Lab-on-a-chip

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https://en.wikipedia.org/wiki/Lab-on-a-chip

A lab-on-a-chip (LOC) is a device that integrates one or several laboratory functions on a single integrated circuit (commonly called a "chip") of only millimeters to a few square centimeters to achieve automation and high-throughput screening. LOCs can handle extremely small fluid volumes down to less than pico-liters. Lab-on-a-chip devices are a subset of microelectromechanical systems (MEMS) devices and sometimes called "micro total analysis systems" (μTAS). LOCs may use microfluidics, the physics, manipulation and study of minute amounts of fluids. However, strictly regarded "lab-on-a-chip" indicates generally the scaling of single or multiple lab processes down to chip-format, whereas "μTAS" is dedicated to the integration of the total sequence of lab processes to perform chemical analysis.

History

Microelectromechanical systems chip, sometimes called "lab on a chip"

After the invention of microtechnology (≈1954) for realizing integrated semiconductor structures for microelectronic chips, these lithography-based technologies were soon applied in pressure sensor manufacturing (1966) as well. Due to further development of these usually CMOS-compatibility limited processes, a tool box became available to create micrometre or sub-micrometre sized mechanical structures in silicon wafers as well: the microelectromechanical systems (MEMS) era had started.

Next to pressure sensors, airbag sensors and other mechanically movable structures, fluid handling devices were developed. Examples are: channels (capillary connections), mixers, valves, pumps and dosing devices. The first LOC analysis system was a gas chromatograph, developed in 1979 by S.C. Terry at Stanford University. However, only at the end of the 1980s and beginning of the 1990s did the LOC research start to seriously grow as a few research groups in Europe developed micropumps, flowsensors and the concepts for integrated fluid treatments for analysis systems. These μTAS concepts demonstrated that integration of pre-treatment steps, usually done at lab-scale, could extend the simple sensor functionality towards a complete laboratory analysis, including additional cleaning and separation steps.

A big boost in research and commercial interest came in the mid-1990s, when μTAS technologies turned out to provide interesting tooling for genomics applications, like capillary electrophoresis and DNA microarrays. A big boost in research support also came from the military, especially from DARPA (Defense Advanced Research Projects Agency), for their interest in portable systems to aid in the detection of biological and chemical warfare agents. The added value was not only limited to integration of lab processes for analysis but also the characteristic possibilities of individual components and the application to other, non-analysis, lab processes. Hence the term "lab-on-a-chip" was introduced.

Although the application of LOCs is still novel and modest, a growing interest of companies and applied research groups is observed in different fields such as chemical analysis, environmental monitoring, medical diagnostics and cellomics, but also in synthetic chemistry such as rapid screening and microreactors for pharmaceutics. Besides further application developments, research in LOC systems is expected to extend towards downscaling of fluid handling structures as well, by using nanotechnology. Sub-micrometre and nano-sized channels, DNA labyrinths, single cell detection and analysis, and nano-sensors, might become feasible, allowing new ways of interaction with biological species and large molecules. Many books have been written that cover various aspects of these devices, including the fluid transport, system properties, sensing techniques, and bioanalytical applications.

The size of the global lab on chip market was estimated at US$5,698 million in 2021 and is projected to increase to US$14,772 million by 2030, at a CAGR of 11.5% from 2022 to 2030 

Chip materials and fabrication technologies

The basis for most LOC fabrication processes is photolithography. Initially most processes were in silicon, as these well-developed technologies were directly derived from semiconductor fabrication. Because of demands for e.g. specific optical characteristics, bio- or chemical compatibility, lower production costs and faster prototyping, new processes have been developed such as glass, ceramics and metal etching, deposition and bonding, polydimethylsiloxane (PDMS) processing (e.g., soft lithography), Off-stoichiometry thiol-ene polymers (OSTEmer) processing, thick-film- and stereolithography-based 3D printing as well as fast replication methods via electroplating, injection molding and embossing. The demand for cheap and easy LOC prototyping resulted in a simple methodology for the fabrication of PDMS microfluidic devices: ESCARGOT (Embedded SCAffold RemovinG Open Technology). This technique allows for the creation of microfluidic channels, in a single block of PDMS, via a dissolvable scaffold (made by e.g. 3D printing). Furthermore, the LOC field more and more exceeds the borders between lithography-based microsystem technology, nanotechnology and precision engineering. Printing is considered as a well-established yet maturing method for rapid prototyping in chip fabrication.

The development of LOC devices using printed circuit board (PCB) substrates is an interesting alternative due to these differentiating characteristics: commercially available substrates with integrated electronics, sensors and actuators; disposable devices at low cost, and very high potential of commercialization. These devices are known as Lab-on-PCBs (LOPCBs). The following are some of the advantages of PCB technology: a) PCB-based circuit design offers great flexibility and can be tailored to specific demands. b) PCB technology enables the integration of electronic and sensing modules on the same platform, reducing device size while maintaining accuracy of detection. c) The standardized and established PCB manufacturing process allows for cost-effective large-scale production of PCB-based detection devices. d) The growth of flexible PCB technology has driven the development of wearable detection devices. As a result, over the past decade, there have been numerous reports on the application of Lab-on-PCB to various biomedical fields, including the fastest SARS-CoV-2 molecular diagnostic test.) PCBs are compatible with wet deposition methods, to allow for the fabrication of sensors using novel nanomaterials (e.g. graphene).

