Biology

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This image is a drawing of Haloquadratum walsbyi. Credit: Rotational.

On the right is a drawing of the archaean Haloquadratum walsbyi.

Biology is the study of living organisms, divided into many specialized fields that cover their morphology, physiology, anatomy, behavior, origin, and distribution.

Theoretical biology[edit]

Def. the "study of all life or living matter"[1] is called biology.

Zoology[edit]

Main source: Zoology
The image shows a full length view of an adult blue whale. Credit: NOAA Fisheries (TBjornstad).

Def. "that part of biology which relates to the animal kingdom, including the structure, embryology, evolution, classification, habits, and distribution of all animals, both living and extinct"[2] is called zoology.

Botany[edit]

Main source: Botany
This is a traditional cultural association between Maize, squash and beans, called Milpa in the region. Credit: Isabelle Fragniere.

Def. "[t]he scientific study of plants, ... [t]ypically those disciplines that involve the whole plant"[3] is called botany.

Usage notes:

"The scientific definition of what organisms should be considered plants changed dramatically during the 20th century. Bacteria, algae, and fungi are no longer considered plants by those who study them. Many textbooks do not reflect the most current thinking on classification."[4]

Archaeaology[edit]

Main source: Archaeaology
This is an electron microscope image the archaean Halobacteria species strain NRC-1. Credit: NASA.

"This path has attracted 'archaeaologists' with great tenacity and drive, impressive creativity and dynamic thinking, and a capacity to expand a mental comfort zone to broker remarkable observations, often in view of reluctant acceptance."[5]

Def. the scientific study of the archaea is called archaeaology.

"The B recognition element (BRE) is a DNA sequence found in the promoter region of most genes in eukaryotes and Archaea.[6][7]"[8]

In the archaean from the Dead Sea imaged at the right, "We have completely fragmented their DNA. I mean we have completely destroyed it by bombarding it with [radiation]. And they can reassemble their entire chromosome and put it back into working order within several hours."[9]

Genetics[edit]

Main source: Genetics

"A recent comparison of the draft sequences of mouse and human genomes has shed light on the selective forces that have predominated in their recent evolutionary histories. In particular, mouse-specific clusters of homologues associated with roles in reproduction, immunity and host defence appear to be under diversifying positive selective pressure, as indicated by high ratios of non-synonymous to synonymous substitution rates. These clusters are also frequently punctuated by homologous pseudogenes. They thus have experienced numerous gene death, as well as gene birth, events. These regions appear, therefore, to have borne the brunt of adaptive evolution that underlies physiological and behavioural innovation in mice. We predict that the availability of numerous animal genomes will give rise to a new field of genome zoology in which differences in animal physiology and ethology are illuminated by the study of genomic sequence variations."[10]

Cytokinesis[edit]

An unknown species of ciliate is imaged in the last stages of mitosis (cytokinesis), with cleavage furrow visible. Credit: TheAlphaWolf.

Cytokinesis is a name applied to the cell separation phase of the cell division process.

Mitosis[edit]

Mitosis is the process by which nucleated cells duplicate.

Mitosis is one of the phases of the cell cycle.

After S phase, there is another interphase, known as Gap 2, or G2. Then mitosis starts off the M phase. In M phase, the two copies of DNA are seperated from each other and one copy each is given to each “daughter”. The daughters are actually the cell itself divided into two halves, each half having what a whole cell needs. During mitosis, the DNA becomes visible within the nucleus of the cell (its home) because the chromosones are duplicates folded up tightly. Then they are lined up across the middle of the nucleus and then the copies are pulled apart to opposite poles of the cell.

After this has occurred, cytokinesis can then ensue. In this process, the cell itself divides, and each “pole” becomes a new nucleus in the new cells.

Ras homolog family members[edit]

Notation: let Rho stand for Ras homolog family members.

