Ancestral Code Research Articles

The Genetic Code Assembles via Division and Fusion, Basic Cellular Events.

Standard Genetic Code (SGC) evolution is quantitatively modeled in up to 2000 independent coding 'environments'. Environments host multiple codes that may fuse or divide, with division yielding identical descendants. Code division may be selected-sophisticated gene products could be required for an orderly separation that preserves the coding. Several unforeseen results emerge: more rapid evolution requires unselective code division rather than its selective form. Combining selective and unselective code division, with/without code fusion, with/without independent environmental coding tables, and with/without wobble defines 25 = 32 possible pathways for SGC evolution. These 32 possible histories are compared, specifically, for evolutionary speed and code accuracy. Pathways differ greatly, for example, by ≈300-fold in time to evolve SGC-like codes. Eight of thirty-two pathways employing code division evolve quickly. Four of these eight that combine fusion and division also unite speed and accuracy. The two most precise, swiftest paths; thus the most likely routes to the SGC are similar, differing only in fusion with independent environmental codes. Code division instead of fusion with unrelated codes implies that exterior codes can be dispensable. Instead, a single ancestral code that divides and fuses can initiate fully encoded peptide biosynthesis. Division and fusion create a 'crescendo of competent coding', facilitating the search for the SGC and also assisting the advent of otherwise uniformly disfavored wobble coding. Code fusion can unite multiple codon assignment mechanisms. However, via code division and fusion, an SGC can emerge from a single primary origin via familiar cellular events.

Contribuții la cercetarea „obiceiului pamântului” pe Valea Cosăului

Our study focuses on an important and interesting aspect of legal ethnology – the habit of the earth, that legal code of great complexity, including unwritten rules, meant to order the social, economic, spiritual, family life, etc., as established and they perpetuated in the archaic area of Cosău Valley from Maramureș County. At the beginning we focused, using the opinions of researchers, on the unwritten ancestral legal code, reflecting how the peasant conceives the idea of concept of justice, how it is resolved according to the rules of this ancestral code, then how its rules materialize in all sectors of village life. We also referred to the durability and resistance of the custom of the land over time, the way in which unwritten laws coexisted in feudal society along with written ones. A developed chapter was reserved for unwritten norms related to the complex of relations between the villagers, in which we emphasized the role played by the implications of the kinship system, then the relations between the villagers and the „village lights”. We have assigned a separate chapter for unwritten agrarian laws, many related to property, to the protection of wealth. We paid attention to the ways of associating the owners in order to be able to break through the work of the agricultural lands, which required a lot of increased labour force. We have assigned another chapter for the unwritten pastoral laws, the sheepfold having a complex status, with numerous rigorously observed norms. We referred to the role of the sheepfold chief in the observance of the unwritten norms from the statute of the sheepfold. Another chapter is about the unwritten norms of the complex of family life, with many normative provisions, some related to the protection of children, others to the complex of marriage, others focused on the relations between children and parents, etc. In our study we also included unwritten normative provisions related to the practice of certain trades or related to the obligations of the community to the calls of the village leadership. In this chapter, we paid attention to the normative provisions related to the transactions between the villagers. A developed chapter of our study is intended to judge the abuses committed by the guilty, due to the violation of the unwritten norms, in which we focused on those invested to apply them: the elderly, the lads’ group or by people with juridical and administrative roles in the rural community. We also did not omit the information related to the categories of punishments: fees. The study concludes with brief references related to the legal customs performed or punishments or the submission to the laughter and mockery of the village, the compensations in kind, etc. in the investigated space: Shouting over the village and „Herdetișurile”. Keywords: Cosau Valley, juridical rules, unwritten norms

Toponyms: Neglected wallflower or pot of lenty

Threats of imminent extinction motivate language documentation; they also allow place name neglect. This paper examines settlement names within Africa’s Edoid group. Village nomenclature converges on a restricted range of conventions; however, interethnic contact has led to non-Edoid toponyms for three villages. Two derive from the trade language Hausa. A third links to Igbo blacksmiths supporting rainforest penetration with iron tools, as is evident in cognate vocabulary. Iron use most naturally follows a pastoral era outside the rainforest, which number prefixes on herd-animal nouns support. Toponymic studies thus remind us of the benefit accrued when documentation looks beyond “the single ancestral code.”

