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What physics knowledge can be applied to biology of organisms and ecosystems?

What physics knowledge can be applied to biology of organisms and ecosystems?


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In the wiki page of Biophysics:

Biophysics spans all scales of biological organization, from the molecular scale to whole organisms and ecosystems.

But after searching on the internet; the dominant application of physics in biology that I see is at the molecular scale. In the wiki page Mathematical biophysics, there is a lot of interesting information, but it is only about mathematical knowledge applied to biophysics, not physics itself.

What, if any, physics knowledge (based on principles and laws of physics) can be applied to biology in the sense of organisms and ecosystems?


This question is really asking for examples, and the list of ways that knowledge of physics can be used in biology could be very long. However, here are a couple of examples:

  • Systems ecology, especially with regard to energy and nutrient flow.
    This type of ecology can be strongly influenced by physics. For one example see the book Theoretical Ecosystem Ecology: Understanding Element Cycles by Ågren & Bosatta (Ågren was originally a physicist)

  • Physical limitations to growth and transport
    This can include for instance mechanical contraints on plant growth (see e.g. the book Plant Physics by Nicklas & Spatz), water transport in trees (see e.g. this BioSE question) or the biomechanics of movement (see e.g. Hudson et al (2012) on the speed and movement of cheetahs or Wikipedia: Biomechanics).

  • Allometric relationships between organisms, e.g. with regard to metabolism
    To explain these types of relationships knowledge in physics is useful. See e.g. Kleiber's law for more.

  • MAXENT as a general approach to ecological patterns or to model species distributions
    This is basically a tool lifted from physics that can be applied to ecological problems. There are many papers to look at, but Harte & Newman (2014) (Harte is another previous physicist) and Elith et al (2010) are two good starting points.

  • Dynamical modelling of populations and communities
    This field use many of the same tools for analysis as physics, e.g. systems of differential equations. One of the pioneers in this field (among many) were Robert May (also started with a PhD in physics), and his classical book Theoretical Ecology: Principles and Applications is still a good starting point.

  • Energy harnessing and conversion by organisms
    This can refer both to how organsims convert prey to energy (e.g. conversion efficiencies) and the physics of photosynthesis (which is an interesting intersection between physics and molecular biology). See Jang et al (2004) and O'Reilly & Olaya-Castro (2013) for examples of the how quantum mechanics can inform us about photosynthesis.

Hopefully this will give you a sense of some different ways that knowledge in physics can be useful for biology.


Viewed from space, Earth offers no clues about the diversity of life forms that reside there. The first forms of life on Earth are thought to have been microorganisms that existed for billions of years in the ocean before plants and animals appeared. The mammals, birds, and flowers so familiar to us are all relatively recent, originating 130 to 200 million years ago. Humans have inhabited this planet for only the last 2.5 million years, and only in the last 200,000 years have humans started looking like we do today.

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

What is biology? In simple terms, biology is the study of living organisms and their interactions with one another and their environment. This is a very broad definition because the scope of biology is vast. Biologists may study anything from the microscopic or submicroscopic view of a cell to ecosystems and the whole living planet (Figure 1.1). Listening to the daily news, you will quickly realize how many aspects of biology are discussed every day. For example, recent news topics include Escherichia coli (Figure 1.2) outbreaks in spinach and Salmonella contamination in peanut butter. Other subjects include efforts toward finding cures for diseases such as AIDS, Alzheimer disease, and cancer. On a global scale, many researchers are committed to finding ways to protect the planet, solve environmental issues, and reduce the effects of climate change. All of these diverse endeavors are related to different facets of the discipline of biology.

Figure 1.2 Escherichia coli (E. coli) bacteria, seen in this scanning electron micrograph, are normal residents of our digestive tracts that aid in the absorption of vitamin K and other nutrients. However, virulent strains are sometimes responsible for disease outbreaks. (Credit: Eric Erbe, digital colorization by Christopher Pooley, both of USDA, ARS, EMU)


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Seeing Emergent Physics Behind Evolution

Nigel Goldenfeld, director of the NASA Astrobiology Institute for Universal Biology, spends little time in his office in the physics department at the University of Illinois, Urbana-Champaign. But even when working on biology studies, he applies to them the informative principles of condensed matter physics and emergent states.

