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What is the most complex biological organism (or precursors) that we have been able to synthesize from raw materials?

What is the most complex biological organism (or precursors) that we have been able to synthesize from raw materials?



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In the Miller-Urey experiment they produced several amino acids. I'm not sure if there were other similar experiments that got further.

http://www.jcvi.org/cms/press/press-releases/full-text/article/first-self-replicating-synthetic-bacterial-cell-constructed-by-j-craig-venter-institute-researcher/ is a reference to making a cell, but they really injected an engineered genome into an existing cell (which is pretty amazing!)

But I'm interested in work to make completely synthetic life with no preexisting biological components.


What is the most complex biological organism (or precursors) that we have been able to synthesize from raw materials? - Biology

Autotrophs (producers) synthesize their own energy, creating organic materials that are utilized as fuel by heterotrophs (consumers).

Learning Objectives

Distinguish between photoautotrophs and chemoautotrophs and the ways in which they acquire energy

Key Takeaways

Key Points

  • Food webs illustrate how energy flows through ecosystems, including how efficiently organisms acquire and use it.
  • Autotrophs, producers in food webs, can be photosynthetic or chemosynthetic.
  • Photoautotrophs use light energy to synthesize their own food, while chemoautotrophs use inorganic molecules.
  • Chemoautotrophs are usually bacteria that live in ecosystems where sunlight is unavailable.
  • Heterotrophs cannot synthesize their own energy, but must obtain it from autotrophs or other heterotrophs they act as consumers in food webs.

Key Terms

  • photoautotroph: an organism that can synthesize its own food by using light as a source of energy
  • chemoautotroph: a simple organism, such as a protozoan, that derives its energy from chemical processes rather than photosynthesis
  • heterotroph: an organism that requires an external supply of energy in the form of food, as it cannot synthesize its own

How Organisms Acquire Energy in a Food Web

All living things require energy in one form or another since energy is required by most, complex, metabolic pathways (often in the form of ATP ) life itself is an energy-driven process. Living organisms would not be able to assemble macromolecules (proteins, lipids, nucleic acids, and complex carbohydrates) from their monomeric subunits without a constant energy input.

It is important to understand how organisms acquire energy and how that energy is passed from one organism to another through food webs and their constituent food chains. Food webs illustrate how energy flows directionally through ecosystems, including how efficiently organisms acquire it, use it, and how much remains for use by other organisms of the food web. Energy is acquired by living things in three ways: photosynthesis, chemosynthesis, and the consumption and digestion of other living or previously-living organisms by heterotrophs.

Photosynthetic and chemosynthetic organisms are grouped into a category known as autotrophs: organisms capable of synthesizing their own food (more specifically, capable of using inorganic carbon as a carbon source ). Photosynthetic autotrophs (photoautotrophs) use sunlight as an energy source, whereas chemosynthetic autotrophs (chemoautotrophs) use inorganic molecules as an energy source. Autotrophs act as producers and are critical for all ecosystems. Without these organisms, energy would not be available to other living organisms and life itself would not be possible.

Photoautotrophs, such as plants, algae, and photosynthetic bacteria, serve as the energy source for a majority of the world’s ecosystems. These ecosystems are often described by grazing food webs. Photoautotrophs harness the solar energy of the sun by converting it to chemical energy in the form of ATP (and NADP). The energy stored in ATP is used to synthesize complex organic molecules, such as glucose.

Chemoautotrophs are primarily bacteria that are found in rare ecosystems where sunlight is not available, such as in those associated with dark caves or hydrothermal vents at the bottom of the ocean. Many chemoautotrophs in hydrothermal vents use hydrogen sulfide (H2S), which is released from the vents, as a source of chemical energy. This allows chemoautotrophs to synthesize complex organic molecules, such as glucose, for their own energy and in turn supplies energy to the rest of the ecosystem.

Chemoautotrophs: Swimming shrimp, a few squat lobsters, and hundreds of vent mussels are seen at a hydrothermal vent at the bottom of the ocean. As no sunlight penetrates to this depth, the ecosystem is supported by chemoautotrophic bacteria and organic material that sinks from the ocean’s surface.

Heterotrophs function as consumers in the food chain they obtain energy in the form of organic carbon by eating autotrophs or other heterotrophs. They break down complex organic compounds produced by autotrophs into simpler compounds, releasing energy by oxidizing carbon and hydrogen atoms into carbon dioxide and water, respectively. Unlike autotrophs, heterotrophs are unable to synthesize their own food. If they cannot eat other organisms, they will die.


Abstract

Oligosaccharides and polysaccharides constitute the principal components of carbohydrates, which are important biomacromolecules that demonstrate considerable bioactivities. However, the variety and structural complexity of oligo/polysaccharides represent a major challenge for biological and structural explorations. To access structurally defined oligo/polysaccharides, biological strategies using glycoenzyme biocatalysts have shown remarkable synthetic potential attributed to their regioselectivity and stereoselectivity that allow mild, structurally controlled reaction without addition of protecting groups necessary in chemical strategies. This review summarizes recent biotechnological approaches of oligo/polysaccharide synthesis, which mainly includes in vitro enzymatic synthesis and cell factory synthesis. We have discussed the important factors involved in the production of nucleotide sugars. Furthermore, the strategies established in the cell factory and enzymatic syntheses are summarized, and we have highlighted concepts like metabolic flux rebuilding and regulation, enzyme engineering, and route design as important strategies. The research challenges and prospects are also outlined and discussed.


Scientists look to synthetic biology and 3-D printing for life support in space

As NASA gears up to send humans back to the moon or even to Mars, they'll need to figure out how to keep these humans healthy and safe, far away from the resource-abundant Earth.

It won't be feasible to pack everything they may need over the course of the mission, and resupply missions like those that keep the International Space Station (ISS) stocked will be prohibitively expensive and lengthy.

What these astronauts can pack are Earth's unique renewable resource: cells. Cells of fungi and bacteria, for example, can be reprogrammed with synthetic DNA to produce specific materials, like bioplastics. These materials can then be fed into 3-D printers to manufacture things the astronauts may need during spaceflight — everything from hardware and medical devices to medicine and food.

In an opinion piece published online in Trends in Biotechnology, researchers from the Universities Space Research Association (USRA), MIT Lincoln Laboratory, and NASA outline ways that synthetic biology and 3-D printing can support life during deep-space human missions. But to make these ideas a reality, NASA is seeking help.

"Our opinion piece is a call to action to get DIY [do-it-yourself] biology and makerspace communities involved," says Peter Carr, who works in Lincoln Laboratory's Bioengineering Systems and Technologies Group. The DIY biology community makes it possible for anyone in the public with an interest to conduct biological engineering. The community operates outside the traditional academic or industry settings and spreads knowledge through open sourcing. Many DIY biologist groups operate makerspaces that provide equipment and supplies for members to do experiments on their own.

"These separate, eclectic communities do bio in unconventional settings all the time and are pioneers at rapid prototyping and developing technologies with limited resources. There are parallels here with space and the needs of NASA crews," Carr says. "But this also requires organizations like ours and NASA to connect more deeply with them in a two-way process, so there's a real pathway to getting people's work into space. We're just getting started."

3-D printers are common staples of makerspaces. Experiments done on the ISS with 3-D printers have proven their utility for manufacturing on-demand items, like replacement hardware. But if 3-D printing is to be a reliable tool for long-duration missions in space, a new problem crops up: the need to supply the ship with the feedstock for the printers.

To meet this need, the authors envision using synthetic biology to produce custom biological "ink" to 3-D print whatever may be needed over the course of a mission. Such a process would give scientists "the autonomy to design for the unknown," says Jessica Snyder, a USRA researcher who leads the synthetic biology task for the NASA Academic Mission Services.

Living organisms can convert sunlight, nitrogen, and water into finished products. Bioengineers can reprogram the inner logic of these organisms' cells to produce target compounds. The building blocks to edit these cells can be digitized and sent to the space crew in the form of a DNA sequence, which can be synthesized, assembled, and inserted into an organism on ship. "The idea is what we call a 'bits-to-biology' converter," says David Walsh, a bioengineer at Lincoln Laboratory.

Here's one example of how this vision could be implemented: Say that astronauts faced a situation that occurred on the ISS in 2007 — a solar panel has torn and needs a repair strap. On Earth, synthetic biologists, whether of the DIY type or not, design and test genetic programs instructing bacteria to produce the polymer feedstock for 3-D printing. (This work could also take place well before the need arises during the space mission.) The maker community works out the design of a strap from those materials. These genetic instructions and 3-D printing instructions are sent digitally from Earth to the space crew. The crew reproduces the genetic program, and the bacteria reproduce and synthesize the raw materials, which are used to 3-D print the strap. At the end of the product's life cycle, the part is recovered and digested, and a new one can be made.

