JoSS: Joy of Sharing Science No: 3

No:3

JoSS

JoyofSharingScience

03July2020

AnindependentinitiativeofUskudarAmericanAcademyvolunteerstudents

Editor: FazılOnuralpArdıç

Pescidesaretakinginnocentlives!

ElifDemir,YaseminYüksel

Yourbrainactualylistenstoyourgutfeeling.

CeylinGün

Yourcalculatorisjustabunchofelectricalswitches.

ZanyarOğurlu,EdaToprak,MehmetEkinDoğan

Joy of Sharing Science 2020

This newspaper is an independent initiative of Uskudar American Academy volunteer students.

The Joy of Sharing Science is a weekly newspaper that explores the physics/biology/chemistry

behind interesting real life phenomena in a concise and easily understandable way. Each week,

3 phenomena concerning physics, chemistry, and biology will be published. The aim of this

project is to explore the science hidden in plain sight, evoke curiosity, and elevate scientific

literacy.

Advisor: Yasemin Sarıhan, Head of Science Department UAA

Editor: Fazıl Onuralp Ardıç, Senior student

Issue Authors:

Yasemin Yüksel,

Elif Demir,

Ceylin Gün,

Zanyar Oğurlu,

Mehmet Ekin Doğan,

Eda Toprak,

Junior student

Junior student

Junior student

Senior student

Junior student

Junior student

For your feedback, suggestions

Contact: uaajoss@gmail.com

Cover art: from free license: <a href='https://www.freepik.com/vectors/background'>Background

vector created by freepik - www.freepik.com</a>

Pesticides are taking

innocent lives!

Elif Demir, Yasemin Yüksel

The pesticide is the term used for comprising a wide scope of

chemicals such as “insecticides, fungicides, herbicides, rodenticides,

molluscicides, nematicides, plant growth regulators, and others”

(Hermann, 16) Within these compounds, organochlorine (OC)

insecticides have been used in economically struggling countries for

the crop yield and in other European countries to reduce the

transmissibility constant of epidemics such as malaria and typhus.

Other inorganic, synthesized insecticides such as organophosphate

(OP), however, took control in agricultural activities since the 1970s by

being able to provide beneficial output as fungicides and herbicides.

The issue of pesticides originates from the fact that while primary

beneficial outcomes are local and short-termed, the hazardous effects

are long-termed and worldwide. As a result of its contamination with

inorganic substances such as soil, water, lawn, and greenery, pesticides

may become toxic out of its target area (insects and weeds) by

toxifying other host animals like fish, birds, beneficial soil

microorganisms. In today’s world, freshwater has become a

widespread problem. One of the most popular reasons for this issue is

Joy of Sharing Science

the contamination of freshwater with pesticides since they tend to reach water through

watering systems of plants and soils and their runoffs. From the chemical analysis of

those water samples, it is evident that more than 150 chemicals from each major class

are utilized for agricultural purposes. It may take centuries for water to purify itself

from toxic chemicals with high cost and complex chemical systems if there is any way

to solve this issue. Thus, the United States Geological Survey has found out that the

concentration is exceeding the legal guidelines about pesticides.

The Hazardous Effects of Pesticides on the Environment

Transformation products are chemical substances that emerged from contaminants

by a combination of biotic and abiotic processes such as advanced oxidation,

photolysis, hydrolysis and can be found in wastewater pretreatment plants. Some

frameworks such as water solubility and persistence define TPs. Additionally, such

parameters by being correlated with soil-sorption constant (Koc), the octanol/water

partition coefficient (Kow), and half-life in soil (DT50) also define the toxicity and

are being used to classify pesticides. These are two main classifications of

pesticides:

1. The main characteristics of this type of pesticides are hydrophobicity, persistence,

and most importantly bioaccumulation since these chemical compounds are able to

establish strong bonds with soil. Even though most of the hydrophobic pesticides

are banned worldwide due to its bioaccumulation, in urban areas, organochlorine

DDT, endosulfan, endrin, heptachlor, lindane, and their TPs are currently used for

agricultural purposes.

