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Monday, February 28, 2022

Conversation analysis

Conversation analysis (CA) is an approach to the study of social interaction, embracing both verbal and non-verbal conduct, in situations of everyday life. CA originated as a sociological method, but has since spread to other fields. CA began with a focus on casual conversation, but its methods were subsequently adapted to embrace more task- and institution-centered interactions, such as those occurring in doctors' offices, courts, law enforcement, helplines, educational settings, and the mass media, and focus on nonverbal activity in interaction, including gaze, body movement and gesture. As a consequence, the term 'conversation analysis' has become something of a misnomer, but it has continued as a term for a distinctive and successful approach to the analysis of sociolinguistic interactions. CA and ethnomethodology are sometimes considered one field and referred to as EMCA.

History

Inspired by Harold Garfinkel's ethnomethodology and Erving Goffman's conception of the what came to be known as the interaction order,[ CA was developed in the late 1960s and early 1970s principally by the sociologist Harvey Sacks and his close associates Emanuel Schegloff and Gail Jefferson. It is distinctive in that its primary focus is on the production of social actions in the context of sequences of actions, rather than messages or propositions. Today CA is an established method used in sociology, anthropology, linguistics, speech-communication and psychology. It is particularly influential in interactional sociolinguistics and interactional linguistics, discourse analysis and discursive psychology.

Method

The method consists of detailed qualitative analysis of stretches of interaction between a number of people, often less than a minute. Most studies rely on a collection of cases, often from different interactions with different people, but some studies also focus on a single-case analysis. Crucially, the method uses the fact that interaction consists of multiple participants and that they make sense of each other, so the method proceeds by considering e.g. how one turn by a specific participant displays an understanding of the previous turn by another participant (or other earlier interaction). This is commonly referred to as the next-turn proof procedure even though proof is not to be taken literally. Research questions revolve around participants' orientation, that is, what features (linguistic or other) that cues people to respond in certain ways and influence the trajectory of an interaction. One key part of the method is about identifying deviant cases in collections, as they show that when a participant does not follow a norm, the interaction is affected in a way that reveals the existence of the norm in focus.

The data used in CA is in the form of video- or audio-recorded conversations, collected with or without researchers' involvement, typically from a video camera or other recording device in the space where the conversation takes place (e.g. a living room, picnic, or doctor's office). The researchers construct detailed transcriptions from the recordings, containing as much detail as is possible.

The transcription often contains additional information about nonverbal communication and the way people say things. Jeffersonian transcription is a commonly used method of transcription and nonverbal details are often transcribed according to Mondadan conventions by Lorenza Mondada.

After transcription, the researchers perform inductive data-driven analysis aiming to find recurring patterns of interaction. Based on the analysis, the researchers identify regularities, rules or models to describe these patterns, enhancing, modifying or replacing initial hypotheses. While this kind of inductive analysis based on collections of data exhibits is basic to fundamental work in CA, it has been more common in recent years to also use statistical analysis in applications of CA to solve problems in medicine and elsewhere.

While Conversation Analysis provides a method of analysing conversation, this method is informed by an underlying theory of what features of conversation are meaningful and the meanings that are likely implied by these features. Additionally there is a body of theory about how to interpret conversation.[12]

Basic structures

Conversation analysis provides a model that can be used to understand interactions, and offers a number of concepts to describe them. The following section contains important concepts and phenomena identified in the conversation analytical literature, and will refer to articles that are centrally concerned with the phenomenon. A conversation is viewed as a collection of turns as speaking; errors or misunderstandings in speech are addressed with repairs, and turns may be marked by the delay between them or other linguistic features.

Turn-taking organization

The analysis of turn-taking started with the description in a model in the paper known as the "Simplest Systematics", which was very programmatic for the field of Conversation analysis and one of the most cited papers published in the journal Language.

The model is designed to explain that when people talk in conversation, they do not always talk all at the same time, but generally, one person speaks at a time, and then another person can follow. Such a contribution to a conversation by one speaker is then a turn. A turn is created through certain forms or units that listeners can recognize and count on, called turn construction units (TCUs), and speakers and listeners will know that such forms can be a word or a clause, and use that knowledge to predict when a speaker is finished so that others can speak, to avoid or minimize both overlap and silence. A listener will look for the places where they can start speaking - so-called transition relevant places (TRPs) - based on how the units appear over time. Turn construction units can be created or recognized via four methods, i.e. types of unit design:

  • Grammatical methods, i.e. morphosyntactic structures.
  • Prosodic methods, e.g. pitch, speed and changes in pronunciation.
  • Pragmatic methods: turns perform actions, and at the point where listeners have heard enough and know enough, a turn can be pragmatically complete.
  • Visual methods: Gesture, gaze and body movement is also used to indicate that a turn is over. For example, a person speaking looks at the next speaker when their turn is about to end.

Each time a turn is over, speakers also have to decide who can talk next, and this is called turn allocation. The rules for turn allocation is commonly formulated in the same way as in the original Simplest Systematics paper, with 2 parts where the first consists of 3 elements:

    • a. If the current speaker selects a next one to speak at the end of current TCU (by name, gaze or contextual aspects of what is said), the selected speaker has the right and obligation to speak next.
    • b. If the current speaker does not select a next speaker, other potential speakers have the right to self-select (the first starter gets the turn)
    • c. If options 1a and 1b have not been implemented, current speaker may continue with another TCU.
  1. At the end of that TCU, the option system applies again.

Based on the turn-taking system, three types of silence may be distinguished:

  • Pause: A period of silence within a speaker's TCU, i.e. during a speaker's turn when a sentence is not finished.
  • Gap: A period of silence between turns, for example after a question has been asked and not yet answered
  • Lapse: A period of silence when no sequence or other structured activity is in progress: the current speaker stops talking, does not select a next speaker, and no one self selects. Lapses are commonly associated with visual or other forms of disengagement between speakers, even if these periods are brief.

