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25.6: Conclusion and Resources - Biology

25.6: Conclusion and Resources - Biology



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25.6: Conclusion and Resources

25.1 Early Plant Life

By the end of this section, you will be able to do the following:

  • Discuss the challenges to plant life on land
  • Describe the adaptations that allowed plants to colonize the land
  • Describe the timeline of plant evolution and the impact of land plants on other living things

The kingdom Plantae constitutes large and varied groups of organisms. There are more than 300,000 species of catalogued plants. Of these, more than 260,000 are seed plants. Mosses, ferns, conifers, and flowering plants are all members of the plant kingdom. Land plants arose within the Archaeplastida, which includes the red algae (Rhodophyta) and two groups of green algae, Chlorophyta and Charaphyta. Most biologists also consider at least some green algae to be plants, although others exclude all algae from the plant kingdom. The reason for this disagreement stems from the fact that only green algae, the Chlorophytes and Charophytes , share common characteristics with land plants (such as using chlorophyll a and b plus carotene in the same proportion as plants). These characteristics are absent from other types of algae.

Evolution Connection

Algae and Evolutionary Paths to Photosynthesis

Some scientists consider all algae to be plants, while others assert that only the green algae belong in the kingdom Plantae. Still others include only the Charophytes among the plants. These divergent opinions are related to the different evolutionary paths to photosynthesis selected for in different types of algae. While all algae are photosynthetic—that is, they contain some form of a chloroplast—they didn’t all become photosynthetic via the same path.

The ancestors to the Archaeplastida became photosynthetic by forming an endosymbiotic relationship with a green, photosynthetic bacterium about 1.65 billion years ago. That algal line evolved into the red and green algae, and eventually into the modern mosses, ferns, gymnosperms, and angiosperms. Their evolutionary trajectory was relatively straight and monophyletic. In contrast, algae outside of the Archaeplastida, e.g., the brown and golden algae of the stramenopiles, and so on—all became photosynthetic by secondary, or even tertiary, endosymbiotic events that is, they engulfed cells that already contained an endosymbiotic cyanobacterium. These latecomers to photosynthesis are parallels to the Archaeplastida in terms of autotrophy, but they did not expand to the same extent as the Archaeplastida, nor did they colonize the land.

Scientists who solely track evolutionary straight lines (that is, monophyly), consider only the Charophytes as plants. The common ancestor of Charophytes and land plants excludes the other members of the Archaeplastida. Charophytes also share other features with the land plants. These will be discussed in more detail in another section.

Link to Learning

Go to this article to get a more in-depth view of the Charophytes.

Plant Adaptations to Life on Land

As organisms adapted to life on land, they had to contend with several challenges in the terrestrial environment. Water has been described as “the stuff of life.” The cell’s interior is a thick soup: in this medium, most small molecules dissolve and diffuse, and the majority of the chemical reactions of metabolism take place. Desiccation, or drying out, is a constant danger for an organism exposed to air. Even when parts of a plant are close to a source of water, the aerial structures are likely to dry out. Water also provides buoyancy to organisms. On land, plants need to develop structural support in a medium that does not give the same lift as water. The organism is also subject to bombardment by mutagenic radiation, because air does not filter out ultraviolet rays of sunlight. Additionally, the male gametes must reach the female gametes using new strategies, because swimming is no longer possible. Therefore, both gametes and zygotes must be protected from desiccation. The successful land plants developed strategies to deal with all of these challenges. Not all adaptations appeared at once. Some species never moved very far from the aquatic environment, whereas others went on to conquer the driest environments on Earth.

To balance these survival challenges, life on land offers several advantages. First, sunlight is abundant. Water acts as a filter, altering the spectral quality of light absorbed by the photosynthetic pigment chlorophyll. Second, carbon dioxide is more readily available in air than in water, since it diffuses faster in air. Third, land plants evolved before land animals therefore, until dry land was colonized by animals, no predators threatened plant life. This situation changed as animals emerged from the water and fed on the abundant sources of nutrients in the established flora. In turn, plants developed strategies to deter predation: from spines and thorns to toxic chemicals.

Early land plants, like the early land animals, did not live very far from an abundant source of water and developed survival strategies to combat dryness. One of these strategies is called tolerance. Many mosses, for example, can dry out to a brown and brittle mat, but as soon as rain or a flood makes water available, mosses will absorb it and are restored to their healthy green appearance. Another strategy is to colonize environments with high humidity, where droughts are uncommon. Ferns, which are considered an early lineage of plants, thrive in damp and cool places such as the understory of temperate forests. Later, plants moved away from moist or aquatic environments using resistance to desiccation, rather than tolerance. These plants, like cacti, minimize the loss of water to such an extent they can survive in extremely dry environments.

The most successful adaptation solution was the development of new structures that gave plants the advantage when colonizing new and dry environments. Four major adaptations contribute to the success of terrestrial plants. The first adaptation is that the life cycle in all land plants exhibits the alternation of generations, a sporophyte in which the spores are formed and a gametophyte that produces gametes. Second is an apical meristem tissue in roots and shoots. Third is the evolution of a waxy cuticle to resist desiccation (absent from some mosses). Finally cell walls with lignin to support structures off the ground. These adaptations all contribute to the success of the land plants, but are noticeably lacking in the closely related green algae—another reason for the debate over their placement in the plant kingdom. They are also not all found in the mosses, which can be regarded as representing an intermediate stage in adaptation to land.

Alternation of Generations

All sexually reproducing organisms have both haploid and diploid cells in their life cycles. In organisms with haplontic life cycles, the haploid stage is dominant, while in organisms with a diplontic life cycle, the diploid stage is the dominant life stage. Dominant in this context means both the stage in which the organism spends most of its time, and the stage in which most mitotic cell reproduction occurs—the multicellular stage. In haplontic life cycles, the only diploid cell is the zygote, which undergoes immediate meiosis to restore the haploid state. In diplontic life cycles, the only haploid cells are the gametes, which combine to restore the diploid state at their earliest convenience. Humans, for example, are diplontic.

