Biological Redox.

Redox reactions are well known to anyone having taken basic chemistry. The concept is fairly straightforward—during a redox chemical reaction, due to changes in connectivity, and often, therefore, electronegativity, certain atoms will change their oxidation states. This can be worded to say that electron “ownership” changes. For example, in respiration, because the two atoms possess equal electronegativity in diatomic oxygen, the 4 double bonded electrons are shared equally. So each oxygen “owns” six electrons. In water, the oxygen now holds the bonding electrons closer to itself, because of its higher electronegativity relative to hydrogen. Thus, it could be said that oxygen has eight electrons, one more from each H-O bond.

So why redox? All living metabolisms deal with redox couplings.That is to say, biological energy generation deals heavily in redox chemistry. Living organisms move electron ownership between chemicals from unfavorable, high energy atomic configurations to favorable, stable ones. This process releases energy used to then power cellular function.

Given this conservation, surely there are reasons for the prevalence of redox in biology:

Being able to modify oxidation states opens up organisms to more energy and more variety. To explain this, we can say that there are more reactions one can do when shuffling electrons instead of just elements. The more degrees of thermodynamic freedom in a system, the more ways you can manipulate the elements contained within.

Non-redox reactions can only take so many forms. Requiring significant chemical remodeling, and usually resulting in a stable product/products that are difficult to further work with, non redox chemistry is not well suited for life. Life that involves countless interacting reactionary pathways.

How the biological electron gets around this problem is by being versatile. Electron ownership can be shuffled between any number of molecules, provided the final result is a favorable reaction. This means there are nearly endless electronic states able to be used by molecular interactions employing redox as a means of reaction power.

The utility this versatility affords can be seen in ATP biogenesis. ATP, to those not familiar, is the standardized molecular fuel of the cell (which, to drive the importance of the concept home, powers reactions by way of redox transfers itself). By and large, the majority of ATP in non-photoautotrophs comes from ATP synthase, powered by electron transport chains (ETCs). A familiar concept in modern biology, we will take a look at probably the best studied of all ETCs—that of the mitochondria.

Starting with a basal hydrocarbon, various “shuttles” strip electrons off the molecule, thereby oxidizing it in the process (eventually into CO2, the most biologically oxidized form of C). These electrons are passed off to mitochondrial transmembrane proteins. What follows is a number of electron transfers (and thus, redox) between these protein groups, and finally onto water. With each transfer, energy is generated to develop a transmembrane ion gradient, which then is processed through kinetic means into ATP.

a very simplified view of phosphorylation redox.

ATP production in this way can be thought of as analogous to combustion, with a carbonaceous compound split into water and carbon dioxide. However, unlike traditionally empirical combustion, the energy otherwise released as a flash of light and heat is split carefully and efficiently into small microtransactions. In this way, redox metabolism is exceedingly efficient. But this is just the surface.

The field of redox biology has a broad scope. There are, of course, the traditional metabolic approaches, looking at fermentation and photoautotrophy, both which make extensive use of redox. Other topics with a redox focus include radical biochemistry and even potential-dependent transcription. In the end, even studies not expressly studying redox chemistry  still would do well to consider it, as it is the basis of much of biochemistry.

2 months ago  3 notes

Environmental Immunology.

Immunology is traditionally thought of as a molecular pursuit. It is, after all, dependent upon binding of antigen molecules to a variety of different receptors (immunoglobulins, T cell receptors, Tolls, MHC, etc). And, of course, it deals with a host’s ability to defend itself from microbial challenges. However, increasingly, immune function is being viewed in an ecological sense.

Why is this unique? It’s rare for ecology to have this kind of fine resolution. Generally speaking, interactions between macro-organisms, especially metazoans, are only examined in as much detail as genomic/phylogenic studies allow. This certainly gives relevant information, but it is more evolutionary than functional. However, as our understanding of science increases, so does the ability to interconnect the disparate worlds of molecular and environmental biology. Organisms, of course, exist not just as a collection of functional proteins and nucleic acid code, but as whole creatures relating with their surroundings. In a sense, this new research allows science to ask bigger “whys” and “hows”.

