HAPPY NEW YEAR!

Its been a while since I have put written something in here. Its time to make up with the lost times hehe. Tama ba yun? :)

Hey! 2 hours nalang New Year na! its 2006! Its time to contemplate and reminisce all the good , together with the bad things that happened in the year 2005.

Its not important how problematic you were in the year 2005 but its how you were able to win all the complicated situation which in turn determines your readiness to face the coming year!

Cheer up, get a cold one and celebrate life!

Julius

Herz, Status of Philippine Education, etc.

Haha. Somebody just got me corrected about my blogspot! The Hertz was not spelled correctly but should be written as "Herz". Actually, it was written that way before the actual interface revamp was made. After that, the settings were all gone so I have to type everything again! That's where the error in spelling probably occured. Nalagyan ng T! lolz. Thanks, Ate Lea! (She's from Germany! Ang galing!
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Our current topic in SCED (Science Education) in UP Open University in Los Baños is pretty interesting.

"Are Filipinos generally scientifically literate? Why or why not?"

Ate Lea and I responded with the following answers which I find it interesting to share. Read on. :)

"...I do not think that the the general Filipino population is scientifically literate --yet."

It all begins with having access to education. Although primary and secondary schooling are compulsary with public schools bearing the responsiblity of educating 50+ students in a classroom, the question here is the quality of education they are receiving. Yes, they may remember that they have "Science" as a subject but how much learning really does occur in the classroom? How much of the topics or processes in science do they really undertand and therefore, use outside the confines of the classroom? Are they able to see the relationship between science and the other subjects taught in the Curriculum? Do they see science as an extension of technology and as a means of improving one's quality of life?

We should re-define our meaning of literacy. It should be beyond the description of having the ability to read and write. Literacy should also mean having understood what has been taught, even welcoming the dissection of one's knowledge if it means gaining more.

And sad to say, we have a long way to go to be literate in science (or on any other subject for that matter).

Lea
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This is a very timely question for all of our compatriots in the field of science education!

Perhaps, I would consider our country as a "sleeping giant" in terms of our potential in science competency given our talents evidenced by famous Filipinos in the field of science and technology (much like China) but the only difference is that our country apparently have never learned to wake up!

Maybe our country have forgotten to wake up scientifically after Bagong Lipunan education was dissolved. This is a very sad truth for most of our students (around 95%) are flanking in National Science and Mathematics achievement examinations.

Worst, according to the latest results of examinations conducted among public and private school teachers by the Commission on Higher Education, a measly 9% among the participants in the said exam successfully passed, while the rest did not even manage to get to the 74% mark!

Others' scores are even dwindling on the twilight zone of intellectual uncertainty as to whether they are even qualified to teach or can be perfectly described as "napadaan lang".

Disappointing as it may seem, I still conclude that the Philippines is not phyically ready to embrace the grandeur Science has to give and therefore are not scientifically literate.

There may be some who are exceptionally gifted in in this field but these people are usually product of prestigious private schools here and abroad. It does not reflect the general status of education in our country and does not provide clear distinction so as to confer us the eligibily to be regarded as intelligble individuals in terms of science and technology.

Julius

Of Influenza Viruses and and strains

I found this information in the Centers for Disease Control and Prevention website and I think is really very informative. It provides information about the different strains of Influenza virus and their mechanism of infection and genetic modification. Youu may read on the article or visit the website directly. Very enlightening. :) Thanks!

Julius

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Types, Subtypes, and Strains

There are three types of influenza viruses: A, B, and C. Only influenza A viruses are further classified by subtype on the basis of the two main surface glycoproteins hemagglutinin (HA) and neuraminidase (NA). Influenza A subtypes and B viruses are further classified by strains.

Human Influenza Viruses and Avian Influenza A Viruses

Humans can be infected with influenza types A, B, and C viruses. Subtypes of influenza A that are currently circulating among people worldwide include H1N1, H1N2, and H3N2 viruses.

Wild birds are the natural host for all known subtypes of influenza A viruses. Typically, wild birds do not become sick when they are infected with avian influenza A viruses. However, domestic poultry, such as turkeys and chickens, can become very sick and die from avian influenza, and some avian influenza A viruses also can cause serious disease and death in wild birds.

Low Pathogenic versus Highly Pathogenic Avian Influenza A Viruses

Avian influenza A virus strains are further classified as low pathogenic (LPAI) or highly pathogenic (HPAI) on the basis of specific molecular genetic and pathogenesis criteria that require specific testing. Most avian influenza A viruses are LPAI viruses that are usually associated with mild disease in poultry. In contrast, HPAI viruses can cause severe illness and high mortality in poultry. More recently, some HPAI viruses (e.g., H5N1) have been found to cause no illness in some poultry, such as ducks. LPAI viruses have the potential to evolve into HPAI viruses and this has been documented in some poultry outbreaks. Avian influenza A viruses of the subtypes H5 and H7,including H5N1, H7N7, and H7N3 viruses, have been associated with HPAI, and human infection with these viruses have ranged from mild (H7N3, H7N7) to severe and fatal disease (H7N7, H5N1). Human illness due to infection with LPAI viruses has been documented, including very mild symptoms (e.g., conjunctivitis) to influenza-like illness. Examples of LPAI viruses that have infected humans include H7N7, H9N2, and H7N2.

In general, direct human infection with avian influenza viruses occurs very infrequently, and has been associated with direct contact (e.g., touching) infected sick or dead infected birds (domestic poultry).

How Influenza Viruses Change: Drift and Shift

Influenza viruses are dynamic and are continuously evolving. Influenza viruses can change in two different ways: antigenic drift and antigenic shift. Influenza viruses are changing by antigenic drift all the time, but antigenic shift happens only occasionally. Influenza type A viruses undergo both kinds of changes; influenza type B viruses change only by the more gradual process of antigenic drift.

Antigenic drift refers to small, gradual changes that occur through point mutations in the two genes that contain the genetic material to produce the main surface proteins, hemagglutinin, and neuraminidase. These point mutations occur unpredictably and result in minor changes to these surface proteins. Antigenic drift produces new virus strains that may not be recognized by antibodies to earlier influenza strains. This process works as follows: a person infected with a particular influenza virus strain develops antibody against that strain. As newer virus strains appear, the antibodies against the older strains might not recognize the "newer" virus, and infection with a new strain can occur. This is one of the main reasons why people can become infected with influenza viruses more than one time and why global surveillance is critical in order to monitor the evolution of human influenza virus stains for selection of which strains should be included in the annual production of influenza vaccine. In most years, one or two of the three virus strains in the influenza vaccine are updated to keep up with the changes in the circulating influenza viruses. For this reason, people who want to be immunized against influenza need to be vaccinated every year.

Antigenic shift refers to an abrupt, major change to produce a novel influenza A virus subtype in humans that was not currently circulating among people (see more information below under Influenza Type A and Its Subtypes). Antigenic shift can occur either through direct animal (poultry)-to-human transmission or through mixing of human influenza A and animal influenza A virus genes to create a new human influenza A subtype virus through a process called genetic reassortment. Antigenic shift results in a new human influenza
A subtype. A global influenza pandemic (worldwide spread) may occur if three conditions are met:

A new subtype of influenza A virus is introduced into the human population.
The virus causes serious illness in humans.
The virus can spread easily from person to person in a sustained manner.

Types, Subtypes, and Strains

Influenza Type A and Its Subtypes

Influenza type A viruses can infect people, birds, pigs, horses, and other animals, but wild birds are the natural hosts for these viruses. Influenza type A viruses are divided into subtypes and named on the basis of two proteins on the surface of the virus: hemagglutinin (HA) and neuraminidase (NA). For example, an “H7N2 virus” designates an influenza A subtype that has an HA 7 protein and an NA 2 protein. Similarly an “H5N1” virus has an HA 5 protein and an NA 1 protein. There are 16 known HA subtypes and 9 known NA subtypes. Many different combinations of HA and NA proteins are possible. Only some influenza A subtypes (i.e., H1N1, H1N2, and H3N2) are currently in general circulation among people. Other subtypes are found most commonly in other animal species. For example, H7N7 and H3N8 viruses cause illness in horses, and H3N8 also has recently been shown to cause illness in dogs.

Only influenza A viruses infect birds, and all known subtypes of influenza A viruses can infect birds. However, there are substantial genetic differences between the influenza A subtypes that typically infect birds and those that infect both people and birds. Three prominent subtypes of the avian influenza A viruses that are known to infect both birds and people are:

Influenza A H5

Nine potential subtypes of H5 are known. H5 infections, such as HPAI H5N1 viruses currently circulating in Asia and Europe, have been documented among humans and sometimes cause severe illness or death.

Influenza A H7

Nine potential subtypes of H7 are known. H7 infection in humans is rare but can occur among persons who have direct contact with infected birds. Symptoms may include conjunctivitis and/or upper respiratory symptoms. H7 viruses have been associated with both LPAI (e.g., H7N2, H7N7) and HPAI (e.g., H7N3, H7N7), and have caused mild to severe and fatal illness in humans.

Influenza A H9

Nine potential subtypes of H9 are known; influenza A H9 has rarely been reported to infect humans. However, this subtype has been documented only in a low pathogenic form.

