Federal Period Architecture: Exploring Neoclassical Influences on American Architecture (1785-1830)

 

Federal Period Architecture: Exploring Neoclassical Influences on American Architecture (1785-1830)

The Federal Period (1785-1830) in American architecture was characterized by the influence of Neoclassical design, which originated from ancient Greek and Roman architectural traditions. This article delves into the architectural aesthetic landscape of the Northern and Southern American colonies during this period, highlighting the key architects and design elements that shaped this era.

I. Classical Period and Architecture: Architecture, as an art form, has played a crucial role in shaping the landscape of early American public buildings and private residences. Looking back to the Classical Period, particularly ancient Greece and Rome, provides a deeper understanding of the Neoclassical influences observed in American architecture during the 17th and 18th centuries.

  1. Greece and Rome: The ruins and elements of classical architecture found in Greece and Rome served as the foundation for Neoclassical architecture in America. These ancient civilizations had a profound impact on the architectural style, as they encompassed physical constructions and philosophical symbolism. From roadways to colosseums and temples, these classical elements resonated with the Neoclassical movement in American design.
  2. Neoclassical Influence and Adaptation: The Neoclassical influence in America coincided with the adaptation of classical elements from their origins and their resurgence in foreign countries. Notably, the French architect who worked on Thomas Jefferson’s renowned estate, Monticello, incorporated some of these classical elements. The appeal of classical architecture extended beyond its visual aspects, as it symbolized the imperial and powerful ruling democracies of the Greco-Roman Empires, which resonated with the newly established American democracy.

II. Neo-Classicism: Neoclassicism, a revival of Classical themes and styles, gained prominence not only in America but also in various European countries. America embraced its own version of Neoclassicism, heavily influencing the architectural landscape of both the Northern and Southern colonies until the Romantic and Victorian styles emerged after the Civil War.

  1. Excavations and Discoveries: One significant catalyst for the Neoclassical movement in America was the exploratory excavations that unearthed artifacts of Classical Antiquity. The discoveries made in ancient Roman architectural ruins, such as Herculaneum and Pompeii, shed light on the architectural achievements of Classical societies. These findings fueled the transition to Neoclassicism, with the Adam style acting as a subtractive source of influence for America’s Federal Style.
  2. European Influence: Neoclassicism in America evolved from the broader European movements, particularly the Georgian style from France and England. The Neoclassical Federal Style, with its meaningful representations and appeal to American ideals and values, found its place in the architectural landscape. Public buildings, schools, churches, banks, and wealthy private residences reflected this style, showcasing its prevalence in both the Northern and Southern states.

III. The American Architects of Neoclassical: Federal Style: Several prominent architects played a crucial role in defining the Federal Style during the Neoclassical period. Their contributions significantly shaped the architectural landscape of America, and here are a few noteworthy architects and their achievements:

  1. Asher Benjamin: Considered a pioneering American architect, Asher Benjamin published books featuring Neoclassical designs and architectural sketches. His work influenced other architects and reflected the adamesque British flare of classical revival architectural style.
  2. Charles Bulfinch: Charles Bulfinch, the first American-born architect of the Neoclassical Federal Style, left a lasting impact on the architectural scene. Notably, he designed the rotunda and dome of the US Capitol building.
  1. James Hoban: James Hoban, an American Freemason of Irish origin, designed buildings across various states, leaving an indelible mark on the Neoclassical architecture of the Federal period. One of his most famous works is the White House, the iconic residence of the President of the United States. Hoban’s design for the White House was heavily influenced by classical Greek and Roman architecture, featuring a grand portico with Ionic columns and a central pediment.
  2. Benjamin Latrobe: Benjamin Latrobe, often referred to as the “Father of American Architecture,” made significant contributions to the development of Neoclassical architecture during the Federal period. He was appointed as the Surveyor of Public Buildings in the United States and was responsible for the design of important structures such as the United States Capitol’s south wing. Latrobe’s designs showcased a blend of Neoclassical elements and innovative engineering techniques, incorporating domes, porticos, and intricate detailing.
  3. William Thornton: William Thornton, a British-born architect, played a pivotal role in shaping the Federal period’s architectural landscape. He won the design competition for the United States Capitol building, and his plan served as the foundation for the iconic structure we see today. Thornton’s design incorporated Neoclassical features, including a grand dome and a central portico with Doric columns, reflecting the influences of ancient Roman and Greek architecture.
  4. Robert Mills: Robert Mills, an American architect and engineer, made significant contributions to Neoclassical architecture during the Federal period. His notable works include the Washington Monument, which stands as a towering tribute to America’s first president. Mills’ design for the monument embraced classical influences, featuring a tall obelisk structure reminiscent of ancient Egyptian architecture, topped with a Neoclassical-style statue of George Washington.
  5. Samuel McIntire: Samuel McIntire, a master woodcarver and architect, made significant contributions to the development of Neoclassical architecture in New England. Known for his exceptional craftsmanship, McIntire’s work incorporated intricate detailing and delicate ornamentation, reflecting the elegance and refinement of the Federal Style. His designs included private residences, public buildings, and decorative elements such as mantelpieces and carvings that became synonymous with the Federal period’s architectural aesthetic.