Alternation of generations describes a life cycle in which an organism has both haploid and diploid multicellular stages (Figure 25.2). This type of life cycle, which is found in all plants, is described as haplodiplontic .

In alternation of generations, the multicellular haploid form, known as a gametophyte, is followed in the developmental sequence by a multicellular diploid form, the sporophyte. The gametophyte gives rise to the gametes (reproductive cells) by mitosis. This can be the most obvious phase of the life cycle of the plant, as in the mosses, or it can occur in a microscopic structure, such as a pollen grain, in the seed plants. The evolution of the land plants is marked by increasing prominence of the sporophyte generation. The sporophyte stage is barely noticeable in non-vascular plants (the collective term for the plants that include the liverworts and mosses). In the seed plants, the sporophyte phase can be a towering tree, as in sequoias and pines.

Protection of the embryo is a major requirement for land plants. The vulnerable embryo must be sheltered from desiccation and other environmental hazards. In both seedless and seed plants, the female gametophyte provides protection and nutrients to the embryo as it develops into the new sporophyte. This distinguishing feature of land plants gave the group its alternate name of embryophytes .

Sporangia in Seedless Plants

The sporophyte of seedless plants is diploid and results from syngamy (fusion) of two gametes. The sporophyte bears the sporangia (singular, sporangium). The term “sporangia” literally means “a vessel for spores,” as it is a reproductive sac in which spores are formed (Figure 25.3). Inside the multicellular sporangia, the diploid sporocytes , or mother cells, produce haploid spores by meiosis, during which the 2n chromosome number is reduced to 1n (note that in many plants, chromosome number is complicated by polyploidy: for example, durum wheat is tetraploid, bread wheat is hexaploid, and some ferns are 1000-ploid). The spores are later released by the sporangia and disperse in the environment. When the haploid spore germinates in a hospitable environment, it generates a multicellular gametophyte by mitosis. The gametophyte supports the zygote formed from the fusion of gametes and the resulting young sporophyte (vegetative form). The cycle then begins anew.

Plants that produce only one type of spore are called homosporous and the resultant gametophyte produces both male and female gametes, usually on the same individual. Non-vascular plants are homosporous, and the gametophyte is the dominant generation in the life cycle. Plants that produce two types of spores are called heterosporous. The male spores are called microspores, because of their smaller size, and develop into the male gametophyte the comparatively larger megaspores develop into the female gametophyte. A few seedless vascular plants and all seed plants are heterosporous, and the sporophyte is the dominant generation.

The spores of seedless plants are surrounded by thick cell walls containing a tough polymer known as sporopollenin . As the name suggests, it is also found in the walls of pollen grains. This complex substance is characterized by long chains of organic molecules related to fatty acids and carotenoids: hence the yellow color of most pollen. Sporopollenin is unusually resistant to chemical and biological degradation. In seed plants, in which pollen is the male gametophyte, the toughness of sporopollenin explains the existence of well-preserved pollen fossils. Sporopollenin was once thought to be an innovation of land plants however, the charophyte Coleochaetes also forms spores that contain sporopollenin.

Gametangia in Seedless Plants

Gametangia (singular, gametangium) are structures observed on multicellular haploid gametophytes. In the gametangia, precursor cells give rise to gametes by mitosis. The male gametangium ( antheridium ) releases sperm. Seedless plants produce sperm equipped with flagella that enable them to swim in a moist environment to the archegonium : the female gametangium. The embryo develops inside the archegonium as the sporophyte. Gametangia are prominent in seedless plants, but are absent or rudimentary in seed plants.

Apical Meristems

Shoots and roots of plants increase in length through rapid cell division in a tissue called the apical meristem, which is a small mitotically active zone of cells found at the shoot tip or root tip (Figure 25.4). The apical meristem is made of undifferentiated cells that continue to proliferate throughout the life of the plant. Meristematic cells give rise to all the specialized tissues of the organism. Elongation of the shoots and roots allows a plant to access additional space and resources: light in the case of the shoot, and water and minerals in the case of roots. A separate meristem, called the lateral meristem, produces cells that increase the diameter of tree trunks.

Additional Land Plant Adaptations

As plants adapted to dry land and became independent from the constant presence of water in damp habitats, new organs and structures made their appearance. Early land plants did not grow more than a few inches off the ground, competing for light on these low mats. By developing a shoot and growing taller, individual plants captured more light. Because air offers substantially less support than water, land plants incorporated more rigid molecules in their stems (and later, tree trunks). In small plants such as single-celled algae, simple diffusion suffices to distribute water and nutrients throughout the organism. However, for plants to evolve larger forms, the evolution of a conductive tissue for the distribution of water and solutes was a prerequisite. The evolution of vascular tissue in plants met both of these needs. The vascular system contains two types of conductive tissue: xylem and phloem. Xylem conducts water and minerals absorbed from the soil up to the shoot, while phloem transports food derived from photosynthesis throughout the entire plant. In xylem, the cells walls are reinforced with lignin, whose tough hydrophobic polymers help prevent the seepage of water across the xylem cell walls. Lignin also adds to the strength of these tissues in supporting the plant. The vascular tissues extend into the root of land plants. The root system evolved to take up water and minerals from the soil, and to anchor the increasingly taller shoot in the soil.

In land plants, a waxy, waterproof cover called a cuticle protects the leaves and stems from desiccation. However, the cuticle also prevents intake of carbon dioxide needed for the synthesis of carbohydrates through photosynthesis. To overcome this, stomata or pores that open and close to regulate traffic of gases and water vapor appeared in plants as they moved away from moist environments into drier habitats.

Water filters ultraviolet-B (UVB) light, which is harmful to all organisms, especially those that must absorb light to survive. This filtering does not occur for land plants. Exposure to damaging radiation presented an additional challenge to land colonization, which was met by the evolution of biosynthetic pathways for the synthesis of protective flavonoids and other pigments that absorb UV wavelengths of light and protect the aerial parts of plants from photodynamic damage.