Influenza Type B

Influenza B viruses are usually found only in humans. Unlike influenza A viruses, these viruses are not classified according to subtype. Influenza B viruses can cause morbidity and mortality among humans, but in general are associated with less severe epidemics than influenza A viruses. Although influenza type B viruses can cause human epidemics, they have not caused pandemics.

Influenza Type C

Influenza type C viruses cause mild illness in humans and do not cause epidemics or pandemics. These viruses are not classified according to subtype.

Strains

Influenza B viruses and subtypes of influenza A virus are further characterized into strains. There are many different strains of influenza B viruses and of influenza A subtypes. New strains of influenza viruses appear and replace older strains. This process occurs through antigenic drift. When a new strain of human influenza virus emerges, antibody protection that may have developed after infection or vaccination with an older strain may not provide protection against the new strain. Therefore, the influenza vaccine is updated on a yearly basis to keep up with the changes in influenza viruses.

Information taken from Centers for Disease Control and Prevention
Visit their website at www.cdc.gov

Welcome Bio Students!

I am delighted to teach again! This coming weeks will be one of the busiest time for me since I need to take some "real" adjustments.

Also, I would like to take this opportunity to thank miss Gloria Bondoc-Abrazado for letting me handle her Genetics and Natural Science 2 (Biological Science) Class. Its great to be in the teaching field again. To my students, welcome!

I have been around in the blogger world for quite some time now and enjoying it! You may use this site for updates on our subject matter and read updates on what's hot in the world of biology.

Our blog will particularly provide additional readings in biology which you will find interesting. Many are updates regarding the recent bird flu outbreak and AIDS pandemic.

This will be a very huge adjustment for all of us but, with your cooperation and diligence, surely, we will be able to accomplish something worthwhile at the end of my teaching substitution career and you being students of Science as well.

Let's make the most out of our pagsasama! Cheers!


Julius

Word Power: Epidemic or Pandemic?

Hello Friends! I am introducing a new segment of our blog which is called WORD POWER!. Whenever you see such posts, it surely tackles about unique words or expressions which you frequently read in medical articles, books and journals.

Being able to understand these words empowers you to read on medical articles without difficulty and keeps you on a competitive edge with other people. So here it is!

Most people tend to interchange the meaning between pandemic and epidemic. These two words are widely used in the medical field, specifially, in the world of microbiology.

With the advent of bird flu virus threat and other related infections, knowing how to distinguish the meaning and the relative differences of the two words will provide you greater advantage and clear understanding on every articles where these words were used.

Entries in Merriam Webster give clear distinctioin between the two words.

Main Entry: 1ep·i·dem·ic

Etymology: French épidémique, from Middle French, from epidemie, n., epidemic, from Late Latin epidemia, from Greek epidEmia visit, epidemic, from epidEmos visiting, epidemic, from epi- + dEmos people -- more at DEMAGOGUE

1 : affecting or tending to affect a disproportionately large number of individuals within a population, community, or region at the same time

Main Entry: 1pan·dem·ic

Etymology: Late Latin pandemus, from Greek pandEmos of all the people, from pan- + dEmos people -- more at DEMAGOGUE

: occurring over a wide geographic area and affecting an exceptionally high proportion of the population

For more information, please click on the Post Title Link to lead you to the website source. Thank you.

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A rather more helpful explanation is available in the site below. It cited the difference between endemi, epidemic and pandemic.

Endemic: a disease that exists permanently in a particular region or population. Malaria is a constant worry in parts of Africa.

Epidemic: An outbreak of disease that attacks many peoples at about the same time and may spread through one or several communities.

Pandemic: When an epidemic spreads throughout the world.

http://www.mansfieldct.org/schools/mms/staff/hand/immnotes.htm

Dictionary.com provides similar explanation:

Pandemic ultimately derives from Greek pandemos, of all the people, from pan-, all + demos, people

Usage: Difference between endemic, epidemic, and pandemic:

Endemic is peculiar to a district or particular locality, or class of persons ("diseases endemic to the tropics"). That which is epidemic is common to, or affecting at the same time, a large number in a community ("an epidemic outbreak of influenza"). Pandemic is epidemic over a wide geographical area.

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See! We are learning! Its nice to know all these stuff for it frees you from reading difficulties! Information is power! :) Keep on reading!

Julius

Pig Flu Virus?

Aside from birds, pigs are one vital candidate in the transmisson of flu.

(Picture taken from CNN)

Hi Readers!

Researchers are eyeing on another source of flu virus that may pose greater threat to humans more than bird flu due to their more-than-close association with us.

Just recently, researchers are looking at the possibility of the spread of a pig flu virus. Pigs are more biologically similar in function and structure with humans than in birds. This fact provides more reason that a subtle pig flu outbreak may expedite a more deadly contamination with humans and may start a world-wide panick which most of us are totally unprepared.

Viruses differ in their ability to infect animals and plants and may well jump from one organism to another and possibly start a whole new strain. This "species jumping" is caused by the virus' ability to change genetically and add another host of animals in their infection list.

As stated in our previous post, viruses lacks the ability to repair specific genome damage during replication of their genetic material. This apparent biological infirmity confers the organism the ability to undergo dramatic change from one strain to another rendering most organisms unable to cope up with attcks due to lack of preformed defenses (antibodies) .

Likewise, dogs, seals, horses, and ferrets are more prone to these attacks and pose greater theat to the the survival of the human population.

Julius

Why do AIDS and Avian Influenza and other diseases caused by viruses difficult to treat?

This week protesters marched to US capitol demanding the reauthorization of Ryan White Care Act which aims to promote basic health care services for AIDS victims who lacks basic health care insurance to support medication and other needs to treat the disease.

It is reported that more than 1 million Americans are afflicted with the disease. More and more people are being infected every year and the numbers would continue to rise as people engage in risky behaviors which put them more susceptible to the disease.

Just how the development of AIDS vaccine so hard to device lies on the ever changing form of the virus. Through laboratory test, it was shown that more than one strain of virus is present in an AIDS patient.

This fact provides us with valuable clues to the nature of the AIDS virus and empower us to device treatment which is tailored to how the virus advance on an infected patient.

This works the same way with Avaian Influenza (H5N1) strain. The killer bird flu virus was believed to have already developed the ability to infect humans. Its mutation works in two ways: through antigenic drift and antigenic shift.

Antigenic drift is a small change to the genetic information contained in the virus due to the virus' lack of proofreading ability during genetic replication. Humans are equipped with this competency and allow us to maintain our genetic integrity and discourage unallowable changes.

This small changes creates an invariably small, unique changes to the genetic composition of the virus. This issue is important for it allows us to predict the strain of virus that will more likely to be prevalent in the coming flu season. It will also give local administrators to adjust the compositon of flu vaccines to be given in the coming season.

In contrast, anti-genetic shift works where a virus can interchange or "mate" its genetic composition with another virus species thereby producing a completely different type which in most cases are more virulent (extremely pathogenic or producing severe disease).

The latter definition is of major concern to scientists working on preventing the spread of avian influenza and eventually acquire the necessary mechanism to infect humans through the process enumerated above.

For your additional readings, please visit the following site below:

www.who.int/mediacentre/factsheets/avian_influenza/en/index.html
www.unaids.org/wad2004/EPIupdate2004_html_en/epi04_00_en.htm

Avian Influenza Menace

Hey guys, got some scary news. Just recently, more and more countries are getting disturbed about the rapid progression of bird flu virus to different regions of the planet. Most countries in the South Asia and Southeast Europe are plagued by dreaded disease. Romania and Turkey just recently announced the menace brought about by the virus. Chickens were culled and some bird species quarantined. I have read that Europe strickly bans the vaccine innoculation of chickens lest it will pave the way for the transformation of H5N1 virus to a different strain and assume a form which infects humans. Despite these recommendations, some countries in Asia are still in the practice of vaccination which are believed inimical to the current research progress conducted by several countries combating this disease. May God help us all. If you would like to know more infomation about Bird flu virus simply click on the link below which will lead you to a different website containing the information in question. Thanks!

http://www.cdc.gov/flu/avian/gen-info/facts.htm
http://www.who.int/csr/don/2004_01_15/en/

The Chemistry Behind Invisible Ink

Hola! Enough of those biological principles! :) I would like to introduce you to the chemistry of the invisible ink and how it works so we will all be familiar with the principles underlying this wonderful Science. Many household products can be used to make this experiment but some that remains popular are lemon juice ink, baking soda and corn starch. Inferring on their pH content, these substances are basic and acidic substances. To the best interest of everybody, the principle behind invisible inks is the process of weakening the molecular bond that holds cellulose together (polysaccharide, glucose molecule) that makes up the paper material. The application of the acidic substances or basic substances weakens the part of the paper where the basic/acidic substance was applied to and made visible when passed over a flame or a hot object or when heat is directly applied to show the damaged part of the paper. I have searched some experiments online which you can use with your students or when making clandestine dates with your girlfriends or boyfriends or sending secret messages. Hehe. Pretty cool, huh! Please use the links below and paste it in your external browser's address field for detailed instructions on how to prepare this cool stuff. :) Enjoy!

