13. 2017-July-25 Comps Day 3- Svenson

13. 2017-July-25 Comps Day 3- Svenson

I'm afraid I won't be able to post the contents of this part of my exam, at least for now, because my prompt was printed out for me, and I had to write it all out by hand. I made a point of photographing everything, but I have no mind right now to either transcribe or post the photos.

On the bright side, I managed to crush all NINE questions in only five hours. Two more days to go!

 

1.

The “Ascent of Man” image, particularly as depicted here, with an arrow underneath, propagates a misunderstanding of the nature of speciation. The image presents the evolution of an as being a stepwise, directional transition through other distinct extant and extinct species, creating a sense of directional order and progression towards an ultimate state. A phylogeny containing these seven taxa would illustrate that each of these groups are tips of interconnected branches, rather than ungs on an evolutionary ladder. The use of phylogenies illuminate the full breadth of change over time indicating the nodes of common ancestry, and suggesting the far more elaborate branching patterns involved in evolutionary time (cf. genealogical trees).

The original image not only fails to convey the more complex state of the taxa’s relationships/ancestry, but it also suggests that each taxa has emerged from and replaced is predecessor. This carries forward the recurring misconception most effectively presented in the question, “if man evolved from monkeys, why are there still monkeys?” (I recognize that none of the taxa depicted are monkeys!).

Time calibration would in turn allow for an understanding not only of which taxa have closet common ancestry, but would allow for a better grasp of when they split from a common ancestor, allowing for better appreciation not only for the amount of time between the branching at the various nodes, but the fat that evolution continues to occur in all branches past the nodes, regardless of their age, as well as the sheer time scale of evolution within this relatively small sample of taxa.

 

2.

In an evolutionary context, the “purpose”, ore more rather, result of natural selection is the propagation of lineages which have etter (not necessarily best) fitness. “Success” in the evolutionary sense, is the successful propagation of ones’ heritable elements (one’s genome, genes, DNA, as you see fit to think of it). Any and all derived traits from such materials are relevant solely in terms of evolutionary fitness, if they aid in successful production of offspring which in turn are fit.

There is no distinct intent or goal in evolutionary processes beyond this basic selective mechanism (although it is of course modulated by arious of the other forces, eg genetic drift). This is frequently misperceived by the public, who focus more often on the traits responsible in visible examples (larger, smarter, faster, etc.) for fitness than the result itself of whatever trait(s) contribute to fitness, namely successful reproduction.

What seems to e clear is that the public is inundated with a number of popular images (such as the Ascent of Man) such that their perception of a number of common scientific concept have been corrupted by the easily drawn upon abstractions, analogies, and oversimplified explanation that without deliberate corrective efforts, these types of inaccurate visual shorthands will continue to be the primary reference points for people's mental models of evolutionary theory. Studies have shown that while abstracted understanding of problem solving facilitates application to novel contexts, it is also know that without explicitly communicating the precise nature of what metaphor, analogy, or abstraction is meant to convey, people will readily interpret such presentations overly literally, which contributes significantly to misunderstanding even when the information being depicted/explained/transformed is accurate from the perspective of the educator.

While it is tempting to try, knowing that people readily build up and reinforce existing knowledge, to directly tackle misconceptions and the related causative media, doing so an unintentionally keep the focus on the source of such misunderstanding, rather than shift them towards new replacement mental models.

What this means for the context of purpose/success/fitness is that efforts must be taken to not look merely at causative elements of fitness (traits), but also the various ways selection can produce current traits and most importantly the “result” *which reiterates a moving goalpost through time) which is reproductive/evolutionary fitness.

 

3.

Biological systematics serves to identify, classify, categorize, describe, and codify living organisms as they relate to each other; historically, this was primarily driven by overall similarity (phenetics). The phylogenetic system allows us to further expand systematics to examine the evolutionary [common] origins of organisms, as well as try and understand the processes and transitions life has gone through over evolutionary time to reach their current states.

