Merge branch 'main' of https://github.com/openstax/osbooks-biology-bu…

…ndle

.gitpod.yml

@@ -1,4 +1,7 @@
+ports:
+- port: 27149
+  visibility: public
 vscode:
   extensions:
-    - openstax.editor
-    - redhat.vscode-xml
+  - openstax.editor
+  - redhat.vscode-xml

modules/m45417/index.cnxml

@@ -40,7 +40,7 @@
 </media>
 <caption>The age of remains that contain carbon and are less than about 50,000 years old, such as this pygmy mammoth, can be determined using carbon dating. (credit: Bill Faulkner/NPS)</caption></figure></note><note id="fs-idm2233728" class="interactive non-majors">
 
-<para id="fs-idp2572512">To learn more about atoms and isotopes, and how you can tell one isotope from another, visit this <link window="new" url="http://openstax.org/l/isotopes">site</link> and run the simulation.</para>
+<para id="fs-idp2572512">To learn more about atoms and isotopes, and how you can tell one isotope from another, visit this <link window="new" url="https://openstax.org/l/isotopes">site</link> and run the simulation.</para>
 </note></section>
 <section id="fs-idp98334368">
 <title>Chemical Bonds</title>

modules/m45419/index.cnxml

@@ -32,7 +32,7 @@
                     <caption>The leaves of this sensitive plant (<emphasis effect="italics">Mimosa pudica</emphasis>) will instantly droop and fold when touched. After a few minutes, the plant returns to its normal state. (credit: Alex Lomas)</caption></figure>
                 <note id="fs-idm74852384" class="interactive non-majors">
 
-                    <para id="fs-idm68222224">Watch this <link window="new" url="http://openstax.org/l/thigmonasty">video</link> to see how the sensitive plant responds to a touch stimulus.</para></note></section>
+                    <para id="fs-idm68222224">Watch this <link window="new" url="https://openstax.org/l/thigmonasty">video</link> to see how the sensitive plant responds to a touch stimulus.</para></note></section>
 
             <section id="fs-idm127740192">
                 <title>Reproduction</title>
@@ -75,7 +75,7 @@ The diversity of life on Earth is a result of mutations, or random changes in he
                 </media>
                     <caption>A molecule, like this large DNA molecule, is composed of atoms. (credit: "Brian0918"/Wikimedia Commons)</caption></figure><note id="fs-idm8353152" class="interactive non-majors">
 
-                <para id="fs-idm17985200">To see an animation of this DNA molecule, click <link window="new" url="http://openstax.org/l/rotating_DNA2">here</link>.</para></note><para id="fs-idm42027712">Some cells contain aggregates of macromolecules surrounded by membranes; these are called <term id="term-00006">organelles</term>. Organelles are small structures that exist within cells and perform specialized functions. All living things are made of cells; the <term id="term-00007">cell</term> itself is the smallest fundamental unit of structure and function in living organisms. (This requirement is why viruses are not considered living: they are not made of cells. To make new viruses, they have to invade and hijack a living cell; only then can they obtain the materials they need to reproduce.) Some organisms consist of a single cell and others are multicellular. Cells are classified as prokaryotic or eukaryotic. <term id="term-00008">Prokaryotes</term> are single-celled organisms that lack organelles surrounded by a membrane and do not have nuclei surrounded by nuclear membranes; in contrast, the cells of <term id="term-00009">eukaryotes</term> do have membrane-bound organelles and nuclei.</para>
+                <para id="fs-idm17985200">To see an animation of this DNA molecule, click <link window="new" url="https://openstax.org/l/rotating_DNA2">here</link>.</para></note><para id="fs-idm42027712">Some cells contain aggregates of macromolecules surrounded by membranes; these are called <term id="term-00006">organelles</term>. Organelles are small structures that exist within cells and perform specialized functions. All living things are made of cells; the <term id="term-00007">cell</term> itself is the smallest fundamental unit of structure and function in living organisms. (This requirement is why viruses are not considered living: they are not made of cells. To make new viruses, they have to invade and hijack a living cell; only then can they obtain the materials they need to reproduce.) Some organisms consist of a single cell and others are multicellular. Cells are classified as prokaryotic or eukaryotic. <term id="term-00008">Prokaryotes</term> are single-celled organisms that lack organelles surrounded by a membrane and do not have nuclei surrounded by nuclear membranes; in contrast, the cells of <term id="term-00009">eukaryotes</term> do have membrane-bound organelles and nuclei.</para>
             <para id="fs-idm28612144">In most multicellular organisms, cells combine to make <term id="term-00010">tissues</term>, which are groups of similar cells carrying out the same function. <term id="term-00011">Organs</term> are collections of tissues grouped together based on a common function. Organs are present not only in animals but also in plants. An <term id="term-00012">organ system</term> is a higher level of organization that consists of functionally related organs. For example vertebrate animals have many organ systems, such as the circulatory system that transports blood throughout the body and to and from the lungs; it includes organs such as the heart and blood vessels. <term id="term-00013">Organisms</term> are individual living entities. For example, each tree in a forest is an organism. Single-celled prokaryotes and single-celled eukaryotes are also considered organisms and are typically referred to as microorganisms.</para>
 
