home		Biological	until 1854	Formalization 1854-1937	Revolutions 1937-1951	Electronic Age
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Comprehensive History of Information and Computing: Biological

• Self-replicating RNA molecules: «Life could not exist until a collection of specific catalysts appeared that could promote the synthesis of more catalysts of the same kind. Early stages in the evolutionary pathway presumably centred on RNA molecules [ribonucleic acid], which not only present specific catalytic surfaces but also contain the potential for their own duplication through the formation of a complementary RNA molecule. It is assumed that a small RNA molecule eventually appeared that was able to catalyze its own duplication. Such an autocatalytic RNA molecule would have multiplied faster than its neighbours, usurping the RNA precursor molecules in the primeval soup» [Britannica].
  RNA is a molecule, a long chain made from the «four nucleotides: adenine (A), guanine (G), cytosine (C), and uracil (U)» [Britannica].

  Encod. + Processor: Ribosomes (rRNA) process mRNA, decode it, synthesize proteins [next processor: Carillons]:
  Proteins are molecules «composed of long chains of amino acids, and the specific sequence of these amino acids dictates the function of each protein» [MS Encarta online: Genetics/C]. They «are more powerful catalysts than RNA molecules.» [Britannica], but since they cannot self-replicate, they must be synthesized (translated) from RNA. Early synthesis worked probably in analogy to synthesis in current cells [MS Encarta online: Genetics/III D; Britannica], where it takes place in ribosomes [ribosomes -- since when?] [Britannica]:

  Special tRNA molecules (transfer RNA), with a short sequence of nucleotides called anticodon, bind a specific amino acid (of those flowing around). [How anticodon and amino acids match is shown below for the modern triplet code.] tRNA molecules match with their anticodon-side to a subsection, called codon, in the long sequence of nucleotides of an mRNA molecule (messenger RNA) so that nucleotides in mRNA's codon and tRNA's anticodon match as follows: A:U, U:A, G:C, C:G. In some anticodons Inosin replaces [Guanin?] Uracil[?] The amino acids bound to the tRNA molecules that were able to match to the mRNA are joined together, where some ribosomes (rRNA = ribosomal RNA molecules) act as catalysator.

  Hence, mRNA molecules encode proteins, in the sense that decoding them with the help of tRNAs and rRNAs synthesizes proteins.

  «[A]s time passed, cells arose in which RNA served primarily as genetic material, being directly replicated in each generation and inherited by all progeny cells in order to specify proteins» [Britannica].

  3.5 bill BC: Cells: «[A]rchaebacteria, the first cells on earth, evolved at least 3.5 billion years ago» [MS Encarta online: Prokaryote], they are anaerobe organisms, living without oxygen.

  Encod. + Processor: DNA, «related to RNA yet chemically stabler, probably appeared rather late in the evolutionary history of cells».

  	DNA is a double chain (twisted to a double helix) where at each link of the chain there can be one of four nucleotide bases: adenine (A), guanine (G), thymine (T), and cytosine (C). Each half of the double chain is a template of/for the other half, where nucleotides on each side match as follows: A:T, T:A, G:C, C:G.
  	This redudancy (duplication) of information allows some kinds of repairs, and allows safer replication: The two halfs are separated, and then each one is ``repaired'' to a double chain by reconstructing its complement. This way each of the new double chains is half new and half old. «This "semiconservative" replication is the key to the stable inheritance of genetic traits» [Britannica].

  «A segment of DNA that codes for the cell's synthesis of a specific protein is called a gene» [Britannica]. «Genes line up in a row along the length of a DNA molecule. In humans a single gene can vary in length from 100 to over 1,000,000 bases [MS Encarta online: Genetics/III C]. However, «not all DNA codes for protein synthesis. ... [S]ome of the noncoding DNA is involved in regulating the biochemical processes of the cell» [Britannica].

  Transcriptase is the enzyme that processes DNA to translate it to mRNA: To synthesize a protein, the two chain of a DNA are separated, to make a gene accessible, so that mRNA can be created to match it, where each DNA base corresponds to an mRNA base as follows: A:U, T:A, G:C, C:G. After this "transcription", the normal "translation" from mRNA to protein can take place [MS Encarta online: Genetics/III D; Britannica].

  Retroviruses have developed the enzyme "reverse transcriptase" which encodes RNA back to DNA [Britannica].

  «Over a period of time, the genetic information in RNA sequences was transferred to DNA sequences, and the ability of RNA molecules to replicate directly was lost.» [Britannica].

  Triplet code: «A sequence of three nucleotide bases, called a triplet, is the genetic code word, or codon, that specifies a particular amino acid» [MS Encarta online: DNA].