Advantages

LOCs may provide advantages, which are specific to their application. Typical advantages are:

• low fluid volumes consumption (less waste, lower reagents costs and less required sample volumes for diagnostics)
• faster analysis and response times due to short diffusion distances, fast heating, high surface to volume ratios, small heat capacities.
• better process control because of a faster response of the system (e.g. thermal control for exothermic chemical reactions)
• compactness of the systems due to integration of much functionality and small volumes
• massive parallelization due to compactness, which allows high-throughput analysis
• lower fabrication costs, allowing cost-effective disposable chips, fabricated in mass production
• part quality may be verified automatically
• safer platform for chemical, radioactive or biological studies because of integration of functionality, smaller fluid volumes and stored energies

Disadvantages

The most prominent disadvantages of labs-on-chip are:

• The micro-manufacturing process required to make them is complex and labor-intensive, requiring both expensive equipment and specialized personnel. It can be overcome by the recent technology advancement on low-cost 3D printing and laser engraving.
• The complex fluidic actuation network requires multiple pumps and connectors, where fine control is difficult. It can be overcome by careful simulation, an intrinsic pump, such as air-bag embed chip, or by using a centrifugal force to replace the pumping, i.e. centrifugal micro-fluidic biochip.
• Most LOCs are novel proof of concept application that are not yet fully developed for widespread use. More validations are needed before practical employment.
• In the microliter scale that LOCs deal with, surface dependent effects like capillary forces, surface roughness or chemical interactions are more dominant. This can sometimes make replicating lab processes in LOCs quite challenging and more complex than in conventional lab equipment.
• Detection principles may not always scale down in a positive way, leading to low signal-to-noise ratios.

Global health

Lab-on-a-chip technology may soon become an important part of efforts to improve global health, particularly through the development of point-of-care testing devices. In countries with few healthcare resources, infectious diseases that would be treatable in a developed nation are often deadly. In some cases, poor healthcare clinics have the drugs to treat a certain illness but lack the diagnostic tools to identify patients who should receive the drugs. Many researchers believe that LOC technology may be the key to powerful new diagnostic instruments. The goal of these researchers is to create microfluidic chips that will allow healthcare providers in poorly equipped clinics to perform diagnostic tests such as microbiological culture assays, immunoassays and nucleic acid assays with no laboratory support.

Global challenges

For the chips to be used in areas with limited resources, many challenges must be overcome. In developed nations, the most highly valued traits for diagnostic tools include speed, sensitivity, and specificity; but in countries where the healthcare infrastructure is less well developed, attributes such as ease of use and shelf life must also be considered. The reagents that come with the chip, for example, must be designed so that they remain effective for months even if the chip is not kept in a climate controlled environment. Chip designers must also keep cost, scalability, and recyclability in mind as they choose what materials and fabrication techniques to use.

Examples of global LOC application

One of the most prominent and well known LOC devices to reach the market is the at home pregnancy test kit, a device that utilizes paper-based microfluidics technology.

Another active area of LOC research involves ways to diagnose and manage common infectious diseases caused by bacteria, e.g. bacteriuria, or viruses, e.g. influenza. A gold standard for diagnosing bacteriuria (urinary tract infections) is microbial culture. A recent study based on lab-on-a-chip technology, Digital Dipstick, miniaturised microbiological culture into a dipstick format and enabled it to be used at the point-of-care. Lab-on-a-chip technology can also be useful for the diagnosis and management of viral infections. In 2023, researchers developed a working prototype of an RT-LAMP lab-on-a-chip system called LoCKAmp, which provided results for SARS-CoV-2 tests within three minutes. Managing HIV infections is another area where lab-on-a-chips may be useful. Around 36.9 million people are infected with HIV in the world today, and 59% of these people receive anti-retroviral treatment. Only 75% of people living with HIV knew their status. Measuring the number of CD4+ T lymphocytes in a person's blood is an accurate way to determine if a person has HIV and to track the progress of an HIV infection. At the moment, flow cytometry is the gold standard for obtaining CD4 counts, but flow cytometry is a complicated technique that is not available in most developing areas because it requires trained technicians and expensive equipment. Recently such a cytometer was developed for just $5. Another active area of LOC research is for controlled separation and mixing. In such devices it is possible to quickly diagnose and potentially treat diseases. As mentioned above, a big motivation for development of these is that they can potentially be manufactured at very low cost. One more area of research that is being looked into with regards to LOC is with home security. Automated monitoring of volatile organic compounds (VOCs) is a desired functionality for LOC. If this application becomes reliable, these micro-devices could be installed on a global scale and notify homeowners of potentially dangerous compounds.

Plant sciences

Lab-on-a-chip devices could be used to characterize pollen tube guidance in Arabidopsis thaliana. Specifically, plant on a chip is a miniaturized device in which pollen tissues and ovules could be incubated for plant sciences studies.

Animal languages

From Wikipedia, the free encyclopedia

Parrots (Australian ringneck)

Animal languages are forms of communication between animals that show similarities to human language. Animals communicate through a variety of signs, such as sounds and movements. Signing among animals may be considered a form of language if the inventory of signs is large enough, the signs are relatively arbitrary, and the animals seem to produce them with a degree of volition (as opposed to relatively automatic conditioned behaviors or unconditioned instincts, usually including facial expressions).

Many researchers argue that animal communication lacks a key aspect of human language, the creation of new patterns of signs under varied circumstances. Humans, by contrast, routinely produce entirely new combinations of words. Some researchers, including the linguist Charles Hockett, argue that human language and animal communication differ so much that the underlying principles are unrelated. Accordingly, linguist Thomas A. Sebeok has proposed to not use the term "language" for animal sign systems. However, other linguists and biologists, including Marc Hauser, Noam Chomsky, and W. Tecumseh Fitch, assert that an evolutionary continuum exists between the communication methods of animal and human language.

