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8: Novelty - Biology

8: Novelty - Biology


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  • 8.1: What is an Evolutionary Novelty?
    A novelty as a new structure or property of an organism that allows it to perform a new function, thus opening a new "adaptive zone". In this reckoning, a novelty allows an organism to exploit a new ecological resource and should lead to an adaptive radiation.
  • 8.2: Case Study - The Evolution of Insect Wings
    Insect wings are an incredibly important novelty associated with the radiation of the insects into one of the most diverse clades on the planet. They occupy land, water, and air and eat almost every food source imaginable. While their origin seems almost "out of the blue," careful developmental and paleontological studies have revealed key insights into their evolutionary history.
  • 8.E: Novelty Discussion
  • 8.S: Novelty (Summary)

Do novel genes drive morphological novelty? An investigation of the nematosomes in the sea anemone Nematostella vectensis

The evolution of novel genes is thought to be a critical component of morphological innovation but few studies have explicitly examined the contribution of novel genes to the evolution of novel tissues. Nematosomes, the free-floating cellular masses that circulate through the body cavity of the sea anemone Nematostella vectensis, are the defining apomorphy of the genus Nematostella and are a useful model for understanding the evolution of novel tissues. Although many hypotheses have been proposed, the function of nematosomes is unknown. To gain insight into their putative function and to test hypotheses about the role of lineage-specific genes in the evolution of novel structures, we have re-examined the cellular and molecular biology of nematosomes.

Results

Using behavioral assays, we demonstrate that nematosomes are capable of immobilizing live brine shrimp (Artemia salina) by discharging their abundant cnidocytes. Additionally, the ability of nematosomes to engulf fluorescently labeled bacteria (E. coli) reveals the presence of phagocytes in this tissue. Using RNA-Seq, we show that the gene expression profile of nematosomes is distinct from that of the tentacles and the mesenteries (their tissue of origin) and, further, that nematosomes (a Nematostella-specific tissue) are enriched in Nematostella-specific genes.

Conclusions

Despite the small number of cell types they contain, nematosomes are distinct among tissues, both functionally and molecularly. We provide the first evidence that nematosomes comprise part of the innate immune system in N. vectensis, and suggest that this tissue is potentially an important place to look for genes associated with pathogen stress. Finally, we demonstrate that Nematostella-specific genes comprise a significant proportion of the differentially expressed genes in all three of the tissues we examined and may play an important role in novel cell functions.


Introduction

Different concepts reflect different priorities in research programs (Wagner 2014)

The biological concept of “novelty” has various applications depending upon which field is utilizing the term. As Wagner points out, there is nothing inherently wrong with this. The view of what a novelty is varies according to the requirements of each field in order to make the term functional. However, while novelties have long been considered an important and neglected problem in evolutionary theory (Mayr 1960), there is debate on whether they are distinct from continuous, adaptational change (Love 2003 Müller and Newman 2005). Although the existence of structures that are not present in ancestral groups is a biological reality, how these structures originate and how they are accounted for in evolutionary theory is a topic of discussion.

At the center of the issue is the question of whether morphological evolution proceeds purely by the accumulation of quantitative variation, with any changes that are qualitative appear as a consequence of the accumulation of small alterations or whether there are instances of discontinuous change that are mechanistically different from continuous modifications, and cannot be extrapolated from the summation of adaptations. The mechanisms underlying discontinuous changes may also affect the likelihood of trait retention and its spread in a population (West-Eberhard 2003). This relates to a corollary problem on the consequences of morphological novelty origination in phenotypic evolution. If these novelties are a subset of continuous change, their appearance is likely explained by selection on a new function combined with, perhaps, innovation at the genetic level. However, if morphological novelties represent discontinuous events of change resulting from higher level processes, selection cannot be invoked without resorting to circular arguments (Moczek 2008). Instead, novelties would represent unrefined variational additions for selection to act on.

This notion of discontinuity is common in usage of the term across various fields of research and indicates a conceptual distinction from standard variation. Some commentators have played down this importance, arguing that novelty is essentially another term for variation or a subset of variational change (Arthur 2000), whereas other accounts emphasize that novelties represent a distinct class of evolutionary change (Müller and Wagner 1991 Wagner 2014). This article details how novelties are studied in evolutionary developmental biology (EvoDevo), particularly at the level of the phenotype, and how they represent autonomous biological entities. Potential practical applications of the novelty concept and implications that have been sidelined in evolutionary theory are equally addressed. This is crucial for giving significance to the concept, as it is too often weighed down in arguments over definitions. To contrast novelty in EvoDevo with uses from other fields, an introductory description of how the novelty concept is employed by geneticists, population geneticists, morphologists, and behavioral biologists is provided. Though each field has its own terminology, and new traits are not always explicitly stated using the word “novelties,” each of these fields offers a means for dealing with traits that were not present in ancestral species. Although the present study relies predominantly on animal examples, plants show an equally broad distribution of novelties across all taxa. The general implications of the phenotypic novelty concept apply to plants as well.