The immune system, in particular, is a very personalized concept in that there are far fewer and more abstract relationships between it and the ecological environment. In contrast, other molecular biosciences, for example developmental bio or endocrinology, are very readily linked to external cues.

So instead of just considering immunology in a few specialized laboratory cases, one can look at the bigger picture. But how does one go about doing that? While there are numerous avenues of this new field being explored, let us take a look at one of the least concrete ecological concepts (mate choice) and tie that in to an immunology framework.

Intersexual selection is where organisms of one sex actively choose mates based on the strength on sexual displays. This prevents taxing and potentially damaging confrontation between members of the same sex. Nowhere is this concept more familiar than it is in the bird world. Indeed, some of the features most attributed to birds are their sexual displays/activities—complex songs, elaborate plumage, nest building, and brooding behaviors.

This being a courtship issue, it is appropriate to look at this through hormones. Specifically, testosterone. There is a long precedence of experimental immunosuppression in birds when testosterone is overexpressed. In general, the antibody response is curtailed, with some data showing an increase in certain lymphocyte subpopulations such as killer (CD8+) T cells.

Now we ask, as one often does in ecology, “why is this so?”. Testosterone increases risk taking ability and aggression, and other stereotyped masculine behavior. During the competition for mates, a male must be in top functional form. While the immune system is used to clear infective agents, inflammation and other immunogenic effects greatly curtail these competitive abilities. Thus, it is only after brooding occurs, when mates are secured, and chicks are not yet hatched, do testosterone levels go down and immune function returns, full force.

What’s more, carotenoids, pigments used in sexual displays and not synthesized de novo by birds have been shown to boost the immune system. Increased testosterone works to increase foraging aggression, giving these males the most access to the pigments. This both strengthens their sexual displays and helps immunity.

Drastic effects of carotenoid limitation in Carpodacus mexicanus (J Exp Biol).

To further explore this concept, we might further look at parasite effects on immunosuppressed males, androgen effects on females and young, oestrogen mediated immunity, immune restructuring under androgen presence, and cost benefit analyses of immunosuppression and mate desirability.

Is this a correct analysis of testosterone immunosuppression? Maybe, maybe not. But it does give an overview of what ecological immunology entails. The problem here is that many of these concepts can be difficult to test, but the scope of such an analysis is great, and it gives a whole new perspective to biology.

2 months ago  1 note

Plant Neurobiology.

Because plants cannot move through muscular action, are too big and static for flagella or cilia, and have less ability to use cytoplasmic locomotion due to restrictive cell walls, they do not have rapid responses to stimuli seen in many other organisms (usually).


M. pudica using vacuolar collapse to move rapidly.

This does not mean however, that plants are not advanced information processing units.

Plants are not thought of being able to store data like animals can, and processes such as phototropism and nasticity can be chalked up to a preprogrammed movement resulting from chemical sensory responses. However, some scientists (admittedly few) are now viewing plants as neural analogs.

What this means is, rather than considering the plant as an organism with a data processing unit, one sees the plant itself as the data processing unit. Doing so allows scientists to ask questions such as “what are the fundamental mechanisms behind neural signaling and memory”, as opposed to “how does signaling function on the plant as a whole?”. Although it doesn’t sound like it, it’s an important distinction to make.

This is not as far-fetched of a notion as you might think. Plant signaling is largely hormone based, not unlike our own mechanisms of body control. More importantly, they produce action potentials (voltage changes across cell membranes to produce current), which are how nerves function. Researchers as of yet do not know what these potentials do for the plant, but they exist.

They communicate with one another through chemical means. They recognize self, foreign species, conspecifics, and perhaps even kin, and adjust their competitive behaviors accordingly. They exhibit complex decision making skills, such as determining which meristems, out of many, to grow. Or modulating anti-predatory defenses to adjust to a particular threat.

They can even store information for periods of time. There are numerous examples, but some of the most striking examples involve germination. Seeds of certain plants germinate a special way based on certain external stimuli. Seeds exposed to these stimuli, and then germinated weeks after removal of said stimuli still germinated peculiarly.