Jordana Cepelewicz

The physicist Nigel Goldenfeld hates biology — “at least the way it was presented to me” when he was in school, he said. “It seemed to be a disconnected collection of facts. There was very little quantitation.” That sentiment may come as a surprise to anyone who glances over the myriad projects Goldenfeld’s lab is working on. He and his colleagues monitor the individual and swarm behaviors of honeybees, analyze biofilms, watch genes jump, assess diversity in ecosystems and probe the ecology of microbiomes. Goldenfeld himself is director of the NASA Astrobiology Institute for Universal Biology, and he spends most of his time not in the physics department at the University of Illinois but in his biology lab on the Urbana-Champaign campus.

Goldenfeld is one in a long list of physicists who have sought to make headway on questions in biology: In the 1930s Max Delbrück transformed the understanding of viruses later, Erwin Schrödinger published What is Life? The Physical Aspect of the Living Cell Francis Crick, a pioneer of X-ray crystallography, helped discover the structure of DNA. Goldenfeld wants to make use of his expertise in condensed matter theory, in which he models how patterns in dynamic physical systems evolve over time, to better understand diverse phenomena including turbulence, phase transitions, geological formations and financial markets. His interest in emergent states of matter has compelled him to explore one of biology’s greatest mysteries: the origins of life itself. And he’s only branched out from there. “Physicists can ask questions in a different way,” Goldenfeld said. “My motivation has always been to look for areas in biology where that kind of approach would be valued. But to be successful, you have to work with biologists and essentially become one yourself. You need both physics and biology.”

Quanta Magazine recently spoke with Goldenfeld about collective phenomena, expanding the Modern Synthesis model of evolution, and using quantitative and theoretical tools from physics to gain insights into mysteries surrounding early life on Earth and the interactions between cyanobacteria and predatory viruses. A condensed and edited version of that conversation follows.

Physics has an underlying conceptual framework, while biology does not. Are you trying to get at a universal theory of biology?

God, no. There’s no unified theory of biology. Evolution is the nearest thing you’re going to get to that. Biology is a product of evolution there aren’t exceptions to the fact that life and its diversity came from evolution. You really have to understand evolution as a process to understand biology.

So how can collective effects in physics inform our understanding of evolution?

When you think about evolution, you typically tend to think about population genetics, the frequency of genes in a population. But if you look to the Last Universal Common Ancestor — the organism ancestral to all others, which we can trace through phylogenetics [the study of evolutionary relationships] — that’s not the beginning of life. There was definitely simpler life before that — life that didn’t even have genes, when there were no species. So we know that evolution is a much broader phenomenon than just population genetics.

The Last Universal Common Ancestor is dated to be about 3.8 billion years ago. The earth is 4.6 billion years old. Life went from zero to essentially the complexity of the modern cell in less than a billion years. In fact, probably a lot less: Since then, relatively little has happened in terms of the evolution of cellular architecture. So evolution was slow for the last 3.5 billion years, but very fast initially. Why did life evolve so fast?

[The late biophysicist] Carl Woese and I felt that it was because it evolved in a different way. The way life evolves in the present era is through vertical descent: You give your genes to your children, they give their genes to your grandchildren, and so on. Horizontal gene transfer gives genes to an organism that’s not related to you. It happens today in bacteria and other organisms, with genes that aren’t really so essential to the structure of the cell. Genes that give you resistance to antibiotics, for example — that’s why bacteria evolve defenses against drugs so quickly. But in the earlier phase of life, even the core machinery of the cell was transmitted horizontally. Life early on would have been a collective state, more of a community held together by gene exchange than simply the sum of a collection of individuals. There are many other well-known examples of collective states: for example, a bee colony or a flock of birds, where the collective seems to have its own identity and behavior, arising from the constituents and the ways that they communicate and respond to each other. Early life communicated through gene transfer.

How do you know?