Often the idea of novelty is treated in papers describing what “novelty” is, or how it is outside the scope of population genetics (Müller and Newman 2005 Pigliucci 2008 Hallgrímsson et al. 2012). While these advances are helpful in their own right, here the concept is taken beyond the descriptive realm or a definitional debate. Practical guidelines and detailed examples are given to show how an EvoDevo-specific approach to novelty can be used in experiments, modeling, databank creation, and more. It is also addressed how this strategy is productive for the advancement of evolutionary theory. Specifically, three themes about researching novel phenotypes in an EvoDevo context are discussed: (1) The generative potential, explanatory power, and predictability of different kinds of novelty generation, (2) The distinction of discontinuous and continuous change of structural traits, (3) The role of novelty generation in evolutionary theory.

These themes indicate how the novelty concept can be used for research in more than a descriptive manner. Crucially, the EvoDevo approach to phenotypic novelty seeks to provide a mechanistic explanation of morphological change. This reinforces recent suggestions that EvoDevo has explanatory power, despite this potential often being attributed solely to (population) genetics (Gilbert et al. 1996 Wagner 2000). These insights are not meant to replace, or modify, the ideas or practices found in other fields. Instead, they relate to events that fall outside of the priorities of other research programs.


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Habituation and Novelty

Introduction

Habituation and novelty paradigms have been used for more than 50 years to study perceptual and mnemonic processes in the human infant. In the first part of this article we provide a brief history and description of the different types of habituation and novelty procedures, critique the major theories and models of infant habituation and novelty preferences, and summarize major developmental trends and debates. In the second part of the article we review more recent advances in our understanding of habituation and novelty preferences using the methods of neuroscience that are now available, and provide a critical review of the debate over what kind of memory supports infant performance in these tasks.


DISCUSSION

In this study, we used a summative assessment to examine students’ ability to apply material learned in an introductory biology course to increasingly novel and more complex situations. In support of our first prediction, students scored highest on questions with familiar content and complexity (category A). As predicted, students scored lowest on questions with higher complexity and novel content (category D), but they also scored equivalently low on questions with higher complexity and familiar content (category C). Our second prediction, that students would be challenged equally by questions of higher complexity and novelty (categories B and C), was not supported. Instead, we found that progressing to a higher complexity reduced student performance to a greater extent than moving to novel subject matter. Student scores on questions were highest when questions contained familiar and low-complexity situations (A) and lowest when questions contained high-complexity situations (C and D), regardless of the novelty of the subject matter.

Variation in student performance based on question category can be partially explained by the familiarity level of exam questions, both in complexity and novelty. Over the course of the semester, via formative assessments and in-class problems, students were exposed to situations that challenged them to apply knowledge laterally in novel contexts and in situations that increased in complexity, but it is possible that this exposure, particularly with respect to complexity, was insufficient to develop proficiency in these skills. With respect to exposure to novelty, students used the scientific method to develop hypotheses and design experiments using different biological topics and organisms in all three course modules. Because the scientific process was a central theme in the course, it is likely that repeated exposure to novel situations in this manner resulted in students struggling to a lesser degree on exam questions in category B (scores reduced by 7.5%) compared with those in categories C and D (scores reduced by 8%). With respect to complexity, students were challenged to apply increasingly sophisticated statistical techniques to data sets and to develop proficiency in writing and interpreting increasingly complicated code in R (R Core Team, 2015). However, it is possible that the emphasis on developing proficiency with increasingly complex situations was too limited, both in scope and time allocation, to develop proficiencies in application of these skills.

While this study was the first to directly test the effects of novelty and complexity in a biology course, reduced student performance on novel and more complex tasks has been reported in linguistics and physical sciences. Novelty has been shown to reduce performance at second language comprehension (Schmidt-Rinehart, 1994), but only in the case of listening (not reading). However, exposure to novel conceptual tasks within a similar level of complexity in an interleaved design has been shown to increase students’ ability to apply knowledge in conceptually related contexts (Rohrer, 2012). Increased complexity has been shown to influence student performance in a simulation-based physics learning environment, but its effect depended on how concepts were represented in simulations (Van der Meij and de Jong, 2006). These contrasting results demonstrate the need for factorial designs such as the one applied in this study that address novel and complex situations compared with a course-based control group (category A in our study).