Plants cannot avoid being eaten by animals. Instead, they synthesize a large range of poisonous secondary metabolites: complex organic molecules such as alkaloids, whose noxious smells and unpleasant taste deter animals. These toxic compounds can also cause severe diseases and even death, thus discouraging predation. Humans have used many of these compounds for centuries as drugs, medications, or spices. In contrast, as plants co-evolved with animals, the development of sweet and nutritious metabolites lured animals into providing valuable assistance in dispersing pollen grains, fruit, or seeds. Plants have been enlisting animals to be their helpers in this way for hundreds of millions of years.

Evolution of Land Plants

No discussion of the evolution of plants on land can be undertaken without a brief review of the timeline of the geological eras. The early era, known as the Paleozoic, is divided into six periods. It starts with the Cambrian period, followed by the Ordovician, Silurian, Devonian, Carboniferous, and Permian. The major event to mark the Ordovician, more than 500 million years ago, was the colonization of land by the ancestors of modern land plants. Fossilized cells, cuticles, and spores of early land plants have been dated as far back as the Ordovician period in the early Paleozoic era. The oldest-known vascular plants have been identified in deposits from the Devonian. One of the richest sources of information is the Rhynie chert, a sedimentary rock deposit found in Rhynie, Scotland (Figure 25.5), where embedded fossils of some of the earliest vascular plants have been identified.

Paleobotanists distinguish between extinct species, as fossils, and extant species, which are still living. The extinct vascular plants most probably lacked true leaves and roots and formed low vegetation mats similar in size to modern-day mosses, although some could reach one meter in height. The later genus Cooksonia, which flourished during the Silurian, has been extensively studied from well-preserved examples. Imprints of Cooksonia show slender branching stems ending in what appear to be sporangia. From the recovered specimens, it is not possible to establish for certain whether Cooksonia possessed vascular tissues. Fossils indicate that by the end of the Devonian period, ferns, horsetails, and seed plants populated the landscape, giving rising to trees and forests. This luxuriant vegetation helped enrich the atmosphere with oxygen, making it easier for air-breathing animals to colonize dry land. Plants also established early symbiotic relationships with fungi, creating mycorrhizae: a relationship in which the fungal network of filaments increases the efficiency of the plant root system, and the plants provide the fungi with byproducts of photosynthesis.

Career Connection

Paleobotanist

How organisms acquired traits that allow them to colonize new environments—and how the contemporary ecosystem is shaped—are fundamental questions of evolution. Paleobotany (the study of extinct plants) addresses these questions through the analysis of fossilized specimens retrieved from field studies, reconstituting the morphology of organisms that disappeared long ago. Paleobotanists trace the evolution of plants by following the modifications in plant morphology: shedding light on the connection between existing plants by identifying common ancestors that display the same traits. This field seeks to find transitional species that bridge gaps in the path to the development of modern organisms. Fossils are formed when organisms are trapped in sediments or environments where their shapes are preserved. Paleobotanists collect fossil specimens in the field and place them in the context of the geological sediments and other fossilized organisms surrounding them. The activity requires great care to preserve the integrity of the delicate fossils and the layers of rock in which they are found.

One of the most exciting recent developments in paleobotany is the use of analytical chemistry and molecular biology to study fossils. Preservation of molecular structures requires an environment free of oxygen, since oxidation and degradation of material through the activity of microorganisms depend on its presence. One example of the use of analytical chemistry and molecular biology is the identification of oleanane, a compound that deters pests. Up to this point, oleanane appeared to be unique to flowering plants however, it has now been recovered from sediments dating from the Permian, much earlier than the current dates given for the appearance of the first flowering plants. Paleobotanists can also study fossil DNA, which can yield a large amount of information, by analyzing and comparing the DNA sequences of extinct plants with those of living and related organisms. Through this analysis, evolutionary relationships can be built for plant lineages.

Some paleobotanists are skeptical of the conclusions drawn from the analysis of molecular fossils. For example, the chemical materials of interest degrade rapidly when exposed to air during their initial isolation, as well as in further manipulations. There is always a high risk of contaminating the specimens with extraneous material, mostly from microorganisms. Nevertheless, as technology is refined, the analysis of DNA from fossilized plants will provide invaluable information on the evolution of plants and their adaptation to an ever-changing environment.

The Major Divisions of Land Plants

The green algae and land plants are grouped together into a subphylum called the Streptophyta, and thus are called Streptophytes. In a further division, land plants are classified into two major groups according to the absence or presence of vascular tissue, as detailed in Figure 25.6. Plants that lack vascular tissue, which is formed of specialized cells for the transport of water and nutrients, are referred to as non-vascular plants . Liverworts, mosses, and hornworts are seedless, non-vascular plants that likely appeared early in land plant evolution. Vascular plants developed a network of cells that conduct water and solutes. The first vascular plants appeared in the late Ordovician (500 to 435 MYA) and were probably similar to lycophytes, which include club mosses (not to be confused with the mosses) and the pterophytes (ferns, horsetails, and whisk ferns). Lycophytes and pterophytes are referred to as seedless vascular plants, because they do not produce seeds. The seed plants, or spermatophytes, form the largest group of all existing plants, and hence dominate the landscape. Seed plants include gymnosperms, most notably conifers, which produce “naked seeds,” and the most successful of all plants, the flowering plants (angiosperms). Angiosperms protect their seeds inside chambers at the center of a flower the walls of the chamber later develop into a fruit.


Abstract

We respond to concerns raised by Baldocchi and Penuelas who question the potential for ecosystems to provide carbon sinks and storage, and conclude that we should focus on decarbonizing our energy systems. While we agree with many of their concerns, we arrive at a different conclusion: we need strong action to advance both clean energy solutions and natural climate solutions (NCS) if we are to stabilize warming well below 2°C. Cost-effective NCS can deliver 11.3 PgCO2e yr -1 or

30% of near-term climate mitigation needs through protection, improved management, and restoration of ecosystems, as we increase overall ambition.

In a recently published opinion piece, Baldocchi and Penuelas ( 2019 ) caution against relying on ecosystems as a major climate mitigation opportunity, counter to our findings (Griscom et al., 2017 ). Interestingly, we agree with many of Baldocchi and Penuelas' concerns, yet we arrive at a different conclusion.

