Lif

For the first part of the 20th century, the study of genetics was considered by many biologists to be separate from, or even irrelevant to, the processes by which darwinian evolution occurred. It did not seem possible that natural selection if it was the mechanism of speciation could work gradually, as Darwin had suggested, through the discrete particles of mendelian inheritance, whose known changes caused discretely different, or worse, grossly disruptive changes to the organism. However, as...

Hormone Evolution

Hormones cannot bind to DNA on their own but must first be bound to a receptor. How this linkage evolved is not clear. Did every mutation in a receptor have to weather the blows of natural selection until a comparable mutation arose in its ligand This seems unlikely, but complex organisms depend extensively on such coevolution, the mechanisms of which in general are not well understood. This is another element of the problems of specificity, cross-reactivity, and coevolution that face systems...

Info

Schematic of genetic drift. Each line represents a separate experiment of an allele starting with a frequency of 0.10 followed over time in a population of size 100. In these computer-simulated data, frequency change is due to chance alone. Any frequency is achievable, but most new alleles quickly disappear while a few are lucky and rise to high frequency. In any population multiple alleles may be segregating, their relative frequencies drifting up or down over time, some being...

Detecting Physical Variability in the Environment

Almost 2500 years ago, in his treatise On the Soul (De Anima), Aristotle wrote, There is nothing in the intellect that was not first in the senses. He enumerated five senses sight, hearing, smell, taste, and touch. To Aristotle, the senses were formed of earth, water, air, and fire, as was all matter, and they came together in the common sense, the heart, which brings us the awareness of sensation, allows us to distinguish between the perceptions of each sense, and yet ultimately combines them...

Tsx

Reaction-diffusion systems can generate repetitive patterns. (A) The principles of a basic model shown at sequential developmental times the horizontal axis represents position along a layer of otherwise similar cells. Cells produce an activator, A, that catalyzes its own continued production. A diffuses across the tissue, where cells detecting it are stimulated to make A as well as a rapidly diffusing inhibitor, I. Cells whose receptors detect I inhibit their production of A. Where...

Light

As we saw in Chapter 14, most organisms in this world, single-celled bacteria, plants, insects, mammals and fish, make use of light energy in some way. Some convert solar into chemical energy, whereas others have receptors that trigger responses ranging from movement toward or away from a light source to conversion of the light into a perception of the surroundings. Plants use light in more ways than do animals and have evolved more pigments to collect and transduce it. They use light for...

Some General Concepts

Uniqueness and Generalization in a Historical Science Evolution is an opportunistic process that builds solely on its present state. There is a large chance component in the environmental and biological variation that exists at any time and place. Evolution has been a one-time history. Each individual organism inherits, and must work with, the products of the events that happened in its unique prior history. Selection may mold organisms in a given direction now but does not and cannot aim...

Xfg

Diffusion, and in the mainly cellular tissue of the wing disk, Dynamin here acts to move Dpp from cell to cell to help it diffuse from its source. Figure 9-3C described the workings of a simple concentration gradient mechanism, for DV patterning in the fly. This establishes the dorsal dominance of Dpp signal that, among other things, inhibits neural development, which takes place more ventrally. This is all part of a broader DV gradient patterning mechanism, that results in regionalized DV...

Conclusion

Diverse biological processes in diverse species use a limited number of genetic regulatory factors and their interactions, raising questions about how local specificity is established or how the requisite complex combinatorial patterns are controlled in a stable way. These processes include ligand-receptor binding for signal trans-duction that alters gene expression, gene regulation by the binding of cis enhancers by TFs, message transduction mechanisms such as the protein kinase networks, and...

Havmpnadhkvnksahlaetpavhslasstvtsk

Consensus Consensus Consensus GASXSALSAS C (Nucleotide substitutions X 100) Figure 5-2. Amino acid sequence comparison of gene family members within a single species' genome. (A) Alignment of human globin proteins (components of hemoglobin) (B) alignment of the mouse Dlx gene family, involved in embryological development (head, limbs, etc.) (C) phylogenetic tree of the Dlx genes based on degrees of sequence similarity, relationships that reflect the genes' history of descent by gene duplication...

Quick And Incomplete Tour Of Animal And Plant Development

A major hallmark of multicellular life is differentiation. Cells reproduce, and a single cell becomes a complete organism. Much of the work done on this subject before and even since our recently increased ability to document genetic mechanisms experimentally has concerned the determination of overall body plans. Multicellu-lar organisms are quite diverse, but in fact there are only about 35 body plans associated with the major animal phyla (e.g., Raff 1996) and an additional set of basic plant...

Gustation

Location of gustatory receptors on a mammalian tongue four major classes. Figure 13-7. Location of gustatory receptors on a mammalian tongue four major classes. The taste mechanism in vertebrates is patterned on the tongue and develops separately from the olfactory and vomeronasal systems. Taste receptor cells have voltage-gated ion channels, which in vertebrates synapse into three of the primary cranial nerves (facial, glosopharyngeal, and vagus) remarkably, this is true even of...

Bacteria

Motility is an important determinant of bacterial survival.Although some only glide, many bacteria can swim by rotating their flagellum, an ability that allows them to move toward a more favorable environment when they detect toxic conditions. Bacteria sense changes in the levels of surrounding nutrients and toxic chemicals, pH, temperature, light, the magnetic field of the Earth, electron transport conditions, and the like, and they respond with osmoregulation, altering internal conditions to...

