environment

# What is environment?

The non-self.

Then what is self?

Note:

* local and global
* Self could be a lipid bilayer container with polysaccharide wall, some flagella, surface receptor proteins to detect noxious and nutritive stimuli, and a cellular core that we call E Coli
* Self could be an epidermal container with hair follicles, bipedal locomotion, and a 1.5kg cell mass of a cerebrum we call human.

* Self is a point of view. A point referenced by at least some combination of other points in multidimensional space
* Multiple positional vectors: centric to earth + centric to solar system + centric to galaxy + centric to galactic superstructure + centric to bigbang

* nucleus, organelle, cell, tissue, organism, community: containers for structured protoplasmic variance that keep the wavelets of life going

## What is environment?

From wordnet:

`wn environment -over`

environment (wn, noun)  
: (the totality of surrounding **conditions**;)  
: (the **area** in which something exists or lives;)

`wn environment -hypon`

Sense 1
environment
       => context, circumstance, setting
       => ecology
       => setting, background, scope
       => home
       => milieu, surroundings
       => sphere, domain, area, orbit, field, arena
       => street

## What is condition, domain, area?

condition (wn, over)  
: (a mode of being or form of existence of a person or thing; "the human condition")  
: (an assumption on which rests the validity or effect of something else)

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domain (wn, noun)  
: sphere, domain, area, orbit, field, arena -- (a particular environment or walk of life;)  
: domain, demesne, land -- (territory over which rule or control is exercised; "his domain extended into Europe";)  
: domain, domain of a function -- ((mathematics) the set of values of the independent variable for which a function is defined)

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area (wn, noun)  
: area, region -- (a part of an animal that has a special function or is supplied by a given artery or nerve;)  
: area -- (a part of a structure having some specific characteristic or function;)  
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region (wn, noun)  
: region, part -- (the extended spatial location of something;)  
: region, neighborhood -- (the approximate amount of something (usually used prepositionally as in 'in the region of'); 
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Note:

Overview of noun "field" in wordnet has seventeen senses, outnumbering form! Here are some:

field (wn, noun)  
: field -- ((mathematics) a set of elements such that addition and multiplication are commutative and associative and multiplication is distributive over addition and there are two elements 0 and 1; "the set of all rational numbers is a field")  
: field, field of force, force field -- (the space around a radiating body within which its electromagnetic oscillations can exert force on another similar body not in contact with it)  
: field -- ((computer science) a set of one or more adjacent characters comprising a unit of information)  
: field, field of view -- (the area that is visible (as through an optical instrument))  
: sphere, domain, area, orbit, field, arena -- (a particular environment or walk of life;)  
: field -- (a geographic region (land or sea) under which something valuable is found;)

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## Living systems are a product of both genes and environment

Life as a set of self-perpetuating protoplasmic containers.

The basic unit for self-perpetuation is a gene.

A living entity is always a set of **interactions** across **time**. Product of self & non-self, gene & environment.

* "nature <del>OR</del> <span style="color:red">AND</span> nurture"
* living things need to detect nutritive and noxious stimuli in their *environment*; during development and beyond

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Note:

- not nature or nurture, nature and nurture
- innate behavior: food, motility, sex
  * E. Coli has 12 surface receptors for detecting noxious or nutritious objects in their environment. sugar (carbohydrate oxidation), amino acids (build blocks), toxins (heavy metal ions)
  * reduces data flow from these 12 inputs combined with recent experience (time scale seconds) into a decision for behavior
  * output: flagellar motors, transmembrane crankshafts using proton gradients
  * adapts behavior based on these inputs: swim or tumble
- behaviors not innate: language, learning to ride a bike
- clones, identical twins: phenotypic similarities and differences, especially over **time** into adulthood..

* Brains as buffers against environmental variability
  - sense presence of resources and hazards that vary in space+time and influence survival
  - evaluate and store input
  -  generate adaptive responses executed by effectors such as muscle (cardiac, smooth, skeletal)
* Redwood trees have evolved buffers against some kinds of environmental variability (fires, drought) but not others (human operated chainsaws)
* unicellular organisms also locate resources, detect hazards, and adapt behavior.
  - done by integrating sensory channels and making adaptive movements

iteration. recursion

recursion  
: ((mathematics) an expression such that each term is generated by repeating a particular mathematical operation)  
: `f(f(x))`  
: `f(f(x),t)`  
: let `x=3`;  
: - if `f(x)=2∙x`, then `f=6`  
: - if `f(x)=2^x`, then `f=8`

iteration, loop  
: ((computer science) a single execution of a set of instructions that are to be repeated; "the solution took hundreds of iterations");  
: ((computer science) executing the same set of instructions a given number of times or until a specified result is obtained; "the solution is obtained by iteration")

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## Maternal environment of the oocyte

Does embryonic patterning rely on maternally inherited mRNAs and proteins from the oocyte before onset of zygotic gene transcription?