Most fundamentally, we debate the question posed by Baldocchi and Penuelas “if it is more feasible to decarbonize our energy system and reduce carbon emissions, rather than rely on ecosystems [to] take up carbon in a slow, incremental way over current baseline?” This is a false dichotomy. The IPCC ( 2018 ) and most recently Anderson et al. ( 2019 ) conclude that the world needs aggressive actions to reduce fossil fuel emissions and pursue land-based options to stabilize warming well below 2°C. Land-based options include natural climate solutions (NCS) which use ecosystems for removal and storage, and off-site storage using options like bioenergy with carbon capture and storage (BECCS). Baldocchi and Penuelas suggest that political capital and resources are insufficient to effectively pursue both fossil fuel emissions reductions and NCS. We are pleased to note that climate policies are already successfully integrating both in places like California (https://www.arb.ca.gov/cc/pillars/pillars.htm#pillars) and New Zealand (https://www.mfe.govt.nz/node/23439), and NCS is prominent in nationally determined contributions to the Paris Climate Agreement (Grassi et al., 2017 ). More options allow greater overall ambition by reducing total cost to society for any abatement goal, given the wide range of marginal abatement costs of potential carbon sequestration strategies (Aldy, Krupnick, Newell, Parry, & Pizer, 2010 ). Furthermore, ecosystem-based options have been disproportionately underinvested in relative to their cost-effective climate mitigation potential (Buchner, Trabacchi, Mazza, Abramskiehn, & Wang, 2015 ), not to mention co-benefits like water filtration, flood control, and biodiversity habitat. While we agree that ecosystems should not be considered an alternative to decarbonizing the energy system, they are nonetheless essential to addressing climate change.

We agree with Baldocchi and Penuelas that one must account for albedo as well as saturation of ecosystem sinks as we have done (Griscom et al., 2017 ). For example, we excluded reforestation in boreal regions due to albedo. We find that saturation will begin in 20–30 years for two of the 20 NCS we analyzed. Most other options are effective beyond 2,100. In any case, saturation is not a concern during the critical first half of this century when we must balance carbon emissions with removals.

We also agree with Baldocchi and Penuelas’ concerns about the permanence of terrestrial ecosystem carbon storage in the face of climate change. Yet, ignoring opportunities to increase terrestrial sinks through NCS would increase rather than avoid this risk. Achieving cost-effective NCS would provide about 30% of near-term climate mitigation needs—and hence reduce climate risks—while increasing resilience to climate change and adding only 1% to terrestrial carbon storage that is exposed to climate risks (Griscom et al., 2017 ). Baldocchi and Penuelas emphasize small carbon fluxes per m 2 of land. Yet, summed to the globe, gross ecosystem carbon fluxes are an order of magnitude larger than anthropogenic emissions (Denman et al., 2007 ). While ecosystem fluxes are nearly balanced, net terrestrial sinks absorb one-fourth of anthropogenic emissions, and could absorb considerably more with NCS. Terrestrial ecosystems also store four times more carbon than the atmosphere (Le Quere et al., 2018 ). Given the large role ecosystems already play in global carbon fluxes and stocks, the threat of climate change is a further reason to restore resilient ecosystems, rather than a reason to disregard them.

The points raised by Baldocchi and Penuelas about competition for land are also important. They state that “Much land is not available or is unsuitable because it is already dedicated to providing food and fiber for a burgeoning world population.” They report our estimate that “48 M km 2 are needed with a portfolio of reforestation, avoided forest conversion, forest and crop management, and peat restoration (Griscom et al., 2017 )” which they suggest is unrealistic. We agree that this extent is unrealistic, as it is the “maximum with safeguards” extent we report for NCS. The needed NCS mitigation potential is about half of this extent (27.1 M km 2 ) that can cost-effectively deliver about 30% of additional terrestrial mitigation in 2030 (11.3 PgCO2e yr -1 ), assuming less mature carbon storage options like BECCS are not yet available (Field & Mach, 2017 ). Only 9% (2.3 M km 2 ) of this needed extent would displace existing land use, primarily by restoring degraded grazing lands with native forest, productive plantations, and agroforestry. The remaining 24.8 M km 2 involves improving management on working forests and farms while maintaining or increasing long-term food and fiber yields, and a relatively small extent of avoided loss of forests, wetlands, and grasslands (see graphical abstract online, derived from numbers in Griscom et al., 2017 ). Nevertheless, we share Baldocchi and Penuelas’ fundamental concern that the major changes we call for in global land use and management must be done with careful consideration of the consequences for food and fiber, not to mention alignment with renewable energy (Kiesecker & Naugle, 2017 ).

Improving global land stewardship and largely eliminating fossil fuel emissions are both massive undertakings. Nevertheless, both can and must be done in the coming decades to avoid greater costs to society posed by climate change. Done together in smart ways, we can grow our economies and improve our quality of life while stabilizing our climate. Indeed, it is now an imperative of self-interest that we protect and restore life on earth at an unprecedented scale.


3. New Insights and Contributions

As pointed out above, the identification of a certain correspondence between phases in Kuhn’s developmental scheme and stages in the history of evolutionary biology is, in itself, quite trivial. The more pertinent question is whether a Kuhnian analysis of that history is heuristically rewarding. We believe that this is indeed the case: such an analysis particularly provides us with a better insight in the so-called eclipse of Darwinism (3.1), in the still poorly understood genesis of the MS (3.2), and in the relatively turbulent normal science period in the history of evolutionary biology (3.3), including the precise nature of the EES. As we shall see, the extreme multidisciplinarity of the science of evolutionary biology (Welch 2017) left a strong mark on each one of these three Kuhnian phases in its history.