Aspects of human language

The Belgian conservationist Claudine André with a bonobo

Some experts argue the following properties separate human language from animal communication:

• Arbitrariness: There is usually no rational relationship between a sound or sign and its meaning. For example, there is nothing intrinsically house-like about the word "house".
• Discreteness: Language is composed of small, separate, and repeatable parts (discrete units, e.g. morphemes) that are used in combination to create meaning.
• Displacement: Language can be used to communicate about things that are not in the immediate vicinity either spatially or temporally.
• Duality of patterning: The smallest meaningful units (words or morphemes) consist of sequences of units without meaning (sounds or phonemes). This is also referred to as double articulation.
• Productivity: Users can understand and create an indefinitely large number of utterances.
• Semanticity: Specific signals have specific meanings.

Research with apes, like that of Francine Patterson with Koko (gorilla) or Allen and Beatrix Gardner with Washoe (chimpanzee), suggested that apes are capable of using language that meets some of these requirements, including arbitrariness, discreteness, and productivity.

In the wild, chimpanzees have been seen "talking" to each other when warning about approaching danger. For example, if one chimpanzee sees a snake, said chimpanzee may make a low, rumbling noise, signaling for all the other chimps to climb into nearby trees. In this case, the chimpanzees' communication does not indicate displacement, as it is entirely contained to an observable event.

Arbitrariness has been noted in meerkat calls; bee dances demonstrate elements of spatial displacement; and cultural transmission has possibly occurred through language between the bonobos named Kanzi and Panbanisha.

Claims that animals have language skills akin to humans, however, are extremely controversial. In his book The Language Instinct, Steven Pinker illustrates that claims of chimpanzees acquiring language are exaggerated and rest on very limited or specious evidence.

The American linguist Charles Hockett theorized that there are sixteen features of human language that distinguish human communication from that of animals. He called these the design features of language. The features mentioned below have so far been found in all spoken human languages, and at least one is missing from any other animal communication system.

• Vocal-auditory channel: Sounds are emitted from the mouth and perceived by the auditory system. While this applies to many animal communication systems, there are many exceptions, such as those relying on visual communication. One example is cobras extending the ribs behind their heads to send the message of intimidation or of feeling threatened. In humans, sign languages provide many examples of fully formed languages that use a visual channel.
• Broadcast transmission and directional reception: This requires that the recipient can tell the direction that the signal comes from and thus the originator of the signal.
• Rapid fading (transitory nature): The signal lasts a short time. This is true of all systems involving sound. It does not take into account audio recording technology and is also not true for written language. It tends not to apply to animal signals involving chemicals and smells which often fade slowly. For example, a skunk's smell, produced in its glands, lingers to deter a predator from attacking.
• Interchangeability: All utterances that are understood can be produced. This is different from some communication systems where, for example, males produce one set of behaviors and females another and they are unable to interchange these messages so that males use the female signal and vice versa. For example, Heliothine moths have differentiated communication: females are able to send a chemical to indicate preparedness to mate, while males cannot send the chemical.
• Total feedback: The sender of a message is aware of the message being sent.
• Specialization: The signal produced is intended for communication and is not due to another behavior. For example, dog panting is a natural reaction to being overheated, but is not produced to specifically relay a particular message.
• Semanticity: There is some fixed relationship between a signal and a meaning.

Primates

Humans are able to distinguish real words from fake words based on the phonological order of the word itself. In a 2013 study, baboons were shown to have this skill as well. The discovery has led researchers to believe that reading is not as advanced a skill as previously believed, but instead based on the ability to recognize and distinguish letters from one another. The experimental setup consisted of six young adult baboons, and results were measured by allowing the animals to use a touch screen and select whether or not the displayed word was a real word, or a non-word such as "dran" or "telk". The study lasted for six weeks, with approximately 50,000 tests completed in that time. The researchers minimized common bigrams, or combinations of two letters, in non-words, and maximized them in real words. Further studies will attempt to teach baboons how to use an artificial alphabet.

In a 2016 study, a team of biologists from several universities concluded that macaques possess vocal tracts physically capable of speech, "but lack a speech-ready brain to control it".

Non-primates

Among the most studied examples of non-primate languages are:

Birds

• Bird songs: Songbirds can be highly articulate. Grey parrots and macaws are well known for their ability to mimic human language. At least one specimen, Alex, appeared able to answer a number of simple questions about objects he was presented with, such as answering simple mathematical equations and identifying colors. Parrots, hummingbirds and songbirds display vocal learning patterns. Crows have been studied for their ability to understand recursion.

Insects

• Bee dancing: Used to communicate the direction and distance of food source in many species of bees. In 2023, James C. Nieh, Associate Dean and Professor of Biology with the University of California, San Diego, performed an experiment to determine if the dances of bees were innate skills or if they were developed through observation of older bees within their hive. The research group determined that the dance bees performed was to some degree innate, but the consistency and accuracy of the dance was a skill passed down by older bees. Although the experimental hive that contained only workers of the same age developed better accuracy when conveying angle and direction as they got older, their ability to communicate distance never reached the level of the control beehives.