One surprising outcome of this study was the strong effect of question complexity on student performance. Students did not perform equally on questions for which either novelty or complexity was altered, and scores on assessments were influenced by the complexity level of the question rather than the novelty of the subject matter. At the high-complexity level, scores were equally reduced compared with scores on questions in category A, even when subject matter was familiar. We also discovered that, while complexity of subject matter influenced student scores regardless of novelty, novelty of subject matter only mattered for lower-complexity questions. This suggests students were challenged by increases in complexity across the board but were only differentially challenged by novel situations when questions were simpler. In contrast to these results, in a physics course exam, Van der Meij and de Jong (2006) discovered differences in student scores between treatments (different types of representations of questions) and student perception of differences in difficulty only when question complexity was high. One difference between this study and the present study was that four scaffolded levels were used by Van der Meij and de Jong (2006) compared with two levels used here (e.g., A versus C questions). These contrasting results may therefore relate to the number of scaffolded levels used in the questioning scheme or the familiarity of scaffolded assessments to students in a given course.

Challenges associated with increasingly complex tasks in assessments are likely related to their degree of complexity compared with the degree of complexity in material encountered by students during a course (Catrambone, 1998). Cortright et al. (2005) showed that the relationship between performance on questions and task complexity is negative but nonlinear, and a sharp decline in performance occurs after a threshold of complexity level. Also, the manner in which complex examples are presented and practiced by students may influence student performance on summative assessments. For example, breaking down complex problems into modular units before solving problems has been shown to facilitate successful problem solving for students compared with less structured approaches (Gerjets et al., 2004). Finally, student perception of the complexity of a task can also influence performance on a question. When questions are perceived to be more complex, they are more frequently answered incorrectly than those perceived to be simpler (Lee, 2004). We did not directly assess student perception of difficulty in the questions administered in this study, though combining quantitative and qualitative feedback in future work would give insight into how perceived difficulty influences student scores, as well as what components of questions led students to perceive them as more or less difficult. Further, considering student perception of difficulty level of questions on a numerical scale would provide an additional variable to potentially explain levels of correctness within and between question categories.

One possible explanation for the negative effect of complexity on student scores is that students may require additional learning strategies before they are prepared to accomplish higher-complexity cognitive tasks. In a psychology course, De Koning et al. (2007) found that visual cuing was essential in meeting learning outcomes using animations of high complexity. This suggests that forms of priming, particularly using the same sensory format, may enhance student ability to apply concepts of familiar complexity to higher-complexity tasks. In this study, we investigated two different types of cognitive tasks: those that were incremental (increasing complexity) and those that were lateral (increasing novelty). It is possible that each of these tasks required different learning strategies and course work succeeded more at developing the lateral framework compared with the incremental one.

Several considerations must be taken into account regarding the level of inference that can be drawn from the current study. First, while course material did include novel (more prominently) and more complex (less prominently) situations for students to grapple with, the majority of assessment techniques experienced by students throughout the semester related directly to course material and contained familiar content and complexity levels. For this reason, it is likely that the familiar and lower-complexity questions in category A were most similar to what they had experienced during the course compared with questions in the other categories. The relatively high performance on category A questions was probably partly due to cognitive mechanisms related to repetition and recall (Roediger and Karpicke, 2006).

Second, the question validation method used, including current course TAs, resulted in variable placement of questions into categories. While 74% of TAs correctly placed questions into category A, only 53% correctly placed the questions into category D. The TAs came from different disciplinary backgrounds (e.g., ecology, evolutionary biology, natural resources, entomology), and both undergraduate and graduate TAs were used for this assessment. The variability in general ability to assess questions based on these differences among TAs could have contributed to the apparent challenges in category placement we observed, particularly in the questions that contained higher-complexity and novel situations. We used an anonymous, Scantron-based question validation procedure and did not ask TAs to self-identify as undergraduate or graduate, though this would be an important component of follow-up studies. Nonetheless, while it would be optimal for agreement percentages to be higher, this study was the first of its kind, and we feel these presented data represent a logical baseline to which other courses or assessments can be compared.