             <note id="fs-idm40888688" class="visual-connection">

modules/m45425/index.cnxml

@@ -27,7 +27,7 @@
 </media>
 <caption>(a) The lattice structure of ice makes it less dense than the freely flowing molecules of liquid water. Ice's lower density enables it to (b) float on water. (credit a: modification of work by Jane Whitney; credit b: modification of work by Carlos Ponte)</caption></figure><note id="fs-idm26183088" class="interactive non-majors">
 
-<para id="fs-idp31871184">Click <link window="new" url="http://openstax.org/l/ice_lattice">here</link> to see a 3-D animation of the structure of an ice lattice.</para></note></section>
+<para id="fs-idp31871184">Click <link window="new" url="https://openstax.org/l/ice_lattice">here</link> to see a 3-D animation of the structure of an ice lattice.</para></note></section>
 <section id="fs-idp27591888">
 <title>Water Is an Excellent Solvent</title>
 <para id="fs-idm8670256">Because water is polar, with slight positive and negative charges, ionic compounds and polar molecules can readily dissolve in it. Water is, therefore, what is referred to as a <term id="term-00005">solvent</term>—a substance capable of dissolving another substance. The charged particles will form hydrogen bonds with a surrounding layer of water molecules. This is referred to as a sphere of hydration and serves to keep the particles separated or dispersed in the water. In the case of table salt (NaCl) mixed in water (<link target-id="fig-ch02_02_03"/>), the sodium and chloride ions separate, or dissociate, in the water, and spheres of hydration are formed around the ions. A positively charged sodium ion is surrounded by the partially negative charges of oxygen atoms in water molecules. A negatively charged chloride ion is surrounded by the partially positive charges of hydrogen atoms in water molecules. These spheres of hydration are also referred to as hydration shells. The polarity of the water molecule makes it an effective solvent and is important in its many roles in living systems.</para>
@@ -43,7 +43,7 @@
 <para id="fs-idm104886816">Cohesive and adhesive forces are important for sustaining life. For example, because of these forces, water can flow up from the roots to the tops of plants to feed the plant.</para>
 <note id="fs-idm26802544" class="interactive non-majors">
 
-<para id="fs-idm2800528">To learn more about water, visit the U.S. Geological Survey Water Science for Schools: All About Water! <link window="new" url="http://openstax.org/l/about_water">website.</link></para></note></section><section id="fs-idp31303616">
+<para id="fs-idm2800528">To learn more about water, visit the U.S. Geological Survey Water Science for Schools: All About Water! <link window="new" url="https://openstax.org/l/about_water">website.</link></para></note></section><section id="fs-idp31303616">
 <title>Buffers, pH, Acids, and Bases</title>
 <para id="fs-idp31791840">The pH of a solution is a measure of its acidity or bascicity. You have probably used <term id="term-00009">litmus</term> <term id="term-00010">paper</term>, paper that has been treated with a natural water-soluble dye so it can be used as a pH indicator, to test how much acid or base (basicity) exists in a solution. You might have even used some to make sure the water in an outdoor swimming pool is properly treated. In both cases, this pH test measures the amount of hydrogen ions that exists in a given solution. High concentrations of hydrogen ions yield a low pH, whereas low levels of hydrogen ions result in a high pH. The overall concentration of hydrogen ions is inversely related to its pH and can be measured on the <term id="term-00011">pH scale</term> (<link target-id="fig-ch02_02_05"/>). Therefore, the more hydrogen ions present, the lower the pH; conversely, the fewer hydrogen ions, the higher the pH.</para><para id="fs-idm16790768">The pH scale ranges from 0 to 14. A change of one unit on the pH scale represents a change in the concentration of hydrogen ions by a factor of 10, a change in two units represents a change in the concentration of hydrogen ions by a factor of 100. Thus, small changes in pH represent large changes in the concentrations of hydrogen ions. Pure water is neutral. It is neither acidic nor basic, and has a pH of 7.0. Anything below 7.0 (ranging from 0.0 to 6.9) is acidic, and anything above 7.0 (from 7.1 to 14.0) is alkaline. The blood in your veins is slightly alkaline (pH = 7.4). The environment in your stomach is highly acidic (pH = 1 to 2). Orange juice is mildly acidic (pH = approximately 3.5), whereas baking soda is basic (pH = 9.0).</para>
 <figure id="fig-ch02_02_05"><media id="fs-idp81684336" alt="The pH scale with representative substances and their pHs.">