Some types of turns may require extra work before they can successfully take place. Speakers wanting a long turn, for example to tell a story or describe important news, must first establish that others will not intervene during the course of the telling through some form of preface and approval by the listener (a so-called go-ahead). The preface and its associated go-ahead comprise a "pre-sequence".Conversations cannot be appropriately ended by 'just stopping', but require a special closing sequence.

The model also leaves puzzles to be solved, for example concerning how turn boundaries are identified and projected, and the role played by gaze and body orientation in the management of turn-taking. It also establishes some questions for other disciplines: for example, the split second timing of turn-transition sets up a cognitive 'bottle neck' problem in which potential speakers must attend to incoming speech while also preparing their own contribution - something which imposes a heavy load of human processing capacity, and which may impact the structure of languages.

However, the original formulation in Sacks et al. 1974 is designed to model turn-taking only in ordinary and informal conversation, and not interaction in more specialized, institutional environments such as meetings, courts, news interviews, mediation hearings, which have distinctive turn-taking organizations that depart in various ways from ordinary conversation. Later studies has looked at institutional interaction and turn-taking in institutional contexts.

Sequence organization

Adjacency pairs

Talk tends to occur in responsive pairs; however, the pairs may be split over a sequence of turns. Adjacency pairs divide utterance types into 'first pair parts' and 'second pair parts' to form a 'pair type'. There are many examples of adjacency pairs including Questions-Answers, Offer-Acceptance/Refusal and Compliment-Response.

Sequence expansion

Sequence expansion allows talk which is made up of more than a single adjacency pair to be constructed and understood as performing the same basic action and the various additional elements are as doing interactional work related to the basic action underway.
Sequence expansion is constructed in relation to a base sequence of a first pair part (FPP) and a second pair part (SPP) in which the core action underway is achieved. It can occur prior to the base FPP, between the base FPP and SPP, and following the base SPP.
1. Pre-expansion: an adjacency pair that may be understood as preliminary to the main course of action. A generic pre-expansion is a summon-answer adjacency pair, as in "Mary?"/ "Yes?".It is generic in the sense that it does not contribute to any particular types of base adjacency pair, such as request or suggestion. There are other types of pre-sequence that work to prepare the interlocutors for the subsequent speech action. For example, "Guess what!"/"What?" as preliminary to an announcement of some sort, or "What are you doing?"/"Nothing" as preliminary to an invitation or a request.
2. Insert expansion: an adjacency pair that comes between the FPP and SPP of the base adjacency pair. Insert expansions interrupt the activity under way, but are still relevant to that action. Insert expansion allows a possibility for a second speaker, the speaker who must produce the SPP, to do interactional work relevant to the projected SPP. An example of this would be a typical conversation between a customer and a shopkeeper:

Customer: I would like a turkey sandwich, please. (FPP base)
Server: White or wholegrain? (Insert FPP)
Customer: Wholegrain. (Insert SPP)
Server: Okay. (SPP base)

3. Post-expansion: a turn or an adjacency pair that comes after, but is still tied to, the base adjacency pair. There are two types: minimal and non-minimal. Minimal expansion is also termed sequence closing thirds, because it is a single turn after the base SPP (hence third) that does not project any further talk beyond their turn (hence closing). Examples of sequence closing thirds include "oh", "I see", "okay", etc.

4. Silence: Silence can occur throughout the entire speech act but in what context it is happening depends what the silence means. Three different assets can be implied through silence:

  • Pause: A period of silence within a speaker's turn.
  • Gap: A period of silence between turns.
  • Lapse: A period of silence when no sequence is in progress: the current speaker stops talking, does not select a next speaker, and no one self selects. Lapses are commonly associated with visual or other forms of disengagement between speakers, even if these periods are brief.

Preference organization

CA may reveal structural (i.e. practice-underwritten) preferences in conversation for some types of actions (within sequences of action) over others, as responses in certain sequential environments. For example, responsive actions which agree with, or accept, positions taken by a first action tend to be performed more straightforwardly and faster than actions that disagree with, or decline, those positions. The former is termed a preferred turn shape, meaning the turn is not preceded by silence nor is it produced with delays, mitigation and accounts. The latter is termed a dispreferred turn shape, which describes a turn with opposite characteristics. One consequence of this is that agreement and acceptance are promoted over their alternatives, and are more likely to be the outcome of the sequence. Pre-sequences are also a component of preference organization and contribute to this outcome.

Repair

Repair organization describes how parties in conversation deal with problems in speaking, hearing, or understanding, and there are various mechanisms through which certain "troubles" in interaction are dealt with. Repair segments are classified by who initiates repair (self or other), by who resolves the problem (self or other), and by how it unfolds within a turn or a sequence of turns. The organization of repair is also a self-righting mechanism in social interaction. Participants in conversation seek to correct the trouble source by initiating and preferring self repair, the speaker of the trouble source, over other repair. Self repair initiations can be placed in three locations in relation to the trouble source, in a first turn, a transition space or in a third turn.

Action formation

Turns in interaction implement actions, and a specific turn may perform one (or more) specific actions. The study of action focuses on the description of the practices by which turns at talk are composed and positioned so as to realize one or more actions. This could include openings and closings of conversations, assessments, storytelling, and complaints. Focus is both on how those actions are formed through linguistic or other activity (the formation of action) and how they are understood (the ascription of action to turns). The study of action also concerns the ways in which the participants’ knowledge, relations, and stances towards the ongoing interactional projects are created, maintained, and negotiated, and thus the intersubjectivity of how people interact. The concept of action within CA resembles, but it different from the concept of speech act in other fields of pragmatics.

Jeffersonian transcription

Gail Jefferson developed a system of transcription while working with Harvey Sacks. In this system, speakers are introduced with a name followed by a colon, as conventionally used in scripts. It is designed to use typographical and orthographical conventions used elsewhere, rather than a strict phonetic system such as the International Phonetic Alphabet. The transcription conventions take into account overlapping speech, delays between speech, pitch, volume and speed based on research showing that these features matter for the conversation in terms of action, turn-taking and more. Transcripts are typically written in a monospaced font to ease the alignment of overlap symbols.