"We have the power of digital information. We can design and work out all of the kinks on Earth and simply send the instructions to space," Walsh says.

The same principles can be used to insert DNA into organisms in space to make target compounds for food or pharmaceuticals, which if brought directly from Earth would degrade over time from radiation in space.

Astronauts would be able to conduct these complex biology experiments by using 3-D-printed microfluidic devices. These tiny "lab-on-a-chip" devices automatically control the flow and mixture of fluids through microchannels and use only trace amounts of chemicals to run hundreds of bioreactions in parallel in seconds. Genetic instructions would be sent directly to electronics controlling these microfluidic devices, enabling them to precisely follow the digital "recipe" to synthetize molecules of DNA.

Earlier this year, Lynn Rothschild, a scientist at the NASA Ames Research Center who co-authored the opinion piece, led a team that ran the first synthetic biology experiments in space. The experiments aimed to test how well bacteria in space take in synthetic DNA inserted into their genome and how well the bacteria produce proteins, while being spun to simulate microgravity (what astronauts in the ISS encounter), lunar gravity, and Martian gravity levels. The experiments took place on the PowerCell payload aboard the German satellite mission Eu:CROPIS (Euglena and Combined Regenerative Organic-Food Production in Space).

There is still a long way to go, however, both in experimenting with synthetic biology and figuring out all of the parameters that would make 3-D printing with biomaterials possible in space. "For example, bacteria will need water and will take up space they need the right environment to live and they'll produce waste. We still need to put these ideas up against the real-world constraints," Carr says.

But there's urgency in developing the concepts now. If synthetic biology and 3-D printing techniques can be proven and practiced in time for missions close to Earth, from which supplies can still be sent relatively quickly, then they can be counted on for a long-term mission to Mars.

"Flexible manufacturing techniques provide an excellent complement to Earth-based supply chains for destinations days away, like the International Space Station and possible lunar infrastructure, for examples. Let's take advantage of this redundancy to build an in-space manufacturing capacity to take us further into space more safely," Snyder says. Do-it-yourself biologists and makers can help today by publishing their designs for 3-D-printed products, microfluidic devices, or synthetic DNA on open-source repositories and by testing and editing published designs. "If DIY bio communities use, iteratively improve, and ultimately approve of a technique, then that technique has been optimized more robustly than most individuals or team could offer without great effort. Partnering with these communities is an invaluable asset," Snyder adds. People who are interested can also see NASA's Centennial Challenges, which outline problems that NASA is seeking the public's help to solve.

"We often hear about the engineer who was inspired by NASA in their youth and works there now. But what about the bio people who are inspired by these grand ideas? How can they contribute? Now is a chance to transition their ideas to space," Carr says. "There is so much opportunity to innovate."


One contribution of 16 to a theme issue ‘The peculiar carbon metabolism in diatoms’.

Published by the Royal Society. All rights reserved.

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Outcomes of glycolysis

Here are a couple of things to consider:

One of the clear outcomes of glycolysis is the biosynthesis of compounds that can enter into a variety of metabolic pathways. Likewise, compounds coming from other metabolic pathways can feed into glycolysis at various points. So, this pathway can be part of a central exchange for carbon flux within the cell.

If glycolysis is run long enough, the constant oxidation of glucose with NAD + can leave the cell with a problem: how to regenerate NAD + from the two molecules of NADH produced. If the NAD + is not regenerated, all of the cell's NAD will be nearly completely transformed into NADH. So how do cells regenerate NAD + ?

Pyruvate is not completely oxidized there is still some energy to be extracted. How might this happen? Also, what should the cell do with all of that NADH? Is there any energy there to extract?

Strongly suggested discussion/exercise

Can you write an energy story for the overall process of glycolysis? For energy terms, just worry about describing things in terms of whether they are exergonic or endergonic. When I say "overall process," I mean overall process: glucose should be listed on the reactant side of the arrow, and pyruvate should be listed on the product side of the arrow.


6.1 Energy and Metabolism

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

  • Explain metabolic pathways and describe the two major types
  • Discuss how chemical reactions play a role in energy transfer

Scientists use the term bioenergetics to discuss the concept of energy flow (Figure 6.2) through living systems, such as cells. Cellular processes such as building and breaking down complex molecules occur through stepwise chemical reactions. Some of these chemical reactions are spontaneous and release energy whereas, others require energy to proceed. Just as living things must continually consume food to replenish what they have used, cells must continually obtain more energy to replenish that which the many energy-requiring chemical reactions that constantly take place use. All of the chemical reactions that transpire inside cells, including those that use and release energy, are the cell’s metabolism .

Carbohydrate Metabolism

Sugar (a simple carbohydrate) metabolism (chemical reactions) is a classic example of the many cellular processes that use and produce energy. Living things consume sugar as a major energy source, because sugar molecules have considerable energy stored within their bonds. The following equation describes the breakdown of glucose, a simple sugar:

Consumed carbohydrates have their origins in photosynthesizing organisms like plants (Figure 6.3). During photosynthesis, plants use the energy of sunlight to convert carbon dioxide gas (CO2) into sugar molecules, like glucose (C6H12O6). Because this process involves synthesizing a larger, energy-storing molecule, it requires an energy input to proceed. The following equation (notice that it is the reverse of the previous equation) describes the synthesis of glucose:

During photosynthesis chemical reactions, energy is in the form of a very high-energy molecule scientists call ATP, or adenosine triphosphate. This is the primary energy currency of all cells. Just as the dollar is the currency we use to buy goods, cells use ATP molecules as energy currency to perform immediate work. The sugar (glucose) is stored as starch or glycogen. Energy-storing polymers like these break down into glucose to supply ATP molecules.

Solar energy is required to synthesize a glucose molecule during the photosynthesis reactions. In photosynthesis, light energy from the sun initially transforms into chemical energy that temporally stores itself in the energy carrier molecules ATP and NADPH (nicotinamide adenine dinucleotide phosphate). Photosynthesis later uses the stored energy in ATP and NADPH to build one glucose molecule from six molecules of CO2. This process is analogous to eating breakfast in the morning to acquire energy for your body that you can use later in the day. Under ideal conditions, energy from 18 molecules of ATP is required to synthesize one glucose molecule during photosynthesis reactions. Glucose molecules can also combine with and convert into other sugar types. When an organism consumes sugars, glucose molecules eventually make their way into each organism's living cell. Inside the cell, each sugar molecule breaks down through a complex series of chemical reactions. The goal of these reactions is to harvest the energy stored inside the sugar molecules. The harvested energy makes high-energy ATP molecules, which perform work, powering many chemical reactions in the cell. The amount of energy needed to make one glucose molecule from six carbon dioxide molecules is 18 ATP molecules and 12 NADPH molecules (each one of which is energetically equivalent to three ATP molecules), or a total of 54 molecule equivalents required for synthesizing one glucose molecule. This process is a fundamental and efficient way for cells to generate the molecular energy that they require.

Metabolic Pathways

The processes of making and breaking down sugar molecules illustrate two types of metabolic pathways. A metabolic pathway is a series of interconnected biochemical reactions that convert a substrate molecule or molecules, step-by-step, through a series of metabolic intermediates, eventually yielding a final product or products. In the case of sugar metabolism, the first metabolic pathway synthesized sugar from smaller molecules, and the other pathway broke sugar down into smaller molecules. Scientists call these two opposite processes—the first requiring energy and the second producing energy—anabolic (building) and catabolic (breaking down) pathways, respectively. Consequently, building (anabolism) and degradation (catabolism) comprise metabolism.

Evolution Connection

Evolution of Metabolic Pathways

There is more to the complexity of metabolism than understanding the metabolic pathways alone. Metabolic complexity varies from organism to organism. Photosynthesis is the primary pathway in which photosynthetic organisms like plants (planktonic algae perform the majority of global photosynthesis) harvest the sun’s energy and convert it into carbohydrates. The by-product of photosynthesis is oxygen, which some cells require to carry out cellular respiration. During cellular respiration, oxygen aids in the catabolic breakdown of carbon compounds, like carbohydrates. Among the products are CO2 and ATP. In addition, some eukaryotes perform catabolic processes without oxygen (fermentation) that is, they perform or use anaerobic metabolism.