  «There are 64 possible codons, three of which do not code for amino acids but indicate the end of a protein. The remaining 61 codons specify the 20 amino acids that make up proteins. The AUG codon [of mRNA], in addition to coding for methionine, is found at the beginning of every mRNA and indicates the start of a protein ... [T]he genetic code is identical in almost all species, with the same codons specifying the same amino acids.» [Britannica]. Amino acids #21 (selenocystein) and #22 (pyrrolysin) were discovered 1986 and 2002 resp. [Spiegel Online 24 May 2002]

  [from exipolis]

  information (amino acid)

  start protein encoding (only in bacteria), and methionine ile...

  thr...

  asn... lysine

  ser... arg...

  his... gln...

  proline

  leucin phenyl- alanine

  cys... trp...

  tyr... end of encoding

  serin

  glycin

  valine

  ala...

  asp... glu...

  tRNA anticodon

  UAC UAA/G/U

  UG*

  UUA/G UUU/C

  UCA/G UCU/C

  - GC*

  GUA/G GUU/C

  GG*

  GA* -

  AAU/C AAA/G

  ACA/G ACC

  AUA/G -

  AG*

  CC*

  CA*

  CG*

  CUA/G CUU/C

  mRNA codon

  AUG AUU/C/A

  AC*

  AAU/C AAA/G

  AGU/C AGA/G

  - CG*

  CAU/C CAA/G

  CC*

  CU* -

  UUA/G UUU/C

  UGU/C UGG

  UAU/C UGA, UAA/G

  UC*

  GG*

  GU*

  GC*

  GAU/C GAA/G

  DNA codogen

  TAC TAA/G/T

  TG*

  TTA/G TTT/C

  TCA/G TCT/C

  - GC*

  GTA/G GTT/C

  GG*

  GA* -

  AAT/C AAA/G

  ACA/G ACC

  ATA/G ACT, ATT/C

  AG*

  CC*

  CA*

  CG*

  CTA/G CTT/C

  3.4 bill. - 2.5 bill. BC: Photosynthesis: «[C]yanobacteria evolved from 2.5 to 3.4 billion years ago. Through the process of photosynthesis, ... cyanobacteria introduced oxygen into the atmosphere. As the oxygen content in the atmosphere increased over the centuries, bacteria evolved that used this oxygen ... [This] set the stage for the evolution of eukaryotic cells --larger, more complex cells that require efficient energy production to carry out their life processes» [MS Encarta online: Prokaryote].

  2.0 bill. BC: Aerobic: «The switch to predominantly aerobic metabolism is thought to have occurred in bacteria approximately 2,000,000,000 years agos» [Britannica].

  1.5 bill. BC: «Aerobic eukaryotic cells (cells containing nuclei and all of the other organelles) probably appeared about 1,500,000,000 years ago, their lineage having branched off much earlier from that of the bacteria. Eukaryotic cells almost certainly became aerobic by engulfing aerobic bacteria ...» The internal structuring of the cell allowed specialization of the parts, e.g. the membrane could specialize for cell-to-cell communication and cell signaling [Britannica].

  «The nucleus is the information centre of the cell in all higher organisms» [Britannica]. Much like a library, the nucleus has collected (nearly) all of the cell's DNA, where they are in a storage and reading area, separated from the other buisness of the cell.

  Encod.: In eukaryotes, for decoding a gene to produce a protein, certain regions of the gene, called introns, are skipped in the transcription step. [MS Encarta online: Genetics/III C].

• 350 mio. BC: Acanthostega, the most primitive tetrapod (with four limbs) has eight fingers on each hand; had they not been reduced to five each over the time, humanity's predominant number system would not have been decimal but hexadecimal!
• Gene, between 350-240 mio. BC, shortly after mamals and reptiles separated: the new male-sex determining gene region SRY separated a pair of normal chromosomes into the Y (with SRY) and X (without SRY) chromosomes. Gene recombination between X and Y (in males) was restricted to prevent the dominant SRY from jumping onto the X chromosome which would result in both X and Y being male determining. [bild der wissenschaft 11/2001, source BMBF].

• Brain [>]: Australopithecus has a 450gr (450cm³) brain (like chimanzes). Males 50% larger than females (indication for `harem' structure).
• 2.5 mio. BC: The ice ages started a time of climate changes every few thousand years. This favoured flexible, not instinctive, behavior.

  Larger brain made a larger head, increasing the change for complications at birth. The limit of head size at birth to the width of the birth channel required humans to be born in a less mature state than normal for mammals, ensuing the need for more (parental) care for the baby.

  Larger brain (and language) improved social skills. Typical clan size increased to 150 members from chimpanzes' and pavians' 50 members.

• Brain [<>]: Hypothesis: Shifting to a diet of meat (and, perhaps, nutritious roots) enabled the first steps of reducing intestine size in favor of increased brain size. (First scavanging, then, with improved hunting techniques, improved spears and improved spear throwing skills, more and more hunting.)
  1. 2 mio. BC: Homo habilis with 600-700gr brain.
  2. 1.7 mio. BC: Homo erectus: 800-1000gr brain. Males reduced to 20% larger than females.
• 1.7 mio. BC: Homo erectus spreaded from Africa to Asia.
• Brain 1 - 0.4 mio. BC [<]: Hypothesis: cooking enabled the second step of intestine reduction and corresponding brain increase.
  1. archaic homo sapiens: 1200gr brain.
  2. modern human being: typically 1300-1400gr (1100-1800gr).
• 100,000 BC: modern humans spreaded from Africa over all continents.