Yes!

* polarized localization of maternal mRNAs and proteins at vegetal and animal poles
* zygotic transcription is temporally and spatially limited initially, occurs relatively late (e.g. 4000 cell stage)[^Heasman:2006]

Note:

Does embryonic patterning rely on maternally inherited mRNAs and proteins from the oocyte before onset of zygotic gene transcription? The answer is yes, zygotic transcription begins at the 4000 cell stage and also newly expressed zygotic genes have localized patterns of expression [^Heasman:2006].

Some of the key genes from the maternal pool localized to the animal or vegetal hemispheres of the oocyte and early embryo include global regulators of transcription Xkaiso and Xtcf3 (Houston 2002; Ruzov 2004), forkhead proteins FoxH1, Foxi1E, cAMP response element binding protein CREB (Sundaram 2003). Zic2 and Xgrhl1 localized to animal hemisphere (Houston 2005, Tao 2005a).

vegetally localized mRNAs: Vg1 (Weeks and Melton 1987), Wnt11 (Ku and Melton 1993), transcription factor Otx1 (Pannese 2000), T box protein VegT (Zhang and King 1996; Stennard 1999). cortical cytokeratin fliment is needed to hold the transcripts in place (Kloc 2005) [^Heasman:2006]. Some of the vegetally localized mRNAs get inherited into primoridal germ cells while others (VegT) to endodermal cells [^Heasman:2006].

[Heasman:2006]: Heasman J. Patterning the early xenopus embryo. Development 2006 133: 1205-1217; doi:10.1242/dev.02304 <https://dev.biologists.org/content/133/7/1205>

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## Frog oocyte: protoplasmic gradients

Non-uniformity The colloidal protoplasmic material of eggs is non-uniform.

Note:

Oocytes already have anisotropic distributions of cellular stuff.

Fundamentals of comparative embryology of the vertebrates. 1941, 1959, 1958 Alfred F. Huettner p. 41
Gametes, Fertilization and Parthenogenesis
> Fig. 20. The telolecithal egg (oocyte) of the wood frog Rana sylvatica prior to maturation. The nucleus is very large and has an irregular outline. Chromosomes are very faint and are difficult to demonstrate by the usual staining methods.

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## Frog ovum: protoplasm flow at fertilization

Note:

Fundamentals of comparative embryology of the vertebrates. 1941, 1959, 1958 Alfred F. Huettner p. 44
Gametes, Fertilization and Parthenogenesis
> Fig. 23. The ovum of the wood frog (Rana sylvatica) during karyogamy. The arrow indicates the movement of pigment graules at fertilization. Many of these granules have moved into the interior of the ovum with the sperm and left a dark streak referred to as the copulation path of the sperm. The outer most membrane is the fertilzation membrane. Teh one nearest the zygoe is teh vitelline membrane (not labeled).

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## Frog gastrulation: polarity and rotation

<div><img src="figs/IMG_0170_frog_gastrula_polarity_1929_2d6315c.jpg" width="400px"><figcaption>from Walther Fogt, Festschrift fur Hans Spemann, funfter Teil. 1929.</figcaption></div>

Note:

fig source: Fundamentals of comparative embryology of the vertebrates. 1941, 1959, 1958 Alfred F. Huettner p. 84

> Fig. 54. Scheme of polarity and rotation in the frog gastrula. (Adapted from Kopsch).

Fundamentals of comparative embryology of the vertebrates. 1941, 1959, 1958 Alfred F. Huettner p. 81

The Frog-- to primitive streak stage

> Fig. 51. Scheme of gastrulation in the amphibian ovum. (a) Gastrula viewed from the blastopore, (b) viewed from the left side. Heavy lines indicate movment of material on hte outer layer of the gastrula and thin lines show disposal of these materials inside, after they have passed over the rim of the bblastopore. From Walther Fogt, Festschrift fur Hans Spemann, funfter Teil. 1929. Gestaltungsanalyse am Amphibienkeim mit ortlicher Vitalfarbung. II. Teil. Gastrulation und Mesodermbildung bei Urodelen und Anuren. pp. 384-706. Archiv fur Entwickelungsmechanik der Organismen, Vol. 120.