Organisms probably evolved anaerobic metabolism to survive (living organisms came into existence about 3.8 billion years ago, when the atmosphere lacked oxygen). Despite the differences between organisms and the complexity of metabolism, researchers have found that all branches of life share some of the same metabolic pathways, suggesting that all organisms evolved from the same ancient common ancestor (Figure 6.4). Evidence indicates that over time, the pathways diverged, adding specialized enzymes to allow organisms to better adapt to their environment, thus increasing their chance to survive. However, the underlying principle remains that all organisms must harvest energy from their environment and convert it to ATP to carry out cellular functions.

Anabolic and Catabolic Pathways

Anabolic pathways require an input of energy to synthesize complex molecules from simpler ones. Synthesizing sugar from CO2 is one example. Other examples are synthesizing large proteins from amino acid building blocks, and synthesizing new DNA strands from nucleic acid building blocks. These biosynthetic processes are critical to the cell's life, take place constantly, and demand energy that ATP and other high-energy molecules like NADH (nicotinamide adenine dinucleotide) and NADPH provide (Figure 6.5).

ATP is an important molecule for cells to have in sufficient supply at all times. The breakdown of sugars illustrates how a single glucose molecule can store enough energy to make a great deal of ATP, 36 to 38 molecules. This is a catabolic pathway. Catabolic pathways involve degrading (or breaking down) complex molecules into simpler ones. Molecular energy stored in complex molecule bonds release in catabolic pathways and harvest in such a way that it can produce ATP. Other energy-storing molecules, such as fats, also break down through similar catabolic reactions to release energy and make ATP (Figure 6.5).

It is important to know that metabolic pathway chemical reactions do not take place spontaneously. A protein called an enzyme facilitates or catalyzes each reaction step. Enzymes are important for catalyzing all types of biological reactions—those that require energy as well as those that release energy.


Course Content

Unit 1 : Driving Question: What is sustainable agriculture?

Unit 1 Description

This introductory unit will focus on the biological classifications of agriculture and their associated industry sectors, what sustainability is, and how the scientific method is the driving force behind advancements and developments in sustainable biological practices within agriculture. Students develop an overview of agricultural industries and biologic practices through research projects on facets of California agriculture, and identify what sustainability and sustainable practices are through individualized lab experiments relating to current practices. Ultimately, students will be able to use the scientific method to complete an extensive laboratory experiment that is designed to evaluate potential feed source varieties for sustainable success within their local community.

Unit 1 Key Assignments

1. “What is sustainable agriculture?”

Students groups will research the various biological divisions of what constitutes agriculture (plant science, animal science, forestry, horticulture, etc.). Within their research they will identify the sub categories of industry that fall within their topic, what career paths are available within each, what are currently identified as “best practices” (such as the three E’s of sustainability -- economics, ecology and equity) and what are some of the sustainability issues and biologic concerns within each of these divisions.  Students will then develop a multimedia presentation to introduce their particular area of agriculture to the class and identify the most prevalent issues facing their particular field of interest.

2.“That’s Ag - The Science Behind Agriculture” – Categorical Based Mini-Labs:

Student groups will design and complete an inquiry based mini-lab experiment to expand on their knowledge of the particular industry sector they researched from the previous activity. Choosing a focus from one of the areas of concern or issues within their sector, students will then design and implement an experiment that tests factors contributing to the issue and potential impacts they have on the population using scientific method learned in class. Examples might include a lab on animal production and energy flow, a lab on soil degradation and plant germination, a lab on food processing practices, a lab on post-harvest preservation, etc.  The labs will introduce the application of inquiry within the agriculture sectors and the importance of the implementation of research in the industry. Design protocols, data, and analysis will be submitted in lab report format.  As part of their analysis, students must use their data to make suggestions on how to improve efficiency or yield, or lessen the impact of processing, relevant to their finding of their particular experiment.

3. Scientific Method and Sustainability Lab – “Work Like a Scientist”

In this lab students are introduced to the scientific method, the basis for all scientific decision making.  The native grasses research will provide students with the foundation of scientific investigation application as well providing key research that will be used in the final unit project as well as the end of course project. Students will research the difference between native grasses versus invasive grasses including specific species. Using this knowledge they will hypothesize germination rates between these two variable groups.  Students will then design and implement an experiment incorporating quantitative data collection, analysis, and draw conclusions reflective to their hypothesis, and evaluate the grasses for potential sustainability within their communities.

As a continuation of the germination experiment, given that the two variables have differing germination rates, students can identify other measures of “success” of a potential feed crop. They will then sample the community environment for the potential factors affecting the continued growth and development of grasses.  Samples would include soil testing, (pH, nutrient composition, structure and texture, and water capacity), water availability, and ambient temperatures. Combining this information with the initial background research regarding natives versus invasive, students will hypothesize on the continued success of their germinating grasses, then transplant their seeds into test plots or fodder trays, and allow for continued growth.  After a predetermined amount of time, sample plots will be analyzed for percent coverage and measurements of species biomass will be completed. Using this information students will determine the most biologically suitable grass species to plant that would be the most sustainable within the local community through a written lab completed in their lab notebook and a powerpoint presentation of their hypothesis, design, data and conclusion.

Unit 2 : Driving Question: How does sustainable agriculture fit into our environment?

Unit 2 Description

While unit one examined whole systems, unit two takes a closer look at components within that system. Students will use evidence gathered from a series of laboratory exercises to be able to describe the transfer of energy from one trophic level to another as well as the cycling of nutrients and energy through ecosystems. Students will be able to draw conclusions about these biogeochemical cycles and how they apply to sustainability of production agriculture. Specifically, students will conduct primary research in the areas of photosynthesis and chemical energy creation, nutrient cycling, transpiration and water use, ecological relationships and global farming practices in order to draw biologically-sound conclusions regarding the effects of agriculture on the natural environment. The students learning will culminate in a synthesis of concepts applied to the development of a three year sustainable crop rotation plan.

Unit 2 Key Assignments

1. “Bacteria at Work” -  Nitrogen Fixation

Students will analyze the effects of nitrogen fixation on plants initially by examining prior studies as well as industry publications regarding the role of nitrogen in plant growth and the methods by which farmers enhance nitrogen levels in soil. This should include a thorough look at the microbiology of nitrogen-fixing bacteria, plant and root physiology, nutrient cycling and uptake in plants, chemical processes and cellular respiration in plants and fertilization methods. After garnering that background information, students will conduct an experiment that compares the effects of added nitrogen fertilizer versus nitrogen fixing bacteria on the growth of clover.  Students will grow clover plants in soil with no nitrogen added, in soil with nitrogen fertilizer added, and in soil containing nitrogen-fixing bacteria (in this case, a species of rhizobia called Rhizobium legominosarium, or R. legominosarium). Students will monitor the nitrogen levels in each type of soil using a nitrogen testing kit. The students will observe the effects of nitrogen on the health of the clover plants by measuring the increase in biomass of each plant during the experiment. Plants should be harvested, soil washed away, and weights taken on plant material produced. Students will use the data collected to create a graph showing the relationship between nitrogen availability in the soil and crop sustainability. This allows students to not only experience agriculture’s role in the nitrogen cycle, but also provides necessary supporting data for decision making in the final end of course project.

2. “Morning Jolt!”- Photosynthesis Lab

Photosynthesis is the basis for the creation of chemical energy in the natural world. Plants require light in order to transform one type of energy into another, and the quantity and type of light determine the optimal photosynthesis rates. Students will conduct a laboratory exercise that examines the effects of shade on the growth of plants and the rates of photosynthesis and will develop a written memorandum to the International Coffee Growers Association regarding optimal shade levels for the growth of coffee trees, including information regarding ecological sustainability involved in the practice. The process will begin by using industry journals to examine coffee production methods primarily comparing and contrasting industrial coffee production with shade-grown, sustainable coffee production. Students should come up with the following information: arabica coffee has the highest yields under 35 to 65% shade. In addition, growing coffee under shade also discourages weed growth, may reduce pathogen infection, protect the crop from frost, and helps to increase numbers of pollinators which results in better fruit set. However, in order to produce faster, higher yields and prevent the spread of coffee leaf rust (Hemileia vastatrix), many coffee plantations began to grow coffee under sunnier conditions. The fewer shade trees that are in coffee plantations, the less biodiversity there is in those plantations.

The laboratory exercise will use several small coffee plant starts (available for purchase online as seeds or a houseplant) and will grow them for a series of days under varying shade levels. Students will conduct visual assessments of plant health and growth, then conduct a traditional floating leaf disc assay protocol to assess photosynthesis levels under varying light conditions. Students will use both the previously gathered background information regarding industry practices, sustainability and plant growth as well results of the primary research to develop the memorandum regarding optimal shade levels for sustainable coffee growth.