3.1. The Misnomer, Called the Eclipse of Darwinism

We will return to the place (or lack thereof) of Darwin’s On the Origin in Kuhn’s (original) scheme and the implications of our Kuhnian analysis for the historical status of his theory of evolution in section 4.1. (see particularly note 17 ). Here, we want to focus on what followed the publication of this seminal work. Largent portrays the phrase ‘eclipse of Darwinism’ as a deterministic and Whiggish metaphor that has served the purposes of certain biologists and historians, at the “expense of our understanding of the research, conclusions, and worldviews of early twentieth-century American evolutionists” (2009, p. 7). It constructed the MS as an inevitable, discontinuous and “predictable solution to the problem of darkness” (2009, p. 4) that supposedly had plagued evolutionary biology after the publication of Origin (1859). He refers more particularly to Vernon Lyman Kellogg’s book Darwinism To-Day (1907) which has erroneously been interpreted from the perspective of this metaphor but which, in reality, “heralded the primacy of Darwinian natural selection (…)” (2009, p. 15). The eclipse metaphor is a lingering relic that is harmful to our ability accurately to depict twentieth-century evolutionary biology and should be replaced with “a new term and a new conception of the work done in evolutionary biology between 1880 and 1940, one that analyzes early twentieth-century evolutionary biology on its own terms, not merely in the context of what followed” (2009, p. 18).

As we explained previously (Tanghe et al. 2018), the phrase ‘eclipse of Darwinism’ is indeed somewhat Whiggish or anachronistic as we can only describe this episode as an eclipse with the benefit of hindsight. It is in several ways very misleading. Firstly, as pointed out above, Darwinism was never the dominant interpretation of evolution (i.e., a paradigm) secondly, it did never completely ‘disappear’ (there were always Darwinists or ultra-Darwinists) thirdly, the eclipse metaphor ignores the fact that, during the so-called eclipse, Darwinism was one of several competing pre-paradigmatic theories (Junker 2008, p. 496) and, fourthly, Darwinism also didn’t reappear unchanged in the twentieth century, like the sun after a literal eclipse. We shouldn’t overestimate the negative impact this metaphor has had on modern historians, though. In 1983, Bowler (1983, p. ix) already claimed that his thesis that the eclipse represented a crucial phase in the development of modern evolutionism “has become widely accepted.” Still, “pre-paradigmatic phase” seems to us to be a better phrase since Kuhn’s characterization of this period is a more accurate description of what evolutionists did between 1860 and 1947 than what is suggested by the phrase ‘eclipse of Darwinism’ (or by Largent’s alternative term “interphase”): they did sometimes important research but within the context of different and quarrelling, pre-paradigmatic schools of thought.

However, in one important way, the pre-paradigmatic phase in the history of evolutionary biology was unlike pre-paradigmatic phases of other sciences: the multidisciplinarity of this science led to a tentative association between pre-paradigmatic approaches of evolution and specific biological disciplines. They each tended to approach evolution from the specific perspective of their own disciplinary specialty, which, as we shall see, highly complicated the construction of the MS. Some Mendelists, for example, were drawn to de Vries’ mutationism because they studied the transmission of discrete and clearly defined characters, field naturalists were attracted to Lamarckism because it seemed a good explanation for the adaptive patterns they observed in the field, whereas many paleontologists were adherents of orthogenesis because of the linear patterns they discerned in the fossil record. Put differently: the specific interpretation of evolution of each one of these disciplines was distorted or lopsided by their specific, disciplinary perspective.

The so-called “population genetics approach to evolution” (Michod 1981, p. 3) which interprets evolution in terms of changes in the relative frequency of alleles, can, as already indicated, be considered one of these pre-paradigmatic theories or approaches, even though we normally don’t interpret it as such from our modern perspective, since it was this approach of evolution that eventually won the pre-paradigmatic competition. 11

3.2. The Complex Construction of the MS

The question of how the MS was constructed, remains “one of the most vexing problems in the history of biology” (Smocovitis 1996, p. xii Amundson 2005, section 8.3), despite the existence of a veritable ‘Synthesis Industry’ (e.g., Mayr and Provine 1980 Mayr 1982 Smocovitis 1996 Bowler [1989] 2009 Gould 2002). From a Kuhnian perspective, its construction is, like the pre-paradigmatic phase, classic and atypical at the same time.

We already know in what way the genesis of the MS can be called a Kuhnian process: it is based on one of the pre-paradigmatic approaches of evolution (population genetics). However, due to the highly multidisciplinary nature of evolutionary biology, its construction was at the same time also atypical. It is not difficult to understand why: since the victorious evolutionary approach was that of one particular biological discipline, the construction of the MS also had to encompass a synthesis of information from other biological disciplines (hence its name). Theodosius Dobzhansky’s Genetics and the Origin of Species (1937) started this synthesis process and inspired a small number of other biologists from various disciplines (Huxley 1942 Mayr 1942 Simpson 1944 Rensch 1947 Stebbins 1950) to elaborate a more or less coherent interpretation of evolution (i.e., the MS). This heterogeneous set of books in its turn inspired many other biologists and started a neo-Darwinian research tradition. They clearly constitute an example of a Kuhnian “universally recognized scientific achievement” and at the same time also form yet another reflection of the extreme disciplinary heterogeneity of evolutionary biology: Kuhn’s paradigms are, typically, elaborated in single books. 12

3.3. The Turbulent Normal Science Period

This complex, binary construction of the MS (constriction and synthesis) helps to explain why it has turned out to be somewhat schizophrenic in its performance as a paradigm: functional and dysfunctional at the same time.

3.3.1. A Run-of-the-Mill Paradigm

Above, we saw how the MS facilitated the start of a still ongoing phase of normal science. It is in that Kuhnian light that we can understand a mystery, pondered by John Maynard Smith. He wondered why a major characteristic of evolutionary biology since 1960 has been the attempt to develop Darwinian explanations of seemingly anomalous biological phenomena such as sex, ageing, sexual ornamentation, and, “most important of all, cooperation” (Maynard Smith 1994, p. x see also Mayr 2004, p. 139). From a Kuhnian perspective, there is no mystery whatsoever: as long as scientists still discuss the fundamental nature of the natural phenomenon that they study (electricity, light, evolution, …), there does not exist much interest in that kind of esoteric puzzles. It is only once a paradigm emerges that they attract widespread attention or that they become the ‘main business’ of scientists and thus can inspire a crisis and a scientific revolution.

