March 12, 2019 | David F. Coppedge

Biological Codes Are Everywhere

Scientists struggle to account for the origin of coded information in biology from a materialistic framework.

A special of BioSystems, called “Code Biology,” contains a rare set of papers tackling the subject of biological codes head on. Though published in Feb 2018, the papers still represent the state of thinking among materialistic evolutionists, because no paradign-shifting breakthroughs have arrived since then. Look at some of the challenges they deal with:

What is code biology? (Mattew Barbieri, Biosystems).

Various independent discoveries have shown that many organic codes exist in living systems, and this implies that they came into being during the history of life and contributed to that history…. After the genetic code and the signal processing codes, on the other hand, only the ancestors of the eukaryotes continued to explore the coding space and gave origin to splicing codes, histone code, tubulin code, compartment codes and many others. A first theoretical consequence of this historical fact is the idea that the Eukarya became increasingly more complex because they maintained the potential to bring new organic codes into existence. A second theoretical consequence comes from the fact that the evolution of the individual rules of a code can take an extremely long time, but the origin of a new organic code corresponds to the appearance of a complete set of rules and from a geological point of view this amounts to a sudden event. The great discontinuities of the history of life, in other words, can be explained as the result of the appearance of new codes. A third theoretical consequence comes from the fact that the organic codes have been highly conserved in evolution, which shows that they are the great invariants of life, the sole entities that have gone intact through billions of years while everything else has changed. This tells us that the organic codes are fundamental components of life and their study – the new research field of Code Biology – is destined to become an increasingly relevant part of the life sciences.

Proteins are coded by triplet codons of DNA “letters” A, C, T, and G. (Illustra Media)

On universal coding events in protein biogenesis (Kubyshkin et al, Biosystems)

The complete ribosomal protein synthesis cycle and codon-amino acids associations are universally preserved in all life taxa on Earth. This process is accompanied by a set of hierarchically organized recognition and controlling events at different complexity levels. It starts with amino acid activation by aminoacyl tRNA synthetases (aaRS) followed by matching with the acceptor units of their cognate tRNAs (“operational RNA code”) and ribosomal codon-anticodon pairing of messenger RNA (“triplet code”). However, this codon-anticodon matching is possible only when protein translation machinery (translation factors, ribosome) accepts an esterified amino acid. This capacity (“charge code”) correlates mainly with the amino acid nature and the identity elements in the tRNA 3D structure. A fourth potential “folding code” (also referred as “stereochemical code”) between the translation dynamics, sequence composition and folding of the resulting protein can also be defined in the frame of the ‘Anfinsen dogma’ followed by post-translational modifications. All these coding events as well as the basic chemistry of life are deemed invariant across biological taxa due to the horizontal gene transfer (HGT) making the ‘universal genetic code’ the ‘lingua franca’ of life of earth.

The splicing code (Baralle and Baralle, Biosystems)

This issue dedicated to the code of life tackles very challenging and open questions in Biology. The genetic code, brilliantly uncovered over 50 years ago is an example of a univocal biological code. In fact, except for very few and marginal variations, it is the same from bacteria to man, the RNA stretch: 5′ GUGUUC 3′ reads as the dipeptide: Val-Phe in bacteria, in yeast, in Arabidopsis, in zebra fish, in mouse and in human…. Given the complexity of the splicing process, the construction of an algorithm that can define exons or their fate with certainty has not yet been achieved.

Evidence for the implication of the histone code in building the genome structure (Prakash and Fournier, Biosystems)

Histones are punctuated with small chemical modifications that alter their interaction with DNA. One attractive hypothesis stipulates that certain combinations of these histone modifications may function, alone or together, as a part of a predictive histone code to provide ground rules for chromatin folding.

The lamin code (Maraldi, Biosystems)

Unicellular eukaryotes and metazoa present a nuclear envelope (NE) and metazoa express in it one or more lamins that give rise to the nuclear lamina. The expression of different types of lamins is related to the complexity of the organism and the expression of type-A lamins is related to the initial steps of tissue-specific cell differentiation. Several posttranslational modifications characterize the expression of lamin A in the course of cell differentiation, and the alteration of this expression pattern leads to impressive phenotypic diseases that are collectively referred to as laminopathies. This indicates a link between differential lamin A expression and tissue-specific cell commitment, and makes it conceivable that the lamin posttranslational modifications constitute a lamin code, utilized by metazoan cells to induce tissue-specific cell differentiation. Although the rules of this code are not yet deciphered, at the moment, the presence of adaptors, represented by NE transmembrane proteins (NETs), and of effectors, constituted by epigenetic repressors that modulate chromatin arrangement and gene expression, strongly supports the possibility that the rules of lamin modification represent one of the organic codes that characterize cell evolution.

The bioelectric code: An ancient computational medium for dynamic control of growth and form (Levin and Martyniuk, Biosystems). These authors present an exciting prospect that electricity guides body form (morphology) from the genetic code.