Of course, much of the above listed behaviors have fairly linear pathways, conceptually. But that’s the point—to view the plant as a neural body, and reduce these signaling aspects down to their individual parts in an attempt to better understand our own complex brain physiology.

Plants, then, are not the static organisms as they are usually perceived but are—like all life—complex and surprising.

compare to:


2 months ago  4 notes

Inverted Ecological Pyramids.

The concept of the ecological pyramid is one of the most important models described in ecology. Classically defined, biomass and energy pyramids are wider at the bottom. This indicates that there are more prey items than predators in a given environment, with cumulative biomass and energy content being greater in prey than predators. Inverted pyramids have predators stably outnumber prey, with the most biomass locked up in the highest rung.

i.e.:

This inverted scheme goes against the convention generally taught in basic biology, and for good reason. They’re rare, and, in fact, their existence is debatable, depending upon semantics. 

A popular example of biomass inversion comes from aquatic environments (particularly closed off, nutrient poor lakes). Here, phytoplankton, the primary producers, can be much reduced in biomass compared to the planktivores that eat them.

This is usually explained by the high turnover of plankton numbers. Their rapid synthesis and mortality ensures that, although their overall biomass is less, because of the fast rates of death and reproduction, more ENERGY is going through these lower rungs. So the energy throughput of the phytoplankton is greatest amongst pyramid levels. Conversely, predators live longer, grow slower, and are predated less often, so it may appear as though there is more biomass there, but the energy flowing through the top is reduced.

This shows that energy pyramids are always bottom up and can never be inverted. Nature is inefficient. Due to requirements of organisms to “waste” energy maintaining homeostasis (for starters), not all the energy taken from the lower food level gets transferred to the next one up.

Another familiarly published inverted system describes coral reef habitats, where shark populations see significantly more accumulated biomass than those of smaller reef fish species.

Problems with the inversion concept include mobile predators with access to multiple ecosystems, inconsistent ratios between predator/prey mass [i.e., in a lake, there may be less algae than small fish (inverted scheme), but there are more small fish than top predators (normal), resulting in only a partially inverted biomass pyramid], and just a lack of understanding of the full complexities of food chains.

3 months ago 

Biological Redox.

Redox reactions are well known to anyone having taken basic chemistry. The concept is fairly straightforward—during a redox chemical reaction, due to changes in connectivity, and often, therefore, electronegativity, certain atoms will change their oxidation states. This can be worded to say that electron “ownership” changes. For example, in respiration, because the two atoms possess equal electronegativity in diatomic oxygen, the 4 double bonded electrons are shared equally. So each oxygen “owns” six electrons. In water, the oxygen now holds the bonding electrons closer to itself, because of its higher electronegativity relative to hydrogen. Thus, it could be said that oxygen has eight electrons, one more from each H-O bond.

So why redox? All living metabolisms deal with redox couplings.That is to say, biological energy generation deals heavily in redox chemistry. Living organisms move electron ownership between chemicals from unfavorable, high energy atomic configurations to favorable, stable ones. This process releases energy used to then power cellular function.

Given this conservation, surely there are reasons for the prevalence of redox in biology:

Being able to modify oxidation states opens up organisms to more energy and more variety. To explain this, we can say that there are more reactions one can do when shuffling electrons instead of just elements. The more degrees of thermodynamic freedom in a system, the more ways you can manipulate the elements contained within.

Non-redox reactions can only take so many forms. Requiring significant chemical remodeling, and usually resulting in a stable product/products that are difficult to further work with, non redox chemistry is not well suited for life. Life that involves countless interacting reactionary pathways.

How the biological electron gets around this problem is by being versatile. Electron ownership can be shuffled between any number of molecules, provided the final result is a favorable reaction. This means there are nearly endless electronic states able to be used by molecular interactions employing redox as a means of reaction power.

The utility this versatility affords can be seen in ATP biogenesis. ATP, to those not familiar, is the standardized molecular fuel of the cell (which, to drive the importance of the concept home, powers reactions by way of redox transfers itself). By and large, the majority of ATP in non-photoautotrophs comes from ATP synthase, powered by electron transport chains (ETCs). A familiar concept in modern biology, we will take a look at probably the best studied of all ETCs—that of the mitochondria.

