Stem Cell Debate

Hi sophies... i've added a new link, "Science and Theology News" which you can visit to while away a stormy day... click on it and find on the home page an interesting, if not enlightening, debate on stem cell research... happy reading!

Covalent and Ionic Bonds

Berea Arts and Sciences High School
Covalent and Ionic Bonds Problem Set

Notes

Ionic bond – a strong attractive force holding ions together. An ionic bond can
form between two atoms by the transfer of electrons from the valence shell of one atom to the valence shell of the other

Covalent bond – a strong attractive force that holds two atoms together by their
sharing of electrons. These bonding electrons are attracted simultaneously to both atomic nuclei, and they spend part of the time near one atom and part of the time near the other

Electronegativities – the unequal abilities of the atoms to draw bonding electrons
to themselves

Lewis electron-dot formulas – simple representations of the valence-shell
electrons of atoms in molecules and ions and are useful for describing the covalent bonding in substances

Problem Set.

1. For each of the following pairs of elements, state whether the binary compound formed is likely to be ionic or covalent. Give the formula and name of the compound.

a. Sr,O b. C,Br c. Ga, F d. N, Br

2. Give the Lewis formula for the arsenate ion, AsO3-4. Write the formula of lead(II) arsenate.

3. Iodic acid, HIO3, is a colorless, crystalline compound. What is the electron dot formula of iodic acid?

4. Write electron dot formulas for the following:

a. SeOCl2 b. CSe2 c. GaCl-4 d. C2-2

5. Why do most monoatomic cations of the main-group elements have a charge equal to the group number? Why do most monoatomic anions of these elements have a charge equal to the group number minus 8?

6. Describe the formation of a covalent bond in H2 from atoms. What does it mean to say that the bonding electrons are shared by the two atoms?

Nuclear Chemistry

Berea Arts and Science High School
Nuclear Chemistry Notes and Problem Set

Notes
Radioactive decay – the process in which a nucleus spontaneously disintegrates, giving
off radiation

Nuclear bombardment reaction – a nuclear reaction in which a nucleus is bombarded, or
struck, by another nucleus or by a nuclear particle

Types of Radioactive Decay
a. Alpha emission – emission of a 42He nucleus, or alpha particle, from an unstable
nucleus. An example is the radioactive decay of radium-22, written as

22688Ra 22286Rn + 42He

The product nucleus has an atomic number that is two less, and a mass number
that is four less, than that of the original nucleus.

b. Beta emission – emission of a high-speed electron from an unstable nucleus. Beta
emission is equivalent to the conversion of a neutron to a proton.

10n 11p + 0-1e

An example of beta emission is the radioactive decay of carbon-14.

146C 147N + 0-1e

the product nucleus has an atomic number that is one more than that of the
original nucleus. The mass number remains the same.

c. Positron emission – emission of a positron from an unstable nucleus. Positron emission
is equivalent to the conversion of a proton to a neutron.

11p 10n + 01e
d. Electron capture – the decay of an unstable nucleus by capturing, or picking up, an
electron from an inner orbital of an atom. In effect, a proton is changed to a neutron as in positron emission

11p + 0-1e 10n

e. Gamma emission – emission from an excited nucleus of a gamma photon,
corresponding to radiation with a wavelength of about 10-12 m. in many cases, radioactive results in a product nucleus that is in an excited state. Often, gamma emission occurs very quickly after radioactive decay

Metastable nucleus – a nucleus in an excited state with a lifetime of at least one
nanosecond (10-9 s). In time, the metastable nucleus decays by gamma emission. An example is metastable technetium-99, denoted 99m43Tc, which is used in medical diagnosis.

99m43Tc 9943Tc + 00

he product nucleus is simply a lower-energy state of the original nucleus, so there is no change of atomic number or mass number.

Radioactive decay series – a sequence in which one radioactive nucleus decays to a
second, which then decays to a third, and so forth. Eventually, a stable nucleus is reached. For the natural radioactive decay series, this stable nucleus is an isotope of lead.

Particle accelerator – a device used to accelerate electrons, protons, and alpha particles
and other ions to very high speeds.

Cyclotron – a type of particle accelerator consisting of two hollow, semicircular metal
electrodes, called dees (because the shape of a dee resembles the letter D) in which charged particles are accelerated by stages to a higher and higher kinetic energies.

Nuclear force – a strong force of attraction between nucleons that acts only at very short
distances (about 10-15 m)

Problem Set
1. Of the following nuclides, two are radioactive. Which are radioactive and which is
stable?
a. 11850Sn b. 7633As c. 22789Ac

2. Potassium-40 is a naturally occurring radioactive isotope. It decays to calcium-40 by
beta emission. When a potassium-40 nucleus decays by beta emission, it emits one beta particle and gives a calcium-40 nucleus. Write the nuclear equation for this decay.

3. Plutonium-239 decays by alpha emission, with each nucleus emitting one alpha
particle. What is the other product of this decay?

4. Cobalt-60, used in cancer therapy, decays by beta and gamma emission. The decay
constant is 4.18 x 10-9/s. what is the half-life in years?

5. A nuclear power plant emits into the atmosphere a very small amount of krypton-85, a
radioactive isotope with a half-life of 10.76 y. What fraction of this krypton-85 remains after 25.0 y?

