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Let the Science Begin!
Let the Science Begin!
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Humans versus the Nitrogen Cycle
(image by Daniel Mayer )
Normally discussions of climate change focus on carbon. Almost daily, new articles are posted on how human activity is altering carbon dioxide, or methane, levels in the atmosphere, and how this is potentially influencing climate around the world. But what about the other biogeochemical cycles? For a quick introduction to a problem with the nitrogen cycle, watch the GeoTimes video below:
Unfortunately, while the nitrogen cycle is often discussed in the classroom, it is rarely given as much attention as the carbon or water cycles. Some of this may be due to time constraints, but usually the lack of coverage seems to be linked to scarce coverage of nitrogen-related current events by the media. However, just last week an article was published in PLoS One which provides an interesting twist of the potential consequences of human interference in the nitrogen cycle.
The articles subject is the potential toxic nature of nitrogen in aquatic ecosystems. Researchers at North Carolina State University, using the water flea Daphnia as a model organism, found that when exposed to nitrates and nitrites in the water, the metabolic pathways of the water flea convert these chemicals to nitric oxide. In living organisms, nitric oxide is an important chemical signal between cells. In humans, nitric oxide levels help regulate the activity of the gastrointestinal tract, respiration, and some aspects of brain activity (including those associated with learning and memory). The drug Viagra regulates nitric oxide levels in the penis, allowing for longer erections. Nitric oxide levels in the body are carefully regulated. What was alarming from the NCSU study was the fact that Daphnia demonstrated developmental problems at nitrate concentrations that were well below those normally found in most water supplies. Now water fleas are not humans, the but question can now be raised as to whether the same effect is occurring in us, and at what concentrations do increased levels of nitrates and nitrites in our water supply produce toxic results.
Unfortunately, while the nitrogen cycle is often discussed in the classroom, it is rarely given as much attention as the carbon or water cycles. Some of this may be due to time constraints, but usually the lack of coverage seems to be linked to scarce coverage of nitrogen-related current events by the media. However, just last week an article was published in PLoS One which provides an interesting twist of the potential consequences of human interference in the nitrogen cycle.
The articles subject is the potential toxic nature of nitrogen in aquatic ecosystems. Researchers at North Carolina State University, using the water flea Daphnia as a model organism, found that when exposed to nitrates and nitrites in the water, the metabolic pathways of the water flea convert these chemicals to nitric oxide. In living organisms, nitric oxide is an important chemical signal between cells. In humans, nitric oxide levels help regulate the activity of the gastrointestinal tract, respiration, and some aspects of brain activity (including those associated with learning and memory). The drug Viagra regulates nitric oxide levels in the penis, allowing for longer erections. Nitric oxide levels in the body are carefully regulated. What was alarming from the NCSU study was the fact that Daphnia demonstrated developmental problems at nitrate concentrations that were well below those normally found in most water supplies. Now water fleas are not humans, the but question can now be raised as to whether the same effect is occurring in us, and at what concentrations do increased levels of nitrates and nitrites in our water supply produce toxic results.
Additional Resources
- PhysicalGeography.net ebook entry on the nitrogen cycle .
- McGraw-Hill Higher Education animation of the nitrogen cycle .
- PLoS article on aquatic nitrogen toxicology .
Application Animations for Engaging Students
Instructors are always looking for new animations, videos, and multimedia to enliven our lectures and engage our students. Recently, I stumbled across the website of Nucleus Medical Media , an animation company based out of Kennesaw Georgia. This is a very impressive site - the company specializes in the development of medical animations. While many of these appears to the targeted towards the education of medical professionals, there is a significant amount of material that could be used on this site in the classrooms. The Interactive multimedia link is especially useful. There you will find short animations in which have been embedded tutorial materials to provide more information on the topic. The animation may be played through with or without watching the interactives, allowing them to be used both in and out of the classroom. Nucleus also has a YouTube channel (NucleusAnimation ). Many of the more applicable animations from the YouTube channel have been cross-linked to our Ricochet Science channel.