2. Another type of TPs is polar pesticides that are commonly regarded as herbicides

while they can be used as carbamates, fungicides, and other organophosphorus

insecticides TPs. They stand a higher risk of contamination to soil and thus the

groundwater provided to the population due to the fact that it could spread on soil

through runoffs. The most recent study focuses on different biotic and abiotic

pathways that could be followed such as hydrolysis, methylation, and ring cleavage

that would result in the productions of these toxicants. The efficacy of

contamination depends on several parameters, and most importantly on the

chemical classification these chemicals belong to. After long surveys and analysis of

samples collected from different regions, the correlation between the absorption of

pesticides and TPs into the soil and the organic matter content of the soil is found as

follows: The increase in the organic matter content in soil results in the enhanced

absorption of these toxicants. The absorption constant of soil is directly

proportional to soil’s capacity to hold positively charged ions since most of the

pesticides are also positively charged, and it enhances the quality of the transaction

of these ions and the bonds created during this process. For the removal of these

chemicals, strong mineral acids are required and the scientists consider it almost

Pesticides are taking innocent lives!

impossible due to high cost,

lack of recent studies, and

lack of proficiency in this

research area.

Especially during the

treatment with pesticide

sprays, there stands a 25%

chance of these chemical

compounds may hit or

volatilize to a non-target

species such as other

vegetations and beneficial soil

microorganisms. Within a few days, it is

estimated that 80-90% of these chemicals

may contaminate other abiotic

substances such as air, soil, and the

range of spreading within those days may differ from a yard to hundreds of

miles. Herbicides undergoing ester-formulation stand a higher chance of

becoming a lethal threat towards vegetations after volatilization due to vapor

energy sufficient. Other than causing health problems in non-target plants,

these pesticides may also cause sublethal problems in aimed plants due to

high exposure. One of the common examples of these herbicides is Phenoxy

herbicides since they are able to drift further away from the target and injure

other vegetations. Those chemicals possess a lethal threat towards species,

especially endangered ones. Those popular pesticides caused worldwide

problems since some samples from the Arctic contain residues. “However,

only recently has it been established that volatilization and vapor-phase

transport are important in the dissipation of even the so-called “nonvolatile

pesticides,” and other organochlorine compounds. Pesticides range in

volatility from fumigants, such as gaseous methyl bromide, to herbicides with

vapor pressures below 10-8 mm.” (Farmer)

The Hazardous Effects of Pesticides on the Soil Microorganisms

The use of pesticides in the long-term has resulted in serious damage to soil

ecology which has led to harming and altering beneficial/plant probiotic soil

microflora as well as general soil microorganisms. This has also resulted in

weathered soils losing their ability to sustain enhanced production of

crops/grains on the same land.


Firstly, it is certainly

useful to mention that

there is a crucial

relationship between

plants

and

microorganisms, in other

words, microbes in

which plants such as

grass, trees, and food

crops highly depend on

soil microorganisms in obtaining nutrients,

protection from pests and pathogens as well as the

break down of compounds that could inhibit growth, etc. However, this

relationship is not only one-sided as soil microbes also benefit from plants

through their root system. Soil microbes including fungi, nematodes,

protozoa, microarthropods, and other beneficial bacteria, decompose organic

material while they absorb water and nutrients that would otherwise get lost

in the soil; the absorbed water and nutrients then get used by more and more

complex

The effect of pesticides is that they include a large group of chemical agents

that attempt to eliminate destructive biological forces in agriculture. For

instance, herbicides are for killing plants, insecticides for killing insects,

fungicides for killing fungus, and bactericides for killing bacteria. While these

chemicals supposedly only target specific species, long-term use has been

inevitably killing microbial life that is beneficial to the soil system and

ecosystem all the way up to the largest mammalian predators. Microbes that

survive can be genetically altered in a way that is no longer beneficial to the

soil ecosystem and is resistant to the chemical intended to kill them.

References:

Additional information Acknowledgements Authors are thankful to the state

government of Punjab. “Effect of Pesticide Application on Soil Microorganisms.”

Taylor & Francis, www.tandfonline.com/doi/abs/10.1080/03650341003787582.

Aktar, Md. Wasim, et al. “Impact of Pesticides Use in Agriculture: Their Benefits and

Hazards.” US National Library of Medicine National Institutes of Health, Mar. 2009,

www.ncbi.nlm.nih.gov/pmc/articles/PMC2984095/.

Damalas, Christos A. “Understanding Benefits and Risks of Pesticide Use.”

Department of Agricultural Development of Pieria, 11 Sept. 2009.

Pesticides are taking innocent lives!

“How Pesticides Affect Soil Microbes.” EMNZ, 13 Mar. 2015,

www.emnz.com/article/how-pesticides-affect-soil-microbes.

Johnson, Nathanael. “The Secret to Richer, Carbon-Capturing Soil? Treat Your

Microbes Well.” Grist, Grist, 1 July 2014, grist.org/food/the-secret-to-richer-carboncapturing-soil-treat-your-microbes-well/.

WAIBEL, HERMANN, et al. “The Economic Benefits Of Pesticides: A Case Study

from Germany.” Jahrgang, 1999,

file:///Users/elifdemir/Downloads/Jahrgang_1999_Artikel_33.pdf.

