Biology

Classical classification

• Boatny: fungi and bacteria were treated as plants
• Zoology

plant (植物)

•microbe •fungus •algae •lichen •moss •fern •gymnospermae •angiospermae

•anatomy •cytology

animal (動物)

•insect •fish •amphibian •reptile •bird •mammal •human (人類)

Proximate and ultimate factors (至近要因と究極要因)

Five kingdoms (5界説)

Three domains

Fig. Evolutionary phylogeny. Super-thermotrophic bacteria (超好熱菌) = Aquifex, Pyrodicticum, Thermoproteus and T. celer

One attempt, not supported well

Domain 1 Aphanobionta (無形生物)

Kingdom 1 Virus (ウイルス)

Division 1 Virus (ウイルス)

Domain 2 Monera (モネラ)

Kingdom 2 Eubacteria (真性細菌)

Subkingdom 1 Gram-negative bacteria (グラム陰性細菌)

Division 2 Thermotogobacteria (始祖好熱細菌)

Division 3 Chloroflexobacteria (緑色糸状細菌)

Division 4 Deinococcus-Thermus

Division 5 Chlorobiobacteria (緑色硫黄細菌)

Division 6 Proteobacteria (プロテオバクテリア)

Division 7 Spirochaetobacteria (スピロヘータ)

Superdivision Cyanobacteria (シアノバクテリア)

Division 8 Cyanobacteria シアノバクテリア(藍藻)

Subkingdom 2 Clamidiobacteria

Division 9 Clamidiobacteria

Subkingdom 3 Gram-native bacteria (グラム陽性細菌)

Division 10 Bacillobacteria (グラム陽性菌)

Subdivision Heliobacteria

Division 11 Actinobacteria (放線菌)

Subdivision Actynomycota (放線菌)

Domain 3 Archaea (古細菌)

Kingdom 3 Metabacteria 後生細菌(古細菌)

Division 12 Thermoproteobacteria (高温・好酸・硫黄依存古細菌)

Division 13 Halobacteria (高度好塩菌)

Division 14 Methanobacteria (メタン生成菌)

Domain 4 Eucaryota (真核生物)

Superkingdom Archaeozoa (原真核生物)

Kingdom 4 Archaeozoa (原真核生物界)

Superkingdom Eucaryota (真核生物)

Kingdom 5 Protoctista (原生生物)

Subkingdom 1 Sarcomastigophora (肉質鞭毛虫)

Subkingdom 2 Sporozoa (胞子虫)

Subkingdom 3 Myxozoa (ミクソゾア/粘液胞子虫)

Subkingdom 4 Rhodophyta (紅藻)

Kingdom 6 Chromista (クロミスタ)

Kingdom 7. Plantae (植物)

Kingdom 8 Fungi (菌)

Kingdom 9 Animalia (動物)

pointed out the mistakes on sheart drawn by Galenus (129?-200?)
corrected by the addition of septum between right and left atria

laying the foundation of medical research of which central approach is anatomy

discovered the principles of blood circulation (the effect of overseas education)
demonstrated by observationss which pipe was inflated after binding, vein (blue pipe) or artery

Morphology (= form)

Anatomy: study of structure, study of basic type
Embryology: phylogenic embryology, individual embryology

Physiology (= function)

Working physiology: plant physiology, animal physiology
Relational physiology: study of distribution, ecology (oecologie)

The nucleus = Natural history → Taxonomy - Descriptive

1922, 25 "The plant species in relation to habitat and imate. Contribution to the knowledge of genecological units" - genecology (遺伝生態学) (Hereditas vols 3, 6)

confirming ecological race (= ecotype), using the transplant experiments of Draba verna, Atriplex subcordata, Epilobium pyrricholophum, etc.

ecotype is a kind of genotype
the ecotype is ranked as:

ecophene < ecotype < ecospeceis < coenospecies
→ interpreted as the stages of variations

Genetics

→ comprehensive obsrvations and descriptions
→ no laws and theorems were found out

1866 Versuche über Pflanzen-Hybriden (Experiments in plant hybridization)

1902-03 proposed chromosome theory of inheritance

chromosomal distribution in sex cells is consistent with Mendelian inheritance

1924 confirming the mutation stated by de Vries is chromosomal mutation, using figwort/antirrhinum/maj.html

Oryza = 23 species. Oryza sativa = A genome type

☛ Greek philosophy

Ancient Greek

→ the everlastingness is formed accidentally by binding the four elements (arche): water, earth, air and fire

Spontaneous generation theory (SGT, 自然発生説)

psyche = logical (logistykon) + spirited (thymoeides) + appetitive (epithymetikon)

Ovoviviparous: ♂: seminal fluid + ♀: menstrual blood → coagulation

Veiw of birth or genesis (発生観)