Coding Cellular Differentiation Information Regulating Information

Except for simple organisms, the number of genes in a given species is somewhat a matter of speculation, even when the complete DNA sequence is known. This is partly because of the multiple splicing of mRNA and overlapping transcription that are sometimes found.The definition of a gene also changes as we continue to learn of ways new functions are encoded in the genome. Even with the simplest classical definition of genes as protein codes, a complex organism typically has tens of thousands of...

Communication within Organisms

The purpose of this section is to review how some fundamental challenges in information transfer within a multicellular organism have been met, and how the mechanisms involved today evolved from simpler precursor states. First, we will look at the ways in which multicellular life has come about. We will look at various ways a modest number of basic strategies that are used have evolved, and how genes are used to achieve them. These strategies have been employed throughout the biosphere. A major...

Conclusions

We referred earlier to Aristotle's defining of the classical separate senses. Here we have noted that not only is each sense a complex problem of perception of detection, but the senses are not really entirely independent in that their perception is often integrative. Indeed, the poet Dante Alighieri even suggested that shades (souls) of the departed were equipped with organs for each of the senses (Alighieri 1314). How else could he have spoken with them on his tour through the postmortem...

Development is Functionally Arbitrary

Just as the codon system for specifying amino acids is completely arbitrary relative to the chemical properties of the proteins being coded for, regulatory DNA sequences are arbitrary relative to the function they enable (Weiss 2002d 2002e). There is nothing about regulatory genes or RE sequences that has anything directly to do with the function of a regulated protein. There is nothing about the chemical nature of SFs or their receptors that is related to the physical or functional properties...

Invad

A substantial fraction of organisms that have ever lived have probably died as a result of predation, and much of evolution and of the structures of organisms can be viewed in the context of the battle to eat or be eaten. And as life would have it, many organisms alive today survive only by consuming other forms of life. Predation, broadly defined as obtaining nutrition from other living organisms, is a primary way in which organisms secure their energy needs. As a consequence, most animals and...

Cns

Photoreception Chemosensation Body axis outgrowth Heart Summed combinations of Hox gene expression specifies region along the axis Segmentation behind CNS Hairy, Engrailed Sog chordin dorsal, dpp TGFb ventral Para-hox genes Anterior, Lab Gsx central, Bcd Xlox, and perhaps an Antp Ubx-like gene posterior, Cdx Abd-B. See (Arendt and Nubler-Jung 1994 Campbell 2002 Carroll, Grenier et al. 2001 De Robertis and Sasai 1996 Gerhart 2000 Scott 1994 Wilkins 2002). similar gene hierarchies and inductions...

The Illusion of Adaptation Revisited

It may now be easier to understand why in Chapter 2 we said that the notion of adaptation was in some senses a seductive illusion, if not a tautology. To be here today, an organism had to have been adaptive sufficiently suited to its ancestral environments for an uninterrupted 3 billion year ancestry. What criterion can we use to infer anything beyond that With genes, unlike phenotypes, we can at least define more directly specific units of evolutionary change, and this allows for somewhat more...

Genetic Aspects Of Information

Basic Genetics A Brief Partly Guided Tour of DNA The large macromolecules, the nucleic acids DNA and RNA, serve many functions. The vital structural property of both molecules is that they are modular, each is a string of concatenated nucleotide bases, of which there are four basic types adenine (A), cytosine (C), guanine (G), and thymine (T) (or in a modified form as uracil (U) in RNA). These are linked by a phosphate-sugar backbone. Each of the two purines (G and A) easily forms a chemical...

Scaling Up How Cells Build an Organism

A single cell can develop, more or less on its own, into a full adult organism. This basic phenomenon was noted nearly as long ago in the history of Western thought as we can go back, by Aristotle. In On the Soul, he wrote, It is a fact of observation that plants and certain insects go on living when divided into segments this means that each of the segments has a soul in it identical in species, though not numerically identical in the different segments, for both of the segments for a time...

Protein is More Than a Polypeptide

Genes are usually portrayed as coding for proteins, and a simple schematic of this relationship is given by Figure 4-10. This shows the modular nature of the coding logic, but it is not entirely accurate. Genes code for polypeptides strings of amino acids. Polypeptides are not mature proteins. Functional proteins often comprise several polypeptides from the same gene (homomultimers) or different genes (heteromultimers). Its shape gives a protein its ability to interact with some other specific...

A

DNA and RNA are illustrated schematically in Figure 4-1. DNA is double-stranded, with one strand having the complementary nucleotides to the other (e.g., AAACGTA would be paired with TTTGCAT). For physicochemical reasons, this arrangement leads to the well-known basic double-helix shape of DNA. However, the DNA molecule in a cell would, if stretched out linearly, greatly exceed the space available in the cell (e.g., in a human cell, the DNA would be more than one meter long) therefore, the...

Table 61

Endoplasmic reticulum (ER) which maintains structural continuity with the cell membrane, is continuous with the nuclear envelope, and synthesizes and transports lipids and membrane proteins. There are two kinds of ER in the cell the rough ER is a flattened sheet, studded with ribosomes carrying out protein synthesis, and the smooth ER is more tubular with no attached ribosomes, but with major lipid synthesis function and for the storage and release of calcium ions into the cytosol, where...