3. “Move on Through” - Transpiration Lab

Students will initially conduct background research into water use in agriculture and the demands placed on farmers to be efficient and careful with this scarce natural resource. Students will then investigate transpiration as part of the hydrologic system, based on different genetic variations of plant structure (leaf type and shape, for example). Students will conduct a research exercise by examining transpiration in plants with various leaf structures. This can occur using locally-grown crops or by using exotic crops and adding a component regarding appropriate plant selection. In this lab, students will use the plant weight protocol to measure the transpiration rates of individual plants. Students give plants a predetermined amount of water, reweigh the plants, and continue weighing the plants over time to contrast weight differentials and determine water loss through transpiration. Students will monitor observable physical changes in the different plants’ condition as water is depleted, collecting qualitative data and measuring the diurnal transpiration rates. Students will apply the individual plant water usage data to larger scale acreage to analyze water usage. Students will create a written case study to justify plant selection within the context of the sustainability of the hydrologic system.

Optional extension: include in the case study how trends in daily transpiration rates change if water losses were replenished through different irrigation management techniques (drip, flood, etc.).

4. “From Trash to Gas” - Sustainable Waste Management

Students will use both primary and secondary research to discover that food scraps, dead plants, manure, and other decaying organic matter, called biomass are a rich source of energy. Energy can be procured from biomass by turning it into a gas called biogas.  The process will begin by students examining agricultural examples of biogas production (small scale composting, dairy lagoon gas extraction, codigestion, etc.) as well as the microbiological basis for biogas production, including aerobic and anaerobic fermentation, cellular respiration, lignocellulosic breakdown, etc. As part of this analysis, students will compare the amounts of biogas produced by different types of biomass. In order to quantify their findings, students will conduct an experiment with three soda bottles filled to the same volume with various types of biomass commonly used in biogas production.  Bottle one will contain cow manure, bottle two will contain cow manure and household kitchen scraps, and bottle three will contain cow manure and a biological waste product of the students choosing (teacher approved). Bottles will be topped with a small balloon. Students will record the circumference of each of the balloons at the same time of day over a period of 10 days as well as record observations of the biomass inside of the bottles. Students will create a graph representing the circumference of balloons and the number of days. Students will compare graphs to determine which biomass type produced the fastest inflation of the balloon.  Upon completion of the experiment, the students will then need to develop a written plan for how this naturally occurring byproduct can be harnessed to benefit a farming situation. In addition to incorporating their data, this plan should include: research on how the gas is used, the scientific processes behind biogas creation (fermentation, anaerobic digestion, etc.), biomass feedstocks that can be used to create efficient quantities of biogas, potential uses of biogas, and potential economic and sustainable benefits of instituting a biomass digester.

5. “Composting, Do the Rot Thing”

Students will examine the principle of composting organic material, and the process of converting complex organic matter into the basic nutrients needed by living organisms. Prior to conducting the experiment, students will use industry and extension publications to learn the processes of composting, as well as the benefits and challenges of compost production (available nutrient levels, community perceptions, hazardous materials, smell, storage, etc.). Following the background research, students will conduct a laboratory exercise that will examine the utilization of organic wastes (household) as nutrients for plants. It will allow students to investigate which waste products can be composted and best utilized by plants. Based off of prior knowledge of an ecosystem and how ecosystems regenerate as well as the interaction of food and fiber systems with natural cycles, students will justify specific nutrient requirements, as well as renewable and nonrenewable natural resources. Students will prepare three test plots, one plot with just soil, one with soil and household waste products collected by students, and one plot with animal waste products. Students will then monitor plant growth and development to graph their results. Students will create an informational, six paneled brochure that explains a waste management plan using compost. Included in the brochure should be information regarding the microbiology of compost production in addition to the practical household application of the research. Additionally, the brochure should outline the removal of organic matter to increase ecological sustainability while having the least environmental impact on the farm and community.

Unit 2. Assessment

Plant, Grow, Rotate, Repeat Sustainable Crop Management Plan

Students will apply concepts of the biogeochemical cycles as well as waste management to create a 3 year sustainable crop rotation plan that produces the highest crop yields for any given location with the least environmental impact. Students must analyze current soil conditions as well as community needs when considering their crops for production. Student focus should be on nitrogen fixation of specified crops. Students will use previous knowledge of ecosystems, invasive species, and producer and consumer relationships as well as research current market prices and local demands, to assess the environmental contribution and the economical impact from each crop. When creating the 3 year crop rotations students will defend their selections and the ecological impacts of their decisions. The synthesis of the students’ research will culminate in written proposal to a local producer.

Unit 3 : Driving Question - What molecular biology principles guide sustainable agriculture?

Unit 3 Description

In this unit, students will examine the science of agriculture and evaluate the efficiency and sustainability of current methods. Students will explore the concepts of taxonomy of plants and nomenclature of animals, cell structure, cellular division, DNA, and chromosomes. Students will apply this knowledge to evaluate desirable inheritable traits in each species to artificially select characteristics to breed more efficient and productive offspring as a part of their created breeding plan. Students will be introduced to genetic markers, genetically modified organisms, and biotechnology. With this knowledge students will examine and evaluate biotechnology, the ethics of genetic manipulation, and its implication on the sustainability of agriculture and our ability to feed a growing population.  As a culminating project for the first two units students will design, conduct, and interpret their own agricultural research project on a biological issue facing agriculture and present their findings with a visual, written, and oral report.

Unit 3 Key Assignments

1. “Breed For The Need”- Sustainable Breeding Evaluation

Animal genetics play a role in sustainability. An animal that is genetically predicted to become heavier muscled in a shorter period of time will utilize less pasture and nutritive resources than one that takes longer to reach the same weight. A female who produces more milk to feed her offspring will utilize less resources for both her and her progeny. Therefore, summative phenotypic traits are important to evaluate in a sustainable ecosystem in order to efficiently utilize natural resources.  By analyzing these traits students can determine the probability of the trait expression in an animal’s offspring. After instruction on chromosomal physiology, multicellular organization, animal anatomy, basic heredity, and genetic expression, students will identify desirable characteristics from a group of four animals of the same species to create a sustainable breeding plan that will include: hybrid vigor, genetic efficiency and other genetic traits. Students will use three components to evaluate the group of four animals that include the farmer’s sustainability scenario, expected progeny difference data and phenotypic evaluation of the animals. First students will read an agricultural producer’s written scenario that describes the targeted phenotypic traits a farmer desires based on the environment that must sustain the health and nutrition of the specific animals while not depleting the natural resources within that biological system. The parameters of the traits the students will evaluate include milk production (the weight of the weaned offspring that was contributed to the amount of milk the mother produced), weaning weight (the weight of the offspring when removed from the mother),  yearling weight ( the weight of the offspring at eighteen months of age and birth weight (the weight of the offspring at birth). Next, the students will read and analyze Expected Progeny Difference (Summative phenotype expression) data. Finally, students will perform visual observations of the phenotypic traits in those four animals. Students will assess and prioritize the three analyzed components based on importance and collectively use them to place the four animals in phenotypic order from the most desirable for the environment to the least desirable according to the farmer’s sustainability scenario. Students will give an oral defense with evidence to support reasoning.

2. “Where Should I Make My Home ?”- Sustainable Production Plan

The students will be put into groups and collectively evaluate the same animals from the previous activity with summative phenotypic traits for each of the bio-geological growing zones in California which are desert and high desert, coastal, valley, foothills and mountains. Instruction should occur on plant taxonomy and livestock anatomical suitability (large animals in areas with poor biomass production, genetic hardiness factors, etc.) prior to the secondary research being done. Research done on each zone will provide information on the possible sustainability plans in which the four animals could be raised. Students will research the ecosystem of each area, analyzing what crops, pasture and range can be grown and the effects of climate and rainfall on the availability of nutrients for the animals’ sustainability. Based on the data accumulated from the research they will reevaluate the four animals from the previous lab including EPD data.  For each zone they will place the animals in order from the one most suited and efficient to the least. Students construct a written defense for their decision in the placing of those animals in each zone based on their data and research. They will argue the merits of their placing based on the data from their zone research: native and nonnative grass and crop survivability in each zone that provides nutrition to the animals, biological merits and disadvantages of each zone on the animals. They will then use the zone information to reevaluate the EPD data and how it can be best utilized to meet the animal’s biological needs. Using the research and accumulated data students can determine a class placing for each region of California.