Contrasting 5' and 3' Evolutionary Histories and Frequent Evolutionary Convergence in Meis/hth Gene Structures

Organisms show striking differences in genome structure; however, the functional implications and fundamental forces that govern these differences remain obscure. The intron–exon organization of nuclear genes is involved in a particularly large variety of structures and functional roles. We performed a 22-species study of Meis/hth genes, intron-rich homeodomain-containing transcription factors involved in a wide range of developmental processes. Our study revealed three surprising results that suggest important and very different functions for Meis intron–exon structures. First, we find unexpected conservation across species of intron positions and lengths along most of the Meis locus. This contrasts with the high degree of structural divergence found in genome-wide studies and may attest to conserved regulatory elements residing within these conserved introns. Second, we find very different evolutionary histories for the 5′ and 3′ regions of the gene. The 5′-most 10 exons, which encode the highly conserved Meis domain and homeodomain, show striking conservation. By contrast, the 3′ of the gene, which encodes several domains implicated in transcriptional activation and response to cell signaling, shows a remarkably active evolutionary history, with diverse isoforms and frequent creation and loss of new exons and splice sites. This region-specific diversity suggests evolutionary “tinkering,” with alternative splicing allowing for more subtle regulation of protein function. Third, we find a large number of cases of convergent evolution in the 3′ region, including 1) parallel losses of ancestral coding sequence, 2) parallel gains of external and internal splice sites, and 3) recurrent truncation of C-terminal coding regions. These results attest to the importance of locus-specific splicing functions in differences in structural evolution across genes, as well as to commonalities of forces shaping the evolution of individual genes along different lineages.

On the origin of the genetic code: signatures of its primordial complementarity in tRNAs and aminoacyl-tRNA synthetases

If the table of the genetic code is rearranged to put complementary codons face-to-face, it becomes apparent that the code displays latent mirror symmetry with respect to two sterically different modes of tRNA recognition. These modes involve distinct classes of aminoacyl-tRNA synthetases (aaRSs I and II) with recognition from the minor or major groove sides of the acceptor stem, respectively. We analyze the anticodon pairs complementary to the face-to-face codon couplets. Taking into account the invariant nucleotides on either side (5' and 3'), we consider the risk of anticodon confusion and subsequent erroneous aminoacylation in the ancestral coding system. This logic leads to the conclusion that ribozymic precursors of tRNA synthetases had the same two complementary modes of tRNA aminoacylation. This surprising case of molecular mimicry (1) shows a key potential selective advantage arising from the partitioning of aaRSs into two classes, (2) is consistent with the hypothesis that the two aaRS classes were originally encoded by the complementary strands of the same primordial gene and (3) provides a 'missing link' between the classic genetic code, embodied in the anticodon, and the second, or RNA operational, code that is embodied mostly in the acceptor stem and is directly responsible for proper tRNA aminoacylation.

Evidence forde NovoEvolution of Testis-Expressed Genes in theDrosophila yakuba/Drosophila erectaClade

The mutational origin and subsequent evolution of de novo genes, which are hypothesized to be genes of recent origin that are not obviously related to ancestral coding sequence, are poorly understood. However, accumulating evidence suggests that such genes may often function in male reproduction. Here we use testis-derived expressed sequence tags (ESTs) from Drosophila yakuba to identify genes that have likely arisen either in D. yakuba or in the D. yakuba/D. erecta ancestor. We found several such genes, which show testis-biased expression and are often X-linked. Comparative data indicate that three of these genes have very short open reading frames, which suggests the possibility that a significant number of testis-biased de novo genes in the D. yakuba/D. erecta clade may be noncoding RNA genes. These data, along with previously published data from D. melanogaster, support the idea that many de novo Drosophila genes function in male reproduction and that a small region of the X chromosome in the melanogaster subgroup may be a hotspot for the evolution of novel testis-biased genes.