Partial table of annotations added in Jeffersonian Transcription
Feature Symbol Used Example
Very quietly spoken °°...°°
Matt: Shoes °°I love shoes°°_
Quietly spoken °...°
Sue: Have you had any °symptoms°,?
Loudly spoken Capital letters
Sara: Why can't you JUST STOP?
Falling pitch .
Fred: That's a good idea.
Unchanging (level) pitch _
Matt: That's a good idea_
Slightly rising pitch ,
Matt: We like to shop, and to eat fish_
Intermediately rising pitch ,?
Alex: We're buying shoes,?
Rising pitch ?
Bill: Should we open the door?
Stressed syllables Underlined letters
Dave: That is a good idea.
Absence of normal pauses =
Lucy:    Perhaps we should leave=
William: =I don't think that's a good idea_
Noticeable pauses (.)
Lucy: James (.) we need to talk.
Pauses of a specific duration (Duration)
Lucy: James (1.0) we need to talk.
Rushed speech ><
Alex: What are you doing?
Jack: >I need to buy the shoes<
Slowed speech <>
Fred: <That's a good idea,> I think 
Overlapping speech [...]
Dave: Perhaps we should [leave.]
Tom:                    [Go inside,?]
Prolonged sounds (non-phonemic) :
Dave: O:h wo::w.
Creaky voice *...*
Lucy:  Do you want to talk?
James: *No* (.) Sorry.

There are various transcription systems based on the jeffersonian conventions with slight differences. Galina Bolden has designed a system for transcribing Russian conversations while Samtalegrammatik.dk uses their own system for Danish. GAT2 (Gesprächsanalytisches Transskriptionssystem 2) was also designed originally for German and to systematize the way some of the prosodic features are handled. The TalkBank also has its own system designed for use with its CLAN (CHILDES Language Analyzer) software.

Different approaches

Interactional linguistics

Interactional linguistics (IL) is Conversation analysis when the focus is on linguistic structure. While CA has worked with language in its data since the beginning, the interest in the structure of it, and possible relations to grammatical theory, was sometimes secondary to sociological (or ethnomethodological) research questions. The field developed during the 90's and got its name with the publication of the 2001 Studies in Interactional Linguistics and is inspired by West Coast functional grammar which is sometimes considered to have effectively merged with IL since then, but has also gained inspiration from British phoneticians doing prosodic analysis. Levinson's former department on Language and Cognition at the Max Planck Institute for Psycholinguistics has been important in connecting CA and IL with linguistic typology. Interactional linguistics has studied topics within syntax, phonetics and semantics as they related to e.g. action and turn-taking. There is a journal called Interactional Linguistics.

Discursive psychology

Discursive psychology (DP) is the use of CA on psychological themes, and studies how psychological phenomena are attended to, understood and construed in interaction. The subfield formed through studies by Jonathan Potter and Margaret Wetherell, most notably their 1987 book Discourse and social psychology: Beyond attitudes and behaviour.

Membership categorization analysis

Membership Categorization Analysis (MCA) was influenced by the work of Harvey Sacks and his work on Membership Categorization Devices (MCD). Sacks argues that members' categories comprise part of the central machinery of organization and developed the notion of MCD to explain how categories can be hearably linked together by native speakers of a culture. His example that is taken from a children's storybook (The baby cried. The mommy picked it up) shows how "mommy" is interpreted as the mother of the baby by speakers of the same culture. In light of this, categories are inference rich – a great deal of knowledge that members of a society have about the society is stored in terms of these categories. Stokoe further contends that members’ practical categorizations form part of ethnomethodology's description of the ongoing production and realization of ‘facts’ about social life and including members’ gendered reality analysis, thus making CA compatible with feminist studies.

Relations to other fields

Contrasts to other theories about language

In contrast to the research inspired by Noam Chomsky, which is based on a distinction between competence and performance and dismisses the particulars of actual speech, conversation analysis studies naturally-occurring talk and shows that spoken interaction is systematically orderly in all its facets (cf. Sacks in Atkinson and Heritage 1984: 21–27). In contrast to the theory developed by John Gumperz, CA maintains it is possible to analyze talk-in-interaction by examining its recordings alone (audio for telephone, video for copresent interaction). CA researchers do not believe that the researcher needs to consult with the talk participants or members of their speech community.

It is distinct from discourse analysis in focus and method. (i) Its focus is on processes involved in social interaction and does not include written texts or larger sociocultural phenomena (for example, 'discourses' in the Foucauldian sense). (ii) Its method, following Garfinkel and Goffman's initiatives, is aimed at determining the methods and resources that the interacting participants use and rely on to produce interactional contributions and make sense of the contributions of others. Thus CA is neither designed for, nor aimed at, examining the production of interaction from a perspective that is external to the participants' own reasoning and understanding about their circumstances and communication. Rather the aim is to model the resources and methods by which those understandings are produced.

In considering methods of qualitative analysis, Braun and Clarke distinguish thematic analysis from conversation analysis and discourse analysis, viewing thematic analysis to be theory agnostic while conversation analysis and discourse analysis are considered to be based on theories.

Application in other fields

CA is important in language revitalization. For example, according to Ghil'ad Zuckermann, Western conversational interaction is typically both "dyadic" (between two particular people, eye contact is important, the speaker controls the interaction) and "contained" (in a relatively short, defined time frame). Accordingly, if one asks a question, one expects to receive an answer immediately thereafter. On the other hand, traditional Aboriginal conversational interaction is "communal" (broadcast to many people, eye contact is not important, the listener controls the interaction) and "continuous" (spread over a longer, indefinite time frame). Accordingly, if one asks a question, one should not expect an immediate answer.