3. “Battle of the Seeds” - Biotechnology Use in Agriculture

Crop decisions made by agricultural producers are often predicated on understanding the climate, rainfall and topography needs of their growing area. These decisions often prioritize crop yield, but also must take into account  the biological health of each system. The previous lab focused on evaluating the efficiency of specific animals introduced into an ecosystem where the biological components were predetermined and consistent. In this activity, students explore the introduction of new plants into predetermined, consistent ecosystems by investigating how germination, growth and efficiency of plants (crops) can be affected by genetic and environmental changes. Prior to the experiment, students should be instructed in cell division and structure as functions of organism growth, genotypic traits and variable expression, traditional hybridization methods and modern genetic manipulation.

For the primary research exercise, students will set up three demonstration plots to compare growth and yield rates of plants.  Half of the class will grow unweeded plots of plants, manually weed-controlled beds, and chemically controlled beds with plants that have been genetically modified to withstand the effects of a widely-used herbicide. The other half of the class will grow hybrid seed, non-hybrid seed, and genetically enhanced seed of the same plant.  Upon analyzing data of plant growth and yield rates students will calculate the cost in time and money for the methods demonstrated. Students will formulate a written opinion/thesis and defend from evidence the most sustainable method of growing food based on their experiment. Students determine the statistical, economical and biological differences of genetically modified organisms as compared to natural organisms. Students will then research public concern of genetically modified organisms to prepare for a class debate. Utilizing their experimental results and research students debate the use of biotechnology and genetically modified organisms playing one of four following roles a leader of a developing nation where hunger is a problem among their citizens, a biotechnology company specializing in producing genetically modified plants, a farmer, or a parent who primarily purchases organic produce.  Students will reflect on their original opinion and write what they learned as a result of this experience.

Unit 3.  Assessment:

“Hypothesize, Analyze, Repeat” - Formal Research Project

Labs and activities have been done in this unit that represent the common applications of biological factors such as genetic potential and variability of plants and animals, the symbiosis of animals and plants within an ecosystem and the impact of new species introduced into an established environment. Students will utilize the science of nature they learned in unit three, how that science fits into the biological systems from unit two and how those systems contribute to sustainability in unit one to develop a comprehensive agriscience experimental research project. Students will identify a problem related to agriculture that is the result of completing the first three units of the course (plant science, animal science, natural resources).  Students will utilize the empirical method to design an experiment that will test their own authentic hypothesis using the skills and processes learned throughout the course that include dissecting published research and studies, testing the hypothesis, collecting, synthesizing, analyzing and interpreting data, accepting or rejecting the hypothesis based upon the data, technical reading and writing, and scientific collaboration. Specific expectations for the written research project are outlined below:

Students will use credible sources to conduct background research on the agricultural issue they are investigating, and they will use this research to generate a testable hypothesis related to the scientific problem they have identified.  The hypothesis developed by the student will be constructed with the independent and dependent variables in mind.

2. Experimental design and conducting experimentation

Students will construct an experimental design to test their hypothesis. A written experimental design should be constructed consistent with scientific protocol using a systematic approach outlined in the previous units. Students will have their experimental designs reviewed by industry experts, agricultural instructors, local growers/producers, researchers or university representatives. After validating the design using the peer review process, students will move to the experimentation phase of their research. Experimental designs should include replicates, control groups, and determine the variables to be controlled and how.  Additionally, a determination should be made as to the type of data that will be collected and in what ways, with the emphasis placed on quantitative data or quantifying data that is qualitative in nature. Students will use their experimental design to test their hypothesis. For example, in a study of primed versus non-treated seeds, seeds would be planted in identical environments, multiple test groups would be established and compared to a control group, and the number of germinated seeds would be counted and recorded to quantify the outcome. Raw data should be recorded using a field book or electronic device.

3. Analyzing data, interpreting data and forming conclusions.

Students will determine the best methods for organizing their data using tables.  Students will use mathematical principles to synthesize their data, calculating a mean, for example. Furthermore, a statistical analysis of the data will help the student determine if the results are due to chance or the independent variable that was tested.  Students will choose the best way to present their data using graphs they believe will most effectively demonstrate their findings, and will further summarize what each graph shows. Finally, students will interpret the data and formulate conclusions based on the results.  In the written conclusion, students will use their data to either accept or reject the original hypothesis. Conclusions should be directly supported by the data and supported by previous research. Students will also identify the limitations of their research, improvements that could be made to the experimental design, as well as future studies that may be conducted that relate the study at hand.

4. Evidence of Performing the AgriScience Research Project

Students will submit their research in a written paper, and it will include the following components: problem/purpose, background research, hypotheses, methodology, results/data, and discussion/ conclusion.  The paper will be written using skills associated with technical and scientific writing, for example, refraining from the use of personal pronouns or keeping discussion limited to what the research and data suggest rather than personal opinion and bias.  APA format will be utilized to reference and cite sources. Students will create a visual display board, using a digital format that mirrors the use of research posters in higher education, which will also include all of the components of the paper, but in a condensed form. The peer group that reviewed the original experimental design will review the final research paper.  The project and its findings will be shared with the class in an oral presentation, with the research board on display to aid in communicating the results of the research.

Unit 4 : Driving Question: How do we make decisions to maximize sustainable agricultural practices within a functioning ecosystem?

Unit 4 Description

Students will understand common practices in the agriculture industry that promote sustainability. They will evaluate and/or refine technological solutions that reduce impacts of human activities on natural systems by using  practices that utilize cellular biology, genetics, energy cycles, biological systems, plant and animal nomenclature and how these units collectively create ecosystems that were covered in the previous units. Students will conduct production practices in the areas of animal science, horticulture, and natural resources.  Students will experience how the biological systems can be changed at the cellular level, promoting the emergence of new energy cycles that produce useful, recyclable products that have a positive impact on the environment, thus decreasing the impact of agriculture on the environment and promoting sustainability. Students will investigate positive sustainable approaches to changing negative impacts agriculture has on the land by testing methods of efficiency in laboratory work. This experience will give students perspective on production costs and resource needs in relation to animal welfare, mechanization versus labor, and use of chemicals to non-use of chemicals. Students will utilize this hands-on production experience to develop their own sustainable farm as a culminating final project to illustrate the management of agricultural systems, management of natural resources , the sustainability of an ecosystem for the future while preserving biodiversity.

Unit 4 Key Assignments

1. “Show Me You Care” - Practice in Animal Health  Management

Common animal production practices are done to ensure multi-system homeostasis and to foster productive animal growth and general welfare. Prior to conducting a laboratory exercise, students will engage in secondary research that seeks to correlate common livestock production practices to maintaining system health in animals. For example, castration, tail banding, hoof trimming and vaccinations prevent pathogen (viral, bacterial, fungal and parasitic) infections and thereby ensuring the health of the immune system, lymphatic system and respiratory system, among others.  Shearing, clipping and dehorning are noninvasive procedures that provide recycling opportunities of animal byproducts but are also designed to maintain homeostasis and to protect vital organs throughout multiple systems (shearing reduces overall stress on the circulatory system, for example). Animal identification requires animals to have a traceable number like the scrapie tag that traces the animal to the breeder in case an animal tests positive for the genetic disease and ensure herd health (preventing disease outbreaks that can stress multiple systems).

After the conclusion of the background research, students will engage in a laboratory experience where they will conduct common livestock production procedures practiced in the United States through the application of: castration methods, dehorning practices, vaccination protocols, identification systems and shearing techniques. Students will divide into groups to demonstrate one or more of the common livestock production practices within several species of livestock and small animals.  After the conclusion of each of these demonstrations, students will choose one method they demonstrated and write an explanatory position paper that correlates the production practice to physiological health in the animal, highlighting homeostatic mechanisms and system nomenclature.

2. “If You Root It, They Will Grow” -  Sustainable Practices in Horticulture

The ability to graft, increase growth rates and clone species of plant, trees and crops is an option that can increase the number of organisms that can be planted in a shorter amount of time. Using one plant to create many or the ability to grow different varieties of fruit on one tree maximizes the efficiency of each organism within an ecosystem.  The ability to utilize this technology increases species diversity while positively affecting land biomass. Students will experience a laboratory activity, conducting propagation techniques that make plants more efficient and in return contribute to the energy cycles within the ecosystem potentially maximizing sustainability of the plant and its production.This laboratory lets students use asexual propagation through the application of auxins directly onto plants used as a common practice in the horticultural industry. Students will also research the role of auxins and make predictions on its effectiveness on their assigned mother stock plant. Through teacher demonstration, students will learn the proper steps of asexual propagation and make cuttings of their plant.  Each student will test the effectiveness of auxins (rooting growth hormone) with one row in a flat being a different concentration of hormone and one control. After two weeks students will collect data every three days and record the rate at which their plant cutting roots. Students will calculate the cost of hormone treatment versus the time for cuttings to root to recommend the use or non-use of auxins on their assigned plant in their lab report.