Phylogenetics, understanding and illustrating the relationships between organisms based on common ancestry,  as opposed to sum similarity, allows for a ore expansive and complete understanding of the evolutionary process as it occurred/occurs over time. Evolution in turn serves as the foundation for all of the biological sciences, as this complex of variation, selection, speciation, and innovation is responsible for the complexities of living things at all levels.

However, in part due to the structure and requirements of educational curricula, compounded by religious opposition, evolution is frequently not a central emphasis in biology programs, and often is not taught until late in courses and without connecting it to other material. What seems eminently clear is that considering the important role of evolution in the understanding of biology, that efforts must be taken to completely integrate evolutionary/phylogenetic thinking into all components of biology instruction (particularly at the introductory levels, both at the primary and secondary levels) to provide greater exposure and reinforcement of these foundational principles to allow for a better infrastructure for later biology learning. Currently most biology textbooks begin with molecular, biochemical, and genetics material (usually the entire first semester’s worth), with organismal level content including biodiversity, ecology and conservation, and evolution deferred to later in courses. So, rather than being able to contextualize biology subjects in the frame and scaffolding of evolution, students are required to learn topics in relative isolation, and uch of the intrinsic connections between subjects must be made by the students independently. Again, as seen elsewhere, nonexplicit learning outcomes (such as thematic linkages between materials) rarely are internalized by learners, greatly dulling their effectiveness

Phylogenetic thinking (tree-thinking) must permeate all elements of biological instruction to distinctly/obvious interrelate all biological subjects. More frustratingly, any biology textbooks focus far more heavily on the nonphylogenetic components of systematics, resulting in a fact-memorization-driven learning paradigm which often does not support or even opposes process and concept based understanding.

This is frequently illustrated by a overly hierarchical focus on classical Linnaean taxonomy, and the rote memorization of frequently/rapidly outdated rankings, rather than a framing of the nature of phylogenetic relationships.

 

4.

Yes and no. The classical definition (preDarwin) of evolution was “change over time”, and now that definition is still applicable within evolutionary contexts (of course, it now is more nuanced). IN this way all species are undergoing evolution as they move forward in time, and so any population of organisms is changing (allele frequencies) and evolving, which would in this simple rationale support the idea that there is no such thing as a “primitive lineage”. In any phylogeny, all species have been evolving equal amounts of time from common ancestors, and so their state, now at the tips of branches are the result of incremental “growth” of these branches over evolutionary time.

However, if we examine certain lineages (the so-called “living fossils”), we find that some of these tips are uncannily alike to their ancestors. In this sense, they seem unchanged from their older, ancestral lineage members (they are similar in appearance to their morphologically “primitive” ancestors). It seems that semantically there is a large amount of weight to the term primitive, conveying a sense of archaic, outdated modes of action; when we think of “primitive” man, the most defining features that differ are behavioural complexity. This carries with it certain cultural valuations that older means less complex, and less complex means inferior, none of which is intrinsically true. As such, with living fossils, a seeming lack of change in “complexity” is perceived negatively, even as these species members continue to exhibit fitness. These “primitive” lineages may be morphologically/behaviorally similar to their ancestors, and this may be a result of evolutionary stasis, but it could also reflect far less visible evolutionary change.

Stasis refers to a selective state where variation is selected against, as the current suite of phenotypes exhibits high fitness in contrast to any significant degree of variation. Provided a change in selective pressures, these organisms (at the population level) can still prove to carry ariation allowing for evolutionary change (provided they carry enough genetic diversity and the selective pressure are not too strong/fast), however their current, and historical environments and factors of fitness have remained unchanged.

As such, whether or not an organism is primitive, that is, it has relatively few apomorphies than other related organisms when compared to their common ancestor, is determined moreso by ones comprehension and usage of the term primitive, rather than a qualitative subjective description of the lineage itself.

 

5.