Jules

Chemistry of Invisible Ink: http://chemistry.about.com/b/a/207468.htm?nl=1
Lesson Plan on making Invisible Ink: http://www.iit.edu/~smile/ch9602.html

Suicide Grasshoppers Brainwashed by Parasite Worms

Hi! Wie geht's? It took me almost a month before I was able to post a message again. . Sorry about that. I have had a very busy month for I was finishing several assignments (TMAs-Teacher-Marked Assignment as they call it in UPOU) in my Bio and Chem class. Well, I was able to read something in National Geographic Website about a parasitic hairworm which infects grasshoppers and ultimately persuade it to commit suicide by drowning itself to make it easier for the worm to continue its life cycle particularly completed in water. The hairworm is actually thrice or four times the length of the host (grasshopper) after showing up when the grasshopper is already drowned in water. Once inside the host, the parasitic worm presumably , as the chain of events suggest it, takes over the insect's nervous government and influence the insect to submit itself completely from the worm's viscious scheme. It will eventually drown itself to favor the continuity of the worm's life cycle. What a horrible fate for grasshoppers! I think ascaris will soon develop the same aptitude and influence us into doing something very stupid. :( Grabe. Gusto ko tuloy magpurga. :( Katakot. Plead read on the article below for full text of the article in question. Thanks again!

Jules

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James Owenfor National Geographic News
September 1, 2005

Parasites were the inspiration behind the creature that terrified moviegoers in Alien. Now sci-fi screenwriters may have a new role model—parasitic worms that brainwash their victims.
Scientists say hairworms, which live inside grasshoppers, pump the insects with a cocktail of chemicals that makes them commit suicide by leaping into water. The parasites then swim away from their drowning hosts to continue their life cycle.

A team of French biologists made the discovery after monitoring grasshoppers that became trapped in a swimming pool in southern France.

Postmortems of the grasshoppers suggest that worms triggered the insects' death leaps by sabotaging their central nervous...

For more information, please click on the Post Title Link to lead you to the website source. Thank you.

On Science and Faith

Bonjour tout le monde! Another week had passed and the posts keep on coming in! What a tiring week that was really! I was so busy preparing my assignment for my Chemistry course at UPOU and still haven't figured out how to finalize it. In fact, I haven't finished reading chapter 7 of the book among the 4 chapters (4 to 7) we were advised to read by our chemistry professor. Well, I visited my virtual classroom and checked on the latest posts for Biology, which also I am currently enrolled, and found that some of my classmates were discussing issues about the stand of Faith in Science which I was quite intrigued. I want to share with you my recent post which details the interplay of Science and Faith in an environment of intellectual discourse in search for truth and how well we can achieve wisdom using the two values mentioned. Enjoy reading!

Julius

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I have always been fascinated by people who has an unrelenting belief about their God, be it classified as paganistic, Islamic or Christian, its truly worth the commendation. I may not be a religious person but definitely I believe in God. Seriously, its not bad to believe in God, neither it is bad not to according to my own belief. I do not usually profess my faith in public unless people are ready to listen which I know is bad. My dad even seconded the motion! (hmpt pero tama sya) :( But that is how "Life" is shaping everybody else's perspective. Life has to adopt to continuing demands for reality and faith. Anything that is regarded as "true" cannot always be regarded as true. The same thing applies to stuff which are classified as untrue. What is just in one society cannot be considered improper to other societies which is why I try to question things and dad don't like it! hahaha. Its like forcing a child to believe that his mother is an alien when he or she see her as a human. Have scientists confirmed the existence of an alien? Why do many people believe them. Everything has to be taken on faith don't you think?

You see, the same reason why people is searching for the truth is because they want to know their God. Science works that way as I see it. People do not do things for nothing. Since the beginning of time, man has endeavored to know the true nature of their own God and that is the same reason they created Science (at the very least). Science is innate to people and so as the process (scientific method) that consolidates the facts that explains a phenomenon. One way to know God is by studying His creation sabi nga ni Stanley White and that is the very same reason why Science operates. Do you even believe that God created the cells? Yes? Fine. Shall we stop from there? I guess not. Humans were endowed of reasoning ability by nature that is why he searched for this answer though he believes there is God though he didn't actually see Him (let's exclude Adam and Eve, that is if they really existed). That is one reason why I do not encouraged my students to engage in religious deliberation inside a Science class. Let's leave that to the Theologians and to subjects which pertain to the very nature of God. How can Science advance if we will never give it a chance?

If we talk about God in a Science class alone, will it advance our understanding on how cells divide and how that same division is manipulated? I think the fact that God created humans with brain is because He wants man to think of his own, and discover how great He is and how compassionate and loving God He is. God never tolerated ignorance that is why He gave us the brain to think. If we question the process that involves Science and stop from there, we will all be like dead humans now for there is no way for Science to advance and reap the vitamins of its fruits as in the case of medicine and other therapeautic machineries. I guess we have to take God on faith and allow Science to progress as a tool to know God through the continued examination of His creation.

An interesting argument about the teacher and the student which I got from a friend is particulary interesting when Science and Faith is viewed as two separate conflicting entities. I always hate forwarded e-mail but this one is an exception! I hope this will serve as a guiding principle to all Science students in order to maintain peace and respect in a world where everybody wants to build their own churches. :( I hope I did not offend anybody with my post. I just want to share. Learning is preserved when everybody respects anybody else's opinion. Should you have contradicting views please do share them in here. I would love to learn from you as well. Peace mga pare at mare?! Fish tayo! ;-)

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Sounds like a good argument.

Subject: Signs vs Science on Sunday

"Let me explain the problem science has with Jesus Christ." The atheist professor of philosophy pauses before his class and then asks one of his new students to stand. "You're a Christian, aren't you, son?" "Yes sir," the student says. "So you believe in God?" "Absolutely." "Is God good?" "Sure! God's good." "Is God all-powerful? Can God do anything?" "Yes." "Are you good or evil?" "The Bible says I'm evil." The professor grins knowingly. "Aha! The Bible!"He considers for a moment. "Here's one for you. Let's say there's a sick person over here and you can cure him. You can do it. Would you help them? Would you try?" "Yes sir, I would." "So you're good ... !" "I wouldn't say that." "But why not say that? You'd help a sick and maimed person if you could. Most of us would if we could. But God doesn't." The student does not answer, so the professor continues. "He doesn't, does he? My brother was a Christian who died of cancer, even though he prayed to Jesus to heal him. How is this Jesus good? Hmmm? Can you answer that one?" The student remains silent. "No, you can't, can you?" the professor says. He takes a sip of water from a glass on his desk to give the student time to relax. "Let's start again, young fella. Is God good?" "Er ... Yes," the student says. "Is Satan good?" The student doesn't hesitate on this one. "No." "Then where does Satan come from?" The student falters. "From ... God ..." "That's right. God made Satan, didn't he? Tell me, son. Is there evil in this world?" "Yes, sir." "Evil's everywhere, isn't it? And God did make everything, correct?" "Yes." "So who created evil?" Again, the student has no answer. "Is there sickness? Immorality? Hatred?Ugliness. All these terrible things, do they exist in this world?" The student squirms on his feet. "Yes." "So who created them?" The student does not answer again, so the professor repeats his question. "Who created them? " There is still no answer. Suddenly the lecturer breaks away to pace in front of the classroom. The class is mesmerized."Tell me," he continues. "Do you believe in Jesus Christ, son?" The student's voice betrays him and cracks."Yes, professor. I do." The old man stops pacing. "Science says you have five senses you use to identify and observe the world around you.Have you ever seen Jesus?" "No sir. I've never seen Him." "Then tell us if you've ever heard your Jesus?" "No, sir. I have not." "Have you ever felt your Jesus, tasted your Jesus or smelt your Jesus? Have you ever had any sensory perception of Jesus Christ, or God for that matter. "No, sir, I'm afraid I haven't." "Yet you still believe in him?" "Yes." "According to the rules of empirical, testable, demonstrable protocol, science says your God doesn't exist. What do you say to that, son?" "Nothing," the student replies. "I only have my faith." "Yes, faith," the professor repeats. "And that is the problem science has with God. There is no evidence, only faith." The student stands quietly for a moment, before asking a question of his own. "Professor, is there such thing as heat?" "Yes," the professor replies. "There's heat." "And is there such a thing as cold?" "Yes, son, there's cold too." "No sir, there isn't." The professor turns to face the student, obviously interested. The room suddenly becomes very quiet. The student begins to explain. "You can have lots of heat, even more heat, super-heat, mega-heat, white heat, a little heat or no heat, but we don't have anything called 'cold'. We can hit 458 degrees below zero, which is no heat, but we can't go any further after that. There is no such thing as cold; otherwise we would be able to go colder than -458 degrees. You see, sir, cold is only a word we use to describe the absence of heat. We cannot measure cold. Heat we can measure in thermal units because heat is energy. Cold is not the opposite of heat, sir, just the absence of it." Silence across the room. A pen drops somewhere in the classroom, sounding like a hammer. "What about darkness, professor. Is there such a thing as darkness?" "Yes," the professor replies without hesitation."What is night if it isn't darkness?" "You're wrong again, sir. Darkness is not something; it is the absence of something. You can have low light, normal light, bright light, flashing light ... but if you have no light constantly you have nothing and it's called darkness, isn't it?That's the meaning we use to define the word. In reality, Darkness isn't.If it were, you would be able to make darkness darker, wouldn't you?" The professor begins to smile at the student in front of him. This will be a good semester. "So what point are you making, young man?" "Yes, professor. My point is, your philosophical premise is flawed to start with and so your conclusion must also be flawed." The professor's face cannot hide his surprise this time. "Flawed? Can you explain how?" "You are working on the premise of duality," the student explains. "You argue that there is life and then there's death; a good God and a bad God. You are viewing the concept of God as something finite, something we can measure. Sir, science can't even explain a thought. It uses electricity and magnetism, but has never seen, much less fully understood either one. To view death as the opposite of life is to be ignorant of the fact that death cannot exist as a substantive thing. Death is not the opposite of life, just the absence of it. "Now tell me, professor. Do you teach your students that they evolved from a monkey?" "If you are referring to the natural evolutionary process, young man, yes, of course I do." "Have you ever observed evolution with your own eyes, sir?" The professor begins to shake his head, still smiling, as he realizes where the argument is going. A very good semester indeed. "Since no one has ever observed the process of evolution at work and cannot even prove that this process is an on-going endeavor, are you not teaching your opinion, sir? Are you now not a scientist, but a preacher?" The class is in uproar. The student remains silent until the commotion has subsided. "To continue the point you were making earlier to the other student, let me give you an example of what I mean?" The student looks around the room. "Is there anyone in the class who has ever seen the professor's brain?" The class breaks out into laughter. "Is there anyone here who has ever heard the professor's brain, felt the professor's brain, touched or smelt the professor's brain? No one appears to have done so. So, according to the established rules of empirical, stable, demonstrable protocol, science says that you have no brain, with all due respect, sir. So if science says you have no brain, how can we trust your lectures, sir?" Now the room is silent. The professor just stares at the student, his face unreadable. Finally, after what seems an eternity, the old man answers. "I guess you'll have to take them on faith."