Fly needs egg for the generation, demonstrated by an experiment

1677 sperms discovered by a self-made microscope

+ microbes discovered in milk and wort

the discovery of Leewenhock is explained by SGT

fertilization is inactivated by the filteration of sperms → sperm is related to fertilization

performation theory (入れ子説), ovium – homunculus

whole embryo – epigenesis ↔ partial embryo – preformation

active maintenance of normal and specific structure

Life emerged from inorganic matter by spontaneous generation

Life emerged when complex substances were produced from organic matter originating inorganic matter

published "The origin of life" (in Russian)

chemical evolution (化学進化)
proposed coacervate hypothesis (コアセルベート仮説)

CH₄ + NH₃ → HCN + 3H₂
C₂H₄ + HCN → CH₃CH₂CN
CH₃CH₂CN + NH₃ → CH₃CH-CN-NH Ala

protenoid: the synthesis of 14 amino acids under high pressure

synthesis of nucleotide from adenines, riboses and ethyl-metaphosphoric acids by UV irradiation

marigranule: artificial sea water + amino acids → coccus-like spherule

self-replicating RNA molecules → DNA and proteins

catalytic reaction of RNA extracted from Tetrahymena

☛ viroid = living fossil of RNA organisms?

Fossil records (初期生物型)

Longevity (寿命)

(v. adapt, a. adaptive)

Adaptation (適応)

Eugenics (優生学)

eu (good, well) + gens (born, come into being and growing/grown)
1865 Hereditary Character and Talent (Macmillan's Magazine)
1869 Hereditary Genius
1873 Africa for the Chinese (The Times)
1874 English men of science: their nature and nurture

1903 American Breeders Association (ABA)
1906 Committee on Eugenics (within ABA)
1910 Eugenics Record Office at Cold Spring Harbor Lab (-1939)
1912 Permanent International Eugenics Committee

renamed International Federation of Eugenics Organizations

the standard is made based on eugenics

1931 Sterilization Laws established in the 30 states of USA

by excluding people and groups judged to be inferior, and vice versa
→ applied by CRISPR and genetic screening

Prior to Darwin

number of (created) species = constant

proposed a term "evolutionism" → evolution

proposed quinarian system (circle theory) - not accepted

(Lamarck 1815-22)

Use-and-disuse theory (用不用説)

━━━━━ TIME ━━━━━▶

Giraffe neck

1. In every animal which has not passed the limit of its development, a more frequent and continuous use of any organ gradually strengthens, develops and enlarges that organ, and gives it a power proportional to the length of time it has been so used; while the permanent disuse of any organ imperceptibly weakens and deteriorates it, and progressively diminishes its functional capacity, until it finally disappears
2. All the acquisitions or losses wrought by nature on individuals, through the influence of the environment in which their race has long been placed, and hence through the influence of the predominant use or permanent disuse of any organ; all these are preserved by reproduction to the new individuals which arise, provided that the acquired modifications are common to both sexes, or at least to the individuals which produce the young

(Darwin)

Natural selection theory (自然淘汰説)

1. Variation
2. Inheritance
3. High rate of population growth
4. Differential survival and reproduction

Panselectionism (淘汰万能主義)

neutral alleles that are not affected by natural selection are not present

1963 "Animal species and evolution

1964 "Ecological genetics (4th edn.)"

(Nei/根井 1972)

Genetic identity (遺伝的同一性)

x_i and y_i are the frequencies of the ith allele in population X and Y, respectively.

The mean over all loci studied (including monomorphic ones) and is most conveniently calculated. I_X, I_Y and I_XY are the arithmetic mean, over all loci of Σx_i², Σy_i² and Σ(x_iy_i).

Red Queen hypothesis (赤の女王仮説)

Now, here, you see, it takes all the running
you can do, to keep in the same place.

☛ defense strategy

Predator avoidance (被食回避) on plants

Poison (secondary metabolites)

about 200 plant species have poison to some extent
also used for UV protection

Flavor
Taste

Specific organs - spine, prickle, thorn, etc.

symbiosis
enemy of predator

(Raven 1964)

Escape and radiate coevolution

Competition

Evolution (+ succession): go towards maximizing energy flux (1922)
→ the amount is changing, at any cost, before and after the species invasion

Intrapopulational-specific competition

Interpopulational-sepcific competition

(Evolutionary) fitness (適応度), w or ω

Game theory (ゲーム理論)

polygamy (一夫多妻) = polygyrous + polyandeous

Sex selection (性淘汰)

1551–1558, 1587 Historiae animalium: developed modern zoology

Vertebrates (脊椎動物)

Thermoregulation

maintaining a stable internal body temperature regardless of external influence

fluctuating body temperature with its external environment
Ex. fish, amphibians and reptiles as well as invertebrates

Invertebrates (無脊椎動物)