Life could only have evolved as rapidly and optimally as it did if we assume this early network effect, rather than a [family] tree. We discovered about 10 years ago that this was the case with the genetic code, the rules that tell the cell which amino acids to use to make protein. Every organism on the planet has the same genetic code, with very minor perturbations. In the 1960s Carl was the first to have the idea that the genetic code we have is about as good as it could possibly be for minimizing errors. Even if you get the wrong amino acid — through a mutation, or because the cell’s translational machinery made a mistake — the genetic code specifies an amino acid that’s probably similar to the one you should have gotten. In that way, you’ve still got a chance that the protein you make will function, so the organism won’t die. David Haig [at Harvard University] and Laurence Hurst [at the University of Bath] were the first to show that this idea could be made quantitative through Monte Carlo simulation — they looked for which genetic code is most resilient against these kinds of errors. And the answer is: the one that we have. It’s really amazing, and not as well known as it should be.

Later, Carl and I, together with Kalin Vetsigian [at the University of Wisconsin-Madison], did a digital life simulation of communities of organisms with many synthetic, hypothetical genetic codes. We made computer virus models that mimicked living systems: They had a genome, expressed proteins, could replicate, experienced selection, and their fitness was a function of the proteins that they had. We found that it was not just their genomes that evolved. Their genetic code evolved, too. If you just have vertical evolution [between generations], the genetic code never becomes unique or optimal. But if you have this collective network effect, then the genetic code evolves rapidly and to a unique, optimal state, as we observe today.

So those findings, and the questions about how life could get this error-minimizing genetic code so quickly, suggest that we should see signatures of horizontal gene transfer earlier than the Last Universal Common Ancestor, for example. Sure enough, some of the enzymes that are associated with the cell’s translation machineries and gene expression show strong evidence of early horizontal gene transfers.

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VIDEO: Nigel Goldenfeld explains how condensed matter physics provides insights into the collective state of early life on Earth.

How have you been able to build on those findings?

Tommaso Biancalani [now at the Massachusetts Institute of Technology] and I discovered in the last year or so — and our paper on this has been accepted for publication — that life automatically shuts off the horizontal gene transfer once it has evolved enough complexity. When we simulate it, it basically shuts itself off on its own. It’s still trying to do horizontal gene transfer, but almost nothing sticks. Then the only evolutionary mechanism that dominates is vertical evolution, which was always present. We’re now trying to do experiments to see whether all the core cellular machinery has gone through this transition from horizontal to vertical transmission.

Is this understanding of early evolution why you’ve said that we need a new way to talk about biology?

People tend to think about evolution as being synonymous with population genetics. I think that’s fine, as far as it goes. But it doesn’t go far enough. Evolution was going on before genes even existed, and that can’t possibly be explained by the statistical models of population genetics alone. There are collective modes of evolution that one needs to take seriously, too. Processes like horizontal gene transfer, for example.

It’s in that sense that I think our view of evolution as a process needs to be expanded — by thinking about dynamical systems, and how it is possible that systems capable of evolving and reproducing can exist at all. If you think about the physical world, it is not at all obvious why you don’t just make more dead stuff. Why does a planet have the capability to sustain life? Why does life even occur? The dynamics of evolution should be able to address that question. Remarkably, we don’t have an idea even in principle of how to address that question — which, given that life started as something physical and not biological, is fundamentally a physics question.

How does your work on cyanobacteria fit into these applications of condensed matter theory?

My graduate student Hong-Yan Shih and I modeled the ecosystem of an organism called Prochlorococcus, a type of cyanobacteria that lives in the ocean through photosynthesis. I think it may well be the most numerous cellular organism on the planet. There are viruses, called phages, that prey on the bacteria. Ten years or so ago, it was discovered that these phages have photosynthesis genes, too. Now, you normally wouldn’t think of a virus as needing to do photosynthesis. So why are they carrying these genes around?

It seems that the bacteria and phages don’t quite behave as the dynamics of a predator-prey ecosystem would predict. The bacteria actually benefit from the phages. In fact, the bacteria could prevent the phages from attacking them in many ways, but they don’t, not entirely. The phages’ photosynthesis genes originally came from the bacteria — and, amazingly, the phages then transferred them back to the bacteria. Photosynthesis genes have shuttled back and forth between the bacteria and the phages several times over the last 150 million years.