Synthesis and Targeting of Mitochondrial and Chloroplast Proteins

Its me again. :) I have been dealing with this research for quite a while, and my readings have confirmed that mitochondria and chloroplasts really share a multitude of similarities be it in their double-membrane structure or the raw materials of their digestion and products of metabolism. Their function and highly specialized membrane structure seems to suggest that these organisms are, at one time of their life, free living species who turned to become endosymbionts to compensate for their structural and functional flaws and live in cahoots with the cell to aid each other for perpetual existence. Please read on the article below for more information about this issue. I will post more articles regarding this topic in the next few days to add to your readings about the two intriguing organelles. Thanks for visiting myBlog and have a nice day!

Julius

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Mitochondria and chloroplasts are surprisingly similar. Both are bounded by two membranes; chloroplasts contain, in addition, an internal membrane compartment — the thylakoids — on which photosynthesis takes place (see Figure 16-34). Both organelles use a proton-motive force and the same type of protein — an F-class ATPase — to synthesize ATP (see Figure 16-2); they also contain similar types of electron-transport proteins. Growth and division of mitochondria and chloroplasts is not coupled to nuclear division. These organelles grow by the incorporation of proteins and lipids, a process that occurs continuously during the interphase period of the cell cycle. As the organelles increase in size, one or more daughters pinch off in a manner similar to the way in which bacterial cells grow and divide. Although the biogenesis of both organelles is similar in many respects, our discussion focuses on mitochondrial biogenesis, about which more is known.

Mitochondria and chloroplasts probably arose by the incorporation of photosynthetic or nonphotosynthetic bacteria into ancestral eukaryotic cells, about 1,500 million years ago, and their subsequent replication in the cytoplasm. Over eons of evolution much of the bacterial DNA in these endosymbionts moved to the nucleus, so that in present-day cells many mitochondrial and chloroplast proteins are imported into the organelles after their synthesis in the cytosol. The mitochondrial and chloroplast DNA found in extant organisms encodes organelle rRNAs and tRNAs but...

References:

Lodish, et.al. "Synthesis and Targeting of Mitochondrial and Chloroplast Proteins". Modern Cell Biology. Fourth EditionW. H. FREEMAN,

Molecular Expressions. “Exploring the World of Optics and Microscopy.” Graphics and Web Programming Team, National High Magnetic Field Laboratory. (diagram for cell organelles).


For more information, please click on the Post Title Link to lead you to the website source. Thank you.

NASA: 10th Planet Discovered

Here is another article from NASA about the 10th planet recently discovered. In my previous post, I mentioned that scientists named it Sedna but this article from NASA shows that the official name is tentative and will still be decided by the International Astronomical Union. However, for purpose of identification, it was given the temporary name 2003 UB313. Enjoy reading. :)


Julius

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Astronomers have found a new planet in the outer reaches of the solar system.

July 29, 2005: "It's definitely bigger than Pluto." So says Dr. Mike Brown of the California Institute of Technology who announced today the discovery of a new planet in the outer solar system.

The planet, which hasn't been officially named yet, was found by Brown and colleagues using the Samuel Oschin Telescope at Palomar Observatory near San Diego. It is currently about 97 times farther from the sun than Earth, or 97 Astronomical Units (AU). For comparison, Pluto is 40 AU from the sun.

This places the new planet more or less in the Kuiper Belt, a dark realm beyond Neptune where thousands of small icy bodies orbit the sun. The planet appears to be typical of Kuiper Belt objects...

The new planet, circled in white, moves across a field of stars on Oct. 21, 2003. The three photos were taken about 90 minutes apart. Image credit: Samuel Oschin Telescope, Palomar Observatory.

For more information, please click on the Post Title Link to lead you to the website sour

Astronomers claim discovery of solar system's 10th planet

Here it is guys! The 10th planet! Not sure though. :-( Well, its worth the information to be given to everybody especially to students and spark their dwindling curiosity for Science. :( I will post more of this info. This is an article I got from CNN. Hopefully, if Pluto, which is believed to be part of Kuiper Belt, is demoted as a planet and Sedna confirmed to be a real planet, Sedna will replace Pluto as the 9th planet. Recently, I read on Discover Magazine that scientists are eyeing on 2 more planets, named planet x and y. Expect more posts regarding this subject on the days to come. Enjoy this article for the meantime. :) Read on!

Julius

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NASA: An artist's rendition shows the newly discovered planet-like object, dubbed "Sedna," in relation to other bodies in the Solar System, including Earth and its Moon, Pluto, and Quaoar.

Sunday, July 31, 2005; Posted: 11:31 a.m. EDT (15:31 GMT)

PASADENA, California (CNN) -- Astronomers announced Friday that an object they discovered in the distant reaches of the solar system is large enough to be the 10th planet -- a claim likely to reignite a debate over just how many objects should be called planets.

The object -- 96 times as far from the Earth as the Earth is from the sun, or nearly 9 billion miles away -- was first photographed in October 2003 by astronomers at the California Institute of Technology's Palomar Observatory, north of San Diego.
While researchers say they aren't yet sure of its actual size, they have determined the object is bigger than Pluto...


For more information, please click on the Post Title Link to lead you to the website source. Thank you.

A Second Look to the Nature of Science and a Revisit to the World of the Cell

Kamusta mga kaibigan! :) Its been months since I created this site but haven't started out a single thread of my own. :( I got loaded with officework and homeworks hehe. :(. Well, I would like to share an interesting TMA (Teacher-Marked Assignment as they call it in UP Open University) in my Biology class which I think you will find interesting as well. Let us explore the intriguing processes of Science, and the immense possibilities it offers us. A revisit to the world of the cell is particularly inspiring for many of the basic functions we associate with organs can be traced back to the cell itself, the fundamental unit of which all of life's characteristics are manifested. Enjoy reading. :)

Julius

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On the Scientific Enterprise

1. What is science? Is science a process? Is it an endpoint? Is it a frame of mind? Is it Science that uncovers or explains? Who creates Science? Who decides what is Science and what is not? What is the scope of Science? How is Science created?

What is Science?

According to JP Siepmann, “Science is the field of study, which attempts to describe and understand the nature of the universe in whole or part.” It’s pretty nice a definition for science J. This definition is very important because it provides us with understanding and viewpoint regarding the nature and scope of science. Science as we know it seeks to explain everything but as we try to unravel the mystery behind everything, the more we get to question things that constitutes a thing until we come to a point that we will realize that everything cannot be explained by science. The scientists’ business is to find answers to the basic phenomena of nature but much of what is happening in nature are not explainable in terms of processes employed by scientists in Science but we do get credit to gaining noble information for the fundamental identity of a certain entity in nature and influence its working on a limited scale.

In a Worldbook Encyclopedia entry, it’s stated that,” Science covers the broad field of knowledge that deals with observed facts and the relationships among those facts. The word science comes from the Latin word scientia, which means knowledge.” If science is knowledge how can we describe subject areas that are categorized under Arts? What makes a certain subject Science and others not? If the prime language of Science is mathematics, ergo it’s the prime knowledge by which Science operates. How can we define subject areas that do not fall under this category? Can we say that subject areas that fall under Humanities have no knowledge at all? Questions like these usually arise because Science is limited to explaining the details of nature and its origin. The very origin of life itself cannot be deduced solely on its workings because the processes that motivate a certain thing to function will never explain its evolution and origin.

In his biology textbook, Neil Campbell expounded further the meaning of Science. He contradicted the idea of providing a concrete definition of science for Science is better understood by observing it than by trying to create a precise definition of it. There is no exact, single statement by which we can define Science for the facts and activities that involve Science far exceed the amount of knowledge of all men put together and their efforts to delineate a satisfactory definition of it through our concerted action.