Sunday, February 27, 2022

Photorespiration

From Wikipedia, the free encyclopedia
 
Simplified C2 cycle
 
Simplified photorespiration and Calvin cycle

Photorespiration (also known as the oxidative photosynthetic carbon cycle, or C2 photosynthesis) refers to a process in plant metabolism where the enzyme RuBisCO oxygenates RuBP, wasting some of the energy produced by photosynthesis. The desired reaction is the addition of carbon dioxide to RuBP (carboxylation), a key step in the Calvin–Benson cycle, but approximately 25% of reactions by RuBisCO instead add oxygen to RuBP (oxygenation), creating a product that cannot be used within the Calvin–Benson cycle. This process reduces the efficiency of photosynthesis, potentially reducing photosynthetic output by 25% in C3 plants. Photorespiration involves a complex network of enzyme reactions that exchange metabolites between chloroplasts, leaf peroxisomes and mitochondria.

The oxygenation reaction of RuBisCO is a wasteful process because 3-phosphoglycerate is created at a reduced rate and higher metabolic cost compared with RuBP carboxylase activity. While photorespiratory carbon cycling results in the formation of G3P eventually, around 25% of carbon fixed by photorespiration is re-released as CO2 and nitrogen, as ammonia. Ammonia must then be detoxified at a substantial cost to the cell. Photorespiration also incurs a direct cost of one ATP and one NAD(P)H.

While it is common to refer to the entire process as photorespiration, technically the term refers only to the metabolic network which acts to rescue the products of the oxygenation reaction (phosphoglycolate).

Photorespiratory reactions

PhotorespirationFrom left to right: chloroplast, peroxisome, and mitochondrion

Addition of molecular oxygen to ribulose-1,5-bisphosphate produces 3-phosphoglycerate (PGA) and 2-phosphoglycolate (2PG, or PG). PGA is the normal product of carboxylation, and productively enters the Calvin cycle. Phosphoglycolate, however, inhibits certain enzymes involved in photosynthetic carbon fixation (hence is often said to be an 'inhibitor of photosynthesis'). It is also relatively difficult to recycle: in higher plants it is salvaged by a series of reactions in the peroxisome, mitochondria, and again in the peroxisome where it is converted into glycerate. Glycerate reenters the chloroplast and by the same transporter that exports glycolate. A cost of 1 ATP is associated with conversion to 3-phosphoglycerate (PGA) (Phosphorylation), within the chloroplast, which is then free to re-enter the Calvin cycle.

Several costs are associated with this metabolic pathway; the production of hydrogen peroxide in the peroxisome (associated with the conversion of glycolate to glyoxylate). Hydrogen peroxide is a dangerously strong oxidant which must be immediately split into water and oxygen by the enzyme catalase. The conversion of 2× 2Carbon glycine to 1 C3 serine in the mitochondria by the enzyme glycine-decarboxylase is a key step, which releases CO2, NH3, and reduces NAD to NADH. Thus, 1 CO
2
molecule is produced for every 2 molecules of O
2
(two deriving from RuBisCO and one from peroxisomal oxidations). The assimilation of NH3 occurs via the GS-GOGAT cycle, at a cost of one ATP and one NADPH.

Cyanobacteria have three possible pathways through which they can metabolise 2-phosphoglycolate. They are unable to grow if all three pathways are knocked out, despite having a carbon concentrating mechanism that should dramatically reduce the rate of photorespiration (see below).

Substrate specificity of RuBisCO

Oxygenase activity of RuBisCO

The oxidative photosynthetic carbon cycle reaction is catalyzed by RuBP oxygenase activity:

RuBP + O
2
→ Phosphoglycolate + 3-phosphoglycerate + 2H+

During the catalysis by RuBisCO, an 'activated' intermediate is formed (an enediol intermediate) in the RuBisCO active site. This intermediate is able to react with either CO
2
or O
2
. It has been demonstrated that the specific shape of the RuBisCO active site acts to encourage reactions with CO
2
. Although there is a significant "failure" rate (~25% of reactions are oxygenation rather than carboxylation), this represents significant favouring of CO
2
, when the relative abundance of the two gases is taken into account: in the current atmosphere, O
2
is approximately 500 times more abundant, and in solution O
2
is 25 times more abundant than CO
2
.

The ability of RuBisCO to specify between the two gases is known as its selectivity factor (or Srel), and it varies between species, with angiosperms more efficient than other plants, but with little variation among the vascular plants.

A suggested explanation of RuBisCO's inability to discriminate completely between CO
2
and O
2
is that it is an evolutionary relic: The early atmosphere in which primitive plants originated contained very little oxygen, the early evolution of RuBisCO was not influenced by its ability to discriminate between O
2
and CO
2
.

Conditions which affect photorespiration


Photorespiration rates are increased by:

Altered substrate availability: lowered CO2 or increased O2

Factors which influence this include the atmospheric abundance of the two gases, the supply of the gases to the site of fixation (i.e. in land plants: whether the stomata are open or closed), the length of the liquid phase (how far these gases have to diffuse through water in order to reach the reaction site). For example, when the stomata are closed to prevent water loss during drought: this limits the CO2 supply, while O
2
production within the leaf will continue. In algae (and plants which photosynthesise underwater); gases have to diffuse significant distances through water, which results in a decrease in the availability of CO2 relative to O
2
. It has been predicted that the increase in ambient CO2 concentrations predicted over the next 100 years may reduce the rate of photorespiration in most plants by around 50%. However, at temperatures higher than the photosynthetic thermal optimum, the increases in turnover rate are not translated into increased CO2 assimilation because of the decreased affinity of Rubisco for CO2.

Increased temperature

At higher temperatures RuBisCO is less able to discriminate between CO2 and O
2
. This is because the enediol intermediate is less stable. Increasing temperatures also reduce the solubility of CO2, thus reducing the concentration of CO2 relative to O
2
in the chloroplast.

