(Upload on November 1 2023) [ 日本語 | English ]

Biology (生物学)

Mount Usu / Sarobetsu post-mined peatland
From left: Crater basin in 1986 and 2006. Cottongrass / Daylily


= biological science: concerned with the study of life and living organisms at various scales, including their structure, function, growth, evolution, distribution, taxonomy, etc.
Classical classification
zoology + botany →
The classification in the faculty of science, Hokkaido University, applied this criteria in 1980 except no ecology lab. ⇓ on each taxon
plant (植物)




animal (動物)

insectfishamphibianreptilebirdmammalhuman (人類)

Proximate and ultimate factors (至近要因と究極要因)
Proximate factor: the general cause of a particular change, such as variations in day length, which affects the behaviour or organisms in various ways
Ultimate factors: environmental factors which in the course of evolution have led, through natural selection, to the relevant restriction (Immelmann 1972)

Five kingdoms (5界説)

1969 Whittaker RH proposed

Three domains

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)

non-cellular life, reproducing only in the cells of the other species
1000-5000(50万) species

Kingdom 1 Virus (ウイルス)

Division 1 Virus (ウイルス)

Domain 2 Monera (モネラ)

= moneran
bacteria, no nuclear membranes between nuclei and between ribosomes, no endothelial reticula and no cellular skeletons
5,000- (40,000-3,000,000) species

Kingdom 2 Eubacteria (真性細菌)

membrane lipids consisting of acylglycerol and peptidoglycan

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

developing plasma membranes and outer membranes
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)
green sulfur bacteria
Division 6 Proteobacteria (プロテオバクテリア)
Class Rhodobacteria (紅色細菌)
Class Omnibacteria (オムニバクテリア)
Class Myxobacteria (粘液細菌)
Class Rickettsiomycota (リケッチア)
chemoautotrophic bacterias, bacteroides-fravobacterium
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
Planctomyces, Clamydia and the relatives
phylogenetically far from eubacteria and archaea
Division 9 Clamidiobacteria
Planctomyces, Clamydia and the relatives

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

no outer membranes
Division 10 Bacillobacteria (グラム陽性菌)
= gram-positive low G+C group
Subdivision Heliobacteria
Mollicutes (mycoplasmomycota ), gram-positive bacteria
Division 11 Actinobacteria (放線菌)
gram-positive high G+C groupe
Subdivision Actynomycota (放線菌)

Domain 3 Archaea (古細菌)

lipids not containing isoprene-ether and peptidoglycan, no outer membranes

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)

nuclei enclosed by nuclear membranes
endomembrane system and cytoskeletal system present
membrane lipids consisting of acylglycerol
cell wall not containing peptidoglyca

Superkingdom Archaeozoa (原真核生物)

70S ribosomes
Golgi apparatus, mitochondria, peroxisome absent in the cells
inhabiting in anaerobic environments
formerly considered as Protoctista, moved into this group because of no mitochondria without oxygen respiration

Kingdom 4 Archaeozoa (原真核生物界)

Superkingdom Eucaryota (真核生物)

80S ribosomes
Golgi apparatus, mitochondria, peroxisome present in the cells (also chloroplasts in some groups)

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)

chloroplast evolved by symbioses twice over, four-layered chloroplast membranes, chloroplast containing ER

Kingdom 7. Plantae (植物)

green plants
chloroplast evolved by symbioses once, two-layered chloroplast membranes, plastids in chloroplast (not in ER)

Kingdom 8 Fungi ()

fungi, mushrooms, yeast
hypha consisting of chitinous cell walls
decomposed and absorbed by exogenous degradative enzymes

Kingdom 9 Animalia (動物)

triploblastic and phagocytic
only multicellular species remaining in this group, because species in "protozoa" are moved to the other taxa, such as Protoctista

[History of natural sciences]

History of biology (生物学史)

Paracelsus (1493-1541, Switzerland)
autonym = Theophrastus von Hohenheim
alchemy → life thought → medicine
human body = mercury (azoth) + sulfur + salt → we get disease when the balance of these three elements is collapsed (derived from evidence on the effectiveness of chemical medicine )
Vesalius Andreas (1514-1564)
1514 De humani corporis fabrica (人体構造図): sharp observation

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

→ recognized importance of observations
Professor of Università degli Studi di Padova (UNIPD, Italy)