modules/m45426/index.cnxml

@@ -87,7 +87,7 @@ A <term id="term-00011">fat</term> molecule, such as a triglyceride, consists of
 <para id="fs-idm127618976">Cholesterol is a steroid. Cholesterol is mainly synthesized in the liver and is the precursor of many steroid hormones, such as testosterone and estradiol. It is also the precursor of vitamins E and K. Cholesterol is the precursor of bile salts, which help in the breakdown of fats and their subsequent absorption by cells. Although cholesterol is often spoken of in negative terms, it is necessary for the proper functioning of the body. It is a key component of the plasma membranes of animal cells.</para>
 <para id="fs-idp33877296">Waxes are made up of a hydrocarbon chain with an alcohol (–OH) group and a fatty acid. Examples of animal waxes include beeswax and lanolin. Plants also have waxes, such as the coating on their leaves, that helps prevent them from drying out.</para><note id="fs-idm18031456" class="interactive non-majors">
 
-<para id="fs-idm71715008">For an additional perspective on lipids, watch this video about <link window="new" url="http://openstax.org/l/lipids">types of fat</link>.</para></note></section></section>
+<para id="fs-idm71715008">For an additional perspective on lipids, watch this video about <link window="new" url="https://openstax.org/l/lipids">types of fat</link>.</para></note></section></section>
 <section id="fs-idp8690560">
 <title>Proteins</title>
 <para id="fs-idm56053456"><term id="term-00019">Proteins</term> are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective; they may serve in transport, storage, or membranes; or they may be toxins or enzymes. Each cell in a living system may contain thousands of different proteins, each with a unique function. Their structures, like their functions, vary greatly. They are all, however, polymers of amino acids, arranged in a linear sequence.</para>
@@ -120,7 +120,7 @@ The chemical nature of the R group determines the chemical nature of the amino a
 <caption>The four levels of protein structure can be observed in these illustrations. (credit: modification of work by National Human Genome Research Institute)</caption></figure><para id="fs-idm54908400">Each protein has its own unique sequence and shape held together by chemical interactions. If the protein is subject to changes in temperature, pH, or exposure to chemicals, the protein structure may change, losing its shape in what is known as denaturation as discussed earlier. Denaturation is often reversible because the primary structure is preserved if the denaturing agent is removed, allowing the protein to resume its function. Sometimes denaturation is irreversible, leading to a loss of function. One example of protein denaturation can be seen when an egg is fried or boiled. The albumin protein in the liquid egg white is denatured when placed in a hot pan, changing from a clear substance to an opaque white substance. Not all proteins are denatured at high temperatures; for instance, bacteria that survive in hot springs have proteins that are adapted to function at those temperatures.</para>
 <note id="fs-idm76093712" class="interactive non-majors">
 