Spencer, W. F., et al. “Pesticide Volatilization.” 1973.


Your brain actually listens

to your gut feeling

Ceylin Gün

The gut-brain axis is a bidirectional communication pathway

between the central nervous system and the enteric nervous system.

The central nervous system consists (CNS) of the brain and the

spinal cord. The enteric nervous system is the largest component of

the autonomic nervous system which controls bodily functions like

breathing, heartbeat, and digestive functions. The enteric nervous

system (ENS) is responsible for the digestive part of the autonomic

nervous system by governing the gastrointestinal tract. The

gastrointestinal tract is shown in the diagram:

(Taken from National Cancer

Institute Cancer Terms

Dictionary, “Gastrointestinal

Tract”)


The gut-brain axis is found to be not only responsible for the maintenance of

gastrointestinal homeostasis, but also highly linked to the cognitive and emotional

parts of the central nervous system. Thus, it appears to have an effect on

motivation, cognitive functions, and some diseases of the central nervous system.

Microbiota in the enteric nervous system has a significant role in the constitution of

this bidirectional communication system. Microbiota refers to the microorganisms

found in particular environments. Since enteric microbiota are located in the enteric

nervous system, they are in communication with the intestinal cells and the ENS,

but also they are in direct contact with the CNS too through metabolic pathways.

(Taken from Quigley, “The Gut-Brain Axis and the Microbiome: Clues to Pathophysiology and

Opportunities for Novel Management Strategies in Irritable Bowel Syndrome (IBS)”)

The microbial colonization is important for the maturation of both the ENS and the

CNS, and the absence of microbial colonization in the gut alters the expression of

neurotransmitters. Experiments on mice also have demonstrated that microbiota

affects stress and anxiety. Microbial colonization reduces the effects of increased

cortisol expression, so it normalizes the stress level. Memory dysfunction in studied

mice has also been reported. The impact of microbiota on stress is also supported by

Your brain actually listens to your gut feeling

the discovery that the probiotics reduce stress-induced cortisol release, anxiety and

depression-like behavior.

So far, only the effects of the “gut to brain” direction have been iscussed. However,

the CNS also has an impact on microbiota. The brain can alter the intestinal

permeability, hence welcoming bacteria antigens and stimulating an immune

response in the mucosa which will, in turn, change the microbiota composition and

function. Overall, the principal mechanism of the gut-brain axis can be seen here:

(Taken from

Carabotti, et al., “The

gut-brain axis:

interactions between

enteric microbiota,

central and enteric

nervous systems”)

One example of a digestive disorder with psychological effects is Irritable bowel

syndrome (IBS), including side effects of anxiety and depression. Now that we

know the link between the CNS and the ENS, we can see how they are connected.

IBS can be a lifelong problem that affects 6-18% of the population. The microbiota is

altered in IBS patients compared to healthy people. The microbiota can predict the

severity of IBS and also responsiveness to low carbohydrate diet treatment.

A very complex system of bidirectional CNS-ENS interactions reveals the link

between cognitive and emotional functions, and the functioning of the

gastrointestinal tract. Considering that the digestive system is said to be the second

brain of the body, it is possible that future studies will reveal more about how the

two nervous systems interact with each other.

References:

Carabotti, Marilia et al. “The gut-brain axis: interactions between enteric microbiota, central

and enteric nervous systems.” Annals of gastroenterology vol. 28,2 (2015): 203-209.

Costa, M. “Anatomy and Physiology of the Enteric Nervous System.” Gut, vol. 47, no.

90004, 2000, pp. 15iv–19., doi:10.1136/gut.47.suppl_4.iv15.

Edermaniger, Leanne. “Microbiome Vs Microbiota: What's The Difference For Your Gut

Bacteria?” Atlas Biomed Blog | Take Control of Your Health with No-Nonsense News on Lifestyle,

Gut Microbes and Genetics, Atlas Biomed Blog | , 14 Jan. 2020,

atlasbiomed.com/blog/whats-the-difference-between-microbiome-and-microbiota/.


“NCI Dictionary of Cancer Terms.” National Cancer Institute,

www.cancer.gov/publications/dictionaries/cancer-terms/def/gastrointestinal-tract.

Quigley, Eamonn. “The Gut-Brain Axis and the Microbiome: Clues to Pathophysiology and

Opportunities for Novel Management Strategies in Irritable Bowel Syndrome (IBS).” Journal

of Clinical Medicine, vol. 7, no. 1, 2018, p. 6., doi:10.3390/jcm7010006.