"Rho regulates cytokinesis".[11]

Gene ID: 387 RHOA ras homolog family member A[edit]

"This gene encodes a member of the Rho family of small GTPases, which cycle between inactive GDP-bound and active GTP-bound states and function as molecular switches in signal transduction cascades. Rho proteins promote reorganization of the actin cytoskeleton and regulate cell shape, attachment, and motility. Overexpression of this gene is associated with tumor cell proliferation and metastasis. Multiple alternatively spliced variants have been identified."[12]

Gene ID: 389 RHOC ras homolog family member C[edit]

"This gene encodes a member of the Rho family of small GTPases, which cycle between inactive GDP-bound and active GTP-bound states and function as molecular switches in signal transduction cascades. Rho proteins promote reorganization of the actin cytoskeleton and regulate cell shape, attachment, and motility. The protein encoded by this gene is prenylated at its C-terminus, and localizes to the cytoplasm and plasma membrane. It is thought to be important in cell locomotion. Overexpression of this gene is associated with tumor cell proliferation and metastasis. Multiple alternatively spliced variants, encoding the same protein, have been identified."[13]

Gene ID: 29984 RHOD ras homolog family member D[edit]

"Ras homolog, or Rho, proteins interact with protein kinases and may serve as targets for activated GTPase. They play a critical role in muscle differentiation. The protein encoded by this gene binds GTP and is a member of the small GTPase superfamily. It is involved in endosome dynamics and reorganization of the actin cytoskeleton, and it may coordinate membrane transport with the function of the cytoskeleton. Two transcript variants encoding different isoforms have been found for this gene."[14]

Parasitology[edit]

Main source: Parasitology

The "Acanthocephala, are descended from, and should be considered as, highly modified rotifers. Genetic research has determined this is unequivocal; the Acanthocephalans are modified rotifers".[15]

Taxonomy[edit]

Main source: Taxonomy
A collage depicts animal diversity using a collection of featured pictures. Credit: Justin.
Composite image illustrates the diversity of plants. Credit: Ryan Kitko.
  1. Superregnum Archaea,
  2. Superregnum Bacteria, and
  3. Superregnum Eukaryota.[16]

Superregnum: Archaea[17]

Regnum (Phyla):

  1. Crenarchaeota
  2. Euryarchaeota
  3. Korarchaeota

Superregnum: Bacteria[18]

Phyla

  1. Acidobacteria
  2. Actinobacteria
  3. Aquificae
  4. Chlamydiae
  5. Chloroflexi
  6. Chrysiogenetes
  7. Cyanobacteria
  8. Deferribacteres
  9. Deinococcus-Thermus
  10. Dictyoglomi
  11. Fibrobacteres
  12. Firmicutes
  13. Fusobacteria
  14. Gemmatimonadetes
  15. Nitrospirae
  16. Planctomycetes
  17. Proteobacteria
  18. Spirochaetes
  19. Thermodesulfobacteria
  20. Thermotogae
  21. Verrucomicrobia

Superregnum: Eukaryota[19] Regnums (Whittaker & Margulis, 1978): Animalia - Plantae - Fungi - Protista Regnums (Cavalier-Smith, 1981): Animalia - Plantae - Fungi - Chromista - Protozoa

Regnum: Animalia Phyla (36):

  1. Acanthocephala
  2. Annelida
  3. Arthropoda
  4. Brachiopoda
  5. Bryozoa
  6. Cephalorhyncha
  7. Chaetognatha
  8. Chordata
  9. Cnidaria
  10. Ctenophora
  11. Cycliophora
  12. Echinodermata
  13. Echiura
  14. Gastrotricha
  15. Gnathostomulida
  16. Hemichordata
  17. Kamptozoa
  18. Kinorhyncha
  19. Loricifera
  20. Micrognathozoa
  21. Mollusca
  22. Myxozoa
  23. Nematoda
  24. Nematomorpha
  25. Nemertea
  26. Onychophora
  27. Orthonectida
  28. Phoronida
  29. Placozoa
  30. Platyhelminthes
  31. Porifera
  32. Rhombozoa
  33. Rotifera
  34. Sipuncula
  35. Tardigrada
  36. Xenacoelomorpha

Regnum: Plantae[20] Divisiones (8): "Algae" (first four)

  1. Charophyta
  2. Chlorophyta
  3. Glaucophyta
  4. Rhodophyta
  5. Anthocerotophyta
  6. Bryophyta
  7. Marchantiophyta
  8. Tracheophyta

Agriculture[edit]

Main source: Agriculture
The image shows a field in China on a fair weather day. Credit: Hijirikyou.

Agriculture is the science, art, or practice of farming, including cultivation of the soil for the growing of crops and the rearing of animals to provide food, wool, and other products.