Additional Links
Additional Links
- Nucleus Medical Media homepage
- Nucleus Animation on YouTube
- Ricochet Science YouTube Channel
Update: Are All Animals Aerobic?
Earlier this year we posted an article,( "All Animals are Aerobic - False "), which briefly mentioned the discovery of an anaerobic animal, called a loriciferan, at the bottom of the Mediterranean Sea. At first, this just seemed like one of the oddities of nature, an example of an organism that failed to read the textbooks on what its characteristics should be. For instead of oxygen, the energy-releasing molecule of the cellular respiration pathways, these loriciferans are hydrogen-based organisms, which utilize a structure called a hydrogenosome. Hydrogenosomes release hydrogen gas as a waste product, which may in turn be used by the cell to generate methane from carbon dioxide. The conversion of CO2 to releases a small amount of energy. Not the same as cellular respiration, but enough to power some cellular processes.
Nick Lane , biochemist and author of Oxygen:The Molecule That Shaped the World ", suggests that we should be taking a closer look at the anaerobic loriciferans and their hydrogen-based lifestyle. Current evolutionary thought follows that path that oxygen, the byproduct of photosynthesis, was the key molecule in the evolution of the eukaryotic organisms. Lane's article discusses an alternate hypothesis, that it was hydrogen that may have played an important role in the evolution of the eukaryotes.
The answer lies within the genetic information packed within the mitochondria and hydrogenosomes. By analyzing the DNA of aerobic and anaerobic organisms, and comparing it to the information found in anaerobic organisms with hydrogenosomes, it may be possible to determine whether hydrogen gas or oxygen gas was first step in the evolution of the eukaryotes. Either way, it seems as if there will have to be some revisions to the textbooks, and a retraction of the statement that all animals are anaerobes.
Nick Lane , biochemist and author of Oxygen:The Molecule That Shaped the World ", suggests that we should be taking a closer look at the anaerobic loriciferans and their hydrogen-based lifestyle. Current evolutionary thought follows that path that oxygen, the byproduct of photosynthesis, was the key molecule in the evolution of the eukaryotic organisms. Lane's article discusses an alternate hypothesis, that it was hydrogen that may have played an important role in the evolution of the eukaryotes.
The answer lies within the genetic information packed within the mitochondria and hydrogenosomes. By analyzing the DNA of aerobic and anaerobic organisms, and comparing it to the information found in anaerobic organisms with hydrogenosomes, it may be possible to determine whether hydrogen gas or oxygen gas was first step in the evolution of the eukaryotes. Either way, it seems as if there will have to be some revisions to the textbooks, and a retraction of the statement that all animals are anaerobes.
Additional Links
- Scientific Activist blogpost on ScienceBlogs
- New Scientist article "Genesis Revisited " (Aug 7, 2010) - subscription required
Frogs, Big Mountains, and Speciation
The formation of new species is always a great way to discuss evolutionary change over time. Most textbooks do an adequate job of providing examples of how geographic isolation contributes to the the process of speciation. However, where many books are lacking is showing how the resulting species then adapt to their new environment following the establishment of the geographic barrier. If you are looking for an interesting way to show the relationship between geographic isolation, adaptation, and speciation, then you need to visit a very special group of frogs in southeast Asia.
A study coming out of UC Berkeley demonstrates how a really big mountain range, the Himalayas, has influenced the speciation of frogs in Southeast Asia. the study focuses on a group of amphibians commonly called the spiny frogs. According to the article , the ancestors of the spiny frogs first occupied the area that is now western China around 27 mya. When the Indian subcontinent collided with south Asia, the uplifting created the Himalayan mountains, and created the Tibetan plateau. Right in the middle of these events were the spiny frogs. And as their environment changed, the spring frogs diverged into several very different species - the Nanorana subgenus, which occupies elevations up to 4,700 meters, and the lowland Quasipaa group.