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## Frog embryo: blastula to gastrula

<div><img src="figs/IMG_0160_frog_embryo_zygote_cleavage_30f9c2c.jpg" height="250px"><figcaption>zygote cleave</figcaption></div>

<div><img src="figs/IMG_0161_frog_embryo_blastulation_39721aa.jpg" height="250px"><figcaption>blastulation</figcaption></div>

<div><img src="figs/IMG_0162_frog_embryo_gastrulation_778b101.jpg" height="250px"><figcaption>gastrulation</figcaption></div>

<div><img src="figs/IMG_0169_frog_embryo_gastrulation_late_f339969.jpg" height="250px"><figcaption>late gastrulation</figcaption></div>

Note:

fig source: Fundamentals of comparative embryology of the vertebrates. 1941, 1959, 1958 Alfred F. Huettner p. 76
The Frog-- To Primitive Streak Stage
> Fig. 46. Cleavages from the zygote of the frog

Fundamentals of comparative embryology of the vertebrates. 1941, 1959, 1958 Alfred F. Huettner 
> Fig. 47. The blastula of the frog, (a) and (b) early, (c) and (d) later stage. (b) is a hemisection of (a), and (d) is a hemisection of (c).

Fundamentals of comparative embryology of the vertebrates. 1941, 1959, 1958 Alfred F. Huettner p. 78
The Frog-- To Primitive Streak Stage
> Fig. 48. The blastula (a) of the frog and its transformation into the gastrula (b-f). The region in which gastrulation will occur on the blastula is on the right side. Begginning of gastrulation (b),. Elimination of blastocoel or segmentation cavity by the gastrocoel or archentreron (c-e). Complete gastrula with mesentoderm (chorda-mesoderm) beneath the ectoderm (f).

Fundamentals of comparative embryology of the vertebrates. 1941, 1959, 1958 Alfred F. Huettner p. 83
> Fig. 53. This figure is continus with Fig. 48. External appearance of gastula (a). Different partial sections of the gasrula (b, c). The entoderm has been delaminated as a single layer of cells. The mesoderm is in the process of delamination from the yolk cells. Late gastrula stages (d, e). The blastopore becomes smaller, the yolk plug is withdrawn, and the embryo is elongating in the antero-posterior axis and enters the neurula stage.

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## Frog embryo: neurula to hatching

<div><img src="figs/IMG_0157_frog_embryo_neurulation_66ae107.jpg" height="250px"><figcaption>neurula 2.1 to 2.4mm</figcaption></div>

<div><img src="figs/IMG_0158_frog_embryo_neurulation_late_292e497.jpg" height="250px"><figcaption>late neurula 2.4mm</figcaption></div>

<div><img src="figs/IMG_0159_frog_embryo_neurula_hatch_7d3faab.jpg" height="250px"><figcaption>hatching embryo 3.0mm</figcaption></div>

Note:

Fundamentals of comparative embryology of the vertebrates. 1941, 1959, 1958 Alfred F. Huettner p. 84
From the primitive streak stage to hatching (2-6.5mm)
> Fig. 60. External appearance of the frog embryo in the neurula stage. Development of the sense plate and the gill plate. (a) and (b) represent the 2.10 mm neurula viewed from the posterior-lateral side, and from the frontal-lateral side. (c) is the 2.40 mm neurula lateral view.

Fundamentals of comparative embryology of the vertebrates. 1941, 1959, 1958 Alfred F. Huettner p. 84
From the primitive streak stage to hatching (2-6.5mm)
> Fig. 66. Late hemisected neurula, 2.40 mm. (a) seen from the anteiro left postiion, (b) seen from the posterior right position. (From plastic reconstruction by Landrock and Huettner.)

Fundamentals of comparative embryology of the vertebrates. 1941, 1959, 1958 Alfred F. Huettner p. 100
From the primitive streak stage to hatching (2-6.5mm)
> Fig. 67. Median longitudnal section through the 3.00 mm from embryo. Vertical lines from (a) to (j) indicate postiions of transverse sections shown in figures 68, 69 and 70.