The basic idea of parsimony in phylogenetics is to produce genealogical arguments that minimize ad hoc argument of homoplasy. This is in principle an application of Occam’s razor, namely that the simplest explanation, based on the available facts, is most likely to be true. When the relationship between two of three species can be argued based on shared derived traits as opposed to independent convergence of those traits, the former has a stronger logical basis. This does not imply an assumption that homoplasy is rare or common, but works from the idea that if we are using changes/differences in character states across multiple characters, smaller series of transitions in individual characters are assortments of character carries greater logical weight than a “just so” argument of repeated convergence of gains/losses of novel character states.

This logic becomes slightly less stable at the molecular level, is the clarity of distinct characters (individual base pairs, conceivably is aligned sequences) becomes more nebulous even when the character states are reduced to only four possible combinations for each character. The simplicity in which base pairs, individually and in larger ensembles, can change, reverse, duplicate, transpose and be deleted, makes not only the measure of orthology (sequence similarity) more difficult, but the various processes producing paralogous genes, transposable genetic elements, and whole genome duplications are far more difficult to infer from these genetic data sets. So, while parsimony still plays a role in molecular phylogenetics, analysis of the data is complicated by its reduction to a pseudophenetic means of comparison.

6.

Homology is central to measuring, assessing, testing, and understanding phylogenetic relationships between lineages (shared ancestry). Replication with errors produces minute changes in alleles, which can accumulate in populations over time causing alterations in the gross genetic, cellular, biochemical, and morphological/behavioral nature of a species, and the fact that these processes of descent with modification underlies the entire genealogical nature of evolutionary relationships means that shared traits derived from a common ancestry is a fundamental component of understanding life’s shared origins.

Homology is tested by constructing hypotheses that suppose/presume that distinct characters/character states are derived from like (or dislike) characters or states of another organism (or another location on the same organism in arguments of serial homology). Phylogenetic analysis is then used to test these proposed character relationships in the framework of a larger character matrix, building trees with maximum parsimony that is, trees which which necessitate the fewest changes in character states to explain them. Any of the most parsimonious trees are compared to one another, and nodes which are common among them (or a statistically significant number of them) are resolved. Then with this new tree informing tentative relationships, the character matrix can be reevaluated, modified as needed to reflect improved understanding of character relations or methods of coding particular states, and repeating the process, (reciprocal illumination). In this way, the data and the means in which it is supplied in the analyses can be refined to produce a tree that is as accurate a depiction of relationships between taxa as possible with the existing data.

This is distinct from phenetic methods in that it works on the idea of organisms sharing common ancestry, and using the data to elucidate these interrelationships. Phonetics, in contrast, focuses entirely on gross morphological similarity, creating groups based upon likeness, which can ignore valuable information regarding their evolutionary origins, which can result in interpretations of convergent morphologies as “like” producing polyphyletic groupings which have no value in examining evolutionary relationships.

Without keeping the framing of evolution in biological systematics, it reduces the functionality of the discipline to merely a surface-level descriptive state akin to stamp collecting.

 

7.

The major microevolutionary processes are natural selection, mutation, gene flow,, and genetic drift. These occurring independently and in combination produce the changes in populations that result in changes in species and speciation over time.

Natural selection as a process can be inferred by examining current allele/phenotype distributions in populations, and by observing the nature of the concept of fitness. As genotypes underlay phenotypes, and phenotypes affects fitness, alleles which improve fitness will, providing other processes do not interfere (which they can and do) the population distribution will shift as those carrying fitness-improving genes reproduce more successfully (producing more offspring which in turn are fit) will produce proportionately more offspring in each generation.

Each of the other processes interacts in differing ways with natural selection.

Mutation is the primary source of novel alleles → genotypes → phenotypes → adaptations, and the intrinsic need for a mechanism of change in heritable material/information carries with it the implicit nature of mutation. Without a means for novel genetic information, variation cannot occur for selection to act upon.