In conclusion, this study illustrates how summative assessments are useful tools for direct evaluation of course learning objectives and for evaluating student performance with novel and more complex problems. Using a 2 × 2 factorial question design in which combinations of novelty and complexity were represented, we discovered that the interaction of these two variables explained variability in student scores on a final exam. Specifically, we found that progressing to questions of a higher complexity reduced student performance to a greater extent than moving to questions of novel subject matter. Returning to the research questions posed earlier in the context of the current course (How can we determine whether the goal of application of course content in diverse ways is met in introductory biology courses?, Which elements of application of course content are most challenging for students?), our data indicate that there was better student performance in demonstrating application of course content to novel situations than skills that allow students to progress to incrementally more complex situations. We show here that increasing the complexity of questions poses a significant challenge to students in introductory biology. Students may require additional cues or learning strategies to make incremental cognitive steps with more complex questions, while novel situations may pose a less challenging lateral step. We propose that scaffolded questions that gradually increase in complexity should be integrated into activities in introductory biology courses to enable students to apply learned material to increasingly complex situations they are likely to encounter in their academic careers.

Accessing Materials

All questions used in the study are available in PDF format in the Supplemental Material.


Evolution of novelty

The evolution of novelty can come about by a significant change in the growth trajectory of a body part. In insects, growth is controlled systemically by hormones, primarily ecdysone and for some tissues by insulin-like growth factors as well ( Nijhout and Grunert 2002 Emlen et al. 2006 Nijhout et al. 2007 Shingleton et al. 2007 Nijhout et al. 2014). Growth in a novel location could come about by the novel expression of the ecdysone or insulin receptor in an area where it was not formerly expressed, whereas increased growth in a particular location could be due to an increased expression of receptors for these hormones. This would result in the origin of a new structure (such as a horn in a beetle ( Emlen et al. 2006 Moczek and Rose 2009 Snell-Rood and Moczek 2012), a disproportionate increase in a structure, or, if the spatial pattern of receptor expression is altered, growth in a different shape-altering direction. Such a change in the regional pattern of growth of a body part would result in a change in its shape, and lead to a change in allometry. The exaggerated traits shown in Fig. 1 are examples of changes in form due to localized changes in growth patterns.


In his lectures at Stanford University, the French philosopher Jean-Pierre Dupuy occasionally compares the confusion between ethics and prudence to the mistake of a physics student who would not make the distinction between weight and mass.

However, it is worth mentioning that some synthetic biologists consider the Biobricks program more as a tool to bring students in contact with the field, through the iGEM competition, rather than as a serious program of engineering.

Descartes: “I don’t recognize any difference between artefacts and natural bodies except that artefacts mostly work through mechanisms that are big enough to be easily perceivable by the senses (they have to be, if humans are to be able to manufacture them!)” (Principles of Philosophy, 1644, Sect. 4, § 203).

This underlying valuation has been the target of an artist’s criticism through an extreme-art project. The exhibit Synth-Ethic in Vienna displayed “le cheval en moi” by Marion Laval-Jeautet who has been injected with horse immunoglobulin for several months and gradually developed tolerance to the point of accepting a transfusion of horse blood. She claims that animal is the future of humans.


Genome doubling, cell size and novelty

In the 2019 Coulter Review, "Polyploidy, the Nucleotype, and Novelty: The Impact of Genome Doubling on the Biology of the Cell," published in the International Journal of Plant Sciences (180:1-52), Jeff J. Doyle and Jeremy E. Coate examine the effects of genome doubling on cell biology and the generation of novelty in plants.

Polyploidy, or the presence of more than two chromosomes in a cell, is common across many plant species. This "genome doubling" generates evolutionary novelty and is a prime facilitator of new species. How polyploidy alters cells to generate novelty, however, is complex, and, as Doyle and Coate illustrate, not well understood even on a fundamental level. Rapidly developing technology, however, will enable researchers to shed light not only on this integral part of plant evolution and biology, but also on the function of cells in general.

Many of the documented effects of genome doubling on cells, such as increases in cell size, nuclear volume and cell cycle duration, are hypothesized to be "nucleotypic—effects induced by changes in bulk DNA amount irrespective of genotype. Doyle and Coate update our understanding of the nucleotype and other mechanisms by which genome doubling can alter cell biology, hightlighting insights gained from studies of synthetic autopolyploids and relating these to the current state of knowledge in the field of cell biology.

Cell size in particular was of great interest to the authors, since it is strongly associated with genome doubling. Though it has long been known that genome size and cell size correlate, recent work shows that this correlation is cell type-specific, and the factors that control cell size, polyploidy or otherwise, remain mysterious.