Four Questions for EnviSci

Hi sophies… I have here four questions for you… I also have provided the answers which you can reflect on as you prepare for your next exam in envisci…

1. Discuss the fate of energy in terrestrial communities. Discuss it on the perspective of the laws of thermodynamics.

My Answer

The first law of thermodynamics is also referred to as the Law of Conservation of Energy. This law purports that energy is neither created nor destroyed. Implicit to this is the principle that energy is simply transferred from one system to another through various forms. As such, the total energy in the universe is constant and will remain constant ad infinitum.

Ecologically, life on this planet is given to be ultimately driven by radiant energy. The energy coming from the sun is trapped in the chlorophyll pigments of chloroplasts prior to getting converted to chemical energy in the form of ATP’s or adenosine triphosphates. This process takes on the complementary roles of both thylakoidal and stromal reactions of photosynthesis among photoautotrophic organisms. Utilization and assimilation of this energy decreases invariably from one trophic level in the food chain to another trophic level.

Among heterotrophs, chemical energy is released from the food and assimilated in the system through aerobic cellular respiration. This process involves the cytoplasmic reactions of the glycolytic pathway where sugar is broken down into pyruvate molecules and the mitochondrial reactions of the tricarboxylic acid cycle and the electron transport chain. Much of the energy assimilated by organisms are released in the form of heat during cellular respiration. A certain fraction also gets locked in the soil during decomposition. It is noted that only about 10% of the total energy in the organism is passed on to the succeeding organisms occupying higher trophic levels in the food chain. This means that the highest amount of energy is assimilated by the photoautotrophs or chemoautotrophs. This assertion is better understood using the following illustrations.

The energy pyramid is an illustration of energy transfer that is representative of the fate of energy as it flows from one system to another. And in the energy flow, one form of energy gets converted to another form as one organism makes use of it to carry out its metabolic requirements.

Implicit to the First Law of Thermodynamics, the energy that gets passed on from one organism to another is the same energy that originated from the sun. They just have assumed different configurations like heat and come in diminishing concentrations like the 10% Rule illustrated above. No new energy is incorporated in the succeeding trophic levels after the direct assimilation of radiant energy by photosynthetic organisms.

Energy and mass (materials) are related concepts. In Einstein’s famous equation E=mc2, a direct relationship between energy and mass is noted. Implicit to this is the fact that the more mass a certain body has, the more energy it possesses. Unlike energy however which is linear, mass can go through cycles. At a certain point, the material that makes up an abiotic system may, at another point make up a living system.
Geographically, different topologies and latitudinal locations on the surface of the earth are invariably heated up. This implies that some areas receive more sunlight than do other areas. This uneven distribution of sunlight effects to a certain extent, different climatic conditions that bring about different effects on the other factors that affect climate like rainfall, humidity, and wind systems. Such differences in the abiotic component of the environment entail differences in primary productivity in different ecosystems. Here is another way of looking at energy flow as pertaining to the amount of primary productivity in ecosystems.

From the premises raised, it can be inferred that the ecosystems with highest average net Primary Productivity are the estuaries and the tropical rainforests. Logically, they are also the ecosystems that exhibit the highest species diversity.

2. Explain the top-down and bottom-up controls of food webs. Identify the factors related to each of these controls.

My Answer

The top-down and bottom-up controls of food webs pertain to the interaction of consumer (top-down) and resource (bottom-up) effects on species composition and abundance. The objectives of identifying these controls are to investigate how species and populations are distributed within food webs and what factors determine biomass and productivity within a trophic level.

It is noted that the biomass of organisms in food webs based on primary productivity is controlled simultaneously by resources (bottom-up) and consumers (top-down).

It is a matter of consequence that the population of certain species is checked either by predatory feeding relationships with other organisms that they share a common functional group with or by the availability (abundance or scarcity) of resources in their respective ecospaces.

In a study conducted by Power and Dietrich of the UC Berkeley titled, “Food Webs in River Networks”, they described food webs as complex adaptive systems with diverse components that are linked by flows and interactions. It was Robert Paine however, who pointed out that “energy flows from more basal resources up to consumers at higher trophic positions (bottom-up) while chains of population control link consumers to the resource populations they regulate or limit (top-down), if these consumers are not suppressed by their own predators.

Given these assertions, how then does a food web illustrate the flow of energy across trophic levels? Power and Dietrich offered that conditions, resource fluxes and biotic interactions all play pivotal role in the determination of functional food chains in food web systems, the length of energy flow paths and the controls on both. They have identified these controls as dependent on two environmental factors: Productivity/Efficiency and Disturbance/Stability; and one evolutionary factor – that of design constraints.

Power and Dietrich argued that in terms of productivity or efficiency, functional food chains should “lengthen as fluxes of limiting resources or energy to food webs increase, or as consumers increase their efficiency of resource capture or conversion”. In terms however, of disturbance or stability, it should follow that functional food chains are shorter in situations that are characterized by frequent disturbance. Conversely, a more stable situation should be able to host a longer functional food chain. Lastly, on the evolutionary factor of design constraints, they argued that “it is impossible for evolution to build a Pterodactyl predator”, for example, because an organism large enough to subdue one could not fly to catch it. While at this, it is important to note that the length of functional food chains in complex adaptive systems is directly related to the length of energy flow paths.