Starting with a basal hydrocarbon, various “shuttles” strip electrons off the molecule, thereby oxidizing it in the process (eventually into CO2, the most biologically oxidized form of C). These electrons are passed off to mitochondrial transmembrane proteins. What follows is a number of electron transfers (and thus, redox) between these protein groups, and finally onto water. With each transfer, energy is generated to develop a transmembrane ion gradient, which then is processed through kinetic means into ATP.

a very simplified view of phosphorylation redox.

ATP production in this way can be thought of as analogous to combustion, with a carbonaceous compound split into water and carbon dioxide. However, unlike traditionally empirical combustion, the energy otherwise released as a flash of light and heat is split carefully and efficiently into small microtransactions. In this way, redox metabolism is exceedingly efficient. But this is just the surface.

The field of redox biology has a broad scope. There are, of course, the traditional metabolic approaches, looking at fermentation and photoautotrophy, both which make extensive use of redox. Other topics with a redox focus include radical biochemistry and even potential-dependent transcription. In the end, even studies not expressly studying redox chemistry  still would do well to consider it, as it is the basis of much of biochemistry.

Environmental Immunology.

Immunology is traditionally thought of as a molecular pursuit. It is, after all, dependent upon binding of antigen molecules to a variety of different receptors (immunoglobulins, T cell receptors, Tolls, MHC, etc). And, of course, it deals with a host’s ability to defend itself from microbial challenges. However, increasingly, immune function is being viewed in an ecological sense.

Why is this unique? It’s rare for ecology to have this kind of fine resolution. Generally speaking, interactions between macro-organisms, especially metazoans, are only examined in as much detail as genomic/phylogenic studies allow. This certainly gives relevant information, but it is more evolutionary than functional. However, as our understanding of science increases, so does the ability to interconnect the disparate worlds of molecular and environmental biology. Organisms, of course, exist not just as a collection of functional proteins and nucleic acid code, but as whole creatures relating with their surroundings. In a sense, this new research allows science to ask bigger “whys” and “hows”.

The immune system, in particular, is a very personalized concept in that there are far fewer and more abstract relationships between it and the ecological environment. In contrast, other molecular biosciences, for example developmental bio or endocrinology, are very readily linked to external cues.

So instead of just considering immunology in a few specialized laboratory cases, one can look at the bigger picture. But how does one go about doing that? While there are numerous avenues of this new field being explored, let us take a look at one of the least concrete ecological concepts (mate choice) and tie that in to an immunology framework.

Intersexual selection is where organisms of one sex actively choose mates based on the strength on sexual displays. This prevents taxing and potentially damaging confrontation between members of the same sex. Nowhere is this concept more familiar than it is in the bird world. Indeed, some of the features most attributed to birds are their sexual displays/activities—complex songs, elaborate plumage, nest building, and brooding behaviors.

This being a courtship issue, it is appropriate to look at this through hormones. Specifically, testosterone. There is a long precedence of experimental immunosuppression in birds when testosterone is overexpressed. In general, the antibody response is curtailed, with some data showing an increase in certain lymphocyte subpopulations such as killer (CD8+) T cells.

Now we ask, as one often does in ecology, “why is this so?”. Testosterone increases risk taking ability and aggression, and other stereotyped masculine behavior. During the competition for mates, a male must be in top functional form. While the immune system is used to clear infective agents, inflammation and other immunogenic effects greatly curtail these competitive abilities. Thus, it is only after brooding occurs, when mates are secured, and chicks are not yet hatched, do testosterone levels go down and immune function returns, full force.

What’s more, carotenoids, pigments used in sexual displays and not synthesized de novo by birds have been shown to boost the immune system. Increased testosterone works to increase foraging aggression, giving these males the most access to the pigments. This both strengthens their sexual displays and helps immunity.

Drastic effects of carotenoid limitation in Carpodacus mexicanus (J Exp Biol).

To further explore this concept, we might further look at parasite effects on immunosuppressed males, androgen effects on females and young, oestrogen mediated immunity, immune restructuring under androgen presence, and cost benefit analyses of immunosuppression and mate desirability.