One of the main Kuhnian puzzles in evolutionary biology, next to cooperation, is the existence of sex. In the preface to his Sex and Evolution (1975), George Williams even claimed that the prevalence of sexual reproduction in higher plants and animals is “inconsistent with current evolutionary theory” and that, consequently, there was “a kind of crisis at hand in evolutionary biology” (p. v). With his book, he wanted to propose “minimal modifications of the theory in order to account for the persistence of so seemingly maladaptive a character” (p. v). Sex may have been (and still be) the “queen of problems in evolutionary biology” (Bell 1982, p. 19), but it is (contra Williams) not serious enough to have inspired (or inspire) a true, Kuhnian crisis. Rather, it is an example of the “omnipresent concomitant of normal science” that, as we saw, most anomalies are. The problem is not that it cannot be explained but rather that we are still not certain which evolutionary explanation(s) is (or are) correct (see, e.g., Barton and Charlesworth 1998).

As stated above, a paradigm implies “a new and more rigid definition of the field. Those unwilling or unable to accommodate their work to it must proceed in isolation (…)” (Kuhn 1962, p. 19). Entire schools can thus endure in “increasing isolation from professional schools” (Kuhn 1962, p. 19). Examples of such groups are or were adherents of astrology (once an integral part of astronomy) and of “romantic” chemistry (i.e., alchemy). Something similar happened to traditional or “naïve” group selectionists (i.e., adherents of the idea that prosocial behaviors will automatically spread in populations because they benefit groups), once the first generation of biologists, educated in the new paradigm, started their career. The fathers of population genetics (Ronald Fisher, John B. S. Haldane, and Sewall Wright) had each considered the question of group selection or multilevel selection, but only briefly. Consequently, group selection did not really form an integral part of the original MS. In the wake of its emergence, individual selection even became the norm. As Borrello puts it:

Essentially, the neo-Darwinian paradigm held that all evolution is due to the accumulation of small genetic changes, guided by natural selection. The theory of group selection clearly did not fit within this definition, and the era of peaceful coexistence came to a decisive end. (2005, p. 45)

Likewise, in the preface to the 1996 edition of Adaptation and Natural Selection: A Critique of Some Current Evolutionary Thought ([1966] 1996), Williams refers to “what seemed to be a pervasive inconsistency in the use of the theory of natural selection” (p. ix). Adaptive changes are, in theory, only caused by the selection of individuals. However, in practice, many biologists continuously spoke of group adaptations, which evolved through group selection and required individual organisms to forgo their own interests for the greater good of the group or the species. A lecture by the renowned ecologist and termite specialist A. E. Emerson about beneficial death, the idea that senescence evolved for the benefit of the species, which Williams attended while on a teaching fellowship at the University of Chicago, was the “triggering event” (p. ix). If that was acceptable biology, he rather wanted to become an insurance salesman. In the introduction, he wrote that, with some minor qualifications, “it can be said that there is no escape from the conclusion that natural selection, as portrayed in elementary texts and in most of the technical contributions of population geneticists, can only produce adaptations for the genetic survival of individuals” (pp. 7–8).

Dawkins, who was “greatly influenced” by “Williams’s great book” (Dawkins 1976, p. 11) wanted with his own more popular book The Selfish Gene (1976) to “examine the biology of selfishness and altruism” (p. 1)—i.e., propound recently published ideas about the evolution of social and particularly altruistic behaviors—, and to falsify the “erroneous assumption” (p. 2) behind books like Konrad Lorenz’ On Agression (1966) and Robert Ardrey’s The Social Contract (1970) “that the important thing in evolution is the good of the species (or the group) rather than the good of the individual (or the gene).” The reason why he sounded so “evangelist” in The Selfish Gene, he later explained (Dawkins 1979), is that he wanted to rebut the still popular group selection mechanism by bringing in gene selectionism as an alternative.

3.3.2. Not-So-Normal Normal Science

In some ways, though, evolutionary biology was and/or is an atypical paradigmatic science. For example, its professionalization proceeded surprisingly slowly (Antonovics 1987). 13 Also, the MS was soon challenged by an ever-increasing plethora of alternative evolutionary models (Huneman and Walsh 2017). Or, as Bowler puts it: the founders of the MS, who had hoped that their paradigm would inspire a long period of what Thomas Kuhn called normal science, “were to be disappointed. The diversity of new theories has never matched that of the ‘eclipse of Darwinism’, but it has been possible to articulate divergent perspectives within the narrower frame of reference established by the synthesis” ([1989] 2009, p. 347). Evidently, not all proponents of those ‘divergent perspectives’ would agree with that last claim. Some scholars even believe that the original MS has ceased to exist and that “there is no longer a single, unifying ‘Darwinian evolutionary theory’” (Kutchera 2013, p. 544).

In any case, as we explained elsewhere in more detail (Tanghe et al. 2018), this unusual degree of disagreement among modern evolutionists can, once again, only be explained by the extreme multidisciplinarity of evolutionary biology. It not only, and evidently, sharply increases the chance of disagreements (among practitioners of various evolutionary disciplines) but was, through the complex construction of the MS, also antecedent to four problematic and contentious features of this paradigm. First, since the approach of evolution that became the basis of the MS was that of one evolutionary discipline (population genetics), the MS was inevitably somewhat lopsided (i.e., quite gene-centric). As aforementioned, it even identified evolution with its genetic dimension and, more particularly, with changes in allele frequencies. Dobzhansky (1937, p. 11) put it as follows: “Since evolution is a change in the genetic composition of populations, the mechanisms of evolution constitute problems of population genetics.”