3. What is a “keystone species”? How does its absence affect the stability of the community where it is once found?

My Answer

Robert D. Davic in his correspondence with the Ohio Environmental Protection Agency titled, “Linking Keystone Species and Functional Groups: A New Operational Definition of the Keystone Species Concept”, redefined the concept of keystone species as one that “is held to be a strongly interacting species whose top-down effect on species diversity and competition is large relative to its biomass dominance within a functional group.” The premise behind this redefinition is anchored on the fact that from 1969, when the term “keystone species” was first defined by Paine up to the present, the concept has gone through linguistic metamorphosis to a point of controversy.

At issue in the keystone species controversy is whether abundance of the keystone relates significantly to impact within its functional group. This is on top of the controversy on how to measure abundance and impact, and where to delineate between abundance and impact.

In 1969 when the concept was first coined, Paine defined keystone species as “a species of high trophic status whose activities exert a disproportionate influence on the pattern of species diversity in a community”. But because it is a given ecological tenet that species in a keystone set are invariably interrelated to each other, it becomes difficult to tell which species is the keystone species. In the case for example of the mycorrhizae and certain species of trees, it is clear that the keystone species is the mycorrhiza – in spite of its low trophic status – for upon whose death depends the survival of the trees.

In Davic’s redefinition of the concept of keystone species, he noted the narrow food-web context that Paine used in his definition of keystone species and provided a divergent line of thought. His redefinition presupposes that the influence of a keystone species should be considered in light of the species’ biomass relative to its functional group. This implies that a keystone species is not necessarily the dominant species or the species of higher trophic status within a biotic community. Further, this also implies that a keystone species may be considered from across a wider width of feeding niches. But while at this, Davic’s premise however, does not preclude nor deviate from the predator-prey relationship model of Paine.

Regardless however of the blurry line that divides between biomass and impact, it is clear that for a species to qualify as a keystone species, it’s presence within a functional group in an ecospace must have an influence on the population of other species that belong to the same functional group and that such influence is taken to mean as a large top-down effect on biodiversity and competition relative to the keystone species’ biomass within a functional group.

Thus said, it is for the same argument that the impact of a keystone species’ absence to the stability of a community must be gleaned.

In a study conducted by the University of Washington on the delicate balance between and among marine organisms inhabiting the coastal areas extending from Baja, California to Alaska, they have figured a species of starfish as a prospective keystone species whose removal from the community may lead to disruption of ecological equilibrium there. The starfish Pisaster ochracues is said to influence negatively on the population of other marine organisms that it shares a functional group with through predatory relationships. If the starfish is taken out of its functional group, it is noted that a skewed population growth of other species, some of which are secondary predators, ensues as a consequence. Such trend in the other species is not noted as a result of their absence.

In Costa Rica, a species of shore crabs is noted to feed primarily on tree saplings. There is however, a tree sapling that is distasteful to the shore crabs. This tree sapling is what eventually grows in number and dominates the entire landscape. The proliferation of these trees makes the landscape an open-space forest that caters to a host of local animals like howler monkeys, tapirs, and coatis. If the shore crabs were to be taken out of this community, the open space forest will revert back to the level of heterogeneity of the off-coast forest and may threaten the extinction of the said local animals with particular preference to the open-type forest.

The examples cited above illustrate two typical influence of keystone species on other species within a functional group. The case of the starfish typifies what a top predator does to skew the population trend negatively. The case of the shore crabs on the other hand typifies an indirect check on the population of the other organisms within its functional group through drastic changes in the community.

4. Discuss the two ecological theories of island communities. Explain supporting evidences of these theories.

My Answer

The concept of “Island” can be broadly defined as patches of land that are, to some extent, isolated from the mainland. In the classical sense, islands are terrestrial habitats that are isolated from continental habitats either by freshwater or marine areas that represent a certain degree of geologic barrier to dispersal between the island and the mainland.

There are two ecological theories of island communities: the Habitat Diversity Theory and the Equilibrium Theory.

The Equilibrium Theory centers on the balance between the rate at which allochthonous organisms (species new to the island) colonize the islands and the rate at which autochthonous organisms (species that are residents/native to the island) go extinct on the islands.

There are three basic characteristics to the Equilibrium Theory of Island Biogeography: species-area relationship; species-isolation relationship; and species turnover. It is given that a larger area works to the advantage of resident species because there will be more resources available for them and therefore, intraspecific competition is less likely. But eventually, when other organisms migrate to the place, the resident species will have to compete with the new species for available resources. To mitigate the effects of intraspecific competition among the resident species, either dispersal ensues among them or niche differentiation is resorted to. In the case of turnover, a study conducted by Jared Diamond on the turnover of birds on California Channel Islands, established that “turnover tends to be lower on larger islands and increases with generation time of the organisms”. This follows the logic that a larger area will play host to a more diverse collection of resources that can be utilized by a wider array of species. Moreover, in an experimental defaunation conducted on arthropods by Wilson and Simberloff, where they exterminated an entire population of arthropods, it was established that turnover tends to increase with rapid colonization that followed the killing of the arthropods. This illustrates the likely scenario that when populations leave a place either for reasons of dispersal or extinction, they leave behind their respective niches which eventually gets assumed by colonizing species that share the same environmental niche.