At right are farm buildings with trees surrounded by fields on a fair weather day.

Farming[edit]

Main source: Farming
These three false-color images demonstrate some of the applications of remote sensing in precision farming. Credit: Susan Moran, Landsat 7 Science Team and USDA Agricultural Research Service.

"These three false-color images [on the right] demonstrate some of the applications of remote sensing in precision farming. The goal of precision farming is to improve farmers’ profits and harvest yields while reducing the negative impacts of farming on the environment that come from over-application of chemicals. The images were acquired by the Daedalus sensor aboard a NASA aircraft flying over the Maricopa Agricultural Center in Arizona."[21]

"The top image shows the color variations determined by crop density (also referred to as #147;Normalized Difference Vegetation Index”, or NDVI), where dark blues and greens indicate lush vegetation and reds show areas of bare soil."[21]

"The middle image is a map of water deficit, derived from the Daedalus’ reflectance and temperature measurements. Greens and blues indicate wet soil and reds are dry soil."[21]

"The bottom image shows where crops are under serious stress, as is particularly the case in Fields 120 and 119 (indicated by red and yellow pixels). These fields were due to be irrigated the following day."[21]

Forestry[edit]

Main source: Forestry
This shows some of the effects of forestry work in Austria. Credit: Queryzo.

Def. the science or practice of planting, managing, and caring for forests is called forestry.

"Continuous cover forestry (CCF) is not a new idea in forest management but there has been renewed interest in it for the potential it has to meet the sustainability requirements which are part of the Rio/Helsinki process and certification. Broadly speaking CCF includes those silvicultural systems which involve continuous and uninterrupted maintenance of forest cover and which avoid clearcutting."[22]

Soils[edit]

Main sources: Sediments/Soils and Soils

"In soil, estimates are that 80 to 99% of the microorganisms remain unidentified (1)."[23]

"The soil at the Arlington site is a Plano silt-loam. The 20-cm-deep A horizon is a silt-loam and contains 4.4% organic matter. The loess mantel is >1.25 m deep. Four 2.5-cm-diameter soil cores were taken from the top 10 cm of a clover-grass pasture at the Arlington Agricultural Research Station. The soil samples were immediately placed on dry ice, mixed, and then stored at -70°C prior to DNA extraction. Soil analysis was done by the Soil Testing Laboratory of the University of Wisconsin—Madison as described by Schulte et al. (40). The soil sample contained 13% sand, 70% silt, 17% clay, 4.4% organic matter, 0.3% total N, 400 ppm of K+, and 98 ppm of P. The soil pH was 6.5. The site is well drained, with groundwater more than 25 m below the surface. Two-thirds of the 79-cm annual rainfall occurs from April to October. The site has an average of 165 frost-free days."[23]

Mycology[edit]

Main source: Mycology

Mycology is the branch of biology concerned with the study of fungi, including their genetic and biochemical properties, their taxonomy and their use to humans as a source for tinder, medicine (e.g., penicillin), food (e.g., beer, wine, cheese, edible mushrooms), and entheogens, as well as their dangers, such as poisoning or infection.[24]

Ammonoids[edit]

This ammonitic ammonoid shows the septal surface (especially at right) with its undulating lobes and saddles. Credit: Jonathan350.

An ammonoid is an extinct cephalopod mollusk with a flat-coiled spiral shell.

An ammonite may be an ammonoid that belongs to the order Ammonitida, typically having elaborately frilled suture lines.

Mollusks[edit]

Def. a "body wall of a mollusc, from which the shell is secreted"[25] is called a mantle.

Def. a "rasping tongue of snails and most other mollusks"[26] is called a radula.

As a mollusk an ammonite may be expected to have

  1. a mantle with a cavity for breathing and excretion,
  2. a radula, and
  3. a structured nervous system.

Ammonites[edit]

The schematic drawings show four growth stages in the ontogeny of Hoploscaphites nicolletii. Credit: Hugo Bucher, Neil H. Landman, Susan M. Klofak, and Jean Guex.

Def. "the scientific study of squid (often extended to all cephalopods)"[27] is called teuthology.

"Teuthology, a branch of malacology, is the study of cephalopods."[28]

Def. "any of numerous flat spiral fossil shells of cephalopods"[29] is called an ammonite.