-<para id="fs-idp14302288">For an additional perspective on proteins, explore “Biomolecules: The Proteins” through this interactive <link window="new" url="http://openstax.org/l/proteins">animation</link>.</para></note></section>
+<para id="fs-idp14302288">For an additional perspective on proteins, explore “Biomolecules: The Proteins” through this interactive <link window="new" url="https://openstax.org/l/proteins">animation</link>.</para></note></section>
 </section>
 <section id="fs-idp46685792">
 <title>Nucleic Acids</title>

modules/m45428/index.cnxml

@@ -27,7 +27,7 @@
 <para id="fs-idp108612400">Light microscopes commonly used in the undergraduate college laboratory magnify up to approximately 400 times. Two parameters that are important in microscopy are magnification and resolving power. Magnification is the degree of enlargement of an object. Resolving power is the ability of a microscope to allow the eye to distinguish two adjacent structures as separate; the higher the resolution, the closer those two objects can be, and the better the clarity and detail of the image. When oil immersion lenses are used, magnification is usually increased to 1,000 times for the study of smaller cells, like most prokaryotic cells. Because light entering a specimen from below is focused onto the eye of an observer, the specimen can be viewed using light microscopy. For this reason, for light to pass through a specimen, the sample must be thin or translucent.</para>
 <note id="fs-idp118198192" class="interactive non-majors">
 
-<para id="fs-idm15412240">For another perspective on cell size, try the <link window="new" url="http://openstax.org/l/cell_sizes2">HowBig</link> interactive.</para>
+<para id="fs-idm15412240">For another perspective on cell size, try the <link window="new" url="https://openstax.org/l/cell_sizes2">HowBig</link> interactive.</para>
 </note><para id="fs-idp263638992">A second type of microscope used in laboratories is the dissecting microscope (<link target-id="fig-ch03_01_01ab"/><emphasis effect="bold">b</emphasis>). These microscopes have a lower magnification (20 to 80 times the object size) than light microscopes and can provide a three-dimensional view of the specimen. Thick objects can be examined with many components in focus at the same time. These microscopes are designed to give a magnified and clear view of tissue structure as well as the anatomy of the whole organism. Like light microscopes, most modern dissecting microscopes are also binocular, meaning that they have two separate lens systems, one for each eye. The lens systems are separated by a certain distance, and therefore provide a sense of depth in the view of their subject to make manipulations by hand easier. Dissecting microscopes also have optics that correct the image so that it appears as if being seen by the naked eye and not as an inverted image. The light illuminating a sample under a dissecting microscope typically comes from above the sample, but may also be directed from below.</para>
 <figure id="fig-ch03_01_01ab">
 <media id="fs-idp53987872" alt="Part a: This light microscope has binocular lenses and three objective lenses. The sample stage is directly beneath the objective lens. The light microscope sits on a tabletop. Part b: The dissecting microscope has binocular eyepieces, one objective lens, and light sources from both above and below the sample stage. There is room on the stage for a three-dimensional specimen.">

modules/m45434/index.cnxml

@@ -37,7 +37,7 @@
 </list>
 <note id="fs-idm44192000" class="interactive non-majors">
 
-<para id="fs-idp114686800">For an animation of the diffusion process in action, view <link window="new" url="http://openstax.org/l/passive_trnsprt">this short video</link> on cell membrane transport.</para>
+<para id="fs-idp114686800">For an animation of the diffusion process in action, view <link window="new" url="https://openstax.org/l/passive_trnsprt">this short video</link> on cell membrane transport.</para>
 </note></section>
 <section id="fs-idm38664720">
 <title>Facilitated transport</title>
@@ -54,7 +54,7 @@
 <para id="fs-idm66021008">A principle of diffusion is that the molecules move around and will spread evenly throughout the medium if they can. However, only the material capable of getting through the membrane will diffuse through it. In this example, the solute cannot diffuse through the membrane, but the water can. Water has a concentration gradient in this system. Therefore, water will diffuse down its concentration gradient, crossing the membrane to the side where it is less concentrated. This diffusion of water through the membrane—osmosis—will continue until the concentration gradient of water goes to zero. Osmosis proceeds constantly in living systems.</para>
 <note id="fs-idm19927952" class="interactive non-majors">
 
-<para id="fs-idp39016320">Watch this <link window="new" url="http://openstax.org/l/dispersion">video</link> that illustrates diffusion in hot versus cold solutions.</para>
+<para id="fs-idp39016320">Watch this <link window="new" url="https://openstax.org/l/dispersion">video</link> that illustrates diffusion in hot versus cold solutions.</para>
 </note></section>
 <section id="fs-idp113325968">
 <title>Tonicity</title>