Iob

Type seem likely to be responsible for a large fraction of the organization of complex organisms. There has been direct molecular demonstration of reaction-diffusion-like patterning in the use of Fgf and Bmp signaling as activators and inhibitors, respectively (Hogan 1999 Jernvall and Jung 2000 Jernvall and Thesleff 2000 Jung et al. 1998 Jung et al. 1999). Here we add the qualifying terminology, reaction-diffusion- like to indicate that these repetitive patterning systems vary in most of their...

Pleiotropy Aplenty

The same TFs, SFs, receptors, and REs are typically used in numerous developmental or histological contexts in an organism or even at different times and different ways during the ontogeny of a single tissue or organ. This in a sense is what is implied by the term toolkit, but there is an important implication if expression control is combinatorial and each gene has many uses, we can't expect to understand the development of a given structure until we know most or all of the regulatory factors...

The Phenomenon Of Evolution

The theory of evolution developed out of earlier ideas, some clearly anticipating what Charles Darwin and Alfred Russel Wallace would introduce to the world in 1858. The important concept was that the diversity of life, present and past, was not static and produced by externally derived creation events but was the product of historical processes, operating since some origin time on Earth and still operating. One can view these as the biological version of the prevalent idea of a universally...

W

Structure of immunoglobulin proteins, showing (A) the joined light and heavy chains, constant and variable regions (B) T cell receptors, showing their similarity to immunoglobulins. Figure 11-3. Antigen presenting cell with signals, T cell and receptors. Redrawn from Medzhitov and Janeway with permission see that reference for details. Original figure copyright 2000, Massachusetts Medical Society, all rights reserved. Figure 11-3. Antigen presenting cell with signals, T cell and...

P

Basic stages of Xenopus development, from fertilization to cleavage (cell divisions that produce the blastula, a spherical layer of cells that surround a fluid-filled cavity), gastrulation (invagination of cells from the blastula to form the gastrula, a two-layered sphere consisting of ectoderm and endoderm surrounding an archenteron that communicates with the exterior via the blastopore that will form the gut), neurulation (embryonic stage at which the neural tube develops),...

Some Basic Developmental Processes And Some Genes They

We have identified a few generic principles by which spatial and temporal differentiation takes place. We can now describe how these same principles are employed in a repertoire of basic developmental processes that characterize much of development in animals and even plants. The same sets of genes appear again and again in different developmental contexts, even in the same organism. Many or even most regulatory pathways have homologs in vertebrates as well as invertebrates, or even in animals...

Table 104

Corticotropin-releasing hormone (CRH), thyrotropin-releasing hormone (TRH), luteinizing hormone-releasing hormone (LHRH), growth hormone-releasing hormone (GHRH), somatostatin, growth factors (fibroblast growth factors), transforming growth factor-a (TGF-a), transforming growth factor-b (TGF-b), insulin-like growth factor I (IGF-I) Erythropoietin, renin, 1,25-dihydroxyvitamin D fibroblasts

Reticulated Variation

In nature, sexual reproduction is widespread and allows for the scrambling of the hierarchically nested variation that a history of mutation produces. In many animal and plant species, this means that individuals bear more than one copy of their species' genomes (humans have two one copy from each parent). Scrambling of variation occurs because of recombination, or crossing-over, between homologous chromosomes during meiosis prior to reproduction, the homologous (corresponding) chromosomes...

Some Concluding Generalizations About Multicellular Life

The organizational advances necessary for the cell as we know it to exist and predominate in the biosphere were many and included a cell membrane and internal structures of some kind in which controlled reactions could take place. Such evolutionary steps alone resulted in single-celled organisms such as bacteria and protozoa, which still comprise more than half of the total biomass on Earth. Of course, we do not know how much more advanced current unicellular organisms are versus those that...

Multisensory Perception

We have largely discussed sensory perception in a Cartesian way, as though each of the senses were an independent function. Although we see orderly ways in which these things are organized, and we can relate that to the known kinds of developmental processes, the emergent nature of perception in each type of sense is still rather elusive. In fact, although many of these sensory systems do function without input from others, higher sensory processing often involves their interaction....

Table

The special case of the Serpentine receptors. A particularly interesting and important class of cell-surface signal receptors are those known as the seven-transmembrane G protein-coupled receptors (7TM-GPCRs, or 7TMRs). There are hundreds of genes in this class, involved in diverse aspects of information transfer to cells. As shown in Scheme 7-2, these receptor molecules contain seven helical transmembrane domains, with additional extra- and intracellular domains. Transmembrane information...

Ommunicatin Between Cells

The specialization in cells and tissues that multicellularity allows depends on mechanisms for regulating and integrating the function of the different cells and organs. One cell must be able to influence the physiology of another, on the basis of its context or conditions. In a sense, this is what makes what we term an organism as a coordinated biological entity possible. The organism coordinates many functions that involve communication between neighboring cells or among more distant cells or...

Table 75

Extracellular workings A G protein cascade is activated when a ligand binds to a receptor (see Scheme 7-2). As 7-spanning transmembrane proteins, the free NH2 terminus of the protein remains outside of the cell, and the COOH terminus floats in the cytoplasm of the cell. The receptor-ligand binding causes a conformational change (phosphorylation) in the three-dimensional structure of the receptor, and this results in the transfer of signal from the receptor to a G protein, which is in the plasma...