The Habitat Diversity Theory on the other hand, hubs on the “suitability of islands as habitats for various species”.

In a study conducted by Ricklefs and Lovette titled, “The Roles of Island Area, per se and Habitat Diversity in the Species-Area Relationships of Four Lesser Antillean Faunal Groups”, they have established strong positive correlations between area and habitat diversity and between elevation and habitat diversity. It was observed that large elevated islands tend to host a more diverse habitat that matches species richness among faunal groups. These correlations however applied differently to other species included in their study like certain species of butterflies and bats. Species richness observed in some species of butterflies and certain groups of bats tend to be correlated to strong habitat-diversity effects. These species are said to exhibit “high degrees of habitat specialization”, large population sizes, high fitness rate, life-cycles that include a resistant resting stage that reduces vulnerability to catastrophic extinction and such other adaptive biological traits.

In other words, habitat diversity is rendered appropriate to a certain group of species only if it translates to species richness. But studies point out that while there may exist strong correlations between habitat diversity and habitat area, and between habitat area and species richness on account of resource availability, the same strong correlation cannot be applied to habitat diversity and species richness. Certain match between geographic features and biological traits must first be established as indeed resulting to or may result to species richness.

Ricklef and Lovette have established that these “taxon-specific differences demonstrate that both biological characteristics of organisms and geographical features of island groups” control the relative influence of island area and habitat diversity to differences in species richness.

References

Bak, P. 1996. How nature works: the science of self-organized criticality.
Springer-Verlag, New York, New York, USA.
Berger, W. H., and F. L. Parker. 1970. Diversity of planktonic Foraminifera in
deep sea sediments. Science 168:1345-1347
Primack, Richard B. Essentials of Conservation Biology
Ricklefs, R. E. et al., Island Biology Illustrated by the Land Birds of Jamaica
The Keystone-Species Concept in Ecology and Conservation," L. Scott Mills,
Michael E. Soule, and Daniel F. Doak, BioScience
"The Keystone Cops Meet in Hilo," Mary E. Power and L. Scott Mills, TREE

Notice

Hi sophies... I've just uploaded my lectures for EnviSci next week. Be sure to check them out at Mikology Correspondence under Sir Miko's Uploads before Tuesday. There are 6 new files for EnviSci in all...

Subic Escape

Hi kids and littluns.... I've posted some pics from our Subic Field Trip.... Check them out! You can also visit Flickr and use "berea pics" as your search words.... And there's Justin's Collection as well... some really good pics there!

Two Versions on the Central Dogma

If you find these illustrations quite small, you can click here to access the reference texts on the Central Dogma of Molecular Biology....

The Water Cycle

Cellular Respiration

Photosynthesis

The Carbon Cycle

Linkage Problems

Solving Linkage Problems

Tip: The most important part is to determine which progeny resulted from parental type gametes, and which from recombinant types.

In a plant, leaf color and leaf shape are controlled by two linked genes. Leaves of the wild-type plant are red. A recessive mutation in this gene causes white leaves. Wild-type leaves are pointed, and a recessive mutation in this gene causes them to be smooth. The following crosses were performed:

pure breeding white, smooth X pure breeding wild type

gives F1: all red, pointed

Now, the next cross:

red, pointed X pure breeding white, smooth

gives F2:
40 white, curly
36 red, pointed
10 white, pointed
14 red, curly

What is the recombination frequency between the gene for color and for shape?

Solution:

First, assign genotype symbols. Since the mutations are recessive to wild-type, use + for the wt allele and lower case letters for the mutant alleles:
w = recessive color allele for white
s = recessive shape allele for smooth
The first cross is: X giving progeny: (red, pointed)

The second cross is: X giving progeny where the genotypes can be unambiguously interpreted from their phenotypes.
The parental gamete types will be: and , resulting in [white, smooth] and [red, pointy] progeny.
The recombinant gamete types will be: and , resulting in [white, pointy] and [red, smooth] progeny.

Therefore, the recombination frequency is:

Mendelian Genetics

Sophies, why don't you give this a try...

Solving Problems: Practicing Crosses

A wild population contains red-eyed and white-eyed flies. A scientist crosses two white-eyed flies and gets all white eyed progeny (cross 1). She crosses two red eyed flies and gets all red-eyed progeny (cross 2). When she crosses a different pair of red-eyed flies, she gets 22 white eyed progeny and 78 red-eyed progeny (cross 3). Explain her observations, giving the most probable genotypes of the parents and progeny of each cross.

- try making a model where white is dominant to red. Appropriate symbols would be:

W - dominant white allele

w - recessive red allele

White eyed flies are either Ww or WW, red eyed flies must be ww.

- cross 1: to get all white progeny, the parents must be WW and WW. The data are compatible with this model.

- cross 2: ww X ww would give all ww - red eyed. This is also compatible with the data.

- cross 3: ww X ww would give no white eyed progeny

This is not compatible with the data. Therefore white cannot be dominant.

- try making a model where red is dominant to white. Appropriate symbols would be:

R - dominant red allele

r - recessive white allele

White eyed flies are rr, red flies are RR or Rr.

- cross 1: to get all white progeny, the parents must be rr and rr. OK.