What determines large-scale anatomy? DNA does not directly specify geometrical arrangements of tissues and organs, and a process of encoding and decoding for morphogenesis is required. Moreover, many species can regenerate and remodel their structure despite drastic injury. The ability to obtain the correct target morphology from a diversity of initial conditions reveals that the morphogenetic code implements a rich system of pattern-homeostatic processes. Here, we describe an important mechanism by which cellular networks implement pattern regulation and plasticity: bioelectricity. All cells, not only nerves and muscles, produce and sense electrical signals; in vivo, these processes form bioelectric circuits that harness individual cell behaviors toward specific anatomical endpoints. We review emerging progress in reading and re-writing anatomical information encoded in bioelectrical states, and discuss the approaches to this problem from the perspectives of information theory, dynamical systems, and computational neuroscience. Cracking the bioelectric code will enable much-improved control over biological patterning, advancing basic evolutionary developmental biology as well as enabling numerous applications in regenerative medicine and synthetic bioengineering.

Fundamental principles of the olfactory code (Grabe and Sachse, Biosystems). These two explore what is known about the “nose code” which involves fundamentally different mechanisms from other senses. (For animation of the olfactory code, see the clip “A Pacific Salmon’s Sense of Smell” from Living Waters by Illustra Media).

Interior of the odor processing center in a salmon (Illustra Media)

Sensory coding represents a basic principle of all phyla in nature: species attempt to perceive their natural surroundings and to make sense of them. Ultimately, sensory coding is the only way to allow a species to make the kinds of crucial decisions that lead to a behavioral response. In this manner, animals are able to detect numerous parameters, ranging from temperature and humidity to light and sound to volatile or non-volatile chemicals. Most of these environmental cues represent a clearly defined stimulus array that can be described along a single physical parameter, such as wavelength or frequency; odorants, in contrast, cannot. The odor space encompasses an enormous and nearly infinite number of diverse stimuli that cannot be classified according to their positions along a single dimension. Hence, the olfactory system has to encode and translate the vast odor array into an accurate neural map in the brain. In this review, we will outline the relevant steps of the olfactory code and describe its progress along the olfactory pathway, i.e., from the peripheral olfactory organs to the first olfactory center in the brain and then to the higher processing areas where the odor perception takes place, enabling an organism to make odor-guided decisions. We will focus mainly on studies from the vinegar fly Drosophila melanogaster, but we will also indicate similarities to and differences from the olfactory system of other invertebrate species as well as of the vertebrate world.

The sugar code: Why glycans are so important (Gabius, Biosystems). The “third alphabet of life” is surprisingly rich, this author shows.

The cell surface is the platform for presentation of biochemical signals that are required for intercellular communication. Their profile necessarily needs to be responsive to internal and external factors in a highly dynamic manner. The structural features of the signals must meet the criterion of high-density information coding in a minimum of space. Thus, only biomolecules that can generate many different oligomers (‘words’) from few building blocks (‘letters’) qualify to meet this challenge. Examining the respective properties of common biocompounds that form natural oligo- and polymers comparatively, starting with nucleotides and amino acids (the first and second alphabets of life), comes up with sugars as clear frontrunner. The enzymatic machinery for the biosynthesis of sugar chains can indeed link monosaccharides, the letters of the third alphabet of life, in a manner to reach an unsurpassed number of oligomers (complex carbohydrates or glycans). Fittingly, the resulting glycome of a cell can be likened to a fingerprint. Conjugates of glycans with proteins and sphingolipids (glycoproteins and glycolipids) are ubiquitous in Nature. This implies a broad (patho)physiologic significance. By looking at the signals, at the writers and the erasers of this information as well as its readers and ensuing consequences, this review intends to introduce a broad readership to the principles of the concept of the sugar code.

The evolution of the Glycomic Codes of extracellular matrices (Buckeridge, Biosystems). Here’s another code most of us knew nothing about: a code system that works outside the cell and between cells.

The extracellular matrices (ECMs) of living organisms are compartments responsible for maintenance of cell shape, cell adhesion, and cell communication. They are also involved in cell signaling and defense against the attack of pathogens. The plant cell walls have been recently defined as encoded structures that combine polysaccharides with other encoded structures (proteins and phenolic compounds). The term Glycomic Code has been used to define the set of mechanisms that generate cell wall architecture (the combination of polymers of different types) and biological function.

How did biological codes originate? That will be the subject of additional papers we will look at in this special issue, “Code Biology.”

This issue is so rich with concepts and principles of interest to intelligent design, we need to show more. Watch the tension develop as these evolutionary biologists observe real coded information exchange within and outside of cells, and try to account for them by blind, unguided processes. We say it cannot be done! That will certainly become evident in articles on the origin of life.

Is a code possible without a mind? Atheists may object that archaea and other microbes do not have minds, and yet use codes. But this dodges the question. Computers don’t have minds either, but their codes (e.g., ASCII) are clearly products of mind that were coded into the hardware. The codes we know in our machines are always products of minds. By the uniformity of experience, therefore, we can infer that a mind or minds were responsible for the codes in biology, many of which are so complex and efficient we are just beginning to appreciate them.

 

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