Mammals

• African forest elephants: Cornell University's Elephant Listening Project began in 1999 when Katy Payne began studying the calls of African forest elephants in Dzanga National Park in the Central African Republic. Andrea Turkalo has continued Payne's work in Dzanga National Park by observing elephant communication. For nearly 20 years, Turkalo has used a spectrogram to record the noises that the elephants make. After extensive observation and research, she has been able to recognize elephants by their voices. Researchers hope to translate these voices into an elephant dictionary, but this will likely not occur for many years. Because elephant calls are often made at very low frequencies, the spectrogram is designed to detect lower frequencies than humans can perceive, allowing Turkalo to better understand the elephants' noise making. Cornell's research on African forest elephants has challenged the idea that humans are considerably better at using language than animals, and that animals only have a small set of information they can convey to others. As Turkalo explained, "many of their calls are in some ways similar to human speech." Elephants in captivity can be taught to remember tone, melody, and recognise more than 20 words.
• Mustached bats: Since these animals spend most of their lives in the dark, they rely heavily on their auditory system to communicate, including via echolocation and using calls to locate each other. Studies have shown that mustached bats use a wide variety of calls to communicate with one another. These calls include 33 different sounds, or "syllables", that the bats either use alone or combine in various ways to form composite syllables.
• Prairie dogs: Con Slobodchikoff studied prairie dog communication and discovered that they use different alarm calls and escape behaviors for different species of predators. Their calls transmit semantic information, which was demonstrated when playbacks of alarm calls in the absence of predators led to escape behavior appropriate for the types of predators associated with the calls. The alarm calls also contain descriptive information about the general size, color, and speed of the predator.

Aquatic mammals

• Bottlenose dolphins: Dolphins can hear one another up to 6 miles apart underwater. Researchers observed a mother dolphin successfully communicating with her baby using a telephone. It appeared that both dolphins knew who they were speaking with and what they were speaking about. Not only do dolphins communicate via nonverbal cues, they also seem to chatter and respond to other dolphins' vocalizations.

Spectrogram of humpback whale vocalizations. Detail is shown for the first 24 seconds of the 37 second humpback whale "song" recording. The whale songs and echolocation "clicks" are visible as horizontal striations and vertical sweeps respectively.

• Whales: Two groups of whales, the humpback whale and a subspecies of blue whale found in the Indian Ocean, are known to produce repeated sounds at varying frequencies, known as whale songs. Male humpback whales perform these vocalizations only during the mating season, and so it is surmised the purpose of songs is to aid sexual selection. Humpbacks also make a sound called a feeding call, which is five to ten seconds in length at a nearly constant frequency. Humpbacks generally feed cooperatively by gathering in groups, swimming underneath shoals of fish and lunging up vertically through the fish and out of the water together. Prior to these lunges, whales make their feeding call. The exact purpose of the call is not known, but research suggests that fish react to it. When the sound was played back to them, a group of herring responded to the sound by moving away from the call, even though no whale was present.
• Sea lions: Since 1971, Ronald J. Schusterman and his research associates have studied sea lions' cognitive ability. They have discovered that sea lions are able to recognize relationships between stimuli based on similar functions or connections made with their peers, rather than only the stimuli's common features. This is called equivalence classification. This ability to recognize equivalence may be a precursor to language. Research is currently being conducted at the Pinniped Cognition & Sensory Systems Laboratory to determine how sea lions form these equivalence relations. Sea lions have also been proven to understand simple syntax and commands when taught an artificial sign language similar to one used with primates. The sea lions studied were able to learn and use a number of syntactic relations between the signs they were taught, such as how the signs should be arranged in relation to each other. However, the sea lions rarely used the signs semantically or logically. In the wild, it is thought that sea lions use reasoning skills associated with equivalence relations in order to make important decisions that can affect their survival, e.g. recognizing friends and relatives or avoiding enemies and predators. Sea lions use various postural positions and a range of barks, chirps, clicks, moans, growls, and squeaks to communicate. It has yet to be proven that sea lions use echolocation as a means of communication.

The effects of learning on auditory signaling in these animals is of interest to researchers. Several investigators have pointed out that some marine mammals appear to have the capacity to alter both the contextual and structural features of their vocalizations as a result of experience. Janik and Slater have stated that learning can modify vocalizations in one of two ways, by influencing the context in which a particular call is used, or by altering the acoustic structure of the call itself. Male California sea lions can learn to inhibit their barking in the presence of any male dominant to them, but vocalize normally when dominant males are absent. The different call types of gray seals can be selectively conditioned and controlled by different cues, and the use of food reinforcement can also modify vocal emissions. A captive male harbor seal named Hoover demonstrated a case of vocal mimicry, but similar observations have not been reported since. Still shows that under the right circumstances pinnipeds may use auditory experience in addition to environmental consequences such as food reinforcement and social feedback to modify their vocal emissions.

In a 1992 study, Robert Gisiner and Schusterman conducted experiments in which they attempted to teach syntax to a female California sea lion named Rocky. Rocky was taught signed words, then she was asked to perform various tasks dependent on word order after viewing a signed instruction. It was found that Rocky was able to determine relations between signs and words, and form basic syntax. A 1993 study by Schusterman and David Kastak found that the California sea lion was capable of understanding abstract concepts such as symmetry, sameness and transitivity. This suggests that equivalence relations can form without language.

The distinctive sounds of sea lions are produced both above and below water. To mark territory, sea lions "bark", with non-alpha males making more noise than alphas. Although females also bark, they do so less frequently and most often in connection with birthing pups or caring for their young. Females produce a highly directional bawling vocalization, the pup attraction call, which helps mothers and pups locate one another. As noted in Animal Behavior, their amphibious lifestyle has made them need acoustic communication for social organization while on land.

Sea lions can hear frequencies between 100 Hz and 40,000 Hz, and vocalize from 100 to 10,000 Hz.

Mollusks

• Caribbean reef squid have been shown to communicate using a variety of color, shape, and texture changes. Squid are capable of rapid changes in skin color and pattern through nervous system control of chromatophores. In addition to camouflage and appearing larger in the face of a threat, squid use color, patterns, and flashing to communicate with one another in various courtship rituals. Caribbean reef squid can send one message via color patterns to a squid on their right, while they send another message to a squid on their left.