- cross 2: as above, if the parents were RR and RR, all the progeny would be RR - red. This is also OK.

- cross 3: RR X RR would give all red progeny

RR X Rr would give all red progeny

Rr X Rr would give 75% red, 25% white - this prediction matches the data.

Therefore, the model that red is dominant to white fits the cross data best.

cross 1: rr X rr gives only rr progeny

cross 2: RR X RR gives only RR progeny

cross 3: Rr X Rr gives 75% R_ (RR or Rr), 25% rr

For problems with more than one trait (if the problem involved red and white eyes and short and long wings, for instance), treat each trait independently (work with eye color alone by counting red-eyed/short-winged and red-eyed/long-winged as simply red-eyed) to break the problem into two smaller problems.

GenSci Competency No. 4

Competency No. 4
Second Quarter

Name: Date:
Directions: Read the selection carefully and answer the items that follow.

The Selection

Metallic Meal

By Incognito

Aurisaur is a golden lizard that is autochthonous or native to the planet Metallandia. It is a gentle creature that feeds mainly on Cupripterans which are winged copper-toned insects that resemble a dragonfly. Both the Aurisaur and the Cupripterans live under an Argentophyte tree whose silver leaves serve as food to the winged creatures. The winged creatures in turn provide fertilizer to the tree through their copper droppings. One morning in autumn, as the Aurisaur clings from one branch of the Argentophyte to another, a beastly Wolframicarpus predator bird arrived and attacked the golden lizard. The predator bird has a tungsten beak that readily reacts and melts with the golden secretions of the dying Aurisaur. As the tungsten bird gobbled on the golden lizard, little did it know that it has already lost its beak and has thereby lost its lethal predatory weapon. The feasting did not escape the attention of a radioactive leaden snake called Plumboa. Without the bird’s weapon, it proved to be vulnerable to the precision-ambush of the snake. The Tungsten bird yielded its last gasp of metallic air to the leaden snake. But the Plumboa is not without its weakness. Its fissile constitution eventually gave way to the reaction caused by the copper droppings of the starving Cupripterans. The autumn season has shed off almost all the leaves of the Argentophyte leaving very little for the winged creatures to eat, and making their copper droppings most reactive. Ultimately, Natribacters - the bacteria that metabolize sodium - have then started decomposing the Plumboa.

I. List all the alien organisms mentioned in the selection. (12 pts)

II. Diagram a complete food chain for the selection. (12 pts)

III. Illustrate energy assimilation by the organisms using an energy pyramid. (12 pts)

IV. In what type of biome did the story take place? Substantiate your answer. (10 pts)

V. Which organisms exhibited a mutualistic relationship? Substantiate your answer (6 pts)

VI. Which organism(s) exhibited predatory instincts? (6 pts)

VII. Which organism(s) occupied the first trophic level? (5 pts)

VIII. What nutritive function did the Natribacters perform in the food chain? (5 pts)

IX. Assuming that 112,233 KJ of energy has been assimilated by the Wolframicarpus, determine the amount of energy invariably assimilated by the other organisms in the food chain. (10 pts)

Start answering here…

Life History Patterns

Explain the concept of life history. What are its various components?

My Answer:

The concept of life history refers to the time spanning the initial origination of species that are now extinct and takes into consideration the process of change in species that are still extant, either through evolutionary mechanisms or ecological influences or through the indispensable interaction between the two forces. For the most part however, life history pertains to the story of how life first came into existence on this planet and how life went through the ramifications of evolution to bring about the level of complexity that characterizes living systems at present. Of course, the assertions inherent in the history of life based on evolutionary claims, take validity on account of the premises of evolution.

Peter J. Bryant of the University of California at Berkeley, in his book titled, “Biodiversity and Conservation”, described the concept of life history as “a complicated series of geological, climatic and biological events that have led up to the present day situation.” He speculated that the history of life and for that matter, the history of global biological diversity is best seen in marine habitats on account of the premise that the first life forms emerged from the bodies of water.

In support of Bryant’s presupposition, the geologic time scale describes the dawn of life as having started from the pre-cambrian phagocytic unicells. Henceforth, it is believed that this primitive life form went through the different evolutionary mechanisms to bring about the level of complexity characteristic of the many species that survived the tests of time.

The underlying premise here is that different species have evolved different structural mechanisms to enable them to shift their reproductive strategies in such a way that they are better able to cope with ecological pressures arising from scarcity of available resources or uncertainty of existing environmental conditions. The species’ continuous interaction with their environment created in them, the needed changes in their gene-pool that either will prepare their generation for changes in their ecospaces or will evolve new generations with new levels of fitness.

Begon in his book titled, “Ecology: Individuals, Populations, and Communities”, enumerated seven of the more apparent components of life history patterns: size, growth rate, pattern of development, reproduction, resource capture and allocation, and dispersal. The underlying premise here is that, variations to this components will have corresponding trade-offs if only to make the individual members of a species better able to utilize available resources or to compete for such resources.