Furthermore, the additional synthesis of data and concepts from a variety of other biological disciplines around this genecentric approach of evolution led to two other problems. That synthesis was not only incomplete—or, as Eldredge (1985) put it, unfinished—but also imperfect. It was incomplete because not all life sciences (fully) participated in the synthesis—some of course only came into being after the establishment of the MS—and it was imperfect because of two related reasons: practitioners of several biological disciplines believed that their field should have made a more substantial contribution to the MS and the MS did not resolve the old, pre-paradigmatic conflict between an organism-focused and a gene-focused approach to the study of (evolving) life (Mayr 1982, pp. 540–50), as soon became painfully clear in the comments of some of its main architects (see, e.g., Mayr 1959, p. 13). Lastly, due to its convoluted construction (a lopsided constriction, followed by a problematic synthesis), the MS is also surprisingly fuzzy, as has often been pointed out: it is a ‘moving target’ and meant and means different things to different people and, particularly, to practitioners of different biological disciplines (see, e.g., Craig 2015, p. 255).

This brings us back to the EES. As we pointed out above, only a minority of its proponents sees it as a potential new paradigm. It can be conceived as an alternative Lakatosian research program but it can also, and maybe more appropriately, be interpreted as a classic, Kuhnian reformulation of the modern, extended MS by more organism-focused biologists. This interpretation is corroborated by Müller’s (2017) remark that the new way of thinking about evolution of the EES is historically rooted in the not-so-new “organicist tradition” (p. 8). The EES is, in any case, at least partly inspired by a strong aversion, among organism-focused biologists, for the baked-in, greedy genecentrism of the MS. This is the theoretical problem that they want to solve through their reformulation.

Laland et al., for example, argue that “important drivers of evolution, ones that cannot be reduced to genes, must be woven into the very fabric of evolutionary theory” (2014, p. 161). Genes are not causally privileged as programs or blueprints, but are rather “parts of the systemic dynamics of interactions that mobilize self-organizing processes in the evolution of development and entire life cycles” (Müller 2017, p. 7). Also, organism-focused biological disciplines like Laland’s ethology or Müller’s developmental biology and the somatic, ecological and epigenetic phenomena that they study, occupy a much more important place in the EES than they do in the MS. The current friction between the MS- and the EES-community can, in this sense, be seen as a continuation or resurgence of the old conflict between an organism-focused and a gene-focused approach to the study of (evolving) life.


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IL1R2 Polymorphisms are Associated with Increased Risk of Esophageal Cancer

Author(s): Jianfeng Liu*, Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi’an 710069, Shaanxi, China Yonghui Yang*, Clinical Laboratory, Xi'an 630 Hospital, Yanliang, Xi’an 710089, Shaanxi, China Haiyue Li, Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi’an 710069, Shaanxi, China Yuanwei Liu, Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi’an 710069, Shaanxi, China Yao Sun, Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi’an 710069, Shaanxi, China Jiamin Wu, Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi’an 710069, Shaanxi, China Zichao Xiong, Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi’an 710069, Shaanxi, China Tianbo Jin Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi’an 710069, Shaanxi, China

Affiliation:

Journal Name: Current Molecular Medicine

Volume 20 , Issue 5 , 2020




Abstract:

Background: Esophageal cancer (EC) is the sixth leading cause of cancer death worldwide, and the overall incidence is increasing.

Objective: The aim of this study was to evaluate the association between single nucleotide polymorphisms in IL1R2 and EC risk in the Chinese population.

Methods: Genotyping of six SNPs of IL1R2 was performed with the Agena MassARRAY platform from 384 EC and 499 controls. The association between polymorphisms and EC risk was assessed by performing genetics models and haplotype analyses.

Results: Overall analysis results showed that the allele C of rs11674595 (odds ratio [OR] = 1.42, 95% confidence interval [CI]: 1.14-1.77, p = 0.002) and allele G of rs2072472 (allele: OR = 1.35, 95% CI: 1.08-1.69, p = 0.008) were associated with an increased EC risk. The rs11674595 and rs2072472 were found to be correlated with EC risk under the codominant, dominant, and additive models. Stratification analysis found that rs11674595 and rs2072472 were associated with increased EC risk in male and in age > 55 years old subgroup. In addition, Crs11674595Grs4851527 haplotype was significantly associated with 1.44-fold increased risk of EC (95% CI: 1.12-1.84, p = 0.004).

Conclusion: Our results reveal the significant association between SNPs (rs11674595 and rs2072472) in the IL1R2 and EC risk in the Chinese Han population. The findings may provide meaningful reference for the prevention and treatment of EC.

Current Molecular Medicine

Title:<i>IL1R2</i> Polymorphisms are Associated with Increased Risk of Esophageal Cancer

VOLUME: 20 ISSUE: 5

Author(s):Jianfeng Liu*, Yonghui Yang*, Haiyue Li, Yuanwei Liu, Yao Sun, Jiamin Wu, Zichao Xiong and Tianbo Jin

Affiliation:Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi’an 710069, Shaanxi, Clinical Laboratory, Xi'an 630 Hospital, Yanliang, Xi’an 710089, Shaanxi, Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi’an 710069, Shaanxi, Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi’an 710069, Shaanxi, Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi’an 710069, Shaanxi, Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi’an 710069, Shaanxi, Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi’an 710069, Shaanxi, Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi’an 710069, Shaanxi

Abstract:Background: Esophageal cancer (EC) is the sixth leading cause of cancer death worldwide, and the overall incidence is increasing.

Objective: The aim of this study was to evaluate the association between single nucleotide polymorphisms in IL1R2 and EC risk in the Chinese population.

Methods: Genotyping of six SNPs of IL1R2 was performed with the Agena MassARRAY platform from 384 EC and 499 controls. The association between polymorphisms and EC risk was assessed by performing genetics models and haplotype analyses.

Results: Overall analysis results showed that the allele C of rs11674595 (odds ratio [OR] = 1.42, 95% confidence interval [CI]: 1.14-1.77, p = 0.002) and allele G of rs2072472 (allele: OR = 1.35, 95% CI: 1.08-1.69, p = 0.008) were associated with an increased EC risk. The rs11674595 and rs2072472 were found to be correlated with EC risk under the codominant, dominant, and additive models. Stratification analysis found that rs11674595 and rs2072472 were associated with increased EC risk in male and in age > 55 years old subgroup. In addition, Crs11674595Grs4851527 haplotype was significantly associated with 1.44-fold increased risk of EC (95% CI: 1.12-1.84, p = 0.004).