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

Harvey W (1578-1657, England)
overseas study in UNIPD
supervised by Fabricius (1537-1619, Italy) who discovered venous valve
Galileo was a professor of UNIPD when Harvecy was in the university → influenced something by Galileo (because the similarity of spirit of experimentation and method)
1628 On the motion of the heart and blood In animals

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

Ray J (1628-1705, England)
1686: descriptions of morphological variations → the concept of species (natural history)
Maupertuis, Pierre Louis de (1698-1759, French)
1745 Vénus physique (name withheld)
1754 Systeme de la Nature
considering the origin of human and animasl
Kaelreuter JG (1761-1766)
tobacco: tring to artificially create the first hybridizer (regoginzing in the present that hybridization experiment is important for breeing and genetics)
→ the Age of Hybridizer
Camerarius RJ (1655-1721) "Observations sur"
anther = male-like vs ovary = female-like
→ sex present in plants, demonstrated by cross-fertilization
follwed by many researchers
Bufforn (1707-1788)
Taxonomy + Morphology + Ecological technique, habit and competition
Lamarck JB (1744-1829): proposed use-and-disuse theory (用不用説) Haeckel, Ernst Heinrich (ヘッケル, 1834.2.16-1919.8.9 Germany, Zoology
1866: Generelle morphologie
The study of the relation of organisms or groups of organisms to their environment, or the science of the interrelations between living organisms and their environment (Haeckel 1866)

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

Schimper KF (1803-1867, Gr): Botanist (Schimper-Brawn's law)
Warming, Johannes Eugenius Bülow (1841.11.3 - 1924.4.2, Denmark)
Plant ecology
Cowels 1899, Tansley 1911: succession determined by the environments, poly-climax
Clements (1904, 14), Shelford (1911): biome, mono-climax (単極相)
Shoröter: 1911 autoecology and synecology
Turesson G (1892-1970, Sweden)

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


Before Mendel: the fact of heredity was known

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

Mendel GJ (1822-1884, Austlia), friar/botanist

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

1900 rediscovery of Mendelian rules (de Vries, Correns & Tschermak)
Sutton & Boveri

1902-03 proposed chromosome theory of inheritance

chromosomal distribution in sex cells is consistent with Mendelian inheritance

Bauer E

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

Vavilov, Nikolai Ivanovich (1887-1943, Russia): classical study on breeding

Oryza = 23 species. Oryza sativa = A genome type

View of life (生命観)

Spontaneous generation theory (SGT, 自然発生説)
spontaneous generation (syn. abiogenesis)
Hippocrates (BC 460-377)

♂: seminal fluid + ♀: seminal fluid → coagulation

Aristoteles (BC384-322)

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

Veiw of birth or genesis (発生観)

17 C:
Redi, Francesco (1626-1698) "Experiments on the generation of insects"

Fly needs egg for the generation, demonstrated by an experiment

Malpighi (1628-1694)
Van Leewenhock (1632-1723): animaliculist

1677 sperms discovered by a self-made microscope

+ microbes discovered in milk and wort

Theesen (1637-1686): confirmed yolk in shark eggs
De Graaf (1641-1673)
Leibniz, Gottfried Wilhelm (1646-1716): animaliculist

the discovery of Leewenhock is explained by SGT

18 C:
Needham, John Turberville (1713-1781): supported SGT
Spllanzani (1729-1799): recjected SGT

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

Bonne C (1720-1793, Switzerland, natural history)

performation theory (入れ子説), ovium – homunculus

Pasteur, Louis (1822-1895): rejected SGT completely ☛ origin of life
19c↑ (scientific = demonstrative)
Wilhelm Roux (1850-1924, Germany)

whole embryo – epigenesis ↔ partial embryo – preformation

causal analysis = experimental embryology
electron microscopy → chemical embryology
____________________↑ developmental physiology ____________________molecular biology
1859 Darwin CR: published Origin of species
1883 Haldane RB & JS (1860-1936): what we call life =

active maintenance of normal and specific structure

Origin of life (生命の起源)

1809 Lamarck: in Philosophie Zoologique

Life emerged from inorganic matter by spontaneous generation

1855 Darwin: letter to friend, Hooker, Joseph Dalton, Sir (1817-1911)

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

1924 Oparin, Alexander Ivanovich (1894-1980) (オパーリン), beiochem

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)

1928 Haldane JBS: proposed primordial soup (原始のスープ)
Miller, Stanley Lloyd (1930-2007)
1952 success in the synthesis of amino acids by atmospheric discharge
1953 [NH3, CH4, H2, H2O] → spark → [CO, CO2, N2, Amino acids]

CH4 + NH3 → HCN + 3H2

1950' Fox SW & Harada (原田馨)

protenoid: the synthesis of 14 amino acids under high pressure

1965 Ponnamperuma et al.

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

1977 Egami (江上) et al.

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

RNA world (RNAワールド) (hypothesis)

self-replicating RNA molecules → DNA and proteins

1962 Rich, Alexander (1924-2015): the concept of the RNA world
1981 Cech, Thomas Robert (1947-), et al.: ribozyme

catalytic reaction of RNA extracted from Tetrahymena

1986 Gilbert, Walter (1932-): proposed the term RNA world

viroid = living fossil of RNA organisms?