In the next step of the laboratory students will practice the proper steps of transplanting and fertilizer use as regular practice in the horticultural industry.  Students will take their rooted cuttings and transplant them to a larger container. After direct instruction on types of fertilizers, students will make predictions on the most effective type of fertilizer for their rooted cuttings liquid, slow release, and organic. Students will be assigned a growing area (landscape plot, or one gallon-containers) to conduct their experiment.  Students will test each type of fertilizer with four rows of plants. One row will be the control, without fertilizer application and the other three rows will have liquid, slow release, and organic fertilizer applications. Students will take daily measurements and make final conclusions of fertilizer effectiveness for their plant. Students also compare cost of fertilizer to effectiveness to determine final recommendations in their lab report.

3. “It’s Easy Being Green - Growing Green Communities” -  Landscaping  

Students will utilize the Horticulture report and experience to create a landscape plan in groups.  Students will utilize the original cuttings from the previous activity which are now grown plants. Each group will use those plants in designing a landscape for a specific area designated by the teacher that could include areas around the school and/or community. Students must consider plant growth requirements, resources such as water, soil quality, and fertilization needs. Students must address the long term needs of their landscape and write a reflection on the positive and negative aspects with recommendations for more sustainable qualities. The students will submit their designs in a written proposal to the school and or community organizations for approval. Those approved will be planted and maintained by the group for the rest of the year.

4. “Use Me Responsibly or Lose Me Forever” -  Using Nature’s Natural Resources Students will delve deeper into natural resources conducting research on bioprospecting. They will use the knowledge gained within this unit regarding the potential to change the future through bioprospecting and the need to prevent the exploitation of those resources to preserve the biospheres for future generations. Students will read articles about the use of plants and animals in nature like coral producing a natural sunscreen named, “Sunscreen 855”.  To prevent the harvest of coral in order to save the barrier reef they isolated the compound and produced it in a lab that will be the most naturally occurring sunscreen developed. Students will discuss the importance of bioprospecting, as well as how the prospect of products from plants and animals argues for the continued maintenance of biodiversity and sustainability as long as the resources are not exploited.(Biology,Prentice Hall) After the discussion students will research other types of bioprospecting happening in agriculture. They will choose one material (natural resource) being prospected and find the following information from their research: what research is being done on the material, how are they utilizing the material and how does the research and use of the material play a role in sustainability. The information accumulated on the material bioprospecting will be utilized in a flyer created by each student. The flyers will be set-up in a walking gallery where the students will use a bioprospecting rubric to score the importance of each natural resource presented as a valuable material for continued research. The students will have a class discussion about which three natural resources are the most valuable source of bioprospecting to contribute to sustainability of the human population.

5. Bioprospecting - “Motoring with Microbes” – Discovering Cellulose Microbes for Biofuel Efficiency

The students will then conduct a research lab on Bioprospecting for Cellulose-Degrading Microbes: Filter Paper Assay Method where Students collect samples that they predict will contain communities of cellulose-degrading microbes and test for the ability of microorganisms in their samples to break down pure cellulose (filter paper). In the process, groups collect evidence to test predictions about which environmental microbial samples will be the most effective for degrading cellulose. By comparing results across groups, students can begin to uncover patterns and develop explanations about the types of environments that support cellulose-degrading microbes. This lab method is nearly identical to that used by researchers and student results could help scientists discover new enzymes for efficient biofuel production that is key in agriculture’s ability to remain sustainable in the next century. Students will turn in a completed lab using scientific method and write an abstract of their research to send to the Great Lakes Bioenergy Research Center as part of their on going research on biofuel. Great Lakes Bioenergy Research Center Classroom Materials 

Unit 4. Assessment and End of Course Project

“I Believe in the Future of Agriculture” - Sustainable Farming Project

Students will design a solution for developing, managing, and utilizing energy and resources through the development of a completely sustainable farm on 400 acres that must include a minimum of three crops and two species of animals.  A comprehensive farming portfolio will be created. The portfolio will include data and research done from each unit within the course to be used to create their farm as well as provide evidence to defend the sustainability of that farm and thus, the best representative of sustainability. The students must research genetic varieties of crops and species of animals based on genetic efficiency and commensalism. Attention to how soil nutrients and deficiencies affect vegetative reproduction, germination, plant growth and crop adaptation within an environment must be utilized in the research.  Based on the data the students will determine the crops to be produced. They will research and evaluate the species of animals that will have a symbiotic relationship with the crops they have chosen above. Phenotypic and genotypic traits, hybrid vigor, commensalism, and other variables should be used to determine the two species of animals that will be best suited for the designed environment while providing for the welfare of the animals’ health and nutrition. Animal welfare must be addressed in the decisions made to create a farm that is positive and biodiverse in nature. Environmental impacts based on the crops and animals raised on the farm need to be identified dealing with biological magnification, depletion of soil /plant nutrients , use of natural resources , pollution issues dealing with waste and desertification. The students will use this information as well as the data and labs from the previous units to determine the carrying capacity of livestock and acres of crops to be grown on the farm . Biological methods of reducing the identified environmental impacts will then be designed by the student, which could include methane digesters, aquaculture, CO2 collectors and irrigation water recycling. Finally, students will  address the management decisions made to reduce the farm’s carbon footprint over a decade of production. The portfolio and presentations will be presented to the local farm bureau as well as other agriculture associations and businesses.


Testing Darwin

If you want to find alien life-forms, hold off on booking that trip to the moons of Saturn. You may only need to catch a plane to East Lansing, Michigan.

The aliens of East Lansing are not made of carbon and water. They have no DNA. Billions of them are quietly colonizing a cluster of 200 computers in the basement of the Plant and Soil Sciences building at Michigan State University. To peer into their world, however, you have to walk a few blocks west on Wilson Road to the engineering department and visit the Digital Evolution Laboratory. Here you’ll find a crew of computer scientists, biologists, and even a philosopher or two gazing at computer monitors, watching the evolution of bizarre new life-forms.

These are digital organisms—strings of commands—akin to computer viruses. Each organism can produce tens of thousands of copies of itself within a matter of minutes. Unlike computer viruses, however, they are made up of digital bits that can mutate in much the same way DNA mutates. A software program called Avida allows researchers to track the birth, life, and death of generation after generation of the digital organisms by scanning columns of numbers that pour down a computer screen like waterfalls.

After more than a decade of development, Avida’s digital organisms are now getting close to fulfilling the definition of biological life. “More and more of the features that biologists have said were necessary for life we can check off,” says Robert Pennock, a philosopher at Michigan State and a member of the Avida team. “Does this, does that, does this. Metabolism? Maybe not quite yet, but getting pretty close.”

One thing the digital organisms do particularly well is evolve. “Avida is not a simulation of evolution it is an instance of it,” Pennock says. “All the core parts of the Darwinian process are there. These things replicate, they mutate, they are competing with one another. The very process of natural selection is happening there. If that’s central to the definition of life, then these things count.”

It may seem strange to talk about a chunk of computer code in the same way you talk about a cherry tree or a dolphin. But the more biologists think about life, the more compelling the equation becomes. Computer programs and DNA are both sets of instructions. Computer programs tell a computer how to process information, while DNA instructs a cell how to assemble proteins.

The ultimate goal of the instructions in DNA is to make new organisms that contain the same genetic instructions. “You could consider a living organism as nothing more than an information channel, where it’s transmitting its genome to its offspring,” says Charles Ofria, director of the Digital Evolution Laboratory. “And the information stored in the channel is how to build a new channel.” So a computer program that contains instructions for making new copies of itself has taken a significant step toward life.

A cherry tree absorbs raw materials and turns them into useful things. In goes carbon dioxide, water, and nutrients. Out comes wood, cherries, and toxins to ward off insects. A computer program works the same way. Consider a program that adds two numbers. The numbers go in like carbon dioxide and water, and the sum comes out like a cherry tree.

In the late 1990s Ofria’s former adviser, physicist Chris Adami of Caltech, set out to create the conditions in which a computer program could evolve the ability to do addition. He created some primitive digital organisms and at regular intervals presented numbers to them. At first they could do nothing. But each time a digital organism replicated, there was a small chance that one of its command lines might mutate. On a rare occasion, these mutations allowed an organism to process one of the numbers in a simple way. An organism might acquire the ability simply to read a number, for example, and then produce an identical output.