In the case of the trade off between size and fitness for example, the energy used to compensate for an increase in the size of organisms is traded off with the energy that is thought to compensate for reproductive functions. This is consistent with the r/K Selection Theory. According to this theory, organisms that have capitalized on the advantages of reproduction (r-selection) will have to bear a multitude of offprings even if in the end, only quite a few of them survive. Organisms that have adapted to this evolutionary predisposition will have to reproduce at a fast-tracked rate and at the soonest time possible in their life cycle. This is an apparent trade off in terms of fitness relative to organisms that have capitalized on body size. This evolutionary predisposition takes on the advantage of bearing “fitter” offsprings (K-selection) even if to trade off the advantage that comes with reproducing in multitude.

In the case of developmental patterns, it is presupposed that the phenotypic attributes of individuals in a population must establish an “appropriateness of fit” with the environment that they will grow into later on in life to make them cope better by adapting a function that corresponds to the habitat’s intrinsic stresses and pressures. Phenotypic plasticity figures significantly in this component of life history. Through phenotypic plasticity, a genotype common among individual organisms of the same species will have variable phenotypic expressions. This is achieved in part through the physiologic response of the organism to fluctuations in environmental conditions and in part through the behavioral match that an organism will have to adapt itself to in order to accommodate a particular environmental setting.

Advisory

Hi kids and littluns... be reminded of your sched for next week:

Sept. 19 - Envi Sci Long Test
Sept. 20 - Gen Sci Long Test
Sept. 21 - Bio Long Test

Do study hard and God bless you in your studies....

Phenotypic Plasticity

What is phenotypic plasticity? How does it affect life history patterns?

My Answer:

Carl D. Schlichting of the University of Connecticut defined Phenotypic Plasticity as “the property of a genotype to produce different phenotypes when exposed to different environments. Phenotypic Plasticity can occur in the morphology and behavior of organisms.”

Thus defined, phenotypic plasticity recognizes individual organisms as complex “genetic and epigenetic” systems that respond according to the different stresses and constraints that figure in the dynamics of a continuously evolving environment. Because no super adapted species exist relative to the heterogeneity of environmental systems, the premise behind phenotypic plasticity is that, certain “incompleteness” in the genotype of organisms is compensated by variations in phenotypic expressions arising from the same genotype. In other words, phenotypic plasticity enables many organisms at different stages of growth and development to adaptively match trait expression to particular environmental settings.

How then does phenotypic plasticity affect life history patterns? It must be recognized that phenotypic plasticity is but a factor in a myriad of other factors that are central to the determination of life history patterns. Therefore, where phenotypic plasticity figures in life history patterns, its function should be taken as correlative to other evolutionary functions such as speciation, acclimatization, heterochrony, and allometry. Thus said, if phenotypic plasticity comes as a consequence of an organism’s juggling of its options to match existing environmental settings through variable expression of phenotypes, life history patterns should logically reflect these variations in the distribution of organisms across all possible geologic ecospaces. Following is an illustration of a trade off in the larvae of echinoids. (At left is an echinoid larva that was starved. Compared to the well-fed larva on the right that developed new adult structures, the starved larva developed feeding structures instead like the elongated ciliated arms.

Kathleen K. Smith of Duke University asserted in her article titled, “Heterochrony Revisited: The Evolution of Developmental Sequences”, the idea that evolutionary innovations can occur at any stage in the life history of organisms. She anchored this premise on the observation that a certain amount of change in developmental timing can produce evolutionary change. Having thus correlated developmental change – which in some cases may constitute phenotypic plasticity, to evolutionary change – which for the most part is about a survey of life history patterns, it bears noting where and how phenotypic plasticity can in fact, effect change in organisms belonging to the same taxonomic category, if not the same phyletic origin.

Stephen Jay Gould of Harvard University recognizes the idea “that morphological diversity among taxa arises from diversity underlying developmental processes responsible for ‘building’ morphological features.” Paul Magwene of Yale University in his article titled, “Comparing Ontogenetic Trajectories Using Growth Process Data”, substantiated this assertion on the correlation between developmental change and diversity among taxa by analyzing variation in phenotypic plasticity, its effect on morphology and behavior, and its influence in ontogenetic trajectories.

The aforesaid studies have shown that life history patterns may have in fact been driven by phenotypic plasticity through the mechanisms of heterochronic developmental changes. But as to whether phenotypic plasticity taken as a process independent of developmental mechanisms have direct influence on life history patterns remains uncertain. This is because phenotypic plasticity is largely on account of an organism’s response to a certain environmental stress or constraint but does not imply change in the genetic makeup of the organism. As such, it may be implied that no amount of genetic modification is introduced into the gene-pool of the population. Therefore, this hardly qualifies as a veritable evolutionary mechanism for organismic change.

Phenotypic Plasticity’s significance figures prominently in the discourse on life history patterns. It may even be made a discourse unto itself that is independent of the discourse in evolution. Is phenotypic plasticity then, to a certain level of validity, an alternative to evolution in mapping out life history patterns? Dr. Lee Spetner has this to say: “A change in phenotype in the fossil record is recognized as evolution. There is no way to tell from the fossils whether the observed changes in continuous records were caused by variation appearing in the genotype or only in the phenotype”

In other words, it cannot be deduced from the premises of evolution whether or not “apparent transitional features of a fossil are truly the results of changes in the genotype (i.e. random mutations)” or are simply the consequence of certain species adapting to varied environmental settings as a result of phenotypic plasticity.