IV. Key Design Elements of Federal Style: The Neoclassical Federal Style of architecture encompassed several key design elements that set it apart from earlier architectural styles:

  1. Symmetry and Balance: Federal-style buildings were characterized by their symmetrical and balanced facades. The use of evenly spaced windows, doors, and ornamentation created a sense of harmony and order.
  2. Classical Motifs and Details: Architects incorporated classical motifs and details, such as columns, pediments, and entablatures, into their designs. These elements were inspired by ancient Greek and Roman architecture and added a sense of grandeur and authority to the buildings.
  3. Porticos and Entryways: Grand porticos with columns, often in the Ionic or Doric order, were a prominent feature of Federal-style buildings. These porticos served as entryways and provided a sense of welcome and importance.
  4. Palladian Windows: Palladian windows, named after the Italian architect Andrea Palladio, were another common feature of Federal-style architecture. These large, arched windows with smaller rectangular windows on either side added elegance and brought in ample natural light.
  5. Rooflines and Cornices: Rooflines in Federal-style buildings were typically low-pitched and often featured decorative cornices. The cornices added a touch of refinement and provided a transition between the walls and the roof.

The Federal period in American architecture, characterized by the prominent influence of Neoclassical design principles, stands as a significant chapter in the nation’s architectural history. During this era, a group of talented American architects, including James Hoban, Benjamin Latrobe, William Thornton, Robert Mills, and Samuel McIntire, emerged as key figures, leaving an indelible mark on the architectural landscape.

The Federal architects drew inspiration from the classical architectural traditions of ancient Greece and Rome, skillfully blending these influences with innovative engineering techniques and a distinct American sensibility. Their designs reflected the ideals of the newly formed nation, emphasizing order, symmetry, and elegance.

One of the most iconic examples of Federal architecture is the White House, designed by James Hoban. Its grand portico with Ionic columns and central pediment became an enduring symbol of presidential power and the nation itself. Benjamin Latrobe, revered as the “Father of American Architecture,” made significant contributions by infusing Neoclassical elements with inventive engineering, exemplified by his work on the United States Capitol.

William Thornton’s design for the Capitol, chosen through a design competition, established the foundation for the monumental structure that stands as a testament to democracy. Thornton’s inclusion of a grand dome and a central portico with Doric columns pays homage to the architectural heritage of ancient Greece and Rome.

Robert Mills contributed to the Federal period with his design of the Washington Monument, a soaring obelisk adorned with a Neoclassical-style statue of George Washington. Mills’ incorporation of classical influences and his masterful execution elevated the monument into a timeless symbol of the nation’s first president and the ideals he represented.

In New England, Samuel McIntire showcased his exceptional craftsmanship and artistry by blending intricate detailing and delicate ornamentation into the Federal architectural style. His work adorned private residences, public buildings, and decorative elements, embodying the refined elegance characteristic of the period.

Key design elements of Federal architecture included symmetrical and balanced facades, the incorporation of classical motifs and details such as columns and pediments, grand porticos with Ionic or Doric columns, the use of Palladian windows to bring in natural light, and the addition of decorative cornices to enhance the rooflines. These design elements created an architectural language that exuded a sense of harmony, authority, and refined aesthetics.

The enduring legacy of the Federal period in American architecture is seen in the many buildings and structures that still grace the nation’s cities and towns today. Its influence extended beyond the Federal era, laying the foundation for subsequent architectural styles and shaping the development of American architectural identity.

In conclusion, the American architects of the Neoclassical Federal Style made significant contributions to the architectural landscape, producing buildings of timeless beauty and embodying the ideals and aspirations of a young nation. Their designs, marked by symmetry, classical motifs, and refined detailing, continue to inspire and captivate, ensuring the enduring relevance of the Federal period in American architectural history.


