Innovations in Biological Engineering: Microbes, Design, and Health

Posted on Jun 26, 2025 in Other university degrees and diplomas

Biomining: Harnessing Microbes for Mineral Extraction

One of the smallest representatives of life forms, bacteria, can be seen as a mixed blessing. They cause diseases in plants and animals, even human beings, such as tuberculosis and leprosy on one side, and they also convert milk into curd. In the last couple of decades, we have identified bacteria as miners. These diminutive diggers have become assets to the mining industry, eliminating traditional offensive methods which use explosives, toxic chemicals, and high temperatures (Science, Vol 264, No 5160). They also offer an economical alternative, especially in extracting minerals from low-grade ores, against the background of depleting high-grade reserves. Biomining contributes to improving the recovery rates of minerals, reducing capital and operating costs.

History of Biomining

The first miners to exploit microbes, albeit unknowingly, were probably the Romans who worked the Rio Tinto copper mine in Spain 2,000 years ago. They noticed that the fluid running off the mine tailings was blue, an indication that it contained copper salts, from which they then recovered the valuable metal. However, not until 40 years ago did it become clear that the copper in the fluid was in fact the handiwork of a bacterium named Thiobacillus ferrooxidans. The tiny miner has proved to be a godsend for the copper mining industry, which has been left with low-grade ores that need to be smelted more to produce the same amount of copper. With each new smelter costing $1 billion, the world is running short of smelters. T. ferrooxidans, however, can chew up the poor-quality ore which has been treated with sulfuric acid, releasing the copper that is collected in a solution at lower costs. Today, at least 25 percent of all copper produced worldwide, worth more than $1 billion annually, is extracted using this bug. Of late, biomining has struck gold, too. With depleting high-grade reserves of gold, not only are these microbes cheaper to use than conventional energy-intensive techniques, they also increase the rate of gold recovery from 70 to 95 percent.

Phosphate Extraction Innovations

Phosphates have traditionally been extracted from ores either by burning them at high temperatures to yield solid phosphorus or by treating them with sulfuric acid to produce phosphoric acid. But last year, Alan Goldstein of California State University in Los Angeles and Robert Rogers of the Idaho National Engineering Laboratory in Idaho Falls evolved a pair of bacterial strains, Pseudomonas cepacia E-37 and Erwinia herbicola, which can remove the phosphate from the ore at room temperatures, without using corrosive sulfuric acid.

Genetically Engineered Microbes

Scientists are now trying to genetically engineer new bacterial strains that can stand up to toxic metals such as mercury and cadmium. However, genetically engineered microbes may take some time to materialize because scientists still know little about Thiobacillus and other bacteria used in biomining.

Source: https://www.downtoearth.org.in/news/biomining-and-bacteria-32220

Biomining is the process of using microorganisms (microbes) to extract metals of economic interest from rock ores or mine waste. Biomining techniques may also be used to clean up sites that have been polluted with metals. Valuable metals are commonly bound up in solid minerals. Some microbes can oxidize those metals, allowing them to dissolve in water. This is the basic process behind most biomining, which is used for metals that can be more easily recovered when dissolved than from solid rocks. A different biomining technique, for metals which are not dissolved by the microbes, uses microbes to break down the surrounding minerals, making it easier to recover the metal of interest directly from the remaining rock.

Metals Currently Biomined

Most current biomining operations target valuable metals like copper, uranium, nickel, and gold that are commonly found in sulfidic (sulfur-bearing) minerals. Microbes are especially good at oxidizing sulfidic minerals, converting metals like iron and copper into forms that can dissolve more easily.

Other metals, like gold, are not directly dissolved by this microbial process, but are made more accessible to traditional mining techniques because the minerals surrounding these metals are dissolved and removed by microbial processes. When the metal of interest is directly dissolved, the biomining process is called “bioleaching,” and when the metal of interest is made more accessible or “enriched” in the material left behind, it is called “biooxidation.” Both processes involve microbial reactions that can happen anywhere the microbes, rocks, and necessary nutrients, like oxygen, occur together.

Approaches to Bioleaching: Direct vs. Indirect

  • Direct Bioleaching: Uses minerals that are easily receptive to oxidation to create a direct enzymatic strike using the microorganisms to separate the metal and the ore.
  • Indirect Bioleaching: Microorganisms are not in direct contact with minerals during the process. However, leaching agents are created by microbes, which still oxidize the ore.