Xer

Generation of antibody diversity in vertebrates (A) Various vertebrate antibody recombination mechanisms including multiple V-region genes in the germ line, somatic mutation, somatic recombination between elements forming a V-region gene, gene conversion, and nucleotide addition (B) antibody diversity in the mouse is due to somatic recombination in sharks to numerous antibody genes rather than somatic recombination chickens have few antibody genes but a high level of gene...

Genes Coding for RNA

Located at various places in the chromosomes of every species are the codes for the various types of RNA molecules. These include the tRNA molecules that transfer (carry) a specific amino acid for use in protein assembly, the ribosomal RNA (rRNA) molecules that are major constituents of ribosomes, where the tRNA-borne amino acids are concatenated, and the small nuclear snRNA molecules that participate in a variety of functions such as splicing mRNA and attending to telomeres (chromosome ends)....

Contents

UNDERSTANDING BIOLOGICAL COMPLEXITY Basic Concepts and Principles 1 1. Prospect The Basic Postulates of Life 3 2. Conceptual and Analytic Approaches to Evolution 21 3. Evolution By Phenotype How Change Happens in Life 43 II. BUILDING BLOCKS OF LIFE A Genetic Repertoire for 4. The Storage and Flow of Biological Information 69 5. Genotypes and Phenotypes 105 7. A Repertoire of Basic Genetic Mechanisms 145 III. AN INTERNAL AWARENESS OF SELF Communication 8. Making More of Life The Many Aspects...

D1

Evolution of the Hox subfamily of homeobox-containing genes involved in developmental patterning (see Table 7-5 for a description of this family). From an original gene, a small set of proto-Hox genes evolved by duplication. From these, subsequent duplication has created chromosomally linked clusters in invertebrates and early vertebrates. These clusters continued to gain and lose genes by tandem duplication and the clusters themselves were duplicated on at least two occasions...

Genes to Keep Things in Balance

If genes are generally thought of as making something, an obvious issue that arises is what happens when enough is enough. Getting rid of something can be as important as making more of it. Excess levels can be toxic, and genes related to development or homeostasis may be very damaging if expressed at the wrong times. At some point, a structure has to stop developing. Not surprisingly, a large number of mechanisms have evolved whose function is to adjust the balance of constituents in a cell,...

Making More of Life The Many Aspects of Reproduction

Reproduction is so fundamental to life that it is one of the characteristics by which we define life. As well as the generation of new life in the short term, in the long term, reproduction provides an opportunity for heritable change of various kinds, and hence for evolution. A key view of 20th century biology was that life is basically a nucleic acid information phenomenon, in the dual senses that biological information flows from DNA to RNA to protein (the Central Dogma), but not the other...

Oh P

Rag1 and Rag2 mediated V(D)J formation (see text). Redrawn from (Ohmori and Hikida 1998) with permission. This somatic recombination happens in cis, that is, along the TCR and heavy and light chain Ig gene regions. At the same time, there is a trans phenomenon of allelic exclusion, by which the same region of the homologous chromosome is inactivated, so that the cell expresses only one combination of its genes (for the TCR or its Ig, depending on the cell type) derived from only...

The Central Dogma

The discovery of the logic DNA mRNA protein as a fundamental characteristic of life led to the formulation of the Central Dogma, referred to in Chapter 2. This states that this information flow goes only one way there is no flow back of information (that is, to DNA sequence) that reflects life experience directly in a her itable, lamarckian way. The causal arrows go only one way. Evolution unfolds but does not involute back upon itself. The Central Dogma asserts an aspect of biological...

Bwb

SEQUENCE Short repeat element SEQUENCE Alu repeat SEQUENCE Exon, untranslated regions B SEQUENCE Exon, coding region including signal peptide, mature peptide, stop. triplet carry their amino acid to the site, where it is concatenated to the previously joined amino acid, thus producing a polypeptide, the precursor of a functional protein. This codon-anticodon matching is how the sequence of DNA specifies, through mRNA as a temporary information carrier, the sequence of amino acids, and this is...

Nhq

Tion plants have because, with their rigid cell wall, they have no need of anchoring junctions. Plasmodesmata connect every cell in a plant with its neighboring cells, allowing the passage of cytoplasm from cell to cell. In a sense, then, plant cells connected in this way form one mega-cell containing many nuclei. The outer membranes of bacteria, mitochondria, and chloroplasts are permeated by pore proteins called porins that function similarly to gap junctions, although they are structurally...

The Development and Structure of Nervous Systems

In previous chapters, we have discussed the open-ended environmental variability that organisms encounter and detect with sight, taste, smell, feel, and so on. In Chapters 15 and 16, we will describe in basic terms what is known about the central problem of how organisms perceive this infinite and constantly changing variety of sensory signals. As humans, we tend to relate these issues to our own personal experience, leading us to equate perception with consciousness. But the two are highly or...