Mathematics and logic are not based on experimental testing. Yet, they are categorized under Science. But they can be considered part of science because they are essential tools in almost all-scientific study. Mathematics enables scientists to prepare exact statements of their findings and theories and to make numerical predictions about what will happen in the future. Logic provides the basis for all scientific reasoning.1

Science can never be a frame of mind for its processes are purely knowledge-based and follow a logical flow. Science can be someone else’s frame of mind if it is manipulated to suit the current intellectual biases of a certain scientist. Thus, pseudoscience develops.
Most books mentions about the tool by which people propagate Science and most of them points mathematical language as its medium of communication by which Science can be best understood. Just like any other languages, the general population may not be able to speak and at the same time understand it unless a leader (which sometimes is the teacher which can be qualified as a scientist himself) has the courage to teach its semantics and syntax to decipher its very meaning. In this way, a common dialect is used to direct the path of our thinking towards the understanding of Science and more often than not, the so-called hypothetico-deductive approach is most effective as proposed by the famous philosopher Karl Popper. In this method, a true Science can be tested by the use of the approach by which the process of deduction is applied using the hypothesis, an educated guess as we usually call it, synthesized at hand. One strong point of this testing is that, it aims to falsify a certain hypothesis laid out to explain the behavior of a certain natural phenomenon. As mentioned in Dela Paz’s book, a hypothesis, to become effective, should be falsifiable so that it could undergo further testing through experimentation and confirm its validity.

The question concerning the creator of science is humans themselves. Humans created Science because they want to know God. Science was founded to study nature (God's works) to better know God1 as what Stanley White stipulated in one of his articles. The founding fathers of science were deeply religious men. They believed in monotheism, a single creator of the universe. These great men did not live in one place, but were scattered [over all of Europe.] They communicated mostly by letter. These early men of science believed that to better know God, one must study his works.

Our search for knowledge has never ended. People tend to ask questions of all the things happening in his environment. With the many questions left unanswered, curiosity pervades every human mind. From time to time, we see philosophers and scientists laid out their theories: explanations to a not well understood natural phenomenon. They may be accepted momentarily but since experimentation, which is one of the chief tools of Science, time will come that a rather comprehensive and scientifically accurate explanation will replace the pervading theory. When new information is discovered, the conclusion must be looked at again. If the new knowledge gives support, fine, but if not, what looked like an answer must be discarded or modified. That means scientific ideas may change. The changing attitudes and practices in medicine throughout history illustrates that science is a process.3 This is probably brought about by our deductive way of thinking and our ever application of the scientific method, the main tool by which scientists test the validity of a certain scientific supposition. As a learner of science we must keep our foot always on the ground by adhering to the basic rules of science otherwise our experiments will fail, although we can see how some scientists do away with some process in scientific method to better portray how their hunches greatly agrees with an observed phenomenon or fact which is not a healthy way of dealing with science.

2. Prepare a model of the cell. Choose a certain specific cell type and work on uncovering/discovering what is in that cell. Explain your model by answering these questions:

What is the cell? What is its purpose?

The cell has been referred to as the simplest unit that is capable of living and assuming all the functions of a living being. The cell in terms of structure is simple - being the smallest unit that is viewed as a dynamic machine that exhibits all the properties that define a living entity as a whole and complex since each structures that make up the entire cell is composed of complex substances intertwined to produce a highly complex organelle that performs varied task that cannot usually identified in a non-living entity. I recalled one instance in our conversations in the discussion board where the phrase “anything that metabolizes and self-perpetuates” was used by Dr. Dela Paz in his/her book which I responded in a reply below: “The problem with the phrase “any structure that metabolizes and self-perpetuates is that metabolism is not just inclusive (a feature) to living beings alone and self-perpetuation connotes something that a living being can reproduce without the aid of environmental instruments and raw materials. I think that the cell itself does not reproduce or “self-perpetuates” but the individual structures that makes up an entire cell and from the raw materials in the environment…thus, a living being cannot “self-perpetuate” without raw materials from its immediate environment. Therefore, a cell is not an independent, basic structure of all living things since it cannot exist alone. To illustrate this, Mitochondria has its own method of metabolism and so do other organelles. They also have their own genome, metabolizes and double during cell division “self-perpetuate” ika nga ni Dr. Dela Paz. If we are to use “self-perpetuation” as a basis in our definition for the word “life” does that gives mitochondrion a license to survive alone outside a host species? Definitely not although it is “a widely accepted belief that mitochondria and plastids (photosynthetic organelles in plant cells) evolved from bacteria that were engulfed by nucleated ancestral cells. As a relic of this evolutionary past, both types of organelles contain their own genomes, as well as their own biosynthetic machinery for making RNA and organelle proteins? (Molecular Biology of the Cell :Bruce Alberts, et. al.)4 Mahirap talagang humanap ng naaangkop na panaguri sa mga bagay na buhay. But as time goes by we can perhaps formulate a meaning that encompasses and clearly identifies a living being.

Surely, the purpose of the cell is to provide life the necessary mechanism to “self-perpetuate” and differentiate to pave the way for the production of a different living unit more complex and better adapted to its present habitat. The environment provides the necessary raw materials for the organism to metabolize, reproduce, and acquire the appropriate skills to survive. Without it, the organism dies due its failure to learn and to unlearn. This might come intrinsically as an organism cannot learn or unlearn without a brain or a primary motor that regulates all of life’s activities. Nonetheless, the environment provides the indispensable training ground for an organism to acquire the best learning equipment there is to survive.

What are found inside the cell? What are their purposes?

Model of a Eukaryotic Animal Cell

Although the animal cell vary differently from the plant cell in terms of shape, size, function and contents, both types of cells actually share many of the same features and organelles that can be found on both cells.

The animal cell is composed of several organelles that make up the entire unicellular entity and these I have enumerated below.

· Cell Membrane/Plasma Membrane/Cell coat

The cell membrane is pictured as a bilayer of phospholipids molecule with embedded protein and enzymes. Its membranes act as a discriminating barrier against unwanted substances that may harm or delimit the ability of the cell to perform its varied functions. Its primary function is to separate the vital chemicals and contents present inside the cell from the outside environment but permit other molecules, which the cell deemed appropriate, to pass through due to its selectively permeable property. Thus, it regulates the amount and type of material that must pass through the membrane of the cell either for cell-to-cell-communication or nutrition.

The cell membrane along with the cell coat promotes intimate contact among cells and plays a very important role in cell-to-cell recognition and thus advancing the organization among the adjacent cells. Some part of a multicellular animal’s body and other unicellular organisms there appears to be thickly distributed (in one part of the cell) cell membrane extensions that plays an important role in increasing the amount of available area (surface area) for additional gateway for the passage of materials into and out of the cell (microvilli). The cell membrane also provides the needed barrier that separates the content of one cell to another and supplies a communication satellite with other cells as in the case of tight junctions, desmosomes and gap junctions.

The cell membrane itself is made of phospholipids bilayer material (tail) and a phosphate group (head). These layer are oriented in such a way that the water loving head portion of the bilayer is situated towards the watery environment (hydrophilic) and its water-fearing portion away from it (hydrophobic) in such a away that the layer will look like a sandwich.

The cell membrane can be perfectly conceptualized using the fluid-mosaic model by Singer and Nicholson. Under this principle, the cell membrane is pictured as a two-dimensional bilipid “fluid” layer where the hydrophobic region of the molecules of the membrane is directed within the layer with integral proteins embedded in it. The word “mosaic” (a surface decoration made by inlaying small pieces of variously colored material to form pictures or patterns-Merriam Webster) is used since majority of the substances found in the bilipid layer are a conglomerate of different molecules such as cholesterol, proteins (integral and peripheral). The picture may represent the material as immobile but theoretically or when observed under a powerful electron microscope, the proteins are lying freely and can move around the sea of molecule created by lipids.

· Nucleus

The nucleus is usually the most prominent organelle in a cell. Most biology books picture it as the center organelle of the cell but most of the time found on one side of the cell under a light microscope. This organelle contains the genetic materials of the cell (DNA) in the form of chromosomes that is conspicuous during cell division. Its content, the nucleoplasm houses another distinct structure, which is called nucleoli, a mass of granular structures in nucleus, not bound by membrane. It is thought to be involved in ribosomal RNA synthesis and ribosome precursor function. We can also see pores surrounding the membranous nuclear envelope. This double membrane structure separates the contents of the nucleus to the rest of the cytoplasm. At the tip of each pore, the inner and outer membranes are fused. The pore, which contains proteins, only allows only a specific type of RNA molecule in and out of the nucleus, which has a direct involvement in the production of other types of protein needed by the cell to maintain life.
Inside the nucleus a dark region of chromatin, involved in making ribosomes called nucleolus can be found. This structure is involved in the production of particles called ribosomes, an organelle which functions in protein synthesis.

· Endoplasmic Reticulum

The Endoplasmic Reticulum (ER) is an extensive network of tubular channels and sacs whose primary function is to transport materials from the nucleus to the plasma membrane and vice versa. It functions much like that of a highway where products from one end of the highway are transported to the other end or to areas along its path. The amount of visible endoplasmic reticulum in the cell varies from one cell type to another depending on the activity and function of the cell as its presence is attributed to a certain function, which I will discuss later. There are two distinct types of ER, which depends on the presence, or absence of another organelle termed ribosomes, which are the primary sites of protein synthesis. These are discussed in more detail in the next section.