Resources:

Kozlowski, M. (Photographer). Monticello [Photograph]. Retrieved from [insert URL]

Classical Period and Architecture:

Ancient Greece. (n.d.). Temple of Athena Nike. Ancient Greece: Architecture. Retrieved from http://ancient-greece.org/architecture/athena-nike.html

The American Architects of Neoclassical: Federal Style:

Monticello. (n.d.). Retrieved from http://www.monticello.org/

Palladian Style. (n.d.). Retrieved from http://www.boglewood.com/palladio/analysis.html

Virginia State Capital. (n.d.). The Library of Congress. Retrieved from [https://www.loc.gov/item/2018666788/]

The History of Mathematics: Coordinate Geometry vs. Non-Euclidean Geometry

Coordinate Geometry vs. Non-Euclidean Geometry

Coordinate Geometry:

During the time that Descartes (1596-1650) and Fermat (1601-1665) were developing their Mathematical Theories there were many Political and Cultural events occurring in Europe and the Americas. A great portion of Descartes life was lived out during the 17th Century AD (1601-1700) as well as Fermat’s, who was born at the turn of the century.

A movement referred to as the Baroque period in Europe began to dominate the cultural byproducts of Artistic endeavors. Partial to the movement were the wealthy class known as aristocrats that enjoyed the opulence and extravagance of Baroque values. The Baroque style and value not only could be found in Western painting but in the dramatic Arts, Literature, Philosophy, Sculpture, Clothing, Furniture, Architecture and Music as well. Patterns were reflected in Baroque styling.

In 1661, Louis XIV (1638 – 1715) assumed the throne of the French Monarchy as King of France, even though he had ascended the thrown at the age of 4. He was culturally known as an egocentric King, arrogantly relating himself to the likenesses of mythological gods. Under his political rule, Feudalism was disregarded and central government established. France was a power force amongst other European Countries at the time.

The Franco-Dutch War, and the War of the Spanish Secession found France at the forefront.

The Scientific Revolution was spurring much scientific investigation- discovery and/or invention- throughout the Western world. At first this predominantly influenced European Cultures prior to spreading to the Americas. It encompasses that of great cultural advancement as science had become an enriching, empowering and notable force. Each progression marked a step toward modern science as we know it. Galileo Galilei left his mark on culture during this time, with his accomplishments in Astronomy and the physicist, mathematician, astronomer, alchemist, and philosopher Sir Isaac lived during this time.

In 1642-1649 a Civil War breaks out in England.

In the Americas, the pilgrims arrive on the Mayflower ship, at Plymouth Rock in 1620. Soon after many English settlers began to colonize the America. In 1622, the Jamestown Massacre was marked by eastern native Americans killing hundreds of English that lived in the colony of Jamestown. A great cultural achievement in the Americas during the 17th century was the founding Harvard University.

Non-Euclidean Geometry:

During the 16th, 17th, 18th, and 19th centuries there were many developments that played a role in the “Scientific Revolution.”

Riemann – German 1826-1866

Germany as a Holy Roman Empire

Immigration by Germans to the United States of America occurred during this time period and the Scientific Revolution was continued in the United States during this time by people such as Thomas Jefferson.

Industrial Revolution

1866 Austro-Prussian War: Prussia overcomes leader Otto Van Bismark

Lobachevsky – Russian 1792-1856

Russia in the 1800’s was under the rule of a Czar (similar to a King). Post social and political Revolution was a time when the Russian people remained oppressed which lead to civil war and eventually influenced the future development of the Soviet Union and communist control.

Workers guilds against post-industrial revolutions factory building

Bolyai – Hungarian 1802-1860

Hungary in the 19th century saw social changes in population class status’ and the nationality of hungarian nationals evolving with the population expansion that peaked in the 1800’s. The Upper class “Magnates” held positions of great power and influence over social political movement. They did not like the idea of the modernization because of its tie to population growth in the more diverse and lower class systems. The Industrial Revolution and modernization caused the hungarian magnates to reach out to Vienna, the Austrian capital for an alliance in bringing about post-modernization social and political structuring dynamics.

Marine Biology: Morphological Change in Model Organisms- Student Blogger Example

Sample Article Review of Scientific Literature for Student Contributors to our Blog: Thoughts on Newton Blvd

Assignments for College Preparatory Science Students
by Academic Tutors 101

Subject: Marine Biology: Morphological Change in Model Organisms (Coral)

Citation: Todd, P.A. et al. An aquarium experiment for identifying the physical factors inducing morphological change in two massive scleractinian corals. Journal of Experimental Marine Biology and Ecology. 299 (2004): 97-113.