Fish

• Freshwater Elephant Fish have been observed to have their own language.
• Mexican Tetra have been observed communicating with a series of clicks, and have also been observed to have regional accents.

Comparison of "animal language" and "animal communication"

It is worth distinguishing "animal language" from "animal communication", although there is some comparative interchange in certain cases (e.g. Cheney & Seyfarth's vervet monkey call studies). Animal language typically does not include bee dancing, bird song, whale song, dolphin signature whistles, prairie dog alarm calls, or the communicative systems found in most social mammals. The features of language as listed above are a dated formulation by Hockett in 1960. Through this formulation Hockett made one of the earliest attempts to break down features of human language for the purpose of applying Darwinian gradualism. Although an influence on early animal language efforts (see below), it is no longer considered the key architecture at the core of animal language research.

Clever Hans, an Orlov Trotter horse that was claimed to have been able to perform arithmetic and other intellectual tasks

Animal language results are controversial for several reasons (for a related controversy, see also Clever Hans). Early chimpanzee work was executed using chimpanzee infants raised as if they were human; a test of the nature vs. nurture hypothesis. Chimpanzees have a laryngeal structure very different from that of humans, and it has been suggested that chimpanzees are not capable of voluntary control of their breathing, although better studies are needed to accurately confirm this. This combination is thought to make it very difficult for the chimpanzees to reproduce the vocal intonations required for human language. Researchers eventually moved towards a gestural (sign language) modality, as well as keyboard devices with buttons with symbols (known as "lexigrams") that the animals could press to produce artificial language. Other chimpanzees learned by observing human subjects performing the task. This latter group of researchers studying chimpanzee communication through symbol recognition (keyboard) as well as through the use of sign language (gestural), are on the forefront of communicative breakthroughs in the study of animal language, and they are familiar with their subjects on a first name basis: Sarah, Lana, Kanzi, Koko, Sherman, Austin and Chantek.

Perhaps the best known critic of animal language is Herbert Terrace. Terrace's 1979 criticism using his own research with the chimpanzee Nim Chimpsky^] was scathing and spelled the end of animal language research in that era, most of which emphasized the production of language by animals. In short, he accused researchers of over-interpreting their results, especially as it is rarely parsimonious to ascribe true intentional "language production" when other simpler explanations for the behaviors (gestural hand signs) could be put forth. Additionally, his animals failed to show generalization of the concept of reference between the modalities of comprehension and production; this generalization is one of many fundamental ones that are trivial for human language use. The simpler explanation according to Terrace was that the animals had learned a sophisticated series of context-based behavioral strategies to obtain either primary (food) or social reinforcement, behaviors that could be over-interpreted as language use.

In 1984 Louis Herman published an account of artificial language found in the bottlenose dolphin in the journal Cognition. A major difference between Herman's work and previous research was his emphasis on a method of studying language comprehension only (rather than language comprehension and production by the animal(s)), which enabled rigorous controls and statistical tests, largely because he was limiting his research to evaluating the animals' physical behaviors (in response to sentences) with blinded observers, rather than attempting to interpret possible language utterances or productions. The dolphins' names here were Akeakamai and Phoenix. Irene Pepperberg used the vocal modality for language production and comprehension in a grey parrot named Alex in the verbal mode, and Sue Savage-Rumbaugh continues to study bonobos such as Kanzi and Panbanisha. R. Schusterman duplicated many of the dolphin results in his California sea lions ("Rocky"), and came from a more behaviorist tradition than Herman's cognitive approach. Schusterman's emphasis is on the importance on a learning structure known as equivalence classes.

However, overall, there has not been any meaningful dialog between the linguistics and animal language spheres, despite capturing the public's imagination in the popular press. Furthermore, the growing field of language evolution is another source of future interchange between these disciplines. Most primate researchers tend to show a bias toward a shared pre-linguistic ability between humans and chimpanzees, dating back to a common ancestor, while dolphin and parrot researchers stress the general cognitive principles underlying these abilities. More recent related controversies regarding animal abilities include the closely linked areas of theory of mind, Imitation (e.g. Nehaniv & Dautenhahn, 2002),^[56] Animal Culture (e.g. Rendell & Whitehead, 2001), and Language Evolution (e.g. Christiansen & Kirby, 2003).

There has been a recent emergence in animal language research which has contested the idea that animal communication is less sophisticated than human communication. Denise Herzing has done research on dolphins in the Bahamas whereby she created a two-way conversation via a submerged keyboard. The keyboard allows divers to communicate with wild dolphins. By using sounds and symbols on each key the dolphins could either press the key with their nose or mimic the whistling sound emitted in order to ask humans for a specific prop. This ongoing experiment has shown that in non-linguistic creatures sophisticated and rapid thinking does occur despite our previous conceptions of animal communication. Further research done with Kanzi using lexigrams has strengthened the idea that animal communication is much more complex than once thought.

Eukaryote

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Eukaryote

The eukaryotes (/juːˈkærioʊts, -əts/ yoo-KARR-ee-ohts, -⁠əts) constitute the domain of Eukaryota or Eukarya, organisms whose cells have a membrane-bound nucleus. All animals, plants, fungi, seaweeds, and many unicellular organisms are eukaryotes. They constitute a major group of life forms alongside the two groups of prokaryotes: the Bacteria and the Archaea. Eukaryotes represent a small minority of the number of organisms, but given their generally much larger size, their collective global biomass is much larger than that of prokaryotes.