· Rough endoplasmic reticulum (RER)

Rough Endoplasmic Reticulum (RER) was so named due to the presence of ribosomes, a protein factory of the cell. They synthesize protein and are transported right into the ER to where they are stuck that is why RER shows to produce protein. It is these same organelles that make the RER unique in a sense that is able to perform protein production from nascent polypeptide.

· Smooth endoplasmic reticulum (SER)

Smooth ER, on the other hand, is NOT covered with ribosomes and processes LIPIDS and CARBOHYDRATES. Being devoid of ribosomes does not make SER devoid of its functions as well. In fact, there several of its various functions are critical for the maintenance of life as a whole when the body or the cell itself is confronted with toxins present in small or considerably large amounts in the food we eat. Many of the important functions of the ER are performed by the SER of which are listed below:

· synthesis of steroids in gland cells
· the regulation of calcium levels in muscle cells
· breakdown of toxic substances by liver cells

From the functions enumerated above, we can summarize that most of Smooth ER’s function is fundamentally related to detoxification since the liver and kidney cells are the most prominent organs in the human body in which most Smooth ER can be located. The abundance of smooth ER among liver cells only indicates an active detoxification effect of the said organs. I believe that it is interesting to note that one spectacular function of the smooth ER is its ability to separate or sequester calcium from the cell’s fluid medium, the cytosol. The lumen of the SER, which is the internal cavity of the endoplasmic reticulum, with its powerful calcium-binding particles allows the continuous influx of calcium ions from the cytosol to the smooth endoplasmic reticulum. A specialized smooth endoplasmic reticulum called sarcoplasmic reticulum is present in muscle cells and performs almost similar functions. An enzyme called CaATPase regulates the process done by this organelle type. From here on, it is but safe to assume that the ability of the muscle cells to regulate the contraction and relaxation of the myofibrils of muscle cell relates to the function of the SER above.

· Golgi Apparatus

Golgi bodies or apparatus are another series of flattened disks, which form channels all throughout the cell. It is manufactured by endoplasmic reticulum and its main function is to modify the contents of the vesicle produced by the endoplasmic reticulum. The Golgi bodies have two distinct faces, one forming a convex area where coalescing vesicles coming from the endoplasmic reticulum discharges its content to the internal content of the Golgi apparatus for modification and further processing (cis face). On the other side, the trans face area, is a place of increased budding activity where the substances modified by the Golgi bodies are packed and transported towards the cell membrane and excreted to the outside of the cell by means of exocytosis, the release of cellular substances (as secretory products) contained in cell vesicles by fusion of the vesicular membrane with the plasma membrane and subsequent release of the contents to the exterior of the cell. (Merriam-Webster Dictionary)

· Ribosomes

Among the organelles listed herein, ribosomes are the only one not bounded by a membrane. They are the primary sites of protein integration and synthesis and are found either attached with the endoplasmic reticulum or lying free in the cytoplasm. If lying free in the cytoplasm, they can be found in clusters called polysomes. Proteins produced by free ribosomes

On the next section, I will introduce you to two (aside from the Nucleus) of some of the most popular organelles high school students generally do not forget after finishing elementary biology which I regard to be true. Part of the reason, I can think of is probably due to giving these organelles the distinguishable phrase that describes their function and in turn aids memory retention.

· Lysosomes

Remember the phrase “suicidal pack of the cell”? Does that ring a bell? J Retention is made rapid when we associate an object to a word, phrase or a situation. In all cases, they employ sounds as a tool for communication. I can define this organelle even when sleeping. J Christian de Duve, a cell biologist discovered lysosomes, cell organelles specialized for recycling and waste disposal. The structures vary in size from 0.2 to 2 micrometers in diameter which is quite small. Most books usually dismiss lysosomes as indistinguishable under a microscope partly due to their varied sizes and appearances. Under a high-resolution microscope, most of these organelles appear black due to their high content of hydrolytic enzymes, which in chemistry translates a high-density electron region. Animal cells have numerous number of this organelle but found very seldom in plant cells. Like most eukaryotic organelles, this tiny organelle is membrane-bound. Its membrane is again a lipid bilayer and protects its content. The fact that the organelle is encased in a lipid membrane suggest one thing: more than protecting its content, this organelle protects the cell since its poisonous or digestive content harms the cell in any way or will result to its premature destruction. It has been identified that lysosome’s content can reach pH of 5 and lower making its content very dangerous in some way but beneficial for nutrition and also works in autolysis (self-destruction) during period of environmental stress and brings balance to the ecosystem. That provides the ecosystem the opportunity to replenish itself through the action of these substances. J They usually fuse with vacuoles and eventually digest its content with a cocktail of enzymes (around 40 different enzymes) present in the organelle’s interior bringing about nutrition to the cell in a way. I also believe that this action neutralizes any harmful substances present in the vacuole itself.

· Mitochondria (sing. Mitochondrion)

Another interesting organelle found in an animal cell is the mitochondrion, from the Greek, "mito-" meaning, "thread" and "chondrion" meaning "body” which probably explains the thread-like appearance of these minute structures in the cell. Just like the previous organelle mentioned, this structure is very popular for it was identified for decades using a phrase that depicts its main function: “The powerhouse of the cell.” Overused a phrase as it may seem but this very phrase provides a substantial overview of the organelle’s fundamental function in a living cell.

A mitochondrion is a double-membrane organelle. Their appearance varies from rod to ovoid structures but all of them share the same internal structures. My college cell biology teacher usually note in most of her discussions that “structure always relate to function” which is true in all circumstances as in the case of mitochondria’s internal structure which we will discuss as we go along. The organelle has an outer membrane, and an inner membrane, which envelopes the organelle. The Inner membrane is folded many times along its length to create a region called crista (sing. cristae) where mitochondrial respiration [energy-yielding oxidative (using oxygen) reactions in living matter] occurs. The inner membrane encloses the internal matrix, a region where the most important proteins needed for aerobic (containing oxygen) respiration are situated.

Mitochondria are the powerhouses, energy-generators, or in other words “power sources” of the cell. Whatever you call it, these distinct organelles’ function only boils down to one: to produce energy when the cell needs it. If we are to observe the structure as shown in the cartoon above, we can describe this organelle having a rod shaped appearance, although some of them are ovoid, and are long and having a distinct stripes inside which are found to be an inner membrane folded many times in several areas the length of the inner membrane. Knowing that the actual ATP (energy-currency/molecule produced by mitochondria that powers most of cell’s cytoplasmic activities) production occurs mostly in the inner membrane of the organelle, this structure is vital to the function of mitochondria for it increases the area by which this process occurs thereby increasing the number of by-products of the ATP production activity of the mitochondrion. One interesting fact about mitochondria is that it does have its own sets of DNA not similar to the one contained in the nucleus. Similarly, ribosomes can be found. During cell division, it divides independently and forms offspring mitochondrion, which are distributed and used by the forming cells. In short, it possesses its own genetic apparatus and mitotic (cell-division) behavior.

· Microbodies

It’s hard to identify microbodies based on their appearance due to their diverse shape and sizes. It has been found out that these organelles are found everywhere in a fungal cell. Among the most common microbodies are peroxisomes (found in plants and animals) and glyoxysomes (found only in plants), although lysosomes are sometimes being included in the list of microbodies due to the similarities in basic functionalities with microbodies, that is, digestive properties. Despite of this similarity, the functions of lysosomes far outweigh that of the function of microbodies for they contain numerous enzymes, which aid them from performing varied functions aside from the one, which will be described later.

Microbodies are membrane bound vesicles (a membranous and usually fluid-filled pouch-Merriam-Webster Dictionary) present in cytoplasm in most animal and plant cells. Each cell possesses their unique microbodies and performs quite different function but share similar characteristics: all of them contain valuable enzymes for degradation of toxic macromolecules, which are intermediate products of cellular metabolism. One enzyme worth mentioning is the enzyme catalase present in animal peroxisomes. The role of this enzyme is critical to the survival of the cell due to its neutralizing effect on toxic hydrogen peroxide (H2O2), intermediate by-products of amino acid and fatty acid metabolism.

To give you a brief detail of the chemical reaction that culminates to the production of oxygen and liquid water in the metabolism of hydrogen peroxide, please refer to the diagram below.

2 H2O2 <-> O2 + 2H2O

As the cell metabolizes amino acid and fatty acids, it creates by-products, which are toxic to the cell itself and as these substances accumulates in the cytoplasm, their potential to damage the cell is enormous. The amount of these harmful substances is counterbalanced by the catalytic action of peroxisomes with the use of catalase enzyme, which breaks toxic hydrogen peroxide into a less toxic form - water and oxygen.

Analysis of enzymes in purified or partially purified microbodies from fungi indicates that they participate in the following biochemical functions8:

· Fatty acid degradation
· Glyoxylate cycle
· Purine metabolism
· methanol oxidation
· Assimilation of nitrogenous compounds
· Amine metabolism
· Oxalate synthesis

Glyoxysomes function in lipid, such as fatty acid, metabolism and its greatest glyoxysomic activity were found mostly in plants especially in fruits and seeds. It is in this organelle where chemical process known as glyoxylate cycle, where the start of the beta-oxidation (stepwise catabolism of fatty acids in which two-carbon fragments are successively removed from the carboxyl end of the chain) of fatty takes place, begins.