Biological adaptation to minimize photorespiration

Maize uses the C4 pathway, minimizing photorespiration

Certain species of plants or algae have mechanisms to reduce uptake of molecular oxygen by RuBisCO. These are commonly referred to as Carbon Concentrating Mechanisms (CCMs), as they increase the concentration of CO
2
so that RuBisCO is less likely to produce glycolate through reaction with O
2
.

Biochemical carbon concentrating mechanisms

Biochemical CCMs concentrate carbon dioxide in one temporal or spatial region, through metabolite exchange. C4 and CAM photosynthesis both use the enzyme Phosphoenolpyruvate carboxylase (PEPC) to add CO
2
to a 4-Carbon sugar. PEPC is faster than RuBisCO, and more selective for CO
2
.

C4

C4 plants capture carbon dioxide in their mesophyll cells (using an enzyme called phosphoenolpyruvate carboxylase which catalyzes the combination of carbon dioxide with a compound called phosphoenolpyruvate (PEP)), forming oxaloacetate. This oxaloacetate is then converted to malate and is transported into the bundle sheath cells (site of carbon dioxide fixation by RuBisCO) where oxygen concentration is low to avoid photorespiration. Here, carbon dioxide is removed from the malate and combined with RuBP by RuBisCO in the usual way, and the Calvin Cycle proceeds as normal. The CO
2
concentrations in the Bundle Sheath are approximately 10–20 fold higher than the concentration in the mesophyll cells.

This ability to avoid photorespiration makes these plants more hardy than other plants in dry and hot environments, wherein stomata are closed and internal carbon dioxide levels are low. Under these conditions, photorespiration does occur in C4 plants, but at a much reduced level compared with C3 plants in the same conditions. C4 plants include sugar cane, corn (maize), and sorghum.

CAM (Crassulacean acid metabolism)

Overnight graph of CO2 absorbed by a CAM plant

CAM plants, such as cacti and succulent plants, also use the enzyme PEP carboxylase to capture carbon dioxide, but only at night. Crassulacean acid metabolism allows plants to conduct most of their gas exchange in the cooler night-time air, sequestering carbon in 4-carbon sugars which can be released to the photosynthesizing cells during the day. This allows CAM plants to reduce water loss (transpiration) by maintaining closed stomata during the day. CAM plants usually display other water-saving characteristics, such as thick cuticles, stomata with small apertures, and typically lose around 1/3 of the amount of water per CO
2
fixed.

Algae

There have been some reports of algae operating a biochemical CCM: shuttling metabolites within single cells to concentrate CO2 in one area. This process is not fully understood.

Biophysical carbon-concentrating mechanisms

This type of carbon-concentrating mechanism (CCM) relies on a contained compartment within the cell into which CO2 is shuttled, and where RuBisCO is highly expressed. In many species, biophysical CCMs are only induced under low carbon dioxide concentrations. Biophysical CCMs are more evolutionarily ancient than biochemical CCMs. There is some debate as to when biophysical CCMs first evolved, but it is likely to have been during a period of low carbon dioxide, after the Great Oxygenation Event (2.4 billion years ago). Low CO
2
periods occurred around 750, 650, and 320–270 million years ago.

Eukaryotic algae

In nearly all species of eukaryotic algae (Chloromonas being one notable exception), upon induction of the CCM, ~95% of RuBisCO is densely packed into a single subcellular compartment: the pyrenoid. Carbon dioxide is concentrated in this compartment using a combination of CO2 pumps, bicarbonate pumps, and carbonic anhydrases. The pyrenoid is not a membrane bound compartment, but is found within the chloroplast, often surrounded by a starch sheath (which is not thought to serve a function in the CCM).

Hornworts

Certain species of hornwort are the only land plants which are known to have a biophysical CCM involving concentration of carbon dioxide within pyrenoids in their chloroplasts.

Cyanobacteria

Cyanobacterial CCMs are similar in principle to those found in eukaryotic algae and hornworts, but the compartment into which carbon dioxide is concentrated has several structural differences. Instead of the pyrenoid, cyanobacteria contain carboxysomes, which have a protein shell, and linker proteins packing RuBisCO inside with a very regular structure. Cyanobacterial CCMs are much better understood than those found in eukaryotes, partly due to the ease of genetic manipulation of prokaryotes.

Possible purpose of photorespiration

Reducing photorespiration may not result in increased growth rates for plants. Photorespiration may be necessary for the assimilation of nitrate from soil. Thus, a reduction in photorespiration by genetic engineering or because of increasing atmospheric carbon dioxide (due to fossil fuel burning) may not benefit plants as has been proposed. Several physiological processes may be responsible for linking photorespiration and nitrogen assimilation. Photorespiration increases availability of NADH, which is required for the conversion of nitrate to nitrite. Certain nitrite transporters also transport bicarbonate, and elevated CO2 has been shown to suppress nitrite transport into chloroplasts. However, in an agricultural setting, replacing the native photorespiration pathway with an engineered synthetic pathway to metabolize glycolate in the chloroplast resulted in a 40 percent increase in crop growth.

Although photorespiration is greatly reduced in C4 species, it is still an essential pathway – mutants without functioning 2-phosphoglycolate metabolism cannot grow in normal conditions. One mutant was shown to rapidly accumulate glycolate.

Although the functions of photorespiration remain controversial, it is widely accepted that this pathway influences a wide range of processes from bioenergetics, photosystem II function, and carbon metabolism to nitrogen assimilation and respiration. The oxygenase reaction of RuBisCO may prevent CO2 depletion near its active sites and contributes to the regulation of CO2. concentration in the atmosphere The photorespiratory pathway is a major source of hydrogen peroxide (H
2
O
2
) in photosynthetic cells. Through H
2
O
2
production and pyrimidine nucleotide interactions, photorespiration makes a key contribution to cellular redox homeostasis. In so doing, it influences multiple signalling pathways, in particular, those that govern plant hormonal responses controlling growth, environmental and defense responses, and programmed cell death.