Abc

Figure 17-1. (A) Aristotle (B) young Darwin (C) young Wallace. (A) Statue in Vienna art museum, copied from (Bowder 1982), (B) 1840 painting by George Richmond. explanatory power. Among our points is that one can accept Darwin and Wallace's deep insight, yet need not overly or uncritically invoke the single force of systematic natural selection as we try to understand the evolution of life. Before there was much formalized history and essentially no paleontology no sense of great time depth in...

Acknowledgments

We are pleased and grateful to acknowledge the help and guidance of a number of people as we wrote this book. Kris Aldridge, for an introduction into the literature on the brain, Mary Silcox for the tip on Linnaeus' classification of bacteria, Frances Hayashida for invaluable assistance with Adobe Illustrator, her provocative questions on the subject of every chapter and her delight in the answers (even though she's an archeologist), Ela and Janusz Sikora for cheering us on (even though they...

Cjn

Rods and cones have inner and outer segments. The outer segments are composed of a series of stacked bilipid membranous disks that contain visual pigment called photopigment. There are two main ways in which these disks can be presented at the apical end of the cell or in cilia formed on that end. These cellular arrangements have been thought to divide protostomes and deuterostomes, respectively, but the photoreceptor phylogeny turns out to be rather more complex and even raises questions about...

Repertoire o Basic Genetic Mechanisms

Observing the very similar chemical constituents of diverse life forms, biologists long ago realized that life (on Earth, at least) is a single subject. This edifying realization did not require knowledge of anything about genes and was basically understood even by Aristotle and others in ancient times. However, we now have genetic knowledge, and it confirms the unity of life in exquisite detail and adds whole new sets of phylogenetic relationships that go beyond and in some ways are...

FROM a Traits Point Of View

What we have described so far is a general quantitative theory of the inheritance and evolution of genes. The assumption is widely made that population genetics is the rigorous theory of evolution and that the study of phenotypes and their development is rather descriptive and ambiguous by comparison. If genes are the ultimate units of evolution, the theory of evolution really only need consider what happens to genes. This needs a bit of clarification. Population genetics gives a plausible...

Ofd

The central body is a way-station through which nerve fibers pass from one hemisphere to the other. The nature of the signal processing that takes place here is unclear it may be involved in visual processing (Burrows 1996). The optic lobes are laminar, that is, organized in layers, and process information from the insect's compound eyes through the layers in a way that, as in vertebrates, retains the retinotopic (spatial) map of the image. The antennal lobes process...

RNA Regulating Gene Expression

If it is true in physics that for every action there is an equal and opposite reaction, there is something like this in genomic information as well. If mRNA represents activation of a coding signal, the same signal can be dampened by antisense RNA, which can bind to mRNA by complementary base pairing. In Chapter 7, we will see that important means to do this do in fact exist. Of course, were this reaction truly equal and opposite, nothing in life would get accomplished. But then, biology is not...

Olfaction

The ability to detect odors varies widely across the animal world.The numbers game can be misleading, but there is a general correspondence between the number of olfactory neurons (ONs) cells specialized for odorant detection that an animal has and the probability that any given odorant will come in contact with an appropriate receptor. Humans have approximately 5-10 million olfactory neurons in the olfactory epithelium, enabling us to detect an estimated 10,000 or more different odorants, but...

Table 76

Homeodomain TFs (coded for by homeobox genes) have a basic 60 or 61-amino acid helix-turn-helix (bHTH) protein domain that, depending on its amino acid sequence, binds specific DNA sequences the third helix extends into the major groove of the DNA that it recognizes. Amino acids in the NH2-terminal portion of the homeodomain also contact the bases in the minor groove of the DNA double helix. A class called POU TFs also has a second DNA-binding domain. Lim and Pax genes comprise two other...

Technical Notes

Genes are being discovered by the hundreds, often by automated means. The nomenclature system is somewhat undisciplined and not entirely consistent. In this book we have discussed results from work in most areas of biology, many of which have their own conventions for gene nomenclature, not always even internally consistent. Designation conventions change and seem likely to do so even more as an ever-larger set of species and their genes are identified, and genes are grouped ever more...

Cell Replication

Perhaps the single most important characteristic of life is its ability to replicate. This will be the topic of Chapter 8, but a few comments can be made here. Today, bio-molecules replicate mainly via the elaborate DNA-RNA-protein coding system, which is an intracellular mechanism. This can be direct, as in the repeated production of the same protein, or indirect, as in the production of a biomolecule through the action of enzymes (proteins coded for by genes). An important stage in evolution...

Gap Junctions

Like ion channels that face intercellular spaces, gap junctions are pores that connect cells directly to each other. The gap junction is formed by a circular complex, a con-nexon, composed of four to six protein subunits called connexins, which can be repeats of the same subcomplex. What can pass through a gap junction is determined by which gene family members code for the proteins of which it is comprised. In invertebrates, the proteins are coded for by members of the innexin gene family...

Genes Are Involved In Everything But Not Everything Is Genetic

The Importance of Genes in Inheritance and Phenotype Determination A century of unprecedented work has led to an understanding of the importance of genes as inherited material, as the molecule that stores the information from the history of life, and as determinants of the traits of organisms. Before genes were discovered and understood, it was difficult to explain inheritance and the evolution of organized traits. Genetics has become the central, theoretical organizing principle of biology....