But what is interesting about this study is not that it is just another example of allopatric speciation. Rather, a closer look at the species of frogs in the report reveals some really interesting adaptations that have occurred in these spiny frogs, most notably the Nanorana species. These frogs are well adapted to life at high-elevation. As frogs, their life cycle is tied to the water environment. However, unlike the rivers and lakes of the lowlands, the waters of high elevation mountains moves fast, which can create some real problems for holding onto a mate. But the Nanorana have evolved some interesting adaptations. The most notable one is that the male frogs have large forearms (see photo) and spines on their chests, allowing them to establish a firm grip on the females despite the rapid rush of water. These features are largely absent in theQuasipaa group. Other adaptations to a cold, oxygen-deprived environment, include evidence of organ degeneration, although the authors of the paper are careful to note that additional studies of these adaptations are needed. Overall, however, the research does provide an interesting look at how new species form due to geographic isolation.
A study coming out of UC Berkeley demonstrates how a really big mountain range, the Himalayas, has influenced the speciation of frogs in Southeast Asia. the study focuses on a group of amphibians commonly called the spiny frogs. According to the article , the ancestors of the spiny frogs first occupied the area that is now western China around 27 mya. When the Indian subcontinent collided with south Asia, the uplifting created the Himalayan mountains, and created the Tibetan plateau. Right in the middle of these events were the spiny frogs. And as their environment changed, the spring frogs diverged into several very different species - the Nanorana subgenus, which occupies elevations up to 4,700 meters, and the lowland Quasipaa group.
But what is interesting about this study is not that it is just another example of allopatric speciation. Rather, a closer look at the species of frogs in the report reveals some really interesting adaptations that have occurred in these spiny frogs, most notably the Nanorana species. These frogs are well adapted to life at high-elevation. As frogs, their life cycle is tied to the water environment. However, unlike the rivers and lakes of the lowlands, the waters of high elevation mountains moves fast, which can create some real problems for holding onto a mate. But the Nanorana have evolved some interesting adaptations. The most notable one is that the male frogs have large forearms (see photo) and spines on their chests, allowing them to establish a firm grip on the females despite the rapid rush of water. These features are largely absent in theQuasipaa group. Other adaptations to a cold, oxygen-deprived environment, include evidence of organ degeneration, although the authors of the paper are careful to note that additional studies of these adaptations are needed. Overall, however, the research does provide an interesting look at how new species form due to geographic isolation.
Additional resources
- UC Berekely News Release (August 2010)
- Understanding Evolution entry on patterns of speciation
- PNAS article on spiny frog evolution (full-text available)
- McGraw-Hill material on allopatric speciation .
Terra Video: A Winning Scenario
The hot summer across the northern hemisphere, coupled with floods in Europe and Pakistan, have many people wondering whether climate change may be responsible for extreme weather events. And as fall classes start across the country, educators can use this opportunity to open the discussion on the long-term influences that climate change will have on human society.
The folks at Terra have once again done a great job of presenting the human side of a hot-topic in the sciences.In their video " A Winning Scenario ", Terra takes a look at the effects of global climate change on the people of sub-Saharan Africa. But what is most interesting for this video, and what makes it an ideal presentation tool for the classroom, is the fact that it is not a gloom-and-doom documentary. While the video does discuss how deforestation and changes in rainfall patterns have led to crop failures and massive soil erosion - it also presents examples of how the people of Kenya are adoption sustainable practices that are reducing the impact of climate change. The video relates very well to classroom lectures about the carbon cycle, sustainable practices, and the influence of forests on regional rain patterns. But it also provides a real measure of hope, for if the people of Kenya, with their limited resources, can find ways to reduce their impact on their environment, then it should be possible for those of us in the developed countries to do the same.
Update - How Fast Have Humans Evolved?
How fast can a species adapt to a new environment? What evidence isthere that humans are evolving?