It turns out that genes evolve much more rapidly in the viruses than they do in the bacteria, because the replication process for the viruses is much shorter and more likely to make mistakes. As a side effect of the phages’ predation on the bacteria, bacterial genes sometimes get transferred into the viruses, where they can spread, evolve quickly and then be given back to the bacteria, which can then reap the benefits. So the phages have been useful to the bacteria. For example, there are two strains of Prochlorococcus, which live at different depths. One of those ecotypes adapted to live closer to the surface, where the light is much more intense and has a different frequency. That adaptation could occur because the viruses made rapid evolution available.

And the viruses benefit from the genes, too. When a virus infects its host and replicates, the number of new viruses it makes depends on how long the hijacked cell can survive. If the virus carries with it a life-support system — the photosynthesis genes — it can keep the cell alive longer to make more copies of the virus. The virus that carries the photosynthesis genes has a competitive advantage over one that doesn’t. There’s a selection pressure on the viruses to carry genes that benefit the host. You’d expect that because the viruses have such a high mutation rate, their genes would deteriorate rapidly. But in the calculations that we’ve done, we’ve found that the bacteria filter the good genes and transfer them to the viruses.

So there’s a nice story here: a collective behavior between the bacteria and the viruses that mimics the kind of things that happen in condensed matter systems — and that we can model, so that we can predict features of the system.


Overview

The food we eat, the water we drink, the air we breathe, many of the materials we use, and much of the recreation and culture we enjoy are products of ecological systems.

We manage ecosystems to provide us with these benefits, and our use and misuse can have grave impacts. Problems like pollution, over-harvesting, acid rain and climate change often arise because we fail to understand our ecosystems properly.

In this specialization/minor, you can develop your understanding of how ecosystems function. You'll build foundational knowledge of living and non-living components of ecosystems, and how they interact. You can also learn to apply systems thinking to the challenges that come with managing ecosystems for agriculture, forestry, fisheries, protected areas and urban development. Upon graduation, you will be able to harness concepts and tools that can help you deal with the complexity that an ecosystem perspective brings.

If taken as a specialization, it must be combined with a major in the B.Sc(AgEnvSc). The suggested major is Environmental Biology


Systems biology approaches towards predictive microbial ecology

Through complex interspecies interactions, microbial processes drive nutrient cycling and biogeochemistry. However, we still struggle to predict specifically which organisms, communities and biotic and abiotic processes are determining ecosystem function and how environmental changes will alter their roles and stability. While the tools to create such a predictive microbial ecology capability exist, cross-disciplinary integration of high-resolution field measurements, detailed laboratory studies and computation is essential. In this perspective, we emphasize the importance of pursuing a multiscale, systems approach to iteratively link ecological processes measured in the field to testable hypotheses that drive high-throughput laboratory experimentation. Mechanistic understanding of microbial processes gained in controlled lab systems will lead to the development of theory that can be tested back in the field. Using N2 O production as an example, we review the current status of field and laboratory research and layout a plausible path to the kind of integration that is needed to enable prediction of how N-cycling microbial communities will respond to environmental changes. We advocate for the development of realistic and predictive gene regulatory network models for environmental responses that extend from single-cell resolution to ecosystems, which is essential to understand how microbial communities involved in N2 O production and consumption will respond to future environmental conditions.


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Ecology

Ecology, or ecological science, is the scientific study of the distribution and abundance of living organisms and how the distribution and abundance are affected by interactions between the organisms and their environment.

The environment of an organism includes both physical properties, which can be described as the sum of local abiotic factors such as insolation (sunlight), climate, and geology, as well as the other organisms that share its habitat.

Ecology is usually considered a branch of biology, the general science that studies living organisms.

Organisms can be studied at many different levels, from proteins and nucleic acids (in biochemistry and molecular biology), to cells (in cellular biology), to individuals (in botany, zoology, and other similar disciplines), and finally at the level of populations, communities, and ecosystems, to the biosphere as a whole these latter strata are the primary subjects of ecological inquiries.