Coz

< Ganglionic neural crest Ectomesenchyme Visceral skeleton Cerebral hemispheres Thalamus Optic lobes Cerebellum Medulla oblongata Spinal cord Mesomere Mesoderm (intermediate mesoderm) Mesonephric tubuje urogenital ducts Renal cortex Blood vascular Mesentery Extraembryonic membranes Mesonephric tubuje urogenital ducts Renal cortex Oral and nasal cavities and derivatives Pharyngeal pouches Esophagus Lung buds Stomach Urogenital sinus Figure 8-3. Continued Esophagus Tracheal tube Stomach Liver...

Ion Channels

Ligand-gated and voltage-gated ion channels are separate types of structure that were described in Chapter 6. Both are formed by complexes of proteins that make controlled passages into the cell. The ion channel may be composed of a single protein with multiple domains that pass through the cell membrane or of homo- or heteromultimers of various channel proteins. Voltage-gated channels typically involve four subunits, with the main subunit having multiple (e.g., five or six), similar...

Tom

Opsin genes. (A) Simplified opsin gene tree in many instances similar but not identical opsins (based on gene sequence and estimated peak sensitivity) are found within the groups tested, but shown here as one branch of similar genes (B) location of the amino acids in the opsin protein structure that have the greatest effect in red-green spectral cone sensitivity among naturally observed opsins, showing their likely important relationship to the retinal molecule bound to the...

Receptormediated Signaling

Larger signaling molecules cannot diffuse through the membranes of receiving cells and instead serve as ligands for specific receptors protruding from the surface of cells sensitized thereby to receive the message. This is true of a variety of growth and signaling factors as well as of protein hormones like insulin and adrenaline. In fact, message exchange among cells is so important that cell membranes are often littered with receptors of many kinds. Cell surface receptors have one or more...

Am

Figure 17-3. (A) Darwin's drawing of developmental divergence of basic body plan components from a common core body plan as proposed by von Baer (B) Darwin's early sketch of the divergent nature of his emerging view of species evolution (C) a somatic tree of development of organs within an organism the sequestered germline cells are shown in gray (D) a fractal pattern of branching as roughly approximates much of organ branching seen in veins, nerves, bronchial trees and real trees. (A,B,D)...

Awe

Bacterial biofilms and slime molds are among the most simply organized coalitions of individual organisms, although social insects are probably the most often-used example of clearcut organization above the level of what is traditionally considered an organism. Of course, human societies and hundreds of less elaborate animal social structures can be thought of in the same way. From a darwinian point of view, of ever-present competition for reproductive gain, social organization should occur...

Uqg

The instruction stop, that is, the end of the amino acid coding sequence. As can be seen from the table, the redundancy is mainly in the third position. The level of code degeneracy (e.g., whether two or four nucleotides in a given position code for the same amino acid) was what was shown in Figure 3-5 concerning the relative amounts of diversity in genes. Thus, the bar for variation found in two-fold degenerate sites refers to sites like the third position in the codons that specify the amino...

Chemical Signaling and Sensation from the Outside World

The light, sound, and chemical environs of an organism are often detected at a distance from their source and, to a great extent, are varied enough that they cannot be specifically anticipated. The properties of the sensory stimuli also vary. Light is fastest, but cannot penetrate solid objects, and an object cannot be seen if the requisite energy is not available (e.g., many animals do not see well at night). Because light travels in a coherent linear way, the information it carries is...

Cqu

Sequence of the opsin protein and its interaction with the chromophore. Modifications in the photoreceptor itself, such as the use of oil droplets by some species, mean that the actual response of the photoreceptor may not correspond to that of the visual pigment alone. Examples are the chicken Rh2 gene that is paired with a green oil droplet and the goldfish Rh2 that is green-shifted because of the modified chromophore it uses (Yokoyama and Yokoyama 2000). Because its different opsins respond...

Qwj

A bestiary of basic anatomical body plans (A) Nematode, experimental model system, C. elegans with tissues identified (for use below) (B) hydra (C) starfish illustrating radial symmetry (D) fossil fern from Carboniferous age around 350 million years ago (Mya) (E) fossil trilobite from the Cambrian (Burgess shale) about 500 Mya (F) Richard Owen's famous archetype of a standard, shared vertebrate body plan. Also see the frog, fly, and plant body plan figures below. Sources Fern,...

Evolution Of The Dna System Of Life Dna Evolved From an RNA World

Because of the diverse enzymatic roles now known for RNA, it is thought by many who speculate on the origin of life that some kind of RNA world preceded the DNA-based coding system (Gilbert 1986 Joyce 2002 Maynard Smith and Szathmary 1995). This was suggested by the discovery in the 1980s that RNA has enzymatic properties that include catalyzing some aspects of RNA replication (e.g., Cech 1986 1990), and many additional active functions of RNA have since been discovered. Indeed, RNA can fulfill...

Final

Evolutionary Order and Disorder between Phenotypes and Genotypes We have reviewed many aspects of the lives and times of complex organisms. It can be seen both in terms of traits and their associated genes that life is a universally connected phenomenon, in many simple but elegant ways. Genes are complicated, but the process by which they have been strung together and used to make the Great Chain of Beings that live today, and that have lived, is a mesh of chemical interactions that follow some...