Source: This article was obtained through the Science Direct database at the www.esc.edu/library. (Note: Use “Export Citation” with the “ASCII” option to obtain the URL, then add “http://library.esc.edu/login?url=” in front of the “http” address. This will give you a stable link to the article.)

Note: You must supply the full and correct citation and whenever possible, a copy of a hotlink to the article itself. Your readers and students will want to read the actual article along with your review.

Summation: Prior research has shown that some species of coral are phenotypically plastic, but no controlled experiments had yet been done in a laboratory setting to try to determine the role of different environmental factors in facilitating morphological change. Researchers collected fragments of coral from different species of coral and grew them in different aquaria designed to represent varied light intensity, sedimentation rates and water current strengths. The corals were analyzed for morphological changes after 4 months of controlled growing experiments. They concluded that the most consistent morphological change seemed to be in response to light intensity.

Original source: Scientists from Scotland, Singapore, and Japan carried out this research at the Raffles Marina Research Station off the coast of Singapore.

What was studied: Fragments of different coral species were sampled during controlled laboratory experiments designed to distinguish phenotypic changes due to one or several environmental factors. Since the fragments were from the same coral colony, they were genetic clones of each other and therefore had the same genotype. Change in response to an environmental factor could then be known to be due to a change in phenotype. This is the coral equivalent of twin studies in Biology and psychology.

How the study was conducted: The control aspect in this study was attempted by leaving clonal fragments under natural conditions so as to have a comparison of any natural change in morphology over time. Many of these fragments were lost at sea and this highlights a difficult problem that often occurs in Marine Biology field studies!

What was concluded: They concluded that the most consistent change in morphology was the result of light intensity.

New questions: Corals seem to be very affected by environmental stresses. The paper mentions concerns about increased sedimentation and about climate change caused by global warming effects. It would be interesting to include water temperature as an environmental feature studied in the aquaria.

My opinion: After 4 months, the aquarium pump broke down and the study was prematurely ended. It is interesting to see that as long as a study is well-designed, something positive can be learned from it even when it doesn’t go as planned. In this case, the scientists learned more about the practical aspects of running the study, but also arrived at the conclusion to focus on light as a prime mover of phenotypic response.

This paper also highlights how little is known about coral biology, the roles, triggers, and biology of phenotypic plasticity in coral. There is also not much known yet about the ecology of phenotypic plasticity. This paper mentions that corals that are plastic are thought to be generalists. However, the cost and benefits of this trait are not yet clear in terms of evolutionary success and role in the community.

Glossary
*Be sure to use the college resources when building your glossary.

Genotype: Genotype refers to the genetic make-up of individuals and organisms. See Genetics.
This is a very important word in this article. Because the coral fragments were genotypically the same, the researchers were able to reason that any differences they saw in the individuals were a phenotypic adaptation to the environmental conditions.

Phenotypically plastic: Plastic means adaptable or malleable. See the Merriam-Webster dictionary. This concept is very important for understanding this study. With the same genotype, organisms showed different phenotypes under different environmental conditions. A phenotype refers to the physical result of a certain genotype. See Genetics.

How to Start Applying to College in New York State in 5 simple steps!

How to Start Applying to College in New York State in 5 simple steps!

REMINDER...

Take note of all submission deadlines for the academic year in which you wish to apply to College, on ALL forms. Some SUNY School’s have separate application deadlines.

1. Submitting your Application

You have some options, the Common Application or The SUNY Application? Which is best for you? Do you want to go to College in a State other then New York? If so, you will follow some different steps then those outlined here. Also, see the CUNY Application.

The Common Application

The SUNY Application

The CUNY Application

2. Qualifying for Financial Aid

To qualify for financial aid at the institution(s) of choice, you must complete and submit the free application for Federal Student Aid (FAFSA)

Note, you can and should list multiple Colleges and Universities even if you are waiting on some admission letters at the time of your FAFSA submission.

After submitting your FAFSA, you will be redirected to the Higher Education Services Corporation to file a separate application for NYS based financial aid programs like the new Excelsior Scholarship.

Types of Financial Aid

3. The Admissions Essay
You should search for Tips on How to Write your Admissions essay on the websites of the colleges and universities that you are applying to. You should consider what they are looking for and if you should apply using the SUNY Common App you will want to be inclusive of the criteria set forth by the institution(s) you are interested in as you respond primarily to the Common Application Essay Prompt of your choice.