Doyle and Coate write that they had hoped the long running literature of cell biology would hold the answers to how polyploidy operates at the cellular level. "Instead, we discovered that these questions, as well as a host of other issues needed to address the question of what polyploidy "does," have yet to be answered satisfactorily," they write. "In many cases, there are competing theories, and often there exists a dearth of compelling data even in mature model systems, such as human and yeast, or in the best plant models, such as Arabidopsis and maize, let alone in non-model plant species."

The authors go on to suggest that in order to understand polyploidy, as well as cellular function in general, researchers must shift their focus to quantitative data, such as time resolution, rate constants, and local molecule concentrations, when analyzing polyploids against their diploid progenitors.

Doyle and Coate outline questions on polyploidy research going forward. These include how nuclear crowdedness varies with nuclear size across cell types and species, whether protein stability is affected by polyploidy, and whether changes in transcriptome size associated with polyploidy is a response to increased nuclear volume or vice versa.

"The technology exists to address such questions quantitatively, with ever-increasing precision and at ever-decreasing scales down to individual cells and molecules," they write. "We are now poised to address these questions and to understand what polyploidy 'does.'"


Remembering novelty

Imagine going to a café you have never been to. You will remember this new environment, but when you visit it again and again fewer new memories about the environment will be formed, only the things that changed will be really memorable. How this long-term memory are regulated is still not fully understood. Ryuichi Shigemoto from the Institute of Science and Technology Austria (IST Austria) in cooperation with researchers from Aarhus University and the National Institute for Physiological Sciences in Japan now have uncovered a new keystone in the formation of memories. In their study published in Current Biology, they investigated a signaling path in the hippocampus area of the brain and showed how it controls making new memories about experiencing new environments.

The hippocampus is a central area in the brain that plays an important role in transferring information from the short-term memory to the long-term memory. Of the many interlocking parts of the hippocampus, the researchers focused on the connection between the so-called mossy cells that receive novelty signals of sensory input about the environment and the so-called granule cells to which this information is relayed. In diseases like Alzheimer's this part of the brain is one of the first ones affected.

The scientists used four different approaches for this study in order to rigorously investigate these new findings. First, they put the hippocampus under the microscope and studied the structure of how the mossy cells are connected to the granule cells showing their many complex connections.

Second, they used the technique of calcium imaging that allows live monitoring of neuron activity as these genetically modified cells light up when activated. When exposing the animals a new environment for several days, the activity of the mossy cells sending signals to the granule cells first was high and then became less and less. When they then put the mice into another new environment, the activity sprung up again, therefore showing that these neurons are specifically relevant to process new environmental input.

Third, the researchers followed traces in the neuron left by the signals. Neural activity in these cells triggers the expression of a certain gene, meaning the production of the corresponding protein that is encoded in it. The more activity there was, the more of this protein they can find afterwards. In the granule cells they found production of this protein, which correlated with activity of the mossy cells.

And lastly, the scientists used behavioral studies to see the effects of this pathway in the hippocampus on memory formation. This is especially important, because the connection between memory formation and behavior can tell them a lot about the brain's functions. They combined a negative sensory stimulus, a small electric shock, with putting the animals in a new environment. The mice then quickly learned to associate the new environment with unpleasant feelings and their negative reaction of freezing on the spot was measured.

When the researches used drugs to inhibit the activity of the mossy cells--the ones receiving the signals about the new environment--and then did the negative conditioning, the mice did not remember the connection between the new environment and the unpleasant feeling. Additionally, when the animals were first accustomed to the new environment and then conditioned, there was also no activation of the mossy cells, and therefore no association between the environment and the shocks.

On the other hand, if the mossy cells were artificially activated, this association could be formed even after the animals were already used to the new environment. This clearly shows how the mossy cells in the hippocampus react to novel input and trigger the formation of new long-term memories in mice.

Next Steps in Understanding

Whether the exact same processes happen in the human brain is still an open question, but these new findings are an important first step in understanding this part of our most complex organ. Ryuichi Shigemoto and his collaborators are conducting fundamental research that may one day help to address degenerative brain diseases that affect memory formation, but this is still a while away.

He cautiously states: "This research field is very competitive and new findings arise quickly. There are many disputed mechanisms on memory formation, but our findings corroborate an existing hypothesis and are very robust, thus opening up a new field of neuroscience research and furthering our understanding of the brain."

Understanding how the brain stores and processes information is only possible by studying the brains of animals while they carry out specific behaviors. No other methods, such as in vitro or in silico models, can serve as alternatives. The animals were raised, kept and treated according to the strict regulations of Austrian law.

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.


Watch the video: Unit 8 Reaction-Diffusion lecture (July 2022).


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