If DNA were a computer program…

_{Denyse O'Leary

October 27, 2018

Design inference, Genomics, Intelligent Design}

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A computer programmer looks at DNA … and finds it to be “amazing” code.

From 2006 through 2017, Dutch entrepreneur and software developer Bert Hubert contributed from time to time to a web page where he listed many of the ways the workings of DNA can be likened to coding decisions by programmers. Some of his thoughts:

The human genome is about 3 gigabases long, which boils down to 750 megabytes. Depressingly enough, this is only 2.8 Mozilla browsers.

DNA is not like C source but more like byte-compiled code for a virtual machine called ‘the nucleus’. It is very doubtful that there is a source to this byte compilation – what you see is all you get.

File:DNA simple.svg It is easier to imagine a potential source with no code than it is to imagine a code with no source but we are offered no further explanation. However, the pace picks up when we get to epigenetics, the changes we acquire during our lifetimes that are passed on through several generations without altering our DNA:

Although the actual relevant changes in the DNA of an organism rarely occur within a generation, substantial tinkering goes on by activating or deactivating parts of our genome, without altering the actual code.

This can be compared to the Linux kernel, which at boot time discovers what CPU it is running on, and actually disables parts of its binary code in case (for example) it is running on a single CPU system.

He also sees a computer analogy to “junk DNA” (non-coding DNA which was, at one time, thought to be accumulated garbage from the meanderings of evolution): … More.

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See also: H. Allen Orr on DNA as information