Ecology is a multi-disciplinary science.

Because of its focus on the higher levels of the organization of life on earth and on the interrelations between organisms and their environment, ecology draws heavily on many other branches of science, especially geology and geography, meteorology, pedology, chemistry, and physics.

Thus, ecology is considered by some to be a holistic science, one that over-arches older disciplines such as biology which in this view become sub-disciplines contributing to ecological knowledge.


CBS Minors

To declare one of the minors listed below, please complete one of our online forms on the Policies, Procedures, and Forms page. In each CBS minor, students must take the courses on an A-F basis and earn at least a C- in all credits counted toward the minor.

As a student with declared CBS minor, you have access to the CBS advisors through daily drop in hours to answer your questions. More information on scheduled drop in times and appropriate drop in issues can be found on the Drop In Advising page.

Behavioral biology is the scientific discipline that aims to understand all aspects of the biological bases of animal behavior. These aspects include the causal mechanisms underlying behaviors, changes in behaviors over the animal’s lifetime, the adaptive value of behaviors, and the evolutionary history of behaviors. Disciplines informing the field of behavioral biology include: cell and developmental biology, endocrinology, ecology, economics, evolution, genetics, neuroscience, physiology, and psychology.

For more information, please see the undergraduate catalog.

*NOTE: Biology majors are not eligible for this minor due to overlap

The Biochemistry minor is available to CBS students pursuing one of the other department majors. It is also available to non-CBS students. Students must complete the courses listed below. For information regarding the pre-requisites and requirements for the biochemistry minor, please see the undergraduate catalog.

*NOTE: Biology majors are not eligible for this minor due to overlap.

The Biology minor is available to non-CBS students only. Due to significant course overlap, the following majors will not be allowed to complete a biology minor: Biology, Society, and the Environment Physiology Medical Laboratory Sciences Nutrition (Nutritional Science sub-plan only) Fisheries and Wildlife (all sub-plans) Environmental Sciences, Policy, and Management major: Environmental Science track Scientific and Technical Communication major (Biological and Health Sciences subplan) Animal Science (Pre-Vet/Science sub-plan only) individually designed programs with a life sciences emphasis Environmental Sciences, Policy, and Management Food Science Applied Plant Science (Environmental Science AND Environmental Education/Curriculum sub-plans). In addition, students pursuing a Biochemistry, Plant Biology, Marine Biology, Microbiology, or Integrative Neuroscience minor are not allowed to receive a biology minor. Transfer courses, AP/IB credit, or courses offered by non-CBS departments are only allowed for use in the biology minor for general biology, general chemistry, and a maximum of three credits of upper division coursework.

*NOTE: GCD 3033 is now an accepted course for the Biology minor. For minor course requirements, view the biology minor in the university catalog.

The Cell Biology minor is available to non-CBS students and students who are not pursuing the Genetics minor.

Cell Biology is focused on the structure and function of individual cells and cell-to-cell interactions. Key areas within Cell Biology include metabolism, cell communication, cell cycle, and cell secretion. This field is responsible for critical discoveries regarding how cells function, ultimately giving insight into understanding larger organisms. Cell Biology has provided pivotal advances in biomedical fields, including the treatment of cancer and other diseases. More information about the minor, please see the University Catalog.

The Cellular and Molecular Neuroscience minor is for CBS students and students from other colleges who have a strong background in molecular biology and biochemistry and are interested in more advanced Neuroscience courses. Like the Integrative Neuroscience major curriculum, students in this minor study the molecular and cellular building blocks that make up the brain and control its function.

For information regarding the pre-requisites and requirements for the Cellular and Molecular Neuroscience minor, please see the undergraduate catalog.

Large-scale data are now a norm in biological and medical research. The ability to properly analyze large-scale biological data requires mathematical and computational skills as well as an understanding of biology. The Computational Biology minor allows students to focus on courses that include mathematical and computational analysis as well as biology content. The number of biology-related jobs that require mathematical and computational skills has rapidly increased in both industry and academia. Completing this minor develops skills that are highly valued by employers as well as by graduate and professional schools.