Processes Used in Biomining

The most common processes used in biomining are:

  • Heap Leaching: Freshly mined material is moved directly into heaps that are then bioleached.
  • Slope/Dump Leaching: Low-value ore or waste rock is placed in a sealed pit and then bioleached to remove more of the valuable metals from the waste pile.
  • Agitated Leaching: Crushed rocks are placed into a large vat that is shaken to distribute the microbes and material evenly and speed up the bioleaching process.

Leaching times vary from days to months, making this process slower than conventional mineral extraction techniques. Dump and heap leaching are the oldest and most established biomining techniques, but the use of agitated leaching is becoming more common for minerals that are resistant to leaching, including some copper sulfides like chalcopyrite.

Advantages of Bioleaching

Some advantages of bioleaching include:

  • Bioleaching can stabilize sulfate toxins from the mine without causing harm to the environment.
  • Poisonous sulfur dioxide emissions harm the environment and can cause health problems for miners, and bioleaching avoids this process entirely.
  • Bioleaching is more cost-effective than smelting processes.
  • Bioleaching offers a different way to extract valuable metals from low-grade ores that have already been processed.

Environmental Risks of Biomining

Most current biomining operations use naturally occurring microbial communities. Because these types of organisms are already common in the environment, the risks from the release of the microbes themselves into the local environment are relatively small. The greatest environmental risks are related to leakage and treatment of the acidic, metal-rich solution created by the microbes, which is similar to the acid mine drainage from some abandoned mines. This risk can be managed by ensuring that biomining is conducted under controlled conditions with proper sealing and waste management protocols.

Prevalence of Biomining

Biomining is currently a small part of the overall mining industry. It is used most frequently when the percentage of the desired metal in a rock is small, or to extract remaining metals from waste rock after conventional mining. In Chile, which currently produces one-third of the world’s copper, many of the most copper-rich ores have already been mined. As a result, biomining is increasingly being used to mine deposits with low percentages of copper, and worldwide, 10-15% of copper is extracted using bioleaching. Biomining is also important in the gold industry, where roughly 5% of global gold is produced using biooxidation. As metal-rich ores are depleted worldwide, and with advances in microbial research and engineering, biomining may become more common in the future.

Other Uses of Biomining

  • New biomining techniques that do not involve oxidation are being tested, which would enable large-scale biomining for different types of minerals and metals.
  • Some researchers and companies are testing the use of biomining for recycling, to recover valuable elements from wastewater and electronic waste.
  • Several smaller operations recover metals from existing acid mine drainage. These operations recover economically valuable metals that would otherwise cause pollution.
  • In Europe, the BIOMOre project is studying the feasibility of biomining deep underground to avoid having to excavate the rocks themselves.

Biological Algorithms

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Contribution of Engineering in Biological Domains

Microscopes: Tools for Biological Discovery

Microscopes have opened up many doors in science. By using microscopes, scientists, researchers, and students were able to discover the existence of microorganisms, study the structure of cells, and see the smallest parts of plants, animals, and fungi. When it comes to biology, microscopes are important because biology mainly deals with the study of cells (and their contents), genes, and all organisms. Some organisms are so small that they can only be seen by using magnifications of 40x-1000x, which can only be achieved with the use of a microscope. Cells are too small to be seen with the naked eye.

Microscopes in Industry and Genetics

Microscopes are not just used to observe cells and their structure but are also used in many industries. For example, electron microscopes help create and observe extremely tiny electrical circuits found on silicon microchips. Scanning microscopes are much more sophisticated and they have higher magnifications than light-refracting microscopes.

Apart from biological research and industrial use, microscopes are also used in the field of genetics. Genetics is the study of variations in an organism generation after generation. Genetic engineering requires the mixing of genes. Genes are even smaller than cells, which is why microscopes are essential in this field.

Microscopes in Medical Diagnosis

Microscopes are also used to diagnose illness in hospitals and clinics all over the world. Microscopes magnify blood samples, so doctors or pathologists can see the viruses and parasites attacking the red blood cells and take the necessary steps to cure it. Without the microscope, mankind would not have been so developed and many diseases would still have no cure.

Microscopic examination confirms laboratory tests that may be positive for a disease. Technicians count the number of red blood cells infected with the virus or parasite to give the doctors an idea of how advanced the disease is in a patient.

Advanced Microscopic Techniques

Microscopes use simple visible light refracting lenses. Electrons, X-rays, and infrared rays are also used. Scanning electron microscopes are able to resolve viruses which are far smaller than any cell. They enlarge the view of tiny viruses, which allows scientists to develop vaccines and cures for infectious diseases in humans and animals.

Scanning electron microscopes have magnifications up to several million times to view molecules, viruses, and nanoparticles. They use corrective software to increase the magnification and resolution of images. Computers help nanotechnologists use high-powered electron microscopes to view objects.