The eukaryotes emerged within the archaeal kingdom Promethearchaeati and its sole phylum Promethearchaeota. This implies that there are only two domains of life, Bacteria and Archaea, with eukaryotes incorporated among the Archaea. Eukaryotes first emerged during the Paleoproterozoic, likely as flagellated cells. The leading evolutionary theory is they were created by symbiogenesis between an anaerobic Promethearchaeati archaean and an aerobic proteobacterium, which formed the mitochondria. A second episode of symbiogenesis with a cyanobacterium created the plants, with chloroplasts.

Eukaryotic cells contain membrane-bound organelles such as the nucleus, the endoplasmic reticulum, and the Golgi apparatus. Eukaryotes may be either unicellular or multicellular. In comparison, prokaryotes are typically unicellular. Unicellular eukaryotes are sometimes called protists. Eukaryotes can reproduce both asexually through mitosis and sexually through meiosis and gamete fusion (fertilization).

Etymology

The word eukaryote is derived from the Greek words "eu" (εὖ) meaning "true" or "good" and "karyon" (κάρυον) meaning "nut" or "kernel", referring to the nucleus of a cell.

Diversity

Further information: Organism

Eukaryotes are organisms that range from microscopic single cells, such as picozoans under 3 micrometres across, to animals like the blue whale, weighing up to 190 tonnes and measuring up to 33.6 metres (110 ft) long, or plants like the coast redwood, up to 120 metres (390 ft) tall. Many eukaryotes are unicellular; the informal grouping called protists includes many of these, with some multicellular forms like the giant kelp up to 200 feet (61 m) long. The multicellular eukaryotes include the animals, plants, and fungi, but again, these groups too contain many unicellular species. Eukaryotic cells are typically much larger than those of prokaryotes—the bacteria and the archaea—having a volume of around 10,000 times greater. Eukaryotes represent a small minority of the number of organisms, but, as many of them are much larger, their collective global biomass (468 gigatons) is far larger than that of prokaryotes (77 gigatons), with plants alone accounting for over 81% of the total biomass of Earth.

• Eukaryotes range in size from single-celled organisms to huge whales
• 
  Prokaryotes (small cylindrical cells, bacteria, on left) and a single-celled eukaryote, Paramecium
   
• 
  Coast redwood
   
• 
  Blue whale

The eukaryotes are a diverse lineage, consisting mainly of microscopic organisms. Multicellularity in some form has evolved independently at least 25 times within the eukaryotes. Complex multicellular organisms, not counting the aggregation of amoebae to form slime molds, have evolved within only six eukaryotic lineages: animals, symbiomycotan fungi, brown algae, red algae, green algae, and land plants. Eukaryotes are grouped by genomic similarities, so that groups often lack visible shared characteristics.

Distinguishing features

Further information: Cell (biology) § Eukaryotic cells

Nucleus

The defining feature of eukaryotes is that their cells have a well-defined, membrane-bound nuclei, distinguishing them from prokaryotes that lack such a structure. Eukaryotic cells have a variety of internal membrane-bound structures, called organelles, and a cytoskeleton which defines the cell's organization and shape. The nucleus stores the cell's DNA, which is divided into linear bundles called chromosomes; these are separated into two matching sets by a microtubular spindle during nuclear division, in the distinctively eukaryotic process of mitosis.

Biochemistry

Eukaryotes differ from prokaryotes in multiple ways, with unique biochemical pathways such as sterane synthesis. The eukaryotic signature proteins have no homology to proteins in other domains of life, but appear to be universal among eukaryotes. They include the proteins of the cytoskeleton, the complex transcription machinery, the membrane-sorting systems, the nuclear pore, and some enzymes in the biochemical pathways.

Internal membranes

Further information: Endomembrane system

Prokaryote, to same scale

Eukaryotic cell with endomembrane system

Eukaryotic cells are some 10,000 times larger than prokaryotic cells by volume, and contain membrane-bound organelles.

Eukaryote cells include a variety of membrane-bound structures, together forming the endomembrane system. Simple compartments, called vesicles and vacuoles, can form by budding off other membranes. Many cells ingest food and other materials through a process of endocytosis, where the outer membrane invaginates and then pinches off to form a vesicle. Some cell products can leave in a vesicle through exocytosis.

The nucleus is surrounded by a double membrane known as the nuclear envelope, with nuclear pores that allow material to move in and out. Various tube- and sheet-like extensions of the nuclear membrane form the endoplasmic reticulum, which is involved in protein transport and maturation. It includes the rough endoplasmic reticulum, covered in ribosomes which synthesize proteins; these enter the interior space or lumen. Subsequently, they generally enter vesicles, which bud off from the smooth endoplasmic reticulum. In most eukaryotes, these protein-carrying vesicles are released and further modified in stacks of flattened vesicles (cisternae), the Golgi apparatus.

Vesicles may be specialized; for instance, lysosomes contain digestive enzymes that break down biomolecules in the cytoplasm.

Mitochondria

Main article: Mitochondrion

Mitochondria are essentially universal in the eukaryotes, and with their own DNA somewhat resemble prokaryotic cells.

Mitochondria are organelles in eukaryotic cells. The mitochondrion is commonly called "the powerhouse of the cell", for its function providing energy by oxidising sugars or fats to produce the energy-storing molecule ATP. Mitochondria have two surrounding membranes, each a phospholipid bilayer, the inner of which is folded into invaginations called cristae where aerobic respiration takes place.

Mitochondria contain their own DNA, which has close structural similarities to bacterial DNA, from which it originated, and which encodes rRNA and tRNA genes that produce RNA which is closer in structure to bacterial RNA than to eukaryote RNA.