· Cilia and Flagella

Cilia and flagella are an important hallmark of a motile organism. Some types of cells may have evolved to become stationary but most of them retain one of these structures as in the case of ciliated cells of trachea and bronchioles of the lungs. They function in the movement of substances over their surface either for the distribution of substances for nutrition or moving particulate wastes out of the organism through its specialized excretory instrumentations. Our respiratory tract is kept clean by the actions made by these organelles especially when cilia present in the cells of trachea beat synchronously in one direction to move the foreign material trapped on the mucus (slippery secretions of the cell which moistens and protects) lining of the cell out towards the nose or the mouth to be swallowed.

Cilia and flagella are extra-cellular extensions that protrude from the cell. Although both structures are composed of the same material, which in this case are microtubules, one distinguishes the other from their length since flagella are longer than the cilia. Microtubules, the cytoskeleton that makes up cilia and flagella are composed of a globular protein tubulin. This globular protein is composed of alpha and beta tubulin dimer (a compound formed by the union of two radicals or two molecules of a simpler compound) suggesting its heterodimeric (composed of more than one dimer) structure. This dimer molecule connects to form a linear pattern called protofilament and these rows of globular proteins conjoin to frame a microtubule molecule.

· Vault

A decade ago (1992, although first reported in mid1980s but was not attributed a function), Leonard Rome and Nancy Kedersha of the UCLA School of Medicine recently discovered these subcellular organelle under a rat liver cell, although it has been observed that such particles/organelles exist in all nucleated cells observed so far. Among its properties are octagonal in structure, composed of RNA, and looks more like a cathedral vaults because of obvious multiple arch-type structure. They are believed to be nuclear pore complex plugs due to their shape although such assumptions alone were not yet verified due to lack of experimental evidence. These structures are usually found in a location where fiber precursors are building up to make actin protein. In that instance, Rome assumed that vaults are responsible for transporting , "mail trucking"as one of my classmate in UPOU calls it, the actin RNA templates in such actin-organizing region of cells. What scientists are trying to do today is that, they are attempting to disable the gene that is responsible for the production of vault protein. If paralyzation is complete and the cells show signs of failure for actin production then scientists are right that such organelles are responsible for actin protein assembly by providing templates for the production of actin (RNA templates). That confirms the "Mail Truck Theory" stipulated for the mobility of these subcellular organelles. They are not only found near the nucleus but througout the cytoplasm, probably due to their transporting ability from the nuclear pore through the rest of the cytoplasm. Additonally, another interesting fact to note here is that vaults are visibly abundant in multi-drug resistant cancer cells. This discovery lead to the hypothesis that these organelles participates in interceding drug resistance conferring the cell its ability to reject medication.

All the characteristics of living things, as outlined in the Module, can be traced back to the cell. Show, using examples, how your cell…

Metabolizes

Nearly all living things share certain basic characteristics. These characteristics include (1) reproduction; (2) growth; (3) metabolism; (4) movement; (5) responsiveness; and (6) adaptation. Not every organism exhibits all these features, and even nonliving things may show some of them. However, these characteristics as a group outline the basic nature of living things.5

Metabolism is one of the unique characteristics of a living thing. It is able to assimilate a component of its environment and transform it into a form that can be used to power the many processes undergone for its continued existence. Almost all books mention at least once in its entire content the more popular meaning of the word: “metabolism involves all the chemical processes by which an organism converts molecules and energy into forms that it can use.”5 All of the biological substrates needed by metabolism come from the environment although the energy that powers this process comes from sunlight, which is the ultimate source of energy of all living beings. Moreover, metabolism offers the organism’s body the opportunity for growth, and repair of damaged parts. It is interesting to note that metabolism is driven by a high-energy molecule (Adenosine Triphosphate) that is unique to living species. It stores and releases energy trapped between the bonds of phosphate that makes up the entire molecule.

Reproduces

Reproduction is a process by which living creatures uses to perpetuate their kind, which is better, or in worst cases, inferior to the parent living creature. All organisms reproduce or use some other mechanisms, which helps them to complete the process, even though some of them cannot reproduce by themselves (as in the case of viruses) and influences others to do it for them. Reproduction can be in many ways but primarily are classified as asexual or sexual, depending on the type of biological tool used (gamete or part of the body of the organism). Humans for example, reproduce by sexual means. This is performed using gametes as a tool to perpetuate its own kind. Major forms of individuals distinguishable among sexually reproducing species includes male or females. Both of these forms bear their own respective sexually active gamete ready to produce a viable offspring by fertilization from one of the other counterpart gamete. Asexual reproduction are usually performed by lower forms of animals such as bacteria where a new organism is produced by budding which is a characteristic of a hydra (small-bodied, freshwater polyps), releasing special kind of cells within the body of the organism which develops into a new, but identical individual as in the case of Sponges [any of a phylum (Porifera) of aquatic chiefly marine lower invertebrate animals that are essentially double-walled cell colonies that are permanently attached as adults(Merriam Webster Dictionary)], fragmentation (body of the parent organism breaks into two forming new individual) and regeneration (formation of a new individual using a lost or detached part) , which are characteristics of planarians and various echinoderms.

This process is an indispensable tool to counteracting the effect of death of an individual species. Reproduction itself is a major characteristic that sets living organisms apart from non-living entities and is a direct manifestation of an organism’s ability to violate the effect of the second law of thermodynamics, to put it simply, the “law of disorder” which is the fate of all matter in the universe.

There are two types of sexual reproduction. It comes in two forms: mitosis and meiosis. Mitosis produces two daughter cells with equal number of genetic material with 2 copies (diploid) of them in each cell while meiosis produces offspring (daughter cells) with half the number of chromosomes or genetic material (haploid) as the parent cell. While mitosis produces two cells during replication meiosis produces 4 daughter cells carrying half the number of genetic material the original cell has.

Responds

All living organisms respond in various ways depending on their learned evolutionary differences but I believe that organisms respond in many ways due to their internal and conscious willingness to survive. Last week when I watched the movie “The Island”, I can’t help but agree with Ewan McGregor’s line, “I will do everything to survive” where he used his ability to pretend in order to mask his true identity and the bad guys from the cloning facility mistook someone else’s as he (in this regard, his source since he is a clone).

In the October 4, 2001 issue of the National Geographic News Online [I kept this one in my mailbox for a year!:-) ] a Swedish scientist named Arne Öhman, a psychologist at the Karolinska Institute and Hospital in Stockholm, Sweden has conducted experiment on the sources of fear of humans and further extrapolated the role of evolution itself from its development and survival use. He stated that, “individuals who have been good at identifying and recruiting defense responses to predators or aggressors have left more offspring than individuals with less efficient defense systems."6

Living species of plants and animals continue to survive because of their continued responsiveness to objects that hinders their survival and perpetuation. Size sometimes does not equate to less efficient in managing the effects of predation but good response mechanisms helps a certain species to be aware of what is happening in its environment and react on how to avoid threats.

Cells particularly do that by way of releasing chemicals or moving away from the location where the threat was detected (chemotaxis). This is dictated by the nucleus to counteract any effect the environment has to its survival and continued stability. For unicellular organisms such as bacteria, the chemicals surrounding them motivate their motility. This behavior is employed to find food in the environment or flee from the source of threat, which comes in form of predator or poison.

Adapts

Perhaps the most popular among the characteristics of living things is adaptation. This is because this topic is hotly debated in almost every biology class I have attended since high school, even when I was still teaching. J The main reason I can think of is our varied and sometimes irreconcilable beliefs as to the origin and diversity of life around us. Our religious belief sometimes gets in the way of our scientific thinking. We often ask questions like, “How did humans evolve?” “Is evolution really true, if yes, is it acceptable according to our own religious belief that we evolve from monkey’s (literally)?” “Is there a God who authored all these things?” Things like that sometimes interferes our scientific understanding and judgment as to what is true and what is not but basically there are evidences that supports evolution where vitalists, people who believe that living things are not governed solely by the laws of physics and chemistry but by which a potent life force present in all living things, fails.

All organisms have a knack on adapting to its environment. This ability helps the organism to survive under extreme environmental conditions and as when surrounded by environmental threats. Throughout the course of an organism’s evolution, organisms change due to internal need to suit their structure to the current environment. They may develop certain structures (modifications), or features not characterized by an organism’s physique such as stamina and endurance, that is employed to adapting to its niche (function in the ecosystem) or environment.

Species of organisms that shows the characteristics necessary to survive in an environment from which it functions most of the time reproduces offspring with similar abilities. They may reproduce more organisms that can survive but the organisms that are able to withstand the stress in the environment are able to pass on their desirable characteristics using reproduction mechanism and contribute to the fitness of the organisms to which their genes will be passed on. This what best describes natural selection; a natural process that results in the survival and reproductive success of individuals or groups best adjusted to their environment and that leads to the perpetuation of genetic qualities best suited to that particular environment (Merriam-Webster Dictionary).

Cells adapt to the environment by manipulating its internal machineries, producing proteins necessary for its survival and moving away from the source of danger by its unique locomotive ability. The cell particularly uses mRNAs to create proteins which direct the cell’s activity and in turn alter its behavior.