Pisay Forum

Pisay-CVC is at a crossroads... It's a bifurcated contest between status quo and hope... But of course, there need not be any dilemma... The problem is as clear as day... So should be the solution. And the Faculty, in their nomination letter (PisayDirekNominationsFaculty.doc), have hinted at possibly, the only right way to go...

Integrated Pest Management

How does integrated pest management support sustainability and biodiversity conservation?

My Answer:

Integrated Pest Management (IPM), properly defined, refers to an “approach which first assesses the pest situation, evaluates the merits of pest management options and then implements a system of complementary management actions within a defined area. The objective of IPM is to mitigate pest damage while protecting human health, the environment and economic viability.”

For an integrated pest management to effectively support prospective thrusts and undertakings on ecological (read: agricultural) sustainability and biodiversity conservation, it must be able to define important components that will provide structure to the planning and implementation of the IPM.

The Minnesota Department of Agriculture has defined six components to their IPM: planning, setting action thresholds, monitoring and detection, proper identification, action/implementation, and evaluation of results.

The component of planning takes on a proactive stance. Elemental to this component is the idea of being clear about specific objectives that shall provide framework to the conceptualization of an IPM. These objectives are anchored upon available data on the history of the pests and the structure of the site. With these considerations being made part of the planning, effective pest management may be resorted to in both the short term and the long term implementation of an IPM and education or expert advice may be sought where needed.

The setting of action thresholds takes on the premise that the implementation of an IPM is not without risk. Action thresholds must be based on realistic triggers that can serve as bases for management action in case of actual damages. Such action thresholds must define both the nature and extent of unacceptable damage – like aesthetics, economics, health considerations, nuisance, and other such elements that may be deemed constitutive of unacceptable damage determined from both personal and social values. It must be noted however that action thresholds vary relative to the dynamics of certain pests and the situation of their habitat. For which reason, the identification of realistic triggers must be made reflective of this dynamics and the factors that figure in the equation.

The IPM component of monitoring and detection has the objective of providing meaningful assessment of the site and the pests that inhabit it and being able to make recommendations on the nature of the pest and the extent of its influence over the place. Early detection of pests, their distribution patterns and their number will certainly help in initiating timely management decisions.

Proper identification is another important component of an IPM. Through this component, biology of the pest is noted and profiled. Without doubt, improper identification may lead to misdirected pest management efforts and may result to ineffective pest control and significant yield loss. Proper identification of pests has the objective of gathering information about the pests’ life cycle, their habits, and their physiology and with the end-in-view of identifying their weak links which serve as possible points of control and regulation.

The praxis of an IPM comes in the component of action and implementation. In this component, decisions as to which management option (biological control, cultural control, chemical control, or genetic control) is to be implemented, is reached. It is important however to note that any management option will have its “good” and “bad” effects on both humans and the environment. On this account therefore, decisions and actions on an IPM’s implementation have to be a case in which the benefits are calculated to far-outweigh the risks.

The last component of an IPM includes the evaluation of results. In this component, data that were gathered throughout the entire duration of the IPM’s implementation will be evaluated on account of its strengths and weaknesses. Results must be able to show in what aspects the IPM succeeded and in what aspects it failed. These results should be able to provide a proactive basis for future planning of IPM’s.

In summary, Integrated Pest Management is a system or a program whose objective is the mitigation of the impact of pests over a certain agricultural domain. It is designed to provide insights as to the nature of the pest, its ecological influence, and its mode of control. With these information about the pest, it is surmised that calibrated decision may be used to rid the domain of the pest but that, such decision should be of very limited harm to the other components of the environment that are rendered beneficial and to human health as well. On this account, integrated pest management is rendered supportive of sustainability – if by sustainability is meant the carrying out of a system that works in favor of the beneficial components and that works against the pests that are the subject of an IPM, and conservation of biodiversity – if by conservation is meant the protection of the natural microbial flora and fauna of a particular domain allowed only by the mitigation of the influence of pests whose proliferation harms the other ecological components.

Mining Disaster

Lafayette Mining, an Australian company, in its information campaign proposes a profitable and
environmentally-clean mining operation in Rapu-Rapu, Albay (http://www.rapurapu.20m.com/mining.html). But environmentalists opposed the proposal. In fact, those who strongly opposed claimed that “gold mining in Rapu-Rapu will eventually destroy this fragile island ecosystem, flora and fauna, water resources, aquatic and marine life, corals, seagrasses, mangroves, fishes, and finally human life” (http://www.rapurapu.20m.com/mining.html). Using the concepts on resources and conditions, is the claim justifiable? Support your answer.

My Answer:

A claim is said to be justifiable if and when it is capable of being shown as reasonable or “merited according to accepted standards”. The claim by environmentalists opposed to the operations of Lafayette Mining that “gold mining in Rapu-Rapu will eventually destroy this fragile island ecosystem, flora and fauna, water resources, aquatic and marine life, corals, seagrasses, mangroves, fishes, and finally human life”, should therefore show that their claim holds ground in reason and can be merited from accepted ecological standards.