Rao, Meenakshi, and Michael D. Gershon. “The Bowel and beyond: the Enteric Nervous

System in Neurological Disorders.” Nature News, Nature Publishing Group, 20 July 2016,

www.nature.com/articles/nrgastro.2016.107.

“What Is IBS?” NHS Choices, NHS, 9 Oct. 2017, www.nhs.uk/conditions/irritable-bowelsyndrome-ibs/.

Your calculator is just a

bunch of electrical

switches

Zanyar Oğurlu, Eda Toprak, Mehmet Ekin Doğan

Revolutionized the electronics industry when it was invented in 1947,

transistors play a huge role in most of the electronic devices today.

They are the building blocks of many integrated circuits and are crucial

for logical operations. For simplicity, we are not going to discuss every

type of transistor but the first invented model called bipolar junction

transistor (BJT); however, we must also take into account that they are

not the most commonly used type of transistor. That title goes to

metal–oxide–semiconductor field-effect transistor (MOSFET) which is

far easier to mass-manufacture.

As you can see in the picture a BJT transistor has three legs, labeled as

E (Emitter), B (Base), and C (Collector) which are classified into two: P,

the material with fewer electrons or more ‘holes’ and N, the material

with more electrons or less ‘holes’ (The term ‘hole’ is used to represent

a missing electron.) The material with more holes is more positive

compared to its counterpart. In the PNP type of transistor, the current’s

direction won’t be aligned with the movement of electrons but

movement of holes. These P and N materials are arranged in such

ways that make the transistor function as if it was an electrical switch.


When there is no voltage difference applied across the base and emitter ends,

electrons from base and holes from the emitter attract each other. So, a chargeneutral

zone in between P and N is formed called EB. A similar process occurs

between the base and collector where electrons and holes attract each other to form

a second neutral zone called CB. In this state, it is not possible for a current to run

from emitter to collector through the transistor. However, when a voltage difference

(VEB) is applied across Emitter and Base, holes start to circulate. They are pushed

from Emitter to the neutral zone due to the voltage difference and then pulled from

the neutral zone to base. This way of applying a voltage difference across the

emitter and the base is called forward bias because it makes the EB neutral zone

thinner and forces holes to move forward. To complete the system and enable a

current from Emitter to Collector, another voltage difference needs to be applied.

This voltage difference is applied across the Collector and Base. The direction of the

voltage difference pulls holes away from the base and widens the CB neutral zone

while also starting another circulation of holes. This type of voltage difference is

called reverse bias.

Your calculator is just a bunch of electrical switches

The holes coming from the emitter are now able to proceed to the collector and a

current is formed.

Transistors are used to make logic gates

Logic gates are the building blocks of digital systems. They accept one or more

inputs to produce an output according to a logical rule. Those inputs and outputs

are “truth-valued,” which are True and False in binary logic. In logic gates, 1 is

considered to be true, whereas 0 is false.

A logic gate is a small transistor circuit and is implemented in several forms to

create seven types of logic gates called AND, OR, NAND, NOR, XOR, XNOR, and

NOT. The circuit operates on two voltage levels called logic 0 and logic 1 and

receives its inputs according to the voltage level to which it is exposed.

Metal Oxide Semiconductor Field Effect Transistor (MOSFET) is another type of a

transistor and one of the most widely used types. Its mechanism will not be

explained in detail here but will be mentioned only in relation to the construction of

the logic gates.

The switch behavior of MOS transistors are used to build the logic gates. A range of

analog voltages are assigned to each logic symbol according to the electrical

properties of the transistors. While the voltage range for 0 is between 0 and 0.5V,

some typical values for 1 are 5V, 3.3V, 2.9V, and 1.1V.

A complementary MOS (CMOS) circuit creates the logic gate. It uses both N-type

and P-type MOS transistors. P-type transistors are attached to the + voltage and

pull the output voltage up when the input is zero. N-type transistors are attached to

the GND, which is the reference point for signals or a common path in the circuit

from which all voltages are measured, and they pull the output voltage down when

the input is one. Hey also, when the input voltage to a P-type transistor is 1 (high),

then the transistor will not open (does not conduct).


(Image taken from Prof.

Guri Sohi, “Transistors

and Logic Gates”)

A NOT gate reverses the input by converting 0 into 1 and 1 into 0. When no voltage

is applied to the input wire, the P-type transistor will pull the output voltage up,

resulting in the output wire to have electricity flowing through itself and an output

of 1. However, when high voltage has an input of 1 applied to the “in wire,” the N-

type transistor will pull the voltage down; the current will be led to the source,

leaving the “out wire” without electricity. This causes the output to be 0. This basic

principle of connecting P-type and N-type transistors in a circuit is similarly used to

implement AND and XOR logic gates.