3. Define an Enzyme.

Putting it simply, an enzyme is protein biocatalyst, which lowers the amount of time a certain substance be modified (or digested) and provides the necessary venue for the chemical reaction to occur rapidly that would proceed otherwise at room temperature. The name enzyme was taken from the Greek énsimo, formed by én = in and simo yeast. This was due to the fact that many of the enzymes studied by scientists during the 1800s were of yeast in origin. Almost all enzymes are proteins. The basic structure and functionalities of enzymes are fully discussed in the next question. As early as 1800, scientists like Louis Pasteur (1822-1895 French chemist & microbiologist) and Hans and Eduard Buchner (1860-1917 German Chemists; awarded 1907 Nobel prize for chemistry for research on alcoholic fermentation) working on the fermentation of sugar to alcohol by yeast cells, were able to conclude that something which Pasteur called “ferments”, were aiding the digestion and eventual degradation of sugar to alcohol and were thought to happen only in living organisms. With our knowledge in basic inorganic chemistry, we can now conclude that such assumption is incorrect since some inorganic substances (and organic substances) can act as much like the workings of an enzyme. Similar experiments were conducted by Buchner in 1897 and observed the same phenomenon though their purpose was purely medical. It was in the year 1926 when James B. Summer, an American Biochemist, confirmed that enzymes present in living systems are protein molecules. He was also the first person to isolate a pure enzyme in the form of crystals. 7

In terms of its composition.

Enzymes are structurally and functionally diverse just as animals are in a certain ecosystem. Diverse as they are, enzymes do share a common structure. An enzyme has an active site where a substrate, a molecule that binds to and acted upon by biological catalysts, fits snugly into the enzyme. The lock and key hypothesis is the most intelligible model by which we can understand the workings of an enzyme. In this model, the substrate, the reacting molecule, binds with an enzyme in the active site producing what we call a reaction intermediate, which also shows how an enzyme-substrate complex forms. This reaction intermediate is important for it provides a way for enzymes to lower the activation energy, the minimum amount of energy required to convert a normal stable molecule into a reactive molecule, of a substance when reacting to another substance than done otherwise. This way, a reaction that usually occurs years to complete is expedited to a minute or seconds upon the intervention of an enzyme molecule. Upon contact with a substrate, it was observed that an enzyme changes its shape to accommodate the shape of the entire substrate. This behavior is a characteristic of a covalent bond that connects the molecules of an enzyme and confers the molecule its apparent flexibility. This discovery led to the formulation of a new model for enzyme activity, which is known as Induced Fit Hypothesis in 1959 by Maxi Koshland. Under this hypothesis, active sites changes shape as substrates interact with it. The amino acids making up the active site is a flexible material, which fits the substrate snugly into the active site and performs the normal catalytic function.

Aside from the aforementioned main structure of an enzyme, an auxiliary molecule that aids the enzymes from performing their catalytic function called co-factors which includes co-enzymes (organic compound like vitamins or any derivative molecule of vitamins), and activators (trace elements such as copper, iron, or magnesium) are worth mentioning in this TMA. Co-factors can come in different shapes, sizes, forms, and kinds. If co-enzymes are firmly associated with an enzyme, they are called prosthetic groups.

In terms of its purpose in the cell

Enzymes function primarily to maneuver chemical reaction rapidly. Without them, a chemical reaction that usually last for a seconds will take years to complete. The presence of enzymes is critical to our biological existence for it helps the organism from performing its varied functions while supplying the correct form of molecule unique to a particular process. Most chemical reactions occur very slowly under ordinary temperature conditions but an enzyme speeds up this process and helps the production and modification of biological molecules by which the cell can readily use for its diverse functionalities. We have seen several cases of diseases where a defective enzyme is involved. One perfect example is for people with Phenylketonuria. Patients suffering from this disease suffer from mild to severe mental retardation, depending on the severity of the condition and blood phenylalanine levels. This condition manifests in patients who lacks the necessary enzyme to initiate the degradation of the essential amino acid phenylalanine, which in this case, the phenylalanine hydroxylase (hydroxylase: any of a group of enzymes that catalyze oxidation reactions in which one of the two atoms of molecular oxygen is incorporated into the substrate and the other is used to oxidize NADH or NADPH – Merriam-Webster’s Dictionary). In phenylketonuric patients, the enzyme responsible for the metabolism of the essential amino acid phenylalanine is completely or partially non-functional or in other cases, the lack of other enzymes necessary for the catabolistic process of the same is absent. Consequently, knowing that the amino acid cannot be metabolized, the unmonitored intake of phenylalanine causes an increase in phenylalanine in the blood and saturates the blood vessels causing organ damage especially the brain. Through genetic screening, it was found that this condition is genetic in origin and was due to a mutation in both alleles coding for the enzyme phenylalanine hydroxylase and can be located in chromosome 12. Patients exhibiting these symptoms and found to be inflicted with this disease are kept in strict dietary supervision to control the intake of dietary phenylalanine thereby avoiding the consequences this disease portends.

Give a metaphor that will allow you to describe an enzyme to a fourteen year old. Explain your metaphor.

Using the descriptions provided above for enzymes, we could use the child eating a lollipop as an analogy to better understand the province of enzymes with the “lollipop” logically substituting the substrate and “saliva” as enzymes to a fourteen-year-old child. I can somehow illustrate to a novice learner of science how saliva acts as a destabilizing agent towards the partial digestion of the lollipop and better prepare it to further digestion in the stomach using the digestive juices (hydrochloric acid and other enzymes) as secondary agent for further enzymatic action. In this way, the basic foundation for the concept of enzymes is established using simple activity that is rather comprehensible to a juvenile pupil.

Find out where the enzymes are in the Central Dogma of Molecular Biology.

DNA <-> RNA > PROTEIN

In the above illustration, it describes the flow of genetic information starting from DNA as the template material for the production of succeeding molecules left of the diagram. According to this tenet, RNA molecules are arranged from the intricate structure of DNA by a process called transcription. In turn, the production of RNA from the DNA template will provide a new pattern to yield another product by translating the information contained in RNA to produce proteins, a process popularly known as translation. To every reaction that is taking place in the process of replication (DNA synthesis from DNA template), transcription (RNA production from DNA template) and translation (protein synthesis from RNA template), enzymes are always involved. Enzymes can be located in the arrows connecting each molecules produced by every reaction. In fact, the skeleton of this doctrine is quite so simple for many enzymes are involved in each reaction as represented by these arrows.

Enzymes are the catalyst of change that aids molecule to be created from one form to another. They provide the proper avenue in order for the chemical modification to takes place. A biochemical reaction cannot move on without the aid of chemical modifiers such as enzymes for they possess the necessary biochemical machinery to process a molecule in a form that an organism can readily use.


REFERENCES:

Online Resources/References:

1Dauben, Joseph W. "Science." World Book Online Reference Center. 2005. World Book, Inc. 17 July 2005.

2 Stanley Fay White, “The Meaning of Science”, 2000

3Science Scope by Kathryn L. Stout, B.S. Ed., M. Ed.

4Bruce Alberts, “Molecular biology of the cell.” 2002. 4th Ed.

5 Morowitz, Harold J. "Life." World Book Online Reference Center. 2005. World Book, Inc. 26 July 2005.

6John Roach. "Fear of Snakes, Spiders Rooted in Evolution, Study Finds." National Geographic News October 4, 2001.

7Rudolph, Frederick B. "Enzyme." World Book Online Reference Center. 2005. World Book, Inc. August 9, 2005.

8Carson, D. B. and Cooney, J. J., (1990), "Microbodies in fungi - a review", Journal of Industrial Microbiology, v 6, n 1, p 1-18

Mark Dalton. ”Online Biology Book.”

Regina Bailey. "Asexual Reproduction". BiologyAbout.com.

Jerry G. Johnson. ”The World of Biology.”

Dr. Michael Pidwirny. "The Hypothetico-deductive Method, the Science of Physical Geography." University of British Columbia - Okanagan 1999-2005

Other Resources (Hardbound and paperback copy Books, Encyclopedia)

Barrion, A. “Principles of Biology”. Philippines: UP Open University Office of the Academic Support and Instructional Services. 1994.

Campbell, N. Biology. California: The Benjamin/ Cummings Publishing Company, Inc. 1996.

Campbell, N. Et.al. Biology: Concepts and Connections. California: The Benjamin/ Cummings Publishing Company, Inc. 2003.

Enger, E. and Ross, F. “Concepts in Biology.” Boston: McGraw-Hill companies, Inc. 2000 International Edition.

Rubenstein, Irwin, and Susan M. Wick. "Cell." World Book Online Reference Center. 2005. World Book, Inc. 2 August. 2005.

Holtzman, N.A., and others: Loss of Dietary Control in Phenylketonuria. The New England Journal of Medicine 314:593-598, March 6, 1986.

Geoffrey M. Cooper. "Expression of Genetic Information" The Cell: A Molecular Approach. Second Edition Sinauer Associates, Inc., Boston University 2000

Harvey Lodish, et.al. “Synthesis of Biopolymers: Rules of Macromolecular Carpentry.”

Molecular Cell Biology,” W. H. Freeman and Company Fourth Edition 2000.