Comments

It seems to me that, in order for DNA code to accomplish so much with so little data (compared to computer code), it must be using an extremely efficient compression mechanism similar to a hierarchical structure. In other words, each branch in the tree is given a code and the code is used or reused wherever it is needed, thereby saving a lot of space. PS. Excellent comments above.FourFaces_{October 28, 2018
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Even more astonishing is the fact that dna existed in the first life forms which appeared soon after life on earth was possible. DNA could not have evolved. This super-complex information system came spontaneously into existence. If this doesn't defy the laws of nature nothing does. The creation of DNA can only be described as miraculous.Peter_{October 28, 2018
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Tom Robbins and bornagain77, Excellent comments. Thanks.PeterA_{October 27, 2018
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Besides greatly outclassing anything man has yet accomplished in 'reversible computation', DNA also greatly outclasses anything man has yet accomplished in terms of quantum computation. Due to, among other things, the extremely fragile nature of quantum coherent states, man has yet, despite extreme effort, to build a quantum computer of any significant, practical, size,,,
Quantum Computation problems 2010 Excerpt: Interference - During the computation phase of a quantum calculation, the slightest disturbance in a quantum system (say a stray photon or wave of EM radiation) causes the quantum computation to collapse, a process known as decoherence. A quantum computer must be totally isolated from all external interference during the computation phase. Some success has been achieved with the use of qubits in intense magnetic fields, with the use of ions. http://whatis.techtarget.com/definition/quantum-computing Scientists achieve critical steps to building first practical quantum computer - April 30, 2015 Excerpt: If a quantum computer could be built with just 50 quantum bits (qubits), no combination of today's TOP500 supercomputers could successfully outperform it (for certain tasks). http://phys.org/news/2015-04-scientists-critical-quantum.html
And yet whereas the slightest environmental noise presents extreme difficulties for man in his quest to build quantum computers of any significant, practical, size, on the other hand, life is apparently designed in such an ingenuous way that “Environmental noise drives a persistent and cyclic generation of new entanglement”
Quantum entanglement in hot systems – 2011 Excerpt: The authors remark that this reverses the previous orthodoxy, which held that quantum effects could not exist in biological systems because of the amount of noise in these systems.,,, Environmental noise here drives a persistent and cyclic generation of new entanglement.,,, In summary, the authors say that they have demonstrated that entanglement can recur even in a hot noisy environment. In biological systems this can be related to changes in the conformation of macromolecules. http://quantum-mind.co.uk/quantum-entanglement-hot-systems/
In fact, the entire DNA molecule can be viewed as quantum information that has classical information information embedded within it:
"What happens is this classical information (of DNA) is embedded, sandwiched, into the quantum information (of DNA). And most likely this classical information is never accessed because it is inside all the quantum information. You can only access the quantum information or the electron clouds and the protons. So mathematically you can describe that as a quantum/classical state." Elisabeth Rieper – Classical and Quantum Information in DNA – video (Longitudinal Quantum Information resides along the entire length of DNA discussed at the 19:30 minute mark; at 24:00 minute mark Dr Rieper remarks that practically the whole DNA molecule can be viewed as quantum information with classical information embedded within it) https://youtu.be/2nqHOnVTxJE?t=1176
This quantum information along the entire DNA molecule, besides providing a method by which to perform quantum computation, and since quantum computation greatly outclasses classical computation in terms of solving 'traveling salesmen problems,,,
Speed Test of Quantum Versus Conventional Computing: Quantum Computer Wins - May 8, 2013 Excerpt: quantum computing is, "in some cases, really, really fast." McGeoch says the calculations the D-Wave excels at involve a specific combinatorial optimization problem, comparable in difficulty to the more famous "travelling salesperson" problem that's been a foundation of theoretical computing for decades.,,, "This type of computer is not intended for surfing the internet, but it does solve this narrow but important type of problem really, really fast," McGeoch says. "There are degrees of what it can do. If you want it to solve the exact problem it's built to solve, at the problem sizes I tested, it's thousands of times faster than anything I'm aware of. If you want it to solve more general problems of that size, I would say it competes -- it does as well as some of the best things I've looked at. At this point it's merely above average but shows a promising scaling trajectory." http://www.sciencedaily.com/releases/2013/05/130508122828.htm
,,, since quantum computation greatly outclasses classical computation in terms of solving 'traveling salesmen' problems, then quantum computation within DNA provides a very plausible solution to the unanswered questions as to how DNA, and the associated molecules, are possibly able to perform such astonishing searches in DNA as they do. For example:
Genes and Organisms: Improvising the Dance of Life - Excerpt: Stephen L. Talbott - Nov. 10, 2015 You may recall from my earlier article, “Getting Over the Code Delusion” (Talbott 2010), that packing DNA into a typical cell nucleus is like packing about 24 miles of very thin, double-stranded string into a tennis ball, with the string cut up (in the normal human case) into 46 pieces, corresponding to our 46 chromosomes. To locate a protein-coding gene of typical size within all that DNA is like homing in on a one-half-inch stretch within those 24 miles. Or, rather, two relevant half-inch stretches located on different pieces of string, since we typically have two copies of any given gene. Except that sometimes one copy differs from the other and one version is not supposed to be expressed, or one version needs to be expressed more than the other, or the product of one needs to be modified relative to the other. So part of the job may be to distinguish one of those half-inch stretches from the other. “Decisions” everywhere, it seems. http://www.natureinstitute.org/txt/st/org/comm/ar/2015/genes_29.htm Scientists' 3-D View of Genes-at-Work Is Paradigm Shift in Genetics - Dec. 2009 Excerpt: Highly coordinated chromosomal choreography leads genes and the sequences controlling them, which are often positioned huge distances apart on chromosomes, to these 'hot spots'. Once close together within the same transcription factory, genes get switched on (a process called transcription) at an appropriate level at the right time in a specific cell type. This is the first demonstration that genes encoding proteins with related physiological role visit the same factory. http://www.sciencedaily.com/releases/2009/12/091215160649.htm
Multiple overlapping codes within DNA, extensive biophotonic communication, etc.. etc.., all of which greatly outclasses anything man has ever accomplished, could be touched upon as well, but for brevity I'll skip those attributes for now. But of one final note, Quantum Biology undermines the entire reductive materialistic foundation which undergirds Darwinian thought:
Darwinian Materialism vs. Quantum Biology - video https://youtu.be/LHdD2Am1g5Y
bornagain77_{October 27, 2018
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Thanks Tom Robbins. Very well put. I just shook my head in disbelief while reading the article, and then sighed heavily when Dawkin's Selfish Gene was mentioned towards the end. To try to add a few glimpses, to your already excellent overview, as to just how far more advanced DNA is compared to our feeble attempts at programming. Firstly, "a cell is (at least) 10,000 times more energy-efficient than a transistor."
Life Leads the Way to Invention - Feb. 2010 Excerpt: a cell is 10,000 times more energy-efficient than a transistor. “In one second, a cell performs about 10 million energy-consuming chemical reactions, which altogether require about one picowatt (one millionth millionth of a watt) of power.” This and other amazing facts lead to an obvious conclusion: inventors ought to look to life for ideas.,,, Essentially, cells may be viewed as circuits that use molecules, ions, proteins and DNA instead of electrons and transistors. That analogy suggests that it should be possible to build electronic chips – what Sarpeshkar calls “cellular chemical computers” – that mimic chemical reactions very efficiently and on a very fast timescale. http://creationsafaris.com/crev201002.htm#20100226a
In order to achieve such amazing energy efficiency as it does, the integrated coding of the cell appears to be ingeniously designed for ‘reversible computation’ in order to achieve such astonishing energy efficiency as it does.
Notes on Landauer’s principle, reversible computation, and Maxwell’s Demon - Charles H. Bennett - September 2003 Excerpt: Of course, in practice, almost all data processing is done on macroscopic apparatus, dissipating macroscopic amounts of energy far in excess of what would be required by Landauer’s principle. Nevertheless, some stages of biomolecular information processing, such as transcription of DNA to RNA, appear to be accomplished by chemical reactions that are reversible not only in principle but in practice.,,,, http://www.sciencedirect.com/science/article/pii/S135521980300039X Logically and Physically Reversible Natural Computing: A Tutorial - 2013 Excerpt: This year marks the 40th anniversary of Charles Bennett’s seminal paper on reversible computing. Bennett’s contribution is remembered as one of the first to demonstrate how any deterministic computation can be simulated by a logically reversible Turing machine. Perhaps less remembered is that the same paper suggests the use of nucleic acids to realise physical reversibility. In context, Bennett’s foresight predates Leonard Adleman’s famous experiments to solve instances of the Hamiltonian path problem using strands of DNA — a landmark date for the field of natural computing — by more than twenty years. http://link.springer.com/chapter/10.1007%2F978-3-642-38986-3_20 Logical Reversibility of Computation* - C. H. Bennett - 1973 Excerpt from last paragraph: The biosynthesis and biodegradation of messenger RNA may be viewed as convenient examples of logically reversible and irreversible computation, respectively. Messenger RNA. a linear polymeric informational macromolecule like DNA, carries the genetic information from one or more genes of a DNA molecule. and serves to direct the synthesis of the proteins encoded by those genes. Messenger RNA is synthesized by the enzyme RNA polymerase in the presence of a double-stranded DNA molecule and a supply of RNA monomers (the four nucleotide pyrophosphates ATP, GTP, CTP, and UTP) [7]. The enzyme attaches to a specific site on the DNA molecule and moves along, sequentially incorporating the RNA monomers into a single-stranded RNA molecule whose nucleotide sequence exactly matches that of the DNA. The pyrophosphate groups are released into the surrounding solution as free pyrophosphate molecules. The enzyme may thus be compared to a simple tape-copying Turing machine that manufactures its output tape rather than merely writing on it. Tape copying is a logically reversible operation. and RNA polymerase is both thermodynamically and logically reversible.,,, http://www.cs.princeton.edu/courses/archive/fall04/cos576/papers/bennett73.html The astonishing efficiency of life - November 17, 2017 by Jenna Marshall Excerpt: All life on earth performs computations – and all computations require energy. From single-celled amoeba to multicellular organisms like humans, one of the most basic biological computations common across life is translation: processing information from a genome and writing that into proteins. Translation, it turns out, is highly efficient. In a new paper published in the journal Philosophical Transactions of the Royal Society A, SFI researchers explore the thermodynamic efficiency of translation.,,, To discover just how efficient translation is, the researchers started with Landauer's Bound. This is a principle of thermodynamics establishing the minimum amount of energy that any physical process needs to perform a computation. "What we found is that biological translation is roughly,,, about 100,000 times more efficient than a computer." https://phys.org/news/2017-11-astonishing-efficiency-life.html