2017-2018 Essay Prompts

4. Follow up with and check your Financial aid status about a month after submitting your FAFSA application. Make sure that there are no additional documents required by FAFSA and/or by the colleges you have applied to that will be receiving your financial aid information. (I.e., tax returns)

5. Await your acceptance letters!

Deadlines:
FAFSA

The Common Application

The SUNY Application (Pg. 4)

The CUNY Application

HESC Applications (SUNY & CUNY)

Evolution and Disease: Exploring the effects of Pathogenesis as a factor driving Natural Selection

Author: Lauren Feist

Affiliation: SUNY Stony Brook University

Publication Year: 2023 (Revised edition)

Title: Pathogens, Evolution, and the Role of Viral Pathogens: Insights into Genetic Variation, Disease Processes, and Evolutionary Change

Abstract:

Pathogens, including viruses, play a significant role in shaping genetic composition and driving evolutionary processes within populations. Through various mechanisms, pathogens introduce genetic mutations into host genomes, leading to new genomic and epigenetic effects. These mutations can contribute to natural selection by conferring advantages or disadvantages in survival and reproduction. The study of pathogenesis and evolution requires collaboration among different scientific disciplines, such as genetics, virology, biology, and chemistry.

By analyzing the genomic composition of infective agents, researchers gain insights into the relationships between pathogens and hosts, as well as the impact of these interactions on evolutionary change. Understanding how pathogens influence genetic variation, frequencies, and mutations provides valuable information about disease processes and the conservation of specific traits. The field of proteogenomics, which combines proteomics and genomics, allows for the exploration of protein structure, function, and expression in relation to genetic variations.

Sequencing entire genomes has revolutionized genetics, providing valuable insights into gene structure and function. Proteomic techniques and the study of post-translational modifications offer new avenues to explore the functions of proteins and their interactions with the genome and epigenome. Mapping protein form and function contributes to a better understanding of disease processes and the development of disease prevention and treatment strategies.
The evolution of pathogens, including antibiotic and disease resistance, is an important area of study within evolutionary development. Pathogens exert selection pressures on populations, leading to the survival and reproduction of resistant variants. Understanding the mechanisms and implications of antibiotic resistance is crucial for developing effective strategies to combat evolving pathogens.

The Borna virus serves as an illustrative example of an endogenous non-retroviral RNA virus. It replicates within human hosts, infiltrating the cell nucleus and transmitting through germ cells. The viral information is distributed within the genomic structure of subsequent generations, influencing gene expression through various mechanisms. The integration of viral genetic material into the host genome raises questions about its potential epigenetic effects and its role in human behavior and mental illnesses.

Further exploration of the human genome and mammal genomes reveals a greater viral component than previously recognized, indicating the existence of fossil viruses with implications for disease understanding and treatment. Viral pathogens, as non-living vectors, uniquely influence their own evolutionary trajectory by invading host organisms. The study of viral pathogens expands our understanding of evolutionary change and selection in living organisms.
Viral evolution can occur within host cells as well as through transmission between different host species, emphasizing the importance of tracking and projecting the evolution of pathogens for effective interventions. Integrating knowledge of viral integration, tumorigenesis, and core transcriptional features associated with neoplastic transformations provides insights into selection pressures, mutagenic changes, and mortalities in global populations. Understanding these mechanisms is crucial for the development of efficient disease management and prevention strategies.

The study of pathogenic populations and their role in evolution provides valuable insights into disease processes, genetic variation, and natural selection. By exploring genomic composition, mutations, and protein functions, researchers unravel the complex relationship between pathogens, hosts, and evolutionary change. This interdisciplinary field of research enhances our understanding of disease prevention, treatment strategies, and the broader implications of evolution in medical sciences.

Overall, this interdisciplinary research field, ( “Evo-Devo Pathogenetics”) contributes to our understanding of disease processes, genetic variation, and natural selection. The exploration of pathogenic populations and their role in evolution has far-reaching implications for disease prevention, treatment strategies, and the broader understanding of evolution in the medical sciences.

Keywords: pathogenesis, evolution, genes, pathogens, genetic variation, proteogenomics, antibiotic resistance.


Here is an expanded section with additional information and a chart highlighting the genes that are potentially involved in the processes described:

Pathogens, including viruses, play a significant role in shaping the genetic composition of populations and driving evolutionary processes. They introduce genetic mutations through various mechanisms, such as integrating their genetic material into the host genome, leading to new genomic and epigenetic effects. These mutations can contribute to natural selection by conferring advantages or disadvantages in survival and reproduction.