From DNA to RNA to Protein A Digital Coding System for the Diversity of Life

The most familiar role of DNA is as a code that specifies the structure of a protein, the role to which the word gene was first applied in regard to DNA. The diverse functions of life are brought about by the chemical properties of the 20 different amino acids (listed in Table 4-2) their number and order determine the interactions of a protein with other molecules. These properties depend on how it is folded, chemically modified, and combined with other molecules (including other proteins)....

Understanding Biological Complexity

In this section, we consider some of the general principles that characterize the nature and evolution of organized, functionally adaptive life on Earth. The mechanisms that determine the nature of organisms and the origin of the traits they possess can be approached at various levels of complexity. First, we will look at general principles. Inheritance is a vital component of diversified, specialized life, and we will consider just what it is that is inherited. We will then consider how that...

The Pace Of Replacement

Organisms approach reproduction in various ways. Evolutionary biologists have sometimes characterized these in two general categories as r and K strategies. This nomenclature derives from an equation for the dynamics of population size, relating the rate of change in size of a population now of size N, to its intrinsic growth capability of the population (r), and the carrying capacity (maximum sustainable population) (K) of the local environment This is the logistic growth equation. At low...

Tsw

The notion of an organizer is somewhat imprecise, but in a general sense there are organizers from head (see Chapter 15) to tail (Agathon et al. 2003) and many places in between, and in subsequent chapters we will see how some of them work. The notion of an organizer, like others in biology that use a term borrowed from everyday life, should be understood with circumspection. The term is used to identify signals in a practical sense and does not mean that these cells somehow come from the...

Detecting Light

Light is the ultimate resource for all forms of life. Organisms use light in three basic ways, the most ubiquitous being in direct physiological processes, the capture of energy via photosynthesis. This is of course what plants do and, in terms of the ecology of the Earth, photosynthesis is probably the most active important use of light energy by living organisms. Second, many organisms simply detect the location of a light source, moving toward or away from it. Third is vision, the...

Mammal

Papilla basilaris basilar membrane lagena cristae utricle macula utriculi saccule macula acculi Figure 12-5. Comparative diagram of the labyrinths and inner ears of fish, amphibians, birds, and mammals. Redrawn based on version in Encyclopedia Britannica (Britannica 2003). organs, the saccule, which detects motion in the vertical plane, and the utricle, which senses motion in the horizontal plane. These sacs and canals are all filled with a fluid called endolymph. As with hearing, the detection...

Multiple Functions via Modularity in RNA

A tRNA molecule folds upon itself via complementary base pairing into a general cloverleaf shape that is characteristic of tRNAs. Over evolutionary time, a considerable amount of variation on this structure has accumulated, although the basic shape is retained. The sequence at one end of a given type of tRNA determines which amino acid will attach there, and a sequence of three nucleotides at the other end of the (folded) tRNA molecule, called the anticodon, determines its specificity to a...

L

Stages in antigen processing and presentation to the surface of the cell by the MHC class I and II gene products. Redrawn after (Paul 1999) with permission. Original figure copyright Lippincott, Williams and Wilkins, 1999. Figure 11-5. Stages in antigen processing and presentation to the surface of the cell by the MHC class I and II gene products. Redrawn after (Paul 1999) with permission. Original figure copyright Lippincott, Williams and Wilkins, 1999. waste disposal. Class I...

Plant Signaling

In plants, as animals, growth and development are controlled by responses to environmental or inter- or extracellular triggers. Environmental triggers of plant responses include features of light signals such as quality (red light activates different genes than blue light), duration, direction, and quantity, changes in temperature that can alter the fluidity of cell membranes, chemical signals (air pollutants, phytotoxins, or elicitors from other organisms), changes in water availability and...

Some Basic Sensory Principles

Whether of internal or external stimuli, sensory perception begins at the level of the cell. This raises two general questions first, what kinds of signals do cells sense and what mechanisms are used Second, what do they do with the signal (Here, inevitably trapped by language, we use words like information or signal without implying an intentional sender or coder nor that incoming data are neatly packaged). Some sensory mechanisms cause cells to change gene expression. Other sensory cells...

How Does It Work

Unlike light and sound, odorants are not sampled from a continuous or coherent frequency spectrum. Similar molecules can smell different, and different compounds can smell the same. But the senses of sight and hearing do have some similarities with smell. Each photoreceptor (Chapter 14) or hair cell (Chapter 12) responds optimally to a particular part of its corresponding spectrum, but a given light or sound frequency can trigger responses in more than one photoreceptor gene or hair cell....

Ggaag

Source (Lander, Linton et al. 2001). Like the codon system for amino acid specification, the recognition sequences are degenerate or redundant that is, the RE sequences for a given TF can vary. An example is given in Table 4-5 for the paired domain of Pax6, a gene involved in the development of eyes and other structures. These enhancer sequences may not have equal binding efficiency, but all are recognized by a given TF protein. The nominal or consensus...

If Dna Is A Book How Does It Get Read

The metaphors are overstated, sometimes misleadingly so, but DNA is widely characterized as the Book of Life a repository of the information of biology and the program from which organisms are computed. But this is very different from a book a human would write for the same reason that an organism is not truly a machine. A book or machine is assembled with a purpose in mind, from parts derived from all sorts of other knowledge. An organism is built from within, and its DNA must function that...