It has been postulated that photorespiration may function as a "safety valve", preventing the excess of reductive potential coming from an overreduced NADPH-pool from reacting with oxygen and producing free radicals, as these can damage the metabolic functions of the cell by subsequent oxidation of membrane lipids, proteins or nucleotides. The mutants deficient in photorespiratory enzymes are characterized by a high redox level in the cell, impaired stomatal regulation, and accumulation of formate.

Food politics

Food politics is a term which encompasses not only food policy and legislation, but all aspects of the production, control, regulation, inspection, distribution and consumption of commercially grown, and even sometimes home grown, food. The commercial aspects of food production are affected by ethical, cultural, and health concerns, as well as environmental concerns about farming and agricultural practices and retailing methods. The term also encompasses biofuels, GMO crops and pesticide use, the international food market, food aid, food security and food sovereignty, obesity, labor practices and immigrant workers, issues of water usage, animal cruelty, and climate change.

Policy

Government policies around food production, distribution, and consumption influence the cost, availability, and safety of the food supply domestically and internationally. On a national scale, food policy work affects farmers, food processors, wholesalers, retailers and consumers. Commodity crops, such as corn, rice, wheat, and soy are most often at the heart of agricultural policy-making.

While most food policy is initiated domestically, there are international ramifications. Globally, protectionist trade policies, international trade agreements, famine, political instability, and development aid are among the primary influences on food policy. Increasingly, climate change concerns and predictions are gaining the attention of those most concern with ensuring an adequate worldwide food supply.

Food politics in the U.S.

A number of contemporary issues around food policy issues have surfaced in the United States due to changes in the production of food and concerns about the nutritional quality of commercially prepared foods.

Technology

As with many industries, the food industry has experienced growth in the capacity to produce food with the use of improved technologies. In developed countries, there are a number of important trends at play. Yields, or the amount of food harvested per acre of cropland, have increased less than one percent per year in since at least the 1960s and the amount of land devoted to crop use is in decline due to development pressures for housing and other economic concerns. In the U.S. alone, about 3000 acres of productive farmland are lost each day.

This places a premium on quality yields from existing acres of farmland. In addition, the demand for meat products worldwide, expected to double by 2020, has accelerated a trend toward raising more animals on fewer acres of land.

Farming of animals

More intensive forms of animal farming have largely replaced traditional methods of raising pigs, cattle, poultry and fish for human consumption in the U.S. The increased development of Concentrated Animal Feeding Operations have been associated with increased risk of foodborne illnesses from e.coli, environmental degradation, and increased emissions of ammonia, carbon dioxide, and methane into the air. In addition to food safety and environmental concerns, organizations such as the People for the Ethical Treatment of Animals and the Humane Society of the United States (HSUS) have drawn attention to a range of practices that allow for the more efficient raising of animals for meat consumption, but these practices stress the animals, the land on which they are raised and the supply of food for human consumption. In a recent report on industrialized animal agriculture, HSUS called on people in Western countries to shift to a plant-based diet because half the world's grain crop is used to raise animals for meat, eggs, and milk. Fish farming has also come under scrutiny due to high concentrations of fish in smaller spaces than is experienced in the wild. For both land and water animals, the prophylactic use of antibiotics to promote growth and stem the spread of infection among the animals has also been questioned due to concerns that this practice may contribute to strains of antibiotic-resistant bacteria.

Genetically modified foods

The use of genetically modified organism seeds to grow commodity and other crops in the U.S. has drawn criticism from organizations such as Greenpeace, The Non-GMO Project, and the Organic Consumers Association among others. Concerns center on both food safety and the erosion of agricultural biodiversity. While the European Union regulates genetically engineered foods as they would any other new product requiring extensive testing to provide it is safe for human consumption, the U.S. does not. The Food and Drug Administration generally considers a food with origins from genetically modified organisms (GMO) to be as safe as its conventional counterpart.

Numerous studies have backed industry claims that GMO foods appear to be safe for human consumption, including an examination of more than 130 research projects conducted in the European Union prior to 2010 and work published by the American Medical Association's Council on Science and Public Health.

In the U.S., the political debate has centered primarily on whether or not to label products with GMO origins to better inform the public about the content of the foods they purchase. A statewide ballot question that would have mandated labeling of GMO products in California was defeated in 2012. The measure, known as Proposition 37 was leading by a wide margin in early polling but was defeated after an advertising blitz bankrolled by Monsanto, the largest supplier of genetically engineered seeds, Kraft Foods, Coca-Cola, PepsiCo., and other large food business interests. The ballot question's results were closely watched across the country as advocates for the measure hoped that it would pass and spur the federal government to mandate labeling of GMO foods as well.

In the wake of the labeling law proposal's defeat, an organization called March Against Monsanto was formed to continue to keep alive the public debate about labeling GMO food products. In 2013, a ballot initiative that would have required labels on GMO foods sold in the state of Washington was defeated by voters, again after a campaign against the initiative was led by major food companies.

Pesticide use

Among the much-heralded impacts of the Green Revolution was the spread of technological advances in the development of pesticides to ensure higher crop yields. Health effects of pesticides have led to a number of regulatory and non-regulatory efforts to control potential harm to human health from these chemicals in the food supply. The US Environmental Protection Agency has jurisdiction of the use of pesticides in crop management and sets tolerances for trace amounts of pesticides that may be found in the food supply. About 12,000 samples of fruits and vegetables available to U.S. consumers are collected each year and tested for residue from pesticides and the results are published in an annual Pesticide Data Program (PDP) hosted by the USDA.

Big food

Food manufacturing and processing is a heavily concentrated industry. The 10 largest food companies in the United States control more than half of all food sales domestically and a growing percentage of packaged food and beverage products on store shelves worldwide. Ranked by food sales, PepsiCo, Inc., is the largest food manufacturer in the U.S., followed by Tyson Foods, Nestlé, JBS USA, and Anheuser-Busch, according to a 2013 list published by Food Processing magazine. Big food influence is evident in Washington, D.C. where companies spend millions on lobbying each year, many of whom are members of the Consumer Goods Forum. Lobbying unfairly benefits large corporations whose deep pockets and connections get them special access to lawmakers, regulators and other influential officials.