Conclusion: Our results reveal the significant association between SNPs (rs11674595 and rs2072472) in the IL1R2 and EC risk in the Chinese Han population. The findings may provide meaningful reference for the prevention and treatment of EC.


Osmosis Lab Example 2

Introduction:
Kinetic energy, a source of energy stored in cells, causes molecules to bump into each other and move in new directions. Diffusion is the result of this contact. Diffusion is the random movement of molecules to an area of lower concentration from an area of higher concentration. Osmosis is a type of diffusion. This is the diffusion of water through a selectively permeable membrane from a region of higher water potential to a region of lower water potential. Water potential is the measure of free energy of water in a solution. A living system also contains an active transport to create movement of particles like ions that move against their concentration gradient. The energy source ATP is used during this process to move the particles across the cell membrane. This experiment takes place to measure the diffusion of small molecules through dialysis tubing. This tubing acts as a selectively permeable membrane, allowing larger molecules to pass through, but slowly. Dialysis is the movement of a solute through a selectively permeable membrane.

When the two solutions on either sides of the membrane are equal and no net movement is detected, the solutions are isotonic. This means that the solutions have the same concentration of solutes. If two solutions differ in the concentration of solutes that each has, the one with more solute is hypertonic. The solution that has less solute is hypotonic.

Water potential is predicting the movement of water into or out of plant cells. It is abbreviated by the Greek letter psi and has two components a physical pressure component, pressure potential, and the effects of solutes, solute potential. Water always moves from an area of high to low water potential. The equation is water potential equals the sum of pressure potential and solute potential.

In a plant cell, turgor pressure is necessary. This is a pressure available to plants in a hypotonic environment. Turgor pressure gives plants their structure and strength. When a plant cell is in an isotonic solution, the turgor pressure decreases, causing wilting in the plant structure. In hypertonic solutions, plants plasma membrane shrinks away from the cell wall, an action termed plasmolysis.

Hypothesis:
Diffusion and osmosis occur between different molar solutions until the solutions are isotonic, effecting the turgor pressure of plant cells.

Materials:
Lab 1A – The materials used in conducting this experiment are as follows: one 30cm strip of dialysis tubing (presoaked), distilled water, 15%glucose/1%starch solution, 250mL beaker, Iodine Potassium Iodide solution, glucose Testape, and string.

Lab 1B – The materials used in conducting this experiment are as follows: six presoaked strips of dialysis tubing, distilled water, 0.2M, 0.4M, 0.6M, 0.8M, and 1.0M solutions of sucrose, six 250mL glass beakers, string, and an electronic balance.

Lab 1C – The materials used in conducting this experiment are as follows: six 250mL glass beakers, a potato, a core borer, a knife, distilled water, , 0.2M, 0.4M, 0.6M, 0.8M, and 1.0M solutions of sucrose, string, a ruler, and an electronic balance.

Lab 1D – The materials used in conducting this experiment are as follows: graph paper, pencil, a ruler, a calculator, and colored pencils.

Lab 1E – The materials used in conducting this experiment are as follows: a light microscope, microscope slide, cover slip, distilled water, NaCl solution, paper, pencil, and onion skin.

Procedure:
Lab 1A: Obtain a 30cm piece of dialysis tubing that has been presoaked in distilled water. Tie off one end securely. Open the other end of the dialysis tube and insert 15mL of 15%glucose/1%starch solution. Tie off the other end of the bag, leaving room for expansion. Record the color of the solution within the bag. Test the 15%glucose/1%starch solution for the presence of glucose using Testape. Fill a 250mL beaker with distilled water and add approximately 4mL of Lugol’s solution (IKI) to the distilled water. Test this solution for the presence of glucose as well with the Testape. Record the results in the data table. Immerse the bag in the beaker of solution. Let this stand for approximately 30min, or until distinct coloration is observed. Record final colors of solutions in the bag and in the beaker. Test both solutions once more for the presence of glucose with the Testape strips.

Lab 1B: Before starting this lab, wash your hands. Obtain six 30cm dialysis strips that have been presoaked in distilled water. Tie off each end securely. Pour approximately 25mL of each sucrose molar solution into its respective bags (that should be labeled, but not on the tubing itself). Tie off the other ends securely with string, careful to get any air bubbles out and leaving room for expansion. Rinse off each bag and blot off the water. Weigh and record the initial mass of the dialysis bags in the data table. Fill six 250mL glass beakers 2/3 full of distilled water and label each beaker with its respective bag’s molarity of sucrose. Immerse each bag into the distilled water. Allow this to stand for thirty minutes. Remove each bag, blot the sides to get off extra solution and weigh and record mass in grams each bag and determine the mass difference and percent change in mass. Next, compare the group percentages to the class.

Lab 1C: Pour 100mL of the assigned sucrose solutions into their 250mL beakers (pre-labeled). Obtain a large potato. Using a core borer, take 24 samples out of the potato, and measure each in centimeters so that they are all equal in length (use the knife to slice off ends). Make sure not to leave any skin with the samples. Place these cores in a covered beaker until an electronic balance can be obtained. Determine the mass of four cores at a time, placing the four in their sucrose solutions. Record this data for each of the six beakers. Allow these potato samples to sit immersed in the solutions overnight, covered. Remove the cores, blot off excess solution, and weigh the samples, recording the mass in the data table. Determine the mass difference, the percent change in mass and the class average percent change in mass. Graph the increase and decrease in mass of the potato cores according to the molarity of the solutions they were placed in on graph 1.2.

Lab 1D: Using paper, a pencil, and a calculator determine the solute potential of the sucrose solution, the pressure potential, and the water potential. Also, obtain graph paper and graph the values given for the zucchini percent change in mass and molarity of sucrose solutions in the graph 1.3.

Lab 1E: Prepare a wet mount slide of onion skin. Observe under a light microscope and sketch what you see. Add a few drops of the NaCl solution, observe, and sketch what you see there as well.

Data:
Table 1.1 The presence of glucose in beaker and bag solutions


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