The study of pathogenesis and evolution requires collaboration among different scientific disciplines, including genetics, virology, biology, and chemistry. By analyzing the genomic composition of infective agents, researchers can gain insights into the relationships between pathogens and their hosts, as well as the impact of these interactions on evolutionary change. Understanding how pathogens influence genetic variation, frequencies, and mutations provides valuable information about disease processes and the conservation of specific traits.

Mutations, which can arise spontaneously or be caused by mutagenic factors, are essential for evolution by natural selection. They contribute to the diversity and polymorphic variances within populations and can be inherited through reproduction. Studying mutations and their effects on gene function and protein production deepens our understanding of the genetic basis of diseases and complex traits. The field of proteogenomics, which combines proteomics and genomics, allows for the exploration of protein structure, function, and expression in relation to genetic variations.

Sequencing entire genomes has been a groundbreaking advancement in genetics, providing insights into the structure and function of genes. Proteomic techniques and the study of post-translational modifications offer new avenues to explore the functions of proteins and their interactions with the genome and epigenome. By mapping the form and function of proteins, researchers can gain a better understanding of disease processes and potentially develop strategies for disease prevention and treatment.

The evolution of pathogens, including antibiotic and disease resistance, is an important area of study within the context of evolutionary development. Pathogens exert selection pressures on populations, leading to the survival and reproduction of resistant variants. Understanding the mechanisms and implications of antibiotic resistance is crucial for developing effective strategies to combat evolving pathogens.

The study of pathogenic populations and their role in evolution provides valuable insights into disease processes, genetic variation, and natural selection. By exploring the genomic composition, mutations, and protein functions, researchers can unravel the complex relationship between pathogens, hosts, and evolutionary change. This interdisciplinary field of research has the potential to enhance our understanding of disease prevention, treatment strategies, and the broader implications of evolution in the medical sciences.

Now, let’s chart some of the genes that are potentially involved in these processes:

Gene Name Function
p53 Tumor suppressor gene, regulates cell cycle and apoptosis
E6 Oncogenic protein of Human Papillomavirus
E7 Oncogenic protein of Human Papillomavirus
LINE Long Interspersed Repetitive Elements
URR Upstream Regulatory Region of HPV
H1N1 Influenza virus strain
HIV Human Immunodeficiency Virus
Various oncogenes and tumor suppressor genes Involved in neoplastic transformation and progression

Please note that this is not an exhaustive list, and there are numerous other genes and genetic elements that play significant roles in pathogenesis, evolution, and disease processes. The specific genes involved can vary depending on the pathogen and the host species under study.

 



Pathogens, including viruses, play a significant role in shaping the genetic composition of populations and driving evolutionary processes. Pathogens can introduce genetic mutations through various mechanisms, such as integrating their genetic material into the host genome, leading to new genomic and epigenetic effects. These mutations, in turn, can contribute to natural selection by conferring advantages or disadvantages in survival and reproduction.
The study of pathogenesis and evolution requires collaboration among different scientific disciplines, including genetics, virology, biology, and chemistry. By analyzing the genomic composition of infective agents, researchers can gain insights into the relationships between pathogens and their hosts, as well as the impact of these interactions on evolutionary change. Understanding how pathogens influence genetic variation, frequencies, and mutations can provide valuable information about disease processes and the conservation of specific traits.

Mutations, which can arise spontaneously or be caused by mutagenic factors, are essential for evolution by natural selection. Mutations can be inherited through reproduction, and they contribute to the diversity and polymorphic variances within populations. By studying mutations and their effects on gene function and protein production, researchers can gain a deeper understanding of the genetic basis of diseases and complex traits. The field of proteogenomics, which combines proteomics and genomics, allows for the exploration of protein structure, function, and expression in relation to genetic variations.

Sequencing entire genomes has been a groundbreaking advancement in genetics and has provided valuable insights into the structure and function of genes. The ongoing development of proteomic techniques and the study of post-translational modifications offer new avenues to explore the functions of proteins and their interactions with the genome and epigenome. By mapping the form and function of proteins, researchers can gain a better understanding of disease processes and potentially develop strategies for disease prevention and treatment.

The evolution of pathogens, including antibiotic and disease resistance, is an important area of study within the context of evolutionary development. Pathogens can exert selection pressures on populations, leading to the survival and reproduction of resistant variants. This phenomenon can be likened to predators and prey, where antibiotics act as the predator, killing some bacteria while allowing resistant variants to survive and proliferate. Understanding the mechanisms and implications of antibiotic resistance is crucial for developing effective strategies to combat evolving pathogens.