These are two common questions that usually come up during classroom discussions of evolution. Most people do not have a problem recognizing that insects adapt to new environments by evolutionary change that provides resistance to certain chemicals, or that bacteria do the same with antibiotic resistance, but often it is difficult to make the connection that the same thing must be occurring for humans. Maybe this is because of the same problem that Aristotle and Plato faced when they proposed the Chain of Being - as far as one can tell, life (and especially humans) has changed little over the relatively brief period of recorded history. The organisms that people are familiar with - oak trees, lizards, and humans, appear to be the same now as they were several thousand years ago. For humans, this unfortunately has resulted in the idea that we are a "fixed" species, operating outside the laws of evolution.Therein lies a the fundamental problem - that if you can't "see" evolution, it isn't happening. But now, due to studies of evolutionary change in human populations living in high-elevation areas of Tibet (see "High Elevation Humans - Evidence of Adaption "), we now know that it is possible to detect the genetic basis of specific adaptations in humans. But what is really interesting about this discovery is not the fact that humans are evolving - since that is a basic characteristic of all life - but rather that this adaptation probably occurred over less than 3,000 years . If we use a 25 year generation time for humans, that means that the high-elevation occurred in less than 120 generations. While not as fast as the evolution of adaptations in the bacteria, or even some insects, this is still fast. More importantly, it can be pointed to as a definite example that humans evolve, and that this evolutionary change can be measured.
Additional Links
- University of Berkeley article on rate of change in high-elevation humans.
High-Elevation Humans - Evidence of Adaptation
Tibetans Display Natural Selection of Hemoglobin Gene
(image source )
(image source )
Sometimes, one of the most difficult aspects of getting people to understand evolutionary change is relating the basic ideas of adaptation and natural selection to humans. Everyone gets the idea that artificial selection is responsible for our dogs and the food that we eat, but few understand that humans are bound by the same principles of natural selection and evolutionary change as all other living organisms.
A recent article coming out of the National Evolutionary Synthesis Center provides a fantastic example of how selection has favored a certain allele in individuals living in the high-elevation areas of Tibet. The study proposes that a small-subset of Tibetans has adapted to high-elevation living by producing less hemoglobin in their blood.
Normally, if a person moves to a higher altitude - their body responds by making more hemoglobin, which thickens the blood. For minor elevation changes, this does not present much of a problem. But for people that live at extreme elevations (some people in the Himalayas can live at elevations of over 13,000 feet, or close to 4,000 meters), this can present a number of health problems.
Since high hemoglobin levels would be a detriment to people at high elevations, it makes sense that natural selection would favor individuals that produced less hemoglobin at high elevations. Such is the case with the Tibetans in this study. Researchers have identified an allele of a gene that reduces hemoglobin production at high elevations. Comparisons between Tibetans at both high and low elevations strongly suggest that selection has played a role in the prevalence of the high-elevation allele.
The gene is EPSA1, a gene on chromosome 2 (2p21 to be exact) that produces a transcription factor (TF). TFs act as regulators of gene expression, and the TF produced by EPSA1 is responsible (among other things) for regulating a series of other genes that are involved with oxygen use by the body, including the amount of hemoglobin present in the blood. The allele in the high-elevation Tibetans down-regulates production of hemoglobin, allowing these individuals to escape the consequences of thick blood.
A recent article coming out of the National Evolutionary Synthesis Center provides a fantastic example of how selection has favored a certain allele in individuals living in the high-elevation areas of Tibet. The study proposes that a small-subset of Tibetans has adapted to high-elevation living by producing less hemoglobin in their blood.
Normally, if a person moves to a higher altitude - their body responds by making more hemoglobin, which thickens the blood. For minor elevation changes, this does not present much of a problem. But for people that live at extreme elevations (some people in the Himalayas can live at elevations of over 13,000 feet, or close to 4,000 meters), this can present a number of health problems.
Since high hemoglobin levels would be a detriment to people at high elevations, it makes sense that natural selection would favor individuals that produced less hemoglobin at high elevations. Such is the case with the Tibetans in this study. Researchers have identified an allele of a gene that reduces hemoglobin production at high elevations. Comparisons between Tibetans at both high and low elevations strongly suggest that selection has played a role in the prevalence of the high-elevation allele.
