Feature Article - September 2018
by Do-While Jones

Object-oriented Creation: Clarifications

Here is Tony’s response to our critique of his hypothesis.

Last month, Tony sent us an email in which he proposed an alternative to the theory of evolution. 1 His idea was to analyze genetics from an object-oriented programming perspective, in which he proposed comparing the instructions coded in the DNA molecule and the instructions coded in a computer program. He asked us to critique his proposal, which we did.

We admitted that there were some parts of his proposal that we did not fully understand, and admitted that our comments were based on what we thought he meant, and that our understanding might not be entirely correct.

For the most part, our comments were based on a correct understanding—but there were a few points that Tony wanted to clarify.

Limited Solution Space

Our understanding of Tony’s points 3 through 6 included this statement: “Tony seems to realize that the genes that produce lungs in one species should not be very much different from genes that produce lungs in any other species.” Tony’s response was,

#3-6 Also apply directly to protein creation and other biochemical factory products.

We didn’t mean to unfairly limit Tony’s observation to just lungs. We suggested the lungs as an example which we hoped would be easy to understand.

It is generally recognized by engineers that given any problem, there usually are only a few good solutions. Therefore, engineers often independently arrive at the same good solution to a particular problem. Since all biology depends upon protein creation, and there are just a few good ways to create proteins, it is not surprising to find similar genetic codes to create proteins across all forms of life. Common genetic codes could certainly be the natural result of a “limited solution space” (to use engineering jargon). It is proof neither of a common ancestor nor an intelligent designer.

“Smart” Membranes

We admitted that we weren’t really sure we understood Tony’s seventh point (“That these Functions will have quality control processes that attempt to validate incoming parameter variables.”) and apparently we, in fact, did not understand. He wrote to tell us,

#7 is referring more to the facts such as that the cellular membrane prohibits most non-needed material from crossing the cellular membrane, thus becoming available for whatever the cellular factory happens to be producing; or that DNA transcription errors are often corrected during replication (http://jonlieffmd.com/blog/dna-proofreading-correcting-mutations-during-replication-cellullar-self-directed-engineering).

It certainly is remarkable that the membranes around cells are selectively permeable. That is, they let the good stuff in and keep the bad stuff out. It is also true that the biological machinery which reads the DNA code has some error-correcting properties.

Error Correction

His clarification of his seventh point mentioned the automatic correction of DNA transcription errors. For those of you who are not familiar with error-correcting codes, here is a quick tutorial.

Some communication systems are designed to provide accurate communication of information even in the presence of noise which can cause some information to be corrupted.

For example, I am a substitute bowler in a bowling league. Everything is recorded electronically now; but in the past I needed to give handwritten bowling scores to the league secretary. My handwriting is not very legible, so my scores could be misinterpreted. Adding checksums would make sure that erroneous scores could be detected and corrected. Here’s how:

These are the actual scores from my last three league-sanctioned weeks. The fourth line is the sum of the three numbers above it.

DateGame 1Game 2Game 3Series
30-Jan-18149138157444
13-Mar-18152164167483
20-Mar-18137135138410
Checksums4384374621337

Suppose I wrote the score for Game 1 on 13 March so badly that the 5 looked like a 6, so my score appeared to be 162 (instead of 152). In that case, the sum of the three games that day would be 493, which does not match the series total of 483. The secretary would know that for 13 March, one of the individual game scores is wrong, or the series total is wrong; but which one is wrong?

The sum of the Game 1 scores is 448, which does not match the checksum (438). Therefore, the secretary would know one of the Game 1 scores (or the checksum for Game 1) is wrong. Since all the checksums and series totals add up to 1337, the secretary would know all the checksums and series totals are correct.

Comparing the sums of the individual game scores with the series totals and checksums would not only alert the league secretary to the fact that there is an error in the first game of my 13 March scores, the secretary would also know that the score I had erroneously written was 10 pins too high. The checksums allow any single error in any row or column to be detected and corrected.

Our point is, even the simplest error-detection and error-correction scheme is complicated. Tony’s point, we think, is that error-detection and error-correction algorithms are too complicated to happen by chance.

Self-limitation

We dismissed Tony’s eighth point as self-evident, saying nothing more than, “There’s nothing you can do that can’t be done.” So, Tony clarified it.

#8 is self-evident and self-limiting. It necessarily excludes our DNA system from being useful in all environments. Our DNA system has been exquisitely tuned to our Earthly environment with all of its many biomes. However, it does not contain the information needed for us to live, unassisted, outside of our Earthen environment, and no amount of time would add that information to our DNA. Having self-limiting features allows for a hypothesis to be falsified. In short, if we could evolve to live on the Moon, Mars, or Venus without technical assistance, I would be wrong.

The problem we have with this argument is that it is too hypothetical. Yes, if we could evolve to live on Mars, it would prove evolution is possible—but without experimental proof that we actually could evolve to live on Mars, the conjecture is irrelevant. And, to get nit-picky, if we “evolved” to live on Mars, that would not really be evolution—it would be adaptation. There’s a subtle difference between evolution and adaptation. Furthermore, proving that we could adapt to live on Mars in the future does not prove that dinosaurs evolved into birds in the past.