The facts are as clear as day. Lafayette Mining was previously fined by the DENR the sum of PhP 10.7 million in penalty for “spilling its mine tailings not once but twice. This is in clear violation of Republic Act 9275 or otherwise known as the Clean Water Act. DENR reported that “the water pollution raps against Lafayette, which operates a polymetallic mining project covering three barangays in Rapu-rapu, Albay, stemmed from two incidents of spillage of mine tailings that occurred on October 11 and 31, 2005, that resulted in fishkills”. It also bears mentioning that the fishkills were attributed by inspectors of the Regional Mines and Geosciences Bureau in Albay to cyanide contamination. Recently, there was another report of spilling to which Lafayette Mining reacted vigorously.

Lafayette Mining in its website denied categorically any and all allegations pertaining to a reported “third toxic spill at the mine” towards the end of July this year. It asserted that it cannot do so since a Temporary Lifting Order issued by government regulatory agencies is in effect to set for the company, a three-stage, 30-day trial period that will monitor its environment management systems. As such, any incident to this effect should have been detected first by the monitoring body. But alas, no such spilling was detected, monitored and reported by the authorities to make the claim “official”. The company even found an ally in Sorsogon’s Governor Lee who issued in his press statement dated August 12, 2006, not only a scathing admonition of the advocacy espoused by environmental activists but even more so, an accusing finger directed at the activists for advertently contaminating the bodies of water and making it appear that Lafayette Mining has not complied with the requirements set forth by the DENR. At this point, there is no doubt that the issue has already been muddled by politics and money, reducing the environmentalists’ claim to the level of “hearsay”. But this is not without good reason and sinister motivation.

Lafayette is not loosening up its hold on Rapu-rapu Island because it knows the vastness of resources embedded in this place. It reported that “the Rapu-rapu mineral resource currently supports an eight-year mine life producing approximately 10,000 tonnes of copper in concentrates, 14,000 tonnes in zinc concentrates, 50,000 ounces of gold, and 600,000 ounces of silver annually”. And obviously, the politicians know very well what Lafayette knows about the place. For which reason, they are not loosening up their hold on Lafayette mining.

As the environmentalists’ claim has already been obfuscated with counter-claims from Lafayette, the validity of the argument stipulating environmental hazards appurtenant to the mining’s operation, can now only find validity from studies that show the same projected hazards stemming out from similarly situated and circumstanced mining operations.

Where then does the evil lurk in all these? The earth’s crust is a rich resource of minerals. These minerals come from ore deposits which are of two components: the ore mineral containing the desired metal, and waste material called gangue. Tailings and gangue are what remain from mining operations. And they are of no economic worth. But sometimes, to cope with operations cost, even these tailings are reprocessed for further extraction of precious metals. Damage to the environment starts with the process of extraction. For, regardless of whatever extraction type may be operated on, harmful substances like cyanide will still have to be resorted to, processed after use, then released to the environment. In heap leaching for instance, the ore is crushed into small chunks and irrigated with solution containing cyanide which serves in leaching out the precious metal from the ore. The role of cyanide in heap leaching is best described by the following equation:

During the extraction phase, the gold ions form complex ions with the cyanide:

Recovery of the gold is readily achieved with a redox-reaction:

In other extraction processes, gold cyanidation is simply replaced with sulfur extracting solutions. Contaminants are still used and they still pose very real hazards. It must be pointed out that in the greater scheme of things, resources go through cycles and depending on what conditions are ripe to effect random combinations of these resources, the contaminants that were supplied to the mining operations will have to end somewhere. Most often, they end up in bodies of water. Or even where so ever they end up, once they get incorporated in the environs of living systems, they stay there for the whole duration of their residence time. Chances are, they get assimilated in living systems which are devoid of any built-in mechanism for metabolizing harmful substances. As such, they just linger for a while in the organism until such time that bioaccumulation piles them up in magnified concentrations resulting to death. Ecologically, death taking its toll on a significant number of organisms in a population, effectively reduces, if not terminates, the fitness of affected species thereby diminishing their capacity for perpetuating their kind.

That spilling has happened twice in a row either by operational negligence or technical aberrations, the sword of Damocles still hangs over the head of Rapu-rapu’s residents. And they can only hope that such accident or incident never happens again. But as they say, hope springs eternal – especially to those who hope even against hope.

GenSci Forum

Hi Freshies... I have here some articles that I think will help you understand better the many concepts that we have covered thus far in general science. You can start clicking here for additional readings on the four fundamental forces... I've also included links on Newton's Three Laws of Motion... also, start reading on Levers...
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Hi... I've just posted Competency No. 4... It's your reviewer for Wednesday's Long Test... Check it out on this blog.

Biology Forum

Hey Sophies... I have added here some links to our previous lectures in Embryology. For more info about fertilization, click here... also, find here some important files on the segmentation of the fertilized ovum, the neural groove and tube, the primitive segments, the development of the cavities, and the different stages in embryonic growth... I hope these links will better help you appreciate the intricate processes of biological systems...
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the endoderm is the innermost germ layer in the developing embryo that will soon differentiate to form the different visceral organs that make up the gastro-intestinal tract... it also provides the basis for the embryonic differentiation of the cardio-pulmonary organs...
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For access to the powerpoint lectures on embryology, click here...
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Genetics is the branch of biology that deals with the study of heredity and variation...
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I have uploaded a powerpoint presentation on the Human Genome at Mikology Correspondence under Sir Miko's uploads...