Fossil records (初期生物型)

Biology (生物学)

= biological science

Longevity (寿命)

typical length of life

(v. adapt, a. adaptive)

Adaptation (適応)
The adaptation of a subpopulation to a particular environmental patch can be maintained in two ways. First, there can be strong opposing selection pressures in different patches. Second, gene flow may be restricted. (Pickett 1976)
Eugenics (優生学)
Aim: to improve the genetic quality of a (human) population

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

Evolution (進化論)

Prior to Darwin
Linne 1751 Philosophia Botanica

number of (created) species = constant

Bonnet, Charles (1720-1793)

proposed a term "evolutionism" → evolution

Macleay or McLeay, William Sharp (1792-1865), entomologist

proposed quinarian system (circle theory) - not accepted

Oken Lorenz (1799-1851), naturalist: prototype of cell theory

(Lamarck 1815-22)

Use-and-disuse theory (用不用説)

Giraffe neck
━━━━━ TIME ━━━━━▶

Giraffe neck
The adaptive force
  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


Natural selection theory (自然淘汰説)

Natural variation: factor of evolution ⇔ natural selection: process of evolution
  1. Variation
  2. Inheritance
  3. High rate of population growth
  4. Differential survival and reproduction
Panselectionism (淘汰万能主義)
every evolution can be explained by natural selection

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

Mayr, Ernst Walter (1904-2005)

1963 "Animal species and evolution

Ford, Edmund Brisco (1901-1988)

1964 "Ecological genetics (4th edn.)"

(Nei/根井 1972)

Genetic identity (遺伝的同一性)

Nei's coefficient of genetic identity, I = Σ(xiyi)/Σ√(Σxi2·Σyi2)

xi and yi are the frequencies of the ith allele in population X and Y, respectively.

Mean genetic identity, I^ = (IXY)/√(IX·IY)

The mean over all loci studied (including monomorphic ones) and is most conveniently calculated. IX, IY and IXY are the arithmetic mean, over all loci of Σxi2, Σyi2 and Σ(xiyi).

Red Queen hypothesis (赤の女王仮説)

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

= Red Queen effect, Red Queen's race and Red Queen dynamics
evolutionary arms race (軍拡競争)
1973 van Valen, Leigh M.: proposed the hypothesis

☛ defense strategy

Predator avoidance (被食回避) on plants
Chemical protection

Poison (secondary metabolites)

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


Physical protection

Specific organs - spine, prickle, thorn, etc.

Biological protection

enemy of predator

(Raven 1964)

Escape and radiate coevolution

Natural selection (自然淘汰)


Lotka, Alfred James (1880-1949): Polish-American (math and statistics)

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

Volterra, Vito (1860-1940)
☛ Lotka-Volterra equation
Intrapopulational-specific competition
= inter-specific competition
Interpopulational-sepcific competition
= inter-specific competition

(Evolutionary) fitness (適応度), w or ω

quantitative representation of natural selection, including sexual selection, within evolutionary biology

Game theory (ゲーム理論)

Def. Zero-sum niche
Def. Zero-sum dynamics

Sex ()

1871 Darwin

polygamy (一夫多妻) = polygyrous + polyandeous

Sex selection (性淘汰)

1) Optimal sex ratio
2) Mating system


Botany (植物学)

= plant science(s) or plant biology

Zoology (動物学)

= animal science(s) or animal biology

Vertebrates (脊椎動物)

Homeotherms (恒温動物) = warm-blooded animals (温血動物) ⇔

maintaining a stable internal body temperature regardless of external influence

Poikilotherms (変温動物) = cold-blooded animals (冷血動物)

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

Thermoregulation Fig. Body temperature and sustained energy controled by a poikilothermal lizard and a homeothermal mouse. The homeotherm has a much higher output but function only over a narrow range of body temperatures.

Invertebrates (無脊椎動物)