Some eukaryotes, such as the metamonads Giardia and Trichomonas, and the amoebozoan Pelomyxa, appear to lack mitochondria, but all contain mitochondrion-derived organelles, like hydrogenosomes or mitosomes, having lost their mitochondria secondarily. They obtain energy by enzymatic action in the cytoplasm. It is thought that mitochondria developed from prokaryotic cells which became endosymbionts living inside eukaryotes.

Plastids

Main article: Plastid

The most common type of plastid is the chloroplast, which contains chlorophyll and produces organic compounds by photosynthesis.

Plants and various groups of algae have plastids as well as mitochondria. Plastids, like mitochondria, have their own DNA and are developed from endosymbionts, in this case cyanobacteria. They usually take the form of chloroplasts which, like cyanobacteria, contain chlorophyll and produce organic compounds (such as glucose) through photosynthesis. Others are involved in storing food. Although plastids probably had a single origin, not all plastid-containing groups are closely related. Instead, some eukaryotes have obtained them from others through secondary endosymbiosis or ingestion. The capture and sequestering of photosynthetic cells and chloroplasts, kleptoplasty, occurs in many types of modern eukaryotic organisms.

Cytoskeletal structures

Main article: Cytoskeleton

The cytoskeleton. Actin filaments are shown in red, microtubules in green. (The nucleus is in blue.)

The cytoskeleton provides stiffening structure and points of attachment for motor structures that enable the cell to move, change shape, or transport materials. The motor structures are microfilaments of actin and actin-binding proteins, including α-actinin, fimbrin, and filamin are present in submembranous cortical layers and bundles. Motor proteins of microtubules, dynein and kinesin, and myosin of actin filaments, provide dynamic character of the network.

Many eukaryotes have long slender motile cytoplasmic projections, called flagella, or multiple shorter structures called cilia. These organelles are variously involved in movement, feeding, and sensation. They are composed mainly of tubulin, and are entirely distinct from prokaryotic flagella. They are supported by a bundle of microtubules arising from a centriole, characteristically arranged as nine doublets surrounding two singlets. Flagella may have hairs (mastigonemes), as in many stramenopiles. Their interior is continuous with the cell's cytoplasm.

Centrioles are often present, even in cells and groups that do not have flagella, but conifers and flowering plants have neither. They generally occur in groups that give rise to various microtubular roots. These form a primary component of the cytoskeleton, and are often assembled over the course of several cell divisions, with one flagellum retained from the parent and the other derived from it. Centrioles produce the spindle during nuclear division.

Cell wall

Main article: Cell wall

The cells of plants, algae, fungi and most chromalveolates, but not animals, are surrounded by a cell wall. This is a layer outside the cell membrane, providing the cell with structural support, protection, and a filtering mechanism. The cell wall also prevents over-expansion when water enters the cell.

The major polysaccharides making up the primary cell wall of land plants are cellulose, hemicellulose, and pectin. The cellulose microfibrils are linked together with hemicellulose, embedded in a pectin matrix. The most common hemicellulose in the primary cell wall is xyloglucan.

Sexual reproduction

Further information: Evolution of sexual reproduction

Sexual reproduction requires a life cycle that alternates between a haploid phase, with one copy of each chromosome in the cell, and a diploid phase, with two copies. In eukaryotes, haploid gametes are produced by meiosis; two gametes fuse to form a diploid zygote.

Eukaryotes have a life cycle that involves sexual reproduction, alternating between a haploid phase, where only one copy of each chromosome is present in each cell, and a diploid phase, with two copies of each chromosome in each cell. The diploid phase is formed by fusion of two haploid gametes, such as eggs and spermatozoa, to form a zygote; this may grow into a body, with its cells dividing by mitosis, and at some stage produce haploid gametes through meiosis, a division that reduces the number of chromosomes and creates genetic variability. There is considerable variation in this pattern. Plants have both haploid and diploid multicellular phases. Eukaryotes have lower metabolic rates and longer generation times than prokaryotes, because they are larger and therefore have a smaller surface area to volume ratio.

The evolution of sexual reproduction may be a primordial characteristic of eukaryotes. Based on a phylogenetic analysis, Dacks and Roger have proposed that facultative sex was present in the group's common ancestor. A core set of genes that function in meiosis is present in both Trichomonas vaginalis and Giardia intestinalis, two organisms previously thought to be asexual. Since these two species are descendants of lineages that diverged early from the eukaryotic evolutionary tree, core meiotic genes, and hence sex, were likely present in the common ancestor of eukaryotes. Species once thought to be asexual, such as Leishmania parasites, have a sexual cycle. Amoebae, previously regarded as asexual, may be anciently sexual; while present-day asexual groups could have arisen recently.

Evolution

History of classification

Further information: History of taxonomy

In antiquity, the two lineages of animals and plants were recognized by Aristotle and Theophrastus. The lineages were given the taxonomic rank of kingdom by Linnaeus in the 18th century. Though he included the fungi with plants with some reservations, it was later realized that they are quite distinct and warrant a separate kingdom. The various single-cell eukaryotes were originally placed with plants or animals when they became known. In 1818, the German biologist Georg A. Goldfuss coined the word Protozoa to refer to organisms such as ciliates, and this group was expanded until Ernst Haeckel made it a kingdom encompassing all single-celled eukaryotes, the Protista, in 1866. The eukaryotes thus came to be seen as four kingdoms:

• Kingdom Protista
• Kingdom Plantae
• Kingdom Fungi
• Kingdom Animalia

The protists were at that time thought to be "primitive forms", and thus an evolutionary grade, united by their primitive unicellular nature. Understanding of the oldest branchings in the tree of life only developed substantially with DNA sequencing, leading to a system of domains rather than kingdoms as top level rank being put forward by Carl Woese, Otto Kandler, and Mark Wheelis in 1990, uniting all the eukaryote kingdoms in the domain "Eucarya", stating, however, that "'eukaryotes' will continue to be an acceptable common synonym". In 1996, the evolutionary biologist Lynn Margulis proposed to replace kingdoms and domains with "inclusive" names to create a "symbiosis-based phylogeny", giving the description "Eukarya (symbiosis-derived nucleated organisms)".