According to figures from the United States Census Bureau from 2007, the most highly concentrated food industries in the country included cane sugar refining, breakfast cereals, bottled water, and cookie/cracker manufacturing using the 4-firm concentration ratio. Consolidation of this industry took place in the 1970s and 1980s through a series of mergers and acquisitions.

"Big food" has come under fire not only because a small number of players are responsible for a large percentage of the food supply chain, but because of concerns about the links between the highly processed foods they produce and the obesity epidemic both in the U.S. and worldwide. A report from Global Health Advocacy Incubator documents the food industry’s strategies to defeat warning labels on ultra-processed food products (UPP).

The director general of the World Health Organization, in a speech given at the 8th Global Conference on Health Promotion in Helsinki, Finland in June 2013, noted that the public health community's efforts to combat chronic diseases such as diabetes, hypertension and cardiovascular disease are pitted against the economic interests of the powerful food industry.

Marketing and other strategies of the food industry have been compared to those of the tobacco industry at the height of its influence in the consumer marketplace. In response, the food industry has engaged in some voluntary efforts to improve the nutritional content of their foods. In 2005, General Mills announced a plan to ensure that all of its breakfast cereals contained at least eight grams of whole grain per serving. In 2006, Campbell Soup Company announced an initiative to reduce sodium in its products by at least 25 percent. Due to slumping sales, Campbell's acknowledged that it was adding more sodium back into some of its soups in 2011.

The World Health Organization published a report in 2022 which highlights food marketing is especially prevalent where children are and what they watch on TV. Predominantly promoting ultra-processed food which includes sugar-sweetened beverages, and chocolate and confectionery. It confirms food marketing is pervasive, persuasive and bad for health.

Food movements

A cultural backlash against an increasingly mechanized food industry has taken a number of different forms.

  • Local food is a movement to shift food expenditures by individuals, families, community organizations, schools, restaurants, and other institutions from foods produced and shipped long distances by larger corporate entities to regional farmers and other local producers of food. Small farming interests, relatively heterogeneous products and short supply chains characterize local food markets, though there is no agreed-upon measure of the distances that constitute "local." Community-supported agriculture is a mechanism for connecting consumers with local farmers. Farm-to-table efforts are also part of the local food movement.
  • Meatless Monday is a public health awareness campaign encouraging individuals and families to eat a meat-free diet at least once each week. Launched in 2003 through the Johns Hopkins Center for a Livable Future, its focus is on preventable diseases associated with excessive meat consumption  but the campaign has also been incorporated by many concerned about sustainable agriculture and the environment.
  • Slow Food is an international movement founded in Italy in 1986, with Slow Food USA established in 2000. The organization stands in opposition to "the standardization of taste and culture, and the unrestrained power of food industry multinationals and industrial agriculture."

Among those influential in the food movement in the United States are writers, including Michael Pollan and Marion Nestle, and celebrity chefs such as Alice Waters, Mario Batali and Jamie Oliver. Popular books and movies on contemporary topics in food include Fast Food Nation, The Omnivore's Dilemma and the documentary Food, Inc. In 2011, the president of the American Farm Bureau Federation referred to this influential group as "self-appointed food elitists" and the Washington Post published an op-ed from Eric Schlosser, author of Fast Food Nation, defending the work he and colleagues have done to improve food systems in the United States.

Social justice

While the production and distribution of food is primarily an economic activity, advocates for a variety of social justice concerns are increasingly aware of the role that food policy plays in issues of greatest concern to causes they espouse.

Biofuel mandates and food supply

The interests of varied sectors of the agricultural industry are not always in alignment  as illustrated by tensions stemming from a drought in 2012 that affected domestic corn production. Described as the most severe and extensive drought in the U.S. in the last 25 years by the USDA Economic Research Service, thousands of acres of mostly corn and soy fields in the Midwest were damaged or destroyed.

This led to increased pressure on the federal government from some domestic farmers and international anti-hunger organizations to relax the Renewable Fuel Standard that call for a portion of the US-grown corn supply to be set aside for ethanol production. Meat and poultry producers, both of whom rely on corn for animal feed and feared rising prices due to the drought conditions, accused the federal government of "picking winners and losers" with its ethanol policy while ethanol producers, many of whom are corn farmers, argued that price spikes would affect them as well and that ethanol production had been scaled back.

Domestic food aid

Offering government food assistance to the lowest income Americans dates back to the administration of President Franklin D. Roosevelt and has continued into the 21st century. In FY 2011, the budget for the USDA Food and Nutrition Service, which is responsible for the major feeding programs, was $107 billion. The largest single food assistance program in the country is the Supplemental Nutrition Assistance Program, the provisions for which are contained in a Farm Bill that is re-authorized by Congress and signed by the president every five years. Benefits to SNAP recipients cost approximately $75 billion in 2012. Largely uncontroversial for most of its history, the SNAP program was targeted for major cuts by members of the House of Representatives in the 2012 Farm Bill re-authorization attempt.

House leaders also endeavored to separate the SNAP program from the Farm Bill, splitting the long-standing coalition of urban and rural legislators who traditionally backed the renewals of funding for the Farm Bill every five years.

Increases in the size of the SNAP caseload during the early 2000s were associated with increases in the unemployment rate and with a number of policy changes made to the program in many states. A series of six measures to better understand employment trends developed by the Bureau of Labor Statistics, three of which are more conservative estimates of unemployment and three of which define it more broadly, all showed correlations with SNAP participation. In particular, it was suggested that longer-term unemployment results in the heaviest utilization of SNAP benefits.