The study of pathogenic populations and their role in evolution provides valuable insights into disease processes, genetic variation, and natural selection. By exploring the genomic composition, mutations, and protein functions, researchers can unravel the complex relationship between pathogens, hosts, and evolutionary change. This interdisciplinary field of research has the potential to enhance our understanding of disease prevention, treatment strategies, and the broader implications of evolution in the medical sciences.

The Borna virus serves as an illustrative example of an endogenous non-retroviral RNA virus. Endogenous viruses originate within the tissues, organisms, or cells themselves and can impact the genetic makeup and functioning of the host. Empirical evidence suggests that the Borna virus is capable of replicating within human hosts by infiltrating the cell nucleus and subsequently transmitting through germ cells such as spermatozoa and oocytes. During gametogenesis, when germ cells from progenitor species merge, the viral information is often distributed within the genomic structure, specifically the chromosomes, of subsequent generations. The offspring’s genome becomes influenced by the provirus, which is the latent or concealed derivative of the Borna virus that has successfully integrated into the genomic structure. This integration occurs in regions where reverse transcriptase activity takes place or is encoded in Long Interspersed Repetitive Elements (LINE) or Long Interspersed Nuclear Elements (LINE).

It is plausible to speculate that this process could potentially trigger an epigenetic effect within certain loci of gene expression, leading to various outcomes such as epigenetic silencing, linkage, epistasis, null effects, or deletion mutations. In addition to these conjectures, the Borna virus has been identified as “replacing” the function of reverse transcriptase activity along LINE-1, where DNA copies of RNA are synthesized and inserted into the genome. Over generations, the viral DNA undergoes mutations, eventually losing its ability to mutate and becoming disabled.

Considering the aforementioned, one might question whether these viral remnants act as mediators of susceptibility to other viruses through overlapping protein sequences in a domain. In fact, an inverse relationship of this nature appears conceivable when examining the research of Dr. Keizo Tomonaga, a virologist at Osaka University, who fortuitously discovered that four segments of human DNA share clear ancestry with the Borna virus. Dr. Tomonaga’s theory proposes that the Borna virus did not invade mammalian genomes but rather that the genomes “kidnapped” the viruses, suggesting a synergistic relationship between human and viral genes. He suggests that LINEs, which have the ability to create copies of themselves, captured genes from the Borna virus and reintegrated them back into the genome. If this hypothesis holds true, it is possible that LINEs have also acquired genes from other viruses and utilized genetic material from those viruses in advantageous ways.

In his article “Hunting Fossil Viruses in Human DNA” (2010), Carl Zimmer mentions that the neurotropic Borna virus is just one of many viruses that infect mammals and birds. It is worth noting that birds, insects, and humans share a unique relationship, as vectors like mosquitoes are known to transmit viruses across species boundaries. Consequently, the presence of the Borna virus in various species is not surprising. Zimmer further explains that some species infected with this virus exhibit no symptoms, thereby rendering the effects of the infectious agent largely enigmatic, with specific exceptions. For instance, horses have been observed to display behavioral effects, such as wild fits that may lead to self-inflicted fatal injuries or starvation. Researchers have postulated a correlation between the Borna virus and human behaviors indicative of disorders such as schizophrenia. However, when considering the recent identification of protozoa affecting human behaviors and their role as pathogens or parasites underlying disorders like schizophrenia, we may gain further insight into the influence of pathogenesis on behaviors. The idea that pathogenesis can contribute to mental illness or influence behavior remains a topic of controversy, analogous to the initial debates surrounding the proposition of humans descending from primates. Anticipating a potential controversy over the notion that humans have limited control over their behaviors, the identification of pathogens responsible for behavioral influences could pave the way for targeted interventions and potentially lead to cures for various mental illnesses.
An alarming hypothesis, should it be considered conclusive, suggests that around 40 million years ago, the Borna virus infected our primate-like ancestors. Viruses are estimated to be present in approximately 8% of the genome in every individual on Earth, primarily in the form of endogenous non-retroviral RNA virus elements in mammalian genomes. To put this percentage into perspective, it is seven times greater than the DNA content of all the 20,000 protein-coding genes in the human genome. The completion of the human genome sequencing in 2001 revealed that several segments of human genes bear resemblance to retroviral genes. While scientists have identified connections between approximately 100,000 viral elements, mostly originating from retroviral infections, imprinted within the human genome, the discovery of the Borna virus as a component of the human genome represents a novel finding. This suggests that many other viruses may still await discovery within the human genome. Consider the implications of unraveling the form and function associated with these viruses—what other insights could be gained about known or unidentified diseases and their potential treatments?