Electron microscopes help prepare small surfaces for sectioning into small slices. Microscopes enlarge the images of silicon chips to help engineers create more efficient electronic devices. When more circuits are fitted onto a small chip, the computational power of silicon microchips increases.

Microscopes in Biological Research

All branches of biology use microscopes, especially in Molecular Biology and Histology (the study of cells). Microscopes are the backbone of studying biology. Biologists use them to view details that cannot be seen by the naked eye, such as small parasites and small organisms, which is important for disease control research.

Ergonomics: Designing Work for Well-being

Ergonomics can roughly be defined as the study of people in their working environment. More specifically, an ergonomist (pronounced like economist) designs or modifies the work to fit the worker, not the other way around. The goal is to eliminate discomfort and risk of injury due to work. In other words, the employee is our first priority in analyzing a workstation.

“Ergonomics (or human factors) is the scientific discipline concerned with the understanding of the interactions among human and other elements of a system, and the profession that applies theory, principles, data and methods to design in order to optimize human well-being and overall system performance.”

Source: International Ergonomics Association Executive Council, August 2000

When evaluating a job, ergonomists look for three main characteristics known as ergonomic stressors: the force required to complete a task, any awkward or static working postures adopted in completing a task, and the repetitiveness of a task. Any of these factors, or any combination of these factors, may place someone at greater risk for discomfort.

Biologically Inspired Technologies: Biomimetics

Biomimetics: Nature-Inspired Materials and Processes

Biomimetics is the innovation process that looks for sustainable solutions to human challenges by emulating nature’s time-tested patterns and strategies.

Notable Examples of Biomimicry

  • Leonardo da Vinci’s Flying Machine (1485): Well over 500 years ago, Leonardo da Vinci was developing plans for a flying machine. With nothing remotely similar in circulation, his inspiration had to come from the world around him. Mimicking the shapes of bird and bat wings, he was able to design a concept that, while ineffective, would inspire others for hundreds of years to come.
  • Camouflage (1890): Sir Edward Poulton, a British zoologist and early adopter of Darwinism, believed that animals mimicked their environments for safety and proposed this as proof for natural selection. In his 1890 publication, The Colours of Animals, he describes this theory and suggests how humans could harness this same technology. While camouflage has changed and improved over the years, most of its many interpretations have been borrowed from nature.
  • Velcro (1941): George de Mestral, a Swiss engineer, turned an inconvenience into an opportunity while out on a hunting trip in the early 1940s. While walking through the hills, he noticed cocklebur seed capsules sticking to his clothing as he walked past. After closer inspection of the burs and their hooks, he developed and patented the hook-and-loop design currently known as Velcro.
  • “Passive” Air Conditioning (1996): Operational for over 20 years now, the Eastgate Complex in Harare, Zimbabwe has been a leader in building cooling technology since its conception. Designed after a termite mound, the building uses “passive cooling” technology to consume 90% less energy than modern air conditioning. Further research has shown that other models may be even more effective and prototypes are currently being designed.
  • Medical Staples (2014): A current leader in many different biomimicry technologies, the Karp lab has drawn inspiration from porcupine needles in their design for a more secure medical staple. Sutures closing dangerous wounds need to be as sturdy as possible. By mimicking the unidirectional barbs found in porcupine quills, the Karp lab has created a design that will hold in soft tissue far more effectively than other staples have before.
  • Japanese Bullet Trains (2016): The Hokkaido Shinkansen, the latest iteration of Japan’s famous bullet trains, is based on the face and beak of the Kingfisher bird. These trains are known to reach speeds in excess of 300 km/h and have an impressive track record boasting 0 fatalities in their greater than 50-year history.
  • Whale Fin Wind Turbines (2018): For the past 10 years, Whalepower Corporation has been doing research, starting in a Harvard lab and growing into a company, to revolutionize wind power. Drawing inspiration from bumps on the leading edge of humpback whale fins, the engineers at Whalepower have designed turbine blades that channel air around artificial tubercles. This maximizes the blades’ ability to operate in low/infrequent wind, while maintaining their ability to function in high wind as well.
  • Woodpecker Football Helmets (2018): When designing a new football helmet to help with chronic prevalence of CTE in the NFL, the team at VICIS turned to the humble woodpecker. These amazing birds spend a lot of time hitting their heads against hard objects, without any serious repercussions. After creating an impact absorption system mimicking the soft tissue surrounding the skull of the woodpecker, they are confident they have a product that will help decrease injury in athletes engaging in high-impact sport.
  • Hydrodynamic Green Energy Solutions (Currently in Development): Currently in late stage development, the bioWAVE aims to harness the fluid dynamic power of waves and convert it into electricity. Designed after coral, the structure is able to be pushed back and forth by shifting tides. This will have major advantages over other sources of green energy as it will provide more constant energy production than either wind or solar.
  • Biohacking Limb Regeneration Technology (Currently in Development): Researchers in labs around the world are pulling inspiration from an aquatic salamander, the axolotl, in designs for medical technologies to aid with regeneration of damaged or removed limbs. This creature can regrow lost limbs over the course of a few weeks, complete with soft, cardiac, and neuronal tissue. By sequencing and searching the axolotl genome, scientists are learning how we may be able to use this technology for ourselves in the future.