AND Gates:

AND is one of the Boolean operations. The AND gates accept two wires. If both

wires are “on” as electricity is flowing through them, they will be in true state

represented by 1. Then, two 1 will output 1.

(Image taken from Pamela Fox, “Logic gates”)

However, if both wires are “off” as no electricity is flowing, then they will represent

the false state as two 0s of input. Consequently, the output will also be 0 as seen in

the figure below.


(Image taken from Pamela Fox, “Logic gates”)

Having one wire with electricity flowing through and one not means that the circuit

has the inputs 1 and 0, and since this is an AND operation, not having both wires in

the true state will output 0.

XOR (Exclusive OR) Gates:

The XOR gate output is at logic 1 when only one of its inputs is 1. If both wires

connected to the gate are on or off, the output will be logic 0. This logic function

and its truth table in a circuit can be seen from the figure below.

The AND and XOR gates are specifically useful in mathematical operations carried

out by the computers in binary.

How does your calculator add numbers?

Let’s take two binary numbers into account as an example: 0101 and 1101. In the

most basic terms, in the way we learned in the 1st grade, how do we add two

numbers?


As illustrated in this figure, firstly, every 2 digit is

added together, and it is checked whether the sum is

smaller or equal to, or greater than 1. The sum of two

binary digits can equal something greater than 1,

only if those digits are both 1. This means that the

digit that will be carried can be decided by an AND

gate. (If we put our two inputs through an AND gate,

we will obtain the carried digit.) Now that the carried

digit is obtained, let’s have a look at what the noncarried

digit will be. Below is a truth table to

demonstrate:

From the table to the right, we can

see that when the inputs are

equivalent to one another, the

resultant non-carried digit will

equal 0. Otherwise, if the inputs

are different, the digit will equal 1. This is called the XOR operation, and computers

do it via the pre-explained XOR gate. What happens now? Well, the non-carried

digit is returned directly. The same operations are made for the second digits, via

the same gates. Then, the non-carried digit from the next digit and the carried digit

from the previous is put through an XOR operation to determine the outputs. Then,

the carried digit needs to be determined. If Input 1 and Input 2 in the second digit

of the sum are both 1, the carried digit will equal 1. However, there is another way

that the carried digit is 1. If one of Input 1 or Input 2 is 1 and the other is 0, and the

carried from previous sum is 1, the carried digit for this digit of the sum will again

be equal to 1. Thus, the process goes as follows:


The subscript of d represents the order of the digit that is being calculated, and

superscript represents the number from which the input is taken. This process will

continue with the same pattern until the two final bits of the input binary numbers

are summed. After the final summation is carried out, the carry from that operation

will directly be returned, since there is no digit that comes after. Below is the visual

representation of the first two parts of the process that is outlined above

mathematically:

Here is a sample addition operation of the two binary numbers 00101 and 01101 (which was

illustrated above) carried out using the method described and visualized above:


As the result of the summation of the numbers 00101 and 01101 in binary, 10010 has

been obtained. Let’s convert these numbers to decimal now and check if our

method was correct. 00101 = 4 + 1 = 5 in decimal form. 01101 = 8 + 4 + 1 = 13 in

decimal form. The result, 10010 = 16 + 2 = 18 in decimal form. Since 5+13 = 18, the

methodology has been validated.

References:

“Binary Adder and Binary Addition Using Ex-OR Gates.” Basic Electronics Tutorials, 20

Sept. 2018, www.electronics-tutorials.ws/combination/comb_7.html.

Electrical4U. “PNP Transistor: How Does It Work? (Symbol & Working Principle).” 11 May

2020, www.electrical4u.com/pnp-transistor/.

Fox, Pamela. “Logic Gates | AP CSP (Article).” Khan Academy, Khan

Academy, www.khanacademy.org/computing/computers-and-theinternet/xcae6f

4a7ff015e7d:computers/xcae6f4a7ff015e7d:logic-gates-andcircuits/a/logic-gates.

“Learnabout Electronics.” Logic Gates, learnabout-electronics.org/Digital/dig21.php.

Logic Gates, faculty.cooper.edu/smyth/cs225/ch10/gates1.htm.

Sohi, Guri. “Introduction to Computer Engineering.” Wisconsin.

pages.cs.wisc.edu/~sohi/cs252/Fall2012/lectures/lec03_digital_logic.pdf.

“The P-Channel Mosfet Transistor (PMOS).” YouTube, Booksofscience, 1 June 2012,

www.youtube.com/watch?v=-wsr0eE3pN4.

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