Economy of Reuse

We frankly admitted that we didn’t know what Tony meant by his 13th point (“That the cellular environment modifies Function expression as an input parameter.”) He sent us this clarification:

#13 means, a particular gene (functional code) in one cellular environment may behave differently than the same gene (functional code) in another cellular environment, depending on how it is coded. Same function. Same Code. Different results. Why this matters is that what we see in nature is the repetitious use of genetic codes across unrelated species. A banana, a chimp, a starfish, and a human all share genetic information, not because we are related through common descent, but because the language of the genetic code is flexible enough to be reusable, like a good function library in C++. Why reinvent the wheel?

Yes, we recognize that every program that runs on a Windows computer needs to be able to recognize a mouse click. Depending upon the situation, a mouse click might open a file, follow a link, or start a program. It would be stupid to write new code to recognize a mouse click every time. It makes much more sense to store the sequence of instructions that recognize a mouse click in a software library and incorporate that same sequence in every program that needs it, no matter what that program does in response to the click.

Junk DNA

Tony’s 14th point was that all DNA is functional, even if scientists haven’t figured out what its function is. We mostly agreed. The professional literature often contains articles written by geneticists who have discovered a previously unrecognized function in some portion of the DNA molecule. However, we believe that there might be a few parts of the DNA molecule that were functional at some time in the past, but a mutation has rendered that function inoperable. If the impairment caused by that mutation isn’t sufficiently harmful, natural selection might not remove it from the gene pool.

Tony’s response was,

#14 I will concede the point if you concede that malfunction does not equal non-functional for the purpose of this hypothesis. Transcription errors and deleterious mutations are exactly the type of mutations this theory predicts we will find in abundance.

Yes, we agree that “malfunction” is different from “non-functional.” The radio in my “new” truck (which I have had since 2004) distorts at even moderate volume. The radio in my old truck didn’t work at all when I sold it. The radio in my new truck malfunctions, and the radio in my old truck was non-functional; but both trucks got me (and my cargo) to my destination and back, which was all I really needed from a truck. The distinction between “malfunction” and “non-function” didn’t really matter to me.

Tony said, “this theory predicts” an “abundance” of mutations. Which theory was he talking about? Evolution or his theory? We presume he was talking about evolution because later in the second email he said,

#19 Agreed. I should have stated that as Random Mutations cannot create new information for Natural Selection to act on. However, if natural selection “filters information, keeping the good information and rejecting the bad information", why are there so many deleterious inherited mutations? Shouldn't they have been rejected?

Apparently Tony thinks there are “so many deleterious inherited mutations,” which is more than he thinks the theory of evolution would predict. That’s more of a subjective opinion than a scientific proof.

Regardless of whether the DNA of a particular species was initially created by evolution or design, eventually the Second Law of Thermodynamics is going to introduce some harmful mutations, many (probably most) of which will be eliminated by natural selection. The term “abundance” is rather vague.

We agree with Tony in principle, but we don’t think it matters as much as Tony apparently does.

Tony’s Conclusion

In our response to his first email, we admitted that we had to guess exactly what Tony’s point was. He ended his second email with a better explanation. We will give him the final word.

#16-18 Your computer analogy is good, but it ignores the Object-oriented Programming portion which is what this hypothesis is about. DNA is one giant code library that is reused throughout all known life. Physics is your computer, the framework that controls the conversion of information into material reality. We have no clue what the operating system is. I am not even sure there has been any research done to answer the question of "Er..just how do all these organisms from vastly different lineages speak the same genetic language?" I mean, it's more complex than binary or ternary, contains the ability to create every biological molecule, and had to be fully functional in the first cell in order for it to survive.

Note that the fact that their genes are different is irrelevant. All life uses the exact same programming language and has since the first cell. The language has never, ever changed. [italics his] If common descent were true, and #19 and #25 are also true, then the first cell had to contain all of the genetic information ever to have existed on the planet. This directly contradicts the theory of evolution. But if common descent is false, how do we account for the same genetic code showing up in unrelated creatures in the given time frame? If common descent is false why do you share genetic information with a banana?

#23 You hit the nail on the head, actually, though it extends far beyond embryology. If your laryngeal nerve didn't grow at the correct rate you would die before you could be born. However, it also applies to other things such as cell death (https://www.sciencealert.com/scientists-discover-a-new-way-to-get-cancer-cells-to-self-destruct) and cell replenishment over a lifetime and other biological processes that are very time sensitive. Our genetic machinery operates so much more efficiently than man-made computers that I could scarcely begin to know how to quantify the difference. Imagine if the timing of the cellular factory somehow 'forgot' to start reproducing the cells that make up your lungs. Too many cells is a deadly problem, as is too few.

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Footnotes:

1 Disclosure, August 2018, “Object-oriented Creation”, http://scienceagainstevolution.info/v22i11e.htm