Genetic drift is many ways in opposition to selection, randomly affecting populations in manners independent of trait dependent selection. This can be observed by recognizing the reduction of genetic diversity in populations that have been reduced in number, or isolated from a larger pool of genetic variation by other means (bottlenecks). Any population which shows limited genetic variation despite the occurrence of mutations over evolutionary time, or show great diversity in spite of implied isolation (e.g. Hawaii, Galapagos) can imply the occurrence of genetic drift.

Finally as suggested in the mechanism of genetic drift, the ability of separate populations gene pools to interact with others can overcome some of the boundaries impose by local selective pressure; this can allow phenotypes that are only selected for in one population to persist in populations where it may contextually impair fitness, as a member of one population under one set of selection pressure may cross with members of another with its own distinct pressures.

Thus by observing ways in which each of these processes “breaks” the rules of the others one can extract the principles behind each in action.

 

8.

Linnaean taxonomy is highly functional in the scheme of evolutionary history as it provides for consistent continuous naming and labeling of groups even as the precise composition of such groups change. While there remain criticisms of its somewhat arbitrary ranking orders and other outdated modes, it has in recent years greatly developed to embrace the ever-shifting topologies it categories.

The PhyloCode set out in its origins to systematically reorganize the way we would render and describe phylogenetic relationships, with a clear goal to eliminate obsolete naming schemes and remove nonmonophyletic names from use. However, as the PhyloCode developed, it became clear that rather than fixing the perceived flaws in Linnaean systems, they were instead implementing stopgap solutions that produced more rigid typing and an inflexibility to adjust with changes to our understanding of phylogenetic relationships.

In the PhyloCode, species and taxa re delineated with harp distinct borders, which neglects the nature of species as states of change that we observe in individual instances in time. The rigidity of the PhyloCode dictates that a name of a clade is defined by strict guidelines, which is rendered infeasible if new knowledge can reflect change in a taxon’s composition (or a change in our understanding of its composition, rather). This with further research developing new phylogenies of hard-coded groups, the PhyloCode system would assuredly strain and break as its semantic capacity obstinately held to preprescribed rules and definitions.

 

9.

Symplesiomorphies provide information about shared ancestral traits between taxa, but fail to provide truly meaningful information about the nature of their relationships. As ancestral traits can be lost and regained, symplesiomorphies can easily produce paraphyletic groupings as members of a clade are excluded due to an apomorphic change in a character. As phylogenetics aims to organize taxa into monophyletic groups, those containing all organisms that share a common ancestor, utilizing symplesiomorphies, which frequently are essentially phenetic features, can muddle, particularly in non-scientific contexts, the public’s meaningful appreciation of what constitute groups, and why.

The public frequently have difficulty in appreciating the difference between organisms outside of obvious phenetic differences. When shown members of a monophyletic group, non-scientists focus on marked differences and similarities, as opposed to the only truly meaningful characteristic for taxonomic grouping, namely a common ancestor. An emphasis on physical similarity, namely shared ancestral traits/characters, in the descriptions of many groups further emphasizes this misperception about the nature of what it means for organisms to be more or less related to each other. People continue to fail to recognize that similarity in appearance alone is not intrinsically meaningful, let alone the complexity of how homology is tested and established.

The nature of characters, especially in the context of more advanced fields like epigenetics and evo-devo, makes the nature of evolutionary change in ways more complex than the public can readily engage with. While people can readily appreciate the concept of genealogy, they struggle to extend this fundamental tree-thinking to any scale even close to that of the macroevolutionary level. While they can trace a lineage linearly, the intrinsically highly branched long-term stepwise changes underlying both homology and evolution broadly continue to create a constant barrier to nonscientists’ understanding.

14. 2017-July-26 Day 4- Barton

14. 2017-July-26 Day 4- Barton

12. 2017-July-25 Comps Day 2- Mitchell

12. 2017-July-25 Comps Day 2- Mitchell