The amazing energy efficiency possible with ‘reversible computation’ has been known about since Charles Bennett laid out the principles for such reversible programming in 1973, but as far as I know, due to the extreme level of complexity involved in achieving such ingenious ‘reversible coding’, has yet to be accomplished in any meaningful way for our computer programs even to this day:
Reversible computing Excerpt: Reversible computing is a model of computing where the computational process to some extent is reversible, i.e., time-invertible.,,, Although achieving this goal presents a significant challenge for the design, manufacturing, and characterization of ultra-precise new physical mechanisms for computing, there is at present no fundamental reason to think that this goal cannot eventually be accomplished, allowing us to someday build computers that generate much less than 1 bit's worth of physical entropy (and dissipate much less than kT ln 2 energy to heat) for each useful logical operation that they carry out internally. http://en.wikipedia.org/wiki/Reversible_computing#The_reversibility_of_physics_and_reversible_computing
bornagain77_{October 27, 2018
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I read the full article, and and it sounds like they just pulled a few rookie star trek fans off the street, who know very little about biology and the current state of the "theory" - the second guy they quoted was fan of the selfish gene!!! And it shows why programmers will see the CODE of DNA to fit their worldview - he says it is OBVIOUS DNA drives the organism and not the other way around, but fans of this sight and many modern biologists know, this is a complete falsehood. The more evidence we collect, the more we know for certain, that the idea of the selfish gene is dead and gone - the organism uses DNA like a read write system - DNA does not a person make, we know this. And the one guy that focuses on JUNK DNA for helping to fold the DNA is missing the HUGE picture - JUNK DNA performs many of the same operations as an operating system - regulation, repair, all the housekeeping tasks. Calling routines, regulating what gets access to the DNA and when, and so many other analogous operations we are just now beginning to understand- oh man it chaps my ass when a programmer, if anyone, should see the incredible similarities but appreciate why it is only similar not identical to computer code in his Windows 7 machine - his Windows 7 machine does not produce a organic based 100 Billion cell person!! And the coding DNA is like the data on the drive, and JUNK DNA very similar but much more complex than any operating system we have. OF COURSE there is not a 1:1 analogy, the main point is the cell, for some unknown reason, "decided" to encode instructions for parts and enzymes, and control systems, feedback systems, on and on and on. The one guy comparing the size of DNA and how much data it is when compared with Mozilla browsers is comparing apples and oranges but for some reason misses the fact hat DNA does not need this HUGE amount of code to achieve something a trillion times more complex than a damn firefox browser - DNA can hold much more data in a small space than man could ever dream of, it can also cut and spice in to make a particular protein, be read forward and backward in an overlapping manner, works in 4 dimensions, all he way up to it's placement on the balled up form of DNA, with more used data located near the outside (how in the hell did it "know" to do this, or how was that selected for - you have to be a pure idiot to understand what it does and think that there is no intelligence behind its design, not to mention other structures in the cell that ALSO contain information. Not to mention ONE gram of DNA can potentially hold up to 455 exabytes of data, according to the New Scientist, and a kilogram could theoretically hold all the data in all the books, on all the hard drives, on all printed material, that man has ever created!! In other words, DNA can't help he fact that it can do so much more than code man can come up with so much more efficiently. My degree is in computer science, and I am a Systems Engineer and I know quite a bit about programing, and as far as object oriented programing is concerned, once again nature invented it first - TOP DOWN DESIGN, this is why reductionists materialists keep failing miserably. The body plans and overall goals come first, and the DNA and other information is definitely front loaded, as we see time and time again, examples where code that was turned off, waiting until it is needed, and then switched on.. These two guys are knuckleheads with very limited understanding of Biology - the one guy shows this by claiming the selfish gene is comfortable to him and is still favored!!! The other tries to do a 1 to one comparison, he does ok with immune system analogies, but we even now know the in the cell, there is a very real type of encryption used - and NO it is not as complex as far as the number of bits used, but it does not have to be!!! It just has to make sure that if this enzyme is only for project A, not B, so has a tag that is only recognized by its receiver - very much like a public key is used in encryption. And as far as not having a processor - the code is already in a form that can go to the 3D printer - the processor has already done his job - the mind that made it.Tom Robbins_{October 27, 2018
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