The gene is EPSA1, a gene on chromosome 2 (2p21 to be exact) that produces a transcription factor (TF). TFs act as regulators of gene expression, and the TF produced by EPSA1 is responsible (among other things) for regulating a series of other genes that are involved with oxygen use by the body, including the amount of hemoglobin present in the blood. The allele in the high-elevation Tibetans down-regulates production of hemoglobin, allowing these individuals to escape the consequences of thick blood.
The study provides an excellent opportunity for discussions on the influence of selection on humans.
Additional Links
- Link to news article -
- National Evolutionary Synthesis Center
- PNAS article (full pdf available)
- MB10 - chapter 13 (gene regulation); chapter 16 (natural selection)
- HB11 - chapter 22 (human evolution)
- MI13 - chapter 27 (evolution)
Scientist at Work - Great Blog for Biodiversity Teaching
If you are looking for a great reference site to enhance either your teaching or understanding of biodiversity, check out the new NY Times blog Scientist at Work:Notes from the Field
The site not only has some fantastic pictures, but is written by actual field biologists who explain both the importance of their work and, in many cases, why they enjoy being field biologists. It is also possible to nominate individuals to prepare pieces for the blog.
Biodiversity loss has been in the news a lot lately, especially after the failure of the world's nations to meet the criteria set forth in the 2002 IUCN Convention on Biological Diversity. In fact, biodiversity loss has actually accelerated, not decreased since the 2002 agreement. Therefore, it is important that the general public be made aware of the tremendous wealth of life on this planet. Sites such as Scientist at Work are a first step in that direction.
Additional Links
The site not only has some fantastic pictures, but is written by actual field biologists who explain both the importance of their work and, in many cases, why they enjoy being field biologists. It is also possible to nominate individuals to prepare pieces for the blog.
Biodiversity loss has been in the news a lot lately, especially after the failure of the world's nations to meet the criteria set forth in the 2002 IUCN Convention on Biological Diversity. In fact, biodiversity loss has actually accelerated, not decreased since the 2002 agreement. Therefore, it is important that the general public be made aware of the tremendous wealth of life on this planet. Sites such as Scientist at Work are a first step in that direction.
Additional Links
Twitter in the Classroom
There can be little doubt that social media is finally making its way into the science classrooms. The video below, produced by Science Nation at NSF , shows how some professors are beginning to use Twitter and Facebook to interact with their classes:
The Science Nation video is suggesting that Twitter may be a replacement for the textbook. This seems to show a misunderstanding of how students really use Twitter, textbooks, social media, and laptops. Twitter is a useful mechanism for delivering small pieces of information, opening up discussions, and posting questions to the class. In today's media-rich textbook environment, with interactive artwork and 3D animations (click here for an example ), Twitter will be a useful way for the instructor to direct students to appropriate content, and not necessarily (yet!) replace the textbook.
Another useful tool for Twitter is as an announcement system. As noted in the video, students don't check email all that often. Instead, they are attached to social networks such as Facebook. At Appalachian State, I am using a Twitter feed as part of my online class in human genetics. I had noticed that students in my online class were missing assignments and quizzes, not because they were bad students, but because they were too busy to be checking their university email. So, I developed a Twitter site for the class. Each day, a tweet is sent out informing the students of the assignments due over the next few days. I keep the amount of spam to a minimum, and do not require that they set up their Twitter accounts to deliver text messages to their phones (but most do). By just setting up this site, the number of missed assignments dropped considerably - and the sending of a tweet actually takes less time on my part than sending a class email. Furthermore, I can send class tweets from my phone, wherever I may be. So far, there has not been a single complaint on the part of the students.
Ricochet Science also has its own Twitter feed and Facebook page . Stop by either site, and feel free to make comments on how you are using social networks for your classes.