Language and ethnicity in the "taboo" region: the U.S.-Mexico border

This article explores the relative values of the Spanish language along the US-Mexico border. It is proposed that Spanish is inextricably linked to Mexican ethnicity. The Spanish language and the Mexican ethnicity operate as an equation. Its relative acceptance or rejection depends on historical, economic, demographic and geographic factors. US border communities in diverse locations (e.g., southern California, southern Arizona, southwest Texas, and the Rio Grande Valley of Texas) are analyzed, discussed and compared. The analysis shows the degree of continuity or discontinuity of language and ethnicity in each Community. Spanish, the ancestral code may be showing signs of a reversed language shift, a process that may more advanced in older communities where the density ofthe Mexican-American population is rather high.

Comma-free and synchronizable codes

Shepherd (1981. Proc. natn. Acad. Sci. U.S.A. 78, 1596-1600), Clarke (1982. J. theor. Biol. 99, 397-403), Crick et al. (1976. Origins of Life 7, 389) have put forward the possibility that there was a code, ancestral to the existing genetic code, which was non-degenerate and comma-free. The point of a comma-free code, as first proposed in Crick et al. (1957), is that it provides immunity from frameshift reading errors. In this paper it is argued that if frameshift error immunity is to be used as a selection factor in guiding the search for a hypothetical ancestral code, then the appropriate mathematical formulation of this characteristic is not comma-freeness but synchronizability. The calling card of the comma-free notion is that it results in a limit of 20 on the number of sense codons when applied to the genetic coding system. But so does synchronizability, which includes comma-freeness as a special case. Further, using synchronizability as a constraint instead of comma-freeness yields roughly 3000 times as many potential models for an ancestral code. In particular, the RNY model becomes more compatible with immunity from frameshift error as an evolutionary constraint.

The murine complement receptor gene family. Analysis of mCRY gene products and their homology to human CR1.

The mouse genome contains two sets of gene sequences which are highly homologous to the gene encoding the human C3b/C4b receptor (CR1). These genes, termed murine CRY (mCRY) and murine CRX (mCRX) reside on murine chromosomes 1 and 8, respectively. Analysis of cDNA isolated by using these sequences as probes indicates that there are two related but distinct mRNA which are expressed in a wide variety of murine tissues including spleen, liver, lung, and brain. Both of these transcripts encode proteins which should contain a signal sequence for membrane insertion, a transmembrane/cytoplasmic tail region for membrane anchoring, and five extracellular domains made up of 60 amino acid consensus repeat sequences. The difference between the two is the presence of an additional exon of 129 bp immediately 3' of the signal sequence. This additional exon does not encode a 60 amino acid repeat. The sizes of the mature proteins predicted from the cDNA sequences are 43,998 Mr and 48,680 Mr; however, antisera raised against carboxy-terminal sequences detects a 70,000 Mr protein from murine fibroblasts suggesting a high degree of post-translational modification of the mature protein. A comparison of these murine gene sequences with a partial human CR1 sequence suggests that the human CR1 gene evolved by direct duplication of the ancestral coding sequences contained within these murine genes including those sequences important for membrane anchoring and cytoplasmic protein attachment.

Homology between coding and noncoding sequences within the human class I HLA antigen gene.

In our previous paper, we identified 32 recurring base oligomers (1 decamer, 4 octamers, 9 heptamers and 18 hexamers) within the coding sequence for the mouse class I major histocompatibility (MHC) antigen H-2Kb. The compilation of these recurring base oligomers led to the conclusion that the entire ancestral coding sequence for class 1 MHC antigens evolved from tandem repeats of the one 45 base-long primordial building block base sequence. As with most other mammalian genes, the gene for each class I MHC antigen is an admixture of coding and noncoding segments interspersed with each other. Thus, the status of noncoding segments should be clarified in relation to the concept of the primordial building block. The published 4,122 base-long sequence of human pHLA 12.4 germline gene afforded me an opportunity for clarification. Since the number of recurring base oligomers residing within the entire 4,000 + base-long sequence proved unmanageably numerous, the two portions 1,200 bases in the total length were singled out. Within these portions containing five noncoding and four coding segments, noncoding and coding segments shared 1 nonomer, 3 octamers, 6 heptamers and 5 hexamers; all the above-noted base oligomers were derived from different parts of the same 45 base-long primordial building block. It was thus concluded that not only the coding segments, but the entire ancestral gene for class I MHC antigens evolved from tandem repeats of the 45-base-long primordial building block. This new concept of primordial building block was discussed in relation to the mechanism of evolution by gene duplication.