In order to know what mechanisms eventually provoke change and if unguided evolution of an organism is a viable explanation, it must be known what mechanisms do form phenotype, body architecture, organs, various cell types, cell migration etc. Development biology ( Evo-devo ) is a rather new branch of biology, but, yesterday, I gave a look at the book Development biology, Gilbert / Barresi. 11th ed 2018. Despite studying biology for years, I had the impression to know almost nothing of what is described there. Development biology might be the most complex branch of biology, and many open questions remain.
Homeoboxes have been found in fungi, plants and animals. In each "kingdom" homeobox genes occupy a key position in the genetic control of either cell differentiation, morphogenesis and or body plan specification.
All Hox genes and many other developmental transcription factors contain the homeobox, known for their colinearity: conserved arrangement on chromosomes that is the same as their order of activation along the body axis. The regulation is very precise. The degree of sequence conservation of the homeodomain is extremely high indicating strong functional constraints leading to a high pressure to retain the homeobox sequences constant.
What the Hox code represents is a somewhat digital mechanism for regulating axial patterning. By mixing and matching combinations of the expression of a small number of Hox genes, organisms generate a greater range of morphological possibilities.
It is obvious that not any arrangement of Homeobox genes will give rise to functional body architecture. The precise arrangement is key to have functional body plans. Mutations in hox genes do produce aberrant body plans..like legs where there should be antennae in fruit flies. But it is a mistake to assume that this is evidence that hox genes causally lay out the body plan, just like it would be a mistake to assume that a fault in a TV, causing a disruption in the reception of the signal, shows that the TV box produces the signal itself. Linear DNA cannot produce 3D form. There is a higher orchestration, which directs the correct linear arrangement of Homeobox genes in the genome.
Hox Genes in Development: The Hox Code
This colinearity, arrangement, order of activation and precise regulation of Hox gene clusters indicates there is a HOX Code, which sets the right pattern of Hox gene cluster arrangement for correct sequential expression of segments and rhombomeres in the embryo.
There is uncertainty in our understanding of homeobox gene cluster evolution at present. This relates to our still rudimentary understanding of the dynamics of genome rearrangements and evolution over the evolutionary timescales being considered when we compare lineages from across the animal kingdom.
The mechanisms responsible for the synchronous regulation of Hox genes and the molecular function of their colinearity remain unknown. Despite 35 years of active research, the mechanisms of Hox gene regulation have remained elusive. It has been argued that chromatin structure and histone demethylation play important roles in activation of Hox genes, but the mechanism precisely directing chromatin modifications to specific loci at the right time remains mysterious.
What does this elucidate? Life is not only composed of organic carbon-based matter but essentially, instructional information. Not any kind of information, but complex, specifying information, blueprints, which precisely orchestrates and directs how to develop, build, adopt animals, plants, fungi, bacterias, and perpetuate life in all its various forms.
1. Cells store codified information in DNA, and at least 18 epigenetic codes, which are complex instructional informational blueprints, essential for cells to make copies of themselves, animal development, adaptation, and body architecture
2. All Codes, and blueprints we know the origin of come from an intelligent mind. Evolution is a non-directed, non-intelligent process and does not suffice to explain the origin of biodiversity and body architecture.
3. Therefore we have 100% inference that DNA comes from an intelligent mind and 0% inference that it is not.
The Hox Code, Code biology, Barbieri, page 107
In 1979, David Elder proposed a model that was capable of accounting for the regularities that exist in the bodies of many segmented worms (annelids). The segments of these animals are often subdivided into annuli whose number varies according to a simple rule: if a segment contains n annuli, the following segment contains either the same number n (repetition) or n plus or minus 1 (digital modification). Elder noticed that this type of rules is known to the designers of electronic circuits as a Gray code, a code that is binary (because it employs circuits that have only one of two states), combinatorial (because its outcomes are obtained by combinations of circuits) and progressive (because consecutive outcomes must be coded by combinations that differ in the state of one circuit only). The results obtained with these rules describe with great accuracy what is observed in segmented worms, and Elder proposed therefore that the body plan of these animals is based on a combinatorial code that is a biological equivalent of the Gray code. He underlined in particular that the coding principle cannot be the classical “one geneone pattern”, but “one combination of genes-one pattern” and for this reason he called it epigenetic code (Elder 1979). After the discovery of the Hox genes, it became increasingly clear that they are used in many different permutations, according to a combinatorial set of rules that became known as Hox code. The term Hox code was introduced independently by Paul Hunt and colleagues (1991) and by Kessel and Gruss (1991) to account for the finding that the individual characteristics of the vertebrae are determined by different combinations of Hox genes. Later on, it was found that this is true in most other organs and it became standard practice to refer to any combination of Hox genes as a Hox code. The epigenetic code proposed by Elder, in particular, is a Hox code because it is Hox genes that are responsible for the body plan of the segmented worms. It must be underlined that the Hox genes can be used in different combinations not only in various parts of a body, but also in different stages of embryonic development. At the phylotypic stage, for example, the Hox genes specify characteristics of the phylum, whereas in later stages they determine characteristics at lower levels of organization. There is, in short, a hierarchy of Hox gene expressions, and therefore a hierarchy of Hox codes. At this point, however, we have to face a key definition problem: is it legitimate to say that the Hox codes are true organic codes? More precisely, that they have the basic features that we find, for example, in the genetic code? An organic code is a mapping between two independent worlds and cannot exist without a set of adaptors that physically realize the mapping. The Hox codes have been defined instead as patterns of combinatorial gene expression and do not require adaptors because a molecular pattern in one world is not a mapping between two independent worlds. We have therefore two different definitions of code, one based on mapping and the other on patterns, or sequences, and it is important to keep them separate because they have different biological implications.
The various codes in the cell
The Genetic Code
The Splicing Codes
The Metabolic Code
The Signal Transduction Codes
The Signal Integration Codes
The Histone Code
The Tubulin Code
The Sugar Code
The Glycomic Code
The non-ribosomal code
The Calcium Code
The RNA code
A domain substrate specificity code of Nonribosomal peptide synthetases (NRPS)
The DNA methylation Code
The coactivator/corepressor/epigenetic code
The transcription factor code
The post-translational modification code for transcription factors
The HOX Code
Last edited by Admin on Tue Nov 20, 2018 5:12 am; edited 2 times in total