We "describe the overall mode of growth of ammonoids with reference to Nautilus, the only externally shelled cephalopod that is still extant. Ammonoids are, in fact, phylogenetically more closely related to coleoids than they are to Nautilus (Engeser, 1990; Jacobs and Landman, 1993; Chapter 1, this volume). However, the retention of an external shell in ammonoids implies that these extinct forms shared with Nautilus basic similarities in their processes of growth, although not necessarily a similarity in their rate of growth or age at maturity."[30]

On the right are schematic drawings of four growth stages of Hoploscaphites nicolletii in lateral and transverse cross-sections:

  1. A is an embryonic shell called the ammonitella, scale bar 500 µm,
  2. B is the first postembryonic stage called the neanic and the animal or shell is called the neanoconch, scale bar 1 mm,
  3. C is a juvenile, scale bar 5 mm, and
  4. D is an adult, scale bar is 1 cm.[30]

Lytocerates[edit]

Fossil shell is of Lytoceras cornucopia from Isère (France). Credit: Hectonichus.

Characteristics:

  1. loosely coiled,
  2. evolute,
  3. gyroconic,
  4. exposed whorls,
  5. whorls touching,
  6. subcircular to narrowly compressed whorls,
  7. broadly arched, or keeled venter,
  8. smooth or ribbed sides,
  9. aptychi are single valved and concentrically striated,
  10. suture saddle endings tend to be rounded but usually not phylloid,
  11. lobes tend to be more jagged with thorn-like endings, and
  12. complex moss-like suture endings with adventious and secondary subdivisions.

Nautiloids[edit]

This is an individual of Nautilus pompilius. Credit: appealtoreason.
The images include an anatomical diagram of Nautilus. Credit: David Darling.

Def. a cephalopod mollusk with a light external spiral shell that is white with brownish bands on the outside and lined with mother-of-pearl on the inside is called a nautiloid.

Nautiloidea is another subclass of cephalopods.

"Nautilus [included in the diagram on the left] is one of the few surviving animals resembling the primitive or original cephalopods. The fossilized shells of these extinct forms, called ammonites (A), are quite common. (B) is a deep-sea species Nautilus pompilius that lives in tropical waters. To the right is a section through Nautilus showing the shell (1) and siphuncle (2) wound in a spiral. Immediately behind the tentacles lies the mouth (4) leading to the intestine (7). Nautilus has an advanced nervous system with a brain (3) and respires by means of gills (6) that are located in the mantle cavity. It swims by forcing a jet of water out of its mantle cavity and through the siphon (5)."[31]

"Nautiluses first evolved in the Cambrian period and became significant marine predators during the Ordovician period."[31]

Nautilids[edit]

This is Nautilus, the only extant exterior-shelled cephalopod. Credit: J. Baecker.
Here are a couple of Nautilus macromphalus. Credit: Pierre Sylvie.

An individual example of the genus Nautilus is on the right.

A couple of Nautilus macromphalus are on the left, photographed during a night dive, at 15 meters, near Lifou, Sandal wood bay, New Caledonia.

"The six living species of nautiluses are:

  1. No common name (Allonautilus perforates),
  2. Crusty Nautilus (Allonautilus scrobiculatus),
  3. Palau Nautilus (Nautilus belauensis),
  4. Bellybutton Nautilus (Nautilus macromphalus),
  5. Chambered Nautilus (Nautilus pompilius), and
  6. White-patch Nautilus (Nautilus stenomphalus)".[31]

Oceanography[edit]

This image shows the Earth's oceans and their bottoms. Credit: NOAA.

"Oceanography..., also called oceanology or marine science, ... studies the ocean. It covers a wide range of topics, including marine organisms and ecosystem dynamics; ocean currents, waves, and geophysical fluid dynamics; plate tectonics and the geology of the sea floor; and fluxes of various chemical substances and physical properties within the ocean and across its boundaries."[32]

Temperatures[edit]

This illustration shows the Earth's sea surface temperature from infrared observations by the Advanced Very High Resolution Radiometer (AVHRR) during July 1984. Credit: NASA.