Phylogeny

Tree of eukaryotes showing major subgroups and thumbnail diagrams of representative members of each group, based on 2023 phylogenomic reconstructions.

By 2014, a rough consensus started to emerge from the phylogenomic studies of the previous two decades. The majority of eukaryotes can be placed in one of two large clades dubbed Amorphea (similar in composition to the unikont hypothesis) and the Diphoda (formerly bikonts), which includes plants and most algal lineages. A third major grouping, the Excavata, has been abandoned as a formal group as it was found to be paraphyletic. The proposed phylogeny below includes two groups of excavates (Discoba and Metamonada), and incorporates the 2021 proposal that picozoans are close relatives of rhodophytes. The Provora are a group of microbial predators discovered in 2022.

One view of the great kingdoms and their stem groups. The Metamonada are hard to place, being sister possibly to Discoba or to Malawimonada or being a paraphyletic group external to all other eukaryotes.

Origin of eukaryotes

Main article: Eukaryogenesis

In the theory of symbiogenesis, a merger of an archaean and an aerobic bacterium created the eukaryotes, with aerobic mitochondria; a second merger added chloroplasts, creating the green plants.

The origin of the eukaryotic cell, or eukaryogenesis, is a milestone in the evolution of life, since eukaryotes include all complex cells and almost all multicellular organisms. The last eukaryotic common ancestor (LECA) is the hypothetical origin of all living eukaryotes, and was most likely a biological population, not a single individual. The LECA is believed to have been a protist with a nucleus, at least one centriole and flagellum, facultatively aerobic mitochondria, sex (meiosis and syngamy), a dormant cyst with a cell wall of chitin or cellulose, and peroxisomes.

An endosymbiotic union between a motile anaerobic archaean and an aerobic alphaproteobacterium gave rise to the LECA and all eukaryotes, with mitochondria. A second, much later endosymbiosis with a cyanobacterium gave rise to the ancestor of plants, with chloroplasts.

The presence of eukaryotic biomarkers in archaea points towards an archaeal origin. The genomes of Promethearchaeati archaea have plenty of eukaryotic signature protein genes, which play a crucial role in the development of the cytoskeleton and complex cellular structures characteristic of eukaryotes. In 2022, cryo-electron tomography demonstrated that Promethearchaeati archaea have a complex actin-based cytoskeleton, providing the first direct visual evidence of the archaeal ancestry of eukaryotes.

Fossils

The timing of the origin of eukaryotes is hard to determine, but the discovery of Qingshania magnificia, the earliest multicelluar eukaryote from North China which lived 1.635 billion years ago, suggests that the crown group eukaryotes originated from the late Paleoproterozoic (Statherian). The earliest unequivocal unicellular eukaryotes, Tappania plana, Shuiyousphaeridium macroreticulatum, Dictyosphaera macroreticulata, Germinosphaera alveolata, and Valeria lophostriata from North China, lived approximately 1.65 billion years ago.

Some acritarchs are known from at least 1.65 billion years ago, and a fossil, Grypania, which may be an alga, is as much as 2.1 billion years old. The "problematic" fossil Diskagma has been found in paleosols 2.2 billion years old.

Reconstruction of the problematic Diskagma buttonii, a terrestrial fossil less than 1mm high, from rocks around 2.2 billion years old

The Neoarchean fossil Thuchomyces shares similarities with eukaryotes, specifically fungi. It especially resembles the problematic fossil Diskagma, with hyphae and multiple differentiated layers. However, it is over 600 million years older than all other possible eukaryotes, and many of its "eukaryote features" are not specific to the clade, meaning it is almost certainly a microbial mat instead.

Structures proposed to represent "large colonial organisms" have been found in the black shales of the Palaeoproterozoic such as the Francevillian B Formation, in Gabon, dubbed the "Francevillian biota" which is dated at 2.1 billion years old. However, the status of these structures as fossils is contested, with other authors suggesting that they might represent pseudofossils. The oldest fossils that can unambiguously be assigned to eukaryotes are from the Ruyang Group of China, dating to approximately 1.8-1.6 billion years ago. Fossils that are clearly related to modern groups start appearing an estimated 1.2 billion years ago, in the form of red algae, though recent work suggests the existence of fossilized filamentous algae in the Vindhya basin dating back perhaps to 1.6 to 1.7 billion years ago.

The presence of steranes, eukaryotic-specific biomarkers, in Australian shales previously indicated that eukaryotes were present in these rocks dated at 2.7 billion years old, but these Archaean biomarkers have been rebutted as later contaminants. The oldest valid biomarker records are only around 800 million years old. In contrast, a molecular clock analysis suggests the emergence of sterol biosynthesis as early as 2.3 billion years ago. The nature of steranes as eukaryotic biomarkers is further complicated by the production of sterols by some bacteria.

Whenever their origins, eukaryotes may not have become ecologically dominant until much later; a massive increase in the zinc composition of marine sediments 800 million years ago has been attributed to the rise of substantial populations of eukaryotes, which preferentially consume and incorporate zinc relative to prokaryotes, approximately a billion years after their origin (at the latest).