In addition to concerns about the cost of the program from fiscal conservatives, leaders in the movement to improve the nutritional content of the American diet suggested changes to the program to preclude the purchase of sugar-sweetened soft drinks or other forms of junk food with low nutritional value. In fact, the House of Representatives’ version of the initial Food Stamp Act of 1964 prohibited using food stamps for the purchase of soft drinks, but the provision was not adopted.

Efforts to more narrowly define the food purchases by SNAP recipients were derided by anti-hunger organizations  as a form of paternalism. The 2008 Farm Bill re-authorization established the Healthy Incentives Pilot, a $20 million effort in five states to learn if offering select SNAP recipients credits on purchases of fresh, frozen, canned, or dried fruits and vegetables with no added sugar, salt, fat, or oil will result in increased purchases of these foods. Results of the pilot study were expected in 2014.

In addition to advocacy work in Washington, D.C., on behalf of those in poverty, public awareness campaigns around the constraints faced by families receiving SNAP were launched. The food stamp challenge or SNAP challenge is one mechanism used by advocates such as Feeding America. Individuals are challenged to restrict food spending for a week to levels typical for families receiving SNAP benefits.

Labor and immigration

Hired farmworkers are among the most economically disadvantaged groups in the United States. Farm labor statistics are published twice yearly by the National Agricultural Statistics Service, a division of the U.S. Department of Agriculture and are compared with similar data from the prior year. In April 2013, the number of workers hired by farm operators was 732,000. Field workers received an average pay of $10.92 per hour and livestock workers earned $11.46 hourly. Average hourly rates for field and livestock work have been on the rise since 1990. Language barriers, fear of deportation, frequent re-locations, and lack of voting status have contributed to difficulties in organizing farm laborers to advocate for wage, benefit, and working condition reforms.

The agricultural industry's reliance on non-native workers has become part of the political debate over immigration policies and enforcement in the country. United States Department of Labor statistics from 2009 indicated that about 50 percent of hired crop workers were not legally authorized to work in the U.S., a figure that remained largely unchanged over the course of the prior decade. During that same time period, intense debate took place in the nation's capital regarding immigration policies and enforcement. Farm interests, concerned about access to a steady workforce, worked on Capitol Hill to secure their interests in the Border Security, Economic Opportunity, and Immigration Modernization Act of 2013. Provisions favored by the farm lobby included: "earned adjustments" that will allow for temporary legal immigration status based on past experience with the possibility of applying for permanent residency by continuing to work in agriculture for a set period of time; and a more flexible guest worker program for agricultural workers.

In addition to farm labor, workers in the nation's food service industry garnered attention in 2012 and 2013 with a series of strikes against fast food outlets demanding higher wages, better working conditions, and the right to form unions. A study by the Labor Center at the University of California, Berkeley in October 2013 demonstrated that 52 percent of families of fast-food workers receive public assistance, in comparison to 25 percent of the workforce as a whole. According to the study, full-time hours were not sufficient to compensate for low wages.

Security

In the past, the denial of food deliveries has been used as a weapon in war. For example, during both world wars, the British naval blockade was intended to starve Germany into submission.

Food security is an important political issue as national leaders attempt to maintain control of sufficient food supplies for their nation. It can drive national policy, encourage the use of subsidies to stimulate farming, or even lead to conflict. This is mostly a national policy because nations have only recognized that there is a negative duty to not disrupt other nations food supply and do not require that one help them attain such secure access by protecting them against other threats.

In 1974, the World Food Summit defined food security as:

availability at all times of adequate world food supplies of basic foodstuffs to sustain a steady expansion of food consumption and to offset fluctuations in production and prices

Food Security & Food Sovereignty in MENA politics

"There are three traditional routes to national food security: 1) domestic production, which contributes to self-sufficiency; 2) commercial food imports; and 3) international food aid". Therefore, we need to make it clear that there is a distinction "between self-sufficiency and food security, in that the former is only one possible route to food security at the national level".

Since 2007/2008, multiple Middle Eastern and North African (MENA) region governments have begun to consider more domestic food production as a part of their national aggregate food security laws. Although from a political view that approach may be justified due to it helping in stabilizing domestic food prices and deducting vulnerability to international markets and reliance on other countries, it comes at an enormous economic cost. This due to the resource endowments of the majority "of MENA countries—water scarcity and lack of arable land—are not well-suited to food production", specifically cereal production, and "these countries’ comparative international advantages lie in other economic activities".

Many of "the international organizations involved in the MENA economies during the 1990s and the 2000s advocated a food security strategy for most countries" that based on diversification away from agriculture towards multiple other activities, "including manufacturing exports, with the resulting foreign exchange used to purchase food imports". "Within the agricultural sector there has also been emphasis on shifting resources into high- value crops that are most efficient in water use, such as fruits, vegetables, and tree crops", with a view on export markets, in replace of cereal production for domestic consumption.

Hunger

Malnutrition and starvation continue to be a persistent problem in some areas of the world. The effects of low agricultural output can be exacerbated by internecine struggles, such as the famine conditions that occurred in Somalia during the 1990s. But even under more stable conditions, hunger persists in some nations. Images of starvation can have a powerful influence, leading to charitable and even military intervention.

Retailing

During the late 1990s and early 21st century a significant amount of discussion and debate has developed surrounding the role of supermarkets in the retailing of food and the impacts of supermarkets both on the supply and production of food. Due to the buying power of the large supermarket chains, they can put huge demands on producers, often pushing prices artificially low, whilst still making large profits on the food themselves, with some products selling at over 400% the price paid to, whilst farmers may only make 50p profit on each animal produced domestically. This buying power also allows supermarkets to transcend national boundaries in sourcing food. For example, in the UK, where the food market is highly dominated by supermarkets, only 25% of apples sold in supermarkets are produced domestically, with out-of-season Cox apples being flown 14,000 miles from New Zealand, despite the UK being a natural producer of apples. Furthermore, due to the national nature of the supply networks used by supermarkets, this often involves domestically produced foodstuffs being transported around the country before being delivered to retailers, creating a huge impact both on traffic and pollution.

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