Engineering Perspectives of Biological Sciences

Bioengineering and Biomedical Engineering

Bioengineering or Biomedical Engineering is a discipline that advances knowledge in engineering, biology, and medicine — and improves human health through cross-disciplinary activities that integrate the engineering sciences with the biomedical sciences and clinical practice. Bioengineering/Biomedical Engineering combines engineering expertise with medical needs for the enhancement of healthcare. It is a branch of engineering in which knowledge and skills from the existing methodologies in such fields as molecular biology, biochemistry, microbiology (study of microorganisms), pharmacology (study of drugs and medicines), cytology (cell biology), immunology (study of the immune system), and neuroscience (study of the nervous system) are utilized and applied to the design of medical devices, diagnostic equipment, biocompatible materials, and other important medical needs.

Bioengineering is not limited to the medical field. Bioengineers have the ability to exploit new opportunities and solve problems within the domain of complex systems. They have a great understanding of complexity within living systems which can be applied to many fields including entrepreneurship. Those working within the bioengineering field are of service to people, work with living systems, and apply advanced technology to the complex problems of medical care.

Categories of Bioengineering

Bioengineering may be categorized as:

  • Biomedical Engineering
  • Biomedical Technology
  • Biomedical Diagnosis
  • Biomedical Therapy
  • Biomechanics
  • Biomaterials
  • Genetic Engineering
  • Cell Engineering

Biomedical Engineering (BME) Explained

By combining biology and medicine with engineering, biomedical engineers develop devices and procedures that solve medical and health-related problems. Biomedical engineers may be called upon to design instruments and devices, to bring together knowledge from many sources to develop new procedures, or to carry out research to acquire knowledge needed to solve problems. Many do research, along with life scientists, chemists, and medical scientists, to develop and evaluate systems and products for use in the fields of biology and health, such as artificial organs, prostheses (artificial devices that replace missing body parts), instrumentation, medical information systems, and health management and care delivery systems. Bioengineers design devices used in a variety of medical procedures, such as the computers used to analyze blood or the laser systems used in corrective eye surgery. They develop artificial organs, imaging systems such as magnetic resonance, ultrasound, and X-ray, and devices for automating insulin injections or controlling body functions. Most engineers in this specialty require a sound background in one of the basic engineering specialties, such as mechanical or electronics engineering, in addition to specialized biomedical training. Some specialties within bioengineering or biomedical engineering include biomaterials, biomechanics, medical imaging, rehabilitation engineering, and orthopedic engineering.

Examples of Biomedical Engineering Work

  • Designing and constructing cardiac pacemakers, defibrillators, artificial kidneys, blood oxygenators, hearts, blood vessels, joints, arms, and legs.
  • Designing computer systems to monitor patients during surgery or in intensive care, or to monitor healthy persons in unusual environments, such as astronauts in space or underwater divers at great depth.
  • Designing and building sensors to measure blood chemistry, such as potassium, sodium, O2, CO2, and pH.
  • Designing instruments and devices for therapeutic uses, such as a laser system for eye surgery or a device for automated delivery of insulin.
  • Developing strategies for clinical decision making based on expert systems and artificial intelligence, such as a computer-based system for selecting seat cushions for paralyzed patients or for managing the care of patients with severe burns or for diagnosing diseases.
  • Designing clinical laboratories and other units within the hospital and healthcare delivery system that utilize advanced technology. Examples would be a computerized analyzer for blood samples, ambulances for use in rural areas, or a cardiac catheterization laboratory.
  • Designing, building, and investigating medical imaging systems based on X-rays (computer assisted tomography), isotopes (positron emission tomography), magnetic fields (magnetic resonance imaging), ultrasound, or newer modalities.
  • Constructing and implementing mathematical/computer models of physiological systems.
  • Designing and constructing biomaterials and determining the mechanical, transport, and biocompatibility properties of implantable artificial materials.
  • Implementing new diagnostic procedures, especially those requiring engineering analyses to determine.