Adami rewarded the digital organisms by speeding up the time it took them to reproduce. If an organism could read two numbers at once, he would speed up its reproduction even more. And if they could add the numbers, he would give them an even bigger reward.Within six months, Adami’s organisms were addition whizzes. “We were able to get them to evolve without fail,” he says. But when he stopped to look at exactly how the organisms were adding numbers, he was more surprised. “Some of the ways were obvious, but with others I’d say, ‘What the hell is happening?’ It seemed completely insane.”

On a trip to Michigan State, Adami met microbiologist Richard Lenski, who studies the evolution of bacteria. Adami later sent Lenski a copy of the Avida software so he could try it out for himself. On a Friday, Lenski loaded the program into his computer and began to create digital worlds. By Monday he was tempted to shut down his laboratory and dedicate himself to Avida. “It just had the smell of life,” says Lenski.

It also mirrored Lenski’s own research, launched in 1988, which is now the longest continuously running experiment in evolution. He began with a single bacterium— Escherichia coli —and used its offspring to found 12 separate colonies of bacteria that he nurtured on a meager diet of glucose, which creates a strong incentive for the evolution of new ways to survive. Over the past 17 years, the colonies have passed through 35,000 generations. In the process, they’ve become one of the clearest demonstrations that natural selection is real. All 12 colonies have evolved to the point at which the bacteria can replicate almost twice as fast as their ancestors. At the same time, the bacterial cells have gotten twice as big. Surprisingly, these changes didn’t unfold in a smooth, linear process. Instead, each colony evolved in sudden jerks, followed by hundreds of generations of little change, followed by more jerks.

Similar patterns occur in the evolution of digital organisms in Avida. So Lenski set up digital versions of his bacterial colonies and has been studying them ever since. He still marvels at the flexibility and speed of Avida, which not only allow him to alter experimental conditions with a few keystrokes but also to automatically record every mutation in every organism. “In an hour I can gather more information than we had been able to gather in years of working on bacteria,” Lenski says. “Avida just spits data at you.”

With this newfound power, the Avida team is putting Darwin to the test in a way that was previously unimaginable. Modern evolutionary biologists have a wealth of fossils to study, and they can compare the biochemistry and genes of living species. But they can’t look at every single generation and every single gene that separates a bird, for example, from its two-legged dinosaur ancestors. By contrast, Avida makes it possible to watch the random mutation and natural selection of digital organisms unfold over millions of generations. In the process, it is beginning to shed light on some of the biggest questions of evolution.

QUESTION #1: WHAT GOOD IS HALF AN EYE?

If life today is the result of evolution by natural selection, Darwin realized, then even the most complex systems in biology must have emerged gradually from simple precursors, like someone crossing a river using stepping-stones. But consider the human eye, which is made of many different parts—lens, iris, jelly, retina, optic nerve—and will not work if even one part is missing. If the eye evolved in a piecemeal fashion, how was it of any use to our ancestors? Darwin argued that even a simpler version of today’s eyes could have helped animals survive. Early eyes might have been nothing more than a patch of photosensitive cells that could tell an animal if it was in light or shadow. If that patch then evolved into a pit, it might also have been able to detect the direction of the light. Gradually, the eye could have taken on new functions, until at last it could produce full-blown images. Even today, you can find these sorts of proto-eyes in flatworms and other animals. Darwin declared that the belief that natural selection cannot produce a complex organ “can hardly be considered real.”

Digital organisms don’t have complex organs such as eyes, but they can process information in complex ways. In order to add two numbers together, for example, a digital organism needs to carry out a lot of simpler operations, such as reading the numbers and holding pieces of those numbers in its memory. Knock out the commands that let a digital organism do one of these simple operations and it may not be able to add. The Avida team realized that by watching a complex organism evolve, they might learn some lessons about how complexity evolves in general.

The researchers set up an experiment to document how one particularly complex operation evolved. The operation, known as equals, consists of comparing pairs of binary numbers, bit by bit, and recording whether each pair of digits is the same. It’s a standard operation found in software, but it’s not a simple one. The shortest equals program Ofria could write is 19 lines long. The chances that random mutations alone could produce it are about one in a thousand trillion trillion.

To test Darwin’s idea that complex systems evolve from simpler precursors, the Avida team set up rewards for simpler operations and bigger rewards for more complex ones. The researchers set up an experiment in which organisms replicate for 16,000 generations. They then repeated the experiment 50 times.

Avida beat the odds. In 23 of the 50 trials, evolution produced organisms that could carry out the equals operation. And when the researchers took away rewards for simpler operations, the organisms never evolved an equals program. “When we looked at the 23 tests, they were all done in completely different ways,” adds Ofria. He was reminded of how Darwin pointed out that many evolutionary paths can produce the same complex organ. A fly and an octopus can both produce an image with their eyes, but their eyes are dramatically different from ours. “Darwin was right on that—there are many different ways of evolving the same function,” says Ofria.

The Avida team then traced the genealogy leading from the first organism to each one that had evolved the equals routine. “The beauty of digital life is that you can watch it happen step by step,” says Adami. “In every step you would ordinarily never see there is a goal you’re going toward.” Indeed, the ancestors of the successful organisms sometimes suffered harmful mutations that made them reproduce at a slower rate. But mutations a few generations later sped them up again.

When the Avida team published their first results on the evolution of complexity in 2003, they were inundated with e-mails from creationists. Their work hit a nerve in the antievolution movement and hit it hard. A popular claim of creationists is that life shows signs of intelligent design, especially in its complexity. They argue that complex things could have never evolved, because they don’t work unless all their parts are in place. But as Adami points out, if creationists were right, then Avida wouldn’t be able to produce complex digital organisms. A digital organism may use 19 or more simple routines in order to carry out the equals operation. If you delete any of the routines, it can’t do the job. “What we show is that there are irreducibly complex things and they can evolve,” says Adami.

The Avida team makes their software freely available on the Internet, and creationists have downloaded it over and over again in hopes of finding a fatal flaw. While they’ve uncovered a few minor glitches, Ofria says they have yet to find anything serious. “We literally have an army of thousands of unpaid bug testers,” he says. “What more could you want?”

QUESTION #2: WHY DOES A FOREST HAVE MORE THAN ONE KIND OF PLANT?

When you walk into a forest, the first thing you see is diversity. Trees tower high overhead, ferns lurk down below, vines wander here and there like tangled snakes. Yet these trees, ferns, and vines are all plants, and as such, they all make a living in the same way, by catching sunlight. If one species was better than all the rest at catching sunlight, then you might expect it to outcompete the other plants and take over the forest. But it’s clear that evolution has taken a different course.

Figuring out why is a full-time job for a small army of biologists. A number of them seek enlightenment by comparing places that are rich and poor in species and trying to figure out the other things that make them different. One intriguing pattern has to do with food. Ecologists have found that the more energy a habitat can provide organisms, the more species it can support. But a habitat can get too productive. Then it supports fewer species. This pattern has emerged time and again in studies on ecosystems ranging from grasslands to Arctic tundra.

Until recently, a typical Avida experiment would end up with a single dominant organism. The Avida researchers suspected that was the result of providing an endless supply of food—in this case, numbers. Perhaps, they reasoned, if they put their digital organisms on a diet, they might evolve into different forms—just as it happens in nature. So the Avida team retooled their software to limit the supply of numbers flowing into their digital worlds. Then they made the numbers even more scarce by splitting them up into smaller supplies, each of which could be used only for a particular operation, such as adding two numbers. As the organisms used the numbers at a faster rate, they got a smaller benefit. And if too many organisms gorged themselves on one supply of numbers, they would stop replicating altogether.

The Avida team subsequently flooded some digital worlds with numbers and limited others to a scant supply, and the same pattern of diversity found in global ecosystems emerged. When the number supply was low, only one type of organism could survive. At intermediate levels, three or four different types emerged and coexisted. Each type evolved into a specialist at one or a few kinds of operations. But when the number supply got too abundant, diversity dropped to a single species again.

Bringing diversity into Avida has brought more bad news for those who think complexity cannot evolve. Ofria decided to run the complexity experiment over again, this time with a limit on the supply of numbers. “It just floored me,” he says. “I went back and checked this so many ways.” In the original experiment, the organisms evolved the equals routine in 23 out of 50 trials. But when the experiment was run with a limited supply of numbers, all the trials produced organisms that could carry out the equals routine. What’s more, they needed only a fifth of the time to do it.

Ofria suspects that the difference comes from the fact that several species are now evolving in the experiment rather than just one. More species mean more opportunities for success.