Hierarchies of Regulatory Circuits Batteries and Networks

Some TFs are known as selectors, meaning that they activate a hierarchical cascade of change in the expression of other, developmentally downstream genes. This is comparable to the notion of an embryological organizer that we will see in later chapters. Another term for the idea is master control genes, but it can be misleading to think of genes so metaphorically in terms of our own culture's social structure rarely if ever is one gene the master of a whole organ in a very meaningful sense....

Wondrous Nature To Be Explained

Naturalists, theologians, philosophers, and poets have written of their wonderment at the panoply of natural forms. Many have been struck by the adaptation of organisms to what they do in life perhaps this insight alone is responsible for our modern view of biology. Different explanations for the origins of adaptation have been offered, but it is worth quoting one of the first advocates of an evolutionary view, the naturalist Henry Walter Bates, who described the following observations on the...

Vertebrate Endocrine System

As in other organisms, because hormones are a fundamental way that multicellular organisms solve the problem of intercellular communication and the regulation of local gene expression to serve the whole, vertebrates have evolved a substantial array of hormone-producing glands, genes, and systems that affect all aspects of life reproduction, growth and development, maintenance of a stable internal environment, mental functions, physical activity, food seeking and satiety, many behaviors, and...

Prospect The Postulates of

Natural history is the descriptive study of the natural world. The ultimate objective of science is to go beyond natural history to find generalizations, or explanatory theories, to account for our observations of nature. Theory enables us to explain a set of observations with fewer bits (a bit being equivalent to the answer to a single yes no question) of information than are contained in the observations themselves. The more dramatic the reduction in the amount of such information needed to...

H

Pyriform and entorhinal cortex (primary olfactory cortex) Figure 13-1. Vertebrate (human) olfactory system showing olfactory epithelium, olfactory bulb of the brain and the pathway of olfactory neurons to the olfactory regions of the brain. Figure 13-1. Vertebrate (human) olfactory system showing olfactory epithelium, olfactory bulb of the brain and the pathway of olfactory neurons to the olfactory regions of the brain. OR genes are the largest subset of this gene family and comprise about 3-4...

DNA A Protected Code

The beauty of the DNA RNA system is that it solves many functions by the one phenomenon of base pairing. The double-stranded nature of DNA and its packaging make it a stable molecule resistant to damage. When a cell divides, the entire complement of DNA must be replicated so that each daughter cell receives a complete copy. To achieve this, the two strands, call them A and B, separate and are matched nucleotide-by-nucleotide by a new concatenation of nucleotides. This generates two new double...

Mro

Sustaining or changing in a contingent way. The state of differentiation is not washed out by being blended with that of neighboring cells. One cell or few cells can be the progenitor of a whole complex structure even if isolated from the rest of the organism (e.g., grown in vitro). As cancer shows, and may be important to many normal traits as well, a mutant somatic cell can generate a clone of cells with altered function. Cellular commitments are achieved in various ways for example, the...

Cooh

Stereotype of 7TMR protein structure. Seven regions are hydrophobic and insert stably in the cell membrane. The intracellular domain is involved in signal transduc-tion. Signal may be received by the extracellular domain(s) or in some instances occurs in the intracellular or membane domains. Specific amino acid variants in the appropriate domains affect the nature of the ligand (or light energy frequency) that triggers a response, and hence is how divergence and specialization in...

What Mapping Genes Tells Us and Doesnt Tell Us

When we do mapping studies, the idea is to find genes that contribute quantitatively or qualitatively (if probabilistically) to a trait. This is an important objective because, without identifying the genes, we can't understand what they do. However, at this stage of knowledge, much of what we do remains in the black-box category. In many if not most instances, especially for complex or quantitative traits, variation in genes identifiable by mapping methods accounts for only a fraction, often a...

Mapping Qualitative and Quantitative Traits

Mapping is an empirical approach to finding genes, that is, it is a technique that makes use of naturally existing or experimentally arranged phenotypic variation to find associated genetic variation, rather than the direct experimental manipulation of known genes. Traits can be treated as qualitative or quantitative, but they are approached in logically similar ways. In mapping a qualitative trait, our statistical analysis searches for associations between the presence, or probability of...

Some General Types Of Genes

The Central Dogma of biology, that genes code for protein, led to the general notion that genes specify individual structural proteins and enzymes that control basic physiology. The idea (not always explicitly stated) was that an organism is built up of separate identifiable functions and that one gene coded for one function. We know this is an overstatement, and one that can be quite misleading, but it is a view that has persistent effects on biology and biological research. The traditional...

Adar

Other RNA editing phenomena affect the translation of a gene's amino acid code. Besides mRNA splice variation, there is at least one other known pre-mRNA editing phenomenon, adenosine deaminase acting on RNA (ADAR), which has been observed in both invertebrates and vertebrates. What ADAR does is change the sequence of particular codons so that the mRNA is translated to contain a different amino acid from that nominally coded in the gene itself (e.g., Reenan 2001). In the target regions, the DNA...

C

Cell division provided the mechanism for reproduction of the cell as an organism. Multicellular organisms are aggregates of differentiated cells that ultimately descend from a single cell (e.g., the fertilized egg). Thus, large complex organisms are built on a process of duplication with variation. Organisms are modular in many ways beyond being aggregates of differentiated cells. Many if not most higher-level structures, like organ systems, are also modular (each themselves built up of...