"The above illustration of Earth's sea surface temperature was obtained from two weeks of infrared observations by the Advanced Very High Resolution Radiometer (AVHRR), an instrument on board NOAA-7 during July 1984. Temperatures are color coded with red being warmest and decreasing through oranges, yellows, greens, and blues. Temperature patterns seen in this image are the result of many influences, including the circulation of the ocean, surface winds, and solar heating. The image indicates a large pool of warm water in the Western Pacific and a tongue of relatively cold water extending along the Equator westward from South America. Every few years, there occurs an interrelated set of changes in the global atmospheric and oceanic circulation known as an El Nino in which the region of warm equatorial water in the West extends eastward across the Pacific and blankets the cool, productive regions along the coast of South America. Fish, birds, and marine mammals that depend upon the normally phytoplankton-rich waters often die in large numbers during El Nino. Images of sea surface temperature such as this help scientists to better monitor and ultimately understand the changes to Earth caused by events such as El Nino."[33]

Aragonites[edit]

This map shows changes in the amount of aragonite dissolved in ocean surface waters between the 1880s and the most recent decade (2003-2012). Credit: US EPA.

"Aragonite is a form of calcium carbonate that many marine animals use to build their skeletons and shells. Aragonite saturation is a ratio that compares the amount of aragonite that is actually present with the total amount of aragonite that the water could hold if it were completely saturated. The more negative the change in aragonite saturation, the larger the decrease in aragonite available in the water, and the harder it is for marine creatures to produce their skeletons and shells."[34]

"Measurements made over the last few decades have demonstrated that ocean carbon dioxide levels have risen in response to increased carbon dioxide in the atmosphere, leading to an increase in acidity (that is, a decrease in pH)"[34].

"Historical modeling suggests that since the 1880s, increased carbon dioxide has led to lower aragonite saturation levels (less availability of minerals) in the oceans around the world (see [above image])."[34]

"The largest decreases in aragonite saturation have occurred in tropical waters (see [above image]). However, decreases in cold areas may be of greater concern because colder waters typically have lower aragonite levels to begin with."[34]

See also[edit]

References[edit]

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  5. Ricardo Cavicchioli (January 2011). "Archaea—timeline of the third domain". Nature Reviews Microbiology 9 (1): 51-61. http://www.nature.com/nrmicro/journal/v9/n1/full/nrmicro2482.html. Retrieved 2015-02-23. 
  6. Lagrange T, Kapanidis AN, Tang H, Reinberg D, Ebright RH (1998). "New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB". Genes & Development 12 (1): 34–44. doi:10.1101/gad.12.1.34. PMID 9420329. PMC 316406. //www.ncbi.nlm.nih.gov/pmc/articles/PMC316406/. 
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  10. Richard D. Emes, Leo Goodstadt, Eitan E. Winter and Chris P. Ponting (2003). "Comparison of the genomes of human and mouse lays the foundation of genome zoology". Human Molecular Genetics 12 (7): 701-9. doi:10.1093/hmg/ddg078. http://hmg.oxfordjournals.org/content/12/7/701.long. Retrieved 2014-05-18. 
  11. F. Oceguera-Yanez, K. Kimura, S. Yasuda, C. Higashida, T. Kitamura, Y. Hiraoka, T. Haraguchi, S. Narumiya (17 January 2005). "Ect2 and MgcRacGAP regulate the activation and function of Cdc42 in mitosis". The Journal of Cell Biology 168 (2): 221-32. doi:10.1083/jcb.200408085. PMID 15642749. https://www.ncbi.nlm.nih.gov/pubmed/15642749. Retrieved 2016-12-10. 
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  22. A. Pommerening and S.T. Murphy (2004). "A review of the history, definitions and methods of continuous cover forestry with special attention to afforestation and restocking". Forestry 77 (1): 27-44. doi:10.1093/forestry/77.1.27. http://forestry.oxfordjournals.org/content/77/1/27.full.pdf. Retrieved 2016-02-07. 
  23. 23.0 23.1 James Borneman, Paul W. Skroch, Katherine M. O'Sullivan, James A. Palus, Norma G. Rumjanek, Jennifer L. Jansen, James Nienhuis, and Eric W. Triplett (June 1996). "Molecular Microbial Diversity of an Agricultural Soil in Wisconsin". Applied and Environmental Microbiology 62 (6): 1935-43. http://aem.asm.org/content/62/6/1935.short. Retrieved 2013-11-21. 
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External links[edit]

{{Anthropology resources}}{{Gene project}}{{Medicine resources}}{{Phosphate biochemistry}}{{Sciences resources}}