Human society depends on countless acts of cooperation and personal sacrifice. But that doesn’t make us unique. Consider Myxococcus xanthus , a species of bacteria that Lenski and his colleagues study. Myxococcus travels in giant swarms 100,000 strong, hunting down E. coli and other bacteria like wolves chasing moose. They kill their prey by spitting out antibiotics then they spit out digestive enzymes that make the E. coli burst open. The swarm then feasts together on the remains. If the Myxococcus swarm senses that they’ve run out of prey to hunt, they gather together to form a stalk. The bacteria at the very top of the stalk turn into spores, which can be carried away by wind or water to another spot where they can start a new pack. Meanwhile, the individuals that formed the stalk die.

This sort of cooperation poses a major puzzle because it could be undermined by the evolution of cheaters. Some bacteria might feast on the prey killed by their swarm mates and avoid wasting their own energy making antibiotics or enzymes. Others might evolve ways of ensuring that they always end up becoming spores and never get left behind in the dead stalk. Such cheaters are not theoretical: Lenski and his colleagues have evolved them in their lab.

The Avida team is now trying to address the mystery of cooperation by creating new commands that will let organisms exchange packages of information. “Once we get them to communicate, can we get them to work together to solve a problem?” asks Ofria. “You can set up an information economy, where one organism can pay another one to do a computation for it.”

If digital organisms cooperate, Ofria thinks it may be possible to get them working together to solve real-world computing problems in the same way Myxococcus swarms attack their prey. “I think we’ll be able to solve much more complex problems, because we won’t have to know how to break them down. The organisms will have to figure it out for themselves,” says Ofria. “We could really change the face of a lot of computing.”

Birds do it, bees do it, and even fleas do it—but why they all do it is another matter. Reproduction is possible without sex. Bacteria and protozoa simply split in two. Some trees send shoots into the ground that sprout up as new trees. There are even lizard species that are all female. Their eggs don’t need sperm to start developing into healthy baby female lizards.

“One of the biggest questions in evolution is, why aren’t all organisms asexual?” says Adami. Given the obvious inefficiency of sex, evolutionary biologists suspect that it must confer some powerful advantage that makes it so common. But they have yet to come to a consensus about what that advantage is.

So Dusan Misevic, a biologist at Michigan State, has spent the past couple of years introducing sex into Avida. While digital sex may lack romance, it features the most important element from an evolutionary point of view: the genetic material from two parents gets mixed together in a child. When a digital organism makes a copy of itself, the copy doesn’t immediately take its own place in Avida and start reproducing. Instead, chunks of its code are swapped with the copy of another new organism. Only after this exchange do the two creatures start to reproduce.

In 1964 the German biologist H. J. Muller proposed that sex allows organisms to mix their genomes together in combinations that can overcome the effects of harmful mutations. Asexual organisms, on the other hand, are stuck with all the mutations their ancestors pass down to them. Over time, Muller argued, they can’t reproduce as quickly as their sexual competitors. Misevic designed an experiment to put Muller’s hypothesis to the test. “It’s a classic explanation, so it seemed like a good place to start,” he says.

Misevic created two kinds of worlds: one full of sexual digital organisms and the other full of asexuals. After they had evolved for tens of thousands of generations, he measured how fast they could replicate. “The overall conclusion we got was that, yes, there are some situations where sex is beneficial,” says Misevic. But there were surprises. Sex is good mainly as a way to escape annihilation from lethal mutations. But in Avida, sexual organisms had to pay a price for that insurance—they carried more nonlethal yet harmful mutations than the asexual organisms.

“We must look to other explanations to help explain sex in general,” says Misevic.

Question #5: What Does Life on Other Planets Look Like?

Life on Earth is based on DNA. But we can’t exclude the possibility that life could evolve from a completely different system of molecules. And that raises some worrying questions about the work going on these days to find signs of extraterrestrial life. NASA is funding a wide range of life-detecting instruments, from rovers that prowl across Mars to telescopes that will gaze at distant solar systems. They are looking for the signs of life that are produced on Earth. Some are looking for high levels of oxygen in the atmospheres of other planets. Others are looking for bits of DNA or fragments of cell walls. But if there’s non-DNA-based life out there, we might overlook it because it doesn’t fit our preconceptions.

“We can look at how known life-forms leave marks on their environment,” says Evan Dorn, a member of Chris Adami’s lab at Caltech, “but we can never make universal statements about them because we have only one example.”

Dorn says Avida is example number two. By finding patterns that are shared by life on Earth and life in Avida, he thinks he will be able to offer some ideas about how to look for life that the universe might be harboring.

Some researchers have suggested the best way to look for signs of life is to look for weird chemistry. Take the building blocks of proteins—amino acids—which are found on meteorites and can also be created in the lab simply by running an electric current through ammonia and other compounds. In a lifeless setting, the most common amino acid that results is the simplest: glycine. Some slightly less simple amino acids are also common, but all the larger ones make up only a trace or are missing altogether. That’s because it takes a lot of energy to make those big amino acids. “There’s a limited repertoire of chemistry in the absence of life,” says Dorn.

If you analyze a scoop of soil or pond water, however, you’ll find a completely different profile of amino acids. Life has evolved ways of building certain big amino acids, and when organisms die, those big amino acids float around in the environment.

What if life on another planet made compounds that were radically different from amino acids? Would it alter its planet’s chemistry in some similar way?

To test this idea, Dorn created a world devoid of life. Instead of containing a self-replicating program, each cell contained a random assortment of commands. All of the commands in the Avida language were present at equal levels. Here was the signature of a lifeless planet.

Then Dorn began dropping organisms into this world, like spores falling to Earth. At the beginning of the experiment, he set the mutation rate so high that no spore could replicate very long on the planet. (Think of Mars, where ultraviolet rays pelt the surface.) Gradually, he lowered the mutation rate until life could survive. “As soon as the environment was habitable, the organism took over and dominated the environment,” Dorn says.

As the digital organisms evolved to adapt to the world, Dorn found that some commands became rare and others became far more common. This distinctive signature stayed stable as long as life could survive on the planet. And no matter how many times Dorn repeated the experiment, the same signature of life appeared. Whether manipulating amino acids or computer commands, life does seem to leave the same mark. “It gives us a pretty strong indication that this process is universal,” says Dorn.

If Dorn is right, discovery of non-DNA life would become a little less spectacular because it would mean that we have already stumbled across it here on Earth—in East Lansing, Michigan.

Question #6: What Will Life on Earth Look Like In The Future?

One of the hallmarks of life is its ability to evolve around our best efforts to control it. Antibiotics, for example, were once considered a magic bullet that would eradicate infectious diseases. In just a few decades, bacteria have evolved an arsenal of defenses that make many antibiotics useless.

Ofria has been finding that digital organisms have a way of outwitting him as well. Not long ago, he decided to see what would happen if he stopped digital organisms from adapting. Whenever an organism mutated, he would run it through a special test to see whether the mutation was beneficial. If it was, he killed the organism off. “You’d think that would turn off any further adaptation,” he says. Instead, the digital organisms kept evolving. They learned to process information in new ways and were able to replicate faster. It took a while for Ofria to realize that they had tricked him. They had evolved a way to tell when Ofria was testing them by looking at the numbers he fed them. As soon as they recognized they were being tested, they stopped processing numbers. “If it was a test environment, they said, ‘Let’s play dead,’ ” says Ofria. “There’s this thing coming to kill them, and so they avoid it and go on with their lives.”

When Ofria describes these evolutionary surprises, admiration and ruefulness mix in his voice. “Here I am touting Avida as a wonderful system where you have full knowledge of everything and can control anything you want—except I can’t get them to stop adapting. Life will always find a way.”

Thinking about such adaptable creatures lurking on the Michigan State campus, furiously feeding on data, can be unsettling. Should the Avida team be working in quarantine? Lenski argues that Avida itself acts as a quarantine, because its organisms can exist only in its computer language. “They’re living in an alien world,” Lenski says. “They may be nasty predators from Mars, but they’d drop dead here.”

Still, Ofria acknowledges that harmful computer viruses may eventually evolve like his caged digital organisms. “Some day it’s going to happen, and it’s going to be scary,” Ofria says. “Better to study them now so we know how to deal with them.”


Section Summary

Land plants acquired traits that made it possible to colonize land and survive out of the water. All land plants share the following characteristics: alternation of generations, with the haploid plant called a gametophyte, and the diploid plant called a sporophyte protection of the embryo, formation of haploid spores in a sporangium, formation of gametes in a gametangium, and an apical meristem. Vascular tissues, roots, leaves, cuticle cover, and a tough outer layer that protects the spores contributed to the adaptation of plants to dry land. Land plants appeared about 500 million years ago in the Ordovician period.