The Borna virus is not the sole instance of fossil viruses revealed through gene mapping and referencing databases containing human genome sequences. Researchers are expanding their scope beyond the human genome and capitalizing on the growing number of mammal genomes available in online databases to elucidate the evolutionary history of viruses dating back millions of years. Collectively, these investigations provide compelling evidence that humans and other species have a greater viral component than previously recognized.
Of all the various pathogens I will discuss, viral pathogens, or “pathogenes” as I prefer to refer to them, hold particular significance. Unlike other pathogenic agents such as prokaryotes, archaea, and protozoa, viruses are technical, non-living vectors. Viruses uniquely possess genetic material that is not alive per se, requiring invasion of host organisms for survival and replication, thereby influencing their own evolutionary trajectory. The optimal conditions for viral evolution often arise when the host organism is not exploited to the point of death, ensuring the virus’s survival and reproduction in greater numbers. This concept theoretically applies to viruses, as it serves as the foundation for evolution through natural selection in living organisms. However, it is also plausible that certain viral pathogens may evolve by exploiting a host to the point of fatality while concurrently being transmitted to another host, facilitating evolutionary changes in both the host and viral populations. Viruses may evolve as they multiply within cells and reproduce. Is there a limited advantage, yet an advantage nonetheless, for viral pathogens gained by integrating into the host genome either during active infection or afterward as proviruses that are inherited by subsequent generations, thereby preventing their complete obsolescence? In my view, the answer is likely affirmative. This driving force of evolution is not limited to humans and animals but may extend to interactions between prokaryotes, archaea, and protozoa—what I term the “pathogen-to-pathogen route.” For example, eubacteria may be exploited by a viral population, presenting a symbiotic advantage in both populations. When examining the relationships between eukaryotes, prokaryotes, and archaea, we should explore a pathogenic phylogeny encompassing all domains and subsequent taxonomies.
Oncoviruses, which promote tumorigenesis in humans and animals, represent another extensively researched topic that expands our understanding of how viral pathogens can drive evolutionary change or at least fulfill the criteria necessary for selection to occur.

Interfering with the action of p53 allows a virus-infected cell to progress into a different stage of the cell cycle, promoting replication of the virus genome. Forcing the cell into the S phase of the cell cycle can potentially lead to cellular transformation (Scheffner et al., 1990).

According to a study conducted by the National Cancer Institute, HPV 16 is the most common type, accounting for 61% of cervical cancers, followed by HPV 18 at 9%. Types 33, 45, 58, and 59 were each found in one specimen. Analysis of the genomic sequences of HPV 16-positive isolates revealed distinct patterns of stability and variability in the upstream regulatory region (URR) and the E6 and E7 genes. Mutations were observed in 5% of the URR, including a large deletion in one isolate and various point mutations affecting regulatory sites. More sequence variations were found in the E6 gene compared to the E7 gene. Mutations in these genes, which encode the oncogenic proteins essential for malignant transformation, may impact the oncogenicity of the virus by altering amino acid sequences or transcription factor binding sites (Human Papillomaviruses and Cancer, National Cancer Institute, 2008; Int. J. Cancer 86:695-701, 2000).

Furthermore, it has been observed that viral evolution can occur not only within host cells but also through transmission between different host species. Examples include the H1N1 influenza virus, which originated in swine populations and crossed the species barrier to infect humans, as well as avian influenza viruses undergoing multi-species crossing-over.

In terms of gene expression and profiling, a large-scale meta-analysis of cancer microarray data revealed common transcriptional profiles associated with neoplastic transformation and progression. This analysis examined 40 published cancer microarray datasets, encompassing over 3,700 cancer samples and 38 million gene expression measurements. The findings indicated a common transcriptional profile in various forms of undifferentiated cancers, suggesting core transcriptional features associated with neoplastic transformations and the perpetuation of cancer development (source: Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression).

These findings highlight the significance of viral integration within the human genome and its role in driving evolutionary changes, with tumorigenesis being one measurable outcome. Understanding these mechanisms is crucial in medical science, as it provides insights into selection pressures, mutagenic changes, and mortalities in global populations. By comprehending the evolutionary aspects, research can be directed towards developing effective treatments and prevention strategies. Targeting the most virulent strains of pathogens while minimizing harm to the host appears to be a promising approach for disease management and prevention of resistance. However, in the case of HIV, all variants of the virus exploit the host in harmful ways, posing challenges for this approach. Thus, closely tracking and projecting the evolution of pathogens is crucial for the development of efficient interventions.


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