For information regarding the pre-requisites and requirements for the Computational Biology minor, please see the undergraduate catalog.

The Genetics minor is available to non-CBS students and students who are not pursuing the Cell Biology minor.

The study of genetics focuses on 1) the relationship between the transmission of genes from parent to offspring and the outcome of the offspring’s traits, 2) molecular understanding of the features of DNA and how these features underlie the expression of genes and 3) genetic variation and how that variation is related to an organism’s environment.More information about the minor, please see the University Catalog.

The Integrative Neuroscience minor provides an in-depth contemporary understanding of how the nervous system functions in both health and disease. The goal of the minor is to provide instruction that will enrich the curriculum through an array of academic majors. As we will all experience the impact of nervous system disease ourselves or through family members and/or friends, instruction in this minor will offer insights into the nervous system that students can utilize throughout their lifetimes.

For information regarding the pre-requisites and requirements for the Integrative Neuroscience minor, please see the undergraduate catalog.

*NOTE: Biology majors are not eligible for this minor due to overlap

Students learn about the foundational concepts of marine biology, and the current issues that affect marine environments. With 71% of our planet covered by oceans, it's important to understand marine ecosystems, organisms, chemistry, and the physics of the oceans. Students in this minor will develop knowledge and skills through which they can explore complex problems such as habitat conservation, sustainability, climate change, and biodiversity in the oceans and on land. This minor also provides students with a base for subsequent studies in marine biology.

For information regarding the pre-requisites and requirements for the Marine Biology minor, please see the undergraduate catalog.

Microbiology is a fascinating and important discipline that integrates information from many majors in the biological sciences. Beginning in the Fall semester of 2011, CBS will offer a 14 credit microbiology minor. Students must have a cumulative GPA of 2.5 in order to declare the minor. This minor is available to both CBS and non-CBS students. If you have taken VBS 2032 (or a non-majors microbiology course at another institution) and wish to pursue this minor, please contact Dr. Leslie Schiff by email (schif002@umn.edu). Transfer credit will only be accepted for the General Microbiology component of the minor.

To declare the minor, please complete the Add/Drop a CBS Minor form. It will be added to the records of students with a 2.5 cumulative GPA effective for Fall 2011.

Prerequisite courses: MCB 3301 and BIOC 3021 or 4331. For information regarding the requirements for the microbiology minor, please see the undergraduate catalog.

*NOTE: Biology majors are not eligible for this minor due to overlap.

Pharmacology is a scientific discipline that studies how drugs affect biological systems. Drugs are defined as chemical/biological agents that act on living organisms, mostly act by interacting with specific target molecules to produce a desired biological effect. Pharmacology is the foundation of medicine, pharmacy, dentistry, veterinary medicine, nursing and many other healthcare professions. Pharmacology is also an interdisciplinary discipline that employs scientific principles and experimental techniques of its own, as well as various biological disciplines such as physiology, biochemistry, cellular/molecular biology, microbiology, immunology, genetics, structural biology, and pathology, etc. A fundamental knowledge of the underlying biological processes is required to achieve the objectives of pharmacology study, including identification of new targets for therapeutic intervention, developing new therapeutics, understanding their mechanisms of action and the potential environmental/toxicological implications. For course descriptions, see the Pharmacology course catalog.

For information regarding the pre-requisites and requirements for the pharmacology minor, please see the undergraduate catalog.


Curriculum

We've designed the Biology course of study to reflect the many different career options available to Biology majors. We pride ourselves on offering students the ability to tailor their education to their interests and career goals. Below, you can see some of the many course options available to you through the Biology program.

Courses To Prepare You For Your Career

SNHU's bachelor's in biology program includes:

General Education Program

Our programs are designed to equip you with the skills and insights you need to move forward. In recent years, employers have stressed the need for graduates with higher order skills - the skills that go beyond technical knowledge - such as:

All bachelor's students are required to take general education classes. Through foundation, exploration and integration courses, students learn to think critically, creatively and collaboratively, giving you the edge employers are looking for.


Watch the video: Ecosystems, Thermodynamics part 2 (January 2023).