings can be made using the same bricks, lumber, tools, etc. Thus, the fact that human and chimp genes are almost 99% the same only means that they are built of the same proteins and their metabolism uses the same enzymes. That is hardly surprising and does not imply that humans are almost the same as chimps, just as a library is not almost the same as a nursing home just because they both use the same framing, concrete and roofing materials. Obviously there are some minor differences even in the coding parts; for example, some houses may have different coloured bricks, or an oil furnace instead of gas. There are similarly some (around 0.1%) DNA differences among human genes due to eye/skin/hair colour, size/build, etc., just as in a given subdivision, there are variations among houses built by the same developer.

As a final note, building blueprints or construction plans also contain considerable information that is not, strictly speaking, needed to build the house. The name of the house model, the architectual firm, drawing inspection and approval dates, building license, surveyor notes, and engineer stamps are not needed to construct the house, but they are included in the information package anyway. Then there is the table of contents and page numbers so you can find what you need quickly, and cross references for related info and prerequisites or next steps. I expect that science will find similar pointers and directions in our DNA at some time, if they haven't already.

Wouldn't it be funny if somehow, some small piece of human "junk DNA" were eventually decoded as, "Then God said, Let us make mankind in our image, in our likeness..." (Gen. 1:26). Or maybe it would say, "Species: Homo sapiens, model No. Adam/Eve; developed Holocene year 136,000, on planet Sol-3, by Archangel team Gabriel under divine directive Our-Image; QC by team Michael, passed inspection; released and ensouled by YHWH Himself into production thereafter; Soli Deo Gloria!"

In summary, just as construction projects need non-material instructions, so cells and humans require non-coding information in their DNA to develop, live well and reproduce properly. Such information should never have been considered as junk, and science should now do more research into the functions of "non-coding" DNA in our genomes. That about wraps up all I can find in this analogy.  I hope you found it at least entertaining, if not educational. Forgive me if I have gotten any biology wrong or misused the terminology somehow. Comment if you can think of other intriguing aspects of this analogy.