Another useful tool for Twitter is as an announcement system. As noted in the video, students don't check email all that often. Instead, they are attached to social networks such as Facebook. At Appalachian State, I am using a Twitter feed as part of my online class in human genetics. I had noticed that students in my online class were missing assignments and quizzes, not because they were bad students, but because they were too busy to be checking their university email. So, I developed a Twitter site for the class. Each day, a tweet is sent out informing the students of the assignments due over the next few days. I keep the amount of spam to a minimum, and do not require that they set up their Twitter accounts to deliver text messages to their phones (but most do). By just setting up this site, the number of missed assignments dropped considerably - and the sending of a tweet actually takes less time on my part than sending a class email. Furthermore, I can send class tweets from my phone, wherever I may be. So far, there has not been a single complaint on the part of the students.
Ricochet Science also has its own Twitter feed and Facebook page . Stop by either site, and feel free to make comments on how you are using social networks for your classes.
Humans as Neanderthals 2.0
Neanderthals are back in the news. there has been a renewed interest in Neanderthals ever since the Neanderthal genome project was announced (see video below). Who were they? Why did they go extinct? How similar were they to modern humans?
As the video below demonstrates- we know that Neanderthals were not terribly different than ourselves. There were adaptations to life in the cold, but they were a far cry from the primitive cavemen image typically associated with the name Neanderthal.
We may be one step closer to getting the answers to our questions. This week, it was announced in Science that the Neanderthal genome project has been "completed" (genome sequencing is never complete - there are always edits to be made). To honor this accomplishment Science magazine has prepared a special feature on the Neanderthal genome. There are some really nice teaching assets at this site, including a time line of discoveries leading up to the sequencing of the genome, maps, and links to a wide array of additional resources on the web. But what is probably most interesting from the discovery, is the identification of genetic changes that have occurred after the divergence of Neanderthals and our species. Most of these at first glance do not appear to be major, but one did catch my eye, and that was ZNHIT2. this gene encodes a transcription factor. Transcription factors are involved in how genes are expressed and regulated. We now know that many genes are very similar across many species - the differences in how these are used are often determined by the tissues that they are expressed in, or the levels at which the proteins are produced. Transcription factors play a major role in that process - so that fact that a transcription factor is difference between Neanderthals and our species is not surprising, but it does give us someplace to start looking for evolutionary differences. In addition to these genes, there appears to be around 20 regions of our genome that have undergone positive selection since the Neanderthal-sapiens split. While specific differences are being examined, these regions do contain genes that are known to be associated with brain development.
One other fascinating fact that is getting a lot of attention in the media (see Nicolas Wade's NY Times article ) is evidence that Neaderthals may have interbred (called admixture) with Homo sapiens in the area of what is now the Middle East. if this turns out to be correct, then the genetic differences between the two species must have been relatively minor (in a genomic sense). It also raises the possibility that we our species may have been upgraded by the influence of the Neanderthal genes (although there is not any current evidence of this), in which case Homo sapiens may really be just Neanderthals 2.0
MI13 - genomics (Chapter 26) and animal evolution (Chapter 31)
MB10 - genomics (Chapter 14) and human evolution (chapter 30)
HB11 - human evolution (chapter 22)
One other fascinating fact that is getting a lot of attention in the media (see Nicolas Wade's NY Times article ) is evidence that Neaderthals may have interbred (called admixture) with Homo sapiens in the area of what is now the Middle East. if this turns out to be correct, then the genetic differences between the two species must have been relatively minor (in a genomic sense). It also raises the possibility that we our species may have been upgraded by the influence of the Neanderthal genes (although there is not any current evidence of this), in which case Homo sapiens may really be just Neanderthals 2.0
Additional Links
- research articles in Science
- Science's special feature on the Neanderthal genome
- "Kissing Cousins" by Olivia Judson
- 'Signs of Neanderthals Mating With Humans " by Nicolas Wade
- Previous blog entries on Neanderthals
Textbook Links
MI13 - genomics (Chapter 26) and animal evolution (Chapter 31)
MB10 - genomics (Chapter 14) and human evolution (chapter 30)
HB11 - human evolution (chapter 22)