Is this a correct analysis of testosterone immunosuppression? Maybe, maybe not. But it does give an overview of what ecological immunology entails. The problem here is that many of these concepts can be difficult to test, but the scope of such an analysis is great, and it gives a whole new perspective to biology.

Plant Neurobiology.

Because plants cannot move through muscular action, are too big and static for flagella or cilia, and have less ability to use cytoplasmic locomotion due to restrictive cell walls, they do not have rapid responses to stimuli seen in many other organisms (usually).


M. pudica using vacuolar collapse to move rapidly.

This does not mean however, that plants are not advanced information processing units.

Plants are not thought of being able to store data like animals can, and processes such as phototropism and nasticity can be chalked up to a preprogrammed movement resulting from chemical sensory responses. However, some scientists (admittedly few) are now viewing plants as neural analogs.

What this means is, rather than considering the plant as an organism with a data processing unit, one sees the plant itself as the data processing unit. Doing so allows scientists to ask questions such as “what are the fundamental mechanisms behind neural signaling and memory”, as opposed to “how does signaling function on the plant as a whole?”. Although it doesn’t sound like it, it’s an important distinction to make.

This is not as far-fetched of a notion as you might think. Plant signaling is largely hormone based, not unlike our own mechanisms of body control. More importantly, they produce action potentials (voltage changes across cell membranes to produce current), which are how nerves function. Researchers as of yet do not know what these potentials do for the plant, but they exist.

They communicate with one another through chemical means. They recognize self, foreign species, conspecifics, and perhaps even kin, and adjust their competitive behaviors accordingly. They exhibit complex decision making skills, such as determining which meristems, out of many, to grow. Or modulating anti-predatory defenses to adjust to a particular threat.

They can even store information for periods of time. There are numerous examples, but some of the most striking examples involve germination. Seeds of certain plants germinate a special way based on certain external stimuli. Seeds exposed to these stimuli, and then germinated weeks after removal of said stimuli still germinated peculiarly.

Of course, much of the above listed behaviors have fairly linear pathways, conceptually. But that’s the point—to view the plant as a neural body, and reduce these signaling aspects down to their individual parts in an attempt to better understand our own complex brain physiology.

Plants, then, are not the static organisms as they are usually perceived but are—like all life—complex and surprising.

compare to:


Inverted Ecological Pyramids.

The concept of the ecological pyramid is one of the most important models described in ecology. Classically defined, biomass and energy pyramids are wider at the bottom. This indicates that there are more prey items than predators in a given environment, with cumulative biomass and energy content being greater in prey than predators. Inverted pyramids have predators stably outnumber prey, with the most biomass locked up in the highest rung.

i.e.:

This inverted scheme goes against the convention generally taught in basic biology, and for good reason. They’re rare, and, in fact, their existence is debatable, depending upon semantics. 

A popular example of biomass inversion comes from aquatic environments (particularly closed off, nutrient poor lakes). Here, phytoplankton, the primary producers, can be much reduced in biomass compared to the planktivores that eat them.

This is usually explained by the high turnover of plankton numbers. Their rapid synthesis and mortality ensures that, although their overall biomass is less, because of the fast rates of death and reproduction, more ENERGY is going through these lower rungs. So the energy throughput of the phytoplankton is greatest amongst pyramid levels. Conversely, predators live longer, grow slower, and are predated less often, so it may appear as though there is more biomass there, but the energy flowing through the top is reduced.

This shows that energy pyramids are always bottom up and can never be inverted. Nature is inefficient. Due to requirements of organisms to “waste” energy maintaining homeostasis (for starters), not all the energy taken from the lower food level gets transferred to the next one up.

Another familiarly published inverted system describes coral reef habitats, where shark populations see significantly more accumulated biomass than those of smaller reef fish species.

Problems with the inversion concept include mobile predators with access to multiple ecosystems, inconsistent ratios between predator/prey mass [i.e., in a lake, there may be less algae than small fish (inverted scheme), but there are more small fish than top predators (normal), resulting in only a partially inverted biomass pyramid], and just a lack of understanding of the full complexities of food chains.

Biological Redox.
Environmental Immunology.
Plant Neurobiology.
Inverted Ecological Pyramids.

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