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## Frog larva at hatching

<div><img src="figs/IMG_0153_frog_embyro_hatching_x1280.jpg" width="400px"><figcaption>frog larva, newly hatched, 6.5mm</figcaption></div>

<div><img src="figs/IMG_0154_frog_larva_hatched_f1a16c8.jpg" width="400px"><figcaption>frog larva, 8 to 11.5mm</figcaption></div>

Note:

fig source: Fundamentals of comparative embryology of the vertebrates. 1941, 1959, 1958 Alfred F. Huettner p. 108
From the primitive streak stage to hatching (2-6.5mm)
> Fig. 73. Young frog larva, 6.5 mm long, immediately after hatching.

Fundamentals of comparative embryology of the vertebrates. 1941, 1959, 1958 Alfred F. Huettner p. 122
The embryology of the frog. The young larva
> Fig. 80. The external appearnce of the frog larva with special reference to the gills and formation of teh operculum. Larva at hatching (a). This is the same stage as shown in Figs. 73, 74, 75. Larva of 8 mm (b) and 11.5 mm in length (c).

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## Mammalian blastulation and gastrulation

<div><img src="figs/IMG_0145-blastulation_mammals_x1280.jpg" height="400px"><figcaption>mammalian blastula formation</figcaption></div>

<div><img src="figs/IMG_0146-gastrulation_mammals_x1280.jpg" height="400px"><figcaption>mammalian gastrula formation</figcaption></div>

Note:

fig source: Fundamentals of comparative embryology of the vertebrates. p. 251

> Fig. 160. Schematic representation of cleavage and blastulation of the mammailan ovum, as for example, that of the rabbit, pig, or monkey.
> (b-e), cleavages; (f) morula; (g) morula hemisected; (h and i) separation of the inner cell mass from the trophectoderm, leading to the blastula (i).

fig source: Fundamentals of comparative embryology of the vertebrates. p. 254:

> Fig. 162. Gastrulation of the mammalian embryo. This series of figuress is consecutive to Fig. 160. The inner cell mass comes to the surface of the blastocyst in the formation of the embryonic knob, wic becomes the embryonic shield after the amnion  has been formed.

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## Human embryo at 25 days gestation

Note:
fig source: Fundamentals of comparative embryology of the vertebrates. p. 293

> Fig. 192. Stereogram of a blastocyst containing a human embryo, twenty-vive days old and 2.4 mm. long, imbedded in the endometrium. The embryo is attached to the chorioin bhy the body stalk. The large cavity is the extraembryonic coelome.

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## Human embryo at 29 days gestation

Note:

fig source: Fundamentals of comparative embryology of the vertebrates. p. 294

> Fig. 193. Stereogram of a blastocyst containing a human embryo, twenty-nine days old and 4.3 mm. long. The blastocyst is bulging slightly over the uterine mucosa into the uterine cavity. The embryo has rotated and is facing the body stalk. The extraembryoinc coelome has been partically replaced by the amniotic cavity.

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## Human embryo at 38 days gestation

Note:

fig source: Fundamentals of comparative embryology of the vertebrates. p. 296

> Fig. 195. Human embryo in the uterus, thirty-eight days old and 7.5 mm. long.

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## Human embryo at 49 days gestation

Note:

fig source: Fundamentals of comparative embryology of the vertebrates. p. 297

> Fig. 196. Human embryo in the uterus seven weeks old and 17 mm. long

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## Embryonic sensory organ development

<div><img src="figs/IMG_0155_frog_larva_eye_1ee705d.jpg" height="500px"><figcaption>frog larva, optic cup, nerve, and lens</figcaption></div>

<div><img src="figs/IMG_0156_mammmal_embryo_otic_capsule_ear_dev_f282169.jpg" height="500px"><figcaption>Development of the otic capsule and labyrinth in mammal</figcaption></div>

Note:

Fundamentals of comparative embryology of the vertebrates. 1941, 1959, 1958 Alfred F. Huettner p. 127
The embryology of the frog. Chp IX. The young larva
> Fig. 82. Stereogram of the optic cup with lens and optic stalk.

Fundamentals of comparative embryology of the vertebrates. 1941, 1959, 1958 Alfred F. Huettner p. 128
The embryology of the frog. Chp IX. The young larva
> Fig. 83. Development of the otic capsule and labyrinth of the left ear in the mammal. (Adapted from various sources).